diff --git a/BinaryFiles b/BinaryFiles new file mode 100644 index 0000000..c76f1a0 --- /dev/null +++ b/BinaryFiles @@ -0,0 +1,8 @@ +inst/bin/clumpp_linux_1.1.2b_32bit +inst/bin/clumpp_linux_1.1.2b_64bit +inst/bin/clumpp_mac_1.1.2b +inst/bin/clumpp_windows_1.1.2b.exe +inst/bin/distruct_linux_1.1_64bit +inst/bin/distruct_macosx_1.1 +inst/bin/distruct_macosx_1.1_2013 +inst/bin/distruct_windows_1.1.exe diff --git a/DESCRIPTION b/DESCRIPTION new file mode 100644 index 0000000..51cc51b --- /dev/null +++ b/DESCRIPTION @@ -0,0 +1,30 @@ +Package: pophelper +Type: Package +Title: Tabulate, analyse and visualise STRUCTURE, TESS, ADMIXTURE and tab-delimited q-matrices + files +Version: 2.2.5 +Date: 2018-01-11 +Author: Roy Mathew Francis +Authors@R: person("Roy", "Francis", email = "roy.m.francis@outlook.com",role = c("aut", "cre")) +Maintainer: Roy Mathew Francis +Description: A set of useful functions for processing output files from the + population structure analysis softwares STRUCTURE, TESS, ADMIXTURE, fastSTRUCTURE etc. The + package contains functions to read runs, tabulate runs, summarise runs, plot runs, estimate + K using Evanno method, export clumpp files, export distruct files and generate barplots. +URL: https://github.com/royfrancis/pophelper +Depends: + R(>= 3.1.2), + Cairo, + ggplot2 +Imports: + grid, + gridExtra, + gtable, + tidyr +Suggests: + knitr, + testthat +License: GPL-3 +Encoding: UTF-8 +VignetteBuilder: knitr +RoxygenNote: 6.0.1 diff --git a/NAMESPACE b/NAMESPACE new file mode 100644 index 0000000..818dd46 --- /dev/null +++ b/NAMESPACE @@ -0,0 +1,26 @@ +# Generated by roxygen2: do not edit by hand + +export(analyseQ) +export(clumppExport) +export(collectClumppOutput) +export(collectRunsTess) +export(distructColours) +export(distructExport) +export(evannoMethodStructure) +export(is.qlist) +export(plotQ) +export(plotQMultiline) +export(readQ) +export(readQBaps) +export(readQBasic) +export(readQClumpp) +export(readQStructure) +export(readQTess) +export(readQTess3) +export(summariseQ) +export(tabulateQ) +export(verifyGrplab) +import(grid) +import(gridExtra) +import(gtable) +import(tidyr) diff --git a/NEWS b/NEWS new file mode 100644 index 0000000..7d83b01 --- /dev/null +++ b/NEWS @@ -0,0 +1,436 @@ +pophelper 2.2.5 +=========== +* 11-Jan-2018 +* A bug in plotQ() caused strip labels to be incorrect. This has been fixed +* plotQMultiline() subtitle by default prints the K value of the run +* plotQ() and plotQMultiline() prints 'Drawing plot ...' when exporting plot + +pophelper 2.2.4 +=========== +* 07-Jan-2018 +* Function readQBaps() added to convert BAPS run files to qlist +* Function readQ() modified to read BAPS run files +* Function checkQ() modified to identify BAPS run files +* Open textConnection() fixed in readQStructure() +* Function readQTess() modified to use textConnection() +* Functions readQStructure(),readQTess(),readQBasic() and readQClumpp() + are now exported to the namespace. +* tabulateQ() has 'quiet=T' set as default +* summariseQ has 'quiet=T' set as default +* Changes to plotQ() + + Argument 'sharedindlab' added to control separate vs common labels in 'join' plots + + Argument 'indlabwithgrplab' added to control if grp labels are concatenated to ind lab + + Argument 'showyaxis' added to turn y-axis on/off + + Argument 'showticks' added to turn x and y axes ticks on/off + + Argument 'ticksize' added to adjust tick size + + Argument 'ticklength' added to adjust tick length + + Argument 'basesize' added to adjust text size of all theme elements + + Argument 'panelratio' added to adjust plot panel to grplab panel ratio + + Argument 'legendmargin' added to adjust margin around the legend + + Argument 'exportplot' added to export plot + + Argument 'returnplot' added to return plot object + + Argument 'returndata' added to return processed data + + Default individual labels are added before sorting, subsetting etc + therefore, individual labels now reflect change is sorting. + + Fixed a bug in sorting where sorting by 'label' didn't work + + Argument 'quiet' added to turn off messages + + Facets are plotted by facet_wrap rather than facet_grid + + Minor adjustments to margins + + Div lines are not drawn with 'join' plot, when sorting by all or cluster. (Bug to be fixed) +* Changes to plotQMultiline() + + Argument 'indlabwithgrplab' added to control if grp labels are concatenated to ind lab + + Arguments 'showlegend','legendlab','legendpos','legendkeysize','legendtextsize','legendmargin' added + + Argument 'ticksize' added to adjust tick size + + Argument 'ticklength' added to adjust tick length + + Argument 'basesize' added to adjust text size of all theme elements + + Argument 'quiet' added to turn off messages + + Argument 'exportplot' added to export plot + + Argument 'returnplot' added to return plot object + + Argument 'returndata' added to return processed data + + Fixed a bug in sorting where sorting by 'label' didn't work +* Changes to evannoMethodStructure() + + Argument 'returnplot' added to return plot object + + Argument 'returndata' added to return processed data + + Argument 'quiet' added to turn off messages + + Argument 'outputfilename' added to specify custom file name + + kPlot is no longer shown by default to the current print device +* Arguments 'showindlab' and 'sharedindlab' added to getDim() to adjust plot height +* grpLabels(): Arguments 'lndlabwithgrplab' and 'indlabsep' added +* sortInd(): Fixed a bug in sorting where sorting by 'label' didn't work + +pophelper 2.2.3 +=========== +* 01-Sep-2017 +* Function readQTess3() added to convert TESS 3 R object to qlist +* Minor changes in tabulateQ() + +pophelper 2.2.2 +=========== +* 25-Aug-2017 +* Fixed an issue where 'barbordersize' could not be turned off +* Changes to plotQ() + + Argument 'barbordersize' set to 0 as default + + Argument 'barbordercolour' set to NA as default +* Changes to plotQMultiline() + + Argument 'barbordersize' set to 0 as default + + Argument 'barbordercolour' set to NA as default + +pophelper 2.2.1 +=========== +* 04-Aug-2017 +* Changes to plotQ() + + Order of arguments changed in plotQ + + Argument 'barbordersize' added to adjust border size on bars + + Argument 'barbordercolour' added to adjust colour of bar borders + + Argument 'indlabspacer' added to control spacing between individual labels and plot area + + Argument 'splabangle' added to control angle of strip panel labels (requested by Gang Liu) + + Argument 'showtitle' added to show/hide plot title + + Argument 'titlelab' added to provide custom title (requested by Gang Liu) + + Argument 'titlehjust' added to adjust horizontal justification of the title + + Argument 'titlevjust' added to adjust vertical justification of the title + + Argument 'titlesize' added to adjust size of the title + + Argument 'titlecol' added to adjust the colour of the title + + Argument 'titleface' added to adjust the font face of the title + + Argument 'titlespacer' added to adjust the space below the title + + Argument 'titleangle' added to adjust the angle of the title + + Argument 'showsubtitle' added to show/hide plot subtitle + + Argument 'subtitlelab' added to provide custom subtitle + + Argument 'subtitlehjust' added to adjust horizontal justification of the subtitle + + Argument 'subtitlevjust' added to adjust vertical justification of the subtitle + + Argument 'subtitlesize' added to adjust size of the subtitle + + Argument 'subtitlecol' added to adjust the colour of the subtitle + + Argument 'subtitleface' added to adjust the font face of the subtitle + + Argument 'subtitlespacer' added to adjust the space below the subtitle + + Argument 'subtitleangle' added to adjust the angle of the subtitle +* Changes to plotQMultiline() + + Order of arguments changed in plotQMultiline. + + Argument 'barbordersize' added to adjust border size on bars + + Argument 'barbordercolour' added to adjust colour of bar borders + + Argument 'indlabspacer' added to control spacing between individual labels and plot area. + + Argument 'showtitle' added to show/hide plot title + + Argument 'titlelab' added to provide custom title (requested by Gang Liu) + + Argument 'titlehjust' added to adjust horizontal justification of the title + + Argument 'titlevjust' added to adjust vertical justification of the title + + Argument 'titlesize' added to adjust size of the title + + Argument 'titlecol' added to adjust the colour of the title + + Argument 'titleface' added to adjust the font face of the title + + Argument 'titlespacer' added to adjust the space below the title + + Argument 'titleangle' added to adjust the angle of the title + + Argument 'showsubtitle' added to show/hide plot subtitle + + Argument 'subtitlelab' added to provide custom subtitle + + Argument 'subtitlehjust' added to adjust horizontal justification of the subtitle + + Argument 'subtitlevjust' added to adjust vertical justification of the subtitle + + Argument 'subtitlesize' added to adjust size of the subtitle + + Argument 'subtitlecol' added to adjust the colour of the subtitle + + Argument 'subtitleface' added to adjust the font face of the subtitle + + Argument 'subtitlespacer' added to adjust the space below the subtitle + + Argument 'subtitleangle' added to adjust the angle of the subtitle + +pophelper 2.2.0 +=========== +* 17-May-2017 +* is.qlist() modified to produce error if input does not meet qlist requirements +* readQ() argument 'indlabfromfile' did not work (fixed) +* evannoMethodStructure() font did not work for pdfs (fixed) +* Changes to plotQ() + + Order of arguments changed in plotQ + + Argument 'grplab' must be data.frame + + Argument 'sp' changed to 'showsp' + + Argument 'div' changed to 'showdiv' + + Argument 'legend' changed to 'showlegend' + + Argument 'labspacer' changed to 'grplabspacer' + + Argument 'labpanelheight' changed to 'grplabheight' + + Argument 'labpos' changed to 'grplabpos' + + Argument 'labsize' changed to 'grplabsize' + + Argument 'labangle' changed to 'grplabangle' + + Argument 'labjust' changed to 'grplabjust' + + Argument 'labcol' changed to 'grplabcol' + + Argument 'labalpha' changed to 'grplabalpha' + + Argument 'labsep' changed to 'indlabsep' + + Argument 'showindlab' added to turn individual labels on/off + + Argument 'indlabheight' added to adjust panel height of individual labels + + Argument 'indlabsize' added to adjust size of individual labels + + Argument 'indlabangle' added to adjust angle of individual labels + + Argument 'indlabvjust' added to adjust vertical adjustment of individual labels + + Argument 'indlabhjust' added to adjust horizontal adjustment of individual labels + + Argument 'indlabcol' added to adjust colour of individual labels + + Argument 'selgrp' added to select active group label set from multiple group label sets + + Argument 'ordergrp' added to reorder group labels + + Argument 'outputfilename' added to name exported files + + Clipping of markers along the edges (fixed) + + New lines in the grplab titles (strip labels) automatically adjust to number of new lines in splab +* Changes to plotQMultiline() + + Argument 'grplab' takes a dataframe + + Argument 'indlab' changed to 'showindlab' + + Argument 'labsep' changed to 'indlabsep' + + Argument 'labsize' changed to 'indlabsize' + + Argument 'labangle' changed to 'indlabangle' + + Argument 'labvjust' changed to 'indlabvjust' + + Argument 'labhjust' changed to 'indlabhjust' + + Argument 'ticks' changed to 'showticks' + + Argument 'yaxislabs' changed to 'showyaxis' + + Argument 'selgrp' added to select active group label set from multiple group label sets + + Argument 'ordergrp' added to reorder group labels + + Argument 'showgrplab' added to turn group labels on/off + + Argument 'indlabcol' added to adjust colour of individual labels + + Argument 'grplabsize' added to adjust size of group labels + + Argument 'grplabcol' added to adjust colour of group labels + + Argument 'grplabbgcol' added to adjust background colour of group label panel + + Argument 'outputfilename' added to name exported files + +pophelper 2.1.0 +=========== +* 17-Apr-2017 +* Changes to plotQMultiline() + + Argument 'grplab' added + + Argument 'grpmean' added + + Argument 'subsetgrp' added + + Argument 'sortind' has extra option 'label' to sort by individual labels + + Argument 'labsep' added + + tiff option added to 'imgtype' + + Argument 'theme' added + + Argument 'font' added + + Argument 'barwidth' changed to 'barsize' + + Arguments 'height' and 'width' must always be in specified units. No special change for pdf + + Argument 'res' changed to 'dpi' to be consistent with other functions in the package + + Uses function is.qlist() to test qlist input validity +* Changes to plotQ() + + Argument 'sortind' has extra option 'label' to sort by individual labels + + Argument 'theme' added + + Argument 'font' added + + Argument 'useindlab' added + + Argument 'labsep' added + + Argument 'barsize' added + + tiff option added to 'imgtype' + + Uses is.qlist() to test qlist input validity + + Argument 'linethick' deprecated and replaced with linesize + + Argument 'divthick' deprecated and replaced with divsize +* tabulateQ() uses is.qlist() to test qlist input validity +* clumppExport() uses is.qlist() to test qlist input validity +* distructExport() uses is.qlist() to test qlist input validity +* Changes to evannoMethodStructure() + + Argument 'pointsize' added + + Argument 'pointtype' added + + Argument 'pointcol' added + + Argument 'linesize' added + + Argument 'linecol' added + + Argument 'ebwidth' added + + Argument 'ebcol' added + + Argument 'textcol' added + + Argument 'gridsize' added + + Argument 'theme' added + + Argument 'font' added + + Argument 'res' changed to dpi + + Arguments 'height' and 'width' must always be in specified units. No special change for pdf + + tiff option added to 'imgtype' + + Default margins slightly increased + + Minor grid lines removed to reduce clutter + + +pophelper 2.0.0 +=========== +* 19-Dec-2016 +* checkRuns modified +* clumppExport.. 'usexe' path issue corrected +* Erroneous warning messages in clumppExport.. fixed +* File name matching issue in clumppExport.. fixed +* tabulateRunsStructure() deprecated +* tabulateRunsTess() deprecated +* tabulateRunsMatrix() deprecated +* summariseRunsStructure() deprecated +* summariseRunsTess() deprecated +* summariseRunsMatrix() deprecated +* clumppExportStructure() deprecated +* clumppExportTess() deprecated +* clumppExportMatrix() deprecated +* runsToDfStructure() deprecated +* runsToDfTess() deprecated +* runsToDfMatrix() deprecated +* readQ() added + + Input files are converted to a qlist. + + Structure specific values such as elpd, mvll etc are preserved as dataframe attributes + + For CLUMPP, multiple runs within a file are suffixed with -1, -2 etc +* tabulateQ() added + + Argument 'qlist' added to accept a qlist input + + Argument 'quiet' removed +* summariseQ() added +* clumppExport() added + + Argument 'qlist' added to accept a qlist input +* plotRuns() error when using subsetpops 'length of poplabels not equal to number of individuals' fixed. +* plotRuns() renamed to plotQ(). + + Argument 'qlist' added to accept a qlist input + + plotRuns() 'imgoutput' argument has two options 'sep' or 'join' + + Argument 'popcol' changed to clustercol + + Argument 'popmean' changed to grpmean + + Argument 'poplab' changed to grplab + + Argument 'grplab' must now be a named list to allow more than one label sets + + Argument 'flab' changed to 'sp' + + Argument 'splab' added to provide custom labels to strip panels + + Argument 'flabsize' changed to 'splabsize' + + Argument 'flabcol' changed to 'splabcol' + + Argument 'flabbackcol' changed to 'spbgcol' + + Argument 'divgrp' added to define which label set(s) must be divider lines based on + + Argument 'labalpha' added to adjust transparency of labels + + Argument 'linealpha' added to adjust transparency of line + + Argument 'pointalpha' added to adjust transparency of points + + Argument 'divalpha' added to adjust transparency of divider line + + Argument 'legend' added to display legend for cluster colours + + Argument 'legendlab' added to provide custom cluster labels + + Argument 'legendpos' added for legend justification + + Argument 'legendkeysize' added to adjust legend key size + + Argument 'legendtextsize' added to adjust legend text size +* plotMultiline() renamed to plotQMultiline() +* plotQMultiline() modified to accept qlist input +* distructExport() modified to accept qlist input +* Deprecated functions show error messages +* analyseRuns() renamed to analyseQ() +* checkRuns() renamed to checkQ() +* Functions related to spatial, plotRunsInterpolate() and plotRunsSpatial() renamed to plotQInterpolate() and plotQSpatial() and moved to a different package pophelperSpatial + + +pophelper 1.2.1 +=========== +* 05-Sep-2016 +* Fixed a critical bug during parsing in runsToDfStructure() when K=1. Thanks to Emily Humble for reporting this. + +pophelper 1.2.0 +=========== +* 25-July-2016 +* exportDistruct() added to generate input files for software DISTRUCT from STRUCTURE, TESS, MATRIX or TAB files. +* Argument 'indlabfromfile' added to runsToDfStructure() to read individual labels from structure file if available and adds as row names. +* Argument 'indlabfromfile' added to plotMultiline() to read individual labels from structure file if available and use as labels. +* Argument 'indlab' added to plotMultiline() to provide individual labels externally. +* Argument 'popmean' added to plotRuns() to plot population mean values rather than individual values. Applicable only when pop labels are in use. +* plotRuns() is able to handle duplicated contiguous block of pop labels except when using argument 'subsetpops'. +* clumppExportStructure(), clumppExportTess() and clumppExportMatrix() now checks for directory write permission before creating directory. +* Argument 'useexe' added to clumppExportStructure(), clumppExportTess() and clumppExportMatrix() to automatically run CLUMPP. +* Incorrect error messages were reported when some logical arguments were incorrectly set. This has been corrected for tabulateRunsStructure(), tabulateRunsTess(),tabulateRunsMatrix(). +* Dependency on plyr and reshape removed. +* New dependency on tidyr. + +pophelper 1.1.9 +=========== +* 31-May-2016 +* For structure files, 'Mean value of alpha' is no longer reported in tabulateRunsStructure(). Reporting of 'Mean value of alpha' and 'Mean value of Fst' may be reimplemented in future if users think it might be be useful. + +pophelper 1.1.8 +=========== +* 19-May-2016 +* In structure files, when more than one line of 'Mean value of alpha' is present, 'mva' was reported as NA. Now, the mean of the values is reported as 'mva'. Thanks to J A Blanco Aguiar for pointing out this issue. + +pophelper 1.1.7 +=========== +* 18-May-2016 +* runsToDfStructure() produced NA columns when STRUCTURE file contains probability intervals. Fixed. Thanks to J A Blanco Aguiar for pointing out this issue. +* plotMultiline() has a new argument sortlabels to show x-axis labels in the original sort order. +* A critical loop variable issue fixed in plotMultiline(). + +pophelper 1.1.6 +=========== +* 02-Jan-2016 +* Sort individuals by one or all clusters in plotRuns() or plotMultiline(). +* Subset/reorder populations when using pop labels in plotRuns(). +* runsToDfMatrix(), tabulateRunsMatrix(), summariseRunsMatrix(), clumppExportMatrix() implemented for tabular data. +* runsToDfAdmixture(), tabulateRunsAdmixture(), summariseRunsAdmixture(), clumppExportAdmixture() deprecated. +* Argument 'barwidth' deprecated from plotMultiline(). +* Fixed space, labeller for compatibility with ggplot2 2.0.0. + +pophelper 1.1.5 +=========== +* 18-Oct-2015 +* Handling of Admixture files. +* checkRuns modified to use grepl instead of grep and checks for Admixture files too. +* plotRuns() handles ADMIXTURE files. +* plotMultiline() handles ADMIXTURE files. +* plotRunsInterpolate() handles ADMIXTURE files. +* Code optimisation. + +pophelper 1.1.4 +=========== +* 27-Sep-2015 +* Fixed runsToDfStructure() error when the structure file has 'Estimated Allele Frequencies in each population' rather than 'each cluster'. + +pophelper 1.1.3 +=========== +* 27-Sep-2015 +* Error in plotMultiline() with table files corrected. + +pophelper 1.1.2 +=========== +* 17-Sep-2015 +* Error fixed in evannoMethodStructure() when using writetable=T. +Error in vapply(x, format, "", ...) : values must be length 1, + but FUN(X[[1]]) result is length 6 +* Same error fixed in tabulateRunsStructure(). +* Same error fixed in tabulateRunsTess(). +* Same error fixed in summariseRunsStructure(). +* Same error fixed in summariseRunsTess(). +* Error fixed in plotRunsInterpolate(). +Error in theme(legend.key.size = unit(legendsize, "cm")) : + could not find function "unit" + +pophelper 1.1.1 +=========== +* 31-Mar-2015 +* Function plotRuns() modified. + + Spacing between bottom plot and second plot was larger than spacing between other plots. This has been corrected. + + New code to plotting labels + + Arguments to control label panel height (labpanelheight), spacing between plots (panelspacer), spacing between label area and plots (labspacer). + + Argument to include or exclude side panels on right side (flab). + + Argument to include a divider line between populations (flab). Further arguments to modify the divider line. + + Figure dimensions and conversions have been improved. Old dimension settings (length, height, res etc) may give different plot dimension in this version. +* Internal helper functions for plotRuns() modified. +* Function evannoMethodStructure() modified. + + Argument doplot is removed. Set plot off using exportplot=F. + + Argument basesize added to generally control size of figure elements. + + Conversion between units and dimensions have been modified. + +pophelper 1.1.0 +=========== +* 16-Mar-2015 +* Several changes in code to enable faster runtime. +* New HTML vignette created. +* Corrections to NAMESPACE and DESCRIPTION +* Function tabulateRunsStructure() modified. +* Function tabulateRunsTess() modified. +* Function summariseRunsStructure() function modified. 2.5x faster. + + ddply() from plyr() package used to summarise table. + + na.rm argument added for summarising table. na.rm is passed to min(), max(), mean() and sd() functions. + + Output table variable order changed. Current column order is loci, ind, k, runs, elpdmean, elpdsd, elpdmin, elpdmax. +* Function summariseRunsTess() function modified. + + Function ddply() from plyr() package used to summarise table. + + Output table variable order changed. Current column order is ind, k, runs. +* evannoMethodStructure() has an improved plot theme. +* Function plotRuns() modified. + + Argument 'labcol' didn't change colour of labels. Fixed. + + Argument 'pointbgcol' added for background colour of marker points + + Argument 'linetype' added for changing line type of marker line +* Function analyseRuns() function added. A wrapper for several other functions. Performs a tabulation of runs, summarising of runs, perform Evanno method (for STRUCTURE runs only), exports clumpp output and generates barplots. + +pophelper 1.0.4 +=========== +* 18-May-2014 +* Cairo plotting for png exports. Better anti-aliasing. +* fig aspect ratio issue fixed in function plotRunsInterpolate() +* Namespace error resolved for some functions. +* Minor changes to plotRunsInterpolate(). +* plotRunsSpatial() function added. STRUCTURE and TESS runs can be used with a coordinate file to spatially plot the points and colour them into clusters based on the highest probability value. The coordinates can be transformed to UTM coordinates for a better spatial representation. + +pophelper 1.0.3 +=========== +* 11-May-2014 +* Function plotRunsInterpolate() added. STRUCTURE and TESS run files can be used with a coordinate file to spatially interpolate clusters using several interpolation methods such as thin splines, inverse distance weighting and kriging. + +pophelper 1.0.2 +=========== +* 25-Apr-2014 +* A bug in functions clumppExportStructure() and clumppExportTess() produced a 'No input' error. This has been fixed. Thanks to Micheal Panasci for pointing this out. + +pophelper 1.0.1 +=========== +* parameter sorttable added to functions tabulateRunsStructure() and tabulateRunsTess(). Useful if unsorted table is required. + +pophelper 1.0.0 +=========== +* 16-Feb-2014 +* the first version of the `pophelper` package diff --git a/R/pophelper.R b/R/pophelper.R new file mode 100644 index 0000000..a2514f2 --- /dev/null +++ b/R/pophelper.R @@ -0,0 +1,4496 @@ +# Begin ------------------------------------------------------------------------ + +# pophelper v2.2.5 +# Functions +# 11-Jan-2018 + +# check packages +pkgs <- c("Cairo","grid","gridExtra","ggplot2","gtable","tidyr") +if(any(!pkgs %in% installed.packages())) +{ + warning(paste0("Package(s) '",paste0(pkgs[which(!pkgs %in% installed.packages())],collapse=", "),"' is not installed.")) +} +rm(pkgs) + +# compiler::enableJIT(3) + +# getColours ------------------------------------------------------------------- + +#' @title Internal: Generate colours based on number of K +#' @description Internal: Generate colours based on number of K. +#' @param k A numeric indicating the number of colours required +#' @return Returns a character vector of k colours in hexadecimal format +#' @details Colours 1 to 12 are custom unique colours. Colours beyond 15 are generated from colour ramp \code{rich.colors()} from package \code{gplots}. +# @export +#' +getColors <- getColours <- function(k) +{ + if(length(k) > 1) stop("getColours: Input has more than one value. Argument k must be a single numeric or integer.") + if(!is.integer(k) && !is.numeric(k) ) stop("getColours: Input is not an integer. Argument k must be a single numeric or integer.") + k <- as.integer(k) + # standard colours + col1 <- c("#2121D9","#9999FF","#DF0101","#04B404","#FFFB23","#FF9326","#A945FF","#0089B2","#B26314","#610B5E","#FE2E9A","#BFF217") + # col1 <- c("#1D72F5","#DF0101","#77CE61", + # "#FF9326","#A945FF","#0089B2", + # "#FDF060","#FFA6B2","#BFF217", + # "#60D5FD","#CC1577","#F2B950", + # "#7FB21D","#EC496F","#326397", + # "#B26314","#027368","#A4A4A4", + # "#610B5E") + if(k <= 12) return(col1[1:k]) + if(k > 12) + { + cr <- colorRampPalette(colors=c("#000040FF","#00004FFF","#000060FF","#000074FF","#000088FF","#00009DFF","#0000B2FF", + "#0000C6FF","#000CD8FF","#0022E7FF","#0037F3FF","#004BFBFF","#005EFFFF","#0070FEFF", + "#0081F8FF","#0091EEFF","#00A0E0FF","#00ADCFFF","#00BABCFF","#00C6A7FF","#01D092FF", + "#02DA7EFF","#03E26AFF","#07E958FF","#0EF047FF","#1BF539FF","#31F92CFF","#54FC22FF", + "#80FE1AFF","#ABFF13FF","#CEFF0EFF","#E4FE0AFF","#F1FB07FF","#F8F805FF","#FCF403FF", + "#FDEE02FF","#FEE801FF","#FFE001FF","#FFD801FF","#FFCE00FF","#FFC300FF","#FFB800FF", + "#FFAB00FF","#FF9D00FF","#FF8E00FF","#FF7E00FF","#FF6D00FF","#FF5B00FF","#FF4700FF", + "#FF3300FF"),space="rgb") + return(cr(k)) + } +} + +# checkQ -------------------------------------------------------------------- + +#' @title Internal: Check input filetype. +#' @description Internal: Check input filetype. +#' @param files A character or character vector of one or more input text files or a list of dataframes. +#' @param warn A logical indicating if a warning must be displayed for file those are not STRUCTURE, TESS or BASIC file. +#' @return A character or character vector indicating input type 'STRUCTURE', 'TESS', 'BASIC', 'CLUMPP', 'list', 'data.frame', 'UNIDENTIFIED' for all selected files. +# @export +#' +checkQ <- function(files=NULL,warn=FALSE) +{ + if(is.null(files)) stop("checkQ: Input is empty.") + if(class(files) != "list" && class(files) != "character") stop("checkQ: Input is not a character or list datatype.") + + len1 <- length(files) + + checkvec <- rep("UNIDENTIFIED",length=len1) + subtype <- rep(NA,length=len1) + for(i in 1:len1) + { + chk <- FALSE + + if(class(files)=="list") + { + if(class(files[[i]])=="data.frame") + { + chk <- TRUE + checkvec[i] <- "data.frame" + } + } + + if(!chk) + { + + read1 <- readLines(files[i],n=7,warn=FALSE) + + # read BAPS file + if(!chk) + { + chk <- any(grepl("RESULTS OF ADMIXTURE ANALYSIS BASED",toupper(read1))) + if(chk) checkvec[i] <- "BAPS" + } + + # read TESS file + if(!chk) + { + chk <- grepl("ESTIMATED CLUSTERING PROBABILITIES",toupper(read1)[1]) + if(chk) checkvec[i] <- "TESS" + } + + # read STRUCTURE file + if(!chk) + { + chk <- grepl("STRUCTURE BY PRITCHARD",toupper(read1)[4]) + if(chk) checkvec[i] <- "STRUCTURE" + } + + # read BASIC files + + rm(read1) + + if(!chk) + { + seps <- c("","\t",",") + subtypes <- c("SPACE","TAB","COMMA") + k=1 + while(!chk) + { + if(class(try(suppressWarnings(read.table(files[i],header=FALSE,sep=seps[k],nrows=1,quote="",stringsAsFactors=FALSE))))!="try-error") + { + df <- read.table(files[i],header=FALSE,sep=seps[k],nrows=1,quote="",stringsAsFactors=FALSE) + if(all(sapply(df,is.numeric))) { + checkvec[i] <- "BASIC" + subtype[i] <- subtypes[k] + chk <- TRUE + }else{ + if((ncol(df) > 2) && (is.character(df[,1]))) + { + checkvec[i] <- "CLUMPP" + chk <- TRUE + } + } + } + k=k+1 + if(k>3) break + } + } + } + if((!chk) && warn) warning(paste0("checkQ: ",files[i]," is not a STRUCTURE, TESS, BAPS, BASIC or CLUMPP file.")) + } + + return(list(type=checkvec,subtype=subtype)) +} + +# is.qlist -------------------------------------------------------------------- + +#' @title Verify if a qlist is formatted correctly. +#' @description Verify if a qlist is formatted correctly. +#' @param qlist A qlist object. +#' @return Nothing. +#' @export +#' +is.qlist <- function(qlist=NULL) +{ + if(is.null(qlist)) stop("is.qlist: Input is empty.") + + # is it a list? + if(!is.list(qlist)) stop("is.qlist: Input is not a list object.") + + # does it have dataframes? + if(!all(sapply(qlist,is.data.frame))) stop("is.qlist: One or more list elements are not data.frame datatype.") + + # any NA? + if(any(is.na(qlist))) stop("is.qlist: One or more list elements are NA.") + + # are dataframe lists named? + if(is.null(names(qlist))) stop("is.qlist: List elements are not named.") + + # are dataframe lists named? + if(any(is.na(names(qlist)))) stop("is.qlist: One or more list element name is NA.") + + # are all dataframe lists named? + if(any(nchar(names(qlist))==0)) stop("is.qlist: One or more list elements are not named.") + + # are there duplicated list names? + if(any(duplicated(names(qlist)))) stop("is.qlist: One or more list element names are duplicated.") + + # are dataframes all numeric? + if(!all(unlist(lapply(qlist,sapply,is.numeric)))) stop("is.qlist: One or more qlist dataframes have non-numeric columns.") + + # are there duplicated rownames? + if(any(unlist(lapply(lapply(qlist,rownames),duplicated)))) stop("is.qlist: One or more qlist dataframes have duplicated row names.") + + # are there duplicated column names? + if(any(unlist(lapply(lapply(qlist,colnames),duplicated)))) stop("is.qlist: One or more qlist dataframes have duplicated column names.") + + # do column names have format Cluster? + if(!all(grepl("Cluster[0-9]+$",unlist(lapply(qlist,colnames))))) warning("is.qlist: One or more qlist dataframes have column names that do not conform to format 'ClusterNumber' like 'Cluster1', 'Cluster12' etc.") +} + +# verifyGrplab -------------------------------------------------------------------- + +#' @title Verify if a grplab dataframe is formatted correctly. +#' @description Verify if a grplab dataframe is formatted correctly. +#' @param grplab A dataframe with character fields. +#' @return Nothing. +#' @export +#' +verifyGrplab <- function(grplab=NULL) +{ + if(is.null(grplab)) stop("verifyGrplab: Argument 'grplab' is empty.") + + # is it a dataframe? + if(!is.data.frame(grplab)) stop("verifyGrplab: Argument 'grplab' is not a data.frame object.") + + # are there NAs in labels? + if(any(sapply(grplab,is.na))) stop("verifyGrplab: Argument 'grplab' contains NAs.") + + # are all elements character datatype? + if(!any(sapply(grplab,is.character))) stop("verifyGrplab: Argument 'grplab' contains one or more fields which are not character datatype.") +} + +# unitConverter ---------------------------------------------------------------- + +#' @title Internal: Convert value between dimension units +#' @description Internal: Convert value between dimension units +#' @param value A numeric value or numeric vector to convert +#' @param fromunit A character indicating the current unit of the value. Options are "cm", "mm", "in" or "px". +#' @param tounit A character indicating the unit to change to. Options are "cm", "mm", "in" or "px". +#' @param dpi A numeric indicating the resolution for pixel conversion. This should be in PPI (pixels per inch). +#' @return Returns a numeric value or numeric vector in changed units. +#' +unitConverter <- function(value=NA,fromunit=NA,tounit=NA,dpi=NA) +{ + # check + if(all(is.na(value))) stop("unitConverter: Argument value is empty.") + if(is.na(fromunit)) stop("unitConverter: Argument fromunit is empty.") + if(is.na(tounit)) stop("unitConverter: Argument tounit is empty.") + + if(fromunit=="cm") + { + if(tounit=="cm") outvalue <- value + if(tounit=="mm") outvalue <- round(value*10,2) + if(tounit=="in") outvalue <- round(value*0.3937,2) + if(tounit=="px") + { + if(is.na(dpi)) stop("unitConverter: Argument dpi is empty.") + #convert dpi to 1 cm + pxpercm <- dpi/2.54 + outvalue <- round(pxpercm*value,0) + } + } + + if(fromunit=="mm") + { + if(tounit=="mm") outvalue <- value + if(tounit=="cm") outvalue <- round(value/10,2) + if(tounit=="in") outvalue <- round(value*0.03937,2) + if(tounit=="px") + { + if(is.na(dpi)) stop("unitConverter: Argument dpi is empty.") + #convert dpi to 1 mm + pxpermm <- dpi/25.4 + outvalue <- round(pxpermm*value,0) + } + } + + if(fromunit=="in") + { + if(tounit=="in") outvalue <- value + if(tounit=="cm") outvalue <- round(value*2.54,2) + if(tounit=="mm") outvalue <- round(value*0.254,2) + if(tounit=="px") + { + if(is.na(dpi)) stop("unitConverter: Argument dpi is empty.") + outvalue <- round(dpi*value,0) + } + } + + if(fromunit=="px") + { + if(tounit=="px") outvalue <- value + if(is.na(dpi)) stop("unitConverter: Argument dpi is empty.") + + if(tounit=="cm") + { + pxpercm <- dpi/2.54 + outvalue <- value/pxpercm + } + + if(tounit=="mm") + { + pxpermm <- dpi/25.4 + outvalue <- value/pxpermm + } + + if(tounit=="in") outvalue <- value/dpi + + } + + return(outvalue) +} + +# readQ ------------------------------------------------------------------------ + +#' @title Convert run files (q-matrices) to qlist. +#' @description Takes one or more STRUCTURE, TESS, BAPS, numeric delimited run files or +#' CLUMPP format files and converts them to a qlist (list of dataframes). +#' @param files A character or character vector of one or more files. +#' @param filetype A character indicating input filetype. Options are 'auto','structure','tess','baps', +#' 'basic' or 'clumpp'. See details. +#' @param indlabfromfile A logical indicating if individual labels must be read +#' from input file and used as row names for resulting dataframe. Spaces in +#' labels may be replaced with _. Currently only applicable to STRUCTURE runs files. +#' @return A list of lists with dataframes is returned. List items are named by input filenames. +#' File extensions such as '.txt','.csv','.tsv' and '.meanQ' are removed from filename. +#' In case filenames are missing or not available, lists are named sample1, sample2 etc. +#' For STRUCTURE runs, if individual labels are present in the run file and \code{indlabfromfile=T}, +#' they are added to the dataframe as row names. Structure metadata including loci, +#' burnin, reps, elpd, mvll, and vll is added as attributes to each dataframe. +#' For CLUMPP files, multiple runs within one file are suffixed by -1, -2 etc. +#' @details +#' STRUCTURE, TESS and BAPS run files have unique layout and format (See vignette). BASIC files can be Admixture run files, +#' fastStructure meanQ files or any tab-delimited, space-delimited or comma-delimited tabular data +#' without a header. CLUMPP files can be COMBINED, ALIGNED or +#' MERGED files. COMBINED files are generated from \code{clumppExport}. ALIGNED and +#' MERGED files are generated by CLUMPP. +#' +#' To convert TESS3 R objects to pophelper qlist, see \code{\link{readQTess3}}. +#' +#' See the \href{http://royfrancis.github.io/pophelper/}{vignette} for more details. +#' +#' @seealso \code{\link{readQTess3}} +#' +#' @examples +#' +#' # STRUCTURE files +#' sfiles <- list.files(path=system.file("files/structure",package="pophelper"),full.names=TRUE) +#' # create a qlist of all runs +#' slist <- readQ(sfiles) +#' slist <- readQ(sfiles,filetype="structure") +#' +#' # use ind names from file +#' readQ(sfiles[1],indlabfromfile=T) +#' +#' # access the first run +#' readQ(sfiles)[[1]] +#' +#' # access names of runs +#' names(slist) +#' +#' # TESS files +#' tfiles <- list.files(path=system.file("files/tess",package="pophelper"),full.names=TRUE) +#' # create a qlist +#' readQ(tfiles) +#' +#' # BASIC files +#' afiles <- list.files(path=system.file("files/admixture",package="pophelper"),full.names=TRUE) +#' # create a qlist +#' readQ(afiles) +#' +#' # CLUMPP files +#' tabs1 <- system.file("files/STRUCTUREpop_K4-combined.txt",package="pophelper") +#' tabs2 <- system.file("files/STRUCTUREpop_K4-combined-aligned.txt",package="pophelper") +#' tabs3 <- system.file("files/STRUCTUREpop_K4-combined-merged.txt",package="pophelper") +#' +#' # create a qlist +#' readQ(tabs1) +#' readQ(tabs2) +#' readQ(tabs3) +#' +#' # manually create qlist +#' df1 <- data.frame(Cluster1=c(0.2,0.4,0.6,0.2),Cluster2=c(0.8,0.6,0.4,0.8)) +#' df2 <- data.frame(Cluster1=c(0.3,0.1,0.5,0.6),Cluster2=c(0.7,0.9,0.5,0.4)) +#' +#' # one-element qlist +#' q1 <- list("sample1"=df1) +#' str(q1) +#' +#' # two-element qlist +#' q2 <- list("sample1"=df1,"sample2"=df2) +#' str(q2) +#' +#' @export +#' +readQ <- function(files=NULL,filetype="auto",indlabfromfile=FALSE) +{ + if(is.null(files) || (length(files)==0)) stop("readQ: No input files.") + if(!is.character(files)) stop("readQ: Argument 'files' is not a character datatype.") + flen <- length(files) + + len <- length(files) + dlist <- vector("list") + for (i in 1:len) + { + # check file + if(filetype=="auto") + { + chk <- tolower(pophelper:::checkQ(files[i])$type) + + if(chk %in% c("structure","tess","baps","basic","clumpp")) + { + if(chk=="structure") dfr <- pophelper:::readQStructure(files[i],indlabfromfile=indlabfromfile) + if(chk=="tess") dfr <- pophelper:::readQTess(files[i]) + if(chk=="basic") dfr <- pophelper:::readQBasic(files[i]) + if(chk=="clumpp") dfr <- pophelper:::readQClumpp(files[i]) + if(chk=="baps") dfr <- pophelper:::readQBaps(files[i]) + dlist <- append(dlist,dfr) + }else{ + warning(paste0("readQ: Input file ",files[i]," was not identified as a STRUCTURE, TESS, BAPS, BASIC or CLUMPP filetype. Specify 'filetype' manually or check input.")) + } + }else{ + if(filetype=="structure") dfr <- pophelper:::readQStructure(files[i],indlabfromfile=indlabfromfile) + if(filetype=="tess") dfr <- pophelper:::readQTess(files[i]) + if(filetype=="basic") dfr <- pophelper:::readQBasic(files[i]) + if(filetype=="clumpp") dfr <- pophelper:::readQClumpp(files[i]) + if(filetype=="baps") dfr <- pophelper:::readQBaps(files[i]) + dlist <- append(dlist,dfr) + } + } + return(dlist) +} + +# readQStructure ------------------------------------------------------------ + +#' @title Convert STRUCTURE run files to qlist. +#' @description Takes one or more STRUCTURE run files and converts them to a list of dataframes. +#' @param files A character or character vector of one or more STRUCTURE run files. Use \code{choose.files(multi=TRUE)} +#' to select interactively. +#' @param indlabfromfile A logical indicating if individual labels must be read from input file and used as row names for resulting dataframe. Spaces in labels may be replaced with _. +#' @return A list of lists with dataframes is returned. If individual labels are +#' present in the STRUCTURE file, they are added to the dataframe as row names. Structure +#' metadata including loci, burnin, reps, elpd, mvll, and vll is added as attributes +#' to each dataframe. List items are named by input filenames. +#' @examples +#' sfiles <- list.files(path=system.file("files/structure",package="pophelper"),full.names=TRUE) +#' # create a qlist of all runs +#' slist <- readQStructure(sfiles) +#' +#' # use ind names from file +#' readQStructure(sfiles[1],indlabfromfile=T) +#' +#' # access the first run +#' readQStructure(sfiles)[[1]] +#' +#' # access names of runs +#' names(slist) +#' @export +#' +readQStructure <- function(files=NULL,indlabfromfile=FALSE) +{ + if(is.null(files) || (length(files)==0)) stop("readQStructure: No input files.") + # number of files selected + flen <- length(files) + + #check file + if(any(pophelper:::checkQ(files)$type != "STRUCTURE")) error("readQStructure: Input may be in incorrect format.") + + i <- 1 + dlist <- vector("list",length=flen) + len1 <- length(files) + for (i in 1:len1) + { + fname <- basename(files[i]) + file1 <- readLines(as.character(files[i]),warn=FALSE) + + # find individuals and get number of individuals + ind <- as.numeric(as.character(base::gsub("\\D","",grep("\\d individuals",file1,perl=TRUE,ignore.case=TRUE,value=TRUE)[1]))) + if(is.na(ind)) cat(paste0("Number of individuals is NA in file: ",fname,"\n")) + + # get value of k & error check + k <- as.numeric(as.character(base::gsub("\\D","",grep("\\d populations assumed",file1,perl=TRUE,ignore.case=TRUE,value=TRUE)[1]))) + if(is.na(k)) cat(paste0("Value of K is NA in file: ",fname,"\n")) + + # get number of loci & error check + loci <- as.numeric(base::gsub("\\D","",grep("\\d loci",file1,perl=TRUE,ignore.case=TRUE,value=TRUE)[1])) + if(is.na(loci)) cat(paste0("Number of Loci is NA in file: ",files[i],"\n")) + + # get burn-in value & error check + burnin <- as.numeric(base::gsub("\\D","",grep("\\d Burn-in period",file1,perl=TRUE,ignore.case=TRUE,value=TRUE)[1])) + if(is.na(burnin)) cat(paste0("Burn-in value is NA in file: ",files[i],"\n")) + + # get burn-in value & error check + reps <- as.numeric(base::gsub("\\D","",grep("\\d Reps",file1,perl=TRUE,ignore.case=TRUE,value=TRUE)[1])) + if(is.na(reps)) cat(paste0("Reps value is NA in file: ",files[i],"\n")) + + # get est ln prob of data & error check + elpd <- as.numeric(base::gsub("=","",base::gsub("Estimated Ln Prob of Data","",grep("Estimated Ln Prob of Data",file1,perl=TRUE,ignore.case=TRUE,value=TRUE)[1]))) + if(is.na(elpd)) cat(paste0("Estimated Ln Prob of Data is NA in file: ",files[i],"\n")) + + # get mn value of ln likelihood & error check + mvll <- as.numeric(base::gsub("=","",base::gsub("Mean value of ln likelihood","",grep("Mean value of ln likelihood",file1,perl=TRUE,ignore.case=TRUE,value=TRUE)[1]))) + if(is.na(mvll)) cat(paste0("Mean value of ln likelihood is NA in file: ",files[i],"\n")) + + # get Variance of ln likelihood else NA + vll <- as.numeric(base::gsub("=","",base::gsub("Variance of ln likelihood","",grep("Variance of ln likelihood",file1,perl=TRUE,ignore.case=TRUE,value=TRUE)[1]))) + if(is.na(vll)) cat(paste0("Variance of ln likelihood is NA in file: ",files[i],"\n")) + + file1 <- file1[grep(".+\\(\\d+\\).+\\:.+",file1)] + if(length(file1)==0) + { + cstart <- base::charmatch("Inferred ancestry of individuals",file1) + cend <- base::charmatch("Estimated Allele Frequencies in each",file1) + file1 <- file1[(cstart+2):(cend-1)] + } + + file_a <- file1[file1 != ""] + rm(file1) + + # error check + tc_file_a <- textConnection(file_a) + file_b <- read.delim(tc_file_a,header=F,sep="",stringsAsFactors=F) + close(tc_file_a) + + suppressWarnings( + errorcheck <- try( + file_b[,as.integer(grep(":",file_b[1,])+1):as.integer(max(grep("^[0-9]|[.]+$",file_b[1,]))),drop=F], + silent=T) + ) + rm(file_b) + + if(class(errorcheck)=="try-error") + { + # using manual substring + file_a <- base::gsub("\\([0-9.,]+\\)","",file_a) + file_b <- base::gsub(": ","",substr(file_a,base::regexpr(":\\W+\\d\\.\\d+",file_a),base::nchar(file_a)-1)) + file_b <- base::sub("\\s+$","",base::sub("^\\s+","",file_b)) + rm(file_a) + file_c <- as.vector(as.numeric(as.character(unlist(base::strsplit(file_b," "))))) + rm(file_b) + dframe <- as.data.frame(matrix(file_c,nrow=ind,byrow=TRUE),stringsAsFactors=FALSE) + }else{ + # using textconnection + tc_file_a <- textConnection(file_a) + file_b <- read.delim(tc_file_a,header=F,sep="",stringsAsFactors=F) + close(tc_file_a) + dframe <- file_b[,as.integer(grep(":",file_b[1,])+1):as.integer(max(grep("^[0-9]|[.]+$",file_b[1,]))),drop=F] + } + + dframe <- as.data.frame(sapply(dframe,as.numeric),stringsAsFactors=FALSE) + colnames(dframe) <- paste0("Cluster",1:ncol(dframe)) + row.names(dframe) <- 1:nrow(dframe) + #row.names(dframe) <- sprintf(paste0("%",paste0(rep(0,nchar(nrow(dframe))),collapse=""),nchar(nrow(dframe)),"d"),1:nrow(dframe)) + + # add labels + if(indlabfromfile) + { + labeldf <- file_b[,(grep("[0-9]",file_b[1,])[1]+1):(grep("[(]",file_b[1,])[1]-1),drop=FALSE] + + if(ncol(labeldf) > 1) labeldf <- data.frame(V2=do.call(paste,c(labeldf,sep="_")),stringsAsFactors=FALSE) + if(nrow(labeldf)==nrow(dframe)) + { + if(any(duplicated(labeldf[,1]))) + { + warning(paste0("readQStructure: Individual names in file ",fname," not used due to presence of duplicate names.")) + }else{ + row.names(dframe) <- as.character(labeldf[,1]) + } + }else{ + warning(paste0("readQStructure: Individual names in file ",fname," not used due to incorrect length.")) + } + } + + attr(dframe,"ind") <- nrow(dframe) + attr(dframe,"k") <- ncol(dframe) + attr(dframe,"loci") <- loci + attr(dframe,"burnin") <- burnin + attr(dframe,"reps") <- reps + attr(dframe,"elpd") <- elpd + attr(dframe,"mvll") <- mvll + attr(dframe,"vll") <- vll + + dlist[[i]] <- dframe + #names(dlist[[i]]) <- as.character(name) + } + + fnames <- sub(".txt","",basename(files)) + names(dlist) <- fnames + return(dlist) +} + +# readQTess ----------------------------------------------------------------- + +#' @title Convert TESS cluster files to qlist. +#' @description Takes one or more TESS cluster run files and converts them to a +#' list of dataframes. +#' @param files A character or character vector of one or more TESS cluster run files. Use \code{choose.files(multi=TRUE)} +#' to select interactively. +#' @return A list of lists with dataframes is returned. List items are named by input filename. +#' @details Use collectRunsTess() to collect TESS runs into one directory. +#' @examples +#' tfiles <- list.files(path=system.file("files/tess",package="pophelper"),full.names=TRUE) +#' # create a qlist +#' readQTess(tfiles) +#' @export +#' +readQTess <- function(files=NULL) +{ + if(is.null(files) || (length(files)==0)) stop("readQTess: No input files.") + # number of files selected + flen <- length(files) + + # check file + if(any(pophelper:::checkQ(files)$type != "TESS")) error("readQTess: Input may contain incorrect input format.") + + i <- 1 + dlist <- vector("list",length=flen) + len1 <- length(files) + for (i in 1:len1) + { + # read whole file in + file1 <- readLines(files[i],warn=FALSE) + + # extract the cluster table part + file1 <- file1[3:c(grep("Estimated Allele Frequencies",file1)-1)] + + # remove empty lines + file1 <- file1[file1 != ""] + + # create a text connection + tc_file1 <- textConnection(file1) + + # read as a table + file2 <- read.delim(tc_file1,header=F,sep="\t",stringsAsFactors=FALSE) + + # close text connection + close(tc_file1) + + # choose columns 2 to numofcols-2 + dframe <- file2[,2:(ncol(file2)-2)] + + # remove temporary files + rm(file1,file2) + + # convert all columns to numeric + dframe <- as.data.frame(sapply(dframe,as.numeric),stringsAsFactors=FALSE) + + # add column names + colnames(dframe) <- paste0("Cluster",1:ncol(dframe)) + + # add attributes + attr(dframe,"ind") <- nrow(dframe) + attr(dframe,"k") <- ncol(dframe) + + # add to list + dlist[[i]] <- dframe + } + + # add file names as qlist names + fnames <- sub(".txt","",basename(files)) + names(dlist) <- fnames + + return(dlist) +} + +# readQBasic --------------------------------------------------------------- + +#' @title Convert delimited text files to qlist. +#' @description Takes one or more delimited numeric text files and converts each of +#' them to separate dataframes. +#' @param files A character or character vector of one or more delimited text files. Use \code{choose.files(multi=TRUE)} +#' to select interactively. +#' @return A list of lists with dataframes is returned. List items are named by input filename. +#' @details Input files can be Admixture run files, fastStructure meanQ files. +#' or any tab-delimited, space-delimited or comma-delimited tabular data without header. +#' @examples +#' afiles <- list.files(path=system.file("files/admixture",package="pophelper"),full.names=TRUE) +#' # create a qlist +#' readQBasic(afiles) +#' @export +#' +readQBasic <- function(files=NULL) +{ + if(is.null(files) || (length(files)==0)) stop("readQBasic: No input files.") + + # number of files selected + flen <- length(files) + + # check input file type + chk <- pophelper:::checkQ(files) + if(any(chk$type != "BASIC")) error("readQBasic: Input may be in incorrect format.") + if(any(is.na(chk$subtype))) warning("readQBasic: Input may be in incorrect format.") + + i <- 1 + dlist <- vector("list",length=flen) + len1 <- length(files) + for (i in 1:len1) + { + # read in delimited files + if(chk$subtype[i]=="SPACE") dframe <- read.delim(files[i],header=F,sep="",dec=".",stringsAsFactors=FALSE) + if(chk$subtype[i]=="TAB") dframe <- read.delim(files[i],header=F,sep="\t",dec=".",stringsAsFactors=FALSE) + if(chk$subtype[i]=="COMMA") dframe <- read.delim(files[i],header=F,sep=",",dec=".",stringsAsFactors=FALSE) + + # error if columns contain non-numeric + if(!all(sapply(dframe,is.numeric))) stop("readQBasic: One or more columns are not numeric.") + colnames(dframe) <- paste0("Cluster",1:ncol(dframe)) + + # add attributes + attr(dframe,"ind") <- nrow(dframe) + attr(dframe,"k") <- ncol(dframe) + + dlist[[i]] <- dframe + } + + # remove file name extensions + fnames <- sub(".txt","",basename(files)) + fnames <- sub(".tsv","",basename(files)) + fnames <- sub(".csv","",basename(files)) + fnames <- sub(".meanQ","",basename(files)) + + # add file names to qlist + names(dlist) <- fnames + + return(dlist) +} + +# readQClumpp --------------------------------------------------------------- + +#' @title Convert CLUMPP format numeric text files to qlist. +#' @description Takes one or more CLUMPP format numeric text files and converts +#' them to a list of dataframes. +#' @param files A character or character vector of one or more COMBINED, ALIGNED or +#' MERGED files. COMBINED files are generated from \code{clumppExport}. ALIGNED and +#' MERGED files are generated by CLUMPP. Use \code{choose.files(multi=TRUE)} to +#' select interactively. +#' @return A list of lists with dataframes is returned. Each list item is named by +#' input filename. Multiple runs within one file are suffixed by -1, -2 etc. +#' @examples +#' tabs1 <- system.file("files/STRUCTUREpop_K4-combined.txt",package="pophelper") +#' tabs2 <- system.file("files/STRUCTUREpop_K4-combined-aligned.txt",package="pophelper") +#' tabs3 <- system.file("files/STRUCTUREpop_K4-combined-merged.txt",package="pophelper") +#' +#' # create a qlist +#' readQClumpp(tabs1) +#' readQClumpp(tabs2) +#' readQClumpp(tabs3) +#' +#' @export +#' +readQClumpp <- function(files=NULL) +{ + if(is.null(files) || (length(files)==0)) stop("readQClumpp: No input files.") + + # number of files selected + flen <- length(files) + + # check file + chk <- pophelper:::checkQ(files) + if(any(chk$type != "CLUMPP")) error("readQClumpp: Input may be in incorrect format.") + + i <- 1 + k <- 1 + dlist <- vector("list") + snames <- vector() + len1 <- length(files) + for (i in 1:len1) + { + fname <- base::gsub(".txt","",basename(files[i])) + + df1 <- read.table(files[i],header=F,sep="",dec=".",quote="",stringsAsFactors=FALSE) + if(class(df1)!="data.frame") stop("readQClumpp: Read error. Check input format.") + + df1[,1] <- factor(df1[ ,1]) + indlev <- levels(df1[,1]) + + # error check + if((nrow(df1) %% length(indlev)) != 0) stop("readQClumpp: Number of individuals is not a multiple of the total number of rows.") + + Ind <- as.numeric(as.character(length(indlev))) + tempb <- as.numeric(nrow(df1)) + numruns <- as.numeric(tempb/Ind) + numk <- ncol(df1) - 2 + + df2 <- data.frame(Num=factor(rep(1:numruns,1,each=Ind)), + Ind=factor(rep(1:Ind,numruns)), + df1[,2:(numk+1)],stringsAsFactors=FALSE) + colnames(df2)[3:ncol(df2)] <- paste0("Cluster",1:(ncol(df2)-2)) + + for(j in 1:numruns) + { + dframe <- subset(df2,df2$Num==j) + dframe$Num <- NULL + dframe$Ind <- NULL + snames <- c(snames,paste0(fname,"-",j)) + + if(!all(sapply(dframe,is.numeric))) stop("readQClumpp: One or more columns are not numeric.") + + attr(dframe,"ind") <- nrow(dframe) + attr(dframe,"k") <- ncol(dframe) + + dlist[[k]] <- dframe + k <- k+1 + } + } + + snames <- sub(".txt","",snames) + snames <- sub(".tsv","",snames) + snames <- sub(".csv","",snames) + snames <- sub(".meanQ","",snames) + + names(dlist) <- snames + return(dlist) +} + +# readQTess3 ------------------------------------------------------------------- + +#' @title Convert TESS3 R object to pophelper qlist. +#' @description Takes a TESS3 R object and convert to pophelper qlist for use with pophelper. +#' @param t3list A TESS3 object. An output from function \code{tess3()} from package \code{tess3r}. +#' @param progressbar A logical indicating if execution progress must be shown. +#' @return A list of lists with dataframes (qlist) is returned. Each list item is named by +#' as sample1, sample2 etc. Within TESS3, 'tess3Main' attributes L, n, ploidy, K, rmse +#' and crossentropy are preserved as attributes in the qlist dataframe. +#' @details See the \href{http://royfrancis.github.io/pophelper/}{vignette} for more details. +#' @examples +#' t3obj <- readRDS(system.file("files/tess3.rds",package="pophelper")) +#' t3list <- readQTess3(t3obj) +#' @export +#' +readQTess3 <- function(t3list=NULL,progressbar=FALSE) +{ + if(is.null(t3list)) stop("readQTess3: Input is empty.") + if(!any("tess3" %in% class(t3list))) warning("readQTess3: Input cannot be identified as a valid tess3 class object.") + length(t3list) + + # initialise loop variables + len <- length(t3list) + qlist <- vector("list",length=len) + if(progressbar) pb <- txtProgressBar(min=0,max=len,style=3) + + # loop to read in data + for(i in 1:len) + { + if(progressbar) setTxtProgressBar(pb,i) + if(!"tess3.run" %in% names(t3list[[i]])) stop("readQTess3: 'tess3.run' slot not found in list item ",i,".") + dlist <- t3list[[i]]$tess3.run[[1]] + dframe <- as.data.frame(dlist$Q,stringsAsFactors=F) + colnames(dframe) <- paste0("Cluster",1:ncol(dframe)) + + # attribute values as added if available else set to NA + if("n" %in% names(dlist)) {attr(dframe,"ind") <- dlist$n} else {attr(dframe,"ind") <-NA} + if("K" %in% names(dlist)) {attr(dframe,"k") <- dlist$K} else {attr(dframe,"k") <- NA} + if("L" %in% names(dlist)) {attr(dframe,"loci") <- dlist$L} else {attr(dframe,"loci") <- NA} + if("gif" %in% names(dlist)) {attr(dframe,"gif") <- dlist$gif} else {attr(dframe,"gif") <- NA} + if("rmse" %in% names(dlist)) {attr(dframe,"rmse") <- dlist$rmse} else {attr(dframe,"rmse") <- NA} + if("crossentropy" %in% names(dlist)) {attr(dframe,"crossentropy") <- dlist$crossentropy} else {attr(dframe,"crossentropy") <- NA} + if("ploidy" %in% names(dlist)) {attr(dframe,"ploidy") <- dlist$ploidy} else {attr(dframe,"ploidy") <- NA} + + qlist[[i]] <- dframe + } + if(progressbar) close(pb) + # list items are labelled + names(qlist) <- paste0("sample",1:len) + + return(qlist) +} + +# readQBaps ----------------------------------------------------------------- + +#' @title Convert BAPS cluster files to qlist. +#' @description Takes one or more BAPS cluster run files and converts them to a +#' list of dataframes. +#' @param files A character or character vector of one or more BAPS cluster run files. Use \code{choose.files(multi=TRUE)} +#' to select interactively. +#' @return A list of lists with dataframes is returned. List items are named by input filename. +#' @details See the \href{http://royfrancis.github.io/pophelper/}{vignette} for more details. +#' @examples +#' bfiles <- list.files(path=system.file("files/baps",package="pophelper"),full.names=TRUE) +#' # create a qlist +#' readQBaps(bfiles) +#' @export +#' +readQBaps <- function(files=NULL) +{ + if(is.null(files) || (length(files)==0)) stop("readQBaps: No input files.") + # number of files selected + flen <- length(files) + + # check if file type is BAPS + if(any(pophelper:::checkQ(files)$type != "BAPS")) error("readQBaps: Input may be in incorrect format.") + + i <- 1 + dlist <- vector("list",length=flen) + len1 <- length(files) + for (i in 1:len1) + { + # read in all lines from file + file1 <- readLines(files[i],warn=FALSE) + + # extract the cluster table part + file1 <- file1[grep("^1:",file1):length(file1)] + + # read table using delimiter : and use column V2 + tc_file1 <- textConnection(file1) + file2 <- read.delim(tc_file1,sep=":",header=F,stringsAsFactors=F)$V2 + + # read table using delimiter space + tc_file2 <- textConnection(file2) + dframe <- read.delim(tc_file2,sep="",header=F,stringsAsFactors=F) + + # close text connections + close(tc_file1,tc_file2) + + # remove temporary objects + rm(file1,file2) + + # convert all columns to numeric + dframe <- as.data.frame(sapply(dframe,as.numeric),stringsAsFactors=FALSE) + + # create valid column names + colnames(dframe) <- paste0("Cluster",1:ncol(dframe)) + + # attach attributes to dataframe + attr(dframe,"ind") <- nrow(dframe) + attr(dframe,"k") <- ncol(dframe) + + # place dataframe in a list + dlist[[i]] <- dframe + } + + # remove .txt in all file names + fnames <- sub(".txt","",basename(files)) + # label qlist objects with file names + names(dlist) <- fnames + + return(dlist) +} + +# tabulateQ -------------------------------------------------------------------- + +#' @title Tabulate runs from a qlist +#' @description Takes a qlist of one of more numeric dataframes and creates a +#' table with filenames, K and number of individuals. +#' @param qlist A qlist (list of dataframes). An output from \code{\link{readQ}}. +#' @param writetable A logical indicating if the output table must be exported as +#' a tab-delimited text file in the working directory. +#' @param sorttable A logical indicating if output table is to be sorted. Sorts table by ind and K. +#' @return Returns a dataframe with filenames (if list is not named, then sample1, sample2 etc. is used), +#' K and number of individuals of all runs sorted by ind and K (if \code{sorttable=T}). +#' The row numbers of the output table denotes the file number selected. This is helpful +#' if a particular file from the table needs to +#' be identified in the selection vector. If input files come from STRUCTURE runs, +#' columns loci, burnin, reps, elpd, mvll and vll are also returned. In input files come +#' from TESS3, columns loci, gif, rmse, crossentropy and ploidy are included as well. +#' @details The input must be a list of dataframes. If one dataframe is used, then it +#' must be inside a list. If the list items are named, then the item name is used as +#' filename, else sample1, sample2 etc. is used. +#' +#' See the \href{http://royfrancis.github.io/pophelper/}{vignette} for more details. +#' +#' @seealso \code{\link{summariseQ}} +#' @examples +#' +#' # STRUCTURE files +#' sfiles <- list.files(path=system.file("files/structure",package="pophelper"),full.names=TRUE) +#' slist <- readQ(sfiles) +#' tabulateQ(qlist=slist) +#' +#' # TESS files +#' tfiles <- list.files(path=system.file("files/tess",package="pophelper"),full.names=TRUE) +#' tlist <- readQ(tfiles) +#' tabulateQ(qlist=tlist) +#' +#' # ADMIXTURE files +#' afiles <- list.files(path=system.file("files/admixture",package="pophelper"),full.names=TRUE) +#' alist <- readQ(afiles) +#' tabulateQ(qlist=alist) +#' +# @import xlsx +#' @export +#' +tabulateQ <- function(qlist=NULL,writetable=FALSE,sorttable=TRUE) +{ + + # check input + is.qlist(qlist) + if(!is.logical(writetable)) stop("tabulateQ: Argument 'writetable' not set correctly. Set as TRUE or FALSE.") + if(!is.logical(sorttable)) stop("tabulateQ: Argument 'sorttable' not set correctly. Set as TRUE or FALSE.") + + # get filenames from selection + filenames <- names(qlist) + if(is.null(filenames)) filenames <- paste0("sample",1:length(qlist)) + #number of files selected + flen <- length(filenames) + + # make dataframe container + main <- data.frame(file=filenames,k=1:flen,ind=1:flen,stringsAsFactors=FALSE) + + # loop to make dataframe with filenames and other variables + # initialise variables + tq_k <- vector(length=flen,mode="numeric") + tq_ind <- vector(length=flen,mode="numeric") + tq_loci <- vector(length=flen,mode="numeric") + tq_burnin <- vector(length=flen,mode="numeric") + tq_reps <- vector(length=flen,mode="numeric") + tq_elpd <- vector(length=flen,mode="numeric") + tq_mvll <- vector(length=flen,mode="numeric") + tq_vll <- vector(length=flen,mode="numeric") + tq_gif <- vector(length=flen,mode="numeric") + tq_rmse <- vector(length=flen,mode="numeric") + tq_crossentropy <- vector(length=flen,mode="numeric") + tq_ploidy <- vector(length=flen,mode="numeric") + + i <- 1 + for (i in i:flen) + { + # read file & error check + df1 <- qlist[[i]] + if(!is.data.frame(df1)) stop(paste0("tabulateQ: List item ",i," is not a data.frame object.")) + if(!any(sapply(df1,is.numeric))) stop(paste0("tabulateQ: List item ",i," has non-numeric columns.")) + + # get k + tq_k[i] <- ncol(df1) + # get ind + tq_ind[i] <- nrow(df1) + # loci + tq_loci[i] <- ifelse(is.null(attr(df1,"loci")),NA,attr(df1,"loci")) + # burnin + tq_burnin[i] <- ifelse(is.null(attr(df1,"burnin")),NA,attr(df1,"burnin")) + # reps + tq_reps[i] <- ifelse(is.null(attr(df1,"reps")),NA,attr(df1,"reps")) + # elpd + tq_elpd[i] <- ifelse(is.null(attr(df1,"elpd")),NA,attr(df1,"elpd")) + # mvll + tq_mvll[i] <- ifelse(is.null(attr(df1,"mvll")),NA,attr(df1,"mvll")) + # vll + tq_vll[i] <- ifelse(is.null(attr(df1,"vll")),NA,attr(df1,"vll")) + # gif + tq_gif[i] <- ifelse(is.null(attr(df1,"gif")),NA,attr(df1,"gif")) + # rmse + tq_rmse[i] <- ifelse(is.null(attr(df1,"rmse")),NA,attr(df1,"rmse")) + # crossentropy + tq_crossentropy[i] <- ifelse(is.null(attr(df1,"crossentropy")),NA,attr(df1,"crossentropy")) + # ploidy + tq_ploidy[i] <- ifelse(is.null(attr(df1,"ploidy")),NA,attr(df1,"ploidy")) + } + + # create dataframe + main <- data.frame(file=filenames,k=tq_k,ind=tq_ind,stringsAsFactors=FALSE) + if(all(!is.na(tq_loci))) main$loci <- tq_loci + if(all(!is.na(tq_burnin))) main$burnin <- tq_burnin + if(all(!is.na(tq_reps))) main$reps <- tq_reps + if(all(!is.na(tq_elpd))) main$elpd <- tq_elpd + if(all(!is.na(tq_mvll))) main$mvll <- tq_mvll + if(all(!is.na(tq_vll))) main$vll <- tq_vll + if(all(!is.na(tq_gif))) main$gif <- tq_gif + if(all(!is.na(tq_rmse))) main$rmse <- tq_rmse + if(all(!is.na(tq_crossentropy))) main$crossentropy <- tq_crossentropy + if(all(!is.na(tq_ploidy))) main$ploidy <- tq_ploidy + + # sort table on K + if(sorttable) main <- main[with(main,order(ind,k)),] + + # write table if opted + if(writetable) write.table(main,"tabulateQ.txt",quote=FALSE,row.names=FALSE,sep="\t",dec=".") + + return(main) +} + +# summariseQ ---------------------------------------------------------------- + +#' @title Summarise a tabulated dataframe +#' @description Creates a summary table from a tabulated dataframe of two or more +#' runs with k, number of runs and individuals. +#' @param data A dataframe with tabulated runs. An output from \code{tabulateQ()}. +#' Must have minimum 2 columns named k and ind. +#' @param writetable A logical indicating if the output table is to be exported as +#' a tab-delimited text file in the working directory. +#' @return Returns a dataframe with all values of K sorted by K. The table has +#' 3 columns namely value of K, number of runs for each K and number of individuals. +#' If the input file is derived from STRUCTURE runs, the table is sorted by loci as well. +#' Other columns include elpdmean, elpdsd, elpdmin and elpdmax. +#' @details See the \href{http://royfrancis.github.io/pophelper/}{vignette} for more details. +#' @aliases summarizeQ +#' @seealso \code{\link{tabulateQ}} +# @import xlsx +#' @examples +#' +#' # STRUCTURE files +#' sfiles <- list.files(path=system.file("files/structure",package="pophelper"),full.names=TRUE) +#' slist <- readQ(sfiles) +#' tr1 <- tabulateQ(slist) +#' summariseQ(tr1) +#' +#' # ADMIXTURE files +#' afiles <- list.files(path=system.file("files/admixture",package="pophelper"),full.names=TRUE) +#' tr1 <- tabulateQ(readQ(afiles)) +#' summariseQ(tr1) +#' +#' @export +#' +summariseQ <- summarizeQ <- function(data=NULL,writetable=FALSE) +{ + # does df data contain any data? + if(is.null(data) || length(data)==0) stop("summariseQ: No input files.") + if(!is.logical(writetable)) stop("summariseQ: Argument 'writetable' not set correctly. Set as TRUE or FALSE.") + + # make sure dataframe + if(class(data) != "data.frame") stop("summariseQ: Input is not a dataframe.") + # convert column names to lowercase + colnames(data) <- tolower(colnames(data)) + # is column k available? + if(length(grep("k",colnames(data)))==0) stop("summariseQ: Column k not available.") + # is column ind available? + if(length(grep("ind",colnames(data)))==0) stop("summariseQ: Column ind not available.") + + # check + if(nrow(data) < 2) stop("summariseQ: At least 2 runs are required for this function.") + + if(all(c("k","ind","loci","elpd") %in% colnames(data))) + { + dframe1 <- stats::aggregate(elpd ~ loci + ind + k,data=data,length) + colnames(dframe1)[4] <- "runs" + dframe2 <- aggregate(elpd ~ loci + ind + k,data=data,FUN=function(x) c(elpdmean =mean(x,na.rm=T),elpdsd=sd(x,na.rm=T),elpdmin=min(x,na.rm=T),elpdmax=max(x,na.rm=T)))[,-c(1:3)] + dframe1 <- cbind(dframe1,dframe2) + }else{ + dframe1 <- stats::aggregate(file ~ ind + k,data=data[,c("file","k","ind")],length) + colnames(dframe1)[3] <- "runs" + } + + # write table if opted + if(writetable) write.table(dframe1,"summariseQ.txt",quote=FALSE,row.names=FALSE,sep="\t",dec=".") + + return(dframe1) +} + +# evannoMethodStructure -------------------------------------------------------- + +#' @title Perform the Evanno method for STRUCTURE runs. +#' @description The Evanno method for detecting the appropriate number of population clusters from STRUCTURE results. Creates table and figure with +#' Evanno method derivatives. Refer to return for detailed list of columns. See details for Evanno method reference. +#' @param data A dataframe with summarised runs. An output from \code{summariseQ()} derived from STRUCTURE runs. Must have minimum 7 columns named elpdmean, elpdsd, k, runs, loci, elpdmax and elpdmin. +#' @param writetable A logical indicating if the output table is to be exported as a file in the working directory. +#' @param exportplot A logical indicating if the Evanno plots are to be exported as an image in the working directory. If Evanno method cannot be computed, a kPlot (elpd over k) is exported instead. +#' @param returndata A logical indicating if the data must be returned. A data.frame object is returned alone when \code{returnplot=F}. When \code{returnplot=T}, the data.frame object is returned in a list. See 'Value'. +#' @param returnplot A logical indicating if the plot must be returned. A gtable object is returned alone when \code{returndata=F}. When \code{returndata=T}, the gtable object is returned in a list. See 'Value'. +#' @param pointsize A numeric indicating size of points. Default for \code{basesize=6} is 1.8. +#' @param pointype A character or number for the type of points. Defaults to 20. Same as pch in standard R. +#' @param pointcol A colour character for the colour of points. Defaults to "steelblue". +#' @param linesize A numeric indicating the thickness of the line. Default for \code{basesize=6} is 0.24. +#' @param linecol A colour character for the colour of line. Defaults to "steelblue". +#' @param ebwidth A numeric indicating size od width of error abrs. Defaults to 0.2. +#' @param ebcol A colour character for colour for errorbar. Defaults to "grey30". +#' @param textcol A colour character for all text elements on the plot. Defaults to "grey30". +#' @param basesize A numeric indicating the base size of various plot elements such as pointsize, linesize etc. Increase basesize with larger figure dimensions. Defaults to 6. Manually specified arguments (eg: pointsize) override basesize. +#' @param gridsize A numeric indicating thickness of background grid. Default for \code{basesize=6} is 0.18. +#' @param imgtype A character indicating the type of exported image. Default set to 'png'. Other possible +#' options are 'jpeg', 'tiff' or 'pdf'. +#' @param height A numeric denoting the height of exported image. Default units in 'cm'. +#' @param width A numeric denoting the width of exported image. Default units in 'cm'. +#' @param dpi A numeric denoting the resolution of exported image. Default set to 300. If \code{imgtype="pdf"}, dpi is fixed at 300. +#' @param units A character denoting the unit of measure of the export image. Default is 'cm'. Other options are 'px', 'in' or 'mm'. +#' @param theme A character indicating ggplot theme to be used. Use like "theme_grey", "theme_bw" etc. +#' @param font A character indicating font family to be used in the plots. Uses default system fonts by default for jpeg, png and tiff. Uses 'Helvetica' as default for pdf. Use package \code{extrafonts} to import custom fonts. See vignette for examples. +#' @param na.rm Default set to FALSE. Does not remove NAs for plot and this +#' generates warnings from \code{ggplot}. If set to TRUE, NAs are removed before +#' plotting and warning messages from \code{ggplot} are avoided. +#' @param quiet A logical indicating if messages must be printed to console. +#' @param outputfilename A character indicating output file name. Defaults to 'evannoMethodStructure'. +#' @return When \code{returndata=T} and \code{returnplot=F}, a data.frame is returned. +#' When \code{returndata=F} and \code{returnplot=T}, a gtable plot object is returned. +#' When \code{returndata=T} and \code{returnplot=T}, a list with data.frame and gtable object is returned. +#' +#' The data.frame contains Evanno results sorted by K. The table has 16 +#' columns namely Mean estimated ln probability of data, Standard deviation, +#' Value of K, Number of runs for each K, Number of runs for each K, Number of +#' individuals for each K, Number of loci for each K, Estimated ln probability +#' of data plus standard deviation, Estimated ln probability of data minus +#' standard deviation, First derivative, Max error of first derivative, Min +#' error of first derivative, Second derivative, Max error of second derivative, +#' Min error of second derivative and the Third derivative. +#' +#' The gtable object is a result of \code{gridExtra::arrangeGrob()}. This is +#' suitable for plotting in a report. +#' +#' @details The Evanno method is based on the paper: Evanno, G., Regnaut, S., +#' and Goudet, J. (2005). Detecting the number of clusters of individuals using +#' the software STRUCTURE: a simulation study. Molecular ecology, 14(8), +#' 2611-2620. The Evanno plot generated from this function can be recreated +#' from the returned dataframe if furthur customisation is required. +#' +#' See the \href{http://royfrancis.github.io/pophelper/}{vignette} for more details. +#' +#' @examples +#' +#' \dontrun{ +#' sfiles <- list.files(path=system.file("files/structure",package="pophelper"),full.names=TRUE) +#' tr1 <- tabulateQ(readQ(sfiles)) +#' sr1 <- summariseQ(tr1) +#' evannoMethodStructure(sr1) +#' evannoMethodStructure(data=sr1,exportplot=T) +#' } +#' +# @import xlsx +#' @import grid +#' @import gridExtra +#' @export +#' +evannoMethodStructure <- function(data=NULL,writetable=FALSE,exportplot=FALSE,returnplot=FALSE,returndata=TRUE, + pointsize=NA,pointtype=20,pointcol="steelblue",linesize=NA,linecol="steelblue", + ebwidth=0.2,ebcol="grey30", + textcol="grey30",basesize=6,gridsize=NA, + imgtype="png",height=NA,width=NA,dpi=300,units="cm", + theme="theme_bw",font="",na.rm=TRUE,quiet=TRUE,outputfilename="evannoMethodStructure") +{ + # does df data contain any data? + if(is.null(data) || length(data)==0) stop("evannoMethodStructure: No input files.") + if(class(data) != "data.frame") stop("evannoMethodStructure: Input is not a dataframe datatype.") + if(!is.logical(writetable)) stop("evannoMethodStructure: Argument 'writetable' not set correctly. Set as TRUE or FALSE.") + if(!is.logical(exportplot)) stop("evannoMethodStructure: Argument 'exportplot' not set correctly. Set as TRUE or FALSE.") + if(!is.logical(na.rm)) stop("evannoMethodStructure: Argument 'na.rm' not set correctly. Set as TRUE or FALSE.") + imgtype <- tolower(imgtype) + if(imgtype != "png" && imgtype != "pdf" && imgtype != "tiff" && imgtype != "jpeg") stop("evannoMethodStructure: Argument 'imgtype' set incorrectly. Options are 'png', 'jpeg', 'tiff' or 'pdf'.") + + # convert column names to lowercase + colnames(data) <- tolower(colnames(data)) + cold <- colnames(data) + + # is column loci available? + if(!"loci" %in% cold) stop("evannoMethodStructure: Column loci not available.") + # is column ind available? + if(!"ind" %in% cold) stop("evannoMethodStructure: Column ind not available.") + # is column k available? + if(!"k" %in% cold) stop("evannoMethodStructure: Column k not available.") + # is column runs available? + if(!"runs" %in% cold) stop("evannoMethodStructure: Column runs not available.") + # is column elpdmean available? + if(!"elpdmean" %in% cold) stop("evannoMethodStructure: Column elpdmean not available.") + # is column elpdsd available? + if(!"elpdsd" %in% cold) stop("evannoMethodStructure: Column elpdsd not available.") + # is column minelpd available? + if(!"elpdmin" %in% cold) stop("evannoMethodStructure: Column elpdmin not available.") + # is column maxelpd available? + if(!"elpdmax" %in% cold) stop("evannoMethodStructure: Column elpdmax not available.") + + + err <- 0 + # are there atleast 3 values of K? + if(length(data$k) < 3) {warning("Error: The Evanno method not computed. Requires at least 3 values of K.\n"); err <- 1} + # do loci vary? + if(!all(data$loci[1]==data$loci)) {warning("Error: The Evanno method not computed. Number of loci vary between runs.\n"); err <- 1} + # do ind vary? + if(!all(data$ind[1]==data$ind)) {warning("Error: The Evanno method not computed. Number of individuals vary between runs.\n"); err <- 1} + # are k values sequential? + is.sequential <- function(x) all(abs(diff(x))==1) + if(!is.sequential(data$k)) {warning("Error: The Evanno method not computed. Requires increasing sequential values of K.\n"); err <- 1} + # are repeats of any k<2? + if(any(data$runs < 2)) warning("evannoMethodStructure: Results may not be meaningful if repeats (runs) for any value of K is less than 2.") + + base_size <- basesize + height1 <- height + width1 <- width + if(imgtype=="pdf") dpi <- 300 + if(imgtype=="pdf" && font=="") font <- "Helvetica" + if(is.na(pointsize)) pointsize <- base_size*0.3 + if(is.na(linesize)) linesize <- base_size*0.04 + if(is.na(gridsize)) gridsize <- base_size*0.03 + + if(err==1) + { + if(exportplot || returnplot) + { + #create plots list + plist <- vector("list",1) + + #settings for kPlot + if(is.na(height)) {height1 <- 7}else{height1 <- height} + if(is.na(width)) {width1 <- 7}else{width1<-width} + if(is.na(basesize)) base_size <- round((5*height1)/7,1) + + if(imgtype=="pdf") height1 <- pophelper:::unitConverter(height1,units,"in",dpi) + if(imgtype=="pdf") width1 <- pophelper:::unitConverter(width1,units,"in",dpi) + + #if(is.na(height) && imgtype=="pdf") height1 <- pophelper:::unitConverter(value=height1, fromunit="cm", tounit="in", dpi) + #if(is.na(width) && imgtype =="pdf") width1 <- pophelper:::unitConverter(value=width1, fromunit="cm", tounit="in", res=res) + #if(!is.na(height) && imgtype=="pdf" && units != "in") height1 <- pophelper:::unitConverter(value=height, fromunit=units, tounit="in", dpi) + #if(!is.na(width) && imgtype =="pdf" && units != "in") width1 <- pophelper:::unitConverter(value=width, fromunit=units, tounit="in", dpi) + + plist[[1]] <- ggplot2::ggplot(data,aes(x=k,y=elpdmean))+ + geom_path(colour=linecol,size=linesize,na.rm=na.rm)+ + geom_point(colour=pointcol,fill=pointcol,size=pointsize,shape=pointtype,na.rm=na.rm)+ + geom_errorbar(aes(x=k,ymax=elpdmax,ymin=elpdmin,width=ebwidth),size=linesize,colour=ebcol,na.rm=na.rm)+ + get(theme)(base_family=font)+ + labs(x=expression(paste(italic(K))), + y=expression(paste("Mean L(",italic(K),") " %+-% " SD")))+ + theme(legend.position="none", + axis.text.y=element_text(angle=90,hjust=0.5,size=base_size,colour=textcol), + axis.text.x=element_text(size=base_size,colour=textcol), + axis.title=element_text(size=base_size+1,colour=textcol,face="bold"), + plot.title=element_text(size=base_size+3,hjust=0,colour=textcol), + axis.ticks=element_blank(), + panel.border=element_blank(), + panel.grid.minor=element_blank(), + panel.grid.major=element_line(size=gridsize), + plot.margin=grid::unit(c(0.2,0.2,0.2,0.2),"cm")) + + if(exportplot) + { + # check image imgtype + if(imgtype=="pdf") pdf(filename=paste0(outputfilename,".pdf"),height=height1,width=width1,fonts=font) + if(imgtype=="png") png(filename=paste0(outputfilename,".png"),height=height1,width=width1,res=dpi,units=units,type="cairo",family=font) + if(imgtype=="jpeg") jpeg(filename=paste0(outputfilename,".jpg"),height=height1,width=width1,res=dpi,units=units,quality=100,family=font) + if(imgtype=="tiff") tiff(filename=paste0(outputfilename,".tiff"),height=height1,width=width1,res=dpi,units=units,compression="lzw",type="cairo",family=font) + + print(plist[[1]]) + dev.off() + + if(imgtype=="tiff" && !quiet) cat(paste0(outputfilename,".tiff exported.\n")) + if(imgtype=="pdf" && !quiet) cat(paste0(outputfilename,".pdf exported.\n")) + if(imgtype=="png" && !quiet) cat(paste0(outputfilename,".png exported.\n")) + if(imgtype=="jpeg" && !quiet) cat(paste0(outputfilename,".jpg exported.\n")) + } + + } + if(returnplot) return(plist[[1]]) + stop("evannoMethodStructure: Evanno method not computed.") + } + + # convert dataframe to list + datal <- as.list(data) + + # Loop to get first derivative of l(K) and its sd + drv1 <- vector(length=nrow(data)-1,mode="numeric") + drv1sd <- vector(length=nrow(data)-1,mode="numeric") + i <- 1 + len1 <- length(datal$elpdmean) + while (i < len1) + { + drv1[i] <- datal$elpdmean[i+1]-datal$elpdmean[i] + drv1sd[i] <- abs(datal$elpdsd[i+1]-datal$elpdsd[i]) + i=i+1 + } + + # Loop to get second derivative of l(K) and its sd + drv2 <- vector(length=nrow(data)-2,mode="numeric") + drv2sd <- vector(length=nrow(data)-2,mode="numeric") + i <- 1 + len1 <- length(drv1) + while (i < len1) + { + drv2[i] <- abs(drv1[i+1]-drv1[i]) + drv2sd[i] <- abs(drv1sd[i+1]-drv1sd[i]) + i=i+1 + } + + # add NA to SD vector 1 and 2 + drv1sdf <- c(NA,drv1sd) + drv2sdf <- c(NA,drv2sd,NA) + + datal$drv1 <- c(NA,drv1) + datal$drv1max <- datal$drv1+drv1sdf + datal$drv1min <- datal$drv1-drv1sdf + datal$drv2 <- c(NA,drv2,NA) + datal$drv2max <- datal$drv2+drv2sdf + datal$drv2min <- datal$drv2-drv2sdf + datal$drv3 <- abs(datal$drv2)/datal$elpdsd + + data <- data.frame(datal,stringsAsFactors=FALSE) + rm(datal) + colnames(data)[9:15] <- c("lnk1","lnk1max","lnk1min","lnk2","lnk2max","lnk2min","deltaK") + + # write table if opted + if(writetable) + { + write.table(data,paste0(outputfilename,".txt"),quote=FALSE,row.names=FALSE,sep="\t",dec=".") + if(!quiet) cat(paste0(outputfilename,".txt exported. \n")) + } + + # show plot + if(exportplot || returnplot) + { + if(is.na(height)) {height1 <- 8}else{height1 <- height} + if(is.na(width)) {width1 <- 8}else{width1 <- width} + if(is.na(basesize)) base_size <- round((5*height1)/7,1) + + if(imgtype=="pdf") height1 <- pophelper:::unitConverter(height1,units,"in",dpi) + if(imgtype=="pdf") width1 <- pophelper:::unitConverter(width1,units,"in",dpi) + + #if(is.na(height) && imgtype=="pdf") height1 <- pophelper:::unitConverter(value=height1, fromunit="cm", tounit="in", res=dpi) + #if(is.na(width) && imgtype =="pdf") width1 <- pophelper:::unitConverter(value=width1, fromunit="cm", tounit="in", res=dpi) + #if(!is.na(height) && imgtype=="pdf" && units != "in") height1 <- pophelper:::unitConverter(value=height, fromunit=units, tounit="in", res=dpi) + #if(!is.na(width) && imgtype =="pdf" && units != "in") width1 <- pophelper:::unitConverter(value=width, fromunit=units, tounit="in", res=dpi) + + #create plots list + plist <- vector("list",4) + + # plot1 + plist[[1]] <- ggplot2::ggplot(data,aes(x=k,y=elpdmean))+ + geom_path(colour=linecol,size=linesize,na.rm=na.rm)+ + geom_point(colour=pointcol,fill=pointcol,size=pointsize,shape=pointtype,na.rm=na.rm)+ + geom_errorbar(aes(x=k,ymax=elpdmax,ymin=elpdmin,width=ebwidth),size=linesize,colour=ebcol,na.rm=na.rm)+ + get(theme)(base_family=font)+ + labs(x=expression(paste(italic(K))),y=expression(paste("Mean L(",italic(K),") " %+-% " SD")),title="A") + + # plot 2 + plist[[2]] <- ggplot2::ggplot(data,aes(x=k,y=lnk1))+ + geom_path(colour=linecol,size=linesize,na.rm=na.rm)+ + geom_point(colour=pointcol,fill=pointcol,size=pointsize,shape=pointtype,na.rm=na.rm)+ + geom_errorbar(aes(x=k,ymax=lnk1max,ymin=lnk1min,width=ebwidth), + size=linesize,colour=ebcol,na.rm=na.rm)+ + get(theme)(base_family=font)+ + labs(x=expression(paste(italic(K))),y=expression(paste("L'(",italic(K),") " %+-% " SD")),title="B") + + # plot 3 + plist[[3]] <- ggplot2::ggplot(data,aes(x=k,y=lnk2))+ + geom_path(colour=linecol,size=linesize,na.rm=na.rm)+ + geom_point(colour=pointcol,fill=pointcol,size=pointsize,shape=pointtype,na.rm=na.rm)+ + geom_errorbar(aes(x=k,ymax=lnk2max,ymin=lnk2min,width=0.2), + size=linesize,colour=ebcol,na.rm=na.rm)+ + get(theme)(base_family=font)+ + labs(x=expression(paste(italic(K))),y=expression(paste("|L\"(",italic(K),")| " %+-% " SD")),title="C") + + # plot 4 + if(is.finite(sum(data$drv3,na.rm=TRUE))) + { + plist[[4]] <- ggplot2::ggplot(data,aes(x=k,y=deltaK))+ + geom_path(colour=linecol,size=linesize,na.rm=na.rm)+ + geom_point(colour=pointcol,fill=pointcol,size=pointsize,shape=pointtype,na.rm=na.rm)+ + get(theme)(base_family=font)+ + labs(x=expression(paste(italic(K))),y=expression(paste(Delta,italic(K))),title="D") + } + + plen <- length(plist) + for (r in 1:plen) + { + plist[[r]] <- plist[[r]] + theme(legend.position="none", + axis.text.y=element_text(angle=90,hjust=0.5,size=base_size-0.5,colour=textcol), + axis.text.x=element_text(size=base_size-0.5,colour=textcol), + axis.title=element_text(size=base_size+0.6,colour=textcol,face="bold"), + plot.title=element_text(size=base_size+2.5,hjust=0,colour=textcol), + panel.border=element_blank(), + axis.ticks=element_blank(), + panel.grid.minor=element_blank(), + panel.grid.major=element_line(size=gridsize), + plot.margin=grid::unit(c(0.2,0.2,0.2,0.2),"cm")) + } + + # export image + if(exportplot) + { + # check image imgtype + if(imgtype=="pdf") pdf(paste0(outputfilename,".pdf"),height=height1,width=width1,fonts=font) + if(imgtype =="png") png(paste0(outputfilename,".png"),height=height1,width=width1,res=dpi,units=units,type="cairo",family=font) + if(imgtype =="tiff") tiff(paste0(outputfilename,".tiff"),height=height1,width=width1,res=dpi,units=units,compression="lzw",type="cairo",family=font) + if(imgtype=="jpeg") jpeg(paste0(outputfilename,".jpg"),height=height1,width=width1,res=dpi,units=units,quality=100,family=font) + + if(plen==3) gridExtra::grid.arrange(plist[[1]],plist[[2]],plist[[3]],ncol=2,nrow=2) + if(plen==4) gridExtra::grid.arrange(plist[[1]],plist[[2]],plist[[3]],plist[[4]],ncol=2,nrow=2) + dev.off() + + if(imgtype=="tiff" && !quiet) cat(paste0(outputfilename,".tiff exported.\n")) + if(imgtype=="pdf" && !quiet) cat(paste0(outputfilename,".pdf exported.\n")) + if(imgtype=="png" && !quiet) cat(paste0(outputfilename,".png exported.\n")) + if(imgtype=="jpeg" && !quiet) cat(paste0(outputfilename,".jpg exported.\n")) + } + + if(returnplot) + { + if(plen==3) p <- gridExtra::arrangeGrob(plist[[1]],plist[[2]],plist[[3]],ncol=2,nrow=2) + if(plen==4) p <- gridExtra::arrangeGrob(plist[[1]],plist[[2]],plist[[3]],plist[[4]],ncol=2,nrow=2) + } + } + + # return + if(returndata && !returnplot) return(data) + if(!returndata && returnplot) return(p) + if(returndata && returnplot) return(list(data=data,plot=p)) +} + + +# clumppExport ----------------------------------------------------------------- + +#' @title Generate CLUMPP output from a qlist +#' @description Takes a qlist and combines several repeats for each K into a +#' single file along with a parameter file suitable for input to CLUMPP. The two +#' output files are organised into folders by K. CLUMPP is executed automatically +#' when \code{useexe=T}, else the CLUMPP executable file can be copied to the +#' output directories and run to reorder the clusters for each K. +#' @param qlist A qlist (list of dataframes). An output from \code{\link{readQ}}. +#' @param prefix A character prefix for folder names. By default, set to 'pop'. +#' @param parammode A numeric 1, 2 or 3 indicating the algorithm option for CLUMPP paramfile. Calculated +#' automatically by default. Set this value to 3 if CLUMPP runs too long. See details. +#' @param paramrep A numeric indicating the number of repeats for CLUMPP paramfile. Calculated +#' automatically by default. See details. +#' @param useexe A logical indicating if CLUMPP executable must be run automatically based on system OS (experimental). May not work on all OS and versions. +#' @return The combined file and paramfile are written into respective folders +#' named by K. +#' @details When multiple repeats are run for each K in runs, the order of +#' clusters may be jumbled for each run. Therefore, when plotting multiple runs +#' within each K, the colours cannot be assigned correctly. The software CLUMPP +#' helps to overcome this issue by reordering the clusters correctly. This +#' function \code{clumppExport()} takes multiple runs for each K and combines +#' them into a single file and generates a parameter file for easy use with +#' CLUMPP. Further details for CLUMPP can be found here: Jakobsson, M., and +#' Rosenberg, N. A. (2007). CLUMPP: a cluster matching and permutation program +#' for dealing with label switching and multimodality in analysis of population +#' structure. Bioinformatics, 23(14), 1801-1806.\cr +#' \cr +#' \strong{parammode}\cr +#' The parammode (M) is the type of algorithm used. Option 1 is 'FullSearch' +#' (takes the longest time), option 2 is 'Greedy' and option 3 is 'LargeKGreedy' +#' (fastest). If clumpp takes more than a few minutes, consider changing parammode +#' to a higher number (ex. from 2 to 3), or open the exported paramfile and manually +#' change GREEDY_OPTION to 3.\cr +#' \cr +#' The parammode and paramrep for CLUMPP paramfile is set based on this calculation. +#' T <- factorial(k)*((runs*(runs-1))/2)*k*ind, where k is number of +#' populations, runs is number of runs for k and ind is number of individuals. +#' If T <= 100000000, then parammode is 2 and paramrep is 20, otherwise +#' parammode is 3 and paramrep is set to 500.\cr +#' \cr +#' To find out more about parammode (algorithm type) and paramrep (repeats), +#' refer to CLUMPP documentation.\cr +#' +#' \strong{useexe}\cr +#' This option automatically runs the CLUMPP executable that is provided with this package. +#' The CLUMPP executable was obtained from \url{https://web.stanford.edu/group/rosenberglab/clumpp.html}. +#' Remember to cite CLUMPP if this option is used.\cr +#' +#' See the \href{http://royfrancis.github.io/pophelper/}{vignette} for more details. +#' +#' @examples +#' +#' \dontrun{ +#' +#' # generate input files for CLUMPP from STRUCTURE files +#' sfiles <- list.files(path=system.file("files/structure",package="pophelper"),full.names=TRUE) +#' clumppExport(readQ(sfiles)) +#' +#' # auto execute CLUMPP +#' clumppExport(readQ(sfiles),useexe=TRUE) +#' +#' # generate input files for CLUMPP from ADMIXTURE files +#' afiles <- list.files(path=system.file("files/admixture",package="pophelper"),full.names=TRUE) +#' clumppExport(readQ(afiles)) +#' +#' } +#' +#' @export +#' +clumppExport <- function(qlist=NULL,prefix=NA,parammode=NA,paramrep=NA,useexe=FALSE) +{ + # check input + is.qlist(qlist) + + if(is.na(prefix)) prefix <- "pop" + prefix <- paste0(prefix,"_K") + if(!is.logical(useexe)) stop("clumppExport: Argument 'useexe' set incorrectly. Set as TRUE or FALSE.") + + # get tabulated runs + df1 <- pophelper::tabulateQ(qlist) + df2 <- pophelper::summariseQ(df1) + df1l <- as.list(df1) + df2l <- as.list(df2) + + if(is.null(names(qlist))) names(qlist) <- paste0("sample",1:length(qlist)) + + # k val duplicated + if(any(duplicated(df2l$k))) stop("clumppExport: Repeating values of K found.") + # do ind vary? + if(!all(df2l$ind[1]==df2l$ind)) warning("clumppExport: Number of individuals vary between runs.") + + e <- 1 + p <- 1 + len1 <- length(df2l$k) + while (e <= len1) + { + k <- df2l$k[e] + ind <- df2l$ind[e] + runs <- df2l$runs[e] + + ldata <- vector("list",length=runs) + f <- 1 + for (f in 1:runs) + { + sel <- which(names(qlist)==as.character(df1l$file[p])) + dframe1 <- qlist[[sel]] + + # generate df + dframe3 <- as.matrix(data.frame(V1=paste0(1:ind,":"),dframe1,last=as.character(rep(1,ind)),stringsAsFactors=FALSE)) + + # add dataframes to list + ldata[[f]] <- dframe3 + rm(dframe3) + p=p+1 + } + + if(runs > 1 && k > 1) + { + currwd <- getwd() + if(as.numeric(file.access(currwd,2))==-1) stop(paste0("clumppExport: Directory ",currwd," has no write permission.")) + + dir.create(paste0(currwd,"/",prefix,k)) + setwd(paste0(currwd,"/",prefix,k)) + cat(paste0("Folder created: ",basename(getwd()),"\n")) + out <- paste0(prefix,k,"-combined.txt") + + ## file output block + + # make 2 line space + spacer <- matrix(rep(" ",(k+2)*2),nrow=2) + + # write file + write(t(format(ldata[[1]],nsmall=15)),paste(out),ncolumns=k+2) + i=2 + for (i in 2:length(ldata)) + { + write(t(spacer),paste(out),ncolumns=k+2,append=TRUE) + write(t(format(ldata[[i]],nsmall=15)),append=TRUE,paste(out),ncolumns=k+2) + } + cat(paste0(out),"exported.\n") + + ## paramfile section + T1 <- factorial(k)*((length(ldata)*(length(ldata)-1))/2)*k*ind + if(T1 <= 100000000) + { + if(is.na(parammode)) parammode <- 2 + if(is.na(paramrep)) paramrep <- 20 + }else{ + if(is.na(parammode)) parammode <- 3 + if(is.na(paramrep)) paramrep <- 500 + } + out1 <- base::gsub(".txt","",out) + params <- c("DATATYPE 1 ", + "INDFILE NOTNEEDED.indfile ", + paste0("POPFILE ",out," "), + paste0("OUTFILE ",out1,"-merged.txt "), + paste0("MISCFILE ",out1,"-miscfile.txt "), + paste0("K ",k," "), + paste0("C ",ind," "), + paste0("R ",length(ldata)," "), + paste0("M ",parammode," "), + "W 0 ", + "S 2 ", + "GREEDY_OPTION 2 ", + paste0("REPEATS ",paramrep," "), + "PERMUTATIONFILE NOTNEEDED.permutationfile ", + "PRINT_PERMUTED_DATA 1 ", + paste0("PERMUTED_DATAFILE ",out1,"-aligned.txt "), + "PRINT_EVERY_PERM 0 ", + paste0("EVERY_PERMFILE ",out1,".every_permfile "), + "PRINT_RANDOM_INPUTORDER 0 ", + paste0("RANDOM_INPUTORDERFILE ",out1,".random_inputorderfile "), + "OVERRIDE_WARNINGS 0 ", + "ORDER_BY_RUN 0 ") + + write(params,"paramfile") + cat(paste0("paramfile exported.\n")) + + # autorun clumpp executable + if(useexe) + { + # identify OS + sysos <- pophelper:::getOS() + if(sysos=="windows") + { + file.copy(system.file("bin/clumpp_windows_1.1.2b.exe",package="pophelper"),".") + system("clumpp_windows_1.1.2b.exe") + unlink("clumpp_windows_1.1.2b.exe",force=TRUE) + } + + if(sysos=="mac") + { + file.copy(system.file("bin/clumpp_mac_1.1.2b",package="pophelper"),".") + system("chmod 777 clumpp_mac_1.1.2b") + system("./clumpp_mac_1.1.2b") + unlink("clumpp_mac_1.1.2b",force=TRUE) + } + + if(sysos=="unix32") + { + file.copy(system.file("bin/clumpp_linux_1.1.2b_32bit",package="pophelper"),".") + system("chmod 777 clumpp_linux_1.1.2b_32bit") + system("./clumpp_linux_1.1.2b_32bit") + unlink("clumpp_linux_1.1.2b_32bit",force=TRUE) + } + + if(sysos=="unix64") + { + file.copy(system.file("bin/clumpp_linux_1.1.2b_64bit",package="pophelper"),".") + system("chmod 777 clumpp_linux_1.1.2b_64bit") + system("./clumpp_linux_1.1.2b_64bit") + unlink("clumpp_linux_1.1.2b_64bit",force=TRUE) + } + + # if OS is unidentified, give error + if(sysos=="unknown") warning("clumppExport: CLUMPP executable not run because system cannot be identified as windows, mac or linux.") + } + + setwd(paste(currwd)) + cat("-----------------------\n") + }else + { + if(k==1) message(paste0(prefix,k," not exported. K less than 2.\n")) + if(runs < 2) message(paste0(prefix,k," not exported. Repeats less than 2.\n")) + cat("-----------------------\n") + } + e <- e + 1 + } + + cat("Run completed.\n") +} + +# collectRunsTess -------------------------------------------------------------- + +#' @title Collect TESS cluster run files from multiple folders +#' @description Collect TESS cluster run files from multiple folders to one folder and rename each run by folder name +#' @param runsdir A character path indicating the directory containing TESS runs in multiple directories. Use \code{choose.dir()} for interactively selecting the directory. If NA, or no directory is selected, the current working directory is used. +#' @param newdir A character indicating the name of the new directory to be created with the collected runs. IF NA, the default name 'AllTESSRuns' is used. +#' @param quiet A logical indicating if a message is to be displayed for directories without TESS runs and number of runs copied and renamed. +#' @details Within each TESS run folder, the function searches for filename ending with 'TR.txt' as the cluster file. This file is copied to the new folder and renamed as the name of the respective run directory. Therefore, DO NOT manually rename original run files or directories. +#' +#' See the \href{http://royfrancis.github.io/pophelper/}{vignette} for more details. +#' +#' @return Two integers are ruturned. The first denotes the number of TESS run files copied and renamed. The second number denotes number of directories without TESS run files. +#' @examples +#' \dontrun{ +#' collectRunsTess("path") +#' } +#' @export +#' +collectRunsTess <- function(runsdir=NA,newdir=NA,quiet=FALSE) +{ + if(!is.logical(quiet)) stop("collectRunsTess: Argument 'quiet' set incorrectly. Set as TRUE or FALSE.") + currwd <- getwd() + if(is.na(newdir)) newdir <- "AllTESSRuns" + if(is.na(runsdir)) runsdir <- currwd + dirs <- list.dirs(path=runsdir,full.names=TRUE,recursive=FALSE) + dir.create(paste0(runsdir,"/",newdir)) + k <- 0 + l <- 0 + len1 <- length(dirs) + for (i in 1:len1) + { + setwd(dirs[i]) + files <- list.files() + sel <- grep("\\w+TR.txt",files) + if(length(sel)==0) + { + if(!quiet) cat(paste0("No TESS cluster file found in directory: ",basename(dirs[i]),"\n")) + l=l+1 + } + if(length(sel) != 0) + { + file.copy(from=paste0(dirs[i],"/",files[sel],sep=""),to=paste0(runsdir,"/",newdir)) + file.rename(from=paste0(runsdir,"/",newdir,"/",files[sel]),to=paste0(runsdir,"/",newdir,"/",basename(dirs[i]),".txt")) + k=k+1 + } + } + setwd(currwd) + if(!quiet) cat(paste0(k," TESS cluster files copied and renamed.\n")) + return(c(k,l)) +} + +# collectClumppOutput ---------------------------------------------------------- + +#' @title Collect CLUMPP output files from multiple folders +#' @description Collect CLUMPP output files from multiple folders to one folder +#' @param prefix A character indicating the prefix of the CLUMPP directories before the underscore. For ex. if the directories are pop_K2, then prefix is pop. +#' @param filetype A character indicating the type of file to be copied. Options are 'aligned' to copy aligned files only, 'merged' to copy merged files only and 'both' to copy both files. +#' @param runsdir A character denoting the directory containing CLUMPP output files in multiple directories. Use \code{choose.dir()} for interactively selecting the directory. If NA, the current working directory is used. +#' @param newdir A character indicating the name of the new directory to be created with the collected runs. IF NA, the a directory name joining prefix and filetype is created. +#' @param quiet A logical indicating if a message is to be displayed showing the number of folders processed and number of files processed. +#' @details Within each CLUMPP output folder, the function searches for filenames containing combination of prefix and filetype. This file is copied to the new folder. Therefore, do not manually rename CLUMPP output files or output directories. +#' +#' See the \href{http://royfrancis.github.io/pophelper/}{vignette} for more details. +#' +#' @return Two integers are ruturned. The first denotes the number of directories processed. The second number denotes the number files copied. +#' @examples +#' \dontrun{ +#' collectClumppOutput(runsdir="path") +#' collectClumppOutput(prefix="pop",runsdir="path") +#' } +#' @export +#' +collectClumppOutput <- function(prefix="pop",filetype="aligned",runsdir=NA,newdir=NA,quiet=FALSE) +{ + if(!is.character(prefix)) stop("Argument 'prefix' must be a character.") + if(!is.character(filetype)) stop("Argument 'filetype' must be a character.") + if(!is.logical(quiet)) stop("collectClumppOutput: Argument 'quiet' set incorrectly. Set as TRUE or FALSE.") + + # check imgoutput + if(tolower(filetype)!="aligned" && tolower(filetype)!="merged" && tolower(filetype)!="both") stop("collectClumppOutput: Argument 'filetype' set incorrectly. Set as 'aligned', 'merged' or 'both'.") + + currwd <- getwd() + if(is.na(newdir)) newdir <- paste0(prefix,"-",filetype) + if(is.na(runsdir)) runsdir <- currwd + dirs <- list.dirs(path=runsdir,full.names=TRUE,recursive=FALSE) + dirs1 <- dirs[grep(paste0(prefix,"_"),dirs)] + dir.create(paste0(runsdir,"/",newdir)) + + k <- 0 + l <- 0 + i <- 1 + len1 <- length(dirs1) + for (i in 1:len1) + { + setwd(dirs1[i]) + files <- list.files() + sel1 <- grep("aligned",files) + sel2 <- grep("merged",files) + if(tolower(filetype)=="aligned") sel3 <- sel1 + if(tolower(filetype)=="merged") sel3 <- sel2 + if(tolower(filetype)=="both") sel3 <- c(sel1,sel2) + if(length(sel3)==0) + { + cat("No suitable file found in directory: ",basename(dirs1[i]),"\n",sep="") + } + if(length(sel3) != 0) + { + file.copy(from=paste0(dirs1[i],"/",files[sel3]),to=paste0(runsdir,"/",newdir)) + k=k+1 + l=l+length(sel3) + } + } + + setwd(currwd) + if(!quiet) cat(paste0("Directories processed: ",k,"\nFiles copied: ",l,"\n")) + + return(c(k,l)) +} + +# getDim ----------------------------------------------------------------------- + +#' @title Internal: Get dimensions for figures. +#' @description Internal: Generate height and width of figure based on number of individuals. +#' @param ind A numeric indicating the number of individuals. +#' @param units A character indicating the unit of dimension: "cm","mm","in". +#' @param height A numeric indicating the height of each plot. +#' @param width A numeric indicating the width of each plot. +#' @param dpi A numeric indicating the resolution of the figure. +#' @param imgtype A character denoting image format. "png", "jpeg" or "pdf". +#' @param grplabheight A numeric denoting the height of the label panel. +#' @param labs An integer denoting number of label groups. +#' @param plotnum A numeric indicating the number of plots in the figure. +#' @param showindlab A logical indicating of indlab is displayed. +#' @param sharedindlab A logical indicating if shared indlab is in use. +#' @return a vector with height and width. +# @export +#' +getDim <- function(ind=NA,units=NA,height=NA,width=NA,dpi=NA,imgtype=NA,grplabheight=NA,labs=NA,plotnum=NA,showindlab=FALSE,sharedindlab=TRUE) +{ + if(is.na(units)) units <- "cm" + if(is.na(units) && imgtype=="pdf") units <- "in" + if(is.na(dpi)) dpi <- 300 + if(is.na(plotnum)) plotnum <- 1 + if(is.na(labs)) labs <- 1 + + # height + if(is.na(height)) + { + if(plotnum==1) height <- 1.8 + if(plotnum > 1) height <- 1.2 + if(!showindlab) + { + height <- height+0.5 + if(!sharedindlab) height <- height+(0.5*plotnum) + } + + if(imgtype=="pdf") height <- pophelper:::unitConverter(value=height,fromunit="cm",tounit="in",dpi=dpi) + }else{ + if(units=="mm" && imgtype != "pdf") height <- pophelper:::unitConverter(value=height,fromunit="mm",tounit="cm",dpi=dpi) + if(units=="px" && imgtype != "pdf") height <- pophelper:::unitConverter(value=height,fromunit="px",tounit="cm",dpi=dpi) + if(units=="in" && imgtype != "pdf") height <- pophelper:::unitConverter(value=height,fromunit="in",tounit="cm",dpi=dpi) + if(units=="cm" && imgtype=="pdf") height <- pophelper:::unitConverter(value=height,fromunit="cm",tounit="in",dpi=dpi) + if(units=="mm" && imgtype=="pdf") height <- pophelper:::unitConverter(value=height,fromunit="mm",tounit="in",dpi=dpi) + if(units=="px" && imgtype=="pdf") height <- pophelper:::unitConverter(value=height,fromunit="px",tounit="in",dpi=dpi) + } + height <- height*plotnum + + # width + if(is.na(width)) + { + if(is.na(ind)) stop("getDim: Argument ind is empty.") + width <- ind*0.020 + if(width < 5) width <- 5 + if(width > 30) width <- 30 + if(imgtype=="pdf") width <- pophelper:::unitConverter(value=width,fromunit="cm",tounit="in",dpi=dpi) + }else{ + if(units=="mm" && imgtype != "pdf") width <- pophelper:::unitConverter(value=width,fromunit="mm",tounit="cm",dpi=dpi) + if(units=="px" && imgtype != "pdf") width <- pophelper:::unitConverter(value=width,fromunit="px",tounit="cm",dpi=dpi) + if(units=="in" && imgtype != "pdf") width <- pophelper:::unitConverter(value=width,fromunit="in",tounit="cm",dpi=dpi) + if(units=="cm" && imgtype=="pdf") width <- pophelper:::unitConverter(value=width,fromunit="cm",tounit="in",dpi=dpi) + if(units=="mm" && imgtype=="pdf") width <- pophelper:::unitConverter(value=width,fromunit="mm",tounit="in",dpi=dpi) + if(units=="px" && imgtype=="pdf") width <- pophelper:::unitConverter(value=width,fromunit="px",tounit="in",dpi=dpi) + } + + # grplabheight + if(is.na(grplabheight)) + { + if(labs==1) grplabheight <- 0.4 + if(labs>1) grplabheight <- 0.3 + grplabheight <- grplabheight * labs + if(imgtype=="pdf") grplabheight <- pophelper:::unitConverter(value=grplabheight,fromunit="cm",tounit="in",dpi=dpi) + }else{ + if(units=="mm" && imgtype != "pdf") grplabheight <- pophelper:::unitConverter(value=grplabheight,fromunit="mm",tounit="cm",dpi=dpi) + if(units=="in" && imgtype != "pdf") grplabheight <- pophelper:::unitConverter(value=grplabheight,fromunit="in",tounit="cm",dpi=dpi) + if(units=="px" && imgtype != "pdf") grplabheight <- pophelper:::unitConverter(value=grplabheight,fromunit="px",tounit="cm",dpi=dpi) + if(units=="mm" && imgtype=="pdf") grplabheight <- pophelper:::unitConverter(value=grplabheight,fromunit="mm",tounit="in",dpi=dpi) + if(units=="cm" && imgtype=="pdf") grplabheight <- pophelper:::unitConverter(value=grplabheight,fromunit="cm",tounit="in",dpi=dpi) + if(units=="px" && imgtype=="pdf") grplabheight <- pophelper:::unitConverter(value=grplabheight,fromunit="px",tounit="in",dpi=dpi) + } + + if(imgtype!="pdf") units1 <- "cm" + if(imgtype=="pdf") units1 <- "in" + + lst <- list(height=round(height,2),width=round(width,2),grplabheight=round(grplabheight,2),units=units1) + return(lst) +} + +# getPlotParams ---------------------------------------------------------------- + +#' @title Internal: Generate parameters for plots with labels +#' @description Internal: Generates various parameters required for plotting with labels. +#' @param grplab A character vector of labels same length as number of individuals. +#' @param plotnum A numeric indicating the number of plots on the figure. +#' @param grplabsize A numeric indicating the size of the labels. +#' @param grplabangle A numeric indicating the angle/rotation of labels. 0 is horizontal while 90 is vertical. +#' @param grplabjust A numeric indicating the justification of labels. Defaults to 0.5 if grplabangle=0 or 1 if grplabangle between 20 and 135. +#' @param pointsize A numeric indicating the size of points on label marker line. +#' @param linesize A numeric indicating the thickness of the label marker line. +#' @return A list with following plot parameters: grplab, plotnum, grplabsize, +#' grplabangle, grplabjust, pointsize, linesize. +# @export +#' +getPlotParams <- function(grplab=NA,plotnum=1,grplabsize=NA,grplabangle=NA,grplabjust=NA,pointsize=NA,linesize=NA) +{ + if(all(is.na(grplab))) stop("getPlotParams: Labels are empty.") + + # estimate ct based on number of labels/ind + lp <- length(as.character(grplab)) + + # calculate grplabangle, just and margins + if(is.na(grplabangle)) grplabangle <- 0 + if(grplabangle==0) + { + if(is.na(grplabjust)) grplabjust <- 0.5 + } + + if(abs(grplabangle) > 20 && abs(grplabangle) < 135) + { + if(is.na(grplabjust)) grplabjust <- 1 + #bmar <- round(max(nchar(as.character(grplab)))/8, 2)+round(lp/900, 3) + #if(all(is.na(fmar))) fmar <- c(0.2, 0.2, bmar, 0) + } + + grplabsize1 <- grplabsize + pointsize1 <- pointsize + linesize1 <- linesize + + if(is.na(grplabsize)) grplabsize1 <- lp*0.00123 + if(is.na(pointsize)) pointsize1 <- lp*0.0015 + if(is.na(linesize)) linesize1 <- lp*0.0003 + + if(is.na(grplabsize)) {if(grplabsize1 < 1.5) grplabsize1 <- 1.5} + if(is.na(pointsize)) {if(pointsize1 < 1.2) pointsize1 <- 1.2} + if(is.na(linesize)) {if(linesize1 < 0.3) linesize1 <- 0.3} + + if(is.na(grplabsize)) {if(grplabsize1 > 2.5) grplabsize1 <- 2.5} + if(is.na(pointsize)) {if(pointsize1 > 3.2) pointsize1 <- 3.2} + if(is.na(linesize)) {if(linesize1 > 0.6) linesize1 <- 0.6} + + dlist <- list(grplab=grplab,plotnum=plotnum,grplabsize=grplabsize1,grplabangle=grplabangle,grplabjust=grplabjust, + pointsize=pointsize1,linesize=linesize1) + return(dlist) +} + +# grpLabels -------------------------------------------------------------------- + +#' @title Internal: Handles grp subset/order +#' @description Internal: Takes a q-matrix dataframe along with grp labels. Pop labels +#' can be reordered or subsetted. The function also creates labelpos and markerpos dfs. +#' @param df A q-matrix dataframe +#' @param grplab A dataframe with group labels +#' @param selgrp A character denoting selected group label set +#' @param ordergrp A logical indicating if individuals must be ordered by group labels +#' @param subsetgrp A character or character vector of grp name(s) to subset/reorder +#' @param grpmean A logical indicating if q-matrix must be converted from individual to group mean. +#' @param grplabpos A numeric indicating y-axis position of labels +#' @param linepos A numeric indicating y-axis position of label line +#' @return Returns a list with subsetted/reordered q-matrix, a character vector +#' of original/subsetted/reordered grplab dataframe, grplabpos and linepos. +# @export +grpLabels <- function(dframe=NULL,grplab=NA,selgrp=NA,subsetgrp=NA,ordergrp=FALSE,grpmean=FALSE,grplabpos=NA,linepos=NA,indlabwithgrplab=TRUE,indlabsep="_") +{ + if(is.null(dframe)) stop("grpLabels: Argument 'dframe' is empty.") + if(!is.data.frame(dframe)) stop("grpLabels: Argument 'dframe' is not a data.frame datatype.") + if(any(is.na(grplab))) stop("grpLabels: Argument 'grplab' contains NA.") + if(!is.data.frame(grplab)) stop("grpLabels: Argument 'grplab' is not a data.frame datatype.") + if(is.na(selgrp)) selgrp <- names(grplab)[1] + if(!all(is.na(selgrp))) {if(!is.character(selgrp)) stop("grpLabels: Argument 'selgrp' is not a character datatype.")} + if(!all(is.na(subsetgrp))) {if(!is.character(subsetgrp)) stop("grpLabels: Argument 'subsetgrp' is not a character datatype.")} + if(is.na(grplabpos)) grplabpos <- 0.25 + if(is.na(linepos)) linepos <- 0.75 + + #check length + if(nrow(dframe) != nrow(grplab)) stop(paste0("grpLabels: Number of individuals (",nrow(dframe),") differ from number of labels in 'grplab' (",nrow(grplab),").")) + #if(is.factor(grplab)) grplablev <- levels(grplab) + #if(is.character(grplab)) grplablev <- factor(grplab,levels=c(rle(grplab)$values)) + + #concatenate grp labs to ind labs + if(indlabwithgrplab) rownames(dframe) <- apply(as.data.frame(list(list(rn=rownames(dframe)),as.list(grplab))),1,paste,collapse=indlabsep) + + gnames <- names(grplab) + onames <- gnames[!gnames %in% selgrp] + + # order groups + # orders dframe and all labels by selgrp + if(ordergrp) + { + dfwork1 <- cbind(dframe,grplab) + #dfwork1 <- dfwork1[order(dfwork1[,selgrp]),] + dfwork1 <- dfwork1[do.call(order,dfwork1[,c(selgrp,onames),drop=FALSE]),,drop=FALSE] + + grplab1 <- dfwork1[,gnames,drop=FALSE] + dfwork1[,gnames] <- NULL + }else{ + dfwork1 <- dframe + grplab1 <- grplab + } + + # group mean by selgrp + if(grpmean) dfwork1 <- as.data.frame(sapply(dfwork1,ave,unlist(grplab1[selgrp])),stringsAsFactors=F) + + # in case of subsetgrp + if(!any(is.na(subsetgrp))) + { + if(any(duplicated(subsetgrp))) stop(paste0("grpLabels: Argument 'subsetgrp' contains duplicate values (",paste0(subsetgrp,collapse=', '),").")) + subsetgrp <- as.character(subsetgrp) + subsetlabs <- as.vector(unlist(grplab1[selgrp])) + #rle grp + rlegrp <- rle(subsetlabs) + + # checks + if(any(duplicated(rlegrp$values))) stop("grpLabels: Duplicated contiguous block of labels in 'selgrp'. Change grplab, selgrp or use 'ordergrp=TRUE'.") + if(any(duplicated(rlegrp$values))) {cont <- "non-contiguous"}else{cont <- "contiguous"} + if(!any(subsetgrp %in% rlegrp$values)) stop(paste0("grpLabels: Subset group label (",subsetgrp,") not present in group label set (",selgrp,") with following ",cont," groups: (",paste0(rlegrp$values,collapse=", "),").")) + + # compute positions and labels of subset grps + posvec=vector() + for(k in 1:length(subsetgrp)) + { + sgrp=subsetgrp[k] + pos=which(subsetlabs==sgrp) + posvec=c(posvec,pos) + } + + if(length(intersect(colnames(dfwork1),colnames(grplab1)))!=0) stop(paste0("grpLabels: One or more header labels in the run file are duplicated in grplab header. Change labels to be unique. Following are the duplicate label(s): (",paste0(intersect(colnames(dfwork1),colnames(grplab1)),collapse=", "),").")) + dfwork2 <- cbind(dfwork1,grplab1) + dfwork2 <- dfwork2[posvec,,drop=FALSE] + dfwork1 <- dfwork2 + dfwork1[,gnames] <- NULL + grplab1 <- dfwork2[,gnames,drop=FALSE] + } + + # create labelpos and markerpos + markerlist <- vector("list",length=length(gnames)) + labellist <- vector("list",length=length(gnames)) + intlablist <- vector("list",length=length(gnames)) + for(k in 1:length(gnames)) + { + rlegrp <- rle(unlist(grplab1[gnames[k]])) + labelpos <- data.frame(label=rlegrp$values,freq=rlegrp$lengths,stringsAsFactors=F) + markerpos <- data.frame(markerxpos=c(0,cumsum(labelpos$freq)),stringsAsFactors=F) + labelpos$labxpos <- round((diff(markerpos$markerxpos)/2)+markerpos$markerxpos[1:length(markerpos$markerxpos)-1],1) + labelpos$labypos <- rep(grplabpos,nrow(labelpos)) + markerpos$temp <- factor(rep(1,nrow(markerpos))) + markerpos$markerypos <- rep(linepos,nrow(markerpos)) + + markerpos$count <- gnames[k] + markerlist[[k]] <- markerpos + labelpos$count <- gnames[k] + labellist[[k]] <- labelpos + } + + markerposbind <- do.call("rbind",markerlist) + markerposbind$count <- factor(markerposbind$count,levels=gnames) + labelposbind <- do.call("rbind",labellist) + labelposbind$count <- factor(labelposbind$count,levels=gnames) + + rownames(markerposbind) <- 1:nrow(markerposbind) + rownames(labelposbind) <- 1:nrow(labelposbind) + + # adjust divider position + markerposbind$divxpos <- markerposbind$markerxpos+0.5 + + return(list(dframe=dfwork1,grplab=grplab1,labelpos=labelposbind,markerpos=markerposbind)) +} + +# sortInd ---------------------------------------------------------------------- + +#' @title Internal: Handles individual sorting +#' @description Internal: Handles individual sorting +#' @param dframe A q-matrix dataframe +#' @param grplab A dataframe with group labels +#' @param selgrp A single character denoting selected group label set. See details. +#' @param sortind A character indicating how individuals are sorted. Default is NA (Same order of individuals as in input file). Other options are 'all' (sorting by values of all clusters), by any one cluster (eg. 'Cluster1') or 'labels' (sorting by individual labels). +#' @param grplabpos A numeric indicating y-axis position of labels +#' @param linepos A numeric indicating y-axis position of label line +#' @return Returns a list with ordered q-matrix dataframe and ordered grplab. +#' @details When multiple group label sets are in use, \code{selgrp} defines which +#' group label set is used for group ordering (\code{ordergrp}), subsetting (\code{subsetgrp}) +#' and group mean (\code{grpmean}). \code{selgrp} is also used for plotting divider +#' lines and and sorting (\code{sortind}). If \code{selgrp} is not specified, the +#' first group label set is used by default. +# @export +sortInd <- function(dframe=NULL,grplab=NA,selgrp=NA,sortind=NA,grplabpos=NA,linepos=NA) +{ + if(is.null(dframe)) stop("sortInd: Argument 'dframe' is empty.") + if(!all(is.na(grplab))) + { + if(is.na(selgrp)) selgrp <- names(grplab)[1] + if(!is.character(selgrp)) stop("sortInd: Argument 'selgrp' must be a character datatype.") + if(length(selgrp)>1) stop("sortInd: Argument 'selgrp' must be a character datatype of length 1.") + if(!any(selgrp %in% names(grplab))) stop(paste0("sortInd: Argument 'selgrp' contains (",selgrp,") which is not in the 'grplab' titles (",paste0(names(grpla),collapse=", "),").")) + } + if(all(!is.na(sortind))) + { + if(length(sortind) > 1) stop("sortInd: Argument 'sortind' must be of length 1. Use 'all','label' or a cluster name like 'Cluster1'.") + #if(sortind != "all" && sortind != "label" && !grepl("Cluster[0-9+]",sortind)) stop("sortInd: Argument 'sortind' must be set to 'all', 'label' or a cluster like 'Cluster1'.") + } + + # sorting without grplab + if(any(is.na(grplab))) + { + if(!is.na(sortind)) + { + if(sortind=="all") + { + maxval <- apply(dframe,1,max) + matchval <- vector(length=nrow(dframe)) + for(j in 1:nrow(dframe)) matchval[j] <- match(maxval[j],dframe[j,]) + dftemp <- dframe + dftemp$maxval <- maxval + dftemp$matchval <- matchval + + dframe <- dframe[with(dftemp,order(matchval,-maxval)),,drop=FALSE] + } + + if(sortind=="label") dframe <- dframe[order(rownames(dframe)),,drop=FALSE] + + if(sortind!="all" && sortind!="label") + { + if(!(sortind %in% colnames(dframe))) stop(paste0("sortInd: 'sortind' value (",sortind,") not found in file header (",paste0(colnames(dframe),collapse=", "),").")) + dframe <- dframe[order(dframe[[sortind]]),,drop=FALSE] + } + } + labelposbind <- NA + markerposbind <- NA + } + + # sorting with grplab + if(!all(is.na(grplab))) + { + gnames <- names(grplab) + + if(!is.na(sortind)) + { + if(sortind=="all") + { + maxval <- apply(dframe,1,max) + matchval <- vector(length=nrow(dframe)) + for(j in 1:nrow(dframe)) matchval[j] <- match(maxval[j],dframe[j,]) + dftemp <- dframe + dftemp$maxval <- maxval + dftemp$matchval <- matchval + + if(length(intersect(colnames(dftemp),colnames(grplab)))!=0) stop(paste0("sortInd: One or more header labels in the run file are duplicated in grplab header. Change labels to be unique. Following are the duplicate label(s): (",paste0(intersect(colnames(dftemp),colnames(grplab)),collapse=", "),").")) + dftemp <- cbind(dftemp,grplab) + + rle1 <- rle(as.character(unlist(grplab[selgrp]))) + grplabnames <- rle1$values + tovec <- cumsum(rle1$lengths) + fromvec <- (tovec - rle1$lengths)+1 + dftemplist <- vector("list",length=length(grplabnames)) + for(k in 1:length(tovec)) + { + dftemp1 <- dftemp[fromvec[k]:tovec[k],,drop=FALSE] + dftemp1$grp <- NULL + dftemplist[[k]] <- dftemp1[with(dftemp1,order(matchval,-maxval)),,drop=FALSE] + } + + dframe <- do.call("rbind",dftemplist) + grplab <- dframe[,gnames,drop=FALSE] + dframe[,gnames] <- NULL + dframe$maxval <- NULL + dframe$matchval <- NULL + } + + if(sortind=="label") + { + dftemp <- dframe + if(length(intersect(colnames(dftemp),colnames(grplab)))!=0) stop(paste0("sortInd: One or more header labels in the run file are duplicated in grplab header. Change labels to be unique. Following are the duplicate label(s): (",paste0(intersect(colnames(dftemp),colnames(grplab)),collapse=", "),").")) + dftemp <- cbind(dftemp,grplab) + + rle1 <- rle(as.character(unlist(grplab[selgrp]))) + grplabnames <- rle1$values + tovec <- cumsum(rle1$lengths) + fromvec <- (tovec - rle1$lengths)+1 + dftemplist <- vector("list",length=length(grplabnames)) + for(k in 1:length(tovec)) + { + dftemp1 <- dftemp[fromvec[k]:tovec[k],,drop=FALSE] + dftemp1$grp <- NULL + dftemplist[[k]] <- dftemp1[order(rownames(dftemp1)),,drop=FALSE] + } + + dframe <- do.call("rbind",dftemplist) + grplab <- dframe[,gnames,drop=FALSE] + dframe[,gnames] <- NULL + } + + + if(sortind!="all" && sortind!="label") + { + if(!(sortind %in% colnames(dframe))) stop(paste0("sortInd: 'sortind' value (",sortind,") not found in file header (",paste0(colnames(dframe),collapse=", "),").")) + clnum <- which(sortind==colnames(dframe)) + dftemp <- dframe + if(length(intersect(colnames(dftemp),colnames(grplab)))!=0) stop(paste0("sortInd: One or more header labels in the run file are duplicated in grplab header. Change labels to be unique. Following are the duplicate label(s): (",paste0(intersect(colnames(dftemp),colnames(grplab)),collapse=", "),").")) + dftemp <- cbind(dftemp,grplab) + + rle1 <- rle(as.character(unlist(grplab[selgrp]))) + grplabnames <- rle1$values + tovec <- cumsum(rle1$lengths) + fromvec <- (tovec - rle1$lengths)+1 + dftemplist <- vector("list",length=length(grplabnames)) + for(k in 1:length(tovec)) + { + dftemp1 <- dftemp[fromvec[k]:tovec[k],,drop=FALSE] + dftemp1$grp <- NULL + dftemplist[[k]] <- dftemp1[order(dftemp1[[sortind]]),,drop=FALSE] + } + + dframe <- do.call("rbind",dftemplist) + grplab <- dframe[,gnames,drop=FALSE] + dframe[,gnames] <- NULL + } + } + + # create labelpos and markerpos + gnames <- names(grplab) + markerlist <- vector("list",length=length(gnames)) + labellist <- vector("list",length=length(gnames)) + intlablist <- vector("list",length=length(gnames)) + for(k in 1:length(gnames)) + { + rlegrp <- rle(unlist(grplab[gnames[k]])) + labelpos <- data.frame(label=rlegrp$values,freq=rlegrp$lengths,stringsAsFactors=F) + markerpos <- data.frame(markerxpos=c(0,cumsum(labelpos$freq)),stringsAsFactors=F) + labelpos$labxpos <- round((diff(markerpos$markerxpos)/2)+markerpos$markerxpos[1:length(markerpos$markerxpos)-1],1) + labelpos$labypos <- rep(grplabpos,nrow(labelpos)) + markerpos$temp <- factor(rep(1,nrow(markerpos))) + markerpos$markerypos <- rep(linepos,nrow(markerpos)) + + markerpos$count <- gnames[k] + markerlist[[k]] <- markerpos + labelpos$count <- gnames[k] + labellist[[k]] <- labelpos + } + + markerposbind <- do.call("rbind",markerlist) + markerposbind$count <- factor(markerposbind$count,levels=gnames) + labelposbind <- do.call("rbind",labellist) + labelposbind$count <- factor(labelposbind$count,levels=gnames) + + rownames(markerposbind) <- 1:nrow(markerposbind) + rownames(labelposbind) <- 1:nrow(labelposbind) + + #adjust divider position + markerposbind$divxpos <- markerposbind$markerxpos+0.5 + } + + + + return(list(dframe=dframe,grplab=grplab,labelpos=labelposbind,markerpos=markerposbind)) +} + +# plotQ --------------------------------------------------------------------- + +#' @title Generate barplots from qlists. +#' @description Generate separate or joined barplots (group-level) from qlists. +#' @param qlist A qlist (list of dataframes). An output from \code{\link{readQ}}. +#' @param imgoutput A character with options: 'sep' or 'join'.If set to "sep", each run is plotted as separate image file. If set to "join", multiple runs are joined into a single image. +#' @param clustercol A vector of colours for clusters. If NA, colours are automatically generated. K=1 to K=12 are custom unique colours while K>12 are coloured by function \code{gplots::rich.colors()}. +#' @param sortind A character indicating how individuals are sorted. Default is NA (Same order of individuals as in input file). Other options are 'all' (sorting by values of all clusters), by any one cluster (eg. 'Cluster1') or 'labels' (sorting by individual labels). See details. +#' @param grplab A dataframe with one or more columns (group label sets), and rows equal to the number of individuals. See details. +#' @param selgrp A single character denoting a selected group label set. The selected label must be a group label title used in \code{grplab}. See details. +#' @param ordergrp A logical indicating if individuals must be grouped into contiguous blocks based on \code{grplab} starting with \code{selgrp}. +#' @param subsetgrp A character or character vector with group names to subset or reorder groups. Only applicable when \code{grplab} is in use. Default is NA. See details. +#' @param grpmean A logical indicating if q-matrix must be converted from individual values to group mean values. Applicable only when \code{grplab} is in use and mean is calculated over \code{selgrp}. +#' @param panelspacer A numeric indicating the spacing between barplot panels in cm. Defaults to 0.06cm. +#' @param showsp A logical indicating if strip panels on right side must be shown. Strip panel by default displays file name and K value. Defaults to TRUE. +#' @param sppos A character indicating position of strip panel. One of 'right' or 'left'. Defaults to 'right'. +#' @param splab A character or character vector denoting items displayed in the strip panels. Length must be equal to number of runs. +#' @param splabsize A numeric indicating the size of the strip panel label. Computed automatically when set to NULL. Note that overall text size can be controlled using \code{basesize}. +#' @param splabangle A numeric indicating angle/rotation of the strip panel label. Defaults to NULL. Automatically set to -90. +#' @param splabcol A character indicating the colour of the strip panel label. Defaults to "grey30". +#' @param splabface A character indicating the font face of strip panel label. One of 'plain', 'italic', 'bold' or 'bold.italic'. Defaults to 'plain'. Applicable only when \code{showsp=T}. +#' @param spbgcol A character denoting the background colour of the strip panel. Defaults to white. +#' @param showtitle A logical indicating if plot title must be shown on the top. Defaults to FALSE. If TRUE and \code{titlelab=NA}, file name is displayed by default. +#' @param titlelab A character or character vector for title text. Defaults to NA, and when \code{showtitle=TRUE} displays file name. +#' @param titlehjust A numeric denoting the horizontal justification of the title. Defaults to 0 (left). +#' @param titlevjust A numeric denoting the vertical justification of the title. Defaults to 0.5 (center). +#' @param titlesize A numeric indicating the size of the title text. Computed automatically when set to NULL. Note that overall text size can be controlled using \code{basesize}. +#' @param titlecol A colour character for title. Defaults to "grey30". +#' @param titleface A character indicating the font face of title label. One of 'plain', 'italic', 'bold' or 'bold.italic'. Defaults to 'plain'. Applicable only when \code{showtitle=T}. +#' @param titlespacer A numeric indicating the space below the title. Defaults to 1.2. +#' @param titleangle A numeric indicating the angle/rotation of the title. Defaults to 0. +#' @param showsubtitle A logical indicating if plot subtitle must be shown on the top. Defaults to FALSE. If TRUE and \code{subtitlelab=NA}, file name is displayed by default. +#' @param subtitlelab A character or character vector for subtitle text. Defaults to NA, and when \code{showsubtitle=TRUE} displays file name. +#' @param subtitlehjust A numeric denoting the horizontal justification of the subtitle. Defaults to 0 (left). +#' @param subtitlevjust A numeric denoting the vertical justification of the subtitle. Defaults to 0.5 (center). +#' @param subtitlesize A numeric indicating the size of the subtitle text. Computed automatically when set to NULL. Note that overall text size can be controlled using \code{basesize}. +#' @param subtitlecol A colour character for subtitle. Defaults to "grey30". +#' @param subtitleface A character indicating the font face of subtitle label. One of 'plain', 'italic', 'bold' or 'bold.italic'. Defaults to 'plain'. Applicable only when \code{showsubtitle=T}. +#' @param subtitlespacer A numeric indicating the space below the subtitle. Defaults to 1.2. +#' @param subtitleangle A numeric indicating the angle/rotation of the subtitle. Defaults to 0. +#' @param grplabspacer A numeric indicating the space between the plot panels and the group label area in cm. Defaults to 0cm. Applicable only when \code{grplab} are in use. +#' @param grplabheight A numeric indicating the height of the group label area in cm. Defaults to 0.4cm. Multiple group sets are multiplied by 0.4. Applicable only with \code{grplab}. See details. +#' @param grplabpos A numeric indicating the y position of the group labels. Applicable only with group labels. Defaults to 0. +#' @param grplabsize A numeric indicating the size of the group labels. Default range between 1.5 - 2.5 depending on number of individuals. This text size is not affected by \code{basesize}. +#' @param grplabangle A numeric indicating the angle/rotation of group labels. 0 is horizontal while 90 is vertical. Default is 0. +#' @param grplabjust A numeric indicating the justification of group labels. Defaults to 0.5 if grplabangle=0 or 1 if grplabangle between 20 and 135. +#' @param grplabcol A colour character for the colour of group labels. Defaults to "grey30". +#' @param grplabalpha A numeric between 0 and 1 denoting transparency of group labels. Defaults to 1. +#' @param showindlab A logical indicating if individual labels must be shown. See details. +#' @param sharedindlab A logical indicating if only one set of shared individual labels must be shown below all plots. Applicable only when \code{imgoutput="join"}. Individual labels are visible only when \code{showindlab=TRUE}. +#' @param useindlab A logical indicating if individual labels must be read from the rownames of qlist dataframes and used as individual labels. See details. +#' @param indlabwithgrplab A logical indicating if individual labels must be concatenated with grplab. Applies only when grplab is in use. Relevant for sorting by label. +#' @param indlabsep A character used as separator when concatenating individual labels and group labels. Defaults to space \code{indlabsep=" "}. +#' @param indlabheight A numeric indicating space below the individual label panel. Increase to 0.1, 0.2 etc if labels are clipped off. +#' @param indlabsize A numeric indicating the size of the individual labels. Computed automatically when set to NULL. Note that overall text size can be controlled using \code{basesize}. +#' @param indlabangle A numeric indicating the angle/rotation of individual labels. 0 is horizontal while 90 is vertical. Defaults to 90. +#' @param indlabvjust A numeric denoting vertical justification of the individual labels. Defaults to 0.5. +#' @param indlabhjust A numeric denoting the horizontal justification of the individual labels. Defaults to 1. +#' @param indlabcol A colour character for the colour of individual labels. Defaults to "grey30". +#' @param indlabspacer A numeric denoting space between the individual label and the plot area. Default set to 0. +#' @param pointsize A numeric indicating the size of points on label marker line. Default range between 1.2 - 3.2 depending on number of individuals. +#' @param pointcol A colour character for the colour of points on the label marker line. Defaults to "grey30". +#' @param pointbgcol A colour character for the background of marker point for certain point types. +#' @param pointtype A character or number for the type of points on the label marker line. Defaults to |. Same as pch in standard R. +#' @param pointalpha A numeric between 0 and 1 denoting transparency of the points. Defaults to 1. +#' @param linepos A numeric indicating the y position of the label marker line and the points. Applicable only with group labels. Defaults to 1. +#' @param linesize A numeric indicating the thickness of the label marker line. Default range between 0.3 and 0.6 depending on number of individuals. +#' @param linecol A colour character for the label marker line. Defaults to "grey30". +#' @param linetype A numeric indicating the type of line for marker line. Same as lty in standard R. Default value is 1. +#' @param linealpha A numeric between 0 and 1 denoting transparency of the marker line. Defaults to 1. +#' @param showdiv A logical indicating if divider lines between groups must be drawn. Applicable only when group labels are in use. +#' @param divgrp A character or character vector with one or more group label titles denoting which groups are used to draw divider lines. This must be a group label title used in \code{grplab}. If not provided, the value in \code{selgrp} is used by default. +#' @param divcol A character or hexadecimal colour denoting the colour of the divider line. Default is white. +#' @param divtype A numeric indicating the type of line for the divider line. Same as lty in standard R. Default value is '21'. +#' @param divsize A numeric indicating the thickness of the divider line. Default is 0.25. +#' @param divalpha A numeric between 0 and 1 denoting transparency of the divider line. Defaults to 1. +#' @param showlegend A logical indicating if legend denoting cluster colours must be plotted. Defaults to FALSE. +#' @param legendlab A character or character vector to for legend cluster labels. Must be equal to max number of clusters. +#' @param legendpos A character 'right' or 'left' denoting position of the legend. Defaults to 'left'. +#' @param legendkeysize A numeric indicating size of the legend key. Defaults to 4. +#' @param legendtextsize A numeric indicating size of the legend text. Defaults to 3. +#' @param legendmargin A numeric vector of length 4 indicating top, right, bottom and left margins of the legend. +#' @param barsize A numeric indicating the width of the bars. Defaults to 1. +#' @param barbordersize A numeric indicating border size of bars. Defaults to 0. Visible only when \code{barbordercolour} is not NA. +#' @param barbordercolour A single colour for bar border. Defaults to NA. Visible only when \code{barbordersize} is larger than zero and set to a colour other than NA. +#' @param showyaxis A logical indicating if y-axis labels should be displayed or not. Defaults to FALSE. Y-axis size is same as \code{indlabsize}. +#' @param showticks A logical indicating if ticks on axis should be displayed or not. Defaults to FALSE. Applies to x and y axis. Y-axis ticks are visible only when \code{showyaxis=TRUE}. Tick colour is same as \code{indlabcol}. +#' @param ticksize A numeric indicating size of ticks. Defaults to 0.2. Applies to both x and y axis. +#' @param ticklength A numeric indicating length of tick marks in cm. Defaults to 0.03. Applies to both x and y axis. +#' @param outputfilename A character or character vector denoting output file name without file extension. See details. +#' @param imgtype A character indicating output image file type. Possible options are "png","jpeg","tiff" or "pdf". +#' @param height A numeric indicating the height of a single run panel. By default, automatically generated based on number of runs. Separate plots use 1.8cm and joined plots use 1.2cm for single panel. See details. +#' @param width A numeric indicating the width of the whole plot. By default, automatically generated based on number of individuals. Ranges between 5cm and 30cm. +#' @param dpi A numeric indicating the image resolution in pixels per inch (PPI). Defaults to 300. If \code{imgtype="pdf"}, dpi is fixed at 300. +#' @param units A numeric indicating the units of height and width. Default set to "cm". Other options are 'px', 'in' or 'mm'. +#' @param theme A character indicating ggplot theme to be used. Use like "theme_grey", "theme_bw" etc. +#' @param basesize A numeric indicating overall text size. Defaults to 5 suitable for export. Set to 11 for returned plot. +#' @param font A character indicating font family to be used in the plots. Uses default system fonts by default for jpeg, png and tiff. Uses 'Helvetica' as default for pdf. Use package \code{extrafonts} to import custom fonts. See vignette for examples. +#' @param na.rm A logical indicating if NAs are removed from data, else \code{ggplot} prints warning messages for NAs. If set to TRUE, NAs are removed before plotting and \code{ggplot} NA warning is suppressed. +#' @param quiet A logical indicating if any messages are printed to console. +#' @param panelratio A two value integer vector denoting ratio of plot panel to grplab panel. Defaults to \code{c(3,1)}. Applicable only when \code{grplab} is in use. +#' @param exportplot A logical indicating if a plot image must be exported into the working directory. +#' @param returnplot A logical indicating if ggplot plot objects must be returned. See 'Value'. +#' @param returndata A logical indicating if processed data must be returned. See 'Value'. +#' @return When \code{returnplot=TRUE}, plot object(s) are returned. When \code{grplab=NA}, +#' a ggplot2 object is returned. When \code{grplab} is in use, a gtable (output from gridExtra::arrangeGrob()) +#' list is returned. When \code{returndata=TRUE}, the input qlist is modified (sorted, subsetted etc) +#' and returned. If \code{grplab} is in use, a list of modified qlist and grplab is returned. +#' If \code{returnplot=TRUE} and \code{returndata=TRUE} are both set, then a named list +#' (plot,data) is returned. The plot item contains the ggplot2 object or gtable and +#' the data contains qlist (and grplab). +#' +#' @details +#' +#' \strong{sortind}\cr +#' This argument takes one character as input. Default NA means individuals are +#' plotted in the same order as input. Individuals can be ordered by any one cluster. +#' For ex. \code{sortind="Cluster1"} or \code{sortind="Cluster2"}. +#' To order by all clusters as the 'Sort by Q' option in STRUCTURE software, +#' use \code{sortind="all"}. When using \code{sortind="label"}, individuals are +#' sorted by individual labels (along with grplab if present). Individual +#' labels can be displayed using \code{showindlab=T}. When using \code{sortind} +#' with \code{grplab}, individuals are sorted within the groups.\cr +#' +#' \strong{grplab}\cr +#' \code{grplab} must be a data.frame. One or more label sets can be provided. Each +#' label set must be a character vector equal to the number of individuals +#' present in the qlist. +#' For example, we can provide one group label set as such:\cr +#' \code{grplab=data.frame(labs=c("Grp A","Grp A","Grp B","Grp B"),stringsAsFactors=F)}\cr +#' +#' Two group label sets can be provided as such:\cr +#' \code{grplab=data.frame(labs=c("Grp A","Grp A","Grp B","Grp B"),loc=c("Loc 1","Loc 2","Loc 2","Loc 2"),stringsAsFactors=F)}\cr +#' +#' \strong{selgrp}\cr +#' When multiple group label sets are in use, \code{selgrp} defines which +#' group label set is used for group ordering (\code{ordergrp}), subsetting (\code{subsetgrp}) +#' and group mean (\code{grpmean}). \code{selgrp} is also used for plotting divider +#' lines and and sorting (\code{sortind}). If \code{selgrp} is not specified, +#' the first group label set is used by default.\cr +#' +#' \strong{ordergrp}\cr +#' When using \code{grplab}, labels may not be in contiguous blocks. Using \code{ordergrp=TRUE}, +#' regroups individuals into contiguous blocks for all group label sets starting with \code{selgrp}.\cr +#' +#' \strong{subsetgrp}\cr +#' This argument takes one or more characters as input. Use only group labels used +#' in one of the group label sets in \code{grplab}. For ex. In case of a group label +#' set 'labs' with two grps in order 'Grp A' and 'Grp B', use \code{subsetgrp=c("Grp B","Grp A")} +#' to change order of groups. Use \code{subsetgrp="Grp B"} to subset only Grp B. +#' When using multiple group label sets, use \code{selgrp} to declare which group label set to subset.\cr +#' +#' \strong{outputfilename}\cr +#' Default is \code{outputfilename=NA} which means that output file names are automatically generated. +#' When \code{imgoutput="sep"}, the names of the qlist are used to create output labels. When \code{imgoutput="join"}, +#' one output label is created for all input files in this format: JoinedNFiles-YYYYMMDDHHMMSS, +#' where N stands for number of runs joined, and the ending stands for current system date and time. +#' If \code{outputfilename} is provided, when \code{imgoutput="sep"}, \code{outputfilename} must be +#' a character vector equal to length of input runs. When \code{imgoutput="join"}, \code{outputfilename} +#' must be a character of length one. File extensions like .png etc must not be provided.\cr +#' +#' \strong{height}\cr +#' Argument \code{height} denotes the height of one run panel. With joined plots, the \code{height} is multiplied by number of runs. The height does not include label panel. The \code{grplabheight} is used to define the full height of the lab panel. If \code{grplabheight} is not provided, it is calculated based on the number of group label sets. +#' final_image_height = (height*num_of_runs)+grplabheight +#' It is possible to set either height or width and leave other as default.\cr +#' +#' \strong{indlab}\cr +#' When \code{showindlab=T}, individual labels are shown/displayed. When \code{showindlab=F}, +#' individual labels are not shown/displayed on the graph, although they are present in the underlying data. +#' Therefore, \code{showindlab} only control display of labels on the plot and nothing to +#' do with label control in the data.\cr +#' The default \code{useindlab=F}, creates labels numerically in the +#' original order of data but with zero padding. For example, if there are 10 individuals, +#' labels are 01, 02 up to 10. if there are 100 individuals, then labels are 001, 002 up +#' to 100. Zero padding to ensure optimal sorting. When \code{useindlab=T}, labels +#' are used from rownames of qlist dataframes. They are usually labelled 1,2,3.. if +#' read in using \code{readQ()}. This can be an issue with sorting by labels \code{sortind="label"}. +#' For STRUCTURE files with individual labels, they can be read +#' in automatically using \code{readQ(indlabfromfile=T)}.\cr +#' When group labels are in use, \code{grplab}, they are added to the individual +#' labels in both cases \code{useindlab=T} and \code{useindlab=F} separated by \code{indlabsep}. +#' Default \code{indlabsep=" "} adds a space between individual label and grplab. For example, +#' group labels 'popA', 'popA'... will be '01 popA', '02 popA'... when \code{useindlab=F} +#' and usually '1 popA', '2 popA'... when \code{useindlab=T}. When multiple group labels +#' are in use, the are similarly concatenated one after the other to individual names +#' in the order in which the group labels were provided. +#' +#' See the \href{http://royfrancis.github.io/pophelper/}{vignette} for more details. +#' +#' @seealso \code{\link{plotQMultiline}} +#' @examples +#' slist <- readQ(list.files(path=system.file("files/structure",package="pophelper"),full.names=TRUE)) +#' +#' # plot one separate figure +#' plotQ(qlist=slist[1]) +#' +#' # plot two separate figures +#' plotQ(qlist=slist[1:2]) +#' +#' # plot a joined figure with multiple plots +#' plotQ(qlist=slist[1:2],imgoutput="join") +#' +#' # sort individuals +#' plotQ(qlist=slist[c(1,3)],sortind="all") +#' plotQ(qlist=slist[c(1,3)],sortind="Cluster1") +#' plotQ(qlist=slist[c(1,3)],sortind="label") +#' plotQ(qlist=slist[c(1,3)],sortind="all",imgoutput="join") +#' +#' # read group labels +#' md <- read.delim(system.file("files/metadata.txt", package="pophelper"), header=T,stringsAsFactors=F) +#' +#' # plot with one group label set +#' plotQ(qlist=slist[1],grplab=md[,2,drop=F]) +#' plotQ(qlist=slist[1:2],grplab=md[,2,drop=F],imgoutput="join") +#' +#' # sort within groups +#' plotQ(qlist=slist[1:2],grplab=md[,2,drop=F],imgoutput="join",sortind="all") +#' plotQ(qlist=slist[1:2],grplab=md[,2,drop=F],imgoutput="join",sortind="Cluster1") +#' plotQ(qlist=slist[1:2],grplab=md[,2,drop=F],imgoutput="join",sortind="label") +#' +#' # reorder groups +#' plotQ(qlist=slist[1],grplab=md[,2,drop=F],subsetgrp=c("CatB","CatA")) +#' +#' # multiple group label sets and ordergrp +#' plotQ(qlist=slist[1],grplab=md,ordergrp=TRUE) +#' plotQ(qlist=slist[1:2],grplab=md,ordergrp=TRUE,imgoutput="join") +#' +#' # sort in second label group set cat +#' plotQ(qlist=slist[1],grplab=md,selgrp="cat",sortind="all") +#' +#' # use default individual labels +#' plotQ(slist[1],showindlab=T,width=15) +#' +#' # use custom individual labels +#' inds <- read.delim(system.file("files/structureindlabels.txt",package="pophelper"),header=FALSE,stringsAsFactors=FALSE) +#' rownames(slist[[1]]) <- inds$V1 +#' plotQ(slist[1],showindlab=T,useindlab=T,width=15) +#' +#' # change cluster colours +#' plotQ(slist[1],clustercol=c("steelblue","coral")) +#' +#' # plot a custom dataframe +#' temp <- list("custom"=data.frame(Cluster1=c(0.2,0.3,0.6,0.8),Cluster2=c(0.8,0.7,0.4,0.2))) +#' plotQ(temp) +#' +#' @import gtable +#' @import grid +#' @import gridExtra +#' @import tidyr +#' @export +#' +plotQ <- function(qlist=NULL,imgoutput="sep",clustercol=NA,sortind=NA,grplab=NA,selgrp=NA,ordergrp=FALSE,subsetgrp=NA,grpmean=FALSE,panelspacer=0.1, + showsp=TRUE,sppos="right",splab=NA,splabsize=NULL,splabangle=NULL,splabcol="grey30",splabface="plain",spbgcol=NA, + showtitle=FALSE,titlelab=NA,titlehjust=0,titlevjust=0.5,titlesize=NULL,titlecol="grey30",titleface="plain",titlespacer=1.4,titleangle=0, + showsubtitle=FALSE,subtitlelab=NA,subtitlehjust=0,subtitlevjust=0.5,subtitlesize=NULL,subtitlecol="grey30",subtitleface="plain",subtitlespacer=1.5,subtitleangle=0, + grplabspacer=0,grplabheight=NA,grplabpos=0.25,grplabsize=NA,grplabangle=NA,grplabjust=NA,grplabcol="grey30",grplabalpha=1, + showindlab=FALSE,sharedindlab=TRUE,useindlab=FALSE,indlabwithgrplab=FALSE,indlabspacer=1.5,indlabheight=0.2,indlabsep=" ",indlabsize=NULL,indlabangle=90,indlabvjust=0.5,indlabhjust=1,indlabcol="grey30", + pointsize=NA,pointcol="grey30",pointbgcol="grey30",pointtype="|",pointalpha=1, + linepos=0.75,linesize=NA,linecol="grey30",linetype=1,linealpha=1, + showdiv=TRUE,divgrp=NA,divcol="white",divtype="21",divsize=0.25,divalpha=1, + showlegend=FALSE,legendlab=NA,legendpos="right",legendkeysize=4,legendtextsize=3,legendmargin=c(0.5,0.5,0.5,0), + barsize=1,barbordersize=0,barbordercolour=NA, + showyaxis=FALSE,showticks=FALSE,ticksize=0.1,ticklength=0.03, + outputfilename=NA,imgtype="png",height=NA,width=NA,dpi=300,units="cm", + theme="theme_grey",basesize=5,font="",na.rm=TRUE,quiet=FALSE,panelratio=c(3,1), + exportplot=TRUE,returnplot=FALSE,returndata=FALSE) +{ + # check qlist + is.qlist(qlist) + + # check imgoutput + imgoutput <- tolower(imgoutput) + if(imgoutput != "sep" && imgoutput != "join") stop("plotQ: Argument 'imgoutput' set incorrectly. Set as 'sep' to export as separate plots. Set as 'join' to export as one joined plot.") + + # check imagetype + imgtype <- tolower(imgtype) + if(imgtype!="png" && imgtype != "pdf" && imgtype != "tiff" && imgtype != "jpeg") stop("plotQ: Argument 'imgtype' set incorrectly. Set as 'png', 'jpeg', 'tiff' or 'pdf'.") + + # check sortind + if(length(sortind) > 1) stop("plotQ: Argument 'sortind' must be of length 1. Use 'all','label' or a cluster name like 'Cluster1'.") + if(is.na(sortind)) {sortindcheck <- "empty"}else{sortindcheck <- sortind} + # if sort not label, set sharedindlab in use, error + if(imgoutput=="join" && sortindcheck != "label" && sortindcheck != "empty" && sharedindlab) stop("plotQ: When 'sortind' is 'all' or a cluster, 'sharedindlab' must be set to FALSE.") + + if(!any(is.na(clustercol))) {if(!is.character(clustercol)) stop("plotQ: Argument 'clustercol' must be a character datatype.")} + if(!is.logical(useindlab)) stop("plotQ: Argument 'useindlab' set incorrectly. Set as TRUE or FALSE.") + if(!is.character(indlabsep)) stop("plotQ: Argument 'indlabsep' must be a character datatype.") + if(!is.logical(grpmean)) stop("plotQ: Argument 'grpmean' set incorrectly. Set as TRUE or FALSE.") + if(!is.logical(na.rm)) stop("plotQ: Argument 'na.rm' set incorrectly. Set as TRUE or FALSE.") + if(!is.logical(showsp)) stop("plotQ: Argument 'showsp' set incorrectly. Set as TRUE or FALSE.") + if(!any(is.na(splab))) {if(!is.character(splab)) stop("plotQ: Argument 'splab' must be a character datatype.")} + if(!any(is.na(splab))) {if(length(splab) != length(qlist)) stop("plotQ: Length of 'splab' is not equal to number of runs.")} + if(!is.character(splabface)) stop("plotQ: Argument 'splabface' must be a character datatype.") + if(is.character(splabface)) {if(!splabface %in% c("plain","italic","bold","bold.italic")) stop("plotQ: Argument 'splabface' must be 'plain', 'italic', 'bold' or 'bold.italic'.")} + if((sppos != "right") && (sppos != "left")) stop("plotQ: Argument 'sppos' set incorrectly. Set as 'right' or 'left'.") + if(!is.logical(showdiv)) stop("plotQ: Argument 'showdiv' set incorrectly. Set as TRUE or FALSE.") + if(!any(is.na(legendlab))) {if(!is.character(legendlab)) stop("plotQ: Argument 'legendlab' must be a character datatype.")} + if((legendpos != "right") && (legendpos != "left")) stop("plotQ: Argument 'legendpos' set incorrectly. Set as 'right' or 'left'.") + if(!is.numeric(legendkeysize)) stop("plotQ: Argument 'legendkeysize' must be a numeric datatype.") + if(!is.numeric(legendtextsize)) stop("plotQ: Argument 'legendtextsize' must be a numeric datatype.") + if(!is.character(font)) stop("plotQ: Argument 'font' must be a character datatype.") + if(imgtype=="pdf" && font=="") font <- "Helvetica" + if(imgtype=="pdf") dpi <- 300 + if(!is.numeric(barsize)) stop("plotQ: Argument 'barsize' must be a numeric datatype.") + if(barsize<0 || barsize>1) stop("plotQ: Argument 'barsize' must be a value between 0 and 1.") + if(is.na(basesize)) stop("plotQ: Argument 'basesize' is NA.") + if(length(panelratio)!=2) stop("plotQ: Argument 'panelratio' must be an integer vector of length 2.") + panelratio <- as.integer(panelratio) + + # ggplot version + ggv <- as.numeric(gsub("\\.","",packageDescription("ggplot2", fields="Version"))) + if(ggv < 220) stop("plotQ: Package ggplot2 must be version 2.2.0 or above.") + + # defaults + col3 <- "grey30" + + if(grplabpos > 1 || grplabpos < 0) stop("plotQ: Argument 'grplabpos' is set incorrectly. Set a numeric value between 0 and 1. To further increase space, adjust argument 'grplabheight'.") + if(grplabpos > 1 || grplabpos < 0) stop("plotQ: Argument 'linepos' is set incorrectly. Set a numeric value between 0 and 1. To further increase space, adjust argument 'grplabheight'.") + + # check grplabels + if(!all(is.na(grplab))) + { + verifyGrplab(grplab) + grplablen <- ncol(grplab) + grplabcheck <- TRUE + + if(length(selgrp)>1) stop("plotQ: Argument 'selgrp' must be of length 1.") + if(any(is.na(selgrp))) selgrp <- names(grplab)[1] + if(!is.character(selgrp)) stop("plotQ: Argument 'selgrp' must be a character datatype.") + if(!any(selgrp %in% names(grplab))) stop(paste0("plotQ: Argument 'selgrp' contains (",selgrp,") which is not in the 'grplab' titles (",paste0(names(grplab),collapse=", "),").")) + if(any(is.na(divgrp))) divgrp <- selgrp + if(!is.character(divgrp)) stop("plotQ: Argument 'divgrp' must be a character datatype.") + if(!any(divgrp %in% names(grplab))) stop(paste0("plotQ: Argument 'divgrp' contains one or more labels (",paste0(divgrp,collapse=", "),") not present in the 'grplab' titles (",paste0(names(grplab),collapse=", "),").")) + }else{ + grplabcheck <- FALSE + } + + # length of files + flen <- length(qlist) + + # check outputfilename + if(!all(is.na(outputfilename))) + { + if(exportplot) {if(imgoutput=="sep") if(length(outputfilename) != flen) stop(paste0("plotQ: Length of argument 'outputfilename' (",length(outputfilename),") is not equal to the number of runs (",flen,") when using 'imgoutput=sep'."))} + if(imgoutput=="join") if(length(outputfilename) != 1) stop("plotQ: Argument 'outputfilename' must be of length equal to 1 when 'imgoutput=join'.") + } + + # check titlelab + if(!all(is.na(titlelab))) + { + if(imgoutput=="sep") if(length(titlelab) != flen) stop(paste0("plotQ: Length of argument 'titlelab' (",length(titlelab),") is not equal to the number of runs (",flen,") when using 'imgoutput=sep'.")) + if(imgoutput=="join") if(length(titlelab) != 1) stop("plotQ: Argument 'titlelab' must be of length equal to 1 when 'imgoutput=join'.") + } + + # check subtitlelab + if(!all(is.na(subtitlelab))) + { + if(imgoutput=="sep") if(length(subtitlelab) != flen) stop(paste0("plotQ: Length of argument 'subtitlelab' (",length(subtitlelab),") is not equal to the number of runs (",flen,") when using 'imgoutput=sep'.")) + if(imgoutput=="join") if(length(subtitlelab) != 1) stop("plotQ: Argument 'subtitlelab' must be of length equal to 1 when 'imgoutput=join'.") + } + + ## sep + sep indlab ---------------------------------------------------------- + if(imgoutput=="sep") + { + if(returndata) + { + list_qlist <- vector("list",length=flen) + list_grplab <- vector("list",length=flen) + } + if(returnplot) list_plot <- vector("list",length=flen) + for (i in 1:flen) + { + #output name + fname <- names(qlist)[i] + fname <- gsub(".txt$|.csv$|.tsv$|.meanq$|.meanQ$|.structure$","",fname) + if(is.null(fname)) fname <- paste0("sample",i) + + # prepare outputfilename + if(exportplot) + { + if(any(is.na(outputfilename))){ + outname <- fname + }else{ + outname <- outputfilename[i] + } + } + + # prepare title + if(any(is.na(titlelab))){ + titlename <- fname + }else{ + titlename <- titlelab[i] + } + + #prepare subtitle + if(any(is.na(subtitlelab))){ + subtitlename <- fname + }else{ + subtitlename <- subtitlelab[i] + } + + df1 <- qlist[[i]] + grplabloop <- grplab + + # add rownames + if(!useindlab) row.names(df1) <- sprintf(paste0("%",paste0(rep(0,nchar(nrow(df1))),collapse=""),nchar(nrow(df1)),"d"),1:nrow(df1)) + + #ordering grps + if(grplabcheck) + { + templist <- pophelper:::grpLabels(dframe=df1,grplab=grplabloop,selgrp=selgrp, + subsetgrp=subsetgrp,ordergrp=ordergrp,grpmean=grpmean, + grplabpos=grplabpos,linepos=linepos, + indlabwithgrplab=indlabwithgrplab, + indlabsep=indlabsep) + df1 <- templist$dframe + grplabloop <- templist$grplab + markerpos <- templist$markerpos + labelpos <- templist$labelpos + rm(templist) + } + + # sorting individuals + if(!is.na(sortind)) + { + templist <- pophelper:::sortInd(dframe=df1,grplab=grplabloop,selgrp=selgrp, + sortind=sortind,grplabpos=grplabpos,linepos=linepos) + df1 <- templist$dframe + grplabloop <- templist$grplab + markerpos <- templist$markerpos + labelpos <- templist$labelpos + rm(templist) + } + + # save modified data for return + if(returndata) + { + list_qlist[[i]] <- df1 + names(list_qlist)[i] <- fname + if(grplabcheck) {list_grplab[[i]] <- grplabloop}else{list_grplab[[i]] <- NA} + } + + k <- ncol(df1) + Ind <- nrow(df1) + df1$ind <- as.character(rownames(df1)) + df1$run <- factor(rep(i,nrow(df1))) + df1$order_ind <- seq(from=1,to=Ind) + df2 <- tidyr::gather(df1,"variable","value",-c(ind,run,order_ind)) + + # legendlab + if(any(is.na(legendlab))) + { + legendlab1 <- levels(factor(as.character(df2$variable))) + }else{ + legendlab1 <- legendlab + } + if(length(legendlab1) != length(levels(factor(as.character(df2$variable))))) stop("plotQ: Length of 'legendlab' is not equal to number of clusters.") + + # strip panel (showsp) labelling + if(any(is.na(splab))) + { + facetnames <- paste0(fname,"\n","K=",k) + }else{ + facetnames <- splab[i] + } + + #names of facets are run id which is i + names(facetnames) <- i + + # get colours + coll <- clustercol + if(any(is.na(clustercol))) coll <- pophelper:::getColours(as.integer(k)) + if(length(coll) < k) stop(paste0("plotQ: Number of colours (",length(coll),") less than number of clusters (",k,").")) + + # get dimensions + dimtemp <- pophelper:::getDim(ind=Ind,height=height,width=width,dpi=dpi,units=units,imgtype=imgtype, + grplabheight=grplabheight,labs=length(grplabloop),plotnum=1, + showindlab=showindlab) + height1 <- as.numeric(dimtemp[1]) + width1 <- as.numeric(dimtemp[2]) + grplabheight1 <- as.numeric(dimtemp[3]) + units1 <- as.character(dimtemp[4]) + + ## COMMON PLOT TOP PANEL --------------------------------------------------- + # create plot + gg_plot_panel <- ggplot2::ggplot(data=df2,aes(x=order_ind,y=value,fill=variable))+ + geom_bar(width=barsize,size=barbordersize,colour=barbordercolour, + stat="identity",position="fill",na.rm=na.rm)+ + scale_x_continuous(breaks=df2$order_ind,labels=df2$ind,expand=c(0,0))+ + scale_y_continuous(expand=c(0,0))+ + scale_fill_manual(values=coll,labels=legendlab1)+ + facet_wrap(~run,labeller=labeller(run=facetnames),strip.position=sppos,scales="fixed",nrow=1)+ + get(theme)(base_family=font,base_size=basesize) + + gg_plot_panel <- gg_plot_panel + labs(x=NULL,y=NULL)+ + theme(legend.position="top", + legend.direction="horizontal", + legend.title=element_blank(), + legend.key.size=grid::unit(legendkeysize,"points"), + legend.text=element_text(size=legendtextsize,colour=indlabcol), + legend.spacing=grid::unit(0,"points"), + legend.justification=legendpos, + legend.margin=margin(legendmargin[1],legendmargin[2],legendmargin[3],legendmargin[4],"points"), + legend.box.spacing=grid::unit(1.5,"points"), + panel.grid=element_blank(), + panel.background=element_blank(), + axis.text.x=element_text(size=indlabsize,colour=indlabcol, + angle=indlabangle,vjust=indlabvjust, + hjust=indlabhjust,margin=margin(t=indlabspacer)), + axis.text.y=element_text(size=indlabsize,colour=indlabcol,margin=margin(r=indlabspacer)), + axis.ticks=element_line(size=ticksize,colour=indlabcol), + axis.ticks.length=unit(ticklength,"cm"), + axis.line=element_blank(), + axis.title=element_blank(), + strip.text.y=element_text(size=splabsize,colour=splabcol,face=splabface,angle=splabangle), + strip.background=element_rect(colour=spbgcol,fill=spbgcol), + plot.margin=grid::unit(c(0.2,0.05,indlabheight,0),"cm"), + panel.spacing=grid::unit(panelspacer,"cm")) + + # remove indlab + if(!showindlab) gg_plot_panel <- gg_plot_panel+theme(axis.text.x=element_blank()) + + # remove y-axis labels + if(!showyaxis) + { + gg_plot_panel <- gg_plot_panel+theme(axis.ticks.y=element_blank(), + axis.text.y=element_blank(), + plot.margin=grid::unit(c(0.2,0.05,indlabheight,0),"cm")) + }else{ + gg_plot_panel <- gg_plot_panel+theme(plot.margin=grid::unit(c(0.2,0.05,indlabheight,0.1),"cm")) + } + + # remove ticks + if(!showticks) gg_plot_panel <- gg_plot_panel+theme(axis.ticks=element_blank()) + + # show title + if(showtitle) gg_plot_panel <- gg_plot_panel+labs(title=titlename)+ + theme(plot.title=element_text(size=titlesize,colour=titlecol, + angle=titleangle,hjust=titlehjust,face=titleface, + vjust=titlevjust,margin=margin(b=titlespacer))) + # show subtitle + if(showsubtitle) gg_plot_panel <- gg_plot_panel+labs(subtitle=subtitlename)+ + theme(plot.subtitle=element_text(size=subtitlesize,colour=subtitlecol, + angle=subtitleangle,hjust=subtitlehjust,face=subtitleface, + vjust=subtitlevjust,margin=margin(b=subtitlespacer))) + + # remove strip panels on right + if(!showsp) gg_plot_panel <- gg_plot_panel+theme(strip.text=element_blank()) + + # remove legend + if(!showlegend) gg_plot_panel <- gg_plot_panel+theme(legend.position="none") + + if(!grplabcheck) + { + if(exportplot) + { + if(!quiet) cat("Drawing plot ...\n") + if(imgtype=="tiff") tiff(paste0(outname,".tiff"),height=height1,width=width1,res=dpi,units=units1,type="cairo",compression="lzw",family=font) + if(imgtype=="png") png(paste0(outname,".png"),height=height1,width=width1,res=dpi,units=units1,type="cairo",family=font) + if(imgtype=="jpeg") jpeg(paste0(outname,".jpg"),height=height1,width=width1,res=dpi,units=units1,quality=100,family=font) + if(imgtype=="pdf") pdf(paste0(outname,".pdf"),height=height1,width=width1,fonts=font) + print(gg_plot_panel) + dev.off() + if(imgtype=="tiff" && !quiet) cat(paste0(outname,".tiff exported.\n")) + if(imgtype=="png" && !quiet) cat(paste0(outname,".png exported.\n")) + if(imgtype=="jpeg" && !quiet) cat(paste0(outname,".jpg exported.\n")) + if(imgtype=="pdf" && !quiet) cat(paste0(outname,".pdf exported.\n")) + } + if(returnplot) list_plot[[i]] <- gg_plot_panel + } + + if(grplabcheck) + { + # add grp divider lines only if 2 grps or more + if(showdiv) + { + markerpos1 <- markerpos[c(markerpos$count %in% divgrp),] + if(nrow(markerpos1) > 2) gg_plot_panel <- gg_plot_panel+geom_vline(xintercept=markerpos1$divxpos[-c(1,length(markerpos1$divxpos))],colour=divcol,linetype=divtype,size=divsize,alpha=divalpha) + } + + ppar <- pophelper:::getPlotParams(grplab=grplabloop[[1]],plotnum=1,grplabsize=grplabsize,grplabangle=grplabangle, + grplabjust=grplabjust,pointsize=pointsize,linesize=linesize) + + # fix facet labels in grplab plot + cnl <- function(str) {length(strsplit(str,"\n")[[1]])-1} + glabfacetnames <- names(grplabloop) + names(glabfacetnames) <- names(grplabloop) + gn <- max(as.vector(sapply(facetnames,cnl))) + if(gn>0) + { + if(all(cnl(glabfacetnames) 2) gg_plot_panel <- gg_plot_panel+geom_segment(data=markerpos1,aes(x=divxpos,xend=divxpos,y=0,yend=1),colour=divcol,linetype=divtype,size=divsize,alpha=divalpha) + if(grplabcheck && sortindcheck!="label" && sortindcheck!="empty" && !sharedindlab) + { + warning("Divider lines are currently not printed on 'join' plots with group labels and sorting other than 'label'.\n") + }else{ + if(nrow(markerpos1) > 0) gg_plot_panel <- gg_plot_panel+geom_vline(data=markerpos1,aes(xintercept=divxpos),colour=divcol,linetype=divtype,size=divsize,alpha=divalpha) + } + } + + # plot with grp labels + ppar <- pophelper:::getPlotParams(grplab=grplabloop[[1]],plotnum=flen,grplabsize=grplabsize,grplabangle=grplabangle,grplabjust=grplabjust, + pointsize=pointsize,linesize=linesize) + + # fix facet labels in grplab plot + cnl <- function(str) {length(strsplit(str,"\n")[[1]])-1} + glabfacetnames <- names(grplabloop) + names(glabfacetnames) <- names(grplabloop) + gn <- max(as.vector(sapply(facetnames,cnl))) + if(gn>0) + { + if(all(cnl(glabfacetnames) 1) stop("plotQMultiline: Argument 'sortind' must be of length 1. Use 'all','label' or a cluster name like 'Cluster1'.") + if(is.na(sortind)) {sortindcheck <- "empty"}else{sortindcheck <- sortind} + + if(!is.character(font)) stop("plotQMultiline: Argument 'font' must be a character datatype.") + if(imgtype=="pdf" && font=="") font <- "Helvetica" + if(!is.numeric(barsize)) stop("plotQMultiline: Argument 'barsize' must be a numeric datatype.") + if(barsize<0 || barsize>1) stop("plotQMultiline: Argument 'barsize' must be a value between 0 and 1.") + + # ggplot version + ggv <- as.numeric(gsub("\\.","",packageDescription("ggplot2", fields="Version"))) + if(ggv < 220) stop("plotQMultiline: Package ggplot2 must be version 2.2.0 or above.") + + # check grplabels + if(!all(is.na(grplab))) + { + verifyGrplab(grplab) + grplablen <- length(grplab) + grplabcheck <- TRUE + + if(!is.logical(showgrplab)) stop("Argument 'showgrplab' must be a logical TRUE or FALSE.") + if(length(selgrp)>1) stop("plotQMultiline: Argument 'selgrp' must be of length 1.") + if(any(is.na(selgrp))) selgrp <- names(grplab)[1] + if(!is.character(selgrp)) stop("plotQMultiline: Argument 'selgrp' must be a character datatype.") + if(!any(selgrp %in% names(grplab))) stop(paste0("plotQMultiline: Argument 'selgrp' contains (",selgrp,") which is not in the 'grplab' titles (",paste0(names(grplab),collapse=", "),").")) + }else{ + grplabcheck <- FALSE + } + + # set NA values + #if(is.na (dpi)) dpi <- 300 + if(imgtype=="pdf") dpi <- 300 + #if(is.na (units)) units <- "cm" + if(is.na (height)) height <- 29.7 + if(is.na (width)) width <- 21 + if(imgtype=="pdf") height <- pophelper:::unitConverter(height,units,"in",dpi) + if(imgtype=="pdf") width <- pophelper:::unitConverter(width,units,"in",dpi) + + len1 <- length(qlist) + + # check outputfilename + if(!all(is.na(outputfilename))) + { + if(length(outputfilename) != len1) stop(paste0("plotQMultiline: Length of argument 'outputfilename' (",length(outputfilename),") is not equal to the number of runs (",len1,").")) + } + + # check titlelab + if(!all(is.na(titlelab))) + { + if(length(titlelab) != len1) stop(paste0("plotQMultiline: Length of argument 'titlelab' (",length(titlelab),") is not equal to the number of runs (",len1,").")) + } + + # check subtitlelab + if(!all(is.na(subtitlelab))) + { + if(length(subtitlelab) != len1) stop(paste0("plotQMultiline: Length of argument 'subtitlelab' (",length(subtitlelab),") is not equal to the number of runs (",len1,").")) + } + + # legendlab + maxk <- max(pophelper::tabulateQ(qlist)$k) + if(all(!is.na(legendlab))) + { + legendlab1 <- legendlab + if(length(legendlab1) < maxk) stop(paste0("plotQ: Length of 'legendlab' (",length(legendlab),") is less than the number of max clusters (",maxk,").")) + } + + if(returndata) + { + list_qlist <- vector("list",length=len1) + list_grplab <- vector("list",length=len1) + } + if(returnplot) list_plot <- vector("list",length=len1) + for (i in 1:len1) + { + # sample name + fname <- names(qlist)[i] + fname <- gsub(".txt$|.csv$|.tsv$|.meanq$|.meanQ$|.structure$","",fname) + if(is.null(fname)) fname <- paste0("sample",i) + + # prepare outputfilename + if(any(is.na(outputfilename))){ + outname <- fname + }else{ + outname <- outputfilename[i] + } + + # check files + dff <- qlist[[i]] + grplabloop <- grplab + + # add rownames + if(!useindlab) row.names(dff) <- sprintf(paste0("%",paste0(rep(0,nchar(nrow(dff))),collapse=""),nchar(nrow(dff)),"d"),1:nrow(dff)) + + # ordering grps + if(grplabcheck) + { + templist <- pophelper:::grpLabels(dframe=dff,grplab=grplabloop,selgrp=selgrp, + subsetgrp=subsetgrp,ordergrp=ordergrp,grpmean=grpmean, + indlabwithgrplab=indlabwithgrplab,indlabsep=indlabsep) + dff <- templist$dframe + grplabloop <- templist$grplab + if(any(duplicated(rle(grplabloop[,selgrp])$values))) stop("plotQMultiline: Group labels cannot be used due to non-contiguous blocks of labels. Change grplab, selgrp or use 'ordergrp=TRUE'.") + rm(templist) + } + + # ordering individuals + if(!is.na(sortind)) + { + templist <- pophelper:::sortInd(dframe=dff,grplab=grplabloop,selgrp=selgrp,sortind=sortind) + dff <- templist$dframe + grplabloop <- templist$grplab + rm(templist) + } + + # prepare title + if(any(is.na(titlelab))){ + titlename <- fname + }else{ + titlename <- titlelab[i] + } + + # prepare subtitle + if(any(is.na(subtitlelab))){ + subtitlename <- paste0("K=",ncol(dff)) + }else{ + subtitlename <- subtitlelab[i] + } + + # save modified data for return + if(returndata) + { + list_qlist[[i]] <- dff + names(list_qlist)[i] <- fname + if(grplabcheck) {list_grplab[[i]] <- grplabloop}else{list_grplab[[i]] <- NA} + } + + # primary calculation of spl + nr1 <- nrow(dff) + + #numrows <- floor(nr1/spl) + #numextra <- nr1-(spl*numrows) + #nr2 <- numrows + #if(numextra > 0) nr2 <- nr2+1 + + if(!is.na(spl)) + { + if(spl > nr1) stop("plotQMultiline: Samples per line (spl) is greater than total number of samples.") + spl1 <- spl + numrows <- floor(nr1/spl1) + numextra <- nr1-(spl1*numrows) + } + + # optimise spl + if(is.na(spl)) + { + if(nr1 <= 60) {spl1 <- nr1} else {spl1 <- 60} + + # automatically optimise number of rows and spl + numextra <- 0 + while(numextra < 0.70*spl1) + { + numrows <- floor(nr1/spl1) + numextra <- nr1-(spl1*numrows) + if(numextra < 0.70*spl1) spl1=spl1+1 + if(spl1 > nr1) + { + spl1 <- nr1 + break + } + } + } + + nr2 <- numrows + if(numextra > 0) nr2 <- nr2+1 + + # get colours + coll <- clustercol + if(any(is.na(clustercol))) coll <- pophelper:::getColours(as.integer(ncol(dff))) + if(length(coll) < ncol(dff)) stop(paste0("plotQMultiline: Number of colours (",length(coll),") is less than the number of clusters (",ncol(dff),").")) + + if(any(is.na(legendlab))) legendlab1 <- colnames(dff) + + dff$ind <- factor(rownames(dff),levels=rownames(dff)) + #dff$ind <- as.character(rownames(dff)) + dff$rows <- factor(c(rep(1:numrows,each=spl1),rep(nr2,each=numextra))) + #dff$order_ind <- seq(from=1,to=nr1) + if(grplabcheck) + { + if(length(intersect(colnames(dff),colnames(grplabloop)))!=0) stop(paste0("sortInd: One or more header labels in the run file are duplicated in grplab header. Change labels to be unique. Following are the duplicate label(s): (",paste0(intersect(colnames(dff),colnames(grplabloop)),collapse=", "),").")) + dff <- cbind(dff,grplabloop) + dff[[selgrp]] <- grplabloop[,selgrp] + dff[[selgrp]] <- factor(dff[[selgrp]],levels=rle(dff[[selgrp]])$values) + } + + # split and plot rows + dlist <- split(dff,dff$rows) + plist <- vector("list",length=nr2) + #widthsvec <- vector(length=nr2) + for (j in 1: nr2) + { + dlist[[j]]$rows <- NULL + + if(grplabcheck) + { + scols <- setdiff(colnames(dlist[[j]]),c("ind",names(grplabloop))) + df2 <- tidyr::gather_(dlist[[j]],key_col="variable",value="value",gather_cols=scols) + }else{ + df2 <- tidyr::gather(dlist[[j]],"variable","value",-ind) + } + + #df2 <- df2[rev(1:nrow(df2)),] + plist[[j]] <- ggplot2::ggplot(data=df2,aes(x=ind,y=value,fill=variable))+ + geom_bar(width=barsize,size=barbordersize,colour=barbordercolour,stat="identity",position="fill",na.rm=na.rm)+ + scale_x_discrete(expand=c(0,0))+ + scale_y_continuous(expand=c(0,0),limits=c(0,1))+ + scale_fill_manual(values=coll,labels=legendlab1)+ + labs(x=NULL,y=NULL)+ + #facet_wrap(~selgrp,nrow=1,scales="free_x")+ + get(theme)(base_family=font,base_size=basesize)+ + theme(legend.position="none", + panel.grid=element_blank(), + panel.background=element_blank(), + axis.line=element_blank(), + axis.title=element_blank(), + axis.text.x=element_text(size=indlabsize,colour=indlabcol,angle=indlabangle,vjust=indlabvjust,hjust=indlabhjust,margin=margin(t=indlabspacer)), + axis.text.y=element_text(size=indlabsize,colour=indlabcol,margin=margin(r=indlabspacer)), + axis.ticks=element_line(size=ticksize,colour=indlabcol), + axis.ticks.length=unit(ticklength,"cm"), + plot.margin=grid::unit(mar,units)) + + if(grplabcheck) + { + plist[[j]] <- plist[[j]] + facet_grid(as.formula(paste0("~",paste0(names(grplabloop),collapse="+"))),scales="free_x",space="free_x")+ + theme(strip.background=element_rect(fill=grplabbgcol), + strip.text=element_text(size=grplabsize,colour=grplabcol)) + if(!showgrplab) plist[[j]] <- plist[[j]] + theme(strip.text=element_blank()) + } + + # remove y-axis + if(!showyaxis) plist[[j]] <- plist[[j]] + theme(axis.ticks.y=element_blank(),axis.text.y=element_blank()) + # remove indlab + if(!showindlab) plist[[j]] <- plist[[j]] + theme(axis.ticks.x=element_blank(),axis.text.x=element_blank()) + # remove ticks + if(!showticks) plist[[j]] <- plist[[j]] + theme(axis.ticks=element_blank()) + + # show title + if(j==1) + { + if(showtitle) plist[[j]] <- plist[[j]]+labs(title=titlename)+ + theme(plot.title=element_text(size=titlesize,colour=titlecol, + angle=titleangle,hjust=titlehjust,face=titleface, + vjust=titlevjust,margin=margin(b=titlespacer))) + # show subtitle + if(showsubtitle) plist[[j]] <- plist[[j]]+labs(subtitle=subtitlename)+ + theme(plot.subtitle=element_text(size=subtitlesize,colour=subtitlecol, + angle=subtitleangle,hjust=subtitlehjust,face=subtitleface, + vjust=subtitlevjust,margin=margin(b=subtitlespacer))) + # show legend + if(showlegend) plist[[j]] <- plist[[j]]+ + theme(legend.position="top", + legend.direction="horizontal", + legend.title=element_blank(), + legend.key.size=grid::unit(legendkeysize,"points"), + legend.text=element_text(size=legendtextsize,colour=indlabcol), + legend.spacing=grid::unit(0,"points"), + legend.justification=legendpos, + legend.margin=margin(legendmargin[1],legendmargin[2],legendmargin[3],legendmargin[4],"points"), + legend.box.spacing=grid::unit(1.5,"points")) + } + + # calculate widths. not implemented. + #widthsvec[j] <- nrow(dlist[[j]])/spl1 + } + + # lpp calculations + if(!is.na(lpp)) lpp1 <- lpp + if(is.na(lpp)) + { + lpp1 <- 11 + if(lpp1 > nr2) lpp1 <- nr2 + } + numpages <- ceiling(nr2/lpp1) + #numpagesextra <- nr2-(lpp*numpages) + #numpages1 <- numpages + #if(numpagesextra > 0) numpages1 <- numpages1+1 + + e <- 0 + r <- 1 + list_panel <- vector("list",length=numpages) + while (r <= numpages) + { + start1 <- e + 1 + stop1 <- e + lpp1 + if(stop1 > length(plist)) stop1 <- length(plist) + + #widths <- widthsvec[start1:stop1] + alist <- c(plist[start1:stop1],lpp1,1) + names(alist) <- c(as.character(start1:stop1),"nrow","ncol") + if(numpages>1) outname1 <- paste0(outname,"-",r) + if(numpages==1) outname1 <- outname + + if(exportplot) + { + if(!quiet) cat("Drawing plot ...\n") + if(imgtype=="tiff") tiff(paste0(outname1,".tiff"),height=height,width=width,res=dpi,units=units,type="cairo",compression="lzw",family=font) + if(imgtype=="png") png(paste0(outname1,".png"),height=height,width=width,res=dpi,units=units,type="cairo",family=font) + if(imgtype=="jpeg") jpeg(paste0(outname1,".jpg"),height=height,width=width,res=dpi,units=units,quality=100,family=font) + if(imgtype=="pdf") pdf(paste0(outname1,".pdf"),height=height,width=width,fonts=font) + + do.call(gridExtra::grid.arrange,alist) + dev.off() + + if(imgtype=="tiff" && !quiet) cat(paste0(outname1,".tiff exported.\n")) + if(imgtype=="png" && !quiet) cat(paste0(outname1,".png exported.\n")) + if(imgtype=="jpeg" && !quiet) cat(paste0(outname1,".jpg exported.\n")) + if(imgtype=="pdf" && !quiet) cat(paste0(outname1,".pdf exported.\n")) + } + + if(returnplot) + { + px <- do.call(gridExtra::arrangeGrob,alist) + list_panel[[r]] <- px + names(list_panel)[r] <- outname1 + } + + e <- stop1 + r=r+1 + } + if(returnplot) list_plot[[i]] <- list_panel + rm(nr1,nr2,numrows,numextra,numpages,start1,stop1,e,r,dlist,plist,df2,dff) + } + + if(returnplot && !returndata) return(list(plot=list_plot,data=list(qlist=NA,grplab=NA))) + if(!returnplot && returndata) return(list(plot=NA,data=list(qlist=list_qlist,grplab=list_grplab))) + if(returnplot && returndata) return(list(plot=list_plot,data=list(qlist=list_qlist,grplab=list_grplab))) +} + +# analyseQ ------------------------------------------------------------------ + +#' @title Analyse STRUCTURE, TESS, BAPS or BASIC text runs. Wrapper around several smaller functions. +#' @description A single function to analyse STRUCTURE, TESS, BAPS or BASIC text runs. Converts runs to a qlist, then tabulate, summarise, perform evanno method, export clumpp and plots runs. +#' @param files A character or character vector of one or more STRUCTURE, TESS, BAPS or BASIC run files. Use \code{choose.files(multi=TRUE)} to choose interactively. +#' @param evannomethod A logical indicating if evanno method should be performed. Applies only to STRUCTURE runs. +#' @param clumppexport A logical indicating if files must be exported for clumpp. +#' @param plotruns A logical indicating if selected files should be exported as barplots. +#' @param imgoutput A character indicating if files are plotted as separate image files ("sep") or joined into a single image ("join"). +#' @param grplab A dataframe with one or more columns (group label sets), and rows equal to the number of individuals. +#' @param clustercol A character vector of colours for colouring clusters. If NA, colours are automatically generated. K 1 to 12 are custom unique colours while K>12 are coloured by function \code{rich.color()}. +#' @param writetable A logical T or F. Setting to TRUE writes the output table to the working directory. +#' @param sorttable A logical indicating if the output table must be sorted. Sorts table by loci, ind and K when available. +#' @details The function \code{analyseQ} is a wrapper around several other \code{pophelper} functions. All arguments for all these other functions are not available. If more arguments/options are required, consider running the functions separately. +#' +#' See the \href{http://royfrancis.github.io/pophelper/}{vignette} for more details. +#' +#' @return If a single file is selected, a single dataframe is returned. If +#' multiple files are selected, a list with multiple dataframes is returned. +#' @examples +#' \dontrun{ +#' # structure files +#' sfiles <- list.files(path=system.file("files/structure",package="pophelper"),full.names=TRUE) +#' analyseQ(sfiles) +#' +#' # tess files +#' tfiles <- list.files(path=system.file("files/tess",package="pophelper"),full.names=TRUE) +#' analyseQ(tfiles) +#' +#' # admixture files +#' afiles <- list.files(path=system.file("files/admixture",package="pophelper"),full.names=TRUE) +#' analyseQ(afiles) +#' } +#' @export +#' +analyseQ <- analyzeQ <- function(files=NULL,evannomethod=TRUE,clumppexport=TRUE,plotruns=TRUE, + imgoutput="sep",grplab=NA,clustercol=NA,writetable=TRUE,sorttable=TRUE) +{ + if(is.null(files) || (length(files)==0)) stop("analyseQ: No input files.") + if(!is.character(files)) stop("analyseQ: Input is not character dataype.") + if(!is.logical(evannomethod)) stop("analyseQ: Argument 'evannoMethod' set incorrectly. Set as TRUE or FALSE.") + if(!is.logical(clumppexport)) stop("analyseQ: Argument 'clumppExport' set incorrectly. Set as TRUE or FALSE.") + if(!is.logical(plotruns)) stop("analyseQ: Argument 'plotQ' set incorrectly. Set as TRUE or FALSE.") + if(!is.logical(writetable)) stop("analyseQ: Argument 'writetable' set incorrectly. Set as TRUE or FALSE.") + if(!is.logical(sorttable)) stop("analyseQ: Argument 'sorttable' set incorrectly. Set as TRUE or FALSE.") + + chk1 <- unique(pophelper:::checkQ(files=files,warn=FALSE)$type) + if(length(chk1) > 1) stop("analyseQ: Mixed runs selected.") + if("CLUMPP" %in% chk1) stop("analyseQ: CLUMPP files cannot be used in this function.") + if("UNIDENTIFIED" %in% chk1) stop("analyseQ: Input file has incorrect format. Check if selected files are STRUCTURE, BAPS, TESS or BASIC runs.") + if(imgoutput != "sep" && imgoutput != "join") stop("analyseQ: Argument 'imgoutput' set incorrectly. Set as 'sep' to export as separate plots. Set as 'join' to export as one joined plot.") + if(!(chk1 %in% c("STRUCTURE","TESS","BAPS","BASIC"))) stop("analyseQ: Input files are not STRUCTURE, BAPS, TESS or BASIC run formats.") + + if(chk1=="STRUCTURE") rlist <- pophelper::readQ(files,filetype="structure",indlabfromfile=TRUE) + if(chk1=="TESS") rlist <- pophelper::readQ(files,filetype="tess") + if(chk1=="BAPS") rlist <- pophelper::readQ(files,filetype="baps") + if(chk1=="BASIC") rlist <- pophelper::readQ(files,filetype="basic") + + df1 <- pophelper::tabulateQ(rlist,writetable=writetable,sorttable=sorttable) + df2 <- pophelper::summariseQ(df1,writetable=writetable) + + if(chk1=="STRUCTURE") + { + if(evannomethod) pophelper::evannoMethodStructure(df2,writetable=writetable,exportplot=TRUE) + } + + if(clumppexport) pophelper::clumppExport(rlist) + if(plotruns) pophelper::plotQ(rlist,imgoutput=imgoutput,grplab=grplab,clustercol=clustercol) + return(rlist) +} + +# distructExport --------------------------------------------------------------- + +#' @title Generate files for DISTRUCT. +#' @description Create DISTRUCT input files from a qlist. +#' @param qlist A qlist (list of dataframes). An output from \code{\link{readQ}}. +#' @param grplabbottom A character vector of group labels to be plotted below the plot. The vector must be the same length as number of individuals. See details. +#' @param grplabtop An optional character vector of group labels to be plotted above the plot. The vector must be the same length as number of individuals. See details. +#' @param grpmean A logical indicating if individual values are to be plotted (F) or group means are to be plotted (T). +#' @param overwritedirs A logical indicating if existing directories must be overwritten (T) automatically or not (F). +#' @param printtitle A logical indicating if the filename must be printed as the title on the plot. +#' @param clustercol A character vector of colours equal to the number of clusters. Note these are not R colours. Use \code{distructColours()} or refer to DISTRUCT manual for colours. +#' With multiple files, number of colours must equal input file with highest number of clusters. +#' @param grayscale A logical indicating if clusters must be shown in grayscale. +#' @param printcolorbrewer A logical indicating if the colours provided in \code{clustercol} are ColorBrewer colours. See details. +#' @param sepline A logical indicating if divider lines must be drawn between groups (T). +#' @param seplinewidth A numeric indicating width of sepline. +#' @param borderlinewidth A numeric indicating width of border around the plot. +#' @param indlinewidth A numeric indicating width of border around individual bars and ticks. +#' @param fontsize A numeric indicating font size of group labels. +#' @param topdist A numeric indicating distance of top labels from the top edge of the plot. +#' @param bottomdist A numeric indicating distance of bottom labels from the bottom edge of the plot. Usually a negative number. +#' @param figheight A numeric indicating height of the plot. +#' @param indwidth A numeric indicating width of each individual bar. The width of the plot depends on this value. +#' @param orientation An integer (0,1,2,3) indicating orientation of the plot. See details. +#' @param xorigin A numeric indicating lower left x-coordinate of the plot. See details. +#' @param yorigin A numeric indicating lower left y-coordinate of the plot. See details. +#' @param xscale A numeric indicating scaling for the x direction. +#' @param yscale A numeric indicating scaling for the y direction. +#' @param toplabangle A numeric between 0 and 180 indicating angle of top labels. +#' @param bottomlabangle A numeric between 0 and 180 indicating angle of bottom labels. +#' @param echodata A logical. Not really sure what this does. +#' @param printdata A logical indicating if head and tail of data must be shown in display on running DISTRUCT. +#' @param quiet A logical TRUE or FALSE. Set to TRUE by default to print verbose statements to screen. +#' @param useexe A logical indicating if DISTRUCT executable is automatically run based on system OS (experimental). Does not work on UNIX systems. +#' @return The function does not return anything. The function creates directories for each input file and +#' populates it with files necessary to run DISTRUCT. The files are individual q-matrix file (xx-indq.txt), +#' population q-matrix file (xx-popq.txt), a cluster colour file (xx-colours.txt) and drawparams file. If +#' group labels were defined, then (xx-poplab-bottom.txt) or (xx-poplab-top.txt) are also exported. The +#' DISTRUCT executable is run in this directory to generate an xx.ps file. +#' @details +#' \strong{Orientation} \cr +#' 0 for horizontal orientation (default) \cr +#' 1 for vertical orientation \cr +#' 2 for reverse horizontal orientation \cr +#' 3 for reverse vertical orientation \cr +#' \cr +#' \strong{Origin} \cr +#' Default values of origin for a given orientation: \cr +#' orientation, xorigin, yorigin \cr +#' 0,72,288 \cr +#' 1,360,72 \cr +#' 2,540,504 \cr +#' 3,288,720 \cr +#' If plot exceeds canvas size, consider shifting \code{xorigin} to the left and/or decreasing \code{indwidth}.\cr +#' \cr +#' \strong{Colorbrewer colours} \cr +#' Colorbrewer colours are not automatically generated for now. Refer to DISTRUCT manual for colour names. \cr +#' Replace the colour names in xx-colours.txt output file with selected colorbrewer colours (ex: Accent_3_qual_1). \cr +#' \cr +#' \strong{useexe}\cr +#' This option automatically runs the DISTRUCT executable that is provided with this package. +#' Note that the executable is 64bit LSB requiring a 64bit system. The DISTRUCT executable was obtained from +#' here \url{https://web.stanford.edu/group/rosenberglab/distruct.html}. Remember to cite DISTRUCT if this option is used.\cr +#' +#' See the \href{http://royfrancis.github.io/pophelper/}{vignette} for more details. +#' +# @import xlsx +#' @examples +#' \dontrun{ +#' # read some data +#' slist <- readQ(list.files(path=system.file("files/structure",package="pophelper"),full.names=TRUE)) +#' grps1 <- read.delim(system.file("files/structuregrplabels.txt",package="pophelper"),header=FALSE, stringsAsFactor=F) +#' grps2 <- read.delim(system.file("files/structuregrplabels2.txt",package="pophelper"),header=FALSE, stringsAsFactor=F) +#' +#' # plot without labels +#' distructExport(slist[1]) +#' +#' # plot with bottom group label +#' distructExport(slist[1],grplabbottom=grps1$V1) +#' +#' # plot with top group label +#' distructExport(slist[1],grplabtop=grps2$V1) +#' +#' # plot group mean values +#' distructExport(slist[1],grplabbottom=grps1$V1,grpmean=T) +#' +#' # automatically run DESTRUCT +#' distructExport(slist[1],useexe=T) +#' } +#' @import tidyr +#' @export +#' +distructExport <- function(qlist=NULL,grplabbottom=NA,grplabtop=NA,grpmean=FALSE,overwritedirs=FALSE, + printtitle=FALSE,clustercol=NA,grayscale=FALSE,printcolorbrewer=FALSE, + sepline=T,seplinewidth=0.2,borderlinewidth=1.2,indlinewidth=0.2, + fontsize=6,topdist=5,bottomdist=-7,figheight=36,indwidth=1, + orientation=0,xorigin=NA,yorigin=NA,xscale=1,yscale=1,toplabangle=60,bottomlabangle=60, + echodata=TRUE,printdata=FALSE,quiet=FALSE,useexe=FALSE) +{ + # check input + is.qlist(qlist) + grplabbottom <- as.character(grplabbottom) + grplabtop <- as.character(grplabtop) + if((length(grplabbottom) > 1) && any(is.na(grplabbottom))) stop("distructExport: Missing values (NA) in grplabbottom.") + if((length(grplabtop) > 1) && any(is.na(grplabtop))) stop("distructExport: Missing values (NA) in grplabtop.") + clustercol <- as.character(clustercol) + if((length(clustercol) > 1) && any(is.na(clustercol))) stop("distructExport: Missing values (NA) in clustercol.") + if(all(!c(0,1,2,3) %in% orientation)) stop("distructExport: Argument 'orientation' must be a numeric value of 0, 1, 2 or 3.") + if(!is.logical(grpmean)) stop("distructExport: Argument 'grpmean' not set correctly. Set as TRUE or FALSE.") + if(!is.logical(overwritedirs)) stop("distructExport: Argument 'overwritedirs' not set correctly. Set as TRUE or FALSE.") + if(!is.logical(printtitle)) stop("distructExport: Argument 'printtitle' not set correctly. Set as TRUE or FALSE.") + if(!is.logical(sepline)) stop("distructExport: Argument 'sepline' not set correctly. Set as TRUE or FALSE.") + if(!is.logical(grayscale)) stop("distructExport: Argument 'grayscale' not set correctly. Set as TRUE or FALSE.") + if(!is.logical(printcolorbrewer)) stop("distructExport: Argument 'printcolorbrewer' not set correctly. Set as TRUE or FALSE.") + if(!is.logical(echodata)) stop("distructExport: Argument 'echodata' not set correctly. Set as TRUE or FALSE.") + if(!is.logical(printdata)) stop("distructExport: Argument 'printdata' not set correctly. Set as TRUE or FALSE.") + if(!is.logical(quiet)) stop("distructExport: Argument 'quiet' not set correctly. Set as TRUE or FALSE.") + if(!is.logical(useexe)) stop("distructExport: Argument 'useexe' set incorrectly. Set as TRUE or FALSE.") + + # number of files selected + flen <- length(qlist) + if(!quiet) cat(paste0("Number of runs in the qlist: ",flen,"\n")) + + currwd <- getwd() + if(as.numeric(file.access(currwd,2))==-1) stop(paste0("distructExport: Directory ",currwd," has no write permission.")) + + for(i in 1:flen) + { + # sample name + fname <- names(qlist)[i] + if(is.null(fname)) fname <- paste0("sample",i) + if(!quiet) cat(paste0("Computing Distruct files for ",fname,"\n")) + + # check file + df <- qlist[[i]] + if(!is.data.frame(df)) stop(paste0("distructExport: List item ",fname," is not a data.frame object.")) + if(!any(sapply(df,is.numeric))) stop(paste0("distructExport: List item ",fname," has non-numeric columns.")) + tab_runs <- 1 + + for(j in 1:tab_runs) + { + + dirname <- paste0(fname,"-distruct") + dop_k <- ncol(df) + dop_n <- nrow(df) + + # top labels & bottom labels + if((!any(is.na(grplabbottom))) && (!any(is.na(grplabtop)))) + { + grplabbottom <- as.character(grplabbottom) + grplabtop <- as.character(grplabtop) + + if(dop_n != length(grplabbottom)) {message(paste0("distructExport: Number of rows of data (",dop_n,") not equal to length of bottom group labels (",length(grplabbottom),").")); next;} + if(dop_n != length(grplabtop)) {message(paste0("distructExport: Number of rows of data (",dop_n,") not equal to length of top group labels (",length(grplabtop),").")); next;} + if(length(grplabbottom) != length(grplabtop)) {message(paste0("distructExport: Length of top group labels (",length(grplabtop),") not equal to length of bottom group labels (",length(grplabbottom),").")); next;} + + dop_bottomlabel <- TRUE + dop_toplabel <- TRUE + + rlevalb <- rle(grplabbottom) + facb <- factor(rep(1:length(rlevalb$values),rlevalb$lengths)) + rlevalt <- rle(grplabtop) + fact <- factor(rep(1:length(rlevalt$values),rlevalt$lengths)) + + if(length(levels(facb)) != length(levels(fact))) {message("distructExport: Number of levels of top labels are not equal to the number of levels of bottom labels."); next;} + + # indq + inames <- sprintf("%08.0f",1:nrow(df)) + indq <- cbind(data.frame(id1=1:nrow(df),sample=inames,id2=1:nrow(df), + grp=sprintf("%06.0f",as.numeric(as.character(facb))), + colon=rep(":",nrow(df)),stringsAsFactors=F),df) + + # grpq + dfb <- df + dfb$grp <- facb + dfb1 <- tidyr::gather(dfb,"variable","value",-grp) + dfb2 <- cbind(aggregate(value~grp+variable,data=dfb1,FUN=mean),aggregate(value~grp+variable,data=dfb1,FUN=length)[,3,drop=F]) + colnames(dfb2) <- c("grp","variable","mean","len") + dfb3 <- tidyr::spread(dfb2,"variable","mean") + rm(dfb1,dfb2) + dfb3$length <- dfb3$len + dfb3 <- dfb3[,!(colnames(dfb3) %in% c("grp","len"))] + pnames <- sprintf("%06.0f",1:nrow(dfb3)) + grpq <- cbind(data.frame(sample=paste0(pnames,":"),stringsAsFactors=F),dfb3) + + # bottomlabels + plb <- data.frame(sample=pnames,label=rlevalb$values,stringsAsFactors=F) + dop_m <- nrow(plb) + + # grpq + dft <- df + dft$grp <- facb + dft1 <- tidyr::gather(dft,"variable","value",-grp) + dft2 <- cbind(aggregate(value~grp+variable,data=dft1,FUN=mean),aggregate(value~grp+variable,data=dft1,FUN=length)[,3,drop=F]) + colnames(dft2) <- c("grp","variable","mean","len") + dft3 <- tidyr::spread(dft2,"variable","mean") + rm(dft1,dft2) + dft3$length <- dft3$len + dft3 <- dft3[,!(colnames(dft3) %in% c("grp","len"))] + pnamest <- sprintf("%06.0f",1:nrow(dft3)) + # grpq <- cbind(data.frame(sample=paste0(pnamesb,":"),stringsAsFactors=F),dft3) + + # tolabels + plt <- data.frame(sample=pnamest,label=rlevalt$values,stringsAsFactors=F) + #dop_m <- nrow(plb) + fname_plb <- paste0(fname,"-grplab-bottom.txt") + fname_plt <- paste0(fname,"-grplab-top.txt") + } + + # bottom labels + if((!any(is.na(grplabbottom))) && (any(is.na(grplabtop)))) + { + grplabbottom <- as.character(grplabbottom) + if(dop_n != length(grplabbottom)) {message(paste0("distructExport: Number of rows of data (",dop_n,") not equal to length of bottom group labels (",length(grplabbottom),").")); next;} + + dop_bottomlabel <- TRUE + dop_toplabel <- FALSE + rleval <- rle(grplabbottom) + fac <- factor(rep(1:length(rleval$values),rleval$lengths)) + + # indq + inames <- sprintf("%08.0f",1:nrow(df)) + indq <- cbind(data.frame(id1=1:nrow(df),sample=inames,id2=1:nrow(df), + grp=sprintf("%06.0f",as.numeric(as.character(fac))), + colon=rep(":",nrow(df)),stringsAsFactors=F),df) + + # grpq + df$grp <- fac + df1 <- tidyr::gather(df,"variable","value",-grp) + df2 <- cbind(aggregate(value~grp+variable,data=df1,FUN=mean),aggregate(value~grp+variable,data=df1,FUN=length)[,3,drop=F]) + colnames(df2) <- c("grp","variable","mean","len") + df3 <- tidyr::spread(df2,"variable","mean") + rm(df1,df2) + df3$length <- df3$len + df3 <- df3[,!(colnames(df3) %in% c("grp","len"))] + pnames <- sprintf("%06.0f",1:nrow(df3)) + grpq <- cbind(data.frame(sample=paste0(pnames,":"),stringsAsFactors=F),df3) + + # bottomlabels + plb <- data.frame(sample=pnames,label=rleval$values,stringsAsFactors=F) + dop_m <- nrow(plb) + + fname_plb <- paste0(fname,"-grplab-bottom.txt") + fname_plt <- "null" + } + + # top labels + if((!any(is.na(grplabtop))) && (any(is.na(grplabbottom)))) + { + grplabtop<- as.character(grplabtop) + if(dop_n != length(grplabtop)) {message(paste0("distructExport: Number of rows of data (",dop_n,") not equal to length of bottom group labels (",length(grplabtop),").")); next;} + + dop_toplabel <- TRUE + dop_bottomlabel <- FALSE + + rleval <- rle(grplabtop) + fac <- factor(rep(1:length(rleval$values),rleval$lengths)) + + # indq + inames <- sprintf("%08.0f",1:nrow(df)) + indq <- cbind(data.frame(id1=1:nrow(df),sample=inames,id2=1:nrow(df), + grp=sprintf("%06.0f",as.numeric(as.character(fac))), + colon=rep(":",nrow(df)),stringsAsFactors=F),df) + + # grpq + df$grp <- fac + df1 <- tidyr::gather(df,"variable","value",-grp) + df2 <- cbind(aggregate(value~grp+variable,data=df1,FUN=mean),aggregate(value~grp+variable,data=df1,FUN=length)[,3,drop=F]) + colnames(df2) <- c("grp","variable","mean","len") + df3 <- tidyr::spread(df2,"variable","mean") + rm(df1,df2) + df3$length <- df3$len + df3 <- df3[,!(colnames(df3) %in% c("grp","len"))] + pnames <- sprintf("%06.0f",1:nrow(df3)) + grpq <- cbind(data.frame(sample=paste0(pnames,":"),stringsAsFactors=F),df3) + + # toplabels + plt <- data.frame(sample=pnames,label=rleval$values,stringsAsFactors=F) + dop_m <- nrow(plt) + + fname_plb <- "null" + fname_plt <- paste0(fname,"-grplab-top.txt") + } + + # top and bottom labels absent + if((any(is.na(grplabbottom))) && (any(is.na(grplabtop)))) + { + + # indq + inames <- sprintf("%08.0f",1:nrow(df)) + indq <- cbind(data.frame(id1=1:nrow(df),sample=inames,id2=1:nrow(df), + grp=sprintf("%06.0f",as.numeric(as.character(rep(1,nrow(df))))), + colon=rep(":",nrow(df)),stringsAsFactors=F),df) + + df1 <- tidyr::gather(df,"variable","value") + df2 <- cbind(aggregate(value~variable,data=df1,FUN=mean),aggregate(value~variable,data=df1,FUN=length)[,2,drop=F]) + colnames(df2) <- c("variable","mean","len") + df3 <- tidyr::spread(df2,"variable","mean") + + rm(df1,df2) + df3$length <- df3$len + df3 <- df3[,!(colnames(df3) %in% c("len"))] + pnames <- sprintf("%06.0f",1:nrow(df3)) + grpq <- cbind(data.frame(sample=paste0(pnames,":"),stringsAsFactors=F),df3) + + dop_m <- 1 + dop_toplabel <- FALSE + dop_bottomlabel <- FALSE + fname_plb <- "null" + fname_plt <- "null" + } + + # colours + if(any(is.na(clustercol))){ + colsdf <- data.frame(sample=1:dop_k,cols=pophelper:::distructColours()[1:dop_k],stringsAsFactors=F) + }else{ + if(length(clustercol) != length(pnames)) stop(paste0("distructExport: Length of colours (",length(clustercol),") not equal to length of groups (",length(pnames),"). Change number of colours in 'clustercol' or set 'clustercol=NA'.")) + #if(any(!clustercol %in% pophelper:::distructColours())) stop(paste0("distructExport: One or more colours provided (",clustercol[which(!clustercol %in% pophelper:::distructColours())],") is not a standard Distruct colour.")) + colsdf <- data.frame(sample=pnames,cols=clustercol,stringsAsFactors=F) + } + + # grayscale + if(grayscale) + { + fngray <- function(n) { + x <- round(seq(0,1,by=1/n),nchar(n)) + x[round(seq(1,length(x),length.out=n))] + } + colsdf <- data.frame(sample=1:dop_k,cols=fngray(dop_k),stringsAsFactors=F) + } + + # xorigin + if(is.na(xorigin)) + { + if(orientation==0) xorigin <- 72 + else if(orientation==1) xorigin <- 360 + else if(orientation==2) xorigin <- 540 + else if(orientation==3) xorigin <- 288 + } + + # yorigin + if(is.na(yorigin)) + { + if(orientation==0) yorigin <- 288 + else if(orientation==1) yorigin <- 72 + else if(orientation==2) yorigin <- 504 + else if(orientation==3) yorigin <- 720 + } + + # output file names + fname_grpq <- paste0(fname,"-grpq.txt") + fname_indq <- paste0(fname,"-indq.txt") + fname_col <- paste0(fname,"-colours.txt") + fname_out <- paste0(fname,".ps") + + # params + params <- c( + "PARAMETERS FOR THE PROGRAM distruct.", + "", + "'(int)' means that this takes an integer value.", + "'(B)' means that this variable is Boolean", + "(1 for True, and 0 for False)", + "'(str)' means that this is a string (but not enclosed in quotes)", + "'(d)' means that this is a double (a real number).", + "", + "Data settings", + "", + paste0("#define INFILE_POPQ ",fname_grpq), + paste0("#define INFILE_INDIVQ ",fname_indq), + paste0("#define INFILE_LABEL_BELOW ",fname_plb), + paste0("#define INFILE_LABEL_ATOP ",fname_plt), + paste0("#define INFILE_CLUST_PERM ",fname_col), + paste0("#define OUTFILE ",fname_out), + "", + "// number of clusters", + paste0("#define K ",dop_k," "), + "// number of pre-defined groups", + paste0("#define NUMPOPS ",dop_m," "), + "// number of individuals", + paste0("#define NUMINDS ",dop_n," "), + "", + "Main usage options", + "", + "// (B) 1 if indiv q\'s are to be printed, 0 if only group q\'s", + paste0("#define PRINT_INDIVS ",as.numeric(!grpmean)," "), + "// (B) print labels above figure", + paste0("#define PRINT_LABEL_ATOP ",as.numeric(dop_toplabel)," "), + "// (B) print labels below figure", + paste0("#define PRINT_LABEL_BELOW ",as.numeric(dop_bottomlabel)," "), + "// (B) print lines to separate groups", + paste0("#define PRINT_SEP ",as.numeric(sepline)," "), + "", + "Figure appearance", + "", + "// (d) size of font", + paste0("#define FONTHEIGHT ",as.numeric(fontsize)," "), + "// (d) distance above plot to place text", + paste0("#define DIST_ABOVE ",as.numeric(topdist)," "), + "// (d) distance below plot to place text", + paste0("#define DIST_BELOW ",as.numeric(bottomdist)," "), + "// (d) height of the figure", + paste0("#define BOXHEIGHT ",as.numeric(figheight)," "), + "// (d) width of an individual", + paste0("#define INDIVWIDTH ",as.numeric(indwidth)," "), + "", + "Extra options", + "", + "// (int) 0 for horizontal orientation (default)", + "// (int) 1 for vertical orientation", + "// (int) 2 for reverse horizontal orientation", + "// (int) 3 for reverse vertical orientation", + paste0("#define ORIENTATION ",as.numeric(orientation)," "), + "// (d) lower-left x-coordinate of figure", + paste0("#define XORIGIN ",as.numeric(xorigin)," "), + "// (d) lower-left y-coordinate of figure", + paste0("#define YORIGIN ",as.numeric(yorigin)," "), + "// (d) scale for x direction", + paste0("#define XSCALE ",as.numeric(xscale)," "), + "// (d) scale for y direction", + paste0("#define YSCALE ",as.numeric(yscale)," "), + "// (d) angle for labels atop figure (in [0,180])", + paste0("#define ANGLE_LABEL_ATOP ",as.numeric(toplabangle)," "), + "// (d) angle for labels below figure (in [0,180])", + paste0("#define ANGLE_LABEL_BELOW ",as.numeric(bottomlabangle)," "), + "// (d) width of 'pen' for rim of box", + paste0("#define LINEWIDTH_RIM ",as.numeric(borderlinewidth)," "), + "// (d) width of 'pen' for separators between grps and for tics", + paste0("#define LINEWIDTH_SEP ",as.numeric(seplinewidth)," "), + "// (d) width of 'pen' used for individuals", + paste0("#define LINEWIDTH_IND ",as.numeric(indlinewidth)," "), + "// (B) use grayscale instead of colors", + paste0("#define GRAYSCALE ",as.numeric(grayscale)," "), + "// (B) print some of the data to the screen", + paste0("#define ECHO_DATA ",as.numeric(printdata)," "), + "// (B) print the data as a comment in the ps file", + paste0("#define REPRINT_DATA ",as.numeric(printdata)," "), + "// (B) print the name of INFILE_POPQ above the figure", + "// this option is meant for use only with ORIENTATION=0", + paste0("#define PRINT_INFILE_NAME ",as.numeric(printtitle)," "), + "// (B) print ColorBrewer settings in the output file", + paste0("#define PRINT_COLOR_BREWER ",as.numeric(printcolorbrewer)," "), + "// this option adds 1689 lines and 104656 bytes to the output and is required if using ColorBrewer colors", + "", + "Command line options:", + "", + "-d drawparams", + paste0("-K ",dop_k), + paste0("-M ",dop_m), + paste0("-N ",dop_n), + paste0("-p ",fname_grpq), + paste0("-i ",fname_indq), + paste0("-a ",fname_plt), + paste0("-b ",fname_plb), + paste0("-c ",fname_col), + paste0("-o ",fname_out)) + + dir.create(dirname) + if(!quiet) cat("-------------------------------\n") + if(!quiet) cat(paste0("Directory ",dirname," created.\n")) + setwd(paste0(currwd,"/",dirname)) + if(as.numeric(file.access(paste0(currwd,"/",dirname),2))==-1) stop(paste0("distructExport: Directory ",paste0(currwd,"/",dirname)," has no write permission.")) + + write.table(grpq,fname_grpq,row.names=F,col.names=F,quote=F,dec=".",sep="\t") + if(!quiet) cat(paste0(fname_grpq," exported.\n")) + write.table(indq,fname_indq,row.names=F,col.names=F,quote=F,dec=".",sep="\t") + if(!quiet) cat(paste0(fname_indq," exported.\n")) + if(!any(is.na(grplabbottom))) + { + write.table(plb,fname_plb,row.names=F,col.names=F,quote=F,dec=".",sep="\t") + if(!quiet) cat(paste0(fname_plb," exported.\n")) + } + if(!any(is.na(grplabtop))) + { + write.table(plt,fname_plt,row.names=F,col.names=F,quote=F,dec=".",sep="\t") + if(!quiet) cat(paste0(fname_plt," exported.\n")) + } + write.table(colsdf,fname_col,row.names=F,col.names=F,quote=F,dec=".",sep="\t") + if(!quiet) cat(paste0(fname_col," exported.\n")) + writeLines(params,"drawparams") + if(!quiet) cat(paste0("drawparams exported.\n")) + + # auto execute distruct + if(useexe) + { + # identify OS + #sysos <- tolower(as.character(Sys.info()['sysname'])) + sysos <- pophelper:::getOS() + if(sysos=="windows") + { + file.copy(system.file("bin/distruct_windows_1.1.exe",package="pophelper"),".") + system("distruct_windows_1.1.exe") + unlink("distruct_windows_1.1.exe",force=TRUE) + } + + if(sysos=="mac") + { + file.copy(system.file("bin/distruct_macosx_1.1_2013",package="pophelper"),".") + system("chmod 777 distruct_macosx_1.1_2013") + system("./distruct_macosx_1.1_2013") + unlink("distruct_macosx_1.1_2013",force=TRUE) + } + + if(sysos=="unix64") + { + file.copy(system.file("bin/distruct_linux_1.1_64bit",package="pophelper"),".") + system("chmod 777 distruct_linux_1.1_64bit") + system("./distruct_linux_1.1_64bit") + unlink("distruct_linux_1.1_64bit",force=TRUE) + } + if(sysos=="unix32") warning("distructExport: DISTRUCT executable not run because system was identified as 32 bit while the executable is 64 bit.") + if(sysos=="unknown") warning("distructExport: DISTRUCT executable not run because system cannot be identified as windows, mac or linux.") + } + + setwd(currwd) + } + } + if(!quiet) cat("===============================\n") +} + +# distructColours -------------------------------------------------------------- + +#' @title Internal: Vector of 90 Distruct colours +#' @description Internal: Vector of 90 Distruct colours. +#' @return Returns a character vector of 90 colours recognised by Distruct. +#' @aliases distructColors +#' @examples +#' distructColours(); +#' distructColours()[1:5]; +#' distructColours()[10:15]; +#' @export +#' +distructColours <- distructColors <- function() +{ + return(c("orange","blue","yellow","pink","green","purple","red","light_green","dark_blue", + "light_purple","light_yellow","brown","light_blue","olive_green","peach","sea_green", + "yellow_green","blue_purple","blue_green","gray","dark_green","light_gray","red2", + "light_blue2","light_orange","dark_gray","light_pink","dark_brown","dark_orange", + "dark_purple","white",paste0("color",32:60),paste0("color",101:130))) +} + +# getOS ------------------------------------------------------------------------ + +#' @title Internal: Find current OS +#' @description Find current OS +#' @return Returns a character in lowercase with OS name 'windows', 'mac' or 'linux'. +#' +getOS <- function() { + if(tolower(.Platform$OS.type)=="windows") { + return("windows") + } else if(tolower(Sys.info()["sysname"])=="darwin") { + return("mac") + } else if(tolower(.Platform$OS.type)=="unix") { + if(grepl("x86_64",as.character(sessionInfo()["platform"]))) {return("unix64")}else{return("unix32")} + } else { + return("unknown") + } +} + +analyzeQ <- analyseQ +summarizeQ <- summariseQ + +# On Load ---------------------------------------------------------------------- + +#ON LOAD +.onLoad <- function(...) { + packageStartupMessage("pophelper v2.2.5 ready.") +} + +# End -------------------------------------------------------------------------- diff --git a/README.md b/README.md new file mode 100644 index 0000000..bbcd63e --- /dev/null +++ b/README.md @@ -0,0 +1,66 @@ +# pophelper 2.2.5 + +`pophelper` is an R package and web app to analyse and visualise population structure. `pophelper` curently supports output run files generated from population analysis programs such as STRUCTURE, TESS, TESS3, BAPS and numeric delimited formats such as ADMIXTURE or fastSTRUCTURE. The `pophelper` package can be used to read run files to R, tabulate runs, summarise runs, estimate *K* using the Evanno method, align clusters within K using CLUMPP, export files for DISTRUCT and generate barplot figures. + +For a detailed demonstration and walkthrough, refer the online [vignette](http://royfrancis.github.io/pophelper/). For information about changes in the latest version, visit [this GitHub page](https://github.com/royfrancis/pophelper/releases). + +## Installation +You need to have R (> 3.3.0) statistical package installed on your system. [R](https://www.r-project.org/) is open-source and freely available to download for Windows, Mac and other OS. Then, install the dependency packages. Then, you can install `pophelper` from `github` using the `devtools` package. + +```coffee +# install dependencies and devtools +install.packages(c("Cairo","ggplot2","gridExtra","gtable","tidyr","devtools"),dependencies=T) + +# install pophelper package from GitHub +devtools::install_github('royfrancis/pophelper') + +# load library for use +library(pophelper) +``` + +Note that `pophelper 1.2.0` and later includes binary executables for CLUMPP and DISTRUCT. This is experimental and may not work on all OS and versions. + +`pophelper` has been tested on the following systems: + ++ Windows 10 64bit, R 3.4.3 ++ Windows 10 64bit, R 3.3.3 ++ Windows 7 64bit, R 3.4.0 (DISTRUCT is unstable) ++ Scientific Linux 6.8 (Carbon) 64bit, R 3.4.0 + +## Web App +An online interactive version of pophelper is available at [pophelper.com](http://www.pophelper.com). The web app is quite outdated and limited in terms of functionality and flexibility. The web app must not be used for major work or large datasets. The web app is also limited in computational power and working hours. The web app will be automatically restricted after 100 hours of use per month. If anyone has ideas for funding `pophelper` web server, please get in touch. + +## Features + ++ Read q-matrices from STRUCTURE, TESS 2.3, TESS 3, BAPS, fastSTRUCTURE, ADMIXTURE runs. ++ Tabulate/summarise reads. ++ Compute Evanno method to estimate K for STRUCTURE runs. ++ Aligned clusters for single K using CLUMPP. ++ Single line and multiline barplots with labelling, sorting and subsetting. ++ Export files for use with DISTRUCT. + +## Sample figures + +![Workflow](vignettes/workflow.png) +__Fig:__ *Workflow for all filetypes.* + +![evanno-method](vignettes/evanno-plot.png) +__Fig:__ *Plots from Evanno method.* + +![plotq](vignettes/plotq.png) +__Fig:__ *Singleline barplots from q-matrices with individual and group labelling.* + +![plotq-multiline](vignettes/plotqmultiline.png) +__Fig:__ *Multiline barplots from q-matrices with individual and group labelling.* + +For detailed demonstration and description, refer the [vignette](http://royfrancis.github.io/pophelper/). + +### Disclaimer + +The `pophelper` R package is offered free and without warranty of any kind, either expressed or implied. I will not be held liable to you for any damage arising out of the use, modification or inability to use this program. `pophelper` R package can be used, redistributed and/or modified freely for non-commercial purposes subject to the original source being properly cited. Licensed under GPL-3. Please make sure you verify all your results. + +### Contact + +If you have an comments, suggestions, corrections or ideas on ways to improve or extend this package, feel free to contact me. Submit a report on the [Github issues page](https://github.com/royfrancis/pophelper/issues). + +2017 Roy M Francis diff --git a/inst/CITATION b/inst/CITATION new file mode 100644 index 0000000..21eaa69 --- /dev/null +++ b/inst/CITATION @@ -0,0 +1,19 @@ +citHeader("To cite the pophelper package, please use:") + +bibentry(bibtype = "Article", + title = "pophelper: An R package and web app to analyse and visualise population structure", + author = person(given="Roy",family="Francis",middle="Mathew",email="roymathewfrancis[at]gmail.com"), + year = "2017", + journal = "Molecular Ecology Resources", + volume = "17", + number = "1", + pages = "27-32", + doi = "10.1111/1755-0998.12509", + url = "https://github.com/royfrancis/pophelper", + note = "pophelper R package version 2.2.5", + textVersion= + paste("Francis, R. M. (2017).", + "pophelper: an R package and web app to analyse and visualize population structure.", + "Mol Ecol Resour, 17: 27–32. ", + "doi:10.1111/1755-0998.12509") +) diff --git a/inst/bin/clumpp_linux_1.1.2b_32bit b/inst/bin/clumpp_linux_1.1.2b_32bit new file mode 100644 index 0000000..f7978a1 Binary files /dev/null and b/inst/bin/clumpp_linux_1.1.2b_32bit differ diff --git a/inst/bin/clumpp_linux_1.1.2b_64bit b/inst/bin/clumpp_linux_1.1.2b_64bit new file mode 100644 index 0000000..2bdd951 Binary files /dev/null and b/inst/bin/clumpp_linux_1.1.2b_64bit differ diff --git a/inst/bin/clumpp_mac_1.1.2b b/inst/bin/clumpp_mac_1.1.2b new file mode 100644 index 0000000..dfe0e63 Binary files /dev/null and b/inst/bin/clumpp_mac_1.1.2b differ diff --git a/inst/bin/clumpp_windows_1.1.2b.exe b/inst/bin/clumpp_windows_1.1.2b.exe new file mode 100644 index 0000000..8b48f65 Binary files /dev/null and b/inst/bin/clumpp_windows_1.1.2b.exe differ diff --git a/inst/bin/distruct_linux_1.1_64bit b/inst/bin/distruct_linux_1.1_64bit new file mode 100644 index 0000000..2987e2f Binary files /dev/null and b/inst/bin/distruct_linux_1.1_64bit differ diff --git a/inst/bin/distruct_macosx_1.1 b/inst/bin/distruct_macosx_1.1 new file mode 100644 index 0000000..27ca1ac Binary files /dev/null and b/inst/bin/distruct_macosx_1.1 differ diff --git a/inst/bin/distruct_macosx_1.1_2013 b/inst/bin/distruct_macosx_1.1_2013 new file mode 100644 index 0000000..e8e7070 Binary files /dev/null and b/inst/bin/distruct_macosx_1.1_2013 differ diff --git a/inst/bin/distruct_windows_1.1.exe b/inst/bin/distruct_windows_1.1.exe new file mode 100644 index 0000000..28e4518 Binary files /dev/null and b/inst/bin/distruct_windows_1.1.exe differ diff --git a/inst/files/PophelperDemo.R b/inst/files/PophelperDemo.R new file mode 100644 index 0000000..24ef65b --- /dev/null +++ b/inst/files/PophelperDemo.R @@ -0,0 +1,181 @@ +#POPHELPER 1.1.6 +#02-JAN-2016 +#DEMO SCRIPT + +library(pophelper) +#create a new folder and set as wd +currwd <- getwd() +dir.create(paste(currwd,"/PophelperDemo",sep="")) +setwd(paste(currwd,"/PophelperDemo",sep="")) +#read sample STRUCTURE files from R package +sfiles <- list.files(path=system.file("/files/structure",package="pophelper"),full.names=T) +#read sample TESS files from R package +tfiles <- list.files(path=system.file("/files/tess",package="pophelper"),full.names=T) +#read sample ADMIXTURE files from R package +afiles <- list.files(path=system.file("/files/admixture",package="pophelper"),full.names=T) +#tabulate STRUCTURE runs +sf1 <- tabulateRunsStructure(files=sfiles, quiet=F) +sf1 <- tabulateRunsStructure(files=sfiles, writetable = T) +sf1 <- tabulateRunsStructure(files=sfiles, writetable = T, sorttable = F, quiet = T) +sf1 +#tabulate TESS runs +tf1 <- tabulateRunsTess(files=tfiles, writetable = T) +tf1 <- tabulateRunsTess(files=tfiles, writetable = T, sorttable = F, quiet = T) +tf1 +#tabulate ADMIXTURE runs +af1 <- tabulateRunsAdmixture(files=afiles, writetable = T) +af1 <- tabulateRunsAdmixture(files=afiles, writetable = T, sorttable = F, quiet = T) +af1 +#summarise STRUCTURE runs +sf2 <- summariseRunsStructure(sf1) +sf2 <- summariseRunsStructure(sf1, writetable = T) +sf2 +#summarise TESS runs +tf2 <- summariseRunsTess(tf1, writetable = F) +tf2 <- summariseRunsTess(tf1, writetable = T) +tf2 +#summarise ADMIXTURE runs +af2 <- summariseRunsAdmixture(af1, writetable = F) +af2 <- summariseRunsAdmixture(af1, writetable = T) +af2 +#perform evanno method +evannoMethodStructure(sf2) +evannoMethodStructure(sf2, writetable = T, exportplot = T) +evannoMethodStructure(sf2, writetable = T, exportplot = T, height = 15, width = 15) +evannoMethodStructure(sf2, height = 20, width = 20, basesize=8) +#convert STRUCTURE run files to R dataframe +runsToDfStructure(files=sfiles) +#convert TESS run files to R dataframe +runsToDfTess(files=tfiles) +#convert ADMIXTURE run files to R dataframe +runsToDfAdmixture(files=afiles) +#convert STRUCTURE runs for CLUMPP +clumppExportStructure(files=sfiles) +clumppExportStructure(files=sfiles, prefix = "Boom", parammode = 3, paramrep = 200) +#convert TESS runs for CLUMPP +clumppExportTess(files=tfiles) +#convert ADMIXTURE runs for CLUMPP +clumppExportAdmixture(files=afiles) +#collect CLUMPP outputs into single directory +#collectClumppOutput(prefix="STRUCTUREpop", filetype="both") +#collectClumppOutput(prefix="TESSpop", filetype="both") +#CANNOT TEST ABOVE WITHOUT CLUMPP.EXE +#plot separate figures STRUCTURE +plotRuns(files=sfiles[1:2]) +plotRuns(files=sfiles[1:2], imgoutput = "sep", height = 5, width = 15) +#plot separate figures TESS +plotRuns(files=tfiles[1:2]) +#plot joined figures STRUCTURE +plotRuns(files=sfiles[1:2], imgoutput="join",na.rm=T) +#plot joined figures TESS +plotRuns(files=tfiles[1:2], imgoutput="join") +#read labels for STRUCTURE +pops<-read.delim(system.file("files/structurepoplabels.txt",package="pophelper"),header=F) +#plot separately with labels +plotRuns(files=sfiles[1:2], imgoutput="sep", poplab=pops$V1) +#plot joined with labels +plotRuns(files=sfiles[1:2], imgoutput="join", poplab=pops$V1) +#create TESS labels +labs1 <- factor(c(rep("PopA",30),rep("PopB",45))) +#plot TESS runs with labels +plotRuns(files=tfiles[1:2], imgoutput="sep", poplab=labs1) +plotRuns(files=tfiles[1:2], imgoutput="join", poplab=labs1) +#plot ADMIXTURE runs +plotRuns(files=afiles[1:2], imgoutput="sep") +plotRuns(files=afiles[1:2], imgoutput="join") +#read labels for ADMIXTURE +admpops<-read.delim(system.file("files/admixturepoplabels.txt",package="pophelper"),header=F) +plotRuns(files=afiles[1:2], imgoutput="sep", poplab=admpops$V1) +plotRuns(files=afiles[1:2], imgoutput="join", poplab=admpops$V1) +#plot TABLE files +tabs1 <- c(system.file("files/STRUCTUREpop_K4-combined.txt",package="pophelper"), + system.file("files/STRUCTUREpop_K4-combined-aligned.txt",package="pophelper"), + system.file("files/STRUCTUREpop_K4-combined-merged.txt",package="pophelper")) +#plot one TABLE file +plotRuns(files=tabs1[1],imgoutput="tab") +#plot all TABLE files +plotRuns(files=tabs1,imgoutput="tab") +#plot all TABLE files with labels +plotRuns(files=tabs1,imgoutput="tab",poplab=pops$V1) +#plot multiline STRUCTURE +plotMultiline(files=sfiles[1]) +#plot multiline TESS +plotMultiline(files=tfiles[1]) +#plot multiline ADMIXTURE +plotMultiline(files=afiles[1]) +#plot multiline ADMIXTURE multiple +plotMultiline(files=afiles[2:3]) +#plotmultiline with custom setting +plotMultiline(files=sfiles[1], spl=75, lpp=10) +#plotmultiline with custom setting +plotMultiline(files=sfiles[1],barspace = 0,barwidth = 1,height = 6,width=16) +#plotmultiline with custom setting +plotMultiline(files=sfiles[1],barspace = 0,barwidth = 1,height = 6,width=16,yaxislabs = T,indlabs = F) +#plotmultiline with custom setting +plotMultiline(files=sfiles[1],barspace = 0,barwidth = 1,height = 6,width=16,yaxislabs = T,labangle = 45,imgtype = "jpeg") +#plotMultiline with one TABLE file +plotMultiline(files=tabs1[1]) +#plotMultiline with all TABLE file +plotMultiline(files=tabs1) +#read coordinate file +cd2 <- system.file("/files/coords75.txt",package="pophelper") +#basic usage +plotRunsInterpolate(datafile=tfiles[2],coordsfile=cd2) +plotRunsInterpolate(datafile=tfiles[2],coordsfile=cd2,imgtype="jpeg") +plotRunsInterpolate(datafile=tfiles[2],coordsfile=cd2,imgtype="pdf") +plotRunsInterpolate(datafile=tfiles[2],coordsfile=cd2,method="bicubic") +plotRunsInterpolate(datafile=tfiles[2],coordsfile=cd2,method="krig") +plotRunsInterpolate(datafile=tfiles[2],coordsfile=cd2,clusters=2) +plotRunsInterpolate(datafile=tfiles[2],coordsfile=cd2,pointcol = "red") +plotRunsInterpolate(datafile=tfiles[2],coordsfile=cd2,clusters=c(1,3)) +#adjusting legend size and legend text +plotRunsInterpolate(datafile=tfiles[2],coordsfile=cd2,legendsize=0.4,legendtextsize=6,method="bilinear") +#removing legend and changing method +plotRunsInterpolate(datafile=tfiles[2],coordsfile=cd2,legend=FALSE,method="idw") +plotRunsInterpolate(datafile=tfiles[2],coordsfile=cd2,legend=FALSE,method="idw",idwpower=5) +#read coordinate file length 239 +cfile239 <- read.delim(system.file("files/coords239.txt",package="pophelper"),header=F) +#select path to STRUCTURE file length 239 +sfile239 <- system.file("files/Structure239_4",package="pophelper") +#basic usage +plotRunsInterpolate(datafile=sfile239,coordsfile=cfile239,cluster=1:2,height=8) +plotRunsSpatial(datafile=sfile239,coordsfile=cfile239) +plotRunsSpatial(datafile=sfile239,coordsfile=cfile239,imgtype="jpeg") +plotRunsSpatial(datafile=sfile239,coordsfile=cfile239,imgtype="pdf") +#needs more height. set height and width as required in cm. +plotRunsSpatial(datafile=sfile239,coordsfile=cfile239,height=12) +plotRunsSpatial(datafile=sfile239,coordsfile=cfile239,height=12,showaxis = T) +plotRunsSpatial(datafile=sfile239,coordsfile=cfile239,height=12,showaxis = T, popcol=c("blue","green","red","steelblue","yellow")) +plotRunsSpatial(datafile=sfile239,coordsfile=cfile239,height=12,showaxis = T, pointcol ="red") +plotRunsSpatial(datafile=sfile239,coordsfile=cfile239,height=12,pointtype=12) +plotRunsSpatial(datafile=sfile239,coordsfile=cfile239,height=12,chull=T,chullsize=2,ellipse=F,) +#set UTM coordinates. Better geographic distance representation over a scale such as normal countries. +plotRunsSpatial(datafile=sfile239,coordsfile=cfile239,height=12,setutm=T) +#without ellipses +plotRunsSpatial(datafile=sfile239,coordsfile=cfile239,height=12,ellipse=F) + +#Create a 2x2 montage with varying parameters +#don't export, export data, add title +p1 <- plotRunsSpatial(datafile=sfile239,coordsfile=cfile239,exportplot=F,dataout=T, plottitle="Fig 1") +#without ellipse, with square points and transparency added +p2 <- plotRunsSpatial(datafile=sfile239,coordsfile=cfile239,exportplot=F,dataout=T, plottitle="Fig 2",ellipse=F,pointtype=15,pointtransp=0.4) +#without ellipse, with convex hulls, coordinates in UTM +p3 <- plotRunsSpatial(datafile=sfile239,coordsfile=cfile239,exportplot=F,dataout=T, plottitle="Fig 3",ellipse=F,chull=T, setutm=T) +#no ellipse, with convex hull, decreased convexhull transparency, change cluster labels +p4 <- plotRunsSpatial(datafile=sfile239,coordsfile=cfile239,exportplot=F,dataout=T, plottitle="Fig 4",ellipse=F,chull=T,chulltransp=0.2,chulltype=3,legendlabels=c("PopA","PopB","PopC","PopD","PopE")) + +#install gridExtra first +#library(gridExtra) +#png("PlotRunsSpatial.png",height=20,width=20,res=250,units="cm",type="cairo") +#grid.arrange(p1,p2,p3,p4,nrow=2,ncol=2) +#dev.off() +setwd(currwd) +dir.create(paste(currwd,"/AnalyseDemo",sep="")) +setwd(paste(currwd,"/AnalyseDemo",sep="")) + +#perform a routine analysis using a wrapper function +analyseRuns(sfiles) +analyseRuns(tfiles) +analyseRuns(afiles) + +setwd(currwd) diff --git a/inst/files/STRUCTUREpop_K4-combined-aligned.txt b/inst/files/STRUCTUREpop_K4-combined-aligned.txt new file mode 100644 index 0000000..959730b --- /dev/null +++ b/inst/files/STRUCTUREpop_K4-combined-aligned.txt @@ -0,0 +1,450 @@ + 1: 0.0350 0.3870 0.0910 0.4870 1 + 2: 0.0360 0.8240 0.0710 0.0690 1 + 3: 0.0390 0.0790 0.8110 0.0710 1 + 4: 0.0360 0.7153 0.0839 0.1648 1 + 5: 0.0340 0.1552 0.7397 0.0711 1 + 6: 0.0310 0.8300 0.0810 0.0580 1 + 7: 0.0501 0.2903 0.5776 0.0821 1 + 8: 0.0521 0.1131 0.5816 0.2533 1 + 9: 0.0500 0.1070 0.7940 0.0490 1 + 10: 0.0240 0.1330 0.8070 0.0360 1 + 11: 0.0240 0.1170 0.4590 0.4000 1 + 12: 0.0290 0.1210 0.7060 0.1440 1 + 13: 0.0649 0.0529 0.7702 0.1119 1 + 14: 0.0400 0.2022 0.2162 0.5415 1 + 15: 0.0521 0.5415 0.3273 0.0791 1 + 16: 0.1450 0.0440 0.7400 0.0710 1 + 17: 0.0871 0.0961 0.4284 0.3884 1 + 18: 0.0280 0.0650 0.8720 0.0350 1 + 19: 0.0530 0.1680 0.3450 0.4340 1 + 20: 0.0550 0.3150 0.5210 0.1090 1 + 21: 0.0230 0.0709 0.8601 0.0460 1 + 22: 0.0300 0.0590 0.8430 0.0680 1 + 23: 0.0380 0.5704 0.2078 0.1838 1 + 24: 0.0710 0.4350 0.0570 0.4370 1 + 25: 0.1300 0.1020 0.7040 0.0640 1 + 26: 0.0521 0.1141 0.7838 0.0501 1 + 27: 0.1260 0.1360 0.3140 0.4240 1 + 28: 0.0580 0.2610 0.2450 0.4360 1 + 29: 0.1790 0.0400 0.6430 0.1380 1 + 30: 0.3810 0.1220 0.2390 0.2580 1 + 31: 0.3574 0.1842 0.2723 0.1862 1 + 32: 0.1430 0.5780 0.0480 0.2310 1 + 33: 0.0350 0.3350 0.2390 0.3910 1 + 34: 0.0230 0.7380 0.1980 0.0410 1 + 35: 0.0450 0.0919 0.3487 0.5145 1 + 36: 0.1011 0.1662 0.4955 0.2372 1 + 37: 0.2970 0.0920 0.3860 0.2250 1 + 38: 0.0680 0.3830 0.1130 0.4360 1 + 39: 0.1530 0.6530 0.1390 0.0550 1 + 40: 0.0300 0.4930 0.4230 0.0540 1 + 41: 0.0330 0.0390 0.8919 0.0360 1 + 42: 0.0380 0.4745 0.1129 0.3746 1 + 43: 0.0400 0.5764 0.2567 0.1269 1 + 44: 0.0320 0.1320 0.7750 0.0610 1 + 45: 0.0690 0.4220 0.0750 0.4340 1 + 46: 0.0240 0.2573 0.6416 0.0771 1 + 47: 0.0190 0.2340 0.6950 0.0520 1 + 48: 0.2713 0.2863 0.2983 0.1441 1 + 49: 0.0730 0.5810 0.0800 0.2660 1 + 50: 0.0360 0.6807 0.1231 0.1602 1 + 51: 0.0850 0.2190 0.6220 0.0740 1 + 52: 0.1429 0.4895 0.2517 0.1159 1 + 53: 0.1530 0.1830 0.6080 0.0560 1 + 54: 0.1502 0.3233 0.4464 0.0801 1 + 55: 0.0300 0.1640 0.3590 0.4470 1 + 56: 0.2210 0.5230 0.1940 0.0620 1 + 57: 0.2660 0.1080 0.5720 0.0540 1 + 58: 0.2550 0.2760 0.3610 0.1080 1 + 59: 0.0990 0.1840 0.2960 0.4210 1 + 60: 0.0601 0.1101 0.7037 0.1261 1 + 61: 0.0910 0.2130 0.5600 0.1360 1 + 62: 0.4144 0.1602 0.1542 0.2713 1 + 63: 0.2202 0.5435 0.1481 0.0881 1 + 64: 0.0510 0.5470 0.1880 0.2140 1 + 65: 0.0250 0.7670 0.0460 0.1620 1 + 66: 0.1241 0.6577 0.0931 0.1251 1 + 67: 0.0680 0.5410 0.0780 0.3130 1 + 68: 0.0810 0.7190 0.1000 0.1000 1 + 69: 0.1171 0.2162 0.0791 0.5876 1 + 70: 0.1000 0.1820 0.5910 0.1270 1 + 71: 0.0370 0.5936 0.3083 0.0611 1 + 72: 0.0210 0.3300 0.6010 0.0480 1 + 73: 0.0270 0.8790 0.0400 0.0540 1 + 74: 0.0851 0.3443 0.1512 0.4194 1 + 75: 0.0500 0.7120 0.1300 0.1080 1 + 76: 0.0770 0.7370 0.0380 0.1480 1 + 77: 0.0430 0.1500 0.1270 0.6800 1 + 78: 0.0260 0.1090 0.4700 0.3950 1 + 79: 0.0330 0.5460 0.3030 0.1180 1 + 80: 0.0690 0.1330 0.0320 0.7660 1 + 81: 0.0570 0.3650 0.1260 0.4520 1 + 82: 0.6500 0.0580 0.1480 0.1440 1 + 83: 0.4190 0.1520 0.1980 0.2310 1 + 84: 0.0460 0.6560 0.1810 0.1170 1 + 85: 0.3636 0.1538 0.3666 0.1159 1 + 86: 0.0460 0.0930 0.1910 0.6700 1 + 87: 0.0370 0.8680 0.0270 0.0680 1 + 88: 0.1311 0.1702 0.3163 0.3824 1 + 89: 0.2180 0.5930 0.0620 0.1270 1 + 90: 0.0190 0.6850 0.2480 0.0480 1 + 91: 0.0660 0.6910 0.1600 0.0830 1 + 92: 0.0180 0.9071 0.0410 0.0340 1 + 93: 0.0870 0.2720 0.0970 0.5440 1 + 94: 0.0580 0.0490 0.8460 0.0470 1 + 95: 0.6080 0.2010 0.0820 0.1090 1 + 96: 0.1290 0.1110 0.6810 0.0790 1 + 97: 0.1988 0.2338 0.5135 0.0539 1 + 98: 0.4780 0.0790 0.3710 0.0720 1 + 99: 0.2830 0.0320 0.6320 0.0530 1 +100: 0.5856 0.1441 0.1812 0.0891 1 +101: 0.1349 0.0969 0.5654 0.2028 1 +102: 0.0310 0.1110 0.7910 0.0670 1 +103: 0.0550 0.0780 0.7440 0.1230 1 +104: 0.3580 0.3500 0.1330 0.1590 1 +105: 0.2640 0.2700 0.1700 0.2960 1 +106: 0.1060 0.6030 0.0570 0.2340 1 +107: 0.5175 0.1451 0.1902 0.1471 1 +108: 0.8062 0.0370 0.0450 0.1119 1 +109: 0.7530 0.0690 0.0480 0.1300 1 +110: 0.6750 0.0250 0.0710 0.2290 1 +111: 0.8650 0.0380 0.0580 0.0390 1 +112: 0.2260 0.0530 0.2200 0.5010 1 +113: 0.8292 0.0579 0.0390 0.0739 1 +114: 0.2780 0.0490 0.0900 0.5830 1 +115: 0.5770 0.0620 0.0350 0.3260 1 +116: 0.8740 0.0350 0.0260 0.0650 1 +117: 0.8650 0.0450 0.0350 0.0550 1 +118: 0.9060 0.0280 0.0370 0.0290 1 +119: 0.8268 0.0220 0.0320 0.1191 1 +120: 0.8050 0.0690 0.0460 0.0800 1 +121: 0.6740 0.0710 0.0710 0.1840 1 +122: 0.9199 0.0170 0.0190 0.0440 1 +123: 0.7772 0.0470 0.0539 0.1219 1 +124: 0.8520 0.0420 0.0220 0.0840 1 +125: 0.8920 0.0330 0.0300 0.0450 1 +126: 0.5600 0.0250 0.0480 0.3670 1 +127: 0.8900 0.0200 0.0310 0.0590 1 +128: 0.4056 0.0350 0.0519 0.5075 1 +129: 0.5165 0.0509 0.0619 0.3706 1 +130: 0.5770 0.1510 0.0440 0.2280 1 +131: 0.8430 0.0700 0.0390 0.0480 1 +132: 0.8250 0.0380 0.0320 0.1050 1 +133: 0.8182 0.0410 0.0440 0.0969 1 +134: 0.6420 0.0430 0.0470 0.2680 1 +135: 0.7490 0.0890 0.0390 0.1230 1 +136: 0.7810 0.0620 0.0340 0.1230 1 +137: 0.8470 0.0250 0.0310 0.0970 1 +138: 0.5946 0.0450 0.0300 0.3303 1 +139: 0.6720 0.0540 0.0510 0.2230 1 +140: 0.8719 0.0310 0.0350 0.0621 1 +141: 0.7628 0.0440 0.0791 0.1141 1 +142: 0.8899 0.0370 0.0250 0.0480 1 +143: 0.8660 0.0340 0.0320 0.0680 1 +144: 0.8840 0.0200 0.0420 0.0540 1 +145: 0.7560 0.0560 0.1120 0.0760 1 +146: 0.6410 0.0700 0.0890 0.2000 1 +147: 0.4990 0.0340 0.0870 0.3800 1 +148: 0.9200 0.0310 0.0180 0.0310 1 +149: 0.8338 0.0310 0.0350 0.1001 1 + + 1: 0.0330 0.4190 0.2240 0.3240 1 + 2: 0.0330 0.8200 0.0670 0.0800 1 + 3: 0.0370 0.0690 0.5220 0.3720 1 + 4: 0.0330 0.7200 0.1070 0.1400 1 + 5: 0.0320 0.1470 0.4780 0.3430 1 + 6: 0.0290 0.8140 0.0760 0.0810 1 + 7: 0.0460 0.2753 0.3994 0.2793 1 + 8: 0.0490 0.1149 0.4525 0.3836 1 + 9: 0.0480 0.1050 0.5050 0.3420 1 + 10: 0.0220 0.1220 0.5070 0.3490 1 + 11: 0.0230 0.1201 0.4434 0.4134 1 + 12: 0.0270 0.1111 0.4815 0.3804 1 + 13: 0.0621 0.0531 0.5225 0.3624 1 + 14: 0.0380 0.2180 0.3480 0.3960 1 + 15: 0.0490 0.5230 0.2450 0.1830 1 + 16: 0.1389 0.0430 0.4805 0.3377 1 + 17: 0.0830 0.0990 0.4170 0.4010 1 + 18: 0.0250 0.0570 0.5500 0.3680 1 + 19: 0.0509 0.1678 0.3866 0.3946 1 + 20: 0.0510 0.3020 0.3700 0.2770 1 + 21: 0.0210 0.0650 0.5400 0.3740 1 + 22: 0.0270 0.0510 0.5420 0.3800 1 + 23: 0.0370 0.5790 0.1880 0.1960 1 + 24: 0.0681 0.4414 0.1992 0.2913 1 + 25: 0.1239 0.0989 0.4635 0.3137 1 + 26: 0.0500 0.1040 0.5030 0.3430 1 + 27: 0.1201 0.1421 0.3694 0.3684 1 + 28: 0.0560 0.2650 0.3270 0.3520 1 + 29: 0.1730 0.0410 0.4550 0.3310 1 + 30: 0.3686 0.1259 0.2597 0.2458 1 + 31: 0.3450 0.1830 0.2520 0.2200 1 + 32: 0.1351 0.5836 0.1231 0.1582 1 + 33: 0.0330 0.3293 0.3103 0.3273 1 + 34: 0.0220 0.7260 0.1360 0.1160 1 + 35: 0.0410 0.0971 0.4234 0.4384 1 + 36: 0.0961 0.1592 0.4164 0.3283 1 + 37: 0.2960 0.0890 0.3270 0.2880 1 + 38: 0.0640 0.3980 0.2410 0.2970 1 + 39: 0.1450 0.6510 0.1080 0.0960 1 + 40: 0.0280 0.4695 0.2913 0.2112 1 + 41: 0.0310 0.0350 0.5576 0.3764 1 + 42: 0.0350 0.4840 0.2030 0.2780 1 + 43: 0.0370 0.5596 0.2202 0.1832 1 + 44: 0.0300 0.1250 0.5010 0.3440 1 + 45: 0.0669 0.4396 0.2018 0.2917 1 + 46: 0.0230 0.2420 0.4320 0.3030 1 + 47: 0.0180 0.2190 0.4510 0.3120 1 + 48: 0.2720 0.2770 0.2420 0.2090 1 + 49: 0.0690 0.5750 0.1570 0.1990 1 + 50: 0.0340 0.6730 0.1360 0.1570 1 + 51: 0.0800 0.2100 0.4080 0.3020 1 + 52: 0.1360 0.4800 0.2040 0.1800 1 + 53: 0.1449 0.1738 0.3956 0.2857 1 + 54: 0.1400 0.3040 0.3140 0.2420 1 + 55: 0.0280 0.1640 0.3810 0.4270 1 + 56: 0.2130 0.5090 0.1450 0.1330 1 + 57: 0.2540 0.1020 0.3750 0.2690 1 + 58: 0.2500 0.2720 0.2670 0.2110 1 + 59: 0.0980 0.1860 0.3460 0.3700 1 + 60: 0.0550 0.1060 0.4910 0.3480 1 + 61: 0.0851 0.2002 0.4004 0.3143 1 + 62: 0.4100 0.1630 0.2070 0.2200 1 + 63: 0.2098 0.5295 0.1359 0.1249 1 + 64: 0.0480 0.5530 0.1940 0.2050 1 + 65: 0.0240 0.7640 0.0840 0.1280 1 + 66: 0.1180 0.6530 0.1130 0.1160 1 + 67: 0.0669 0.5455 0.1628 0.2248 1 + 68: 0.0741 0.7217 0.0991 0.1051 1 + 69: 0.1150 0.2200 0.2810 0.3840 1 + 70: 0.0930 0.1720 0.4180 0.3170 1 + 71: 0.0350 0.5770 0.2110 0.1770 1 + 72: 0.0200 0.3120 0.3890 0.2790 1 + 73: 0.0250 0.8699 0.0450 0.0601 1 + 74: 0.0821 0.3544 0.2492 0.3143 1 + 75: 0.0460 0.6980 0.1280 0.1280 1 + 76: 0.0720 0.7450 0.0750 0.1080 1 + 77: 0.0410 0.1588 0.3437 0.4565 1 + 78: 0.0240 0.1171 0.4354 0.4234 1 + 79: 0.0310 0.5220 0.2460 0.2010 1 + 80: 0.0661 0.1562 0.3133 0.4645 1 + 81: 0.0540 0.3700 0.2520 0.3240 1 + 82: 0.6630 0.0570 0.1430 0.1370 1 + 83: 0.4296 0.1518 0.2068 0.2118 1 + 84: 0.0450 0.6380 0.1570 0.1600 1 + 85: 0.3500 0.1490 0.2840 0.2170 1 + 86: 0.0440 0.1029 0.3856 0.4675 1 + 87: 0.0340 0.8610 0.0420 0.0630 1 + 88: 0.1320 0.1720 0.3530 0.3430 1 + 89: 0.2050 0.5880 0.0940 0.1130 1 + 90: 0.0180 0.6850 0.1600 0.1370 1 + 91: 0.0611 0.6767 0.1401 0.1221 1 + 92: 0.0170 0.8990 0.0370 0.0470 1 + 93: 0.0860 0.2900 0.2660 0.3580 1 + 94: 0.0550 0.0450 0.5350 0.3650 1 + 95: 0.6170 0.1950 0.0900 0.0980 1 + 96: 0.1219 0.0989 0.4525 0.3267 1 + 97: 0.1880 0.2260 0.3390 0.2470 1 + 98: 0.4650 0.0770 0.2590 0.1990 1 + 99: 0.2733 0.0310 0.4094 0.2863 1 +100: 0.5760 0.1380 0.1530 0.1330 1 +101: 0.1290 0.1030 0.4250 0.3430 1 +102: 0.0290 0.1030 0.5070 0.3610 1 +103: 0.0511 0.0751 0.5075 0.3664 1 +104: 0.3596 0.3497 0.1389 0.1518 1 +105: 0.2580 0.2730 0.2260 0.2430 1 +106: 0.1010 0.6110 0.1250 0.1630 1 +107: 0.5015 0.1479 0.1818 0.1688 1 +108: 0.8142 0.0360 0.0669 0.0829 1 +109: 0.7620 0.0650 0.0780 0.0950 1 +110: 0.6920 0.0250 0.1230 0.1600 1 +111: 0.8719 0.0360 0.0480 0.0440 1 +112: 0.2340 0.0590 0.3320 0.3750 1 +113: 0.8400 0.0550 0.0490 0.0560 1 +114: 0.3017 0.0559 0.2697 0.3726 1 +115: 0.5916 0.0651 0.1371 0.2062 1 +116: 0.8810 0.0330 0.0380 0.0480 1 +117: 0.8720 0.0430 0.0390 0.0460 1 +118: 0.9100 0.0260 0.0330 0.0310 1 +119: 0.8410 0.0220 0.0570 0.0800 1 +120: 0.8142 0.0669 0.0559 0.0629 1 +121: 0.6870 0.0690 0.1090 0.1350 1 +122: 0.9251 0.0170 0.0260 0.0320 1 +123: 0.7990 0.0440 0.0720 0.0850 1 +124: 0.8640 0.0400 0.0410 0.0550 1 +125: 0.9009 0.0310 0.0320 0.0360 1 +126: 0.5806 0.0270 0.1622 0.2302 1 +127: 0.8970 0.0200 0.0380 0.0450 1 +128: 0.4170 0.0410 0.2210 0.3210 1 +129: 0.5465 0.0561 0.1672 0.2302 1 +130: 0.6000 0.1480 0.1090 0.1430 1 +131: 0.8510 0.0650 0.0400 0.0440 1 +132: 0.8350 0.0370 0.0550 0.0730 1 +133: 0.8300 0.0390 0.0590 0.0720 1 +134: 0.6710 0.0420 0.1160 0.1710 1 +135: 0.7640 0.0860 0.0650 0.0850 1 +136: 0.7880 0.0600 0.0650 0.0870 1 +137: 0.8550 0.0250 0.0530 0.0670 1 +138: 0.6234 0.0470 0.1299 0.1998 1 +139: 0.6900 0.0540 0.1120 0.1440 1 +140: 0.8769 0.0300 0.0440 0.0490 1 +141: 0.7700 0.0430 0.0920 0.0950 1 +142: 0.8969 0.0350 0.0310 0.0370 1 +143: 0.8760 0.0330 0.0410 0.0500 1 +144: 0.8930 0.0190 0.0430 0.0450 1 +145: 0.7658 0.0531 0.0941 0.0871 1 +146: 0.6630 0.0690 0.1230 0.1450 1 +147: 0.5345 0.0350 0.1812 0.2492 1 +148: 0.9259 0.0290 0.0210 0.0240 1 +149: 0.8450 0.0300 0.0540 0.0710 1 + + 1: 0.0340 0.4166 0.0849 0.4645 1 + 2: 0.0340 0.8218 0.0711 0.0731 1 + 3: 0.0370 0.0761 0.8198 0.0671 1 + 4: 0.0340 0.7300 0.0760 0.1600 1 + 5: 0.0330 0.1522 0.7437 0.0711 1 + 6: 0.0300 0.8210 0.0820 0.0670 1 + 7: 0.0480 0.2760 0.5680 0.1080 1 + 8: 0.0500 0.1180 0.5780 0.2540 1 + 9: 0.0490 0.1060 0.7870 0.0580 1 + 10: 0.0220 0.1271 0.8148 0.0360 1 + 11: 0.0230 0.1170 0.4450 0.4150 1 + 12: 0.0280 0.1149 0.7213 0.1359 1 + 13: 0.0619 0.0529 0.7592 0.1259 1 + 14: 0.0380 0.2010 0.2090 0.5520 1 + 15: 0.0490 0.5265 0.3283 0.0961 1 + 16: 0.1381 0.0440 0.7457 0.0721 1 + 17: 0.0830 0.0990 0.4390 0.3790 1 + 18: 0.0260 0.0610 0.8770 0.0360 1 + 19: 0.0510 0.1760 0.3460 0.4270 1 + 20: 0.0520 0.3060 0.5270 0.1150 1 + 21: 0.0220 0.0690 0.8650 0.0440 1 + 22: 0.0280 0.0560 0.8490 0.0670 1 + 23: 0.0380 0.5760 0.2050 0.1810 1 + 24: 0.0680 0.4410 0.0550 0.4360 1 + 25: 0.1260 0.1000 0.6920 0.0820 1 + 26: 0.0510 0.1080 0.7890 0.0520 1 + 27: 0.1200 0.1360 0.3130 0.4310 1 + 28: 0.0541 0.2663 0.2362 0.4434 1 + 29: 0.1708 0.0420 0.6364 0.1508 1 + 30: 0.3700 0.1230 0.2340 0.2730 1 + 31: 0.3480 0.1810 0.2650 0.2060 1 + 32: 0.1360 0.5750 0.0450 0.2440 1 + 33: 0.0330 0.3290 0.2280 0.4100 1 + 34: 0.0220 0.7390 0.1910 0.0480 1 + 35: 0.0420 0.0900 0.3400 0.5280 1 + 36: 0.0959 0.1598 0.4805 0.2637 1 + 37: 0.2953 0.0911 0.3944 0.2192 1 + 38: 0.0650 0.3900 0.1070 0.4380 1 + 39: 0.1460 0.6550 0.1370 0.0620 1 + 40: 0.0290 0.4810 0.4310 0.0590 1 + 41: 0.0320 0.0380 0.8941 0.0360 1 + 42: 0.0350 0.4830 0.1180 0.3640 1 + 43: 0.0380 0.5550 0.2560 0.1510 1 + 44: 0.0310 0.1330 0.7670 0.0690 1 + 45: 0.0671 0.4384 0.0731 0.4214 1 + 46: 0.0230 0.2442 0.6456 0.0871 1 + 47: 0.0180 0.2362 0.6917 0.0541 1 + 48: 0.2687 0.2877 0.3037 0.1399 1 + 49: 0.0710 0.5820 0.0790 0.2680 1 + 50: 0.0350 0.6823 0.1179 0.1648 1 + 51: 0.0830 0.2150 0.6220 0.0800 1 + 52: 0.1370 0.4850 0.2470 0.1310 1 + 53: 0.1470 0.1820 0.6130 0.0580 1 + 54: 0.1430 0.3160 0.4590 0.0820 1 + 55: 0.0290 0.1718 0.3726 0.4266 1 + 56: 0.2130 0.5130 0.2090 0.0650 1 + 57: 0.2530 0.1060 0.5870 0.0540 1 + 58: 0.2520 0.2750 0.3650 0.1080 1 + 59: 0.0990 0.1890 0.2920 0.4200 1 + 60: 0.0560 0.1060 0.6980 0.1400 1 + 61: 0.0850 0.2060 0.5690 0.1400 1 + 62: 0.4136 0.1608 0.1508 0.2747 1 + 63: 0.2130 0.5300 0.1540 0.1030 1 + 64: 0.0490 0.5580 0.1850 0.2080 1 + 65: 0.0240 0.7772 0.0430 0.1558 1 + 66: 0.1190 0.6520 0.0900 0.1390 1 + 67: 0.0671 0.5526 0.0781 0.3023 1 + 68: 0.0770 0.7160 0.0950 0.1120 1 + 69: 0.1150 0.2200 0.0770 0.5880 1 + 70: 0.0951 0.1742 0.6006 0.1301 1 + 71: 0.0350 0.5900 0.3100 0.0650 1 + 72: 0.0200 0.3220 0.6040 0.0540 1 + 73: 0.0260 0.8710 0.0390 0.0640 1 + 74: 0.0810 0.3470 0.1530 0.4190 1 + 75: 0.0480 0.7050 0.1260 0.1210 1 + 76: 0.0730 0.7430 0.0360 0.1480 1 + 77: 0.0410 0.1630 0.1280 0.6680 1 + 78: 0.0240 0.1151 0.4855 0.3754 1 + 79: 0.0320 0.5300 0.3050 0.1330 1 + 80: 0.0661 0.1421 0.0310 0.7608 1 + 81: 0.0560 0.3760 0.1250 0.4430 1 + 82: 0.6600 0.0570 0.1440 0.1390 1 + 83: 0.4240 0.1510 0.1940 0.2310 1 + 84: 0.0450 0.6597 0.1772 0.1181 1 + 85: 0.3566 0.1469 0.3656 0.1309 1 + 86: 0.0430 0.0951 0.1812 0.6807 1 + 87: 0.0350 0.8650 0.0250 0.0750 1 + 88: 0.1310 0.1670 0.3080 0.3940 1 + 89: 0.2100 0.5860 0.0610 0.1430 1 + 90: 0.0190 0.6923 0.2368 0.0519 1 + 91: 0.0630 0.6760 0.1590 0.1020 1 + 92: 0.0170 0.9010 0.0380 0.0440 1 + 93: 0.0870 0.2820 0.0940 0.5370 1 + 94: 0.0559 0.0490 0.8472 0.0480 1 + 95: 0.6140 0.1960 0.0820 0.1080 1 + 96: 0.1229 0.1089 0.6863 0.0819 1 + 97: 0.1900 0.2300 0.5190 0.0610 1 + 98: 0.4635 0.0769 0.3856 0.0739 1 + 99: 0.2693 0.0320 0.6406 0.0581 1 +100: 0.5780 0.1390 0.1870 0.0960 1 +101: 0.1290 0.1030 0.5570 0.2110 1 +102: 0.0290 0.1110 0.7930 0.0670 1 +103: 0.0530 0.0740 0.7520 0.1210 1 +104: 0.3586 0.3566 0.1319 0.1528 1 +105: 0.2570 0.2750 0.1660 0.3020 1 +106: 0.1010 0.6070 0.0550 0.2370 1 +107: 0.5050 0.1440 0.1870 0.1640 1 +108: 0.8120 0.0360 0.0430 0.1090 1 +109: 0.7550 0.0660 0.0450 0.1340 1 +110: 0.6887 0.0250 0.0661 0.2202 1 +111: 0.8690 0.0370 0.0550 0.0390 1 +112: 0.2310 0.0590 0.2060 0.5040 1 +113: 0.8360 0.0560 0.0380 0.0700 1 +114: 0.3003 0.0551 0.0861 0.5586 1 +115: 0.5830 0.0660 0.0330 0.3180 1 +116: 0.8790 0.0330 0.0250 0.0630 1 +117: 0.8710 0.0440 0.0330 0.0520 1 +118: 0.9080 0.0270 0.0360 0.0290 1 +119: 0.8388 0.0220 0.0300 0.1091 1 +120: 0.8140 0.0670 0.0450 0.0740 1 +121: 0.6830 0.0710 0.0670 0.1790 1 +122: 0.9221 0.0170 0.0190 0.0420 1 +123: 0.7882 0.0450 0.0509 0.1159 1 +124: 0.8581 0.0410 0.0210 0.0799 1 +125: 0.8970 0.0310 0.0290 0.0430 1 +126: 0.5720 0.0270 0.0470 0.3540 1 +127: 0.8950 0.0200 0.0290 0.0560 1 +128: 0.4150 0.0400 0.0510 0.4940 1 +129: 0.5415 0.0551 0.0611 0.3423 1 +130: 0.5980 0.1510 0.0420 0.2090 1 +131: 0.8490 0.0660 0.0380 0.0470 1 +132: 0.8322 0.0370 0.0310 0.0999 1 +133: 0.8260 0.0400 0.0420 0.0920 1 +134: 0.6580 0.0410 0.0460 0.2550 1 +135: 0.7610 0.0880 0.0380 0.1130 1 +136: 0.7860 0.0600 0.0320 0.1220 1 +137: 0.8510 0.0250 0.0300 0.0940 1 +138: 0.6130 0.0460 0.0300 0.3110 1 +139: 0.6853 0.0539 0.0490 0.2118 1 +140: 0.8741 0.0300 0.0340 0.0619 1 +141: 0.7660 0.0440 0.0770 0.1130 1 +142: 0.8940 0.0360 0.0240 0.0460 1 +143: 0.8730 0.0330 0.0300 0.0640 1 +144: 0.8900 0.0190 0.0400 0.0510 1 +145: 0.7618 0.0551 0.1101 0.0731 1 +146: 0.6590 0.0700 0.0870 0.1840 1 +147: 0.5145 0.0350 0.0859 0.3646 1 +148: 0.9240 0.0290 0.0170 0.0300 1 +149: 0.8408 0.0300 0.0340 0.0951 1 + diff --git a/inst/files/STRUCTUREpop_K4-combined-merged.txt b/inst/files/STRUCTUREpop_K4-combined-merged.txt new file mode 100644 index 0000000..5a4662f --- /dev/null +++ b/inst/files/STRUCTUREpop_K4-combined-merged.txt @@ -0,0 +1,149 @@ + 1: 0.0340 0.4075 0.1333 0.4252 1 + 2: 0.0343 0.8219 0.0697 0.0740 1 + 3: 0.0377 0.0747 0.7176 0.1700 1 + 4: 0.0343 0.7218 0.0890 0.1549 1 + 5: 0.0330 0.1514 0.6538 0.1617 1 + 6: 0.0300 0.8217 0.0797 0.0687 1 + 7: 0.0480 0.2805 0.5150 0.1565 1 + 8: 0.0503 0.1153 0.5374 0.2970 1 + 9: 0.0490 0.1060 0.6953 0.1497 1 + 10: 0.0227 0.1274 0.7096 0.1403 1 + 11: 0.0233 0.1180 0.4491 0.4095 1 + 12: 0.0280 0.1157 0.6363 0.2201 1 + 13: 0.0630 0.0530 0.6840 0.2000 1 + 14: 0.0387 0.2071 0.2577 0.4965 1 + 15: 0.0500 0.5304 0.3002 0.1194 1 + 16: 0.1407 0.0437 0.6554 0.1602 1 + 17: 0.0844 0.0980 0.4281 0.3895 1 + 18: 0.0263 0.0610 0.7663 0.1463 1 + 19: 0.0516 0.1706 0.3592 0.4185 1 + 20: 0.0527 0.3077 0.4727 0.1670 1 + 21: 0.0220 0.0683 0.7550 0.1547 1 + 22: 0.0283 0.0553 0.7447 0.1717 1 + 23: 0.0377 0.5751 0.2003 0.1869 1 + 24: 0.0690 0.4391 0.1037 0.3881 1 + 25: 0.1266 0.1003 0.6198 0.1532 1 + 26: 0.0510 0.1087 0.6919 0.1484 1 + 27: 0.1220 0.1380 0.3321 0.4078 1 + 28: 0.0560 0.2641 0.2694 0.4105 1 + 29: 0.1743 0.0410 0.5781 0.2066 1 + 30: 0.3732 0.1236 0.2442 0.2589 1 + 31: 0.3501 0.1827 0.2631 0.2041 1 + 32: 0.1380 0.5789 0.0720 0.2111 1 + 33: 0.0337 0.3311 0.2591 0.3761 1 + 34: 0.0223 0.7343 0.1750 0.0683 1 + 35: 0.0427 0.0930 0.3707 0.4936 1 + 36: 0.0977 0.1617 0.4641 0.2764 1 + 37: 0.2961 0.0907 0.3691 0.2441 1 + 38: 0.0657 0.3903 0.1537 0.3903 1 + 39: 0.1480 0.6530 0.1280 0.0710 1 + 40: 0.0290 0.4812 0.3818 0.1081 1 + 41: 0.0320 0.0373 0.7812 0.1495 1 + 42: 0.0360 0.4805 0.1446 0.3389 1 + 43: 0.0383 0.5637 0.2443 0.1537 1 + 44: 0.0310 0.1300 0.6810 0.1580 1 + 45: 0.0677 0.4333 0.1166 0.3824 1 + 46: 0.0233 0.2478 0.5731 0.1557 1 + 47: 0.0183 0.2297 0.6126 0.1394 1 + 48: 0.2707 0.2837 0.2813 0.1643 1 + 49: 0.0710 0.5793 0.1053 0.2443 1 + 50: 0.0350 0.6787 0.1257 0.1607 1 + 51: 0.0827 0.2147 0.5507 0.1520 1 + 52: 0.1386 0.4848 0.2342 0.1423 1 + 53: 0.1483 0.1796 0.5389 0.1332 1 + 54: 0.1444 0.3144 0.4065 0.1347 1 + 55: 0.0290 0.1666 0.3709 0.4335 1 + 56: 0.2157 0.5150 0.1827 0.0867 1 + 57: 0.2577 0.1053 0.5113 0.1257 1 + 58: 0.2523 0.2743 0.3310 0.1423 1 + 59: 0.0987 0.1863 0.3113 0.4037 1 + 60: 0.0570 0.1074 0.6309 0.2047 1 + 61: 0.0870 0.2064 0.5098 0.1968 1 + 62: 0.4127 0.1613 0.1707 0.2553 1 + 63: 0.2143 0.5343 0.1460 0.1053 1 + 64: 0.0493 0.5527 0.1890 0.2090 1 + 65: 0.0243 0.7694 0.0577 0.1486 1 + 66: 0.1204 0.6542 0.0987 0.1267 1 + 67: 0.0673 0.5463 0.1063 0.2800 1 + 68: 0.0774 0.7189 0.0980 0.1057 1 + 69: 0.1157 0.2187 0.1457 0.5199 1 + 70: 0.0960 0.1761 0.5365 0.1914 1 + 71: 0.0357 0.5869 0.2764 0.1010 1 + 72: 0.0203 0.3213 0.5313 0.1270 1 + 73: 0.0260 0.8733 0.0413 0.0594 1 + 74: 0.0827 0.3486 0.1845 0.3842 1 + 75: 0.0480 0.7050 0.1280 0.1190 1 + 76: 0.0740 0.7417 0.0497 0.1347 1 + 77: 0.0417 0.1573 0.1996 0.6015 1 + 78: 0.0247 0.1137 0.4636 0.3979 1 + 79: 0.0320 0.5327 0.2847 0.1507 1 + 80: 0.0670 0.1438 0.1254 0.6637 1 + 81: 0.0557 0.3703 0.1677 0.4063 1 + 82: 0.6577 0.0573 0.1450 0.1400 1 + 83: 0.4242 0.1516 0.1996 0.2246 1 + 84: 0.0453 0.6512 0.1717 0.1317 1 + 85: 0.3568 0.1499 0.3388 0.1546 1 + 86: 0.0443 0.0970 0.2526 0.6061 1 + 87: 0.0353 0.8647 0.0313 0.0687 1 + 88: 0.1314 0.1697 0.3258 0.3731 1 + 89: 0.2110 0.5890 0.0723 0.1277 1 + 90: 0.0187 0.6874 0.2149 0.0790 1 + 91: 0.0634 0.6812 0.1530 0.1024 1 + 92: 0.0173 0.9024 0.0387 0.0417 1 + 93: 0.0867 0.2813 0.1523 0.4797 1 + 94: 0.0563 0.0477 0.7427 0.1533 1 + 95: 0.6130 0.1973 0.0847 0.1050 1 + 96: 0.1246 0.1063 0.6066 0.1625 1 + 97: 0.1923 0.2299 0.4572 0.1206 1 + 98: 0.4688 0.0776 0.3385 0.1150 1 + 99: 0.2752 0.0317 0.5607 0.1324 1 +100: 0.5799 0.1404 0.1737 0.1060 1 +101: 0.1310 0.1010 0.5158 0.2523 1 +102: 0.0297 0.1083 0.6970 0.1650 1 +103: 0.0530 0.0757 0.6678 0.2035 1 +104: 0.3588 0.3521 0.1346 0.1546 1 +105: 0.2597 0.2727 0.1873 0.2803 1 +106: 0.1027 0.6070 0.0790 0.2113 1 +107: 0.5080 0.1457 0.1863 0.1600 1 +108: 0.8108 0.0363 0.0516 0.1013 1 +109: 0.7567 0.0667 0.0570 0.1197 1 +110: 0.6852 0.0250 0.0867 0.2031 1 +111: 0.8686 0.0370 0.0537 0.0407 1 +112: 0.2303 0.0570 0.2527 0.4600 1 +113: 0.8351 0.0563 0.0420 0.0666 1 +114: 0.2933 0.0533 0.1486 0.5047 1 +115: 0.5839 0.0644 0.0684 0.2834 1 +116: 0.8780 0.0337 0.0297 0.0587 1 +117: 0.8693 0.0440 0.0357 0.0510 1 +118: 0.9080 0.0270 0.0353 0.0297 1 +119: 0.8356 0.0220 0.0397 0.1027 1 +120: 0.8111 0.0676 0.0490 0.0723 1 +121: 0.6813 0.0703 0.0823 0.1660 1 +122: 0.9224 0.0170 0.0213 0.0393 1 +123: 0.7881 0.0453 0.0590 0.1076 1 +124: 0.8580 0.0410 0.0280 0.0730 1 +125: 0.8966 0.0317 0.0303 0.0413 1 +126: 0.5709 0.0263 0.0857 0.3171 1 +127: 0.8940 0.0200 0.0327 0.0533 1 +128: 0.4125 0.0387 0.1080 0.4408 1 +129: 0.5349 0.0540 0.0967 0.3144 1 +130: 0.5917 0.1500 0.0650 0.1933 1 +131: 0.8477 0.0670 0.0390 0.0463 1 +132: 0.8307 0.0373 0.0393 0.0926 1 +133: 0.8247 0.0400 0.0483 0.0870 1 +134: 0.6570 0.0420 0.0697 0.2313 1 +135: 0.7580 0.0877 0.0473 0.1070 1 +136: 0.7850 0.0607 0.0437 0.1107 1 +137: 0.8510 0.0250 0.0380 0.0860 1 +138: 0.6103 0.0460 0.0633 0.2804 1 +139: 0.6824 0.0540 0.0707 0.1929 1 +140: 0.8743 0.0303 0.0377 0.0577 1 +141: 0.7663 0.0437 0.0827 0.1074 1 +142: 0.8936 0.0360 0.0267 0.0437 1 +143: 0.8717 0.0333 0.0343 0.0607 1 +144: 0.8890 0.0193 0.0417 0.0500 1 +145: 0.7612 0.0547 0.1054 0.0787 1 +146: 0.6543 0.0697 0.0997 0.1763 1 +147: 0.5160 0.0347 0.1180 0.3313 1 +148: 0.9233 0.0297 0.0187 0.0283 1 +149: 0.8399 0.0304 0.0410 0.0887 1 diff --git a/inst/files/STRUCTUREpop_K4-combined.txt b/inst/files/STRUCTUREpop_K4-combined.txt new file mode 100644 index 0000000..b82a609 --- /dev/null +++ b/inst/files/STRUCTUREpop_K4-combined.txt @@ -0,0 +1,451 @@ +1: 0.035 0.387 0.091 0.487 1 +2: 0.036 0.824 0.071 0.069 1 +3: 0.039 0.079 0.811 0.071 1 +4: 0.036 0.716 0.084 0.165 1 +5: 0.034 0.155 0.739 0.071 1 +6: 0.031 0.830 0.081 0.058 1 +7: 0.050 0.290 0.577 0.082 1 +8: 0.052 0.113 0.581 0.253 1 +9: 0.050 0.107 0.794 0.049 1 +10: 0.024 0.133 0.807 0.036 1 +11: 0.024 0.117 0.459 0.400 1 +12: 0.029 0.121 0.706 0.144 1 +13: 0.065 0.053 0.771 0.112 1 +14: 0.040 0.202 0.216 0.541 1 +15: 0.052 0.541 0.327 0.079 1 +16: 0.145 0.044 0.740 0.071 1 +17: 0.087 0.096 0.428 0.388 1 +18: 0.028 0.065 0.872 0.035 1 +19: 0.053 0.168 0.345 0.434 1 +20: 0.055 0.315 0.521 0.109 1 +21: 0.023 0.071 0.861 0.046 1 +22: 0.030 0.059 0.843 0.068 1 +23: 0.038 0.571 0.208 0.184 1 +24: 0.071 0.435 0.057 0.437 1 +25: 0.130 0.102 0.704 0.064 1 +26: 0.052 0.114 0.783 0.050 1 +27: 0.126 0.136 0.314 0.424 1 +28: 0.058 0.261 0.245 0.436 1 +29: 0.179 0.040 0.643 0.138 1 +30: 0.381 0.122 0.239 0.258 1 +31: 0.357 0.184 0.272 0.186 1 +32: 0.143 0.578 0.048 0.231 1 +33: 0.035 0.335 0.239 0.391 1 +34: 0.023 0.738 0.198 0.041 1 +35: 0.045 0.092 0.349 0.515 1 +36: 0.101 0.166 0.495 0.237 1 +37: 0.297 0.092 0.386 0.225 1 +38: 0.068 0.383 0.113 0.436 1 +39: 0.153 0.653 0.139 0.055 1 +40: 0.030 0.493 0.423 0.054 1 +41: 0.033 0.039 0.891 0.036 1 +42: 0.038 0.475 0.113 0.375 1 +43: 0.040 0.577 0.257 0.127 1 +44: 0.032 0.132 0.775 0.061 1 +45: 0.069 0.422 0.075 0.434 1 +46: 0.024 0.257 0.641 0.077 1 +47: 0.019 0.234 0.695 0.052 1 +48: 0.271 0.286 0.298 0.144 1 +49: 0.073 0.581 0.080 0.266 1 +50: 0.036 0.680 0.123 0.160 1 +51: 0.085 0.219 0.622 0.074 1 +52: 0.143 0.490 0.252 0.116 1 +53: 0.153 0.183 0.608 0.056 1 +54: 0.150 0.323 0.446 0.080 1 +55: 0.030 0.164 0.359 0.447 1 +56: 0.221 0.523 0.194 0.062 1 +57: 0.266 0.108 0.572 0.054 1 +58: 0.255 0.276 0.361 0.108 1 +59: 0.099 0.184 0.296 0.421 1 +60: 0.060 0.110 0.703 0.126 1 +61: 0.091 0.213 0.560 0.136 1 +62: 0.414 0.160 0.154 0.271 1 +63: 0.220 0.543 0.148 0.088 1 +64: 0.051 0.547 0.188 0.214 1 +65: 0.025 0.767 0.046 0.162 1 +66: 0.124 0.657 0.093 0.125 1 +67: 0.068 0.541 0.078 0.313 1 +68: 0.081 0.719 0.100 0.100 1 +69: 0.117 0.216 0.079 0.587 1 +70: 0.100 0.182 0.591 0.127 1 +71: 0.037 0.593 0.308 0.061 1 +72: 0.021 0.330 0.601 0.048 1 +73: 0.027 0.879 0.040 0.054 1 +74: 0.085 0.344 0.151 0.419 1 +75: 0.050 0.712 0.130 0.108 1 +76: 0.077 0.737 0.038 0.148 1 +77: 0.043 0.150 0.127 0.680 1 +78: 0.026 0.109 0.470 0.395 1 +79: 0.033 0.546 0.303 0.118 1 +80: 0.069 0.133 0.032 0.766 1 +81: 0.057 0.365 0.126 0.452 1 +82: 0.650 0.058 0.148 0.144 1 +83: 0.419 0.152 0.198 0.231 1 +84: 0.046 0.656 0.181 0.117 1 +85: 0.364 0.154 0.367 0.116 1 +86: 0.046 0.093 0.191 0.670 1 +87: 0.037 0.868 0.027 0.068 1 +88: 0.131 0.170 0.316 0.382 1 +89: 0.218 0.593 0.062 0.127 1 +90: 0.019 0.685 0.248 0.048 1 +91: 0.066 0.691 0.160 0.083 1 +92: 0.018 0.908 0.041 0.034 1 +93: 0.087 0.272 0.097 0.544 1 +94: 0.058 0.049 0.846 0.047 1 +95: 0.608 0.201 0.082 0.109 1 +96: 0.129 0.111 0.681 0.079 1 +97: 0.199 0.234 0.514 0.054 1 +98: 0.478 0.079 0.371 0.072 1 +99: 0.283 0.032 0.632 0.053 1 +100: 0.585 0.144 0.181 0.089 1 +101: 0.135 0.097 0.566 0.203 1 +102: 0.031 0.111 0.791 0.067 1 +103: 0.055 0.078 0.744 0.123 1 +104: 0.358 0.350 0.133 0.159 1 +105: 0.264 0.270 0.170 0.296 1 +106: 0.106 0.603 0.057 0.234 1 +107: 0.517 0.145 0.190 0.147 1 +108: 0.807 0.037 0.045 0.112 1 +109: 0.753 0.069 0.048 0.130 1 +110: 0.675 0.025 0.071 0.229 1 +111: 0.865 0.038 0.058 0.039 1 +112: 0.226 0.053 0.220 0.501 1 +113: 0.830 0.058 0.039 0.074 1 +114: 0.278 0.049 0.090 0.583 1 +115: 0.577 0.062 0.035 0.326 1 +116: 0.874 0.035 0.026 0.065 1 +117: 0.865 0.045 0.035 0.055 1 +118: 0.906 0.028 0.037 0.029 1 +119: 0.826 0.022 0.032 0.119 1 +120: 0.805 0.069 0.046 0.080 1 +121: 0.674 0.071 0.071 0.184 1 +122: 0.919 0.017 0.019 0.044 1 +123: 0.778 0.047 0.054 0.122 1 +124: 0.852 0.042 0.022 0.084 1 +125: 0.892 0.033 0.030 0.045 1 +126: 0.560 0.025 0.048 0.367 1 +127: 0.890 0.020 0.031 0.059 1 +128: 0.406 0.035 0.052 0.508 1 +129: 0.517 0.051 0.062 0.371 1 +130: 0.577 0.151 0.044 0.228 1 +131: 0.843 0.070 0.039 0.048 1 +132: 0.825 0.038 0.032 0.105 1 +133: 0.819 0.041 0.044 0.097 1 +134: 0.642 0.043 0.047 0.268 1 +135: 0.749 0.089 0.039 0.123 1 +136: 0.781 0.062 0.034 0.123 1 +137: 0.847 0.025 0.031 0.097 1 +138: 0.594 0.045 0.030 0.330 1 +139: 0.672 0.054 0.051 0.223 1 +140: 0.871 0.031 0.035 0.062 1 +141: 0.762 0.044 0.079 0.114 1 +142: 0.889 0.037 0.025 0.048 1 +143: 0.866 0.034 0.032 0.068 1 +144: 0.884 0.020 0.042 0.054 1 +145: 0.756 0.056 0.112 0.076 1 +146: 0.641 0.070 0.089 0.200 1 +147: 0.499 0.034 0.087 0.380 1 +148: 0.920 0.031 0.018 0.031 1 +149: 0.833 0.031 0.035 0.100 1 + + +1: 0.324 0.419 0.033 0.224 1 +2: 0.080 0.820 0.033 0.067 1 +3: 0.372 0.069 0.037 0.522 1 +4: 0.140 0.720 0.033 0.107 1 +5: 0.343 0.147 0.032 0.478 1 +6: 0.081 0.814 0.029 0.076 1 +7: 0.279 0.275 0.046 0.399 1 +8: 0.384 0.115 0.049 0.453 1 +9: 0.342 0.105 0.048 0.505 1 +10: 0.349 0.122 0.022 0.507 1 +11: 0.413 0.120 0.023 0.443 1 +12: 0.380 0.111 0.027 0.481 1 +13: 0.362 0.053 0.062 0.522 1 +14: 0.396 0.218 0.038 0.348 1 +15: 0.183 0.523 0.049 0.245 1 +16: 0.338 0.043 0.139 0.481 1 +17: 0.401 0.099 0.083 0.417 1 +18: 0.368 0.057 0.025 0.550 1 +19: 0.395 0.168 0.051 0.387 1 +20: 0.277 0.302 0.051 0.370 1 +21: 0.374 0.065 0.021 0.540 1 +22: 0.380 0.051 0.027 0.542 1 +23: 0.196 0.579 0.037 0.188 1 +24: 0.291 0.441 0.068 0.199 1 +25: 0.314 0.099 0.124 0.464 1 +26: 0.343 0.104 0.050 0.503 1 +27: 0.368 0.142 0.120 0.369 1 +28: 0.352 0.265 0.056 0.327 1 +29: 0.331 0.041 0.173 0.455 1 +30: 0.246 0.126 0.369 0.260 1 +31: 0.220 0.183 0.345 0.252 1 +32: 0.158 0.583 0.135 0.123 1 +33: 0.327 0.329 0.033 0.310 1 +34: 0.116 0.726 0.022 0.136 1 +35: 0.438 0.097 0.041 0.423 1 +36: 0.328 0.159 0.096 0.416 1 +37: 0.288 0.089 0.296 0.327 1 +38: 0.297 0.398 0.064 0.241 1 +39: 0.096 0.651 0.145 0.108 1 +40: 0.211 0.469 0.028 0.291 1 +41: 0.376 0.035 0.031 0.557 1 +42: 0.278 0.484 0.035 0.203 1 +43: 0.183 0.559 0.037 0.220 1 +44: 0.344 0.125 0.030 0.501 1 +45: 0.292 0.440 0.067 0.202 1 +46: 0.303 0.242 0.023 0.432 1 +47: 0.312 0.219 0.018 0.451 1 +48: 0.209 0.277 0.272 0.242 1 +49: 0.199 0.575 0.069 0.157 1 +50: 0.157 0.673 0.034 0.136 1 +51: 0.302 0.210 0.080 0.408 1 +52: 0.180 0.480 0.136 0.204 1 +53: 0.286 0.174 0.145 0.396 1 +54: 0.242 0.304 0.140 0.314 1 +55: 0.427 0.164 0.028 0.381 1 +56: 0.133 0.509 0.213 0.145 1 +57: 0.269 0.102 0.254 0.375 1 +58: 0.211 0.272 0.250 0.267 1 +59: 0.370 0.186 0.098 0.346 1 +60: 0.348 0.106 0.055 0.491 1 +61: 0.314 0.200 0.085 0.400 1 +62: 0.220 0.163 0.410 0.207 1 +63: 0.125 0.530 0.210 0.136 1 +64: 0.205 0.553 0.048 0.194 1 +65: 0.128 0.764 0.024 0.084 1 +66: 0.116 0.653 0.118 0.113 1 +67: 0.225 0.546 0.067 0.163 1 +68: 0.105 0.721 0.074 0.099 1 +69: 0.384 0.220 0.115 0.281 1 +70: 0.317 0.172 0.093 0.418 1 +71: 0.177 0.577 0.035 0.211 1 +72: 0.279 0.312 0.020 0.389 1 +73: 0.060 0.869 0.025 0.045 1 +74: 0.314 0.354 0.082 0.249 1 +75: 0.128 0.698 0.046 0.128 1 +76: 0.108 0.745 0.072 0.075 1 +77: 0.457 0.159 0.041 0.344 1 +78: 0.423 0.117 0.024 0.435 1 +79: 0.201 0.522 0.031 0.246 1 +80: 0.464 0.156 0.066 0.313 1 +81: 0.324 0.370 0.054 0.252 1 +82: 0.137 0.057 0.663 0.143 1 +83: 0.212 0.152 0.430 0.207 1 +84: 0.160 0.638 0.045 0.157 1 +85: 0.217 0.149 0.350 0.284 1 +86: 0.468 0.103 0.044 0.386 1 +87: 0.063 0.861 0.034 0.042 1 +88: 0.343 0.172 0.132 0.353 1 +89: 0.113 0.588 0.205 0.094 1 +90: 0.137 0.685 0.018 0.160 1 +91: 0.122 0.676 0.061 0.140 1 +92: 0.047 0.899 0.017 0.037 1 +93: 0.358 0.290 0.086 0.266 1 +94: 0.365 0.045 0.055 0.535 1 +95: 0.098 0.195 0.617 0.090 1 +96: 0.327 0.099 0.122 0.453 1 +97: 0.247 0.226 0.188 0.339 1 +98: 0.199 0.077 0.465 0.259 1 +99: 0.286 0.031 0.273 0.409 1 +100: 0.133 0.138 0.576 0.153 1 +101: 0.343 0.103 0.129 0.425 1 +102: 0.361 0.103 0.029 0.507 1 +103: 0.366 0.075 0.051 0.507 1 +104: 0.152 0.350 0.360 0.139 1 +105: 0.243 0.273 0.258 0.226 1 +106: 0.163 0.611 0.101 0.125 1 +107: 0.169 0.148 0.502 0.182 1 +108: 0.083 0.036 0.815 0.067 1 +109: 0.095 0.065 0.762 0.078 1 +110: 0.160 0.025 0.692 0.123 1 +111: 0.044 0.036 0.871 0.048 1 +112: 0.375 0.059 0.234 0.332 1 +113: 0.056 0.055 0.840 0.049 1 +114: 0.373 0.056 0.302 0.270 1 +115: 0.206 0.065 0.591 0.137 1 +116: 0.048 0.033 0.881 0.038 1 +117: 0.046 0.043 0.872 0.039 1 +118: 0.031 0.026 0.910 0.033 1 +119: 0.080 0.022 0.841 0.057 1 +120: 0.063 0.067 0.815 0.056 1 +121: 0.135 0.069 0.687 0.109 1 +122: 0.032 0.017 0.926 0.026 1 +123: 0.085 0.044 0.799 0.072 1 +124: 0.055 0.040 0.864 0.041 1 +125: 0.036 0.031 0.900 0.032 1 +126: 0.230 0.027 0.580 0.162 1 +127: 0.045 0.020 0.897 0.038 1 +128: 0.321 0.041 0.417 0.221 1 +129: 0.230 0.056 0.546 0.167 1 +130: 0.143 0.148 0.600 0.109 1 +131: 0.044 0.065 0.851 0.040 1 +132: 0.073 0.037 0.835 0.055 1 +133: 0.072 0.039 0.830 0.059 1 +134: 0.171 0.042 0.671 0.116 1 +135: 0.085 0.086 0.764 0.065 1 +136: 0.087 0.060 0.788 0.065 1 +137: 0.067 0.025 0.855 0.053 1 +138: 0.200 0.047 0.624 0.130 1 +139: 0.144 0.054 0.690 0.112 1 +140: 0.049 0.030 0.876 0.044 1 +141: 0.095 0.043 0.770 0.092 1 +142: 0.037 0.035 0.896 0.031 1 +143: 0.050 0.033 0.876 0.041 1 +144: 0.045 0.019 0.893 0.043 1 +145: 0.087 0.053 0.765 0.094 1 +146: 0.145 0.069 0.663 0.123 1 +147: 0.249 0.035 0.534 0.181 1 +148: 0.024 0.029 0.925 0.021 1 +149: 0.071 0.030 0.845 0.054 1 + + +1: 0.417 0.034 0.465 0.085 1 +2: 0.821 0.034 0.073 0.071 1 +3: 0.076 0.037 0.067 0.819 1 +4: 0.730 0.034 0.160 0.076 1 +5: 0.152 0.033 0.071 0.743 1 +6: 0.821 0.030 0.067 0.082 1 +7: 0.276 0.048 0.108 0.568 1 +8: 0.118 0.050 0.254 0.578 1 +9: 0.106 0.049 0.058 0.787 1 +10: 0.127 0.022 0.036 0.814 1 +11: 0.117 0.023 0.415 0.445 1 +12: 0.115 0.028 0.136 0.722 1 +13: 0.053 0.062 0.126 0.760 1 +14: 0.201 0.038 0.552 0.209 1 +15: 0.526 0.049 0.096 0.328 1 +16: 0.044 0.138 0.072 0.745 1 +17: 0.099 0.083 0.379 0.439 1 +18: 0.061 0.026 0.036 0.877 1 +19: 0.176 0.051 0.427 0.346 1 +20: 0.306 0.052 0.115 0.527 1 +21: 0.069 0.022 0.044 0.865 1 +22: 0.056 0.028 0.067 0.849 1 +23: 0.576 0.038 0.181 0.205 1 +24: 0.441 0.068 0.436 0.055 1 +25: 0.100 0.126 0.082 0.692 1 +26: 0.108 0.051 0.052 0.789 1 +27: 0.136 0.120 0.431 0.313 1 +28: 0.266 0.054 0.443 0.236 1 +29: 0.042 0.171 0.151 0.637 1 +30: 0.123 0.370 0.273 0.234 1 +31: 0.181 0.348 0.206 0.265 1 +32: 0.575 0.136 0.244 0.045 1 +33: 0.329 0.033 0.410 0.228 1 +34: 0.739 0.022 0.048 0.191 1 +35: 0.090 0.042 0.528 0.340 1 +36: 0.160 0.096 0.264 0.481 1 +37: 0.091 0.295 0.219 0.394 1 +38: 0.390 0.065 0.438 0.107 1 +39: 0.655 0.146 0.062 0.137 1 +40: 0.481 0.029 0.059 0.431 1 +41: 0.038 0.032 0.036 0.895 1 +42: 0.483 0.035 0.364 0.118 1 +43: 0.555 0.038 0.151 0.256 1 +44: 0.133 0.031 0.069 0.767 1 +45: 0.438 0.067 0.421 0.073 1 +46: 0.244 0.023 0.087 0.645 1 +47: 0.236 0.018 0.054 0.691 1 +48: 0.288 0.269 0.140 0.304 1 +49: 0.582 0.071 0.268 0.079 1 +50: 0.683 0.035 0.165 0.118 1 +51: 0.215 0.083 0.080 0.622 1 +52: 0.485 0.137 0.131 0.247 1 +53: 0.182 0.147 0.058 0.613 1 +54: 0.316 0.143 0.082 0.459 1 +55: 0.172 0.029 0.427 0.373 1 +56: 0.513 0.213 0.065 0.209 1 +57: 0.106 0.253 0.054 0.587 1 +58: 0.275 0.252 0.108 0.365 1 +59: 0.189 0.099 0.420 0.292 1 +60: 0.106 0.056 0.140 0.698 1 +61: 0.206 0.085 0.140 0.569 1 +62: 0.161 0.414 0.275 0.151 1 +63: 0.530 0.213 0.103 0.154 1 +64: 0.558 0.049 0.208 0.185 1 +65: 0.778 0.024 0.156 0.043 1 +66: 0.652 0.119 0.139 0.090 1 +67: 0.552 0.067 0.302 0.078 1 +68: 0.716 0.077 0.112 0.095 1 +69: 0.220 0.115 0.588 0.077 1 +70: 0.174 0.095 0.130 0.600 1 +71: 0.590 0.035 0.065 0.310 1 +72: 0.322 0.020 0.054 0.604 1 +73: 0.871 0.026 0.064 0.039 1 +74: 0.347 0.081 0.419 0.153 1 +75: 0.705 0.048 0.121 0.126 1 +76: 0.743 0.073 0.148 0.036 1 +77: 0.163 0.041 0.668 0.128 1 +78: 0.115 0.024 0.375 0.485 1 +79: 0.530 0.032 0.133 0.305 1 +80: 0.142 0.066 0.760 0.031 1 +81: 0.376 0.056 0.443 0.125 1 +82: 0.057 0.660 0.139 0.144 1 +83: 0.151 0.424 0.231 0.194 1 +84: 0.659 0.045 0.118 0.177 1 +85: 0.147 0.357 0.131 0.366 1 +86: 0.095 0.043 0.680 0.181 1 +87: 0.865 0.035 0.075 0.025 1 +88: 0.167 0.131 0.394 0.308 1 +89: 0.586 0.210 0.143 0.061 1 +90: 0.693 0.019 0.052 0.237 1 +91: 0.676 0.063 0.102 0.159 1 +92: 0.901 0.017 0.044 0.038 1 +93: 0.282 0.087 0.537 0.094 1 +94: 0.049 0.056 0.048 0.848 1 +95: 0.196 0.614 0.108 0.082 1 +96: 0.109 0.123 0.082 0.687 1 +97: 0.230 0.190 0.061 0.519 1 +98: 0.077 0.464 0.074 0.386 1 +99: 0.032 0.269 0.058 0.640 1 +100: 0.139 0.578 0.096 0.187 1 +101: 0.103 0.129 0.211 0.557 1 +102: 0.111 0.029 0.067 0.793 1 +103: 0.074 0.053 0.121 0.752 1 +104: 0.357 0.359 0.153 0.132 1 +105: 0.275 0.257 0.302 0.166 1 +106: 0.607 0.101 0.237 0.055 1 +107: 0.144 0.505 0.164 0.187 1 +108: 0.036 0.812 0.109 0.043 1 +109: 0.066 0.755 0.134 0.045 1 +110: 0.025 0.688 0.220 0.066 1 +111: 0.037 0.869 0.039 0.055 1 +112: 0.059 0.231 0.504 0.206 1 +113: 0.056 0.836 0.070 0.038 1 +114: 0.055 0.300 0.558 0.086 1 +115: 0.066 0.583 0.318 0.033 1 +116: 0.033 0.879 0.063 0.025 1 +117: 0.044 0.871 0.052 0.033 1 +118: 0.027 0.908 0.029 0.036 1 +119: 0.022 0.838 0.109 0.030 1 +120: 0.067 0.814 0.074 0.045 1 +121: 0.071 0.683 0.179 0.067 1 +122: 0.017 0.923 0.042 0.019 1 +123: 0.045 0.789 0.116 0.051 1 +124: 0.041 0.859 0.080 0.021 1 +125: 0.031 0.897 0.043 0.029 1 +126: 0.027 0.572 0.354 0.047 1 +127: 0.020 0.895 0.056 0.029 1 +128: 0.040 0.415 0.494 0.051 1 +129: 0.055 0.541 0.342 0.061 1 +130: 0.151 0.598 0.209 0.042 1 +131: 0.066 0.849 0.047 0.038 1 +132: 0.037 0.833 0.100 0.031 1 +133: 0.040 0.826 0.092 0.042 1 +134: 0.041 0.658 0.255 0.046 1 +135: 0.088 0.761 0.113 0.038 1 +136: 0.060 0.786 0.122 0.032 1 +137: 0.025 0.851 0.094 0.030 1 +138: 0.046 0.613 0.311 0.030 1 +139: 0.054 0.686 0.212 0.049 1 +140: 0.030 0.875 0.062 0.034 1 +141: 0.044 0.766 0.113 0.077 1 +142: 0.036 0.894 0.046 0.024 1 +143: 0.033 0.873 0.064 0.030 1 +144: 0.019 0.890 0.051 0.040 1 +145: 0.055 0.761 0.073 0.110 1 +146: 0.070 0.659 0.184 0.087 1 +147: 0.035 0.515 0.365 0.086 1 +148: 0.029 0.924 0.030 0.017 1 +149: 0.030 0.840 0.095 0.034 1 diff --git a/inst/files/Structure239_2 b/inst/files/Structure239_2 new file mode 100644 index 0000000..01e5e3b --- /dev/null +++ b/inst/files/Structure239_2 @@ -0,0 +1,636 @@ + + +---------------------------------------------------- +STRUCTURE by Pritchard, Stephens and Donnelly (2000) + and Falush, Stephens and Pritchard (2003) + Code by Pritchard, Falush and Hubisz + Version 2.3.2.1 (Oct 2009) +---------------------------------------------------- + + + +Command line arguments: bin\structure -m E:\AU\Alexander\alex3\STRUCTURE\alex3\long\mainparams -e E:\AU\Alexander\alex3\STRUCTURE\alex3\long\extraparams +Input File: E:\AU\Alexander\alex3\STRUCTURE\alex3\project_data + +Run parameters: + 239 individuals + 24 loci + 3 populations assumed + 100000 Burn-in period + 1000000 Reps + + +-------------------------------------------- +Overall proportion of membership of the +sample in each of the 3 clusters + +Inferred Clusters + 1 2 3 +0.372 0.348 0.280 + +-------------------------------------------- + +Allele-freq. divergence among pops (Net nucleotide distance), +computed using point estimates of P. + + 1 2 3 + 1 - 0.1941 0.0315 + 2 0.1941 - 0.2830 + 3 0.0315 0.2830 - + +Average distances (expected heterozygosity) between individuals in same cluster: +cluster 1 : 0.4859 +cluster 2 : 0.4867 +cluster 3 : 0.4502 + +-------------------------------------------- +Estimated Ln Prob of Data = -12068.0 +Mean value of ln likelihood = -11852.6 +Variance of ln likelihood = 430.7 +Mean value of alpha = 0.1955 + +Mean value of Fst_1 = 0.1755 +Mean value of Fst_2 = 0.2232 +Mean value of Fst_3 = 0.1559 + + +Inferred ancestry of individuals: + Label (%Miss) : Inferred clusters + 1 I13825 (0) : 0.749 0.173 0.078 + 2 I13826 (0) : 0.489 0.389 0.122 + 3 I13827 (20) : 0.864 0.080 0.056 + 4 I13828 (0) : 0.856 0.082 0.062 + 5 I13829 (8) : 0.940 0.030 0.030 + 6 I13830 (0) : 0.612 0.309 0.079 + 7 I13831 (0) : 0.918 0.040 0.042 + 8 I13832 (16) : 0.905 0.016 0.080 + 9 I13833 (0) : 0.938 0.022 0.040 + 10 I13834 (0) : 0.922 0.054 0.024 + 11 I13835 (0) : 0.946 0.026 0.029 + 12 I13836 (0) : 0.917 0.041 0.042 + 13 I13377 (0) : 0.882 0.017 0.102 + 14 I13378 (0) : 0.842 0.029 0.129 + 15 I13379 (0) : 0.865 0.077 0.058 + 16 I13380 (0) : 0.835 0.021 0.144 + 17 I13381 (0) : 0.832 0.047 0.121 + 18 I13382 (0) : 0.929 0.045 0.026 + 19 I13383 (0) : 0.765 0.049 0.185 + 20 I13384 (0) : 0.880 0.048 0.072 + 21 I13385 (0) : 0.967 0.011 0.022 + 22 I13386 (0) : 0.761 0.176 0.063 + 23 I13387 (0) : 0.727 0.209 0.064 + 24 I13388 (0) : 0.318 0.149 0.533 + 25 I13389 (0) : 0.889 0.010 0.101 + 26 I13390 (0) : 0.918 0.032 0.050 + 27 I13391 (0) : 0.705 0.039 0.257 + 28 I13392 (0) : 0.854 0.027 0.119 + 29 I13393 (0) : 0.719 0.014 0.267 + 30 I13394 (4) : 0.407 0.026 0.567 + 31 I13395 (0) : 0.516 0.036 0.448 + 32 I13396 (0) : 0.616 0.044 0.340 + 33 I13397 (0) : 0.767 0.176 0.058 + 34 I13398 (0) : 0.896 0.070 0.035 + 35 I13399 (4) : 0.687 0.142 0.171 + 36 I13400 (0) : 0.824 0.026 0.150 + 37 I13401 (0) : 0.588 0.013 0.399 + 38 I13402 (0) : 0.764 0.068 0.168 + 39 I13403 (0) : 0.790 0.026 0.184 + 40 I13404 (0) : 0.895 0.074 0.031 + 41 I13405 (0) : 0.945 0.012 0.044 + 42 I13406 (16) : 0.880 0.083 0.037 + 43 I13407 (0) : 0.745 0.172 0.084 + 44 I13408 (0) : 0.959 0.011 0.029 + 45 I13409 (0) : 0.781 0.025 0.194 + 46 I13410 (0) : 0.830 0.140 0.030 + 47 I13411 (0) : 0.790 0.187 0.023 + 48 I13412 (0) : 0.585 0.025 0.390 + 49 I13413 (0) : 0.616 0.099 0.286 + 50 I13414 (0) : 0.577 0.273 0.150 + 51 I13415 (4) : 0.890 0.023 0.087 + 52 I13416 (4) : 0.789 0.020 0.190 + 53 I13417 (4) : 0.807 0.034 0.159 + 54 I13418 (0) : 0.604 0.117 0.279 + 55 I13419 (0) : 0.745 0.181 0.074 + 56 I13420 (0) : 0.627 0.087 0.286 + 57 I13421 (0) : 0.760 0.010 0.229 + 58 I13422 (0) : 0.609 0.048 0.343 + 59 I13423 (0) : 0.692 0.026 0.282 + 60 I13424 (0) : 0.901 0.030 0.068 + 61 I13425 (0) : 0.851 0.051 0.098 + 62 I13426 (0) : 0.386 0.012 0.602 + 63 I13870 (0) : 0.288 0.191 0.522 + 64 I13871 (12) : 0.882 0.034 0.084 + 65 I13872 (0) : 0.626 0.224 0.150 + 66 I13873 (4) : 0.610 0.078 0.313 + 67 I13874 (0) : 0.291 0.308 0.401 + 68 I13875 (8) : 0.561 0.212 0.227 + 69 I13876 (0) : 0.096 0.227 0.676 + 70 I13877 (20) : 0.746 0.146 0.108 + 71 I13878 (29) : 0.830 0.109 0.061 + 72 I13879 (4) : 0.922 0.054 0.024 + 73 I13880 (4) : 0.441 0.363 0.196 + 74 I13881 (0) : 0.209 0.332 0.459 + 75 I13882 (0) : 0.711 0.178 0.111 + 76 I13883 (4) : 0.218 0.329 0.452 + 77 I13884 (16) : 0.555 0.149 0.296 + 78 I13885 (16) : 0.813 0.156 0.030 + 79 I13886 (8) : 0.811 0.144 0.045 + 80 I13887 (0) : 0.282 0.160 0.558 + 81 I13888 (0) : 0.555 0.130 0.315 + 82 I13889 (0) : 0.313 0.018 0.670 + 83 I13890 (33) : 0.445 0.026 0.528 + 84 I13891 (0) : 0.876 0.050 0.074 + 85 I13892 (0) : 0.597 0.015 0.388 + 86 I13893 (8) : 0.522 0.209 0.269 + 87 I13894 (0) : 0.493 0.311 0.196 + 88 I13895 (4) : 0.515 0.092 0.394 + 89 I13896 (0) : 0.466 0.111 0.423 + 90 I13897 (0) : 0.757 0.219 0.024 + 91 I13898 (4) : 0.697 0.190 0.114 + 92 I13899 (0) : 0.502 0.452 0.046 + 93 I13900 (33) : 0.319 0.238 0.443 + 94 I13837 (0) : 0.901 0.030 0.070 + 95 I13838 (0) : 0.163 0.057 0.780 + 96 I13839 (0) : 0.747 0.070 0.183 + 97 I13840 (0) : 0.829 0.010 0.161 + 98 I13841 (0) : 0.567 0.014 0.419 + 99 I13842 (0) : 0.520 0.014 0.466 +100 I13843 (4) : 0.347 0.019 0.634 +101 I13844 (16) : 0.850 0.021 0.129 +102 I13845 (0) : 0.949 0.018 0.033 +103 I13846 (0) : 0.948 0.010 0.043 +104 I13847 (0) : 0.265 0.094 0.641 +105 I13848 (0) : 0.599 0.009 0.392 +106 I13849 (0) : 0.419 0.149 0.432 +107 I13850 (0) : 0.623 0.010 0.367 +108 I12577 (4) : 0.040 0.011 0.949 +109 I12578 (4) : 0.077 0.018 0.905 +110 I12579 (8) : 0.072 0.015 0.913 +111 I12580 (8) : 0.057 0.010 0.933 +112 I12581 (4) : 0.444 0.011 0.545 +113 I12582 (4) : 0.047 0.007 0.946 +114 I12583 (8) : 0.169 0.019 0.811 +115 I12584 (4) : 0.097 0.010 0.894 +116 I12585 (4) : 0.032 0.010 0.957 +117 I12586 (4) : 0.040 0.010 0.950 +118 I12587 (8) : 0.039 0.010 0.951 +119 I12588 (4) : 0.031 0.012 0.957 +120 I12589 (0) : 0.053 0.028 0.919 +121 I12590 (0) : 0.073 0.021 0.905 +122 I12591 (12) : 0.018 0.012 0.970 +123 I12592 (4) : 0.047 0.027 0.927 +124 I12593 (4) : 0.022 0.014 0.964 +125 I12594 (8) : 0.024 0.013 0.963 +126 I12595 (0) : 0.121 0.009 0.870 +127 I12596 (0) : 0.028 0.007 0.965 +128 I12597 (4) : 0.072 0.016 0.912 +129 I12598 (0) : 0.150 0.015 0.835 +130 I12599 (0) : 0.083 0.035 0.882 +131 I12600 (4) : 0.063 0.014 0.923 +132 I12601 (8) : 0.034 0.014 0.952 +133 I12602 (12) : 0.050 0.009 0.940 +134 I12603 (0) : 0.053 0.012 0.936 +135 I12604 (4) : 0.067 0.019 0.914 +136 I12605 (4) : 0.059 0.014 0.927 +137 I12606 (8) : 0.027 0.019 0.954 +138 I12607 (4) : 0.046 0.034 0.920 +139 I12608 (8) : 0.052 0.011 0.938 +140 I12609 (8) : 0.029 0.011 0.960 +141 I12610 (50) : 0.061 0.015 0.924 +142 I12611 (0) : 0.021 0.007 0.972 +143 I12612 (0) : 0.031 0.009 0.960 +144 I12613 (0) : 0.041 0.014 0.945 +145 I12614 (4) : 0.089 0.031 0.880 +146 I12615 (0) : 0.126 0.020 0.853 +147 I12616 (4) : 0.109 0.031 0.860 +148 I12617 (4) : 0.019 0.011 0.970 +149 I12618 (45) : 0.031 0.015 0.954 +150 I14107 (0) : 0.279 0.613 0.108 +151 I14108 (4) : 0.031 0.903 0.066 +152 I14109 (0) : 0.244 0.610 0.145 +153 I14110 (0) : 0.074 0.880 0.046 +154 I14111 (25) : 0.406 0.488 0.106 +155 I14113 (0) : 0.012 0.978 0.009 +156 I14114 (0) : 0.055 0.900 0.045 +157 I14115 (8) : 0.408 0.542 0.050 +158 I14116 (0) : 0.123 0.817 0.060 +159 I14117 (0) : 0.267 0.619 0.115 +160 I14118 (0) : 0.045 0.908 0.047 +161 I14119 (20) : 0.287 0.643 0.070 +162 I14120 (4) : 0.025 0.920 0.054 +163 I14121 (8) : 0.190 0.752 0.058 +164 I14122 (4) : 0.015 0.974 0.011 +165 I14123 (0) : 0.124 0.751 0.125 +166 I14124 (4) : 0.190 0.698 0.112 +167 I14125 (4) : 0.355 0.615 0.030 +168 I14126 (0) : 0.289 0.653 0.058 +169 I14127 (0) : 0.043 0.938 0.019 +170 I14128 (0) : 0.223 0.718 0.058 +171 I14129 (0) : 0.088 0.857 0.055 +172 I14130 (0) : 0.181 0.677 0.142 +173 I14131 (20) : 0.172 0.674 0.155 +174 I14132 (33) : 0.411 0.452 0.137 +175 I14017 (0) : 0.273 0.618 0.109 +176 I14018 (25) : 0.095 0.820 0.085 +177 I14019 (0) : 0.252 0.702 0.046 +178 I14020 (0) : 0.479 0.485 0.036 +179 I14021 (0) : 0.197 0.690 0.113 +180 I14022 (0) : 0.107 0.854 0.038 +181 I14023 (0) : 0.130 0.848 0.023 +182 I14024 (12) : 0.068 0.425 0.507 +183 I14025 (0) : 0.057 0.823 0.120 +184 I14026 (0) : 0.324 0.638 0.038 +185 I14027 (0) : 0.324 0.579 0.097 +186 I14028 (4) : 0.079 0.866 0.055 +187 I14029 (4) : 0.115 0.794 0.091 +188 I14030 (0) : 0.503 0.467 0.030 +189 I14031 (4) : 0.051 0.929 0.020 +190 I14032 (0) : 0.240 0.647 0.113 +191 I14033 (0) : 0.260 0.712 0.027 +192 I14034 (8) : 0.160 0.808 0.031 +193 I14035 (4) : 0.122 0.789 0.089 +194 I14036 (0) : 0.446 0.524 0.031 +195 I14037 (0) : 0.127 0.591 0.282 +196 I14038 (0) : 0.128 0.764 0.108 +197 I14039 (4) : 0.332 0.647 0.021 +198 I14040 (8) : 0.064 0.770 0.166 +199 I14041 (4) : 0.016 0.925 0.059 +200 I14042 (4) : 0.260 0.688 0.052 +201 I14043 (0) : 0.052 0.904 0.043 +202 I14044 (0) : 0.012 0.978 0.010 +203 I14045 (4) : 0.009 0.985 0.006 +204 I14046 (0) : 0.019 0.968 0.013 +205 I14047 (4) : 0.019 0.914 0.067 +206 I14048 (0) : 0.017 0.956 0.027 +207 I14049 (0) : 0.023 0.950 0.027 +208 I14050 (0) : 0.013 0.976 0.011 +209 I14051 (0) : 0.012 0.980 0.007 +210 I14052 (0) : 0.633 0.304 0.063 +211 I14054 (4) : 0.272 0.486 0.242 +212 I14055 (4) : 0.741 0.240 0.019 +213 I14056 (0) : 0.262 0.590 0.148 +214 I14057 (0) : 0.035 0.946 0.019 +215 I14058 (0) : 0.030 0.946 0.024 +216 I14059 (4) : 0.015 0.966 0.020 +217 I14060 (16) : 0.018 0.967 0.015 +218 I14062 (0) : 0.018 0.967 0.015 +219 I14063 (0) : 0.009 0.984 0.007 +220 I14064 (4) : 0.009 0.985 0.006 +221 I14065 (0) : 0.011 0.981 0.008 +222 I14066 (0) : 0.053 0.916 0.031 +223 I14067 (8) : 0.018 0.967 0.015 +224 I14068 (4) : 0.029 0.910 0.060 +225 I14069 (0) : 0.015 0.976 0.009 +226 I14070 (4) : 0.014 0.977 0.010 +227 I14071 (0) : 0.010 0.983 0.007 +228 I14072 (0) : 0.014 0.974 0.013 +229 I14073 (0) : 0.114 0.866 0.019 +230 I14074 (0) : 0.026 0.950 0.024 +231 I14075 (0) : 0.011 0.980 0.008 +232 I14076 (4) : 0.028 0.955 0.017 +233 I14077 (4) : 0.067 0.919 0.014 +234 I14078 (0) : 0.024 0.963 0.014 +235 I14079 (0) : 0.022 0.964 0.014 +236 I14080 (0) : 0.015 0.965 0.020 +237 I14081 (4) : 0.068 0.902 0.030 +238 I14082 (0) : 0.017 0.971 0.011 +239 I14083 (4) : 0.071 0.815 0.114 + + +Estimated Allele Frequencies in each cluster +First column gives estimated ancestral frequencies + + +Locus 1 : A8 +8 alleles +5.0% missing data + 177 (0.352) 0.492 0.125 0.586 + 179 (0.124) 0.133 0.017 0.051 + 175 (0.138) 0.197 0.690 0.008 + 173 (0.100) 0.057 0.150 0.008 + 181 (0.142) 0.094 0.009 0.303 + 165 (0.064) 0.009 0.003 0.034 + 183 (0.044) 0.014 0.001 0.007 + 171 (0.036) 0.004 0.003 0.002 + +Locus 2 : A14 +5 alleles +0.4% missing data + 112 (0.264) 0.256 0.900 0.028 + 110 (0.522) 0.726 0.046 0.845 + 114 (0.078) 0.010 0.049 0.006 + 118 (0.072) 0.005 0.002 0.086 + 116 (0.063) 0.003 0.003 0.035 + +Locus 3 : A24 +6 alleles +2.5% missing data + 104 (0.329) 0.376 0.321 0.378 + 106 (0.452) 0.603 0.570 0.562 + 101 (0.036) 0.006 0.001 0.002 + 108 (0.064) 0.010 0.055 0.006 + 96 (0.079) 0.003 0.041 0.050 + 102 (0.040) 0.002 0.012 0.002 + +Locus 4 : A29 +31 alleles +6.7% missing data + 143 (0.038) 0.050 0.215 0.003 + 149 (0.041) 0.027 0.008 0.060 + 147 (0.036) 0.004 0.051 0.032 + 153 (0.053) 0.083 0.035 0.084 + 169 (0.037) 0.045 0.003 0.048 + 151 (0.040) 0.062 0.007 0.036 + 145 (0.038) 0.006 0.088 0.021 + 157 (0.043) 0.069 0.006 0.152 + 155 (0.060) 0.081 0.074 0.174 + 159 (0.051) 0.088 0.061 0.043 + 161 (0.035) 0.081 0.036 0.005 + 141 (0.041) 0.027 0.243 0.008 + 139 (0.028) 0.009 0.043 0.002 + 144 (0.021) 0.045 0.001 0.001 + 171 (0.036) 0.078 0.004 0.032 + 163 (0.037) 0.111 0.002 0.051 + 167 (0.047) 0.026 0.035 0.060 + 173 (0.024) 0.026 0.001 0.005 + 142 (0.019) 0.005 0.002 0.002 + 177 (0.025) 0.004 0.001 0.035 + 175 (0.024) 0.005 0.001 0.019 + 165 (0.048) 0.037 0.041 0.044 + 146 (0.020) 0.023 0.001 0.001 + 137 (0.021) 0.002 0.001 0.014 + 183 (0.020) 0.001 0.000 0.016 + 179 (0.021) 0.001 0.000 0.016 + 191 (0.019) 0.001 0.000 0.008 + 185 (0.019) 0.001 0.000 0.008 + 180 (0.020) 0.001 0.000 0.017 + 129 (0.020) 0.001 0.039 0.001 + 187 (0.018) 0.002 0.003 0.003 + +Locus 5 : A43 +7 alleles +2.1% missing data + 123 (0.152) 0.127 0.024 0.170 + 141 (0.046) 0.003 0.047 0.002 + 137 (0.542) 0.835 0.777 0.694 + 139 (0.130) 0.030 0.143 0.063 + 124 (0.045) 0.001 0.001 0.052 + 143 (0.050) 0.002 0.006 0.010 + 128 (0.035) 0.001 0.001 0.008 + +Locus 6 : A79 +13 alleles +2.9% missing data + 103 (0.173) 0.332 0.256 0.198 + 97 (0.128) 0.095 0.435 0.068 + 101 (0.115) 0.177 0.222 0.034 + 107 (0.108) 0.151 0.031 0.072 + 109 (0.073) 0.075 0.002 0.087 + 105 (0.136) 0.122 0.042 0.383 + 111 (0.051) 0.015 0.001 0.036 + 113 (0.035) 0.004 0.004 0.007 + 91 (0.037) 0.001 0.001 0.063 + 99 (0.049) 0.012 0.001 0.025 + 115 (0.036) 0.009 0.001 0.013 + 117 (0.030) 0.002 0.002 0.005 + 121 (0.029) 0.001 0.001 0.007 + +Locus 7 : A88 +9 alleles +6.3% missing data + 133 (0.049) 0.003 0.023 0.003 + 149 (0.353) 0.516 0.073 0.770 + 137 (0.136) 0.102 0.346 0.017 + 147 (0.144) 0.354 0.009 0.100 + 141 (0.133) 0.013 0.504 0.076 + 152 (0.037) 0.005 0.002 0.003 + 143 (0.048) 0.003 0.024 0.004 + 151 (0.060) 0.003 0.019 0.010 + 144 (0.040) 0.001 0.001 0.017 + +Locus 8 : A113 +15 alleles +5.4% missing data + 214 (0.229) 0.834 0.072 0.730 + 226 (0.100) 0.040 0.164 0.047 + 218 (0.040) 0.005 0.009 0.002 + 220 (0.096) 0.023 0.044 0.115 + 216 (0.073) 0.015 0.016 0.047 + 230 (0.069) 0.047 0.072 0.006 + 234 (0.056) 0.012 0.080 0.006 + 232 (0.053) 0.005 0.086 0.008 + 228 (0.061) 0.005 0.259 0.013 + 224 (0.036) 0.001 0.050 0.002 + 222 (0.053) 0.003 0.060 0.014 + 208 (0.030) 0.006 0.001 0.002 + 236 (0.036) 0.001 0.057 0.002 + 212 (0.033) 0.002 0.012 0.002 + 239 (0.035) 0.001 0.019 0.003 + +Locus 9 : Ac11 +11 alleles +3.8% missing data + 111 (0.154) 0.151 0.857 0.025 + 117 (0.211) 0.421 0.067 0.204 + 115 (0.181) 0.326 0.027 0.246 + 113 (0.134) 0.081 0.015 0.269 + 119 (0.080) 0.010 0.009 0.148 + 121 (0.050) 0.002 0.003 0.051 + 123 (0.041) 0.002 0.001 0.023 + 127 (0.043) 0.003 0.001 0.022 + 125 (0.034) 0.002 0.001 0.008 + 105 (0.037) 0.001 0.013 0.002 + 109 (0.035) 0.001 0.006 0.002 + +Locus 10 : Ac88 +10 alleles +0.4% missing data + 214 (0.509) 0.886 0.237 0.892 + 216 (0.048) 0.020 0.003 0.003 + 220 (0.159) 0.082 0.729 0.030 + 230 (0.044) 0.002 0.001 0.022 + 221 (0.036) 0.001 0.001 0.009 + 212 (0.039) 0.001 0.001 0.016 + 217 (0.049) 0.005 0.003 0.009 + 224 (0.040) 0.001 0.001 0.016 + 222 (0.036) 0.001 0.006 0.002 + 210 (0.039) 0.001 0.019 0.002 + +Locus 11 : Ac139 +9 alleles +9.6% missing data + 327 (0.228) 0.517 0.007 0.732 + 329 (0.314) 0.380 0.611 0.152 + 331 (0.134) 0.054 0.187 0.029 + 328 (0.094) 0.041 0.124 0.007 + 341 (0.038) 0.001 0.001 0.010 + 337 (0.046) 0.002 0.001 0.043 + 323 (0.038) 0.002 0.001 0.009 + 339 (0.061) 0.002 0.015 0.016 + 333 (0.048) 0.002 0.053 0.003 + +Locus 12 : Ap15 +7 alleles +4.6% missing data + 202 (0.669) 0.971 0.935 0.820 + 212 (0.062) 0.013 0.025 0.003 + 204 (0.088) 0.008 0.033 0.041 + 208 (0.050) 0.003 0.001 0.053 + 220 (0.048) 0.002 0.001 0.062 + 219 (0.036) 0.001 0.001 0.009 + 210 (0.047) 0.002 0.004 0.012 + +Locus 13 : Ap68 +9 alleles +5.9% missing data + 158 (0.290) 0.367 0.564 0.337 + 160 (0.108) 0.134 0.047 0.023 + 156 (0.239) 0.321 0.175 0.334 + 162 (0.071) 0.006 0.117 0.017 + 154 (0.059) 0.140 0.002 0.011 + 152 (0.081) 0.019 0.004 0.230 + 164 (0.082) 0.009 0.089 0.025 + 170 (0.033) 0.003 0.001 0.006 + 166 (0.036) 0.001 0.001 0.017 + +Locus 14 : Ap85 +11 alleles +4.2% missing data + 202 (0.225) 0.297 0.096 0.523 + 186 (0.228) 0.425 0.821 0.110 + 204 (0.086) 0.040 0.011 0.040 + 188 (0.080) 0.148 0.005 0.032 + 194 (0.102) 0.066 0.038 0.033 + 196 (0.078) 0.009 0.014 0.106 + 200 (0.049) 0.003 0.001 0.089 + 192 (0.038) 0.003 0.001 0.013 + 190 (0.033) 0.006 0.001 0.002 + 198 (0.048) 0.001 0.004 0.051 + 208 (0.032) 0.001 0.006 0.002 + +Locus 15 : Ap90 +14 alleles +0.4% missing data + 131 (0.249) 0.512 0.581 0.498 + 135 (0.104) 0.048 0.077 0.084 + 133 (0.168) 0.286 0.192 0.236 + 129 (0.114) 0.109 0.075 0.086 + 137 (0.070) 0.017 0.058 0.015 + 141 (0.029) 0.005 0.001 0.003 + 143 (0.034) 0.009 0.001 0.004 + 151 (0.037) 0.004 0.001 0.011 + 155 (0.030) 0.002 0.002 0.005 + 145 (0.029) 0.001 0.001 0.008 + 130 (0.031) 0.001 0.001 0.016 + 139 (0.044) 0.003 0.009 0.011 + 153 (0.032) 0.001 0.001 0.016 + 147 (0.029) 0.001 0.002 0.006 + +Locus 16 : Ap223 +9 alleles +1.7% missing data + 183 (0.458) 0.659 0.264 0.884 + 187 (0.146) 0.275 0.398 0.014 + 189 (0.069) 0.021 0.034 0.003 + 173 (0.122) 0.019 0.278 0.048 + 182 (0.043) 0.016 0.001 0.004 + 180 (0.043) 0.004 0.001 0.013 + 179 (0.045) 0.002 0.001 0.030 + 177 (0.035) 0.002 0.005 0.002 + 185 (0.041) 0.002 0.017 0.002 + +Locus 17 : Ap224 +7 alleles +2.5% missing data + 283 (0.137) 0.199 0.090 0.021 + 287 (0.277) 0.481 0.037 0.499 + 281 (0.202) 0.146 0.777 0.046 + 289 (0.222) 0.132 0.058 0.387 + 291 (0.068) 0.037 0.010 0.006 + 285 (0.048) 0.003 0.028 0.002 + 279 (0.044) 0.001 0.001 0.039 + +Locus 18 : Ap226 +7 alleles +11.7% missing data + 237 (0.273) 0.389 0.021 0.361 + 239 (0.336) 0.488 0.023 0.584 + 247 (0.212) 0.108 0.915 0.032 + 235 (0.042) 0.006 0.001 0.003 + 241 (0.043) 0.001 0.001 0.013 + 249 (0.052) 0.002 0.037 0.004 + 233 (0.042) 0.005 0.002 0.004 + +Locus 19 : Ap249 +10 alleles +2.5% missing data + 209 (0.355) 0.666 0.071 0.729 + 211 (0.056) 0.055 0.002 0.006 + 217 (0.134) 0.122 0.140 0.023 + 219 (0.146) 0.117 0.641 0.018 + 215 (0.103) 0.027 0.006 0.204 + 208 (0.036) 0.005 0.001 0.003 + 225 (0.046) 0.002 0.029 0.004 + 223 (0.053) 0.004 0.106 0.002 + 213 (0.036) 0.001 0.001 0.008 + 207 (0.036) 0.003 0.004 0.002 + +Locus 20 : Ap273 +4 alleles +3.3% missing data + 106 (0.770) 0.967 0.648 0.941 + 108 (0.101) 0.023 0.017 0.026 + 104 (0.064) 0.005 0.330 0.003 + 102 (0.065) 0.005 0.005 0.030 + +Locus 21 : Ap274 +3 alleles +2.5% missing data + 120 (0.897) 0.993 0.992 0.919 + 122 (0.064) 0.006 0.001 0.079 + 112 (0.039) 0.001 0.006 0.002 + +Locus 22 : Ap288 +7 alleles +0.0% missing data + 123 (0.506) 0.741 0.109 0.936 + 131 (0.247) 0.227 0.742 0.051 + 139 (0.077) 0.019 0.047 0.004 + 121 (0.038) 0.004 0.002 0.003 + 124 (0.038) 0.006 0.001 0.002 + 133 (0.048) 0.002 0.053 0.002 + 127 (0.046) 0.001 0.048 0.002 + +Locus 23 : At163 +7 alleles +1.3% missing data + 128 (0.570) 0.737 0.425 0.903 + 134 (0.231) 0.245 0.555 0.066 + 130 (0.042) 0.009 0.001 0.005 + 136 (0.048) 0.004 0.016 0.002 + 140 (0.037) 0.002 0.001 0.008 + 146 (0.037) 0.002 0.001 0.008 + 142 (0.037) 0.001 0.001 0.008 + +Locus 24 : At188 +15 alleles +2.9% missing data + 189 (0.265) 0.789 0.070 0.879 + 205 (0.057) 0.014 0.122 0.003 + 207 (0.044) 0.056 0.003 0.002 + 219 (0.054) 0.013 0.018 0.004 + 209 (0.073) 0.035 0.135 0.005 + 217 (0.066) 0.021 0.064 0.005 + 215 (0.054) 0.009 0.084 0.003 + 199 (0.096) 0.016 0.175 0.056 + 212 (0.049) 0.020 0.007 0.008 + 213 (0.060) 0.015 0.145 0.004 + 211 (0.044) 0.002 0.115 0.002 + 191 (0.031) 0.006 0.001 0.002 + 187 (0.035) 0.001 0.001 0.023 + 203 (0.034) 0.001 0.012 0.002 + 221 (0.036) 0.001 0.049 0.002 + +Values of parameters used in structure: +DATAFILE=E:\AU\Alexander\alex3\STRUCTURE\alex3\project_data, OUTFILE=E:\AU\Alexander\alex3\STRUCTURE\alex3\long\Results\long_run_2, NUMINDS=239, NUMLOCI=24, MISSING=-9, LABEL=1, POPDATA=0, POPFLAG=1, PHENOTYPE=0, EXTRACOLS=1, MAXPOPS=3, BURNIN=100000, NUMREPS=1000000, USEPOPINFO=0, INFERALPHA=1, INFERLAMBDA=0, POPSPECIFICLAMBDA=0, POPALPHAS=0, COMPUTEPROB=1, NOADMIX=0, ADMBURNIN=2500, UPDATEFREQ=1, PRINTLIKES=0, INTERMEDSAVE=0, PRINTKLD=0, PRINTNET=0, PRINTLAMBDA=0, ANCESTDIST=0, NUMBOXES=1000, ANCESTPINT=0.90000, GENSBACK=2, MIGRPRIOR=0.05000, PRINTQHAT=0, PRINTQSUM=0, ALPHA=1.0000, FREQSCORR=1, FPRIORMEAN=0.0100, FPRIORSD=0.0500, ONEFST=0, LAMBDA=1.0000, UNIFPRIORALPHA=1, ALPHAMAX=10.0000, ALPHAPRIORA=1.0000, ALPHAPRIORB=2.0000, ALPHAPROPSD=0.0250, STARTATPOPINFO=0, RANDOMIZE=1, LINKAGE=0, METROFREQ=10, REPORTHITRATE=0, MARKOVPHASE=-1, PHASED=0, PLOIDY=2, PHASEINFO=0 LOCPRIOR=0, LOCPRIORINIT=1.000000, LOCDATA=0, LOCISPOP=0, LOCPRIORSTEP=0.100000, MAXLOCPRIOR=20.000000, SEED=1335131429, +[STRAT parameters]: NUMSIMSTATS=1000, PHENOTYPECOL=-9, POOLFREQ=10, LOCUSxONLY=0, EMERROR=0.00100, MISSINGPHENO=-9, \ No newline at end of file diff --git a/inst/files/Structure239_3 b/inst/files/Structure239_3 new file mode 100644 index 0000000..e0135ac --- /dev/null +++ b/inst/files/Structure239_3 @@ -0,0 +1,639 @@ + + +---------------------------------------------------- +STRUCTURE by Pritchard, Stephens and Donnelly (2000) + and Falush, Stephens and Pritchard (2003) + Code by Pritchard, Falush and Hubisz + Version 2.3.2.1 (Oct 2009) +---------------------------------------------------- + + + +Command line arguments: bin\structure -m E:\AU\Alexander\alex3\STRUCTURE\alex3\long\mainparams -e E:\AU\Alexander\alex3\STRUCTURE\alex3\long\extraparams +Input File: E:\AU\Alexander\alex3\STRUCTURE\alex3\project_data + +Run parameters: + 239 individuals + 24 loci + 4 populations assumed + 100000 Burn-in period + 1000000 Reps + + +-------------------------------------------- +Overall proportion of membership of the +sample in each of the 4 clusters + +Inferred Clusters + 1 2 3 4 +0.241 0.214 0.217 0.328 + +-------------------------------------------- + +Allele-freq. divergence among pops (Net nucleotide distance), +computed using point estimates of P. + + 1 2 3 4 + 1 - 0.0314 0.0322 0.2876 + 2 0.0314 - 0.0002 0.1874 + 3 0.0322 0.0002 - 0.1883 + 4 0.2876 0.1874 0.1883 - + +Average distances (expected heterozygosity) between individuals in same cluster: +cluster 1 : 0.4513 +cluster 2 : 0.5083 +cluster 3 : 0.5042 +cluster 4 : 0.4813 + +-------------------------------------------- +Estimated Ln Prob of Data = -12036.3 +Mean value of ln likelihood = -11736.8 +Variance of ln likelihood = 598.9 +Mean value of alpha = 0.1494 + +Mean value of Fst_1 = 0.1401 +Mean value of Fst_2 = 0.1516 +Mean value of Fst_3 = 0.1563 +Mean value of Fst_4 = 0.2272 + + +Inferred ancestry of individuals: + Label (%Miss) : Inferred clusters + 1 I13825 (0) : 0.032 0.472 0.413 0.083 + 2 I13826 (0) : 0.073 0.289 0.303 0.336 + 3 I13827 (20) : 0.034 0.427 0.494 0.045 + 4 I13828 (0) : 0.031 0.490 0.435 0.044 + 5 I13829 (8) : 0.027 0.447 0.499 0.027 + 6 I13830 (0) : 0.048 0.326 0.349 0.277 + 7 I13831 (0) : 0.032 0.458 0.475 0.035 + 8 I13832 (16) : 0.066 0.443 0.478 0.013 + 9 I13833 (0) : 0.037 0.462 0.483 0.019 + 10 I13834 (0) : 0.020 0.438 0.495 0.047 + 11 I13835 (0) : 0.018 0.504 0.461 0.017 + 12 I13836 (0) : 0.032 0.441 0.497 0.030 + 13 I13377 (0) : 0.096 0.430 0.461 0.012 + 14 I13378 (0) : 0.043 0.500 0.440 0.018 + 15 I13379 (0) : 0.044 0.444 0.433 0.078 + 16 I13380 (0) : 0.143 0.394 0.448 0.015 + 17 I13381 (0) : 0.089 0.409 0.474 0.028 + 18 I13382 (0) : 0.019 0.435 0.519 0.026 + 19 I13383 (0) : 0.089 0.437 0.443 0.031 + 20 I13384 (0) : 0.053 0.424 0.480 0.043 + 21 I13385 (0) : 0.018 0.461 0.512 0.008 + 22 I13386 (0) : 0.031 0.384 0.457 0.128 + 23 I13387 (0) : 0.039 0.414 0.405 0.143 + 24 I13388 (0) : 0.295 0.329 0.307 0.069 + 25 I13389 (0) : 0.098 0.431 0.463 0.008 + 26 I13390 (0) : 0.041 0.429 0.509 0.021 + 27 I13391 (0) : 0.208 0.390 0.380 0.023 + 28 I13392 (0) : 0.077 0.474 0.432 0.017 + 29 I13393 (0) : 0.191 0.370 0.430 0.010 + 30 I13394 (4) : 0.477 0.249 0.257 0.018 + 31 I13395 (0) : 0.404 0.281 0.289 0.026 + 32 I13396 (0) : 0.116 0.473 0.391 0.020 + 33 I13397 (0) : 0.034 0.433 0.405 0.128 + 34 I13398 (0) : 0.022 0.479 0.449 0.050 + 35 I13399 (4) : 0.118 0.379 0.384 0.118 + 36 I13400 (0) : 0.100 0.457 0.424 0.019 + 37 I13401 (0) : 0.419 0.295 0.276 0.011 + 38 I13402 (0) : 0.050 0.504 0.427 0.019 + 39 I13403 (0) : 0.135 0.445 0.402 0.018 + 40 I13404 (0) : 0.029 0.427 0.479 0.065 + 41 I13405 (0) : 0.026 0.441 0.524 0.008 + 42 I13406 (16) : 0.028 0.461 0.454 0.057 + 43 I13407 (0) : 0.038 0.462 0.402 0.098 + 44 I13408 (0) : 0.024 0.468 0.498 0.010 + 45 I13409 (0) : 0.068 0.495 0.422 0.015 + 46 I13410 (0) : 0.025 0.389 0.444 0.142 + 47 I13411 (0) : 0.017 0.397 0.448 0.139 + 48 I13412 (0) : 0.335 0.305 0.342 0.019 + 49 I13413 (0) : 0.134 0.432 0.381 0.053 + 50 I13414 (0) : 0.072 0.349 0.383 0.197 + 51 I13415 (4) : 0.077 0.438 0.467 0.018 + 52 I13416 (4) : 0.161 0.413 0.412 0.015 + 53 I13417 (4) : 0.162 0.401 0.411 0.027 + 54 I13418 (0) : 0.146 0.368 0.422 0.063 + 55 I13419 (0) : 0.048 0.405 0.406 0.141 + 56 I13420 (0) : 0.249 0.347 0.336 0.068 + 57 I13421 (0) : 0.203 0.365 0.425 0.008 + 58 I13422 (0) : 0.316 0.319 0.331 0.035 + 59 I13423 (0) : 0.143 0.434 0.408 0.014 + 60 I13424 (0) : 0.046 0.433 0.497 0.024 + 61 I13425 (0) : 0.074 0.447 0.443 0.036 + 62 I13426 (0) : 0.528 0.236 0.228 0.009 + 63 I13870 (0) : 0.454 0.194 0.190 0.162 + 64 I13871 (12) : 0.056 0.455 0.460 0.029 + 65 I13872 (0) : 0.053 0.437 0.368 0.141 + 66 I13873 (4) : 0.203 0.390 0.359 0.048 + 67 I13874 (0) : 0.312 0.227 0.212 0.249 + 68 I13875 (8) : 0.146 0.365 0.331 0.158 + 69 I13876 (0) : 0.597 0.107 0.102 0.195 + 70 I13877 (20) : 0.057 0.386 0.463 0.093 + 71 I13878 (29) : 0.050 0.439 0.421 0.090 + 72 I13879 (4) : 0.020 0.439 0.493 0.048 + 73 I13880 (4) : 0.092 0.320 0.280 0.308 + 74 I13881 (0) : 0.398 0.142 0.142 0.317 + 75 I13882 (0) : 0.049 0.458 0.394 0.099 + 76 I13883 (4) : 0.291 0.243 0.217 0.248 + 77 I13884 (16) : 0.123 0.431 0.366 0.079 + 78 I13885 (16) : 0.023 0.389 0.469 0.120 + 79 I13886 (8) : 0.034 0.434 0.416 0.116 + 80 I13887 (0) : 0.228 0.376 0.321 0.075 + 81 I13888 (0) : 0.209 0.336 0.367 0.088 + 82 I13889 (0) : 0.681 0.152 0.153 0.014 + 83 I13890 (33) : 0.444 0.272 0.267 0.018 + 84 I13891 (0) : 0.049 0.477 0.440 0.035 + 85 I13892 (0) : 0.252 0.354 0.385 0.009 + 86 I13893 (8) : 0.190 0.298 0.322 0.191 + 87 I13894 (0) : 0.034 0.459 0.377 0.131 + 88 I13895 (4) : 0.290 0.309 0.341 0.060 + 89 I13896 (0) : 0.211 0.409 0.342 0.037 + 90 I13897 (0) : 0.017 0.407 0.405 0.171 + 91 I13898 (4) : 0.070 0.394 0.399 0.137 + 92 I13899 (0) : 0.028 0.291 0.255 0.426 + 93 I13900 (33) : 0.268 0.295 0.277 0.161 + 94 I13837 (0) : 0.058 0.430 0.488 0.023 + 95 I13838 (0) : 0.723 0.126 0.114 0.036 + 96 I13839 (0) : 0.165 0.375 0.412 0.048 + 97 I13840 (0) : 0.140 0.424 0.429 0.008 + 98 I13841 (0) : 0.410 0.277 0.302 0.011 + 99 I13842 (0) : 0.466 0.248 0.275 0.011 +100 I13843 (4) : 0.594 0.191 0.201 0.014 +101 I13844 (16) : 0.117 0.413 0.452 0.017 +102 I13845 (0) : 0.024 0.458 0.504 0.014 +103 I13846 (0) : 0.031 0.435 0.527 0.007 +104 I13847 (0) : 0.565 0.190 0.177 0.068 +105 I13848 (0) : 0.295 0.363 0.335 0.007 +106 I13849 (0) : 0.192 0.388 0.341 0.079 +107 I13850 (0) : 0.260 0.385 0.348 0.007 +108 I12577 (4) : 0.917 0.038 0.036 0.009 +109 I12578 (4) : 0.867 0.065 0.056 0.013 +110 I12579 (8) : 0.886 0.051 0.052 0.011 +111 I12580 (8) : 0.909 0.041 0.043 0.008 +112 I12581 (4) : 0.488 0.245 0.259 0.008 +113 I12582 (4) : 0.926 0.034 0.034 0.005 +114 I12583 (8) : 0.706 0.144 0.139 0.012 +115 I12584 (4) : 0.745 0.131 0.118 0.007 +116 I12585 (4) : 0.939 0.027 0.026 0.008 +117 I12586 (4) : 0.923 0.034 0.034 0.008 +118 I12587 (8) : 0.937 0.028 0.028 0.008 +119 I12588 (4) : 0.943 0.024 0.024 0.009 +120 I12589 (0) : 0.896 0.042 0.042 0.021 +121 I12590 (0) : 0.865 0.060 0.058 0.016 +122 I12591 (12) : 0.962 0.014 0.015 0.009 +123 I12592 (4) : 0.909 0.035 0.037 0.020 +124 I12593 (4) : 0.942 0.025 0.023 0.010 +125 I12594 (8) : 0.950 0.020 0.020 0.010 +126 I12595 (0) : 0.819 0.087 0.087 0.006 +127 I12596 (0) : 0.950 0.022 0.023 0.005 +128 I12597 (4) : 0.829 0.083 0.077 0.011 +129 I12598 (0) : 0.805 0.089 0.096 0.010 +130 I12599 (0) : 0.792 0.098 0.087 0.023 +131 I12600 (4) : 0.896 0.047 0.047 0.010 +132 I12601 (8) : 0.925 0.033 0.031 0.011 +133 I12602 (12) : 0.907 0.044 0.042 0.007 +134 I12603 (0) : 0.899 0.046 0.046 0.009 +135 I12604 (4) : 0.868 0.062 0.055 0.014 +136 I12605 (4) : 0.819 0.092 0.080 0.009 +137 I12606 (8) : 0.940 0.023 0.023 0.014 +138 I12607 (4) : 0.883 0.046 0.043 0.028 +139 I12608 (8) : 0.910 0.041 0.041 0.008 +140 I12609 (8) : 0.944 0.024 0.024 0.008 +141 I12610 (50) : 0.898 0.044 0.046 0.012 +142 I12611 (0) : 0.961 0.017 0.017 0.005 +143 I12612 (0) : 0.943 0.025 0.025 0.007 +144 I12613 (0) : 0.936 0.026 0.028 0.010 +145 I12614 (4) : 0.834 0.067 0.076 0.023 +146 I12615 (0) : 0.812 0.087 0.086 0.014 +147 I12616 (4) : 0.822 0.074 0.082 0.021 +148 I12617 (4) : 0.960 0.016 0.016 0.008 +149 I12618 (45) : 0.937 0.026 0.026 0.011 +150 I14107 (0) : 0.080 0.163 0.154 0.603 +151 I14108 (4) : 0.053 0.026 0.026 0.895 +152 I14109 (0) : 0.083 0.184 0.177 0.557 +153 I14110 (0) : 0.028 0.066 0.062 0.844 +154 I14111 (25) : 0.043 0.294 0.271 0.392 +155 I14113 (0) : 0.007 0.009 0.010 0.974 +156 I14114 (0) : 0.034 0.042 0.042 0.882 +157 I14115 (8) : 0.037 0.202 0.225 0.536 +158 I14116 (0) : 0.041 0.085 0.089 0.784 +159 I14117 (0) : 0.071 0.179 0.161 0.590 +160 I14118 (0) : 0.036 0.034 0.035 0.895 +161 I14119 (20) : 0.036 0.186 0.176 0.601 +162 I14120 (4) : 0.047 0.020 0.021 0.913 +163 I14121 (8) : 0.036 0.115 0.131 0.717 +164 I14122 (4) : 0.009 0.012 0.012 0.967 +165 I14123 (0) : 0.081 0.100 0.093 0.726 +166 I14124 (4) : 0.068 0.138 0.128 0.666 +167 I14125 (4) : 0.024 0.177 0.181 0.617 +168 I14126 (0) : 0.038 0.158 0.182 0.622 +169 I14127 (0) : 0.014 0.033 0.031 0.922 +170 I14128 (0) : 0.036 0.126 0.147 0.691 +171 I14129 (0) : 0.036 0.072 0.067 0.825 +172 I14130 (0) : 0.103 0.122 0.118 0.657 +173 I14131 (20) : 0.107 0.127 0.130 0.636 +174 I14132 (33) : 0.082 0.260 0.233 0.425 +175 I14017 (0) : 0.070 0.161 0.178 0.591 +176 I14018 (25) : 0.060 0.067 0.065 0.808 +177 I14019 (0) : 0.030 0.144 0.147 0.679 +178 I14020 (0) : 0.021 0.284 0.259 0.436 +179 I14021 (0) : 0.073 0.128 0.131 0.668 +180 I14022 (0) : 0.025 0.081 0.076 0.819 +181 I14023 (0) : 0.015 0.076 0.081 0.828 +182 I14024 (12) : 0.408 0.102 0.095 0.395 +183 I14025 (0) : 0.097 0.049 0.049 0.806 +184 I14026 (0) : 0.030 0.161 0.178 0.630 +185 I14027 (0) : 0.057 0.196 0.195 0.552 +186 I14028 (4) : 0.042 0.049 0.050 0.859 +187 I14029 (4) : 0.056 0.089 0.081 0.774 +188 I14030 (0) : 0.022 0.239 0.276 0.463 +189 I14031 (4) : 0.015 0.035 0.038 0.911 +190 I14032 (0) : 0.050 0.172 0.173 0.604 +191 I14033 (0) : 0.017 0.144 0.153 0.685 +192 I14034 (8) : 0.022 0.098 0.101 0.779 +193 I14035 (4) : 0.066 0.083 0.085 0.765 +194 I14036 (0) : 0.022 0.226 0.242 0.510 +195 I14037 (0) : 0.227 0.107 0.104 0.562 +196 I14038 (0) : 0.075 0.092 0.089 0.744 +197 I14039 (4) : 0.015 0.171 0.184 0.631 +198 I14040 (8) : 0.141 0.054 0.052 0.753 +199 I14041 (4) : 0.059 0.015 0.014 0.912 +200 I14042 (4) : 0.037 0.145 0.160 0.658 +201 I14043 (0) : 0.029 0.049 0.046 0.876 +202 I14044 (0) : 0.007 0.009 0.009 0.974 +203 I14045 (4) : 0.005 0.008 0.008 0.980 +204 I14046 (0) : 0.010 0.015 0.015 0.960 +205 I14047 (4) : 0.066 0.017 0.017 0.900 +206 I14048 (0) : 0.021 0.019 0.018 0.943 +207 I14049 (0) : 0.020 0.024 0.021 0.935 +208 I14050 (0) : 0.008 0.011 0.011 0.970 +209 I14051 (0) : 0.006 0.010 0.010 0.975 +210 I14052 (0) : 0.039 0.327 0.366 0.267 +211 I14054 (4) : 0.157 0.208 0.194 0.441 +212 I14055 (4) : 0.014 0.362 0.437 0.187 +213 I14056 (0) : 0.089 0.166 0.188 0.558 +214 I14057 (0) : 0.013 0.034 0.031 0.921 +215 I14058 (0) : 0.019 0.022 0.023 0.936 +216 I14059 (4) : 0.016 0.012 0.012 0.959 +217 I14060 (16) : 0.011 0.014 0.014 0.962 +218 I14062 (0) : 0.012 0.014 0.013 0.961 +219 I14063 (0) : 0.006 0.007 0.007 0.981 +220 I14064 (4) : 0.005 0.007 0.007 0.982 +221 I14065 (0) : 0.006 0.009 0.009 0.976 +222 I14066 (0) : 0.023 0.034 0.036 0.908 +223 I14067 (8) : 0.011 0.014 0.014 0.961 +224 I14068 (4) : 0.050 0.032 0.030 0.887 +225 I14069 (0) : 0.007 0.011 0.011 0.970 +226 I14070 (4) : 0.007 0.012 0.011 0.970 +227 I14071 (0) : 0.006 0.008 0.008 0.979 +228 I14072 (0) : 0.010 0.010 0.010 0.970 +229 I14073 (0) : 0.014 0.066 0.073 0.847 +230 I14074 (0) : 0.018 0.022 0.021 0.939 +231 I14075 (0) : 0.007 0.009 0.009 0.975 +232 I14076 (4) : 0.013 0.021 0.021 0.944 +233 I14077 (4) : 0.010 0.050 0.054 0.886 +234 I14078 (0) : 0.010 0.017 0.017 0.955 +235 I14079 (0) : 0.011 0.019 0.018 0.952 +236 I14080 (0) : 0.017 0.013 0.013 0.957 +237 I14081 (4) : 0.023 0.055 0.059 0.864 +238 I14082 (0) : 0.008 0.014 0.014 0.964 +239 I14083 (4) : 0.074 0.084 0.073 0.769 + + +Estimated Allele Frequencies in each cluster +First column gives estimated ancestral frequencies + + +Locus 1 : A8 +8 alleles +5.0% missing data + 177 (0.400) 0.572 0.515 0.494 0.119 + 179 (0.110) 0.052 0.111 0.127 0.013 + 175 (0.141) 0.010 0.183 0.193 0.699 + 173 (0.094) 0.010 0.056 0.053 0.154 + 181 (0.138) 0.319 0.099 0.098 0.009 + 165 (0.055) 0.032 0.015 0.014 0.003 + 183 (0.034) 0.004 0.015 0.016 0.001 + 171 (0.028) 0.002 0.006 0.005 0.002 + +Locus 2 : A14 +5 alleles +0.4% missing data + 112 (0.266) 0.029 0.273 0.268 0.906 + 110 (0.569) 0.834 0.694 0.702 0.047 + 114 (0.062) 0.004 0.020 0.017 0.044 + 118 (0.054) 0.095 0.007 0.006 0.001 + 116 (0.049) 0.037 0.006 0.006 0.002 + +Locus 3 : A24 +6 alleles +2.5% missing data + 104 (0.356) 0.357 0.412 0.386 0.318 + 106 (0.468) 0.581 0.551 0.582 0.577 + 101 (0.027) 0.002 0.007 0.006 0.001 + 108 (0.055) 0.004 0.021 0.018 0.050 + 96 (0.061) 0.055 0.006 0.005 0.043 + 102 (0.032) 0.002 0.004 0.004 0.011 + +Locus 4 : A29 +31 alleles +6.7% missing data + 143 (0.040) 0.004 0.049 0.047 0.220 + 149 (0.039) 0.058 0.035 0.030 0.007 + 147 (0.034) 0.034 0.008 0.008 0.050 + 153 (0.052) 0.093 0.068 0.076 0.036 + 169 (0.035) 0.037 0.056 0.047 0.002 + 151 (0.041) 0.037 0.051 0.057 0.008 + 145 (0.037) 0.022 0.011 0.010 0.090 + 157 (0.047) 0.148 0.074 0.074 0.006 + 155 (0.069) 0.177 0.089 0.088 0.073 + 159 (0.055) 0.036 0.098 0.087 0.056 + 161 (0.041) 0.006 0.074 0.077 0.028 + 141 (0.042) 0.010 0.026 0.027 0.253 + 139 (0.026) 0.002 0.010 0.011 0.042 + 144 (0.020) 0.002 0.034 0.040 0.001 + 171 (0.034) 0.030 0.065 0.072 0.003 + 163 (0.047) 0.049 0.103 0.100 0.002 + 167 (0.047) 0.059 0.032 0.029 0.035 + 173 (0.022) 0.005 0.020 0.024 0.001 + 142 (0.016) 0.001 0.005 0.005 0.001 + 177 (0.024) 0.040 0.006 0.005 0.001 + 175 (0.022) 0.019 0.006 0.006 0.001 + 165 (0.048) 0.042 0.043 0.040 0.039 + 146 (0.020) 0.001 0.019 0.020 0.001 + 137 (0.022) 0.013 0.005 0.005 0.001 + 183 (0.017) 0.019 0.002 0.001 0.000 + 179 (0.017) 0.017 0.002 0.002 0.000 + 191 (0.016) 0.009 0.002 0.002 0.000 + 185 (0.016) 0.009 0.002 0.002 0.000 + 180 (0.017) 0.019 0.001 0.001 0.000 + 129 (0.018) 0.001 0.001 0.001 0.041 + 187 (0.016) 0.003 0.004 0.003 0.002 + +Locus 5 : A43 +7 alleles +2.1% missing data + 123 (0.155) 0.158 0.145 0.135 0.022 + 141 (0.040) 0.002 0.006 0.006 0.047 + 137 (0.605) 0.697 0.808 0.815 0.777 + 139 (0.100) 0.065 0.032 0.036 0.146 + 124 (0.035) 0.059 0.003 0.003 0.001 + 143 (0.038) 0.009 0.004 0.004 0.006 + 128 (0.027) 0.009 0.002 0.002 0.001 + +Locus 6 : A79 +13 alleles +2.9% missing data + 103 (0.205) 0.186 0.325 0.326 0.254 + 97 (0.126) 0.058 0.129 0.114 0.435 + 101 (0.114) 0.038 0.146 0.158 0.228 + 107 (0.104) 0.071 0.127 0.144 0.029 + 109 (0.079) 0.090 0.072 0.070 0.002 + 105 (0.149) 0.402 0.139 0.127 0.043 + 111 (0.047) 0.032 0.022 0.019 0.001 + 113 (0.028) 0.004 0.009 0.008 0.002 + 91 (0.030) 0.072 0.002 0.002 0.001 + 99 (0.041) 0.025 0.013 0.014 0.001 + 115 (0.030) 0.010 0.011 0.011 0.001 + 117 (0.024) 0.004 0.004 0.004 0.001 + 121 (0.024) 0.007 0.003 0.002 0.001 + +Locus 7 : A88 +9 alleles +6.3% missing data + 133 (0.042) 0.003 0.008 0.007 0.021 + 149 (0.405) 0.774 0.531 0.518 0.068 + 137 (0.128) 0.017 0.102 0.109 0.343 + 147 (0.167) 0.088 0.314 0.324 0.009 + 141 (0.112) 0.083 0.026 0.025 0.515 + 152 (0.028) 0.003 0.006 0.005 0.001 + 143 (0.039) 0.003 0.006 0.005 0.022 + 151 (0.046) 0.011 0.004 0.004 0.019 + 144 (0.031) 0.018 0.003 0.003 0.001 + +Locus 8 : A113 +15 alleles +5.4% missing data + 214 (0.315) 0.719 0.784 0.793 0.066 + 226 (0.096) 0.042 0.053 0.050 0.164 + 218 (0.034) 0.003 0.006 0.006 0.008 + 220 (0.083) 0.130 0.024 0.024 0.046 + 216 (0.067) 0.049 0.020 0.018 0.015 + 230 (0.067) 0.008 0.041 0.043 0.074 + 234 (0.052) 0.006 0.022 0.019 0.074 + 232 (0.046) 0.007 0.010 0.010 0.087 + 228 (0.056) 0.015 0.012 0.011 0.266 + 224 (0.030) 0.003 0.002 0.002 0.052 + 222 (0.049) 0.011 0.012 0.010 0.058 + 208 (0.024) 0.002 0.005 0.006 0.001 + 236 (0.028) 0.002 0.002 0.002 0.060 + 212 (0.026) 0.002 0.004 0.003 0.011 + 239 (0.028) 0.003 0.002 0.002 0.019 + +Locus 9 : Ac11 +11 alleles +3.8% missing data + 111 (0.160) 0.027 0.162 0.164 0.869 + 117 (0.239) 0.191 0.393 0.398 0.059 + 115 (0.208) 0.236 0.308 0.310 0.026 + 113 (0.135) 0.271 0.101 0.093 0.015 + 119 (0.065) 0.165 0.014 0.014 0.008 + 121 (0.040) 0.057 0.004 0.004 0.002 + 123 (0.037) 0.021 0.006 0.006 0.001 + 127 (0.035) 0.022 0.005 0.005 0.001 + 125 (0.026) 0.007 0.003 0.003 0.001 + 105 (0.028) 0.002 0.002 0.002 0.013 + 109 (0.027) 0.002 0.002 0.002 0.006 + +Locus 10 : Ac88 +10 alleles +0.4% missing data + 214 (0.591) 0.892 0.847 0.861 0.228 + 216 (0.040) 0.003 0.018 0.019 0.003 + 220 (0.148) 0.028 0.111 0.098 0.739 + 230 (0.037) 0.019 0.006 0.006 0.001 + 221 (0.028) 0.009 0.002 0.002 0.001 + 212 (0.030) 0.018 0.002 0.002 0.001 + 217 (0.038) 0.008 0.007 0.007 0.002 + 224 (0.030) 0.018 0.002 0.002 0.001 + 222 (0.028) 0.002 0.003 0.002 0.005 + 210 (0.030) 0.002 0.002 0.002 0.020 + +Locus 11 : Ac139 +9 alleles +9.6% missing data + 327 (0.308) 0.746 0.499 0.488 0.010 + 329 (0.325) 0.135 0.381 0.391 0.607 + 331 (0.119) 0.027 0.065 0.061 0.186 + 328 (0.072) 0.006 0.039 0.044 0.125 + 341 (0.029) 0.010 0.002 0.002 0.001 + 337 (0.035) 0.048 0.003 0.003 0.001 + 323 (0.029) 0.009 0.003 0.003 0.001 + 339 (0.047) 0.017 0.005 0.004 0.015 + 333 (0.036) 0.002 0.004 0.003 0.055 + +Locus 12 : Ap15 +7 alleles +4.6% missing data + 202 (0.740) 0.807 0.953 0.957 0.940 + 212 (0.051) 0.003 0.019 0.017 0.021 + 204 (0.071) 0.041 0.013 0.012 0.033 + 208 (0.038) 0.059 0.004 0.004 0.001 + 220 (0.037) 0.069 0.003 0.003 0.001 + 219 (0.028) 0.009 0.002 0.002 0.001 + 210 (0.037) 0.011 0.005 0.005 0.003 + +Locus 13 : Ap68 +9 alleles +5.9% missing data + 158 (0.320) 0.316 0.413 0.382 0.560 + 160 (0.107) 0.023 0.115 0.122 0.045 + 156 (0.247) 0.343 0.292 0.310 0.178 + 162 (0.061) 0.013 0.017 0.016 0.118 + 154 (0.070) 0.012 0.115 0.122 0.002 + 152 (0.072) 0.246 0.025 0.027 0.003 + 164 (0.069) 0.023 0.017 0.015 0.092 + 170 (0.026) 0.006 0.004 0.004 0.001 + 166 (0.028) 0.018 0.002 0.002 0.001 + +Locus 14 : Ap85 +11 alleles +4.2% missing data + 202 (0.261) 0.522 0.318 0.306 0.093 + 186 (0.245) 0.104 0.386 0.410 0.834 + 204 (0.078) 0.042 0.038 0.039 0.011 + 188 (0.085) 0.023 0.141 0.137 0.004 + 194 (0.097) 0.029 0.075 0.068 0.033 + 196 (0.069) 0.113 0.016 0.015 0.013 + 200 (0.044) 0.095 0.008 0.008 0.001 + 192 (0.032) 0.011 0.006 0.006 0.001 + 190 (0.026) 0.002 0.006 0.006 0.001 + 198 (0.038) 0.057 0.003 0.003 0.004 + 208 (0.026) 0.002 0.003 0.003 0.005 + +Locus 15 : Ap90 +14 alleles +0.4% missing data + 131 (0.296) 0.521 0.484 0.493 0.586 + 135 (0.099) 0.082 0.059 0.057 0.073 + 133 (0.195) 0.216 0.296 0.287 0.191 + 129 (0.115) 0.085 0.102 0.108 0.075 + 137 (0.058) 0.016 0.017 0.017 0.060 + 141 (0.023) 0.002 0.006 0.005 0.001 + 143 (0.027) 0.002 0.011 0.010 0.001 + 151 (0.031) 0.008 0.008 0.007 0.001 + 155 (0.023) 0.004 0.004 0.004 0.001 + 145 (0.024) 0.009 0.002 0.002 0.001 + 130 (0.025) 0.018 0.002 0.002 0.001 + 139 (0.036) 0.012 0.005 0.005 0.008 + 153 (0.026) 0.018 0.002 0.002 0.001 + 147 (0.023) 0.006 0.003 0.002 0.002 + +Locus 16 : Ap223 +9 alleles +1.7% missing data + 183 (0.516) 0.882 0.662 0.665 0.258 + 187 (0.164) 0.016 0.255 0.256 0.397 + 189 (0.054) 0.003 0.018 0.020 0.035 + 173 (0.101) 0.051 0.028 0.026 0.286 + 182 (0.036) 0.004 0.016 0.015 0.001 + 180 (0.033) 0.009 0.008 0.007 0.001 + 179 (0.037) 0.030 0.006 0.005 0.001 + 177 (0.027) 0.002 0.003 0.003 0.004 + 185 (0.031) 0.002 0.003 0.003 0.017 + +Locus 17 : Ap224 +7 alleles +2.5% missing data + 283 (0.144) 0.022 0.182 0.179 0.084 + 287 (0.327) 0.475 0.485 0.481 0.034 + 281 (0.186) 0.048 0.143 0.155 0.788 + 289 (0.216) 0.405 0.140 0.142 0.058 + 291 (0.056) 0.004 0.042 0.036 0.007 + 285 (0.038) 0.002 0.005 0.005 0.028 + 279 (0.034) 0.044 0.002 0.002 0.001 + +Locus 18 : Ap226 +7 alleles +11.7% missing data + 237 (0.297) 0.360 0.369 0.376 0.019 + 239 (0.380) 0.579 0.490 0.482 0.022 + 247 (0.192) 0.037 0.124 0.125 0.917 + 235 (0.031) 0.003 0.006 0.006 0.001 + 241 (0.031) 0.014 0.002 0.002 0.001 + 249 (0.038) 0.004 0.003 0.003 0.038 + 233 (0.031) 0.003 0.005 0.006 0.002 + +Locus 19 : Ap249 +10 alleles +2.5% missing data + 209 (0.419) 0.712 0.644 0.655 0.068 + 211 (0.058) 0.005 0.049 0.051 0.001 + 217 (0.129) 0.021 0.127 0.118 0.134 + 219 (0.144) 0.019 0.128 0.124 0.648 + 215 (0.089) 0.225 0.028 0.030 0.006 + 208 (0.028) 0.002 0.007 0.006 0.001 + 225 (0.035) 0.004 0.003 0.003 0.030 + 223 (0.042) 0.002 0.006 0.007 0.108 + 213 (0.028) 0.009 0.002 0.002 0.001 + 207 (0.028) 0.002 0.005 0.004 0.003 + +Locus 20 : Ap273 +4 alleles +3.3% missing data + 106 (0.813) 0.943 0.956 0.957 0.635 + 108 (0.082) 0.024 0.025 0.025 0.016 + 104 (0.051) 0.003 0.008 0.008 0.345 + 102 (0.054) 0.029 0.011 0.010 0.004 + +Locus 21 : Ap274 +3 alleles +2.5% missing data + 120 (0.918) 0.912 0.989 0.989 0.993 + 122 (0.053) 0.086 0.009 0.009 0.001 + 112 (0.029) 0.002 0.002 0.002 0.006 + +Locus 22 : Ap288 +7 alleles +0.0% missing data + 123 (0.570) 0.938 0.724 0.730 0.105 + 131 (0.243) 0.050 0.238 0.235 0.742 + 139 (0.060) 0.004 0.022 0.020 0.047 + 121 (0.029) 0.002 0.005 0.005 0.001 + 124 (0.029) 0.002 0.006 0.006 0.001 + 133 (0.036) 0.002 0.003 0.003 0.055 + 127 (0.033) 0.002 0.002 0.002 0.050 + +Locus 23 : At163 +7 alleles +1.3% missing data + 128 (0.614) 0.912 0.718 0.733 0.425 + 134 (0.234) 0.061 0.257 0.244 0.557 + 130 (0.031) 0.002 0.012 0.010 0.001 + 136 (0.037) 0.002 0.005 0.005 0.015 + 140 (0.028) 0.007 0.003 0.003 0.001 + 146 (0.028) 0.007 0.003 0.003 0.001 + 142 (0.028) 0.009 0.002 0.002 0.001 + +Locus 24 : At188 +15 alleles +2.9% missing data + 189 (0.366) 0.878 0.753 0.757 0.069 + 205 (0.054) 0.003 0.030 0.025 0.112 + 207 (0.040) 0.003 0.044 0.049 0.002 + 219 (0.046) 0.003 0.014 0.013 0.019 + 209 (0.062) 0.006 0.030 0.033 0.141 + 217 (0.056) 0.004 0.026 0.023 0.063 + 215 (0.043) 0.003 0.010 0.010 0.087 + 199 (0.088) 0.057 0.030 0.031 0.173 + 212 (0.041) 0.006 0.021 0.020 0.005 + 213 (0.056) 0.004 0.024 0.021 0.143 + 211 (0.038) 0.002 0.006 0.005 0.119 + 191 (0.025) 0.001 0.006 0.006 0.001 + 187 (0.028) 0.026 0.002 0.002 0.001 + 203 (0.028) 0.002 0.003 0.002 0.012 + 221 (0.028) 0.002 0.002 0.002 0.052 + +Values of parameters used in structure: +DATAFILE=E:\AU\Alexander\alex3\STRUCTURE\alex3\project_data, OUTFILE=E:\AU\Alexander\alex3\STRUCTURE\alex3\long\Results\long_run_3, NUMINDS=239, NUMLOCI=24, MISSING=-9, LABEL=1, POPDATA=0, POPFLAG=1, PHENOTYPE=0, EXTRACOLS=1, MAXPOPS=4, BURNIN=100000, NUMREPS=1000000, USEPOPINFO=0, INFERALPHA=1, INFERLAMBDA=0, POPSPECIFICLAMBDA=0, POPALPHAS=0, COMPUTEPROB=1, NOADMIX=0, ADMBURNIN=2500, UPDATEFREQ=1, PRINTLIKES=0, INTERMEDSAVE=0, PRINTKLD=0, PRINTNET=0, PRINTLAMBDA=0, ANCESTDIST=0, NUMBOXES=1000, ANCESTPINT=0.90000, GENSBACK=2, MIGRPRIOR=0.05000, PRINTQHAT=0, PRINTQSUM=0, ALPHA=1.0000, FREQSCORR=1, FPRIORMEAN=0.0100, FPRIORSD=0.0500, ONEFST=0, LAMBDA=1.0000, UNIFPRIORALPHA=1, ALPHAMAX=10.0000, ALPHAPRIORA=1.0000, ALPHAPRIORB=2.0000, ALPHAPROPSD=0.0250, STARTATPOPINFO=0, RANDOMIZE=1, LINKAGE=0, METROFREQ=10, REPORTHITRATE=0, MARKOVPHASE=-1, PHASED=0, PLOIDY=2, PHASEINFO=0 LOCPRIOR=0, LOCPRIORINIT=1.000000, LOCDATA=0, LOCISPOP=0, LOCPRIORSTEP=0.100000, MAXLOCPRIOR=20.000000, SEED=1335135174, +[STRAT parameters]: NUMSIMSTATS=1000, PHENOTYPECOL=-9, POOLFREQ=10, LOCUSxONLY=0, EMERROR=0.00100, MISSINGPHENO=-9, \ No newline at end of file diff --git a/inst/files/Structure239_4 b/inst/files/Structure239_4 new file mode 100644 index 0000000..c03bdec --- /dev/null +++ b/inst/files/Structure239_4 @@ -0,0 +1,642 @@ + + +---------------------------------------------------- +STRUCTURE by Pritchard, Stephens and Donnelly (2000) + and Falush, Stephens and Pritchard (2003) + Code by Pritchard, Falush and Hubisz + Version 2.3.2.1 (Oct 2009) +---------------------------------------------------- + + + +Command line arguments: bin\structure -m E:\AU\Alexander\alex3\STRUCTURE\alex3\long\mainparams -e E:\AU\Alexander\alex3\STRUCTURE\alex3\long\extraparams +Input File: E:\AU\Alexander\alex3\STRUCTURE\alex3\project_data + +Run parameters: + 239 individuals + 24 loci + 5 populations assumed + 100000 Burn-in period + 1000000 Reps + + +-------------------------------------------- +Overall proportion of membership of the +sample in each of the 5 clusters + +Inferred Clusters + 1 2 3 4 5 +0.153 0.157 0.156 0.219 0.315 + +-------------------------------------------- + +Allele-freq. divergence among pops (Net nucleotide distance), +computed using point estimates of P. + + 1 2 3 4 5 + 1 - 0.0008 0.0010 0.0352 0.1788 + 2 0.0008 - 0.0004 0.0318 0.1868 + 3 0.0010 0.0004 - 0.0312 0.1851 + 4 0.0352 0.0318 0.0312 - 0.2904 + 5 0.1788 0.1868 0.1851 0.2904 - + +Average distances (expected heterozygosity) between individuals in same cluster: +cluster 1 : 0.5177 +cluster 2 : 0.5109 +cluster 3 : 0.5176 +cluster 4 : 0.4508 +cluster 5 : 0.4787 + +-------------------------------------------- +Estimated Ln Prob of Data = -12082.0 +Mean value of ln likelihood = -11653.7 +Variance of ln likelihood = 856.5 +Mean value of alpha = 0.1177 + +Mean value of Fst_1 = 0.1431 +Mean value of Fst_2 = 0.1457 +Mean value of Fst_3 = 0.1396 +Mean value of Fst_4 = 0.1320 +Mean value of Fst_5 = 0.2303 + + +Inferred ancestry of individuals: + Label (%Miss) : Inferred clusters + 1 I13825 (0) : 0.275 0.283 0.364 0.023 0.056 + 2 I13826 (0) : 0.260 0.195 0.218 0.046 0.281 + 3 I13827 (20) : 0.296 0.329 0.306 0.025 0.043 + 4 I13828 (0) : 0.283 0.300 0.364 0.023 0.030 + 5 I13829 (8) : 0.347 0.303 0.306 0.022 0.022 + 6 I13830 (0) : 0.275 0.256 0.207 0.035 0.227 + 7 I13831 (0) : 0.234 0.394 0.317 0.023 0.031 + 8 I13832 (16) : 0.308 0.322 0.314 0.046 0.010 + 9 I13833 (0) : 0.238 0.383 0.338 0.027 0.014 + 10 I13834 (0) : 0.307 0.320 0.317 0.017 0.039 + 11 I13835 (0) : 0.294 0.301 0.379 0.013 0.013 + 12 I13836 (0) : 0.380 0.294 0.283 0.025 0.017 + 13 I13377 (0) : 0.236 0.383 0.312 0.059 0.009 + 14 I13378 (0) : 0.255 0.326 0.375 0.030 0.014 + 15 I13379 (0) : 0.230 0.358 0.311 0.030 0.072 + 16 I13380 (0) : 0.256 0.329 0.311 0.092 0.012 + 17 I13381 (0) : 0.403 0.260 0.251 0.070 0.016 + 18 I13382 (0) : 0.412 0.288 0.263 0.017 0.020 + 19 I13383 (0) : 0.349 0.297 0.272 0.059 0.023 + 20 I13384 (0) : 0.368 0.314 0.243 0.048 0.027 + 21 I13385 (0) : 0.289 0.345 0.346 0.014 0.007 + 22 I13386 (0) : 0.416 0.239 0.230 0.023 0.091 + 23 I13387 (0) : 0.273 0.279 0.312 0.027 0.109 + 24 I13388 (0) : 0.287 0.267 0.253 0.161 0.032 + 25 I13389 (0) : 0.221 0.389 0.310 0.074 0.006 + 26 I13390 (0) : 0.377 0.320 0.247 0.038 0.017 + 27 I13391 (0) : 0.195 0.353 0.304 0.132 0.016 + 28 I13392 (0) : 0.255 0.310 0.359 0.062 0.014 + 29 I13393 (0) : 0.350 0.242 0.236 0.165 0.007 + 30 I13394 (4) : 0.158 0.279 0.224 0.327 0.012 + 31 I13395 (0) : 0.152 0.268 0.213 0.347 0.021 + 32 I13396 (0) : 0.256 0.276 0.363 0.090 0.015 + 33 I13397 (0) : 0.225 0.313 0.318 0.024 0.119 + 34 I13398 (0) : 0.288 0.321 0.336 0.016 0.039 + 35 I13399 (4) : 0.196 0.378 0.291 0.051 0.084 + 36 I13400 (0) : 0.229 0.338 0.353 0.065 0.015 + 37 I13401 (0) : 0.184 0.216 0.237 0.356 0.008 + 38 I13402 (0) : 0.254 0.313 0.384 0.035 0.015 + 39 I13403 (0) : 0.261 0.267 0.335 0.124 0.014 + 40 I13404 (0) : 0.344 0.324 0.261 0.024 0.047 + 41 I13405 (0) : 0.287 0.368 0.314 0.024 0.007 + 42 I13406 (16) : 0.327 0.285 0.327 0.022 0.039 + 43 I13407 (0) : 0.257 0.266 0.359 0.031 0.087 + 44 I13408 (0) : 0.299 0.349 0.326 0.019 0.008 + 45 I13409 (0) : 0.280 0.281 0.379 0.049 0.010 + 46 I13410 (0) : 0.318 0.291 0.254 0.020 0.118 + 47 I13411 (0) : 0.310 0.297 0.247 0.014 0.133 + 48 I13412 (0) : 0.307 0.220 0.190 0.270 0.012 + 49 I13413 (0) : 0.247 0.304 0.315 0.094 0.040 + 50 I13414 (0) : 0.378 0.259 0.229 0.037 0.098 + 51 I13415 (4) : 0.270 0.335 0.328 0.052 0.015 + 52 I13416 (4) : 0.244 0.348 0.287 0.110 0.011 + 53 I13417 (4) : 0.254 0.313 0.303 0.111 0.019 + 54 I13418 (0) : 0.386 0.255 0.215 0.109 0.035 + 55 I13419 (0) : 0.308 0.271 0.290 0.028 0.103 + 56 I13420 (0) : 0.261 0.243 0.260 0.189 0.048 + 57 I13421 (0) : 0.280 0.266 0.228 0.220 0.006 + 58 I13422 (0) : 0.215 0.258 0.225 0.272 0.029 + 59 I13423 (0) : 0.317 0.259 0.318 0.097 0.009 + 60 I13424 (0) : 0.317 0.345 0.282 0.036 0.020 + 61 I13425 (0) : 0.297 0.308 0.314 0.057 0.024 + 62 I13426 (0) : 0.133 0.204 0.183 0.474 0.007 + 63 I13870 (0) : 0.130 0.176 0.163 0.392 0.139 + 64 I13871 (12) : 0.258 0.377 0.303 0.037 0.026 + 65 I13872 (0) : 0.261 0.261 0.346 0.032 0.100 + 66 I13873 (4) : 0.282 0.238 0.284 0.165 0.031 + 67 I13874 (0) : 0.192 0.158 0.189 0.258 0.203 + 68 I13875 (8) : 0.205 0.304 0.279 0.083 0.129 + 69 I13876 (0) : 0.122 0.116 0.114 0.495 0.152 + 70 I13877 (20) : 0.432 0.246 0.241 0.035 0.045 + 71 I13878 (29) : 0.282 0.290 0.317 0.038 0.072 + 72 I13879 (4) : 0.341 0.305 0.301 0.015 0.037 + 73 I13880 (4) : 0.202 0.245 0.231 0.056 0.266 + 74 I13881 (0) : 0.107 0.129 0.129 0.333 0.302 + 75 I13882 (0) : 0.285 0.264 0.344 0.036 0.071 + 76 I13883 (4) : 0.156 0.185 0.219 0.227 0.213 + 77 I13884 (16) : 0.247 0.265 0.334 0.090 0.064 + 78 I13885 (16) : 0.399 0.279 0.237 0.015 0.070 + 79 I13886 (8) : 0.237 0.324 0.308 0.025 0.107 + 80 I13887 (0) : 0.245 0.234 0.320 0.151 0.050 + 81 I13888 (0) : 0.331 0.254 0.219 0.146 0.050 + 82 I13889 (0) : 0.087 0.147 0.125 0.631 0.011 + 83 I13890 (33) : 0.170 0.195 0.197 0.424 0.014 + 84 I13891 (0) : 0.335 0.285 0.319 0.038 0.023 + 85 I13892 (0) : 0.260 0.303 0.224 0.205 0.007 + 86 I13893 (8) : 0.236 0.269 0.218 0.119 0.159 + 87 I13894 (0) : 0.256 0.258 0.366 0.025 0.095 + 88 I13895 (4) : 0.282 0.256 0.224 0.198 0.039 + 89 I13896 (0) : 0.230 0.244 0.313 0.184 0.029 + 90 I13897 (0) : 0.246 0.309 0.299 0.012 0.134 + 91 I13898 (4) : 0.308 0.244 0.296 0.054 0.098 + 92 I13899 (0) : 0.165 0.182 0.210 0.023 0.420 + 93 I13900 (33) : 0.194 0.286 0.255 0.148 0.117 + 94 I13837 (0) : 0.273 0.365 0.305 0.041 0.016 + 95 I13838 (0) : 0.087 0.080 0.092 0.712 0.029 + 96 I13839 (0) : 0.261 0.315 0.281 0.108 0.035 + 97 I13840 (0) : 0.235 0.360 0.299 0.100 0.006 + 98 I13841 (0) : 0.230 0.175 0.188 0.399 0.008 + 99 I13842 (0) : 0.158 0.230 0.196 0.409 0.008 +100 I13843 (4) : 0.171 0.133 0.134 0.552 0.010 +101 I13844 (16) : 0.246 0.344 0.309 0.087 0.015 +102 I13845 (0) : 0.353 0.312 0.305 0.019 0.011 +103 I13846 (0) : 0.382 0.322 0.262 0.029 0.006 +104 I13847 (0) : 0.137 0.152 0.164 0.495 0.052 +105 I13848 (0) : 0.225 0.279 0.269 0.223 0.005 +106 I13849 (0) : 0.257 0.248 0.314 0.130 0.050 +107 I13850 (0) : 0.222 0.224 0.294 0.255 0.006 +108 I12577 (4) : 0.030 0.031 0.032 0.900 0.007 +109 I12578 (4) : 0.041 0.054 0.053 0.841 0.010 +110 I12579 (8) : 0.042 0.050 0.045 0.854 0.009 +111 I12580 (8) : 0.032 0.033 0.030 0.898 0.006 +112 I12581 (4) : 0.158 0.217 0.198 0.421 0.006 +113 I12582 (4) : 0.026 0.026 0.026 0.918 0.004 +114 I12583 (8) : 0.113 0.115 0.124 0.640 0.009 +115 I12584 (4) : 0.087 0.081 0.108 0.718 0.005 +116 I12585 (4) : 0.022 0.021 0.023 0.928 0.006 +117 I12586 (4) : 0.033 0.030 0.028 0.903 0.006 +118 I12587 (8) : 0.023 0.022 0.022 0.927 0.006 +119 I12588 (4) : 0.019 0.022 0.021 0.930 0.008 +120 I12589 (0) : 0.034 0.036 0.035 0.878 0.016 +121 I12590 (0) : 0.047 0.047 0.048 0.846 0.012 +122 I12591 (12) : 0.012 0.012 0.012 0.957 0.007 +123 I12592 (4) : 0.032 0.033 0.030 0.889 0.016 +124 I12593 (4) : 0.020 0.018 0.021 0.932 0.008 +125 I12594 (8) : 0.018 0.017 0.017 0.941 0.007 +126 I12595 (0) : 0.073 0.080 0.074 0.767 0.005 +127 I12596 (0) : 0.021 0.018 0.019 0.938 0.004 +128 I12597 (4) : 0.068 0.074 0.081 0.769 0.008 +129 I12598 (0) : 0.080 0.069 0.065 0.778 0.008 +130 I12599 (0) : 0.065 0.064 0.074 0.779 0.018 +131 I12600 (4) : 0.036 0.035 0.037 0.884 0.008 +132 I12601 (8) : 0.027 0.032 0.031 0.902 0.009 +133 I12602 (12) : 0.031 0.036 0.035 0.892 0.006 +134 I12603 (0) : 0.042 0.042 0.040 0.869 0.007 +135 I12604 (4) : 0.042 0.043 0.048 0.857 0.011 +136 I12605 (4) : 0.057 0.052 0.071 0.812 0.007 +137 I12606 (8) : 0.021 0.021 0.020 0.927 0.011 +138 I12607 (4) : 0.040 0.042 0.044 0.850 0.024 +139 I12608 (8) : 0.033 0.036 0.035 0.890 0.006 +140 I12609 (8) : 0.020 0.020 0.021 0.932 0.006 +141 I12610 (50) : 0.035 0.040 0.036 0.880 0.009 +142 I12611 (0) : 0.013 0.014 0.014 0.955 0.004 +143 I12612 (0) : 0.019 0.020 0.021 0.934 0.005 +144 I12613 (0) : 0.021 0.023 0.021 0.926 0.008 +145 I12614 (4) : 0.086 0.056 0.055 0.787 0.016 +146 I12615 (0) : 0.062 0.085 0.074 0.768 0.011 +147 I12616 (4) : 0.072 0.068 0.055 0.790 0.015 +148 I12617 (4) : 0.013 0.013 0.013 0.955 0.006 +149 I12618 (45) : 0.021 0.023 0.022 0.924 0.009 +150 I14107 (0) : 0.103 0.121 0.119 0.063 0.594 +151 I14108 (4) : 0.022 0.022 0.023 0.043 0.890 +152 I14109 (0) : 0.152 0.122 0.146 0.056 0.525 +153 I14110 (0) : 0.056 0.047 0.055 0.020 0.822 +154 I14111 (25) : 0.219 0.195 0.231 0.026 0.329 +155 I14113 (0) : 0.008 0.008 0.008 0.006 0.971 +156 I14114 (0) : 0.034 0.033 0.034 0.026 0.873 +157 I14115 (8) : 0.182 0.138 0.134 0.029 0.518 +158 I14116 (0) : 0.072 0.073 0.064 0.029 0.763 +159 I14117 (0) : 0.119 0.124 0.137 0.050 0.569 +160 I14118 (0) : 0.029 0.029 0.029 0.028 0.886 +161 I14119 (20) : 0.127 0.118 0.145 0.026 0.584 +162 I14120 (4) : 0.018 0.018 0.017 0.039 0.908 +163 I14121 (8) : 0.099 0.094 0.077 0.026 0.704 +164 I14122 (4) : 0.010 0.010 0.010 0.007 0.963 +165 I14123 (0) : 0.074 0.072 0.077 0.063 0.714 +166 I14124 (4) : 0.089 0.093 0.110 0.052 0.656 +167 I14125 (4) : 0.107 0.139 0.123 0.019 0.612 +168 I14126 (0) : 0.152 0.121 0.100 0.026 0.600 +169 I14127 (0) : 0.029 0.026 0.027 0.011 0.907 +170 I14128 (0) : 0.115 0.095 0.087 0.027 0.676 +171 I14129 (0) : 0.055 0.055 0.058 0.026 0.807 +172 I14130 (0) : 0.091 0.096 0.089 0.081 0.643 +173 I14131 (20) : 0.117 0.095 0.102 0.074 0.611 +174 I14132 (33) : 0.161 0.166 0.194 0.069 0.410 +175 I14017 (0) : 0.139 0.123 0.111 0.050 0.576 +176 I14018 (25) : 0.045 0.057 0.054 0.045 0.800 +177 I14019 (0) : 0.105 0.099 0.109 0.022 0.665 +178 I14020 (0) : 0.177 0.170 0.223 0.015 0.415 +179 I14021 (0) : 0.091 0.100 0.094 0.056 0.659 +180 I14022 (0) : 0.062 0.056 0.066 0.018 0.799 +181 I14023 (0) : 0.060 0.062 0.057 0.010 0.812 +182 I14024 (12) : 0.133 0.119 0.129 0.277 0.344 +183 I14025 (0) : 0.049 0.043 0.040 0.078 0.789 +184 I14026 (0) : 0.095 0.138 0.117 0.021 0.628 +185 I14027 (0) : 0.143 0.156 0.136 0.036 0.529 +186 I14028 (4) : 0.036 0.043 0.040 0.031 0.851 +187 I14029 (4) : 0.067 0.060 0.070 0.042 0.761 +188 I14030 (0) : 0.238 0.175 0.146 0.014 0.427 +189 I14031 (4) : 0.036 0.028 0.027 0.011 0.898 +190 I14032 (0) : 0.157 0.130 0.119 0.027 0.567 +191 I14033 (0) : 0.142 0.100 0.098 0.012 0.648 +192 I14034 (8) : 0.076 0.070 0.072 0.017 0.766 +193 I14035 (4) : 0.063 0.067 0.065 0.051 0.753 +194 I14036 (0) : 0.200 0.146 0.152 0.016 0.486 +195 I14037 (0) : 0.096 0.095 0.090 0.182 0.537 +196 I14038 (0) : 0.064 0.076 0.072 0.055 0.734 +197 I14039 (4) : 0.133 0.121 0.116 0.012 0.619 +198 I14040 (8) : 0.047 0.049 0.048 0.118 0.738 +199 I14041 (4) : 0.014 0.013 0.014 0.055 0.904 +200 I14042 (4) : 0.124 0.104 0.107 0.027 0.638 +201 I14043 (0) : 0.043 0.038 0.042 0.021 0.855 +202 I14044 (0) : 0.008 0.008 0.008 0.006 0.971 +203 I14045 (4) : 0.007 0.007 0.007 0.004 0.976 +204 I14046 (0) : 0.013 0.012 0.013 0.008 0.955 +205 I14047 (4) : 0.018 0.017 0.017 0.057 0.891 +206 I14048 (0) : 0.017 0.016 0.018 0.016 0.933 +207 I14049 (0) : 0.017 0.017 0.020 0.015 0.931 +208 I14050 (0) : 0.009 0.008 0.009 0.007 0.968 +209 I14051 (0) : 0.009 0.008 0.008 0.005 0.971 +210 I14052 (0) : 0.301 0.254 0.198 0.027 0.220 +211 I14054 (4) : 0.137 0.185 0.176 0.098 0.404 +212 I14055 (4) : 0.351 0.273 0.250 0.010 0.116 +213 I14056 (0) : 0.164 0.119 0.108 0.070 0.540 +214 I14057 (0) : 0.027 0.025 0.030 0.010 0.908 +215 I14058 (0) : 0.019 0.018 0.018 0.015 0.931 +216 I14059 (4) : 0.011 0.010 0.011 0.013 0.955 +217 I14060 (16) : 0.011 0.010 0.011 0.008 0.959 +218 I14062 (0) : 0.011 0.011 0.011 0.009 0.959 +219 I14063 (0) : 0.006 0.005 0.005 0.004 0.979 +220 I14064 (4) : 0.005 0.005 0.005 0.004 0.980 +221 I14065 (0) : 0.007 0.007 0.007 0.005 0.974 +222 I14066 (0) : 0.028 0.025 0.025 0.018 0.903 +223 I14067 (8) : 0.011 0.011 0.011 0.009 0.958 +224 I14068 (4) : 0.029 0.026 0.030 0.042 0.873 +225 I14069 (0) : 0.009 0.009 0.009 0.005 0.967 +226 I14070 (4) : 0.011 0.010 0.010 0.006 0.963 +227 I14071 (0) : 0.007 0.006 0.006 0.005 0.976 +228 I14072 (0) : 0.008 0.008 0.008 0.007 0.967 +229 I14073 (0) : 0.048 0.050 0.047 0.011 0.844 +230 I14074 (0) : 0.017 0.018 0.018 0.014 0.933 +231 I14075 (0) : 0.008 0.008 0.008 0.005 0.971 +232 I14076 (4) : 0.017 0.019 0.018 0.010 0.936 +233 I14077 (4) : 0.055 0.039 0.041 0.008 0.858 +234 I14078 (0) : 0.013 0.014 0.014 0.008 0.951 +235 I14079 (0) : 0.016 0.015 0.016 0.008 0.945 +236 I14080 (0) : 0.012 0.012 0.012 0.014 0.950 +237 I14081 (4) : 0.057 0.044 0.046 0.017 0.836 +238 I14082 (0) : 0.012 0.011 0.011 0.007 0.960 +239 I14083 (4) : 0.056 0.061 0.070 0.058 0.754 + + +Estimated Allele Frequencies in each cluster +First column gives estimated ancestral frequencies + + +Locus 1 : A8 +8 alleles +5.0% missing data + 177 (0.421) 0.456 0.484 0.520 0.575 0.119 + 179 (0.108) 0.135 0.114 0.105 0.053 0.011 + 175 (0.151) 0.226 0.189 0.176 0.012 0.700 + 173 (0.083) 0.044 0.056 0.057 0.009 0.157 + 181 (0.138) 0.098 0.122 0.108 0.315 0.009 + 165 (0.048) 0.016 0.015 0.016 0.032 0.003 + 183 (0.028) 0.020 0.015 0.013 0.003 0.001 + 171 (0.023) 0.006 0.005 0.006 0.002 0.001 + +Locus 2 : A14 +5 alleles +0.4% missing data + 112 (0.268) 0.294 0.256 0.276 0.031 0.905 + 110 (0.596) 0.676 0.713 0.690 0.824 0.046 + 114 (0.052) 0.016 0.016 0.020 0.004 0.045 + 118 (0.044) 0.008 0.007 0.008 0.103 0.001 + 116 (0.040) 0.007 0.007 0.007 0.038 0.002 + +Locus 3 : A24 +6 alleles +2.5% missing data + 104 (0.365) 0.364 0.381 0.406 0.359 0.320 + 106 (0.488) 0.601 0.585 0.554 0.575 0.575 + 101 (0.022) 0.006 0.006 0.007 0.001 0.001 + 108 (0.048) 0.017 0.018 0.022 0.004 0.050 + 96 (0.049) 0.006 0.006 0.007 0.058 0.045 + 102 (0.028) 0.005 0.005 0.005 0.002 0.010 + +Locus 4 : A29 +31 alleles +6.7% missing data + 143 (0.041) 0.044 0.047 0.050 0.004 0.225 + 149 (0.040) 0.026 0.031 0.036 0.058 0.007 + 147 (0.035) 0.017 0.012 0.012 0.035 0.047 + 153 (0.056) 0.070 0.076 0.070 0.093 0.036 + 169 (0.036) 0.042 0.042 0.054 0.037 0.002 + 151 (0.040) 0.061 0.051 0.048 0.037 0.008 + 145 (0.036) 0.012 0.012 0.013 0.024 0.092 + 157 (0.049) 0.071 0.087 0.072 0.146 0.007 + 155 (0.075) 0.090 0.091 0.092 0.178 0.073 + 159 (0.058) 0.081 0.076 0.095 0.036 0.057 + 161 (0.039) 0.085 0.066 0.074 0.006 0.021 + 141 (0.039) 0.025 0.030 0.030 0.009 0.259 + 139 (0.025) 0.019 0.011 0.011 0.002 0.039 + 144 (0.024) 0.035 0.038 0.032 0.002 0.001 + 171 (0.037) 0.073 0.077 0.058 0.027 0.003 + 163 (0.052) 0.086 0.094 0.099 0.050 0.002 + 167 (0.047) 0.032 0.035 0.033 0.057 0.035 + 173 (0.020) 0.027 0.022 0.017 0.005 0.001 + 142 (0.014) 0.005 0.005 0.005 0.001 0.001 + 177 (0.022) 0.005 0.006 0.007 0.042 0.001 + 175 (0.020) 0.006 0.011 0.009 0.015 0.001 + 165 (0.050) 0.045 0.041 0.044 0.041 0.037 + 146 (0.019) 0.020 0.018 0.017 0.001 0.001 + 137 (0.020) 0.005 0.005 0.006 0.013 0.001 + 183 (0.016) 0.002 0.002 0.002 0.020 0.000 + 179 (0.016) 0.003 0.003 0.003 0.017 0.000 + 191 (0.015) 0.002 0.002 0.002 0.009 0.000 + 185 (0.015) 0.003 0.002 0.002 0.009 0.000 + 180 (0.015) 0.001 0.001 0.001 0.021 0.000 + 129 (0.016) 0.002 0.001 0.002 0.001 0.043 + 187 (0.014) 0.004 0.004 0.004 0.002 0.002 + +Locus 5 : A43 +7 alleles +2.1% missing data + 123 (0.152) 0.137 0.130 0.147 0.155 0.020 + 141 (0.035) 0.007 0.007 0.008 0.002 0.048 + 137 (0.646) 0.793 0.819 0.800 0.696 0.777 + 139 (0.085) 0.052 0.034 0.034 0.066 0.148 + 124 (0.028) 0.003 0.003 0.003 0.064 0.001 + 143 (0.031) 0.005 0.005 0.006 0.009 0.005 + 128 (0.022) 0.002 0.002 0.002 0.010 0.001 + +Locus 6 : A79 +13 alleles +2.9% missing data + 103 (0.230) 0.334 0.304 0.320 0.185 0.251 + 97 (0.130) 0.115 0.111 0.135 0.059 0.438 + 101 (0.112) 0.126 0.171 0.148 0.035 0.232 + 107 (0.103) 0.181 0.126 0.115 0.069 0.026 + 109 (0.074) 0.059 0.080 0.071 0.088 0.002 + 105 (0.151) 0.118 0.140 0.146 0.409 0.044 + 111 (0.043) 0.019 0.021 0.021 0.032 0.001 + 113 (0.024) 0.011 0.009 0.009 0.003 0.002 + 91 (0.026) 0.003 0.003 0.003 0.077 0.001 + 99 (0.039) 0.015 0.014 0.013 0.026 0.001 + 115 (0.027) 0.012 0.014 0.011 0.008 0.001 + 117 (0.020) 0.005 0.004 0.005 0.004 0.001 + 121 (0.020) 0.004 0.003 0.004 0.006 0.001 + +Locus 7 : A88 +9 alleles +6.3% missing data + 133 (0.036) 0.008 0.008 0.009 0.003 0.020 + 149 (0.435) 0.497 0.530 0.528 0.780 0.067 + 137 (0.121) 0.131 0.102 0.105 0.016 0.339 + 147 (0.181) 0.307 0.301 0.299 0.083 0.009 + 141 (0.105) 0.036 0.036 0.036 0.084 0.523 + 152 (0.023) 0.005 0.007 0.006 0.002 0.001 + 143 (0.034) 0.007 0.007 0.007 0.003 0.021 + 151 (0.038) 0.006 0.005 0.006 0.011 0.019 + 144 (0.026) 0.004 0.003 0.004 0.018 0.001 + +Locus 8 : A113 +15 alleles +5.4% missing data + 214 (0.385) 0.763 0.761 0.759 0.722 0.066 + 226 (0.088) 0.065 0.051 0.055 0.040 0.160 + 218 (0.028) 0.006 0.007 0.006 0.002 0.007 + 220 (0.071) 0.022 0.031 0.029 0.133 0.047 + 216 (0.061) 0.020 0.023 0.024 0.047 0.014 + 230 (0.063) 0.040 0.047 0.040 0.008 0.075 + 234 (0.050) 0.021 0.022 0.024 0.005 0.073 + 232 (0.042) 0.011 0.014 0.012 0.006 0.087 + 228 (0.053) 0.018 0.016 0.017 0.015 0.270 + 224 (0.024) 0.003 0.003 0.003 0.002 0.054 + 222 (0.042) 0.012 0.011 0.014 0.010 0.058 + 208 (0.021) 0.007 0.006 0.005 0.002 0.000 + 236 (0.024) 0.003 0.002 0.003 0.002 0.062 + 212 (0.024) 0.005 0.004 0.005 0.002 0.010 + 239 (0.025) 0.004 0.003 0.003 0.003 0.019 + +Locus 9 : Ac11 +11 alleles +3.8% missing data + 111 (0.165) 0.183 0.168 0.168 0.028 0.874 + 117 (0.257) 0.377 0.380 0.378 0.189 0.056 + 115 (0.226) 0.307 0.298 0.299 0.232 0.025 + 113 (0.126) 0.082 0.108 0.106 0.272 0.015 + 119 (0.060) 0.020 0.019 0.019 0.169 0.007 + 121 (0.035) 0.007 0.006 0.006 0.059 0.002 + 123 (0.032) 0.008 0.007 0.008 0.020 0.001 + 127 (0.031) 0.007 0.006 0.006 0.021 0.001 + 125 (0.022) 0.004 0.004 0.004 0.007 0.001 + 105 (0.023) 0.003 0.002 0.002 0.001 0.013 + 109 (0.022) 0.003 0.003 0.003 0.002 0.005 + +Locus 10 : Ac88 +10 alleles +0.4% missing data + 214 (0.640) 0.847 0.851 0.837 0.893 0.222 + 216 (0.035) 0.023 0.017 0.016 0.003 0.002 + 220 (0.143) 0.100 0.104 0.117 0.029 0.747 + 230 (0.032) 0.009 0.009 0.009 0.015 0.001 + 221 (0.022) 0.002 0.002 0.002 0.010 0.001 + 212 (0.024) 0.002 0.002 0.002 0.020 0.001 + 217 (0.031) 0.008 0.007 0.008 0.008 0.002 + 224 (0.024) 0.003 0.003 0.003 0.019 0.001 + 222 (0.023) 0.003 0.003 0.003 0.002 0.005 + 210 (0.025) 0.002 0.002 0.002 0.002 0.020 + +Locus 11 : Ac139 +9 alleles +9.6% missing data + 327 (0.342) 0.423 0.490 0.498 0.756 0.011 + 329 (0.343) 0.429 0.387 0.373 0.126 0.605 + 331 (0.106) 0.063 0.062 0.070 0.026 0.187 + 328 (0.061) 0.063 0.040 0.038 0.005 0.125 + 341 (0.025) 0.003 0.003 0.003 0.010 0.001 + 337 (0.029) 0.004 0.003 0.003 0.050 0.001 + 323 (0.025) 0.004 0.004 0.004 0.009 0.001 + 339 (0.039) 0.006 0.006 0.006 0.016 0.015 + 333 (0.031) 0.005 0.004 0.005 0.002 0.056 + +Locus 12 : Ap15 +7 alleles +4.6% missing data + 202 (0.777) 0.951 0.949 0.943 0.803 0.942 + 212 (0.043) 0.016 0.016 0.020 0.003 0.020 + 204 (0.062) 0.015 0.017 0.017 0.039 0.033 + 208 (0.034) 0.005 0.006 0.006 0.062 0.001 + 220 (0.031) 0.004 0.004 0.004 0.073 0.001 + 219 (0.023) 0.003 0.003 0.003 0.009 0.001 + 210 (0.030) 0.006 0.006 0.006 0.010 0.003 + +Locus 13 : Ap68 +9 alleles +5.9% missing data + 158 (0.341) 0.374 0.397 0.418 0.306 0.560 + 160 (0.106) 0.118 0.121 0.111 0.022 0.043 + 156 (0.260) 0.331 0.290 0.285 0.347 0.177 + 162 (0.054) 0.019 0.017 0.021 0.012 0.119 + 154 (0.068) 0.097 0.123 0.110 0.010 0.002 + 152 (0.066) 0.039 0.028 0.028 0.257 0.003 + 164 (0.059) 0.016 0.017 0.019 0.023 0.094 + 170 (0.022) 0.004 0.005 0.005 0.005 0.001 + 166 (0.024) 0.003 0.002 0.003 0.019 0.001 + +Locus 14 : Ap85 +11 alleles +4.2% missing data + 202 (0.281) 0.296 0.299 0.325 0.528 0.094 + 186 (0.261) 0.416 0.427 0.370 0.098 0.838 + 204 (0.070) 0.038 0.042 0.041 0.038 0.010 + 188 (0.089) 0.123 0.119 0.136 0.023 0.004 + 194 (0.091) 0.071 0.063 0.076 0.028 0.031 + 196 (0.062) 0.021 0.017 0.019 0.117 0.012 + 200 (0.043) 0.013 0.013 0.012 0.094 0.001 + 192 (0.028) 0.008 0.007 0.007 0.010 0.001 + 190 (0.022) 0.007 0.006 0.006 0.002 0.001 + 198 (0.032) 0.004 0.004 0.004 0.061 0.004 + 208 (0.022) 0.004 0.003 0.004 0.002 0.004 + +Locus 15 : Ap90 +14 alleles +0.4% missing data + 131 (0.328) 0.476 0.485 0.484 0.529 0.592 + 135 (0.094) 0.070 0.063 0.061 0.082 0.069 + 133 (0.210) 0.271 0.286 0.290 0.213 0.191 + 129 (0.113) 0.122 0.100 0.098 0.084 0.075 + 137 (0.050) 0.016 0.022 0.019 0.014 0.060 + 141 (0.020) 0.005 0.005 0.007 0.002 0.000 + 143 (0.024) 0.010 0.010 0.010 0.002 0.001 + 151 (0.027) 0.007 0.007 0.009 0.008 0.001 + 155 (0.020) 0.004 0.005 0.005 0.003 0.001 + 145 (0.021) 0.002 0.002 0.002 0.010 0.000 + 130 (0.022) 0.002 0.002 0.002 0.019 0.000 + 139 (0.032) 0.008 0.007 0.006 0.012 0.007 + 153 (0.021) 0.002 0.002 0.002 0.019 0.000 + 147 (0.020) 0.004 0.004 0.004 0.004 0.001 + +Locus 16 : Ap223 +9 alleles +1.7% missing data + 183 (0.548) 0.674 0.662 0.662 0.882 0.254 + 187 (0.175) 0.237 0.255 0.245 0.018 0.397 + 189 (0.047) 0.019 0.019 0.020 0.003 0.035 + 173 (0.089) 0.033 0.029 0.033 0.050 0.291 + 182 (0.031) 0.014 0.013 0.015 0.004 0.001 + 180 (0.029) 0.008 0.007 0.009 0.008 0.001 + 179 (0.032) 0.006 0.006 0.007 0.031 0.001 + 177 (0.022) 0.004 0.004 0.004 0.002 0.004 + 185 (0.026) 0.005 0.004 0.004 0.002 0.017 + +Locus 17 : Ap224 +7 alleles +2.5% missing data + 283 (0.134) 0.140 0.190 0.178 0.020 0.083 + 287 (0.362) 0.484 0.467 0.470 0.467 0.033 + 281 (0.185) 0.191 0.154 0.149 0.049 0.791 + 289 (0.206) 0.144 0.148 0.151 0.411 0.058 + 291 (0.052) 0.033 0.033 0.042 0.004 0.006 + 285 (0.033) 0.006 0.006 0.006 0.002 0.028 + 279 (0.028) 0.003 0.003 0.003 0.047 0.001 + +Locus 18 : Ap226 +7 alleles +11.7% missing data + 237 (0.309) 0.370 0.374 0.362 0.356 0.018 + 239 (0.401) 0.463 0.473 0.489 0.582 0.022 + 247 (0.182) 0.145 0.135 0.131 0.038 0.919 + 235 (0.025) 0.007 0.006 0.006 0.003 0.001 + 241 (0.025) 0.003 0.003 0.003 0.015 0.001 + 249 (0.031) 0.004 0.003 0.004 0.004 0.038 + 233 (0.025) 0.007 0.006 0.005 0.003 0.001 + +Locus 19 : Ap249 +10 alleles +2.5% missing data + 209 (0.460) 0.636 0.669 0.633 0.701 0.067 + 211 (0.057) 0.048 0.045 0.048 0.005 0.001 + 217 (0.122) 0.111 0.105 0.126 0.022 0.134 + 219 (0.144) 0.139 0.120 0.133 0.019 0.651 + 215 (0.081) 0.034 0.034 0.032 0.235 0.006 + 208 (0.023) 0.005 0.006 0.007 0.002 0.001 + 225 (0.030) 0.004 0.004 0.004 0.003 0.030 + 223 (0.038) 0.014 0.010 0.009 0.003 0.107 + 213 (0.023) 0.003 0.003 0.003 0.009 0.001 + 207 (0.022) 0.005 0.005 0.005 0.002 0.002 + +Locus 20 : Ap273 +4 alleles +3.3% missing data + 106 (0.837) 0.946 0.951 0.950 0.945 0.628 + 108 (0.072) 0.030 0.026 0.026 0.024 0.015 + 104 (0.046) 0.012 0.012 0.011 0.003 0.353 + 102 (0.045) 0.012 0.011 0.013 0.028 0.004 + +Locus 21 : Ap274 +3 alleles +2.5% missing data + 120 (0.930) 0.985 0.986 0.986 0.909 0.993 + 122 (0.046) 0.013 0.011 0.011 0.089 0.001 + 112 (0.024) 0.003 0.003 0.003 0.002 0.006 + +Locus 22 : Ap288 +7 alleles +0.0% missing data + 123 (0.600) 0.711 0.730 0.721 0.938 0.103 + 131 (0.243) 0.250 0.233 0.239 0.051 0.742 + 139 (0.052) 0.019 0.019 0.022 0.004 0.047 + 121 (0.023) 0.007 0.006 0.005 0.002 0.001 + 124 (0.024) 0.006 0.007 0.006 0.002 0.001 + 133 (0.031) 0.004 0.004 0.005 0.002 0.055 + 127 (0.027) 0.003 0.002 0.002 0.002 0.052 + +Locus 23 : At163 +7 alleles +1.3% missing data + 128 (0.637) 0.742 0.728 0.717 0.913 0.422 + 134 (0.235) 0.230 0.246 0.254 0.061 0.562 + 130 (0.026) 0.009 0.010 0.012 0.002 0.001 + 136 (0.033) 0.009 0.007 0.006 0.002 0.014 + 140 (0.023) 0.004 0.004 0.004 0.007 0.001 + 146 (0.023) 0.004 0.003 0.004 0.007 0.001 + 142 (0.023) 0.003 0.003 0.003 0.008 0.001 + +Locus 24 : At188 +15 alleles +2.9% missing data + 189 (0.436) 0.746 0.739 0.731 0.882 0.069 + 205 (0.050) 0.026 0.026 0.033 0.003 0.111 + 207 (0.038) 0.041 0.046 0.044 0.003 0.002 + 219 (0.040) 0.013 0.013 0.014 0.003 0.019 + 209 (0.054) 0.027 0.036 0.031 0.005 0.144 + 217 (0.051) 0.021 0.025 0.028 0.004 0.063 + 215 (0.039) 0.014 0.012 0.011 0.003 0.087 + 199 (0.084) 0.051 0.037 0.039 0.055 0.167 + 212 (0.035) 0.016 0.024 0.022 0.004 0.004 + 213 (0.049) 0.023 0.022 0.026 0.004 0.145 + 211 (0.032) 0.007 0.006 0.007 0.002 0.122 + 191 (0.021) 0.007 0.006 0.006 0.001 0.001 + 187 (0.023) 0.003 0.002 0.002 0.027 0.001 + 203 (0.023) 0.003 0.003 0.003 0.002 0.012 + 221 (0.024) 0.002 0.002 0.002 0.001 0.054 + +Values of parameters used in structure: +DATAFILE=E:\AU\Alexander\alex3\STRUCTURE\alex3\project_data, OUTFILE=E:\AU\Alexander\alex3\STRUCTURE\alex3\long\Results\long_run_4, NUMINDS=239, NUMLOCI=24, MISSING=-9, LABEL=1, POPDATA=0, POPFLAG=1, PHENOTYPE=0, EXTRACOLS=1, MAXPOPS=5, BURNIN=100000, NUMREPS=1000000, USEPOPINFO=0, INFERALPHA=1, INFERLAMBDA=0, POPSPECIFICLAMBDA=0, POPALPHAS=0, COMPUTEPROB=1, NOADMIX=0, ADMBURNIN=2500, UPDATEFREQ=1, PRINTLIKES=0, INTERMEDSAVE=0, PRINTKLD=0, PRINTNET=0, PRINTLAMBDA=0, ANCESTDIST=0, NUMBOXES=1000, ANCESTPINT=0.90000, GENSBACK=2, MIGRPRIOR=0.05000, PRINTQHAT=0, PRINTQSUM=0, ALPHA=1.0000, FREQSCORR=1, FPRIORMEAN=0.0100, FPRIORSD=0.0500, ONEFST=0, LAMBDA=1.0000, UNIFPRIORALPHA=1, ALPHAMAX=10.0000, ALPHAPRIORA=1.0000, ALPHAPRIORB=2.0000, ALPHAPROPSD=0.0250, STARTATPOPINFO=0, RANDOMIZE=1, LINKAGE=0, METROFREQ=10, REPORTHITRATE=0, MARKOVPHASE=-1, PHASED=0, PLOIDY=2, PHASEINFO=0 LOCPRIOR=0, LOCPRIORINIT=1.000000, LOCDATA=0, LOCISPOP=0, LOCPRIORSTEP=0.100000, MAXLOCPRIOR=20.000000, SEED=1335139730, +[STRAT parameters]: NUMSIMSTATS=1000, PHENOTYPECOL=-9, POOLFREQ=10, LOCUSxONLY=0, EMERROR=0.00100, MISSINGPHENO=-9, \ No newline at end of file diff --git a/inst/files/TESSpop_K5-combined-aligned.txt b/inst/files/TESSpop_K5-combined-aligned.txt new file mode 100644 index 0000000..853520c --- /dev/null +++ b/inst/files/TESSpop_K5-combined-aligned.txt @@ -0,0 +1,228 @@ + 1: 0.0217 0.7877 0.1490 0.0061 0.0355 1 + 2: 0.0226 0.8176 0.0541 0.0102 0.0955 1 + 3: 0.0070 0.9355 0.0307 0.0017 0.0252 1 + 4: 0.0299 0.7678 0.1316 0.0061 0.0646 1 + 5: 0.0428 0.8366 0.0952 0.0024 0.0231 1 + 6: 0.0118 0.9169 0.0562 0.0026 0.0125 1 + 7: 0.1507 0.4146 0.3227 0.0045 0.1075 1 + 8: 0.0707 0.7231 0.1031 0.0054 0.0977 1 + 9: 0.1301 0.7621 0.0620 0.0028 0.0429 1 +10: 0.0564 0.7007 0.1619 0.0093 0.0717 1 +11: 0.0550 0.5866 0.2967 0.0074 0.0543 1 +12: 0.0162 0.8653 0.0494 0.0048 0.0642 1 +13: 0.0256 0.7424 0.1386 0.0072 0.0863 1 +14: 0.0165 0.8477 0.0981 0.0063 0.0314 1 +15: 0.0200 0.8146 0.0938 0.0076 0.0640 1 +16: 0.0100 0.9374 0.0290 0.0024 0.0212 1 +17: 0.0303 0.7487 0.1251 0.0093 0.0865 1 +18: 0.0317 0.8006 0.1025 0.0119 0.0533 1 +19: 0.0242 0.5744 0.3303 0.0149 0.0562 1 +20: 0.0353 0.7326 0.1417 0.0158 0.0745 1 +21: 0.0221 0.5035 0.2858 0.0144 0.1742 1 +22: 0.0336 0.3958 0.2804 0.0195 0.2707 1 +23: 0.0020 0.9226 0.0658 0.0015 0.0081 1 +24: 0.0077 0.8097 0.1107 0.0046 0.0673 1 +25: 0.0079 0.8692 0.0792 0.0050 0.0388 1 +26: 0.0127 0.7785 0.0945 0.0059 0.1084 1 +27: 0.0089 0.8957 0.0426 0.0083 0.0445 1 +28: 0.0052 0.9083 0.0418 0.0023 0.0424 1 +29: 0.0067 0.8683 0.0319 0.0150 0.0780 1 +30: 0.0093 0.5627 0.0205 0.0098 0.3976 1 +31: 0.0058 0.5112 0.0139 0.0011 0.4681 1 +32: 0.0106 0.7734 0.0153 0.0024 0.1982 1 +33: 0.0151 0.4200 0.0102 0.0039 0.5509 1 +34: 0.0052 0.4017 0.0053 0.0022 0.5856 1 +35: 0.0106 0.7192 0.0320 0.0063 0.2319 1 +36: 0.0257 0.8384 0.0601 0.0111 0.0647 1 +37: 0.0162 0.8669 0.0585 0.0050 0.0535 1 +38: 0.0254 0.8885 0.0274 0.0025 0.0561 1 +39: 0.0068 0.8497 0.0108 0.0058 0.1269 1 +40: 0.0025 0.9362 0.0211 0.0037 0.0365 1 +41: 0.0100 0.9406 0.0131 0.0023 0.0341 1 +42: 0.0090 0.7539 0.0136 0.0012 0.2223 1 +43: 0.0134 0.8961 0.0546 0.0018 0.0342 1 +44: 0.0238 0.8957 0.0227 0.0023 0.0555 1 +45: 0.1015 0.7445 0.1400 0.0052 0.0088 1 +46: 0.0233 0.8192 0.1521 0.0019 0.0035 1 +47: 0.0499 0.8545 0.0813 0.0042 0.0102 1 +48: 0.3931 0.5951 0.0111 0.0003 0.0005 1 +49: 0.1428 0.5959 0.2327 0.0037 0.0249 1 +50: 0.1004 0.6127 0.2692 0.0030 0.0147 1 +51: 0.1175 0.7095 0.1434 0.0043 0.0253 1 +52: 0.0324 0.8671 0.0950 0.0009 0.0047 1 +53: 0.0205 0.8871 0.0707 0.0035 0.0183 1 +54: 0.1639 0.6682 0.1426 0.0074 0.0179 1 +55: 0.0813 0.7168 0.1701 0.0068 0.0250 1 +56: 0.0434 0.8120 0.1238 0.0058 0.0150 1 +57: 0.0340 0.6568 0.2966 0.0057 0.0069 1 +58: 0.0163 0.8736 0.1023 0.0026 0.0052 1 +59: 0.0397 0.5721 0.3592 0.0064 0.0227 1 +60: 0.0632 0.5645 0.2891 0.0108 0.0723 1 +61: 0.0328 0.8698 0.0660 0.0107 0.0207 1 +62: 0.0512 0.5776 0.2127 0.0223 0.1362 1 +63: 0.0281 0.6658 0.2685 0.0104 0.0272 1 +64: 0.0926 0.5004 0.3456 0.0193 0.0420 1 +65: 0.0036 0.4667 0.4980 0.0078 0.0239 1 +66: 0.0060 0.7695 0.1816 0.0056 0.0374 1 +67: 0.0037 0.8562 0.1089 0.0040 0.0272 1 +68: 0.0049 0.8321 0.1223 0.0094 0.0313 1 +69: 0.0044 0.9140 0.0609 0.0070 0.0137 1 +70: 0.0062 0.8378 0.1171 0.0112 0.0278 1 +71: 0.0035 0.9365 0.0429 0.0044 0.0127 1 +72: 0.0045 0.9062 0.0291 0.0040 0.0562 1 +73: 0.0004 0.2769 0.0004 0.0003 0.7219 1 +74: 0.0054 0.7236 0.0255 0.0046 0.2409 1 +75: 0.0104 0.8404 0.0330 0.0087 0.1074 1 + + 1: 0.0083 0.9713 0.0076 0.0059 0.0069 1 + 2: 0.0070 0.9748 0.0069 0.0050 0.0063 1 + 3: 0.0033 0.9869 0.0036 0.0029 0.0034 1 + 4: 0.0110 0.9593 0.0109 0.0091 0.0097 1 + 5: 0.0099 0.9656 0.0091 0.0069 0.0086 1 + 6: 0.0041 0.9850 0.0039 0.0028 0.0043 1 + 7: 0.0616 0.7769 0.0609 0.0424 0.0582 1 + 8: 0.0141 0.9489 0.0135 0.0111 0.0123 1 + 9: 0.0218 0.9202 0.0211 0.0185 0.0183 1 +10: 0.0192 0.9298 0.0187 0.0150 0.0174 1 +11: 0.0250 0.9172 0.0226 0.0150 0.0201 1 +12: 0.0058 0.9789 0.0052 0.0048 0.0054 1 +13: 0.0126 0.9560 0.0109 0.0090 0.0116 1 +14: 0.0107 0.9585 0.0107 0.0087 0.0114 1 +15: 0.0111 0.9595 0.0106 0.0082 0.0106 1 +16: 0.0026 0.9898 0.0027 0.0021 0.0028 1 +17: 0.0105 0.9595 0.0101 0.0091 0.0108 1 +18: 0.0128 0.9523 0.0126 0.0097 0.0125 1 +19: 0.0434 0.8218 0.0457 0.0442 0.0449 1 +20: 0.0230 0.9081 0.0237 0.0203 0.0249 1 +21: 0.0286 0.8874 0.0305 0.0239 0.0296 1 +22: 0.0549 0.7848 0.0529 0.0489 0.0585 1 +23: 0.0032 0.9863 0.0036 0.0032 0.0036 1 +24: 0.0058 0.9781 0.0055 0.0050 0.0056 1 +25: 0.0067 0.9710 0.0073 0.0067 0.0083 1 +26: 0.0077 0.9695 0.0077 0.0067 0.0084 1 +27: 0.0080 0.9684 0.0083 0.0071 0.0082 1 +28: 0.0030 0.9879 0.0031 0.0026 0.0034 1 +29: 0.0084 0.9613 0.0102 0.0092 0.0110 1 +30: 0.0128 0.9467 0.0143 0.0115 0.0147 1 +31: 0.0053 0.9803 0.0050 0.0041 0.0053 1 +32: 0.0034 0.9868 0.0035 0.0028 0.0036 1 +33: 0.0088 0.9663 0.0091 0.0067 0.0091 1 +34: 0.0048 0.9816 0.0046 0.0039 0.0051 1 +35: 0.0069 0.9745 0.0068 0.0049 0.0069 1 +36: 0.0057 0.9773 0.0060 0.0046 0.0063 1 +37: 0.0063 0.9751 0.0066 0.0054 0.0066 1 +38: 0.0096 0.9642 0.0097 0.0068 0.0097 1 +39: 0.0111 0.9583 0.0108 0.0080 0.0118 1 +40: 0.0044 0.9839 0.0043 0.0030 0.0045 1 +41: 0.0066 0.9720 0.0083 0.0057 0.0075 1 +42: 0.0049 0.9818 0.0050 0.0034 0.0048 1 +43: 0.0061 0.9771 0.0062 0.0047 0.0059 1 +44: 0.0046 0.9828 0.0046 0.0036 0.0044 1 +45: 0.0288 0.8981 0.0271 0.0235 0.0224 1 +46: 0.0106 0.9616 0.0105 0.0087 0.0087 1 +47: 0.0314 0.8898 0.0293 0.0250 0.0246 1 +48: 0.0457 0.8309 0.0454 0.0396 0.0383 1 +49: 0.0483 0.8329 0.0447 0.0342 0.0399 1 +50: 0.0395 0.8567 0.0386 0.0294 0.0358 1 +51: 0.0523 0.8064 0.0487 0.0447 0.0479 1 +52: 0.0133 0.9510 0.0130 0.0117 0.0111 1 +53: 0.0073 0.9737 0.0067 0.0060 0.0063 1 +54: 0.0382 0.8610 0.0371 0.0296 0.0341 1 +55: 0.0149 0.9457 0.0141 0.0107 0.0146 1 +56: 0.0156 0.9448 0.0143 0.0118 0.0134 1 +57: 0.0289 0.8959 0.0266 0.0252 0.0235 1 +58: 0.0107 0.9620 0.0098 0.0089 0.0086 1 +59: 0.0439 0.8443 0.0429 0.0316 0.0372 1 +60: 0.0341 0.8779 0.0343 0.0231 0.0305 1 +61: 0.0126 0.9497 0.0135 0.0114 0.0128 1 +62: 0.0429 0.8396 0.0406 0.0375 0.0395 1 +63: 0.0211 0.9215 0.0213 0.0170 0.0192 1 +64: 0.0690 0.7436 0.0693 0.0553 0.0627 1 +65: 0.0184 0.9121 0.0238 0.0214 0.0243 1 +66: 0.0100 0.9493 0.0130 0.0126 0.0151 1 +67: 0.0037 0.9837 0.0040 0.0037 0.0048 1 +68: 0.0097 0.9564 0.0113 0.0104 0.0122 1 +69: 0.0039 0.9825 0.0047 0.0044 0.0046 1 +70: 0.0063 0.9705 0.0081 0.0070 0.0081 1 +71: 0.0031 0.9862 0.0036 0.0033 0.0038 1 +72: 0.0034 0.9864 0.0035 0.0028 0.0039 1 +73: 0.0043 0.9844 0.0037 0.0034 0.0042 1 +74: 0.0081 0.9686 0.0082 0.0068 0.0083 1 +75: 0.0059 0.9763 0.0064 0.0049 0.0065 1 + + 1: 0.0005 0.9987 0.0008 0.0000 0.0001 1 + 2: 0.0000 0.9999 0.0000 0.0000 0.0001 1 + 3: 0.0000 1.0000 0.0000 0.0000 0.0000 1 + 4: 0.0005 0.9981 0.0003 0.0002 0.0009 1 + 5: 0.0012 0.9944 0.0009 0.0024 0.0012 1 + 6: 0.0000 1.0000 0.0000 0.0000 0.0000 1 + 7: 0.0337 0.8689 0.0336 0.0277 0.0361 1 + 8: 0.0000 0.9998 0.0000 0.0000 0.0002 1 + 9: 0.0006 0.9936 0.0017 0.0019 0.0022 1 +10: 0.0052 0.9752 0.0077 0.0083 0.0036 1 +11: 0.0001 0.9986 0.0008 0.0003 0.0003 1 +12: 0.0000 1.0000 0.0000 0.0000 0.0000 1 +13: 0.0000 1.0000 0.0000 0.0000 0.0000 1 +14: 0.0000 1.0000 0.0000 0.0000 0.0000 1 +15: 0.0079 0.9681 0.0090 0.0066 0.0084 1 +16: 0.0000 1.0000 0.0000 0.0000 0.0000 1 +17: 0.0016 0.9961 0.0008 0.0006 0.0009 1 +18: 0.0004 0.9955 0.0018 0.0008 0.0015 1 +19: 0.0256 0.8800 0.0271 0.0314 0.0359 1 +20: 0.0166 0.9374 0.0140 0.0103 0.0217 1 +21: 0.0066 0.9725 0.0085 0.0058 0.0066 1 +22: 0.2326 0.1078 0.1923 0.2563 0.2110 1 +23: 0.0000 0.9999 0.0000 0.0001 0.0000 1 +24: 0.0000 1.0000 0.0000 0.0000 0.0000 1 +25: 0.0000 0.9999 0.0001 0.0000 0.0000 1 +26: 0.0000 0.9995 0.0004 0.0000 0.0001 1 +27: 0.0000 1.0000 0.0001 0.0000 0.0000 1 +28: 0.0000 0.9999 0.0000 0.0001 0.0000 1 +29: 0.0049 0.9738 0.0080 0.0056 0.0076 1 +30: 0.0868 0.6468 0.1000 0.0637 0.1027 1 +31: 0.0040 0.9743 0.0055 0.0046 0.0116 1 +32: 0.0000 0.9999 0.0001 0.0000 0.0000 1 +33: 0.0011 0.9855 0.0023 0.0022 0.0091 1 +34: 0.0003 0.9919 0.0000 0.0001 0.0076 1 +35: 0.0048 0.9755 0.0048 0.0084 0.0065 1 +36: 0.0017 0.9942 0.0015 0.0021 0.0006 1 +37: 0.0000 1.0000 0.0000 0.0000 0.0000 1 +38: 0.0009 0.9959 0.0014 0.0009 0.0009 1 +39: 0.0012 0.9954 0.0013 0.0001 0.0020 1 +40: 0.0000 0.9999 0.0000 0.0000 0.0000 1 +41: 0.0001 0.9973 0.0012 0.0006 0.0008 1 +42: 0.0000 0.9994 0.0000 0.0000 0.0006 1 +43: 0.0000 0.9998 0.0000 0.0001 0.0001 1 +44: 0.0014 0.9931 0.0018 0.0015 0.0022 1 +45: 0.0374 0.8635 0.0318 0.0343 0.0331 1 +46: 0.0000 0.9999 0.0000 0.0000 0.0001 1 +47: 0.0011 0.9967 0.0007 0.0004 0.0011 1 +48: 0.0085 0.9678 0.0087 0.0059 0.0092 1 +49: 0.0473 0.8338 0.0330 0.0318 0.0540 1 +50: 0.0003 0.9952 0.0023 0.0010 0.0012 1 +51: 0.1142 0.5607 0.1043 0.1113 0.1094 1 +52: 0.0112 0.9604 0.0067 0.0096 0.0121 1 +53: 0.0000 1.0000 0.0000 0.0000 0.0000 1 +54: 0.0010 0.9893 0.0024 0.0017 0.0056 1 +55: 0.0001 0.9994 0.0002 0.0002 0.0001 1 +56: 0.0002 0.9980 0.0005 0.0006 0.0007 1 +57: 0.0031 0.9840 0.0031 0.0038 0.0061 1 +58: 0.0002 0.9995 0.0003 0.0000 0.0000 1 +59: 0.0817 0.6247 0.1129 0.0825 0.0982 1 +60: 0.0294 0.8869 0.0224 0.0242 0.0371 1 +61: 0.0002 0.9991 0.0004 0.0000 0.0004 1 +62: 0.0017 0.9914 0.0030 0.0009 0.0030 1 +63: 0.0004 0.9970 0.0015 0.0006 0.0005 1 +64: 0.1258 0.4149 0.1686 0.1278 0.1630 1 +65: 0.0019 0.9778 0.0062 0.0058 0.0082 1 +66: 0.0015 0.9877 0.0047 0.0018 0.0043 1 +67: 0.0003 0.9972 0.0007 0.0011 0.0006 1 +68: 0.0001 0.9993 0.0002 0.0003 0.0001 1 +69: 0.0165 0.9379 0.0124 0.0215 0.0118 1 +70: 0.0020 0.9910 0.0023 0.0030 0.0017 1 +71: 0.0002 0.9991 0.0004 0.0002 0.0000 1 +72: 0.0033 0.9888 0.0025 0.0021 0.0033 1 +73: 0.0008 0.9889 0.0016 0.0018 0.0068 1 +74: 0.0039 0.9922 0.0012 0.0015 0.0013 1 +75: 0.0022 0.9864 0.0033 0.0024 0.0056 1 + diff --git a/inst/files/TESSpop_K5-combined-merged.txt b/inst/files/TESSpop_K5-combined-merged.txt new file mode 100644 index 0000000..d839f53 --- /dev/null +++ b/inst/files/TESSpop_K5-combined-merged.txt @@ -0,0 +1,75 @@ + 1: 0.0101 0.9192 0.0524 0.0040 0.0142 1 + 2: 0.0099 0.9307 0.0204 0.0051 0.0340 1 + 3: 0.0035 0.9741 0.0114 0.0015 0.0095 1 + 4: 0.0138 0.9084 0.0476 0.0051 0.0250 1 + 5: 0.0180 0.9322 0.0351 0.0039 0.0109 1 + 6: 0.0053 0.9673 0.0200 0.0018 0.0056 1 + 7: 0.0820 0.6868 0.1391 0.0248 0.0673 1 + 8: 0.0283 0.8906 0.0389 0.0055 0.0367 1 + 9: 0.0508 0.8920 0.0283 0.0077 0.0212 1 +10: 0.0269 0.8686 0.0628 0.0109 0.0309 1 +11: 0.0267 0.8341 0.1067 0.0076 0.0249 1 +12: 0.0074 0.9481 0.0182 0.0032 0.0232 1 +13: 0.0127 0.8995 0.0498 0.0054 0.0326 1 +14: 0.0091 0.9354 0.0363 0.0050 0.0143 1 +15: 0.0130 0.9141 0.0378 0.0075 0.0277 1 +16: 0.0042 0.9757 0.0106 0.0015 0.0080 1 +17: 0.0141 0.9014 0.0453 0.0064 0.0327 1 +18: 0.0150 0.9161 0.0390 0.0075 0.0224 1 +19: 0.0311 0.7587 0.1343 0.0302 0.0457 1 +20: 0.0250 0.8594 0.0598 0.0155 0.0404 1 +21: 0.0191 0.7878 0.1082 0.0147 0.0701 1 +22: 0.1070 0.4295 0.1752 0.1083 0.1801 1 +23: 0.0018 0.9696 0.0231 0.0016 0.0039 1 +24: 0.0045 0.9292 0.0387 0.0032 0.0243 1 +25: 0.0048 0.9467 0.0288 0.0039 0.0157 1 +26: 0.0068 0.9158 0.0342 0.0042 0.0390 1 +27: 0.0056 0.9547 0.0170 0.0051 0.0175 1 +28: 0.0027 0.9654 0.0150 0.0017 0.0153 1 +29: 0.0067 0.9345 0.0167 0.0099 0.0322 1 +30: 0.0363 0.7188 0.0449 0.0283 0.1717 1 +31: 0.0050 0.8219 0.0081 0.0033 0.1617 1 +32: 0.0047 0.9200 0.0063 0.0017 0.0673 1 +33: 0.0083 0.7906 0.0072 0.0043 0.1897 1 +34: 0.0034 0.7917 0.0033 0.0020 0.1995 1 +35: 0.0074 0.8897 0.0145 0.0066 0.0818 1 +36: 0.0110 0.9366 0.0225 0.0060 0.0239 1 +37: 0.0075 0.9473 0.0217 0.0035 0.0200 1 +38: 0.0120 0.9495 0.0129 0.0034 0.0222 1 +39: 0.0064 0.9344 0.0076 0.0047 0.0469 1 +40: 0.0023 0.9733 0.0085 0.0022 0.0137 1 +41: 0.0056 0.9699 0.0075 0.0029 0.0141 1 +42: 0.0046 0.9117 0.0062 0.0016 0.0759 1 +43: 0.0065 0.9577 0.0203 0.0022 0.0134 1 +44: 0.0100 0.9572 0.0097 0.0025 0.0207 1 +45: 0.0559 0.8354 0.0663 0.0210 0.0214 1 +46: 0.0113 0.9269 0.0542 0.0035 0.0041 1 +47: 0.0274 0.9137 0.0371 0.0099 0.0120 1 +48: 0.1491 0.7979 0.0217 0.0153 0.0160 1 +49: 0.0795 0.7542 0.1035 0.0232 0.0396 1 +50: 0.0468 0.8216 0.1033 0.0111 0.0172 1 +51: 0.0947 0.6922 0.0988 0.0534 0.0609 1 +52: 0.0189 0.9261 0.0382 0.0074 0.0093 1 +53: 0.0093 0.9536 0.0258 0.0031 0.0082 1 +54: 0.0677 0.8395 0.0607 0.0129 0.0192 1 +55: 0.0321 0.8873 0.0615 0.0059 0.0132 1 +56: 0.0198 0.9183 0.0462 0.0061 0.0097 1 +57: 0.0220 0.8456 0.1087 0.0115 0.0122 1 +58: 0.0091 0.9450 0.0375 0.0038 0.0046 1 +59: 0.0551 0.6804 0.1717 0.0401 0.0527 1 +60: 0.0422 0.7765 0.1153 0.0194 0.0467 1 +61: 0.0152 0.9395 0.0266 0.0074 0.0113 1 +62: 0.0319 0.8029 0.0854 0.0202 0.0595 1 +63: 0.0165 0.8614 0.0971 0.0093 0.0156 1 +64: 0.0958 0.5530 0.1945 0.0675 0.0893 1 +65: 0.0080 0.7855 0.1760 0.0117 0.0188 1 +66: 0.0058 0.9021 0.0664 0.0067 0.0190 1 +67: 0.0026 0.9457 0.0379 0.0029 0.0109 1 +68: 0.0049 0.9293 0.0446 0.0067 0.0145 1 +69: 0.0082 0.9448 0.0260 0.0110 0.0100 1 +70: 0.0048 0.9331 0.0425 0.0071 0.0125 1 +71: 0.0023 0.9740 0.0157 0.0026 0.0055 1 +72: 0.0037 0.9605 0.0117 0.0030 0.0211 1 +73: 0.0019 0.7501 0.0019 0.0018 0.2443 1 +74: 0.0058 0.8948 0.0116 0.0043 0.0835 1 +75: 0.0062 0.9344 0.0142 0.0053 0.0399 1 diff --git a/inst/files/TESSpop_K5-combined.txt b/inst/files/TESSpop_K5-combined.txt new file mode 100644 index 0000000..c44c092 --- /dev/null +++ b/inst/files/TESSpop_K5-combined.txt @@ -0,0 +1,229 @@ +1: 0.787660 0.035545 0.021665 0.148980 0.006150 1 +2: 0.817585 0.095465 0.022575 0.054130 0.010245 1 +3: 0.935455 0.025210 0.007015 0.030660 0.001660 1 +4: 0.767805 0.064570 0.029915 0.131635 0.006075 1 +5: 0.836550 0.023065 0.042845 0.095180 0.002360 1 +6: 0.916895 0.012525 0.011800 0.056220 0.002560 1 +7: 0.414585 0.107505 0.150730 0.322700 0.004480 1 +8: 0.723070 0.097715 0.070690 0.103095 0.005430 1 +9: 0.762105 0.042930 0.130130 0.062035 0.002800 1 +10: 0.700740 0.071655 0.056360 0.161935 0.009310 1 +11: 0.586635 0.054310 0.054970 0.296680 0.007405 1 +12: 0.865345 0.064235 0.016240 0.049420 0.004760 1 +13: 0.742435 0.086295 0.025555 0.138560 0.007155 1 +14: 0.847705 0.031365 0.016500 0.098125 0.006305 1 +15: 0.814595 0.063985 0.020000 0.093790 0.007630 1 +16: 0.937370 0.021225 0.010020 0.029015 0.002370 1 +17: 0.748705 0.086540 0.030325 0.125095 0.009335 1 +18: 0.800610 0.053275 0.031685 0.102520 0.011910 1 +19: 0.574400 0.056205 0.024215 0.330255 0.014925 1 +20: 0.732615 0.074540 0.035340 0.141665 0.015840 1 +21: 0.503500 0.174230 0.022075 0.285750 0.014445 1 +22: 0.395820 0.270670 0.033610 0.280365 0.019535 1 +23: 0.922555 0.008115 0.002015 0.065815 0.001500 1 +24: 0.809655 0.067335 0.007700 0.110700 0.004610 1 +25: 0.869160 0.038795 0.007870 0.079160 0.005015 1 +26: 0.778535 0.108365 0.012665 0.094500 0.005935 1 +27: 0.895745 0.044455 0.008870 0.042595 0.008335 1 +28: 0.908325 0.042380 0.005220 0.041770 0.002305 1 +29: 0.868345 0.078020 0.006740 0.031870 0.015025 1 +30: 0.562750 0.397610 0.009310 0.020535 0.009795 1 +31: 0.511225 0.468060 0.005765 0.013875 0.001075 1 +32: 0.773375 0.198245 0.010645 0.015295 0.002440 1 +33: 0.419985 0.550890 0.015080 0.010195 0.003850 1 +34: 0.401690 0.585635 0.005240 0.005285 0.002150 1 +35: 0.719160 0.231900 0.010600 0.032000 0.006340 1 +36: 0.838430 0.064685 0.025690 0.060065 0.011130 1 +37: 0.866880 0.053490 0.016175 0.058465 0.004990 1 +38: 0.888505 0.056145 0.025365 0.027445 0.002540 1 +39: 0.849665 0.126890 0.006785 0.010825 0.005835 1 +40: 0.936230 0.036545 0.002460 0.021080 0.003685 1 +41: 0.940560 0.034055 0.010030 0.013065 0.002290 1 +42: 0.753860 0.222330 0.008965 0.013600 0.001245 1 +43: 0.896105 0.034175 0.013355 0.054600 0.001765 1 +44: 0.895730 0.055500 0.023825 0.022680 0.002265 1 +45: 0.744490 0.008810 0.101545 0.139980 0.005175 1 +46: 0.819225 0.003525 0.023335 0.152060 0.001855 1 +47: 0.854465 0.010190 0.049865 0.081295 0.004185 1 +48: 0.595100 0.000515 0.393050 0.011060 0.000275 1 +49: 0.595900 0.024860 0.142800 0.232720 0.003720 1 +50: 0.612745 0.014675 0.100440 0.269185 0.002955 1 +51: 0.709530 0.025255 0.117545 0.143400 0.004270 1 +52: 0.867065 0.004685 0.032370 0.094960 0.000920 1 +53: 0.887065 0.018265 0.020470 0.070735 0.003465 1 +54: 0.668190 0.017880 0.163935 0.142560 0.007435 1 +55: 0.716825 0.024995 0.081275 0.170090 0.006815 1 +56: 0.812025 0.014975 0.043445 0.123760 0.005795 1 +57: 0.656825 0.006890 0.034025 0.296610 0.005650 1 +58: 0.873575 0.005165 0.016310 0.102345 0.002605 1 +59: 0.572085 0.022730 0.039660 0.359160 0.006365 1 +60: 0.564520 0.072335 0.063200 0.289110 0.010835 1 +61: 0.869835 0.020690 0.032750 0.066020 0.010705 1 +62: 0.577630 0.136195 0.051195 0.212715 0.022265 1 +63: 0.665770 0.027180 0.028125 0.268480 0.010445 1 +64: 0.500445 0.042015 0.092590 0.345610 0.019340 1 +65: 0.466745 0.023915 0.003565 0.498015 0.007760 1 +66: 0.769470 0.037415 0.005950 0.181610 0.005555 1 +67: 0.856160 0.027240 0.003685 0.108950 0.003965 1 +68: 0.832130 0.031305 0.004875 0.122325 0.009365 1 +69: 0.914005 0.013695 0.004350 0.060940 0.007010 1 +70: 0.837785 0.027755 0.006190 0.117055 0.011215 1 +71: 0.936495 0.012705 0.003520 0.042920 0.004360 1 +72: 0.906210 0.056205 0.004510 0.029120 0.003955 1 +73: 0.276935 0.721920 0.000435 0.000370 0.000340 1 +74: 0.723590 0.240885 0.005445 0.025530 0.004550 1 +75: 0.840400 0.107435 0.010435 0.032995 0.008735 1 + + +1: 0.0058935 0.9713445 0.0075575 0.0082620 0.0069425 1 +2: 0.0049525 0.9747720 0.0069390 0.0070255 0.0063110 1 +3: 0.0028710 0.9868710 0.0035705 0.0033375 0.0033500 1 +4: 0.0090965 0.9593120 0.0108940 0.0109855 0.0097120 1 +5: 0.0068960 0.9655860 0.0090810 0.0098575 0.0085795 1 +6: 0.0028060 0.9849570 0.0039040 0.0040640 0.0042690 1 +7: 0.0423900 0.7769025 0.0608730 0.0616475 0.0581870 1 +8: 0.0111065 0.9488845 0.0135210 0.0141500 0.0123380 1 +9: 0.0185415 0.9202125 0.0211265 0.0217775 0.0183420 1 +10: 0.0150095 0.9297750 0.0186810 0.0191520 0.0173825 1 +11: 0.0150345 0.9171770 0.0226360 0.0250110 0.0201415 1 +12: 0.0047575 0.9788545 0.0051720 0.0058255 0.0053905 1 +13: 0.0089755 0.9559960 0.0108740 0.0125610 0.0115935 1 +14: 0.0086680 0.9585350 0.0107075 0.0107190 0.0113705 1 +15: 0.0081650 0.9595240 0.0106225 0.0110665 0.0106220 1 +16: 0.0021405 0.9898200 0.0026870 0.0025860 0.0027665 1 +17: 0.0091180 0.9594530 0.0101395 0.0104755 0.0108140 1 +18: 0.0097025 0.9523145 0.0126225 0.0128220 0.0125385 1 +19: 0.0442270 0.8218060 0.0457145 0.0433645 0.0448880 1 +20: 0.0203435 0.9081285 0.0237070 0.0229685 0.0248525 1 +21: 0.0239455 0.8874025 0.0305085 0.0285885 0.0295550 1 +22: 0.0489265 0.7847730 0.0528875 0.0548875 0.0585255 1 +23: 0.0032500 0.9863415 0.0035545 0.0032375 0.0036165 1 +24: 0.0050180 0.9780895 0.0054690 0.0058320 0.0055915 1 +25: 0.0066995 0.9710115 0.0072660 0.0066755 0.0083475 1 +26: 0.0066715 0.9695165 0.0077210 0.0076905 0.0084005 1 +27: 0.0070885 0.9684075 0.0082970 0.0080480 0.0081590 1 +28: 0.0026370 0.9878565 0.0030935 0.0030260 0.0033870 1 +29: 0.0091615 0.9612695 0.0101740 0.0083910 0.0110040 1 +30: 0.0114755 0.9467330 0.0142810 0.0127610 0.0147495 1 +31: 0.0041220 0.9802500 0.0049825 0.0053295 0.0053160 1 +32: 0.0027665 0.9867575 0.0035060 0.0034025 0.0035675 1 +33: 0.0067485 0.9663380 0.0090525 0.0087675 0.0090935 1 +34: 0.0038770 0.9815775 0.0046485 0.0047860 0.0051110 1 +35: 0.0049240 0.9744520 0.0067985 0.0068935 0.0069320 1 +36: 0.0046460 0.9773385 0.0060295 0.0056540 0.0063320 1 +37: 0.0053630 0.9750925 0.0066225 0.0063265 0.0065955 1 +38: 0.0067900 0.9642015 0.0096685 0.0096275 0.0097125 1 +39: 0.0080075 0.9582590 0.0108340 0.0111190 0.0117805 1 +40: 0.0029655 0.9838610 0.0042835 0.0044275 0.0044625 1 +41: 0.0057020 0.9719515 0.0083020 0.0065780 0.0074665 1 +42: 0.0034180 0.9818265 0.0050500 0.0049365 0.0047690 1 +43: 0.0046820 0.9770750 0.0062145 0.0060950 0.0059335 1 +44: 0.0036095 0.9827770 0.0046160 0.0046430 0.0043545 1 +45: 0.0235225 0.8981460 0.0271305 0.0287945 0.0224065 1 +46: 0.0087335 0.9615635 0.0104530 0.0105640 0.0086860 1 +47: 0.0249875 0.8897725 0.0292595 0.0313530 0.0246275 1 +48: 0.0396410 0.8309170 0.0454375 0.0456665 0.0383380 1 +49: 0.0341720 0.8329330 0.0446610 0.0483110 0.0399230 1 +50: 0.0293930 0.8566985 0.0385740 0.0394960 0.0358385 1 +51: 0.0447275 0.8064180 0.0486820 0.0522975 0.0478750 1 +52: 0.0117135 0.9509540 0.0130010 0.0132760 0.0110555 1 +53: 0.0059550 0.9737445 0.0066590 0.0073490 0.0062925 1 +54: 0.0296010 0.8609895 0.0371300 0.0382215 0.0340580 1 +55: 0.0107045 0.9457290 0.0140635 0.0148560 0.0146470 1 +56: 0.0118425 0.9448470 0.0142970 0.0156365 0.0133770 1 +57: 0.0251700 0.8958710 0.0265755 0.0288555 0.0235280 1 +58: 0.0088810 0.9620225 0.0098265 0.0106975 0.0085725 1 +59: 0.0316020 0.8443185 0.0429495 0.0439175 0.0372125 1 +60: 0.0231100 0.8779420 0.0342925 0.0341140 0.0305415 1 +61: 0.0114085 0.9497005 0.0135100 0.0125615 0.0128195 1 +62: 0.0375030 0.8395875 0.0405510 0.0429050 0.0394535 1 +63: 0.0169640 0.9214610 0.0212665 0.0210955 0.0192130 1 +64: 0.0553385 0.7436260 0.0692795 0.0690480 0.0627080 1 +65: 0.0214350 0.9120610 0.0238270 0.0184045 0.0242725 1 +66: 0.0126385 0.9493105 0.0129595 0.0099585 0.0151330 1 +67: 0.0036890 0.9837380 0.0040440 0.0036895 0.0048395 1 +68: 0.0103870 0.9563725 0.0113265 0.0096975 0.0122165 1 +69: 0.0044230 0.9824645 0.0046535 0.0038655 0.0045935 1 +70: 0.0070085 0.9704785 0.0080590 0.0063480 0.0081060 1 +71: 0.0032700 0.9862165 0.0036155 0.0031075 0.0037905 1 +72: 0.0028445 0.9864145 0.0034655 0.0033510 0.0039245 1 +73: 0.0033680 0.9843790 0.0036930 0.0043295 0.0042305 1 +74: 0.0067955 0.9685910 0.0082085 0.0080610 0.0083440 1 +75: 0.0048615 0.9762830 0.0063940 0.0059310 0.0065305 1 + + +1: 0.00045 0.99871 0.00076 0.00002 0.00006 1 +2: 0.00000 0.99988 0.00000 0.00000 0.00012 1 +3: 0.00004 0.99996 0.00000 0.00000 0.00000 1 +4: 0.00051 0.99808 0.00031 0.00024 0.00086 1 +5: 0.00117 0.99436 0.00090 0.00238 0.00119 1 +6: 0.00000 1.00000 0.00000 0.00000 0.00000 1 +7: 0.03374 0.86885 0.03363 0.02766 0.03612 1 +8: 0.00000 0.99981 0.00000 0.00000 0.00019 1 +9: 0.00062 0.99364 0.00168 0.00186 0.00220 1 +10: 0.00523 0.97517 0.00767 0.00829 0.00364 1 +11: 0.00006 0.99855 0.00085 0.00027 0.00027 1 +12: 0.00000 1.00000 0.00000 0.00000 0.00000 1 +13: 0.00000 1.00000 0.00000 0.00000 0.00000 1 +14: 0.00000 0.99997 0.00000 0.00000 0.00003 1 +15: 0.00789 0.96814 0.00896 0.00662 0.00839 1 +16: 0.00000 1.00000 0.00000 0.00000 0.00000 1 +17: 0.00157 0.99614 0.00077 0.00063 0.00089 1 +18: 0.00044 0.99550 0.00179 0.00080 0.00147 1 +19: 0.02563 0.88004 0.02708 0.03139 0.03586 1 +20: 0.01664 0.93736 0.01396 0.01029 0.02175 1 +21: 0.00656 0.97247 0.00849 0.00584 0.00664 1 +22: 0.23261 0.10782 0.19227 0.25633 0.21097 1 +23: 0.00000 0.99994 0.00000 0.00006 0.00000 1 +24: 0.00002 0.99998 0.00000 0.00000 0.00000 1 +25: 0.00000 0.99993 0.00007 0.00000 0.00000 1 +26: 0.00000 0.99946 0.00037 0.00002 0.00015 1 +27: 0.00000 0.99995 0.00005 0.00000 0.00000 1 +28: 0.00000 0.99994 0.00000 0.00005 0.00001 1 +29: 0.00488 0.97385 0.00803 0.00565 0.00759 1 +30: 0.08676 0.64682 0.09999 0.06370 0.10273 1 +31: 0.00401 0.97426 0.00550 0.00461 0.01162 1 +32: 0.00000 0.99992 0.00005 0.00003 0.00000 1 +33: 0.00106 0.98545 0.00228 0.00216 0.00905 1 +34: 0.00032 0.99192 0.00003 0.00009 0.00764 1 +35: 0.00480 0.97554 0.00478 0.00842 0.00646 1 +36: 0.00166 0.99416 0.00146 0.00214 0.00058 1 +37: 0.00000 1.00000 0.00000 0.00000 0.00000 1 +38: 0.00094 0.99586 0.00144 0.00087 0.00089 1 +39: 0.00122 0.99542 0.00126 0.00011 0.00199 1 +40: 0.00000 0.99994 0.00004 0.00000 0.00002 1 +41: 0.00012 0.99726 0.00120 0.00059 0.00083 1 +42: 0.00000 0.99943 0.00000 0.00000 0.00057 1 +43: 0.00000 0.99980 0.00000 0.00014 0.00006 1 +44: 0.00140 0.99314 0.00179 0.00151 0.00216 1 +45: 0.03736 0.86349 0.03178 0.03431 0.03306 1 +46: 0.00000 0.99991 0.00000 0.00003 0.00006 1 +47: 0.00109 0.99674 0.00070 0.00041 0.00106 1 +48: 0.00847 0.96777 0.00871 0.00585 0.00920 1 +49: 0.04733 0.83381 0.03299 0.03183 0.05404 1 +50: 0.00034 0.99521 0.00227 0.00097 0.00121 1 +51: 0.11419 0.56072 0.10432 0.11134 0.10943 1 +52: 0.01120 0.96035 0.00675 0.00962 0.01208 1 +53: 0.00000 1.00000 0.00000 0.00000 0.00000 1 +54: 0.00098 0.98930 0.00243 0.00172 0.00557 1 +55: 0.00012 0.99937 0.00023 0.00019 0.00009 1 +56: 0.00022 0.99797 0.00051 0.00061 0.00069 1 +57: 0.00307 0.98399 0.00305 0.00376 0.00613 1 +58: 0.00018 0.99950 0.00028 0.00000 0.00004 1 +59: 0.08173 0.62471 0.11293 0.08246 0.09817 1 +60: 0.02940 0.88692 0.02237 0.02419 0.03712 1 +61: 0.00018 0.99905 0.00037 0.00000 0.00040 1 +62: 0.00169 0.99141 0.00304 0.00090 0.00296 1 +63: 0.00039 0.99697 0.00152 0.00058 0.00054 1 +64: 0.12575 0.41490 0.16857 0.12775 0.16303 1 +65: 0.00195 0.97782 0.00620 0.00582 0.00821 1 +66: 0.00153 0.98765 0.00468 0.00179 0.00435 1 +67: 0.00034 0.99722 0.00073 0.00113 0.00058 1 +68: 0.00015 0.99930 0.00016 0.00028 0.00011 1 +69: 0.01646 0.93788 0.01236 0.02153 0.01177 1 +70: 0.00197 0.99102 0.00229 0.00299 0.00173 1 +71: 0.00024 0.99915 0.00044 0.00017 0.00000 1 +72: 0.00328 0.98884 0.00249 0.00209 0.00330 1 +73: 0.00085 0.98889 0.00163 0.00183 0.00680 1 +74: 0.00391 0.99220 0.00118 0.00145 0.00126 1 +75: 0.00221 0.98641 0.00334 0.00240 0.00564 1 diff --git a/inst/files/admixture/admixture_01 b/inst/files/admixture/admixture_01 new file mode 100644 index 0000000..70efa39 --- /dev/null +++ b/inst/files/admixture/admixture_01 @@ -0,0 +1,1592 @@ +0.942995 0.057005 +0.950609 0.049391 +0.972208 0.027792 +0.943619 0.056381 +0.931674 0.068326 +0.944011 0.055989 +0.926197 0.073803 +0.976136 0.023864 +0.950896 0.049104 +0.928412 0.071588 +0.947400 0.052600 +0.932082 0.067918 +0.946954 0.053046 +0.983766 0.016234 +0.946589 0.053411 +0.969502 0.030498 +0.922055 0.077945 +0.894128 0.105872 +0.943422 0.056578 +0.954252 0.045748 +0.947033 0.052967 +0.999715 0.000285 +0.946819 0.053181 +0.954604 0.045396 +0.909505 0.090495 +0.940332 0.059668 +0.639082 0.360918 +0.622274 0.377726 +0.616732 0.383268 +0.642448 0.357552 +0.641160 0.358840 +0.641540 0.358460 +0.627042 0.372958 +0.657607 0.342393 +0.621644 0.378356 +0.648931 0.351069 +0.634822 0.365178 +0.679026 0.320974 +0.626667 0.373333 +0.619516 0.380484 +0.646198 0.353802 +0.654603 0.345397 +0.573052 0.426948 +0.985093 0.014907 +0.602255 0.397745 +0.587242 0.412758 +0.643819 0.356181 +0.972257 0.027743 +0.581180 0.418820 +0.644561 0.355439 +0.164249 0.835751 +0.162269 0.837731 +0.167845 0.832155 +0.151826 0.848174 +0.164632 0.835368 +0.155068 0.844932 +0.151798 0.848202 +0.181025 0.818975 +0.142317 0.857683 +0.155925 0.844075 +0.148766 0.851234 +0.165721 0.834279 +0.159381 0.840619 +0.150911 0.849089 +0.168392 0.831608 +0.150043 0.849957 +0.201719 0.798281 +0.147663 0.852337 +0.151050 0.848950 +0.148403 0.851597 +0.159187 0.840813 +0.153258 0.846742 +0.122764 0.877236 +0.213414 0.786586 +0.194961 0.805039 +0.132046 0.867954 +0.134036 0.865964 +0.141651 0.858349 +0.198572 0.801428 +0.149309 0.850691 +0.144015 0.855985 +0.131570 0.868430 +0.133412 0.866588 +0.149752 0.850248 +0.134842 0.865158 +0.141232 0.858768 +0.191372 0.808628 +0.186282 0.813718 +0.185707 0.814293 +0.163154 0.836846 +0.179260 0.820740 +0.571463 0.428537 +0.578038 0.421962 +0.541042 0.458958 +0.560782 0.439218 +0.523809 0.476191 +0.562594 0.437406 +0.553884 0.446116 +0.543402 0.456598 +0.534428 0.465572 +0.560314 0.439686 +0.558593 0.441407 +0.527709 0.472291 +0.553371 0.446629 +0.543995 0.456005 +0.119573 0.880427 +0.120956 0.879044 +0.136804 0.863196 +0.133869 0.866131 +0.142549 0.857451 +0.122443 0.877557 +0.153973 0.846027 +0.134830 0.865170 +0.133720 0.866280 +0.134511 0.865489 +0.122410 0.877590 +0.150112 0.849888 +0.126873 0.873127 +0.134195 0.865805 +0.125169 0.874831 +0.140622 0.859378 +0.139578 0.860422 +0.134243 0.865757 +0.138198 0.861802 +0.137962 0.862038 +0.240188 0.759812 +0.241234 0.758766 +0.222397 0.777603 +0.210561 0.789439 +0.219998 0.780002 +0.238631 0.761369 +0.207886 0.792114 +0.223897 0.776103 +0.222110 0.777890 +0.237594 0.762406 +0.246692 0.753308 +0.247636 0.752364 +0.243291 0.756709 +0.220667 0.779333 +0.211611 0.788389 +0.274211 0.725789 +0.240787 0.759213 +0.241614 0.758386 +0.154886 0.845114 +0.236905 0.763095 +0.192030 0.807970 +0.223977 0.776023 +0.193600 0.806400 +0.211718 0.788282 +0.225955 0.774045 +0.210629 0.789371 +0.233264 0.766736 +0.176103 0.823897 +0.168992 0.831008 +0.215410 0.784590 +0.216387 0.783613 +0.222145 0.777855 +0.189504 0.810496 +0.231347 0.768653 +0.177212 0.822788 +0.196519 0.803481 +0.231271 0.768729 +0.185412 0.814588 +0.170804 0.829196 +0.190611 0.809389 +0.175766 0.824234 +0.195705 0.804295 +0.186995 0.813005 +0.189301 0.810699 +0.174363 0.825637 +0.191333 0.808667 +0.192460 0.807540 +0.199431 0.800569 +0.217483 0.782517 +0.203554 0.796446 +0.176466 0.823534 +0.181714 0.818286 +0.197697 0.802303 +0.197210 0.802790 +0.188035 0.811965 +0.314655 0.685345 +0.285147 0.714853 +0.319773 0.680227 +0.309741 0.690259 +0.296053 0.703947 +0.300771 0.699229 +0.318884 0.681116 +0.288333 0.711667 +0.320885 0.679115 +0.328158 0.671842 +0.298413 0.701587 +0.292423 0.707577 +0.309995 0.690005 +0.299384 0.700616 +0.321439 0.678561 +0.304927 0.695073 +0.307185 0.692815 +0.314489 0.685511 +0.284032 0.715968 +0.284324 0.715676 +0.306208 0.693792 +0.295563 0.704437 +0.305400 0.694600 +0.000010 0.999990 +0.007281 0.992719 +0.018005 0.981995 +0.018397 0.981603 +0.000805 0.999195 +0.007315 0.992685 +0.000010 0.999990 +0.010807 0.989193 +0.000010 0.999990 +0.002709 0.997291 +0.002519 0.997481 +0.000010 0.999990 +0.006906 0.993094 +0.013072 0.986928 +0.021639 0.978361 +0.002534 0.997466 +0.017685 0.982315 +0.000649 0.999351 +0.020842 0.979158 +0.012251 0.987749 +0.016319 0.983681 +0.017077 0.982923 +0.000010 0.999990 +0.015193 0.984807 +0.013065 0.986935 +0.008774 0.991226 +0.000010 0.999990 +0.018078 0.981922 +0.000010 0.999990 +0.014982 0.985018 +0.014962 0.985038 +0.013217 0.986783 +0.001860 0.998140 +0.011005 0.988995 +0.018212 0.981788 +0.002353 0.997647 +0.013871 0.986129 +0.006293 0.993707 +0.019067 0.980933 +0.019597 0.980403 +0.006948 0.993052 +0.000010 0.999990 +0.002766 0.997234 +0.021753 0.978247 +0.019081 0.980919 +0.000010 0.999990 +0.013589 0.986411 +0.030431 0.969569 +0.008318 0.991682 +0.000010 0.999990 +0.019501 0.980499 +0.001109 0.998891 +0.014468 0.985532 +0.014519 0.985481 +0.006192 0.993808 +0.011596 0.988404 +0.009586 0.990414 +0.005238 0.994762 +0.000010 0.999990 +0.019040 0.980960 +0.006968 0.993032 +0.028239 0.971761 +0.012197 0.987803 +0.019413 0.980587 +0.025213 0.974787 +0.009685 0.990315 +0.037480 0.962520 +0.005901 0.994099 +0.061978 0.938022 +0.013382 0.986618 +0.035431 0.964569 +0.040886 0.959114 +0.038554 0.961446 +0.019488 0.980512 +0.012195 0.987805 +0.032678 0.967322 +0.040318 0.959682 +0.031612 0.968388 +0.021638 0.978362 +0.009472 0.990528 +0.036827 0.963173 +0.036646 0.963354 +0.048283 0.951717 +0.035199 0.964801 +0.008645 0.991355 +0.001855 0.998145 +0.043275 0.956725 +0.047952 0.952048 +0.049620 0.950380 +0.026709 0.973291 +0.040982 0.959018 +0.051989 0.948011 +0.022620 0.977380 +0.052563 0.947437 +0.013935 0.986065 +0.019552 0.980448 +0.011597 0.988403 +0.026091 0.973909 +0.037376 0.962624 +0.049630 0.950370 +0.043179 0.956821 +0.021794 0.978206 +0.012211 0.987789 +0.018542 0.981458 +0.023346 0.976654 +0.022687 0.977313 +0.042101 0.957899 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.035633 0.964367 +0.021804 0.978196 +0.018228 0.981772 +0.023758 0.976242 +0.040496 0.959504 +0.048059 0.951941 +0.038407 0.961593 +0.033230 0.966770 +0.046240 0.953760 +0.011119 0.988881 +0.026206 0.973794 +0.017391 0.982609 +0.023035 0.976965 +0.039899 0.960101 +0.006370 0.993630 +0.021977 0.978023 +0.024581 0.975419 +0.027461 0.972539 +0.013266 0.986734 +0.034596 0.965404 +0.015887 0.984113 +0.890153 0.109847 +0.933520 0.066480 +0.870529 0.129471 +0.929497 0.070503 +0.891075 0.108925 +0.930078 0.069922 +0.901775 0.098225 +0.880743 0.119257 +0.032138 0.967862 +0.024051 0.975949 +0.033764 0.966236 +0.027322 0.972678 +0.028574 0.971426 +0.026645 0.973355 +0.034956 0.965044 +0.039772 0.960228 +0.021937 0.978063 +0.026404 0.973596 +0.037409 0.962591 +0.025125 0.974875 +0.036361 0.963639 +0.026498 0.973502 +0.042642 0.957358 +0.033494 0.966506 +0.024775 0.975225 +0.059867 0.940133 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.023971 0.976029 +0.025440 0.974560 +0.017796 0.982204 +0.009748 0.990252 +0.021779 0.978221 +0.022224 0.977776 +0.009652 0.990348 +0.009357 0.990643 +0.015814 0.984186 +0.000010 0.999990 +0.005174 0.994826 +0.013307 0.986693 +0.000010 0.999990 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.093060 0.906940 +0.105193 0.894807 +0.136446 0.863554 +0.114488 0.885512 +0.075223 0.924777 +0.116199 0.883801 +0.088111 0.911889 +0.096470 0.903530 +0.111890 0.888110 +0.114615 0.885385 +0.112163 0.887837 +0.120312 0.879688 +0.114269 0.885731 +0.136636 0.863364 +0.119261 0.880739 +0.107157 0.892843 +0.124955 0.875045 +0.103486 0.896514 +0.080137 0.919863 +0.114810 0.885190 +0.122908 0.877092 +0.108451 0.891549 +0.899951 0.100049 +0.900652 0.099348 +0.872189 0.127811 +0.826736 0.173264 +0.814660 0.185340 +0.911389 0.088611 +0.890804 0.109196 +0.907690 0.092310 +0.924602 0.075398 +0.906416 0.093584 +0.843808 0.156192 +0.931406 0.068594 +0.894713 0.105287 +0.915845 0.084155 +0.901115 0.098885 +0.883824 0.116176 +0.904707 0.095293 +0.870585 0.129415 +0.901530 0.098470 +0.857796 0.142204 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.006743 0.993257 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.010337 0.989663 +0.002162 0.997838 +0.007624 0.992376 +0.000010 0.999990 +0.005011 0.994989 +0.000010 0.999990 +0.000010 0.999990 +0.001660 0.998340 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.996358 0.003642 +0.999990 0.000010 +0.999990 0.000010 +0.998608 0.001392 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.983815 0.016185 +0.969365 0.030635 +0.975583 0.024417 +0.970023 0.029977 +0.999990 0.000010 +0.999990 0.000010 +0.995764 0.004236 +0.964236 0.035764 +0.991261 0.008739 +0.958045 0.041955 +0.956321 0.043679 +0.971256 0.028744 +0.969817 0.030183 +0.980639 0.019361 +0.985133 0.014867 +0.979998 0.020002 +0.984587 0.015413 +0.961036 0.038964 +0.976192 0.023808 +0.943347 0.056653 +0.971128 0.028872 +0.981979 0.018021 +0.953968 0.046032 +0.999990 0.000010 +0.980509 0.019491 +0.998124 0.001876 +0.980913 0.019087 +0.989282 0.010718 +0.999990 0.000010 +0.997481 0.002519 +0.998995 0.001005 +0.966571 0.033429 +0.978865 0.021135 +0.992114 0.007886 +0.930644 0.069356 +0.982495 0.017505 +0.952298 0.047702 +0.999990 0.000010 +0.053647 0.946353 +0.046205 0.953795 +0.044773 0.955227 +0.059369 0.940631 +0.050422 0.949578 +0.038296 0.961704 +0.067023 0.932977 +0.067908 0.932092 +0.031468 0.968532 +0.043506 0.956494 +0.040867 0.959133 +0.044845 0.955155 +0.046174 0.953826 +0.067780 0.932220 +0.054658 0.945342 +0.062993 0.937007 +0.060365 0.939635 +0.041359 0.958641 +0.058456 0.941544 +0.033677 0.966323 +0.035411 0.964589 +0.993568 0.006432 +0.987974 0.012026 +0.989769 0.010231 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.986429 0.013571 +0.999990 0.000010 +0.998265 0.001735 +0.972237 0.027763 +0.521852 0.478148 +0.496525 0.503475 +0.562437 0.437563 +0.519227 0.480773 +0.543730 0.456270 +0.629575 0.370425 +0.499000 0.501000 +0.613211 0.386789 +0.582066 0.417934 +0.566926 0.433074 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999903 0.000097 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.945661 0.054339 +0.924130 0.075870 +0.963230 0.036770 +0.922556 0.077444 +0.949536 0.050464 +0.955558 0.044442 +0.925347 0.074653 +0.956830 0.043170 +0.955265 0.044735 +0.929180 0.070820 +0.000010 0.999990 +0.001078 0.998922 +0.007028 0.992972 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.013131 0.986869 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.107710 0.892290 +0.054189 0.945811 +0.066879 0.933121 +0.082428 0.917572 +0.062448 0.937552 +0.050110 0.949890 +0.109156 0.890844 +0.090137 0.909863 +0.055602 0.944398 +0.056879 0.943121 +0.062758 0.937242 +0.074187 0.925813 +0.068075 0.931925 +0.042522 0.957478 +0.108144 0.891856 +0.916029 0.083971 +0.926130 0.073870 +0.936489 0.063511 +0.924070 0.075930 +0.928402 0.071598 +0.929964 0.070036 +0.958493 0.041507 +0.954640 0.045360 +0.969512 0.030488 +0.948042 0.051958 +0.935469 0.064531 +0.943302 0.056698 +0.927937 0.072063 +0.953663 0.046337 +0.952809 0.047191 +0.927056 0.072944 +0.935008 0.064992 +0.959238 0.040762 +0.947772 0.052228 +0.961622 0.038378 +0.923089 0.076911 +0.943531 0.056469 +0.955491 0.044509 +0.964112 0.035888 +0.972758 0.027242 +0.938893 0.061107 +0.950505 0.049495 +0.688179 0.311821 +0.682066 0.317934 +0.679279 0.320721 +0.682138 0.317862 +0.680368 0.319632 +0.670708 0.329292 +0.688973 0.311027 +0.692555 0.307445 +0.667268 0.332732 +0.691929 0.308071 +0.679038 0.320962 +0.403731 0.596269 +0.435276 0.564724 +0.440756 0.559244 +0.437255 0.562745 +0.448806 0.551194 +0.433304 0.566696 +0.437957 0.562043 +0.443802 0.556198 +0.430225 0.569775 +0.446053 0.553947 +0.445023 0.554977 +0.457956 0.542044 +0.452683 0.547317 +0.278725 0.721275 +0.288449 0.711551 +0.293124 0.706876 +0.278518 0.721482 +0.244895 0.755105 +0.295910 0.704090 +0.285911 0.714089 +0.276732 0.723268 +0.283050 0.716950 +0.272386 0.727614 +0.281185 0.718815 +0.271408 0.728592 +0.293267 0.706733 +0.277626 0.722374 +0.280879 0.719121 +0.656462 0.343538 +0.646239 0.353761 +0.642605 0.357395 +0.649153 0.350847 +0.642710 0.357290 +0.652111 0.347889 +0.635522 0.364478 +0.640284 0.359716 +0.649382 0.350618 +0.652478 0.347522 +0.634084 0.365916 +0.636849 0.363151 +0.364422 0.635578 +0.406176 0.593824 +0.375817 0.624183 +0.395043 0.604957 +0.403163 0.596837 +0.378892 0.621108 +0.367651 0.632349 +0.380010 0.619990 +0.351597 0.648403 +0.377211 0.622789 +0.369394 0.630606 +0.375444 0.624556 +0.379532 0.620468 +0.418829 0.581171 +0.406181 0.593819 +0.413878 0.586122 +0.426317 0.573683 +0.397196 0.602804 +0.403358 0.596642 +0.391069 0.608931 +0.422159 0.577841 +0.425521 0.574479 +0.422347 0.577653 +0.398456 0.601544 +0.437919 0.562081 +0.413303 0.586697 +0.234834 0.765166 +0.062047 0.937953 +0.044291 0.955709 +0.067708 0.932292 +0.039765 0.960235 +0.055759 0.944241 +0.023616 0.976384 +0.019272 0.980728 +0.000010 0.999990 +0.119522 0.880478 +0.048843 0.951157 +0.027404 0.972596 +0.033587 0.966413 +0.025517 0.974483 +0.065485 0.934515 +0.042882 0.957118 +0.040343 0.959657 +0.123885 0.876115 +0.014449 0.985551 +0.037702 0.962298 +0.007714 0.992286 +0.020104 0.979896 +0.014108 0.985892 +0.020520 0.979480 +0.013370 0.986630 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.014171 0.985829 +0.000827 0.999173 +0.010724 0.989276 +0.005603 0.994397 +0.003213 0.996787 +0.000010 0.999990 +0.010881 0.989119 +0.000010 0.999990 +0.002910 0.997090 +0.012543 0.987457 +0.015550 0.984450 +0.009789 0.990211 +0.012542 0.987458 +0.005717 0.994283 +0.010601 0.989399 +0.015299 0.984701 +0.021493 0.978507 +0.013900 0.986100 +0.033302 0.966698 +0.071907 0.928093 +0.104826 0.895174 +0.065305 0.934695 +0.034289 0.965711 +0.024534 0.975466 +0.000304 0.999696 +0.024837 0.975163 +0.018485 0.981515 +0.011372 0.988628 +0.084779 0.915221 +0.094336 0.905664 +0.000010 0.999990 +0.076924 0.923076 +0.003495 0.996505 +0.032447 0.967553 +0.098972 0.901028 +0.032289 0.967711 +0.026015 0.973985 +0.032646 0.967354 +0.036530 0.963470 +0.034089 0.965911 +0.062410 0.937590 +0.029226 0.970774 +0.033585 0.966415 +0.028507 0.971493 +0.011768 0.988232 +0.105712 0.894288 +0.010721 0.989279 +0.037765 0.962235 +0.011950 0.988050 +0.041664 0.958336 +0.050393 0.949607 +0.010969 0.989031 +0.059864 0.940136 +0.017637 0.982363 +0.040985 0.959015 +0.003975 0.996025 +0.035971 0.964029 +0.020366 0.979634 +0.031151 0.968849 +0.025379 0.974621 +0.076797 0.923203 +0.065878 0.934122 +0.005169 0.994831 +0.011624 0.988376 +0.051868 0.948132 +0.087421 0.912579 +0.027073 0.972927 +0.011613 0.988387 +0.022731 0.977269 +0.035769 0.964231 +0.034543 0.965457 +0.081944 0.918056 +0.024013 0.975987 +0.014622 0.985378 +0.015339 0.984661 +0.043694 0.956306 +0.006323 0.993677 +0.028205 0.971795 +0.029278 0.970722 +0.070137 0.929863 +0.049412 0.950588 +0.095862 0.904138 +0.050233 0.949767 +0.013732 0.986268 +0.063812 0.936188 +0.049912 0.950088 +0.002550 0.997450 +0.019421 0.980579 +0.013737 0.986263 +0.055526 0.944474 +0.057480 0.942520 +0.058326 0.941674 +0.043537 0.956463 +0.019714 0.980286 +0.055654 0.944346 +0.043860 0.956140 +0.027958 0.972042 +0.094169 0.905831 +0.125198 0.874802 +0.023811 0.976189 +0.102121 0.897879 +0.056789 0.943211 +0.029229 0.970771 +0.007006 0.992994 +0.058259 0.941741 +0.234466 0.765534 +0.077839 0.922161 +0.111367 0.888633 +0.025472 0.974528 +0.105076 0.894924 +0.066959 0.933041 +0.045881 0.954119 +0.041018 0.958982 +0.021218 0.978782 +0.065315 0.934685 +0.087147 0.912853 +0.288301 0.711699 +0.225466 0.774534 +0.094917 0.905083 +0.010976 0.989024 +0.012087 0.987913 +0.121691 0.878309 +0.056447 0.943553 +0.041664 0.958336 +0.019794 0.980206 +0.015096 0.984904 +0.315416 0.684584 +0.816178 0.183822 +0.104434 0.895566 +0.018232 0.981768 +0.002190 0.997810 +0.108680 0.891320 +0.051942 0.948058 +0.042551 0.957449 +0.016728 0.983272 +0.016654 0.983346 +0.046457 0.953543 +0.087097 0.912903 +0.369176 0.630824 +0.821046 0.178954 +0.112244 0.887756 +0.028382 0.971618 +0.113530 0.886470 +0.097106 0.902894 +0.043022 0.956978 +0.029561 0.970439 +0.019517 0.980483 +0.070250 0.929750 +0.060084 0.939916 +0.064935 0.935065 +0.256404 0.743596 +0.793961 0.206039 +0.119560 0.880440 +0.013296 0.986704 +0.100684 0.899316 +0.106224 0.893776 +0.075733 0.924267 +0.027707 0.972293 +0.003712 0.996288 +0.048702 0.951298 +0.066386 0.933614 +0.080073 0.919927 +0.250534 0.749466 +0.838876 0.161124 +0.088527 0.911473 +0.010446 0.989554 +0.102153 0.897847 +0.063749 0.936251 +0.030427 0.969573 +0.000010 0.999990 +0.063098 0.936902 +0.017069 0.982931 +0.100887 0.899113 +0.239285 0.760715 +0.818010 0.181990 +0.088408 0.911592 +0.031528 0.968472 +0.084007 0.915993 +0.060874 0.939126 +0.044187 0.955813 +0.021228 0.978772 +0.020182 0.979818 +0.067849 0.932151 +0.093985 0.906015 +0.102083 0.897917 +0.259465 0.740535 +0.832381 0.167619 +0.859554 0.140446 +0.754493 0.245507 +0.839641 0.160359 +0.937481 0.062519 +0.700953 0.299047 +0.033120 0.966880 +0.028234 0.971766 +0.042581 0.957419 +0.103840 0.896160 +0.263980 0.736020 +0.451188 0.548812 +0.836593 0.163407 +0.738626 0.261374 +0.821180 0.178820 +0.792487 0.207513 +0.021549 0.978451 +0.045846 0.954154 +0.070595 0.929405 +0.106464 0.893536 +0.295802 0.704198 +0.493811 0.506189 +0.821306 0.178694 +0.745401 0.254599 +0.872078 0.127922 +0.876815 0.123185 +0.054194 0.945806 +0.051617 0.948383 +0.047877 0.952123 +0.125739 0.874261 +0.283573 0.716427 +0.447326 0.552674 +0.819179 0.180821 +0.835981 0.164019 +0.561191 0.438809 +0.703569 0.296431 +0.026804 0.973196 +0.062184 0.937816 +0.125998 0.874002 +0.088069 0.911931 +0.265328 0.734672 +0.562943 0.437057 +0.724458 0.275542 +0.849825 0.150175 +0.840571 0.159429 +0.377242 0.622758 +0.676102 0.323898 +0.048137 0.951863 +0.042388 0.957612 +0.089005 0.910995 +0.092779 0.907221 +0.283040 0.716960 +0.461097 0.538903 +0.758980 0.241020 +0.866936 0.133064 +0.856254 0.143746 +0.659239 0.340761 +0.049816 0.950184 +0.100524 0.899476 +0.243328 0.756672 +0.288660 0.711340 +0.333704 0.666296 +0.721441 0.278559 +0.852941 0.147059 +0.843656 0.156344 +0.609138 0.390862 +0.048202 0.951798 +0.048536 0.951464 +0.105441 0.894559 +0.279806 0.720194 +0.238312 0.761688 +0.326365 0.673635 +0.774015 0.225985 +0.810488 0.189512 +0.791352 0.208648 +0.768858 0.231142 +0.045181 0.954819 +0.028562 0.971438 +0.039942 0.960058 +0.083856 0.916144 +0.250848 0.749152 +0.503155 0.496845 +0.351878 0.648122 +0.447070 0.552930 +0.170834 0.829166 +0.149689 0.850311 +0.147954 0.852046 +0.411469 0.588531 +0.206505 0.793495 +0.157637 0.842363 +0.358446 0.641554 +0.197652 0.802348 +0.253772 0.746228 +0.021560 0.978440 +0.198816 0.801184 +0.308357 0.691643 +0.064131 0.935869 +0.480029 0.519971 +0.179315 0.820685 +0.320447 0.679553 +0.320347 0.679653 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.025792 0.974208 +0.015979 0.984021 +0.043829 0.956171 +0.014263 0.985737 +0.000010 0.999990 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.021451 0.978549 +0.022450 0.977550 +0.012371 0.987629 +0.022571 0.977429 +0.000010 0.999990 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.019429 0.980571 +0.028695 0.971305 +0.012926 0.987074 +0.005192 0.994808 +0.025457 0.974543 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.026476 0.973524 +0.000010 0.999990 +0.000010 0.999990 +0.023325 0.976675 +0.006089 0.993911 +0.999990 0.000010 +0.999990 0.000010 +0.108447 0.891553 +0.023298 0.976702 +0.017906 0.982094 +0.014235 0.985765 +0.021009 0.978991 +0.011474 0.988526 +0.999990 0.000010 +0.999990 0.000010 +0.015776 0.984224 +0.035729 0.964271 +0.032836 0.967164 +0.000010 0.999990 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.067630 0.932370 +0.027316 0.972684 +0.001419 0.998581 +0.022088 0.977912 +0.008763 0.991237 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.025400 0.974600 +0.008077 0.991923 +0.013160 0.986840 +0.023243 0.976757 +0.008671 0.991329 +0.999990 0.000010 +0.015501 0.984499 +0.012953 0.987047 +0.012580 0.987420 +0.018097 0.981903 +0.000010 0.999990 +0.000010 0.999990 +0.008906 0.991094 +0.008203 0.991797 +0.000010 0.999990 +0.003683 0.996317 +0.000010 0.999990 +0.004048 0.995952 +0.013059 0.986941 +0.000010 0.999990 +0.003611 0.996389 +0.008446 0.991554 +0.010344 0.989656 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.002975 0.997025 +0.000010 0.999990 +0.000010 0.999990 +0.011356 0.988644 +0.009846 0.990154 +0.000010 0.999990 +0.014904 0.985096 +0.000010 0.999990 +0.000010 0.999990 +0.006080 0.993920 +0.002962 0.997038 +0.000010 0.999990 +0.019029 0.980971 +0.023705 0.976295 +0.007274 0.992726 +0.020705 0.979295 +0.000010 0.999990 +0.007263 0.992737 +0.000010 0.999990 +0.002493 0.997507 +0.118946 0.881054 +0.085754 0.914246 +0.092983 0.907017 +0.090256 0.909744 +0.013672 0.986328 +0.107102 0.892898 +0.007093 0.992907 +0.084252 0.915748 +0.081076 0.918924 +0.106763 0.893237 +0.000010 0.999990 +0.003748 0.996252 +0.000010 0.999990 +0.001760 0.998240 +0.000010 0.999990 +0.000010 0.999990 +0.009899 0.990101 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.003370 0.996630 +0.010866 0.989134 +0.000010 0.999990 +0.000010 0.999990 +0.012733 0.987267 +0.000256 0.999744 +0.012203 0.987797 +0.011660 0.988340 +0.000010 0.999990 +0.021586 0.978414 +0.006742 0.993258 +0.008764 0.991236 +0.998925 0.001075 +0.983557 0.016443 +0.979072 0.020928 +0.999990 0.000010 +0.980887 0.019113 +0.987236 0.012764 +0.994182 0.005818 +0.987743 0.012257 +0.001759 0.998241 +0.000010 0.999990 +0.003539 0.996461 +0.000712 0.999288 +0.008089 0.991911 +0.375731 0.624269 +0.280970 0.719030 +0.368096 0.631904 +0.363688 0.636312 +0.373066 0.626934 +0.007459 0.992541 +0.429276 0.570724 +0.427570 0.572430 +0.420283 0.579717 +0.376285 0.623715 +0.336802 0.663198 +0.340484 0.659516 +0.428986 0.571014 +0.415993 0.584007 +0.438262 0.561738 +0.428546 0.571454 +0.885661 0.114339 +0.979162 0.020838 +0.854839 0.145161 +0.845303 0.154697 +0.957872 0.042128 +0.843427 0.156573 +0.915795 0.084205 +0.858970 0.141030 +0.877905 0.122095 +0.863453 0.136547 +0.017844 0.982156 +0.011038 0.988962 +0.000010 0.999990 +0.762966 0.237034 +0.046008 0.953992 +0.010396 0.989604 +0.009740 0.990260 +0.021283 0.978717 +0.021002 0.978998 +0.793520 0.206480 +0.022256 0.977744 +0.011741 0.988259 +0.739613 0.260387 +0.006832 0.993168 +0.001399 0.998601 +0.018843 0.981157 +0.701044 0.298956 +0.934191 0.065809 +0.012387 0.987613 +0.930387 0.069613 +0.005134 0.994866 +0.024876 0.975124 +0.834953 0.165047 +0.831489 0.168511 +0.064057 0.935943 +0.000010 0.999990 +0.015731 0.984269 +0.022769 0.977231 +0.020998 0.979002 +0.007361 0.992639 +0.922408 0.077592 +0.857881 0.142119 +0.001853 0.998147 +0.007644 0.992356 +0.000010 0.999990 +0.032173 0.967827 +0.015762 0.984238 +0.017070 0.982930 +0.752750 0.247250 +0.006704 0.993296 +0.081630 0.918370 +0.041556 0.958444 +0.017264 0.982736 +0.000113 0.999887 +0.029783 0.970217 +0.788600 0.211400 +0.923221 0.076779 +0.000010 0.999990 +0.013698 0.986302 +0.940903 0.059097 +0.981095 0.018905 +0.032568 0.967432 +0.024273 0.975727 +0.016460 0.983540 +0.000010 0.999990 +0.000309 0.999691 +0.000010 0.999990 +0.000010 0.999990 +0.009025 0.990975 +0.009021 0.990979 +0.016584 0.983416 +0.016507 0.983493 +0.000010 0.999990 +0.010857 0.989143 +0.021035 0.978965 +0.000010 0.999990 +0.000010 0.999990 +0.007197 0.992803 +0.006811 0.993189 +0.000010 0.999990 +0.015880 0.984120 +0.005359 0.994641 +0.000010 0.999990 +0.008085 0.991915 +0.010392 0.989608 +0.017333 0.982667 +0.000010 0.999990 +0.002299 0.997701 +0.020364 0.979636 +0.128579 0.871421 +0.000010 0.999990 +0.009861 0.990139 +0.046527 0.953473 +0.000010 0.999990 +0.046279 0.953721 +0.854933 0.145067 +0.000010 0.999990 +0.006499 0.993501 +0.010898 0.989102 +0.010603 0.989397 +0.061164 0.938836 +0.044159 0.955841 +0.015014 0.984986 +0.110012 0.889988 +0.000010 0.999990 +0.053067 0.946933 +0.008145 0.991855 +0.022222 0.977778 +0.147615 0.852385 +0.015696 0.984304 +0.014420 0.985580 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.056565 0.943435 +0.064326 0.935674 +0.017851 0.982149 +0.012336 0.987664 +0.003375 0.996625 +0.005414 0.994586 +0.007458 0.992542 +0.022856 0.977144 +0.026527 0.973473 +0.124319 0.875681 +0.000010 0.999990 +0.005282 0.994718 +0.000010 0.999990 +0.047031 0.952969 +0.004807 0.995193 +0.041071 0.958929 +0.056482 0.943518 +0.001161 0.998839 +0.004575 0.995425 +0.059166 0.940834 +0.009543 0.990457 +0.018827 0.981173 +0.087898 0.912102 +0.000010 0.999990 +0.067979 0.932021 +0.000010 0.999990 +0.017631 0.982369 +0.007289 0.992711 +0.005233 0.994767 +0.061744 0.938256 +0.019818 0.980182 +0.005843 0.994157 +0.069160 0.930840 +0.141902 0.858098 +0.015322 0.984678 +0.058372 0.941628 +0.021536 0.978464 +0.016939 0.983061 +0.047839 0.952161 +0.019643 0.980357 +0.008345 0.991655 +0.026655 0.973345 +0.015316 0.984684 +0.065853 0.934147 +0.017545 0.982455 +0.021902 0.978098 +0.000010 0.999990 +0.017150 0.982850 +0.060982 0.939018 +0.015939 0.984061 +0.045261 0.954739 +0.017116 0.982884 +0.000010 0.999990 +0.047821 0.952179 +0.055596 0.944404 +0.003834 0.996166 +0.043440 0.956560 +0.023236 0.976764 +0.015620 0.984380 +0.002263 0.997737 +0.000097 0.999903 +0.061761 0.938239 +0.000750 0.999250 +0.008419 0.991581 +0.057071 0.942929 +0.000010 0.999990 +0.140798 0.859202 +0.007056 0.992944 +0.087757 0.912243 +0.005546 0.994454 +0.011405 0.988595 +0.022473 0.977527 +0.017477 0.982523 +0.017943 0.982057 +0.006106 0.993894 +0.000010 0.999990 +0.037591 0.962409 +0.048574 0.951426 +0.007120 0.992880 +0.023738 0.976262 +0.058103 0.941897 +0.000010 0.999990 +0.000010 0.999990 +0.018608 0.981392 +0.708502 0.291498 +0.056667 0.943333 +0.006798 0.993202 +0.026689 0.973311 +0.012466 0.987534 +0.000010 0.999990 +0.001699 0.998301 +0.006597 0.993403 +0.113425 0.886575 +0.053396 0.946604 +0.061568 0.938432 +0.059140 0.940860 +0.033016 0.966984 +0.017631 0.982369 +0.010068 0.989932 +0.006184 0.993816 +0.015190 0.984810 +0.008244 0.991756 +0.165715 0.834285 +0.023153 0.976847 +0.030966 0.969034 +0.696983 0.303017 +0.000010 0.999990 +0.025608 0.974392 +0.021272 0.978728 +0.000010 0.999990 +0.073048 0.926952 +0.153863 0.846137 +0.087788 0.912212 +0.144776 0.855224 +0.096355 0.903645 +0.075118 0.924882 +0.175695 0.824305 +0.112188 0.887812 +0.001278 0.998722 +0.681658 0.318342 +0.051190 0.948810 +0.713065 0.286935 +0.000010 0.999990 +0.014098 0.985902 +0.052713 0.947287 +0.701591 0.298409 +0.029248 0.970752 +0.121796 0.878204 +0.060402 0.939598 +0.155841 0.844159 +0.162542 0.837458 +0.091277 0.908723 +0.029214 0.970786 +0.000010 0.999990 +0.134714 0.865286 +0.698270 0.301730 +0.100421 0.899579 +0.091723 0.908277 +0.029824 0.970176 +0.081849 0.918151 +0.000010 0.999990 +0.094227 0.905773 +0.098937 0.901063 +0.002315 0.997685 +0.075717 0.924283 +0.054068 0.945932 +0.020651 0.979349 +0.056504 0.943496 +0.675849 0.324151 +0.058223 0.941777 +0.175464 0.824536 +0.153668 0.846332 +0.146132 0.853868 +0.062613 0.937387 +0.681573 0.318427 +0.152224 0.847776 +0.000010 0.999990 +0.127466 0.872534 +0.710462 0.289538 +0.087236 0.912764 +0.060247 0.939753 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.087592 0.912408 +0.000010 0.999990 +0.046795 0.953205 +0.066227 0.933773 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.035763 0.964237 diff --git a/inst/files/admixture/admixture_02 b/inst/files/admixture/admixture_02 new file mode 100644 index 0000000..1f971c0 --- /dev/null +++ b/inst/files/admixture/admixture_02 @@ -0,0 +1,1592 @@ +0.057005 0.942995 +0.049391 0.950609 +0.027792 0.972208 +0.056381 0.943619 +0.068326 0.931674 +0.055989 0.944011 +0.073803 0.926197 +0.023864 0.976136 +0.049104 0.950896 +0.071588 0.928412 +0.052600 0.947400 +0.067918 0.932082 +0.053046 0.946954 +0.016234 0.983766 +0.053412 0.946588 +0.030498 0.969502 +0.077945 0.922055 +0.105872 0.894128 +0.056578 0.943422 +0.045748 0.954252 +0.052967 0.947033 +0.000286 0.999714 +0.053181 0.946819 +0.045396 0.954604 +0.090495 0.909505 +0.059668 0.940332 +0.360918 0.639082 +0.377726 0.622274 +0.383268 0.616732 +0.357552 0.642448 +0.358840 0.641160 +0.358460 0.641540 +0.372958 0.627042 +0.342393 0.657607 +0.378356 0.621644 +0.351069 0.648931 +0.365178 0.634822 +0.320974 0.679026 +0.373333 0.626667 +0.380484 0.619516 +0.353802 0.646198 +0.345397 0.654603 +0.426948 0.573052 +0.014908 0.985092 +0.397745 0.602255 +0.412758 0.587242 +0.356181 0.643819 +0.027744 0.972256 +0.418820 0.581180 +0.355439 0.644561 +0.835751 0.164249 +0.837731 0.162269 +0.832155 0.167845 +0.848174 0.151826 +0.835368 0.164632 +0.844932 0.155068 +0.848202 0.151798 +0.818975 0.181025 +0.857683 0.142317 +0.844075 0.155925 +0.851234 0.148766 +0.834279 0.165721 +0.840619 0.159381 +0.849089 0.150911 +0.831608 0.168392 +0.849957 0.150043 +0.798281 0.201719 +0.852337 0.147663 +0.848950 0.151050 +0.851597 0.148403 +0.840813 0.159187 +0.846742 0.153258 +0.877236 0.122764 +0.786585 0.213415 +0.805039 0.194961 +0.867954 0.132046 +0.865964 0.134036 +0.858349 0.141651 +0.801428 0.198572 +0.850691 0.149309 +0.855985 0.144015 +0.868430 0.131570 +0.866588 0.133412 +0.850248 0.149752 +0.865158 0.134842 +0.858768 0.141232 +0.808628 0.191372 +0.813718 0.186282 +0.814293 0.185707 +0.836846 0.163154 +0.820740 0.179260 +0.428537 0.571463 +0.421962 0.578038 +0.458958 0.541042 +0.439218 0.560782 +0.476191 0.523809 +0.437406 0.562594 +0.446116 0.553884 +0.456598 0.543402 +0.465572 0.534428 +0.439686 0.560314 +0.441407 0.558593 +0.472291 0.527709 +0.446629 0.553371 +0.456005 0.543995 +0.880426 0.119574 +0.879044 0.120956 +0.863196 0.136804 +0.866131 0.133869 +0.857451 0.142549 +0.877557 0.122443 +0.846027 0.153973 +0.865170 0.134830 +0.866280 0.133720 +0.865489 0.134511 +0.877590 0.122410 +0.849888 0.150112 +0.873127 0.126873 +0.865805 0.134195 +0.874831 0.125169 +0.859377 0.140623 +0.860422 0.139578 +0.865757 0.134243 +0.861802 0.138198 +0.862038 0.137962 +0.759812 0.240188 +0.758766 0.241234 +0.777603 0.222397 +0.789439 0.210561 +0.780001 0.219999 +0.761369 0.238631 +0.792114 0.207886 +0.776103 0.223897 +0.777890 0.222110 +0.762406 0.237594 +0.753308 0.246692 +0.752364 0.247636 +0.756709 0.243291 +0.779333 0.220667 +0.788389 0.211611 +0.725789 0.274211 +0.759213 0.240787 +0.758386 0.241614 +0.845114 0.154886 +0.763095 0.236905 +0.807970 0.192030 +0.776023 0.223977 +0.806400 0.193600 +0.788282 0.211718 +0.774045 0.225955 +0.789371 0.210629 +0.766736 0.233264 +0.823897 0.176103 +0.831008 0.168992 +0.784590 0.215410 +0.783613 0.216387 +0.777855 0.222145 +0.810495 0.189505 +0.768653 0.231347 +0.822788 0.177212 +0.803481 0.196519 +0.768729 0.231271 +0.814588 0.185412 +0.829196 0.170804 +0.809389 0.190611 +0.824234 0.175766 +0.804295 0.195705 +0.813005 0.186995 +0.810699 0.189301 +0.825637 0.174363 +0.808667 0.191333 +0.807540 0.192460 +0.800569 0.199431 +0.782517 0.217483 +0.796446 0.203554 +0.823534 0.176466 +0.818286 0.181714 +0.802303 0.197697 +0.802789 0.197211 +0.811965 0.188035 +0.685345 0.314655 +0.714853 0.285147 +0.680227 0.319773 +0.690259 0.309741 +0.703947 0.296053 +0.699229 0.300771 +0.681116 0.318884 +0.711667 0.288333 +0.679115 0.320885 +0.671842 0.328158 +0.701587 0.298413 +0.707577 0.292423 +0.690005 0.309995 +0.700616 0.299384 +0.678561 0.321439 +0.695073 0.304927 +0.692815 0.307185 +0.685511 0.314489 +0.715968 0.284032 +0.715676 0.284324 +0.693792 0.306208 +0.704437 0.295563 +0.694600 0.305400 +0.999990 0.000010 +0.992719 0.007281 +0.981995 0.018005 +0.981603 0.018397 +0.999195 0.000805 +0.992685 0.007315 +0.999990 0.000010 +0.989193 0.010807 +0.999990 0.000010 +0.997291 0.002709 +0.997481 0.002519 +0.999990 0.000010 +0.993094 0.006906 +0.986928 0.013072 +0.978361 0.021639 +0.997466 0.002534 +0.982314 0.017686 +0.999351 0.000649 +0.979158 0.020842 +0.987749 0.012251 +0.983681 0.016319 +0.982923 0.017077 +0.999990 0.000010 +0.984807 0.015193 +0.986935 0.013065 +0.991226 0.008774 +0.999990 0.000010 +0.981922 0.018078 +0.999990 0.000010 +0.985018 0.014982 +0.985038 0.014962 +0.986783 0.013217 +0.998140 0.001860 +0.988994 0.011006 +0.981788 0.018212 +0.997647 0.002353 +0.986129 0.013871 +0.993707 0.006293 +0.980933 0.019067 +0.980402 0.019598 +0.993052 0.006948 +0.999990 0.000010 +0.997234 0.002766 +0.978247 0.021753 +0.980919 0.019081 +0.999990 0.000010 +0.986411 0.013589 +0.969569 0.030431 +0.991682 0.008318 +0.999990 0.000010 +0.980499 0.019501 +0.998891 0.001109 +0.985532 0.014468 +0.985481 0.014519 +0.993808 0.006192 +0.988404 0.011596 +0.990414 0.009586 +0.994762 0.005238 +0.999990 0.000010 +0.980960 0.019040 +0.993032 0.006968 +0.971761 0.028239 +0.987803 0.012197 +0.980587 0.019413 +0.974787 0.025213 +0.990315 0.009685 +0.962520 0.037480 +0.994099 0.005901 +0.938021 0.061979 +0.986618 0.013382 +0.964569 0.035431 +0.959114 0.040886 +0.961445 0.038555 +0.980512 0.019488 +0.987805 0.012195 +0.967322 0.032678 +0.959682 0.040318 +0.968388 0.031612 +0.978362 0.021638 +0.990527 0.009473 +0.963173 0.036827 +0.963354 0.036646 +0.951717 0.048283 +0.964801 0.035199 +0.991355 0.008645 +0.998145 0.001855 +0.956725 0.043275 +0.952048 0.047952 +0.950380 0.049620 +0.973291 0.026709 +0.959018 0.040982 +0.948011 0.051989 +0.977380 0.022620 +0.947437 0.052563 +0.986065 0.013935 +0.980448 0.019552 +0.988403 0.011597 +0.973908 0.026092 +0.962624 0.037376 +0.950370 0.049630 +0.956821 0.043179 +0.978206 0.021794 +0.987788 0.012212 +0.981458 0.018542 +0.976654 0.023346 +0.977313 0.022687 +0.957899 0.042101 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.964367 0.035633 +0.978196 0.021804 +0.981772 0.018228 +0.976242 0.023758 +0.959504 0.040496 +0.951941 0.048059 +0.961593 0.038407 +0.966770 0.033230 +0.953760 0.046240 +0.988881 0.011119 +0.973794 0.026206 +0.982609 0.017391 +0.976965 0.023035 +0.960101 0.039899 +0.993630 0.006370 +0.978023 0.021977 +0.975419 0.024581 +0.972539 0.027461 +0.986733 0.013267 +0.965404 0.034596 +0.984113 0.015887 +0.109847 0.890153 +0.066480 0.933520 +0.129471 0.870529 +0.070503 0.929497 +0.108925 0.891075 +0.069922 0.930078 +0.098225 0.901775 +0.119258 0.880742 +0.967862 0.032138 +0.975949 0.024051 +0.966236 0.033764 +0.972678 0.027322 +0.971426 0.028574 +0.973355 0.026645 +0.965044 0.034956 +0.960228 0.039772 +0.978063 0.021937 +0.973596 0.026404 +0.962591 0.037409 +0.974875 0.025125 +0.963639 0.036361 +0.973502 0.026498 +0.957358 0.042642 +0.966506 0.033494 +0.975225 0.024775 +0.940133 0.059867 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.976029 0.023971 +0.974560 0.025440 +0.982204 0.017796 +0.990252 0.009748 +0.978221 0.021779 +0.977776 0.022224 +0.990348 0.009652 +0.990643 0.009357 +0.984186 0.015814 +0.999990 0.000010 +0.994826 0.005174 +0.986693 0.013307 +0.999990 0.000010 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.906940 0.093060 +0.894807 0.105193 +0.863554 0.136446 +0.885512 0.114488 +0.924777 0.075223 +0.883801 0.116199 +0.911889 0.088111 +0.903530 0.096470 +0.888110 0.111890 +0.885385 0.114615 +0.887837 0.112163 +0.879687 0.120313 +0.885731 0.114269 +0.863364 0.136636 +0.880739 0.119261 +0.892843 0.107157 +0.875045 0.124955 +0.896514 0.103486 +0.919863 0.080137 +0.885190 0.114810 +0.877092 0.122908 +0.891549 0.108451 +0.100049 0.899951 +0.099348 0.900652 +0.127811 0.872189 +0.173264 0.826736 +0.185340 0.814660 +0.088611 0.911389 +0.109196 0.890804 +0.092310 0.907690 +0.075398 0.924602 +0.093584 0.906416 +0.156192 0.843808 +0.068594 0.931406 +0.105287 0.894713 +0.084155 0.915845 +0.098885 0.901115 +0.116176 0.883824 +0.095293 0.904707 +0.129415 0.870585 +0.098470 0.901530 +0.142204 0.857796 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.993257 0.006743 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.989663 0.010337 +0.997838 0.002162 +0.992376 0.007624 +0.999990 0.000010 +0.994989 0.005011 +0.999990 0.000010 +0.999990 0.000010 +0.998340 0.001660 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.003642 0.996358 +0.000010 0.999990 +0.000010 0.999990 +0.001394 0.998606 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.016185 0.983815 +0.030635 0.969365 +0.024417 0.975583 +0.029977 0.970023 +0.000010 0.999990 +0.000010 0.999990 +0.004236 0.995764 +0.035764 0.964236 +0.008739 0.991261 +0.041955 0.958045 +0.043679 0.956321 +0.028744 0.971256 +0.030183 0.969817 +0.019361 0.980639 +0.014867 0.985133 +0.020002 0.979998 +0.015413 0.984587 +0.038964 0.961036 +0.023808 0.976192 +0.056653 0.943347 +0.028872 0.971128 +0.018021 0.981979 +0.046033 0.953967 +0.000010 0.999990 +0.019491 0.980509 +0.001877 0.998123 +0.019087 0.980913 +0.010720 0.989280 +0.000010 0.999990 +0.002520 0.997480 +0.001007 0.998993 +0.033429 0.966571 +0.021135 0.978865 +0.007886 0.992114 +0.069356 0.930644 +0.017505 0.982495 +0.047702 0.952298 +0.000010 0.999990 +0.946353 0.053647 +0.953794 0.046206 +0.955227 0.044773 +0.940631 0.059369 +0.949578 0.050422 +0.961704 0.038296 +0.932977 0.067023 +0.932092 0.067908 +0.968531 0.031469 +0.956494 0.043506 +0.959133 0.040867 +0.955155 0.044845 +0.953826 0.046174 +0.932220 0.067780 +0.945342 0.054658 +0.937007 0.062993 +0.939635 0.060365 +0.958641 0.041359 +0.941544 0.058456 +0.966323 0.033677 +0.964589 0.035411 +0.006433 0.993567 +0.012026 0.987974 +0.010231 0.989769 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.013571 0.986429 +0.000010 0.999990 +0.001738 0.998262 +0.027763 0.972237 +0.478148 0.521852 +0.503475 0.496525 +0.437563 0.562437 +0.480773 0.519227 +0.456270 0.543730 +0.370425 0.629575 +0.501000 0.499000 +0.386789 0.613211 +0.417934 0.582066 +0.433074 0.566926 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000097 0.999903 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.054339 0.945661 +0.075870 0.924130 +0.036771 0.963229 +0.077445 0.922555 +0.050464 0.949536 +0.044442 0.955558 +0.074653 0.925347 +0.043170 0.956830 +0.044735 0.955265 +0.070820 0.929180 +0.999990 0.000010 +0.998921 0.001079 +0.992972 0.007028 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.986869 0.013131 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.892290 0.107710 +0.945811 0.054189 +0.933121 0.066879 +0.917572 0.082428 +0.937551 0.062449 +0.949890 0.050110 +0.890844 0.109156 +0.909863 0.090137 +0.944398 0.055602 +0.943121 0.056879 +0.937241 0.062759 +0.925813 0.074187 +0.931925 0.068075 +0.957478 0.042522 +0.891856 0.108144 +0.083971 0.916029 +0.073870 0.926130 +0.063511 0.936489 +0.075931 0.924069 +0.071598 0.928402 +0.070036 0.929964 +0.041507 0.958493 +0.045360 0.954640 +0.030488 0.969512 +0.051958 0.948042 +0.064531 0.935469 +0.056698 0.943302 +0.072063 0.927937 +0.046337 0.953663 +0.047191 0.952809 +0.072945 0.927055 +0.064992 0.935008 +0.040762 0.959238 +0.052229 0.947771 +0.038378 0.961622 +0.076911 0.923089 +0.056469 0.943531 +0.044509 0.955491 +0.035888 0.964112 +0.027242 0.972758 +0.061107 0.938893 +0.049495 0.950505 +0.311821 0.688179 +0.317934 0.682066 +0.320721 0.679279 +0.317862 0.682138 +0.319632 0.680368 +0.329292 0.670708 +0.311027 0.688973 +0.307445 0.692555 +0.332732 0.667268 +0.308071 0.691929 +0.320962 0.679038 +0.596269 0.403731 +0.564724 0.435276 +0.559244 0.440756 +0.562745 0.437255 +0.551194 0.448806 +0.566696 0.433304 +0.562043 0.437957 +0.556198 0.443802 +0.569775 0.430225 +0.553947 0.446053 +0.554977 0.445023 +0.542044 0.457956 +0.547317 0.452683 +0.721275 0.278725 +0.711551 0.288449 +0.706876 0.293124 +0.721482 0.278518 +0.755105 0.244895 +0.704089 0.295911 +0.714089 0.285911 +0.723267 0.276733 +0.716950 0.283050 +0.727614 0.272386 +0.718815 0.281185 +0.728592 0.271408 +0.706732 0.293268 +0.722374 0.277626 +0.719121 0.280879 +0.343538 0.656462 +0.353761 0.646239 +0.357395 0.642605 +0.350847 0.649153 +0.357290 0.642710 +0.347889 0.652111 +0.364478 0.635522 +0.359717 0.640283 +0.350618 0.649382 +0.347522 0.652478 +0.365916 0.634084 +0.363151 0.636849 +0.635578 0.364422 +0.593824 0.406176 +0.624183 0.375817 +0.604957 0.395043 +0.596837 0.403163 +0.621108 0.378892 +0.632349 0.367651 +0.619990 0.380010 +0.648403 0.351597 +0.622789 0.377211 +0.630606 0.369394 +0.624556 0.375444 +0.620468 0.379532 +0.581171 0.418829 +0.593819 0.406181 +0.586122 0.413878 +0.573683 0.426317 +0.602804 0.397196 +0.596642 0.403358 +0.608931 0.391069 +0.577841 0.422159 +0.574479 0.425521 +0.577653 0.422347 +0.601544 0.398456 +0.562081 0.437919 +0.586697 0.413303 +0.765166 0.234834 +0.937953 0.062047 +0.955709 0.044291 +0.932292 0.067708 +0.960235 0.039765 +0.944241 0.055759 +0.976384 0.023616 +0.980728 0.019272 +0.999990 0.000010 +0.880478 0.119522 +0.951157 0.048843 +0.972596 0.027404 +0.966413 0.033587 +0.974483 0.025517 +0.934515 0.065485 +0.957118 0.042882 +0.959657 0.040343 +0.876115 0.123885 +0.985551 0.014449 +0.962298 0.037702 +0.992286 0.007714 +0.979896 0.020104 +0.985892 0.014108 +0.979480 0.020520 +0.986630 0.013370 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.985829 0.014171 +0.999173 0.000827 +0.989276 0.010724 +0.994397 0.005603 +0.996787 0.003213 +0.999990 0.000010 +0.989119 0.010881 +0.999990 0.000010 +0.997090 0.002910 +0.987457 0.012543 +0.984450 0.015550 +0.990211 0.009789 +0.987458 0.012542 +0.994283 0.005717 +0.989399 0.010601 +0.984701 0.015299 +0.978507 0.021493 +0.986100 0.013900 +0.966698 0.033302 +0.928093 0.071907 +0.895174 0.104826 +0.934695 0.065305 +0.965711 0.034289 +0.975466 0.024534 +0.999696 0.000304 +0.975163 0.024837 +0.981515 0.018485 +0.988628 0.011372 +0.915221 0.084779 +0.905664 0.094336 +0.999990 0.000010 +0.923076 0.076924 +0.996504 0.003496 +0.967552 0.032448 +0.901028 0.098972 +0.967711 0.032289 +0.973985 0.026015 +0.967354 0.032646 +0.963470 0.036530 +0.965911 0.034089 +0.937590 0.062410 +0.970774 0.029226 +0.966415 0.033585 +0.971493 0.028507 +0.988232 0.011768 +0.894288 0.105712 +0.989279 0.010721 +0.962235 0.037765 +0.988050 0.011950 +0.958336 0.041664 +0.949607 0.050393 +0.989031 0.010969 +0.940136 0.059864 +0.982363 0.017637 +0.959015 0.040985 +0.996025 0.003975 +0.964029 0.035971 +0.979634 0.020366 +0.968849 0.031151 +0.974621 0.025379 +0.923203 0.076797 +0.934122 0.065878 +0.994831 0.005169 +0.988376 0.011624 +0.948132 0.051868 +0.912579 0.087421 +0.972927 0.027073 +0.988387 0.011613 +0.977269 0.022731 +0.964231 0.035769 +0.965457 0.034543 +0.918056 0.081944 +0.975987 0.024013 +0.985377 0.014623 +0.984661 0.015339 +0.956306 0.043694 +0.993677 0.006323 +0.971795 0.028205 +0.970722 0.029278 +0.929863 0.070137 +0.950588 0.049412 +0.904138 0.095862 +0.949767 0.050233 +0.986268 0.013732 +0.936188 0.063812 +0.950088 0.049912 +0.997449 0.002551 +0.980579 0.019421 +0.986263 0.013737 +0.944474 0.055526 +0.942520 0.057480 +0.941674 0.058326 +0.956463 0.043537 +0.980285 0.019715 +0.944346 0.055654 +0.956140 0.043860 +0.972042 0.027958 +0.905831 0.094169 +0.874802 0.125198 +0.976189 0.023811 +0.897879 0.102121 +0.943211 0.056789 +0.970771 0.029229 +0.992994 0.007006 +0.941741 0.058259 +0.765534 0.234466 +0.922161 0.077839 +0.888633 0.111367 +0.974528 0.025472 +0.894924 0.105076 +0.933040 0.066960 +0.954119 0.045881 +0.958982 0.041018 +0.978782 0.021218 +0.934685 0.065315 +0.912853 0.087147 +0.711699 0.288301 +0.774534 0.225466 +0.905083 0.094917 +0.989024 0.010976 +0.987913 0.012087 +0.878309 0.121691 +0.943553 0.056447 +0.958336 0.041664 +0.980206 0.019794 +0.984904 0.015096 +0.684584 0.315416 +0.183822 0.816178 +0.895566 0.104434 +0.981767 0.018233 +0.997810 0.002190 +0.891320 0.108680 +0.948058 0.051942 +0.957449 0.042551 +0.983272 0.016728 +0.983346 0.016654 +0.953543 0.046457 +0.912903 0.087097 +0.630824 0.369176 +0.178954 0.821046 +0.887756 0.112244 +0.971618 0.028382 +0.886470 0.113530 +0.902894 0.097106 +0.956978 0.043022 +0.970439 0.029561 +0.980483 0.019517 +0.929750 0.070250 +0.939915 0.060085 +0.935065 0.064935 +0.743596 0.256404 +0.206039 0.793961 +0.880440 0.119560 +0.986704 0.013296 +0.899316 0.100684 +0.893776 0.106224 +0.924267 0.075733 +0.972293 0.027707 +0.996288 0.003712 +0.951298 0.048702 +0.933614 0.066386 +0.919927 0.080073 +0.749466 0.250534 +0.161124 0.838876 +0.911473 0.088527 +0.989553 0.010447 +0.897847 0.102153 +0.936251 0.063749 +0.969573 0.030427 +0.999990 0.000010 +0.936902 0.063098 +0.982931 0.017069 +0.899113 0.100887 +0.760715 0.239285 +0.181990 0.818010 +0.911592 0.088408 +0.968472 0.031528 +0.915992 0.084008 +0.939126 0.060874 +0.955813 0.044187 +0.978772 0.021228 +0.979818 0.020182 +0.932151 0.067849 +0.906015 0.093985 +0.897917 0.102083 +0.740535 0.259465 +0.167619 0.832381 +0.140446 0.859554 +0.245507 0.754493 +0.160359 0.839641 +0.062519 0.937481 +0.299047 0.700953 +0.966880 0.033120 +0.971766 0.028234 +0.957419 0.042581 +0.896160 0.103840 +0.736020 0.263980 +0.548812 0.451188 +0.163407 0.836593 +0.261374 0.738626 +0.178821 0.821179 +0.207513 0.792487 +0.978451 0.021549 +0.954154 0.045846 +0.929405 0.070595 +0.893536 0.106464 +0.704198 0.295802 +0.506189 0.493811 +0.178694 0.821306 +0.254599 0.745401 +0.127922 0.872078 +0.123185 0.876815 +0.945806 0.054194 +0.948383 0.051617 +0.952123 0.047877 +0.874261 0.125739 +0.716427 0.283573 +0.552674 0.447326 +0.180821 0.819179 +0.164019 0.835981 +0.438809 0.561191 +0.296431 0.703569 +0.973196 0.026804 +0.937816 0.062184 +0.874002 0.125998 +0.911931 0.088069 +0.734672 0.265328 +0.437057 0.562943 +0.275542 0.724458 +0.150175 0.849825 +0.159429 0.840571 +0.622758 0.377242 +0.323898 0.676102 +0.951863 0.048137 +0.957612 0.042388 +0.910995 0.089005 +0.907221 0.092779 +0.716960 0.283040 +0.538903 0.461097 +0.241020 0.758980 +0.133064 0.866936 +0.143746 0.856254 +0.340761 0.659239 +0.950184 0.049816 +0.899476 0.100524 +0.756672 0.243328 +0.711340 0.288660 +0.666296 0.333704 +0.278559 0.721441 +0.147059 0.852941 +0.156344 0.843656 +0.390862 0.609138 +0.951798 0.048202 +0.951464 0.048536 +0.894559 0.105441 +0.720194 0.279806 +0.761688 0.238312 +0.673635 0.326365 +0.225985 0.774015 +0.189513 0.810487 +0.208648 0.791352 +0.231142 0.768858 +0.954819 0.045181 +0.971438 0.028562 +0.960058 0.039942 +0.916144 0.083856 +0.749152 0.250848 +0.496845 0.503155 +0.648122 0.351878 +0.552930 0.447070 +0.829166 0.170834 +0.850311 0.149689 +0.852046 0.147954 +0.588531 0.411469 +0.793495 0.206505 +0.842363 0.157637 +0.641554 0.358446 +0.802348 0.197652 +0.746228 0.253772 +0.978440 0.021560 +0.801184 0.198816 +0.691643 0.308357 +0.935869 0.064131 +0.519971 0.480029 +0.820685 0.179315 +0.679553 0.320447 +0.679653 0.320347 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.974208 0.025792 +0.984021 0.015979 +0.956171 0.043829 +0.985737 0.014263 +0.999990 0.000010 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.978549 0.021451 +0.977549 0.022451 +0.987629 0.012371 +0.977429 0.022571 +0.999990 0.000010 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.980571 0.019429 +0.971305 0.028695 +0.987074 0.012926 +0.994808 0.005192 +0.974542 0.025458 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.973523 0.026477 +0.999990 0.000010 +0.999990 0.000010 +0.976675 0.023325 +0.993911 0.006089 +0.000010 0.999990 +0.000010 0.999990 +0.891553 0.108447 +0.976702 0.023298 +0.982094 0.017906 +0.985765 0.014235 +0.978991 0.021009 +0.988526 0.011474 +0.000010 0.999990 +0.000010 0.999990 +0.984224 0.015776 +0.964271 0.035729 +0.967164 0.032836 +0.999990 0.000010 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.932370 0.067630 +0.972684 0.027316 +0.998581 0.001419 +0.977912 0.022088 +0.991237 0.008763 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.974600 0.025400 +0.991923 0.008077 +0.986840 0.013160 +0.976757 0.023243 +0.991329 0.008671 +0.000010 0.999990 +0.984499 0.015501 +0.987047 0.012953 +0.987420 0.012580 +0.981903 0.018097 +0.999990 0.000010 +0.999990 0.000010 +0.991093 0.008907 +0.991797 0.008203 +0.999990 0.000010 +0.996317 0.003683 +0.999990 0.000010 +0.995952 0.004048 +0.986941 0.013059 +0.999990 0.000010 +0.996389 0.003611 +0.991554 0.008446 +0.989656 0.010344 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.997025 0.002975 +0.999990 0.000010 +0.999990 0.000010 +0.988644 0.011356 +0.990154 0.009846 +0.999990 0.000010 +0.985096 0.014904 +0.999990 0.000010 +0.999990 0.000010 +0.993920 0.006080 +0.997038 0.002962 +0.999990 0.000010 +0.980971 0.019029 +0.976295 0.023705 +0.992726 0.007274 +0.979295 0.020705 +0.999990 0.000010 +0.992737 0.007263 +0.999990 0.000010 +0.997507 0.002493 +0.881054 0.118946 +0.914245 0.085755 +0.907017 0.092983 +0.909744 0.090256 +0.986328 0.013672 +0.892898 0.107102 +0.992907 0.007093 +0.915748 0.084252 +0.918924 0.081076 +0.893237 0.106763 +0.999990 0.000010 +0.996252 0.003748 +0.999990 0.000010 +0.998240 0.001760 +0.999990 0.000010 +0.999990 0.000010 +0.990101 0.009899 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.996630 0.003370 +0.989134 0.010866 +0.999990 0.000010 +0.999990 0.000010 +0.987267 0.012733 +0.999744 0.000256 +0.987796 0.012204 +0.988340 0.011660 +0.999990 0.000010 +0.978414 0.021586 +0.993258 0.006742 +0.991236 0.008764 +0.001076 0.998924 +0.016443 0.983557 +0.020928 0.979072 +0.000010 0.999990 +0.019113 0.980887 +0.012764 0.987236 +0.005818 0.994182 +0.012257 0.987743 +0.998241 0.001759 +0.999990 0.000010 +0.996461 0.003539 +0.999288 0.000712 +0.991910 0.008090 +0.624269 0.375731 +0.719030 0.280970 +0.631904 0.368096 +0.636312 0.363688 +0.626934 0.373066 +0.992541 0.007459 +0.570724 0.429276 +0.572430 0.427570 +0.579717 0.420283 +0.623715 0.376285 +0.663198 0.336802 +0.659516 0.340484 +0.571014 0.428986 +0.584007 0.415993 +0.561738 0.438262 +0.571454 0.428546 +0.114339 0.885661 +0.020838 0.979162 +0.145161 0.854839 +0.154697 0.845303 +0.042128 0.957872 +0.156573 0.843427 +0.084205 0.915795 +0.141030 0.858970 +0.122095 0.877905 +0.136547 0.863453 +0.982156 0.017844 +0.988962 0.011038 +0.999990 0.000010 +0.237034 0.762966 +0.953992 0.046008 +0.989604 0.010396 +0.990259 0.009741 +0.978717 0.021283 +0.978998 0.021002 +0.206480 0.793520 +0.977744 0.022256 +0.988259 0.011741 +0.260387 0.739613 +0.993168 0.006832 +0.998601 0.001399 +0.981157 0.018843 +0.298956 0.701044 +0.065809 0.934191 +0.987613 0.012387 +0.069614 0.930386 +0.994866 0.005134 +0.975124 0.024876 +0.165047 0.834953 +0.168511 0.831489 +0.935943 0.064057 +0.999990 0.000010 +0.984269 0.015731 +0.977231 0.022769 +0.979002 0.020998 +0.992639 0.007361 +0.077592 0.922408 +0.142119 0.857881 +0.998147 0.001853 +0.992356 0.007644 +0.999990 0.000010 +0.967827 0.032173 +0.984238 0.015762 +0.982930 0.017070 +0.247250 0.752750 +0.993296 0.006704 +0.918370 0.081630 +0.958444 0.041556 +0.982736 0.017264 +0.999887 0.000113 +0.970217 0.029783 +0.211400 0.788600 +0.076779 0.923221 +0.999990 0.000010 +0.986302 0.013698 +0.059097 0.940903 +0.018905 0.981095 +0.967432 0.032568 +0.975727 0.024273 +0.983540 0.016460 +0.999990 0.000010 +0.999691 0.000309 +0.999990 0.000010 +0.999990 0.000010 +0.990975 0.009025 +0.990979 0.009021 +0.983416 0.016584 +0.983493 0.016507 +0.999990 0.000010 +0.989143 0.010857 +0.978965 0.021035 +0.999990 0.000010 +0.999990 0.000010 +0.992803 0.007197 +0.993189 0.006811 +0.999990 0.000010 +0.984120 0.015880 +0.994641 0.005359 +0.999990 0.000010 +0.991915 0.008085 +0.989608 0.010392 +0.982667 0.017333 +0.999990 0.000010 +0.997701 0.002299 +0.979636 0.020364 +0.871421 0.128579 +0.999990 0.000010 +0.990139 0.009861 +0.953473 0.046527 +0.999990 0.000010 +0.953721 0.046279 +0.145067 0.854933 +0.999990 0.000010 +0.993501 0.006499 +0.989101 0.010899 +0.989397 0.010603 +0.938836 0.061164 +0.955841 0.044159 +0.984986 0.015014 +0.889988 0.110012 +0.999990 0.000010 +0.946933 0.053067 +0.991854 0.008146 +0.977778 0.022222 +0.852385 0.147615 +0.984304 0.015696 +0.985580 0.014420 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.943434 0.056566 +0.935674 0.064326 +0.982149 0.017851 +0.987663 0.012337 +0.996625 0.003375 +0.994586 0.005414 +0.992542 0.007458 +0.977144 0.022856 +0.973472 0.026528 +0.875681 0.124319 +0.999990 0.000010 +0.994718 0.005282 +0.999990 0.000010 +0.952969 0.047031 +0.995192 0.004808 +0.958929 0.041071 +0.943518 0.056482 +0.998839 0.001161 +0.995425 0.004575 +0.940834 0.059166 +0.990457 0.009543 +0.981173 0.018827 +0.912102 0.087898 +0.999990 0.000010 +0.932021 0.067979 +0.999990 0.000010 +0.982369 0.017631 +0.992711 0.007289 +0.994767 0.005233 +0.938256 0.061744 +0.980181 0.019819 +0.994157 0.005843 +0.930840 0.069160 +0.858098 0.141902 +0.984678 0.015322 +0.941628 0.058372 +0.978464 0.021536 +0.983061 0.016939 +0.952160 0.047840 +0.980357 0.019643 +0.991655 0.008345 +0.973345 0.026655 +0.984684 0.015316 +0.934147 0.065853 +0.982455 0.017545 +0.978098 0.021902 +0.999990 0.000010 +0.982850 0.017150 +0.939018 0.060982 +0.984061 0.015939 +0.954739 0.045261 +0.982884 0.017116 +0.999990 0.000010 +0.952179 0.047821 +0.944404 0.055596 +0.996166 0.003834 +0.956560 0.043440 +0.976764 0.023236 +0.984379 0.015621 +0.997737 0.002263 +0.999903 0.000097 +0.938238 0.061762 +0.999250 0.000750 +0.991581 0.008419 +0.942929 0.057071 +0.999990 0.000010 +0.859202 0.140798 +0.992944 0.007056 +0.912243 0.087757 +0.994454 0.005546 +0.988595 0.011405 +0.977527 0.022473 +0.982523 0.017477 +0.982057 0.017943 +0.993894 0.006106 +0.999990 0.000010 +0.962409 0.037591 +0.951425 0.048575 +0.992880 0.007120 +0.976262 0.023738 +0.941897 0.058103 +0.999990 0.000010 +0.999990 0.000010 +0.981392 0.018608 +0.291498 0.708502 +0.943333 0.056667 +0.993202 0.006798 +0.973311 0.026689 +0.987534 0.012466 +0.999990 0.000010 +0.998301 0.001699 +0.993403 0.006597 +0.886574 0.113426 +0.946603 0.053397 +0.938432 0.061568 +0.940860 0.059140 +0.966984 0.033016 +0.982368 0.017632 +0.989932 0.010068 +0.993816 0.006184 +0.984810 0.015190 +0.991756 0.008244 +0.834285 0.165715 +0.976847 0.023153 +0.969034 0.030966 +0.303017 0.696983 +0.999990 0.000010 +0.974392 0.025608 +0.978728 0.021272 +0.999990 0.000010 +0.926952 0.073048 +0.846137 0.153863 +0.912212 0.087788 +0.855224 0.144776 +0.903645 0.096355 +0.924882 0.075118 +0.824304 0.175696 +0.887812 0.112188 +0.998722 0.001278 +0.318342 0.681658 +0.948810 0.051190 +0.286935 0.713065 +0.999990 0.000010 +0.985901 0.014099 +0.947287 0.052713 +0.298409 0.701591 +0.970752 0.029248 +0.878204 0.121796 +0.939598 0.060402 +0.844159 0.155841 +0.837458 0.162542 +0.908723 0.091277 +0.970786 0.029214 +0.999990 0.000010 +0.865286 0.134714 +0.301730 0.698270 +0.899579 0.100421 +0.908277 0.091723 +0.970176 0.029824 +0.918151 0.081849 +0.999990 0.000010 +0.905773 0.094227 +0.901063 0.098937 +0.997685 0.002315 +0.924282 0.075718 +0.945932 0.054068 +0.979349 0.020651 +0.943496 0.056504 +0.324151 0.675849 +0.941777 0.058223 +0.824536 0.175464 +0.846332 0.153668 +0.853867 0.146133 +0.937387 0.062613 +0.318427 0.681573 +0.847776 0.152224 +0.999990 0.000010 +0.872534 0.127466 +0.289538 0.710462 +0.912764 0.087236 +0.939753 0.060247 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.912408 0.087592 +0.999990 0.000010 +0.953205 0.046795 +0.933773 0.066227 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.964237 0.035763 diff --git a/inst/files/admixture/admixture_03 b/inst/files/admixture/admixture_03 new file mode 100644 index 0000000..275cc62 --- /dev/null +++ b/inst/files/admixture/admixture_03 @@ -0,0 +1,1592 @@ +0.057005 0.942995 +0.049391 0.950609 +0.027792 0.972208 +0.056381 0.943619 +0.068326 0.931674 +0.055989 0.944011 +0.073803 0.926197 +0.023864 0.976136 +0.049104 0.950896 +0.071588 0.928412 +0.052600 0.947400 +0.067918 0.932082 +0.053046 0.946954 +0.016234 0.983766 +0.053411 0.946589 +0.030498 0.969502 +0.077945 0.922055 +0.105872 0.894128 +0.056578 0.943422 +0.045748 0.954252 +0.052967 0.947033 +0.000286 0.999714 +0.053181 0.946819 +0.045396 0.954604 +0.090495 0.909505 +0.059668 0.940332 +0.360918 0.639082 +0.377726 0.622274 +0.383268 0.616732 +0.357552 0.642448 +0.358840 0.641160 +0.358460 0.641540 +0.372958 0.627042 +0.342393 0.657607 +0.378356 0.621644 +0.351069 0.648931 +0.365178 0.634822 +0.320974 0.679026 +0.373333 0.626667 +0.380484 0.619516 +0.353802 0.646198 +0.345397 0.654603 +0.426948 0.573052 +0.014907 0.985093 +0.397745 0.602255 +0.412758 0.587242 +0.356181 0.643819 +0.027744 0.972256 +0.418820 0.581180 +0.355439 0.644561 +0.835751 0.164249 +0.837731 0.162269 +0.832155 0.167845 +0.848174 0.151826 +0.835368 0.164632 +0.844932 0.155068 +0.848202 0.151798 +0.818975 0.181025 +0.857683 0.142317 +0.844075 0.155925 +0.851234 0.148766 +0.834279 0.165721 +0.840619 0.159381 +0.849089 0.150911 +0.831608 0.168392 +0.849957 0.150043 +0.798281 0.201719 +0.852337 0.147663 +0.848950 0.151050 +0.851597 0.148403 +0.840813 0.159187 +0.846742 0.153258 +0.877236 0.122764 +0.786585 0.213415 +0.805039 0.194961 +0.867954 0.132046 +0.865964 0.134036 +0.858349 0.141651 +0.801428 0.198572 +0.850691 0.149309 +0.855985 0.144015 +0.868430 0.131570 +0.866588 0.133412 +0.850248 0.149752 +0.865158 0.134842 +0.858768 0.141232 +0.808628 0.191372 +0.813718 0.186282 +0.814293 0.185707 +0.836846 0.163154 +0.820740 0.179260 +0.428537 0.571463 +0.421962 0.578038 +0.458958 0.541042 +0.439218 0.560782 +0.476191 0.523809 +0.437406 0.562594 +0.446116 0.553884 +0.456598 0.543402 +0.465572 0.534428 +0.439686 0.560314 +0.441407 0.558593 +0.472291 0.527709 +0.446629 0.553371 +0.456005 0.543995 +0.880426 0.119574 +0.879044 0.120956 +0.863196 0.136804 +0.866131 0.133869 +0.857451 0.142549 +0.877557 0.122443 +0.846027 0.153973 +0.865170 0.134830 +0.866280 0.133720 +0.865489 0.134511 +0.877590 0.122410 +0.849888 0.150112 +0.873127 0.126873 +0.865805 0.134195 +0.874831 0.125169 +0.859377 0.140623 +0.860422 0.139578 +0.865757 0.134243 +0.861802 0.138198 +0.862038 0.137962 +0.759812 0.240188 +0.758766 0.241234 +0.777603 0.222397 +0.789439 0.210561 +0.780001 0.219999 +0.761369 0.238631 +0.792114 0.207886 +0.776103 0.223897 +0.777890 0.222110 +0.762406 0.237594 +0.753308 0.246692 +0.752364 0.247636 +0.756709 0.243291 +0.779333 0.220667 +0.788389 0.211611 +0.725789 0.274211 +0.759213 0.240787 +0.758386 0.241614 +0.845114 0.154886 +0.763095 0.236905 +0.807970 0.192030 +0.776023 0.223977 +0.806400 0.193600 +0.788282 0.211718 +0.774045 0.225955 +0.789371 0.210629 +0.766736 0.233264 +0.823897 0.176103 +0.831008 0.168992 +0.784590 0.215410 +0.783613 0.216387 +0.777855 0.222145 +0.810495 0.189505 +0.768653 0.231347 +0.822788 0.177212 +0.803481 0.196519 +0.768729 0.231271 +0.814588 0.185412 +0.829196 0.170804 +0.809389 0.190611 +0.824234 0.175766 +0.804295 0.195705 +0.813005 0.186995 +0.810699 0.189301 +0.825637 0.174363 +0.808667 0.191333 +0.807540 0.192460 +0.800569 0.199431 +0.782517 0.217483 +0.796446 0.203554 +0.823534 0.176466 +0.818286 0.181714 +0.802303 0.197697 +0.802789 0.197211 +0.811965 0.188035 +0.685345 0.314655 +0.714853 0.285147 +0.680227 0.319773 +0.690259 0.309741 +0.703947 0.296053 +0.699229 0.300771 +0.681116 0.318884 +0.711667 0.288333 +0.679115 0.320885 +0.671842 0.328158 +0.701587 0.298413 +0.707577 0.292423 +0.690005 0.309995 +0.700616 0.299384 +0.678561 0.321439 +0.695073 0.304927 +0.692815 0.307185 +0.685511 0.314489 +0.715968 0.284032 +0.715676 0.284324 +0.693792 0.306208 +0.704437 0.295563 +0.694600 0.305400 +0.999990 0.000010 +0.992719 0.007281 +0.981995 0.018005 +0.981603 0.018397 +0.999195 0.000805 +0.992685 0.007315 +0.999990 0.000010 +0.989193 0.010807 +0.999990 0.000010 +0.997291 0.002709 +0.997481 0.002519 +0.999990 0.000010 +0.993094 0.006906 +0.986928 0.013072 +0.978361 0.021639 +0.997466 0.002534 +0.982314 0.017686 +0.999351 0.000649 +0.979158 0.020842 +0.987749 0.012251 +0.983681 0.016319 +0.982923 0.017077 +0.999990 0.000010 +0.984807 0.015193 +0.986935 0.013065 +0.991226 0.008774 +0.999990 0.000010 +0.981922 0.018078 +0.999990 0.000010 +0.985018 0.014982 +0.985038 0.014962 +0.986783 0.013217 +0.998140 0.001860 +0.988994 0.011006 +0.981788 0.018212 +0.997647 0.002353 +0.986129 0.013871 +0.993707 0.006293 +0.980933 0.019067 +0.980402 0.019598 +0.993052 0.006948 +0.999990 0.000010 +0.997234 0.002766 +0.978247 0.021753 +0.980919 0.019081 +0.999990 0.000010 +0.986411 0.013589 +0.969569 0.030431 +0.991682 0.008318 +0.999990 0.000010 +0.980499 0.019501 +0.998891 0.001109 +0.985532 0.014468 +0.985481 0.014519 +0.993808 0.006192 +0.988404 0.011596 +0.990414 0.009586 +0.994762 0.005238 +0.999990 0.000010 +0.980960 0.019040 +0.993032 0.006968 +0.971761 0.028239 +0.987803 0.012197 +0.980587 0.019413 +0.974787 0.025213 +0.990315 0.009685 +0.962520 0.037480 +0.994099 0.005901 +0.938021 0.061979 +0.986618 0.013382 +0.964569 0.035431 +0.959114 0.040886 +0.961445 0.038555 +0.980512 0.019488 +0.987805 0.012195 +0.967322 0.032678 +0.959682 0.040318 +0.968388 0.031612 +0.978362 0.021638 +0.990527 0.009473 +0.963173 0.036827 +0.963354 0.036646 +0.951717 0.048283 +0.964801 0.035199 +0.991355 0.008645 +0.998145 0.001855 +0.956725 0.043275 +0.952048 0.047952 +0.950380 0.049620 +0.973291 0.026709 +0.959018 0.040982 +0.948011 0.051989 +0.977380 0.022620 +0.947437 0.052563 +0.986065 0.013935 +0.980448 0.019552 +0.988403 0.011597 +0.973908 0.026092 +0.962624 0.037376 +0.950370 0.049630 +0.956821 0.043179 +0.978206 0.021794 +0.987788 0.012212 +0.981458 0.018542 +0.976654 0.023346 +0.977313 0.022687 +0.957899 0.042101 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.964367 0.035633 +0.978196 0.021804 +0.981772 0.018228 +0.976242 0.023758 +0.959504 0.040496 +0.951941 0.048059 +0.961593 0.038407 +0.966770 0.033230 +0.953760 0.046240 +0.988881 0.011119 +0.973794 0.026206 +0.982609 0.017391 +0.976965 0.023035 +0.960101 0.039899 +0.993630 0.006370 +0.978023 0.021977 +0.975419 0.024581 +0.972539 0.027461 +0.986733 0.013267 +0.965404 0.034596 +0.984113 0.015887 +0.109847 0.890153 +0.066480 0.933520 +0.129471 0.870529 +0.070503 0.929497 +0.108925 0.891075 +0.069922 0.930078 +0.098225 0.901775 +0.119257 0.880743 +0.967862 0.032138 +0.975949 0.024051 +0.966236 0.033764 +0.972678 0.027322 +0.971426 0.028574 +0.973355 0.026645 +0.965044 0.034956 +0.960228 0.039772 +0.978063 0.021937 +0.973596 0.026404 +0.962591 0.037409 +0.974875 0.025125 +0.963639 0.036361 +0.973502 0.026498 +0.957358 0.042642 +0.966506 0.033494 +0.975225 0.024775 +0.940133 0.059867 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.976029 0.023971 +0.974560 0.025440 +0.982204 0.017796 +0.990252 0.009748 +0.978221 0.021779 +0.977776 0.022224 +0.990348 0.009652 +0.990643 0.009357 +0.984186 0.015814 +0.999990 0.000010 +0.994826 0.005174 +0.986693 0.013307 +0.999990 0.000010 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.906940 0.093060 +0.894807 0.105193 +0.863554 0.136446 +0.885512 0.114488 +0.924777 0.075223 +0.883801 0.116199 +0.911889 0.088111 +0.903530 0.096470 +0.888110 0.111890 +0.885385 0.114615 +0.887837 0.112163 +0.879687 0.120313 +0.885731 0.114269 +0.863364 0.136636 +0.880739 0.119261 +0.892843 0.107157 +0.875045 0.124955 +0.896514 0.103486 +0.919863 0.080137 +0.885190 0.114810 +0.877092 0.122908 +0.891549 0.108451 +0.100049 0.899951 +0.099348 0.900652 +0.127811 0.872189 +0.173264 0.826736 +0.185340 0.814660 +0.088611 0.911389 +0.109196 0.890804 +0.092310 0.907690 +0.075398 0.924602 +0.093584 0.906416 +0.156192 0.843808 +0.068594 0.931406 +0.105287 0.894713 +0.084155 0.915845 +0.098885 0.901115 +0.116176 0.883824 +0.095293 0.904707 +0.129415 0.870585 +0.098470 0.901530 +0.142204 0.857796 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.993257 0.006743 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.989663 0.010337 +0.997838 0.002162 +0.992376 0.007624 +0.999990 0.000010 +0.994989 0.005011 +0.999990 0.000010 +0.999990 0.000010 +0.998341 0.001659 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.003642 0.996358 +0.000010 0.999990 +0.000010 0.999990 +0.001394 0.998606 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.016185 0.983815 +0.030635 0.969365 +0.024417 0.975583 +0.029977 0.970023 +0.000010 0.999990 +0.000010 0.999990 +0.004236 0.995764 +0.035764 0.964236 +0.008739 0.991261 +0.041955 0.958045 +0.043679 0.956321 +0.028744 0.971256 +0.030183 0.969817 +0.019361 0.980639 +0.014867 0.985133 +0.020002 0.979998 +0.015413 0.984587 +0.038964 0.961036 +0.023808 0.976192 +0.056653 0.943347 +0.028872 0.971128 +0.018021 0.981979 +0.046033 0.953967 +0.000010 0.999990 +0.019491 0.980509 +0.001877 0.998123 +0.019087 0.980913 +0.010720 0.989280 +0.000010 0.999990 +0.002520 0.997480 +0.001007 0.998993 +0.033429 0.966571 +0.021135 0.978865 +0.007886 0.992114 +0.069356 0.930644 +0.017505 0.982495 +0.047702 0.952298 +0.000010 0.999990 +0.946353 0.053647 +0.953794 0.046206 +0.955227 0.044773 +0.940631 0.059369 +0.949578 0.050422 +0.961704 0.038296 +0.932977 0.067023 +0.932092 0.067908 +0.968531 0.031469 +0.956494 0.043506 +0.959133 0.040867 +0.955155 0.044845 +0.953826 0.046174 +0.932220 0.067780 +0.945342 0.054658 +0.937007 0.062993 +0.939635 0.060365 +0.958641 0.041359 +0.941544 0.058456 +0.966323 0.033677 +0.964589 0.035411 +0.006433 0.993567 +0.012026 0.987974 +0.010231 0.989769 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.013571 0.986429 +0.000010 0.999990 +0.001736 0.998264 +0.027763 0.972237 +0.478148 0.521852 +0.503475 0.496525 +0.437563 0.562437 +0.480773 0.519227 +0.456270 0.543730 +0.370425 0.629575 +0.501000 0.499000 +0.386789 0.613211 +0.417934 0.582066 +0.433074 0.566926 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000097 0.999903 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.054339 0.945661 +0.075870 0.924130 +0.036771 0.963229 +0.077444 0.922556 +0.050464 0.949536 +0.044442 0.955558 +0.074653 0.925347 +0.043170 0.956830 +0.044735 0.955265 +0.070820 0.929180 +0.999990 0.000010 +0.998921 0.001079 +0.992972 0.007028 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.986869 0.013131 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.892290 0.107710 +0.945811 0.054189 +0.933121 0.066879 +0.917572 0.082428 +0.937551 0.062449 +0.949890 0.050110 +0.890844 0.109156 +0.909863 0.090137 +0.944398 0.055602 +0.943121 0.056879 +0.937241 0.062759 +0.925813 0.074187 +0.931925 0.068075 +0.957478 0.042522 +0.891856 0.108144 +0.083971 0.916029 +0.073870 0.926130 +0.063511 0.936489 +0.075930 0.924070 +0.071598 0.928402 +0.070036 0.929964 +0.041507 0.958493 +0.045360 0.954640 +0.030488 0.969512 +0.051958 0.948042 +0.064531 0.935469 +0.056698 0.943302 +0.072063 0.927937 +0.046337 0.953663 +0.047191 0.952809 +0.072944 0.927056 +0.064992 0.935008 +0.040762 0.959238 +0.052228 0.947772 +0.038378 0.961622 +0.076911 0.923089 +0.056469 0.943531 +0.044509 0.955491 +0.035888 0.964112 +0.027242 0.972758 +0.061107 0.938893 +0.049495 0.950505 +0.311821 0.688179 +0.317934 0.682066 +0.320721 0.679279 +0.317862 0.682138 +0.319632 0.680368 +0.329292 0.670708 +0.311027 0.688973 +0.307445 0.692555 +0.332732 0.667268 +0.308071 0.691929 +0.320962 0.679038 +0.596269 0.403731 +0.564724 0.435276 +0.559244 0.440756 +0.562745 0.437255 +0.551194 0.448806 +0.566696 0.433304 +0.562043 0.437957 +0.556198 0.443802 +0.569775 0.430225 +0.553947 0.446053 +0.554977 0.445023 +0.542044 0.457956 +0.547317 0.452683 +0.721275 0.278725 +0.711551 0.288449 +0.706876 0.293124 +0.721482 0.278518 +0.755105 0.244895 +0.704089 0.295911 +0.714089 0.285911 +0.723267 0.276733 +0.716950 0.283050 +0.727614 0.272386 +0.718815 0.281185 +0.728592 0.271408 +0.706732 0.293268 +0.722374 0.277626 +0.719121 0.280879 +0.343538 0.656462 +0.353761 0.646239 +0.357395 0.642605 +0.350847 0.649153 +0.357290 0.642710 +0.347889 0.652111 +0.364478 0.635522 +0.359716 0.640284 +0.350618 0.649382 +0.347522 0.652478 +0.365916 0.634084 +0.363151 0.636849 +0.635578 0.364422 +0.593824 0.406176 +0.624183 0.375817 +0.604957 0.395043 +0.596837 0.403163 +0.621108 0.378892 +0.632349 0.367651 +0.619990 0.380010 +0.648403 0.351597 +0.622789 0.377211 +0.630606 0.369394 +0.624556 0.375444 +0.620468 0.379532 +0.581171 0.418829 +0.593819 0.406181 +0.586122 0.413878 +0.573683 0.426317 +0.602804 0.397196 +0.596642 0.403358 +0.608931 0.391069 +0.577841 0.422159 +0.574479 0.425521 +0.577653 0.422347 +0.601544 0.398456 +0.562081 0.437919 +0.586697 0.413303 +0.765166 0.234834 +0.937953 0.062047 +0.955709 0.044291 +0.932292 0.067708 +0.960235 0.039765 +0.944241 0.055759 +0.976384 0.023616 +0.980728 0.019272 +0.999990 0.000010 +0.880478 0.119522 +0.951157 0.048843 +0.972596 0.027404 +0.966413 0.033587 +0.974483 0.025517 +0.934515 0.065485 +0.957118 0.042882 +0.959657 0.040343 +0.876115 0.123885 +0.985551 0.014449 +0.962298 0.037702 +0.992286 0.007714 +0.979896 0.020104 +0.985892 0.014108 +0.979480 0.020520 +0.986630 0.013370 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.985829 0.014171 +0.999173 0.000827 +0.989276 0.010724 +0.994397 0.005603 +0.996787 0.003213 +0.999990 0.000010 +0.989119 0.010881 +0.999990 0.000010 +0.997090 0.002910 +0.987457 0.012543 +0.984450 0.015550 +0.990211 0.009789 +0.987458 0.012542 +0.994283 0.005717 +0.989399 0.010601 +0.984701 0.015299 +0.978507 0.021493 +0.986100 0.013900 +0.966698 0.033302 +0.928093 0.071907 +0.895174 0.104826 +0.934695 0.065305 +0.965711 0.034289 +0.975466 0.024534 +0.999696 0.000304 +0.975163 0.024837 +0.981515 0.018485 +0.988628 0.011372 +0.915221 0.084779 +0.905664 0.094336 +0.999990 0.000010 +0.923076 0.076924 +0.996504 0.003496 +0.967553 0.032447 +0.901028 0.098972 +0.967711 0.032289 +0.973985 0.026015 +0.967354 0.032646 +0.963470 0.036530 +0.965911 0.034089 +0.937590 0.062410 +0.970774 0.029226 +0.966415 0.033585 +0.971493 0.028507 +0.988232 0.011768 +0.894288 0.105712 +0.989279 0.010721 +0.962235 0.037765 +0.988050 0.011950 +0.958336 0.041664 +0.949607 0.050393 +0.989031 0.010969 +0.940136 0.059864 +0.982363 0.017637 +0.959015 0.040985 +0.996025 0.003975 +0.964029 0.035971 +0.979634 0.020366 +0.968849 0.031151 +0.974621 0.025379 +0.923203 0.076797 +0.934122 0.065878 +0.994831 0.005169 +0.988376 0.011624 +0.948132 0.051868 +0.912579 0.087421 +0.972927 0.027073 +0.988387 0.011613 +0.977269 0.022731 +0.964231 0.035769 +0.965457 0.034543 +0.918056 0.081944 +0.975987 0.024013 +0.985378 0.014622 +0.984661 0.015339 +0.956306 0.043694 +0.993677 0.006323 +0.971795 0.028205 +0.970722 0.029278 +0.929863 0.070137 +0.950588 0.049412 +0.904138 0.095862 +0.949767 0.050233 +0.986268 0.013732 +0.936188 0.063812 +0.950088 0.049912 +0.997449 0.002551 +0.980579 0.019421 +0.986263 0.013737 +0.944474 0.055526 +0.942520 0.057480 +0.941674 0.058326 +0.956463 0.043537 +0.980286 0.019714 +0.944346 0.055654 +0.956140 0.043860 +0.972042 0.027958 +0.905831 0.094169 +0.874802 0.125198 +0.976189 0.023811 +0.897879 0.102121 +0.943211 0.056789 +0.970771 0.029229 +0.992994 0.007006 +0.941741 0.058259 +0.765534 0.234466 +0.922161 0.077839 +0.888633 0.111367 +0.974528 0.025472 +0.894924 0.105076 +0.933040 0.066960 +0.954119 0.045881 +0.958982 0.041018 +0.978782 0.021218 +0.934685 0.065315 +0.912853 0.087147 +0.711699 0.288301 +0.774534 0.225466 +0.905083 0.094917 +0.989024 0.010976 +0.987913 0.012087 +0.878309 0.121691 +0.943553 0.056447 +0.958336 0.041664 +0.980206 0.019794 +0.984904 0.015096 +0.684584 0.315416 +0.183822 0.816178 +0.895566 0.104434 +0.981767 0.018233 +0.997810 0.002190 +0.891320 0.108680 +0.948058 0.051942 +0.957449 0.042551 +0.983272 0.016728 +0.983346 0.016654 +0.953543 0.046457 +0.912903 0.087097 +0.630824 0.369176 +0.178954 0.821046 +0.887756 0.112244 +0.971618 0.028382 +0.886470 0.113530 +0.902894 0.097106 +0.956978 0.043022 +0.970439 0.029561 +0.980483 0.019517 +0.929750 0.070250 +0.939915 0.060085 +0.935065 0.064935 +0.743596 0.256404 +0.206039 0.793961 +0.880440 0.119560 +0.986704 0.013296 +0.899316 0.100684 +0.893776 0.106224 +0.924267 0.075733 +0.972293 0.027707 +0.996288 0.003712 +0.951298 0.048702 +0.933614 0.066386 +0.919927 0.080073 +0.749466 0.250534 +0.161124 0.838876 +0.911473 0.088527 +0.989553 0.010447 +0.897847 0.102153 +0.936251 0.063749 +0.969573 0.030427 +0.999990 0.000010 +0.936902 0.063098 +0.982931 0.017069 +0.899113 0.100887 +0.760715 0.239285 +0.181990 0.818010 +0.911592 0.088408 +0.968472 0.031528 +0.915992 0.084008 +0.939126 0.060874 +0.955813 0.044187 +0.978772 0.021228 +0.979818 0.020182 +0.932151 0.067849 +0.906015 0.093985 +0.897917 0.102083 +0.740535 0.259465 +0.167619 0.832381 +0.140446 0.859554 +0.245507 0.754493 +0.160359 0.839641 +0.062519 0.937481 +0.299047 0.700953 +0.966880 0.033120 +0.971766 0.028234 +0.957419 0.042581 +0.896160 0.103840 +0.736020 0.263980 +0.548812 0.451188 +0.163407 0.836593 +0.261374 0.738626 +0.178821 0.821179 +0.207513 0.792487 +0.978451 0.021549 +0.954154 0.045846 +0.929405 0.070595 +0.893536 0.106464 +0.704198 0.295802 +0.506189 0.493811 +0.178694 0.821306 +0.254599 0.745401 +0.127922 0.872078 +0.123185 0.876815 +0.945806 0.054194 +0.948383 0.051617 +0.952123 0.047877 +0.874261 0.125739 +0.716427 0.283573 +0.552674 0.447326 +0.180821 0.819179 +0.164019 0.835981 +0.438809 0.561191 +0.296431 0.703569 +0.973196 0.026804 +0.937816 0.062184 +0.874002 0.125998 +0.911931 0.088069 +0.734672 0.265328 +0.437057 0.562943 +0.275542 0.724458 +0.150175 0.849825 +0.159429 0.840571 +0.622758 0.377242 +0.323898 0.676102 +0.951863 0.048137 +0.957612 0.042388 +0.910995 0.089005 +0.907221 0.092779 +0.716960 0.283040 +0.538903 0.461097 +0.241020 0.758980 +0.133064 0.866936 +0.143746 0.856254 +0.340761 0.659239 +0.950184 0.049816 +0.899476 0.100524 +0.756672 0.243328 +0.711340 0.288660 +0.666296 0.333704 +0.278559 0.721441 +0.147059 0.852941 +0.156344 0.843656 +0.390862 0.609138 +0.951798 0.048202 +0.951464 0.048536 +0.894559 0.105441 +0.720194 0.279806 +0.761688 0.238312 +0.673635 0.326365 +0.225985 0.774015 +0.189512 0.810488 +0.208648 0.791352 +0.231142 0.768858 +0.954819 0.045181 +0.971438 0.028562 +0.960058 0.039942 +0.916144 0.083856 +0.749152 0.250848 +0.496845 0.503155 +0.648122 0.351878 +0.552930 0.447070 +0.829166 0.170834 +0.850311 0.149689 +0.852046 0.147954 +0.588531 0.411469 +0.793495 0.206505 +0.842363 0.157637 +0.641554 0.358446 +0.802348 0.197652 +0.746228 0.253772 +0.978440 0.021560 +0.801184 0.198816 +0.691643 0.308357 +0.935869 0.064131 +0.519971 0.480029 +0.820685 0.179315 +0.679553 0.320447 +0.679653 0.320347 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.974208 0.025792 +0.984021 0.015979 +0.956171 0.043829 +0.985737 0.014263 +0.999990 0.000010 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.978549 0.021451 +0.977550 0.022450 +0.987629 0.012371 +0.977429 0.022571 +0.999990 0.000010 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.980571 0.019429 +0.971305 0.028695 +0.987074 0.012926 +0.994808 0.005192 +0.974543 0.025457 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.973523 0.026477 +0.999990 0.000010 +0.999990 0.000010 +0.976675 0.023325 +0.993911 0.006089 +0.000010 0.999990 +0.000010 0.999990 +0.891553 0.108447 +0.976702 0.023298 +0.982094 0.017906 +0.985765 0.014235 +0.978991 0.021009 +0.988526 0.011474 +0.000010 0.999990 +0.000010 0.999990 +0.984224 0.015776 +0.964271 0.035729 +0.967164 0.032836 +0.999990 0.000010 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.932370 0.067630 +0.972684 0.027316 +0.998581 0.001419 +0.977912 0.022088 +0.991237 0.008763 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.974600 0.025400 +0.991923 0.008077 +0.986840 0.013160 +0.976757 0.023243 +0.991328 0.008672 +0.000010 0.999990 +0.984499 0.015501 +0.987047 0.012953 +0.987420 0.012580 +0.981903 0.018097 +0.999990 0.000010 +0.999990 0.000010 +0.991094 0.008906 +0.991797 0.008203 +0.999990 0.000010 +0.996317 0.003683 +0.999990 0.000010 +0.995952 0.004048 +0.986941 0.013059 +0.999990 0.000010 +0.996389 0.003611 +0.991554 0.008446 +0.989656 0.010344 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.997025 0.002975 +0.999990 0.000010 +0.999990 0.000010 +0.988644 0.011356 +0.990154 0.009846 +0.999990 0.000010 +0.985096 0.014904 +0.999990 0.000010 +0.999990 0.000010 +0.993920 0.006080 +0.997038 0.002962 +0.999990 0.000010 +0.980971 0.019029 +0.976295 0.023705 +0.992726 0.007274 +0.979295 0.020705 +0.999990 0.000010 +0.992737 0.007263 +0.999990 0.000010 +0.997507 0.002493 +0.881054 0.118946 +0.914246 0.085754 +0.907017 0.092983 +0.909744 0.090256 +0.986328 0.013672 +0.892898 0.107102 +0.992907 0.007093 +0.915748 0.084252 +0.918924 0.081076 +0.893237 0.106763 +0.999990 0.000010 +0.996252 0.003748 +0.999990 0.000010 +0.998240 0.001760 +0.999990 0.000010 +0.999990 0.000010 +0.990101 0.009899 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.996630 0.003370 +0.989134 0.010866 +0.999990 0.000010 +0.999990 0.000010 +0.987267 0.012733 +0.999744 0.000256 +0.987796 0.012204 +0.988340 0.011660 +0.999990 0.000010 +0.978414 0.021586 +0.993258 0.006742 +0.991236 0.008764 +0.001076 0.998924 +0.016443 0.983557 +0.020928 0.979072 +0.000010 0.999990 +0.019113 0.980887 +0.012764 0.987236 +0.005818 0.994182 +0.012257 0.987743 +0.998241 0.001759 +0.999990 0.000010 +0.996461 0.003539 +0.999288 0.000712 +0.991910 0.008090 +0.624269 0.375731 +0.719030 0.280970 +0.631904 0.368096 +0.636312 0.363688 +0.626934 0.373066 +0.992541 0.007459 +0.570724 0.429276 +0.572430 0.427570 +0.579717 0.420283 +0.623715 0.376285 +0.663198 0.336802 +0.659516 0.340484 +0.571014 0.428986 +0.584007 0.415993 +0.561738 0.438262 +0.571454 0.428546 +0.114339 0.885661 +0.020838 0.979162 +0.145161 0.854839 +0.154697 0.845303 +0.042128 0.957872 +0.156573 0.843427 +0.084205 0.915795 +0.141030 0.858970 +0.122095 0.877905 +0.136547 0.863453 +0.982156 0.017844 +0.988962 0.011038 +0.999990 0.000010 +0.237034 0.762966 +0.953992 0.046008 +0.989604 0.010396 +0.990259 0.009741 +0.978717 0.021283 +0.978998 0.021002 +0.206480 0.793520 +0.977744 0.022256 +0.988259 0.011741 +0.260387 0.739613 +0.993168 0.006832 +0.998601 0.001399 +0.981157 0.018843 +0.298956 0.701044 +0.065809 0.934191 +0.987613 0.012387 +0.069613 0.930387 +0.994866 0.005134 +0.975124 0.024876 +0.165047 0.834953 +0.168511 0.831489 +0.935943 0.064057 +0.999990 0.000010 +0.984269 0.015731 +0.977231 0.022769 +0.979002 0.020998 +0.992639 0.007361 +0.077592 0.922408 +0.142119 0.857881 +0.998147 0.001853 +0.992356 0.007644 +0.999990 0.000010 +0.967827 0.032173 +0.984238 0.015762 +0.982930 0.017070 +0.247250 0.752750 +0.993296 0.006704 +0.918370 0.081630 +0.958444 0.041556 +0.982736 0.017264 +0.999887 0.000113 +0.970217 0.029783 +0.211400 0.788600 +0.076779 0.923221 +0.999990 0.000010 +0.986302 0.013698 +0.059097 0.940903 +0.018905 0.981095 +0.967432 0.032568 +0.975727 0.024273 +0.983540 0.016460 +0.999990 0.000010 +0.999691 0.000309 +0.999990 0.000010 +0.999990 0.000010 +0.990975 0.009025 +0.990979 0.009021 +0.983416 0.016584 +0.983493 0.016507 +0.999990 0.000010 +0.989143 0.010857 +0.978965 0.021035 +0.999990 0.000010 +0.999990 0.000010 +0.992803 0.007197 +0.993189 0.006811 +0.999990 0.000010 +0.984120 0.015880 +0.994641 0.005359 +0.999990 0.000010 +0.991915 0.008085 +0.989608 0.010392 +0.982667 0.017333 +0.999990 0.000010 +0.997701 0.002299 +0.979636 0.020364 +0.871421 0.128579 +0.999990 0.000010 +0.990139 0.009861 +0.953473 0.046527 +0.999990 0.000010 +0.953721 0.046279 +0.145067 0.854933 +0.999990 0.000010 +0.993501 0.006499 +0.989102 0.010898 +0.989397 0.010603 +0.938836 0.061164 +0.955841 0.044159 +0.984986 0.015014 +0.889988 0.110012 +0.999990 0.000010 +0.946933 0.053067 +0.991854 0.008146 +0.977778 0.022222 +0.852385 0.147615 +0.984304 0.015696 +0.985580 0.014420 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.943434 0.056566 +0.935674 0.064326 +0.982149 0.017851 +0.987663 0.012337 +0.996625 0.003375 +0.994586 0.005414 +0.992542 0.007458 +0.977144 0.022856 +0.973472 0.026528 +0.875681 0.124319 +0.999990 0.000010 +0.994718 0.005282 +0.999990 0.000010 +0.952969 0.047031 +0.995192 0.004808 +0.958929 0.041071 +0.943518 0.056482 +0.998839 0.001161 +0.995425 0.004575 +0.940834 0.059166 +0.990457 0.009543 +0.981173 0.018827 +0.912102 0.087898 +0.999990 0.000010 +0.932021 0.067979 +0.999990 0.000010 +0.982369 0.017631 +0.992711 0.007289 +0.994767 0.005233 +0.938256 0.061744 +0.980182 0.019818 +0.994157 0.005843 +0.930840 0.069160 +0.858098 0.141902 +0.984678 0.015322 +0.941628 0.058372 +0.978464 0.021536 +0.983061 0.016939 +0.952160 0.047840 +0.980357 0.019643 +0.991655 0.008345 +0.973345 0.026655 +0.984684 0.015316 +0.934147 0.065853 +0.982455 0.017545 +0.978098 0.021902 +0.999990 0.000010 +0.982850 0.017150 +0.939018 0.060982 +0.984061 0.015939 +0.954739 0.045261 +0.982884 0.017116 +0.999990 0.000010 +0.952179 0.047821 +0.944404 0.055596 +0.996166 0.003834 +0.956560 0.043440 +0.976764 0.023236 +0.984379 0.015621 +0.997737 0.002263 +0.999903 0.000097 +0.938238 0.061762 +0.999250 0.000750 +0.991581 0.008419 +0.942929 0.057071 +0.999990 0.000010 +0.859202 0.140798 +0.992944 0.007056 +0.912243 0.087757 +0.994454 0.005546 +0.988595 0.011405 +0.977527 0.022473 +0.982523 0.017477 +0.982057 0.017943 +0.993894 0.006106 +0.999990 0.000010 +0.962409 0.037591 +0.951425 0.048575 +0.992880 0.007120 +0.976262 0.023738 +0.941897 0.058103 +0.999990 0.000010 +0.999990 0.000010 +0.981392 0.018608 +0.291498 0.708502 +0.943333 0.056667 +0.993202 0.006798 +0.973311 0.026689 +0.987534 0.012466 +0.999990 0.000010 +0.998301 0.001699 +0.993403 0.006597 +0.886574 0.113426 +0.946603 0.053397 +0.938432 0.061568 +0.940860 0.059140 +0.966984 0.033016 +0.982368 0.017632 +0.989932 0.010068 +0.993816 0.006184 +0.984810 0.015190 +0.991756 0.008244 +0.834285 0.165715 +0.976847 0.023153 +0.969034 0.030966 +0.303017 0.696983 +0.999990 0.000010 +0.974392 0.025608 +0.978728 0.021272 +0.999990 0.000010 +0.926952 0.073048 +0.846137 0.153863 +0.912212 0.087788 +0.855224 0.144776 +0.903645 0.096355 +0.924882 0.075118 +0.824304 0.175696 +0.887812 0.112188 +0.998722 0.001278 +0.318342 0.681658 +0.948810 0.051190 +0.286935 0.713065 +0.999990 0.000010 +0.985901 0.014099 +0.947287 0.052713 +0.298409 0.701591 +0.970752 0.029248 +0.878204 0.121796 +0.939598 0.060402 +0.844159 0.155841 +0.837458 0.162542 +0.908723 0.091277 +0.970786 0.029214 +0.999990 0.000010 +0.865286 0.134714 +0.301730 0.698270 +0.899579 0.100421 +0.908277 0.091723 +0.970176 0.029824 +0.918151 0.081849 +0.999990 0.000010 +0.905773 0.094227 +0.901063 0.098937 +0.997685 0.002315 +0.924282 0.075718 +0.945932 0.054068 +0.979349 0.020651 +0.943496 0.056504 +0.324151 0.675849 +0.941777 0.058223 +0.824536 0.175464 +0.846332 0.153668 +0.853867 0.146133 +0.937387 0.062613 +0.318427 0.681573 +0.847776 0.152224 +0.999990 0.000010 +0.872534 0.127466 +0.289538 0.710462 +0.912764 0.087236 +0.939753 0.060247 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.912408 0.087592 +0.999990 0.000010 +0.953205 0.046795 +0.933773 0.066227 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.964237 0.035763 diff --git a/inst/files/admixture/admixture_04 b/inst/files/admixture/admixture_04 new file mode 100644 index 0000000..e187cc0 --- /dev/null +++ b/inst/files/admixture/admixture_04 @@ -0,0 +1,1592 @@ +0.057005 0.942995 +0.049391 0.950609 +0.027792 0.972208 +0.056381 0.943619 +0.068326 0.931674 +0.055989 0.944011 +0.073803 0.926197 +0.023864 0.976136 +0.049104 0.950896 +0.071588 0.928412 +0.052600 0.947400 +0.067918 0.932082 +0.053046 0.946954 +0.016234 0.983766 +0.053411 0.946589 +0.030498 0.969502 +0.077945 0.922055 +0.105872 0.894128 +0.056578 0.943422 +0.045748 0.954252 +0.052967 0.947033 +0.000286 0.999714 +0.053181 0.946819 +0.045396 0.954604 +0.090495 0.909505 +0.059668 0.940332 +0.360918 0.639082 +0.377726 0.622274 +0.383268 0.616732 +0.357552 0.642448 +0.358840 0.641160 +0.358460 0.641540 +0.372958 0.627042 +0.342393 0.657607 +0.378356 0.621644 +0.351069 0.648931 +0.365178 0.634822 +0.320974 0.679026 +0.373333 0.626667 +0.380484 0.619516 +0.353801 0.646199 +0.345397 0.654603 +0.426948 0.573052 +0.014908 0.985092 +0.397745 0.602255 +0.412757 0.587243 +0.356181 0.643819 +0.027744 0.972256 +0.418820 0.581180 +0.355439 0.644561 +0.835750 0.164250 +0.837731 0.162269 +0.832154 0.167846 +0.848174 0.151826 +0.835367 0.164633 +0.844932 0.155068 +0.848201 0.151799 +0.818975 0.181025 +0.857683 0.142317 +0.844074 0.155926 +0.851234 0.148766 +0.834278 0.165722 +0.840619 0.159381 +0.849088 0.150912 +0.831608 0.168392 +0.849957 0.150043 +0.798281 0.201719 +0.852336 0.147664 +0.848949 0.151051 +0.851597 0.148403 +0.840813 0.159187 +0.846742 0.153258 +0.877235 0.122765 +0.786585 0.213415 +0.805039 0.194961 +0.867954 0.132046 +0.865963 0.134037 +0.858348 0.141652 +0.801427 0.198573 +0.850690 0.149310 +0.855985 0.144015 +0.868430 0.131570 +0.866587 0.133413 +0.850247 0.149753 +0.865157 0.134843 +0.858768 0.141232 +0.808628 0.191372 +0.813717 0.186283 +0.814292 0.185708 +0.836846 0.163154 +0.820739 0.179261 +0.428537 0.571463 +0.421962 0.578038 +0.458958 0.541042 +0.439218 0.560782 +0.476191 0.523809 +0.437405 0.562595 +0.446116 0.553884 +0.456598 0.543402 +0.465571 0.534429 +0.439686 0.560314 +0.441407 0.558593 +0.472291 0.527709 +0.446629 0.553371 +0.456004 0.543996 +0.880426 0.119574 +0.879043 0.120957 +0.863195 0.136805 +0.866130 0.133870 +0.857451 0.142549 +0.877556 0.122444 +0.846027 0.153973 +0.865170 0.134830 +0.866280 0.133720 +0.865489 0.134511 +0.877590 0.122410 +0.849887 0.150113 +0.873126 0.126874 +0.865804 0.134196 +0.874831 0.125169 +0.859377 0.140623 +0.860421 0.139579 +0.865757 0.134243 +0.861801 0.138199 +0.862037 0.137963 +0.759812 0.240188 +0.758765 0.241235 +0.777603 0.222397 +0.789439 0.210561 +0.780001 0.219999 +0.761368 0.238632 +0.792113 0.207887 +0.776102 0.223898 +0.777890 0.222110 +0.762406 0.237594 +0.753307 0.246693 +0.752363 0.247637 +0.756709 0.243291 +0.779332 0.220668 +0.788388 0.211612 +0.725789 0.274211 +0.759212 0.240788 +0.758386 0.241614 +0.845113 0.154887 +0.763094 0.236906 +0.807970 0.192030 +0.776022 0.223978 +0.806399 0.193601 +0.788282 0.211718 +0.774045 0.225955 +0.789370 0.210630 +0.766736 0.233264 +0.823897 0.176103 +0.831008 0.168992 +0.784589 0.215411 +0.783613 0.216387 +0.777855 0.222145 +0.810495 0.189505 +0.768652 0.231348 +0.822788 0.177212 +0.803481 0.196519 +0.768728 0.231272 +0.814588 0.185412 +0.829196 0.170804 +0.809389 0.190611 +0.824233 0.175767 +0.804294 0.195706 +0.813005 0.186995 +0.810699 0.189301 +0.825636 0.174364 +0.808666 0.191334 +0.807540 0.192460 +0.800568 0.199432 +0.782516 0.217484 +0.796446 0.203554 +0.823534 0.176466 +0.818286 0.181714 +0.802302 0.197698 +0.802789 0.197211 +0.811965 0.188035 +0.685345 0.314655 +0.714853 0.285147 +0.680226 0.319774 +0.690258 0.309742 +0.703946 0.296054 +0.699228 0.300772 +0.681116 0.318884 +0.711667 0.288333 +0.679115 0.320885 +0.671842 0.328158 +0.701587 0.298413 +0.707577 0.292423 +0.690005 0.309995 +0.700616 0.299384 +0.678561 0.321439 +0.695072 0.304928 +0.692815 0.307185 +0.685511 0.314489 +0.715967 0.284033 +0.715675 0.284325 +0.693792 0.306208 +0.704437 0.295563 +0.694599 0.305401 +0.999990 0.000010 +0.992719 0.007281 +0.981994 0.018006 +0.981603 0.018397 +0.999194 0.000806 +0.992684 0.007316 +0.999990 0.000010 +0.989192 0.010808 +0.999990 0.000010 +0.997291 0.002709 +0.997481 0.002519 +0.999990 0.000010 +0.993093 0.006907 +0.986928 0.013072 +0.978361 0.021639 +0.997465 0.002535 +0.982314 0.017686 +0.999350 0.000650 +0.979157 0.020843 +0.987749 0.012251 +0.983681 0.016319 +0.982923 0.017077 +0.999990 0.000010 +0.984806 0.015194 +0.986934 0.013066 +0.991225 0.008775 +0.999990 0.000010 +0.981921 0.018079 +0.999990 0.000010 +0.985018 0.014982 +0.985038 0.014962 +0.986783 0.013217 +0.998139 0.001861 +0.988994 0.011006 +0.981787 0.018213 +0.997647 0.002353 +0.986129 0.013871 +0.993707 0.006293 +0.980932 0.019068 +0.980402 0.019598 +0.993052 0.006948 +0.999990 0.000010 +0.997233 0.002767 +0.978247 0.021753 +0.980919 0.019081 +0.999990 0.000010 +0.986410 0.013590 +0.969568 0.030432 +0.991681 0.008319 +0.999990 0.000010 +0.980498 0.019502 +0.998890 0.001110 +0.985532 0.014468 +0.985480 0.014520 +0.993808 0.006192 +0.988403 0.011597 +0.990413 0.009587 +0.994762 0.005238 +0.999990 0.000010 +0.980960 0.019040 +0.993031 0.006969 +0.971760 0.028240 +0.987803 0.012197 +0.980586 0.019414 +0.974786 0.025214 +0.990314 0.009686 +0.962520 0.037480 +0.994099 0.005901 +0.938021 0.061979 +0.986617 0.013383 +0.964569 0.035431 +0.959113 0.040887 +0.961445 0.038555 +0.980511 0.019489 +0.987805 0.012195 +0.967321 0.032679 +0.959682 0.040318 +0.968388 0.031612 +0.978362 0.021638 +0.990527 0.009473 +0.963173 0.036827 +0.963354 0.036646 +0.951716 0.048284 +0.964800 0.035200 +0.991354 0.008646 +0.998144 0.001856 +0.956725 0.043275 +0.952048 0.047952 +0.950380 0.049620 +0.973291 0.026709 +0.959018 0.040982 +0.948010 0.051990 +0.977380 0.022620 +0.947436 0.052564 +0.986064 0.013936 +0.980447 0.019553 +0.988402 0.011598 +0.973908 0.026092 +0.962624 0.037376 +0.950369 0.049631 +0.956820 0.043180 +0.978205 0.021795 +0.987788 0.012212 +0.981458 0.018542 +0.976654 0.023346 +0.977313 0.022687 +0.957899 0.042101 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.964366 0.035634 +0.978196 0.021804 +0.981771 0.018229 +0.976242 0.023758 +0.959503 0.040497 +0.951941 0.048059 +0.961593 0.038407 +0.966769 0.033231 +0.953759 0.046241 +0.988880 0.011120 +0.973794 0.026206 +0.982609 0.017391 +0.976965 0.023035 +0.960100 0.039900 +0.993630 0.006370 +0.978022 0.021978 +0.975418 0.024582 +0.972539 0.027461 +0.986733 0.013267 +0.965403 0.034597 +0.984112 0.015888 +0.109847 0.890153 +0.066480 0.933520 +0.129471 0.870529 +0.070503 0.929497 +0.108925 0.891075 +0.069922 0.930078 +0.098225 0.901775 +0.119257 0.880743 +0.967861 0.032139 +0.975948 0.024052 +0.966235 0.033765 +0.972677 0.027323 +0.971426 0.028574 +0.973355 0.026645 +0.965043 0.034957 +0.960228 0.039772 +0.978063 0.021937 +0.973595 0.026405 +0.962590 0.037410 +0.974875 0.025125 +0.963639 0.036361 +0.973502 0.026498 +0.957358 0.042642 +0.966506 0.033494 +0.975225 0.024775 +0.940132 0.059868 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.976028 0.023972 +0.974560 0.025440 +0.982203 0.017797 +0.990251 0.009749 +0.978220 0.021780 +0.977776 0.022224 +0.990347 0.009653 +0.990643 0.009357 +0.984185 0.015815 +0.999990 0.000010 +0.994826 0.005174 +0.986692 0.013308 +0.999990 0.000010 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.906939 0.093061 +0.894807 0.105193 +0.863554 0.136446 +0.885512 0.114488 +0.924777 0.075223 +0.883801 0.116199 +0.911888 0.088112 +0.903530 0.096470 +0.888109 0.111891 +0.885384 0.114616 +0.887837 0.112163 +0.879687 0.120313 +0.885731 0.114269 +0.863364 0.136636 +0.880738 0.119262 +0.892842 0.107158 +0.875045 0.124955 +0.896513 0.103487 +0.919863 0.080137 +0.885190 0.114810 +0.877091 0.122909 +0.891548 0.108452 +0.100049 0.899951 +0.099348 0.900652 +0.127811 0.872189 +0.173264 0.826736 +0.185340 0.814660 +0.088611 0.911389 +0.109196 0.890804 +0.092310 0.907690 +0.075398 0.924602 +0.093584 0.906416 +0.156192 0.843808 +0.068594 0.931406 +0.105287 0.894713 +0.084155 0.915845 +0.098885 0.901115 +0.116176 0.883824 +0.095293 0.904707 +0.129415 0.870585 +0.098470 0.901530 +0.142204 0.857796 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.993257 0.006743 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.989662 0.010338 +0.997837 0.002163 +0.992376 0.007624 +0.999990 0.000010 +0.994989 0.005011 +0.999990 0.000010 +0.999990 0.000010 +0.998338 0.001662 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.003642 0.996358 +0.000010 0.999990 +0.000010 0.999990 +0.001394 0.998606 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.016185 0.983815 +0.030635 0.969365 +0.024417 0.975583 +0.029977 0.970023 +0.000010 0.999990 +0.000010 0.999990 +0.004236 0.995764 +0.035764 0.964236 +0.008739 0.991261 +0.041955 0.958045 +0.043679 0.956321 +0.028744 0.971256 +0.030183 0.969817 +0.019361 0.980639 +0.014867 0.985133 +0.020002 0.979998 +0.015413 0.984587 +0.038964 0.961036 +0.023808 0.976192 +0.056653 0.943347 +0.028872 0.971128 +0.018021 0.981979 +0.046032 0.953968 +0.000010 0.999990 +0.019491 0.980509 +0.001877 0.998123 +0.019087 0.980913 +0.010720 0.989280 +0.000010 0.999990 +0.002520 0.997480 +0.001007 0.998993 +0.033429 0.966571 +0.021135 0.978865 +0.007886 0.992114 +0.069356 0.930644 +0.017505 0.982495 +0.047702 0.952298 +0.000010 0.999990 +0.946352 0.053648 +0.953794 0.046206 +0.955226 0.044774 +0.940630 0.059370 +0.949577 0.050423 +0.961704 0.038296 +0.932976 0.067024 +0.932091 0.067909 +0.968531 0.031469 +0.956493 0.043507 +0.959132 0.040868 +0.955154 0.044846 +0.953825 0.046175 +0.932219 0.067781 +0.945342 0.054658 +0.937006 0.062994 +0.939635 0.060365 +0.958641 0.041359 +0.941543 0.058457 +0.966323 0.033677 +0.964589 0.035411 +0.006433 0.993567 +0.012026 0.987974 +0.010231 0.989769 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.013571 0.986429 +0.000010 0.999990 +0.001737 0.998263 +0.027763 0.972237 +0.478148 0.521852 +0.503475 0.496525 +0.437563 0.562437 +0.480772 0.519228 +0.456269 0.543731 +0.370425 0.629575 +0.501000 0.499000 +0.386788 0.613212 +0.417934 0.582066 +0.433074 0.566926 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000097 0.999903 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.054339 0.945661 +0.075870 0.924130 +0.036771 0.963229 +0.077444 0.922556 +0.050464 0.949536 +0.044442 0.955558 +0.074653 0.925347 +0.043170 0.956830 +0.044735 0.955265 +0.070820 0.929180 +0.999990 0.000010 +0.998921 0.001079 +0.992971 0.007029 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.986868 0.013132 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.892290 0.107710 +0.945811 0.054189 +0.933121 0.066879 +0.917572 0.082428 +0.937551 0.062449 +0.949889 0.050111 +0.890844 0.109156 +0.909862 0.090138 +0.944397 0.055603 +0.943121 0.056879 +0.937241 0.062759 +0.925813 0.074187 +0.931925 0.068075 +0.957477 0.042523 +0.891856 0.108144 +0.083971 0.916029 +0.073870 0.926130 +0.063511 0.936489 +0.075930 0.924070 +0.071598 0.928402 +0.070036 0.929964 +0.041507 0.958493 +0.045360 0.954640 +0.030488 0.969512 +0.051958 0.948042 +0.064531 0.935469 +0.056698 0.943302 +0.072063 0.927937 +0.046337 0.953663 +0.047191 0.952809 +0.072944 0.927056 +0.064991 0.935009 +0.040762 0.959238 +0.052228 0.947772 +0.038378 0.961622 +0.076911 0.923089 +0.056469 0.943531 +0.044509 0.955491 +0.035888 0.964112 +0.027242 0.972758 +0.061107 0.938893 +0.049495 0.950505 +0.311821 0.688179 +0.317934 0.682066 +0.320721 0.679279 +0.317862 0.682138 +0.319632 0.680368 +0.329292 0.670708 +0.311027 0.688973 +0.307445 0.692555 +0.332731 0.667269 +0.308071 0.691929 +0.320962 0.679038 +0.596269 0.403731 +0.564723 0.435277 +0.559244 0.440756 +0.562745 0.437255 +0.551193 0.448807 +0.566696 0.433304 +0.562043 0.437957 +0.556198 0.443802 +0.569775 0.430225 +0.553946 0.446054 +0.554976 0.445024 +0.542043 0.457957 +0.547316 0.452684 +0.721274 0.278726 +0.711551 0.288449 +0.706876 0.293124 +0.721482 0.278518 +0.755105 0.244895 +0.704089 0.295911 +0.714089 0.285911 +0.723267 0.276733 +0.716950 0.283050 +0.727613 0.272387 +0.718814 0.281186 +0.728592 0.271408 +0.706732 0.293268 +0.722374 0.277626 +0.719120 0.280880 +0.343538 0.656462 +0.353760 0.646240 +0.357394 0.642606 +0.350847 0.649153 +0.357289 0.642711 +0.347888 0.652112 +0.364478 0.635522 +0.359716 0.640284 +0.350618 0.649382 +0.347522 0.652478 +0.365916 0.634084 +0.363150 0.636850 +0.635578 0.364422 +0.593824 0.406176 +0.624183 0.375817 +0.604957 0.395043 +0.596836 0.403164 +0.621108 0.378892 +0.632348 0.367652 +0.619990 0.380010 +0.648403 0.351597 +0.622789 0.377211 +0.630606 0.369394 +0.624556 0.375444 +0.620468 0.379532 +0.581171 0.418829 +0.593818 0.406182 +0.586122 0.413878 +0.573682 0.426318 +0.602803 0.397197 +0.596642 0.403358 +0.608931 0.391069 +0.577841 0.422159 +0.574478 0.425522 +0.577653 0.422347 +0.601544 0.398456 +0.562081 0.437919 +0.586697 0.413303 +0.765165 0.234835 +0.937953 0.062047 +0.955708 0.044292 +0.932292 0.067708 +0.960234 0.039766 +0.944241 0.055759 +0.976383 0.023617 +0.980728 0.019272 +0.999990 0.000010 +0.880477 0.119523 +0.951157 0.048843 +0.972596 0.027404 +0.966412 0.033588 +0.974482 0.025518 +0.934514 0.065486 +0.957117 0.042883 +0.959656 0.040344 +0.876115 0.123885 +0.985551 0.014449 +0.962297 0.037703 +0.992285 0.007715 +0.979895 0.020105 +0.985892 0.014108 +0.979480 0.020520 +0.986630 0.013370 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.985829 0.014171 +0.999172 0.000828 +0.989276 0.010724 +0.994396 0.005604 +0.996786 0.003214 +0.999990 0.000010 +0.989119 0.010881 +0.999990 0.000010 +0.997089 0.002911 +0.987456 0.012544 +0.984449 0.015551 +0.990210 0.009790 +0.987458 0.012542 +0.994282 0.005718 +0.989399 0.010601 +0.984700 0.015300 +0.978506 0.021494 +0.986100 0.013900 +0.966698 0.033302 +0.928093 0.071907 +0.895174 0.104826 +0.934694 0.065306 +0.965710 0.034290 +0.975465 0.024535 +0.999695 0.000305 +0.975162 0.024838 +0.981515 0.018485 +0.988628 0.011372 +0.915220 0.084780 +0.905664 0.094336 +0.999990 0.000010 +0.923075 0.076925 +0.996504 0.003496 +0.967552 0.032448 +0.901027 0.098973 +0.967710 0.032290 +0.973985 0.026015 +0.967353 0.032647 +0.963470 0.036530 +0.965911 0.034089 +0.937589 0.062411 +0.970774 0.029226 +0.966415 0.033585 +0.971493 0.028507 +0.988232 0.011768 +0.894288 0.105712 +0.989278 0.010722 +0.962235 0.037765 +0.988049 0.011951 +0.958336 0.041664 +0.949607 0.050393 +0.989031 0.010969 +0.940136 0.059864 +0.982362 0.017638 +0.959015 0.040985 +0.996025 0.003975 +0.964029 0.035971 +0.979634 0.020366 +0.968849 0.031151 +0.974620 0.025380 +0.923203 0.076797 +0.934122 0.065878 +0.994830 0.005170 +0.988376 0.011624 +0.948132 0.051868 +0.912578 0.087422 +0.972927 0.027073 +0.988386 0.011614 +0.977268 0.022732 +0.964231 0.035769 +0.965457 0.034543 +0.918055 0.081945 +0.975987 0.024013 +0.985377 0.014623 +0.984660 0.015340 +0.956306 0.043694 +0.993677 0.006323 +0.971794 0.028206 +0.970722 0.029278 +0.929863 0.070137 +0.950587 0.049413 +0.904138 0.095862 +0.949767 0.050233 +0.986268 0.013732 +0.936188 0.063812 +0.950087 0.049913 +0.997449 0.002551 +0.980578 0.019422 +0.986263 0.013737 +0.944474 0.055526 +0.942519 0.057481 +0.941674 0.058326 +0.956463 0.043537 +0.980285 0.019715 +0.944346 0.055654 +0.956139 0.043861 +0.972041 0.027959 +0.905830 0.094170 +0.874801 0.125199 +0.976189 0.023811 +0.897879 0.102121 +0.943211 0.056789 +0.970770 0.029230 +0.992994 0.007006 +0.941741 0.058259 +0.765534 0.234466 +0.922161 0.077839 +0.888633 0.111367 +0.974528 0.025472 +0.894923 0.105077 +0.933040 0.066960 +0.954118 0.045882 +0.958982 0.041018 +0.978781 0.021219 +0.934685 0.065315 +0.912852 0.087148 +0.711699 0.288301 +0.774534 0.225466 +0.905082 0.094918 +0.989023 0.010977 +0.987913 0.012087 +0.878309 0.121691 +0.943552 0.056448 +0.958335 0.041665 +0.980206 0.019794 +0.984903 0.015097 +0.684583 0.315417 +0.183821 0.816179 +0.895565 0.104435 +0.981767 0.018233 +0.997809 0.002191 +0.891320 0.108680 +0.948058 0.051942 +0.957449 0.042551 +0.983271 0.016729 +0.983346 0.016654 +0.953542 0.046458 +0.912902 0.087098 +0.630824 0.369176 +0.178953 0.821047 +0.887755 0.112245 +0.971618 0.028382 +0.886470 0.113530 +0.902894 0.097106 +0.956978 0.043022 +0.970439 0.029561 +0.980482 0.019518 +0.929749 0.070251 +0.939915 0.060085 +0.935064 0.064936 +0.743596 0.256404 +0.206039 0.793961 +0.880440 0.119560 +0.986704 0.013296 +0.899316 0.100684 +0.893775 0.106225 +0.924266 0.075734 +0.972292 0.027708 +0.996288 0.003712 +0.951297 0.048703 +0.933613 0.066387 +0.919926 0.080074 +0.749466 0.250534 +0.161124 0.838876 +0.911472 0.088528 +0.989553 0.010447 +0.897847 0.102153 +0.936251 0.063749 +0.969573 0.030427 +0.999990 0.000010 +0.936901 0.063099 +0.982930 0.017070 +0.899112 0.100888 +0.760715 0.239285 +0.181990 0.818010 +0.911591 0.088409 +0.968471 0.031529 +0.915992 0.084008 +0.939125 0.060875 +0.955813 0.044187 +0.978771 0.021229 +0.979817 0.020183 +0.932150 0.067850 +0.906015 0.093985 +0.897917 0.102083 +0.740535 0.259465 +0.167619 0.832381 +0.140446 0.859554 +0.245507 0.754493 +0.160359 0.839641 +0.062519 0.937481 +0.299047 0.700953 +0.966880 0.033120 +0.971765 0.028235 +0.957418 0.042582 +0.896160 0.103840 +0.736020 0.263980 +0.548812 0.451188 +0.163407 0.836593 +0.261374 0.738626 +0.178820 0.821180 +0.207513 0.792487 +0.978451 0.021549 +0.954153 0.045847 +0.929405 0.070595 +0.893536 0.106464 +0.704197 0.295803 +0.506189 0.493811 +0.178694 0.821306 +0.254599 0.745401 +0.127922 0.872078 +0.123185 0.876815 +0.945805 0.054195 +0.948382 0.051618 +0.952123 0.047877 +0.874261 0.125739 +0.716426 0.283574 +0.552674 0.447326 +0.180821 0.819179 +0.164019 0.835981 +0.438809 0.561191 +0.296430 0.703570 +0.973196 0.026804 +0.937816 0.062184 +0.874001 0.125999 +0.911930 0.088070 +0.734671 0.265329 +0.437057 0.562943 +0.275541 0.724459 +0.150174 0.849826 +0.159429 0.840571 +0.622758 0.377242 +0.323898 0.676102 +0.951862 0.048138 +0.957611 0.042389 +0.910994 0.089006 +0.907221 0.092779 +0.716959 0.283041 +0.538902 0.461098 +0.241020 0.758980 +0.133064 0.866936 +0.143746 0.856254 +0.340761 0.659239 +0.950184 0.049816 +0.899475 0.100525 +0.756671 0.243329 +0.711340 0.288660 +0.666296 0.333704 +0.278559 0.721441 +0.147059 0.852941 +0.156343 0.843657 +0.390862 0.609138 +0.951797 0.048203 +0.951464 0.048536 +0.894559 0.105441 +0.720193 0.279807 +0.761688 0.238312 +0.673635 0.326365 +0.225985 0.774015 +0.189512 0.810488 +0.208648 0.791352 +0.231142 0.768858 +0.954818 0.045182 +0.971437 0.028563 +0.960057 0.039943 +0.916144 0.083856 +0.749152 0.250848 +0.496845 0.503155 +0.648121 0.351879 +0.552930 0.447070 +0.829165 0.170835 +0.850310 0.149690 +0.852045 0.147955 +0.588531 0.411469 +0.793495 0.206505 +0.842362 0.157638 +0.641554 0.358446 +0.802348 0.197652 +0.746227 0.253773 +0.978439 0.021561 +0.801183 0.198817 +0.691642 0.308358 +0.935868 0.064132 +0.519970 0.480030 +0.820685 0.179315 +0.679553 0.320447 +0.679653 0.320347 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.974207 0.025793 +0.984021 0.015979 +0.956171 0.043829 +0.985736 0.014264 +0.999990 0.000010 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.978549 0.021451 +0.977549 0.022451 +0.987628 0.012372 +0.977428 0.022572 +0.999990 0.000010 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.980570 0.019430 +0.971304 0.028696 +0.987074 0.012926 +0.994807 0.005193 +0.974542 0.025458 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.973523 0.026477 +0.999990 0.000010 +0.999990 0.000010 +0.976675 0.023325 +0.993911 0.006089 +0.000010 0.999990 +0.000010 0.999990 +0.891553 0.108447 +0.976701 0.023299 +0.982094 0.017906 +0.985765 0.014235 +0.978990 0.021010 +0.988525 0.011475 +0.000010 0.999990 +0.000010 0.999990 +0.984223 0.015777 +0.964270 0.035730 +0.967163 0.032837 +0.999990 0.000010 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.932370 0.067630 +0.972684 0.027316 +0.998580 0.001420 +0.977912 0.022088 +0.991237 0.008763 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.974600 0.025400 +0.991922 0.008078 +0.986839 0.013161 +0.976757 0.023243 +0.991328 0.008672 +0.000010 0.999990 +0.984498 0.015502 +0.987046 0.012954 +0.987420 0.012580 +0.981903 0.018097 +0.999990 0.000010 +0.999990 0.000010 +0.991093 0.008907 +0.991797 0.008203 +0.999990 0.000010 +0.996317 0.003683 +0.999990 0.000010 +0.995951 0.004049 +0.986940 0.013060 +0.999990 0.000010 +0.996388 0.003612 +0.991554 0.008446 +0.989655 0.010345 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.997024 0.002976 +0.999990 0.000010 +0.999990 0.000010 +0.988644 0.011356 +0.990153 0.009847 +0.999990 0.000010 +0.985095 0.014905 +0.999990 0.000010 +0.999990 0.000010 +0.993919 0.006081 +0.997038 0.002962 +0.999990 0.000010 +0.980970 0.019030 +0.976295 0.023705 +0.992725 0.007275 +0.979294 0.020706 +0.999990 0.000010 +0.992737 0.007263 +0.999990 0.000010 +0.997507 0.002493 +0.881054 0.118946 +0.914245 0.085755 +0.907016 0.092984 +0.909743 0.090257 +0.986327 0.013673 +0.892898 0.107102 +0.992907 0.007093 +0.915747 0.084253 +0.918923 0.081077 +0.893236 0.106764 +0.999990 0.000010 +0.996252 0.003748 +0.999990 0.000010 +0.998239 0.001761 +0.999990 0.000010 +0.999990 0.000010 +0.990101 0.009899 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.996630 0.003370 +0.989133 0.010867 +0.999990 0.000010 +0.999990 0.000010 +0.987266 0.012734 +0.999744 0.000256 +0.987796 0.012204 +0.988340 0.011660 +0.999990 0.000010 +0.978413 0.021587 +0.993258 0.006742 +0.991236 0.008764 +0.001076 0.998924 +0.016443 0.983557 +0.020928 0.979072 +0.000010 0.999990 +0.019113 0.980887 +0.012764 0.987236 +0.005818 0.994182 +0.012257 0.987743 +0.998241 0.001759 +0.999990 0.000010 +0.996460 0.003540 +0.999287 0.000713 +0.991910 0.008090 +0.624269 0.375731 +0.719029 0.280971 +0.631904 0.368096 +0.636312 0.363688 +0.626933 0.373067 +0.992541 0.007459 +0.570724 0.429276 +0.572429 0.427571 +0.579717 0.420283 +0.623715 0.376285 +0.663198 0.336802 +0.659515 0.340485 +0.571013 0.428987 +0.584007 0.415993 +0.561737 0.438263 +0.571454 0.428546 +0.114339 0.885661 +0.020838 0.979162 +0.145161 0.854839 +0.154697 0.845303 +0.042128 0.957872 +0.156573 0.843427 +0.084205 0.915795 +0.141030 0.858970 +0.122095 0.877905 +0.136547 0.863453 +0.982156 0.017844 +0.988961 0.011039 +0.999990 0.000010 +0.237034 0.762966 +0.953992 0.046008 +0.989604 0.010396 +0.990259 0.009741 +0.978717 0.021283 +0.978998 0.021002 +0.206480 0.793520 +0.977743 0.022257 +0.988259 0.011741 +0.260386 0.739614 +0.993167 0.006833 +0.998601 0.001399 +0.981157 0.018843 +0.298956 0.701044 +0.065809 0.934191 +0.987613 0.012387 +0.069613 0.930387 +0.994865 0.005135 +0.975123 0.024877 +0.165047 0.834953 +0.168511 0.831489 +0.935942 0.064058 +0.999990 0.000010 +0.984268 0.015732 +0.977231 0.022769 +0.979001 0.020999 +0.992638 0.007362 +0.077592 0.922408 +0.142119 0.857881 +0.998147 0.001853 +0.992356 0.007644 +0.999990 0.000010 +0.967827 0.032173 +0.984237 0.015763 +0.982930 0.017070 +0.247250 0.752750 +0.993295 0.006705 +0.918369 0.081631 +0.958444 0.041556 +0.982735 0.017265 +0.999886 0.000114 +0.970216 0.029784 +0.211400 0.788600 +0.076779 0.923221 +0.999990 0.000010 +0.986301 0.013699 +0.059097 0.940903 +0.018905 0.981095 +0.967432 0.032568 +0.975726 0.024274 +0.983540 0.016460 +0.999990 0.000010 +0.999691 0.000309 +0.999990 0.000010 +0.999990 0.000010 +0.990975 0.009025 +0.990979 0.009021 +0.983416 0.016584 +0.983493 0.016507 +0.999990 0.000010 +0.989143 0.010857 +0.978965 0.021035 +0.999990 0.000010 +0.999990 0.000010 +0.992803 0.007197 +0.993188 0.006812 +0.999990 0.000010 +0.984119 0.015881 +0.994640 0.005360 +0.999990 0.000010 +0.991915 0.008085 +0.989608 0.010392 +0.982667 0.017333 +0.999990 0.000010 +0.997701 0.002299 +0.979636 0.020364 +0.871420 0.128580 +0.999990 0.000010 +0.990138 0.009862 +0.953473 0.046527 +0.999990 0.000010 +0.953720 0.046280 +0.145067 0.854933 +0.999990 0.000010 +0.993500 0.006500 +0.989100 0.010900 +0.989396 0.010604 +0.938836 0.061164 +0.955841 0.044159 +0.984985 0.015015 +0.889987 0.110013 +0.999990 0.000010 +0.946932 0.053068 +0.991854 0.008146 +0.977777 0.022223 +0.852385 0.147615 +0.984303 0.015697 +0.985579 0.014421 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.943434 0.056566 +0.935673 0.064327 +0.982148 0.017852 +0.987663 0.012337 +0.996625 0.003375 +0.994586 0.005414 +0.992541 0.007459 +0.977143 0.022857 +0.973472 0.026528 +0.875680 0.124320 +0.999990 0.000010 +0.994718 0.005282 +0.999990 0.000010 +0.952969 0.047031 +0.995192 0.004808 +0.958929 0.041071 +0.943517 0.056483 +0.998839 0.001161 +0.995425 0.004575 +0.940834 0.059166 +0.990457 0.009543 +0.981172 0.018828 +0.912101 0.087899 +0.999990 0.000010 +0.932021 0.067979 +0.999990 0.000010 +0.982368 0.017632 +0.992711 0.007289 +0.994766 0.005234 +0.938255 0.061745 +0.980181 0.019819 +0.994157 0.005843 +0.930840 0.069160 +0.858097 0.141903 +0.984678 0.015322 +0.941627 0.058373 +0.978464 0.021536 +0.983060 0.016940 +0.952160 0.047840 +0.980356 0.019644 +0.991654 0.008346 +0.973345 0.026655 +0.984684 0.015316 +0.934146 0.065854 +0.982455 0.017545 +0.978097 0.021903 +0.999990 0.000010 +0.982849 0.017151 +0.939017 0.060983 +0.984060 0.015940 +0.954738 0.045262 +0.982884 0.017116 +0.999990 0.000010 +0.952178 0.047822 +0.944404 0.055596 +0.996165 0.003835 +0.956560 0.043440 +0.976764 0.023236 +0.984379 0.015621 +0.997736 0.002264 +0.999903 0.000097 +0.938238 0.061762 +0.999250 0.000750 +0.991581 0.008419 +0.942928 0.057072 +0.999990 0.000010 +0.859202 0.140798 +0.992943 0.007057 +0.912243 0.087757 +0.994453 0.005547 +0.988594 0.011406 +0.977527 0.022473 +0.982522 0.017478 +0.982056 0.017944 +0.993893 0.006107 +0.999990 0.000010 +0.962409 0.037591 +0.951425 0.048575 +0.992880 0.007120 +0.976262 0.023738 +0.941897 0.058103 +0.999990 0.000010 +0.999990 0.000010 +0.981391 0.018609 +0.291498 0.708502 +0.943332 0.056668 +0.993202 0.006798 +0.973310 0.026690 +0.987534 0.012466 +0.999990 0.000010 +0.998300 0.001700 +0.993402 0.006598 +0.886574 0.113426 +0.946603 0.053397 +0.938432 0.061568 +0.940860 0.059140 +0.966983 0.033017 +0.982368 0.017632 +0.989931 0.010069 +0.993815 0.006185 +0.984809 0.015191 +0.991756 0.008244 +0.834284 0.165716 +0.976846 0.023154 +0.969033 0.030967 +0.303017 0.696983 +0.999990 0.000010 +0.974391 0.025609 +0.978728 0.021272 +0.999990 0.000010 +0.926952 0.073048 +0.846136 0.153864 +0.912211 0.087789 +0.855223 0.144777 +0.903645 0.096355 +0.924882 0.075118 +0.824304 0.175696 +0.887811 0.112189 +0.998722 0.001278 +0.318342 0.681658 +0.948809 0.051191 +0.286935 0.713065 +0.999990 0.000010 +0.985901 0.014099 +0.947286 0.052714 +0.298409 0.701591 +0.970752 0.029248 +0.878204 0.121796 +0.939597 0.060403 +0.844159 0.155841 +0.837458 0.162542 +0.908723 0.091277 +0.970786 0.029214 +0.999990 0.000010 +0.865286 0.134714 +0.301729 0.698271 +0.899578 0.100422 +0.908276 0.091724 +0.970175 0.029825 +0.918150 0.081850 +0.999990 0.000010 +0.905772 0.094228 +0.901062 0.098938 +0.997684 0.002316 +0.924282 0.075718 +0.945931 0.054069 +0.979349 0.020651 +0.943495 0.056505 +0.324151 0.675849 +0.941776 0.058224 +0.824536 0.175464 +0.846332 0.153668 +0.853867 0.146133 +0.937387 0.062613 +0.318427 0.681573 +0.847775 0.152225 +0.999990 0.000010 +0.872533 0.127467 +0.289538 0.710462 +0.912763 0.087237 +0.939752 0.060248 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.912407 0.087593 +0.999990 0.000010 +0.953205 0.046795 +0.933772 0.066228 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.964236 0.035764 diff --git a/inst/files/admixture/admixture_05 b/inst/files/admixture/admixture_05 new file mode 100644 index 0000000..f5a826d --- /dev/null +++ b/inst/files/admixture/admixture_05 @@ -0,0 +1,1592 @@ +0.942995 0.057005 +0.950609 0.049391 +0.972208 0.027792 +0.943619 0.056381 +0.931674 0.068326 +0.944011 0.055989 +0.926197 0.073803 +0.976136 0.023864 +0.950896 0.049104 +0.928412 0.071588 +0.947400 0.052600 +0.932082 0.067918 +0.946955 0.053045 +0.983766 0.016234 +0.946589 0.053411 +0.969502 0.030498 +0.922055 0.077945 +0.894128 0.105872 +0.943422 0.056578 +0.954252 0.045748 +0.947033 0.052967 +0.999714 0.000286 +0.946819 0.053181 +0.954604 0.045396 +0.909505 0.090495 +0.940332 0.059668 +0.639082 0.360918 +0.622274 0.377726 +0.616732 0.383268 +0.642448 0.357552 +0.641160 0.358840 +0.641540 0.358460 +0.627042 0.372958 +0.657607 0.342393 +0.621644 0.378356 +0.648931 0.351069 +0.634822 0.365178 +0.679026 0.320974 +0.626667 0.373333 +0.619516 0.380484 +0.646198 0.353802 +0.654603 0.345397 +0.573052 0.426948 +0.985093 0.014907 +0.602255 0.397745 +0.587243 0.412757 +0.643819 0.356181 +0.972256 0.027744 +0.581180 0.418820 +0.644561 0.355439 +0.164249 0.835751 +0.162269 0.837731 +0.167845 0.832155 +0.151826 0.848174 +0.164632 0.835368 +0.155068 0.844932 +0.151798 0.848202 +0.181025 0.818975 +0.142317 0.857683 +0.155926 0.844074 +0.148766 0.851234 +0.165721 0.834279 +0.159381 0.840619 +0.150911 0.849089 +0.168392 0.831608 +0.150043 0.849957 +0.201719 0.798281 +0.147663 0.852337 +0.151050 0.848950 +0.148403 0.851597 +0.159187 0.840813 +0.153258 0.846742 +0.122765 0.877235 +0.213415 0.786585 +0.194961 0.805039 +0.132046 0.867954 +0.134036 0.865964 +0.141651 0.858349 +0.198573 0.801427 +0.149309 0.850691 +0.144015 0.855985 +0.131570 0.868430 +0.133412 0.866588 +0.149753 0.850247 +0.134842 0.865158 +0.141232 0.858768 +0.191372 0.808628 +0.186282 0.813718 +0.185707 0.814293 +0.163154 0.836846 +0.179260 0.820740 +0.571463 0.428537 +0.578038 0.421962 +0.541042 0.458958 +0.560782 0.439218 +0.523809 0.476191 +0.562594 0.437406 +0.553884 0.446116 +0.543402 0.456598 +0.534429 0.465571 +0.560314 0.439686 +0.558593 0.441407 +0.527709 0.472291 +0.553371 0.446629 +0.543996 0.456004 +0.119574 0.880426 +0.120956 0.879044 +0.136804 0.863196 +0.133869 0.866131 +0.142549 0.857451 +0.122443 0.877557 +0.153973 0.846027 +0.134830 0.865170 +0.133720 0.866280 +0.134511 0.865489 +0.122410 0.877590 +0.150112 0.849888 +0.126873 0.873127 +0.134195 0.865805 +0.125169 0.874831 +0.140623 0.859377 +0.139578 0.860422 +0.134243 0.865757 +0.138198 0.861802 +0.137962 0.862038 +0.240188 0.759812 +0.241234 0.758766 +0.222397 0.777603 +0.210561 0.789439 +0.219999 0.780001 +0.238631 0.761369 +0.207886 0.792114 +0.223897 0.776103 +0.222110 0.777890 +0.237594 0.762406 +0.246692 0.753308 +0.247636 0.752364 +0.243291 0.756709 +0.220667 0.779333 +0.211611 0.788389 +0.274211 0.725789 +0.240787 0.759213 +0.241614 0.758386 +0.154886 0.845114 +0.236905 0.763095 +0.192030 0.807970 +0.223978 0.776022 +0.193600 0.806400 +0.211718 0.788282 +0.225955 0.774045 +0.210629 0.789371 +0.233264 0.766736 +0.176103 0.823897 +0.168992 0.831008 +0.215410 0.784590 +0.216387 0.783613 +0.222145 0.777855 +0.189505 0.810495 +0.231348 0.768652 +0.177212 0.822788 +0.196519 0.803481 +0.231271 0.768729 +0.185412 0.814588 +0.170804 0.829196 +0.190611 0.809389 +0.175766 0.824234 +0.195705 0.804295 +0.186995 0.813005 +0.189301 0.810699 +0.174363 0.825637 +0.191334 0.808666 +0.192460 0.807540 +0.199432 0.800568 +0.217484 0.782516 +0.203554 0.796446 +0.176466 0.823534 +0.181714 0.818286 +0.197697 0.802303 +0.197211 0.802789 +0.188035 0.811965 +0.314655 0.685345 +0.285147 0.714853 +0.319774 0.680226 +0.309741 0.690259 +0.296054 0.703946 +0.300771 0.699229 +0.318884 0.681116 +0.288333 0.711667 +0.320885 0.679115 +0.328158 0.671842 +0.298413 0.701587 +0.292423 0.707577 +0.309995 0.690005 +0.299384 0.700616 +0.321439 0.678561 +0.304927 0.695073 +0.307185 0.692815 +0.314489 0.685511 +0.284032 0.715968 +0.284324 0.715676 +0.306208 0.693792 +0.295563 0.704437 +0.305400 0.694600 +0.000010 0.999990 +0.007281 0.992719 +0.018005 0.981995 +0.018397 0.981603 +0.000805 0.999195 +0.007315 0.992685 +0.000010 0.999990 +0.010807 0.989193 +0.000010 0.999990 +0.002709 0.997291 +0.002519 0.997481 +0.000010 0.999990 +0.006906 0.993094 +0.013072 0.986928 +0.021639 0.978361 +0.002534 0.997466 +0.017686 0.982314 +0.000649 0.999351 +0.020842 0.979158 +0.012251 0.987749 +0.016319 0.983681 +0.017077 0.982923 +0.000010 0.999990 +0.015193 0.984807 +0.013065 0.986935 +0.008775 0.991225 +0.000010 0.999990 +0.018078 0.981922 +0.000010 0.999990 +0.014982 0.985018 +0.014962 0.985038 +0.013217 0.986783 +0.001860 0.998140 +0.011006 0.988994 +0.018212 0.981788 +0.002353 0.997647 +0.013871 0.986129 +0.006293 0.993707 +0.019067 0.980933 +0.019598 0.980402 +0.006948 0.993052 +0.000010 0.999990 +0.002767 0.997233 +0.021753 0.978247 +0.019081 0.980919 +0.000010 0.999990 +0.013590 0.986410 +0.030431 0.969569 +0.008318 0.991682 +0.000010 0.999990 +0.019501 0.980499 +0.001110 0.998890 +0.014468 0.985532 +0.014519 0.985481 +0.006192 0.993808 +0.011596 0.988404 +0.009586 0.990414 +0.005238 0.994762 +0.000010 0.999990 +0.019040 0.980960 +0.006968 0.993032 +0.028240 0.971760 +0.012197 0.987803 +0.019414 0.980586 +0.025213 0.974787 +0.009685 0.990315 +0.037480 0.962520 +0.005901 0.994099 +0.061979 0.938021 +0.013382 0.986618 +0.035431 0.964569 +0.040886 0.959114 +0.038555 0.961445 +0.019489 0.980511 +0.012195 0.987805 +0.032679 0.967321 +0.040318 0.959682 +0.031612 0.968388 +0.021638 0.978362 +0.009473 0.990527 +0.036827 0.963173 +0.036646 0.963354 +0.048283 0.951717 +0.035199 0.964801 +0.008646 0.991354 +0.001855 0.998145 +0.043275 0.956725 +0.047952 0.952048 +0.049620 0.950380 +0.026709 0.973291 +0.040982 0.959018 +0.051989 0.948011 +0.022620 0.977380 +0.052563 0.947437 +0.013935 0.986065 +0.019552 0.980448 +0.011597 0.988403 +0.026092 0.973908 +0.037376 0.962624 +0.049630 0.950370 +0.043179 0.956821 +0.021794 0.978206 +0.012212 0.987788 +0.018542 0.981458 +0.023346 0.976654 +0.022687 0.977313 +0.042101 0.957899 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.035634 0.964366 +0.021804 0.978196 +0.018228 0.981772 +0.023758 0.976242 +0.040496 0.959504 +0.048059 0.951941 +0.038407 0.961593 +0.033230 0.966770 +0.046240 0.953760 +0.011119 0.988881 +0.026206 0.973794 +0.017391 0.982609 +0.023035 0.976965 +0.039899 0.960101 +0.006370 0.993630 +0.021977 0.978023 +0.024581 0.975419 +0.027461 0.972539 +0.013267 0.986733 +0.034596 0.965404 +0.015887 0.984113 +0.890153 0.109847 +0.933520 0.066480 +0.870529 0.129471 +0.929497 0.070503 +0.891075 0.108925 +0.930078 0.069922 +0.901775 0.098225 +0.880743 0.119257 +0.032139 0.967861 +0.024051 0.975949 +0.033764 0.966236 +0.027322 0.972678 +0.028574 0.971426 +0.026645 0.973355 +0.034956 0.965044 +0.039772 0.960228 +0.021937 0.978063 +0.026404 0.973596 +0.037409 0.962591 +0.025125 0.974875 +0.036361 0.963639 +0.026498 0.973502 +0.042642 0.957358 +0.033494 0.966506 +0.024775 0.975225 +0.059867 0.940133 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.023971 0.976029 +0.025440 0.974560 +0.017796 0.982204 +0.009748 0.990252 +0.021780 0.978220 +0.022224 0.977776 +0.009652 0.990348 +0.009357 0.990643 +0.015814 0.984186 +0.000010 0.999990 +0.005174 0.994826 +0.013307 0.986693 +0.000010 0.999990 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.093060 0.906940 +0.105193 0.894807 +0.136446 0.863554 +0.114488 0.885512 +0.075223 0.924777 +0.116199 0.883801 +0.088111 0.911889 +0.096470 0.903530 +0.111890 0.888110 +0.114616 0.885384 +0.112163 0.887837 +0.120313 0.879687 +0.114269 0.885731 +0.136636 0.863364 +0.119261 0.880739 +0.107158 0.892842 +0.124955 0.875045 +0.103486 0.896514 +0.080137 0.919863 +0.114810 0.885190 +0.122908 0.877092 +0.108452 0.891548 +0.899951 0.100049 +0.900652 0.099348 +0.872189 0.127811 +0.826736 0.173264 +0.814660 0.185340 +0.911389 0.088611 +0.890804 0.109196 +0.907690 0.092310 +0.924602 0.075398 +0.906416 0.093584 +0.843808 0.156192 +0.931406 0.068594 +0.894713 0.105287 +0.915845 0.084155 +0.901115 0.098885 +0.883824 0.116176 +0.904707 0.095293 +0.870585 0.129415 +0.901530 0.098470 +0.857796 0.142204 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.006743 0.993257 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.010337 0.989663 +0.002162 0.997838 +0.007624 0.992376 +0.000010 0.999990 +0.005011 0.994989 +0.000010 0.999990 +0.000010 0.999990 +0.001661 0.998339 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.996358 0.003642 +0.999990 0.000010 +0.999990 0.000010 +0.998605 0.001395 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.983815 0.016185 +0.969365 0.030635 +0.975583 0.024417 +0.970023 0.029977 +0.999990 0.000010 +0.999990 0.000010 +0.995765 0.004235 +0.964236 0.035764 +0.991261 0.008739 +0.958045 0.041955 +0.956321 0.043679 +0.971256 0.028744 +0.969817 0.030183 +0.980639 0.019361 +0.985133 0.014867 +0.979998 0.020002 +0.984588 0.015412 +0.961036 0.038964 +0.976192 0.023808 +0.943347 0.056653 +0.971128 0.028872 +0.981980 0.018020 +0.953968 0.046032 +0.999990 0.000010 +0.980509 0.019491 +0.998123 0.001877 +0.980913 0.019087 +0.989279 0.010721 +0.999990 0.000010 +0.997480 0.002520 +0.998992 0.001008 +0.966571 0.033429 +0.978865 0.021135 +0.992114 0.007886 +0.930644 0.069356 +0.982494 0.017506 +0.952298 0.047702 +0.999990 0.000010 +0.053647 0.946353 +0.046206 0.953794 +0.044773 0.955227 +0.059369 0.940631 +0.050422 0.949578 +0.038296 0.961704 +0.067024 0.932976 +0.067908 0.932092 +0.031469 0.968531 +0.043506 0.956494 +0.040867 0.959133 +0.044845 0.955155 +0.046174 0.953826 +0.067780 0.932220 +0.054658 0.945342 +0.062993 0.937007 +0.060365 0.939635 +0.041359 0.958641 +0.058456 0.941544 +0.033677 0.966323 +0.035411 0.964589 +0.993567 0.006433 +0.987974 0.012026 +0.989769 0.010231 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.986429 0.013571 +0.999990 0.000010 +0.998263 0.001737 +0.972237 0.027763 +0.521852 0.478148 +0.496525 0.503475 +0.562437 0.437563 +0.519227 0.480773 +0.543730 0.456270 +0.629575 0.370425 +0.499000 0.501000 +0.613212 0.386788 +0.582066 0.417934 +0.566926 0.433074 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999904 0.000096 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.945661 0.054339 +0.924130 0.075870 +0.963229 0.036771 +0.922556 0.077444 +0.949536 0.050464 +0.955558 0.044442 +0.925347 0.074653 +0.956830 0.043170 +0.955265 0.044735 +0.929180 0.070820 +0.000010 0.999990 +0.001079 0.998921 +0.007028 0.992972 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.013131 0.986869 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.107710 0.892290 +0.054189 0.945811 +0.066879 0.933121 +0.082428 0.917572 +0.062449 0.937551 +0.050110 0.949890 +0.109156 0.890844 +0.090137 0.909863 +0.055603 0.944397 +0.056879 0.943121 +0.062759 0.937241 +0.074187 0.925813 +0.068075 0.931925 +0.042522 0.957478 +0.108144 0.891856 +0.916029 0.083971 +0.926130 0.073870 +0.936489 0.063511 +0.924070 0.075930 +0.928402 0.071598 +0.929964 0.070036 +0.958493 0.041507 +0.954640 0.045360 +0.969512 0.030488 +0.948042 0.051958 +0.935469 0.064531 +0.943302 0.056698 +0.927937 0.072063 +0.953663 0.046337 +0.952809 0.047191 +0.927056 0.072944 +0.935009 0.064991 +0.959238 0.040762 +0.947772 0.052228 +0.961622 0.038378 +0.923089 0.076911 +0.943531 0.056469 +0.955491 0.044509 +0.964112 0.035888 +0.972758 0.027242 +0.938893 0.061107 +0.950505 0.049495 +0.688179 0.311821 +0.682066 0.317934 +0.679279 0.320721 +0.682138 0.317862 +0.680368 0.319632 +0.670708 0.329292 +0.688973 0.311027 +0.692555 0.307445 +0.667269 0.332731 +0.691929 0.308071 +0.679038 0.320962 +0.403731 0.596269 +0.435277 0.564723 +0.440756 0.559244 +0.437255 0.562745 +0.448807 0.551193 +0.433304 0.566696 +0.437957 0.562043 +0.443802 0.556198 +0.430225 0.569775 +0.446053 0.553947 +0.445023 0.554977 +0.457956 0.542044 +0.452683 0.547317 +0.278725 0.721275 +0.288449 0.711551 +0.293124 0.706876 +0.278518 0.721482 +0.244895 0.755105 +0.295911 0.704089 +0.285911 0.714089 +0.276733 0.723267 +0.283050 0.716950 +0.272386 0.727614 +0.281185 0.718815 +0.271408 0.728592 +0.293268 0.706732 +0.277626 0.722374 +0.280879 0.719121 +0.656462 0.343538 +0.646240 0.353760 +0.642606 0.357394 +0.649153 0.350847 +0.642710 0.357290 +0.652111 0.347889 +0.635522 0.364478 +0.640284 0.359716 +0.649382 0.350618 +0.652478 0.347522 +0.634084 0.365916 +0.636849 0.363151 +0.364422 0.635578 +0.406176 0.593824 +0.375817 0.624183 +0.395043 0.604957 +0.403163 0.596837 +0.378892 0.621108 +0.367651 0.632349 +0.380010 0.619990 +0.351597 0.648403 +0.377211 0.622789 +0.369394 0.630606 +0.375444 0.624556 +0.379532 0.620468 +0.418829 0.581171 +0.406182 0.593818 +0.413878 0.586122 +0.426317 0.573683 +0.397196 0.602804 +0.403358 0.596642 +0.391069 0.608931 +0.422159 0.577841 +0.425521 0.574479 +0.422347 0.577653 +0.398456 0.601544 +0.437919 0.562081 +0.413303 0.586697 +0.234834 0.765166 +0.062047 0.937953 +0.044291 0.955709 +0.067708 0.932292 +0.039766 0.960234 +0.055759 0.944241 +0.023616 0.976384 +0.019272 0.980728 +0.000010 0.999990 +0.119522 0.880478 +0.048843 0.951157 +0.027404 0.972596 +0.033587 0.966413 +0.025517 0.974483 +0.065486 0.934514 +0.042882 0.957118 +0.040343 0.959657 +0.123885 0.876115 +0.014449 0.985551 +0.037702 0.962298 +0.007714 0.992286 +0.020105 0.979895 +0.014108 0.985892 +0.020520 0.979480 +0.013370 0.986630 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.014171 0.985829 +0.000827 0.999173 +0.010724 0.989276 +0.005604 0.994396 +0.003214 0.996786 +0.000010 0.999990 +0.010881 0.989119 +0.000010 0.999990 +0.002910 0.997090 +0.012543 0.987457 +0.015551 0.984449 +0.009790 0.990210 +0.012542 0.987458 +0.005717 0.994283 +0.010601 0.989399 +0.015299 0.984701 +0.021493 0.978507 +0.013900 0.986100 +0.033302 0.966698 +0.071907 0.928093 +0.104826 0.895174 +0.065305 0.934695 +0.034289 0.965711 +0.024534 0.975466 +0.000304 0.999696 +0.024837 0.975163 +0.018485 0.981515 +0.011372 0.988628 +0.084779 0.915221 +0.094336 0.905664 +0.000010 0.999990 +0.076924 0.923076 +0.003496 0.996504 +0.032448 0.967552 +0.098972 0.901028 +0.032290 0.967710 +0.026015 0.973985 +0.032646 0.967354 +0.036530 0.963470 +0.034089 0.965911 +0.062410 0.937590 +0.029226 0.970774 +0.033585 0.966415 +0.028507 0.971493 +0.011768 0.988232 +0.105712 0.894288 +0.010721 0.989279 +0.037765 0.962235 +0.011950 0.988050 +0.041664 0.958336 +0.050393 0.949607 +0.010969 0.989031 +0.059864 0.940136 +0.017637 0.982363 +0.040985 0.959015 +0.003975 0.996025 +0.035971 0.964029 +0.020366 0.979634 +0.031151 0.968849 +0.025379 0.974621 +0.076797 0.923203 +0.065878 0.934122 +0.005169 0.994831 +0.011624 0.988376 +0.051868 0.948132 +0.087421 0.912579 +0.027073 0.972927 +0.011613 0.988387 +0.022731 0.977269 +0.035769 0.964231 +0.034543 0.965457 +0.081944 0.918056 +0.024013 0.975987 +0.014623 0.985377 +0.015339 0.984661 +0.043694 0.956306 +0.006323 0.993677 +0.028206 0.971794 +0.029278 0.970722 +0.070137 0.929863 +0.049412 0.950588 +0.095862 0.904138 +0.050233 0.949767 +0.013732 0.986268 +0.063812 0.936188 +0.049912 0.950088 +0.002551 0.997449 +0.019422 0.980578 +0.013737 0.986263 +0.055526 0.944474 +0.057481 0.942519 +0.058326 0.941674 +0.043537 0.956463 +0.019715 0.980285 +0.055654 0.944346 +0.043860 0.956140 +0.027958 0.972042 +0.094169 0.905831 +0.125198 0.874802 +0.023811 0.976189 +0.102121 0.897879 +0.056789 0.943211 +0.029229 0.970771 +0.007006 0.992994 +0.058259 0.941741 +0.234466 0.765534 +0.077839 0.922161 +0.111367 0.888633 +0.025472 0.974528 +0.105076 0.894924 +0.066960 0.933040 +0.045881 0.954119 +0.041018 0.958982 +0.021218 0.978782 +0.065315 0.934685 +0.087148 0.912852 +0.288301 0.711699 +0.225466 0.774534 +0.094917 0.905083 +0.010976 0.989024 +0.012087 0.987913 +0.121691 0.878309 +0.056447 0.943553 +0.041664 0.958336 +0.019794 0.980206 +0.015096 0.984904 +0.315416 0.684584 +0.816178 0.183822 +0.104434 0.895566 +0.018233 0.981767 +0.002190 0.997810 +0.108680 0.891320 +0.051942 0.948058 +0.042551 0.957449 +0.016728 0.983272 +0.016654 0.983346 +0.046457 0.953543 +0.087097 0.912903 +0.369176 0.630824 +0.821047 0.178953 +0.112244 0.887756 +0.028382 0.971618 +0.113530 0.886470 +0.097106 0.902894 +0.043022 0.956978 +0.029561 0.970439 +0.019518 0.980482 +0.070251 0.929749 +0.060085 0.939915 +0.064935 0.935065 +0.256404 0.743596 +0.793961 0.206039 +0.119560 0.880440 +0.013296 0.986704 +0.100684 0.899316 +0.106224 0.893776 +0.075733 0.924267 +0.027707 0.972293 +0.003712 0.996288 +0.048702 0.951298 +0.066386 0.933614 +0.080073 0.919927 +0.250534 0.749466 +0.838876 0.161124 +0.088527 0.911473 +0.010447 0.989553 +0.102153 0.897847 +0.063749 0.936251 +0.030427 0.969573 +0.000010 0.999990 +0.063098 0.936902 +0.017069 0.982931 +0.100887 0.899113 +0.239285 0.760715 +0.818010 0.181990 +0.088408 0.911592 +0.031528 0.968472 +0.084008 0.915992 +0.060874 0.939126 +0.044187 0.955813 +0.021228 0.978772 +0.020183 0.979817 +0.067850 0.932150 +0.093985 0.906015 +0.102083 0.897917 +0.259465 0.740535 +0.832381 0.167619 +0.859554 0.140446 +0.754493 0.245507 +0.839641 0.160359 +0.937481 0.062519 +0.700953 0.299047 +0.033120 0.966880 +0.028234 0.971766 +0.042582 0.957418 +0.103840 0.896160 +0.263980 0.736020 +0.451188 0.548812 +0.836593 0.163407 +0.738626 0.261374 +0.821180 0.178820 +0.792487 0.207513 +0.021549 0.978451 +0.045846 0.954154 +0.070595 0.929405 +0.106464 0.893536 +0.295802 0.704198 +0.493811 0.506189 +0.821306 0.178694 +0.745401 0.254599 +0.872078 0.127922 +0.876815 0.123185 +0.054195 0.945805 +0.051617 0.948383 +0.047877 0.952123 +0.125739 0.874261 +0.283573 0.716427 +0.447326 0.552674 +0.819179 0.180821 +0.835981 0.164019 +0.561191 0.438809 +0.703569 0.296431 +0.026804 0.973196 +0.062184 0.937816 +0.125999 0.874001 +0.088069 0.911931 +0.265328 0.734672 +0.562943 0.437057 +0.724459 0.275541 +0.849825 0.150175 +0.840571 0.159429 +0.377242 0.622758 +0.676102 0.323898 +0.048137 0.951863 +0.042388 0.957612 +0.089005 0.910995 +0.092779 0.907221 +0.283041 0.716959 +0.461097 0.538903 +0.758980 0.241020 +0.866936 0.133064 +0.856254 0.143746 +0.659239 0.340761 +0.049816 0.950184 +0.100525 0.899475 +0.243328 0.756672 +0.288660 0.711340 +0.333704 0.666296 +0.721441 0.278559 +0.852941 0.147059 +0.843657 0.156343 +0.609138 0.390862 +0.048202 0.951798 +0.048536 0.951464 +0.105441 0.894559 +0.279806 0.720194 +0.238312 0.761688 +0.326365 0.673635 +0.774015 0.225985 +0.810488 0.189512 +0.791352 0.208648 +0.768858 0.231142 +0.045181 0.954819 +0.028563 0.971437 +0.039943 0.960057 +0.083856 0.916144 +0.250848 0.749152 +0.503155 0.496845 +0.351879 0.648121 +0.447070 0.552930 +0.170834 0.829166 +0.149689 0.850311 +0.147954 0.852046 +0.411469 0.588531 +0.206505 0.793495 +0.157637 0.842363 +0.358446 0.641554 +0.197652 0.802348 +0.253773 0.746227 +0.021560 0.978440 +0.198816 0.801184 +0.308357 0.691643 +0.064132 0.935868 +0.480029 0.519971 +0.179315 0.820685 +0.320447 0.679553 +0.320347 0.679653 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.025792 0.974208 +0.015979 0.984021 +0.043829 0.956171 +0.014264 0.985736 +0.000010 0.999990 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.021451 0.978549 +0.022451 0.977549 +0.012372 0.987628 +0.022572 0.977428 +0.000010 0.999990 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.019429 0.980571 +0.028695 0.971305 +0.012926 0.987074 +0.005192 0.994808 +0.025458 0.974542 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.026477 0.973523 +0.000010 0.999990 +0.000010 0.999990 +0.023325 0.976675 +0.006089 0.993911 +0.999990 0.000010 +0.999990 0.000010 +0.108447 0.891553 +0.023298 0.976702 +0.017906 0.982094 +0.014235 0.985765 +0.021009 0.978991 +0.011474 0.988526 +0.999990 0.000010 +0.999990 0.000010 +0.015776 0.984224 +0.035729 0.964271 +0.032836 0.967164 +0.000010 0.999990 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.067630 0.932370 +0.027316 0.972684 +0.001419 0.998581 +0.022088 0.977912 +0.008763 0.991237 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.025400 0.974600 +0.008078 0.991922 +0.013161 0.986839 +0.023243 0.976757 +0.008672 0.991328 +0.999990 0.000010 +0.015501 0.984499 +0.012953 0.987047 +0.012580 0.987420 +0.018097 0.981903 +0.000010 0.999990 +0.000010 0.999990 +0.008907 0.991093 +0.008203 0.991797 +0.000010 0.999990 +0.003683 0.996317 +0.000010 0.999990 +0.004048 0.995952 +0.013059 0.986941 +0.000010 0.999990 +0.003611 0.996389 +0.008446 0.991554 +0.010345 0.989655 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.002975 0.997025 +0.000010 0.999990 +0.000010 0.999990 +0.011356 0.988644 +0.009847 0.990153 +0.000010 0.999990 +0.014904 0.985096 +0.000010 0.999990 +0.000010 0.999990 +0.006081 0.993919 +0.002962 0.997038 +0.000010 0.999990 +0.019029 0.980971 +0.023705 0.976295 +0.007274 0.992726 +0.020705 0.979295 +0.000010 0.999990 +0.007263 0.992737 +0.000010 0.999990 +0.002493 0.997507 +0.118946 0.881054 +0.085755 0.914245 +0.092983 0.907017 +0.090257 0.909743 +0.013672 0.986328 +0.107102 0.892898 +0.007093 0.992907 +0.084252 0.915748 +0.081077 0.918923 +0.106764 0.893236 +0.000010 0.999990 +0.003748 0.996252 +0.000010 0.999990 +0.001760 0.998240 +0.000010 0.999990 +0.000010 0.999990 +0.009899 0.990101 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.003370 0.996630 +0.010866 0.989134 +0.000010 0.999990 +0.000010 0.999990 +0.012733 0.987267 +0.000256 0.999744 +0.012204 0.987796 +0.011660 0.988340 +0.000010 0.999990 +0.021586 0.978414 +0.006743 0.993257 +0.008764 0.991236 +0.998924 0.001076 +0.983557 0.016443 +0.979072 0.020928 +0.999990 0.000010 +0.980887 0.019113 +0.987236 0.012764 +0.994182 0.005818 +0.987744 0.012256 +0.001759 0.998241 +0.000010 0.999990 +0.003539 0.996461 +0.000712 0.999288 +0.008090 0.991910 +0.375731 0.624269 +0.280971 0.719029 +0.368096 0.631904 +0.363688 0.636312 +0.373066 0.626934 +0.007459 0.992541 +0.429276 0.570724 +0.427571 0.572429 +0.420283 0.579717 +0.376285 0.623715 +0.336802 0.663198 +0.340484 0.659516 +0.428987 0.571013 +0.415993 0.584007 +0.438262 0.561738 +0.428546 0.571454 +0.885661 0.114339 +0.979162 0.020838 +0.854839 0.145161 +0.845303 0.154697 +0.957872 0.042128 +0.843427 0.156573 +0.915795 0.084205 +0.858970 0.141030 +0.877905 0.122095 +0.863453 0.136547 +0.017844 0.982156 +0.011038 0.988962 +0.000010 0.999990 +0.762966 0.237034 +0.046008 0.953992 +0.010396 0.989604 +0.009741 0.990259 +0.021283 0.978717 +0.021002 0.978998 +0.793520 0.206480 +0.022256 0.977744 +0.011741 0.988259 +0.739614 0.260386 +0.006832 0.993168 +0.001399 0.998601 +0.018843 0.981157 +0.701044 0.298956 +0.934191 0.065809 +0.012387 0.987613 +0.930387 0.069613 +0.005134 0.994866 +0.024876 0.975124 +0.834953 0.165047 +0.831489 0.168511 +0.064057 0.935943 +0.000010 0.999990 +0.015731 0.984269 +0.022769 0.977231 +0.020999 0.979001 +0.007362 0.992638 +0.922408 0.077592 +0.857881 0.142119 +0.001853 0.998147 +0.007644 0.992356 +0.000010 0.999990 +0.032173 0.967827 +0.015763 0.984237 +0.017070 0.982930 +0.752750 0.247250 +0.006704 0.993296 +0.081630 0.918370 +0.041556 0.958444 +0.017264 0.982736 +0.000113 0.999887 +0.029784 0.970216 +0.788600 0.211400 +0.923221 0.076779 +0.000010 0.999990 +0.013698 0.986302 +0.940903 0.059097 +0.981095 0.018905 +0.032568 0.967432 +0.024273 0.975727 +0.016460 0.983540 +0.000010 0.999990 +0.000309 0.999691 +0.000010 0.999990 +0.000010 0.999990 +0.009025 0.990975 +0.009021 0.990979 +0.016584 0.983416 +0.016507 0.983493 +0.000010 0.999990 +0.010857 0.989143 +0.021035 0.978965 +0.000010 0.999990 +0.000010 0.999990 +0.007197 0.992803 +0.006811 0.993189 +0.000010 0.999990 +0.015880 0.984120 +0.005359 0.994641 +0.000010 0.999990 +0.008085 0.991915 +0.010392 0.989608 +0.017333 0.982667 +0.000010 0.999990 +0.002299 0.997701 +0.020364 0.979636 +0.128579 0.871421 +0.000010 0.999990 +0.009861 0.990139 +0.046527 0.953473 +0.000010 0.999990 +0.046279 0.953721 +0.854933 0.145067 +0.000010 0.999990 +0.006499 0.993501 +0.010899 0.989101 +0.010603 0.989397 +0.061164 0.938836 +0.044159 0.955841 +0.015014 0.984986 +0.110012 0.889988 +0.000010 0.999990 +0.053067 0.946933 +0.008146 0.991854 +0.022222 0.977778 +0.147615 0.852385 +0.015696 0.984304 +0.014420 0.985580 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.056566 0.943434 +0.064327 0.935673 +0.017851 0.982149 +0.012337 0.987663 +0.003375 0.996625 +0.005414 0.994586 +0.007458 0.992542 +0.022857 0.977143 +0.026528 0.973472 +0.124320 0.875680 +0.000010 0.999990 +0.005282 0.994718 +0.000010 0.999990 +0.047031 0.952969 +0.004808 0.995192 +0.041071 0.958929 +0.056482 0.943518 +0.001161 0.998839 +0.004575 0.995425 +0.059166 0.940834 +0.009543 0.990457 +0.018827 0.981173 +0.087898 0.912102 +0.000010 0.999990 +0.067979 0.932021 +0.000010 0.999990 +0.017631 0.982369 +0.007289 0.992711 +0.005233 0.994767 +0.061744 0.938256 +0.019819 0.980181 +0.005843 0.994157 +0.069160 0.930840 +0.141902 0.858098 +0.015322 0.984678 +0.058372 0.941628 +0.021536 0.978464 +0.016940 0.983060 +0.047840 0.952160 +0.019644 0.980356 +0.008345 0.991655 +0.026655 0.973345 +0.015316 0.984684 +0.065854 0.934146 +0.017545 0.982455 +0.021902 0.978098 +0.000010 0.999990 +0.017150 0.982850 +0.060982 0.939018 +0.015939 0.984061 +0.045261 0.954739 +0.017116 0.982884 +0.000010 0.999990 +0.047821 0.952179 +0.055596 0.944404 +0.003835 0.996165 +0.043440 0.956560 +0.023236 0.976764 +0.015621 0.984379 +0.002263 0.997737 +0.000097 0.999903 +0.061762 0.938238 +0.000750 0.999250 +0.008419 0.991581 +0.057071 0.942929 +0.000010 0.999990 +0.140798 0.859202 +0.007056 0.992944 +0.087757 0.912243 +0.005546 0.994454 +0.011406 0.988594 +0.022473 0.977527 +0.017477 0.982523 +0.017943 0.982057 +0.006106 0.993894 +0.000010 0.999990 +0.037591 0.962409 +0.048575 0.951425 +0.007120 0.992880 +0.023738 0.976262 +0.058103 0.941897 +0.000010 0.999990 +0.000010 0.999990 +0.018608 0.981392 +0.708502 0.291498 +0.056667 0.943333 +0.006798 0.993202 +0.026690 0.973310 +0.012466 0.987534 +0.000010 0.999990 +0.001699 0.998301 +0.006597 0.993403 +0.113426 0.886574 +0.053397 0.946603 +0.061568 0.938432 +0.059140 0.940860 +0.033016 0.966984 +0.017632 0.982368 +0.010068 0.989932 +0.006184 0.993816 +0.015190 0.984810 +0.008244 0.991756 +0.165715 0.834285 +0.023153 0.976847 +0.030967 0.969033 +0.696983 0.303017 +0.000010 0.999990 +0.025608 0.974392 +0.021272 0.978728 +0.000010 0.999990 +0.073048 0.926952 +0.153864 0.846136 +0.087788 0.912212 +0.144777 0.855223 +0.096355 0.903645 +0.075118 0.924882 +0.175696 0.824304 +0.112188 0.887812 +0.001278 0.998722 +0.681658 0.318342 +0.051190 0.948810 +0.713065 0.286935 +0.000010 0.999990 +0.014099 0.985901 +0.052714 0.947286 +0.701591 0.298409 +0.029248 0.970752 +0.121796 0.878204 +0.060402 0.939598 +0.155841 0.844159 +0.162542 0.837458 +0.091277 0.908723 +0.029214 0.970786 +0.000010 0.999990 +0.134714 0.865286 +0.698271 0.301729 +0.100422 0.899578 +0.091723 0.908277 +0.029824 0.970176 +0.081849 0.918151 +0.000010 0.999990 +0.094227 0.905773 +0.098937 0.901063 +0.002315 0.997685 +0.075718 0.924282 +0.054069 0.945931 +0.020651 0.979349 +0.056504 0.943496 +0.675849 0.324151 +0.058223 0.941777 +0.175464 0.824536 +0.153668 0.846332 +0.146133 0.853867 +0.062613 0.937387 +0.681573 0.318427 +0.152224 0.847776 +0.000010 0.999990 +0.127466 0.872534 +0.710462 0.289538 +0.087236 0.912764 +0.060247 0.939753 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.087592 0.912408 +0.000010 0.999990 +0.046795 0.953205 +0.066227 0.933773 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.035763 0.964237 diff --git a/inst/files/admixture/admixture_06 b/inst/files/admixture/admixture_06 new file mode 100644 index 0000000..e02f409 --- /dev/null +++ b/inst/files/admixture/admixture_06 @@ -0,0 +1,1592 @@ +0.942995 0.057005 +0.950609 0.049391 +0.972207 0.027793 +0.943618 0.056382 +0.931674 0.068326 +0.944011 0.055989 +0.926197 0.073803 +0.976136 0.023864 +0.950896 0.049104 +0.928412 0.071588 +0.947400 0.052600 +0.932082 0.067918 +0.946954 0.053046 +0.983766 0.016234 +0.946588 0.053412 +0.969502 0.030498 +0.922055 0.077945 +0.894128 0.105872 +0.943422 0.056578 +0.954252 0.045748 +0.947032 0.052968 +0.999714 0.000286 +0.946819 0.053181 +0.954604 0.045396 +0.909505 0.090495 +0.940332 0.059668 +0.639082 0.360918 +0.622274 0.377726 +0.616731 0.383269 +0.642448 0.357552 +0.641160 0.358840 +0.641540 0.358460 +0.627042 0.372958 +0.657607 0.342393 +0.621644 0.378356 +0.648931 0.351069 +0.634822 0.365178 +0.679026 0.320974 +0.626667 0.373333 +0.619516 0.380484 +0.646198 0.353802 +0.654603 0.345397 +0.573052 0.426948 +0.985092 0.014908 +0.602255 0.397745 +0.587242 0.412758 +0.643819 0.356181 +0.972256 0.027744 +0.581180 0.418820 +0.644561 0.355439 +0.164249 0.835751 +0.162269 0.837731 +0.167845 0.832155 +0.151826 0.848174 +0.164632 0.835368 +0.155068 0.844932 +0.151798 0.848202 +0.181025 0.818975 +0.142317 0.857683 +0.155926 0.844074 +0.148766 0.851234 +0.165721 0.834279 +0.159381 0.840619 +0.150911 0.849089 +0.168392 0.831608 +0.150043 0.849957 +0.201719 0.798281 +0.147663 0.852337 +0.151050 0.848950 +0.148403 0.851597 +0.159187 0.840813 +0.153258 0.846742 +0.122764 0.877236 +0.213415 0.786585 +0.194961 0.805039 +0.132046 0.867954 +0.134036 0.865964 +0.141651 0.858349 +0.198572 0.801428 +0.149309 0.850691 +0.144015 0.855985 +0.131570 0.868430 +0.133412 0.866588 +0.149752 0.850248 +0.134842 0.865158 +0.141232 0.858768 +0.191372 0.808628 +0.186282 0.813718 +0.185707 0.814293 +0.163154 0.836846 +0.179260 0.820740 +0.571463 0.428537 +0.578038 0.421962 +0.541042 0.458958 +0.560782 0.439218 +0.523809 0.476191 +0.562594 0.437406 +0.553884 0.446116 +0.543402 0.456598 +0.534428 0.465572 +0.560314 0.439686 +0.558593 0.441407 +0.527709 0.472291 +0.553371 0.446629 +0.543995 0.456005 +0.119574 0.880426 +0.120956 0.879044 +0.136804 0.863196 +0.133869 0.866131 +0.142549 0.857451 +0.122443 0.877557 +0.153973 0.846027 +0.134830 0.865170 +0.133720 0.866280 +0.134511 0.865489 +0.122410 0.877590 +0.150112 0.849888 +0.126873 0.873127 +0.134195 0.865805 +0.125169 0.874831 +0.140623 0.859377 +0.139578 0.860422 +0.134243 0.865757 +0.138198 0.861802 +0.137962 0.862038 +0.240188 0.759812 +0.241234 0.758766 +0.222397 0.777603 +0.210561 0.789439 +0.219999 0.780001 +0.238631 0.761369 +0.207886 0.792114 +0.223897 0.776103 +0.222110 0.777890 +0.237594 0.762406 +0.246692 0.753308 +0.247636 0.752364 +0.243291 0.756709 +0.220667 0.779333 +0.211611 0.788389 +0.274211 0.725789 +0.240787 0.759213 +0.241614 0.758386 +0.154886 0.845114 +0.236905 0.763095 +0.192030 0.807970 +0.223977 0.776023 +0.193600 0.806400 +0.211718 0.788282 +0.225955 0.774045 +0.210629 0.789371 +0.233264 0.766736 +0.176103 0.823897 +0.168992 0.831008 +0.215410 0.784590 +0.216387 0.783613 +0.222145 0.777855 +0.189505 0.810495 +0.231347 0.768653 +0.177212 0.822788 +0.196519 0.803481 +0.231271 0.768729 +0.185412 0.814588 +0.170804 0.829196 +0.190611 0.809389 +0.175766 0.824234 +0.195705 0.804295 +0.186995 0.813005 +0.189301 0.810699 +0.174363 0.825637 +0.191334 0.808666 +0.192460 0.807540 +0.199431 0.800569 +0.217483 0.782517 +0.203554 0.796446 +0.176466 0.823534 +0.181714 0.818286 +0.197697 0.802303 +0.197211 0.802789 +0.188035 0.811965 +0.314655 0.685345 +0.285147 0.714853 +0.319773 0.680227 +0.309741 0.690259 +0.296053 0.703947 +0.300771 0.699229 +0.318884 0.681116 +0.288333 0.711667 +0.320885 0.679115 +0.328158 0.671842 +0.298413 0.701587 +0.292423 0.707577 +0.309995 0.690005 +0.299384 0.700616 +0.321439 0.678561 +0.304927 0.695073 +0.307185 0.692815 +0.314489 0.685511 +0.284032 0.715968 +0.284324 0.715676 +0.306208 0.693792 +0.295563 0.704437 +0.305400 0.694600 +0.000010 0.999990 +0.007281 0.992719 +0.018005 0.981995 +0.018397 0.981603 +0.000805 0.999195 +0.007315 0.992685 +0.000010 0.999990 +0.010807 0.989193 +0.000010 0.999990 +0.002709 0.997291 +0.002519 0.997481 +0.000010 0.999990 +0.006906 0.993094 +0.013072 0.986928 +0.021639 0.978361 +0.002534 0.997466 +0.017686 0.982314 +0.000649 0.999351 +0.020842 0.979158 +0.012251 0.987749 +0.016319 0.983681 +0.017077 0.982923 +0.000010 0.999990 +0.015193 0.984807 +0.013065 0.986935 +0.008774 0.991226 +0.000010 0.999990 +0.018078 0.981922 +0.000010 0.999990 +0.014982 0.985018 +0.014962 0.985038 +0.013217 0.986783 +0.001860 0.998140 +0.011006 0.988994 +0.018212 0.981788 +0.002353 0.997647 +0.013871 0.986129 +0.006293 0.993707 +0.019067 0.980933 +0.019598 0.980402 +0.006948 0.993052 +0.000010 0.999990 +0.002767 0.997233 +0.021753 0.978247 +0.019081 0.980919 +0.000010 0.999990 +0.013589 0.986411 +0.030431 0.969569 +0.008318 0.991682 +0.000010 0.999990 +0.019501 0.980499 +0.001109 0.998891 +0.014468 0.985532 +0.014519 0.985481 +0.006192 0.993808 +0.011596 0.988404 +0.009586 0.990414 +0.005238 0.994762 +0.000010 0.999990 +0.019040 0.980960 +0.006968 0.993032 +0.028240 0.971760 +0.012197 0.987803 +0.019414 0.980586 +0.025213 0.974787 +0.009685 0.990315 +0.037480 0.962520 +0.005901 0.994099 +0.061979 0.938021 +0.013382 0.986618 +0.035431 0.964569 +0.040886 0.959114 +0.038555 0.961445 +0.019489 0.980511 +0.012195 0.987805 +0.032679 0.967321 +0.040318 0.959682 +0.031612 0.968388 +0.021638 0.978362 +0.009473 0.990527 +0.036827 0.963173 +0.036646 0.963354 +0.048283 0.951717 +0.035199 0.964801 +0.008645 0.991355 +0.001855 0.998145 +0.043275 0.956725 +0.047952 0.952048 +0.049620 0.950380 +0.026709 0.973291 +0.040982 0.959018 +0.051989 0.948011 +0.022620 0.977380 +0.052563 0.947437 +0.013935 0.986065 +0.019552 0.980448 +0.011597 0.988403 +0.026092 0.973908 +0.037376 0.962624 +0.049630 0.950370 +0.043179 0.956821 +0.021794 0.978206 +0.012212 0.987788 +0.018542 0.981458 +0.023346 0.976654 +0.022687 0.977313 +0.042101 0.957899 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.035633 0.964367 +0.021804 0.978196 +0.018228 0.981772 +0.023758 0.976242 +0.040496 0.959504 +0.048059 0.951941 +0.038407 0.961593 +0.033230 0.966770 +0.046240 0.953760 +0.011119 0.988881 +0.026206 0.973794 +0.017391 0.982609 +0.023035 0.976965 +0.039899 0.960101 +0.006370 0.993630 +0.021977 0.978023 +0.024581 0.975419 +0.027461 0.972539 +0.013267 0.986733 +0.034596 0.965404 +0.015887 0.984113 +0.890153 0.109847 +0.933520 0.066480 +0.870529 0.129471 +0.929497 0.070503 +0.891075 0.108925 +0.930078 0.069922 +0.901775 0.098225 +0.880742 0.119258 +0.032139 0.967861 +0.024051 0.975949 +0.033764 0.966236 +0.027322 0.972678 +0.028574 0.971426 +0.026645 0.973355 +0.034956 0.965044 +0.039772 0.960228 +0.021937 0.978063 +0.026404 0.973596 +0.037409 0.962591 +0.025125 0.974875 +0.036361 0.963639 +0.026498 0.973502 +0.042642 0.957358 +0.033494 0.966506 +0.024775 0.975225 +0.059867 0.940133 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.023971 0.976029 +0.025440 0.974560 +0.017796 0.982204 +0.009748 0.990252 +0.021780 0.978220 +0.022224 0.977776 +0.009652 0.990348 +0.009357 0.990643 +0.015814 0.984186 +0.000010 0.999990 +0.005174 0.994826 +0.013307 0.986693 +0.000010 0.999990 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.093060 0.906940 +0.105193 0.894807 +0.136446 0.863554 +0.114488 0.885512 +0.075223 0.924777 +0.116199 0.883801 +0.088111 0.911889 +0.096470 0.903530 +0.111890 0.888110 +0.114615 0.885385 +0.112163 0.887837 +0.120313 0.879687 +0.114269 0.885731 +0.136636 0.863364 +0.119261 0.880739 +0.107158 0.892842 +0.124955 0.875045 +0.103486 0.896514 +0.080137 0.919863 +0.114810 0.885190 +0.122908 0.877092 +0.108451 0.891549 +0.899951 0.100049 +0.900652 0.099348 +0.872189 0.127811 +0.826736 0.173264 +0.814660 0.185340 +0.911389 0.088611 +0.890804 0.109196 +0.907690 0.092310 +0.924602 0.075398 +0.906416 0.093584 +0.843808 0.156192 +0.931406 0.068594 +0.894713 0.105287 +0.915845 0.084155 +0.901115 0.098885 +0.883823 0.116177 +0.904707 0.095293 +0.870585 0.129415 +0.901530 0.098470 +0.857796 0.142204 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.006743 0.993257 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.010337 0.989663 +0.002162 0.997838 +0.007624 0.992376 +0.000010 0.999990 +0.005011 0.994989 +0.000010 0.999990 +0.000010 0.999990 +0.001660 0.998340 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.996358 0.003642 +0.999990 0.000010 +0.999990 0.000010 +0.998606 0.001394 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.983815 0.016185 +0.969365 0.030635 +0.975583 0.024417 +0.970023 0.029977 +0.999990 0.000010 +0.999990 0.000010 +0.995764 0.004236 +0.964236 0.035764 +0.991261 0.008739 +0.958045 0.041955 +0.956321 0.043679 +0.971256 0.028744 +0.969816 0.030184 +0.980639 0.019361 +0.985133 0.014867 +0.979998 0.020002 +0.984587 0.015413 +0.961036 0.038964 +0.976192 0.023808 +0.943347 0.056653 +0.971128 0.028872 +0.981979 0.018021 +0.953967 0.046033 +0.999990 0.000010 +0.980509 0.019491 +0.998123 0.001877 +0.980913 0.019087 +0.989280 0.010720 +0.999990 0.000010 +0.997481 0.002519 +0.998992 0.001008 +0.966571 0.033429 +0.978865 0.021135 +0.992113 0.007887 +0.930644 0.069356 +0.982495 0.017505 +0.952298 0.047702 +0.999990 0.000010 +0.053647 0.946353 +0.046206 0.953794 +0.044773 0.955227 +0.059369 0.940631 +0.050422 0.949578 +0.038296 0.961704 +0.067023 0.932977 +0.067908 0.932092 +0.031469 0.968531 +0.043506 0.956494 +0.040867 0.959133 +0.044845 0.955155 +0.046174 0.953826 +0.067780 0.932220 +0.054658 0.945342 +0.062993 0.937007 +0.060365 0.939635 +0.041359 0.958641 +0.058456 0.941544 +0.033677 0.966323 +0.035411 0.964589 +0.993567 0.006433 +0.987973 0.012027 +0.989769 0.010231 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.986429 0.013571 +0.999990 0.000010 +0.998258 0.001742 +0.972237 0.027763 +0.521852 0.478148 +0.496525 0.503475 +0.562437 0.437563 +0.519227 0.480773 +0.543730 0.456270 +0.629575 0.370425 +0.499000 0.501000 +0.613211 0.386789 +0.582066 0.417934 +0.566926 0.433074 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999903 0.000097 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.945660 0.054340 +0.924130 0.075870 +0.963229 0.036771 +0.922555 0.077445 +0.949535 0.050465 +0.955558 0.044442 +0.925347 0.074653 +0.956830 0.043170 +0.955265 0.044735 +0.929180 0.070820 +0.000010 0.999990 +0.001079 0.998921 +0.007028 0.992972 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.013131 0.986869 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.107710 0.892290 +0.054189 0.945811 +0.066879 0.933121 +0.082428 0.917572 +0.062449 0.937551 +0.050110 0.949890 +0.109156 0.890844 +0.090137 0.909863 +0.055602 0.944398 +0.056879 0.943121 +0.062759 0.937241 +0.074187 0.925813 +0.068075 0.931925 +0.042522 0.957478 +0.108144 0.891856 +0.916029 0.083971 +0.926130 0.073870 +0.936488 0.063512 +0.924069 0.075931 +0.928402 0.071598 +0.929964 0.070036 +0.958493 0.041507 +0.954640 0.045360 +0.969511 0.030489 +0.948042 0.051958 +0.935468 0.064532 +0.943302 0.056698 +0.927937 0.072063 +0.953663 0.046337 +0.952809 0.047191 +0.927055 0.072945 +0.935008 0.064992 +0.959238 0.040762 +0.947771 0.052229 +0.961622 0.038378 +0.923089 0.076911 +0.943531 0.056469 +0.955491 0.044509 +0.964112 0.035888 +0.972758 0.027242 +0.938893 0.061107 +0.950504 0.049496 +0.688179 0.311821 +0.682066 0.317934 +0.679279 0.320721 +0.682138 0.317862 +0.680368 0.319632 +0.670708 0.329292 +0.688973 0.311027 +0.692555 0.307445 +0.667268 0.332732 +0.691929 0.308071 +0.679038 0.320962 +0.403731 0.596269 +0.435276 0.564724 +0.440756 0.559244 +0.437255 0.562745 +0.448806 0.551194 +0.433304 0.566696 +0.437957 0.562043 +0.443802 0.556198 +0.430225 0.569775 +0.446053 0.553947 +0.445023 0.554977 +0.457956 0.542044 +0.452683 0.547317 +0.278725 0.721275 +0.288449 0.711551 +0.293124 0.706876 +0.278518 0.721482 +0.244895 0.755105 +0.295911 0.704089 +0.285911 0.714089 +0.276733 0.723267 +0.283050 0.716950 +0.272386 0.727614 +0.281185 0.718815 +0.271408 0.728592 +0.293268 0.706732 +0.277626 0.722374 +0.280879 0.719121 +0.656462 0.343538 +0.646239 0.353761 +0.642605 0.357395 +0.649153 0.350847 +0.642710 0.357290 +0.652111 0.347889 +0.635522 0.364478 +0.640283 0.359717 +0.649382 0.350618 +0.652478 0.347522 +0.634084 0.365916 +0.636849 0.363151 +0.364422 0.635578 +0.406176 0.593824 +0.375817 0.624183 +0.395043 0.604957 +0.403163 0.596837 +0.378892 0.621108 +0.367651 0.632349 +0.380010 0.619990 +0.351597 0.648403 +0.377211 0.622789 +0.369394 0.630606 +0.375444 0.624556 +0.379532 0.620468 +0.418829 0.581171 +0.406181 0.593819 +0.413878 0.586122 +0.426317 0.573683 +0.397196 0.602804 +0.403358 0.596642 +0.391069 0.608931 +0.422159 0.577841 +0.425521 0.574479 +0.422347 0.577653 +0.398456 0.601544 +0.437919 0.562081 +0.413303 0.586697 +0.234834 0.765166 +0.062047 0.937953 +0.044291 0.955709 +0.067708 0.932292 +0.039765 0.960235 +0.055759 0.944241 +0.023616 0.976384 +0.019272 0.980728 +0.000010 0.999990 +0.119522 0.880478 +0.048843 0.951157 +0.027404 0.972596 +0.033587 0.966413 +0.025517 0.974483 +0.065485 0.934515 +0.042882 0.957118 +0.040343 0.959657 +0.123885 0.876115 +0.014449 0.985551 +0.037702 0.962298 +0.007714 0.992286 +0.020104 0.979896 +0.014108 0.985892 +0.020520 0.979480 +0.013370 0.986630 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.014171 0.985829 +0.000827 0.999173 +0.010724 0.989276 +0.005603 0.994397 +0.003214 0.996786 +0.000010 0.999990 +0.010881 0.989119 +0.000010 0.999990 +0.002910 0.997090 +0.012543 0.987457 +0.015550 0.984450 +0.009789 0.990211 +0.012542 0.987458 +0.005717 0.994283 +0.010601 0.989399 +0.015299 0.984701 +0.021493 0.978507 +0.013900 0.986100 +0.033302 0.966698 +0.071907 0.928093 +0.104826 0.895174 +0.065305 0.934695 +0.034289 0.965711 +0.024534 0.975466 +0.000304 0.999696 +0.024837 0.975163 +0.018485 0.981515 +0.011372 0.988628 +0.084779 0.915221 +0.094336 0.905664 +0.000010 0.999990 +0.076924 0.923076 +0.003496 0.996504 +0.032448 0.967552 +0.098972 0.901028 +0.032289 0.967711 +0.026015 0.973985 +0.032646 0.967354 +0.036530 0.963470 +0.034089 0.965911 +0.062410 0.937590 +0.029226 0.970774 +0.033585 0.966415 +0.028507 0.971493 +0.011768 0.988232 +0.105712 0.894288 +0.010721 0.989279 +0.037765 0.962235 +0.011950 0.988050 +0.041664 0.958336 +0.050393 0.949607 +0.010969 0.989031 +0.059864 0.940136 +0.017637 0.982363 +0.040985 0.959015 +0.003975 0.996025 +0.035971 0.964029 +0.020366 0.979634 +0.031151 0.968849 +0.025379 0.974621 +0.076797 0.923203 +0.065878 0.934122 +0.005169 0.994831 +0.011624 0.988376 +0.051868 0.948132 +0.087421 0.912579 +0.027073 0.972927 +0.011613 0.988387 +0.022731 0.977269 +0.035769 0.964231 +0.034543 0.965457 +0.081944 0.918056 +0.024013 0.975987 +0.014623 0.985377 +0.015339 0.984661 +0.043694 0.956306 +0.006323 0.993677 +0.028205 0.971795 +0.029278 0.970722 +0.070137 0.929863 +0.049412 0.950588 +0.095862 0.904138 +0.050233 0.949767 +0.013732 0.986268 +0.063812 0.936188 +0.049912 0.950088 +0.002551 0.997449 +0.019421 0.980579 +0.013737 0.986263 +0.055526 0.944474 +0.057480 0.942520 +0.058326 0.941674 +0.043537 0.956463 +0.019715 0.980285 +0.055654 0.944346 +0.043860 0.956140 +0.027958 0.972042 +0.094169 0.905831 +0.125198 0.874802 +0.023811 0.976189 +0.102121 0.897879 +0.056789 0.943211 +0.029229 0.970771 +0.007006 0.992994 +0.058259 0.941741 +0.234466 0.765534 +0.077839 0.922161 +0.111367 0.888633 +0.025472 0.974528 +0.105076 0.894924 +0.066960 0.933040 +0.045881 0.954119 +0.041018 0.958982 +0.021218 0.978782 +0.065315 0.934685 +0.087147 0.912853 +0.288301 0.711699 +0.225466 0.774534 +0.094917 0.905083 +0.010976 0.989024 +0.012087 0.987913 +0.121691 0.878309 +0.056447 0.943553 +0.041664 0.958336 +0.019794 0.980206 +0.015096 0.984904 +0.315416 0.684584 +0.816178 0.183822 +0.104434 0.895566 +0.018233 0.981767 +0.002190 0.997810 +0.108680 0.891320 +0.051942 0.948058 +0.042551 0.957449 +0.016728 0.983272 +0.016654 0.983346 +0.046457 0.953543 +0.087097 0.912903 +0.369176 0.630824 +0.821046 0.178954 +0.112244 0.887756 +0.028382 0.971618 +0.113530 0.886470 +0.097106 0.902894 +0.043022 0.956978 +0.029561 0.970439 +0.019518 0.980482 +0.070250 0.929750 +0.060085 0.939915 +0.064935 0.935065 +0.256404 0.743596 +0.793961 0.206039 +0.119560 0.880440 +0.013296 0.986704 +0.100684 0.899316 +0.106224 0.893776 +0.075733 0.924267 +0.027707 0.972293 +0.003712 0.996288 +0.048702 0.951298 +0.066386 0.933614 +0.080073 0.919927 +0.250534 0.749466 +0.838876 0.161124 +0.088527 0.911473 +0.010447 0.989553 +0.102153 0.897847 +0.063749 0.936251 +0.030427 0.969573 +0.000010 0.999990 +0.063098 0.936902 +0.017069 0.982931 +0.100887 0.899113 +0.239285 0.760715 +0.818009 0.181991 +0.088408 0.911592 +0.031528 0.968472 +0.084008 0.915992 +0.060874 0.939126 +0.044187 0.955813 +0.021228 0.978772 +0.020182 0.979818 +0.067849 0.932151 +0.093985 0.906015 +0.102083 0.897917 +0.259465 0.740535 +0.832381 0.167619 +0.859554 0.140446 +0.754493 0.245507 +0.839641 0.160359 +0.937481 0.062519 +0.700953 0.299047 +0.033120 0.966880 +0.028234 0.971766 +0.042581 0.957419 +0.103840 0.896160 +0.263980 0.736020 +0.451188 0.548812 +0.836593 0.163407 +0.738626 0.261374 +0.821179 0.178821 +0.792487 0.207513 +0.021549 0.978451 +0.045846 0.954154 +0.070595 0.929405 +0.106464 0.893536 +0.295802 0.704198 +0.493811 0.506189 +0.821306 0.178694 +0.745401 0.254599 +0.872078 0.127922 +0.876815 0.123185 +0.054195 0.945805 +0.051617 0.948383 +0.047877 0.952123 +0.125739 0.874261 +0.283573 0.716427 +0.447326 0.552674 +0.819179 0.180821 +0.835980 0.164020 +0.561190 0.438810 +0.703569 0.296431 +0.026804 0.973196 +0.062184 0.937816 +0.125999 0.874001 +0.088069 0.911931 +0.265328 0.734672 +0.562943 0.437057 +0.724458 0.275542 +0.849825 0.150175 +0.840571 0.159429 +0.377242 0.622758 +0.676102 0.323898 +0.048137 0.951863 +0.042388 0.957612 +0.089005 0.910995 +0.092779 0.907221 +0.283040 0.716960 +0.461097 0.538903 +0.758980 0.241020 +0.866936 0.133064 +0.856254 0.143746 +0.659239 0.340761 +0.049816 0.950184 +0.100524 0.899476 +0.243328 0.756672 +0.288660 0.711340 +0.333704 0.666296 +0.721441 0.278559 +0.852941 0.147059 +0.843656 0.156344 +0.609138 0.390862 +0.048202 0.951798 +0.048536 0.951464 +0.105441 0.894559 +0.279806 0.720194 +0.238312 0.761688 +0.326365 0.673635 +0.774015 0.225985 +0.810487 0.189513 +0.791352 0.208648 +0.768858 0.231142 +0.045181 0.954819 +0.028563 0.971437 +0.039942 0.960058 +0.083856 0.916144 +0.250848 0.749152 +0.503155 0.496845 +0.351878 0.648122 +0.447070 0.552930 +0.170834 0.829166 +0.149689 0.850311 +0.147954 0.852046 +0.411469 0.588531 +0.206505 0.793495 +0.157637 0.842363 +0.358446 0.641554 +0.197652 0.802348 +0.253772 0.746228 +0.021560 0.978440 +0.198816 0.801184 +0.308357 0.691643 +0.064132 0.935868 +0.480029 0.519971 +0.179315 0.820685 +0.320447 0.679553 +0.320347 0.679653 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.025792 0.974208 +0.015979 0.984021 +0.043829 0.956171 +0.014263 0.985737 +0.000010 0.999990 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.021451 0.978549 +0.022451 0.977549 +0.012371 0.987629 +0.022571 0.977429 +0.000010 0.999990 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.019429 0.980571 +0.028695 0.971305 +0.012926 0.987074 +0.005192 0.994808 +0.025458 0.974542 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.026477 0.973523 +0.000010 0.999990 +0.000010 0.999990 +0.023325 0.976675 +0.006089 0.993911 +0.999990 0.000010 +0.999990 0.000010 +0.108447 0.891553 +0.023298 0.976702 +0.017906 0.982094 +0.014235 0.985765 +0.021009 0.978991 +0.011474 0.988526 +0.999990 0.000010 +0.999990 0.000010 +0.015776 0.984224 +0.035729 0.964271 +0.032836 0.967164 +0.000010 0.999990 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.067630 0.932370 +0.027316 0.972684 +0.001419 0.998581 +0.022088 0.977912 +0.008763 0.991237 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.025400 0.974600 +0.008078 0.991922 +0.013160 0.986840 +0.023243 0.976757 +0.008672 0.991328 +0.999990 0.000010 +0.015501 0.984499 +0.012953 0.987047 +0.012580 0.987420 +0.018097 0.981903 +0.000010 0.999990 +0.000010 0.999990 +0.008907 0.991093 +0.008203 0.991797 +0.000010 0.999990 +0.003683 0.996317 +0.000010 0.999990 +0.004048 0.995952 +0.013059 0.986941 +0.000010 0.999990 +0.003611 0.996389 +0.008446 0.991554 +0.010344 0.989656 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.002975 0.997025 +0.000010 0.999990 +0.000010 0.999990 +0.011356 0.988644 +0.009846 0.990154 +0.000010 0.999990 +0.014904 0.985096 +0.000010 0.999990 +0.000010 0.999990 +0.006080 0.993920 +0.002962 0.997038 +0.000010 0.999990 +0.019029 0.980971 +0.023705 0.976295 +0.007274 0.992726 +0.020705 0.979295 +0.000010 0.999990 +0.007263 0.992737 +0.000010 0.999990 +0.002493 0.997507 +0.118946 0.881054 +0.085755 0.914245 +0.092983 0.907017 +0.090256 0.909744 +0.013672 0.986328 +0.107102 0.892898 +0.007093 0.992907 +0.084252 0.915748 +0.081076 0.918924 +0.106763 0.893237 +0.000010 0.999990 +0.003748 0.996252 +0.000010 0.999990 +0.001760 0.998240 +0.000010 0.999990 +0.000010 0.999990 +0.009899 0.990101 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.003370 0.996630 +0.010866 0.989134 +0.000010 0.999990 +0.000010 0.999990 +0.012733 0.987267 +0.000256 0.999744 +0.012204 0.987796 +0.011660 0.988340 +0.000010 0.999990 +0.021586 0.978414 +0.006742 0.993258 +0.008764 0.991236 +0.998924 0.001076 +0.983557 0.016443 +0.979072 0.020928 +0.999990 0.000010 +0.980887 0.019113 +0.987236 0.012764 +0.994182 0.005818 +0.987743 0.012257 +0.001759 0.998241 +0.000010 0.999990 +0.003539 0.996461 +0.000712 0.999288 +0.008090 0.991910 +0.375731 0.624269 +0.280970 0.719030 +0.368096 0.631904 +0.363688 0.636312 +0.373066 0.626934 +0.007459 0.992541 +0.429276 0.570724 +0.427570 0.572430 +0.420283 0.579717 +0.376285 0.623715 +0.336802 0.663198 +0.340484 0.659516 +0.428986 0.571014 +0.415993 0.584007 +0.438262 0.561738 +0.428546 0.571454 +0.885661 0.114339 +0.979162 0.020838 +0.854839 0.145161 +0.845302 0.154698 +0.957872 0.042128 +0.843426 0.156574 +0.915795 0.084205 +0.858970 0.141030 +0.877905 0.122095 +0.863453 0.136547 +0.017844 0.982156 +0.011038 0.988962 +0.000010 0.999990 +0.762966 0.237034 +0.046008 0.953992 +0.010396 0.989604 +0.009741 0.990259 +0.021283 0.978717 +0.021002 0.978998 +0.793520 0.206480 +0.022256 0.977744 +0.011741 0.988259 +0.739613 0.260387 +0.006832 0.993168 +0.001399 0.998601 +0.018843 0.981157 +0.701044 0.298956 +0.934191 0.065809 +0.012387 0.987613 +0.930386 0.069614 +0.005134 0.994866 +0.024876 0.975124 +0.834953 0.165047 +0.831489 0.168511 +0.064057 0.935943 +0.000010 0.999990 +0.015731 0.984269 +0.022769 0.977231 +0.020998 0.979002 +0.007361 0.992639 +0.922408 0.077592 +0.857881 0.142119 +0.001853 0.998147 +0.007644 0.992356 +0.000010 0.999990 +0.032173 0.967827 +0.015762 0.984238 +0.017070 0.982930 +0.752750 0.247250 +0.006704 0.993296 +0.081630 0.918370 +0.041556 0.958444 +0.017264 0.982736 +0.000113 0.999887 +0.029783 0.970217 +0.788600 0.211400 +0.923221 0.076779 +0.000010 0.999990 +0.013698 0.986302 +0.940902 0.059098 +0.981095 0.018905 +0.032568 0.967432 +0.024273 0.975727 +0.016460 0.983540 +0.000010 0.999990 +0.000309 0.999691 +0.000010 0.999990 +0.000010 0.999990 +0.009025 0.990975 +0.009021 0.990979 +0.016584 0.983416 +0.016507 0.983493 +0.000010 0.999990 +0.010857 0.989143 +0.021035 0.978965 +0.000010 0.999990 +0.000010 0.999990 +0.007197 0.992803 +0.006811 0.993189 +0.000010 0.999990 +0.015880 0.984120 +0.005359 0.994641 +0.000010 0.999990 +0.008085 0.991915 +0.010392 0.989608 +0.017333 0.982667 +0.000010 0.999990 +0.002299 0.997701 +0.020364 0.979636 +0.128579 0.871421 +0.000010 0.999990 +0.009861 0.990139 +0.046527 0.953473 +0.000010 0.999990 +0.046279 0.953721 +0.854933 0.145067 +0.000010 0.999990 +0.006499 0.993501 +0.010899 0.989101 +0.010603 0.989397 +0.061164 0.938836 +0.044159 0.955841 +0.015014 0.984986 +0.110012 0.889988 +0.000010 0.999990 +0.053067 0.946933 +0.008146 0.991854 +0.022222 0.977778 +0.147615 0.852385 +0.015696 0.984304 +0.014420 0.985580 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.056566 0.943434 +0.064326 0.935674 +0.017851 0.982149 +0.012337 0.987663 +0.003375 0.996625 +0.005414 0.994586 +0.007458 0.992542 +0.022857 0.977143 +0.026528 0.973472 +0.124319 0.875681 +0.000010 0.999990 +0.005282 0.994718 +0.000010 0.999990 +0.047031 0.952969 +0.004808 0.995192 +0.041071 0.958929 +0.056482 0.943518 +0.001161 0.998839 +0.004575 0.995425 +0.059166 0.940834 +0.009543 0.990457 +0.018827 0.981173 +0.087898 0.912102 +0.000010 0.999990 +0.067979 0.932021 +0.000010 0.999990 +0.017631 0.982369 +0.007289 0.992711 +0.005233 0.994767 +0.061744 0.938256 +0.019819 0.980181 +0.005843 0.994157 +0.069160 0.930840 +0.141902 0.858098 +0.015322 0.984678 +0.058372 0.941628 +0.021536 0.978464 +0.016939 0.983061 +0.047840 0.952160 +0.019644 0.980356 +0.008345 0.991655 +0.026655 0.973345 +0.015316 0.984684 +0.065853 0.934147 +0.017545 0.982455 +0.021902 0.978098 +0.000010 0.999990 +0.017150 0.982850 +0.060982 0.939018 +0.015939 0.984061 +0.045261 0.954739 +0.017116 0.982884 +0.000010 0.999990 +0.047821 0.952179 +0.055596 0.944404 +0.003835 0.996165 +0.043440 0.956560 +0.023236 0.976764 +0.015621 0.984379 +0.002263 0.997737 +0.000097 0.999903 +0.061762 0.938238 +0.000750 0.999250 +0.008419 0.991581 +0.057071 0.942929 +0.000010 0.999990 +0.140798 0.859202 +0.007056 0.992944 +0.087757 0.912243 +0.005546 0.994454 +0.011406 0.988594 +0.022473 0.977527 +0.017477 0.982523 +0.017943 0.982057 +0.006106 0.993894 +0.000010 0.999990 +0.037591 0.962409 +0.048575 0.951425 +0.007120 0.992880 +0.023738 0.976262 +0.058103 0.941897 +0.000010 0.999990 +0.000010 0.999990 +0.018608 0.981392 +0.708502 0.291498 +0.056667 0.943333 +0.006798 0.993202 +0.026689 0.973311 +0.012466 0.987534 +0.000010 0.999990 +0.001699 0.998301 +0.006597 0.993403 +0.113426 0.886574 +0.053397 0.946603 +0.061568 0.938432 +0.059140 0.940860 +0.033016 0.966984 +0.017632 0.982368 +0.010068 0.989932 +0.006184 0.993816 +0.015190 0.984810 +0.008244 0.991756 +0.165715 0.834285 +0.023153 0.976847 +0.030967 0.969033 +0.696983 0.303017 +0.000010 0.999990 +0.025608 0.974392 +0.021272 0.978728 +0.000010 0.999990 +0.073048 0.926952 +0.153863 0.846137 +0.087788 0.912212 +0.144776 0.855224 +0.096355 0.903645 +0.075118 0.924882 +0.175696 0.824304 +0.112188 0.887812 +0.001278 0.998722 +0.681658 0.318342 +0.051190 0.948810 +0.713065 0.286935 +0.000010 0.999990 +0.014099 0.985901 +0.052713 0.947287 +0.701591 0.298409 +0.029248 0.970752 +0.121796 0.878204 +0.060402 0.939598 +0.155841 0.844159 +0.162542 0.837458 +0.091277 0.908723 +0.029214 0.970786 +0.000010 0.999990 +0.134714 0.865286 +0.698270 0.301730 +0.100421 0.899579 +0.091723 0.908277 +0.029824 0.970176 +0.081849 0.918151 +0.000010 0.999990 +0.094227 0.905773 +0.098937 0.901063 +0.002315 0.997685 +0.075718 0.924282 +0.054068 0.945932 +0.020651 0.979349 +0.056504 0.943496 +0.675849 0.324151 +0.058223 0.941777 +0.175464 0.824536 +0.153668 0.846332 +0.146133 0.853867 +0.062613 0.937387 +0.681573 0.318427 +0.152224 0.847776 +0.000010 0.999990 +0.127466 0.872534 +0.710462 0.289538 +0.087236 0.912764 +0.060247 0.939753 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.087592 0.912408 +0.000010 0.999990 +0.046795 0.953205 +0.066227 0.933773 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.035763 0.964237 diff --git a/inst/files/admixture/admixture_07 b/inst/files/admixture/admixture_07 new file mode 100644 index 0000000..8342cbc --- /dev/null +++ b/inst/files/admixture/admixture_07 @@ -0,0 +1,1592 @@ +0.942995 0.057005 +0.950609 0.049391 +0.972207 0.027793 +0.943618 0.056382 +0.931674 0.068326 +0.944011 0.055989 +0.926197 0.073803 +0.976136 0.023864 +0.950896 0.049104 +0.928412 0.071588 +0.947400 0.052600 +0.932082 0.067918 +0.946954 0.053046 +0.983766 0.016234 +0.946588 0.053412 +0.969502 0.030498 +0.922055 0.077945 +0.894128 0.105872 +0.943422 0.056578 +0.954252 0.045748 +0.947032 0.052968 +0.999714 0.000286 +0.946819 0.053181 +0.954604 0.045396 +0.909505 0.090495 +0.940332 0.059668 +0.639082 0.360918 +0.622274 0.377726 +0.616732 0.383268 +0.642448 0.357552 +0.641160 0.358840 +0.641540 0.358460 +0.627042 0.372958 +0.657607 0.342393 +0.621644 0.378356 +0.648931 0.351069 +0.634822 0.365178 +0.679026 0.320974 +0.626667 0.373333 +0.619516 0.380484 +0.646198 0.353802 +0.654603 0.345397 +0.573052 0.426948 +0.985092 0.014908 +0.602255 0.397745 +0.587242 0.412758 +0.643819 0.356181 +0.972256 0.027744 +0.581180 0.418820 +0.644561 0.355439 +0.164249 0.835751 +0.162269 0.837731 +0.167845 0.832155 +0.151826 0.848174 +0.164632 0.835368 +0.155068 0.844932 +0.151798 0.848202 +0.181025 0.818975 +0.142317 0.857683 +0.155926 0.844074 +0.148766 0.851234 +0.165721 0.834279 +0.159381 0.840619 +0.150911 0.849089 +0.168392 0.831608 +0.150043 0.849957 +0.201719 0.798281 +0.147663 0.852337 +0.151050 0.848950 +0.148403 0.851597 +0.159187 0.840813 +0.153258 0.846742 +0.122764 0.877236 +0.213415 0.786585 +0.194961 0.805039 +0.132046 0.867954 +0.134036 0.865964 +0.141651 0.858349 +0.198572 0.801428 +0.149309 0.850691 +0.144015 0.855985 +0.131570 0.868430 +0.133412 0.866588 +0.149752 0.850248 +0.134842 0.865158 +0.141232 0.858768 +0.191372 0.808628 +0.186282 0.813718 +0.185707 0.814293 +0.163154 0.836846 +0.179260 0.820740 +0.571463 0.428537 +0.578038 0.421962 +0.541042 0.458958 +0.560782 0.439218 +0.523809 0.476191 +0.562594 0.437406 +0.553884 0.446116 +0.543402 0.456598 +0.534428 0.465572 +0.560314 0.439686 +0.558593 0.441407 +0.527709 0.472291 +0.553371 0.446629 +0.543995 0.456005 +0.119574 0.880426 +0.120956 0.879044 +0.136804 0.863196 +0.133869 0.866131 +0.142549 0.857451 +0.122443 0.877557 +0.153973 0.846027 +0.134830 0.865170 +0.133720 0.866280 +0.134511 0.865489 +0.122410 0.877590 +0.150112 0.849888 +0.126873 0.873127 +0.134195 0.865805 +0.125169 0.874831 +0.140623 0.859377 +0.139578 0.860422 +0.134243 0.865757 +0.138198 0.861802 +0.137962 0.862038 +0.240188 0.759812 +0.241234 0.758766 +0.222397 0.777603 +0.210561 0.789439 +0.219999 0.780001 +0.238631 0.761369 +0.207886 0.792114 +0.223897 0.776103 +0.222110 0.777890 +0.237594 0.762406 +0.246692 0.753308 +0.247636 0.752364 +0.243291 0.756709 +0.220667 0.779333 +0.211611 0.788389 +0.274211 0.725789 +0.240787 0.759213 +0.241614 0.758386 +0.154886 0.845114 +0.236905 0.763095 +0.192030 0.807970 +0.223977 0.776023 +0.193600 0.806400 +0.211718 0.788282 +0.225955 0.774045 +0.210629 0.789371 +0.233264 0.766736 +0.176103 0.823897 +0.168992 0.831008 +0.215410 0.784590 +0.216387 0.783613 +0.222145 0.777855 +0.189505 0.810495 +0.231347 0.768653 +0.177212 0.822788 +0.196519 0.803481 +0.231271 0.768729 +0.185412 0.814588 +0.170804 0.829196 +0.190611 0.809389 +0.175766 0.824234 +0.195705 0.804295 +0.186995 0.813005 +0.189301 0.810699 +0.174363 0.825637 +0.191334 0.808666 +0.192460 0.807540 +0.199431 0.800569 +0.217483 0.782517 +0.203554 0.796446 +0.176466 0.823534 +0.181714 0.818286 +0.197697 0.802303 +0.197211 0.802789 +0.188035 0.811965 +0.314655 0.685345 +0.285147 0.714853 +0.319773 0.680227 +0.309741 0.690259 +0.296053 0.703947 +0.300771 0.699229 +0.318884 0.681116 +0.288333 0.711667 +0.320885 0.679115 +0.328158 0.671842 +0.298413 0.701587 +0.292423 0.707577 +0.309995 0.690005 +0.299384 0.700616 +0.321439 0.678561 +0.304927 0.695073 +0.307185 0.692815 +0.314489 0.685511 +0.284032 0.715968 +0.284324 0.715676 +0.306208 0.693792 +0.295563 0.704437 +0.305400 0.694600 +0.000010 0.999990 +0.007281 0.992719 +0.018005 0.981995 +0.018397 0.981603 +0.000805 0.999195 +0.007315 0.992685 +0.000010 0.999990 +0.010807 0.989193 +0.000010 0.999990 +0.002709 0.997291 +0.002519 0.997481 +0.000010 0.999990 +0.006906 0.993094 +0.013072 0.986928 +0.021639 0.978361 +0.002534 0.997466 +0.017686 0.982314 +0.000649 0.999351 +0.020842 0.979158 +0.012251 0.987749 +0.016319 0.983681 +0.017077 0.982923 +0.000010 0.999990 +0.015193 0.984807 +0.013065 0.986935 +0.008775 0.991225 +0.000010 0.999990 +0.018078 0.981922 +0.000010 0.999990 +0.014982 0.985018 +0.014962 0.985038 +0.013217 0.986783 +0.001860 0.998140 +0.011006 0.988994 +0.018212 0.981788 +0.002353 0.997647 +0.013871 0.986129 +0.006293 0.993707 +0.019067 0.980933 +0.019598 0.980402 +0.006948 0.993052 +0.000010 0.999990 +0.002767 0.997233 +0.021753 0.978247 +0.019081 0.980919 +0.000010 0.999990 +0.013589 0.986411 +0.030431 0.969569 +0.008318 0.991682 +0.000010 0.999990 +0.019501 0.980499 +0.001109 0.998891 +0.014468 0.985532 +0.014519 0.985481 +0.006192 0.993808 +0.011596 0.988404 +0.009586 0.990414 +0.005238 0.994762 +0.000010 0.999990 +0.019040 0.980960 +0.006968 0.993032 +0.028239 0.971761 +0.012197 0.987803 +0.019414 0.980586 +0.025213 0.974787 +0.009685 0.990315 +0.037480 0.962520 +0.005901 0.994099 +0.061979 0.938021 +0.013382 0.986618 +0.035431 0.964569 +0.040886 0.959114 +0.038555 0.961445 +0.019489 0.980511 +0.012195 0.987805 +0.032679 0.967321 +0.040318 0.959682 +0.031612 0.968388 +0.021638 0.978362 +0.009473 0.990527 +0.036827 0.963173 +0.036646 0.963354 +0.048283 0.951717 +0.035199 0.964801 +0.008646 0.991354 +0.001855 0.998145 +0.043275 0.956725 +0.047952 0.952048 +0.049620 0.950380 +0.026709 0.973291 +0.040982 0.959018 +0.051989 0.948011 +0.022620 0.977380 +0.052563 0.947437 +0.013935 0.986065 +0.019552 0.980448 +0.011597 0.988403 +0.026092 0.973908 +0.037376 0.962624 +0.049630 0.950370 +0.043179 0.956821 +0.021794 0.978206 +0.012211 0.987789 +0.018542 0.981458 +0.023346 0.976654 +0.022687 0.977313 +0.042101 0.957899 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.035633 0.964367 +0.021804 0.978196 +0.018228 0.981772 +0.023758 0.976242 +0.040496 0.959504 +0.048059 0.951941 +0.038407 0.961593 +0.033230 0.966770 +0.046240 0.953760 +0.011119 0.988881 +0.026206 0.973794 +0.017391 0.982609 +0.023035 0.976965 +0.039899 0.960101 +0.006370 0.993630 +0.021977 0.978023 +0.024581 0.975419 +0.027461 0.972539 +0.013267 0.986733 +0.034596 0.965404 +0.015887 0.984113 +0.890153 0.109847 +0.933520 0.066480 +0.870529 0.129471 +0.929497 0.070503 +0.891075 0.108925 +0.930078 0.069922 +0.901775 0.098225 +0.880742 0.119258 +0.032139 0.967861 +0.024051 0.975949 +0.033764 0.966236 +0.027322 0.972678 +0.028574 0.971426 +0.026645 0.973355 +0.034956 0.965044 +0.039772 0.960228 +0.021937 0.978063 +0.026404 0.973596 +0.037409 0.962591 +0.025125 0.974875 +0.036361 0.963639 +0.026498 0.973502 +0.042642 0.957358 +0.033494 0.966506 +0.024775 0.975225 +0.059867 0.940133 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.023971 0.976029 +0.025440 0.974560 +0.017796 0.982204 +0.009748 0.990252 +0.021780 0.978220 +0.022224 0.977776 +0.009652 0.990348 +0.009357 0.990643 +0.015814 0.984186 +0.000010 0.999990 +0.005174 0.994826 +0.013307 0.986693 +0.000010 0.999990 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.093060 0.906940 +0.105193 0.894807 +0.136446 0.863554 +0.114488 0.885512 +0.075223 0.924777 +0.116199 0.883801 +0.088111 0.911889 +0.096470 0.903530 +0.111890 0.888110 +0.114615 0.885385 +0.112163 0.887837 +0.120313 0.879687 +0.114269 0.885731 +0.136636 0.863364 +0.119261 0.880739 +0.107158 0.892842 +0.124955 0.875045 +0.103486 0.896514 +0.080137 0.919863 +0.114810 0.885190 +0.122908 0.877092 +0.108451 0.891549 +0.899951 0.100049 +0.900652 0.099348 +0.872189 0.127811 +0.826736 0.173264 +0.814660 0.185340 +0.911389 0.088611 +0.890804 0.109196 +0.907690 0.092310 +0.924602 0.075398 +0.906416 0.093584 +0.843808 0.156192 +0.931406 0.068594 +0.894713 0.105287 +0.915845 0.084155 +0.901115 0.098885 +0.883824 0.116176 +0.904707 0.095293 +0.870585 0.129415 +0.901530 0.098470 +0.857796 0.142204 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.006743 0.993257 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.010337 0.989663 +0.002162 0.997838 +0.007624 0.992376 +0.000010 0.999990 +0.005011 0.994989 +0.000010 0.999990 +0.000010 0.999990 +0.001660 0.998340 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.996357 0.003643 +0.999990 0.000010 +0.999990 0.000010 +0.998605 0.001395 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.983815 0.016185 +0.969365 0.030635 +0.975583 0.024417 +0.970023 0.029977 +0.999990 0.000010 +0.999990 0.000010 +0.995764 0.004236 +0.964236 0.035764 +0.991261 0.008739 +0.958045 0.041955 +0.956321 0.043679 +0.971256 0.028744 +0.969816 0.030184 +0.980639 0.019361 +0.985133 0.014867 +0.979998 0.020002 +0.984587 0.015413 +0.961036 0.038964 +0.976192 0.023808 +0.943347 0.056653 +0.971128 0.028872 +0.981979 0.018021 +0.953967 0.046033 +0.999990 0.000010 +0.980509 0.019491 +0.998123 0.001877 +0.980913 0.019087 +0.989279 0.010721 +0.999990 0.000010 +0.997480 0.002520 +0.998992 0.001008 +0.966571 0.033429 +0.978865 0.021135 +0.992113 0.007887 +0.930644 0.069356 +0.982494 0.017506 +0.952298 0.047702 +0.999990 0.000010 +0.053647 0.946353 +0.046206 0.953794 +0.044773 0.955227 +0.059369 0.940631 +0.050422 0.949578 +0.038296 0.961704 +0.067023 0.932977 +0.067908 0.932092 +0.031469 0.968531 +0.043506 0.956494 +0.040867 0.959133 +0.044845 0.955155 +0.046174 0.953826 +0.067780 0.932220 +0.054658 0.945342 +0.062993 0.937007 +0.060365 0.939635 +0.041359 0.958641 +0.058456 0.941544 +0.033677 0.966323 +0.035411 0.964589 +0.993567 0.006433 +0.987974 0.012026 +0.989769 0.010231 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.986429 0.013571 +0.999990 0.000010 +0.998262 0.001738 +0.972237 0.027763 +0.521852 0.478148 +0.496525 0.503475 +0.562437 0.437563 +0.519227 0.480773 +0.543730 0.456270 +0.629575 0.370425 +0.499000 0.501000 +0.613211 0.386789 +0.582066 0.417934 +0.566926 0.433074 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999903 0.000097 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.945660 0.054340 +0.924130 0.075870 +0.963229 0.036771 +0.922555 0.077445 +0.949536 0.050464 +0.955558 0.044442 +0.925347 0.074653 +0.956830 0.043170 +0.955265 0.044735 +0.929180 0.070820 +0.000010 0.999990 +0.001079 0.998921 +0.007028 0.992972 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.013131 0.986869 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.107710 0.892290 +0.054189 0.945811 +0.066879 0.933121 +0.082428 0.917572 +0.062449 0.937551 +0.050110 0.949890 +0.109156 0.890844 +0.090137 0.909863 +0.055603 0.944397 +0.056879 0.943121 +0.062759 0.937241 +0.074187 0.925813 +0.068075 0.931925 +0.042522 0.957478 +0.108144 0.891856 +0.916029 0.083971 +0.926130 0.073870 +0.936488 0.063512 +0.924069 0.075931 +0.928402 0.071598 +0.929964 0.070036 +0.958493 0.041507 +0.954640 0.045360 +0.969511 0.030489 +0.948042 0.051958 +0.935468 0.064532 +0.943302 0.056698 +0.927937 0.072063 +0.953663 0.046337 +0.952809 0.047191 +0.927055 0.072945 +0.935008 0.064992 +0.959238 0.040762 +0.947771 0.052229 +0.961622 0.038378 +0.923089 0.076911 +0.943531 0.056469 +0.955491 0.044509 +0.964112 0.035888 +0.972758 0.027242 +0.938893 0.061107 +0.950504 0.049496 +0.688179 0.311821 +0.682066 0.317934 +0.679279 0.320721 +0.682138 0.317862 +0.680368 0.319632 +0.670708 0.329292 +0.688973 0.311027 +0.692555 0.307445 +0.667268 0.332732 +0.691929 0.308071 +0.679038 0.320962 +0.403731 0.596269 +0.435276 0.564724 +0.440756 0.559244 +0.437255 0.562745 +0.448806 0.551194 +0.433304 0.566696 +0.437957 0.562043 +0.443802 0.556198 +0.430225 0.569775 +0.446053 0.553947 +0.445023 0.554977 +0.457956 0.542044 +0.452683 0.547317 +0.278725 0.721275 +0.288449 0.711551 +0.293124 0.706876 +0.278518 0.721482 +0.244895 0.755105 +0.295911 0.704089 +0.285911 0.714089 +0.276733 0.723267 +0.283050 0.716950 +0.272386 0.727614 +0.281185 0.718815 +0.271408 0.728592 +0.293268 0.706732 +0.277626 0.722374 +0.280879 0.719121 +0.656462 0.343538 +0.646239 0.353761 +0.642605 0.357395 +0.649153 0.350847 +0.642710 0.357290 +0.652111 0.347889 +0.635522 0.364478 +0.640283 0.359717 +0.649382 0.350618 +0.652478 0.347522 +0.634084 0.365916 +0.636849 0.363151 +0.364422 0.635578 +0.406176 0.593824 +0.375817 0.624183 +0.395043 0.604957 +0.403163 0.596837 +0.378892 0.621108 +0.367651 0.632349 +0.380010 0.619990 +0.351597 0.648403 +0.377211 0.622789 +0.369394 0.630606 +0.375444 0.624556 +0.379532 0.620468 +0.418829 0.581171 +0.406181 0.593819 +0.413878 0.586122 +0.426317 0.573683 +0.397196 0.602804 +0.403358 0.596642 +0.391069 0.608931 +0.422159 0.577841 +0.425521 0.574479 +0.422347 0.577653 +0.398456 0.601544 +0.437919 0.562081 +0.413303 0.586697 +0.234834 0.765166 +0.062047 0.937953 +0.044291 0.955709 +0.067708 0.932292 +0.039765 0.960235 +0.055759 0.944241 +0.023616 0.976384 +0.019272 0.980728 +0.000010 0.999990 +0.119522 0.880478 +0.048843 0.951157 +0.027404 0.972596 +0.033587 0.966413 +0.025517 0.974483 +0.065485 0.934515 +0.042882 0.957118 +0.040343 0.959657 +0.123885 0.876115 +0.014449 0.985551 +0.037702 0.962298 +0.007714 0.992286 +0.020104 0.979896 +0.014108 0.985892 +0.020520 0.979480 +0.013370 0.986630 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.014171 0.985829 +0.000827 0.999173 +0.010724 0.989276 +0.005603 0.994397 +0.003214 0.996786 +0.000010 0.999990 +0.010881 0.989119 +0.000010 0.999990 +0.002910 0.997090 +0.012543 0.987457 +0.015550 0.984450 +0.009789 0.990211 +0.012542 0.987458 +0.005717 0.994283 +0.010601 0.989399 +0.015299 0.984701 +0.021493 0.978507 +0.013900 0.986100 +0.033302 0.966698 +0.071907 0.928093 +0.104826 0.895174 +0.065305 0.934695 +0.034289 0.965711 +0.024534 0.975466 +0.000304 0.999696 +0.024837 0.975163 +0.018485 0.981515 +0.011372 0.988628 +0.084779 0.915221 +0.094336 0.905664 +0.000010 0.999990 +0.076924 0.923076 +0.003496 0.996504 +0.032448 0.967552 +0.098972 0.901028 +0.032289 0.967711 +0.026015 0.973985 +0.032646 0.967354 +0.036530 0.963470 +0.034089 0.965911 +0.062410 0.937590 +0.029226 0.970774 +0.033585 0.966415 +0.028507 0.971493 +0.011768 0.988232 +0.105712 0.894288 +0.010721 0.989279 +0.037765 0.962235 +0.011950 0.988050 +0.041664 0.958336 +0.050393 0.949607 +0.010969 0.989031 +0.059864 0.940136 +0.017637 0.982363 +0.040985 0.959015 +0.003975 0.996025 +0.035971 0.964029 +0.020366 0.979634 +0.031151 0.968849 +0.025379 0.974621 +0.076797 0.923203 +0.065878 0.934122 +0.005169 0.994831 +0.011624 0.988376 +0.051868 0.948132 +0.087421 0.912579 +0.027073 0.972927 +0.011613 0.988387 +0.022731 0.977269 +0.035769 0.964231 +0.034543 0.965457 +0.081944 0.918056 +0.024013 0.975987 +0.014622 0.985378 +0.015339 0.984661 +0.043694 0.956306 +0.006323 0.993677 +0.028206 0.971794 +0.029278 0.970722 +0.070137 0.929863 +0.049412 0.950588 +0.095862 0.904138 +0.050233 0.949767 +0.013732 0.986268 +0.063812 0.936188 +0.049912 0.950088 +0.002551 0.997449 +0.019421 0.980579 +0.013737 0.986263 +0.055526 0.944474 +0.057480 0.942520 +0.058326 0.941674 +0.043537 0.956463 +0.019715 0.980285 +0.055654 0.944346 +0.043860 0.956140 +0.027958 0.972042 +0.094169 0.905831 +0.125198 0.874802 +0.023811 0.976189 +0.102121 0.897879 +0.056789 0.943211 +0.029229 0.970771 +0.007006 0.992994 +0.058259 0.941741 +0.234466 0.765534 +0.077839 0.922161 +0.111367 0.888633 +0.025472 0.974528 +0.105076 0.894924 +0.066960 0.933040 +0.045881 0.954119 +0.041018 0.958982 +0.021218 0.978782 +0.065315 0.934685 +0.087147 0.912853 +0.288301 0.711699 +0.225466 0.774534 +0.094917 0.905083 +0.010976 0.989024 +0.012087 0.987913 +0.121691 0.878309 +0.056447 0.943553 +0.041664 0.958336 +0.019794 0.980206 +0.015096 0.984904 +0.315416 0.684584 +0.816178 0.183822 +0.104434 0.895566 +0.018233 0.981767 +0.002190 0.997810 +0.108680 0.891320 +0.051942 0.948058 +0.042551 0.957449 +0.016728 0.983272 +0.016654 0.983346 +0.046457 0.953543 +0.087097 0.912903 +0.369176 0.630824 +0.821046 0.178954 +0.112244 0.887756 +0.028382 0.971618 +0.113530 0.886470 +0.097106 0.902894 +0.043022 0.956978 +0.029561 0.970439 +0.019518 0.980482 +0.070250 0.929750 +0.060085 0.939915 +0.064935 0.935065 +0.256404 0.743596 +0.793961 0.206039 +0.119560 0.880440 +0.013296 0.986704 +0.100684 0.899316 +0.106224 0.893776 +0.075733 0.924267 +0.027707 0.972293 +0.003712 0.996288 +0.048702 0.951298 +0.066386 0.933614 +0.080073 0.919927 +0.250534 0.749466 +0.838876 0.161124 +0.088527 0.911473 +0.010447 0.989553 +0.102153 0.897847 +0.063749 0.936251 +0.030427 0.969573 +0.000010 0.999990 +0.063098 0.936902 +0.017069 0.982931 +0.100887 0.899113 +0.239285 0.760715 +0.818010 0.181990 +0.088408 0.911592 +0.031528 0.968472 +0.084008 0.915992 +0.060874 0.939126 +0.044187 0.955813 +0.021228 0.978772 +0.020182 0.979818 +0.067849 0.932151 +0.093985 0.906015 +0.102083 0.897917 +0.259465 0.740535 +0.832381 0.167619 +0.859554 0.140446 +0.754493 0.245507 +0.839641 0.160359 +0.937481 0.062519 +0.700953 0.299047 +0.033120 0.966880 +0.028234 0.971766 +0.042581 0.957419 +0.103840 0.896160 +0.263980 0.736020 +0.451188 0.548812 +0.836593 0.163407 +0.738626 0.261374 +0.821179 0.178821 +0.792487 0.207513 +0.021549 0.978451 +0.045846 0.954154 +0.070595 0.929405 +0.106464 0.893536 +0.295802 0.704198 +0.493811 0.506189 +0.821306 0.178694 +0.745401 0.254599 +0.872078 0.127922 +0.876815 0.123185 +0.054195 0.945805 +0.051617 0.948383 +0.047877 0.952123 +0.125739 0.874261 +0.283573 0.716427 +0.447326 0.552674 +0.819179 0.180821 +0.835980 0.164020 +0.561191 0.438809 +0.703569 0.296431 +0.026804 0.973196 +0.062184 0.937816 +0.125999 0.874001 +0.088069 0.911931 +0.265328 0.734672 +0.562943 0.437057 +0.724458 0.275542 +0.849825 0.150175 +0.840571 0.159429 +0.377242 0.622758 +0.676102 0.323898 +0.048137 0.951863 +0.042388 0.957612 +0.089005 0.910995 +0.092779 0.907221 +0.283040 0.716960 +0.461097 0.538903 +0.758980 0.241020 +0.866936 0.133064 +0.856254 0.143746 +0.659239 0.340761 +0.049816 0.950184 +0.100524 0.899476 +0.243328 0.756672 +0.288660 0.711340 +0.333704 0.666296 +0.721441 0.278559 +0.852941 0.147059 +0.843656 0.156344 +0.609138 0.390862 +0.048202 0.951798 +0.048536 0.951464 +0.105441 0.894559 +0.279806 0.720194 +0.238312 0.761688 +0.326365 0.673635 +0.774015 0.225985 +0.810487 0.189513 +0.791352 0.208648 +0.768858 0.231142 +0.045181 0.954819 +0.028563 0.971437 +0.039942 0.960058 +0.083856 0.916144 +0.250848 0.749152 +0.503155 0.496845 +0.351878 0.648122 +0.447070 0.552930 +0.170834 0.829166 +0.149689 0.850311 +0.147954 0.852046 +0.411469 0.588531 +0.206505 0.793495 +0.157637 0.842363 +0.358446 0.641554 +0.197652 0.802348 +0.253772 0.746228 +0.021560 0.978440 +0.198816 0.801184 +0.308357 0.691643 +0.064131 0.935869 +0.480029 0.519971 +0.179315 0.820685 +0.320447 0.679553 +0.320347 0.679653 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.025792 0.974208 +0.015979 0.984021 +0.043829 0.956171 +0.014264 0.985736 +0.000010 0.999990 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.021451 0.978549 +0.022451 0.977549 +0.012371 0.987629 +0.022571 0.977429 +0.000010 0.999990 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.019429 0.980571 +0.028695 0.971305 +0.012926 0.987074 +0.005192 0.994808 +0.025458 0.974542 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.026477 0.973523 +0.000010 0.999990 +0.000010 0.999990 +0.023325 0.976675 +0.006089 0.993911 +0.999990 0.000010 +0.999990 0.000010 +0.108447 0.891553 +0.023298 0.976702 +0.017906 0.982094 +0.014235 0.985765 +0.021009 0.978991 +0.011474 0.988526 +0.999990 0.000010 +0.999990 0.000010 +0.015776 0.984224 +0.035729 0.964271 +0.032836 0.967164 +0.000010 0.999990 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.067630 0.932370 +0.027316 0.972684 +0.001419 0.998581 +0.022088 0.977912 +0.008763 0.991237 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.025400 0.974600 +0.008077 0.991923 +0.013161 0.986839 +0.023243 0.976757 +0.008672 0.991328 +0.999990 0.000010 +0.015501 0.984499 +0.012953 0.987047 +0.012580 0.987420 +0.018097 0.981903 +0.000010 0.999990 +0.000010 0.999990 +0.008907 0.991093 +0.008203 0.991797 +0.000010 0.999990 +0.003683 0.996317 +0.000010 0.999990 +0.004048 0.995952 +0.013059 0.986941 +0.000010 0.999990 +0.003611 0.996389 +0.008446 0.991554 +0.010344 0.989656 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.002975 0.997025 +0.000010 0.999990 +0.000010 0.999990 +0.011356 0.988644 +0.009846 0.990154 +0.000010 0.999990 +0.014904 0.985096 +0.000010 0.999990 +0.000010 0.999990 +0.006080 0.993920 +0.002962 0.997038 +0.000010 0.999990 +0.019029 0.980971 +0.023705 0.976295 +0.007274 0.992726 +0.020705 0.979295 +0.000010 0.999990 +0.007263 0.992737 +0.000010 0.999990 +0.002493 0.997507 +0.118946 0.881054 +0.085755 0.914245 +0.092983 0.907017 +0.090256 0.909744 +0.013672 0.986328 +0.107102 0.892898 +0.007093 0.992907 +0.084252 0.915748 +0.081076 0.918924 +0.106763 0.893237 +0.000010 0.999990 +0.003748 0.996252 +0.000010 0.999990 +0.001760 0.998240 +0.000010 0.999990 +0.000010 0.999990 +0.009899 0.990101 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.003370 0.996630 +0.010866 0.989134 +0.000010 0.999990 +0.000010 0.999990 +0.012733 0.987267 +0.000256 0.999744 +0.012204 0.987796 +0.011660 0.988340 +0.000010 0.999990 +0.021586 0.978414 +0.006742 0.993258 +0.008764 0.991236 +0.998924 0.001076 +0.983557 0.016443 +0.979072 0.020928 +0.999990 0.000010 +0.980887 0.019113 +0.987236 0.012764 +0.994182 0.005818 +0.987743 0.012257 +0.001759 0.998241 +0.000010 0.999990 +0.003539 0.996461 +0.000712 0.999288 +0.008090 0.991910 +0.375731 0.624269 +0.280971 0.719029 +0.368096 0.631904 +0.363688 0.636312 +0.373066 0.626934 +0.007459 0.992541 +0.429276 0.570724 +0.427570 0.572430 +0.420283 0.579717 +0.376285 0.623715 +0.336802 0.663198 +0.340484 0.659516 +0.428986 0.571014 +0.415993 0.584007 +0.438262 0.561738 +0.428546 0.571454 +0.885661 0.114339 +0.979162 0.020838 +0.854839 0.145161 +0.845303 0.154697 +0.957872 0.042128 +0.843427 0.156573 +0.915795 0.084205 +0.858970 0.141030 +0.877905 0.122095 +0.863453 0.136547 +0.017844 0.982156 +0.011038 0.988962 +0.000010 0.999990 +0.762966 0.237034 +0.046008 0.953992 +0.010396 0.989604 +0.009741 0.990259 +0.021283 0.978717 +0.021002 0.978998 +0.793520 0.206480 +0.022256 0.977744 +0.011741 0.988259 +0.739613 0.260387 +0.006832 0.993168 +0.001399 0.998601 +0.018843 0.981157 +0.701044 0.298956 +0.934191 0.065809 +0.012387 0.987613 +0.930386 0.069614 +0.005134 0.994866 +0.024876 0.975124 +0.834953 0.165047 +0.831489 0.168511 +0.064057 0.935943 +0.000010 0.999990 +0.015731 0.984269 +0.022769 0.977231 +0.020998 0.979002 +0.007361 0.992639 +0.922408 0.077592 +0.857881 0.142119 +0.001853 0.998147 +0.007644 0.992356 +0.000010 0.999990 +0.032173 0.967827 +0.015762 0.984238 +0.017070 0.982930 +0.752750 0.247250 +0.006704 0.993296 +0.081630 0.918370 +0.041556 0.958444 +0.017264 0.982736 +0.000113 0.999887 +0.029783 0.970217 +0.788600 0.211400 +0.923221 0.076779 +0.000010 0.999990 +0.013698 0.986302 +0.940903 0.059097 +0.981095 0.018905 +0.032568 0.967432 +0.024273 0.975727 +0.016460 0.983540 +0.000010 0.999990 +0.000309 0.999691 +0.000010 0.999990 +0.000010 0.999990 +0.009025 0.990975 +0.009021 0.990979 +0.016584 0.983416 +0.016507 0.983493 +0.000010 0.999990 +0.010857 0.989143 +0.021035 0.978965 +0.000010 0.999990 +0.000010 0.999990 +0.007197 0.992803 +0.006811 0.993189 +0.000010 0.999990 +0.015880 0.984120 +0.005359 0.994641 +0.000010 0.999990 +0.008085 0.991915 +0.010392 0.989608 +0.017333 0.982667 +0.000010 0.999990 +0.002299 0.997701 +0.020364 0.979636 +0.128579 0.871421 +0.000010 0.999990 +0.009861 0.990139 +0.046527 0.953473 +0.000010 0.999990 +0.046279 0.953721 +0.854933 0.145067 +0.000010 0.999990 +0.006499 0.993501 +0.010899 0.989101 +0.010603 0.989397 +0.061164 0.938836 +0.044159 0.955841 +0.015014 0.984986 +0.110012 0.889988 +0.000010 0.999990 +0.053067 0.946933 +0.008146 0.991854 +0.022222 0.977778 +0.147615 0.852385 +0.015696 0.984304 +0.014420 0.985580 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.056566 0.943434 +0.064326 0.935674 +0.017851 0.982149 +0.012337 0.987663 +0.003375 0.996625 +0.005414 0.994586 +0.007458 0.992542 +0.022857 0.977143 +0.026528 0.973472 +0.124319 0.875681 +0.000010 0.999990 +0.005282 0.994718 +0.000010 0.999990 +0.047031 0.952969 +0.004808 0.995192 +0.041071 0.958929 +0.056482 0.943518 +0.001161 0.998839 +0.004575 0.995425 +0.059166 0.940834 +0.009543 0.990457 +0.018827 0.981173 +0.087898 0.912102 +0.000010 0.999990 +0.067979 0.932021 +0.000010 0.999990 +0.017631 0.982369 +0.007289 0.992711 +0.005233 0.994767 +0.061744 0.938256 +0.019819 0.980181 +0.005843 0.994157 +0.069160 0.930840 +0.141902 0.858098 +0.015322 0.984678 +0.058372 0.941628 +0.021536 0.978464 +0.016939 0.983061 +0.047840 0.952160 +0.019644 0.980356 +0.008345 0.991655 +0.026655 0.973345 +0.015316 0.984684 +0.065853 0.934147 +0.017545 0.982455 +0.021902 0.978098 +0.000010 0.999990 +0.017150 0.982850 +0.060982 0.939018 +0.015939 0.984061 +0.045261 0.954739 +0.017116 0.982884 +0.000010 0.999990 +0.047821 0.952179 +0.055596 0.944404 +0.003835 0.996165 +0.043440 0.956560 +0.023236 0.976764 +0.015621 0.984379 +0.002263 0.997737 +0.000097 0.999903 +0.061762 0.938238 +0.000750 0.999250 +0.008419 0.991581 +0.057071 0.942929 +0.000010 0.999990 +0.140798 0.859202 +0.007056 0.992944 +0.087757 0.912243 +0.005546 0.994454 +0.011406 0.988594 +0.022473 0.977527 +0.017477 0.982523 +0.017943 0.982057 +0.006106 0.993894 +0.000010 0.999990 +0.037591 0.962409 +0.048575 0.951425 +0.007120 0.992880 +0.023738 0.976262 +0.058103 0.941897 +0.000010 0.999990 +0.000010 0.999990 +0.018608 0.981392 +0.708502 0.291498 +0.056667 0.943333 +0.006798 0.993202 +0.026689 0.973311 +0.012466 0.987534 +0.000010 0.999990 +0.001699 0.998301 +0.006597 0.993403 +0.113426 0.886574 +0.053397 0.946603 +0.061568 0.938432 +0.059140 0.940860 +0.033016 0.966984 +0.017632 0.982368 +0.010068 0.989932 +0.006184 0.993816 +0.015190 0.984810 +0.008244 0.991756 +0.165715 0.834285 +0.023153 0.976847 +0.030967 0.969033 +0.696983 0.303017 +0.000010 0.999990 +0.025608 0.974392 +0.021272 0.978728 +0.000010 0.999990 +0.073048 0.926952 +0.153863 0.846137 +0.087788 0.912212 +0.144776 0.855224 +0.096355 0.903645 +0.075118 0.924882 +0.175696 0.824304 +0.112188 0.887812 +0.001278 0.998722 +0.681658 0.318342 +0.051190 0.948810 +0.713065 0.286935 +0.000010 0.999990 +0.014099 0.985901 +0.052713 0.947287 +0.701591 0.298409 +0.029248 0.970752 +0.121796 0.878204 +0.060402 0.939598 +0.155841 0.844159 +0.162542 0.837458 +0.091277 0.908723 +0.029214 0.970786 +0.000010 0.999990 +0.134714 0.865286 +0.698270 0.301730 +0.100421 0.899579 +0.091723 0.908277 +0.029824 0.970176 +0.081849 0.918151 +0.000010 0.999990 +0.094227 0.905773 +0.098937 0.901063 +0.002315 0.997685 +0.075718 0.924282 +0.054068 0.945932 +0.020651 0.979349 +0.056504 0.943496 +0.675849 0.324151 +0.058223 0.941777 +0.175464 0.824536 +0.153668 0.846332 +0.146133 0.853867 +0.062613 0.937387 +0.681573 0.318427 +0.152224 0.847776 +0.000010 0.999990 +0.127466 0.872534 +0.710462 0.289538 +0.087236 0.912764 +0.060247 0.939753 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.087592 0.912408 +0.000010 0.999990 +0.046795 0.953205 +0.066227 0.933773 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.035763 0.964237 diff --git a/inst/files/admixture/admixture_08 b/inst/files/admixture/admixture_08 new file mode 100644 index 0000000..3b25ccd --- /dev/null +++ b/inst/files/admixture/admixture_08 @@ -0,0 +1,1592 @@ +0.942995 0.057005 +0.950609 0.049391 +0.972208 0.027792 +0.943619 0.056381 +0.931674 0.068326 +0.944011 0.055989 +0.926197 0.073803 +0.976136 0.023864 +0.950896 0.049104 +0.928412 0.071588 +0.947400 0.052600 +0.932082 0.067918 +0.946954 0.053046 +0.983766 0.016234 +0.946589 0.053411 +0.969502 0.030498 +0.922055 0.077945 +0.894128 0.105872 +0.943422 0.056578 +0.954252 0.045748 +0.947033 0.052967 +0.999714 0.000286 +0.946819 0.053181 +0.954604 0.045396 +0.909505 0.090495 +0.940332 0.059668 +0.639082 0.360918 +0.622274 0.377726 +0.616732 0.383268 +0.642448 0.357552 +0.641160 0.358840 +0.641540 0.358460 +0.627042 0.372958 +0.657607 0.342393 +0.621644 0.378356 +0.648931 0.351069 +0.634822 0.365178 +0.679026 0.320974 +0.626667 0.373333 +0.619516 0.380484 +0.646198 0.353802 +0.654603 0.345397 +0.573052 0.426948 +0.985093 0.014907 +0.602255 0.397745 +0.587243 0.412757 +0.643819 0.356181 +0.972257 0.027743 +0.581180 0.418820 +0.644561 0.355439 +0.164249 0.835751 +0.162269 0.837731 +0.167845 0.832155 +0.151826 0.848174 +0.164632 0.835368 +0.155068 0.844932 +0.151798 0.848202 +0.181025 0.818975 +0.142317 0.857683 +0.155926 0.844074 +0.148766 0.851234 +0.165721 0.834279 +0.159381 0.840619 +0.150911 0.849089 +0.168392 0.831608 +0.150043 0.849957 +0.201719 0.798281 +0.147663 0.852337 +0.151050 0.848950 +0.148403 0.851597 +0.159187 0.840813 +0.153258 0.846742 +0.122765 0.877235 +0.213415 0.786585 +0.194961 0.805039 +0.132046 0.867954 +0.134036 0.865964 +0.141651 0.858349 +0.198573 0.801427 +0.149309 0.850691 +0.144015 0.855985 +0.131570 0.868430 +0.133412 0.866588 +0.149753 0.850247 +0.134842 0.865158 +0.141232 0.858768 +0.191372 0.808628 +0.186282 0.813718 +0.185707 0.814293 +0.163154 0.836846 +0.179260 0.820740 +0.571463 0.428537 +0.578038 0.421962 +0.541042 0.458958 +0.560782 0.439218 +0.523809 0.476191 +0.562594 0.437406 +0.553884 0.446116 +0.543402 0.456598 +0.534429 0.465571 +0.560314 0.439686 +0.558593 0.441407 +0.527709 0.472291 +0.553371 0.446629 +0.543995 0.456005 +0.119574 0.880426 +0.120956 0.879044 +0.136804 0.863196 +0.133869 0.866131 +0.142549 0.857451 +0.122443 0.877557 +0.153973 0.846027 +0.134830 0.865170 +0.133720 0.866280 +0.134511 0.865489 +0.122410 0.877590 +0.150112 0.849888 +0.126873 0.873127 +0.134195 0.865805 +0.125169 0.874831 +0.140623 0.859377 +0.139578 0.860422 +0.134243 0.865757 +0.138198 0.861802 +0.137962 0.862038 +0.240188 0.759812 +0.241234 0.758766 +0.222397 0.777603 +0.210561 0.789439 +0.219999 0.780001 +0.238631 0.761369 +0.207886 0.792114 +0.223897 0.776103 +0.222110 0.777890 +0.237594 0.762406 +0.246692 0.753308 +0.247636 0.752364 +0.243291 0.756709 +0.220667 0.779333 +0.211611 0.788389 +0.274211 0.725789 +0.240787 0.759213 +0.241614 0.758386 +0.154886 0.845114 +0.236905 0.763095 +0.192030 0.807970 +0.223978 0.776022 +0.193600 0.806400 +0.211718 0.788282 +0.225955 0.774045 +0.210629 0.789371 +0.233264 0.766736 +0.176103 0.823897 +0.168992 0.831008 +0.215410 0.784590 +0.216387 0.783613 +0.222145 0.777855 +0.189505 0.810495 +0.231347 0.768653 +0.177212 0.822788 +0.196519 0.803481 +0.231271 0.768729 +0.185412 0.814588 +0.170804 0.829196 +0.190611 0.809389 +0.175766 0.824234 +0.195705 0.804295 +0.186995 0.813005 +0.189301 0.810699 +0.174363 0.825637 +0.191334 0.808666 +0.192460 0.807540 +0.199432 0.800568 +0.217484 0.782516 +0.203554 0.796446 +0.176466 0.823534 +0.181714 0.818286 +0.197697 0.802303 +0.197211 0.802789 +0.188035 0.811965 +0.314655 0.685345 +0.285147 0.714853 +0.319774 0.680226 +0.309741 0.690259 +0.296054 0.703946 +0.300771 0.699229 +0.318884 0.681116 +0.288333 0.711667 +0.320885 0.679115 +0.328158 0.671842 +0.298413 0.701587 +0.292423 0.707577 +0.309995 0.690005 +0.299384 0.700616 +0.321439 0.678561 +0.304927 0.695073 +0.307185 0.692815 +0.314489 0.685511 +0.284032 0.715968 +0.284324 0.715676 +0.306208 0.693792 +0.295563 0.704437 +0.305400 0.694600 +0.000010 0.999990 +0.007281 0.992719 +0.018005 0.981995 +0.018397 0.981603 +0.000805 0.999195 +0.007315 0.992685 +0.000010 0.999990 +0.010807 0.989193 +0.000010 0.999990 +0.002709 0.997291 +0.002519 0.997481 +0.000010 0.999990 +0.006906 0.993094 +0.013072 0.986928 +0.021639 0.978361 +0.002534 0.997466 +0.017686 0.982314 +0.000649 0.999351 +0.020842 0.979158 +0.012251 0.987749 +0.016319 0.983681 +0.017077 0.982923 +0.000010 0.999990 +0.015193 0.984807 +0.013065 0.986935 +0.008775 0.991225 +0.000010 0.999990 +0.018078 0.981922 +0.000010 0.999990 +0.014982 0.985018 +0.014962 0.985038 +0.013217 0.986783 +0.001860 0.998140 +0.011006 0.988994 +0.018212 0.981788 +0.002353 0.997647 +0.013871 0.986129 +0.006293 0.993707 +0.019067 0.980933 +0.019598 0.980402 +0.006948 0.993052 +0.000010 0.999990 +0.002767 0.997233 +0.021753 0.978247 +0.019081 0.980919 +0.000010 0.999990 +0.013589 0.986411 +0.030431 0.969569 +0.008318 0.991682 +0.000010 0.999990 +0.019501 0.980499 +0.001110 0.998890 +0.014468 0.985532 +0.014519 0.985481 +0.006192 0.993808 +0.011596 0.988404 +0.009586 0.990414 +0.005238 0.994762 +0.000010 0.999990 +0.019040 0.980960 +0.006968 0.993032 +0.028240 0.971760 +0.012197 0.987803 +0.019414 0.980586 +0.025213 0.974787 +0.009685 0.990315 +0.037480 0.962520 +0.005901 0.994099 +0.061979 0.938021 +0.013382 0.986618 +0.035431 0.964569 +0.040886 0.959114 +0.038555 0.961445 +0.019489 0.980511 +0.012195 0.987805 +0.032679 0.967321 +0.040318 0.959682 +0.031612 0.968388 +0.021638 0.978362 +0.009473 0.990527 +0.036827 0.963173 +0.036646 0.963354 +0.048283 0.951717 +0.035199 0.964801 +0.008646 0.991354 +0.001855 0.998145 +0.043275 0.956725 +0.047952 0.952048 +0.049620 0.950380 +0.026709 0.973291 +0.040982 0.959018 +0.051989 0.948011 +0.022620 0.977380 +0.052563 0.947437 +0.013935 0.986065 +0.019552 0.980448 +0.011597 0.988403 +0.026092 0.973908 +0.037376 0.962624 +0.049630 0.950370 +0.043179 0.956821 +0.021794 0.978206 +0.012212 0.987788 +0.018542 0.981458 +0.023346 0.976654 +0.022687 0.977313 +0.042101 0.957899 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.035634 0.964366 +0.021804 0.978196 +0.018228 0.981772 +0.023758 0.976242 +0.040496 0.959504 +0.048059 0.951941 +0.038407 0.961593 +0.033230 0.966770 +0.046240 0.953760 +0.011119 0.988881 +0.026206 0.973794 +0.017391 0.982609 +0.023035 0.976965 +0.039899 0.960101 +0.006370 0.993630 +0.021977 0.978023 +0.024581 0.975419 +0.027461 0.972539 +0.013267 0.986733 +0.034596 0.965404 +0.015887 0.984113 +0.890153 0.109847 +0.933520 0.066480 +0.870529 0.129471 +0.929497 0.070503 +0.891075 0.108925 +0.930078 0.069922 +0.901775 0.098225 +0.880743 0.119257 +0.032139 0.967861 +0.024051 0.975949 +0.033764 0.966236 +0.027322 0.972678 +0.028574 0.971426 +0.026645 0.973355 +0.034956 0.965044 +0.039772 0.960228 +0.021937 0.978063 +0.026404 0.973596 +0.037409 0.962591 +0.025125 0.974875 +0.036361 0.963639 +0.026498 0.973502 +0.042642 0.957358 +0.033494 0.966506 +0.024775 0.975225 +0.059867 0.940133 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.023971 0.976029 +0.025440 0.974560 +0.017796 0.982204 +0.009748 0.990252 +0.021780 0.978220 +0.022224 0.977776 +0.009652 0.990348 +0.009357 0.990643 +0.015814 0.984186 +0.000010 0.999990 +0.005174 0.994826 +0.013307 0.986693 +0.000010 0.999990 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.093060 0.906940 +0.105193 0.894807 +0.136446 0.863554 +0.114488 0.885512 +0.075223 0.924777 +0.116199 0.883801 +0.088111 0.911889 +0.096470 0.903530 +0.111890 0.888110 +0.114616 0.885384 +0.112163 0.887837 +0.120313 0.879687 +0.114269 0.885731 +0.136636 0.863364 +0.119261 0.880739 +0.107158 0.892842 +0.124955 0.875045 +0.103486 0.896514 +0.080137 0.919863 +0.114810 0.885190 +0.122908 0.877092 +0.108452 0.891548 +0.899951 0.100049 +0.900652 0.099348 +0.872189 0.127811 +0.826736 0.173264 +0.814660 0.185340 +0.911389 0.088611 +0.890804 0.109196 +0.907690 0.092310 +0.924602 0.075398 +0.906416 0.093584 +0.843808 0.156192 +0.931406 0.068594 +0.894713 0.105287 +0.915845 0.084155 +0.901115 0.098885 +0.883824 0.116176 +0.904707 0.095293 +0.870585 0.129415 +0.901530 0.098470 +0.857796 0.142204 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.006742 0.993258 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.010337 0.989663 +0.002162 0.997838 +0.007624 0.992376 +0.000010 0.999990 +0.005011 0.994989 +0.000010 0.999990 +0.000010 0.999990 +0.001660 0.998340 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.996358 0.003642 +0.999990 0.000010 +0.999990 0.000010 +0.998607 0.001393 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.983815 0.016185 +0.969365 0.030635 +0.975583 0.024417 +0.970023 0.029977 +0.999990 0.000010 +0.999990 0.000010 +0.995764 0.004236 +0.964236 0.035764 +0.991261 0.008739 +0.958045 0.041955 +0.956321 0.043679 +0.971256 0.028744 +0.969817 0.030183 +0.980639 0.019361 +0.985133 0.014867 +0.979998 0.020002 +0.984587 0.015413 +0.961036 0.038964 +0.976192 0.023808 +0.943347 0.056653 +0.971128 0.028872 +0.981979 0.018021 +0.953968 0.046032 +0.999990 0.000010 +0.980509 0.019491 +0.998123 0.001877 +0.980913 0.019087 +0.989281 0.010719 +0.999990 0.000010 +0.997481 0.002519 +0.998994 0.001006 +0.966571 0.033429 +0.978865 0.021135 +0.992114 0.007886 +0.930644 0.069356 +0.982495 0.017505 +0.952298 0.047702 +0.999990 0.000010 +0.053647 0.946353 +0.046206 0.953794 +0.044773 0.955227 +0.059369 0.940631 +0.050422 0.949578 +0.038296 0.961704 +0.067024 0.932976 +0.067908 0.932092 +0.031469 0.968531 +0.043506 0.956494 +0.040867 0.959133 +0.044845 0.955155 +0.046174 0.953826 +0.067780 0.932220 +0.054658 0.945342 +0.062993 0.937007 +0.060365 0.939635 +0.041359 0.958641 +0.058456 0.941544 +0.033677 0.966323 +0.035411 0.964589 +0.993567 0.006433 +0.987974 0.012026 +0.989769 0.010231 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.986429 0.013571 +0.999990 0.000010 +0.998264 0.001736 +0.972237 0.027763 +0.521852 0.478148 +0.496525 0.503475 +0.562437 0.437563 +0.519227 0.480773 +0.543730 0.456270 +0.629575 0.370425 +0.499000 0.501000 +0.613211 0.386789 +0.582066 0.417934 +0.566926 0.433074 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999903 0.000097 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.945661 0.054339 +0.924130 0.075870 +0.963229 0.036771 +0.922556 0.077444 +0.949536 0.050464 +0.955558 0.044442 +0.925347 0.074653 +0.956830 0.043170 +0.955265 0.044735 +0.929180 0.070820 +0.000010 0.999990 +0.001079 0.998921 +0.007028 0.992972 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.013131 0.986869 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.107710 0.892290 +0.054189 0.945811 +0.066879 0.933121 +0.082428 0.917572 +0.062449 0.937551 +0.050110 0.949890 +0.109156 0.890844 +0.090137 0.909863 +0.055603 0.944397 +0.056879 0.943121 +0.062759 0.937241 +0.074187 0.925813 +0.068075 0.931925 +0.042522 0.957478 +0.108144 0.891856 +0.916029 0.083971 +0.926130 0.073870 +0.936489 0.063511 +0.924070 0.075930 +0.928402 0.071598 +0.929964 0.070036 +0.958493 0.041507 +0.954640 0.045360 +0.969512 0.030488 +0.948042 0.051958 +0.935469 0.064531 +0.943302 0.056698 +0.927937 0.072063 +0.953663 0.046337 +0.952809 0.047191 +0.927056 0.072944 +0.935009 0.064991 +0.959238 0.040762 +0.947772 0.052228 +0.961622 0.038378 +0.923089 0.076911 +0.943531 0.056469 +0.955491 0.044509 +0.964112 0.035888 +0.972758 0.027242 +0.938893 0.061107 +0.950505 0.049495 +0.688179 0.311821 +0.682066 0.317934 +0.679279 0.320721 +0.682138 0.317862 +0.680368 0.319632 +0.670708 0.329292 +0.688973 0.311027 +0.692555 0.307445 +0.667268 0.332732 +0.691929 0.308071 +0.679038 0.320962 +0.403731 0.596269 +0.435276 0.564724 +0.440756 0.559244 +0.437255 0.562745 +0.448806 0.551194 +0.433304 0.566696 +0.437957 0.562043 +0.443802 0.556198 +0.430225 0.569775 +0.446053 0.553947 +0.445023 0.554977 +0.457956 0.542044 +0.452683 0.547317 +0.278725 0.721275 +0.288449 0.711551 +0.293124 0.706876 +0.278518 0.721482 +0.244895 0.755105 +0.295911 0.704089 +0.285911 0.714089 +0.276733 0.723267 +0.283050 0.716950 +0.272386 0.727614 +0.281185 0.718815 +0.271408 0.728592 +0.293268 0.706732 +0.277626 0.722374 +0.280879 0.719121 +0.656462 0.343538 +0.646240 0.353760 +0.642606 0.357394 +0.649153 0.350847 +0.642710 0.357290 +0.652111 0.347889 +0.635522 0.364478 +0.640284 0.359716 +0.649382 0.350618 +0.652478 0.347522 +0.634084 0.365916 +0.636849 0.363151 +0.364422 0.635578 +0.406176 0.593824 +0.375817 0.624183 +0.395043 0.604957 +0.403163 0.596837 +0.378892 0.621108 +0.367651 0.632349 +0.380010 0.619990 +0.351597 0.648403 +0.377211 0.622789 +0.369394 0.630606 +0.375444 0.624556 +0.379532 0.620468 +0.418829 0.581171 +0.406182 0.593818 +0.413878 0.586122 +0.426317 0.573683 +0.397196 0.602804 +0.403358 0.596642 +0.391069 0.608931 +0.422159 0.577841 +0.425521 0.574479 +0.422347 0.577653 +0.398456 0.601544 +0.437919 0.562081 +0.413303 0.586697 +0.234834 0.765166 +0.062047 0.937953 +0.044291 0.955709 +0.067708 0.932292 +0.039766 0.960234 +0.055759 0.944241 +0.023616 0.976384 +0.019272 0.980728 +0.000010 0.999990 +0.119522 0.880478 +0.048843 0.951157 +0.027404 0.972596 +0.033587 0.966413 +0.025517 0.974483 +0.065486 0.934514 +0.042882 0.957118 +0.040343 0.959657 +0.123885 0.876115 +0.014449 0.985551 +0.037702 0.962298 +0.007714 0.992286 +0.020104 0.979896 +0.014108 0.985892 +0.020520 0.979480 +0.013370 0.986630 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.014171 0.985829 +0.000827 0.999173 +0.010724 0.989276 +0.005603 0.994397 +0.003214 0.996786 +0.000010 0.999990 +0.010881 0.989119 +0.000010 0.999990 +0.002910 0.997090 +0.012543 0.987457 +0.015550 0.984450 +0.009790 0.990210 +0.012542 0.987458 +0.005717 0.994283 +0.010601 0.989399 +0.015299 0.984701 +0.021493 0.978507 +0.013900 0.986100 +0.033302 0.966698 +0.071907 0.928093 +0.104826 0.895174 +0.065305 0.934695 +0.034289 0.965711 +0.024534 0.975466 +0.000304 0.999696 +0.024837 0.975163 +0.018485 0.981515 +0.011372 0.988628 +0.084779 0.915221 +0.094336 0.905664 +0.000010 0.999990 +0.076924 0.923076 +0.003496 0.996504 +0.032448 0.967552 +0.098972 0.901028 +0.032290 0.967710 +0.026015 0.973985 +0.032646 0.967354 +0.036530 0.963470 +0.034089 0.965911 +0.062410 0.937590 +0.029226 0.970774 +0.033585 0.966415 +0.028507 0.971493 +0.011768 0.988232 +0.105712 0.894288 +0.010721 0.989279 +0.037765 0.962235 +0.011950 0.988050 +0.041664 0.958336 +0.050393 0.949607 +0.010969 0.989031 +0.059864 0.940136 +0.017637 0.982363 +0.040985 0.959015 +0.003975 0.996025 +0.035971 0.964029 +0.020366 0.979634 +0.031151 0.968849 +0.025379 0.974621 +0.076797 0.923203 +0.065878 0.934122 +0.005169 0.994831 +0.011624 0.988376 +0.051868 0.948132 +0.087421 0.912579 +0.027073 0.972927 +0.011613 0.988387 +0.022731 0.977269 +0.035769 0.964231 +0.034543 0.965457 +0.081944 0.918056 +0.024013 0.975987 +0.014623 0.985377 +0.015339 0.984661 +0.043694 0.956306 +0.006323 0.993677 +0.028206 0.971794 +0.029278 0.970722 +0.070137 0.929863 +0.049412 0.950588 +0.095862 0.904138 +0.050233 0.949767 +0.013732 0.986268 +0.063812 0.936188 +0.049912 0.950088 +0.002551 0.997449 +0.019422 0.980578 +0.013737 0.986263 +0.055526 0.944474 +0.057480 0.942520 +0.058326 0.941674 +0.043537 0.956463 +0.019715 0.980285 +0.055654 0.944346 +0.043860 0.956140 +0.027958 0.972042 +0.094169 0.905831 +0.125198 0.874802 +0.023811 0.976189 +0.102121 0.897879 +0.056789 0.943211 +0.029229 0.970771 +0.007006 0.992994 +0.058259 0.941741 +0.234466 0.765534 +0.077839 0.922161 +0.111367 0.888633 +0.025472 0.974528 +0.105076 0.894924 +0.066960 0.933040 +0.045881 0.954119 +0.041018 0.958982 +0.021218 0.978782 +0.065315 0.934685 +0.087148 0.912852 +0.288301 0.711699 +0.225466 0.774534 +0.094917 0.905083 +0.010976 0.989024 +0.012087 0.987913 +0.121691 0.878309 +0.056447 0.943553 +0.041664 0.958336 +0.019794 0.980206 +0.015096 0.984904 +0.315416 0.684584 +0.816178 0.183822 +0.104434 0.895566 +0.018233 0.981767 +0.002190 0.997810 +0.108680 0.891320 +0.051942 0.948058 +0.042551 0.957449 +0.016728 0.983272 +0.016654 0.983346 +0.046457 0.953543 +0.087097 0.912903 +0.369176 0.630824 +0.821047 0.178953 +0.112244 0.887756 +0.028382 0.971618 +0.113530 0.886470 +0.097106 0.902894 +0.043022 0.956978 +0.029561 0.970439 +0.019518 0.980482 +0.070250 0.929750 +0.060085 0.939915 +0.064935 0.935065 +0.256404 0.743596 +0.793961 0.206039 +0.119560 0.880440 +0.013296 0.986704 +0.100684 0.899316 +0.106224 0.893776 +0.075733 0.924267 +0.027707 0.972293 +0.003712 0.996288 +0.048702 0.951298 +0.066386 0.933614 +0.080073 0.919927 +0.250534 0.749466 +0.838876 0.161124 +0.088527 0.911473 +0.010447 0.989553 +0.102153 0.897847 +0.063749 0.936251 +0.030427 0.969573 +0.000010 0.999990 +0.063098 0.936902 +0.017069 0.982931 +0.100887 0.899113 +0.239285 0.760715 +0.818010 0.181990 +0.088408 0.911592 +0.031528 0.968472 +0.084008 0.915992 +0.060874 0.939126 +0.044187 0.955813 +0.021228 0.978772 +0.020183 0.979817 +0.067849 0.932151 +0.093985 0.906015 +0.102083 0.897917 +0.259465 0.740535 +0.832381 0.167619 +0.859554 0.140446 +0.754493 0.245507 +0.839641 0.160359 +0.937481 0.062519 +0.700953 0.299047 +0.033120 0.966880 +0.028234 0.971766 +0.042582 0.957418 +0.103840 0.896160 +0.263980 0.736020 +0.451188 0.548812 +0.836593 0.163407 +0.738626 0.261374 +0.821180 0.178820 +0.792487 0.207513 +0.021549 0.978451 +0.045846 0.954154 +0.070595 0.929405 +0.106464 0.893536 +0.295802 0.704198 +0.493811 0.506189 +0.821306 0.178694 +0.745401 0.254599 +0.872078 0.127922 +0.876815 0.123185 +0.054195 0.945805 +0.051617 0.948383 +0.047877 0.952123 +0.125739 0.874261 +0.283573 0.716427 +0.447326 0.552674 +0.819179 0.180821 +0.835981 0.164019 +0.561191 0.438809 +0.703569 0.296431 +0.026804 0.973196 +0.062184 0.937816 +0.125999 0.874001 +0.088069 0.911931 +0.265328 0.734672 +0.562943 0.437057 +0.724459 0.275541 +0.849825 0.150175 +0.840571 0.159429 +0.377242 0.622758 +0.676102 0.323898 +0.048137 0.951863 +0.042388 0.957612 +0.089005 0.910995 +0.092779 0.907221 +0.283041 0.716959 +0.461097 0.538903 +0.758980 0.241020 +0.866936 0.133064 +0.856254 0.143746 +0.659239 0.340761 +0.049816 0.950184 +0.100525 0.899475 +0.243328 0.756672 +0.288660 0.711340 +0.333704 0.666296 +0.721441 0.278559 +0.852941 0.147059 +0.843657 0.156343 +0.609138 0.390862 +0.048202 0.951798 +0.048536 0.951464 +0.105441 0.894559 +0.279806 0.720194 +0.238312 0.761688 +0.326365 0.673635 +0.774015 0.225985 +0.810488 0.189512 +0.791352 0.208648 +0.768858 0.231142 +0.045181 0.954819 +0.028563 0.971437 +0.039943 0.960057 +0.083856 0.916144 +0.250848 0.749152 +0.503155 0.496845 +0.351878 0.648122 +0.447070 0.552930 +0.170834 0.829166 +0.149689 0.850311 +0.147954 0.852046 +0.411469 0.588531 +0.206505 0.793495 +0.157637 0.842363 +0.358446 0.641554 +0.197652 0.802348 +0.253773 0.746227 +0.021560 0.978440 +0.198816 0.801184 +0.308357 0.691643 +0.064132 0.935868 +0.480029 0.519971 +0.179315 0.820685 +0.320447 0.679553 +0.320347 0.679653 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.025792 0.974208 +0.015979 0.984021 +0.043829 0.956171 +0.014264 0.985736 +0.000010 0.999990 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.021451 0.978549 +0.022451 0.977549 +0.012371 0.987629 +0.022572 0.977428 +0.000010 0.999990 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.019429 0.980571 +0.028695 0.971305 +0.012926 0.987074 +0.005192 0.994808 +0.025458 0.974542 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.026477 0.973523 +0.000010 0.999990 +0.000010 0.999990 +0.023325 0.976675 +0.006089 0.993911 +0.999990 0.000010 +0.999990 0.000010 +0.108447 0.891553 +0.023298 0.976702 +0.017906 0.982094 +0.014235 0.985765 +0.021009 0.978991 +0.011474 0.988526 +0.999990 0.000010 +0.999990 0.000010 +0.015776 0.984224 +0.035729 0.964271 +0.032836 0.967164 +0.000010 0.999990 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.067630 0.932370 +0.027316 0.972684 +0.001419 0.998581 +0.022088 0.977912 +0.008763 0.991237 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.025400 0.974600 +0.008078 0.991922 +0.013161 0.986839 +0.023243 0.976757 +0.008672 0.991328 +0.999990 0.000010 +0.015501 0.984499 +0.012953 0.987047 +0.012580 0.987420 +0.018097 0.981903 +0.000010 0.999990 +0.000010 0.999990 +0.008907 0.991093 +0.008203 0.991797 +0.000010 0.999990 +0.003683 0.996317 +0.000010 0.999990 +0.004048 0.995952 +0.013059 0.986941 +0.000010 0.999990 +0.003611 0.996389 +0.008446 0.991554 +0.010345 0.989655 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.002975 0.997025 +0.000010 0.999990 +0.000010 0.999990 +0.011356 0.988644 +0.009847 0.990153 +0.000010 0.999990 +0.014904 0.985096 +0.000010 0.999990 +0.000010 0.999990 +0.006081 0.993919 +0.002962 0.997038 +0.000010 0.999990 +0.019029 0.980971 +0.023705 0.976295 +0.007274 0.992726 +0.020705 0.979295 +0.000010 0.999990 +0.007263 0.992737 +0.000010 0.999990 +0.002493 0.997507 +0.118946 0.881054 +0.085755 0.914245 +0.092983 0.907017 +0.090256 0.909744 +0.013672 0.986328 +0.107102 0.892898 +0.007093 0.992907 +0.084252 0.915748 +0.081077 0.918923 +0.106764 0.893236 +0.000010 0.999990 +0.003748 0.996252 +0.000010 0.999990 +0.001760 0.998240 +0.000010 0.999990 +0.000010 0.999990 +0.009899 0.990101 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.003370 0.996630 +0.010866 0.989134 +0.000010 0.999990 +0.000010 0.999990 +0.012733 0.987267 +0.000256 0.999744 +0.012204 0.987796 +0.011660 0.988340 +0.000010 0.999990 +0.021586 0.978414 +0.006742 0.993258 +0.008764 0.991236 +0.998924 0.001076 +0.983557 0.016443 +0.979072 0.020928 +0.999990 0.000010 +0.980887 0.019113 +0.987236 0.012764 +0.994182 0.005818 +0.987743 0.012257 +0.001759 0.998241 +0.000010 0.999990 +0.003539 0.996461 +0.000712 0.999288 +0.008090 0.991910 +0.375731 0.624269 +0.280971 0.719029 +0.368096 0.631904 +0.363688 0.636312 +0.373066 0.626934 +0.007459 0.992541 +0.429276 0.570724 +0.427571 0.572429 +0.420283 0.579717 +0.376285 0.623715 +0.336802 0.663198 +0.340484 0.659516 +0.428987 0.571013 +0.415993 0.584007 +0.438262 0.561738 +0.428546 0.571454 +0.885661 0.114339 +0.979162 0.020838 +0.854839 0.145161 +0.845303 0.154697 +0.957872 0.042128 +0.843427 0.156573 +0.915795 0.084205 +0.858970 0.141030 +0.877905 0.122095 +0.863453 0.136547 +0.017844 0.982156 +0.011038 0.988962 +0.000010 0.999990 +0.762966 0.237034 +0.046008 0.953992 +0.010396 0.989604 +0.009741 0.990259 +0.021283 0.978717 +0.021002 0.978998 +0.793520 0.206480 +0.022256 0.977744 +0.011741 0.988259 +0.739613 0.260387 +0.006832 0.993168 +0.001399 0.998601 +0.018843 0.981157 +0.701044 0.298956 +0.934191 0.065809 +0.012387 0.987613 +0.930387 0.069613 +0.005134 0.994866 +0.024876 0.975124 +0.834953 0.165047 +0.831489 0.168511 +0.064057 0.935943 +0.000010 0.999990 +0.015731 0.984269 +0.022769 0.977231 +0.020999 0.979001 +0.007361 0.992639 +0.922408 0.077592 +0.857881 0.142119 +0.001853 0.998147 +0.007644 0.992356 +0.000010 0.999990 +0.032173 0.967827 +0.015763 0.984237 +0.017070 0.982930 +0.752750 0.247250 +0.006704 0.993296 +0.081630 0.918370 +0.041556 0.958444 +0.017264 0.982736 +0.000113 0.999887 +0.029784 0.970216 +0.788600 0.211400 +0.923221 0.076779 +0.000010 0.999990 +0.013698 0.986302 +0.940903 0.059097 +0.981095 0.018905 +0.032568 0.967432 +0.024273 0.975727 +0.016460 0.983540 +0.000010 0.999990 +0.000309 0.999691 +0.000010 0.999990 +0.000010 0.999990 +0.009025 0.990975 +0.009021 0.990979 +0.016584 0.983416 +0.016507 0.983493 +0.000010 0.999990 +0.010857 0.989143 +0.021035 0.978965 +0.000010 0.999990 +0.000010 0.999990 +0.007197 0.992803 +0.006811 0.993189 +0.000010 0.999990 +0.015880 0.984120 +0.005359 0.994641 +0.000010 0.999990 +0.008085 0.991915 +0.010392 0.989608 +0.017333 0.982667 +0.000010 0.999990 +0.002299 0.997701 +0.020364 0.979636 +0.128579 0.871421 +0.000010 0.999990 +0.009861 0.990139 +0.046527 0.953473 +0.000010 0.999990 +0.046279 0.953721 +0.854933 0.145067 +0.000010 0.999990 +0.006499 0.993501 +0.010899 0.989101 +0.010603 0.989397 +0.061164 0.938836 +0.044159 0.955841 +0.015014 0.984986 +0.110012 0.889988 +0.000010 0.999990 +0.053067 0.946933 +0.008146 0.991854 +0.022222 0.977778 +0.147615 0.852385 +0.015696 0.984304 +0.014420 0.985580 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.056566 0.943434 +0.064326 0.935674 +0.017851 0.982149 +0.012337 0.987663 +0.003375 0.996625 +0.005414 0.994586 +0.007458 0.992542 +0.022857 0.977143 +0.026528 0.973472 +0.124320 0.875680 +0.000010 0.999990 +0.005282 0.994718 +0.000010 0.999990 +0.047031 0.952969 +0.004808 0.995192 +0.041071 0.958929 +0.056482 0.943518 +0.001161 0.998839 +0.004575 0.995425 +0.059166 0.940834 +0.009543 0.990457 +0.018827 0.981173 +0.087898 0.912102 +0.000010 0.999990 +0.067979 0.932021 +0.000010 0.999990 +0.017631 0.982369 +0.007289 0.992711 +0.005233 0.994767 +0.061744 0.938256 +0.019819 0.980181 +0.005843 0.994157 +0.069160 0.930840 +0.141902 0.858098 +0.015322 0.984678 +0.058372 0.941628 +0.021536 0.978464 +0.016940 0.983060 +0.047840 0.952160 +0.019644 0.980356 +0.008345 0.991655 +0.026655 0.973345 +0.015316 0.984684 +0.065853 0.934147 +0.017545 0.982455 +0.021902 0.978098 +0.000010 0.999990 +0.017150 0.982850 +0.060982 0.939018 +0.015939 0.984061 +0.045261 0.954739 +0.017116 0.982884 +0.000010 0.999990 +0.047821 0.952179 +0.055596 0.944404 +0.003835 0.996165 +0.043440 0.956560 +0.023236 0.976764 +0.015621 0.984379 +0.002263 0.997737 +0.000097 0.999903 +0.061762 0.938238 +0.000750 0.999250 +0.008419 0.991581 +0.057071 0.942929 +0.000010 0.999990 +0.140798 0.859202 +0.007056 0.992944 +0.087757 0.912243 +0.005546 0.994454 +0.011406 0.988594 +0.022473 0.977527 +0.017477 0.982523 +0.017943 0.982057 +0.006106 0.993894 +0.000010 0.999990 +0.037591 0.962409 +0.048575 0.951425 +0.007120 0.992880 +0.023738 0.976262 +0.058103 0.941897 +0.000010 0.999990 +0.000010 0.999990 +0.018608 0.981392 +0.708502 0.291498 +0.056667 0.943333 +0.006798 0.993202 +0.026690 0.973310 +0.012466 0.987534 +0.000010 0.999990 +0.001699 0.998301 +0.006597 0.993403 +0.113426 0.886574 +0.053397 0.946603 +0.061568 0.938432 +0.059140 0.940860 +0.033016 0.966984 +0.017632 0.982368 +0.010069 0.989931 +0.006184 0.993816 +0.015191 0.984809 +0.008244 0.991756 +0.165715 0.834285 +0.023153 0.976847 +0.030967 0.969033 +0.696983 0.303017 +0.000010 0.999990 +0.025608 0.974392 +0.021272 0.978728 +0.000010 0.999990 +0.073048 0.926952 +0.153864 0.846136 +0.087788 0.912212 +0.144777 0.855223 +0.096355 0.903645 +0.075118 0.924882 +0.175696 0.824304 +0.112188 0.887812 +0.001278 0.998722 +0.681658 0.318342 +0.051190 0.948810 +0.713065 0.286935 +0.000010 0.999990 +0.014099 0.985901 +0.052714 0.947286 +0.701591 0.298409 +0.029248 0.970752 +0.121796 0.878204 +0.060402 0.939598 +0.155841 0.844159 +0.162542 0.837458 +0.091277 0.908723 +0.029214 0.970786 +0.000010 0.999990 +0.134714 0.865286 +0.698270 0.301730 +0.100421 0.899579 +0.091723 0.908277 +0.029824 0.970176 +0.081849 0.918151 +0.000010 0.999990 +0.094227 0.905773 +0.098937 0.901063 +0.002315 0.997685 +0.075718 0.924282 +0.054068 0.945932 +0.020651 0.979349 +0.056504 0.943496 +0.675849 0.324151 +0.058223 0.941777 +0.175464 0.824536 +0.153668 0.846332 +0.146133 0.853867 +0.062613 0.937387 +0.681573 0.318427 +0.152224 0.847776 +0.000010 0.999990 +0.127466 0.872534 +0.710462 0.289538 +0.087236 0.912764 +0.060247 0.939753 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.087592 0.912408 +0.000010 0.999990 +0.046795 0.953205 +0.066227 0.933773 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.035763 0.964237 diff --git a/inst/files/admixture/admixture_09 b/inst/files/admixture/admixture_09 new file mode 100644 index 0000000..d288317 --- /dev/null +++ b/inst/files/admixture/admixture_09 @@ -0,0 +1,1592 @@ +0.942995 0.057005 +0.950609 0.049391 +0.972207 0.027793 +0.943618 0.056382 +0.931674 0.068326 +0.944011 0.055989 +0.926197 0.073803 +0.976136 0.023864 +0.950896 0.049104 +0.928412 0.071588 +0.947400 0.052600 +0.932082 0.067918 +0.946954 0.053046 +0.983766 0.016234 +0.946588 0.053412 +0.969502 0.030498 +0.922055 0.077945 +0.894128 0.105872 +0.943422 0.056578 +0.954252 0.045748 +0.947032 0.052968 +0.999713 0.000287 +0.946819 0.053181 +0.954604 0.045396 +0.909505 0.090495 +0.940332 0.059668 +0.639082 0.360918 +0.622274 0.377726 +0.616732 0.383268 +0.642448 0.357552 +0.641160 0.358840 +0.641540 0.358460 +0.627042 0.372958 +0.657607 0.342393 +0.621644 0.378356 +0.648931 0.351069 +0.634822 0.365178 +0.679026 0.320974 +0.626667 0.373333 +0.619516 0.380484 +0.646198 0.353802 +0.654603 0.345397 +0.573052 0.426948 +0.985092 0.014908 +0.602255 0.397745 +0.587243 0.412757 +0.643819 0.356181 +0.972256 0.027744 +0.581180 0.418820 +0.644561 0.355439 +0.164249 0.835751 +0.162269 0.837731 +0.167845 0.832155 +0.151826 0.848174 +0.164632 0.835368 +0.155068 0.844932 +0.151798 0.848202 +0.181025 0.818975 +0.142317 0.857683 +0.155926 0.844074 +0.148766 0.851234 +0.165722 0.834278 +0.159381 0.840619 +0.150911 0.849089 +0.168392 0.831608 +0.150043 0.849957 +0.201719 0.798281 +0.147663 0.852337 +0.151051 0.848949 +0.148403 0.851597 +0.159187 0.840813 +0.153258 0.846742 +0.122765 0.877235 +0.213415 0.786585 +0.194961 0.805039 +0.132046 0.867954 +0.134036 0.865964 +0.141651 0.858349 +0.198573 0.801427 +0.149310 0.850690 +0.144015 0.855985 +0.131570 0.868430 +0.133412 0.866588 +0.149753 0.850247 +0.134842 0.865158 +0.141232 0.858768 +0.191372 0.808628 +0.186282 0.813718 +0.185707 0.814293 +0.163154 0.836846 +0.179260 0.820740 +0.571463 0.428537 +0.578038 0.421962 +0.541042 0.458958 +0.560782 0.439218 +0.523809 0.476191 +0.562594 0.437406 +0.553884 0.446116 +0.543402 0.456598 +0.534429 0.465571 +0.560314 0.439686 +0.558593 0.441407 +0.527709 0.472291 +0.553371 0.446629 +0.543996 0.456004 +0.119574 0.880426 +0.120956 0.879044 +0.136804 0.863196 +0.133869 0.866131 +0.142549 0.857451 +0.122444 0.877556 +0.153973 0.846027 +0.134830 0.865170 +0.133720 0.866280 +0.134511 0.865489 +0.122410 0.877590 +0.150113 0.849887 +0.126873 0.873127 +0.134196 0.865804 +0.125169 0.874831 +0.140623 0.859377 +0.139578 0.860422 +0.134243 0.865757 +0.138199 0.861801 +0.137962 0.862038 +0.240188 0.759812 +0.241234 0.758766 +0.222397 0.777603 +0.210561 0.789439 +0.219999 0.780001 +0.238632 0.761368 +0.207887 0.792113 +0.223898 0.776102 +0.222110 0.777890 +0.237594 0.762406 +0.246692 0.753308 +0.247636 0.752364 +0.243291 0.756709 +0.220667 0.779333 +0.211612 0.788388 +0.274211 0.725789 +0.240787 0.759213 +0.241614 0.758386 +0.154886 0.845114 +0.236905 0.763095 +0.192030 0.807970 +0.223978 0.776022 +0.193600 0.806400 +0.211718 0.788282 +0.225955 0.774045 +0.210630 0.789370 +0.233264 0.766736 +0.176103 0.823897 +0.168992 0.831008 +0.215410 0.784590 +0.216387 0.783613 +0.222145 0.777855 +0.189505 0.810495 +0.231348 0.768652 +0.177212 0.822788 +0.196519 0.803481 +0.231272 0.768728 +0.185412 0.814588 +0.170804 0.829196 +0.190611 0.809389 +0.175767 0.824233 +0.195706 0.804294 +0.186995 0.813005 +0.189301 0.810699 +0.174363 0.825637 +0.191334 0.808666 +0.192460 0.807540 +0.199432 0.800568 +0.217484 0.782516 +0.203554 0.796446 +0.176466 0.823534 +0.181714 0.818286 +0.197697 0.802303 +0.197211 0.802789 +0.188035 0.811965 +0.314655 0.685345 +0.285147 0.714853 +0.319774 0.680226 +0.309742 0.690258 +0.296054 0.703946 +0.300772 0.699228 +0.318884 0.681116 +0.288333 0.711667 +0.320885 0.679115 +0.328158 0.671842 +0.298413 0.701587 +0.292423 0.707577 +0.309995 0.690005 +0.299384 0.700616 +0.321439 0.678561 +0.304927 0.695073 +0.307185 0.692815 +0.314489 0.685511 +0.284032 0.715968 +0.284325 0.715675 +0.306208 0.693792 +0.295563 0.704437 +0.305400 0.694600 +0.000010 0.999990 +0.007281 0.992719 +0.018005 0.981995 +0.018397 0.981603 +0.000805 0.999195 +0.007316 0.992684 +0.000010 0.999990 +0.010807 0.989193 +0.000010 0.999990 +0.002709 0.997291 +0.002519 0.997481 +0.000010 0.999990 +0.006907 0.993093 +0.013072 0.986928 +0.021639 0.978361 +0.002534 0.997466 +0.017686 0.982314 +0.000649 0.999351 +0.020842 0.979158 +0.012251 0.987749 +0.016319 0.983681 +0.017077 0.982923 +0.000010 0.999990 +0.015193 0.984807 +0.013065 0.986935 +0.008775 0.991225 +0.000010 0.999990 +0.018079 0.981921 +0.000010 0.999990 +0.014982 0.985018 +0.014962 0.985038 +0.013217 0.986783 +0.001861 0.998139 +0.011006 0.988994 +0.018213 0.981787 +0.002353 0.997647 +0.013871 0.986129 +0.006293 0.993707 +0.019068 0.980932 +0.019598 0.980402 +0.006948 0.993052 +0.000010 0.999990 +0.002767 0.997233 +0.021753 0.978247 +0.019081 0.980919 +0.000010 0.999990 +0.013590 0.986410 +0.030432 0.969568 +0.008319 0.991681 +0.000010 0.999990 +0.019502 0.980498 +0.001110 0.998890 +0.014468 0.985532 +0.014520 0.985480 +0.006192 0.993808 +0.011596 0.988404 +0.009586 0.990414 +0.005238 0.994762 +0.000010 0.999990 +0.019040 0.980960 +0.006969 0.993031 +0.028240 0.971760 +0.012197 0.987803 +0.019414 0.980586 +0.025214 0.974786 +0.009686 0.990314 +0.037480 0.962520 +0.005901 0.994099 +0.061979 0.938021 +0.013383 0.986617 +0.035431 0.964569 +0.040886 0.959114 +0.038555 0.961445 +0.019489 0.980511 +0.012195 0.987805 +0.032679 0.967321 +0.040318 0.959682 +0.031612 0.968388 +0.021638 0.978362 +0.009473 0.990527 +0.036827 0.963173 +0.036646 0.963354 +0.048284 0.951716 +0.035199 0.964801 +0.008646 0.991354 +0.001855 0.998145 +0.043275 0.956725 +0.047952 0.952048 +0.049620 0.950380 +0.026709 0.973291 +0.040982 0.959018 +0.051989 0.948011 +0.022620 0.977380 +0.052563 0.947437 +0.013936 0.986064 +0.019553 0.980447 +0.011598 0.988402 +0.026092 0.973908 +0.037376 0.962624 +0.049631 0.950369 +0.043180 0.956820 +0.021795 0.978205 +0.012212 0.987788 +0.018542 0.981458 +0.023346 0.976654 +0.022687 0.977313 +0.042101 0.957899 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.035634 0.964366 +0.021804 0.978196 +0.018228 0.981772 +0.023758 0.976242 +0.040497 0.959503 +0.048059 0.951941 +0.038407 0.961593 +0.033231 0.966769 +0.046241 0.953759 +0.011119 0.988881 +0.026206 0.973794 +0.017391 0.982609 +0.023035 0.976965 +0.039899 0.960101 +0.006371 0.993629 +0.021978 0.978022 +0.024581 0.975419 +0.027461 0.972539 +0.013267 0.986733 +0.034597 0.965403 +0.015887 0.984113 +0.890153 0.109847 +0.933520 0.066480 +0.870529 0.129471 +0.929497 0.070503 +0.891075 0.108925 +0.930078 0.069922 +0.901775 0.098225 +0.880742 0.119258 +0.032139 0.967861 +0.024051 0.975949 +0.033765 0.966235 +0.027323 0.972677 +0.028574 0.971426 +0.026645 0.973355 +0.034957 0.965043 +0.039772 0.960228 +0.021937 0.978063 +0.026405 0.973595 +0.037410 0.962590 +0.025125 0.974875 +0.036361 0.963639 +0.026498 0.973502 +0.042642 0.957358 +0.033494 0.966506 +0.024775 0.975225 +0.059867 0.940133 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.023972 0.976028 +0.025440 0.974560 +0.017797 0.982203 +0.009748 0.990252 +0.021780 0.978220 +0.022224 0.977776 +0.009653 0.990347 +0.009357 0.990643 +0.015814 0.984186 +0.000010 0.999990 +0.005174 0.994826 +0.013307 0.986693 +0.000010 0.999990 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.093061 0.906939 +0.105193 0.894807 +0.136446 0.863554 +0.114488 0.885512 +0.075223 0.924777 +0.116199 0.883801 +0.088111 0.911889 +0.096470 0.903530 +0.111891 0.888109 +0.114616 0.885384 +0.112163 0.887837 +0.120313 0.879687 +0.114269 0.885731 +0.136636 0.863364 +0.119261 0.880739 +0.107158 0.892842 +0.124955 0.875045 +0.103486 0.896514 +0.080137 0.919863 +0.114810 0.885190 +0.122909 0.877091 +0.108452 0.891548 +0.899951 0.100049 +0.900652 0.099348 +0.872189 0.127811 +0.826736 0.173264 +0.814660 0.185340 +0.911389 0.088611 +0.890804 0.109196 +0.907690 0.092310 +0.924602 0.075398 +0.906416 0.093584 +0.843808 0.156192 +0.931406 0.068594 +0.894713 0.105287 +0.915845 0.084155 +0.901115 0.098885 +0.883824 0.116176 +0.904707 0.095293 +0.870585 0.129415 +0.901530 0.098470 +0.857796 0.142204 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.006743 0.993257 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.010338 0.989662 +0.002163 0.997837 +0.007624 0.992376 +0.000010 0.999990 +0.005011 0.994989 +0.000010 0.999990 +0.000010 0.999990 +0.001660 0.998340 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.996357 0.003643 +0.999990 0.000010 +0.999990 0.000010 +0.998605 0.001395 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.983815 0.016185 +0.969365 0.030635 +0.975583 0.024417 +0.970023 0.029977 +0.999990 0.000010 +0.999990 0.000010 +0.995764 0.004236 +0.964236 0.035764 +0.991261 0.008739 +0.958045 0.041955 +0.956321 0.043679 +0.971256 0.028744 +0.969816 0.030184 +0.980639 0.019361 +0.985133 0.014867 +0.979998 0.020002 +0.984587 0.015413 +0.961036 0.038964 +0.976192 0.023808 +0.943347 0.056653 +0.971128 0.028872 +0.981979 0.018021 +0.953967 0.046033 +0.999990 0.000010 +0.980509 0.019491 +0.998123 0.001877 +0.980913 0.019087 +0.989279 0.010721 +0.999990 0.000010 +0.997480 0.002520 +0.998992 0.001008 +0.966571 0.033429 +0.978865 0.021135 +0.992113 0.007887 +0.930644 0.069356 +0.982494 0.017506 +0.952298 0.047702 +0.999990 0.000010 +0.053648 0.946352 +0.046206 0.953794 +0.044773 0.955227 +0.059369 0.940631 +0.050423 0.949577 +0.038296 0.961704 +0.067024 0.932976 +0.067909 0.932091 +0.031469 0.968531 +0.043506 0.956494 +0.040867 0.959133 +0.044846 0.955154 +0.046174 0.953826 +0.067780 0.932220 +0.054658 0.945342 +0.062994 0.937006 +0.060365 0.939635 +0.041359 0.958641 +0.058456 0.941544 +0.033677 0.966323 +0.035411 0.964589 +0.993567 0.006433 +0.987974 0.012026 +0.989769 0.010231 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.986429 0.013571 +0.999990 0.000010 +0.998264 0.001736 +0.972237 0.027763 +0.521852 0.478148 +0.496525 0.503475 +0.562437 0.437563 +0.519227 0.480773 +0.543730 0.456270 +0.629575 0.370425 +0.499000 0.501000 +0.613212 0.386788 +0.582066 0.417934 +0.566926 0.433074 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999903 0.000097 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.945660 0.054340 +0.924130 0.075870 +0.963229 0.036771 +0.922555 0.077445 +0.949536 0.050464 +0.955558 0.044442 +0.925347 0.074653 +0.956830 0.043170 +0.955265 0.044735 +0.929180 0.070820 +0.000010 0.999990 +0.001079 0.998921 +0.007028 0.992972 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.013132 0.986868 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.107710 0.892290 +0.054189 0.945811 +0.066879 0.933121 +0.082428 0.917572 +0.062449 0.937551 +0.050111 0.949889 +0.109156 0.890844 +0.090137 0.909863 +0.055603 0.944397 +0.056879 0.943121 +0.062759 0.937241 +0.074187 0.925813 +0.068075 0.931925 +0.042523 0.957477 +0.108144 0.891856 +0.916029 0.083971 +0.926130 0.073870 +0.936488 0.063512 +0.924069 0.075931 +0.928402 0.071598 +0.929964 0.070036 +0.958493 0.041507 +0.954640 0.045360 +0.969511 0.030489 +0.948042 0.051958 +0.935468 0.064532 +0.943302 0.056698 +0.927937 0.072063 +0.953663 0.046337 +0.952809 0.047191 +0.927055 0.072945 +0.935008 0.064992 +0.959238 0.040762 +0.947771 0.052229 +0.961622 0.038378 +0.923089 0.076911 +0.943531 0.056469 +0.955491 0.044509 +0.964112 0.035888 +0.972758 0.027242 +0.938893 0.061107 +0.950504 0.049496 +0.688179 0.311821 +0.682066 0.317934 +0.679279 0.320721 +0.682138 0.317862 +0.680368 0.319632 +0.670708 0.329292 +0.688973 0.311027 +0.692555 0.307445 +0.667268 0.332732 +0.691929 0.308071 +0.679038 0.320962 +0.403731 0.596269 +0.435277 0.564723 +0.440756 0.559244 +0.437255 0.562745 +0.448807 0.551193 +0.433304 0.566696 +0.437957 0.562043 +0.443802 0.556198 +0.430225 0.569775 +0.446053 0.553947 +0.445023 0.554977 +0.457957 0.542043 +0.452683 0.547317 +0.278726 0.721274 +0.288449 0.711551 +0.293124 0.706876 +0.278518 0.721482 +0.244895 0.755105 +0.295911 0.704089 +0.285911 0.714089 +0.276733 0.723267 +0.283050 0.716950 +0.272387 0.727613 +0.281186 0.718814 +0.271408 0.728592 +0.293268 0.706732 +0.277626 0.722374 +0.280880 0.719120 +0.656462 0.343538 +0.646240 0.353760 +0.642606 0.357394 +0.649153 0.350847 +0.642710 0.357290 +0.652111 0.347889 +0.635522 0.364478 +0.640284 0.359716 +0.649382 0.350618 +0.652478 0.347522 +0.634084 0.365916 +0.636849 0.363151 +0.364422 0.635578 +0.406176 0.593824 +0.375817 0.624183 +0.395043 0.604957 +0.403163 0.596837 +0.378892 0.621108 +0.367652 0.632348 +0.380010 0.619990 +0.351597 0.648403 +0.377211 0.622789 +0.369394 0.630606 +0.375444 0.624556 +0.379532 0.620468 +0.418829 0.581171 +0.406182 0.593818 +0.413878 0.586122 +0.426317 0.573683 +0.397196 0.602804 +0.403358 0.596642 +0.391069 0.608931 +0.422159 0.577841 +0.425521 0.574479 +0.422347 0.577653 +0.398456 0.601544 +0.437919 0.562081 +0.413303 0.586697 +0.234834 0.765166 +0.062047 0.937953 +0.044291 0.955709 +0.067708 0.932292 +0.039766 0.960234 +0.055759 0.944241 +0.023616 0.976384 +0.019272 0.980728 +0.000010 0.999990 +0.119522 0.880478 +0.048843 0.951157 +0.027404 0.972596 +0.033588 0.966412 +0.025517 0.974483 +0.065486 0.934514 +0.042882 0.957118 +0.040344 0.959656 +0.123885 0.876115 +0.014449 0.985551 +0.037703 0.962297 +0.007715 0.992285 +0.020105 0.979895 +0.014108 0.985892 +0.020520 0.979480 +0.013370 0.986630 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.014171 0.985829 +0.000827 0.999173 +0.010724 0.989276 +0.005604 0.994396 +0.003214 0.996786 +0.000010 0.999990 +0.010881 0.989119 +0.000010 0.999990 +0.002911 0.997089 +0.012544 0.987456 +0.015551 0.984449 +0.009790 0.990210 +0.012542 0.987458 +0.005717 0.994283 +0.010601 0.989399 +0.015300 0.984700 +0.021493 0.978507 +0.013900 0.986100 +0.033302 0.966698 +0.071907 0.928093 +0.104826 0.895174 +0.065306 0.934694 +0.034290 0.965710 +0.024534 0.975466 +0.000305 0.999695 +0.024838 0.975162 +0.018485 0.981515 +0.011372 0.988628 +0.084780 0.915220 +0.094336 0.905664 +0.000010 0.999990 +0.076925 0.923075 +0.003496 0.996504 +0.032448 0.967552 +0.098973 0.901027 +0.032290 0.967710 +0.026015 0.973985 +0.032646 0.967354 +0.036530 0.963470 +0.034089 0.965911 +0.062410 0.937590 +0.029226 0.970774 +0.033585 0.966415 +0.028507 0.971493 +0.011768 0.988232 +0.105712 0.894288 +0.010722 0.989278 +0.037765 0.962235 +0.011950 0.988050 +0.041664 0.958336 +0.050393 0.949607 +0.010969 0.989031 +0.059864 0.940136 +0.017638 0.982362 +0.040985 0.959015 +0.003975 0.996025 +0.035971 0.964029 +0.020366 0.979634 +0.031151 0.968849 +0.025379 0.974621 +0.076797 0.923203 +0.065878 0.934122 +0.005169 0.994831 +0.011624 0.988376 +0.051868 0.948132 +0.087421 0.912579 +0.027073 0.972927 +0.011614 0.988386 +0.022731 0.977269 +0.035769 0.964231 +0.034543 0.965457 +0.081944 0.918056 +0.024013 0.975987 +0.014623 0.985377 +0.015339 0.984661 +0.043694 0.956306 +0.006323 0.993677 +0.028206 0.971794 +0.029278 0.970722 +0.070137 0.929863 +0.049412 0.950588 +0.095862 0.904138 +0.050233 0.949767 +0.013732 0.986268 +0.063812 0.936188 +0.049912 0.950088 +0.002551 0.997449 +0.019422 0.980578 +0.013737 0.986263 +0.055526 0.944474 +0.057481 0.942519 +0.058326 0.941674 +0.043537 0.956463 +0.019715 0.980285 +0.055654 0.944346 +0.043860 0.956140 +0.027958 0.972042 +0.094169 0.905831 +0.125199 0.874801 +0.023811 0.976189 +0.102121 0.897879 +0.056789 0.943211 +0.029230 0.970770 +0.007006 0.992994 +0.058259 0.941741 +0.234466 0.765534 +0.077839 0.922161 +0.111367 0.888633 +0.025472 0.974528 +0.105077 0.894923 +0.066960 0.933040 +0.045882 0.954118 +0.041018 0.958982 +0.021219 0.978781 +0.065315 0.934685 +0.087148 0.912852 +0.288301 0.711699 +0.225466 0.774534 +0.094917 0.905083 +0.010977 0.989023 +0.012087 0.987913 +0.121691 0.878309 +0.056448 0.943552 +0.041665 0.958335 +0.019794 0.980206 +0.015097 0.984903 +0.315416 0.684584 +0.816178 0.183822 +0.104434 0.895566 +0.018233 0.981767 +0.002191 0.997809 +0.108680 0.891320 +0.051942 0.948058 +0.042551 0.957449 +0.016728 0.983272 +0.016654 0.983346 +0.046458 0.953542 +0.087097 0.912903 +0.369176 0.630824 +0.821046 0.178954 +0.112245 0.887755 +0.028382 0.971618 +0.113530 0.886470 +0.097106 0.902894 +0.043022 0.956978 +0.029561 0.970439 +0.019518 0.980482 +0.070251 0.929749 +0.060085 0.939915 +0.064936 0.935064 +0.256404 0.743596 +0.793961 0.206039 +0.119560 0.880440 +0.013296 0.986704 +0.100684 0.899316 +0.106224 0.893776 +0.075733 0.924267 +0.027708 0.972292 +0.003712 0.996288 +0.048702 0.951298 +0.066386 0.933614 +0.080073 0.919927 +0.250534 0.749466 +0.838876 0.161124 +0.088528 0.911472 +0.010447 0.989553 +0.102153 0.897847 +0.063749 0.936251 +0.030427 0.969573 +0.000010 0.999990 +0.063098 0.936902 +0.017069 0.982931 +0.100887 0.899113 +0.239285 0.760715 +0.818010 0.181990 +0.088408 0.911592 +0.031529 0.968471 +0.084008 0.915992 +0.060874 0.939126 +0.044187 0.955813 +0.021229 0.978771 +0.020183 0.979817 +0.067850 0.932150 +0.093985 0.906015 +0.102083 0.897917 +0.259465 0.740535 +0.832381 0.167619 +0.859554 0.140446 +0.754493 0.245507 +0.839641 0.160359 +0.937481 0.062519 +0.700953 0.299047 +0.033120 0.966880 +0.028234 0.971766 +0.042582 0.957418 +0.103840 0.896160 +0.263980 0.736020 +0.451188 0.548812 +0.836593 0.163407 +0.738626 0.261374 +0.821179 0.178821 +0.792487 0.207513 +0.021549 0.978451 +0.045847 0.954153 +0.070595 0.929405 +0.106464 0.893536 +0.295802 0.704198 +0.493811 0.506189 +0.821306 0.178694 +0.745401 0.254599 +0.872078 0.127922 +0.876815 0.123185 +0.054195 0.945805 +0.051617 0.948383 +0.047877 0.952123 +0.125739 0.874261 +0.283573 0.716427 +0.447326 0.552674 +0.819179 0.180821 +0.835980 0.164020 +0.561191 0.438809 +0.703569 0.296431 +0.026804 0.973196 +0.062184 0.937816 +0.125999 0.874001 +0.088069 0.911931 +0.265328 0.734672 +0.562943 0.437057 +0.724458 0.275542 +0.849825 0.150175 +0.840571 0.159429 +0.377242 0.622758 +0.676102 0.323898 +0.048138 0.951862 +0.042388 0.957612 +0.089005 0.910995 +0.092779 0.907221 +0.283041 0.716959 +0.461097 0.538903 +0.758980 0.241020 +0.866936 0.133064 +0.856254 0.143746 +0.659239 0.340761 +0.049816 0.950184 +0.100525 0.899475 +0.243328 0.756672 +0.288660 0.711340 +0.333704 0.666296 +0.721441 0.278559 +0.852941 0.147059 +0.843656 0.156344 +0.609138 0.390862 +0.048203 0.951797 +0.048536 0.951464 +0.105441 0.894559 +0.279807 0.720193 +0.238312 0.761688 +0.326365 0.673635 +0.774015 0.225985 +0.810487 0.189513 +0.791352 0.208648 +0.768858 0.231142 +0.045181 0.954819 +0.028563 0.971437 +0.039943 0.960057 +0.083856 0.916144 +0.250848 0.749152 +0.503155 0.496845 +0.351879 0.648121 +0.447070 0.552930 +0.170835 0.829165 +0.149689 0.850311 +0.147955 0.852045 +0.411469 0.588531 +0.206505 0.793495 +0.157638 0.842362 +0.358446 0.641554 +0.197652 0.802348 +0.253773 0.746227 +0.021560 0.978440 +0.198816 0.801184 +0.308357 0.691643 +0.064132 0.935868 +0.480029 0.519971 +0.179315 0.820685 +0.320447 0.679553 +0.320347 0.679653 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.025792 0.974208 +0.015979 0.984021 +0.043829 0.956171 +0.014264 0.985736 +0.000010 0.999990 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.021451 0.978549 +0.022451 0.977549 +0.012372 0.987628 +0.022572 0.977428 +0.000010 0.999990 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.019429 0.980571 +0.028695 0.971305 +0.012926 0.987074 +0.005192 0.994808 +0.025458 0.974542 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.026477 0.973523 +0.000010 0.999990 +0.000010 0.999990 +0.023325 0.976675 +0.006089 0.993911 +0.999990 0.000010 +0.999990 0.000010 +0.108447 0.891553 +0.023299 0.976701 +0.017906 0.982094 +0.014235 0.985765 +0.021009 0.978991 +0.011475 0.988525 +0.999990 0.000010 +0.999990 0.000010 +0.015776 0.984224 +0.035729 0.964271 +0.032837 0.967163 +0.000010 0.999990 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.067630 0.932370 +0.027316 0.972684 +0.001420 0.998580 +0.022088 0.977912 +0.008763 0.991237 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.025400 0.974600 +0.008078 0.991922 +0.013161 0.986839 +0.023243 0.976757 +0.008672 0.991328 +0.999990 0.000010 +0.015501 0.984499 +0.012954 0.987046 +0.012580 0.987420 +0.018097 0.981903 +0.000010 0.999990 +0.000010 0.999990 +0.008907 0.991093 +0.008203 0.991797 +0.000010 0.999990 +0.003683 0.996317 +0.000010 0.999990 +0.004049 0.995951 +0.013059 0.986941 +0.000010 0.999990 +0.003612 0.996388 +0.008446 0.991554 +0.010345 0.989655 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.002975 0.997025 +0.000010 0.999990 +0.000010 0.999990 +0.011356 0.988644 +0.009847 0.990153 +0.000010 0.999990 +0.014905 0.985095 +0.000010 0.999990 +0.000010 0.999990 +0.006081 0.993919 +0.002962 0.997038 +0.000010 0.999990 +0.019030 0.980970 +0.023705 0.976295 +0.007275 0.992725 +0.020706 0.979294 +0.000010 0.999990 +0.007263 0.992737 +0.000010 0.999990 +0.002493 0.997507 +0.118946 0.881054 +0.085755 0.914245 +0.092983 0.907017 +0.090257 0.909743 +0.013672 0.986328 +0.107102 0.892898 +0.007093 0.992907 +0.084252 0.915748 +0.081077 0.918923 +0.106764 0.893236 +0.000010 0.999990 +0.003748 0.996252 +0.000010 0.999990 +0.001760 0.998240 +0.000010 0.999990 +0.000010 0.999990 +0.009899 0.990101 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.003370 0.996630 +0.010867 0.989133 +0.000010 0.999990 +0.000010 0.999990 +0.012734 0.987266 +0.000256 0.999744 +0.012204 0.987796 +0.011660 0.988340 +0.000010 0.999990 +0.021586 0.978414 +0.006742 0.993258 +0.008765 0.991235 +0.998924 0.001076 +0.983557 0.016443 +0.979072 0.020928 +0.999990 0.000010 +0.980887 0.019113 +0.987236 0.012764 +0.994182 0.005818 +0.987743 0.012257 +0.001759 0.998241 +0.000010 0.999990 +0.003539 0.996461 +0.000712 0.999288 +0.008090 0.991910 +0.375731 0.624269 +0.280971 0.719029 +0.368096 0.631904 +0.363688 0.636312 +0.373067 0.626933 +0.007460 0.992540 +0.429276 0.570724 +0.427571 0.572429 +0.420283 0.579717 +0.376285 0.623715 +0.336802 0.663198 +0.340484 0.659516 +0.428987 0.571013 +0.415993 0.584007 +0.438262 0.561738 +0.428546 0.571454 +0.885661 0.114339 +0.979162 0.020838 +0.854839 0.145161 +0.845303 0.154697 +0.957872 0.042128 +0.843427 0.156573 +0.915795 0.084205 +0.858970 0.141030 +0.877905 0.122095 +0.863453 0.136547 +0.017844 0.982156 +0.011039 0.988961 +0.000010 0.999990 +0.762966 0.237034 +0.046008 0.953992 +0.010396 0.989604 +0.009741 0.990259 +0.021283 0.978717 +0.021002 0.978998 +0.793520 0.206480 +0.022256 0.977744 +0.011741 0.988259 +0.739613 0.260387 +0.006833 0.993167 +0.001399 0.998601 +0.018843 0.981157 +0.701044 0.298956 +0.934191 0.065809 +0.012387 0.987613 +0.930386 0.069614 +0.005135 0.994865 +0.024876 0.975124 +0.834953 0.165047 +0.831489 0.168511 +0.064058 0.935942 +0.000010 0.999990 +0.015731 0.984269 +0.022769 0.977231 +0.020999 0.979001 +0.007362 0.992638 +0.922408 0.077592 +0.857881 0.142119 +0.001853 0.998147 +0.007644 0.992356 +0.000010 0.999990 +0.032173 0.967827 +0.015763 0.984237 +0.017070 0.982930 +0.752750 0.247250 +0.006705 0.993295 +0.081630 0.918370 +0.041556 0.958444 +0.017264 0.982736 +0.000114 0.999886 +0.029784 0.970216 +0.788600 0.211400 +0.923221 0.076779 +0.000010 0.999990 +0.013699 0.986301 +0.940902 0.059098 +0.981095 0.018905 +0.032568 0.967432 +0.024274 0.975726 +0.016460 0.983540 +0.000010 0.999990 +0.000309 0.999691 +0.000010 0.999990 +0.000010 0.999990 +0.009025 0.990975 +0.009021 0.990979 +0.016584 0.983416 +0.016507 0.983493 +0.000010 0.999990 +0.010857 0.989143 +0.021035 0.978965 +0.000010 0.999990 +0.000010 0.999990 +0.007197 0.992803 +0.006812 0.993188 +0.000010 0.999990 +0.015881 0.984119 +0.005360 0.994640 +0.000010 0.999990 +0.008085 0.991915 +0.010392 0.989608 +0.017333 0.982667 +0.000010 0.999990 +0.002299 0.997701 +0.020364 0.979636 +0.128579 0.871421 +0.000010 0.999990 +0.009862 0.990138 +0.046527 0.953473 +0.000010 0.999990 +0.046279 0.953721 +0.854933 0.145067 +0.000010 0.999990 +0.006499 0.993501 +0.010899 0.989101 +0.010604 0.989396 +0.061164 0.938836 +0.044159 0.955841 +0.015014 0.984986 +0.110013 0.889987 +0.000010 0.999990 +0.053068 0.946932 +0.008146 0.991854 +0.022223 0.977777 +0.147615 0.852385 +0.015697 0.984303 +0.014421 0.985579 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.056566 0.943434 +0.064327 0.935673 +0.017851 0.982149 +0.012337 0.987663 +0.003375 0.996625 +0.005414 0.994586 +0.007459 0.992541 +0.022857 0.977143 +0.026528 0.973472 +0.124320 0.875680 +0.000010 0.999990 +0.005282 0.994718 +0.000010 0.999990 +0.047031 0.952969 +0.004808 0.995192 +0.041071 0.958929 +0.056483 0.943517 +0.001161 0.998839 +0.004575 0.995425 +0.059166 0.940834 +0.009543 0.990457 +0.018827 0.981173 +0.087898 0.912102 +0.000010 0.999990 +0.067979 0.932021 +0.000010 0.999990 +0.017632 0.982368 +0.007289 0.992711 +0.005234 0.994766 +0.061745 0.938255 +0.019819 0.980181 +0.005843 0.994157 +0.069160 0.930840 +0.141902 0.858098 +0.015322 0.984678 +0.058372 0.941628 +0.021536 0.978464 +0.016940 0.983060 +0.047840 0.952160 +0.019644 0.980356 +0.008346 0.991654 +0.026655 0.973345 +0.015316 0.984684 +0.065854 0.934146 +0.017545 0.982455 +0.021903 0.978097 +0.000010 0.999990 +0.017151 0.982849 +0.060983 0.939017 +0.015939 0.984061 +0.045261 0.954739 +0.017116 0.982884 +0.000010 0.999990 +0.047821 0.952179 +0.055596 0.944404 +0.003835 0.996165 +0.043440 0.956560 +0.023236 0.976764 +0.015621 0.984379 +0.002264 0.997736 +0.000097 0.999903 +0.061762 0.938238 +0.000750 0.999250 +0.008419 0.991581 +0.057071 0.942929 +0.000010 0.999990 +0.140798 0.859202 +0.007057 0.992943 +0.087757 0.912243 +0.005546 0.994454 +0.011406 0.988594 +0.022473 0.977527 +0.017477 0.982523 +0.017944 0.982056 +0.006107 0.993893 +0.000010 0.999990 +0.037591 0.962409 +0.048575 0.951425 +0.007120 0.992880 +0.023738 0.976262 +0.058103 0.941897 +0.000010 0.999990 +0.000010 0.999990 +0.018609 0.981391 +0.708502 0.291498 +0.056668 0.943332 +0.006798 0.993202 +0.026690 0.973310 +0.012466 0.987534 +0.000010 0.999990 +0.001700 0.998300 +0.006597 0.993403 +0.113426 0.886574 +0.053397 0.946603 +0.061568 0.938432 +0.059140 0.940860 +0.033017 0.966983 +0.017632 0.982368 +0.010069 0.989931 +0.006185 0.993815 +0.015191 0.984809 +0.008244 0.991756 +0.165715 0.834285 +0.023153 0.976847 +0.030967 0.969033 +0.696983 0.303017 +0.000010 0.999990 +0.025609 0.974391 +0.021272 0.978728 +0.000010 0.999990 +0.073048 0.926952 +0.153864 0.846136 +0.087788 0.912212 +0.144777 0.855223 +0.096355 0.903645 +0.075118 0.924882 +0.175696 0.824304 +0.112188 0.887812 +0.001278 0.998722 +0.681658 0.318342 +0.051191 0.948809 +0.713065 0.286935 +0.000010 0.999990 +0.014099 0.985901 +0.052714 0.947286 +0.701591 0.298409 +0.029248 0.970752 +0.121796 0.878204 +0.060402 0.939598 +0.155841 0.844159 +0.162542 0.837458 +0.091277 0.908723 +0.029214 0.970786 +0.000010 0.999990 +0.134714 0.865286 +0.698270 0.301730 +0.100422 0.899578 +0.091724 0.908276 +0.029824 0.970176 +0.081849 0.918151 +0.000010 0.999990 +0.094227 0.905773 +0.098937 0.901063 +0.002315 0.997685 +0.075718 0.924282 +0.054069 0.945931 +0.020651 0.979349 +0.056505 0.943495 +0.675849 0.324151 +0.058224 0.941776 +0.175464 0.824536 +0.153668 0.846332 +0.146133 0.853867 +0.062613 0.937387 +0.681573 0.318427 +0.152225 0.847775 +0.000010 0.999990 +0.127467 0.872533 +0.710462 0.289538 +0.087237 0.912763 +0.060248 0.939752 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.087593 0.912407 +0.000010 0.999990 +0.046795 0.953205 +0.066228 0.933772 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.035763 0.964237 diff --git a/inst/files/admixture/admixture_10 b/inst/files/admixture/admixture_10 new file mode 100644 index 0000000..34f4e42 --- /dev/null +++ b/inst/files/admixture/admixture_10 @@ -0,0 +1,1592 @@ +0.057005 0.942995 +0.049391 0.950609 +0.027792 0.972208 +0.056381 0.943619 +0.068326 0.931674 +0.055989 0.944011 +0.073803 0.926197 +0.023864 0.976136 +0.049104 0.950896 +0.071588 0.928412 +0.052600 0.947400 +0.067918 0.932082 +0.053046 0.946954 +0.016234 0.983766 +0.053411 0.946589 +0.030498 0.969502 +0.077945 0.922055 +0.105872 0.894128 +0.056578 0.943422 +0.045748 0.954252 +0.052967 0.947033 +0.000286 0.999714 +0.053181 0.946819 +0.045396 0.954604 +0.090495 0.909505 +0.059668 0.940332 +0.360918 0.639082 +0.377726 0.622274 +0.383268 0.616732 +0.357552 0.642448 +0.358840 0.641160 +0.358460 0.641540 +0.372958 0.627042 +0.342393 0.657607 +0.378356 0.621644 +0.351069 0.648931 +0.365178 0.634822 +0.320974 0.679026 +0.373333 0.626667 +0.380484 0.619516 +0.353802 0.646198 +0.345397 0.654603 +0.426948 0.573052 +0.014907 0.985093 +0.397745 0.602255 +0.412758 0.587242 +0.356181 0.643819 +0.027744 0.972256 +0.418820 0.581180 +0.355439 0.644561 +0.835751 0.164249 +0.837731 0.162269 +0.832155 0.167845 +0.848174 0.151826 +0.835368 0.164632 +0.844932 0.155068 +0.848202 0.151798 +0.818975 0.181025 +0.857683 0.142317 +0.844075 0.155925 +0.851234 0.148766 +0.834279 0.165721 +0.840619 0.159381 +0.849089 0.150911 +0.831608 0.168392 +0.849957 0.150043 +0.798281 0.201719 +0.852337 0.147663 +0.848950 0.151050 +0.851597 0.148403 +0.840813 0.159187 +0.846742 0.153258 +0.877236 0.122764 +0.786585 0.213415 +0.805039 0.194961 +0.867954 0.132046 +0.865964 0.134036 +0.858349 0.141651 +0.801428 0.198572 +0.850691 0.149309 +0.855985 0.144015 +0.868430 0.131570 +0.866588 0.133412 +0.850248 0.149752 +0.865158 0.134842 +0.858768 0.141232 +0.808628 0.191372 +0.813718 0.186282 +0.814293 0.185707 +0.836846 0.163154 +0.820740 0.179260 +0.428537 0.571463 +0.421962 0.578038 +0.458958 0.541042 +0.439218 0.560782 +0.476191 0.523809 +0.437406 0.562594 +0.446116 0.553884 +0.456598 0.543402 +0.465572 0.534428 +0.439686 0.560314 +0.441407 0.558593 +0.472291 0.527709 +0.446629 0.553371 +0.456005 0.543995 +0.880426 0.119574 +0.879044 0.120956 +0.863196 0.136804 +0.866131 0.133869 +0.857451 0.142549 +0.877557 0.122443 +0.846027 0.153973 +0.865170 0.134830 +0.866280 0.133720 +0.865489 0.134511 +0.877590 0.122410 +0.849888 0.150112 +0.873127 0.126873 +0.865805 0.134195 +0.874831 0.125169 +0.859377 0.140623 +0.860422 0.139578 +0.865757 0.134243 +0.861802 0.138198 +0.862038 0.137962 +0.759812 0.240188 +0.758766 0.241234 +0.777603 0.222397 +0.789439 0.210561 +0.780001 0.219999 +0.761369 0.238631 +0.792114 0.207886 +0.776103 0.223897 +0.777890 0.222110 +0.762406 0.237594 +0.753308 0.246692 +0.752364 0.247636 +0.756709 0.243291 +0.779333 0.220667 +0.788389 0.211611 +0.725789 0.274211 +0.759213 0.240787 +0.758386 0.241614 +0.845114 0.154886 +0.763095 0.236905 +0.807970 0.192030 +0.776023 0.223977 +0.806400 0.193600 +0.788282 0.211718 +0.774045 0.225955 +0.789371 0.210629 +0.766736 0.233264 +0.823897 0.176103 +0.831008 0.168992 +0.784590 0.215410 +0.783613 0.216387 +0.777855 0.222145 +0.810496 0.189504 +0.768653 0.231347 +0.822788 0.177212 +0.803481 0.196519 +0.768729 0.231271 +0.814588 0.185412 +0.829196 0.170804 +0.809389 0.190611 +0.824234 0.175766 +0.804295 0.195705 +0.813005 0.186995 +0.810699 0.189301 +0.825637 0.174363 +0.808667 0.191333 +0.807540 0.192460 +0.800569 0.199431 +0.782517 0.217483 +0.796446 0.203554 +0.823534 0.176466 +0.818286 0.181714 +0.802303 0.197697 +0.802789 0.197211 +0.811965 0.188035 +0.685345 0.314655 +0.714853 0.285147 +0.680227 0.319773 +0.690259 0.309741 +0.703947 0.296053 +0.699229 0.300771 +0.681116 0.318884 +0.711667 0.288333 +0.679115 0.320885 +0.671842 0.328158 +0.701587 0.298413 +0.707577 0.292423 +0.690005 0.309995 +0.700616 0.299384 +0.678561 0.321439 +0.695073 0.304927 +0.692815 0.307185 +0.685511 0.314489 +0.715968 0.284032 +0.715676 0.284324 +0.693792 0.306208 +0.704437 0.295563 +0.694600 0.305400 +0.999990 0.000010 +0.992719 0.007281 +0.981995 0.018005 +0.981603 0.018397 +0.999195 0.000805 +0.992685 0.007315 +0.999990 0.000010 +0.989193 0.010807 +0.999990 0.000010 +0.997291 0.002709 +0.997481 0.002519 +0.999990 0.000010 +0.993094 0.006906 +0.986928 0.013072 +0.978361 0.021639 +0.997466 0.002534 +0.982314 0.017686 +0.999351 0.000649 +0.979158 0.020842 +0.987749 0.012251 +0.983681 0.016319 +0.982923 0.017077 +0.999990 0.000010 +0.984807 0.015193 +0.986935 0.013065 +0.991226 0.008774 +0.999990 0.000010 +0.981922 0.018078 +0.999990 0.000010 +0.985018 0.014982 +0.985038 0.014962 +0.986783 0.013217 +0.998140 0.001860 +0.988994 0.011006 +0.981788 0.018212 +0.997647 0.002353 +0.986129 0.013871 +0.993707 0.006293 +0.980933 0.019067 +0.980402 0.019598 +0.993053 0.006947 +0.999990 0.000010 +0.997234 0.002766 +0.978247 0.021753 +0.980919 0.019081 +0.999990 0.000010 +0.986411 0.013589 +0.969569 0.030431 +0.991682 0.008318 +0.999990 0.000010 +0.980499 0.019501 +0.998891 0.001109 +0.985532 0.014468 +0.985481 0.014519 +0.993808 0.006192 +0.988404 0.011596 +0.990414 0.009586 +0.994762 0.005238 +0.999990 0.000010 +0.980960 0.019040 +0.993032 0.006968 +0.971761 0.028239 +0.987803 0.012197 +0.980587 0.019413 +0.974787 0.025213 +0.990315 0.009685 +0.962520 0.037480 +0.994099 0.005901 +0.938021 0.061979 +0.986618 0.013382 +0.964569 0.035431 +0.959114 0.040886 +0.961445 0.038555 +0.980512 0.019488 +0.987805 0.012195 +0.967322 0.032678 +0.959682 0.040318 +0.968388 0.031612 +0.978362 0.021638 +0.990527 0.009473 +0.963173 0.036827 +0.963354 0.036646 +0.951717 0.048283 +0.964801 0.035199 +0.991355 0.008645 +0.998145 0.001855 +0.956725 0.043275 +0.952048 0.047952 +0.950380 0.049620 +0.973291 0.026709 +0.959018 0.040982 +0.948011 0.051989 +0.977380 0.022620 +0.947437 0.052563 +0.986065 0.013935 +0.980448 0.019552 +0.988403 0.011597 +0.973908 0.026092 +0.962624 0.037376 +0.950370 0.049630 +0.956821 0.043179 +0.978206 0.021794 +0.987788 0.012212 +0.981458 0.018542 +0.976654 0.023346 +0.977313 0.022687 +0.957899 0.042101 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.964367 0.035633 +0.978196 0.021804 +0.981772 0.018228 +0.976242 0.023758 +0.959504 0.040496 +0.951941 0.048059 +0.961593 0.038407 +0.966770 0.033230 +0.953760 0.046240 +0.988881 0.011119 +0.973794 0.026206 +0.982609 0.017391 +0.976965 0.023035 +0.960101 0.039899 +0.993630 0.006370 +0.978023 0.021977 +0.975419 0.024581 +0.972539 0.027461 +0.986734 0.013266 +0.965404 0.034596 +0.984113 0.015887 +0.109847 0.890153 +0.066480 0.933520 +0.129471 0.870529 +0.070503 0.929497 +0.108925 0.891075 +0.069922 0.930078 +0.098225 0.901775 +0.119257 0.880743 +0.967862 0.032138 +0.975949 0.024051 +0.966236 0.033764 +0.972678 0.027322 +0.971426 0.028574 +0.973355 0.026645 +0.965044 0.034956 +0.960228 0.039772 +0.978063 0.021937 +0.973596 0.026404 +0.962591 0.037409 +0.974875 0.025125 +0.963639 0.036361 +0.973502 0.026498 +0.957358 0.042642 +0.966506 0.033494 +0.975225 0.024775 +0.940133 0.059867 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.976029 0.023971 +0.974560 0.025440 +0.982204 0.017796 +0.990252 0.009748 +0.978221 0.021779 +0.977776 0.022224 +0.990348 0.009652 +0.990643 0.009357 +0.984186 0.015814 +0.999990 0.000010 +0.994826 0.005174 +0.986693 0.013307 +0.999990 0.000010 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.906940 0.093060 +0.894807 0.105193 +0.863554 0.136446 +0.885512 0.114488 +0.924777 0.075223 +0.883801 0.116199 +0.911889 0.088111 +0.903530 0.096470 +0.888110 0.111890 +0.885385 0.114615 +0.887837 0.112163 +0.879687 0.120313 +0.885731 0.114269 +0.863364 0.136636 +0.880739 0.119261 +0.892843 0.107157 +0.875045 0.124955 +0.896514 0.103486 +0.919863 0.080137 +0.885190 0.114810 +0.877092 0.122908 +0.891549 0.108451 +0.100049 0.899951 +0.099348 0.900652 +0.127811 0.872189 +0.173264 0.826736 +0.185340 0.814660 +0.088611 0.911389 +0.109196 0.890804 +0.092310 0.907690 +0.075398 0.924602 +0.093584 0.906416 +0.156192 0.843808 +0.068594 0.931406 +0.105287 0.894713 +0.084155 0.915845 +0.098885 0.901115 +0.116176 0.883824 +0.095293 0.904707 +0.129415 0.870585 +0.098470 0.901530 +0.142204 0.857796 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.993258 0.006742 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.989663 0.010337 +0.997838 0.002162 +0.992376 0.007624 +0.999990 0.000010 +0.994989 0.005011 +0.999990 0.000010 +0.999990 0.000010 +0.998340 0.001660 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.003642 0.996358 +0.000010 0.999990 +0.000010 0.999990 +0.001394 0.998606 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.016185 0.983815 +0.030635 0.969365 +0.024417 0.975583 +0.029977 0.970023 +0.000010 0.999990 +0.000010 0.999990 +0.004236 0.995764 +0.035764 0.964236 +0.008739 0.991261 +0.041955 0.958045 +0.043679 0.956321 +0.028744 0.971256 +0.030183 0.969817 +0.019361 0.980639 +0.014867 0.985133 +0.020002 0.979998 +0.015413 0.984587 +0.038964 0.961036 +0.023808 0.976192 +0.056653 0.943347 +0.028872 0.971128 +0.018021 0.981979 +0.046033 0.953967 +0.000010 0.999990 +0.019491 0.980509 +0.001877 0.998123 +0.019087 0.980913 +0.010720 0.989280 +0.000010 0.999990 +0.002520 0.997480 +0.001007 0.998993 +0.033429 0.966571 +0.021135 0.978865 +0.007886 0.992114 +0.069356 0.930644 +0.017505 0.982495 +0.047702 0.952298 +0.000010 0.999990 +0.946353 0.053647 +0.953794 0.046206 +0.955227 0.044773 +0.940631 0.059369 +0.949578 0.050422 +0.961704 0.038296 +0.932977 0.067023 +0.932092 0.067908 +0.968531 0.031469 +0.956494 0.043506 +0.959133 0.040867 +0.955155 0.044845 +0.953826 0.046174 +0.932220 0.067780 +0.945342 0.054658 +0.937007 0.062993 +0.939635 0.060365 +0.958641 0.041359 +0.941544 0.058456 +0.966323 0.033677 +0.964589 0.035411 +0.006433 0.993567 +0.012026 0.987974 +0.010231 0.989769 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.013571 0.986429 +0.000010 0.999990 +0.001736 0.998264 +0.027763 0.972237 +0.478148 0.521852 +0.503475 0.496525 +0.437563 0.562437 +0.480773 0.519227 +0.456270 0.543730 +0.370425 0.629575 +0.501000 0.499000 +0.386789 0.613211 +0.417934 0.582066 +0.433074 0.566926 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000097 0.999903 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.054339 0.945661 +0.075870 0.924130 +0.036771 0.963229 +0.077444 0.922556 +0.050464 0.949536 +0.044442 0.955558 +0.074653 0.925347 +0.043170 0.956830 +0.044735 0.955265 +0.070820 0.929180 +0.999990 0.000010 +0.998922 0.001078 +0.992972 0.007028 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.986869 0.013131 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.892290 0.107710 +0.945811 0.054189 +0.933121 0.066879 +0.917572 0.082428 +0.937552 0.062448 +0.949890 0.050110 +0.890844 0.109156 +0.909863 0.090137 +0.944398 0.055602 +0.943121 0.056879 +0.937241 0.062759 +0.925813 0.074187 +0.931925 0.068075 +0.957478 0.042522 +0.891856 0.108144 +0.083971 0.916029 +0.073870 0.926130 +0.063511 0.936489 +0.075930 0.924070 +0.071598 0.928402 +0.070036 0.929964 +0.041507 0.958493 +0.045360 0.954640 +0.030488 0.969512 +0.051958 0.948042 +0.064531 0.935469 +0.056698 0.943302 +0.072063 0.927937 +0.046337 0.953663 +0.047191 0.952809 +0.072944 0.927056 +0.064992 0.935008 +0.040762 0.959238 +0.052228 0.947772 +0.038378 0.961622 +0.076911 0.923089 +0.056469 0.943531 +0.044509 0.955491 +0.035888 0.964112 +0.027242 0.972758 +0.061107 0.938893 +0.049495 0.950505 +0.311821 0.688179 +0.317934 0.682066 +0.320721 0.679279 +0.317862 0.682138 +0.319632 0.680368 +0.329292 0.670708 +0.311027 0.688973 +0.307445 0.692555 +0.332732 0.667268 +0.308071 0.691929 +0.320962 0.679038 +0.596269 0.403731 +0.564724 0.435276 +0.559244 0.440756 +0.562745 0.437255 +0.551194 0.448806 +0.566696 0.433304 +0.562043 0.437957 +0.556198 0.443802 +0.569775 0.430225 +0.553947 0.446053 +0.554977 0.445023 +0.542044 0.457956 +0.547317 0.452683 +0.721275 0.278725 +0.711551 0.288449 +0.706876 0.293124 +0.721482 0.278518 +0.755105 0.244895 +0.704089 0.295911 +0.714089 0.285911 +0.723267 0.276733 +0.716950 0.283050 +0.727614 0.272386 +0.718815 0.281185 +0.728592 0.271408 +0.706732 0.293268 +0.722374 0.277626 +0.719121 0.280879 +0.343538 0.656462 +0.353761 0.646239 +0.357394 0.642606 +0.350847 0.649153 +0.357290 0.642710 +0.347889 0.652111 +0.364478 0.635522 +0.359716 0.640284 +0.350618 0.649382 +0.347522 0.652478 +0.365916 0.634084 +0.363151 0.636849 +0.635578 0.364422 +0.593824 0.406176 +0.624183 0.375817 +0.604957 0.395043 +0.596837 0.403163 +0.621108 0.378892 +0.632349 0.367651 +0.619990 0.380010 +0.648403 0.351597 +0.622789 0.377211 +0.630606 0.369394 +0.624556 0.375444 +0.620468 0.379532 +0.581171 0.418829 +0.593819 0.406181 +0.586122 0.413878 +0.573683 0.426317 +0.602804 0.397196 +0.596642 0.403358 +0.608931 0.391069 +0.577841 0.422159 +0.574479 0.425521 +0.577653 0.422347 +0.601544 0.398456 +0.562081 0.437919 +0.586697 0.413303 +0.765166 0.234834 +0.937953 0.062047 +0.955709 0.044291 +0.932292 0.067708 +0.960235 0.039765 +0.944241 0.055759 +0.976384 0.023616 +0.980728 0.019272 +0.999990 0.000010 +0.880478 0.119522 +0.951157 0.048843 +0.972596 0.027404 +0.966413 0.033587 +0.974483 0.025517 +0.934515 0.065485 +0.957118 0.042882 +0.959657 0.040343 +0.876115 0.123885 +0.985551 0.014449 +0.962298 0.037702 +0.992286 0.007714 +0.979896 0.020104 +0.985892 0.014108 +0.979480 0.020520 +0.986630 0.013370 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.985829 0.014171 +0.999173 0.000827 +0.989277 0.010723 +0.994397 0.005603 +0.996787 0.003213 +0.999990 0.000010 +0.989119 0.010881 +0.999990 0.000010 +0.997090 0.002910 +0.987457 0.012543 +0.984450 0.015550 +0.990211 0.009789 +0.987458 0.012542 +0.994283 0.005717 +0.989399 0.010601 +0.984701 0.015299 +0.978507 0.021493 +0.986100 0.013900 +0.966698 0.033302 +0.928093 0.071907 +0.895174 0.104826 +0.934695 0.065305 +0.965711 0.034289 +0.975466 0.024534 +0.999696 0.000304 +0.975163 0.024837 +0.981515 0.018485 +0.988628 0.011372 +0.915221 0.084779 +0.905664 0.094336 +0.999990 0.000010 +0.923076 0.076924 +0.996504 0.003496 +0.967553 0.032447 +0.901028 0.098972 +0.967711 0.032289 +0.973985 0.026015 +0.967354 0.032646 +0.963470 0.036530 +0.965911 0.034089 +0.937590 0.062410 +0.970774 0.029226 +0.966415 0.033585 +0.971493 0.028507 +0.988232 0.011768 +0.894288 0.105712 +0.989279 0.010721 +0.962235 0.037765 +0.988050 0.011950 +0.958336 0.041664 +0.949607 0.050393 +0.989031 0.010969 +0.940136 0.059864 +0.982363 0.017637 +0.959015 0.040985 +0.996025 0.003975 +0.964029 0.035971 +0.979634 0.020366 +0.968849 0.031151 +0.974621 0.025379 +0.923203 0.076797 +0.934122 0.065878 +0.994831 0.005169 +0.988376 0.011624 +0.948132 0.051868 +0.912579 0.087421 +0.972927 0.027073 +0.988387 0.011613 +0.977269 0.022731 +0.964231 0.035769 +0.965457 0.034543 +0.918056 0.081944 +0.975987 0.024013 +0.985378 0.014622 +0.984661 0.015339 +0.956306 0.043694 +0.993677 0.006323 +0.971795 0.028205 +0.970722 0.029278 +0.929863 0.070137 +0.950588 0.049412 +0.904138 0.095862 +0.949767 0.050233 +0.986268 0.013732 +0.936188 0.063812 +0.950088 0.049912 +0.997449 0.002551 +0.980579 0.019421 +0.986263 0.013737 +0.944474 0.055526 +0.942520 0.057480 +0.941674 0.058326 +0.956463 0.043537 +0.980286 0.019714 +0.944346 0.055654 +0.956140 0.043860 +0.972042 0.027958 +0.905831 0.094169 +0.874802 0.125198 +0.976189 0.023811 +0.897879 0.102121 +0.943211 0.056789 +0.970771 0.029229 +0.992994 0.007006 +0.941741 0.058259 +0.765534 0.234466 +0.922161 0.077839 +0.888633 0.111367 +0.974528 0.025472 +0.894924 0.105076 +0.933040 0.066960 +0.954119 0.045881 +0.958982 0.041018 +0.978782 0.021218 +0.934685 0.065315 +0.912853 0.087147 +0.711699 0.288301 +0.774534 0.225466 +0.905083 0.094917 +0.989024 0.010976 +0.987913 0.012087 +0.878309 0.121691 +0.943553 0.056447 +0.958336 0.041664 +0.980206 0.019794 +0.984904 0.015096 +0.684584 0.315416 +0.183822 0.816178 +0.895566 0.104434 +0.981767 0.018233 +0.997810 0.002190 +0.891320 0.108680 +0.948058 0.051942 +0.957449 0.042551 +0.983272 0.016728 +0.983346 0.016654 +0.953543 0.046457 +0.912903 0.087097 +0.630824 0.369176 +0.178954 0.821046 +0.887756 0.112244 +0.971618 0.028382 +0.886470 0.113530 +0.902894 0.097106 +0.956978 0.043022 +0.970439 0.029561 +0.980483 0.019517 +0.929750 0.070250 +0.939915 0.060085 +0.935065 0.064935 +0.743596 0.256404 +0.206039 0.793961 +0.880440 0.119560 +0.986704 0.013296 +0.899316 0.100684 +0.893776 0.106224 +0.924267 0.075733 +0.972293 0.027707 +0.996288 0.003712 +0.951298 0.048702 +0.933614 0.066386 +0.919927 0.080073 +0.749466 0.250534 +0.161124 0.838876 +0.911473 0.088527 +0.989553 0.010447 +0.897847 0.102153 +0.936251 0.063749 +0.969573 0.030427 +0.999990 0.000010 +0.936902 0.063098 +0.982931 0.017069 +0.899113 0.100887 +0.760715 0.239285 +0.181990 0.818010 +0.911592 0.088408 +0.968472 0.031528 +0.915992 0.084008 +0.939126 0.060874 +0.955813 0.044187 +0.978772 0.021228 +0.979818 0.020182 +0.932151 0.067849 +0.906015 0.093985 +0.897917 0.102083 +0.740535 0.259465 +0.167619 0.832381 +0.140446 0.859554 +0.245507 0.754493 +0.160359 0.839641 +0.062519 0.937481 +0.299047 0.700953 +0.966880 0.033120 +0.971766 0.028234 +0.957419 0.042581 +0.896160 0.103840 +0.736020 0.263980 +0.548812 0.451188 +0.163407 0.836593 +0.261374 0.738626 +0.178820 0.821180 +0.207513 0.792487 +0.978451 0.021549 +0.954154 0.045846 +0.929405 0.070595 +0.893536 0.106464 +0.704198 0.295802 +0.506189 0.493811 +0.178694 0.821306 +0.254599 0.745401 +0.127922 0.872078 +0.123185 0.876815 +0.945806 0.054194 +0.948383 0.051617 +0.952123 0.047877 +0.874261 0.125739 +0.716427 0.283573 +0.552674 0.447326 +0.180821 0.819179 +0.164019 0.835981 +0.438809 0.561191 +0.296431 0.703569 +0.973196 0.026804 +0.937816 0.062184 +0.874002 0.125998 +0.911931 0.088069 +0.734672 0.265328 +0.437057 0.562943 +0.275542 0.724458 +0.150175 0.849825 +0.159429 0.840571 +0.622758 0.377242 +0.323898 0.676102 +0.951863 0.048137 +0.957612 0.042388 +0.910995 0.089005 +0.907221 0.092779 +0.716960 0.283040 +0.538903 0.461097 +0.241020 0.758980 +0.133064 0.866936 +0.143746 0.856254 +0.340761 0.659239 +0.950184 0.049816 +0.899476 0.100524 +0.756672 0.243328 +0.711340 0.288660 +0.666296 0.333704 +0.278559 0.721441 +0.147059 0.852941 +0.156344 0.843656 +0.390862 0.609138 +0.951798 0.048202 +0.951464 0.048536 +0.894559 0.105441 +0.720194 0.279806 +0.761688 0.238312 +0.673635 0.326365 +0.225985 0.774015 +0.189512 0.810488 +0.208648 0.791352 +0.231142 0.768858 +0.954819 0.045181 +0.971438 0.028562 +0.960058 0.039942 +0.916144 0.083856 +0.749152 0.250848 +0.496845 0.503155 +0.648122 0.351878 +0.552930 0.447070 +0.829166 0.170834 +0.850311 0.149689 +0.852046 0.147954 +0.588531 0.411469 +0.793495 0.206505 +0.842363 0.157637 +0.641554 0.358446 +0.802348 0.197652 +0.746228 0.253772 +0.978440 0.021560 +0.801184 0.198816 +0.691643 0.308357 +0.935869 0.064131 +0.519971 0.480029 +0.820685 0.179315 +0.679553 0.320447 +0.679653 0.320347 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.974208 0.025792 +0.984021 0.015979 +0.956171 0.043829 +0.985737 0.014263 +0.999990 0.000010 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.978549 0.021451 +0.977550 0.022450 +0.987629 0.012371 +0.977429 0.022571 +0.999990 0.000010 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.980571 0.019429 +0.971305 0.028695 +0.987074 0.012926 +0.994808 0.005192 +0.974543 0.025457 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.973523 0.026477 +0.999990 0.000010 +0.999990 0.000010 +0.976675 0.023325 +0.993911 0.006089 +0.000010 0.999990 +0.000010 0.999990 +0.891553 0.108447 +0.976702 0.023298 +0.982094 0.017906 +0.985765 0.014235 +0.978991 0.021009 +0.988526 0.011474 +0.000010 0.999990 +0.000010 0.999990 +0.984224 0.015776 +0.964271 0.035729 +0.967164 0.032836 +0.999990 0.000010 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.932370 0.067630 +0.972684 0.027316 +0.998581 0.001419 +0.977912 0.022088 +0.991237 0.008763 +0.000010 0.999990 +0.000010 0.999990 +0.000010 0.999990 +0.974600 0.025400 +0.991923 0.008077 +0.986840 0.013160 +0.976757 0.023243 +0.991329 0.008671 +0.000010 0.999990 +0.984499 0.015501 +0.987047 0.012953 +0.987420 0.012580 +0.981903 0.018097 +0.999990 0.000010 +0.999990 0.000010 +0.991094 0.008906 +0.991797 0.008203 +0.999990 0.000010 +0.996317 0.003683 +0.999990 0.000010 +0.995952 0.004048 +0.986941 0.013059 +0.999990 0.000010 +0.996389 0.003611 +0.991554 0.008446 +0.989656 0.010344 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.997026 0.002974 +0.999990 0.000010 +0.999990 0.000010 +0.988644 0.011356 +0.990154 0.009846 +0.999990 0.000010 +0.985096 0.014904 +0.999990 0.000010 +0.999990 0.000010 +0.993920 0.006080 +0.997038 0.002962 +0.999990 0.000010 +0.980971 0.019029 +0.976295 0.023705 +0.992726 0.007274 +0.979295 0.020705 +0.999990 0.000010 +0.992737 0.007263 +0.999990 0.000010 +0.997507 0.002493 +0.881054 0.118946 +0.914246 0.085754 +0.907017 0.092983 +0.909744 0.090256 +0.986328 0.013672 +0.892898 0.107102 +0.992907 0.007093 +0.915748 0.084252 +0.918924 0.081076 +0.893237 0.106763 +0.999990 0.000010 +0.996253 0.003747 +0.999990 0.000010 +0.998240 0.001760 +0.999990 0.000010 +0.999990 0.000010 +0.990101 0.009899 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.996630 0.003370 +0.989134 0.010866 +0.999990 0.000010 +0.999990 0.000010 +0.987267 0.012733 +0.999744 0.000256 +0.987797 0.012203 +0.988340 0.011660 +0.999990 0.000010 +0.978414 0.021586 +0.993258 0.006742 +0.991236 0.008764 +0.001076 0.998924 +0.016443 0.983557 +0.020928 0.979072 +0.000010 0.999990 +0.019113 0.980887 +0.012764 0.987236 +0.005818 0.994182 +0.012257 0.987743 +0.998241 0.001759 +0.999990 0.000010 +0.996461 0.003539 +0.999288 0.000712 +0.991910 0.008090 +0.624269 0.375731 +0.719030 0.280970 +0.631904 0.368096 +0.636312 0.363688 +0.626934 0.373066 +0.992541 0.007459 +0.570724 0.429276 +0.572430 0.427570 +0.579717 0.420283 +0.623715 0.376285 +0.663198 0.336802 +0.659516 0.340484 +0.571014 0.428986 +0.584007 0.415993 +0.561738 0.438262 +0.571454 0.428546 +0.114339 0.885661 +0.020838 0.979162 +0.145161 0.854839 +0.154697 0.845303 +0.042128 0.957872 +0.156573 0.843427 +0.084205 0.915795 +0.141030 0.858970 +0.122095 0.877905 +0.136547 0.863453 +0.982156 0.017844 +0.988962 0.011038 +0.999990 0.000010 +0.237034 0.762966 +0.953992 0.046008 +0.989604 0.010396 +0.990259 0.009741 +0.978717 0.021283 +0.978998 0.021002 +0.206480 0.793520 +0.977744 0.022256 +0.988259 0.011741 +0.260387 0.739613 +0.993168 0.006832 +0.998601 0.001399 +0.981157 0.018843 +0.298956 0.701044 +0.065809 0.934191 +0.987613 0.012387 +0.069613 0.930387 +0.994866 0.005134 +0.975124 0.024876 +0.165047 0.834953 +0.168511 0.831489 +0.935943 0.064057 +0.999990 0.000010 +0.984269 0.015731 +0.977231 0.022769 +0.979002 0.020998 +0.992639 0.007361 +0.077592 0.922408 +0.142119 0.857881 +0.998147 0.001853 +0.992356 0.007644 +0.999990 0.000010 +0.967827 0.032173 +0.984238 0.015762 +0.982930 0.017070 +0.247250 0.752750 +0.993296 0.006704 +0.918370 0.081630 +0.958444 0.041556 +0.982736 0.017264 +0.999887 0.000113 +0.970217 0.029783 +0.211400 0.788600 +0.076779 0.923221 +0.999990 0.000010 +0.986302 0.013698 +0.059097 0.940903 +0.018905 0.981095 +0.967432 0.032568 +0.975727 0.024273 +0.983540 0.016460 +0.999990 0.000010 +0.999691 0.000309 +0.999990 0.000010 +0.999990 0.000010 +0.990975 0.009025 +0.990979 0.009021 +0.983416 0.016584 +0.983493 0.016507 +0.999990 0.000010 +0.989143 0.010857 +0.978965 0.021035 +0.999990 0.000010 +0.999990 0.000010 +0.992803 0.007197 +0.993189 0.006811 +0.999990 0.000010 +0.984120 0.015880 +0.994641 0.005359 +0.999990 0.000010 +0.991915 0.008085 +0.989608 0.010392 +0.982667 0.017333 +0.999990 0.000010 +0.997701 0.002299 +0.979636 0.020364 +0.871421 0.128579 +0.999990 0.000010 +0.990139 0.009861 +0.953473 0.046527 +0.999990 0.000010 +0.953721 0.046279 +0.145067 0.854933 +0.999990 0.000010 +0.993501 0.006499 +0.989101 0.010899 +0.989397 0.010603 +0.938836 0.061164 +0.955841 0.044159 +0.984986 0.015014 +0.889988 0.110012 +0.999990 0.000010 +0.946933 0.053067 +0.991854 0.008146 +0.977778 0.022222 +0.852385 0.147615 +0.984304 0.015696 +0.985580 0.014420 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.943434 0.056566 +0.935674 0.064326 +0.982149 0.017851 +0.987663 0.012337 +0.996625 0.003375 +0.994586 0.005414 +0.992542 0.007458 +0.977144 0.022856 +0.973472 0.026528 +0.875681 0.124319 +0.999990 0.000010 +0.994718 0.005282 +0.999990 0.000010 +0.952969 0.047031 +0.995193 0.004807 +0.958929 0.041071 +0.943518 0.056482 +0.998840 0.001160 +0.995425 0.004575 +0.940834 0.059166 +0.990457 0.009543 +0.981173 0.018827 +0.912102 0.087898 +0.999990 0.000010 +0.932021 0.067979 +0.999990 0.000010 +0.982369 0.017631 +0.992711 0.007289 +0.994767 0.005233 +0.938256 0.061744 +0.980182 0.019818 +0.994157 0.005843 +0.930840 0.069160 +0.858098 0.141902 +0.984678 0.015322 +0.941628 0.058372 +0.978464 0.021536 +0.983061 0.016939 +0.952161 0.047839 +0.980357 0.019643 +0.991655 0.008345 +0.973345 0.026655 +0.984684 0.015316 +0.934147 0.065853 +0.982455 0.017545 +0.978098 0.021902 +0.999990 0.000010 +0.982850 0.017150 +0.939018 0.060982 +0.984061 0.015939 +0.954739 0.045261 +0.982884 0.017116 +0.999990 0.000010 +0.952179 0.047821 +0.944404 0.055596 +0.996166 0.003834 +0.956560 0.043440 +0.976764 0.023236 +0.984379 0.015621 +0.997737 0.002263 +0.999903 0.000097 +0.938238 0.061762 +0.999250 0.000750 +0.991581 0.008419 +0.942929 0.057071 +0.999990 0.000010 +0.859202 0.140798 +0.992944 0.007056 +0.912243 0.087757 +0.994454 0.005546 +0.988595 0.011405 +0.977527 0.022473 +0.982523 0.017477 +0.982057 0.017943 +0.993894 0.006106 +0.999990 0.000010 +0.962409 0.037591 +0.951425 0.048575 +0.992880 0.007120 +0.976262 0.023738 +0.941897 0.058103 +0.999990 0.000010 +0.999990 0.000010 +0.981392 0.018608 +0.291498 0.708502 +0.943333 0.056667 +0.993202 0.006798 +0.973311 0.026689 +0.987534 0.012466 +0.999990 0.000010 +0.998301 0.001699 +0.993403 0.006597 +0.886574 0.113426 +0.946603 0.053397 +0.938432 0.061568 +0.940860 0.059140 +0.966984 0.033016 +0.982368 0.017632 +0.989932 0.010068 +0.993816 0.006184 +0.984810 0.015190 +0.991756 0.008244 +0.834285 0.165715 +0.976847 0.023153 +0.969034 0.030966 +0.303017 0.696983 +0.999990 0.000010 +0.974392 0.025608 +0.978728 0.021272 +0.999990 0.000010 +0.926952 0.073048 +0.846137 0.153863 +0.912212 0.087788 +0.855224 0.144776 +0.903645 0.096355 +0.924882 0.075118 +0.824304 0.175696 +0.887812 0.112188 +0.998722 0.001278 +0.318342 0.681658 +0.948810 0.051190 +0.286935 0.713065 +0.999990 0.000010 +0.985902 0.014098 +0.947287 0.052713 +0.298409 0.701591 +0.970752 0.029248 +0.878204 0.121796 +0.939598 0.060402 +0.844159 0.155841 +0.837458 0.162542 +0.908723 0.091277 +0.970786 0.029214 +0.999990 0.000010 +0.865286 0.134714 +0.301730 0.698270 +0.899579 0.100421 +0.908277 0.091723 +0.970176 0.029824 +0.918151 0.081849 +0.999990 0.000010 +0.905773 0.094227 +0.901063 0.098937 +0.997685 0.002315 +0.924283 0.075717 +0.945932 0.054068 +0.979349 0.020651 +0.943496 0.056504 +0.324151 0.675849 +0.941777 0.058223 +0.824536 0.175464 +0.846332 0.153668 +0.853868 0.146132 +0.937387 0.062613 +0.318427 0.681573 +0.847776 0.152224 +0.999990 0.000010 +0.872534 0.127466 +0.289538 0.710462 +0.912764 0.087236 +0.939753 0.060247 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.912408 0.087592 +0.999990 0.000010 +0.953205 0.046795 +0.933773 0.066227 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.999990 0.000010 +0.964237 0.035763 diff --git a/inst/files/admixturegrplabels.txt b/inst/files/admixturegrplabels.txt new file mode 100644 index 0000000..3fab99e --- /dev/null +++ b/inst/files/admixturegrplabels.txt @@ -0,0 +1,1592 @@ +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop C +Pop C +Pop C +Pop C +Pop C +Pop C +Pop C +Pop C +Pop C +Pop C +Pop C +Pop C +Pop C +Pop C +Pop C +Pop C +Pop C +Pop C +Pop C +Pop C +Pop C +Pop C +Pop C +Pop C +Pop C +Pop C +Pop C +Pop C +Pop C +Pop C +Pop C +Pop C +Pop C +Pop C +Pop C +Pop C +Pop C +Pop C +Pop C +Pop C +Pop C +Pop D +Pop D +Pop D +Pop D +Pop D +Pop D +Pop D +Pop D +Pop D +Pop D +Pop D +Pop D +Pop D +Pop D +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop G +Pop G +Pop G +Pop G +Pop G +Pop G +Pop G +Pop G +Pop H +Pop H +Pop H +Pop H +Pop H +Pop H +Pop H +Pop H +Pop H +Pop H +Pop H +Pop H +Pop H +Pop H +Pop H +Pop H +Pop H +Pop H +Pop I +Pop I +Pop I +Pop I +Pop I +Pop I +Pop I +Pop I +Pop I +Pop I +Pop I +Pop I +Pop I +Pop I +Pop I +Pop I +Pop I +Pop I +Pop I +Pop I +Pop I +Pop I +Pop I +Pop I +Pop I +Pop I +Pop I +Pop I +Pop I +Pop I +Pop I +Pop I +Pop I +Pop I +Pop I +Pop I +Pop I +Pop I +Pop I +Pop I +Pop J +Pop J +Pop J +Pop J +Pop J +Pop J +Pop J +Pop J +Pop J +Pop J +Pop J +Pop J +Pop J +Pop K +Pop K +Pop K +Pop K +Pop K +Pop K +Pop K +Pop K +Pop K +Pop K +Pop K +Pop K +Pop L +Pop L +Pop L +Pop L +Pop L +Pop L +Pop L +Pop L +Pop L +Pop L +Pop L +Pop L +Pop L +Pop L +Pop L +Pop L +Pop L +Pop L +Pop L +Pop L +Pop L +Pop L +Pop M +Pop M +Pop M +Pop M +Pop M +Pop M +Pop M +Pop M +Pop M +Pop M +Pop M +Pop M +Pop M +Pop M +Pop M +Pop M +Pop M +Pop M +Pop M +Pop M +Pop M +Pop M +Pop M +Pop M +Pop M +Pop M +Pop M +Pop M +Pop M +Pop M +Pop N +Pop N +Pop N +Pop N +Pop N +Pop N +Pop N +Pop N +Pop N +Pop N +Pop N +Pop N +Pop N +Pop N +Pop N +Pop N +Pop N +Pop N +Pop O +Pop O +Pop O +Pop O +Pop O +Pop O +Pop O +Pop O +Pop O +Pop O +Pop P +Pop P +Pop P +Pop P +Pop P +Pop P +Pop P +Pop P +Pop P +Pop P +Pop P +Pop P +Pop P +Pop P +Pop P +Pop P +Pop P +Pop P +Pop P +Pop P +Pop Q +Pop Q +Pop Q +Pop Q +Pop Q +Pop Q +Pop Q +Pop Q +Pop Q +Pop Q +Pop Q +Pop Q +Pop Q +Pop Q +Pop Q +Pop Q +Pop Q +Pop Q +Pop Q +Pop Q +Pop Q +Pop Q +Pop Q +Pop Q +Pop Q +Pop Q +Pop Q +Pop Q +Pop Q +Pop Q +Pop Q +Pop Q +Pop Q +Pop Q +Pop Q +Pop Q +Pop Q +Pop Q +Pop Q +Pop Q +Pop Q +Pop Q +Pop Q +Pop Q +Pop Q +Pop Q +Pop Q +Pop Q +Pop Q +Pop Q +Pop Q +Pop Q +Pop Q +Pop Q +Pop Q +Pop Q +Pop Q +Pop Q +Pop Q +Pop R +Pop R +Pop R +Pop R +Pop R +Pop R +Pop R +Pop R +Pop R +Pop R +Pop R +Pop R +Pop R +Pop R +Pop R +Pop R +Pop R +Pop R +Pop R +Pop R +Pop R +Pop S +Pop S +Pop S +Pop S +Pop S +Pop S +Pop S +Pop S +Pop S +Pop S +Pop T +Pop T +Pop T +Pop T +Pop T +Pop T +Pop T +Pop T +Pop T +Pop T +Pop U +Pop U +Pop U +Pop U +Pop U +Pop U +Pop U +Pop U +Pop U +Pop U +Pop U +Pop U +Pop U +Pop U +Pop U +Pop U +Pop U +Pop U +Pop U +Pop U +Pop U +Pop U +Pop U +Pop U +Pop U +Pop U +Pop U +Pop U +Pop U +Pop U +Pop U +Pop U +Pop U +Pop U +Pop U +Pop U +Pop U +Pop U +Pop U +Pop U +Pop U +Pop U +Pop U +Pop U +Pop U +Pop U +Pop U +Pop V +Pop V +Pop V +Pop V +Pop V +Pop V +Pop V +Pop V +Pop V +Pop V +Pop V +Pop V +Pop V +Pop V +Pop V +Pop V +Pop V +Pop V +Pop V +Pop V +Pop V +Pop V +Pop V +Pop V +Pop V +Pop V +Pop V +Pop V +Pop V +Pop V +Pop V +Pop V +Pop V +Pop V +Pop V +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA diff --git a/inst/files/admixturepoplabels.txt b/inst/files/admixturepoplabels.txt new file mode 100644 index 0000000..3fab99e --- /dev/null +++ b/inst/files/admixturepoplabels.txt @@ -0,0 +1,1592 @@ +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop C +Pop C +Pop C +Pop C +Pop C +Pop C +Pop C +Pop C +Pop C +Pop C +Pop C +Pop C +Pop C +Pop C +Pop C +Pop C +Pop C +Pop C +Pop C +Pop C +Pop C +Pop C +Pop C +Pop C +Pop C +Pop C +Pop C +Pop C +Pop C +Pop C +Pop C +Pop C +Pop C +Pop C +Pop C +Pop C +Pop C +Pop C +Pop C +Pop C +Pop C +Pop D +Pop D +Pop D +Pop D +Pop D +Pop D +Pop D +Pop D +Pop D +Pop D +Pop D +Pop D +Pop D +Pop D +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop E +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop F +Pop G +Pop G +Pop G +Pop G +Pop G +Pop G +Pop G +Pop G +Pop H +Pop H +Pop H +Pop H +Pop H +Pop H +Pop H +Pop H +Pop H +Pop H +Pop H +Pop H +Pop H +Pop H +Pop H +Pop H +Pop H +Pop H +Pop I +Pop I +Pop I +Pop I +Pop I +Pop I +Pop I +Pop I +Pop I +Pop I +Pop I +Pop I +Pop I +Pop I +Pop I +Pop I +Pop I +Pop I +Pop I +Pop I +Pop I +Pop I +Pop I +Pop I +Pop I +Pop I +Pop I +Pop I +Pop I +Pop I +Pop I +Pop I +Pop I +Pop I +Pop I +Pop I +Pop I +Pop I +Pop I +Pop I +Pop J +Pop J +Pop J +Pop J +Pop J +Pop J +Pop J +Pop J +Pop J +Pop J +Pop J +Pop J +Pop J +Pop K +Pop K +Pop K +Pop K +Pop K +Pop K +Pop K +Pop K +Pop K +Pop K +Pop K +Pop K +Pop L +Pop L +Pop L +Pop L +Pop L +Pop L +Pop L +Pop L +Pop L +Pop L +Pop L +Pop L +Pop L +Pop L +Pop L +Pop L +Pop L +Pop L +Pop L +Pop L +Pop L +Pop L +Pop M +Pop M +Pop M +Pop M +Pop M +Pop M +Pop M +Pop M +Pop M +Pop M +Pop M +Pop M +Pop M +Pop M +Pop M +Pop M +Pop M +Pop M +Pop M +Pop M +Pop M +Pop M +Pop M +Pop M +Pop M +Pop M +Pop M +Pop M +Pop M +Pop M +Pop N +Pop N +Pop N +Pop N +Pop N +Pop N +Pop N +Pop N +Pop N +Pop N +Pop N +Pop N +Pop N +Pop N +Pop N +Pop N +Pop N +Pop N +Pop O +Pop O +Pop O +Pop O +Pop O +Pop O +Pop O +Pop O +Pop O +Pop O +Pop P +Pop P +Pop P +Pop P +Pop P +Pop P +Pop P +Pop P +Pop P +Pop P +Pop P +Pop P +Pop P +Pop P +Pop P +Pop P +Pop P +Pop P +Pop P +Pop P +Pop Q +Pop Q +Pop Q +Pop Q +Pop Q +Pop Q +Pop Q +Pop Q +Pop Q +Pop Q +Pop Q +Pop Q +Pop Q +Pop Q +Pop Q +Pop Q +Pop Q +Pop Q +Pop Q +Pop Q +Pop Q +Pop Q +Pop Q +Pop Q +Pop Q +Pop Q +Pop Q +Pop Q +Pop Q +Pop Q +Pop Q +Pop Q +Pop Q +Pop Q +Pop Q +Pop Q +Pop Q +Pop Q +Pop Q +Pop Q +Pop Q +Pop Q +Pop Q +Pop Q +Pop Q +Pop Q +Pop Q +Pop Q +Pop Q +Pop Q +Pop Q +Pop Q +Pop Q +Pop Q +Pop Q +Pop Q +Pop Q +Pop Q +Pop Q +Pop R +Pop R +Pop R +Pop R +Pop R +Pop R +Pop R +Pop R +Pop R +Pop R +Pop R +Pop R +Pop R +Pop R +Pop R +Pop R +Pop R +Pop R +Pop R +Pop R +Pop R +Pop S +Pop S +Pop S +Pop S +Pop S +Pop S +Pop S +Pop S +Pop S +Pop S +Pop T +Pop T +Pop T +Pop T +Pop T +Pop T +Pop T +Pop T +Pop T +Pop T +Pop U +Pop U +Pop U +Pop U +Pop U +Pop U +Pop U +Pop U +Pop U +Pop U +Pop U +Pop U +Pop U +Pop U +Pop U +Pop U +Pop U +Pop U +Pop U +Pop U +Pop U +Pop U +Pop U +Pop U +Pop U +Pop U +Pop U +Pop U +Pop U +Pop U +Pop U +Pop U +Pop U +Pop U +Pop U +Pop U +Pop U +Pop U +Pop U +Pop U +Pop U +Pop U +Pop U +Pop U +Pop U +Pop U +Pop U +Pop V +Pop V +Pop V +Pop V +Pop V +Pop V +Pop V +Pop V +Pop V +Pop V +Pop V +Pop V +Pop V +Pop V +Pop V +Pop V +Pop V +Pop V +Pop V +Pop V +Pop V +Pop V +Pop V +Pop V +Pop V +Pop V +Pop V +Pop V +Pop V +Pop V +Pop V +Pop V +Pop V +Pop V +Pop V +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop W +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop X +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Y +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop Z +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA +Pop AA diff --git a/inst/files/baps/baps_k2-1.txt b/inst/files/baps/baps_k2-1.txt new file mode 100644 index 0000000..5328c5d --- /dev/null +++ b/inst/files/baps/baps_k2-1.txt @@ -0,0 +1,56 @@ + +--------------------------------------------------- +RESULTS OF ADMIXTURE ANALYSIS BASED +ON MIXTURE CLUSTERING OF INDIVIDUALS +Data file: virosu_m3n3_23484_47_pop_from_grad_mixtured.mat +Number of individuals: 47 +Results based on 50 simulations from posterior allele frequencies. + + 1 2 p +1: 1.00 0.00: 1 +2: 1.00 0.00: 1 +3: 1.00 0.00: 1 +4: 1.00 0.00: 1 +5: 1.00 0.00: 1 +6: 1.00 0.00: 1 +7: 1.00 0.00: 1 +8: 1.00 0.00: 1 +9: 1.00 0.00: 1 +10: 1.00 0.00: 1 +11: 1.00 0.00: 1 +12: 1.00 0.00: 1 +13: 1.00 0.00: 1 +14: 1.00 0.00: 1 +15: 0.85 0.15: 0 +16: 1.00 0.00: 1 +17: 0.61 0.39: 0 +18: 1.00 0.00: 1 +19: 0.81 0.19: 0 +20: 0.74 0.26: 0 +21: 0.00 1.00: 1 +22: 0.00 1.00: 1 +23: 0.00 1.00: 1 +24: 0.00 1.00: 1 +25: 0.12 0.88: 0 +26: 0.16 0.84: 0 +27: 0.00 1.00: 1 +28: 0.00 1.00: 1 +29: 0.00 1.00: 1 +30: 0.00 1.00: 1 +31: 0.00 1.00: 1 +32: 0.00 1.00: 1 +33: 0.00 1.00: 1 +34: 0.16 0.84: 0 +35: 0.00 1.00: 1 +36: 0.00 1.00: 1 +37: 0.00 1.00: 1 +38: 0.00 1.00: 1 +39: 0.00 1.00: 1 +40: 0.14 0.86: 0 +41: 0.23 0.77: 0 +42: 0.22 0.78: 0 +43: 0.15 0.85: 0 +44: 0.00 1.00: 1 +45: 0.27 0.73: 0 +46: 0.00 1.00: 1 +47: 0.42 0.58: 0 diff --git a/inst/files/baps/baps_k2.txt b/inst/files/baps/baps_k2.txt new file mode 100644 index 0000000..5328c5d --- /dev/null +++ b/inst/files/baps/baps_k2.txt @@ -0,0 +1,56 @@ + +--------------------------------------------------- +RESULTS OF ADMIXTURE ANALYSIS BASED +ON MIXTURE CLUSTERING OF INDIVIDUALS +Data file: virosu_m3n3_23484_47_pop_from_grad_mixtured.mat +Number of individuals: 47 +Results based on 50 simulations from posterior allele frequencies. + + 1 2 p +1: 1.00 0.00: 1 +2: 1.00 0.00: 1 +3: 1.00 0.00: 1 +4: 1.00 0.00: 1 +5: 1.00 0.00: 1 +6: 1.00 0.00: 1 +7: 1.00 0.00: 1 +8: 1.00 0.00: 1 +9: 1.00 0.00: 1 +10: 1.00 0.00: 1 +11: 1.00 0.00: 1 +12: 1.00 0.00: 1 +13: 1.00 0.00: 1 +14: 1.00 0.00: 1 +15: 0.85 0.15: 0 +16: 1.00 0.00: 1 +17: 0.61 0.39: 0 +18: 1.00 0.00: 1 +19: 0.81 0.19: 0 +20: 0.74 0.26: 0 +21: 0.00 1.00: 1 +22: 0.00 1.00: 1 +23: 0.00 1.00: 1 +24: 0.00 1.00: 1 +25: 0.12 0.88: 0 +26: 0.16 0.84: 0 +27: 0.00 1.00: 1 +28: 0.00 1.00: 1 +29: 0.00 1.00: 1 +30: 0.00 1.00: 1 +31: 0.00 1.00: 1 +32: 0.00 1.00: 1 +33: 0.00 1.00: 1 +34: 0.16 0.84: 0 +35: 0.00 1.00: 1 +36: 0.00 1.00: 1 +37: 0.00 1.00: 1 +38: 0.00 1.00: 1 +39: 0.00 1.00: 1 +40: 0.14 0.86: 0 +41: 0.23 0.77: 0 +42: 0.22 0.78: 0 +43: 0.15 0.85: 0 +44: 0.00 1.00: 1 +45: 0.27 0.73: 0 +46: 0.00 1.00: 1 +47: 0.42 0.58: 0 diff --git a/inst/files/basic/comma/basic-comma-k3.csv b/inst/files/basic/comma/basic-comma-k3.csv new file mode 100644 index 0000000..0cbd156 --- /dev/null +++ b/inst/files/basic/comma/basic-comma-k3.csv @@ -0,0 +1,75 @@ +0.92633,0.057885,0.015785 +0.68248,0.307585,0.009935 +0.935345,0.05991,0.004745 +0.877755,0.108125,0.01412 +0.855695,0.128085,0.01622 +0.94049,0.053025,0.006485 +0.4792,0.393205,0.127595 +0.67483,0.311105,0.014065 +0.71559,0.263975,0.020435 +0.760645,0.19124,0.048115 +0.736425,0.21584,0.047735 +0.79977,0.191755,0.008475 +0.74638,0.233435,0.020185 +0.91399,0.06757,0.01844 +0.813655,0.167695,0.01865 +0.961345,0.034485,0.00417 +0.664755,0.317515,0.01773 +0.8359,0.14073,0.02337 +0.784935,0.120195,0.09487 +0.813735,0.142155,0.04411 +0.669755,0.27439,0.055855 +0.696605,0.136065,0.16733 +0.95993,0.035815,0.004255 +0.765655,0.225335,0.00901 +0.93428,0.057075,0.008645 +0.721295,0.261755,0.01695 +0.90934,0.079875,0.010785 +0.963815,0.03178,0.004405 +0.91296,0.068685,0.018355 +0.64133,0.32156,0.03711 +0.58481,0.40821,0.00698 +0.77754,0.21508,0.00738 +0.52871,0.457225,0.014065 +0.55024,0.44282,0.00694 +0.796835,0.1804,0.022765 +0.931815,0.05093,0.017255 +0.915155,0.07507,0.009775 +0.685855,0.30715,0.006995 +0.66243,0.321105,0.016465 +0.731645,0.26421,0.004145 +0.91696,0.076265,0.006775 +0.67236,0.32263,0.00501 +0.89296,0.102485,0.004555 +0.752315,0.244275,0.00341 +0.91062,0.064775,0.024605 +0.88845,0.10221,0.00934 +0.90092,0.073475,0.025605 +0.690555,0.27085,0.038595 +0.62902,0.29397,0.07701 +0.92489,0.04776,0.02735 +0.856255,0.0875,0.056245 +0.94584,0.043995,0.010165 +0.8982,0.09126,0.01054 +0.88973,0.06803,0.04224 +0.764175,0.220515,0.01531 +0.933695,0.05207,0.014235 +0.93678,0.044045,0.019175 +0.949515,0.041625,0.00886 +0.892755,0.063405,0.04384 +0.67181,0.26196,0.06623 +0.94439,0.042755,0.012855 +0.683955,0.269325,0.04672 +0.885265,0.08908,0.025655 +0.84537,0.08784,0.06679 +0.943995,0.027945,0.02806 +0.970395,0.01639,0.013215 +0.9156,0.080305,0.004095 +0.96383,0.024145,0.012025 +0.98202,0.010825,0.007155 +0.946585,0.04552,0.007895 +0.979385,0.01676,0.003855 +0.712255,0.27954,0.008205 +0.655345,0.340465,0.00419 +0.706595,0.283935,0.00947 +0.87072,0.120915,0.008365 diff --git a/inst/files/basic/comma/basic-comma-k4.csv b/inst/files/basic/comma/basic-comma-k4.csv new file mode 100644 index 0000000..c702123 --- /dev/null +++ b/inst/files/basic/comma/basic-comma-k4.csv @@ -0,0 +1,75 @@ +0.955705,0.02329,0.010225,0.01078 +0.97025,0.00978,0.011555,0.008415 +0.988065,0.0045,0.004015,0.00342 +0.956495,0.016455,0.01188,0.01517 +0.975235,0.010725,0.007525,0.006515 +0.9846,0.00728,0.00515,0.00297 +0.6624,0.171935,0.096505,0.06916 +0.953795,0.01761,0.017365,0.01123 +0.947975,0.014595,0.02233,0.0151 +0.871835,0.059255,0.024305,0.044605 +0.894005,0.049685,0.024755,0.031555 +0.977285,0.00981,0.006085,0.00682 +0.94224,0.022565,0.012215,0.02298 +0.94773,0.03007,0.01202,0.01018 +0.956865,0.01837,0.01221,0.012555 +0.988305,0.004275,0.004155,0.003265 +0.92505,0.038375,0.017735,0.01884 +0.919855,0.035305,0.018225,0.026615 +0.56458,0.329155,0.018835,0.08743 +0.778205,0.108265,0.006135,0.107395 +0.82095,0.113005,0.013575,0.05247 +0.51192,0.37259,0.018025,0.097465 +0.983605,0.010075,0.001605,0.004715 +0.96554,0.021285,0.00327,0.009905 +0.97407,0.016685,0.002805,0.00644 +0.948345,0.02342,0.01071,0.017525 +0.94937,0.02445,0.011645,0.014535 +0.97971,0.0102,0.00413,0.00596 +0.92199,0.02293,0.03244,0.02264 +0.885585,0.032595,0.04551,0.03631 +0.96793,0.010835,0.00997,0.011265 +0.98554,0.004815,0.005455,0.00419 +0.940185,0.013145,0.02165,0.02502 +0.963735,0.00625,0.01634,0.013675 +0.956795,0.0125,0.01349,0.017215 +0.94098,0.01704,0.02271,0.01927 +0.972195,0.00999,0.010835,0.00698 +0.981735,0.003055,0.010665,0.004545 +0.971005,0.00665,0.01679,0.005555 +0.98738,0.00299,0.005655,0.003975 +0.987855,0.003515,0.005265,0.003365 +0.9918,0.00269,0.00394,0.00157 +0.985485,0.00453,0.006025,0.00396 +0.98447,0.0048,0.006375,0.004355 +0.917025,0.03599,0.024245,0.02274 +0.97876,0.00874,0.006855,0.005645 +0.91806,0.03041,0.02809,0.02344 +0.908525,0.02561,0.03833,0.027535 +0.777225,0.07074,0.07886,0.073175 +0.89878,0.052275,0.031945,0.017 +0.855605,0.052475,0.06131,0.03061 +0.972265,0.009335,0.008475,0.009925 +0.97398,0.01123,0.005605,0.009185 +0.89581,0.037245,0.03086,0.036085 +0.94447,0.01938,0.01964,0.01651 +0.9557,0.01858,0.012855,0.012865 +0.924785,0.036545,0.020675,0.017995 +0.974025,0.01013,0.00777,0.008075 +0.90148,0.041965,0.028315,0.02824 +0.829025,0.060805,0.04,0.07017 +0.93776,0.03093,0.010225,0.021085 +0.79285,0.119565,0.03256,0.055025 +0.904355,0.05374,0.01133,0.030575 +0.83107,0.07136,0.05018,0.04739 +0.832325,0.124045,0.012075,0.031555 +0.88716,0.08679,0.006475,0.019575 +0.97331,0.0142,0.00405,0.00844 +0.91785,0.04062,0.01191,0.02962 +0.97859,0.008935,0.00536,0.007115 +0.9638,0.013895,0.007115,0.01519 +0.97802,0.009835,0.005215,0.00693 +0.978475,0.005615,0.00879,0.00712 +0.98059,0.00449,0.00887,0.00605 +0.950055,0.011995,0.022745,0.015205 +0.971085,0.007535,0.012945,0.008435 diff --git a/inst/files/basic/comma/basic-comma-k5.csv b/inst/files/basic/comma/basic-comma-k5.csv new file mode 100644 index 0000000..0cd9798 --- /dev/null +++ b/inst/files/basic/comma/basic-comma-k5.csv @@ -0,0 +1,75 @@ +0.78766,0.035545,0.021665,0.14898,0.00615 +0.817585,0.095465,0.022575,0.05413,0.010245 +0.935455,0.02521,0.007015,0.03066,0.00166 +0.767805,0.06457,0.029915,0.131635,0.006075 +0.83655,0.023065,0.042845,0.09518,0.00236 +0.916895,0.012525,0.0118,0.05622,0.00256 +0.414585,0.107505,0.15073,0.3227,0.00448 +0.72307,0.097715,0.07069,0.103095,0.00543 +0.762105,0.04293,0.13013,0.062035,0.0028 +0.70074,0.071655,0.05636,0.161935,0.00931 +0.586635,0.05431,0.05497,0.29668,0.007405 +0.865345,0.064235,0.01624,0.04942,0.00476 +0.742435,0.086295,0.025555,0.13856,0.007155 +0.847705,0.031365,0.0165,0.098125,0.006305 +0.814595,0.063985,0.02,0.09379,0.00763 +0.93737,0.021225,0.01002,0.029015,0.00237 +0.748705,0.08654,0.030325,0.125095,0.009335 +0.80061,0.053275,0.031685,0.10252,0.01191 +0.5744,0.056205,0.024215,0.330255,0.014925 +0.732615,0.07454,0.03534,0.141665,0.01584 +0.5035,0.17423,0.022075,0.28575,0.014445 +0.39582,0.27067,0.03361,0.280365,0.019535 +0.922555,0.008115,0.002015,0.065815,0.0015 +0.809655,0.067335,0.0077,0.1107,0.00461 +0.86916,0.038795,0.00787,0.07916,0.005015 +0.778535,0.108365,0.012665,0.0945,0.005935 +0.895745,0.044455,0.00887,0.042595,0.008335 +0.908325,0.04238,0.00522,0.04177,0.002305 +0.868345,0.07802,0.00674,0.03187,0.015025 +0.56275,0.39761,0.00931,0.020535,0.009795 +0.511225,0.46806,0.005765,0.013875,0.001075 +0.773375,0.198245,0.010645,0.015295,0.00244 +0.419985,0.55089,0.01508,0.010195,0.00385 +0.40169,0.585635,0.00524,0.005285,0.00215 +0.71916,0.2319,0.0106,0.032,0.00634 +0.83843,0.064685,0.02569,0.060065,0.01113 +0.86688,0.05349,0.016175,0.058465,0.00499 +0.888505,0.056145,0.025365,0.027445,0.00254 +0.849665,0.12689,0.006785,0.010825,0.005835 +0.93623,0.036545,0.00246,0.02108,0.003685 +0.94056,0.034055,0.01003,0.013065,0.00229 +0.75386,0.22233,0.008965,0.0136,0.001245 +0.896105,0.034175,0.013355,0.0546,0.001765 +0.89573,0.0555,0.023825,0.02268,0.002265 +0.74449,0.00881,0.101545,0.13998,0.005175 +0.819225,0.003525,0.023335,0.15206,0.001855 +0.854465,0.01019,0.049865,0.081295,0.004185 +0.5951,0.000515,0.39305,0.01106,0.000275 +0.5959,0.02486,0.1428,0.23272,0.00372 +0.612745,0.014675,0.10044,0.269185,0.002955 +0.70953,0.025255,0.117545,0.1434,0.00427 +0.867065,0.004685,0.03237,0.09496,0.00092 +0.887065,0.018265,0.02047,0.070735,0.003465 +0.66819,0.01788,0.163935,0.14256,0.007435 +0.716825,0.024995,0.081275,0.17009,0.006815 +0.812025,0.014975,0.043445,0.12376,0.005795 +0.656825,0.00689,0.034025,0.29661,0.00565 +0.873575,0.005165,0.01631,0.102345,0.002605 +0.572085,0.02273,0.03966,0.35916,0.006365 +0.56452,0.072335,0.0632,0.28911,0.010835 +0.869835,0.02069,0.03275,0.06602,0.010705 +0.57763,0.136195,0.051195,0.212715,0.022265 +0.66577,0.02718,0.028125,0.26848,0.010445 +0.500445,0.042015,0.09259,0.34561,0.01934 +0.466745,0.023915,0.003565,0.498015,0.00776 +0.76947,0.037415,0.00595,0.18161,0.005555 +0.85616,0.02724,0.003685,0.10895,0.003965 +0.83213,0.031305,0.004875,0.122325,0.009365 +0.914005,0.013695,0.00435,0.06094,0.00701 +0.837785,0.027755,0.00619,0.117055,0.011215 +0.936495,0.012705,0.00352,0.04292,0.00436 +0.90621,0.056205,0.00451,0.02912,0.003955 +0.276935,0.72192,0.000435,0.00037,0.00034 +0.72359,0.240885,0.005445,0.02553,0.00455 +0.8404,0.107435,0.010435,0.032995,0.008735 diff --git a/inst/files/basic/space/basic-space-k3.txt b/inst/files/basic/space/basic-space-k3.txt new file mode 100644 index 0000000..82da734 --- /dev/null +++ b/inst/files/basic/space/basic-space-k3.txt @@ -0,0 +1,75 @@ +0.92633 0.057885 0.015785 +0.68248 0.307585 0.009935 +0.935345 0.05991 0.004745 +0.877755 0.108125 0.01412 +0.855695 0.128085 0.01622 +0.94049 0.053025 0.006485 +0.4792 0.393205 0.127595 +0.67483 0.311105 0.014065 +0.71559 0.263975 0.020435 +0.760645 0.19124 0.048115 +0.736425 0.21584 0.047735 +0.79977 0.191755 0.008475 +0.74638 0.233435 0.020185 +0.91399 0.06757 0.01844 +0.813655 0.167695 0.01865 +0.961345 0.034485 0.00417 +0.664755 0.317515 0.01773 +0.8359 0.14073 0.02337 +0.784935 0.120195 0.09487 +0.813735 0.142155 0.04411 +0.669755 0.27439 0.055855 +0.696605 0.136065 0.16733 +0.95993 0.035815 0.004255 +0.765655 0.225335 0.00901 +0.93428 0.057075 0.008645 +0.721295 0.261755 0.01695 +0.90934 0.079875 0.010785 +0.963815 0.03178 0.004405 +0.91296 0.068685 0.018355 +0.64133 0.32156 0.03711 +0.58481 0.40821 0.00698 +0.77754 0.21508 0.00738 +0.52871 0.457225 0.014065 +0.55024 0.44282 0.00694 +0.796835 0.1804 0.022765 +0.931815 0.05093 0.017255 +0.915155 0.07507 0.009775 +0.685855 0.30715 0.006995 +0.66243 0.321105 0.016465 +0.731645 0.26421 0.004145 +0.91696 0.076265 0.006775 +0.67236 0.32263 0.00501 +0.89296 0.102485 0.004555 +0.752315 0.244275 0.00341 +0.91062 0.064775 0.024605 +0.88845 0.10221 0.00934 +0.90092 0.073475 0.025605 +0.690555 0.27085 0.038595 +0.62902 0.29397 0.07701 +0.92489 0.04776 0.02735 +0.856255 0.0875 0.056245 +0.94584 0.043995 0.010165 +0.8982 0.09126 0.01054 +0.88973 0.06803 0.04224 +0.764175 0.220515 0.01531 +0.933695 0.05207 0.014235 +0.93678 0.044045 0.019175 +0.949515 0.041625 0.00886 +0.892755 0.063405 0.04384 +0.67181 0.26196 0.06623 +0.94439 0.042755 0.012855 +0.683955 0.269325 0.04672 +0.885265 0.08908 0.025655 +0.84537 0.08784 0.06679 +0.943995 0.027945 0.02806 +0.970395 0.01639 0.013215 +0.9156 0.080305 0.004095 +0.96383 0.024145 0.012025 +0.98202 0.010825 0.007155 +0.946585 0.04552 0.007895 +0.979385 0.01676 0.003855 +0.712255 0.27954 0.008205 +0.655345 0.340465 0.00419 +0.706595 0.283935 0.00947 +0.87072 0.120915 0.008365 diff --git a/inst/files/basic/space/basic-space-k4.txt b/inst/files/basic/space/basic-space-k4.txt new file mode 100644 index 0000000..41c944f --- /dev/null +++ b/inst/files/basic/space/basic-space-k4.txt @@ -0,0 +1,75 @@ +0.955705 0.02329 0.010225 0.01078 +0.97025 0.00978 0.011555 0.008415 +0.988065 0.0045 0.004015 0.00342 +0.956495 0.016455 0.01188 0.01517 +0.975235 0.010725 0.007525 0.006515 +0.9846 0.00728 0.00515 0.00297 +0.6624 0.171935 0.096505 0.06916 +0.953795 0.01761 0.017365 0.01123 +0.947975 0.014595 0.02233 0.0151 +0.871835 0.059255 0.024305 0.044605 +0.894005 0.049685 0.024755 0.031555 +0.977285 0.00981 0.006085 0.00682 +0.94224 0.022565 0.012215 0.02298 +0.94773 0.03007 0.01202 0.01018 +0.956865 0.01837 0.01221 0.012555 +0.988305 0.004275 0.004155 0.003265 +0.92505 0.038375 0.017735 0.01884 +0.919855 0.035305 0.018225 0.026615 +0.56458 0.329155 0.018835 0.08743 +0.778205 0.108265 0.006135 0.107395 +0.82095 0.113005 0.013575 0.05247 +0.51192 0.37259 0.018025 0.097465 +0.983605 0.010075 0.001605 0.004715 +0.96554 0.021285 0.00327 0.009905 +0.97407 0.016685 0.002805 0.00644 +0.948345 0.02342 0.01071 0.017525 +0.94937 0.02445 0.011645 0.014535 +0.97971 0.0102 0.00413 0.00596 +0.92199 0.02293 0.03244 0.02264 +0.885585 0.032595 0.04551 0.03631 +0.96793 0.010835 0.00997 0.011265 +0.98554 0.004815 0.005455 0.00419 +0.940185 0.013145 0.02165 0.02502 +0.963735 0.00625 0.01634 0.013675 +0.956795 0.0125 0.01349 0.017215 +0.94098 0.01704 0.02271 0.01927 +0.972195 0.00999 0.010835 0.00698 +0.981735 0.003055 0.010665 0.004545 +0.971005 0.00665 0.01679 0.005555 +0.98738 0.00299 0.005655 0.003975 +0.987855 0.003515 0.005265 0.003365 +0.9918 0.00269 0.00394 0.00157 +0.985485 0.00453 0.006025 0.00396 +0.98447 0.0048 0.006375 0.004355 +0.917025 0.03599 0.024245 0.02274 +0.97876 0.00874 0.006855 0.005645 +0.91806 0.03041 0.02809 0.02344 +0.908525 0.02561 0.03833 0.027535 +0.777225 0.07074 0.07886 0.073175 +0.89878 0.052275 0.031945 0.017 +0.855605 0.052475 0.06131 0.03061 +0.972265 0.009335 0.008475 0.009925 +0.97398 0.01123 0.005605 0.009185 +0.89581 0.037245 0.03086 0.036085 +0.94447 0.01938 0.01964 0.01651 +0.9557 0.01858 0.012855 0.012865 +0.924785 0.036545 0.020675 0.017995 +0.974025 0.01013 0.00777 0.008075 +0.90148 0.041965 0.028315 0.02824 +0.829025 0.060805 0.04 0.07017 +0.93776 0.03093 0.010225 0.021085 +0.79285 0.119565 0.03256 0.055025 +0.904355 0.05374 0.01133 0.030575 +0.83107 0.07136 0.05018 0.04739 +0.832325 0.124045 0.012075 0.031555 +0.88716 0.08679 0.006475 0.019575 +0.97331 0.0142 0.00405 0.00844 +0.91785 0.04062 0.01191 0.02962 +0.97859 0.008935 0.00536 0.007115 +0.9638 0.013895 0.007115 0.01519 +0.97802 0.009835 0.005215 0.00693 +0.978475 0.005615 0.00879 0.00712 +0.98059 0.00449 0.00887 0.00605 +0.950055 0.011995 0.022745 0.015205 +0.971085 0.007535 0.012945 0.008435 diff --git a/inst/files/basic/space/basic-space-k5.txt b/inst/files/basic/space/basic-space-k5.txt new file mode 100644 index 0000000..6901c7d --- /dev/null +++ b/inst/files/basic/space/basic-space-k5.txt @@ -0,0 +1,75 @@ +0.78766 0.035545 0.021665 0.14898 0.00615 +0.817585 0.095465 0.022575 0.05413 0.010245 +0.935455 0.02521 0.007015 0.03066 0.00166 +0.767805 0.06457 0.029915 0.131635 0.006075 +0.83655 0.023065 0.042845 0.09518 0.00236 +0.916895 0.012525 0.0118 0.05622 0.00256 +0.414585 0.107505 0.15073 0.3227 0.00448 +0.72307 0.097715 0.07069 0.103095 0.00543 +0.762105 0.04293 0.13013 0.062035 0.0028 +0.70074 0.071655 0.05636 0.161935 0.00931 +0.586635 0.05431 0.05497 0.29668 0.007405 +0.865345 0.064235 0.01624 0.04942 0.00476 +0.742435 0.086295 0.025555 0.13856 0.007155 +0.847705 0.031365 0.0165 0.098125 0.006305 +0.814595 0.063985 0.02 0.09379 0.00763 +0.93737 0.021225 0.01002 0.029015 0.00237 +0.748705 0.08654 0.030325 0.125095 0.009335 +0.80061 0.053275 0.031685 0.10252 0.01191 +0.5744 0.056205 0.024215 0.330255 0.014925 +0.732615 0.07454 0.03534 0.141665 0.01584 +0.5035 0.17423 0.022075 0.28575 0.014445 +0.39582 0.27067 0.03361 0.280365 0.019535 +0.922555 0.008115 0.002015 0.065815 0.0015 +0.809655 0.067335 0.0077 0.1107 0.00461 +0.86916 0.038795 0.00787 0.07916 0.005015 +0.778535 0.108365 0.012665 0.0945 0.005935 +0.895745 0.044455 0.00887 0.042595 0.008335 +0.908325 0.04238 0.00522 0.04177 0.002305 +0.868345 0.07802 0.00674 0.03187 0.015025 +0.56275 0.39761 0.00931 0.020535 0.009795 +0.511225 0.46806 0.005765 0.013875 0.001075 +0.773375 0.198245 0.010645 0.015295 0.00244 +0.419985 0.55089 0.01508 0.010195 0.00385 +0.40169 0.585635 0.00524 0.005285 0.00215 +0.71916 0.2319 0.0106 0.032 0.00634 +0.83843 0.064685 0.02569 0.060065 0.01113 +0.86688 0.05349 0.016175 0.058465 0.00499 +0.888505 0.056145 0.025365 0.027445 0.00254 +0.849665 0.12689 0.006785 0.010825 0.005835 +0.93623 0.036545 0.00246 0.02108 0.003685 +0.94056 0.034055 0.01003 0.013065 0.00229 +0.75386 0.22233 0.008965 0.0136 0.001245 +0.896105 0.034175 0.013355 0.0546 0.001765 +0.89573 0.0555 0.023825 0.02268 0.002265 +0.74449 0.00881 0.101545 0.13998 0.005175 +0.819225 0.003525 0.023335 0.15206 0.001855 +0.854465 0.01019 0.049865 0.081295 0.004185 +0.5951 0.000515 0.39305 0.01106 0.000275 +0.5959 0.02486 0.1428 0.23272 0.00372 +0.612745 0.014675 0.10044 0.269185 0.002955 +0.70953 0.025255 0.117545 0.1434 0.00427 +0.867065 0.004685 0.03237 0.09496 0.00092 +0.887065 0.018265 0.02047 0.070735 0.003465 +0.66819 0.01788 0.163935 0.14256 0.007435 +0.716825 0.024995 0.081275 0.17009 0.006815 +0.812025 0.014975 0.043445 0.12376 0.005795 +0.656825 0.00689 0.034025 0.29661 0.00565 +0.873575 0.005165 0.01631 0.102345 0.002605 +0.572085 0.02273 0.03966 0.35916 0.006365 +0.56452 0.072335 0.0632 0.28911 0.010835 +0.869835 0.02069 0.03275 0.06602 0.010705 +0.57763 0.136195 0.051195 0.212715 0.022265 +0.66577 0.02718 0.028125 0.26848 0.010445 +0.500445 0.042015 0.09259 0.34561 0.01934 +0.466745 0.023915 0.003565 0.498015 0.00776 +0.76947 0.037415 0.00595 0.18161 0.005555 +0.85616 0.02724 0.003685 0.10895 0.003965 +0.83213 0.031305 0.004875 0.122325 0.009365 +0.914005 0.013695 0.00435 0.06094 0.00701 +0.837785 0.027755 0.00619 0.117055 0.011215 +0.936495 0.012705 0.00352 0.04292 0.00436 +0.90621 0.056205 0.00451 0.02912 0.003955 +0.276935 0.72192 0.000435 0.00037 0.00034 +0.72359 0.240885 0.005445 0.02553 0.00455 +0.8404 0.107435 0.010435 0.032995 0.008735 diff --git a/inst/files/basic/tab/basic-tab-k3.txt b/inst/files/basic/tab/basic-tab-k3.txt new file mode 100644 index 0000000..6dc008f --- /dev/null +++ b/inst/files/basic/tab/basic-tab-k3.txt @@ -0,0 +1,75 @@ +0.92633 0.057885 0.015785 +0.68248 0.307585 0.009935 +0.935345 0.05991 0.004745 +0.877755 0.108125 0.01412 +0.855695 0.128085 0.01622 +0.94049 0.053025 0.006485 +0.4792 0.393205 0.127595 +0.67483 0.311105 0.014065 +0.71559 0.263975 0.020435 +0.760645 0.19124 0.048115 +0.736425 0.21584 0.047735 +0.79977 0.191755 0.008475 +0.74638 0.233435 0.020185 +0.91399 0.06757 0.01844 +0.813655 0.167695 0.01865 +0.961345 0.034485 0.00417 +0.664755 0.317515 0.01773 +0.8359 0.14073 0.02337 +0.784935 0.120195 0.09487 +0.813735 0.142155 0.04411 +0.669755 0.27439 0.055855 +0.696605 0.136065 0.16733 +0.95993 0.035815 0.004255 +0.765655 0.225335 0.00901 +0.93428 0.057075 0.008645 +0.721295 0.261755 0.01695 +0.90934 0.079875 0.010785 +0.963815 0.03178 0.004405 +0.91296 0.068685 0.018355 +0.64133 0.32156 0.03711 +0.58481 0.40821 0.00698 +0.77754 0.21508 0.00738 +0.52871 0.457225 0.014065 +0.55024 0.44282 0.00694 +0.796835 0.1804 0.022765 +0.931815 0.05093 0.017255 +0.915155 0.07507 0.009775 +0.685855 0.30715 0.006995 +0.66243 0.321105 0.016465 +0.731645 0.26421 0.004145 +0.91696 0.076265 0.006775 +0.67236 0.32263 0.00501 +0.89296 0.102485 0.004555 +0.752315 0.244275 0.00341 +0.91062 0.064775 0.024605 +0.88845 0.10221 0.00934 +0.90092 0.073475 0.025605 +0.690555 0.27085 0.038595 +0.62902 0.29397 0.07701 +0.92489 0.04776 0.02735 +0.856255 0.0875 0.056245 +0.94584 0.043995 0.010165 +0.8982 0.09126 0.01054 +0.88973 0.06803 0.04224 +0.764175 0.220515 0.01531 +0.933695 0.05207 0.014235 +0.93678 0.044045 0.019175 +0.949515 0.041625 0.00886 +0.892755 0.063405 0.04384 +0.67181 0.26196 0.06623 +0.94439 0.042755 0.012855 +0.683955 0.269325 0.04672 +0.885265 0.08908 0.025655 +0.84537 0.08784 0.06679 +0.943995 0.027945 0.02806 +0.970395 0.01639 0.013215 +0.9156 0.080305 0.004095 +0.96383 0.024145 0.012025 +0.98202 0.010825 0.007155 +0.946585 0.04552 0.007895 +0.979385 0.01676 0.003855 +0.712255 0.27954 0.008205 +0.655345 0.340465 0.00419 +0.706595 0.283935 0.00947 +0.87072 0.120915 0.008365 diff --git a/inst/files/basic/tab/basic-tab-k4.txt b/inst/files/basic/tab/basic-tab-k4.txt new file mode 100644 index 0000000..d5c783e --- /dev/null +++ b/inst/files/basic/tab/basic-tab-k4.txt @@ -0,0 +1,75 @@ +0.955705 0.02329 0.010225 0.01078 +0.97025 0.00978 0.011555 0.008415 +0.988065 0.0045 0.004015 0.00342 +0.956495 0.016455 0.01188 0.01517 +0.975235 0.010725 0.007525 0.006515 +0.9846 0.00728 0.00515 0.00297 +0.6624 0.171935 0.096505 0.06916 +0.953795 0.01761 0.017365 0.01123 +0.947975 0.014595 0.02233 0.0151 +0.871835 0.059255 0.024305 0.044605 +0.894005 0.049685 0.024755 0.031555 +0.977285 0.00981 0.006085 0.00682 +0.94224 0.022565 0.012215 0.02298 +0.94773 0.03007 0.01202 0.01018 +0.956865 0.01837 0.01221 0.012555 +0.988305 0.004275 0.004155 0.003265 +0.92505 0.038375 0.017735 0.01884 +0.919855 0.035305 0.018225 0.026615 +0.56458 0.329155 0.018835 0.08743 +0.778205 0.108265 0.006135 0.107395 +0.82095 0.113005 0.013575 0.05247 +0.51192 0.37259 0.018025 0.097465 +0.983605 0.010075 0.001605 0.004715 +0.96554 0.021285 0.00327 0.009905 +0.97407 0.016685 0.002805 0.00644 +0.948345 0.02342 0.01071 0.017525 +0.94937 0.02445 0.011645 0.014535 +0.97971 0.0102 0.00413 0.00596 +0.92199 0.02293 0.03244 0.02264 +0.885585 0.032595 0.04551 0.03631 +0.96793 0.010835 0.00997 0.011265 +0.98554 0.004815 0.005455 0.00419 +0.940185 0.013145 0.02165 0.02502 +0.963735 0.00625 0.01634 0.013675 +0.956795 0.0125 0.01349 0.017215 +0.94098 0.01704 0.02271 0.01927 +0.972195 0.00999 0.010835 0.00698 +0.981735 0.003055 0.010665 0.004545 +0.971005 0.00665 0.01679 0.005555 +0.98738 0.00299 0.005655 0.003975 +0.987855 0.003515 0.005265 0.003365 +0.9918 0.00269 0.00394 0.00157 +0.985485 0.00453 0.006025 0.00396 +0.98447 0.0048 0.006375 0.004355 +0.917025 0.03599 0.024245 0.02274 +0.97876 0.00874 0.006855 0.005645 +0.91806 0.03041 0.02809 0.02344 +0.908525 0.02561 0.03833 0.027535 +0.777225 0.07074 0.07886 0.073175 +0.89878 0.052275 0.031945 0.017 +0.855605 0.052475 0.06131 0.03061 +0.972265 0.009335 0.008475 0.009925 +0.97398 0.01123 0.005605 0.009185 +0.89581 0.037245 0.03086 0.036085 +0.94447 0.01938 0.01964 0.01651 +0.9557 0.01858 0.012855 0.012865 +0.924785 0.036545 0.020675 0.017995 +0.974025 0.01013 0.00777 0.008075 +0.90148 0.041965 0.028315 0.02824 +0.829025 0.060805 0.04 0.07017 +0.93776 0.03093 0.010225 0.021085 +0.79285 0.119565 0.03256 0.055025 +0.904355 0.05374 0.01133 0.030575 +0.83107 0.07136 0.05018 0.04739 +0.832325 0.124045 0.012075 0.031555 +0.88716 0.08679 0.006475 0.019575 +0.97331 0.0142 0.00405 0.00844 +0.91785 0.04062 0.01191 0.02962 +0.97859 0.008935 0.00536 0.007115 +0.9638 0.013895 0.007115 0.01519 +0.97802 0.009835 0.005215 0.00693 +0.978475 0.005615 0.00879 0.00712 +0.98059 0.00449 0.00887 0.00605 +0.950055 0.011995 0.022745 0.015205 +0.971085 0.007535 0.012945 0.008435 diff --git a/inst/files/basic/tab/basic-tab-k5.txt b/inst/files/basic/tab/basic-tab-k5.txt new file mode 100644 index 0000000..a0e8e0b --- /dev/null +++ b/inst/files/basic/tab/basic-tab-k5.txt @@ -0,0 +1,75 @@ +0.78766 0.035545 0.021665 0.14898 0.00615 +0.817585 0.095465 0.022575 0.05413 0.010245 +0.935455 0.02521 0.007015 0.03066 0.00166 +0.767805 0.06457 0.029915 0.131635 0.006075 +0.83655 0.023065 0.042845 0.09518 0.00236 +0.916895 0.012525 0.0118 0.05622 0.00256 +0.414585 0.107505 0.15073 0.3227 0.00448 +0.72307 0.097715 0.07069 0.103095 0.00543 +0.762105 0.04293 0.13013 0.062035 0.0028 +0.70074 0.071655 0.05636 0.161935 0.00931 +0.586635 0.05431 0.05497 0.29668 0.007405 +0.865345 0.064235 0.01624 0.04942 0.00476 +0.742435 0.086295 0.025555 0.13856 0.007155 +0.847705 0.031365 0.0165 0.098125 0.006305 +0.814595 0.063985 0.02 0.09379 0.00763 +0.93737 0.021225 0.01002 0.029015 0.00237 +0.748705 0.08654 0.030325 0.125095 0.009335 +0.80061 0.053275 0.031685 0.10252 0.01191 +0.5744 0.056205 0.024215 0.330255 0.014925 +0.732615 0.07454 0.03534 0.141665 0.01584 +0.5035 0.17423 0.022075 0.28575 0.014445 +0.39582 0.27067 0.03361 0.280365 0.019535 +0.922555 0.008115 0.002015 0.065815 0.0015 +0.809655 0.067335 0.0077 0.1107 0.00461 +0.86916 0.038795 0.00787 0.07916 0.005015 +0.778535 0.108365 0.012665 0.0945 0.005935 +0.895745 0.044455 0.00887 0.042595 0.008335 +0.908325 0.04238 0.00522 0.04177 0.002305 +0.868345 0.07802 0.00674 0.03187 0.015025 +0.56275 0.39761 0.00931 0.020535 0.009795 +0.511225 0.46806 0.005765 0.013875 0.001075 +0.773375 0.198245 0.010645 0.015295 0.00244 +0.419985 0.55089 0.01508 0.010195 0.00385 +0.40169 0.585635 0.00524 0.005285 0.00215 +0.71916 0.2319 0.0106 0.032 0.00634 +0.83843 0.064685 0.02569 0.060065 0.01113 +0.86688 0.05349 0.016175 0.058465 0.00499 +0.888505 0.056145 0.025365 0.027445 0.00254 +0.849665 0.12689 0.006785 0.010825 0.005835 +0.93623 0.036545 0.00246 0.02108 0.003685 +0.94056 0.034055 0.01003 0.013065 0.00229 +0.75386 0.22233 0.008965 0.0136 0.001245 +0.896105 0.034175 0.013355 0.0546 0.001765 +0.89573 0.0555 0.023825 0.02268 0.002265 +0.74449 0.00881 0.101545 0.13998 0.005175 +0.819225 0.003525 0.023335 0.15206 0.001855 +0.854465 0.01019 0.049865 0.081295 0.004185 +0.5951 0.000515 0.39305 0.01106 0.000275 +0.5959 0.02486 0.1428 0.23272 0.00372 +0.612745 0.014675 0.10044 0.269185 0.002955 +0.70953 0.025255 0.117545 0.1434 0.00427 +0.867065 0.004685 0.03237 0.09496 0.00092 +0.887065 0.018265 0.02047 0.070735 0.003465 +0.66819 0.01788 0.163935 0.14256 0.007435 +0.716825 0.024995 0.081275 0.17009 0.006815 +0.812025 0.014975 0.043445 0.12376 0.005795 +0.656825 0.00689 0.034025 0.29661 0.00565 +0.873575 0.005165 0.01631 0.102345 0.002605 +0.572085 0.02273 0.03966 0.35916 0.006365 +0.56452 0.072335 0.0632 0.28911 0.010835 +0.869835 0.02069 0.03275 0.06602 0.010705 +0.57763 0.136195 0.051195 0.212715 0.022265 +0.66577 0.02718 0.028125 0.26848 0.010445 +0.500445 0.042015 0.09259 0.34561 0.01934 +0.466745 0.023915 0.003565 0.498015 0.00776 +0.76947 0.037415 0.00595 0.18161 0.005555 +0.85616 0.02724 0.003685 0.10895 0.003965 +0.83213 0.031305 0.004875 0.122325 0.009365 +0.914005 0.013695 0.00435 0.06094 0.00701 +0.837785 0.027755 0.00619 0.117055 0.011215 +0.936495 0.012705 0.00352 0.04292 0.00436 +0.90621 0.056205 0.00451 0.02912 0.003955 +0.276935 0.72192 0.000435 0.00037 0.00034 +0.72359 0.240885 0.005445 0.02553 0.00455 +0.8404 0.107435 0.010435 0.032995 0.008735 diff --git a/inst/files/basicgrplabels.txt b/inst/files/basicgrplabels.txt new file mode 100644 index 0000000..6da0c17 --- /dev/null +++ b/inst/files/basicgrplabels.txt @@ -0,0 +1,75 @@ +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B diff --git a/inst/files/coords1592.txt b/inst/files/coords1592.txt new file mode 100644 index 0000000..d003e7f --- /dev/null +++ b/inst/files/coords1592.txt @@ -0,0 +1,1592 @@ +40.9018181 21.5116103 +40.9016623 21.5117316 +40.90217 21.5120367 +40.9071067 21.5030733 +40.9065417 21.5025575 +40.9070548 21.5030808 +40.8590889 21.4020477 +40.8589216 21.4020291 +40.8591833 21.40175 +40.8480467 21.3852633 +40.847581 21.3846472 +40.8480022 21.3852284 +42.0538356 21.1131689 +42.05297845 21.11223496 +41.6615644 20.7346756 +41.6618469 20.73545287 +41.4946867 20.4993533 +41.49478254 20.49863206 +41.27309016 20.59281233 +41.2720044 20.59156 +41.15792245 22.49473896 +41.1586833 22.4953222 +40.9018181 21.5116103 +40.9016623 21.5117316 +40.90217 21.5120367 +40.9071067 21.5030733 +40.9065417 21.5025575 +40.9070548 21.5030808 +40.8590889 21.4020477 +40.8589216 21.4020291 +40.8591833 21.40175 +40.8480467 21.3852633 +40.847581 21.3846472 +40.8480022 21.3852284 +42.0538356 21.1131689 +42.05297845 21.11223496 +41.6615644 20.7346756 +41.6618469 20.73545287 +41.4946867 20.4993533 +41.49478254 20.49863206 +41.27309016 20.59281233 +41.2720044 20.59156 +41.15792245 22.49473896 +41.1586833 22.4953222 +41.15782122 22.4947102 +41.36074832 22.04990014 +41.3602256 22.04992 +41.3604707 22.05085131 +41.80550613 22.66250867 +41.80404624 22.66264441 +41.80444695 22.66334864 +41.8041938 22.66222045 +41.8050233 22.66294 +41.76237188 22.8715954 +41.7620722 22.87235 +41.3965011 22.6176956 +41.39723759 22.61788885 +41.11698374 21.61068069 +41.1169878 21.6109322 +41.1037344 21.6481789 +41.10322212 21.64740863 +41.08371472 21.76333803 +41.0846422 21.7638367 +41.01151 21.2476767 +41.01167868 21.24840614 +41.0117969 21.24736222 +42.1618222 21.8708222 +42.16219127 21.87209361 +42.16966354 22.11741311 +42.1698067 22.1165844 +42.00048883 22.14171517 +42.0001444 22.1409222 +41.5723711 21.9163989 +41.57180759 21.91642962 +41.57399553 21.27912497 +41.5744956 21.2786067 +41.36958814 21.24922897 +41.3702489 21.2492489 +40.9496011 20.9010178 +40.94958371 20.90091111 +41.71291737 22.15859214 +41.7128522 22.1582967 +41.94525847 21.49500328 +41.9447822 21.49431 +43.3761792 26.6932076 +42.1520289 22.7953622 +42.1376112 25.1348601 +42.2071885 22.8415741 +42.0700834 23.1498048 +43.124379 24.6946724 +42.6601523 27.566739 +42.2348682 27.7751855 +43.2049353 24.5044025 +42.5325236 26.740262 +43.300986 24.6027577 +42.1999609 25.3255252 +42.1447209 24.7504415 +42.5030972 24.0008741 +41.5518422 24.0290194 +43.6716945 26.1742714 +41.6431363 25.3691085 +42.8187429 23.2253047 +43.6313419 23.5562046 +41.5748969 24.7110201 +43.5972509 23.1172636 +43.4653552 27.6001985 +42.85032 25.6336533 +42.4978379 27.4701854 +42.1981817 24.4333358 +43.248015 26.5737087 +43.1351081 24.7175323 +41.464715 23.7985163 +42.1791549 24.0971473 +41.5603459 24.9737821 +43.6114291 27.2829397 +40.89911 20.6743053 +40.8992088 20.6744875 +40.8992642 20.6745657 +40.8820333 20.6838167 +41.0683067 20.6296233 +41.0681792 20.6296806 +41.068167 20.6295305 +41.1364031 20.3783984 +41.13694 20.37904 +41.18528 20.32393 +41.1852187 20.3239808 +41.1637467 20.23358 +41.1633733 20.2331458 +41.1632734 20.2329669 +45.63540571 15.21185932 +46.2602521 15.3271815 +46.835056 16.142801 +46.83636881 16.14345144 +46.6373823 16.3018427 +46.0323162 14.7175494 +46.0601379 14.7586124 +46.6701967 15.9476135 +46.665051 16.052197 +46.7533019 16.1674449 +45.980295 14.80594 +46.044601 14.750788 +46.3046308 14.2483693 +46.28685 14.2247711 +46.05929461 14.75820837 +46.0252871 14.7610678 +46.06021552 14.75728007 +45.671462 15.217156 +45.6360353 15.2121075 +46.162412 13.8699702 +46.2051453 13.8923817 +46.3259585 14.2022067 +46.573511 16.344767 +46.269841 14.5988551 +46.3292027 14.5880788 +46.0115703 15.0354362 +46.0313919 14.9756585 +46.1024727 14.4140562 +45.9744151 13.7425328 +46.5843436 16.4509887 +46.5829546 16.45029436 +46.507624 16.009805 +46.5881775 16.2692164 +46.5748473 16.2957718 +46.5546899 16.3523873 +46.32986289 14.31747987 +46.32835326 14.3176347 +46.32964497 14.31757184 +46.3291349 14.3172529 +46.6995947 15.9076394 +46.3528021 15.8322341 +46.3935046 14.1568821 +41.02545803 27.37479513 +41.02565798 27.37643592 +41.0266663 27.37550187 +41.02705637 27.37592145 +41.0257384 27.3752089 +41.02541979 27.52614954 +41.0255694 27.5251111 +41.02559663 27.52597266 +41.02633602 27.52642596 +41.02640852 27.52488855 +41.0462964 27.38248865 +41.04684626 27.38314892 +41.04632102 27.38339332 +41.0469611 27.3828028 +41.04624147 27.38241352 +41.0878206 27.54539 +41.08808109 27.54515537 +41.08768807 27.54629788 +41.08790613 27.544653 +41.08765265 27.54549046 +40.98924677 27.42248882 +40.9884306 27.4213306 +40.98866286 27.42235483 +40.98956833 27.42264911 +40.98846807 27.42083019 +40.98813858 27.42190525 +40.9589183 31.3332989 +40.9584617 31.476145 +40.9168572 31.3850683 +40.99553 31.3610633 +40.96476388 31.44562654 +40.9567017 31.4605989 +40.98749655 31.47264559 +40.9485228 31.3526117 +40.9421017 31.3052072 +41.9469189 27.1560189 +41.7283044 27.3409267 +41.8058761 27.3024344 +41.9466072 27.0483044 +40.96607039 31.61054606 +40.95783001 31.46065027 +40.9671706 31.4769372 +40.9654106 31.4449328 +40.9663856 31.6101939 +40.95728494 31.46068803 +40.9601361 31.5436611 +40.9862049 31.47280319 +40.9868133 31.4731939 +40.95705984 31.45965075 +40.9871778 31.6873361 +40.98744269 31.68837421 +40.8005751 30.74493893 +40.799369 30.7443297 +40.800146 30.7451097 +40.79930923 30.74441196 +40.799597 30.7445597 +40.79883365 30.74483688 +40.79973985 30.74473845 +40.80019422 30.74447766 +40.79909512 30.74411067 +40.79936694 30.74546205 +40.79922346 30.74511745 +40.79939045 30.74494972 +40.79907218 30.74383784 +40.800008 30.7449697 +41.6940744 26.5251078 +41.69360886 26.52375392 +41.69393445 26.52595384 +40.725405 26.08896425 +40.7265522 26.0895717 +40.72661545 26.08854415 +40.72575791 26.08976465 +41.27285804 26.68594113 +41.27226108 26.68443718 +41.27211185 26.68550093 +41.2724878 26.6849378 +40.85935427 26.62600131 +40.8581778 26.62659096 +40.8579794 26.6255656 +40.85819641 26.62557891 +40.92744306 26.39547896 +40.92729855 26.39690685 +40.92679773 26.39642599 +40.926775 26.3958028 +40.92674661 26.39673329 +40.92698794 26.39672838 +41.55034838 26.81855832 +41.54870378 26.81906694 +41.5500033 26.8191811 +41.5486203 26.81874789 +40.9018181 21.5116103 +40.9016623 21.5117316 +40.90217 21.5120367 +40.9071067 21.5030733 +40.9065417 21.5025575 +40.9070548 21.5030808 +40.8590889 21.4020477 +40.8589216 21.4020291 +40.8591833 21.40175 +40.8480467 21.3852633 +40.847581 21.3846472 +40.8480022 21.3852284 +42.0538356 21.1131689 +42.05297845 21.11223496 +41.6615644 20.7346756 +41.6618469 20.73545287 +41.4946867 20.4993533 +41.49478254 20.49863206 +41.27309016 20.59281233 +41.2720044 20.59156 +41.15792245 22.49473896 +41.1586833 22.4953222 +41.15782122 22.4947102 +41.36074832 22.04990014 +41.3602256 22.04992 +41.3604707 22.05085131 +41.80550613 22.66250867 +41.80404624 22.66264441 +41.80444695 22.66334864 +41.8041938 22.66222045 +41.8050233 22.66294 +41.76237188 22.8715954 +41.7620722 22.87235 +41.3965011 22.6176956 +41.39723759 22.61788885 +41.11698374 21.61068069 +41.1169878 21.6109322 +41.1037344 21.6481789 +41.10322212 21.64740863 +41.08371472 21.76333803 +41.0846422 21.7638367 +41.01151 21.2476767 +41.01167868 21.24840614 +41.0117969 21.24736222 +42.1618222 21.8708222 +42.16219127 21.87209361 +42.16966354 22.11741311 +42.1698067 22.1165844 +42.00048883 22.14171517 +42.0001444 22.1409222 +41.5723711 21.9163989 +41.57180759 21.91642962 +41.57399553 21.27912497 +41.5744956 21.2786067 +41.36958814 21.24922897 +41.3702489 21.2492489 +40.9496011 20.9010178 +40.94958371 20.90091111 +41.71291737 22.15859214 +41.7128522 22.1582967 +41.94525847 21.49500328 +41.9447822 21.49431 +43.3761792 26.6932076 +42.1520289 22.7953622 +42.1376112 25.1348601 +42.2071885 22.8415741 +42.0700834 23.1498048 +43.124379 24.6946724 +42.6601523 27.566739 +42.2348682 27.7751855 +43.2049353 24.5044025 +42.5325236 26.740262 +43.300986 24.6027577 +42.1999609 25.3255252 +42.1447209 24.7504415 +42.5030972 24.0008741 +41.5518422 24.0290194 +43.6716945 26.1742714 +41.6431363 25.3691085 +42.8187429 23.2253047 +43.6313419 23.5562046 +41.5748969 24.7110201 +43.5972509 23.1172636 +43.4653552 27.6001985 +42.85032 25.6336533 +42.4978379 27.4701854 +42.1981817 24.4333358 +43.248015 26.5737087 +43.1351081 24.7175323 +41.464715 23.7985163 +42.1791549 24.0971473 +41.5603459 24.9737821 +43.6114291 27.2829397 +40.89911 20.6743053 +40.8992088 20.6744875 +40.8992642 20.6745657 +40.8820333 20.6838167 +41.0683067 20.6296233 +41.0681792 20.6296806 +41.068167 20.6295305 +41.1364031 20.3783984 +41.13694 20.37904 +41.18528 20.32393 +41.1852187 20.3239808 +41.1637467 20.23358 +41.1633733 20.2331458 +41.1632734 20.2329669 +45.63540571 15.21185932 +46.2602521 15.3271815 +46.835056 16.142801 +46.83636881 16.14345144 +46.6373823 16.3018427 +46.0323162 14.7175494 +46.0601379 14.7586124 +46.6701967 15.9476135 +46.665051 16.052197 +46.7533019 16.1674449 +45.980295 14.80594 +46.044601 14.750788 +46.3046308 14.2483693 +46.28685 14.2247711 +46.05929461 14.75820837 +46.0252871 14.7610678 +46.06021552 14.75728007 +45.671462 15.217156 +45.6360353 15.2121075 +46.162412 13.8699702 +46.2051453 13.8923817 +46.3259585 14.2022067 +46.573511 16.344767 +46.269841 14.5988551 +46.3292027 14.5880788 +46.0115703 15.0354362 +46.0313919 14.9756585 +46.1024727 14.4140562 +45.9744151 13.7425328 +46.5843436 16.4509887 +46.5829546 16.45029436 +46.507624 16.009805 +46.5881775 16.2692164 +46.5748473 16.2957718 +46.5546899 16.3523873 +46.32986289 14.31747987 +46.32835326 14.3176347 +46.32964497 14.31757184 +46.3291349 14.3172529 +46.6995947 15.9076394 +46.3528021 15.8322341 +46.3935046 14.1568821 +41.02545803 27.37479513 +41.02565798 27.37643592 +41.0266663 27.37550187 +41.02705637 27.37592145 +41.0257384 27.3752089 +41.02541979 27.52614954 +41.0255694 27.5251111 +41.02559663 27.52597266 +41.02633602 27.52642596 +41.02640852 27.52488855 +41.0462964 27.38248865 +41.04684626 27.38314892 +41.04632102 27.38339332 +41.0469611 27.3828028 +41.04624147 27.38241352 +41.0878206 27.54539 +41.08808109 27.54515537 +41.08768807 27.54629788 +41.08790613 27.544653 +41.08765265 27.54549046 +40.98924677 27.42248882 +40.9884306 27.4213306 +40.98866286 27.42235483 +40.98956833 27.42264911 +40.98846807 27.42083019 +40.98813858 27.42190525 +40.9589183 31.3332989 +40.9584617 31.476145 +40.9168572 31.3850683 +40.99553 31.3610633 +40.96476388 31.44562654 +40.9567017 31.4605989 +40.98749655 31.47264559 +40.9485228 31.3526117 +40.9421017 31.3052072 +41.9469189 27.1560189 +41.7283044 27.3409267 +41.8058761 27.3024344 +41.9466072 27.0483044 +40.96607039 31.61054606 +40.95783001 31.46065027 +40.9671706 31.4769372 +40.9654106 31.4449328 +40.9663856 31.6101939 +40.95728494 31.46068803 +40.9601361 31.5436611 +40.9862049 31.47280319 +40.9868133 31.4731939 +40.95705984 31.45965075 +40.9871778 31.6873361 +40.98744269 31.68837421 +40.8005751 30.74493893 +40.799369 30.7443297 +40.800146 30.7451097 +40.79930923 30.74441196 +40.799597 30.7445597 +40.79883365 30.74483688 +40.79973985 30.74473845 +40.80019422 30.74447766 +40.79909512 30.74411067 +40.79936694 30.74546205 +40.79922346 30.74511745 +40.79939045 30.74494972 +40.79907218 30.74383784 +40.800008 30.7449697 +41.6940744 26.5251078 +41.69360886 26.52375392 +41.69393445 26.52595384 +40.725405 26.08896425 +40.7265522 26.0895717 +40.72661545 26.08854415 +40.72575791 26.08976465 +41.27285804 26.68594113 +41.27226108 26.68443718 +41.27211185 26.68550093 +41.2724878 26.6849378 +40.85935427 26.62600131 +40.8581778 26.62659096 +40.8579794 26.6255656 +40.85819641 26.62557891 +40.92744306 26.39547896 +40.92729855 26.39690685 +40.92679773 26.39642599 +40.926775 26.3958028 +40.92674661 26.39673329 +40.92698794 26.39672838 +41.55034838 26.81855832 +41.54870378 26.81906694 +41.5500033 26.8191811 +41.5486203 26.81874789 +40.9018181 21.5116103 +40.9016623 21.5117316 +40.90217 21.5120367 +40.9071067 21.5030733 +40.9065417 21.5025575 +40.9070548 21.5030808 +40.8590889 21.4020477 +40.8589216 21.4020291 +40.8591833 21.40175 +40.8480467 21.3852633 +40.847581 21.3846472 +40.8480022 21.3852284 +42.0538356 21.1131689 +42.05297845 21.11223496 +41.6615644 20.7346756 +41.6618469 20.73545287 +41.4946867 20.4993533 +41.49478254 20.49863206 +41.27309016 20.59281233 +41.2720044 20.59156 +41.15792245 22.49473896 +41.1586833 22.4953222 +41.15782122 22.4947102 +41.36074832 22.04990014 +41.3602256 22.04992 +41.3604707 22.05085131 +41.80550613 22.66250867 +41.80404624 22.66264441 +41.80444695 22.66334864 +41.8041938 22.66222045 +41.8050233 22.66294 +41.76237188 22.8715954 +41.7620722 22.87235 +41.3965011 22.6176956 +41.39723759 22.61788885 +41.11698374 21.61068069 +41.1169878 21.6109322 +41.1037344 21.6481789 +41.10322212 21.64740863 +41.08371472 21.76333803 +41.0846422 21.7638367 +41.01151 21.2476767 +41.01167868 21.24840614 +41.0117969 21.24736222 +42.1618222 21.8708222 +42.16219127 21.87209361 +42.16966354 22.11741311 +42.1698067 22.1165844 +42.00048883 22.14171517 +42.0001444 22.1409222 +41.5723711 21.9163989 +41.57180759 21.91642962 +41.57399553 21.27912497 +41.5744956 21.2786067 +41.36958814 21.24922897 +41.3702489 21.2492489 +40.9496011 20.9010178 +40.94958371 20.90091111 +41.71291737 22.15859214 +41.7128522 22.1582967 +41.94525847 21.49500328 +41.9447822 21.49431 +43.3761792 26.6932076 +42.1520289 22.7953622 +42.1376112 25.1348601 +42.2071885 22.8415741 +42.0700834 23.1498048 +43.124379 24.6946724 +42.6601523 27.566739 +42.2348682 27.7751855 +43.2049353 24.5044025 +42.5325236 26.740262 +43.300986 24.6027577 +42.1999609 25.3255252 +42.1447209 24.7504415 +42.5030972 24.0008741 +41.5518422 24.0290194 +43.6716945 26.1742714 +41.6431363 25.3691085 +42.8187429 23.2253047 +43.6313419 23.5562046 +41.5748969 24.7110201 +43.5972509 23.1172636 +43.4653552 27.6001985 +42.85032 25.6336533 +42.4978379 27.4701854 +42.1981817 24.4333358 +43.248015 26.5737087 +43.1351081 24.7175323 +41.464715 23.7985163 +42.1791549 24.0971473 +41.5603459 24.9737821 +43.6114291 27.2829397 +40.89911 20.6743053 +40.8992088 20.6744875 +40.8992642 20.6745657 +40.8820333 20.6838167 +41.0683067 20.6296233 +41.0681792 20.6296806 +41.068167 20.6295305 +41.1364031 20.3783984 +41.13694 20.37904 +41.18528 20.32393 +41.1852187 20.3239808 +41.1637467 20.23358 +41.1633733 20.2331458 +41.1632734 20.2329669 +45.63540571 15.21185932 +46.2602521 15.3271815 +46.835056 16.142801 +46.83636881 16.14345144 +46.6373823 16.3018427 +46.0323162 14.7175494 +46.0601379 14.7586124 +46.6701967 15.9476135 +46.665051 16.052197 +46.7533019 16.1674449 +45.980295 14.80594 +46.044601 14.750788 +46.3046308 14.2483693 +46.28685 14.2247711 +46.05929461 14.75820837 +46.0252871 14.7610678 +46.06021552 14.75728007 +45.671462 15.217156 +45.6360353 15.2121075 +46.162412 13.8699702 +46.2051453 13.8923817 +46.3259585 14.2022067 +46.573511 16.344767 +46.269841 14.5988551 +46.3292027 14.5880788 +46.0115703 15.0354362 +46.0313919 14.9756585 +46.1024727 14.4140562 +45.9744151 13.7425328 +46.5843436 16.4509887 +46.5829546 16.45029436 +46.507624 16.009805 +46.5881775 16.2692164 +46.5748473 16.2957718 +46.5546899 16.3523873 +46.32986289 14.31747987 +46.32835326 14.3176347 +46.32964497 14.31757184 +46.3291349 14.3172529 +46.6995947 15.9076394 +46.3528021 15.8322341 +46.3935046 14.1568821 +41.02545803 27.37479513 +41.02565798 27.37643592 +41.0266663 27.37550187 +41.02705637 27.37592145 +41.0257384 27.3752089 +41.02541979 27.52614954 +41.0255694 27.5251111 +41.02559663 27.52597266 +41.02633602 27.52642596 +41.02640852 27.52488855 +41.0462964 27.38248865 +41.04684626 27.38314892 +41.04632102 27.38339332 +41.0469611 27.3828028 +41.04624147 27.38241352 +41.0878206 27.54539 +41.08808109 27.54515537 +41.08768807 27.54629788 +41.08790613 27.544653 +41.08765265 27.54549046 +40.98924677 27.42248882 +40.9884306 27.4213306 +40.98866286 27.42235483 +40.98956833 27.42264911 +40.98846807 27.42083019 +40.98813858 27.42190525 +40.9589183 31.3332989 +40.9584617 31.476145 +40.9168572 31.3850683 +40.99553 31.3610633 +40.96476388 31.44562654 +40.9567017 31.4605989 +40.98749655 31.47264559 +40.9485228 31.3526117 +40.9421017 31.3052072 +41.9469189 27.1560189 +41.7283044 27.3409267 +41.8058761 27.3024344 +41.9466072 27.0483044 +40.96607039 31.61054606 +40.95783001 31.46065027 +40.9671706 31.4769372 +40.9654106 31.4449328 +40.9663856 31.6101939 +40.95728494 31.46068803 +40.9601361 31.5436611 +40.9862049 31.47280319 +40.9868133 31.4731939 +40.95705984 31.45965075 +40.9871778 31.6873361 +40.98744269 31.68837421 +40.8005751 30.74493893 +40.799369 30.7443297 +40.800146 30.7451097 +40.79930923 30.74441196 +40.799597 30.7445597 +40.79883365 30.74483688 +40.79973985 30.74473845 +40.80019422 30.74447766 +40.79909512 30.74411067 +40.79936694 30.74546205 +40.79922346 30.74511745 +40.79939045 30.74494972 +40.79907218 30.74383784 +40.800008 30.7449697 +41.6940744 26.5251078 +41.69360886 26.52375392 +41.69393445 26.52595384 +40.725405 26.08896425 +40.7265522 26.0895717 +40.72661545 26.08854415 +40.72575791 26.08976465 +41.27285804 26.68594113 +41.27226108 26.68443718 +41.27211185 26.68550093 +41.2724878 26.6849378 +40.85935427 26.62600131 +40.8581778 26.62659096 +40.8579794 26.6255656 +40.85819641 26.62557891 +40.92744306 26.39547896 +40.92729855 26.39690685 +40.92679773 26.39642599 +40.926775 26.3958028 +40.92674661 26.39673329 +40.92698794 26.39672838 +41.55034838 26.81855832 +41.54870378 26.81906694 +41.5500033 26.8191811 +41.5486203 26.81874789 +40.9018181 21.5116103 +40.9016623 21.5117316 +40.90217 21.5120367 +40.9071067 21.5030733 +40.9065417 21.5025575 +40.9070548 21.5030808 +40.8590889 21.4020477 +40.8589216 21.4020291 +40.8591833 21.40175 +40.8480467 21.3852633 +40.847581 21.3846472 +40.8480022 21.3852284 +42.0538356 21.1131689 +42.05297845 21.11223496 +41.6615644 20.7346756 +41.6618469 20.73545287 +41.4946867 20.4993533 +41.49478254 20.49863206 +41.27309016 20.59281233 +41.2720044 20.59156 +41.15792245 22.49473896 +41.1586833 22.4953222 +41.15782122 22.4947102 +41.36074832 22.04990014 +41.3602256 22.04992 +41.3604707 22.05085131 +41.80550613 22.66250867 +41.80404624 22.66264441 +41.80444695 22.66334864 +41.8041938 22.66222045 +41.8050233 22.66294 +41.76237188 22.8715954 +41.7620722 22.87235 +41.3965011 22.6176956 +41.39723759 22.61788885 +41.11698374 21.61068069 +41.1169878 21.6109322 +41.1037344 21.6481789 +41.10322212 21.64740863 +41.08371472 21.76333803 +41.0846422 21.7638367 +41.01151 21.2476767 +41.01167868 21.24840614 +41.0117969 21.24736222 +42.1618222 21.8708222 +42.16219127 21.87209361 +42.16966354 22.11741311 +42.1698067 22.1165844 +42.00048883 22.14171517 +42.0001444 22.1409222 +41.5723711 21.9163989 +41.57180759 21.91642962 +41.57399553 21.27912497 +41.5744956 21.2786067 +41.36958814 21.24922897 +41.3702489 21.2492489 +40.9496011 20.9010178 +40.94958371 20.90091111 +41.71291737 22.15859214 +41.7128522 22.1582967 +41.94525847 21.49500328 +41.9447822 21.49431 +43.3761792 26.6932076 +42.1520289 22.7953622 +42.1376112 25.1348601 +42.2071885 22.8415741 +42.0700834 23.1498048 +43.124379 24.6946724 +42.6601523 27.566739 +42.2348682 27.7751855 +43.2049353 24.5044025 +42.5325236 26.740262 +43.300986 24.6027577 +42.1999609 25.3255252 +42.1447209 24.7504415 +42.5030972 24.0008741 +41.5518422 24.0290194 +43.6716945 26.1742714 +41.6431363 25.3691085 +42.8187429 23.2253047 +43.6313419 23.5562046 +41.5748969 24.7110201 +43.5972509 23.1172636 +43.4653552 27.6001985 +42.85032 25.6336533 +42.4978379 27.4701854 +42.1981817 24.4333358 +43.248015 26.5737087 +43.1351081 24.7175323 +41.464715 23.7985163 +42.1791549 24.0971473 +41.5603459 24.9737821 +43.6114291 27.2829397 +40.89911 20.6743053 +40.8992088 20.6744875 +40.8992642 20.6745657 +40.8820333 20.6838167 +41.0683067 20.6296233 +41.0681792 20.6296806 +41.068167 20.6295305 +41.1364031 20.3783984 +41.13694 20.37904 +41.18528 20.32393 +41.1852187 20.3239808 +41.1637467 20.23358 +41.1633733 20.2331458 +41.1632734 20.2329669 +45.63540571 15.21185932 +46.2602521 15.3271815 +46.835056 16.142801 +46.83636881 16.14345144 +46.6373823 16.3018427 +46.0323162 14.7175494 +46.0601379 14.7586124 +46.6701967 15.9476135 +46.665051 16.052197 +46.7533019 16.1674449 +45.980295 14.80594 +46.044601 14.750788 +46.3046308 14.2483693 +46.28685 14.2247711 +46.05929461 14.75820837 +46.0252871 14.7610678 +46.06021552 14.75728007 +45.671462 15.217156 +45.6360353 15.2121075 +46.162412 13.8699702 +46.2051453 13.8923817 +46.3259585 14.2022067 +46.573511 16.344767 +46.269841 14.5988551 +46.3292027 14.5880788 +46.0115703 15.0354362 +46.0313919 14.9756585 +46.1024727 14.4140562 +45.9744151 13.7425328 +46.5843436 16.4509887 +46.5829546 16.45029436 +46.507624 16.009805 +46.5881775 16.2692164 +46.5748473 16.2957718 +46.5546899 16.3523873 +46.32986289 14.31747987 +46.32835326 14.3176347 +46.32964497 14.31757184 +46.3291349 14.3172529 +46.6995947 15.9076394 +46.3528021 15.8322341 +46.3935046 14.1568821 +41.02545803 27.37479513 +41.02565798 27.37643592 +41.0266663 27.37550187 +41.02705637 27.37592145 +41.0257384 27.3752089 +41.02541979 27.52614954 +41.0255694 27.5251111 +41.02559663 27.52597266 +41.02633602 27.52642596 +41.02640852 27.52488855 +41.0462964 27.38248865 +41.04684626 27.38314892 +41.04632102 27.38339332 +41.0469611 27.3828028 +41.04624147 27.38241352 +41.0878206 27.54539 +41.08808109 27.54515537 +41.08768807 27.54629788 +41.08790613 27.544653 +41.08765265 27.54549046 +40.98924677 27.42248882 +40.9884306 27.4213306 +40.98866286 27.42235483 +40.98956833 27.42264911 +40.98846807 27.42083019 +40.98813858 27.42190525 +40.9589183 31.3332989 +40.9584617 31.476145 +40.9168572 31.3850683 +40.99553 31.3610633 +40.96476388 31.44562654 +40.9567017 31.4605989 +40.98749655 31.47264559 +40.9485228 31.3526117 +40.9421017 31.3052072 +41.9469189 27.1560189 +41.7283044 27.3409267 +41.8058761 27.3024344 +41.9466072 27.0483044 +40.96607039 31.61054606 +40.95783001 31.46065027 +40.9671706 31.4769372 +40.9654106 31.4449328 +40.9663856 31.6101939 +40.95728494 31.46068803 +40.9601361 31.5436611 +40.9862049 31.47280319 +40.9868133 31.4731939 +40.95705984 31.45965075 +40.9871778 31.6873361 +40.98744269 31.68837421 +40.8005751 30.74493893 +40.799369 30.7443297 +40.800146 30.7451097 +40.79930923 30.74441196 +40.799597 30.7445597 +40.79883365 30.74483688 +40.79973985 30.74473845 +40.80019422 30.74447766 +40.79909512 30.74411067 +40.79936694 30.74546205 +40.79922346 30.74511745 +40.79939045 30.74494972 +40.79907218 30.74383784 +40.800008 30.7449697 +41.6940744 26.5251078 +41.69360886 26.52375392 +41.69393445 26.52595384 +40.725405 26.08896425 +40.7265522 26.0895717 +40.72661545 26.08854415 +40.72575791 26.08976465 +41.27285804 26.68594113 +41.27226108 26.68443718 +41.27211185 26.68550093 +41.2724878 26.6849378 +40.85935427 26.62600131 +40.8581778 26.62659096 +40.8579794 26.6255656 +40.85819641 26.62557891 +40.92744306 26.39547896 +40.92729855 26.39690685 +40.92679773 26.39642599 +40.926775 26.3958028 +40.92674661 26.39673329 +40.92698794 26.39672838 +41.55034838 26.81855832 +41.54870378 26.81906694 +41.5500033 26.8191811 +41.5486203 26.81874789 +40.9018181 21.5116103 +40.9016623 21.5117316 +40.90217 21.5120367 +40.9071067 21.5030733 +40.9065417 21.5025575 +40.9070548 21.5030808 +40.8590889 21.4020477 +40.8589216 21.4020291 +40.8591833 21.40175 +40.8480467 21.3852633 +40.847581 21.3846472 +40.8480022 21.3852284 +42.0538356 21.1131689 +42.05297845 21.11223496 +41.6615644 20.7346756 +41.6618469 20.73545287 +41.4946867 20.4993533 +41.49478254 20.49863206 +41.27309016 20.59281233 +41.2720044 20.59156 +41.15792245 22.49473896 +41.1586833 22.4953222 +41.15782122 22.4947102 +41.36074832 22.04990014 +41.3602256 22.04992 +41.3604707 22.05085131 +41.80550613 22.66250867 +41.80404624 22.66264441 +41.80444695 22.66334864 +41.8041938 22.66222045 +41.8050233 22.66294 +41.76237188 22.8715954 +41.7620722 22.87235 +41.3965011 22.6176956 +41.39723759 22.61788885 +41.11698374 21.61068069 +41.1169878 21.6109322 +41.1037344 21.6481789 +41.10322212 21.64740863 +41.08371472 21.76333803 +41.0846422 21.7638367 +41.01151 21.2476767 +41.01167868 21.24840614 +41.0117969 21.24736222 +42.1618222 21.8708222 +42.16219127 21.87209361 +42.16966354 22.11741311 +42.1698067 22.1165844 +42.00048883 22.14171517 +42.0001444 22.1409222 +41.5723711 21.9163989 +41.57180759 21.91642962 +41.57399553 21.27912497 +41.5744956 21.2786067 +41.36958814 21.24922897 +41.3702489 21.2492489 +40.9496011 20.9010178 +40.94958371 20.90091111 +41.71291737 22.15859214 +41.7128522 22.1582967 +41.94525847 21.49500328 +41.9447822 21.49431 +43.3761792 26.6932076 +42.1520289 22.7953622 +42.1376112 25.1348601 +42.2071885 22.8415741 +42.0700834 23.1498048 +43.124379 24.6946724 +42.6601523 27.566739 +42.2348682 27.7751855 +43.2049353 24.5044025 +42.5325236 26.740262 +43.300986 24.6027577 +42.1999609 25.3255252 +42.1447209 24.7504415 +42.5030972 24.0008741 +41.5518422 24.0290194 +43.6716945 26.1742714 +41.6431363 25.3691085 +42.8187429 23.2253047 +43.6313419 23.5562046 +41.5748969 24.7110201 +43.5972509 23.1172636 +43.4653552 27.6001985 +42.85032 25.6336533 +42.4978379 27.4701854 +42.1981817 24.4333358 +43.248015 26.5737087 +43.1351081 24.7175323 +41.464715 23.7985163 +42.1791549 24.0971473 +41.5603459 24.9737821 +43.6114291 27.2829397 +40.89911 20.6743053 +40.8992088 20.6744875 +40.8992642 20.6745657 +40.8820333 20.6838167 +41.0683067 20.6296233 +41.0681792 20.6296806 +41.068167 20.6295305 +41.1364031 20.3783984 +41.13694 20.37904 +41.18528 20.32393 +41.1852187 20.3239808 +41.1637467 20.23358 +41.1633733 20.2331458 +41.1632734 20.2329669 +45.63540571 15.21185932 +46.2602521 15.3271815 +46.835056 16.142801 +46.83636881 16.14345144 +46.6373823 16.3018427 +46.0323162 14.7175494 +46.0601379 14.7586124 +46.6701967 15.9476135 +46.665051 16.052197 +46.7533019 16.1674449 +45.980295 14.80594 +46.044601 14.750788 +46.3046308 14.2483693 +46.28685 14.2247711 +46.05929461 14.75820837 +46.0252871 14.7610678 +46.06021552 14.75728007 +45.671462 15.217156 +45.6360353 15.2121075 +46.162412 13.8699702 +46.2051453 13.8923817 +46.3259585 14.2022067 +46.573511 16.344767 +46.269841 14.5988551 +46.3292027 14.5880788 +46.0115703 15.0354362 +46.0313919 14.9756585 +46.1024727 14.4140562 +45.9744151 13.7425328 +46.5843436 16.4509887 +46.5829546 16.45029436 +46.507624 16.009805 +46.5881775 16.2692164 +46.5748473 16.2957718 +46.5546899 16.3523873 +46.32986289 14.31747987 +46.32835326 14.3176347 +46.32964497 14.31757184 +46.3291349 14.3172529 +46.6995947 15.9076394 +46.3528021 15.8322341 +46.3935046 14.1568821 +41.02545803 27.37479513 +41.02565798 27.37643592 +41.0266663 27.37550187 +41.02705637 27.37592145 +41.0257384 27.3752089 +41.02541979 27.52614954 +41.0255694 27.5251111 +41.02559663 27.52597266 +41.02633602 27.52642596 +41.02640852 27.52488855 +41.0462964 27.38248865 +41.04684626 27.38314892 +41.04632102 27.38339332 +41.0469611 27.3828028 +41.04624147 27.38241352 +41.0878206 27.54539 +41.08808109 27.54515537 +41.08768807 27.54629788 +41.08790613 27.544653 +41.08765265 27.54549046 +40.98924677 27.42248882 +40.9884306 27.4213306 +40.98866286 27.42235483 +40.98956833 27.42264911 +40.98846807 27.42083019 +40.98813858 27.42190525 +40.9589183 31.3332989 +40.9584617 31.476145 +40.9168572 31.3850683 +40.99553 31.3610633 +40.96476388 31.44562654 +40.9567017 31.4605989 +40.98749655 31.47264559 +40.9485228 31.3526117 +40.9421017 31.3052072 +41.9469189 27.1560189 +41.7283044 27.3409267 +41.8058761 27.3024344 +41.9466072 27.0483044 +40.96607039 31.61054606 +40.95783001 31.46065027 +40.9671706 31.4769372 +40.9654106 31.4449328 +40.9663856 31.6101939 +40.95728494 31.46068803 +40.9601361 31.5436611 +40.9862049 31.47280319 +40.9868133 31.4731939 +40.95705984 31.45965075 +40.9871778 31.6873361 +40.98744269 31.68837421 +40.8005751 30.74493893 +40.799369 30.7443297 +40.800146 30.7451097 +40.79930923 30.74441196 +40.799597 30.7445597 +40.79883365 30.74483688 +40.79973985 30.74473845 +40.80019422 30.74447766 +40.79909512 30.74411067 +40.79936694 30.74546205 +40.79922346 30.74511745 +40.79939045 30.74494972 +40.79907218 30.74383784 +40.800008 30.7449697 +41.6940744 26.5251078 +41.69360886 26.52375392 +41.69393445 26.52595384 +40.725405 26.08896425 +40.7265522 26.0895717 +40.72661545 26.08854415 +40.72575791 26.08976465 +41.27285804 26.68594113 +41.27226108 26.68443718 +41.27211185 26.68550093 +41.2724878 26.6849378 +40.85935427 26.62600131 +40.8581778 26.62659096 +40.8579794 26.6255656 +40.85819641 26.62557891 +40.92744306 26.39547896 +40.92729855 26.39690685 +40.92679773 26.39642599 +40.926775 26.3958028 +40.92674661 26.39673329 +40.92698794 26.39672838 +41.55034838 26.81855832 +41.54870378 26.81906694 +41.5500033 26.8191811 +41.5486203 26.81874789 +40.9018181 21.5116103 +40.9016623 21.5117316 +40.90217 21.5120367 +40.9071067 21.5030733 +40.9065417 21.5025575 +40.9070548 21.5030808 +40.8590889 21.4020477 +40.8589216 21.4020291 +40.8591833 21.40175 +40.8480467 21.3852633 +40.847581 21.3846472 +40.8480022 21.3852284 +42.0538356 21.1131689 +42.05297845 21.11223496 +41.6615644 20.7346756 +41.6618469 20.73545287 +41.4946867 20.4993533 +41.49478254 20.49863206 +41.27309016 20.59281233 +41.2720044 20.59156 +41.15792245 22.49473896 +41.1586833 22.4953222 +41.15782122 22.4947102 +41.36074832 22.04990014 +41.3602256 22.04992 +41.3604707 22.05085131 +41.80550613 22.66250867 +41.80404624 22.66264441 +41.80444695 22.66334864 +41.8041938 22.66222045 +41.8050233 22.66294 +41.76237188 22.8715954 +41.7620722 22.87235 +41.3965011 22.6176956 +41.39723759 22.61788885 +41.11698374 21.61068069 +41.1169878 21.6109322 +41.1037344 21.6481789 +41.10322212 21.64740863 +41.08371472 21.76333803 +41.0846422 21.7638367 +41.01151 21.2476767 +41.01167868 21.24840614 +41.0117969 21.24736222 +42.1618222 21.8708222 +42.16219127 21.87209361 +42.16966354 22.11741311 +42.1698067 22.1165844 +42.00048883 22.14171517 +42.0001444 22.1409222 +41.5723711 21.9163989 +41.57180759 21.91642962 +41.57399553 21.27912497 +41.5744956 21.2786067 +41.36958814 21.24922897 +41.3702489 21.2492489 +40.9496011 20.9010178 +40.94958371 20.90091111 +41.71291737 22.15859214 +41.7128522 22.1582967 +41.94525847 21.49500328 +41.9447822 21.49431 +43.3761792 26.6932076 +42.1520289 22.7953622 +42.1376112 25.1348601 +42.2071885 22.8415741 +42.0700834 23.1498048 +43.124379 24.6946724 +42.6601523 27.566739 +42.2348682 27.7751855 +43.2049353 24.5044025 +42.5325236 26.740262 +43.300986 24.6027577 +42.1999609 25.3255252 +42.1447209 24.7504415 +42.5030972 24.0008741 +41.5518422 24.0290194 +43.6716945 26.1742714 +41.6431363 25.3691085 +42.8187429 23.2253047 +43.6313419 23.5562046 +41.5748969 24.7110201 +43.5972509 23.1172636 +43.4653552 27.6001985 +42.85032 25.6336533 +42.4978379 27.4701854 +42.1981817 24.4333358 +43.248015 26.5737087 +43.1351081 24.7175323 +41.464715 23.7985163 +42.1791549 24.0971473 +41.5603459 24.9737821 +43.6114291 27.2829397 +40.89911 20.6743053 +40.8992088 20.6744875 +40.8992642 20.6745657 +40.8820333 20.6838167 +41.0683067 20.6296233 +41.0681792 20.6296806 +41.068167 20.6295305 +41.1364031 20.3783984 +41.13694 20.37904 +41.18528 20.32393 +41.1852187 20.3239808 +41.1637467 20.23358 +41.1633733 20.2331458 +41.1632734 20.2329669 +45.63540571 15.21185932 +46.2602521 15.3271815 +46.835056 16.142801 +46.83636881 16.14345144 +46.6373823 16.3018427 +46.0323162 14.7175494 +46.0601379 14.7586124 +46.6701967 15.9476135 +46.665051 16.052197 +46.7533019 16.1674449 +45.980295 14.80594 +46.044601 14.750788 +46.3046308 14.2483693 +46.28685 14.2247711 +46.05929461 14.75820837 +46.0252871 14.7610678 +46.06021552 14.75728007 +45.671462 15.217156 +45.6360353 15.2121075 +46.162412 13.8699702 +46.2051453 13.8923817 +46.3259585 14.2022067 +46.573511 16.344767 +46.269841 14.5988551 +46.3292027 14.5880788 +46.0115703 15.0354362 +46.0313919 14.9756585 +46.1024727 14.4140562 +45.9744151 13.7425328 +46.5843436 16.4509887 +46.5829546 16.45029436 +46.507624 16.009805 +46.5881775 16.2692164 +46.5748473 16.2957718 +46.5546899 16.3523873 +46.32986289 14.31747987 +46.32835326 14.3176347 +46.32964497 14.31757184 +46.3291349 14.3172529 +46.6995947 15.9076394 +46.3528021 15.8322341 +46.3935046 14.1568821 +41.02545803 27.37479513 +41.02565798 27.37643592 +41.0266663 27.37550187 +41.02705637 27.37592145 +41.0257384 27.3752089 +41.02541979 27.52614954 +41.0255694 27.5251111 +41.02559663 27.52597266 +41.02633602 27.52642596 +41.02640852 27.52488855 +41.0462964 27.38248865 +41.04684626 27.38314892 +41.04632102 27.38339332 +41.0469611 27.3828028 +41.04624147 27.38241352 +41.0878206 27.54539 +41.08808109 27.54515537 +41.08768807 27.54629788 +41.08790613 27.544653 +41.08765265 27.54549046 +40.98924677 27.42248882 +40.9884306 27.4213306 +40.98866286 27.42235483 +40.98956833 27.42264911 +40.98846807 27.42083019 +40.98813858 27.42190525 +40.9589183 31.3332989 +40.9584617 31.476145 +40.9168572 31.3850683 +40.99553 31.3610633 +40.96476388 31.44562654 +40.9567017 31.4605989 +40.98749655 31.47264559 +40.9485228 31.3526117 +40.9421017 31.3052072 +41.9469189 27.1560189 +41.7283044 27.3409267 +41.8058761 27.3024344 +41.9466072 27.0483044 +40.96607039 31.61054606 +40.95783001 31.46065027 +40.9671706 31.4769372 +40.9654106 31.4449328 +40.9663856 31.6101939 +40.95728494 31.46068803 +40.9601361 31.5436611 +40.9862049 31.47280319 +40.9868133 31.4731939 +40.95705984 31.45965075 +40.9871778 31.6873361 +40.98744269 31.68837421 +40.8005751 30.74493893 +40.799369 30.7443297 +40.800146 30.7451097 +40.79930923 30.74441196 +40.799597 30.7445597 +40.79883365 30.74483688 +40.79973985 30.74473845 +40.80019422 30.74447766 +40.79909512 30.74411067 +40.79936694 30.74546205 +40.79922346 30.74511745 +40.79939045 30.74494972 +40.79907218 30.74383784 +40.800008 30.7449697 +41.6940744 26.5251078 +41.69360886 26.52375392 +41.69393445 26.52595384 +40.725405 26.08896425 +40.7265522 26.0895717 +40.72661545 26.08854415 +40.72575791 26.08976465 +41.27285804 26.68594113 +41.27226108 26.68443718 +41.27211185 26.68550093 +41.2724878 26.6849378 +40.85935427 26.62600131 +40.8581778 26.62659096 +40.8579794 26.6255656 +40.85819641 26.62557891 +40.92744306 26.39547896 +40.92729855 26.39690685 +40.92679773 26.39642599 +40.926775 26.3958028 +40.92674661 26.39673329 +40.92698794 26.39672838 +41.55034838 26.81855832 +41.54870378 26.81906694 +41.5500033 26.8191811 +41.5486203 26.81874789 +40.9018181 21.5116103 +40.9016623 21.5117316 +40.90217 21.5120367 +40.9071067 21.5030733 +40.9065417 21.5025575 +40.9070548 21.5030808 +40.8590889 21.4020477 +40.8589216 21.4020291 +40.8591833 21.40175 +40.8480467 21.3852633 +40.847581 21.3846472 +40.8480022 21.3852284 +42.0538356 21.1131689 +42.05297845 21.11223496 +41.6615644 20.7346756 +41.6618469 20.73545287 +41.4946867 20.4993533 +41.49478254 20.49863206 +41.27309016 20.59281233 +41.2720044 20.59156 +41.15792245 22.49473896 +41.1586833 22.4953222 +41.15782122 22.4947102 +41.36074832 22.04990014 +41.3602256 22.04992 +41.3604707 22.05085131 +41.80550613 22.66250867 +41.80404624 22.66264441 +41.80444695 22.66334864 +41.8041938 22.66222045 +41.8050233 22.66294 +41.76237188 22.8715954 +41.7620722 22.87235 +41.3965011 22.6176956 +41.39723759 22.61788885 +41.11698374 21.61068069 +41.1169878 21.6109322 +41.1037344 21.6481789 +41.10322212 21.64740863 +41.08371472 21.76333803 +41.0846422 21.7638367 +41.01151 21.2476767 +41.01167868 21.24840614 +41.0117969 21.24736222 +42.1618222 21.8708222 +42.16219127 21.87209361 +42.16966354 22.11741311 +42.1698067 22.1165844 +42.00048883 22.14171517 +42.0001444 22.1409222 +41.5723711 21.9163989 +41.57180759 21.91642962 +41.57399553 21.27912497 +41.5744956 21.2786067 +41.36958814 21.24922897 +41.3702489 21.2492489 +40.9496011 20.9010178 +40.94958371 20.90091111 +41.71291737 22.15859214 +41.7128522 22.1582967 +41.94525847 21.49500328 +41.9447822 21.49431 +43.3761792 26.6932076 +42.1520289 22.7953622 +42.1376112 25.1348601 +42.2071885 22.8415741 +42.0700834 23.1498048 +43.124379 24.6946724 +42.6601523 27.566739 +42.2348682 27.7751855 +43.2049353 24.5044025 +42.5325236 26.740262 +43.300986 24.6027577 +42.1999609 25.3255252 +42.1447209 24.7504415 +42.5030972 24.0008741 +41.5518422 24.0290194 +43.6716945 26.1742714 +41.6431363 25.3691085 +42.8187429 23.2253047 +43.6313419 23.5562046 +41.5748969 24.7110201 +43.5972509 23.1172636 +43.4653552 27.6001985 +42.85032 25.6336533 +42.4978379 27.4701854 +42.1981817 24.4333358 +43.248015 26.5737087 +43.1351081 24.7175323 +41.464715 23.7985163 +42.1791549 24.0971473 +41.5603459 24.9737821 +43.6114291 27.2829397 +40.89911 20.6743053 +40.8992088 20.6744875 +40.8992642 20.6745657 +40.8820333 20.6838167 +41.0683067 20.6296233 +41.0681792 20.6296806 +41.068167 20.6295305 +41.1364031 20.3783984 +41.13694 20.37904 +41.18528 20.32393 +41.1852187 20.3239808 +41.1637467 20.23358 +41.1633733 20.2331458 +41.1632734 20.2329669 +45.63540571 15.21185932 +46.2602521 15.3271815 +46.835056 16.142801 +46.83636881 16.14345144 +46.6373823 16.3018427 +46.0323162 14.7175494 +46.0601379 14.7586124 +46.6701967 15.9476135 +46.665051 16.052197 +46.7533019 16.1674449 +45.980295 14.80594 +46.044601 14.750788 +46.3046308 14.2483693 +46.28685 14.2247711 +46.05929461 14.75820837 +46.0252871 14.7610678 +46.06021552 14.75728007 +45.671462 15.217156 +45.6360353 15.2121075 +46.162412 13.8699702 +46.2051453 13.8923817 +46.3259585 14.2022067 +46.573511 16.344767 +46.269841 14.5988551 +46.3292027 14.5880788 +46.0115703 15.0354362 +46.0313919 14.9756585 +46.1024727 14.4140562 +45.9744151 13.7425328 diff --git a/inst/files/coords22.txt b/inst/files/coords22.txt new file mode 100644 index 0000000..c5dcb5b --- /dev/null +++ b/inst/files/coords22.txt @@ -0,0 +1,22 @@ +40.9018181 21.5116103 +40.9016623 21.5117316 +40.90217 21.5120367 +40.9071067 21.5030733 +40.9065417 21.5025575 +40.9070548 21.5030808 +40.8590889 21.4020477 +40.8589216 21.4020291 +40.8591833 21.40175 +40.8480467 21.3852633 +40.847581 21.3846472 +40.8480022 21.3852284 +42.0538356 21.1131689 +42.05297845 21.11223496 +41.6615644 20.7346756 +41.6618469 20.73545287 +41.4946867 20.4993533 +41.49478254 20.49863206 +41.27309016 20.59281233 +41.2720044 20.59156 +41.15792245 22.49473896 +41.1586833 22.4953222 diff --git a/inst/files/coords239.txt b/inst/files/coords239.txt new file mode 100644 index 0000000..4042035 --- /dev/null +++ b/inst/files/coords239.txt @@ -0,0 +1,239 @@ +40.9018181 21.5116103 +40.9016623 21.5117316 +40.90217 21.5120367 +40.9071067 21.5030733 +40.9065417 21.5025575 +40.9070548 21.5030808 +40.8590889 21.4020477 +40.8589216 21.4020291 +40.8591833 21.40175 +40.8480467 21.3852633 +40.847581 21.3846472 +40.8480022 21.3852284 +42.0538356 21.1131689 +42.05297845 21.11223496 +41.6615644 20.7346756 +41.6618469 20.73545287 +41.4946867 20.4993533 +41.49478254 20.49863206 +41.27309016 20.59281233 +41.2720044 20.59156 +41.15792245 22.49473896 +41.1586833 22.4953222 +41.15782122 22.4947102 +41.36074832 22.04990014 +41.3602256 22.04992 +41.3604707 22.05085131 +41.80550613 22.66250867 +41.80404624 22.66264441 +41.80444695 22.66334864 +41.8041938 22.66222045 +41.8050233 22.66294 +41.76237188 22.8715954 +41.7620722 22.87235 +41.3965011 22.6176956 +41.39723759 22.61788885 +41.11698374 21.61068069 +41.1169878 21.6109322 +41.1037344 21.6481789 +41.10322212 21.64740863 +41.08371472 21.76333803 +41.0846422 21.7638367 +41.01151 21.2476767 +41.01167868 21.24840614 +41.0117969 21.24736222 +42.1618222 21.8708222 +42.16219127 21.87209361 +42.16966354 22.11741311 +42.1698067 22.1165844 +42.00048883 22.14171517 +42.0001444 22.1409222 +41.5723711 21.9163989 +41.57180759 21.91642962 +41.57399553 21.27912497 +41.5744956 21.2786067 +41.36958814 21.24922897 +41.3702489 21.2492489 +40.9496011 20.9010178 +40.94958371 20.90091111 +41.71291737 22.15859214 +41.7128522 22.1582967 +41.94525847 21.49500328 +41.9447822 21.49431 +43.3761792 26.6932076 +42.1520289 22.7953622 +42.1376112 25.1348601 +42.2071885 22.8415741 +42.0700834 23.1498048 +43.124379 24.6946724 +42.6601523 27.566739 +42.2348682 27.7751855 +43.2049353 24.5044025 +42.5325236 26.740262 +43.300986 24.6027577 +42.1999609 25.3255252 +42.1447209 24.7504415 +42.5030972 24.0008741 +41.5518422 24.0290194 +43.6716945 26.1742714 +41.6431363 25.3691085 +42.8187429 23.2253047 +43.6313419 23.5562046 +41.5748969 24.7110201 +43.5972509 23.1172636 +43.4653552 27.6001985 +42.85032 25.6336533 +42.4978379 27.4701854 +42.1981817 24.4333358 +43.248015 26.5737087 +43.1351081 24.7175323 +41.464715 23.7985163 +42.1791549 24.0971473 +41.5603459 24.9737821 +43.6114291 27.2829397 +40.89911 20.6743053 +40.8992088 20.6744875 +40.8992642 20.6745657 +40.8820333 20.6838167 +41.0683067 20.6296233 +41.0681792 20.6296806 +41.068167 20.6295305 +41.1364031 20.3783984 +41.13694 20.37904 +41.18528 20.32393 +41.1852187 20.3239808 +41.1637467 20.23358 +41.1633733 20.2331458 +41.1632734 20.2329669 +45.63540571 15.21185932 +46.2602521 15.3271815 +46.835056 16.142801 +46.83636881 16.14345144 +46.6373823 16.3018427 +46.0323162 14.7175494 +46.0601379 14.7586124 +46.6701967 15.9476135 +46.665051 16.052197 +46.7533019 16.1674449 +45.980295 14.80594 +46.044601 14.750788 +46.3046308 14.2483693 +46.28685 14.2247711 +46.05929461 14.75820837 +46.0252871 14.7610678 +46.06021552 14.75728007 +45.671462 15.217156 +45.6360353 15.2121075 +46.162412 13.8699702 +46.2051453 13.8923817 +46.3259585 14.2022067 +46.573511 16.344767 +46.269841 14.5988551 +46.3292027 14.5880788 +46.0115703 15.0354362 +46.0313919 14.9756585 +46.1024727 14.4140562 +45.9744151 13.7425328 +46.5843436 16.4509887 +46.5829546 16.45029436 +46.507624 16.009805 +46.5881775 16.2692164 +46.5748473 16.2957718 +46.5546899 16.3523873 +46.32986289 14.31747987 +46.32835326 14.3176347 +46.32964497 14.31757184 +46.3291349 14.3172529 +46.6995947 15.9076394 +46.3528021 15.8322341 +46.3935046 14.1568821 +41.02545803 27.37479513 +41.02565798 27.37643592 +41.0266663 27.37550187 +41.02705637 27.37592145 +41.0257384 27.3752089 +41.02541979 27.52614954 +41.0255694 27.5251111 +41.02559663 27.52597266 +41.02633602 27.52642596 +41.02640852 27.52488855 +41.0462964 27.38248865 +41.04684626 27.38314892 +41.04632102 27.38339332 +41.0469611 27.3828028 +41.04624147 27.38241352 +41.0878206 27.54539 +41.08808109 27.54515537 +41.08768807 27.54629788 +41.08790613 27.544653 +41.08765265 27.54549046 +40.98924677 27.42248882 +40.9884306 27.4213306 +40.98866286 27.42235483 +40.98956833 27.42264911 +40.98846807 27.42083019 +40.98813858 27.42190525 +40.9589183 31.3332989 +40.9584617 31.476145 +40.9168572 31.3850683 +40.99553 31.3610633 +40.96476388 31.44562654 +40.9567017 31.4605989 +40.98749655 31.47264559 +40.9485228 31.3526117 +40.9421017 31.3052072 +41.9469189 27.1560189 +41.7283044 27.3409267 +41.8058761 27.3024344 +41.9466072 27.0483044 +40.96607039 31.61054606 +40.95783001 31.46065027 +40.9671706 31.4769372 +40.9654106 31.4449328 +40.9663856 31.6101939 +40.95728494 31.46068803 +40.9601361 31.5436611 +40.9862049 31.47280319 +40.9868133 31.4731939 +40.95705984 31.45965075 +40.9871778 31.6873361 +40.98744269 31.68837421 +40.8005751 30.74493893 +40.799369 30.7443297 +40.800146 30.7451097 +40.79930923 30.74441196 +40.799597 30.7445597 +40.79883365 30.74483688 +40.79973985 30.74473845 +40.80019422 30.74447766 +40.79909512 30.74411067 +40.79936694 30.74546205 +40.79922346 30.74511745 +40.79939045 30.74494972 +40.79907218 30.74383784 +40.800008 30.7449697 +41.6940744 26.5251078 +41.69360886 26.52375392 +41.69393445 26.52595384 +40.725405 26.08896425 +40.7265522 26.0895717 +40.72661545 26.08854415 +40.72575791 26.08976465 +41.27285804 26.68594113 +41.27226108 26.68443718 +41.27211185 26.68550093 +41.2724878 26.6849378 +40.85935427 26.62600131 +40.8581778 26.62659096 +40.8579794 26.6255656 +40.85819641 26.62557891 +40.92744306 26.39547896 +40.92729855 26.39690685 +40.92679773 26.39642599 +40.926775 26.3958028 +40.92674661 26.39673329 +40.92698794 26.39672838 +41.55034838 26.81855832 +41.54870378 26.81906694 +41.5500033 26.8191811 +41.5486203 26.81874789 diff --git a/inst/files/coords75.txt b/inst/files/coords75.txt new file mode 100644 index 0000000..a1febaf --- /dev/null +++ b/inst/files/coords75.txt @@ -0,0 +1,75 @@ +19.526914 45.505108 +19.526914 45.505108 +20.439163 45.794199 +20.439163 45.794199 +21.006053 45.171846 +21.006053 45.171846 +20.327675 45.258111 +20.327675 45.258111 +19.110586 45.517777 +19.110586 45.517777 +19.40905 45.996946 +19.524578 45.1179897 +19.524578 45.1179897 +20.260653 45.137065 +20.260653 45.137065 +19.264371 45.042895 +19.264371 45.042895 +19.385321 45.70459 +21.420223 44.382758 +19.646409 43.38478 +19.236739 45.121332 +19.826382 43.866279 +20.694367 42.918264 +22.402966 43.057643 +19.851461 44.272764 +22.256316 43.597383 +20.119577 43.082878 +20.643677 43.751678 +20.643677 43.751678 +21.43415 45.182659 +22.256316 43.597383 +21.57655 42.573187 +21.43415 45.182659 +20.694367 42.918264 +20.119577 43.082878 +20.978816 43.635875 +21.154814 45.044254 +20.119577 43.082878 +19.385321 45.70459 +19.385321 45.70459 +19.385321 45.70459 +19.385321 45.70459 +20.465275 45.828333 +20.465275 45.828333 +20.694367 42.918264 +20.804007 43.104876 +20.846434 42.908099 +20.846434 42.908099 +20.501142 44.142126 +19.866667 45.25 +19.866667 45.25 +20.035228 45.214242 +19.451342 45.226466 +19.535247 45.216429 +21.037778 43.381389 +21.327213 43.574243 +21.200146 43.421908 +21.353255 43.592706 +21.022472 43.323498 +20.978816 43.635875 +19.826382 43.866279 +20.228299 44.747398 +21.43415 45.182659 +21.43415 45.182659 +21.43415 45.182659 +21.43415 45.182659 +21.43415 45.182659 +21.43415 45.182659 +21.43415 45.182659 +21.420223 44.382758 +21.420223 44.382758 +19.560833 43.946644 +20.326674 44.602431 +20.326674 44.602431 +20.326674 44.602431 diff --git a/inst/files/faststructure/fast-structure_01.meanQ b/inst/files/faststructure/fast-structure_01.meanQ new file mode 100644 index 0000000..e32ae75 --- /dev/null +++ b/inst/files/faststructure/fast-structure_01.meanQ @@ -0,0 +1,22 @@ +1.000000 +1.000000 +1.000000 +1.000000 +1.000000 +1.000000 +1.000000 +1.000000 +1.000000 +1.000000 +1.000000 +1.000000 +1.000000 +1.000000 +1.000000 +1.000000 +1.000000 +1.000000 +1.000000 +1.000000 +1.000000 +1.000000 diff --git a/inst/files/faststructure/fast-structure_02.meanQ b/inst/files/faststructure/fast-structure_02.meanQ new file mode 100644 index 0000000..5b66aed --- /dev/null +++ b/inst/files/faststructure/fast-structure_02.meanQ @@ -0,0 +1,22 @@ +0.000025 0.999975 +0.999965 0.000035 +0.000038 0.999962 +0.778755 0.221245 +0.000036 0.999964 +0.000037 0.999963 +0.000036 0.999964 +0.000041 0.999959 +0.000035 0.999965 +0.000040 0.999960 +0.548726 0.451274 +0.000036 0.999964 +0.503467 0.496533 +0.000039 0.999961 +0.000036 0.999964 +0.000033 0.999967 +0.999944 0.000056 +0.999959 0.000041 +0.999904 0.000096 +0.999952 0.000048 +0.999963 0.000037 +0.999955 0.000045 diff --git a/inst/files/faststructure/fast-structure_03.meanQ b/inst/files/faststructure/fast-structure_03.meanQ new file mode 100644 index 0000000..abe5912 --- /dev/null +++ b/inst/files/faststructure/fast-structure_03.meanQ @@ -0,0 +1,22 @@ +0.000012 0.000011 0.999977 +0.999977 0.000011 0.000012 +0.000012 0.000011 0.999977 +0.756188 0.000011 0.243801 +0.000011 0.000010 0.999978 +0.000012 0.999975 0.000013 +0.000012 0.000012 0.999977 +0.000012 0.000012 0.999976 +0.000012 0.000010 0.999978 +0.000011 0.000011 0.999978 +0.547187 0.000012 0.452801 +0.000012 0.000011 0.999977 +0.495716 0.000011 0.504273 +0.000012 0.000010 0.999978 +0.000012 0.000011 0.999977 +0.000012 0.000011 0.999977 +0.999976 0.000012 0.000012 +0.999977 0.000011 0.000012 +0.999409 0.000011 0.000580 +0.999978 0.000011 0.000011 +0.999977 0.000012 0.000012 +0.999977 0.000011 0.000012 diff --git a/inst/files/faststructure/fast-structure_04.meanQ b/inst/files/faststructure/fast-structure_04.meanQ new file mode 100644 index 0000000..cf06ead --- /dev/null +++ b/inst/files/faststructure/fast-structure_04.meanQ @@ -0,0 +1,22 @@ +0.000007 0.000008 0.000007 0.999977 +0.000007 0.999978 0.000007 0.000008 +0.000007 0.000008 0.000007 0.999978 +0.000008 0.778682 0.000008 0.221303 +0.000007 0.000007 0.000007 0.999978 +0.000007 0.000007 0.000007 0.999978 +0.000007 0.000008 0.000007 0.999977 +0.000008 0.000008 0.000008 0.999977 +0.000007 0.000008 0.000007 0.999978 +0.000007 0.000007 0.000007 0.999978 +0.000008 0.548609 0.000008 0.451376 +0.000007 0.000008 0.000007 0.999978 +0.000007 0.503341 0.000007 0.496644 +0.000007 0.000008 0.000007 0.999978 +0.000008 0.000008 0.000008 0.999977 +0.000007 0.000008 0.000007 0.999977 +0.000008 0.999977 0.000008 0.000008 +0.000007 0.999978 0.000007 0.000007 +0.000007 0.999979 0.000007 0.000007 +0.000007 0.999978 0.000007 0.000007 +0.000008 0.999977 0.000008 0.000008 +0.000007 0.999978 0.000007 0.000007 diff --git a/inst/files/faststructure/fast-structure_05.meanQ b/inst/files/faststructure/fast-structure_05.meanQ new file mode 100644 index 0000000..8a299e0 --- /dev/null +++ b/inst/files/faststructure/fast-structure_05.meanQ @@ -0,0 +1,22 @@ +0.000006 0.000006 0.000006 0.000006 0.999977 +0.000006 0.000006 0.999977 0.000006 0.000006 +0.000006 0.000006 0.000006 0.000006 0.999977 +0.000006 0.000006 0.999977 0.000006 0.000006 +0.000006 0.000006 0.000006 0.000006 0.999977 +0.000006 0.000006 0.000006 0.000006 0.999977 +0.000006 0.000006 0.000006 0.000006 0.999977 +0.000006 0.000006 0.000006 0.000006 0.999976 +0.000006 0.000006 0.000006 0.000006 0.999977 +0.000006 0.000006 0.000006 0.000006 0.999978 +0.000006 0.000006 0.999976 0.000006 0.000006 +0.000006 0.000006 0.000006 0.000006 0.999977 +0.000006 0.000006 0.999977 0.000006 0.000006 +0.000006 0.000006 0.000006 0.000006 0.999977 +0.000006 0.000006 0.000006 0.000006 0.999976 +0.000006 0.000006 0.000006 0.000006 0.999977 +0.000006 0.000006 0.999976 0.000006 0.000006 +0.000006 0.000006 0.999977 0.000006 0.000006 +0.000005 0.000005 0.999978 0.000005 0.000005 +0.000006 0.000006 0.999978 0.000006 0.000006 +0.000006 0.000006 0.999976 0.000006 0.000006 +0.000006 0.000006 0.999977 0.000006 0.000006 diff --git a/inst/files/faststructure/fast-structure_06.meanQ b/inst/files/faststructure/fast-structure_06.meanQ new file mode 100644 index 0000000..94c57e4 --- /dev/null +++ b/inst/files/faststructure/fast-structure_06.meanQ @@ -0,0 +1,22 @@ +0.000005 0.999976 0.000005 0.000005 0.000005 0.000005 +0.000005 0.000005 0.999976 0.000005 0.000005 0.000005 +0.000005 0.999976 0.000005 0.000005 0.000005 0.000005 +0.000005 0.221107 0.778873 0.000005 0.000005 0.000005 +0.000005 0.999977 0.000005 0.000005 0.000005 0.000005 +0.000005 0.999977 0.000005 0.000005 0.000005 0.000005 +0.000005 0.999976 0.000005 0.000005 0.000005 0.000005 +0.000005 0.999976 0.000005 0.000005 0.000005 0.000005 +0.000005 0.999976 0.000005 0.000005 0.000005 0.000005 +0.000005 0.999977 0.000005 0.000005 0.000005 0.000005 +0.000005 0.451276 0.548705 0.000005 0.000005 0.000005 +0.000005 0.999976 0.000005 0.000005 0.000005 0.000005 +0.000005 0.496540 0.503441 0.000005 0.000005 0.000005 +0.000005 0.999976 0.000005 0.000005 0.000005 0.000005 +0.000005 0.999976 0.000005 0.000005 0.000005 0.000005 +0.000005 0.999976 0.000005 0.000005 0.000005 0.000005 +0.000005 0.000005 0.999976 0.000005 0.000005 0.000005 +0.000005 0.000005 0.999977 0.000005 0.000005 0.000005 +0.000004 0.000004 0.999978 0.000004 0.000004 0.000004 +0.000005 0.000005 0.999977 0.000005 0.000005 0.000005 +0.000005 0.000005 0.999976 0.000005 0.000005 0.000005 +0.000005 0.000005 0.999977 0.000005 0.000005 0.000005 diff --git a/inst/files/faststructure/fast-structure_07.meanQ b/inst/files/faststructure/fast-structure_07.meanQ new file mode 100644 index 0000000..7298ee1 --- /dev/null +++ b/inst/files/faststructure/fast-structure_07.meanQ @@ -0,0 +1,22 @@ +0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.999975 +0.000004 0.000004 0.000004 0.999976 0.000004 0.000004 0.000004 +0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.999976 +0.000004 0.000004 0.000004 0.778775 0.000004 0.000004 0.221204 +0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.999976 +0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.999976 +0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.999975 +0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.999975 +0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.999976 +0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.999977 +0.000004 0.000004 0.000004 0.548637 0.000004 0.000004 0.451342 +0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.999976 +0.000004 0.000004 0.000004 0.503369 0.000004 0.000004 0.496611 +0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.999976 +0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.999975 +0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.999975 +0.000004 0.000004 0.000004 0.999975 0.000004 0.000004 0.000004 +0.000004 0.000004 0.000004 0.999976 0.000004 0.000004 0.000004 +0.000004 0.000004 0.000004 0.999977 0.000004 0.000004 0.000004 +0.000004 0.000004 0.000004 0.999977 0.000004 0.000004 0.000004 +0.000004 0.000004 0.000004 0.999975 0.000004 0.000004 0.000004 +0.000004 0.000004 0.000004 0.999976 0.000004 0.000004 0.000004 diff --git a/inst/files/faststructure/fast-structure_08.meanQ b/inst/files/faststructure/fast-structure_08.meanQ new file mode 100644 index 0000000..411543a --- /dev/null +++ b/inst/files/faststructure/fast-structure_08.meanQ @@ -0,0 +1,22 @@ +0.000004 0.999975 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 +0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.999975 +0.000004 0.999975 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 +0.000004 0.124838 0.000004 0.000004 0.000004 0.000004 0.000004 0.875140 +0.000003 0.999976 0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 +0.000003 0.999976 0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 +0.000004 0.999975 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 +0.000004 0.999975 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 +0.000004 0.999975 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 +0.000003 0.999976 0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 +0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.999975 +0.000004 0.999975 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 +0.000003 0.403971 0.000003 0.000003 0.000003 0.000003 0.000003 0.596008 +0.000004 0.999975 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 +0.000004 0.999975 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 +0.000004 0.999975 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 +0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.999975 +0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 0.999976 +0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 0.999977 +0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 0.999976 +0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.999975 +0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 0.999976 diff --git a/inst/files/faststructure/fast-structure_09.meanQ b/inst/files/faststructure/fast-structure_09.meanQ new file mode 100644 index 0000000..f077dae --- /dev/null +++ b/inst/files/faststructure/fast-structure_09.meanQ @@ -0,0 +1,22 @@ +0.000003 0.000003 0.000003 0.000003 0.999975 0.000003 0.000003 0.000003 0.000003 +0.000003 0.999975 0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 +0.000003 0.000003 0.000003 0.000003 0.999975 0.000003 0.000003 0.000003 0.000003 +0.000003 0.778810 0.000003 0.000003 0.221167 0.000003 0.000003 0.000003 0.000003 +0.000003 0.000003 0.000003 0.000003 0.999976 0.000003 0.000003 0.000003 0.000003 +0.000003 0.000003 0.000003 0.000003 0.999975 0.000003 0.000003 0.000003 0.000003 +0.000003 0.000003 0.000003 0.000003 0.999974 0.000003 0.000003 0.000003 0.000003 +0.000003 0.000003 0.000003 0.000003 0.999974 0.000003 0.000003 0.000003 0.000003 +0.000003 0.000003 0.000003 0.000003 0.999975 0.000003 0.000003 0.000003 0.000003 +0.000003 0.000003 0.000003 0.000003 0.999976 0.000003 0.000003 0.000003 0.000003 +0.000003 0.548650 0.000003 0.000003 0.451327 0.000003 0.000003 0.000003 0.000003 +0.000003 0.000003 0.000003 0.000003 0.999975 0.000003 0.000003 0.000003 0.000003 +0.000003 0.503383 0.000003 0.000003 0.496596 0.000003 0.000003 0.000003 0.000003 +0.000003 0.000003 0.000003 0.000003 0.999975 0.000003 0.000003 0.000003 0.000003 +0.000003 0.000003 0.000003 0.000003 0.999974 0.000003 0.000003 0.000003 0.000003 +0.000003 0.000003 0.000003 0.000003 0.999975 0.000003 0.000003 0.000003 0.000003 +0.000003 0.999974 0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 +0.000003 0.999975 0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 +0.000003 0.999976 0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 +0.000003 0.999976 0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 +0.000003 0.999974 0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 +0.000003 0.999975 0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 diff --git a/inst/files/faststructure/fast-structure_10.meanQ b/inst/files/faststructure/fast-structure_10.meanQ new file mode 100644 index 0000000..d261d29 --- /dev/null +++ b/inst/files/faststructure/fast-structure_10.meanQ @@ -0,0 +1,22 @@ +0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 0.999974 +0.000003 0.000003 0.000003 0.000003 0.999975 0.000003 0.000003 0.000003 0.000003 0.000003 +0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 0.999975 +0.000003 0.000003 0.000003 0.000003 0.651464 0.000003 0.000003 0.000003 0.000003 0.348513 +0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 0.999975 +0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 0.999975 +0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 0.999974 +0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 0.999974 +0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 0.999975 +0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 0.999975 +0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 0.999974 +0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 0.999974 +0.000003 0.000003 0.000003 0.000003 0.380442 0.000003 0.000003 0.000003 0.000003 0.619536 +0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 0.999974 +0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 0.999974 +0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 0.999974 +0.000003 0.000003 0.000003 0.000003 0.999974 0.000003 0.000003 0.000003 0.000003 0.000003 +0.000003 0.000003 0.000003 0.000003 0.999975 0.000003 0.000003 0.000003 0.000003 0.000003 +0.000003 0.000003 0.000003 0.000003 0.975322 0.000003 0.000003 0.000003 0.000003 0.024657 +0.000003 0.000003 0.000003 0.000003 0.999975 0.000003 0.000003 0.000003 0.000003 0.000003 +0.000003 0.000003 0.000003 0.000003 0.999974 0.000003 0.000003 0.000003 0.000003 0.000003 +0.000003 0.000003 0.000003 0.000003 0.999975 0.000003 0.000003 0.000003 0.000003 0.000003 diff --git a/inst/files/faststructure/fast-structure_11.meanQ b/inst/files/faststructure/fast-structure_11.meanQ new file mode 100644 index 0000000..51af10e --- /dev/null +++ b/inst/files/faststructure/fast-structure_11.meanQ @@ -0,0 +1,22 @@ +0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 0.999974 0.000003 0.000003 0.000003 +0.000003 0.999974 0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 +0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 0.999974 0.000003 0.000003 0.000003 +0.000003 0.778827 0.000003 0.000003 0.000003 0.000003 0.000003 0.221149 0.000003 0.000003 0.000003 +0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 0.999975 0.000003 0.000003 0.000003 +0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 0.999975 0.000003 0.000003 0.000003 +0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 0.999974 0.000003 0.000003 0.000003 +0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 0.999974 0.000003 0.000003 0.000003 +0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 0.999974 0.000003 0.000003 0.000003 +0.000002 0.000002 0.000002 0.000002 0.000002 0.000002 0.000002 0.999975 0.000002 0.000002 0.000002 +0.000003 0.548655 0.000003 0.000003 0.000003 0.000003 0.000003 0.451321 0.000003 0.000003 0.000003 +0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 0.999974 0.000003 0.000003 0.000003 +0.000003 0.503388 0.000003 0.000003 0.000003 0.000003 0.000003 0.496590 0.000003 0.000003 0.000003 +0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 0.999974 0.000003 0.000003 0.000003 +0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 0.999974 0.000003 0.000003 0.000003 +0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 0.999974 0.000003 0.000003 0.000003 +0.000003 0.999974 0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 +0.000003 0.999975 0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 +0.000002 0.999976 0.000002 0.000002 0.000002 0.000002 0.000002 0.000002 0.000002 0.000002 0.000002 +0.000002 0.999975 0.000002 0.000002 0.000002 0.000002 0.000002 0.000002 0.000002 0.000002 0.000002 +0.000003 0.999974 0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 +0.000003 0.999975 0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 0.000003 diff --git a/inst/files/faststructuregrplabels.txt b/inst/files/faststructuregrplabels.txt new file mode 100644 index 0000000..89da61a --- /dev/null +++ b/inst/files/faststructuregrplabels.txt @@ -0,0 +1,22 @@ +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop C +Pop C +Pop C +Pop C +Pop C +Pop C diff --git a/inst/files/faststructurepoplabels.txt b/inst/files/faststructurepoplabels.txt new file mode 100644 index 0000000..89da61a --- /dev/null +++ b/inst/files/faststructurepoplabels.txt @@ -0,0 +1,22 @@ +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop C +Pop C +Pop C +Pop C +Pop C +Pop C diff --git a/inst/files/grplab.txt b/inst/files/grplab.txt new file mode 100644 index 0000000..cf6c31e --- /dev/null +++ b/inst/files/grplab.txt @@ -0,0 +1,150 @@ +lab1 lab2 mixed +c sd qwe +c sd qwe +c sd qwe +c sd qwe +c sd erd +c sd erd +c sd erd +c sd erd +c sd erd +c sd erd +c sd erd +c sd erd +c sd erd +c as erd +c as erd +c as erd +c as erd +c as erd +c as erd +c as rga +c as rga +c as rga +c as rga +c as rga +c as rga +c as rga +a as erd +a as asf +a as asf +a as asf +a as asf +a as asf +a as asf +a as asf +a fg asf +a fg asf +a fg asf +a fg asf +a fg asf +a fg asf +a fg asf +a fg asf +a fg asf +a fg asf +a fg asf +a fg asf +a fg asf +a fg asf +a fg asf +a fg asf +a fg asf +a fg asf +a fg asf +a fg asf +a fg asf +a fg asf +a fg qwe +a fg qwe +a fg qwe +a fg qwe +a fg qwe +a fg qwe +a fg qwe +a fg qwe +a fg qwe +a fg qwe +a fg qwe +a er qwe +a er qwe +a er erd +a er erd +a er erd +a er erd +a er erd +a er erd +a er fds +a er fds +a er fds +a er fds +a er fds +a er fds +a er fds +a er fds +a er fds +a er fds +a er fds +a er fds +a er fds +a er fds +a er fds +a er fds +a er fds +a er fds +a er fds +a er fds +a er fds +a er asf +a er asf +a er asf +a er asf +a er asf +a er asf +a er asf +a er asf +a er asf +a er asf +a er asf +a er asf +a er erd +a er erd +a er erd +a er erd +a er erd +a er erd +a er erd +a er erd +a er erd +a er erd +a er erd +a er erd +a er erd +b er erd +b er erd +b er fds +b er fds +b kj fds +b kj fds +b kj fds +b kj fds +b kj fds +b kj fds +b kj fds +b kj fds +b kj fds +b kj fds +b kj fds +b kj fds +b kj fds +b pp fds +b pp fds +b pp fds +b pp fds +b pp fds +b pp fds +b pp fds +b pp fds +b pp fds +b pp fds +b pp fds diff --git a/inst/files/matrix/comma/matrix-comma-k3.csv b/inst/files/matrix/comma/matrix-comma-k3.csv new file mode 100644 index 0000000..0cbd156 --- /dev/null +++ b/inst/files/matrix/comma/matrix-comma-k3.csv @@ -0,0 +1,75 @@ +0.92633,0.057885,0.015785 +0.68248,0.307585,0.009935 +0.935345,0.05991,0.004745 +0.877755,0.108125,0.01412 +0.855695,0.128085,0.01622 +0.94049,0.053025,0.006485 +0.4792,0.393205,0.127595 +0.67483,0.311105,0.014065 +0.71559,0.263975,0.020435 +0.760645,0.19124,0.048115 +0.736425,0.21584,0.047735 +0.79977,0.191755,0.008475 +0.74638,0.233435,0.020185 +0.91399,0.06757,0.01844 +0.813655,0.167695,0.01865 +0.961345,0.034485,0.00417 +0.664755,0.317515,0.01773 +0.8359,0.14073,0.02337 +0.784935,0.120195,0.09487 +0.813735,0.142155,0.04411 +0.669755,0.27439,0.055855 +0.696605,0.136065,0.16733 +0.95993,0.035815,0.004255 +0.765655,0.225335,0.00901 +0.93428,0.057075,0.008645 +0.721295,0.261755,0.01695 +0.90934,0.079875,0.010785 +0.963815,0.03178,0.004405 +0.91296,0.068685,0.018355 +0.64133,0.32156,0.03711 +0.58481,0.40821,0.00698 +0.77754,0.21508,0.00738 +0.52871,0.457225,0.014065 +0.55024,0.44282,0.00694 +0.796835,0.1804,0.022765 +0.931815,0.05093,0.017255 +0.915155,0.07507,0.009775 +0.685855,0.30715,0.006995 +0.66243,0.321105,0.016465 +0.731645,0.26421,0.004145 +0.91696,0.076265,0.006775 +0.67236,0.32263,0.00501 +0.89296,0.102485,0.004555 +0.752315,0.244275,0.00341 +0.91062,0.064775,0.024605 +0.88845,0.10221,0.00934 +0.90092,0.073475,0.025605 +0.690555,0.27085,0.038595 +0.62902,0.29397,0.07701 +0.92489,0.04776,0.02735 +0.856255,0.0875,0.056245 +0.94584,0.043995,0.010165 +0.8982,0.09126,0.01054 +0.88973,0.06803,0.04224 +0.764175,0.220515,0.01531 +0.933695,0.05207,0.014235 +0.93678,0.044045,0.019175 +0.949515,0.041625,0.00886 +0.892755,0.063405,0.04384 +0.67181,0.26196,0.06623 +0.94439,0.042755,0.012855 +0.683955,0.269325,0.04672 +0.885265,0.08908,0.025655 +0.84537,0.08784,0.06679 +0.943995,0.027945,0.02806 +0.970395,0.01639,0.013215 +0.9156,0.080305,0.004095 +0.96383,0.024145,0.012025 +0.98202,0.010825,0.007155 +0.946585,0.04552,0.007895 +0.979385,0.01676,0.003855 +0.712255,0.27954,0.008205 +0.655345,0.340465,0.00419 +0.706595,0.283935,0.00947 +0.87072,0.120915,0.008365 diff --git a/inst/files/matrix/comma/matrix-comma-k4.csv b/inst/files/matrix/comma/matrix-comma-k4.csv new file mode 100644 index 0000000..c702123 --- /dev/null +++ b/inst/files/matrix/comma/matrix-comma-k4.csv @@ -0,0 +1,75 @@ +0.955705,0.02329,0.010225,0.01078 +0.97025,0.00978,0.011555,0.008415 +0.988065,0.0045,0.004015,0.00342 +0.956495,0.016455,0.01188,0.01517 +0.975235,0.010725,0.007525,0.006515 +0.9846,0.00728,0.00515,0.00297 +0.6624,0.171935,0.096505,0.06916 +0.953795,0.01761,0.017365,0.01123 +0.947975,0.014595,0.02233,0.0151 +0.871835,0.059255,0.024305,0.044605 +0.894005,0.049685,0.024755,0.031555 +0.977285,0.00981,0.006085,0.00682 +0.94224,0.022565,0.012215,0.02298 +0.94773,0.03007,0.01202,0.01018 +0.956865,0.01837,0.01221,0.012555 +0.988305,0.004275,0.004155,0.003265 +0.92505,0.038375,0.017735,0.01884 +0.919855,0.035305,0.018225,0.026615 +0.56458,0.329155,0.018835,0.08743 +0.778205,0.108265,0.006135,0.107395 +0.82095,0.113005,0.013575,0.05247 +0.51192,0.37259,0.018025,0.097465 +0.983605,0.010075,0.001605,0.004715 +0.96554,0.021285,0.00327,0.009905 +0.97407,0.016685,0.002805,0.00644 +0.948345,0.02342,0.01071,0.017525 +0.94937,0.02445,0.011645,0.014535 +0.97971,0.0102,0.00413,0.00596 +0.92199,0.02293,0.03244,0.02264 +0.885585,0.032595,0.04551,0.03631 +0.96793,0.010835,0.00997,0.011265 +0.98554,0.004815,0.005455,0.00419 +0.940185,0.013145,0.02165,0.02502 +0.963735,0.00625,0.01634,0.013675 +0.956795,0.0125,0.01349,0.017215 +0.94098,0.01704,0.02271,0.01927 +0.972195,0.00999,0.010835,0.00698 +0.981735,0.003055,0.010665,0.004545 +0.971005,0.00665,0.01679,0.005555 +0.98738,0.00299,0.005655,0.003975 +0.987855,0.003515,0.005265,0.003365 +0.9918,0.00269,0.00394,0.00157 +0.985485,0.00453,0.006025,0.00396 +0.98447,0.0048,0.006375,0.004355 +0.917025,0.03599,0.024245,0.02274 +0.97876,0.00874,0.006855,0.005645 +0.91806,0.03041,0.02809,0.02344 +0.908525,0.02561,0.03833,0.027535 +0.777225,0.07074,0.07886,0.073175 +0.89878,0.052275,0.031945,0.017 +0.855605,0.052475,0.06131,0.03061 +0.972265,0.009335,0.008475,0.009925 +0.97398,0.01123,0.005605,0.009185 +0.89581,0.037245,0.03086,0.036085 +0.94447,0.01938,0.01964,0.01651 +0.9557,0.01858,0.012855,0.012865 +0.924785,0.036545,0.020675,0.017995 +0.974025,0.01013,0.00777,0.008075 +0.90148,0.041965,0.028315,0.02824 +0.829025,0.060805,0.04,0.07017 +0.93776,0.03093,0.010225,0.021085 +0.79285,0.119565,0.03256,0.055025 +0.904355,0.05374,0.01133,0.030575 +0.83107,0.07136,0.05018,0.04739 +0.832325,0.124045,0.012075,0.031555 +0.88716,0.08679,0.006475,0.019575 +0.97331,0.0142,0.00405,0.00844 +0.91785,0.04062,0.01191,0.02962 +0.97859,0.008935,0.00536,0.007115 +0.9638,0.013895,0.007115,0.01519 +0.97802,0.009835,0.005215,0.00693 +0.978475,0.005615,0.00879,0.00712 +0.98059,0.00449,0.00887,0.00605 +0.950055,0.011995,0.022745,0.015205 +0.971085,0.007535,0.012945,0.008435 diff --git a/inst/files/matrix/comma/matrix-comma-k5.csv b/inst/files/matrix/comma/matrix-comma-k5.csv new file mode 100644 index 0000000..0cd9798 --- /dev/null +++ b/inst/files/matrix/comma/matrix-comma-k5.csv @@ -0,0 +1,75 @@ +0.78766,0.035545,0.021665,0.14898,0.00615 +0.817585,0.095465,0.022575,0.05413,0.010245 +0.935455,0.02521,0.007015,0.03066,0.00166 +0.767805,0.06457,0.029915,0.131635,0.006075 +0.83655,0.023065,0.042845,0.09518,0.00236 +0.916895,0.012525,0.0118,0.05622,0.00256 +0.414585,0.107505,0.15073,0.3227,0.00448 +0.72307,0.097715,0.07069,0.103095,0.00543 +0.762105,0.04293,0.13013,0.062035,0.0028 +0.70074,0.071655,0.05636,0.161935,0.00931 +0.586635,0.05431,0.05497,0.29668,0.007405 +0.865345,0.064235,0.01624,0.04942,0.00476 +0.742435,0.086295,0.025555,0.13856,0.007155 +0.847705,0.031365,0.0165,0.098125,0.006305 +0.814595,0.063985,0.02,0.09379,0.00763 +0.93737,0.021225,0.01002,0.029015,0.00237 +0.748705,0.08654,0.030325,0.125095,0.009335 +0.80061,0.053275,0.031685,0.10252,0.01191 +0.5744,0.056205,0.024215,0.330255,0.014925 +0.732615,0.07454,0.03534,0.141665,0.01584 +0.5035,0.17423,0.022075,0.28575,0.014445 +0.39582,0.27067,0.03361,0.280365,0.019535 +0.922555,0.008115,0.002015,0.065815,0.0015 +0.809655,0.067335,0.0077,0.1107,0.00461 +0.86916,0.038795,0.00787,0.07916,0.005015 +0.778535,0.108365,0.012665,0.0945,0.005935 +0.895745,0.044455,0.00887,0.042595,0.008335 +0.908325,0.04238,0.00522,0.04177,0.002305 +0.868345,0.07802,0.00674,0.03187,0.015025 +0.56275,0.39761,0.00931,0.020535,0.009795 +0.511225,0.46806,0.005765,0.013875,0.001075 +0.773375,0.198245,0.010645,0.015295,0.00244 +0.419985,0.55089,0.01508,0.010195,0.00385 +0.40169,0.585635,0.00524,0.005285,0.00215 +0.71916,0.2319,0.0106,0.032,0.00634 +0.83843,0.064685,0.02569,0.060065,0.01113 +0.86688,0.05349,0.016175,0.058465,0.00499 +0.888505,0.056145,0.025365,0.027445,0.00254 +0.849665,0.12689,0.006785,0.010825,0.005835 +0.93623,0.036545,0.00246,0.02108,0.003685 +0.94056,0.034055,0.01003,0.013065,0.00229 +0.75386,0.22233,0.008965,0.0136,0.001245 +0.896105,0.034175,0.013355,0.0546,0.001765 +0.89573,0.0555,0.023825,0.02268,0.002265 +0.74449,0.00881,0.101545,0.13998,0.005175 +0.819225,0.003525,0.023335,0.15206,0.001855 +0.854465,0.01019,0.049865,0.081295,0.004185 +0.5951,0.000515,0.39305,0.01106,0.000275 +0.5959,0.02486,0.1428,0.23272,0.00372 +0.612745,0.014675,0.10044,0.269185,0.002955 +0.70953,0.025255,0.117545,0.1434,0.00427 +0.867065,0.004685,0.03237,0.09496,0.00092 +0.887065,0.018265,0.02047,0.070735,0.003465 +0.66819,0.01788,0.163935,0.14256,0.007435 +0.716825,0.024995,0.081275,0.17009,0.006815 +0.812025,0.014975,0.043445,0.12376,0.005795 +0.656825,0.00689,0.034025,0.29661,0.00565 +0.873575,0.005165,0.01631,0.102345,0.002605 +0.572085,0.02273,0.03966,0.35916,0.006365 +0.56452,0.072335,0.0632,0.28911,0.010835 +0.869835,0.02069,0.03275,0.06602,0.010705 +0.57763,0.136195,0.051195,0.212715,0.022265 +0.66577,0.02718,0.028125,0.26848,0.010445 +0.500445,0.042015,0.09259,0.34561,0.01934 +0.466745,0.023915,0.003565,0.498015,0.00776 +0.76947,0.037415,0.00595,0.18161,0.005555 +0.85616,0.02724,0.003685,0.10895,0.003965 +0.83213,0.031305,0.004875,0.122325,0.009365 +0.914005,0.013695,0.00435,0.06094,0.00701 +0.837785,0.027755,0.00619,0.117055,0.011215 +0.936495,0.012705,0.00352,0.04292,0.00436 +0.90621,0.056205,0.00451,0.02912,0.003955 +0.276935,0.72192,0.000435,0.00037,0.00034 +0.72359,0.240885,0.005445,0.02553,0.00455 +0.8404,0.107435,0.010435,0.032995,0.008735 diff --git a/inst/files/matrix/space/matrix-space-k3.txt b/inst/files/matrix/space/matrix-space-k3.txt new file mode 100644 index 0000000..82da734 --- /dev/null +++ b/inst/files/matrix/space/matrix-space-k3.txt @@ -0,0 +1,75 @@ +0.92633 0.057885 0.015785 +0.68248 0.307585 0.009935 +0.935345 0.05991 0.004745 +0.877755 0.108125 0.01412 +0.855695 0.128085 0.01622 +0.94049 0.053025 0.006485 +0.4792 0.393205 0.127595 +0.67483 0.311105 0.014065 +0.71559 0.263975 0.020435 +0.760645 0.19124 0.048115 +0.736425 0.21584 0.047735 +0.79977 0.191755 0.008475 +0.74638 0.233435 0.020185 +0.91399 0.06757 0.01844 +0.813655 0.167695 0.01865 +0.961345 0.034485 0.00417 +0.664755 0.317515 0.01773 +0.8359 0.14073 0.02337 +0.784935 0.120195 0.09487 +0.813735 0.142155 0.04411 +0.669755 0.27439 0.055855 +0.696605 0.136065 0.16733 +0.95993 0.035815 0.004255 +0.765655 0.225335 0.00901 +0.93428 0.057075 0.008645 +0.721295 0.261755 0.01695 +0.90934 0.079875 0.010785 +0.963815 0.03178 0.004405 +0.91296 0.068685 0.018355 +0.64133 0.32156 0.03711 +0.58481 0.40821 0.00698 +0.77754 0.21508 0.00738 +0.52871 0.457225 0.014065 +0.55024 0.44282 0.00694 +0.796835 0.1804 0.022765 +0.931815 0.05093 0.017255 +0.915155 0.07507 0.009775 +0.685855 0.30715 0.006995 +0.66243 0.321105 0.016465 +0.731645 0.26421 0.004145 +0.91696 0.076265 0.006775 +0.67236 0.32263 0.00501 +0.89296 0.102485 0.004555 +0.752315 0.244275 0.00341 +0.91062 0.064775 0.024605 +0.88845 0.10221 0.00934 +0.90092 0.073475 0.025605 +0.690555 0.27085 0.038595 +0.62902 0.29397 0.07701 +0.92489 0.04776 0.02735 +0.856255 0.0875 0.056245 +0.94584 0.043995 0.010165 +0.8982 0.09126 0.01054 +0.88973 0.06803 0.04224 +0.764175 0.220515 0.01531 +0.933695 0.05207 0.014235 +0.93678 0.044045 0.019175 +0.949515 0.041625 0.00886 +0.892755 0.063405 0.04384 +0.67181 0.26196 0.06623 +0.94439 0.042755 0.012855 +0.683955 0.269325 0.04672 +0.885265 0.08908 0.025655 +0.84537 0.08784 0.06679 +0.943995 0.027945 0.02806 +0.970395 0.01639 0.013215 +0.9156 0.080305 0.004095 +0.96383 0.024145 0.012025 +0.98202 0.010825 0.007155 +0.946585 0.04552 0.007895 +0.979385 0.01676 0.003855 +0.712255 0.27954 0.008205 +0.655345 0.340465 0.00419 +0.706595 0.283935 0.00947 +0.87072 0.120915 0.008365 diff --git a/inst/files/matrix/space/matrix-space-k4.txt b/inst/files/matrix/space/matrix-space-k4.txt new file mode 100644 index 0000000..41c944f --- /dev/null +++ b/inst/files/matrix/space/matrix-space-k4.txt @@ -0,0 +1,75 @@ +0.955705 0.02329 0.010225 0.01078 +0.97025 0.00978 0.011555 0.008415 +0.988065 0.0045 0.004015 0.00342 +0.956495 0.016455 0.01188 0.01517 +0.975235 0.010725 0.007525 0.006515 +0.9846 0.00728 0.00515 0.00297 +0.6624 0.171935 0.096505 0.06916 +0.953795 0.01761 0.017365 0.01123 +0.947975 0.014595 0.02233 0.0151 +0.871835 0.059255 0.024305 0.044605 +0.894005 0.049685 0.024755 0.031555 +0.977285 0.00981 0.006085 0.00682 +0.94224 0.022565 0.012215 0.02298 +0.94773 0.03007 0.01202 0.01018 +0.956865 0.01837 0.01221 0.012555 +0.988305 0.004275 0.004155 0.003265 +0.92505 0.038375 0.017735 0.01884 +0.919855 0.035305 0.018225 0.026615 +0.56458 0.329155 0.018835 0.08743 +0.778205 0.108265 0.006135 0.107395 +0.82095 0.113005 0.013575 0.05247 +0.51192 0.37259 0.018025 0.097465 +0.983605 0.010075 0.001605 0.004715 +0.96554 0.021285 0.00327 0.009905 +0.97407 0.016685 0.002805 0.00644 +0.948345 0.02342 0.01071 0.017525 +0.94937 0.02445 0.011645 0.014535 +0.97971 0.0102 0.00413 0.00596 +0.92199 0.02293 0.03244 0.02264 +0.885585 0.032595 0.04551 0.03631 +0.96793 0.010835 0.00997 0.011265 +0.98554 0.004815 0.005455 0.00419 +0.940185 0.013145 0.02165 0.02502 +0.963735 0.00625 0.01634 0.013675 +0.956795 0.0125 0.01349 0.017215 +0.94098 0.01704 0.02271 0.01927 +0.972195 0.00999 0.010835 0.00698 +0.981735 0.003055 0.010665 0.004545 +0.971005 0.00665 0.01679 0.005555 +0.98738 0.00299 0.005655 0.003975 +0.987855 0.003515 0.005265 0.003365 +0.9918 0.00269 0.00394 0.00157 +0.985485 0.00453 0.006025 0.00396 +0.98447 0.0048 0.006375 0.004355 +0.917025 0.03599 0.024245 0.02274 +0.97876 0.00874 0.006855 0.005645 +0.91806 0.03041 0.02809 0.02344 +0.908525 0.02561 0.03833 0.027535 +0.777225 0.07074 0.07886 0.073175 +0.89878 0.052275 0.031945 0.017 +0.855605 0.052475 0.06131 0.03061 +0.972265 0.009335 0.008475 0.009925 +0.97398 0.01123 0.005605 0.009185 +0.89581 0.037245 0.03086 0.036085 +0.94447 0.01938 0.01964 0.01651 +0.9557 0.01858 0.012855 0.012865 +0.924785 0.036545 0.020675 0.017995 +0.974025 0.01013 0.00777 0.008075 +0.90148 0.041965 0.028315 0.02824 +0.829025 0.060805 0.04 0.07017 +0.93776 0.03093 0.010225 0.021085 +0.79285 0.119565 0.03256 0.055025 +0.904355 0.05374 0.01133 0.030575 +0.83107 0.07136 0.05018 0.04739 +0.832325 0.124045 0.012075 0.031555 +0.88716 0.08679 0.006475 0.019575 +0.97331 0.0142 0.00405 0.00844 +0.91785 0.04062 0.01191 0.02962 +0.97859 0.008935 0.00536 0.007115 +0.9638 0.013895 0.007115 0.01519 +0.97802 0.009835 0.005215 0.00693 +0.978475 0.005615 0.00879 0.00712 +0.98059 0.00449 0.00887 0.00605 +0.950055 0.011995 0.022745 0.015205 +0.971085 0.007535 0.012945 0.008435 diff --git a/inst/files/matrix/space/matrix-space-k5.txt b/inst/files/matrix/space/matrix-space-k5.txt new file mode 100644 index 0000000..6901c7d --- /dev/null +++ b/inst/files/matrix/space/matrix-space-k5.txt @@ -0,0 +1,75 @@ +0.78766 0.035545 0.021665 0.14898 0.00615 +0.817585 0.095465 0.022575 0.05413 0.010245 +0.935455 0.02521 0.007015 0.03066 0.00166 +0.767805 0.06457 0.029915 0.131635 0.006075 +0.83655 0.023065 0.042845 0.09518 0.00236 +0.916895 0.012525 0.0118 0.05622 0.00256 +0.414585 0.107505 0.15073 0.3227 0.00448 +0.72307 0.097715 0.07069 0.103095 0.00543 +0.762105 0.04293 0.13013 0.062035 0.0028 +0.70074 0.071655 0.05636 0.161935 0.00931 +0.586635 0.05431 0.05497 0.29668 0.007405 +0.865345 0.064235 0.01624 0.04942 0.00476 +0.742435 0.086295 0.025555 0.13856 0.007155 +0.847705 0.031365 0.0165 0.098125 0.006305 +0.814595 0.063985 0.02 0.09379 0.00763 +0.93737 0.021225 0.01002 0.029015 0.00237 +0.748705 0.08654 0.030325 0.125095 0.009335 +0.80061 0.053275 0.031685 0.10252 0.01191 +0.5744 0.056205 0.024215 0.330255 0.014925 +0.732615 0.07454 0.03534 0.141665 0.01584 +0.5035 0.17423 0.022075 0.28575 0.014445 +0.39582 0.27067 0.03361 0.280365 0.019535 +0.922555 0.008115 0.002015 0.065815 0.0015 +0.809655 0.067335 0.0077 0.1107 0.00461 +0.86916 0.038795 0.00787 0.07916 0.005015 +0.778535 0.108365 0.012665 0.0945 0.005935 +0.895745 0.044455 0.00887 0.042595 0.008335 +0.908325 0.04238 0.00522 0.04177 0.002305 +0.868345 0.07802 0.00674 0.03187 0.015025 +0.56275 0.39761 0.00931 0.020535 0.009795 +0.511225 0.46806 0.005765 0.013875 0.001075 +0.773375 0.198245 0.010645 0.015295 0.00244 +0.419985 0.55089 0.01508 0.010195 0.00385 +0.40169 0.585635 0.00524 0.005285 0.00215 +0.71916 0.2319 0.0106 0.032 0.00634 +0.83843 0.064685 0.02569 0.060065 0.01113 +0.86688 0.05349 0.016175 0.058465 0.00499 +0.888505 0.056145 0.025365 0.027445 0.00254 +0.849665 0.12689 0.006785 0.010825 0.005835 +0.93623 0.036545 0.00246 0.02108 0.003685 +0.94056 0.034055 0.01003 0.013065 0.00229 +0.75386 0.22233 0.008965 0.0136 0.001245 +0.896105 0.034175 0.013355 0.0546 0.001765 +0.89573 0.0555 0.023825 0.02268 0.002265 +0.74449 0.00881 0.101545 0.13998 0.005175 +0.819225 0.003525 0.023335 0.15206 0.001855 +0.854465 0.01019 0.049865 0.081295 0.004185 +0.5951 0.000515 0.39305 0.01106 0.000275 +0.5959 0.02486 0.1428 0.23272 0.00372 +0.612745 0.014675 0.10044 0.269185 0.002955 +0.70953 0.025255 0.117545 0.1434 0.00427 +0.867065 0.004685 0.03237 0.09496 0.00092 +0.887065 0.018265 0.02047 0.070735 0.003465 +0.66819 0.01788 0.163935 0.14256 0.007435 +0.716825 0.024995 0.081275 0.17009 0.006815 +0.812025 0.014975 0.043445 0.12376 0.005795 +0.656825 0.00689 0.034025 0.29661 0.00565 +0.873575 0.005165 0.01631 0.102345 0.002605 +0.572085 0.02273 0.03966 0.35916 0.006365 +0.56452 0.072335 0.0632 0.28911 0.010835 +0.869835 0.02069 0.03275 0.06602 0.010705 +0.57763 0.136195 0.051195 0.212715 0.022265 +0.66577 0.02718 0.028125 0.26848 0.010445 +0.500445 0.042015 0.09259 0.34561 0.01934 +0.466745 0.023915 0.003565 0.498015 0.00776 +0.76947 0.037415 0.00595 0.18161 0.005555 +0.85616 0.02724 0.003685 0.10895 0.003965 +0.83213 0.031305 0.004875 0.122325 0.009365 +0.914005 0.013695 0.00435 0.06094 0.00701 +0.837785 0.027755 0.00619 0.117055 0.011215 +0.936495 0.012705 0.00352 0.04292 0.00436 +0.90621 0.056205 0.00451 0.02912 0.003955 +0.276935 0.72192 0.000435 0.00037 0.00034 +0.72359 0.240885 0.005445 0.02553 0.00455 +0.8404 0.107435 0.010435 0.032995 0.008735 diff --git a/inst/files/matrix/tab/matrix-tab-k3.txt b/inst/files/matrix/tab/matrix-tab-k3.txt new file mode 100644 index 0000000..6dc008f --- /dev/null +++ b/inst/files/matrix/tab/matrix-tab-k3.txt @@ -0,0 +1,75 @@ +0.92633 0.057885 0.015785 +0.68248 0.307585 0.009935 +0.935345 0.05991 0.004745 +0.877755 0.108125 0.01412 +0.855695 0.128085 0.01622 +0.94049 0.053025 0.006485 +0.4792 0.393205 0.127595 +0.67483 0.311105 0.014065 +0.71559 0.263975 0.020435 +0.760645 0.19124 0.048115 +0.736425 0.21584 0.047735 +0.79977 0.191755 0.008475 +0.74638 0.233435 0.020185 +0.91399 0.06757 0.01844 +0.813655 0.167695 0.01865 +0.961345 0.034485 0.00417 +0.664755 0.317515 0.01773 +0.8359 0.14073 0.02337 +0.784935 0.120195 0.09487 +0.813735 0.142155 0.04411 +0.669755 0.27439 0.055855 +0.696605 0.136065 0.16733 +0.95993 0.035815 0.004255 +0.765655 0.225335 0.00901 +0.93428 0.057075 0.008645 +0.721295 0.261755 0.01695 +0.90934 0.079875 0.010785 +0.963815 0.03178 0.004405 +0.91296 0.068685 0.018355 +0.64133 0.32156 0.03711 +0.58481 0.40821 0.00698 +0.77754 0.21508 0.00738 +0.52871 0.457225 0.014065 +0.55024 0.44282 0.00694 +0.796835 0.1804 0.022765 +0.931815 0.05093 0.017255 +0.915155 0.07507 0.009775 +0.685855 0.30715 0.006995 +0.66243 0.321105 0.016465 +0.731645 0.26421 0.004145 +0.91696 0.076265 0.006775 +0.67236 0.32263 0.00501 +0.89296 0.102485 0.004555 +0.752315 0.244275 0.00341 +0.91062 0.064775 0.024605 +0.88845 0.10221 0.00934 +0.90092 0.073475 0.025605 +0.690555 0.27085 0.038595 +0.62902 0.29397 0.07701 +0.92489 0.04776 0.02735 +0.856255 0.0875 0.056245 +0.94584 0.043995 0.010165 +0.8982 0.09126 0.01054 +0.88973 0.06803 0.04224 +0.764175 0.220515 0.01531 +0.933695 0.05207 0.014235 +0.93678 0.044045 0.019175 +0.949515 0.041625 0.00886 +0.892755 0.063405 0.04384 +0.67181 0.26196 0.06623 +0.94439 0.042755 0.012855 +0.683955 0.269325 0.04672 +0.885265 0.08908 0.025655 +0.84537 0.08784 0.06679 +0.943995 0.027945 0.02806 +0.970395 0.01639 0.013215 +0.9156 0.080305 0.004095 +0.96383 0.024145 0.012025 +0.98202 0.010825 0.007155 +0.946585 0.04552 0.007895 +0.979385 0.01676 0.003855 +0.712255 0.27954 0.008205 +0.655345 0.340465 0.00419 +0.706595 0.283935 0.00947 +0.87072 0.120915 0.008365 diff --git a/inst/files/matrix/tab/matrix-tab-k4.txt b/inst/files/matrix/tab/matrix-tab-k4.txt new file mode 100644 index 0000000..d5c783e --- /dev/null +++ b/inst/files/matrix/tab/matrix-tab-k4.txt @@ -0,0 +1,75 @@ +0.955705 0.02329 0.010225 0.01078 +0.97025 0.00978 0.011555 0.008415 +0.988065 0.0045 0.004015 0.00342 +0.956495 0.016455 0.01188 0.01517 +0.975235 0.010725 0.007525 0.006515 +0.9846 0.00728 0.00515 0.00297 +0.6624 0.171935 0.096505 0.06916 +0.953795 0.01761 0.017365 0.01123 +0.947975 0.014595 0.02233 0.0151 +0.871835 0.059255 0.024305 0.044605 +0.894005 0.049685 0.024755 0.031555 +0.977285 0.00981 0.006085 0.00682 +0.94224 0.022565 0.012215 0.02298 +0.94773 0.03007 0.01202 0.01018 +0.956865 0.01837 0.01221 0.012555 +0.988305 0.004275 0.004155 0.003265 +0.92505 0.038375 0.017735 0.01884 +0.919855 0.035305 0.018225 0.026615 +0.56458 0.329155 0.018835 0.08743 +0.778205 0.108265 0.006135 0.107395 +0.82095 0.113005 0.013575 0.05247 +0.51192 0.37259 0.018025 0.097465 +0.983605 0.010075 0.001605 0.004715 +0.96554 0.021285 0.00327 0.009905 +0.97407 0.016685 0.002805 0.00644 +0.948345 0.02342 0.01071 0.017525 +0.94937 0.02445 0.011645 0.014535 +0.97971 0.0102 0.00413 0.00596 +0.92199 0.02293 0.03244 0.02264 +0.885585 0.032595 0.04551 0.03631 +0.96793 0.010835 0.00997 0.011265 +0.98554 0.004815 0.005455 0.00419 +0.940185 0.013145 0.02165 0.02502 +0.963735 0.00625 0.01634 0.013675 +0.956795 0.0125 0.01349 0.017215 +0.94098 0.01704 0.02271 0.01927 +0.972195 0.00999 0.010835 0.00698 +0.981735 0.003055 0.010665 0.004545 +0.971005 0.00665 0.01679 0.005555 +0.98738 0.00299 0.005655 0.003975 +0.987855 0.003515 0.005265 0.003365 +0.9918 0.00269 0.00394 0.00157 +0.985485 0.00453 0.006025 0.00396 +0.98447 0.0048 0.006375 0.004355 +0.917025 0.03599 0.024245 0.02274 +0.97876 0.00874 0.006855 0.005645 +0.91806 0.03041 0.02809 0.02344 +0.908525 0.02561 0.03833 0.027535 +0.777225 0.07074 0.07886 0.073175 +0.89878 0.052275 0.031945 0.017 +0.855605 0.052475 0.06131 0.03061 +0.972265 0.009335 0.008475 0.009925 +0.97398 0.01123 0.005605 0.009185 +0.89581 0.037245 0.03086 0.036085 +0.94447 0.01938 0.01964 0.01651 +0.9557 0.01858 0.012855 0.012865 +0.924785 0.036545 0.020675 0.017995 +0.974025 0.01013 0.00777 0.008075 +0.90148 0.041965 0.028315 0.02824 +0.829025 0.060805 0.04 0.07017 +0.93776 0.03093 0.010225 0.021085 +0.79285 0.119565 0.03256 0.055025 +0.904355 0.05374 0.01133 0.030575 +0.83107 0.07136 0.05018 0.04739 +0.832325 0.124045 0.012075 0.031555 +0.88716 0.08679 0.006475 0.019575 +0.97331 0.0142 0.00405 0.00844 +0.91785 0.04062 0.01191 0.02962 +0.97859 0.008935 0.00536 0.007115 +0.9638 0.013895 0.007115 0.01519 +0.97802 0.009835 0.005215 0.00693 +0.978475 0.005615 0.00879 0.00712 +0.98059 0.00449 0.00887 0.00605 +0.950055 0.011995 0.022745 0.015205 +0.971085 0.007535 0.012945 0.008435 diff --git a/inst/files/matrix/tab/matrix-tab-k5.txt b/inst/files/matrix/tab/matrix-tab-k5.txt new file mode 100644 index 0000000..a0e8e0b --- /dev/null +++ b/inst/files/matrix/tab/matrix-tab-k5.txt @@ -0,0 +1,75 @@ +0.78766 0.035545 0.021665 0.14898 0.00615 +0.817585 0.095465 0.022575 0.05413 0.010245 +0.935455 0.02521 0.007015 0.03066 0.00166 +0.767805 0.06457 0.029915 0.131635 0.006075 +0.83655 0.023065 0.042845 0.09518 0.00236 +0.916895 0.012525 0.0118 0.05622 0.00256 +0.414585 0.107505 0.15073 0.3227 0.00448 +0.72307 0.097715 0.07069 0.103095 0.00543 +0.762105 0.04293 0.13013 0.062035 0.0028 +0.70074 0.071655 0.05636 0.161935 0.00931 +0.586635 0.05431 0.05497 0.29668 0.007405 +0.865345 0.064235 0.01624 0.04942 0.00476 +0.742435 0.086295 0.025555 0.13856 0.007155 +0.847705 0.031365 0.0165 0.098125 0.006305 +0.814595 0.063985 0.02 0.09379 0.00763 +0.93737 0.021225 0.01002 0.029015 0.00237 +0.748705 0.08654 0.030325 0.125095 0.009335 +0.80061 0.053275 0.031685 0.10252 0.01191 +0.5744 0.056205 0.024215 0.330255 0.014925 +0.732615 0.07454 0.03534 0.141665 0.01584 +0.5035 0.17423 0.022075 0.28575 0.014445 +0.39582 0.27067 0.03361 0.280365 0.019535 +0.922555 0.008115 0.002015 0.065815 0.0015 +0.809655 0.067335 0.0077 0.1107 0.00461 +0.86916 0.038795 0.00787 0.07916 0.005015 +0.778535 0.108365 0.012665 0.0945 0.005935 +0.895745 0.044455 0.00887 0.042595 0.008335 +0.908325 0.04238 0.00522 0.04177 0.002305 +0.868345 0.07802 0.00674 0.03187 0.015025 +0.56275 0.39761 0.00931 0.020535 0.009795 +0.511225 0.46806 0.005765 0.013875 0.001075 +0.773375 0.198245 0.010645 0.015295 0.00244 +0.419985 0.55089 0.01508 0.010195 0.00385 +0.40169 0.585635 0.00524 0.005285 0.00215 +0.71916 0.2319 0.0106 0.032 0.00634 +0.83843 0.064685 0.02569 0.060065 0.01113 +0.86688 0.05349 0.016175 0.058465 0.00499 +0.888505 0.056145 0.025365 0.027445 0.00254 +0.849665 0.12689 0.006785 0.010825 0.005835 +0.93623 0.036545 0.00246 0.02108 0.003685 +0.94056 0.034055 0.01003 0.013065 0.00229 +0.75386 0.22233 0.008965 0.0136 0.001245 +0.896105 0.034175 0.013355 0.0546 0.001765 +0.89573 0.0555 0.023825 0.02268 0.002265 +0.74449 0.00881 0.101545 0.13998 0.005175 +0.819225 0.003525 0.023335 0.15206 0.001855 +0.854465 0.01019 0.049865 0.081295 0.004185 +0.5951 0.000515 0.39305 0.01106 0.000275 +0.5959 0.02486 0.1428 0.23272 0.00372 +0.612745 0.014675 0.10044 0.269185 0.002955 +0.70953 0.025255 0.117545 0.1434 0.00427 +0.867065 0.004685 0.03237 0.09496 0.00092 +0.887065 0.018265 0.02047 0.070735 0.003465 +0.66819 0.01788 0.163935 0.14256 0.007435 +0.716825 0.024995 0.081275 0.17009 0.006815 +0.812025 0.014975 0.043445 0.12376 0.005795 +0.656825 0.00689 0.034025 0.29661 0.00565 +0.873575 0.005165 0.01631 0.102345 0.002605 +0.572085 0.02273 0.03966 0.35916 0.006365 +0.56452 0.072335 0.0632 0.28911 0.010835 +0.869835 0.02069 0.03275 0.06602 0.010705 +0.57763 0.136195 0.051195 0.212715 0.022265 +0.66577 0.02718 0.028125 0.26848 0.010445 +0.500445 0.042015 0.09259 0.34561 0.01934 +0.466745 0.023915 0.003565 0.498015 0.00776 +0.76947 0.037415 0.00595 0.18161 0.005555 +0.85616 0.02724 0.003685 0.10895 0.003965 +0.83213 0.031305 0.004875 0.122325 0.009365 +0.914005 0.013695 0.00435 0.06094 0.00701 +0.837785 0.027755 0.00619 0.117055 0.011215 +0.936495 0.012705 0.00352 0.04292 0.00436 +0.90621 0.056205 0.00451 0.02912 0.003955 +0.276935 0.72192 0.000435 0.00037 0.00034 +0.72359 0.240885 0.005445 0.02553 0.00455 +0.8404 0.107435 0.010435 0.032995 0.008735 diff --git a/inst/files/metadata.txt b/inst/files/metadata.txt new file mode 100644 index 0000000..12bc1da --- /dev/null +++ b/inst/files/metadata.txt @@ -0,0 +1,150 @@ +type cat loc +Tropical CatA Panama +Tropical CatA Panama +Tropical CatA Panama +Tropical CatA Panama +Tropical CatA Panama +Tropical CatA Panama +Tropical CatA Panama +Tropical CatA Panama +Tropical CatA Panama +Tropical CatA Panama +Tropical CatA Panama +Tropical CatA Panama +Tropical CatA Panama +Tropical CatA Panama +Tropical CatA Panama +Tropical CatA Panama +Tropical CatA Panama +Tropical CatA Panama +Tropical CatA Panama +Tropical CatA Panama +Tropical CatA Panama +Tropical CatA Panama +Tropical CatA Panama +Tropical CatA Panama +Tropical CatA Panama +Tropical CatA Panama +Tropical CatA Panama +Tropical CatA Panama +Temperate CatA Greece +Temperate CatA Greece +Temperate CatA Greece +Tropical CatA Panama +Tropical CatA Panama +Tropical CatA Panama +Tropical CatA Panama +Temperate CatA Greece +Tropical CatA Panama +Tropical CatA Panama +Tropical CatA Panama +Tropical CatA Panama +Tropical CatA Panama +Tropical CatA Panama +Tropical CatA Panama +Tropical CatA Panama +Tropical CatA Panama +Tropical CatA Panama +Tropical CatA Panama +Tropical CatA Panama +Tropical CatA Panama +Tropical CatA Panama +Tropical CatA Panama +Tropical CatA Panama +Tropical CatA Panama +Tropical CatA Panama +Tropical CatA Panama +Tropical CatA Panama +Tropical CatA Panama +Tropical CatA Panama +Tropical CatA Panama +Tropical CatA Panama +Tropical CatA Panama +Tropical CatA Brazil +Tropical CatA Panama +Tropical CatA Panama +Tropical CatA Panama +Tropical CatA Panama +Tropical CatA Panama +Tropical CatA Panama +Temperate CatA Greece +Tropical CatA Panama +Tropical CatA Panama +Tropical CatA Panama +Tropical CatA Panama +Tropical CatA Panama +Tropical CatA Panama +Tropical CatA Panama +Tropical CatA Panama +Tropical CatA Panama +Tropical CatA Panama +Temperate CatA Greece +Tropical CatA Panama +Tropical CatA Brazil +Tropical CatA Brazil +Tropical CatA Panama +Temperate CatA Greece +Tropical CatA Panama +Tropical CatA Panama +Tropical CatA Panama +Tropical CatA Panama +Tropical CatA Panama +Tropical CatA Panama +Tropical CatA Panama +Tropical CatA Panama +Tropical CatA Panama +Temperate CatA Greece +Tropical CatA Panama +Tropical CatA Panama +Temperate CatA Greece +Tropical CatA Panama +Temperate CatA Greece +Tropical CatA Panama +Tropical CatA Panama +Tropical CatA Panama +Temperate CatA Greece +Temperate CatA Greece +Tropical CatA Panama +Temperate CatA Greece +Tropical CatB Brazil +Tropical CatB Brazil +Tropical CatB Brazil +Tropical CatB Brazil +Tropical CatB Brazil +Tropical CatB Brazil +Tropical CatB Brazil +Tropical CatB Brazil +Tropical CatB Brazil +Tropical CatB Brazil +Tropical CatB Brazil +Tropical CatB Brazil +Tropical CatB Brazil +Tropical CatB Brazil +Tropical CatB Brazil +Tropical CatB Brazil +Tropical CatB Brazil +Tropical CatB Brazil +Tropical CatB Brazil +Tropical CatB Brazil +Tropical CatB Brazil +Tropical CatB Brazil +Tropical CatB Brazil +Tropical CatB Brazil +Tropical CatB Brazil +Tropical CatB Brazil +Tropical CatB Brazil +Tropical CatB Brazil +Tropical CatB Brazil +Tropical CatB Brazil +Tropical CatB Brazil +Tropical CatB Brazil +Tropical CatB Brazil +Tropical CatB Brazil +Tropical CatB Brazil +Tropical CatB Brazil +Tropical CatB Brazil +Tropical CatB Brazil +Tropical CatB Brazil +Tropical CatB Brazil +Tropical CatB Brazil +Tropical CatB Brazil diff --git a/inst/files/structure-ci/structure_4_f b/inst/files/structure-ci/structure_4_f new file mode 100644 index 0000000..1a89002 --- /dev/null +++ b/inst/files/structure-ci/structure_4_f @@ -0,0 +1,1395 @@ + + +---------------------------------------------------- +STRUCTURE by Pritchard, Stephens and Donnelly (2000) + and Falush, Stephens and Pritchard (2003) + Code by Pritchard, Falush and Hubisz + Version 2.3.4 (Jul 2012) +---------------------------------------------------- + + + +Command line arguments: bin\structure -m C:\Users\jota.blanco\Desktop\SAmer_reduc\OC_SA2\pop250y500mil\mainparams -e C:\Users\jota.blanco\Desktop\SAmer_reduc\OC_SA2\pop250y500mil\extraparams +Input File: C:\Users\jota.blanco\Desktop\SAmer_reduc\OC_SA2\project_data + +Run parameters: + 551 individuals + 39 loci + 2 populations assumed + 250000 Burn-in period + 500000 Reps +RANDOMIZE turned off + + +-------------------------------------------- +Proportion of membership of each pre-defined + population in each of the 2 clusters + +Given Inferred Clusters Number of + Pop 1 2 Individuals + + 1: 0.852 0.148 49 + 2: 0.015 0.985 52 + 3: 0.994 0.006 326 + 4: 0.435 0.565 85 + 5: 0.113 0.887 39 +-------------------------------------------- + +Allele-freq. divergence among pops (Net nucleotide distance), +computed using point estimates of P. + + 1 2 + 1 - 0.1577 + 2 0.1577 - + +Average distances (expected heterozygosity) between individuals in same cluster: +cluster 1 : 0.6075 +cluster 2 : 0.8553 + +-------------------------------------------- +Estimated Ln Prob of Data = -67802.5 +Mean value of ln likelihood = -61134.7 +Variance of ln likelihood = 13335.5 + +Mean value of alpha_1 = 0.2415 +Mean value of alpha_2 = 0.0820 + +Mean value of Fst_1 = 0.3846 +Mean value of Fst_2 = 0.0018 +Allele frequencies updated using individuals with POPFLAG=1 ONLY. + + +Inferred ancestry of individuals: + Label (%Miss) Pop: Inferred clusters (and 90% probability intervals) + 1 ArgAL-01 (20) 1 : 0.785 0.215 (0.641,0.908) (0.092,0.359) + 2 ArgAL-02 (25) 1 : 0.832 0.168 (0.691,0.945) (0.055,0.309) + 3 ArgAL-03 (17) 1 : 0.736 0.264 (0.589,0.864) (0.136,0.411) + 4 ArgAL-06 (0) 1 : 0.595 0.405 (0.451,0.731) (0.269,0.549) + 5 ArgAL-08 (17) 1 : 0.749 0.251 (0.620,0.862) (0.138,0.380) + 6 ArgAL-09 (23) 1 : 0.743 0.257 (0.596,0.872) (0.128,0.404) + 7 ArgAL-11 (25) 1 : 0.623 0.377 (0.448,0.786) (0.214,0.552) + 8 ArgAL-12 (20) 1 : 0.663 0.337 (0.508,0.805) (0.195,0.492) + 9 ArgAL-13 (5) 1 : 0.642 0.358 (0.505,0.769) (0.231,0.495) + 10 ArgAL-14 (25) 1 : 0.462 0.538 (0.286,0.635) (0.365,0.714) + 11 ArgAL-15 (5) 1 : 0.560 0.440 (0.415,0.699) (0.301,0.585) + 12 ArgRT-01 (2) 1 : 0.885 0.115 (0.795,0.956) (0.044,0.205) + 13 ArgRT-02 (12) 1 : 0.996 0.004 (0.972,1.000) (0.000,0.028) + 14 ArgRT-03 (0) 1 : 0.926 0.074 (0.836,0.991) (0.009,0.164) + 15 ArgRT-04 (10) 1 : 0.865 0.135 (0.766,0.944) (0.056,0.234) + 16 ArgRT-05 (10) 1 : 0.975 0.025 (0.906,1.000) (0.000,0.094) + 17 ArgRT-06 (12) 1 : 0.985 0.015 (0.928,1.000) (0.000,0.072) + 18 ArgRT-07 (5) 1 : 0.849 0.151 (0.742,0.936) (0.064,0.258) + 19 ArgRT-08 (0) 1 : 0.962 0.038 (0.878,1.000) (0.000,0.122) + 20 ArgRT-09 (5) 1 : 0.902 0.098 (0.785,1.000) (0.000,0.215) + 21 ArgRT-10 (2) 1 : 0.944 0.056 (0.843,1.000) (0.000,0.157) + 22 ArgRT-11 (0) 1 : 0.988 0.012 (0.943,1.000) (0.000,0.057) + 23 ArgRT-12 (5) 1 : 0.997 0.003 (0.980,1.000) (0.000,0.020) + 24 ArgRT-13 (2) 1 : 0.963 0.037 (0.902,0.999) (0.001,0.098) + 25 ArgRT-14 (0) 1 : 0.962 0.038 (0.883,1.000) (0.000,0.117) + 26 ArgRT-15 (2) 1 : 0.888 0.112 (0.787,0.970) (0.030,0.213) + 27 ArgTF-01 (23) 1 : 0.908 0.092 (0.818,0.973) (0.027,0.182) + 28 ArgTF-02 (12) 1 : 0.902 0.098 (0.813,0.967) (0.033,0.187) + 29 ArgTF-03 (23) 1 : 0.947 0.053 (0.875,0.992) (0.008,0.125) + 30 ArgTF-04 (25) 1 : 0.920 0.080 (0.837,0.978) (0.022,0.163) + 31 ArgTF-06 (2) 1 : 0.884 0.116 (0.793,0.954) (0.046,0.207) + 32 ArgTF-07 (25) 1 : 0.861 0.139 (0.752,0.945) (0.055,0.248) + 33 ArgTF-08 (20) 1 : 0.865 0.135 (0.760,0.947) (0.053,0.240) + 34 ArgTF-09 (0) 1 : 0.894 0.106 (0.803,0.963) (0.037,0.197) + 35 ArgTF-10 (7) 1 : 0.931 0.069 (0.857,0.984) (0.016,0.143) + 36 ArgTF-11 (17) 1 : 0.988 0.012 (0.941,1.000) (0.000,0.059) + 37 ArgTF-12 (2) 1 : 0.881 0.119 (0.787,0.955) (0.045,0.213) + 38 ArgTF-13 (10) 1 : 0.927 0.073 (0.844,0.985) (0.015,0.156) + 39 ArgTF-14 (2) 1 : 0.887 0.113 (0.795,0.958) (0.042,0.205) + 40 ArgTF-15 (12) 1 : 0.868 0.132 (0.771,0.945) (0.055,0.229) + 41 FALK01 (0) 1 : 0.790 0.210 (0.678,0.886) (0.114,0.322) + 42 FALK04 (0) 1 : 0.874 0.126 (0.780,0.948) (0.052,0.220) + 43 FALK06 (0) 1 : 0.867 0.133 (0.769,0.944) (0.056,0.231) + 44 FALK07 (2) 1 : 0.826 0.174 (0.719,0.914) (0.086,0.281) + 45 FALK08 (2) 1 : 0.873 0.127 (0.776,0.948) (0.052,0.224) + 46 FALK09 (5) 1 : 0.817 0.183 (0.707,0.908) (0.092,0.293) + 47 FALK10 (2) 1 : 0.815 0.185 (0.705,0.907) (0.093,0.295) + 48 FALK11 (0) 1 : 0.793 0.207 (0.682,0.888) (0.112,0.318) + 49 FALK14 (2) 1 : 0.970 0.030 (0.911,1.000) (0.000,0.089) + 50 DON-1 (12) 2 : 0.008 0.992 (0.000,0.039) (0.961,1.000) + 51 DON-3 (5) 2 : 0.009 0.991 (0.000,0.045) (0.955,1.000) + 52 DON-5 (20) 2 : 0.007 0.993 (0.000,0.033) (0.967,1.000) + 53 DON-5722 (10) 2 : 0.018 0.982 (0.000,0.077) (0.923,1.000) + 54 DON-5785 (23) 2 : 0.016 0.984 (0.000,0.075) (0.925,1.000) + 55 DON-5819 (7) 2 : 0.007 0.993 (0.000,0.036) (0.964,1.000) + 56 DON-5930 (7) 2 : 0.015 0.985 (0.000,0.072) (0.928,1.000) + 57 DON-6116 (33) 2 : 0.013 0.987 (0.000,0.061) (0.939,1.000) + 58 DON-6143 (12) 2 : 0.006 0.994 (0.000,0.029) (0.971,1.000) + 59 DON-6241 (15) 2 : 0.021 0.979 (0.000,0.093) (0.907,1.000) + 60 DON-6281 (2) 2 : 0.014 0.986 (0.000,0.061) (0.939,1.000) + 61 DON-7 (12) 2 : 0.012 0.988 (0.000,0.058) (0.942,1.000) + 62 DON-8 (5) 2 : 0.005 0.995 (0.000,0.027) (0.973,1.000) + 63 HUE-1 (5) 2 : 0.006 0.994 (0.000,0.030) (0.970,1.000) + 64 HUE-34 (0) 2 : 0.016 0.984 (0.000,0.074) (0.926,1.000) + 65 HUE-4224 (15) 2 : 0.033 0.967 (0.000,0.129) (0.871,1.000) + 66 HUE-4225 (28) 2 : 0.008 0.992 (0.000,0.042) (0.958,1.000) + 67 HUE-4232 (25) 2 : 0.014 0.986 (0.000,0.066) (0.934,1.000) + 68 HUE-4235 (20) 2 : 0.009 0.991 (0.000,0.045) (0.955,1.000) + 69 HUE-4236 (12) 2 : 0.012 0.988 (0.000,0.057) (0.943,1.000) + 70 HUE-4239 (17) 2 : 0.036 0.964 (0.000,0.121) (0.879,1.000) + 71 HUE-4250 (30) 2 : 0.033 0.967 (0.000,0.133) (0.867,1.000) + 72 HUE-4258 (25) 2 : 0.007 0.993 (0.000,0.034) (0.966,1.000) + 73 HUE-4259 (5) 2 : 0.010 0.990 (0.000,0.050) (0.950,1.000) + 74 HUE-4260 (2) 2 : 0.010 0.990 (0.000,0.051) (0.949,1.000) + 75 HUE-53 (2) 2 : 0.037 0.963 (0.000,0.120) (0.880,1.000) + 76 LLO-11 (25) 2 : 0.013 0.987 (0.000,0.058) (0.942,1.000) + 77 LLO-14 (30) 2 : 0.042 0.958 (0.000,0.137) (0.863,1.000) + 78 LLO-16 (17) 2 : 0.010 0.990 (0.000,0.046) (0.954,1.000) + 79 LLO-17 (5) 2 : 0.007 0.993 (0.000,0.037) (0.963,1.000) + 80 LLO-18 (10) 2 : 0.019 0.981 (0.000,0.084) (0.916,1.000) + 81 LLO-19 (5) 2 : 0.007 0.993 (0.000,0.034) (0.966,1.000) + 82 LLO-20 (15) 2 : 0.041 0.959 (0.000,0.123) (0.877,1.000) + 83 LLO-24 (10) 2 : 0.017 0.983 (0.000,0.074) (0.926,1.000) + 84 LLO-28 (15) 2 : 0.022 0.978 (0.000,0.091) (0.909,1.000) + 85 LLO-29 (10) 2 : 0.005 0.995 (0.000,0.027) (0.973,1.000) + 86 LLO-31 (7) 2 : 0.006 0.994 (0.000,0.030) (0.970,1.000) + 87 LLO-7 (5) 2 : 0.015 0.985 (0.000,0.071) (0.929,1.000) + 88 LLO-8 (7) 2 : 0.019 0.981 (0.000,0.087) (0.913,1.000) + 89 SAN-10 (7) 2 : 0.008 0.992 (0.000,0.041) (0.959,1.000) + 90 SAN-14 (5) 2 : 0.007 0.993 (0.000,0.033) (0.967,1.000) + 91 SAN-15 (5) 2 : 0.006 0.994 (0.000,0.029) (0.971,1.000) + 92 SAN-17 (2) 2 : 0.010 0.990 (0.000,0.050) (0.950,1.000) + 93 SAN-18 (0) 2 : 0.007 0.993 (0.000,0.035) (0.965,1.000) + 94 SAN-20 (7) 2 : 0.061 0.939 (0.000,0.169) (0.831,1.000) + 95 SAN-21 (5) 2 : 0.008 0.992 (0.000,0.038) (0.962,1.000) + 96 SAN-23 (7) 2 : 0.023 0.977 (0.000,0.102) (0.898,1.000) + 97 SAN-3 (2) 2 : 0.009 0.991 (0.000,0.044) (0.956,1.000) + 98 SAN-5 (10) 2 : 0.007 0.993 (0.000,0.033) (0.967,1.000) + 99 SAN-6 (12) 2 : 0.007 0.993 (0.000,0.032) (0.968,1.000) +100 SAN-7 (5) 2 : 0.008 0.992 (0.000,0.040) (0.960,1.000) +101 SAN-8 (7) 2 : 0.008 0.992 (0.000,0.040) (0.960,1.000) +102 AN_AT01 (5) 3 : 0.994 0.006 (0.963,1.000) (0.000,0.037) +103 AN_AT02 (10) 3 : 0.975 0.025 (0.898,1.000) (0.000,0.102) +104 AN_AT03 (10) 3 : 0.998 0.002 (0.986,1.000) (0.000,0.014) +105 AN_AT06 (7) 3 : 0.997 0.003 (0.980,1.000) (0.000,0.020) +106 AN_AT07 (5) 3 : 0.997 0.003 (0.979,1.000) (0.000,0.021) +107 AN_AT08 (2) 3 : 0.995 0.005 (0.971,1.000) (0.000,0.029) +108 AN_AT09 (2) 3 : 0.998 0.002 (0.989,1.000) (0.000,0.011) +109 AN_AT10 (2) 3 : 0.998 0.002 (0.985,1.000) (0.000,0.015) +110 AN_AT28 (2) 3 : 0.985 0.015 (0.931,1.000) (0.000,0.069) +111 AN_AT29 (5) 3 : 0.950 0.050 (0.860,1.000) (0.000,0.140) +112 AN_AT30 (7) 3 : 0.998 0.002 (0.987,1.000) (0.000,0.013) +113 AN_AT31 (2) 3 : 0.949 0.051 (0.870,1.000) (0.000,0.130) +114 AN_AT32 (2) 3 : 0.967 0.033 (0.883,1.000) (0.000,0.117) +115 AN_AT33 (5) 3 : 0.995 0.005 (0.966,1.000) (0.000,0.034) +116 AN_AT34 (2) 3 : 0.997 0.003 (0.984,1.000) (0.000,0.016) +117 AN_AT35 (5) 3 : 0.996 0.004 (0.976,1.000) (0.000,0.024) +118 AN_AT46 (2) 3 : 0.988 0.012 (0.938,1.000) (0.000,0.062) +119 AN_AT47 (2) 3 : 0.998 0.002 (0.985,1.000) (0.000,0.015) +120 AN_AT48 (2) 3 : 0.995 0.005 (0.967,1.000) (0.000,0.033) +121 AN_AT49 (5) 3 : 0.997 0.003 (0.983,1.000) (0.000,0.017) +122 AN_AT50 (7) 3 : 0.959 0.041 (0.860,1.000) (0.000,0.140) +123 AN_AT51 (2) 3 : 0.998 0.002 (0.988,1.000) (0.000,0.012) +124 AN_AT52 (12) 3 : 0.996 0.004 (0.976,1.000) (0.000,0.024) +125 AN_AT53 (5) 3 : 0.997 0.003 (0.981,1.000) (0.000,0.019) +126 BH_A22 (0) 3 : 0.998 0.002 (0.990,1.000) (0.000,0.010) +127 BH_A23 (0) 3 : 0.998 0.002 (0.990,1.000) (0.000,0.010) +128 BH_A24 (0) 3 : 0.998 0.002 (0.990,1.000) (0.000,0.010) +129 BH_A29 (5) 3 : 0.998 0.002 (0.990,1.000) (0.000,0.010) +130 BH_A30 (5) 3 : 0.998 0.002 (0.985,1.000) (0.000,0.015) +131 BH_A31 (2) 3 : 0.998 0.002 (0.990,1.000) (0.000,0.010) +132 BH_A32 (17) 3 : 0.996 0.004 (0.979,1.000) (0.000,0.021) +133 BH_A35 (5) 3 : 0.998 0.002 (0.986,1.000) (0.000,0.014) +134 BH_A36 (0) 3 : 0.998 0.002 (0.989,1.000) (0.000,0.011) +135 BH_A37 (0) 3 : 0.998 0.002 (0.989,1.000) (0.000,0.011) +136 BH_A38 (6) 3 : 0.948 0.052 (0.853,1.000) (0.000,0.147) +137 BH_A39 (7) 3 : 0.998 0.002 (0.987,1.000) (0.000,0.013) +138 BH_A41 (0) 3 : 0.998 0.002 (0.988,1.000) (0.000,0.012) +139 BH_AT01 (5) 3 : 0.998 0.002 (0.986,1.000) (0.000,0.014) +140 BH_AT02 (7) 3 : 0.998 0.002 (0.985,1.000) (0.000,0.015) +141 BH_AT03 (5) 3 : 0.998 0.002 (0.985,1.000) (0.000,0.015) +142 BH_AT04 (2) 3 : 0.982 0.018 (0.927,1.000) (0.000,0.073) +143 BH_ES1 (8) 3 : 0.998 0.002 (0.987,1.000) (0.000,0.013) +144 BH_SP1 (8) 3 : 0.998 0.002 (0.989,1.000) (0.000,0.011) +145 BH_T7 (24) 3 : 0.995 0.005 (0.970,1.000) (0.000,0.030) +146 BH_T8 (2) 3 : 0.997 0.003 (0.982,1.000) (0.000,0.018) +147 CH_A207 (10) 3 : 0.998 0.002 (0.987,1.000) (0.000,0.013) +148 CH_A209 (2) 3 : 0.997 0.003 (0.979,1.000) (0.000,0.021) +149 CH_A213 (2) 3 : 0.997 0.003 (0.979,1.000) (0.000,0.021) +150 CH_A216 (5) 3 : 0.997 0.003 (0.983,1.000) (0.000,0.017) +151 CH_A238 (5) 3 : 0.984 0.016 (0.929,1.000) (0.000,0.071) +152 CH_A243 (7) 3 : 0.994 0.006 (0.965,1.000) (0.000,0.035) +153 CH_A260 (5) 3 : 0.993 0.007 (0.954,1.000) (0.000,0.046) +154 CH_A258 (15) 3 : 0.998 0.002 (0.986,1.000) (0.000,0.014) +155 CH_A274 (2) 3 : 0.995 0.005 (0.968,1.000) (0.000,0.032) +156 CH_A347 (7) 3 : 0.997 0.003 (0.984,1.000) (0.000,0.016) +157 CH_R13 (12) 3 : 0.996 0.004 (0.975,1.000) (0.000,0.025) +158 CH_R14 (7) 3 : 0.989 0.011 (0.941,1.000) (0.000,0.059) +159 CH_R17 (2) 3 : 0.998 0.002 (0.988,1.000) (0.000,0.012) +160 CH_R18 (5) 3 : 0.996 0.004 (0.974,1.000) (0.000,0.026) +161 CH_R19 (7) 3 : 0.997 0.003 (0.980,1.000) (0.000,0.020) +162 CH_R20 (8) 3 : 0.997 0.003 (0.984,1.000) (0.000,0.016) +163 CH_R21 (7) 3 : 0.996 0.004 (0.977,1.000) (0.000,0.023) +164 CH_R22 (7) 3 : 0.988 0.012 (0.926,1.000) (0.000,0.074) +165 CH_R23 (0) 3 : 0.998 0.002 (0.987,1.000) (0.000,0.013) +166 CH_R24 (0) 3 : 0.979 0.021 (0.914,1.000) (0.000,0.086) +167 AC_A214 (0) 3 : 0.998 0.002 (0.987,1.000) (0.000,0.013) +168 AC_A219 (10) 3 : 0.998 0.002 (0.986,1.000) (0.000,0.014) +169 AC_A240 (2) 3 : 0.998 0.002 (0.991,1.000) (0.000,0.009) +170 AC_A241 (5) 3 : 0.998 0.002 (0.990,1.000) (0.000,0.010) +171 AC_A250 (7) 3 : 0.998 0.002 (0.989,1.000) (0.000,0.011) +172 AC_A264 (7) 3 : 0.998 0.002 (0.989,1.000) (0.000,0.011) +173 AC_A267 (5) 3 : 0.998 0.002 (0.990,1.000) (0.000,0.010) +174 AC_A093 (7) 3 : 0.992 0.008 (0.958,1.000) (0.000,0.042) +175 AC_A094 (7) 3 : 0.998 0.002 (0.987,1.000) (0.000,0.013) +176 AC_A095 (2) 3 : 0.997 0.003 (0.980,1.000) (0.000,0.020) +177 AC_A096 (0) 3 : 0.998 0.002 (0.989,1.000) (0.000,0.011) +178 AC_A097 (10) 3 : 0.998 0.002 (0.989,1.000) (0.000,0.011) +179 AC_A099 (5) 3 : 0.998 0.002 (0.988,1.000) (0.000,0.012) +180 AC_A100 (7) 3 : 0.943 0.057 (0.869,0.997) (0.003,0.131) +181 AC_A101 (7) 3 : 0.997 0.003 (0.983,1.000) (0.000,0.017) +182 AC_A104 (5) 3 : 0.998 0.002 (0.988,1.000) (0.000,0.012) +183 AC_A105 (0) 3 : 0.998 0.002 (0.990,1.000) (0.000,0.010) +184 AC_A106 (5) 3 : 0.991 0.009 (0.948,1.000) (0.000,0.052) +185 AC_A110 (5) 3 : 0.998 0.002 (0.989,1.000) (0.000,0.011) +186 AC_A111 (2) 3 : 0.998 0.002 (0.989,1.000) (0.000,0.011) +187 AC_A112 (5) 3 : 0.998 0.002 (0.986,1.000) (0.000,0.014) +188 AC_A113 (0) 3 : 0.997 0.003 (0.982,1.000) (0.000,0.018) +189 AC_A114 (0) 3 : 0.992 0.008 (0.953,1.000) (0.000,0.047) +190 AC_AT03 (5) 3 : 0.998 0.002 (0.989,1.000) (0.000,0.011) +191 EN_A069 (0) 3 : 0.998 0.002 (0.987,1.000) (0.000,0.013) +192 EN_A070 (0) 3 : 0.998 0.002 (0.986,1.000) (0.000,0.014) +193 EN_A071 (0) 3 : 0.997 0.003 (0.984,1.000) (0.000,0.016) +194 EN_A074 (5) 3 : 0.998 0.002 (0.986,1.000) (0.000,0.014) +195 EN_A077 (12) 3 : 0.998 0.002 (0.985,1.000) (0.000,0.015) +196 EN_A078 (17) 3 : 0.997 0.003 (0.984,1.000) (0.000,0.016) +197 EN_A079 (0) 3 : 0.997 0.003 (0.984,1.000) (0.000,0.016) +198 EN_A080 (0) 3 : 0.997 0.003 (0.985,1.000) (0.000,0.015) +199 EN_A081 (5) 3 : 0.988 0.012 (0.935,1.000) (0.000,0.065) +200 EN_A083 (2) 3 : 0.998 0.002 (0.989,1.000) (0.000,0.011) +201 EN_A086 (0) 3 : 0.998 0.002 (0.987,1.000) (0.000,0.013) +202 EN_A087 (7) 3 : 0.998 0.002 (0.986,1.000) (0.000,0.014) +203 EN_A088 (20) 3 : 0.998 0.002 (0.986,1.000) (0.000,0.014) +204 EN_A089 (7) 3 : 0.998 0.002 (0.988,1.000) (0.000,0.012) +205 EN_A090 (5) 3 : 0.998 0.002 (0.985,1.000) (0.000,0.015) +206 EN_A091 (0) 3 : 0.998 0.002 (0.985,1.000) (0.000,0.015) +207 EN_A092 (5) 3 : 0.997 0.003 (0.979,1.000) (0.000,0.021) +208 EN_A205 (5) 3 : 0.997 0.003 (0.979,1.000) (0.000,0.021) +209 EN_A210 (5) 3 : 0.997 0.003 (0.981,1.000) (0.000,0.019) +210 EN_A218 (12) 3 : 0.996 0.004 (0.976,1.000) (0.000,0.024) +211 EN_A220 (0) 3 : 0.998 0.002 (0.985,1.000) (0.000,0.015) +212 EN_A228 (5) 3 : 0.985 0.015 (0.935,1.000) (0.000,0.065) +213 EN_A231 (0) 3 : 0.997 0.003 (0.984,1.000) (0.000,0.016) +214 EN_A234 (0) 3 : 0.998 0.002 (0.985,1.000) (0.000,0.015) +215 EN_A246 (0) 3 : 0.978 0.022 (0.913,1.000) (0.000,0.087) +216 AA_AT01 (5) 3 : 0.997 0.003 (0.980,1.000) (0.000,0.020) +217 AA_AT02 (0) 3 : 0.998 0.002 (0.988,1.000) (0.000,0.012) +218 AA_AT03 (7) 3 : 0.995 0.005 (0.970,1.000) (0.000,0.030) +219 AA_ES2 (5) 3 : 0.996 0.004 (0.973,1.000) (0.000,0.027) +220 AA_ES3 (5) 3 : 0.996 0.004 (0.972,1.000) (0.000,0.028) +221 AA_SP1 (2) 3 : 0.968 0.032 (0.884,1.000) (0.000,0.116) +222 AA_ES1 (2) 3 : 0.994 0.006 (0.958,1.000) (0.000,0.042) +223 AA_SP2 (5) 3 : 0.996 0.004 (0.974,1.000) (0.000,0.026) +224 FB_A001 (5) 3 : 0.996 0.004 (0.975,1.000) (0.000,0.025) +225 FB_A002 (7) 3 : 0.998 0.002 (0.987,1.000) (0.000,0.013) +226 FB_A005 (0) 3 : 0.997 0.003 (0.979,1.000) (0.000,0.021) +227 FB_A017 (17) 3 : 0.994 0.006 (0.963,1.000) (0.000,0.037) +228 FB_A020 (17) 3 : 0.997 0.003 (0.984,1.000) (0.000,0.016) +229 FB_A059 (17) 3 : 0.998 0.002 (0.986,1.000) (0.000,0.014) +230 FB_A060 (23) 3 : 0.996 0.004 (0.976,1.000) (0.000,0.024) +231 FB_T25 (7) 3 : 0.997 0.003 (0.983,1.000) (0.000,0.017) +232 FB_T27 (0) 3 : 0.997 0.003 (0.983,1.000) (0.000,0.017) +233 FB_T45 (2) 3 : 0.997 0.003 (0.982,1.000) (0.000,0.018) +234 FB_T46 (0) 3 : 0.997 0.003 (0.979,1.000) (0.000,0.021) +235 FB_T47 (2) 3 : 0.979 0.021 (0.914,1.000) (0.000,0.086) +236 FG_ES05 (7) 3 : 0.998 0.002 (0.988,1.000) (0.000,0.012) +237 FG_ES06 (7) 3 : 0.997 0.003 (0.981,1.000) (0.000,0.019) +238 FG_ES07 (2) 3 : 0.998 0.002 (0.989,1.000) (0.000,0.011) +239 FG_ES08 (15) 3 : 0.998 0.002 (0.988,1.000) (0.000,0.012) +240 FG_ES09 (11) 3 : 0.998 0.002 (0.985,1.000) (0.000,0.015) +241 FG_ES10 (0) 3 : 0.998 0.002 (0.988,1.000) (0.000,0.012) +242 FG_ES01 (2) 3 : 0.997 0.003 (0.978,1.000) (0.000,0.022) +243 FG_ES02 (2) 3 : 0.998 0.002 (0.991,1.000) (0.000,0.009) +244 FG_ES03 (5) 3 : 0.998 0.002 (0.985,1.000) (0.000,0.015) +245 FG_ES04 (5) 3 : 0.998 0.002 (0.986,1.000) (0.000,0.014) +246 FG_ES11 (0) 3 : 0.992 0.008 (0.961,1.000) (0.000,0.039) +247 FG_ES12 (7) 3 : 0.998 0.002 (0.989,1.000) (0.000,0.011) +248 FG_SP01 (5) 3 : 0.998 0.002 (0.988,1.000) (0.000,0.012) +249 FG_SP02 (5) 3 : 0.992 0.008 (0.951,1.000) (0.000,0.049) +250 FG_SP03 (0) 3 : 0.997 0.003 (0.984,1.000) (0.000,0.016) +251 FG_SP04 (7) 3 : 0.998 0.002 (0.986,1.000) (0.000,0.014) +252 FG_SP05 (7) 3 : 0.985 0.015 (0.935,1.000) (0.000,0.065) +253 FG_SP06 (7) 3 : 0.998 0.002 (0.989,1.000) (0.000,0.011) +254 FG_SP07 (5) 3 : 0.998 0.002 (0.990,1.000) (0.000,0.010) +255 FG_SP08 (8) 3 : 0.970 0.030 (0.898,1.000) (0.000,0.102) +256 FG_SP09 (20) 3 : 0.998 0.002 (0.985,1.000) (0.000,0.015) +257 FG_SP10 (2) 3 : 0.998 0.002 (0.988,1.000) (0.000,0.012) +258 FG_T31 (7) 3 : 0.998 0.002 (0.989,1.000) (0.000,0.011) +259 FG_T32 (0) 3 : 0.997 0.003 (0.981,1.000) (0.000,0.019) +260 FG_T52 (0) 3 : 0.992 0.008 (0.957,1.000) (0.000,0.043) +261 HG_H004 (2) 3 : 0.998 0.002 (0.987,1.000) (0.000,0.013) +262 HG_H006 (0) 3 : 0.997 0.003 (0.984,1.000) (0.000,0.016) +263 HG_H008 (2) 3 : 0.998 0.002 (0.986,1.000) (0.000,0.014) +264 HG_H211 (17) 3 : 0.996 0.004 (0.976,1.000) (0.000,0.024) +265 HG_H217 (0) 3 : 0.998 0.002 (0.988,1.000) (0.000,0.012) +266 HG_H235 (12) 3 : 0.994 0.006 (0.958,1.000) (0.000,0.042) +267 HG_H291 (7) 3 : 0.997 0.003 (0.983,1.000) (0.000,0.017) +268 HG_H293 (7) 3 : 0.998 0.002 (0.989,1.000) (0.000,0.011) +269 FL_H011 (7) 3 : 0.998 0.002 (0.988,1.000) (0.000,0.012) +270 FL_H012 (0) 3 : 0.998 0.002 (0.989,1.000) (0.000,0.011) +271 FL_H013 (5) 3 : 0.998 0.002 (0.990,1.000) (0.000,0.010) +272 FL_H014 (2) 3 : 0.998 0.002 (0.987,1.000) (0.000,0.013) +273 FL_H015 (7) 3 : 0.998 0.002 (0.987,1.000) (0.000,0.013) +274 FL_H016 (0) 3 : 0.998 0.002 (0.989,1.000) (0.000,0.011) +275 FL_H017 (8) 3 : 0.998 0.002 (0.989,1.000) (0.000,0.011) +276 FL_H018 (7) 3 : 0.998 0.002 (0.989,1.000) (0.000,0.011) +277 FL_H019 (5) 3 : 0.997 0.003 (0.984,1.000) (0.000,0.016) +278 FL_H020 (5) 3 : 0.998 0.002 (0.986,1.000) (0.000,0.014) +279 FL_H219 (12) 3 : 0.997 0.003 (0.981,1.000) (0.000,0.019) +280 FL_H220 (2) 3 : 0.995 0.005 (0.968,1.000) (0.000,0.032) +281 FL_H228 (0) 3 : 0.998 0.002 (0.987,1.000) (0.000,0.013) +282 FL_H229 (0) 3 : 0.949 0.051 (0.862,1.000) (0.000,0.138) +283 FL_H232 (5) 3 : 0.943 0.057 (0.850,1.000) (0.000,0.150) +284 FL_H221 (10) 3 : 0.983 0.017 (0.911,1.000) (0.000,0.089) +285 FL_H222 (7) 3 : 0.981 0.019 (0.909,1.000) (0.000,0.091) +286 FL_H223 (0) 3 : 0.997 0.003 (0.981,1.000) (0.000,0.019) +287 FL_H224 (5) 3 : 0.998 0.002 (0.988,1.000) (0.000,0.012) +288 FL_H225 (0) 3 : 0.998 0.002 (0.988,1.000) (0.000,0.012) +289 FL_H226 (7) 3 : 0.996 0.004 (0.974,1.000) (0.000,0.026) +290 FL_H230 (0) 3 : 0.970 0.030 (0.895,1.000) (0.000,0.105) +291 FL_H231 (2) 3 : 0.997 0.003 (0.982,1.000) (0.000,0.018) +292 FL_ES1 (7) 3 : 0.955 0.045 (0.858,1.000) (0.000,0.142) +293 FL_R27 (7) 3 : 0.992 0.008 (0.949,1.000) (0.000,0.051) +294 HI_A212 (0) 3 : 0.996 0.004 (0.973,1.000) (0.000,0.027) +295 HI_A215 (5) 3 : 0.984 0.016 (0.932,1.000) (0.000,0.068) +296 HI_A217 (6) 3 : 0.998 0.002 (0.986,1.000) (0.000,0.014) +297 HI_A222 (0) 3 : 0.996 0.004 (0.977,1.000) (0.000,0.023) +298 HI_A225 (0) 3 : 0.998 0.002 (0.988,1.000) (0.000,0.012) +299 HI_A227 (5) 3 : 0.996 0.004 (0.974,1.000) (0.000,0.026) +300 HI_A229 (5) 3 : 0.998 0.002 (0.986,1.000) (0.000,0.014) +301 HI_A236 (0) 3 : 0.998 0.002 (0.985,1.000) (0.000,0.015) +302 HI_A245 (11) 3 : 0.998 0.002 (0.987,1.000) (0.000,0.013) +303 HI_A261 (0) 3 : 0.998 0.002 (0.990,1.000) (0.000,0.010) +304 HI_A263 (0) 3 : 0.998 0.002 (0.986,1.000) (0.000,0.014) +305 HI_A265 (7) 3 : 0.998 0.002 (0.988,1.000) (0.000,0.012) +306 HI_A266 (0) 3 : 0.998 0.002 (0.989,1.000) (0.000,0.011) +307 HI_A317 (5) 3 : 0.997 0.003 (0.985,1.000) (0.000,0.015) +308 HI_R01 (0) 3 : 0.997 0.003 (0.980,1.000) (0.000,0.020) +309 HI_R03 (5) 3 : 0.997 0.003 (0.979,1.000) (0.000,0.021) +310 HI_R04 (5) 3 : 0.995 0.005 (0.968,1.000) (0.000,0.032) +311 HI_R05 (5) 3 : 0.955 0.045 (0.835,1.000) (0.000,0.165) +312 HI_R06 (5) 3 : 0.997 0.003 (0.981,1.000) (0.000,0.019) +313 HI_R07 (5) 3 : 0.981 0.019 (0.920,1.000) (0.000,0.080) +314 HI_R08 (0) 3 : 0.998 0.002 (0.987,1.000) (0.000,0.013) +315 HI_R10 (0) 3 : 0.998 0.002 (0.987,1.000) (0.000,0.013) +316 HI_R11 (17) 3 : 0.995 0.005 (0.968,1.000) (0.000,0.032) +317 ND_A05 (23) 3 : 0.997 0.003 (0.983,1.000) (0.000,0.017) +318 ND_A10 (7) 3 : 0.995 0.005 (0.968,1.000) (0.000,0.032) +319 ND_A11 (23) 3 : 0.998 0.002 (0.987,1.000) (0.000,0.013) +320 ND_A22 (5) 3 : 0.992 0.008 (0.949,1.000) (0.000,0.051) +321 ND_A24 (5) 3 : 0.995 0.005 (0.970,1.000) (0.000,0.030) +322 ND_A25 (23) 3 : 0.998 0.002 (0.986,1.000) (0.000,0.014) +323 ND_A13 (10) 3 : 0.998 0.002 (0.985,1.000) (0.000,0.015) +324 ND_A02 (20) 3 : 0.997 0.003 (0.983,1.000) (0.000,0.017) +325 ND_A03 (20) 3 : 0.997 0.003 (0.984,1.000) (0.000,0.016) +326 ND_A06 (5) 3 : 0.997 0.003 (0.982,1.000) (0.000,0.018) +327 ND_A07 (5) 3 : 0.998 0.002 (0.988,1.000) (0.000,0.012) +328 ND_A09 (15) 3 : 0.995 0.005 (0.970,1.000) (0.000,0.030) +329 ND_A12 (12) 3 : 0.974 0.026 (0.872,1.000) (0.000,0.128) +330 ND_A14 (12) 3 : 0.997 0.003 (0.979,1.000) (0.000,0.021) +331 ND_A15 (7) 3 : 0.998 0.002 (0.988,1.000) (0.000,0.012) +332 ND_A16 (17) 3 : 0.962 0.038 (0.867,1.000) (0.000,0.133) +333 ND_A17 (17) 3 : 0.998 0.002 (0.986,1.000) (0.000,0.014) +334 ND_A19 (7) 3 : 0.998 0.002 (0.987,1.000) (0.000,0.013) +335 ND_A23 (5) 3 : 0.997 0.003 (0.983,1.000) (0.000,0.017) +336 ND_A26 (23) 3 : 0.998 0.002 (0.987,1.000) (0.000,0.013) +337 NZ_26 (2) 3 : 0.998 0.002 (0.990,1.000) (0.000,0.010) +338 NZ_27 (7) 3 : 0.998 0.002 (0.989,1.000) (0.000,0.011) +339 NZ_28 (2) 3 : 0.998 0.002 (0.989,1.000) (0.000,0.011) +340 NZ_29 (7) 3 : 0.998 0.002 (0.988,1.000) (0.000,0.012) +341 NZ_30 (17) 3 : 0.998 0.002 (0.988,1.000) (0.000,0.012) +342 NZ_31 (10) 3 : 0.998 0.002 (0.987,1.000) (0.000,0.013) +343 NZ_32 (5) 3 : 0.998 0.002 (0.989,1.000) (0.000,0.011) +344 NZ_33 (2) 3 : 0.998 0.002 (0.991,1.000) (0.000,0.009) +345 NZ_34 (16) 3 : 0.998 0.002 (0.988,1.000) (0.000,0.012) +346 NZ_36 (2) 3 : 0.995 0.005 (0.968,1.000) (0.000,0.032) +347 NZ_37 (10) 3 : 0.998 0.002 (0.987,1.000) (0.000,0.013) +348 NZ_38 (11) 3 : 0.956 0.044 (0.887,1.000) (0.000,0.113) +349 NZ_39 (10) 3 : 0.997 0.003 (0.980,1.000) (0.000,0.020) +350 NZ_40 (0) 3 : 0.998 0.002 (0.991,1.000) (0.000,0.009) +351 NZ_41 (0) 3 : 0.998 0.002 (0.990,1.000) (0.000,0.010) +352 NZ_43 (16) 3 : 0.981 0.019 (0.922,1.000) (0.000,0.078) +353 NZ_44 (8) 3 : 0.998 0.002 (0.988,1.000) (0.000,0.012) +354 NZ_45 (14) 3 : 0.997 0.003 (0.984,1.000) (0.000,0.016) +355 NZ_46 (7) 3 : 0.998 0.002 (0.988,1.000) (0.000,0.012) +356 NZ_47 (14) 3 : 0.998 0.002 (0.988,1.000) (0.000,0.012) +357 NZ_48 (5) 3 : 0.998 0.002 (0.989,1.000) (0.000,0.011) +358 NZ_49 (7) 3 : 0.998 0.002 (0.988,1.000) (0.000,0.012) +359 NZ_50 (10) 3 : 0.998 0.002 (0.987,1.000) (0.000,0.013) +360 9_A301 (5) 3 : 0.998 0.002 (0.987,1.000) (0.000,0.013) +361 9_A303 (21) 3 : 0.998 0.002 (0.985,1.000) (0.000,0.015) +362 9_A304 (5) 3 : 0.997 0.003 (0.981,1.000) (0.000,0.019) +363 9_A334 (0) 3 : 0.998 0.002 (0.987,1.000) (0.000,0.013) +364 9_A337 (2) 3 : 0.998 0.002 (0.986,1.000) (0.000,0.014) +365 9_A342 (17) 3 : 0.997 0.003 (0.982,1.000) (0.000,0.018) +366 9_A343 (10) 3 : 0.993 0.007 (0.953,1.000) (0.000,0.047) +367 9_A348 (14) 3 : 0.983 0.017 (0.913,1.000) (0.000,0.087) +368 9_A349 (12) 3 : 0.998 0.002 (0.986,1.000) (0.000,0.014) +369 9_A350 (2) 3 : 0.994 0.006 (0.962,1.000) (0.000,0.038) +370 9_A351 (12) 3 : 0.997 0.003 (0.984,1.000) (0.000,0.016) +371 9_A352 (0) 3 : 0.997 0.003 (0.984,1.000) (0.000,0.016) +372 9_A353 (21) 3 : 0.998 0.002 (0.987,1.000) (0.000,0.013) +373 9_A354 (5) 3 : 0.997 0.003 (0.982,1.000) (0.000,0.018) +374 9_A355 (5) 3 : 0.997 0.003 (0.984,1.000) (0.000,0.016) +375 9_A357 (7) 3 : 0.995 0.005 (0.967,1.000) (0.000,0.033) +376 9_A358 (2) 3 : 0.998 0.002 (0.989,1.000) (0.000,0.011) +377 RXCA_03 (5) 3 : 0.998 0.002 (0.987,1.000) (0.000,0.013) +378 RXCA_04 (12) 3 : 0.998 0.002 (0.986,1.000) (0.000,0.014) +379 RXCA_07 (5) 3 : 0.998 0.002 (0.988,1.000) (0.000,0.012) +380 RXCA_12 (0) 3 : 0.998 0.002 (0.988,1.000) (0.000,0.012) +381 RXCA_19 (5) 3 : 0.998 0.002 (0.987,1.000) (0.000,0.013) +382 RXCA_20 (5) 3 : 0.998 0.002 (0.986,1.000) (0.000,0.014) +383 RXCA_22 (5) 3 : 0.997 0.003 (0.982,1.000) (0.000,0.018) +384 RXCA_26 (5) 3 : 0.998 0.002 (0.987,1.000) (0.000,0.013) +385 RXCH_01 (0) 3 : 0.998 0.002 (0.989,1.000) (0.000,0.011) +386 RXCH_02 (7) 3 : 0.998 0.002 (0.987,1.000) (0.000,0.013) +387 RXCH_13 (11) 3 : 0.998 0.002 (0.985,1.000) (0.000,0.015) +388 RXCH_14 (5) 3 : 0.998 0.002 (0.985,1.000) (0.000,0.015) +389 RXCH_15 (0) 3 : 0.998 0.002 (0.988,1.000) (0.000,0.012) +390 RXCH_16 (0) 3 : 0.986 0.014 (0.924,1.000) (0.000,0.076) +391 RXCH_18 (7) 3 : 0.998 0.002 (0.987,1.000) (0.000,0.013) +392 RXCH_27 (2) 3 : 0.998 0.002 (0.986,1.000) (0.000,0.014) +393 RXCH_29 (0) 3 : 0.998 0.002 (0.988,1.000) (0.000,0.012) +394 RXWH_05 (5) 3 : 0.998 0.002 (0.985,1.000) (0.000,0.015) +395 RXWH_06 (5) 3 : 0.998 0.002 (0.987,1.000) (0.000,0.013) +396 RXWH_08 (5) 3 : 0.998 0.002 (0.987,1.000) (0.000,0.013) +397 RXWH_09 (5) 3 : 0.998 0.002 (0.986,1.000) (0.000,0.014) +398 RXWH_17 (5) 3 : 0.997 0.003 (0.981,1.000) (0.000,0.019) +399 RXWH_21 (0) 3 : 0.998 0.002 (0.987,1.000) (0.000,0.013) +400 RXWH_23 (5) 3 : 0.998 0.002 (0.987,1.000) (0.000,0.013) +401 RXWH_28 (2) 3 : 0.997 0.003 (0.979,1.000) (0.000,0.021) +402 TH_T50 (20) 3 : 0.996 0.004 (0.975,1.000) (0.000,0.025) +403 TH_A244 (2) 3 : 0.998 0.002 (0.985,1.000) (0.000,0.015) +404 TH_A252 (0) 3 : 0.997 0.003 (0.980,1.000) (0.000,0.020) +405 TH_A254 (0) 3 : 0.997 0.003 (0.984,1.000) (0.000,0.016) +406 TH_A276 (7) 3 : 0.996 0.004 (0.974,1.000) (0.000,0.026) +407 TH_A308 (0) 3 : 0.997 0.003 (0.980,1.000) (0.000,0.020) +408 TH_A309 (5) 3 : 0.988 0.012 (0.943,1.000) (0.000,0.057) +409 TH_A313 (5) 3 : 0.992 0.008 (0.951,1.000) (0.000,0.049) +410 TH_A314 (16) 3 : 0.992 0.008 (0.955,1.000) (0.000,0.045) +411 TH_A322 (5) 3 : 0.994 0.006 (0.961,1.000) (0.000,0.039) +412 TH_A326 (7) 3 : 0.997 0.003 (0.982,1.000) (0.000,0.018) +413 TH_A333 (0) 3 : 0.998 0.002 (0.985,1.000) (0.000,0.015) +414 VW_A046 (2) 3 : 0.998 0.002 (0.990,1.000) (0.000,0.010) +415 VW_A047 (2) 3 : 0.998 0.002 (0.990,1.000) (0.000,0.010) +416 VW_A048 (2) 3 : 0.998 0.002 (0.988,1.000) (0.000,0.012) +417 VW_A043 (5) 3 : 0.998 0.002 (0.987,1.000) (0.000,0.013) +418 VW_A050 (7) 3 : 0.998 0.002 (0.989,1.000) (0.000,0.011) +419 VW_A045 (5) 3 : 0.998 0.002 (0.985,1.000) (0.000,0.015) +420 VW_A066 (12) 3 : 0.997 0.003 (0.983,1.000) (0.000,0.017) +421 VW_A068 (2) 3 : 0.998 0.002 (0.986,1.000) (0.000,0.014) +422 VW_A201 (2) 3 : 0.988 0.012 (0.946,1.000) (0.000,0.054) +423 VW_A311 (7) 3 : 0.998 0.002 (0.986,1.000) (0.000,0.014) +424 VW_A332 (0) 3 : 0.998 0.002 (0.988,1.000) (0.000,0.012) +425 VW_A344 (20) 3 : 0.997 0.003 (0.979,1.000) (0.000,0.021) +426 VW_A345 (0) 3 : 0.997 0.003 (0.984,1.000) (0.000,0.016) +427 VW_A346 (0) 3 : 0.998 0.002 (0.986,1.000) (0.000,0.014) +428 Causse_06 (23) 4 : 0.548 0.452 (0.388,0.705) (0.295,0.612) +429 Causse_16 (23) 4 : 0.439 0.561 (0.265,0.613) (0.387,0.735) +430 Causse_22 (14) 4 : 0.432 0.568 (0.260,0.603) (0.397,0.740) +431 Causse_27 (0) 4 : 0.347 0.653 (0.207,0.493) (0.507,0.793) +432 Causse_29 (10) 4 : 0.351 0.649 (0.183,0.525) (0.475,0.817) +433 Causse_30 (10) 4 : 0.458 0.542 (0.309,0.606) (0.394,0.691) +434 Causse_32 (0) 4 : 0.410 0.590 (0.259,0.561) (0.439,0.741) +435 Causse_33 (2) 4 : 0.269 0.731 (0.135,0.415) (0.585,0.865) +436 Causse_36 (5) 4 : 0.442 0.558 (0.280,0.601) (0.399,0.720) +437 EST_1 (0) 4 : 0.330 0.670 (0.187,0.476) (0.524,0.813) +438 EST_2 (2) 4 : 0.600 0.400 (0.457,0.736) (0.264,0.543) +439 EST_3 (2) 4 : 0.529 0.471 (0.385,0.669) (0.331,0.615) +440 EST_5 (5) 4 : 0.518 0.482 (0.375,0.656) (0.344,0.625) +441 FOS_1 (2) 4 : 0.323 0.677 (0.175,0.475) (0.525,0.825) +442 FOS_4 (8) 4 : 0.382 0.618 (0.222,0.543) (0.457,0.778) +443 FOS_5 (5) 4 : 0.600 0.400 (0.449,0.742) (0.258,0.551) +444 FRE_2 (0) 4 : 0.224 0.776 (0.085,0.371) (0.629,0.915) +445 FRE_3 (10) 4 : 0.175 0.825 (0.008,0.345) (0.655,0.992) +446 FRE_4 (0) 4 : 0.122 0.878 (0.002,0.266) (0.734,0.998) +447 FRE_5 (19) 4 : 0.227 0.773 (0.061,0.396) (0.604,0.939) +448 Lyon_34 (5) 4 : 0.193 0.807 (0.050,0.343) (0.657,0.950) +449 Lyon_37 (5) 4 : 0.503 0.497 (0.354,0.649) (0.351,0.646) +450 Lyon_38 (10) 4 : 0.455 0.545 (0.292,0.616) (0.384,0.708) +451 Lyon_39 (7) 4 : 0.405 0.595 (0.253,0.560) (0.440,0.747) +452 Lyon_42 (7) 4 : 0.399 0.601 (0.243,0.556) (0.444,0.757) +453 Lyon_43 (2) 4 : 0.418 0.582 (0.274,0.563) (0.437,0.726) +454 Lyon_44 (15) 4 : 0.288 0.712 (0.131,0.452) (0.548,0.869) +455 Lyon_45 (7) 4 : 0.407 0.593 (0.247,0.568) (0.432,0.753) +456 Lyon_46 (7) 4 : 0.384 0.616 (0.237,0.533) (0.467,0.763) +457 Lyon_48 (7) 4 : 0.296 0.704 (0.146,0.455) (0.545,0.854) +458 Lyon_50 (10) 4 : 0.251 0.749 (0.109,0.401) (0.599,0.891) +459 Lyon_51 (7) 4 : 0.355 0.645 (0.188,0.525) (0.475,0.812) +460 Lyon_52 (7) 4 : 0.327 0.673 (0.168,0.493) (0.507,0.832) +461 Lyon_55 (7) 4 : 0.439 0.561 (0.276,0.602) (0.398,0.724) +462 Lyon_56 (10) 4 : 0.314 0.686 (0.148,0.485) (0.515,0.852) +463 Lyon_57 (5) 4 : 0.378 0.622 (0.219,0.538) (0.462,0.781) +464 Lyon_60 (10) 4 : 0.458 0.542 (0.303,0.613) (0.387,0.697) +465 Lyon_61 (10) 4 : 0.390 0.610 (0.230,0.552) (0.448,0.770) +466 Lyon_63 (0) 4 : 0.473 0.527 (0.312,0.632) (0.368,0.688) +467 Lyon_64 (15) 4 : 0.552 0.448 (0.366,0.732) (0.268,0.634) +468 Lyon_66 (12) 4 : 0.319 0.681 (0.160,0.484) (0.516,0.840) +469 Lyon_67 (8) 4 : 0.440 0.560 (0.287,0.592) (0.408,0.713) +470 Lyon_69 (7) 4 : 0.357 0.643 (0.200,0.518) (0.482,0.800) +471 Lyon_70 (17) 4 : 0.476 0.524 (0.314,0.639) (0.361,0.686) +472 Lyon_71 (5) 4 : 0.292 0.708 (0.135,0.453) (0.547,0.865) +473 PP_06 (15) 4 : 0.326 0.674 (0.153,0.502) (0.498,0.847) +474 PP_12 (5) 4 : 0.294 0.706 (0.153,0.442) (0.558,0.847) +475 PP_15 (23) 4 : 0.331 0.669 (0.172,0.495) (0.505,0.828) +476 PP_16 (17) 4 : 0.443 0.557 (0.286,0.599) (0.401,0.714) +477 PP_18 (15) 4 : 0.359 0.641 (0.199,0.522) (0.478,0.801) +478 PP_19 (0) 4 : 0.313 0.687 (0.174,0.459) (0.541,0.826) +479 PP_20 (14) 4 : 0.159 0.841 (0.046,0.289) (0.711,0.954) +480 PP_21 (17) 4 : 0.309 0.691 (0.172,0.453) (0.547,0.828) +481 PP_24 (0) 4 : 0.257 0.743 (0.130,0.392) (0.608,0.870) +482 PP_26 (10) 4 : 0.296 0.704 (0.159,0.440) (0.560,0.841) +483 Roi_41 (11) 4 : 0.492 0.508 (0.337,0.644) (0.356,0.663) +484 Roi_42 (5) 4 : 0.446 0.554 (0.283,0.607) (0.393,0.717) +485 Roi_44 (5) 4 : 0.529 0.471 (0.388,0.667) (0.333,0.612) +486 Roi_47 (7) 4 : 0.613 0.387 (0.459,0.758) (0.242,0.541) +487 Roi_48 (2) 4 : 0.580 0.420 (0.421,0.733) (0.267,0.579) +488 Roi_49 (5) 4 : 0.495 0.505 (0.326,0.660) (0.340,0.674) +489 Roi_50 (0) 4 : 0.632 0.368 (0.474,0.783) (0.217,0.526) +490 Roi_51 (5) 4 : 0.567 0.433 (0.410,0.717) (0.283,0.590) +491 Roi_52 (5) 4 : 0.660 0.340 (0.513,0.795) (0.205,0.487) +492 Roi_53 (5) 4 : 0.596 0.404 (0.446,0.736) (0.264,0.554) +493 Ver_129 (5) 4 : 0.602 0.398 (0.454,0.743) (0.257,0.546) +494 Ver_152 (10) 4 : 0.718 0.282 (0.557,0.862) (0.138,0.443) +495 Ver_170 (12) 4 : 0.592 0.408 (0.426,0.750) (0.250,0.574) +496 Ver_1743 (2) 4 : 0.455 0.545 (0.310,0.599) (0.401,0.690) +497 Ver_1950 (17) 4 : 0.567 0.433 (0.409,0.718) (0.282,0.591) +498 Ver_1990 (0) 4 : 0.541 0.459 (0.393,0.684) (0.316,0.607) +499 Ver_2469 (12) 4 : 0.639 0.361 (0.475,0.789) (0.211,0.525) +500 Ver_2488 (5) 4 : 0.392 0.608 (0.237,0.552) (0.448,0.763) +501 Ver_2550 (0) 4 : 0.457 0.543 (0.295,0.617) (0.383,0.705) +502 Ver_2593 (0) 4 : 0.579 0.421 (0.422,0.729) (0.271,0.578) +503 Ver_2692 (7) 4 : 0.632 0.368 (0.470,0.782) (0.218,0.530) +504 Ver_2696 (5) 4 : 0.504 0.496 (0.353,0.651) (0.349,0.647) +505 Ver_2701 (7) 4 : 0.518 0.482 (0.367,0.665) (0.335,0.633) +506 Ver_2787 (10) 4 : 0.780 0.220 (0.636,0.904) (0.096,0.364) +507 Ver_2813 (0) 4 : 0.479 0.521 (0.341,0.615) (0.385,0.659) +508 Ver_2911 (7) 4 : 0.651 0.349 (0.499,0.792) (0.208,0.501) +509 Ver_9766 (10) 4 : 0.571 0.429 (0.417,0.718) (0.282,0.583) +510 VIL_3 (5) 4 : 0.409 0.591 (0.253,0.566) (0.434,0.747) +511 VIL_4 (0) 4 : 0.381 0.619 (0.230,0.533) (0.467,0.770) +512 VIL_5 (0) 4 : 0.482 0.518 (0.320,0.642) (0.358,0.680) +513 ALT_018 (2) 5 : 0.283 0.717 (0.151,0.421) (0.579,0.849) +514 ALT_106 (0) 5 : 0.256 0.744 (0.141,0.379) (0.621,0.859) +515 ALT_121 (0) 5 : 0.416 0.584 (0.280,0.552) (0.448,0.720) +516 ALT_125 (5) 5 : 0.313 0.687 (0.188,0.443) (0.557,0.812) +517 ALT_129 (2) 5 : 0.215 0.785 (0.092,0.347) (0.653,0.908) +518 ALT_131 (5) 5 : 0.203 0.797 (0.085,0.332) (0.668,0.915) +519 ALT_140 (0) 5 : 0.369 0.631 (0.243,0.498) (0.502,0.757) +520 ALT_143 (0) 5 : 0.319 0.681 (0.189,0.453) (0.547,0.811) +521 RSL_01 (0) 5 : 0.012 0.988 (0.000,0.058) (0.942,1.000) +522 RSL_02 (0) 5 : 0.059 0.941 (0.000,0.156) (0.844,1.000) +523 RSL_03 (2) 5 : 0.014 0.986 (0.000,0.067) (0.933,1.000) +524 RSL_04 (0) 5 : 0.053 0.947 (0.000,0.160) (0.840,1.000) +525 RSL_05 (5) 5 : 0.013 0.987 (0.000,0.064) (0.936,1.000) +526 RSL_06 (0) 5 : 0.046 0.954 (0.000,0.151) (0.849,1.000) +527 RSL_07 (0) 5 : 0.035 0.965 (0.000,0.131) (0.869,1.000) +528 RSL_08 (0) 5 : 0.015 0.985 (0.000,0.071) (0.929,1.000) +529 RSL_14 (10) 5 : 0.643 0.357 (0.511,0.767) (0.233,0.489) +530 TAR_006 (5) 5 : 0.015 0.985 (0.000,0.072) (0.928,1.000) +531 TAR_009 (10) 5 : 0.023 0.977 (0.000,0.100) (0.900,1.000) +532 TAR_010 (11) 5 : 0.011 0.989 (0.000,0.054) (0.946,1.000) +533 TAR_102 (7) 5 : 0.048 0.952 (0.000,0.167) (0.833,1.000) +534 TAR_103 (7) 5 : 0.170 0.830 (0.003,0.337) (0.663,0.997) +535 TAR_105 (2) 5 : 0.043 0.957 (0.000,0.143) (0.857,1.000) +536 TAR_106 (5) 5 : 0.012 0.988 (0.000,0.060) (0.940,1.000) +537 TAR_107 (7) 5 : 0.136 0.864 (0.033,0.250) (0.750,0.967) +538 TAR_111 (5) 5 : 0.021 0.979 (0.000,0.091) (0.909,1.000) +539 ZRG_02 (0) 5 : 0.076 0.924 (0.000,0.199) (0.801,1.000) +540 ZRG_03 (0) 5 : 0.103 0.897 (0.000,0.258) (0.742,1.000) +541 ZRG_04 (0) 5 : 0.025 0.975 (0.000,0.104) (0.896,1.000) +542 ZRG_06 (0) 5 : 0.018 0.982 (0.000,0.083) (0.917,1.000) +543 ZRG_07 (0) 5 : 0.016 0.984 (0.000,0.074) (0.926,1.000) +544 ZRG_08 (2) 5 : 0.166 0.834 (0.032,0.307) (0.693,0.968) +545 ZRG_10 (0) 5 : 0.014 0.986 (0.000,0.065) (0.935,1.000) +546 ZRG_11 (5) 5 : 0.049 0.951 (0.000,0.172) (0.828,1.000) +547 ZRG_12 (1) 5 : 0.045 0.955 (0.000,0.158) (0.842,1.000) +548 ZRG_13 (0) 5 : 0.067 0.933 (0.000,0.201) (0.799,1.000) +549 ZRG_14 (0) 5 : 0.042 0.958 (0.000,0.162) (0.838,1.000) +550 ZRG_20 (10) 5 : 0.027 0.973 (0.000,0.118) (0.882,1.000) +551 ZRG_24 (7) 5 : 0.013 0.987 (0.000,0.064) (0.936,1.000) + + +Estimated Allele Frequencies in each cluster +First column gives estimated ancestral frequencies + + +Locus 1 : mOC101 +12 alleles +4.7% missing data + 162 (0.091) 0.746 0.089 + 160 (0.043) 0.192 0.040 + 156 (0.128) 0.010 0.129 + 154 (0.176) 0.000 0.180 + 174 (0.083) 0.000 0.084 + 158 (0.050) 0.000 0.050 + 152 (0.024) 0.000 0.023 + 172 (0.102) 0.000 0.104 + 170 (0.013) 0.000 0.012 + 178 (0.212) 0.043 0.214 + 164 (0.065) 0.008 0.063 + 168 (0.013) 0.000 0.011 + +Locus 2 : mOC106 +13 alleles +6.4% missing data + 169 (0.152) 0.032 0.154 + 179 (0.151) 0.001 0.155 + 171 (0.076) 0.365 0.074 + 177 (0.051) 0.156 0.049 + 173 (0.050) 0.349 0.048 + 175 (0.132) 0.004 0.134 + 167 (0.174) 0.093 0.176 + 165 (0.083) 0.000 0.085 + 159 (0.037) 0.000 0.037 + 163 (0.062) 0.000 0.063 + 161 (0.012) 0.000 0.011 + 183 (0.009) 0.000 0.007 + 142 (0.009) 0.000 0.007 + +Locus 3 : mOC108 +11 alleles +6.0% missing data + 144 (0.328) 0.446 0.331 + 152 (0.017) 0.219 0.014 + 146 (0.312) 0.003 0.320 + 150 (0.065) 0.325 0.063 + 158 (0.004) 0.000 0.003 + 142 (0.152) 0.003 0.154 + 148 (0.068) 0.005 0.066 + 140 (0.022) 0.000 0.021 + 156 (0.012) 0.000 0.010 + 138 (0.012) 0.000 0.010 + 136 (0.008) 0.000 0.007 + +Locus 4 : mOC139 +7 alleles +3.8% missing data + 129 (0.133) 0.387 0.132 + 133 (0.125) 0.148 0.124 + 131 (0.455) 0.308 0.461 + 137 (0.047) 0.038 0.045 + 135 (0.167) 0.119 0.167 + 139 (0.040) 0.000 0.040 + 127 (0.033) 0.000 0.032 + +Locus 5 : mOC172 +8 alleles +14.5% missing data + 97 (0.264) 0.369 0.264 + 103 (0.017) 0.455 0.014 + 105 (0.036) 0.007 0.033 + 101 (0.195) 0.001 0.199 + 95 (0.164) 0.000 0.167 + 93 (0.056) 0.000 0.056 + 99 (0.208) 0.167 0.207 + 91 (0.060) 0.000 0.060 + +Locus 6 : mOC176 +26 alleles +8.2% missing data + 227 (0.105) 0.872 0.106 + 233 (0.032) 0.000 0.032 + 235 (0.065) 0.000 0.067 + 236 (0.038) 0.002 0.037 + 244 (0.058) 0.000 0.060 + 225 (0.013) 0.000 0.012 + 238 (0.070) 0.005 0.071 + 234 (0.070) 0.032 0.070 + 237 (0.020) 0.000 0.020 + 240 (0.084) 0.000 0.087 + 229 (0.044) 0.083 0.042 + 231 (0.024) 0.000 0.024 + 247 (0.028) 0.000 0.028 + 241 (0.017) 0.000 0.016 + 251 (0.028) 0.000 0.028 + 242 (0.028) 0.000 0.028 + 230 (0.066) 0.000 0.068 + 224 (0.009) 0.000 0.008 + 219 (0.010) 0.005 0.007 + 249 (0.035) 0.000 0.036 + 239 (0.028) 0.000 0.028 + 246 (0.043) 0.000 0.043 + 228 (0.043) 0.000 0.044 + 223 (0.021) 0.000 0.020 + 226 (0.009) 0.000 0.008 + 232 (0.013) 0.000 0.012 + +Locus 7 : mOC203 +16 alleles +8.5% missing data + 212 (0.206) 0.345 0.209 + 214 (0.144) 0.112 0.146 + 204 (0.048) 0.358 0.046 + 208 (0.048) 0.088 0.046 + 206 (0.055) 0.061 0.053 + 202 (0.050) 0.000 0.050 + 186 (0.167) 0.000 0.173 + 196 (0.050) 0.000 0.051 + 200 (0.040) 0.000 0.040 + 198 (0.033) 0.000 0.032 + 182 (0.022) 0.000 0.022 + 216 (0.048) 0.034 0.046 + 188 (0.019) 0.000 0.018 + 210 (0.050) 0.000 0.050 + 203 (0.009) 0.000 0.007 + 192 (0.012) 0.000 0.011 + +Locus 8 : mOC119 +14 alleles +3.1% missing data + 231 (0.050) 0.575 0.048 + 233 (0.157) 0.236 0.157 + 215 (0.026) 0.000 0.025 + 223 (0.053) 0.000 0.054 + 229 (0.216) 0.173 0.218 + 227 (0.067) 0.000 0.068 + 237 (0.133) 0.000 0.136 + 225 (0.060) 0.000 0.061 + 221 (0.050) 0.000 0.050 + 235 (0.094) 0.013 0.094 + 213 (0.008) 0.000 0.007 + 239 (0.060) 0.000 0.061 + 245 (0.015) 0.000 0.014 + 219 (0.010) 0.002 0.007 + +Locus 9 : mOC140 +13 alleles +1.5% missing data + 182 (0.235) 0.295 0.237 + 184 (0.238) 0.609 0.239 + 186 (0.025) 0.092 0.022 + 188 (0.009) 0.001 0.007 + 192 (0.004) 0.000 0.003 + 177 (0.238) 0.001 0.245 + 179 (0.098) 0.000 0.100 + 175 (0.020) 0.000 0.019 + 181 (0.048) 0.000 0.048 + 183 (0.009) 0.000 0.007 + 185 (0.009) 0.003 0.006 + 180 (0.055) 0.000 0.056 + 190 (0.012) 0.000 0.011 + +Locus 10 : mOC157 +13 alleles +12.9% missing data + 141 (0.120) 0.253 0.120 + 143 (0.145) 0.165 0.146 + 149 (0.142) 0.000 0.146 + 147 (0.142) 0.001 0.146 + 151 (0.030) 0.002 0.029 + 137 (0.084) 0.174 0.082 + 139 (0.208) 0.401 0.209 + 155 (0.009) 0.000 0.008 + 142 (0.013) 0.000 0.012 + 145 (0.047) 0.000 0.047 + 135 (0.027) 0.004 0.024 + 131 (0.009) 0.000 0.008 + 140 (0.025) 0.000 0.024 + +Locus 11 : mOC201 +23 alleles +0.4% missing data + 137 (0.137) 0.246 0.139 + 143 (0.099) 0.059 0.100 + 144 (0.014) 0.567 0.012 + 133 (0.111) 0.032 0.113 + 135 (0.164) 0.000 0.171 + 139 (0.060) 0.000 0.061 + 145 (0.083) 0.020 0.084 + 155 (0.007) 0.000 0.006 + 151 (0.010) 0.000 0.009 + 129 (0.016) 0.000 0.015 + 141 (0.051) 0.000 0.052 + 149 (0.042) 0.000 0.043 + 148 (0.017) 0.055 0.015 + 131 (0.019) 0.000 0.018 + 153 (0.010) 0.000 0.009 + 150 (0.007) 0.000 0.006 + 161 (0.010) 0.000 0.009 + 157 (0.007) 0.000 0.006 + 146 (0.014) 0.018 0.012 + 147 (0.068) 0.000 0.070 + 142 (0.007) 0.000 0.006 + 134 (0.033) 0.000 0.033 + 136 (0.010) 0.000 0.009 + +Locus 12 : mOC87 +13 alleles +3.3% missing data + 220 (0.095) 0.262 0.095 + 228 (0.032) 0.120 0.030 + 224 (0.123) 0.145 0.124 + 212 (0.082) 0.157 0.081 + 230 (0.009) 0.059 0.006 + 236 (0.004) 0.000 0.003 + 232 (0.008) 0.072 0.006 + 214 (0.076) 0.000 0.078 + 216 (0.123) 0.053 0.125 + 210 (0.011) 0.000 0.010 + 218 (0.179) 0.045 0.183 + 222 (0.153) 0.019 0.156 + 226 (0.104) 0.069 0.104 + +Locus 13 : mOC89 +7 alleles +3.4% missing data + 94 (0.324) 0.794 0.325 + 92 (0.191) 0.022 0.192 + 90 (0.353) 0.037 0.358 + 88 (0.025) 0.000 0.024 + 84 (0.009) 0.000 0.008 + 98 (0.026) 0.001 0.024 + 96 (0.071) 0.146 0.068 + +Locus 14 : Sat13 +11 alleles +5.1% missing data + 131 (0.238) 0.159 0.241 + 145 (0.103) 0.695 0.102 + 143 (0.190) 0.001 0.195 + 137 (0.052) 0.041 0.050 + 130 (0.034) 0.000 0.034 + 139 (0.013) 0.000 0.011 + 147 (0.088) 0.002 0.088 + 149 (0.033) 0.031 0.030 + 141 (0.027) 0.000 0.026 + 129 (0.111) 0.000 0.113 + 133 (0.111) 0.070 0.110 + +Locus 15 : mOC102 +21 alleles +2.4% missing data + 231 (0.066) 0.000 0.068 + 235 (0.112) 0.386 0.112 + 233 (0.036) 0.166 0.034 + 234 (0.004) 0.000 0.003 + 236 (0.004) 0.000 0.003 + 237 (0.098) 0.128 0.098 + 215 (0.037) 0.000 0.038 + 239 (0.159) 0.281 0.162 + 251 (0.051) 0.000 0.051 + 241 (0.132) 0.037 0.135 + 247 (0.028) 0.000 0.027 + 245 (0.076) 0.000 0.079 + 219 (0.018) 0.000 0.017 + 229 (0.021) 0.000 0.020 + 249 (0.021) 0.000 0.020 + 221 (0.021) 0.000 0.020 + 243 (0.057) 0.000 0.058 + 225 (0.015) 0.000 0.014 + 223 (0.021) 0.000 0.021 + 227 (0.015) 0.000 0.014 + 250 (0.008) 0.000 0.007 + +Locus 16 : mOC104 +10 alleles +2.4% missing data + 126 (0.297) 0.253 0.301 + 122 (0.048) 0.593 0.046 + 128 (0.125) 0.036 0.125 + 132 (0.137) 0.022 0.138 + 115 (0.020) 0.000 0.019 + 130 (0.210) 0.088 0.212 + 138 (0.016) 0.000 0.015 + 124 (0.075) 0.000 0.076 + 134 (0.044) 0.008 0.042 + 136 (0.027) 0.000 0.026 + +Locus 17 : mOC169 +12 alleles +1.6% missing data + 159 (0.255) 0.319 0.258 + 163 (0.107) 0.311 0.106 + 169 (0.035) 0.287 0.032 + 167 (0.107) 0.001 0.109 + 165 (0.273) 0.044 0.279 + 161 (0.097) 0.000 0.099 + 157 (0.012) 0.000 0.010 + 171 (0.060) 0.002 0.059 + 173 (0.026) 0.036 0.024 + 183 (0.012) 0.000 0.010 + 164 (0.008) 0.000 0.007 + 175 (0.008) 0.000 0.007 + +Locus 18 : mOC192 +20 alleles +3.3% missing data + 133 (0.064) 0.183 0.063 + 137 (0.156) 0.023 0.160 + 139 (0.049) 0.000 0.050 + 135 (0.061) 0.051 0.060 + 115 (0.143) 0.442 0.145 + 129 (0.046) 0.250 0.044 + 113 (0.152) 0.033 0.156 + 109 (0.014) 0.000 0.013 + 131 (0.045) 0.018 0.043 + 141 (0.018) 0.000 0.017 + 111 (0.008) 0.000 0.007 + 117 (0.040) 0.000 0.040 + 121 (0.053) 0.000 0.054 + 127 (0.034) 0.000 0.034 + 151 (0.011) 0.000 0.010 + 155 (0.011) 0.000 0.010 + 125 (0.040) 0.000 0.040 + 119 (0.033) 0.000 0.034 + 143 (0.011) 0.000 0.010 + 149 (0.011) 0.000 0.010 + +Locus 19 : mOC205 +33 alleles +14.2% missing data + 192 (0.034) 0.033 0.033 + 185 (0.097) 0.000 0.104 + 181 (0.124) 0.121 0.130 + 193 (0.023) 0.577 0.021 + 196 (0.015) 0.008 0.013 + 179 (0.072) 0.000 0.076 + 183 (0.074) 0.000 0.079 + 173 (0.056) 0.006 0.057 + 177 (0.027) 0.000 0.028 + 175 (0.021) 0.000 0.021 + 187 (0.053) 0.000 0.055 + 180 (0.011) 0.000 0.010 + 189 (0.035) 0.003 0.035 + 170 (0.011) 0.000 0.010 + 198 (0.011) 0.000 0.010 + 191 (0.024) 0.000 0.024 + 203 (0.008) 0.000 0.007 + 195 (0.030) 0.049 0.029 + 171 (0.028) 0.000 0.028 + 194 (0.011) 0.041 0.009 + 200 (0.015) 0.047 0.013 + 169 (0.040) 0.104 0.039 + 190 (0.053) 0.001 0.055 + 199 (0.008) 0.003 0.006 + 197 (0.024) 0.003 0.023 + 188 (0.024) 0.001 0.023 + 201 (0.008) 0.001 0.006 + 186 (0.024) 0.000 0.024 + 184 (0.008) 0.000 0.007 + 202 (0.008) 0.000 0.007 + 165 (0.008) 0.000 0.007 + 182 (0.008) 0.000 0.007 + 167 (0.008) 0.000 0.007 + +Locus 20 : mOC228 +13 alleles +2.7% missing data + 230 (0.135) 0.619 0.135 + 232 (0.155) 0.126 0.156 + 234 (0.224) 0.114 0.227 + 240 (0.218) 0.140 0.220 + 242 (0.070) 0.000 0.071 + 238 (0.067) 0.000 0.068 + 244 (0.028) 0.000 0.027 + 220 (0.031) 0.000 0.031 + 228 (0.015) 0.000 0.014 + 224 (0.021) 0.000 0.020 + 236 (0.018) 0.000 0.017 + 226 (0.008) 0.000 0.007 + 246 (0.008) 0.000 0.007 + +Locus 21 : Sat3 +25 alleles +1.1% missing data + 169 (0.114) 0.458 0.116 + 175 (0.080) 0.040 0.081 + 179 (0.068) 0.000 0.070 + 165 (0.062) 0.268 0.062 + 167 (0.033) 0.000 0.033 + 177 (0.036) 0.204 0.034 + 170 (0.039) 0.000 0.040 + 173 (0.086) 0.003 0.087 + 171 (0.036) 0.000 0.036 + 183 (0.033) 0.000 0.033 + 178 (0.042) 0.000 0.043 + 181 (0.072) 0.020 0.073 + 163 (0.030) 0.000 0.030 + 174 (0.030) 0.000 0.030 + 185 (0.008) 0.004 0.006 + 187 (0.008) 0.001 0.006 + 168 (0.030) 0.000 0.030 + 164 (0.049) 0.000 0.050 + 162 (0.021) 0.000 0.020 + 166 (0.024) 0.000 0.023 + 160 (0.011) 0.000 0.010 + 172 (0.017) 0.000 0.017 + 180 (0.020) 0.000 0.020 + 176 (0.024) 0.000 0.023 + 158 (0.027) 0.000 0.027 + +Locus 22 : Sat4 +23 alleles +5.8% missing data + 209 (0.147) 0.266 0.151 + 252 (0.033) 0.238 0.031 + 255 (0.090) 0.115 0.091 + 253 (0.041) 0.308 0.040 + 239 (0.192) 0.046 0.200 + 241 (0.074) 0.000 0.077 + 245 (0.021) 0.000 0.020 + 251 (0.049) 0.008 0.049 + 235 (0.052) 0.000 0.054 + 249 (0.040) 0.001 0.040 + 234 (0.024) 0.000 0.023 + 243 (0.049) 0.000 0.050 + 261 (0.014) 0.000 0.013 + 247 (0.011) 0.000 0.010 + 233 (0.011) 0.000 0.010 + 257 (0.011) 0.003 0.009 + 248 (0.016) 0.004 0.013 + 254 (0.043) 0.002 0.043 + 208 (0.011) 0.007 0.009 + 250 (0.030) 0.000 0.030 + 246 (0.021) 0.000 0.020 + 256 (0.008) 0.000 0.007 + 211 (0.011) 0.000 0.010 + +Locus 23 : Sat5 +19 alleles +6.0% missing data + 246 (0.028) 0.655 0.026 + 250 (0.040) 0.033 0.039 + 224 (0.152) 0.063 0.155 + 252 (0.049) 0.015 0.047 + 248 (0.012) 0.217 0.010 + 230 (0.091) 0.000 0.094 + 220 (0.027) 0.000 0.027 + 234 (0.030) 0.000 0.030 + 238 (0.037) 0.000 0.037 + 228 (0.184) 0.008 0.189 + 240 (0.056) 0.000 0.057 + 222 (0.030) 0.000 0.030 + 236 (0.011) 0.000 0.010 + 232 (0.065) 0.000 0.067 + 216 (0.046) 0.000 0.047 + 226 (0.076) 0.001 0.077 + 254 (0.024) 0.000 0.023 + 242 (0.025) 0.001 0.023 + 244 (0.017) 0.007 0.014 + +Locus 24 : Sat7 +16 alleles +1.5% missing data + 205 (0.062) 0.143 0.061 + 216 (0.137) 0.207 0.138 + 204 (0.013) 0.289 0.011 + 214 (0.157) 0.049 0.159 + 212 (0.085) 0.303 0.084 + 208 (0.127) 0.000 0.131 + 210 (0.161) 0.004 0.165 + 196 (0.083) 0.000 0.085 + 206 (0.076) 0.000 0.078 + 220 (0.008) 0.000 0.007 + 203 (0.015) 0.000 0.014 + 200 (0.008) 0.000 0.007 + 202 (0.012) 0.000 0.011 + 207 (0.009) 0.002 0.006 + 218 (0.029) 0.000 0.028 + 198 (0.015) 0.000 0.014 + +Locus 25 : Sat8 +26 alleles +0.7% missing data + 157 (0.012) 0.461 0.009 + 177 (0.079) 0.361 0.079 + 173 (0.080) 0.000 0.083 + 170 (0.008) 0.000 0.006 + 181 (0.040) 0.000 0.040 + 175 (0.036) 0.000 0.037 + 183 (0.040) 0.000 0.040 + 185 (0.011) 0.000 0.010 + 189 (0.018) 0.000 0.017 + 161 (0.386) 0.176 0.401 + 169 (0.014) 0.000 0.013 + 193 (0.008) 0.000 0.007 + 163 (0.039) 0.000 0.040 + 165 (0.027) 0.000 0.027 + 195 (0.011) 0.000 0.010 + 167 (0.034) 0.001 0.033 + 179 (0.033) 0.000 0.033 + 164 (0.018) 0.000 0.017 + 166 (0.011) 0.000 0.010 + 187 (0.017) 0.000 0.017 + 171 (0.021) 0.000 0.020 + 147 (0.008) 0.000 0.007 + 168 (0.017) 0.000 0.017 + 159 (0.014) 0.000 0.013 + 155 (0.008) 0.000 0.006 + 180 (0.011) 0.000 0.010 + +Locus 26 : mOC182 +17 alleles +11.4% missing data + 112 (0.020) 0.000 0.019 + 108 (0.037) 0.000 0.037 + 98 (0.103) 0.004 0.103 + 100 (0.129) 0.395 0.129 + 104 (0.050) 0.000 0.051 + 110 (0.037) 0.000 0.037 + 106 (0.073) 0.000 0.074 + 102 (0.082) 0.000 0.083 + 114 (0.011) 0.000 0.009 + 94 (0.028) 0.000 0.028 + 96 (0.038) 0.001 0.037 + 90 (0.046) 0.000 0.046 + 113 (0.080) 0.474 0.079 + 111 (0.057) 0.123 0.055 + 115 (0.091) 0.001 0.092 + 109 (0.104) 0.000 0.107 + 116 (0.015) 0.000 0.014 + +Locus 27 : mOC185 +9 alleles +5.8% missing data + 166 (0.631) 0.041 0.643 + 170 (0.165) 0.241 0.164 + 176 (0.048) 0.011 0.046 + 175 (0.012) 0.701 0.009 + 172 (0.027) 0.000 0.026 + 164 (0.068) 0.007 0.066 + 174 (0.016) 0.000 0.015 + 168 (0.023) 0.000 0.022 + 162 (0.009) 0.000 0.007 + +Locus 28 : mOC259 +26 alleles +1.3% missing data + 187 (0.064) 0.512 0.064 + 191 (0.015) 0.003 0.013 + 189 (0.074) 0.199 0.074 + 183 (0.073) 0.030 0.074 + 175 (0.075) 0.000 0.079 + 177 (0.057) 0.000 0.059 + 185 (0.215) 0.075 0.224 + 181 (0.059) 0.038 0.059 + 173 (0.080) 0.137 0.081 + 182 (0.023) 0.000 0.023 + 174 (0.011) 0.000 0.010 + 186 (0.017) 0.000 0.016 + 190 (0.017) 0.000 0.016 + 192 (0.008) 0.000 0.007 + 184 (0.042) 0.001 0.042 + 197 (0.008) 0.000 0.006 + 196 (0.014) 0.000 0.013 + 199 (0.032) 0.000 0.033 + 179 (0.051) 0.000 0.053 + 178 (0.011) 0.000 0.010 + 180 (0.008) 0.000 0.006 + 171 (0.011) 0.000 0.010 + 193 (0.012) 0.004 0.009 + 195 (0.008) 0.000 0.006 + 176 (0.008) 0.000 0.006 + 168 (0.008) 0.000 0.006 + +Locus 29 : mOC313 +16 alleles +7.4% missing data + 239 (0.093) 0.272 0.092 + 249 (0.136) 0.020 0.138 + 255 (0.116) 0.421 0.116 + 251 (0.044) 0.147 0.042 + 240 (0.005) 0.000 0.004 + 241 (0.119) 0.135 0.120 + 245 (0.081) 0.000 0.083 + 264 (0.029) 0.000 0.029 + 237 (0.029) 0.000 0.029 + 247 (0.045) 0.000 0.045 + 257 (0.081) 0.004 0.081 + 243 (0.093) 0.000 0.095 + 259 (0.014) 0.000 0.012 + 253 (0.092) 0.001 0.094 + 250 (0.010) 0.000 0.008 + 266 (0.014) 0.000 0.012 + +Locus 30 : mOC40 +16 alleles +0.7% missing data + 207 (0.013) 0.493 0.010 + 217 (0.142) 0.162 0.143 + 221 (0.205) 0.001 0.213 + 219 (0.134) 0.193 0.135 + 223 (0.105) 0.002 0.106 + 225 (0.096) 0.071 0.096 + 213 (0.014) 0.000 0.013 + 215 (0.035) 0.000 0.035 + 229 (0.023) 0.000 0.022 + 211 (0.017) 0.000 0.016 + 227 (0.110) 0.078 0.110 + 201 (0.020) 0.000 0.019 + 231 (0.026) 0.000 0.025 + 235 (0.014) 0.000 0.013 + 233 (0.026) 0.000 0.025 + 209 (0.020) 0.000 0.019 + +Locus 31 : EDNRA +11 alleles +1.8% missing data + 247 (0.129) 0.413 0.127 + 249 (0.032) 0.584 0.028 + 239 (0.046) 0.000 0.045 + 235 (0.331) 0.001 0.338 + 251 (0.008) 0.000 0.007 + 233 (0.026) 0.000 0.025 + 243 (0.066) 0.000 0.066 + 245 (0.121) 0.001 0.122 + 232 (0.019) 0.000 0.017 + 237 (0.063) 0.000 0.063 + 241 (0.158) 0.000 0.161 + +Locus 32 : GPR64 +9 alleles +22.1% missing data + 141 (0.056) 0.016 0.053 + 137 (0.270) 0.025 0.272 + 129 (0.120) 0.955 0.117 + 131 (0.106) 0.000 0.108 + 135 (0.124) 0.000 0.125 + 139 (0.199) 0.001 0.203 + 125 (0.014) 0.000 0.013 + 133 (0.072) 0.003 0.071 + 123 (0.040) 0.000 0.039 + +Locus 33 : KLH13 +11 alleles +20.1% missing data + 251 (0.015) 0.187 0.012 + 255 (0.241) 0.098 0.244 + 263 (0.104) 0.023 0.104 + 257 (0.082) 0.251 0.081 + 265 (0.101) 0.300 0.100 + 259 (0.102) 0.001 0.104 + 261 (0.156) 0.000 0.161 + 249 (0.036) 0.000 0.036 + 253 (0.087) 0.001 0.088 + 267 (0.054) 0.139 0.051 + 245 (0.021) 0.000 0.020 + +Locus 34 : Proc +12 alleles +4.0% missing data + 117 (0.163) 0.016 0.166 + 133 (0.016) 0.128 0.013 + 119 (0.155) 0.020 0.157 + 115 (0.047) 0.259 0.045 + 127 (0.134) 0.531 0.134 + 121 (0.119) 0.025 0.119 + 129 (0.098) 0.019 0.097 + 123 (0.120) 0.000 0.123 + 125 (0.078) 0.000 0.080 + 131 (0.037) 0.001 0.036 + 109 (0.011) 0.000 0.010 + 135 (0.021) 0.000 0.020 + +Locus 35 : HPRT +23 alleles +21.3% missing data + 167 (0.050) 0.461 0.048 + 157 (0.070) 0.292 0.069 + 153 (0.020) 0.133 0.017 + 161 (0.056) 0.000 0.058 + 163 (0.096) 0.065 0.097 + 165 (0.120) 0.040 0.122 + 139 (0.017) 0.000 0.017 + 141 (0.033) 0.000 0.033 + 143 (0.064) 0.000 0.066 + 135 (0.009) 0.000 0.008 + 145 (0.072) 0.000 0.074 + 171 (0.025) 0.000 0.025 + 159 (0.060) 0.000 0.062 + 148 (0.029) 0.000 0.029 + 144 (0.017) 0.000 0.016 + 155 (0.021) 0.000 0.021 + 147 (0.060) 0.000 0.062 + 149 (0.029) 0.000 0.029 + 169 (0.082) 0.007 0.083 + 137 (0.013) 0.000 0.012 + 179 (0.009) 0.000 0.008 + 151 (0.017) 0.000 0.017 + 146 (0.029) 0.000 0.029 + +Locus 36 : mc342 +18 alleles +1.5% missing data + 192 (0.010) 0.307 0.008 + 194 (0.023) 0.040 0.020 + 190 (0.033) 0.445 0.030 + 188 (0.088) 0.050 0.088 + 196 (0.016) 0.039 0.013 + 172 (0.170) 0.015 0.174 + 178 (0.055) 0.000 0.056 + 176 (0.070) 0.000 0.072 + 180 (0.073) 0.000 0.075 + 170 (0.084) 0.084 0.084 + 182 (0.058) 0.000 0.059 + 184 (0.093) 0.001 0.095 + 174 (0.033) 0.000 0.033 + 164 (0.014) 0.000 0.013 + 166 (0.045) 0.000 0.046 + 186 (0.091) 0.018 0.092 + 177 (0.017) 0.000 0.016 + 183 (0.027) 0.000 0.026 + +Locus 37 : AMOT +9 alleles +22.7% missing data + 205 (0.147) 0.513 0.147 + 211 (0.238) 0.163 0.240 + 221 (0.026) 0.195 0.023 + 215 (0.145) 0.084 0.145 + 207 (0.184) 0.042 0.185 + 213 (0.119) 0.000 0.122 + 217 (0.030) 0.000 0.029 + 219 (0.027) 0.001 0.025 + 209 (0.083) 0.000 0.084 + +Locus 38 : EXT +18 alleles +15.4% missing data + 154 (0.414) 0.159 0.426 + 184 (0.022) 0.663 0.019 + 158 (0.166) 0.169 0.168 + 166 (0.046) 0.000 0.047 + 150 (0.039) 0.000 0.039 + 156 (0.020) 0.000 0.019 + 164 (0.009) 0.000 0.008 + 168 (0.009) 0.000 0.008 + 172 (0.009) 0.000 0.008 + 180 (0.057) 0.000 0.058 + 190 (0.017) 0.000 0.016 + 160 (0.019) 0.002 0.017 + 162 (0.097) 0.000 0.100 + 182 (0.024) 0.000 0.023 + 176 (0.013) 0.000 0.012 + 178 (0.017) 0.000 0.016 + 186 (0.014) 0.007 0.011 + 146 (0.009) 0.000 0.008 + +Locus 39 : CRYL +16 alleles +13.2% missing data + 196 (0.193) 0.506 0.195 + 202 (0.284) 0.395 0.289 + 206 (0.072) 0.071 0.070 + 198 (0.074) 0.001 0.075 + 204 (0.052) 0.000 0.053 + 192 (0.038) 0.000 0.038 + 208 (0.027) 0.026 0.024 + 190 (0.045) 0.000 0.045 + 194 (0.067) 0.000 0.068 + 200 (0.070) 0.000 0.072 + 224 (0.009) 0.000 0.007 + 188 (0.013) 0.000 0.011 + 214 (0.009) 0.000 0.007 + 210 (0.013) 0.000 0.011 + 212 (0.023) 0.000 0.023 + 184 (0.013) 0.000 0.011 + +Values of parameters used in structure: +DATAFILE=C:\Users\jota.blanco\Desktop\SAmer_reduc\OC_SA2\project_data, OUTFILE=C:\Users\jota.blanco\Desktop\SAmer_reduc\OC_SA2\pop250y500mil\Results\pop250y500mil_run_4, NUMINDS=551, NUMLOCI=39, MISSING=-9, LABEL=1, POPDATA=1, POPFLAG=1, PHENOTYPE=0, EXTRACOLS=0, MAXPOPS=2, BURNIN=250000, NUMREPS=500000, USEPOPINFO=0, INFERALPHA=1, INFERLAMBDA=0, POPSPECIFICLAMBDA=0, POPALPHAS=1, COMPUTEPROB=1, NOADMIX=0, ADMBURNIN=2500, UPDATEFREQ=1, PRINTLIKES=0, INTERMEDSAVE=0, PRINTKLD=0, PRINTNET=0, PRINTLAMBDA=0, ANCESTDIST=1, NUMBOXES=1000, ANCESTPINT=0.90000, GENSBACK=2, MIGRPRIOR=0.05000, PRINTQHAT=0, PRINTQSUM=0, ALPHA=1.0000, FREQSCORR=1, FPRIORMEAN=0.0100, FPRIORSD=0.0500, ONEFST=0, LAMBDA=1.0000, UNIFPRIORALPHA=1, ALPHAMAX=10.0000, ALPHAPRIORA=1.0000, ALPHAPRIORB=2.0000, ALPHAPROPSD=0.0250, STARTATPOPINFO=0, RANDOMIZE=0, LINKAGE=0, METROFREQ=10, REPORTHITRATE=0, MARKOVPHASE=-1, PHASED=0, PLOIDY=2, PHASEINFO=0 LOCPRIOR=0, LOCPRIORINIT=1.000000, LOCDATA=0, LOCISPOP=0, LOCPRIORSTEP=0.100000, MAXLOCPRIOR=20.000000, SEED=5690, +[STRAT parameters]: NUMSIMSTATS=1000, PHENOTYPECOL=-9, POOLFREQ=10, LOCUSxONLY=0, EMERROR=0.00100, MISSINGPHENO=-9, \ No newline at end of file diff --git a/inst/files/structure-ci/structure_5_f b/inst/files/structure-ci/structure_5_f new file mode 100644 index 0000000..baed254 --- /dev/null +++ b/inst/files/structure-ci/structure_5_f @@ -0,0 +1,1395 @@ + + +---------------------------------------------------- +STRUCTURE by Pritchard, Stephens and Donnelly (2000) + and Falush, Stephens and Pritchard (2003) + Code by Pritchard, Falush and Hubisz + Version 2.3.4 (Jul 2012) +---------------------------------------------------- + + + +Command line arguments: bin\structure -m C:\Users\jota.blanco\Desktop\SAmer_reduc\OC_SA2\pop250y500mil\mainparams -e C:\Users\jota.blanco\Desktop\SAmer_reduc\OC_SA2\pop250y500mil\extraparams +Input File: C:\Users\jota.blanco\Desktop\SAmer_reduc\OC_SA2\project_data + +Run parameters: + 551 individuals + 39 loci + 2 populations assumed + 250000 Burn-in period + 500000 Reps +RANDOMIZE turned off + + +-------------------------------------------- +Proportion of membership of each pre-defined + population in each of the 2 clusters + +Given Inferred Clusters Number of + Pop 1 2 Individuals + + 1: 0.148 0.852 49 + 2: 0.985 0.015 52 + 3: 0.006 0.994 326 + 4: 0.567 0.433 85 + 5: 0.888 0.112 39 +-------------------------------------------- + +Allele-freq. divergence among pops (Net nucleotide distance), +computed using point estimates of P. + + 1 2 + 1 - 0.1573 + 2 0.1573 - + +Average distances (expected heterozygosity) between individuals in same cluster: +cluster 1 : 0.8554 +cluster 2 : 0.6074 + +-------------------------------------------- +Estimated Ln Prob of Data = -68314.6 +Mean value of ln likelihood = -61129.6 +Variance of ln likelihood = 14369.9 + +Mean value of alpha_1 = 0.0828 +Mean value of alpha_2 = 0.2417 + +Mean value of Fst_1 = 0.0011 +Mean value of Fst_2 = 0.3851 +Allele frequencies updated using individuals with POPFLAG=1 ONLY. + + +Inferred ancestry of individuals: + Label (%Miss) Pop: Inferred clusters (and 90% probability intervals) + 1 ArgAL-01 (20) 1 : 0.216 0.784 (0.093,0.360) (0.640,0.907) + 2 ArgAL-02 (25) 1 : 0.170 0.830 (0.056,0.310) (0.690,0.944) + 3 ArgAL-03 (17) 1 : 0.265 0.735 (0.137,0.412) (0.588,0.863) + 4 ArgAL-06 (0) 1 : 0.406 0.594 (0.270,0.550) (0.450,0.730) + 5 ArgAL-08 (17) 1 : 0.252 0.748 (0.138,0.382) (0.618,0.862) + 6 ArgAL-09 (23) 1 : 0.257 0.743 (0.128,0.404) (0.596,0.872) + 7 ArgAL-11 (25) 1 : 0.378 0.622 (0.215,0.553) (0.447,0.785) + 8 ArgAL-12 (20) 1 : 0.339 0.661 (0.196,0.495) (0.505,0.804) + 9 ArgAL-13 (5) 1 : 0.359 0.641 (0.232,0.497) (0.503,0.768) + 10 ArgAL-14 (25) 1 : 0.540 0.460 (0.367,0.716) (0.284,0.633) + 11 ArgAL-15 (5) 1 : 0.441 0.559 (0.302,0.587) (0.413,0.698) + 12 ArgRT-01 (2) 1 : 0.116 0.884 (0.044,0.207) (0.793,0.956) + 13 ArgRT-02 (12) 1 : 0.005 0.995 (0.000,0.029) (0.971,1.000) + 14 ArgRT-03 (0) 1 : 0.075 0.925 (0.009,0.164) (0.836,0.991) + 15 ArgRT-04 (10) 1 : 0.136 0.864 (0.056,0.235) (0.765,0.944) + 16 ArgRT-05 (10) 1 : 0.026 0.974 (0.000,0.096) (0.904,1.000) + 17 ArgRT-06 (12) 1 : 0.015 0.985 (0.000,0.072) (0.928,1.000) + 18 ArgRT-07 (5) 1 : 0.152 0.848 (0.064,0.260) (0.740,0.936) + 19 ArgRT-08 (0) 1 : 0.039 0.961 (0.000,0.124) (0.876,1.000) + 20 ArgRT-09 (5) 1 : 0.100 0.900 (0.000,0.216) (0.784,1.000) + 21 ArgRT-10 (2) 1 : 0.057 0.943 (0.000,0.158) (0.842,1.000) + 22 ArgRT-11 (0) 1 : 0.012 0.988 (0.000,0.058) (0.942,1.000) + 23 ArgRT-12 (5) 1 : 0.003 0.997 (0.000,0.020) (0.980,1.000) + 24 ArgRT-13 (2) 1 : 0.037 0.963 (0.002,0.098) (0.902,0.998) + 25 ArgRT-14 (0) 1 : 0.040 0.960 (0.000,0.119) (0.881,1.000) + 26 ArgRT-15 (2) 1 : 0.113 0.887 (0.031,0.213) (0.787,0.969) + 27 ArgTF-01 (23) 1 : 0.093 0.907 (0.027,0.183) (0.817,0.973) + 28 ArgTF-02 (12) 1 : 0.099 0.901 (0.033,0.188) (0.812,0.967) + 29 ArgTF-03 (23) 1 : 0.053 0.947 (0.008,0.125) (0.875,0.992) + 30 ArgTF-04 (25) 1 : 0.080 0.920 (0.022,0.163) (0.837,0.978) + 31 ArgTF-06 (2) 1 : 0.117 0.883 (0.046,0.208) (0.792,0.954) + 32 ArgTF-07 (25) 1 : 0.140 0.860 (0.056,0.248) (0.752,0.944) + 33 ArgTF-08 (20) 1 : 0.136 0.864 (0.053,0.241) (0.759,0.947) + 34 ArgTF-09 (0) 1 : 0.107 0.893 (0.037,0.197) (0.803,0.963) + 35 ArgTF-10 (7) 1 : 0.069 0.931 (0.016,0.143) (0.857,0.984) + 36 ArgTF-11 (17) 1 : 0.012 0.988 (0.000,0.060) (0.940,1.000) + 37 ArgTF-12 (2) 1 : 0.119 0.881 (0.046,0.214) (0.786,0.954) + 38 ArgTF-13 (10) 1 : 0.073 0.927 (0.015,0.157) (0.843,0.985) + 39 ArgTF-14 (2) 1 : 0.113 0.887 (0.043,0.205) (0.795,0.957) + 40 ArgTF-15 (12) 1 : 0.133 0.867 (0.055,0.230) (0.770,0.945) + 41 FALK01 (0) 1 : 0.211 0.789 (0.114,0.323) (0.677,0.886) + 42 FALK04 (0) 1 : 0.126 0.874 (0.052,0.220) (0.780,0.948) + 43 FALK06 (0) 1 : 0.134 0.866 (0.056,0.232) (0.768,0.944) + 44 FALK07 (2) 1 : 0.174 0.826 (0.086,0.280) (0.720,0.914) + 45 FALK08 (2) 1 : 0.127 0.873 (0.052,0.224) (0.776,0.948) + 46 FALK09 (5) 1 : 0.183 0.817 (0.092,0.293) (0.707,0.908) + 47 FALK10 (2) 1 : 0.186 0.814 (0.093,0.296) (0.704,0.907) + 48 FALK11 (0) 1 : 0.207 0.793 (0.111,0.318) (0.682,0.889) + 49 FALK14 (2) 1 : 0.030 0.970 (0.000,0.088) (0.912,1.000) + 50 DON-1 (12) 2 : 0.992 0.008 (0.961,1.000) (0.000,0.039) + 51 DON-3 (5) 2 : 0.991 0.009 (0.956,1.000) (0.000,0.044) + 52 DON-5 (20) 2 : 0.994 0.006 (0.968,1.000) (0.000,0.032) + 53 DON-5722 (10) 2 : 0.982 0.018 (0.924,1.000) (0.000,0.076) + 54 DON-5785 (23) 2 : 0.984 0.016 (0.927,1.000) (0.000,0.073) + 55 DON-5819 (7) 2 : 0.993 0.007 (0.964,1.000) (0.000,0.036) + 56 DON-5930 (7) 2 : 0.985 0.015 (0.928,1.000) (0.000,0.072) + 57 DON-6116 (33) 2 : 0.988 0.012 (0.939,1.000) (0.000,0.061) + 58 DON-6143 (12) 2 : 0.994 0.006 (0.970,1.000) (0.000,0.030) + 59 DON-6241 (15) 2 : 0.980 0.020 (0.908,1.000) (0.000,0.092) + 60 DON-6281 (2) 2 : 0.986 0.014 (0.939,1.000) (0.000,0.061) + 61 DON-7 (12) 2 : 0.988 0.012 (0.942,1.000) (0.000,0.058) + 62 DON-8 (5) 2 : 0.995 0.005 (0.974,1.000) (0.000,0.026) + 63 HUE-1 (5) 2 : 0.994 0.006 (0.970,1.000) (0.000,0.030) + 64 HUE-34 (0) 2 : 0.984 0.016 (0.926,1.000) (0.000,0.074) + 65 HUE-4224 (15) 2 : 0.968 0.032 (0.873,1.000) (0.000,0.127) + 66 HUE-4225 (28) 2 : 0.992 0.008 (0.958,1.000) (0.000,0.042) + 67 HUE-4232 (25) 2 : 0.986 0.014 (0.934,1.000) (0.000,0.066) + 68 HUE-4235 (20) 2 : 0.991 0.009 (0.955,1.000) (0.000,0.045) + 69 HUE-4236 (12) 2 : 0.989 0.011 (0.944,1.000) (0.000,0.056) + 70 HUE-4239 (17) 2 : 0.965 0.035 (0.881,1.000) (0.000,0.119) + 71 HUE-4250 (30) 2 : 0.968 0.032 (0.870,1.000) (0.000,0.130) + 72 HUE-4258 (25) 2 : 0.993 0.007 (0.967,1.000) (0.000,0.033) + 73 HUE-4259 (5) 2 : 0.990 0.010 (0.951,1.000) (0.000,0.049) + 74 HUE-4260 (2) 2 : 0.990 0.010 (0.950,1.000) (0.000,0.050) + 75 HUE-53 (2) 2 : 0.964 0.036 (0.881,1.000) (0.000,0.119) + 76 LLO-11 (25) 2 : 0.988 0.012 (0.943,1.000) (0.000,0.057) + 77 LLO-14 (30) 2 : 0.959 0.041 (0.865,1.000) (0.000,0.135) + 78 LLO-16 (17) 2 : 0.990 0.010 (0.954,1.000) (0.000,0.046) + 79 LLO-17 (5) 2 : 0.993 0.007 (0.963,1.000) (0.000,0.037) + 80 LLO-18 (10) 2 : 0.981 0.019 (0.917,1.000) (0.000,0.083) + 81 LLO-19 (5) 2 : 0.993 0.007 (0.966,1.000) (0.000,0.034) + 82 LLO-20 (15) 2 : 0.960 0.040 (0.879,1.000) (0.000,0.121) + 83 LLO-24 (10) 2 : 0.984 0.016 (0.927,1.000) (0.000,0.073) + 84 LLO-28 (15) 2 : 0.979 0.021 (0.910,1.000) (0.000,0.090) + 85 LLO-29 (10) 2 : 0.995 0.005 (0.974,1.000) (0.000,0.026) + 86 LLO-31 (7) 2 : 0.994 0.006 (0.971,1.000) (0.000,0.029) + 87 LLO-7 (5) 2 : 0.985 0.015 (0.930,1.000) (0.000,0.070) + 88 LLO-8 (7) 2 : 0.981 0.019 (0.915,1.000) (0.000,0.085) + 89 SAN-10 (7) 2 : 0.992 0.008 (0.959,1.000) (0.000,0.041) + 90 SAN-14 (5) 2 : 0.993 0.007 (0.967,1.000) (0.000,0.033) + 91 SAN-15 (5) 2 : 0.994 0.006 (0.971,1.000) (0.000,0.029) + 92 SAN-17 (2) 2 : 0.990 0.010 (0.951,1.000) (0.000,0.049) + 93 SAN-18 (0) 2 : 0.993 0.007 (0.965,1.000) (0.000,0.035) + 94 SAN-20 (7) 2 : 0.941 0.059 (0.832,1.000) (0.000,0.168) + 95 SAN-21 (5) 2 : 0.992 0.008 (0.962,1.000) (0.000,0.038) + 96 SAN-23 (7) 2 : 0.977 0.023 (0.900,1.000) (0.000,0.100) + 97 SAN-3 (2) 2 : 0.991 0.009 (0.957,1.000) (0.000,0.043) + 98 SAN-5 (10) 2 : 0.993 0.007 (0.967,1.000) (0.000,0.033) + 99 SAN-6 (12) 2 : 0.993 0.007 (0.968,1.000) (0.000,0.032) +100 SAN-7 (5) 2 : 0.992 0.008 (0.961,1.000) (0.000,0.039) +101 SAN-8 (7) 2 : 0.992 0.008 (0.960,1.000) (0.000,0.040) +102 AN_AT01 (5) 3 : 0.006 0.994 (0.000,0.038) (0.962,1.000) +103 AN_AT02 (10) 3 : 0.026 0.974 (0.000,0.104) (0.896,1.000) +104 AN_AT03 (10) 3 : 0.002 0.998 (0.000,0.014) (0.986,1.000) +105 AN_AT06 (7) 3 : 0.003 0.997 (0.000,0.021) (0.979,1.000) +106 AN_AT07 (5) 3 : 0.003 0.997 (0.000,0.021) (0.979,1.000) +107 AN_AT08 (2) 3 : 0.005 0.995 (0.000,0.030) (0.970,1.000) +108 AN_AT09 (2) 3 : 0.002 0.998 (0.000,0.011) (0.989,1.000) +109 AN_AT10 (2) 3 : 0.003 0.997 (0.000,0.016) (0.984,1.000) +110 AN_AT28 (2) 3 : 0.015 0.985 (0.000,0.069) (0.931,1.000) +111 AN_AT29 (5) 3 : 0.051 0.949 (0.000,0.141) (0.859,1.000) +112 AN_AT30 (7) 3 : 0.002 0.998 (0.000,0.014) (0.986,1.000) +113 AN_AT31 (2) 3 : 0.051 0.949 (0.000,0.130) (0.870,1.000) +114 AN_AT32 (2) 3 : 0.033 0.967 (0.000,0.117) (0.883,1.000) +115 AN_AT33 (5) 3 : 0.006 0.994 (0.000,0.038) (0.962,1.000) +116 AN_AT34 (2) 3 : 0.003 0.997 (0.000,0.017) (0.983,1.000) +117 AN_AT35 (5) 3 : 0.004 0.996 (0.000,0.025) (0.975,1.000) +118 AN_AT46 (2) 3 : 0.012 0.988 (0.000,0.062) (0.938,1.000) +119 AN_AT47 (2) 3 : 0.003 0.997 (0.000,0.016) (0.984,1.000) +120 AN_AT48 (2) 3 : 0.005 0.995 (0.000,0.035) (0.965,1.000) +121 AN_AT49 (5) 3 : 0.003 0.997 (0.000,0.018) (0.982,1.000) +122 AN_AT50 (7) 3 : 0.041 0.959 (0.000,0.141) (0.859,1.000) +123 AN_AT51 (2) 3 : 0.002 0.998 (0.000,0.012) (0.988,1.000) +124 AN_AT52 (12) 3 : 0.004 0.996 (0.000,0.024) (0.976,1.000) +125 AN_AT53 (5) 3 : 0.003 0.997 (0.000,0.020) (0.980,1.000) +126 BH_A22 (0) 3 : 0.002 0.998 (0.000,0.011) (0.989,1.000) +127 BH_A23 (0) 3 : 0.002 0.998 (0.000,0.011) (0.989,1.000) +128 BH_A24 (0) 3 : 0.002 0.998 (0.000,0.011) (0.989,1.000) +129 BH_A29 (5) 3 : 0.002 0.998 (0.000,0.011) (0.989,1.000) +130 BH_A30 (5) 3 : 0.003 0.997 (0.000,0.015) (0.985,1.000) +131 BH_A31 (2) 3 : 0.002 0.998 (0.000,0.011) (0.989,1.000) +132 BH_A32 (17) 3 : 0.004 0.996 (0.000,0.023) (0.977,1.000) +133 BH_A35 (5) 3 : 0.002 0.998 (0.000,0.015) (0.985,1.000) +134 BH_A36 (0) 3 : 0.002 0.998 (0.000,0.011) (0.989,1.000) +135 BH_A37 (0) 3 : 0.002 0.998 (0.000,0.012) (0.988,1.000) +136 BH_A38 (6) 3 : 0.052 0.948 (0.000,0.148) (0.852,1.000) +137 BH_A39 (7) 3 : 0.002 0.998 (0.000,0.014) (0.986,1.000) +138 BH_A41 (0) 3 : 0.002 0.998 (0.000,0.013) (0.987,1.000) +139 BH_AT01 (5) 3 : 0.002 0.998 (0.000,0.015) (0.985,1.000) +140 BH_AT02 (7) 3 : 0.002 0.998 (0.000,0.015) (0.985,1.000) +141 BH_AT03 (5) 3 : 0.002 0.998 (0.000,0.015) (0.985,1.000) +142 BH_AT04 (2) 3 : 0.018 0.982 (0.000,0.074) (0.926,1.000) +143 BH_ES1 (8) 3 : 0.002 0.998 (0.000,0.013) (0.987,1.000) +144 BH_SP1 (8) 3 : 0.002 0.998 (0.000,0.012) (0.988,1.000) +145 BH_T7 (24) 3 : 0.005 0.995 (0.000,0.031) (0.969,1.000) +146 BH_T8 (2) 3 : 0.003 0.997 (0.000,0.018) (0.982,1.000) +147 CH_A207 (10) 3 : 0.002 0.998 (0.000,0.014) (0.986,1.000) +148 CH_A209 (2) 3 : 0.004 0.996 (0.000,0.022) (0.978,1.000) +149 CH_A213 (2) 3 : 0.003 0.997 (0.000,0.021) (0.979,1.000) +150 CH_A216 (5) 3 : 0.003 0.997 (0.000,0.018) (0.982,1.000) +151 CH_A238 (5) 3 : 0.017 0.983 (0.000,0.073) (0.927,1.000) +152 CH_A243 (7) 3 : 0.006 0.994 (0.000,0.036) (0.964,1.000) +153 CH_A260 (5) 3 : 0.008 0.992 (0.000,0.050) (0.950,1.000) +154 CH_A258 (15) 3 : 0.002 0.998 (0.000,0.014) (0.986,1.000) +155 CH_A274 (2) 3 : 0.005 0.995 (0.000,0.033) (0.967,1.000) +156 CH_A347 (7) 3 : 0.003 0.997 (0.000,0.017) (0.983,1.000) +157 CH_R13 (12) 3 : 0.004 0.996 (0.000,0.026) (0.974,1.000) +158 CH_R14 (7) 3 : 0.011 0.989 (0.000,0.059) (0.941,1.000) +159 CH_R17 (2) 3 : 0.002 0.998 (0.000,0.013) (0.987,1.000) +160 CH_R18 (5) 3 : 0.004 0.996 (0.000,0.027) (0.973,1.000) +161 CH_R19 (7) 3 : 0.003 0.997 (0.000,0.021) (0.979,1.000) +162 CH_R20 (8) 3 : 0.003 0.997 (0.000,0.016) (0.984,1.000) +163 CH_R21 (7) 3 : 0.004 0.996 (0.000,0.024) (0.976,1.000) +164 CH_R22 (7) 3 : 0.012 0.988 (0.000,0.075) (0.925,1.000) +165 CH_R23 (0) 3 : 0.002 0.998 (0.000,0.014) (0.986,1.000) +166 CH_R24 (0) 3 : 0.021 0.979 (0.000,0.087) (0.913,1.000) +167 AC_A214 (0) 3 : 0.002 0.998 (0.000,0.014) (0.986,1.000) +168 AC_A219 (10) 3 : 0.002 0.998 (0.000,0.015) (0.985,1.000) +169 AC_A240 (2) 3 : 0.002 0.998 (0.000,0.010) (0.990,1.000) +170 AC_A241 (5) 3 : 0.002 0.998 (0.000,0.010) (0.990,1.000) +171 AC_A250 (7) 3 : 0.002 0.998 (0.000,0.011) (0.989,1.000) +172 AC_A264 (7) 3 : 0.002 0.998 (0.000,0.011) (0.989,1.000) +173 AC_A267 (5) 3 : 0.002 0.998 (0.000,0.011) (0.989,1.000) +174 AC_A093 (7) 3 : 0.009 0.991 (0.000,0.043) (0.957,1.000) +175 AC_A094 (7) 3 : 0.002 0.998 (0.000,0.014) (0.986,1.000) +176 AC_A095 (2) 3 : 0.003 0.997 (0.000,0.021) (0.979,1.000) +177 AC_A096 (0) 3 : 0.002 0.998 (0.000,0.011) (0.989,1.000) +178 AC_A097 (10) 3 : 0.002 0.998 (0.000,0.012) (0.988,1.000) +179 AC_A099 (5) 3 : 0.002 0.998 (0.000,0.013) (0.987,1.000) +180 AC_A100 (7) 3 : 0.058 0.942 (0.004,0.132) (0.868,0.996) +181 AC_A101 (7) 3 : 0.003 0.997 (0.000,0.018) (0.982,1.000) +182 AC_A104 (5) 3 : 0.002 0.998 (0.000,0.013) (0.987,1.000) +183 AC_A105 (0) 3 : 0.002 0.998 (0.000,0.011) (0.989,1.000) +184 AC_A106 (5) 3 : 0.009 0.991 (0.000,0.053) (0.947,1.000) +185 AC_A110 (5) 3 : 0.002 0.998 (0.000,0.011) (0.989,1.000) +186 AC_A111 (2) 3 : 0.002 0.998 (0.000,0.011) (0.989,1.000) +187 AC_A112 (5) 3 : 0.002 0.998 (0.000,0.015) (0.985,1.000) +188 AC_A113 (0) 3 : 0.003 0.997 (0.000,0.020) (0.980,1.000) +189 AC_A114 (0) 3 : 0.008 0.992 (0.000,0.049) (0.951,1.000) +190 AC_AT03 (5) 3 : 0.002 0.998 (0.000,0.011) (0.989,1.000) +191 EN_A069 (0) 3 : 0.002 0.998 (0.000,0.013) (0.987,1.000) +192 EN_A070 (0) 3 : 0.002 0.998 (0.000,0.014) (0.986,1.000) +193 EN_A071 (0) 3 : 0.003 0.997 (0.000,0.016) (0.984,1.000) +194 EN_A074 (5) 3 : 0.002 0.998 (0.000,0.014) (0.986,1.000) +195 EN_A077 (12) 3 : 0.003 0.997 (0.000,0.015) (0.985,1.000) +196 EN_A078 (17) 3 : 0.003 0.997 (0.000,0.016) (0.984,1.000) +197 EN_A079 (0) 3 : 0.003 0.997 (0.000,0.016) (0.984,1.000) +198 EN_A080 (0) 3 : 0.003 0.997 (0.000,0.016) (0.984,1.000) +199 EN_A081 (5) 3 : 0.012 0.988 (0.000,0.065) (0.935,1.000) +200 EN_A083 (2) 3 : 0.002 0.998 (0.000,0.011) (0.989,1.000) +201 EN_A086 (0) 3 : 0.002 0.998 (0.000,0.013) (0.987,1.000) +202 EN_A087 (7) 3 : 0.002 0.998 (0.000,0.015) (0.985,1.000) +203 EN_A088 (20) 3 : 0.002 0.998 (0.000,0.014) (0.986,1.000) +204 EN_A089 (7) 3 : 0.002 0.998 (0.000,0.013) (0.987,1.000) +205 EN_A090 (5) 3 : 0.002 0.998 (0.000,0.015) (0.985,1.000) +206 EN_A091 (0) 3 : 0.003 0.997 (0.000,0.016) (0.984,1.000) +207 EN_A092 (5) 3 : 0.003 0.997 (0.000,0.022) (0.978,1.000) +208 EN_A205 (5) 3 : 0.003 0.997 (0.000,0.021) (0.979,1.000) +209 EN_A210 (5) 3 : 0.003 0.997 (0.000,0.020) (0.980,1.000) +210 EN_A218 (12) 3 : 0.004 0.996 (0.000,0.024) (0.976,1.000) +211 EN_A220 (0) 3 : 0.003 0.997 (0.000,0.015) (0.985,1.000) +212 EN_A228 (5) 3 : 0.016 0.984 (0.000,0.066) (0.934,1.000) +213 EN_A231 (0) 3 : 0.003 0.997 (0.000,0.017) (0.983,1.000) +214 EN_A234 (0) 3 : 0.003 0.997 (0.000,0.016) (0.984,1.000) +215 EN_A246 (0) 3 : 0.023 0.977 (0.000,0.088) (0.912,1.000) +216 AA_AT01 (5) 3 : 0.003 0.997 (0.000,0.021) (0.979,1.000) +217 AA_AT02 (0) 3 : 0.002 0.998 (0.000,0.012) (0.988,1.000) +218 AA_AT03 (7) 3 : 0.005 0.995 (0.000,0.030) (0.970,1.000) +219 AA_ES2 (5) 3 : 0.004 0.996 (0.000,0.027) (0.973,1.000) +220 AA_ES3 (5) 3 : 0.005 0.995 (0.000,0.030) (0.970,1.000) +221 AA_SP1 (2) 3 : 0.033 0.967 (0.000,0.117) (0.883,1.000) +222 AA_ES1 (2) 3 : 0.007 0.993 (0.000,0.043) (0.957,1.000) +223 AA_SP2 (5) 3 : 0.004 0.996 (0.000,0.026) (0.974,1.000) +224 FB_A001 (5) 3 : 0.004 0.996 (0.000,0.026) (0.974,1.000) +225 FB_A002 (7) 3 : 0.002 0.998 (0.000,0.013) (0.987,1.000) +226 FB_A005 (0) 3 : 0.003 0.997 (0.000,0.022) (0.978,1.000) +227 FB_A017 (17) 3 : 0.006 0.994 (0.000,0.038) (0.962,1.000) +228 FB_A020 (17) 3 : 0.003 0.997 (0.000,0.016) (0.984,1.000) +229 FB_A059 (17) 3 : 0.002 0.998 (0.000,0.015) (0.985,1.000) +230 FB_A060 (23) 3 : 0.004 0.996 (0.000,0.025) (0.975,1.000) +231 FB_T25 (7) 3 : 0.003 0.997 (0.000,0.018) (0.982,1.000) +232 FB_T27 (0) 3 : 0.003 0.997 (0.000,0.018) (0.982,1.000) +233 FB_T45 (2) 3 : 0.003 0.997 (0.000,0.019) (0.981,1.000) +234 FB_T46 (0) 3 : 0.003 0.997 (0.000,0.021) (0.979,1.000) +235 FB_T47 (2) 3 : 0.022 0.978 (0.000,0.086) (0.914,1.000) +236 FG_ES05 (7) 3 : 0.002 0.998 (0.000,0.012) (0.988,1.000) +237 FG_ES06 (7) 3 : 0.003 0.997 (0.000,0.019) (0.981,1.000) +238 FG_ES07 (2) 3 : 0.002 0.998 (0.000,0.012) (0.988,1.000) +239 FG_ES08 (15) 3 : 0.002 0.998 (0.000,0.012) (0.988,1.000) +240 FG_ES09 (11) 3 : 0.002 0.998 (0.000,0.015) (0.985,1.000) +241 FG_ES10 (0) 3 : 0.002 0.998 (0.000,0.012) (0.988,1.000) +242 FG_ES01 (2) 3 : 0.003 0.997 (0.000,0.022) (0.978,1.000) +243 FG_ES02 (2) 3 : 0.002 0.998 (0.000,0.010) (0.990,1.000) +244 FG_ES03 (5) 3 : 0.002 0.998 (0.000,0.015) (0.985,1.000) +245 FG_ES04 (5) 3 : 0.002 0.998 (0.000,0.014) (0.986,1.000) +246 FG_ES11 (0) 3 : 0.008 0.992 (0.000,0.041) (0.959,1.000) +247 FG_ES12 (7) 3 : 0.002 0.998 (0.000,0.011) (0.989,1.000) +248 FG_SP01 (5) 3 : 0.002 0.998 (0.000,0.013) (0.987,1.000) +249 FG_SP02 (5) 3 : 0.009 0.991 (0.000,0.050) (0.950,1.000) +250 FG_SP03 (0) 3 : 0.003 0.997 (0.000,0.016) (0.984,1.000) +251 FG_SP04 (7) 3 : 0.002 0.998 (0.000,0.014) (0.986,1.000) +252 FG_SP05 (7) 3 : 0.015 0.985 (0.000,0.066) (0.934,1.000) +253 FG_SP06 (7) 3 : 0.002 0.998 (0.000,0.011) (0.989,1.000) +254 FG_SP07 (5) 3 : 0.002 0.998 (0.000,0.011) (0.989,1.000) +255 FG_SP08 (8) 3 : 0.030 0.970 (0.000,0.102) (0.898,1.000) +256 FG_SP09 (20) 3 : 0.003 0.997 (0.000,0.015) (0.985,1.000) +257 FG_SP10 (2) 3 : 0.002 0.998 (0.000,0.013) (0.987,1.000) +258 FG_T31 (7) 3 : 0.002 0.998 (0.000,0.012) (0.988,1.000) +259 FG_T32 (0) 3 : 0.003 0.997 (0.000,0.020) (0.980,1.000) +260 FG_T52 (0) 3 : 0.009 0.991 (0.000,0.045) (0.955,1.000) +261 HG_H004 (2) 3 : 0.002 0.998 (0.000,0.014) (0.986,1.000) +262 HG_H006 (0) 3 : 0.003 0.997 (0.000,0.016) (0.984,1.000) +263 HG_H008 (2) 3 : 0.002 0.998 (0.000,0.015) (0.985,1.000) +264 HG_H211 (17) 3 : 0.004 0.996 (0.000,0.026) (0.974,1.000) +265 HG_H217 (0) 3 : 0.002 0.998 (0.000,0.013) (0.987,1.000) +266 HG_H235 (12) 3 : 0.007 0.993 (0.000,0.043) (0.957,1.000) +267 HG_H291 (7) 3 : 0.003 0.997 (0.000,0.018) (0.982,1.000) +268 HG_H293 (7) 3 : 0.002 0.998 (0.000,0.012) (0.988,1.000) +269 FL_H011 (7) 3 : 0.002 0.998 (0.000,0.013) (0.987,1.000) +270 FL_H012 (0) 3 : 0.002 0.998 (0.000,0.012) (0.988,1.000) +271 FL_H013 (5) 3 : 0.002 0.998 (0.000,0.011) (0.989,1.000) +272 FL_H014 (2) 3 : 0.002 0.998 (0.000,0.014) (0.986,1.000) +273 FL_H015 (7) 3 : 0.002 0.998 (0.000,0.013) (0.987,1.000) +274 FL_H016 (0) 3 : 0.002 0.998 (0.000,0.011) (0.989,1.000) +275 FL_H017 (8) 3 : 0.002 0.998 (0.000,0.011) (0.989,1.000) +276 FL_H018 (7) 3 : 0.002 0.998 (0.000,0.011) (0.989,1.000) +277 FL_H019 (5) 3 : 0.003 0.997 (0.000,0.017) (0.983,1.000) +278 FL_H020 (5) 3 : 0.002 0.998 (0.000,0.015) (0.985,1.000) +279 FL_H219 (12) 3 : 0.003 0.997 (0.000,0.020) (0.980,1.000) +280 FL_H220 (2) 3 : 0.005 0.995 (0.000,0.033) (0.967,1.000) +281 FL_H228 (0) 3 : 0.002 0.998 (0.000,0.014) (0.986,1.000) +282 FL_H229 (0) 3 : 0.051 0.949 (0.000,0.139) (0.861,1.000) +283 FL_H232 (5) 3 : 0.059 0.941 (0.000,0.152) (0.848,1.000) +284 FL_H221 (10) 3 : 0.018 0.982 (0.000,0.091) (0.909,1.000) +285 FL_H222 (7) 3 : 0.020 0.980 (0.000,0.092) (0.908,1.000) +286 FL_H223 (0) 3 : 0.003 0.997 (0.000,0.020) (0.980,1.000) +287 FL_H224 (5) 3 : 0.002 0.998 (0.000,0.013) (0.987,1.000) +288 FL_H225 (0) 3 : 0.002 0.998 (0.000,0.012) (0.988,1.000) +289 FL_H226 (7) 3 : 0.004 0.996 (0.000,0.026) (0.974,1.000) +290 FL_H230 (0) 3 : 0.030 0.970 (0.000,0.107) (0.893,1.000) +291 FL_H231 (2) 3 : 0.003 0.997 (0.000,0.018) (0.982,1.000) +292 FL_ES1 (7) 3 : 0.046 0.954 (0.000,0.143) (0.857,1.000) +293 FL_R27 (7) 3 : 0.009 0.991 (0.000,0.057) (0.943,1.000) +294 HI_A212 (0) 3 : 0.004 0.996 (0.000,0.028) (0.972,1.000) +295 HI_A215 (5) 3 : 0.017 0.983 (0.000,0.070) (0.930,1.000) +296 HI_A217 (6) 3 : 0.002 0.998 (0.000,0.015) (0.985,1.000) +297 HI_A222 (0) 3 : 0.004 0.996 (0.000,0.024) (0.976,1.000) +298 HI_A225 (0) 3 : 0.002 0.998 (0.000,0.012) (0.988,1.000) +299 HI_A227 (5) 3 : 0.004 0.996 (0.000,0.027) (0.973,1.000) +300 HI_A229 (5) 3 : 0.002 0.998 (0.000,0.015) (0.985,1.000) +301 HI_A236 (0) 3 : 0.003 0.997 (0.000,0.016) (0.984,1.000) +302 HI_A245 (11) 3 : 0.002 0.998 (0.000,0.014) (0.986,1.000) +303 HI_A261 (0) 3 : 0.002 0.998 (0.000,0.010) (0.990,1.000) +304 HI_A263 (0) 3 : 0.002 0.998 (0.000,0.015) (0.985,1.000) +305 HI_A265 (7) 3 : 0.002 0.998 (0.000,0.013) (0.987,1.000) +306 HI_A266 (0) 3 : 0.002 0.998 (0.000,0.012) (0.988,1.000) +307 HI_A317 (5) 3 : 0.003 0.997 (0.000,0.016) (0.984,1.000) +308 HI_R01 (0) 3 : 0.003 0.997 (0.000,0.021) (0.979,1.000) +309 HI_R03 (5) 3 : 0.004 0.996 (0.000,0.023) (0.977,1.000) +310 HI_R04 (5) 3 : 0.005 0.995 (0.000,0.032) (0.968,1.000) +311 HI_R05 (5) 3 : 0.046 0.954 (0.000,0.165) (0.835,1.000) +312 HI_R06 (5) 3 : 0.003 0.997 (0.000,0.020) (0.980,1.000) +313 HI_R07 (5) 3 : 0.020 0.980 (0.000,0.083) (0.917,1.000) +314 HI_R08 (0) 3 : 0.002 0.998 (0.000,0.013) (0.987,1.000) +315 HI_R10 (0) 3 : 0.002 0.998 (0.000,0.014) (0.986,1.000) +316 HI_R11 (17) 3 : 0.005 0.995 (0.000,0.032) (0.968,1.000) +317 ND_A05 (23) 3 : 0.003 0.997 (0.000,0.018) (0.982,1.000) +318 ND_A10 (7) 3 : 0.005 0.995 (0.000,0.033) (0.967,1.000) +319 ND_A11 (23) 3 : 0.002 0.998 (0.000,0.014) (0.986,1.000) +320 ND_A22 (5) 3 : 0.009 0.991 (0.000,0.052) (0.948,1.000) +321 ND_A24 (5) 3 : 0.005 0.995 (0.000,0.030) (0.970,1.000) +322 ND_A25 (23) 3 : 0.002 0.998 (0.000,0.015) (0.985,1.000) +323 ND_A13 (10) 3 : 0.003 0.997 (0.000,0.016) (0.984,1.000) +324 ND_A02 (20) 3 : 0.003 0.997 (0.000,0.018) (0.982,1.000) +325 ND_A03 (20) 3 : 0.003 0.997 (0.000,0.017) (0.983,1.000) +326 ND_A06 (5) 3 : 0.003 0.997 (0.000,0.018) (0.982,1.000) +327 ND_A07 (5) 3 : 0.002 0.998 (0.000,0.013) (0.987,1.000) +328 ND_A09 (15) 3 : 0.005 0.995 (0.000,0.031) (0.969,1.000) +329 ND_A12 (12) 3 : 0.030 0.970 (0.000,0.133) (0.867,1.000) +330 ND_A14 (12) 3 : 0.003 0.997 (0.000,0.021) (0.979,1.000) +331 ND_A15 (7) 3 : 0.002 0.998 (0.000,0.012) (0.988,1.000) +332 ND_A16 (17) 3 : 0.039 0.961 (0.000,0.135) (0.865,1.000) +333 ND_A17 (17) 3 : 0.002 0.998 (0.000,0.014) (0.986,1.000) +334 ND_A19 (7) 3 : 0.002 0.998 (0.000,0.013) (0.987,1.000) +335 ND_A23 (5) 3 : 0.003 0.997 (0.000,0.017) (0.983,1.000) +336 ND_A26 (23) 3 : 0.002 0.998 (0.000,0.014) (0.986,1.000) +337 NZ_26 (2) 3 : 0.002 0.998 (0.000,0.010) (0.990,1.000) +338 NZ_27 (7) 3 : 0.002 0.998 (0.000,0.011) (0.989,1.000) +339 NZ_28 (2) 3 : 0.002 0.998 (0.000,0.012) (0.988,1.000) +340 NZ_29 (7) 3 : 0.002 0.998 (0.000,0.012) (0.988,1.000) +341 NZ_30 (17) 3 : 0.002 0.998 (0.000,0.012) (0.988,1.000) +342 NZ_31 (10) 3 : 0.002 0.998 (0.000,0.013) (0.987,1.000) +343 NZ_32 (5) 3 : 0.002 0.998 (0.000,0.011) (0.989,1.000) +344 NZ_33 (2) 3 : 0.002 0.998 (0.000,0.010) (0.990,1.000) +345 NZ_34 (16) 3 : 0.002 0.998 (0.000,0.012) (0.988,1.000) +346 NZ_36 (2) 3 : 0.005 0.995 (0.000,0.033) (0.967,1.000) +347 NZ_37 (10) 3 : 0.002 0.998 (0.000,0.013) (0.987,1.000) +348 NZ_38 (11) 3 : 0.044 0.956 (0.000,0.114) (0.886,1.000) +349 NZ_39 (10) 3 : 0.003 0.997 (0.000,0.021) (0.979,1.000) +350 NZ_40 (0) 3 : 0.002 0.998 (0.000,0.010) (0.990,1.000) +351 NZ_41 (0) 3 : 0.002 0.998 (0.000,0.011) (0.989,1.000) +352 NZ_43 (16) 3 : 0.019 0.981 (0.000,0.078) (0.922,1.000) +353 NZ_44 (8) 3 : 0.002 0.998 (0.000,0.012) (0.988,1.000) +354 NZ_45 (14) 3 : 0.003 0.997 (0.000,0.016) (0.984,1.000) +355 NZ_46 (7) 3 : 0.002 0.998 (0.000,0.013) (0.987,1.000) +356 NZ_47 (14) 3 : 0.002 0.998 (0.000,0.012) (0.988,1.000) +357 NZ_48 (5) 3 : 0.002 0.998 (0.000,0.011) (0.989,1.000) +358 NZ_49 (7) 3 : 0.002 0.998 (0.000,0.012) (0.988,1.000) +359 NZ_50 (10) 3 : 0.002 0.998 (0.000,0.014) (0.986,1.000) +360 9_A301 (5) 3 : 0.002 0.998 (0.000,0.014) (0.986,1.000) +361 9_A303 (21) 3 : 0.002 0.998 (0.000,0.015) (0.985,1.000) +362 9_A304 (5) 3 : 0.003 0.997 (0.000,0.019) (0.981,1.000) +363 9_A334 (0) 3 : 0.002 0.998 (0.000,0.013) (0.987,1.000) +364 9_A337 (2) 3 : 0.002 0.998 (0.000,0.014) (0.986,1.000) +365 9_A342 (17) 3 : 0.003 0.997 (0.000,0.018) (0.982,1.000) +366 9_A343 (10) 3 : 0.007 0.993 (0.000,0.047) (0.953,1.000) +367 9_A348 (14) 3 : 0.018 0.982 (0.000,0.087) (0.913,1.000) +368 9_A349 (12) 3 : 0.002 0.998 (0.000,0.015) (0.985,1.000) +369 9_A350 (2) 3 : 0.006 0.994 (0.000,0.039) (0.961,1.000) +370 9_A351 (12) 3 : 0.003 0.997 (0.000,0.016) (0.984,1.000) +371 9_A352 (0) 3 : 0.003 0.997 (0.000,0.017) (0.983,1.000) +372 9_A353 (21) 3 : 0.002 0.998 (0.000,0.013) (0.987,1.000) +373 9_A354 (5) 3 : 0.003 0.997 (0.000,0.019) (0.981,1.000) +374 9_A355 (5) 3 : 0.003 0.997 (0.000,0.016) (0.984,1.000) +375 9_A357 (7) 3 : 0.005 0.995 (0.000,0.034) (0.966,1.000) +376 9_A358 (2) 3 : 0.002 0.998 (0.000,0.012) (0.988,1.000) +377 RXCA_03 (5) 3 : 0.002 0.998 (0.000,0.014) (0.986,1.000) +378 RXCA_04 (12) 3 : 0.002 0.998 (0.000,0.014) (0.986,1.000) +379 RXCA_07 (5) 3 : 0.002 0.998 (0.000,0.013) (0.987,1.000) +380 RXCA_12 (0) 3 : 0.002 0.998 (0.000,0.013) (0.987,1.000) +381 RXCA_19 (5) 3 : 0.002 0.998 (0.000,0.014) (0.986,1.000) +382 RXCA_20 (5) 3 : 0.002 0.998 (0.000,0.014) (0.986,1.000) +383 RXCA_22 (5) 3 : 0.003 0.997 (0.000,0.019) (0.981,1.000) +384 RXCA_26 (5) 3 : 0.002 0.998 (0.000,0.013) (0.987,1.000) +385 RXCH_01 (0) 3 : 0.002 0.998 (0.000,0.012) (0.988,1.000) +386 RXCH_02 (7) 3 : 0.002 0.998 (0.000,0.014) (0.986,1.000) +387 RXCH_13 (11) 3 : 0.002 0.998 (0.000,0.015) (0.985,1.000) +388 RXCH_14 (5) 3 : 0.003 0.997 (0.000,0.015) (0.985,1.000) +389 RXCH_15 (0) 3 : 0.002 0.998 (0.000,0.013) (0.987,1.000) +390 RXCH_16 (0) 3 : 0.014 0.986 (0.000,0.078) (0.922,1.000) +391 RXCH_18 (7) 3 : 0.002 0.998 (0.000,0.013) (0.987,1.000) +392 RXCH_27 (2) 3 : 0.002 0.998 (0.000,0.015) (0.985,1.000) +393 RXCH_29 (0) 3 : 0.002 0.998 (0.000,0.012) (0.988,1.000) +394 RXWH_05 (5) 3 : 0.002 0.998 (0.000,0.015) (0.985,1.000) +395 RXWH_06 (5) 3 : 0.002 0.998 (0.000,0.013) (0.987,1.000) +396 RXWH_08 (5) 3 : 0.002 0.998 (0.000,0.014) (0.986,1.000) +397 RXWH_09 (5) 3 : 0.002 0.998 (0.000,0.015) (0.985,1.000) +398 RXWH_17 (5) 3 : 0.003 0.997 (0.000,0.021) (0.979,1.000) +399 RXWH_21 (0) 3 : 0.002 0.998 (0.000,0.013) (0.987,1.000) +400 RXWH_23 (5) 3 : 0.002 0.998 (0.000,0.013) (0.987,1.000) +401 RXWH_28 (2) 3 : 0.004 0.996 (0.000,0.022) (0.978,1.000) +402 TH_T50 (20) 3 : 0.004 0.996 (0.000,0.026) (0.974,1.000) +403 TH_A244 (2) 3 : 0.002 0.998 (0.000,0.015) (0.985,1.000) +404 TH_A252 (0) 3 : 0.003 0.997 (0.000,0.020) (0.980,1.000) +405 TH_A254 (0) 3 : 0.003 0.997 (0.000,0.017) (0.983,1.000) +406 TH_A276 (7) 3 : 0.004 0.996 (0.000,0.027) (0.973,1.000) +407 TH_A308 (0) 3 : 0.003 0.997 (0.000,0.021) (0.979,1.000) +408 TH_A309 (5) 3 : 0.012 0.988 (0.000,0.057) (0.943,1.000) +409 TH_A313 (5) 3 : 0.009 0.991 (0.000,0.049) (0.951,1.000) +410 TH_A314 (16) 3 : 0.008 0.992 (0.000,0.045) (0.955,1.000) +411 TH_A322 (5) 3 : 0.006 0.994 (0.000,0.041) (0.959,1.000) +412 TH_A326 (7) 3 : 0.003 0.997 (0.000,0.019) (0.981,1.000) +413 TH_A333 (0) 3 : 0.003 0.997 (0.000,0.015) (0.985,1.000) +414 VW_A046 (2) 3 : 0.002 0.998 (0.000,0.011) (0.989,1.000) +415 VW_A047 (2) 3 : 0.002 0.998 (0.000,0.011) (0.989,1.000) +416 VW_A048 (2) 3 : 0.002 0.998 (0.000,0.013) (0.987,1.000) +417 VW_A043 (5) 3 : 0.002 0.998 (0.000,0.013) (0.987,1.000) +418 VW_A050 (7) 3 : 0.002 0.998 (0.000,0.011) (0.989,1.000) +419 VW_A045 (5) 3 : 0.003 0.997 (0.000,0.016) (0.984,1.000) +420 VW_A066 (12) 3 : 0.003 0.997 (0.000,0.017) (0.983,1.000) +421 VW_A068 (2) 3 : 0.002 0.998 (0.000,0.015) (0.985,1.000) +422 VW_A201 (2) 3 : 0.013 0.987 (0.000,0.055) (0.945,1.000) +423 VW_A311 (7) 3 : 0.002 0.998 (0.000,0.015) (0.985,1.000) +424 VW_A332 (0) 3 : 0.002 0.998 (0.000,0.013) (0.987,1.000) +425 VW_A344 (20) 3 : 0.003 0.997 (0.000,0.021) (0.979,1.000) +426 VW_A345 (0) 3 : 0.003 0.997 (0.000,0.017) (0.983,1.000) +427 VW_A346 (0) 3 : 0.002 0.998 (0.000,0.015) (0.985,1.000) +428 Causse_06 (23) 4 : 0.453 0.547 (0.296,0.614) (0.386,0.704) +429 Causse_16 (23) 4 : 0.562 0.438 (0.387,0.737) (0.263,0.613) +430 Causse_22 (14) 4 : 0.569 0.431 (0.398,0.741) (0.259,0.602) +431 Causse_27 (0) 4 : 0.655 0.345 (0.510,0.794) (0.206,0.490) +432 Causse_29 (10) 4 : 0.650 0.350 (0.476,0.818) (0.182,0.524) +433 Causse_30 (10) 4 : 0.543 0.457 (0.394,0.692) (0.308,0.606) +434 Causse_32 (0) 4 : 0.591 0.409 (0.440,0.742) (0.258,0.560) +435 Causse_33 (2) 4 : 0.731 0.269 (0.585,0.866) (0.134,0.415) +436 Causse_36 (5) 4 : 0.560 0.440 (0.399,0.722) (0.278,0.601) +437 EST_1 (0) 4 : 0.673 0.327 (0.527,0.816) (0.184,0.473) +438 EST_2 (2) 4 : 0.402 0.598 (0.265,0.545) (0.455,0.735) +439 EST_3 (2) 4 : 0.472 0.528 (0.333,0.616) (0.384,0.667) +440 EST_5 (5) 4 : 0.484 0.516 (0.346,0.627) (0.373,0.654) +441 FOS_1 (2) 4 : 0.679 0.321 (0.527,0.827) (0.173,0.473) +442 FOS_4 (8) 4 : 0.620 0.380 (0.458,0.780) (0.220,0.542) +443 FOS_5 (5) 4 : 0.401 0.599 (0.258,0.553) (0.447,0.742) +444 FRE_2 (0) 4 : 0.777 0.223 (0.630,0.915) (0.085,0.370) +445 FRE_3 (10) 4 : 0.827 0.173 (0.657,0.994) (0.006,0.343) +446 FRE_4 (0) 4 : 0.880 0.120 (0.738,0.999) (0.001,0.262) +447 FRE_5 (19) 4 : 0.774 0.226 (0.605,0.942) (0.058,0.395) +448 Lyon_34 (5) 4 : 0.808 0.192 (0.658,0.952) (0.048,0.342) +449 Lyon_37 (5) 4 : 0.498 0.502 (0.351,0.648) (0.352,0.649) +450 Lyon_38 (10) 4 : 0.546 0.454 (0.386,0.708) (0.292,0.614) +451 Lyon_39 (7) 4 : 0.596 0.404 (0.441,0.747) (0.253,0.559) +452 Lyon_42 (7) 4 : 0.603 0.397 (0.445,0.758) (0.242,0.555) +453 Lyon_43 (2) 4 : 0.583 0.417 (0.438,0.728) (0.272,0.562) +454 Lyon_44 (15) 4 : 0.714 0.286 (0.549,0.870) (0.130,0.451) +455 Lyon_45 (7) 4 : 0.595 0.405 (0.432,0.755) (0.245,0.568) +456 Lyon_46 (7) 4 : 0.617 0.383 (0.467,0.764) (0.236,0.533) +457 Lyon_48 (7) 4 : 0.705 0.295 (0.546,0.857) (0.143,0.454) +458 Lyon_50 (10) 4 : 0.750 0.250 (0.599,0.891) (0.109,0.401) +459 Lyon_51 (7) 4 : 0.646 0.354 (0.476,0.812) (0.188,0.524) +460 Lyon_52 (7) 4 : 0.675 0.325 (0.508,0.834) (0.166,0.492) +461 Lyon_55 (7) 4 : 0.562 0.438 (0.399,0.725) (0.275,0.601) +462 Lyon_56 (10) 4 : 0.687 0.313 (0.517,0.853) (0.147,0.483) +463 Lyon_57 (5) 4 : 0.623 0.377 (0.463,0.783) (0.217,0.537) +464 Lyon_60 (10) 4 : 0.543 0.457 (0.388,0.698) (0.302,0.612) +465 Lyon_61 (10) 4 : 0.611 0.389 (0.449,0.771) (0.229,0.551) +466 Lyon_63 (0) 4 : 0.529 0.471 (0.370,0.690) (0.310,0.630) +467 Lyon_64 (15) 4 : 0.449 0.551 (0.269,0.635) (0.365,0.731) +468 Lyon_66 (12) 4 : 0.684 0.316 (0.519,0.842) (0.158,0.481) +469 Lyon_67 (8) 4 : 0.561 0.439 (0.408,0.713) (0.287,0.592) +470 Lyon_69 (7) 4 : 0.644 0.356 (0.483,0.802) (0.198,0.517) +471 Lyon_70 (17) 4 : 0.525 0.475 (0.363,0.687) (0.313,0.637) +472 Lyon_71 (5) 4 : 0.710 0.290 (0.548,0.866) (0.134,0.452) +473 PP_06 (15) 4 : 0.676 0.324 (0.499,0.849) (0.151,0.501) +474 PP_12 (5) 4 : 0.707 0.293 (0.560,0.849) (0.151,0.440) +475 PP_15 (23) 4 : 0.670 0.330 (0.506,0.829) (0.171,0.494) +476 PP_16 (17) 4 : 0.558 0.442 (0.401,0.716) (0.284,0.599) +477 PP_18 (15) 4 : 0.643 0.357 (0.480,0.803) (0.197,0.520) +478 PP_19 (0) 4 : 0.688 0.312 (0.542,0.828) (0.172,0.458) +479 PP_20 (14) 4 : 0.844 0.156 (0.714,0.956) (0.044,0.286) +480 PP_21 (17) 4 : 0.693 0.307 (0.548,0.830) (0.170,0.452) +481 PP_24 (0) 4 : 0.744 0.256 (0.608,0.872) (0.128,0.392) +482 PP_26 (10) 4 : 0.704 0.296 (0.560,0.841) (0.159,0.440) +483 Roi_41 (11) 4 : 0.508 0.492 (0.356,0.664) (0.336,0.644) +484 Roi_42 (5) 4 : 0.555 0.445 (0.394,0.719) (0.281,0.606) +485 Roi_44 (5) 4 : 0.472 0.528 (0.333,0.614) (0.386,0.667) +486 Roi_47 (7) 4 : 0.388 0.612 (0.244,0.542) (0.458,0.756) +487 Roi_48 (2) 4 : 0.421 0.579 (0.268,0.582) (0.418,0.732) +488 Roi_49 (5) 4 : 0.507 0.493 (0.340,0.677) (0.323,0.660) +489 Roi_50 (0) 4 : 0.370 0.630 (0.219,0.529) (0.471,0.781) +490 Roi_51 (5) 4 : 0.434 0.566 (0.285,0.592) (0.408,0.715) +491 Roi_52 (5) 4 : 0.340 0.660 (0.205,0.487) (0.513,0.795) +492 Roi_53 (5) 4 : 0.405 0.595 (0.265,0.555) (0.445,0.735) +493 Ver_129 (5) 4 : 0.398 0.602 (0.258,0.546) (0.454,0.742) +494 Ver_152 (10) 4 : 0.284 0.716 (0.139,0.445) (0.555,0.861) +495 Ver_170 (12) 4 : 0.409 0.591 (0.252,0.575) (0.425,0.748) +496 Ver_1743 (2) 4 : 0.547 0.453 (0.402,0.692) (0.308,0.598) +497 Ver_1950 (17) 4 : 0.434 0.566 (0.283,0.591) (0.409,0.717) +498 Ver_1990 (0) 4 : 0.460 0.540 (0.317,0.608) (0.392,0.683) +499 Ver_2469 (12) 4 : 0.362 0.638 (0.212,0.526) (0.474,0.788) +500 Ver_2488 (5) 4 : 0.610 0.390 (0.450,0.765) (0.235,0.550) +501 Ver_2550 (0) 4 : 0.544 0.456 (0.384,0.707) (0.293,0.616) +502 Ver_2593 (0) 4 : 0.421 0.579 (0.271,0.578) (0.422,0.729) +503 Ver_2692 (7) 4 : 0.368 0.632 (0.218,0.530) (0.470,0.782) +504 Ver_2696 (5) 4 : 0.497 0.503 (0.350,0.648) (0.352,0.650) +505 Ver_2701 (7) 4 : 0.484 0.516 (0.336,0.634) (0.366,0.664) +506 Ver_2787 (10) 4 : 0.221 0.779 (0.096,0.365) (0.635,0.904) +507 Ver_2813 (0) 4 : 0.522 0.478 (0.385,0.660) (0.340,0.615) +508 Ver_2911 (7) 4 : 0.350 0.650 (0.209,0.503) (0.497,0.791) +509 Ver_9766 (10) 4 : 0.430 0.570 (0.283,0.584) (0.416,0.717) +510 VIL_3 (5) 4 : 0.594 0.406 (0.435,0.750) (0.250,0.565) +511 VIL_4 (0) 4 : 0.620 0.380 (0.468,0.771) (0.229,0.532) +512 VIL_5 (0) 4 : 0.520 0.480 (0.359,0.682) (0.318,0.641) +513 ALT_018 (2) 5 : 0.719 0.281 (0.579,0.851) (0.149,0.421) +514 ALT_106 (0) 5 : 0.745 0.255 (0.621,0.860) (0.140,0.379) +515 ALT_121 (0) 5 : 0.585 0.415 (0.448,0.721) (0.279,0.552) +516 ALT_125 (5) 5 : 0.688 0.312 (0.557,0.813) (0.187,0.443) +517 ALT_129 (2) 5 : 0.786 0.214 (0.653,0.910) (0.090,0.347) +518 ALT_131 (5) 5 : 0.798 0.202 (0.668,0.917) (0.083,0.332) +519 ALT_140 (0) 5 : 0.631 0.369 (0.503,0.758) (0.242,0.497) +520 ALT_143 (0) 5 : 0.682 0.318 (0.547,0.812) (0.188,0.453) +521 RSL_01 (0) 5 : 0.988 0.012 (0.943,1.000) (0.000,0.057) +522 RSL_02 (0) 5 : 0.943 0.057 (0.846,1.000) (0.000,0.154) +523 RSL_03 (2) 5 : 0.986 0.014 (0.933,1.000) (0.000,0.067) +524 RSL_04 (0) 5 : 0.948 0.052 (0.843,1.000) (0.000,0.157) +525 RSL_05 (5) 5 : 0.987 0.013 (0.938,1.000) (0.000,0.062) +526 RSL_06 (0) 5 : 0.956 0.044 (0.851,1.000) (0.000,0.149) +527 RSL_07 (0) 5 : 0.966 0.034 (0.871,1.000) (0.000,0.129) +528 RSL_08 (0) 5 : 0.985 0.015 (0.931,1.000) (0.000,0.069) +529 RSL_14 (10) 5 : 0.357 0.643 (0.234,0.489) (0.511,0.766) +530 TAR_006 (5) 5 : 0.985 0.015 (0.929,1.000) (0.000,0.071) +531 TAR_009 (10) 5 : 0.977 0.023 (0.900,1.000) (0.000,0.100) +532 TAR_010 (11) 5 : 0.989 0.011 (0.946,1.000) (0.000,0.054) +533 TAR_102 (7) 5 : 0.954 0.046 (0.835,1.000) (0.000,0.165) +534 TAR_103 (7) 5 : 0.832 0.168 (0.665,0.998) (0.002,0.335) +535 TAR_105 (2) 5 : 0.958 0.042 (0.858,1.000) (0.000,0.142) +536 TAR_106 (5) 5 : 0.988 0.012 (0.940,1.000) (0.000,0.060) +537 TAR_107 (7) 5 : 0.866 0.134 (0.751,0.970) (0.030,0.249) +538 TAR_111 (5) 5 : 0.980 0.020 (0.910,1.000) (0.000,0.090) +539 ZRG_02 (0) 5 : 0.925 0.075 (0.803,1.000) (0.000,0.197) +540 ZRG_03 (0) 5 : 0.899 0.101 (0.744,1.000) (0.000,0.256) +541 ZRG_04 (0) 5 : 0.975 0.025 (0.897,1.000) (0.000,0.103) +542 ZRG_06 (0) 5 : 0.982 0.018 (0.917,1.000) (0.000,0.083) +543 ZRG_07 (0) 5 : 0.984 0.016 (0.926,1.000) (0.000,0.074) +544 ZRG_08 (2) 5 : 0.836 0.164 (0.696,0.968) (0.032,0.304) +545 ZRG_10 (0) 5 : 0.986 0.014 (0.936,1.000) (0.000,0.064) +546 ZRG_11 (5) 5 : 0.951 0.049 (0.829,1.000) (0.000,0.171) +547 ZRG_12 (1) 5 : 0.955 0.045 (0.842,1.000) (0.000,0.158) +548 ZRG_13 (0) 5 : 0.934 0.066 (0.801,1.000) (0.000,0.199) +549 ZRG_14 (0) 5 : 0.959 0.041 (0.841,1.000) (0.000,0.159) +550 ZRG_20 (10) 5 : 0.974 0.026 (0.884,1.000) (0.000,0.116) +551 ZRG_24 (7) 5 : 0.987 0.013 (0.937,1.000) (0.000,0.063) + + +Estimated Allele Frequencies in each cluster +First column gives estimated ancestral frequencies + + +Locus 1 : mOC101 +12 alleles +4.7% missing data + 162 (0.091) 0.090 0.746 + 160 (0.042) 0.040 0.192 + 156 (0.128) 0.129 0.010 + 154 (0.177) 0.180 0.000 + 174 (0.083) 0.084 0.000 + 158 (0.050) 0.050 0.000 + 152 (0.023) 0.023 0.000 + 172 (0.102) 0.103 0.000 + 170 (0.012) 0.011 0.000 + 178 (0.213) 0.215 0.043 + 164 (0.065) 0.064 0.008 + 168 (0.012) 0.011 0.000 + +Locus 2 : mOC106 +13 alleles +6.4% missing data + 169 (0.153) 0.154 0.032 + 179 (0.152) 0.154 0.001 + 171 (0.076) 0.075 0.365 + 177 (0.050) 0.049 0.156 + 173 (0.050) 0.048 0.349 + 175 (0.133) 0.134 0.004 + 167 (0.175) 0.176 0.093 + 165 (0.084) 0.085 0.000 + 159 (0.037) 0.037 0.000 + 163 (0.062) 0.062 0.000 + 161 (0.012) 0.011 0.000 + 183 (0.008) 0.007 0.000 + 142 (0.008) 0.007 0.000 + +Locus 3 : mOC108 +11 alleles +6.0% missing data + 144 (0.330) 0.331 0.445 + 152 (0.016) 0.015 0.219 + 146 (0.315) 0.320 0.003 + 150 (0.065) 0.064 0.325 + 158 (0.004) 0.003 0.000 + 142 (0.152) 0.153 0.003 + 148 (0.067) 0.066 0.005 + 140 (0.021) 0.021 0.000 + 156 (0.011) 0.010 0.000 + 138 (0.011) 0.010 0.000 + 136 (0.008) 0.007 0.000 + +Locus 4 : mOC139 +7 alleles +3.8% missing data + 129 (0.133) 0.132 0.387 + 133 (0.124) 0.124 0.148 + 131 (0.457) 0.460 0.308 + 137 (0.046) 0.045 0.038 + 135 (0.167) 0.167 0.119 + 139 (0.040) 0.040 0.000 + 127 (0.033) 0.032 0.000 + +Locus 5 : mOC172 +8 alleles +14.5% missing data + 97 (0.265) 0.265 0.369 + 103 (0.017) 0.015 0.456 + 105 (0.035) 0.033 0.007 + 101 (0.196) 0.198 0.001 + 95 (0.164) 0.166 0.000 + 93 (0.055) 0.055 0.000 + 99 (0.207) 0.207 0.167 + 91 (0.060) 0.060 0.000 + +Locus 6 : mOC176 +26 alleles +8.2% missing data + 227 (0.107) 0.107 0.872 + 233 (0.032) 0.032 0.000 + 235 (0.066) 0.067 0.000 + 236 (0.038) 0.037 0.002 + 244 (0.058) 0.059 0.000 + 225 (0.012) 0.012 0.000 + 238 (0.070) 0.071 0.005 + 234 (0.070) 0.070 0.032 + 237 (0.020) 0.020 0.000 + 240 (0.085) 0.087 0.000 + 229 (0.043) 0.042 0.083 + 231 (0.024) 0.024 0.000 + 247 (0.028) 0.028 0.000 + 241 (0.016) 0.016 0.000 + 251 (0.028) 0.028 0.000 + 242 (0.028) 0.028 0.000 + 230 (0.066) 0.067 0.000 + 224 (0.009) 0.008 0.000 + 219 (0.009) 0.008 0.005 + 249 (0.035) 0.036 0.000 + 239 (0.028) 0.028 0.000 + 246 (0.043) 0.043 0.000 + 228 (0.043) 0.043 0.000 + 223 (0.020) 0.020 0.000 + 226 (0.009) 0.008 0.000 + 232 (0.012) 0.012 0.000 + +Locus 7 : mOC203 +16 alleles +8.5% missing data + 212 (0.207) 0.209 0.345 + 214 (0.145) 0.145 0.112 + 204 (0.047) 0.046 0.358 + 208 (0.048) 0.046 0.089 + 206 (0.054) 0.053 0.061 + 202 (0.050) 0.050 0.000 + 186 (0.169) 0.173 0.000 + 196 (0.050) 0.050 0.000 + 200 (0.040) 0.040 0.000 + 198 (0.033) 0.032 0.000 + 182 (0.022) 0.022 0.000 + 216 (0.047) 0.046 0.034 + 188 (0.019) 0.018 0.000 + 210 (0.050) 0.050 0.000 + 203 (0.008) 0.007 0.000 + 192 (0.012) 0.011 0.000 + +Locus 8 : mOC119 +14 alleles +3.1% missing data + 231 (0.050) 0.048 0.575 + 233 (0.157) 0.157 0.236 + 215 (0.025) 0.025 0.000 + 223 (0.054) 0.054 0.000 + 229 (0.216) 0.217 0.173 + 227 (0.067) 0.068 0.000 + 237 (0.133) 0.136 0.000 + 225 (0.060) 0.061 0.000 + 221 (0.050) 0.050 0.000 + 235 (0.094) 0.094 0.013 + 213 (0.008) 0.007 0.000 + 239 (0.061) 0.061 0.000 + 245 (0.015) 0.014 0.000 + 219 (0.009) 0.008 0.002 + +Locus 9 : mOC140 +13 alleles +1.5% missing data + 182 (0.235) 0.236 0.295 + 184 (0.239) 0.240 0.609 + 186 (0.024) 0.022 0.092 + 188 (0.008) 0.007 0.001 + 192 (0.004) 0.003 0.000 + 177 (0.240) 0.244 0.001 + 179 (0.099) 0.100 0.000 + 175 (0.019) 0.018 0.000 + 181 (0.048) 0.048 0.000 + 183 (0.008) 0.007 0.000 + 185 (0.008) 0.007 0.003 + 180 (0.056) 0.056 0.000 + 190 (0.012) 0.011 0.000 + +Locus 10 : mOC157 +13 alleles +12.9% missing data + 141 (0.119) 0.119 0.253 + 143 (0.146) 0.146 0.165 + 149 (0.143) 0.146 0.000 + 147 (0.143) 0.146 0.001 + 151 (0.030) 0.029 0.002 + 137 (0.083) 0.082 0.174 + 139 (0.209) 0.210 0.401 + 155 (0.009) 0.008 0.000 + 142 (0.013) 0.012 0.000 + 145 (0.047) 0.047 0.000 + 135 (0.026) 0.024 0.004 + 131 (0.009) 0.008 0.000 + 140 (0.024) 0.024 0.000 + +Locus 11 : mOC201 +23 alleles +0.4% missing data + 137 (0.138) 0.139 0.246 + 143 (0.099) 0.100 0.059 + 144 (0.014) 0.012 0.568 + 133 (0.111) 0.112 0.032 + 135 (0.166) 0.171 0.000 + 139 (0.060) 0.061 0.000 + 145 (0.084) 0.084 0.020 + 155 (0.007) 0.006 0.000 + 151 (0.010) 0.009 0.000 + 129 (0.016) 0.015 0.000 + 141 (0.051) 0.052 0.000 + 149 (0.042) 0.043 0.000 + 148 (0.017) 0.015 0.055 + 131 (0.019) 0.018 0.000 + 153 (0.010) 0.009 0.000 + 150 (0.007) 0.006 0.000 + 161 (0.010) 0.009 0.000 + 157 (0.007) 0.006 0.000 + 146 (0.014) 0.012 0.018 + 147 (0.069) 0.070 0.000 + 142 (0.007) 0.006 0.000 + 134 (0.033) 0.034 0.000 + 136 (0.010) 0.009 0.000 + +Locus 12 : mOC87 +13 alleles +3.3% missing data + 220 (0.095) 0.095 0.262 + 228 (0.031) 0.030 0.120 + 224 (0.124) 0.124 0.145 + 212 (0.082) 0.082 0.157 + 230 (0.008) 0.007 0.059 + 236 (0.004) 0.003 0.000 + 232 (0.008) 0.006 0.072 + 214 (0.077) 0.078 0.000 + 216 (0.124) 0.124 0.053 + 210 (0.011) 0.010 0.000 + 218 (0.179) 0.182 0.045 + 222 (0.153) 0.155 0.019 + 226 (0.104) 0.104 0.069 + +Locus 13 : mOC89 +7 alleles +3.4% missing data + 94 (0.325) 0.326 0.794 + 92 (0.191) 0.192 0.022 + 90 (0.355) 0.357 0.037 + 88 (0.025) 0.024 0.000 + 84 (0.009) 0.008 0.000 + 98 (0.025) 0.024 0.001 + 96 (0.070) 0.068 0.146 + +Locus 14 : Sat13 +11 alleles +5.1% missing data + 131 (0.239) 0.240 0.159 + 145 (0.104) 0.103 0.695 + 143 (0.191) 0.195 0.001 + 137 (0.052) 0.051 0.041 + 130 (0.034) 0.034 0.000 + 139 (0.012) 0.011 0.000 + 147 (0.088) 0.088 0.002 + 149 (0.032) 0.030 0.031 + 141 (0.027) 0.026 0.000 + 129 (0.111) 0.112 0.000 + 133 (0.111) 0.110 0.070 + +Locus 15 : mOC102 +21 alleles +2.4% missing data + 231 (0.067) 0.068 0.000 + 235 (0.112) 0.113 0.386 + 233 (0.035) 0.034 0.166 + 234 (0.004) 0.003 0.000 + 236 (0.004) 0.003 0.000 + 237 (0.098) 0.098 0.128 + 215 (0.037) 0.037 0.000 + 239 (0.161) 0.162 0.281 + 251 (0.050) 0.051 0.000 + 241 (0.134) 0.135 0.037 + 247 (0.028) 0.027 0.000 + 245 (0.077) 0.078 0.000 + 219 (0.018) 0.017 0.000 + 229 (0.021) 0.020 0.000 + 249 (0.021) 0.020 0.000 + 221 (0.021) 0.020 0.000 + 243 (0.057) 0.058 0.000 + 225 (0.014) 0.014 0.000 + 223 (0.021) 0.020 0.000 + 227 (0.014) 0.014 0.000 + 250 (0.008) 0.007 0.000 + +Locus 16 : mOC104 +10 alleles +2.4% missing data + 126 (0.299) 0.301 0.253 + 122 (0.048) 0.047 0.593 + 128 (0.125) 0.125 0.036 + 132 (0.137) 0.138 0.022 + 115 (0.020) 0.019 0.000 + 130 (0.210) 0.211 0.088 + 138 (0.016) 0.015 0.000 + 124 (0.075) 0.076 0.000 + 134 (0.044) 0.042 0.008 + 136 (0.027) 0.026 0.000 + +Locus 17 : mOC169 +12 alleles +1.6% missing data + 159 (0.256) 0.258 0.319 + 163 (0.107) 0.107 0.311 + 169 (0.034) 0.032 0.287 + 167 (0.108) 0.109 0.001 + 165 (0.275) 0.279 0.044 + 161 (0.097) 0.098 0.000 + 157 (0.011) 0.010 0.000 + 171 (0.060) 0.059 0.002 + 173 (0.025) 0.024 0.036 + 183 (0.011) 0.010 0.000 + 164 (0.008) 0.007 0.000 + 175 (0.008) 0.007 0.000 + +Locus 18 : mOC192 +20 alleles +3.3% missing data + 133 (0.064) 0.063 0.183 + 137 (0.157) 0.159 0.023 + 139 (0.050) 0.050 0.000 + 135 (0.061) 0.060 0.051 + 115 (0.144) 0.145 0.442 + 129 (0.045) 0.044 0.250 + 113 (0.154) 0.156 0.033 + 109 (0.014) 0.013 0.000 + 131 (0.044) 0.043 0.018 + 141 (0.017) 0.017 0.000 + 111 (0.007) 0.007 0.000 + 117 (0.040) 0.040 0.000 + 121 (0.053) 0.054 0.000 + 127 (0.033) 0.033 0.000 + 151 (0.011) 0.010 0.000 + 155 (0.011) 0.010 0.000 + 125 (0.040) 0.040 0.000 + 119 (0.033) 0.033 0.000 + 143 (0.011) 0.010 0.000 + 149 (0.011) 0.010 0.000 + +Locus 19 : mOC205 +33 alleles +14.2% missing data + 192 (0.033) 0.033 0.033 + 185 (0.099) 0.103 0.000 + 181 (0.125) 0.129 0.121 + 193 (0.022) 0.021 0.578 + 196 (0.015) 0.013 0.008 + 179 (0.073) 0.076 0.000 + 183 (0.076) 0.079 0.000 + 173 (0.056) 0.057 0.006 + 177 (0.027) 0.027 0.000 + 175 (0.021) 0.021 0.000 + 187 (0.053) 0.055 0.000 + 180 (0.011) 0.010 0.000 + 189 (0.035) 0.035 0.003 + 170 (0.011) 0.010 0.000 + 198 (0.011) 0.010 0.000 + 191 (0.024) 0.024 0.000 + 203 (0.007) 0.007 0.000 + 195 (0.029) 0.029 0.049 + 171 (0.027) 0.027 0.000 + 194 (0.011) 0.009 0.041 + 200 (0.015) 0.013 0.047 + 169 (0.039) 0.039 0.104 + 190 (0.053) 0.054 0.001 + 199 (0.008) 0.006 0.003 + 197 (0.024) 0.023 0.003 + 188 (0.024) 0.023 0.001 + 201 (0.008) 0.006 0.001 + 186 (0.024) 0.024 0.000 + 184 (0.007) 0.007 0.000 + 202 (0.008) 0.007 0.000 + 165 (0.008) 0.007 0.000 + 182 (0.007) 0.007 0.000 + 167 (0.008) 0.007 0.000 + +Locus 20 : mOC228 +13 alleles +2.7% missing data + 230 (0.136) 0.136 0.620 + 232 (0.155) 0.156 0.126 + 234 (0.225) 0.227 0.114 + 240 (0.218) 0.220 0.140 + 242 (0.071) 0.072 0.000 + 238 (0.067) 0.068 0.000 + 244 (0.028) 0.027 0.000 + 220 (0.031) 0.031 0.000 + 228 (0.014) 0.014 0.000 + 224 (0.021) 0.020 0.000 + 236 (0.018) 0.017 0.000 + 226 (0.008) 0.007 0.000 + 246 (0.008) 0.007 0.000 + +Locus 21 : Sat3 +25 alleles +1.1% missing data + 169 (0.114) 0.116 0.458 + 175 (0.081) 0.081 0.040 + 179 (0.068) 0.070 0.000 + 165 (0.062) 0.062 0.268 + 167 (0.033) 0.033 0.000 + 177 (0.035) 0.034 0.204 + 170 (0.040) 0.040 0.000 + 173 (0.086) 0.087 0.003 + 171 (0.036) 0.036 0.000 + 183 (0.033) 0.033 0.000 + 178 (0.043) 0.043 0.000 + 181 (0.072) 0.072 0.020 + 163 (0.030) 0.030 0.000 + 174 (0.030) 0.030 0.000 + 185 (0.008) 0.006 0.004 + 187 (0.007) 0.006 0.001 + 168 (0.030) 0.030 0.000 + 164 (0.049) 0.050 0.000 + 162 (0.020) 0.020 0.000 + 166 (0.023) 0.023 0.000 + 160 (0.011) 0.010 0.000 + 172 (0.017) 0.017 0.000 + 180 (0.020) 0.020 0.000 + 176 (0.023) 0.023 0.000 + 158 (0.027) 0.027 0.000 + +Locus 22 : Sat4 +23 alleles +5.8% missing data + 209 (0.149) 0.151 0.266 + 252 (0.032) 0.031 0.238 + 255 (0.091) 0.091 0.115 + 253 (0.041) 0.040 0.308 + 239 (0.195) 0.200 0.046 + 241 (0.075) 0.077 0.000 + 245 (0.020) 0.020 0.000 + 251 (0.049) 0.048 0.008 + 235 (0.052) 0.053 0.000 + 249 (0.040) 0.040 0.001 + 234 (0.024) 0.023 0.000 + 243 (0.050) 0.050 0.000 + 261 (0.014) 0.013 0.000 + 247 (0.011) 0.010 0.000 + 233 (0.011) 0.010 0.000 + 257 (0.010) 0.009 0.003 + 248 (0.015) 0.013 0.004 + 254 (0.043) 0.043 0.002 + 208 (0.011) 0.009 0.007 + 250 (0.030) 0.030 0.000 + 246 (0.020) 0.020 0.000 + 256 (0.007) 0.007 0.000 + 211 (0.011) 0.010 0.000 + +Locus 23 : Sat5 +19 alleles +6.0% missing data + 246 (0.028) 0.026 0.655 + 250 (0.040) 0.038 0.033 + 224 (0.153) 0.155 0.063 + 252 (0.048) 0.047 0.015 + 248 (0.012) 0.010 0.217 + 230 (0.091) 0.093 0.000 + 220 (0.027) 0.027 0.000 + 234 (0.030) 0.030 0.000 + 238 (0.037) 0.037 0.000 + 228 (0.185) 0.188 0.008 + 240 (0.056) 0.057 0.000 + 222 (0.030) 0.030 0.000 + 236 (0.011) 0.010 0.000 + 232 (0.066) 0.067 0.000 + 216 (0.046) 0.047 0.000 + 226 (0.076) 0.077 0.001 + 254 (0.024) 0.023 0.000 + 242 (0.024) 0.023 0.001 + 244 (0.016) 0.015 0.007 + +Locus 24 : Sat7 +16 alleles +1.5% missing data + 205 (0.062) 0.061 0.143 + 216 (0.138) 0.138 0.207 + 204 (0.013) 0.011 0.290 + 214 (0.157) 0.159 0.049 + 212 (0.085) 0.084 0.303 + 208 (0.128) 0.131 0.000 + 210 (0.163) 0.165 0.004 + 196 (0.084) 0.085 0.000 + 206 (0.077) 0.078 0.000 + 220 (0.008) 0.007 0.000 + 203 (0.015) 0.014 0.000 + 200 (0.008) 0.007 0.000 + 202 (0.011) 0.011 0.000 + 207 (0.009) 0.007 0.002 + 218 (0.029) 0.028 0.000 + 198 (0.015) 0.014 0.000 + +Locus 25 : Sat8 +26 alleles +0.7% missing data + 157 (0.011) 0.010 0.461 + 177 (0.079) 0.079 0.361 + 173 (0.081) 0.083 0.000 + 170 (0.007) 0.007 0.000 + 181 (0.039) 0.040 0.000 + 175 (0.036) 0.037 0.000 + 183 (0.039) 0.040 0.000 + 185 (0.011) 0.010 0.000 + 189 (0.017) 0.017 0.000 + 161 (0.392) 0.401 0.176 + 169 (0.014) 0.013 0.000 + 193 (0.007) 0.007 0.000 + 163 (0.039) 0.040 0.000 + 165 (0.027) 0.026 0.000 + 195 (0.011) 0.010 0.000 + 167 (0.033) 0.033 0.001 + 179 (0.033) 0.033 0.000 + 164 (0.017) 0.016 0.000 + 166 (0.011) 0.010 0.000 + 187 (0.017) 0.017 0.000 + 171 (0.020) 0.020 0.000 + 147 (0.007) 0.007 0.000 + 168 (0.017) 0.017 0.000 + 159 (0.014) 0.013 0.000 + 155 (0.007) 0.007 0.000 + 180 (0.011) 0.010 0.000 + +Locus 26 : mOC182 +17 alleles +11.4% missing data + 112 (0.019) 0.018 0.000 + 108 (0.037) 0.037 0.000 + 98 (0.103) 0.103 0.004 + 100 (0.129) 0.129 0.395 + 104 (0.051) 0.051 0.000 + 110 (0.037) 0.037 0.000 + 106 (0.073) 0.074 0.000 + 102 (0.082) 0.083 0.000 + 114 (0.010) 0.009 0.000 + 94 (0.028) 0.028 0.000 + 96 (0.037) 0.037 0.001 + 90 (0.046) 0.046 0.000 + 113 (0.079) 0.079 0.474 + 111 (0.057) 0.056 0.123 + 115 (0.091) 0.092 0.001 + 109 (0.105) 0.106 0.000 + 116 (0.015) 0.014 0.000 + +Locus 27 : mOC185 +9 alleles +5.8% missing data + 166 (0.635) 0.642 0.040 + 170 (0.165) 0.164 0.241 + 176 (0.048) 0.046 0.011 + 175 (0.012) 0.010 0.701 + 172 (0.027) 0.026 0.000 + 164 (0.067) 0.066 0.007 + 174 (0.016) 0.015 0.000 + 168 (0.023) 0.022 0.000 + 162 (0.008) 0.008 0.000 + +Locus 28 : mOC259 +26 alleles +1.3% missing data + 187 (0.064) 0.064 0.512 + 191 (0.014) 0.013 0.003 + 189 (0.074) 0.074 0.199 + 183 (0.073) 0.074 0.030 + 175 (0.077) 0.079 0.000 + 177 (0.058) 0.059 0.000 + 185 (0.218) 0.224 0.075 + 181 (0.059) 0.059 0.038 + 173 (0.080) 0.081 0.137 + 182 (0.023) 0.023 0.000 + 174 (0.011) 0.010 0.000 + 186 (0.017) 0.016 0.000 + 190 (0.017) 0.016 0.000 + 192 (0.007) 0.007 0.000 + 184 (0.042) 0.042 0.001 + 197 (0.007) 0.006 0.000 + 196 (0.014) 0.013 0.000 + 199 (0.032) 0.033 0.000 + 179 (0.051) 0.052 0.000 + 178 (0.011) 0.010 0.000 + 180 (0.007) 0.007 0.000 + 171 (0.010) 0.010 0.000 + 193 (0.011) 0.009 0.004 + 195 (0.007) 0.006 0.000 + 176 (0.007) 0.006 0.000 + 168 (0.007) 0.006 0.000 + +Locus 29 : mOC313 +16 alleles +7.4% missing data + 239 (0.092) 0.092 0.272 + 249 (0.136) 0.137 0.020 + 255 (0.117) 0.117 0.421 + 251 (0.044) 0.042 0.147 + 240 (0.005) 0.004 0.000 + 241 (0.120) 0.120 0.135 + 245 (0.081) 0.082 0.000 + 264 (0.029) 0.029 0.000 + 237 (0.029) 0.029 0.000 + 247 (0.045) 0.045 0.000 + 257 (0.081) 0.081 0.004 + 243 (0.093) 0.094 0.000 + 259 (0.013) 0.012 0.000 + 253 (0.093) 0.094 0.001 + 250 (0.009) 0.008 0.000 + 266 (0.013) 0.012 0.000 + +Locus 30 : mOC40 +16 alleles +0.7% missing data + 207 (0.013) 0.011 0.493 + 217 (0.143) 0.143 0.162 + 221 (0.207) 0.212 0.001 + 219 (0.135) 0.135 0.193 + 223 (0.105) 0.106 0.002 + 225 (0.096) 0.096 0.071 + 213 (0.013) 0.013 0.000 + 215 (0.035) 0.035 0.000 + 229 (0.023) 0.022 0.000 + 211 (0.017) 0.016 0.000 + 227 (0.110) 0.110 0.078 + 201 (0.020) 0.019 0.000 + 231 (0.026) 0.025 0.000 + 235 (0.013) 0.013 0.000 + 233 (0.026) 0.025 0.000 + 209 (0.020) 0.019 0.000 + +Locus 31 : EDNRA +11 alleles +1.8% missing data + 247 (0.129) 0.128 0.413 + 249 (0.031) 0.029 0.584 + 239 (0.046) 0.045 0.000 + 235 (0.334) 0.338 0.001 + 251 (0.008) 0.007 0.000 + 233 (0.025) 0.024 0.000 + 243 (0.066) 0.066 0.000 + 245 (0.121) 0.122 0.001 + 232 (0.018) 0.017 0.000 + 237 (0.063) 0.063 0.000 + 241 (0.159) 0.160 0.000 + +Locus 32 : GPR64 +9 alleles +22.1% missing data + 141 (0.055) 0.053 0.016 + 137 (0.270) 0.272 0.025 + 129 (0.119) 0.118 0.955 + 131 (0.107) 0.107 0.000 + 135 (0.124) 0.125 0.000 + 139 (0.200) 0.202 0.001 + 125 (0.014) 0.013 0.000 + 133 (0.072) 0.071 0.003 + 123 (0.039) 0.039 0.000 + +Locus 33 : KLH13 +11 alleles +20.1% missing data + 251 (0.014) 0.012 0.188 + 255 (0.242) 0.244 0.098 + 263 (0.104) 0.104 0.023 + 257 (0.082) 0.081 0.251 + 265 (0.101) 0.100 0.300 + 259 (0.103) 0.104 0.001 + 261 (0.157) 0.160 0.000 + 249 (0.036) 0.036 0.000 + 253 (0.087) 0.088 0.001 + 267 (0.053) 0.051 0.139 + 245 (0.021) 0.020 0.000 + +Locus 34 : Proc +12 alleles +4.0% missing data + 117 (0.164) 0.165 0.016 + 133 (0.016) 0.014 0.128 + 119 (0.156) 0.157 0.020 + 115 (0.047) 0.045 0.259 + 127 (0.134) 0.134 0.531 + 121 (0.119) 0.119 0.025 + 129 (0.098) 0.097 0.019 + 123 (0.121) 0.123 0.000 + 125 (0.079) 0.080 0.000 + 131 (0.037) 0.036 0.001 + 109 (0.011) 0.010 0.000 + 135 (0.020) 0.020 0.000 + +Locus 35 : HPRT +23 alleles +21.3% missing data + 167 (0.051) 0.050 0.461 + 157 (0.069) 0.069 0.292 + 153 (0.019) 0.018 0.133 + 161 (0.057) 0.058 0.000 + 163 (0.096) 0.096 0.065 + 165 (0.120) 0.122 0.040 + 139 (0.017) 0.016 0.000 + 141 (0.033) 0.033 0.000 + 143 (0.065) 0.066 0.000 + 135 (0.009) 0.008 0.000 + 145 (0.072) 0.074 0.000 + 171 (0.025) 0.025 0.000 + 159 (0.061) 0.062 0.000 + 148 (0.029) 0.029 0.000 + 144 (0.017) 0.016 0.000 + 155 (0.021) 0.021 0.000 + 147 (0.061) 0.062 0.000 + 149 (0.029) 0.029 0.000 + 169 (0.083) 0.083 0.007 + 137 (0.013) 0.012 0.000 + 179 (0.009) 0.008 0.000 + 151 (0.017) 0.016 0.000 + 146 (0.029) 0.029 0.000 + +Locus 36 : mc342 +18 alleles +1.5% missing data + 192 (0.010) 0.008 0.307 + 194 (0.022) 0.021 0.040 + 190 (0.032) 0.031 0.445 + 188 (0.089) 0.089 0.050 + 196 (0.015) 0.013 0.039 + 172 (0.171) 0.174 0.015 + 178 (0.055) 0.055 0.000 + 176 (0.071) 0.072 0.000 + 180 (0.074) 0.075 0.000 + 170 (0.084) 0.084 0.084 + 182 (0.058) 0.059 0.000 + 184 (0.093) 0.094 0.001 + 174 (0.033) 0.033 0.000 + 164 (0.014) 0.013 0.000 + 166 (0.045) 0.046 0.000 + 186 (0.091) 0.092 0.018 + 177 (0.017) 0.016 0.000 + 183 (0.026) 0.026 0.000 + +Locus 37 : AMOT +9 alleles +22.7% missing data + 205 (0.147) 0.147 0.513 + 211 (0.239) 0.241 0.163 + 221 (0.025) 0.023 0.195 + 215 (0.145) 0.145 0.084 + 207 (0.184) 0.185 0.042 + 213 (0.120) 0.121 0.000 + 217 (0.030) 0.029 0.000 + 219 (0.026) 0.025 0.001 + 209 (0.083) 0.084 0.000 + +Locus 38 : EXT +18 alleles +15.4% missing data + 154 (0.418) 0.425 0.159 + 184 (0.021) 0.020 0.663 + 158 (0.167) 0.168 0.168 + 166 (0.046) 0.046 0.000 + 150 (0.039) 0.039 0.000 + 156 (0.020) 0.019 0.000 + 164 (0.009) 0.008 0.000 + 168 (0.009) 0.008 0.000 + 172 (0.009) 0.008 0.000 + 180 (0.057) 0.058 0.000 + 190 (0.016) 0.015 0.000 + 160 (0.018) 0.017 0.002 + 162 (0.098) 0.100 0.000 + 182 (0.024) 0.023 0.000 + 176 (0.012) 0.012 0.000 + 178 (0.016) 0.015 0.000 + 186 (0.013) 0.011 0.006 + 146 (0.008) 0.008 0.000 + +Locus 39 : CRYL +16 alleles +13.2% missing data + 196 (0.193) 0.195 0.506 + 202 (0.287) 0.290 0.395 + 206 (0.071) 0.070 0.071 + 198 (0.074) 0.075 0.001 + 204 (0.052) 0.053 0.000 + 192 (0.038) 0.038 0.000 + 208 (0.026) 0.024 0.026 + 190 (0.045) 0.045 0.000 + 194 (0.067) 0.068 0.000 + 200 (0.070) 0.071 0.000 + 224 (0.008) 0.007 0.000 + 188 (0.012) 0.011 0.000 + 214 (0.008) 0.007 0.000 + 210 (0.012) 0.011 0.000 + 212 (0.023) 0.023 0.000 + 184 (0.012) 0.011 0.000 + +Values of parameters used in structure: +DATAFILE=C:\Users\jota.blanco\Desktop\SAmer_reduc\OC_SA2\project_data, OUTFILE=C:\Users\jota.blanco\Desktop\SAmer_reduc\OC_SA2\pop250y500mil\Results\pop250y500mil_run_5, NUMINDS=551, NUMLOCI=39, MISSING=-9, LABEL=1, POPDATA=1, POPFLAG=1, PHENOTYPE=0, EXTRACOLS=0, MAXPOPS=2, BURNIN=250000, NUMREPS=500000, USEPOPINFO=0, INFERALPHA=1, INFERLAMBDA=0, POPSPECIFICLAMBDA=0, POPALPHAS=1, COMPUTEPROB=1, NOADMIX=0, ADMBURNIN=2500, UPDATEFREQ=1, PRINTLIKES=0, INTERMEDSAVE=0, PRINTKLD=0, PRINTNET=0, PRINTLAMBDA=0, ANCESTDIST=1, NUMBOXES=1000, ANCESTPINT=0.90000, GENSBACK=2, MIGRPRIOR=0.05000, PRINTQHAT=0, PRINTQSUM=0, ALPHA=1.0000, FREQSCORR=1, FPRIORMEAN=0.0100, FPRIORSD=0.0500, ONEFST=0, LAMBDA=1.0000, UNIFPRIORALPHA=1, ALPHAMAX=10.0000, ALPHAPRIORA=1.0000, ALPHAPRIORB=2.0000, ALPHAPROPSD=0.0250, STARTATPOPINFO=0, RANDOMIZE=0, LINKAGE=0, METROFREQ=10, REPORTHITRATE=0, MARKOVPHASE=-1, PHASED=0, PLOIDY=2, PHASEINFO=0 LOCPRIOR=0, LOCPRIORINIT=1.000000, LOCDATA=0, LOCISPOP=0, LOCPRIORSTEP=0.100000, MAXLOCPRIOR=20.000000, SEED=5691, +[STRAT parameters]: NUMSIMSTATS=1000, PHENOTYPECOL=-9, POOLFREQ=10, LOCUSxONLY=0, EMERROR=0.00100, MISSINGPHENO=-9, \ No newline at end of file diff --git a/inst/files/structure/structure_01 b/inst/files/structure/structure_01 new file mode 100644 index 0000000..336e58a --- /dev/null +++ b/inst/files/structure/structure_01 @@ -0,0 +1,529 @@ + + +---------------------------------------------------- +STRUCTURE by Pritchard, Stephens and Donnelly (2000) + and Falush, Stephens and Pritchard (2003) + Code by Pritchard, Falush and Hubisz + Version 2.3.2.1 (Oct 2009) +---------------------------------------------------- + + + +Command line arguments: +Input File: + +Run parameters: + 149 individuals + 25 loci + 2 populations assumed + 100000 Burn-in period + 1000000 Reps + + +-------------------------------------------- +Overall proportion of membership of the +sample in each of the 2 clusters + +Inferred Clusters + 1 2 +0.630 0.370 + +-------------------------------------------- + +Allele-freq. divergence among pops (Net nucleotide distance), +computed using point estimates of P. + + 1 2 + 1 - 0.0283 + 2 0.0283 - + +Average distances (expected heterozygosity) between individuals in same cluster: +cluster 1 : 0.5131 +cluster 2 : 0.4622 + +-------------------------------------------- +Estimated Ln Prob of Data = -7509.5 +Mean value of ln likelihood = -7387.2 +Variance of ln likelihood = 244.6 +Mean value of alpha = 0.1280 + +Mean value of Fst_1 = 0.0718 +Mean value of Fst_2 = 0.0681 + + +Inferred ancestry of individuals: + Label (%Miss) : Inferred clusters + 1 I13825 (0) : 0.965 0.035 + 2 I13826 (0) : 0.977 0.023 + 3 I13827 (20) : 0.961 0.039 + 4 I13828 (0) : 0.975 0.025 + 5 I13829 (8) : 0.974 0.026 + 6 I13830 (0) : 0.982 0.018 + 7 I13831 (0) : 0.976 0.024 + 8 I13832 (16) : 0.958 0.042 + 9 I13833 (0) : 0.971 0.029 + 10 I13834 (0) : 0.985 0.015 + 11 I13835 (0) : 0.979 0.021 + 12 I13836 (0) : 0.978 0.022 + 13 I13377 (0) : 0.946 0.054 + 14 I13378 (0) : 0.953 0.047 + 15 I13379 (0) : 0.972 0.028 + 16 I13380 (0) : 0.881 0.119 + 17 I13381 (0) : 0.908 0.092 + 18 I13382 (0) : 0.981 0.019 + 19 I13383 (0) : 0.943 0.057 + 20 I13384 (0) : 0.963 0.037 + 21 I13385 (0) : 0.984 0.016 + 22 I13386 (0) : 0.979 0.021 + 23 I13387 (0) : 0.965 0.035 + 24 I13388 (0) : 0.823 0.177 + 25 I13389 (0) : 0.892 0.108 + 26 I13390 (0) : 0.961 0.039 + 27 I13391 (0) : 0.878 0.122 + 28 I13392 (0) : 0.943 0.057 + 29 I13393 (0) : 0.601 0.399 + 30 I13394 (4) : 0.546 0.454 + 31 I13395 (0) : 0.654 0.346 + 32 I13396 (0) : 0.828 0.172 + 33 I13397 (0) : 0.977 0.023 + 34 I13398 (0) : 0.986 0.014 + 35 I13399 (4) : 0.934 0.066 + 36 I13400 (0) : 0.902 0.098 + 37 I13401 (0) : 0.549 0.451 + 38 I13402 (0) : 0.916 0.084 + 39 I13403 (0) : 0.913 0.087 + 40 I13404 (0) : 0.982 0.018 + 41 I13405 (0) : 0.972 0.028 + 42 I13406 (16) : 0.970 0.030 + 43 I13407 (0) : 0.977 0.023 + 44 I13408 (0) : 0.972 0.028 + 45 I13409 (0) : 0.870 0.130 + 46 I13410 (0) : 0.983 0.017 + 47 I13411 (0) : 0.988 0.012 + 48 I13412 (0) : 0.717 0.283 + 49 I13413 (0) : 0.940 0.060 + 50 I13414 (0) : 0.975 0.025 + 51 I13415 (4) : 0.943 0.057 + 52 I13416 (4) : 0.922 0.078 + 53 I13417 (4) : 0.896 0.104 + 54 I13418 (0) : 0.914 0.086 + 55 I13419 (0) : 0.976 0.024 + 56 I13420 (0) : 0.874 0.126 + 57 I13421 (0) : 0.831 0.169 + 58 I13422 (0) : 0.822 0.178 + 59 I13423 (0) : 0.818 0.182 + 60 I13424 (0) : 0.962 0.038 + 61 I13425 (4) : 0.943 0.057 + 62 I13426 (4) : 0.374 0.626 + 63 I13870 (0) : 0.841 0.159 + 64 I13871 (16) : 0.964 0.036 + 65 I13872 (0) : 0.975 0.025 + 66 I13873 (4) : 0.899 0.101 + 67 I13874 (0) : 0.880 0.120 + 68 I13875 (8) : 0.948 0.052 + 69 I13876 (0) : 0.686 0.314 + 70 I13877 (20) : 0.934 0.066 + 71 I13878 (28) : 0.978 0.022 + 72 I13879 (4) : 0.986 0.014 + 73 I13880 (4) : 0.980 0.020 + 74 I13881 (0) : 0.919 0.081 + 75 I13882 (0) : 0.974 0.026 + 76 I13883 (4) : 0.913 0.087 + 77 I13884 (16) : 0.899 0.101 + 78 I13885 (20) : 0.974 0.026 + 79 I13886 (8) : 0.982 0.018 + 80 I13887 (0) : 0.614 0.386 + 81 I13888 (0) : 0.914 0.086 + 82 I13889 (0) : 0.142 0.858 + 83 I13890 (32) : 0.323 0.677 + 84 I13891 (0) : 0.961 0.039 + 85 I13892 (0) : 0.505 0.495 + 86 I13893 (8) : 0.866 0.134 + 87 I13894 (0) : 0.966 0.034 + 88 I13895 (4) : 0.706 0.294 + 89 I13896 (0) : 0.840 0.160 + 90 I13897 (0) : 0.989 0.011 + 91 I13898 (4) : 0.968 0.032 + 92 I13899 (0) : 0.987 0.013 + 93 I13900 (32) : 0.850 0.150 + 94 I13837 (0) : 0.959 0.041 + 95 I13838 (0) : 0.228 0.772 + 96 I13839 (0) : 0.930 0.070 + 97 I13840 (0) : 0.911 0.089 + 98 I13841 (0) : 0.340 0.660 + 99 I13842 (0) : 0.683 0.317 +100 I13843 (4) : 0.275 0.725 +101 I13844 (16) : 0.849 0.151 +102 I13845 (0) : 0.976 0.024 +103 I13846 (0) : 0.942 0.058 +104 I13847 (0) : 0.648 0.352 +105 I13848 (0) : 0.580 0.420 +106 I13849 (0) : 0.908 0.092 +107 I13850 (0) : 0.449 0.551 +108 I12577 (4) : 0.030 0.970 +109 I12578 (4) : 0.061 0.939 +110 I12579 (8) : 0.024 0.976 +111 I12580 (8) : 0.032 0.968 +112 I12581 (4) : 0.279 0.721 +113 I12582 (4) : 0.037 0.963 +114 I12583 (8) : 0.096 0.904 +115 I12584 (4) : 0.054 0.946 +116 I12585 (4) : 0.019 0.981 +117 I12586 (4) : 0.027 0.973 +118 I12587 (8) : 0.021 0.979 +119 I12588 (4) : 0.018 0.982 +120 I12589 (0) : 0.044 0.956 +121 I12590 (0) : 0.051 0.949 +122 I12591 (12) : 0.011 0.989 +123 I12592 (4) : 0.030 0.970 +124 I12593 (4) : 0.018 0.982 +125 I12594 (8) : 0.019 0.981 +126 I12595 (0) : 0.028 0.972 +127 I12596 (0) : 0.018 0.982 +128 I12597 (4) : 0.070 0.930 +129 I12598 (0) : 0.105 0.895 +130 I12599 (0) : 0.092 0.908 +131 I12600 (4) : 0.036 0.964 +132 I12601 (8) : 0.025 0.975 +133 I12602 (12) : 0.027 0.973 +134 I12603 (0) : 0.030 0.970 +135 I12604 (4) : 0.050 0.950 +136 I12605 (4) : 0.035 0.965 +137 I12606 (8) : 0.021 0.979 +138 I12607 (4) : 0.028 0.972 +139 I12608 (8) : 0.039 0.961 +140 I12609 (8) : 0.023 0.977 +141 I12610 (52) : 0.037 0.963 +142 I12611 (0) : 0.019 0.981 +143 I12612 (0) : 0.022 0.978 +144 I12613 (0) : 0.018 0.982 +145 I12614 (4) : 0.056 0.944 +146 I12615 (0) : 0.073 0.927 +147 I12616 (4) : 0.063 0.937 +148 I12617 (8) : 0.016 0.984 +149 I12618 (48) : 0.021 0.979 + + +Estimated Allele Frequencies in each cluster +First column gives estimated ancestral frequencies + + +Locus 1 : A8 +7 alleles +4.0% missing data + 177 (0.476) 0.467 0.603 + 179 (0.110) 0.105 0.057 + 175 (0.075) 0.231 0.010 + 173 (0.052) 0.054 0.009 + 181 (0.196) 0.112 0.283 + 165 (0.056) 0.013 0.032 + 183 (0.036) 0.017 0.005 + +Locus 2 : A14 +5 alleles +0.0% missing data + 112 (0.133) 0.294 0.035 + 110 (0.723) 0.679 0.824 + 114 (0.038) 0.016 0.006 + 118 (0.066) 0.008 0.099 + 116 (0.040) 0.003 0.036 + +Locus 3 : A24 +5 alleles +2.7% missing data + 104 (0.364) 0.380 0.375 + 106 (0.529) 0.593 0.562 + 101 (0.028) 0.007 0.004 + 108 (0.036) 0.017 0.005 + 96 (0.043) 0.003 0.054 + +Locus 4 : A29 +29 alleles +6.7% missing data + 143 (0.027) 0.062 0.005 + 149 (0.043) 0.029 0.060 + 147 (0.036) 0.020 0.028 + 153 (0.055) 0.073 0.084 + 169 (0.043) 0.047 0.037 + 151 (0.045) 0.045 0.050 + 145 (0.034) 0.017 0.024 + 157 (0.060) 0.081 0.117 + 155 (0.066) 0.107 0.145 + 159 (0.049) 0.085 0.043 + 161 (0.031) 0.061 0.009 + 141 (0.032) 0.033 0.013 + 139 (0.020) 0.011 0.003 + 144 (0.025) 0.042 0.004 + 171 (0.044) 0.048 0.044 + 163 (0.054) 0.088 0.066 + 167 (0.044) 0.038 0.052 + 173 (0.030) 0.023 0.011 + 142 (0.018) 0.006 0.003 + 177 (0.031) 0.008 0.038 + 175 (0.028) 0.008 0.019 + 165 (0.042) 0.032 0.044 + 146 (0.022) 0.022 0.003 + 137 (0.025) 0.005 0.015 + 183 (0.020) 0.002 0.020 + 179 (0.021) 0.002 0.020 + 191 (0.018) 0.001 0.011 + 185 (0.018) 0.002 0.011 + 180 (0.020) 0.001 0.021 + +Locus 5 : A43 +7 alleles +1.3% missing data + 123 (0.161) 0.121 0.166 + 141 (0.028) 0.007 0.004 + 137 (0.630) 0.831 0.679 + 139 (0.083) 0.034 0.069 + 124 (0.043) 0.003 0.061 + 143 (0.028) 0.002 0.011 + 128 (0.028) 0.002 0.011 + +Locus 6 : A79 +13 alleles +3.4% missing data + 103 (0.184) 0.289 0.203 + 97 (0.099) 0.136 0.067 + 101 (0.093) 0.157 0.047 + 107 (0.104) 0.127 0.083 + 109 (0.092) 0.079 0.085 + 105 (0.177) 0.145 0.349 + 111 (0.055) 0.021 0.037 + 113 (0.025) 0.005 0.005 + 91 (0.039) 0.004 0.071 + 99 (0.048) 0.017 0.026 + 115 (0.035) 0.011 0.016 + 117 (0.025) 0.006 0.004 + 121 (0.024) 0.005 0.006 + +Locus 7 : A88 +9 alleles +6.0% missing data + 133 (0.028) 0.007 0.004 + 149 (0.514) 0.494 0.764 + 137 (0.076) 0.119 0.020 + 147 (0.169) 0.312 0.085 + 141 (0.098) 0.051 0.085 + 152 (0.028) 0.007 0.004 + 143 (0.028) 0.006 0.005 + 151 (0.028) 0.002 0.012 + 144 (0.032) 0.002 0.021 + +Locus 8 : A113 +12 alleles +7.4% missing data + 214 (0.489) 0.725 0.711 + 226 (0.076) 0.069 0.042 + 218 (0.026) 0.006 0.004 + 220 (0.084) 0.030 0.126 + 216 (0.062) 0.026 0.043 + 230 (0.043) 0.047 0.009 + 234 (0.035) 0.022 0.006 + 232 (0.038) 0.021 0.009 + 228 (0.054) 0.031 0.022 + 224 (0.026) 0.006 0.005 + 222 (0.042) 0.010 0.020 + 208 (0.026) 0.006 0.004 + +Locus 9 : Ac11 +9 alleles +4.7% missing data + 111 (0.110) 0.203 0.042 + 117 (0.250) 0.356 0.222 + 115 (0.239) 0.298 0.237 + 113 (0.163) 0.099 0.247 + 119 (0.087) 0.023 0.142 + 121 (0.044) 0.005 0.052 + 123 (0.040) 0.008 0.022 + 127 (0.039) 0.006 0.025 + 125 (0.027) 0.002 0.011 + +Locus 10 : Ac88 +8 alleles +0.7% missing data + 214 (0.708) 0.825 0.880 + 216 (0.034) 0.017 0.004 + 220 (0.103) 0.145 0.038 + 230 (0.037) 0.006 0.015 + 221 (0.028) 0.002 0.011 + 212 (0.031) 0.002 0.020 + 217 (0.028) 0.002 0.011 + 224 (0.032) 0.002 0.020 + +Locus 11 : Ac139 +8 alleles +13.4% missing data + 327 (0.527) 0.515 0.736 + 329 (0.225) 0.368 0.144 + 331 (0.076) 0.071 0.027 + 328 (0.045) 0.037 0.009 + 341 (0.029) 0.002 0.012 + 337 (0.040) 0.003 0.048 + 323 (0.029) 0.003 0.012 + 339 (0.029) 0.002 0.012 + +Locus 12 : Ac306 +6 alleles +4.7% missing data + 165 (0.674) 0.761 0.800 + 177 (0.107) 0.054 0.097 + 173 (0.102) 0.118 0.041 + 169 (0.050) 0.059 0.008 + 171 (0.028) 0.005 0.007 + 179 (0.040) 0.003 0.047 + +Locus 13 : Ap15 +7 alleles +6.0% missing data + 202 (0.754) 0.955 0.805 + 212 (0.035) 0.018 0.004 + 204 (0.052) 0.010 0.038 + 208 (0.048) 0.005 0.062 + 220 (0.054) 0.007 0.068 + 219 (0.028) 0.002 0.011 + 210 (0.028) 0.002 0.011 + +Locus 14 : Ap68 +9 alleles +4.7% missing data + 158 (0.302) 0.434 0.302 + 160 (0.084) 0.096 0.033 + 156 (0.271) 0.294 0.335 + 162 (0.051) 0.021 0.020 + 154 (0.076) 0.105 0.025 + 152 (0.106) 0.030 0.228 + 164 (0.053) 0.016 0.028 + 170 (0.027) 0.003 0.010 + 166 (0.030) 0.002 0.020 + +Locus 15 : Ap85 +10 alleles +3.4% missing data + 202 (0.323) 0.324 0.484 + 186 (0.205) 0.414 0.128 + 204 (0.069) 0.027 0.054 + 188 (0.088) 0.120 0.035 + 194 (0.076) 0.067 0.034 + 196 (0.068) 0.014 0.108 + 200 (0.069) 0.018 0.085 + 192 (0.037) 0.007 0.014 + 190 (0.026) 0.007 0.004 + 198 (0.038) 0.003 0.054 + +Locus 16 : Ap90 +13 alleles +0.7% missing data + 131 (0.349) 0.512 0.505 + 135 (0.084) 0.054 0.077 + 133 (0.199) 0.277 0.227 + 129 (0.103) 0.100 0.087 + 137 (0.047) 0.021 0.017 + 141 (0.025) 0.006 0.004 + 143 (0.028) 0.011 0.004 + 151 (0.035) 0.007 0.012 + 155 (0.025) 0.006 0.004 + 145 (0.025) 0.002 0.011 + 130 (0.028) 0.002 0.020 + 139 (0.025) 0.002 0.011 + 153 (0.028) 0.002 0.020 + +Locus 17 : Ap223 +7 alleles +2.0% missing data + 183 (0.654) 0.654 0.864 + 187 (0.106) 0.258 0.027 + 189 (0.035) 0.017 0.004 + 173 (0.082) 0.041 0.050 + 182 (0.038) 0.016 0.008 + 180 (0.037) 0.006 0.016 + 179 (0.048) 0.008 0.031 + +Locus 18 : Ap224 +7 alleles +4.0% missing data + 283 (0.094) 0.186 0.023 + 287 (0.423) 0.461 0.470 + 281 (0.130) 0.166 0.063 + 289 (0.244) 0.145 0.388 + 291 (0.042) 0.033 0.006 + 285 (0.028) 0.007 0.004 + 279 (0.039) 0.003 0.046 + +Locus 19 : Ap226 +5 alleles +17.4% missing data + 237 (0.349) 0.346 0.372 + 239 (0.485) 0.477 0.568 + 247 (0.103) 0.168 0.035 + 235 (0.031) 0.007 0.006 + 241 (0.031) 0.002 0.019 + +Locus 20 : Ap249 +9 alleles +1.3% missing data + 209 (0.552) 0.655 0.684 + 211 (0.052) 0.045 0.012 + 217 (0.087) 0.102 0.033 + 219 (0.093) 0.150 0.030 + 215 (0.106) 0.027 0.218 + 208 (0.027) 0.006 0.004 + 225 (0.027) 0.006 0.004 + 223 (0.027) 0.007 0.003 + 213 (0.027) 0.002 0.011 + +Locus 21 : Ap273 +4 alleles +1.3% missing data + 106 (0.851) 0.939 0.944 + 108 (0.065) 0.028 0.026 + 104 (0.041) 0.027 0.006 + 102 (0.044) 0.006 0.024 + +Locus 22 : Ap274 +2 alleles +2.0% missing data + 120 (0.926) 0.986 0.914 + 122 (0.074) 0.014 0.086 + +Locus 23 : Ap288 +5 alleles +0.0% missing data + 123 (0.752) 0.706 0.929 + 131 (0.155) 0.263 0.060 + 139 (0.036) 0.017 0.004 + 121 (0.029) 0.007 0.004 + 124 (0.029) 0.007 0.004 + +Locus 24 : At163 +7 alleles +0.0% missing data + 128 (0.692) 0.695 0.887 + 134 (0.163) 0.281 0.072 + 130 (0.033) 0.011 0.005 + 136 (0.028) 0.007 0.004 + 140 (0.028) 0.002 0.011 + 146 (0.028) 0.002 0.011 + 142 (0.028) 0.002 0.011 + +Locus 25 : At188 +13 alleles +1.3% missing data + 189 (0.558) 0.734 0.866 + 205 (0.036) 0.033 0.004 + 207 (0.040) 0.048 0.005 + 219 (0.030) 0.012 0.004 + 209 (0.040) 0.037 0.006 + 217 (0.038) 0.026 0.007 + 215 (0.029) 0.012 0.004 + 199 (0.076) 0.041 0.056 + 212 (0.033) 0.016 0.006 + 213 (0.038) 0.027 0.006 + 211 (0.026) 0.006 0.004 + 191 (0.026) 0.007 0.003 + 187 (0.032) 0.002 0.028 + +Values of parameters used in structure: +DATAFILE=, OUTFILE=, NUMINDS=149, NUMLOCI=25, MISSING=-9, LABEL=1, POPDATA=0, POPFLAG=1, PHENOTYPE=0, EXTRACOLS=1, MAXPOPS=2, BURNIN=100000, NUMREPS=1000000, USEPOPINFO=0, INFERALPHA=1, INFERLAMBDA=0, POPSPECIFICLAMBDA=0, POPALPHAS=0, COMPUTEPROB=1, NOADMIX=0, ADMBURNIN=2500, UPDATEFREQ=1, PRINTLIKES=0, INTERMEDSAVE=0, PRINTKLD=0, PRINTNET=0, PRINTLAMBDA=0, ANCESTDIST=0, NUMBOXES=1000, ANCESTPINT=0.90000, GENSBACK=2, MIGRPRIOR=0.05000, PRINTQHAT=0, PRINTQSUM=0, ALPHA=1.0000, FREQSCORR=1, FPRIORMEAN=0.0100, FPRIORSD=0.0500, ONEFST=0, LAMBDA=1.0000, UNIFPRIORALPHA=1, ALPHAMAX=10.0000, ALPHAPRIORA=1.0000, ALPHAPRIORB=2.0000, ALPHAPROPSD=0.0250, STARTATPOPINFO=0, RANDOMIZE=1, LINKAGE=0, METROFREQ=10, REPORTHITRATE=0, MARKOVPHASE=-1, PHASED=0, PLOIDY=2, PHASEINFO=0 LOCPRIOR=0, LOCPRIORINIT=1.000000, LOCDATA=0, LOCISPOP=0, LOCPRIORSTEP=0.100000, MAXLOCPRIOR=20.000000, SEED=1335105564, +[STRAT parameters]: NUMSIMSTATS=1000, PHENOTYPECOL=-9, POOLFREQ=10, LOCUSxONLY=0, EMERROR=0.00100, MISSINGPHENO=-9, \ No newline at end of file diff --git a/inst/files/structure/structure_02 b/inst/files/structure/structure_02 new file mode 100644 index 0000000..d97eb37 --- /dev/null +++ b/inst/files/structure/structure_02 @@ -0,0 +1,529 @@ + + +---------------------------------------------------- +STRUCTURE by Pritchard, Stephens and Donnelly (2000) + and Falush, Stephens and Pritchard (2003) + Code by Pritchard, Falush and Hubisz + Version 2.3.2.1 (Oct 2009) +---------------------------------------------------- + + + +Command line arguments: +Input File: + +Run parameters: + 149 individuals + 25 loci + 2 populations assumed + 100000 Burn-in period + 1000000 Reps + + +-------------------------------------------- +Overall proportion of membership of the +sample in each of the 2 clusters + +Inferred Clusters + 1 2 +0.630 0.370 + +-------------------------------------------- + +Allele-freq. divergence among pops (Net nucleotide distance), +computed using point estimates of P. + + 1 2 + 1 - 0.0282 + 2 0.0282 - + +Average distances (expected heterozygosity) between individuals in same cluster: +cluster 1 : 0.5131 +cluster 2 : 0.4623 + +-------------------------------------------- +Estimated Ln Prob of Data = -7508.5 +Mean value of ln likelihood = -7387.2 +Variance of ln likelihood = 242.6 +Mean value of alpha = 0.1270 + +Mean value of Fst_1 = 0.0718 +Mean value of Fst_2 = 0.0679 + + +Inferred ancestry of individuals: + Label (%Miss) : Inferred clusters + 1 I13825 (0) : 0.965 0.035 + 2 I13826 (0) : 0.977 0.023 + 3 I13827 (20) : 0.962 0.038 + 4 I13828 (0) : 0.975 0.025 + 5 I13829 (8) : 0.974 0.026 + 6 I13830 (0) : 0.982 0.018 + 7 I13831 (0) : 0.975 0.025 + 8 I13832 (16) : 0.959 0.041 + 9 I13833 (0) : 0.971 0.029 + 10 I13834 (0) : 0.985 0.015 + 11 I13835 (0) : 0.979 0.021 + 12 I13836 (0) : 0.978 0.022 + 13 I13377 (0) : 0.947 0.053 + 14 I13378 (0) : 0.953 0.047 + 15 I13379 (0) : 0.973 0.027 + 16 I13380 (0) : 0.881 0.119 + 17 I13381 (0) : 0.909 0.091 + 18 I13382 (0) : 0.981 0.019 + 19 I13383 (0) : 0.943 0.057 + 20 I13384 (0) : 0.963 0.037 + 21 I13385 (0) : 0.984 0.016 + 22 I13386 (0) : 0.979 0.021 + 23 I13387 (0) : 0.965 0.035 + 24 I13388 (0) : 0.824 0.176 + 25 I13389 (0) : 0.891 0.109 + 26 I13390 (0) : 0.962 0.038 + 27 I13391 (0) : 0.877 0.123 + 28 I13392 (0) : 0.944 0.056 + 29 I13393 (0) : 0.599 0.401 + 30 I13394 (4) : 0.541 0.459 + 31 I13395 (0) : 0.653 0.347 + 32 I13396 (0) : 0.827 0.173 + 33 I13397 (0) : 0.978 0.022 + 34 I13398 (0) : 0.986 0.014 + 35 I13399 (4) : 0.933 0.067 + 36 I13400 (0) : 0.902 0.098 + 37 I13401 (0) : 0.544 0.456 + 38 I13402 (0) : 0.917 0.083 + 39 I13403 (0) : 0.915 0.085 + 40 I13404 (0) : 0.982 0.018 + 41 I13405 (0) : 0.972 0.028 + 42 I13406 (16) : 0.971 0.029 + 43 I13407 (0) : 0.977 0.023 + 44 I13408 (0) : 0.972 0.028 + 45 I13409 (0) : 0.872 0.128 + 46 I13410 (0) : 0.983 0.017 + 47 I13411 (0) : 0.988 0.012 + 48 I13412 (0) : 0.717 0.283 + 49 I13413 (0) : 0.940 0.060 + 50 I13414 (0) : 0.975 0.025 + 51 I13415 (4) : 0.941 0.059 + 52 I13416 (4) : 0.922 0.078 + 53 I13417 (4) : 0.899 0.101 + 54 I13418 (0) : 0.914 0.086 + 55 I13419 (0) : 0.976 0.024 + 56 I13420 (0) : 0.878 0.122 + 57 I13421 (0) : 0.832 0.168 + 58 I13422 (0) : 0.819 0.181 + 59 I13423 (0) : 0.815 0.185 + 60 I13424 (0) : 0.963 0.037 + 61 I13425 (4) : 0.943 0.057 + 62 I13426 (4) : 0.373 0.627 + 63 I13870 (0) : 0.841 0.159 + 64 I13871 (16) : 0.964 0.036 + 65 I13872 (0) : 0.975 0.025 + 66 I13873 (4) : 0.898 0.102 + 67 I13874 (0) : 0.882 0.118 + 68 I13875 (8) : 0.948 0.052 + 69 I13876 (0) : 0.693 0.307 + 70 I13877 (20) : 0.934 0.066 + 71 I13878 (28) : 0.979 0.021 + 72 I13879 (4) : 0.986 0.014 + 73 I13880 (4) : 0.980 0.020 + 74 I13881 (0) : 0.920 0.080 + 75 I13882 (0) : 0.974 0.026 + 76 I13883 (4) : 0.913 0.087 + 77 I13884 (16) : 0.900 0.100 + 78 I13885 (20) : 0.974 0.026 + 79 I13886 (8) : 0.982 0.018 + 80 I13887 (0) : 0.614 0.386 + 81 I13888 (0) : 0.915 0.085 + 82 I13889 (0) : 0.140 0.860 + 83 I13890 (32) : 0.328 0.672 + 84 I13891 (0) : 0.962 0.038 + 85 I13892 (0) : 0.501 0.499 + 86 I13893 (8) : 0.865 0.135 + 87 I13894 (0) : 0.966 0.034 + 88 I13895 (4) : 0.703 0.297 + 89 I13896 (0) : 0.841 0.159 + 90 I13897 (0) : 0.989 0.011 + 91 I13898 (4) : 0.968 0.032 + 92 I13899 (0) : 0.988 0.012 + 93 I13900 (32) : 0.853 0.147 + 94 I13837 (0) : 0.959 0.041 + 95 I13838 (0) : 0.230 0.770 + 96 I13839 (0) : 0.931 0.069 + 97 I13840 (0) : 0.912 0.088 + 98 I13841 (0) : 0.340 0.660 + 99 I13842 (0) : 0.682 0.318 +100 I13843 (4) : 0.274 0.726 +101 I13844 (16) : 0.851 0.149 +102 I13845 (0) : 0.976 0.024 +103 I13846 (0) : 0.943 0.057 +104 I13847 (0) : 0.647 0.353 +105 I13848 (0) : 0.576 0.424 +106 I13849 (0) : 0.908 0.092 +107 I13850 (0) : 0.450 0.550 +108 I12577 (4) : 0.030 0.970 +109 I12578 (4) : 0.059 0.941 +110 I12579 (8) : 0.025 0.975 +111 I12580 (8) : 0.032 0.968 +112 I12581 (4) : 0.278 0.722 +113 I12582 (4) : 0.036 0.964 +114 I12583 (8) : 0.096 0.904 +115 I12584 (4) : 0.054 0.946 +116 I12585 (4) : 0.019 0.981 +117 I12586 (4) : 0.027 0.973 +118 I12587 (8) : 0.021 0.979 +119 I12588 (4) : 0.017 0.983 +120 I12589 (0) : 0.044 0.956 +121 I12590 (0) : 0.050 0.950 +122 I12591 (12) : 0.011 0.989 +123 I12592 (4) : 0.030 0.970 +124 I12593 (4) : 0.017 0.983 +125 I12594 (8) : 0.019 0.981 +126 I12595 (0) : 0.027 0.973 +127 I12596 (0) : 0.017 0.983 +128 I12597 (4) : 0.069 0.931 +129 I12598 (0) : 0.104 0.896 +130 I12599 (0) : 0.091 0.909 +131 I12600 (4) : 0.036 0.964 +132 I12601 (8) : 0.025 0.975 +133 I12602 (12) : 0.027 0.973 +134 I12603 (0) : 0.030 0.970 +135 I12604 (4) : 0.050 0.950 +136 I12605 (4) : 0.034 0.966 +137 I12606 (8) : 0.021 0.979 +138 I12607 (4) : 0.029 0.971 +139 I12608 (8) : 0.038 0.962 +140 I12609 (8) : 0.023 0.977 +141 I12610 (52) : 0.037 0.963 +142 I12611 (0) : 0.019 0.981 +143 I12612 (0) : 0.022 0.978 +144 I12613 (0) : 0.018 0.982 +145 I12614 (4) : 0.055 0.945 +146 I12615 (0) : 0.072 0.928 +147 I12616 (4) : 0.062 0.938 +148 I12617 (8) : 0.015 0.985 +149 I12618 (48) : 0.021 0.979 + + +Estimated Allele Frequencies in each cluster +First column gives estimated ancestral frequencies + + +Locus 1 : A8 +7 alleles +4.0% missing data + 177 (0.477) 0.467 0.603 + 179 (0.110) 0.105 0.057 + 175 (0.075) 0.231 0.010 + 173 (0.052) 0.054 0.010 + 181 (0.196) 0.113 0.283 + 165 (0.056) 0.013 0.032 + 183 (0.035) 0.018 0.005 + +Locus 2 : A14 +5 alleles +0.0% missing data + 112 (0.133) 0.294 0.035 + 110 (0.723) 0.679 0.824 + 114 (0.038) 0.016 0.006 + 118 (0.066) 0.008 0.099 + 116 (0.040) 0.003 0.036 + +Locus 3 : A24 +5 alleles +2.7% missing data + 104 (0.365) 0.380 0.375 + 106 (0.528) 0.593 0.561 + 101 (0.028) 0.007 0.004 + 108 (0.036) 0.017 0.005 + 96 (0.043) 0.003 0.054 + +Locus 4 : A29 +29 alleles +6.7% missing data + 143 (0.027) 0.062 0.005 + 149 (0.043) 0.029 0.060 + 147 (0.036) 0.020 0.028 + 153 (0.055) 0.073 0.084 + 169 (0.043) 0.047 0.037 + 151 (0.045) 0.045 0.050 + 145 (0.034) 0.017 0.024 + 157 (0.060) 0.081 0.117 + 155 (0.067) 0.107 0.145 + 159 (0.048) 0.085 0.043 + 161 (0.031) 0.061 0.009 + 141 (0.032) 0.033 0.013 + 139 (0.020) 0.011 0.003 + 144 (0.025) 0.042 0.004 + 171 (0.044) 0.048 0.044 + 163 (0.054) 0.088 0.066 + 167 (0.044) 0.038 0.052 + 173 (0.030) 0.023 0.011 + 142 (0.018) 0.006 0.003 + 177 (0.031) 0.009 0.038 + 175 (0.028) 0.008 0.019 + 165 (0.042) 0.032 0.044 + 146 (0.022) 0.022 0.003 + 137 (0.025) 0.006 0.015 + 183 (0.020) 0.002 0.020 + 179 (0.020) 0.002 0.020 + 191 (0.018) 0.001 0.011 + 185 (0.018) 0.002 0.011 + 180 (0.020) 0.001 0.021 + +Locus 5 : A43 +7 alleles +1.3% missing data + 123 (0.161) 0.121 0.166 + 141 (0.027) 0.007 0.004 + 137 (0.631) 0.831 0.679 + 139 (0.083) 0.034 0.069 + 124 (0.043) 0.003 0.061 + 143 (0.027) 0.002 0.011 + 128 (0.027) 0.002 0.011 + +Locus 6 : A79 +13 alleles +3.4% missing data + 103 (0.183) 0.289 0.203 + 97 (0.100) 0.136 0.067 + 101 (0.092) 0.157 0.047 + 107 (0.105) 0.127 0.083 + 109 (0.093) 0.079 0.085 + 105 (0.177) 0.146 0.349 + 111 (0.055) 0.021 0.037 + 113 (0.024) 0.005 0.005 + 91 (0.039) 0.004 0.071 + 99 (0.048) 0.017 0.026 + 115 (0.035) 0.011 0.016 + 117 (0.025) 0.006 0.004 + 121 (0.025) 0.005 0.006 + +Locus 7 : A88 +9 alleles +6.0% missing data + 133 (0.028) 0.007 0.004 + 149 (0.515) 0.494 0.764 + 137 (0.076) 0.119 0.020 + 147 (0.169) 0.312 0.085 + 141 (0.097) 0.051 0.085 + 152 (0.028) 0.007 0.004 + 143 (0.028) 0.006 0.005 + 151 (0.028) 0.002 0.012 + 144 (0.032) 0.002 0.021 + +Locus 8 : A113 +12 alleles +7.4% missing data + 214 (0.488) 0.725 0.711 + 226 (0.077) 0.069 0.042 + 218 (0.026) 0.006 0.004 + 220 (0.084) 0.030 0.126 + 216 (0.062) 0.026 0.043 + 230 (0.044) 0.047 0.009 + 234 (0.035) 0.022 0.006 + 232 (0.038) 0.021 0.009 + 228 (0.054) 0.031 0.022 + 224 (0.026) 0.006 0.005 + 222 (0.042) 0.010 0.020 + 208 (0.026) 0.006 0.004 + +Locus 9 : Ac11 +9 alleles +4.7% missing data + 111 (0.110) 0.203 0.042 + 117 (0.250) 0.356 0.222 + 115 (0.240) 0.298 0.237 + 113 (0.163) 0.099 0.247 + 119 (0.087) 0.023 0.142 + 121 (0.044) 0.005 0.052 + 123 (0.040) 0.008 0.022 + 127 (0.039) 0.006 0.025 + 125 (0.027) 0.002 0.011 + +Locus 10 : Ac88 +8 alleles +0.7% missing data + 214 (0.709) 0.825 0.880 + 216 (0.034) 0.017 0.004 + 220 (0.102) 0.144 0.038 + 230 (0.037) 0.006 0.015 + 221 (0.028) 0.002 0.011 + 212 (0.031) 0.002 0.020 + 217 (0.027) 0.002 0.011 + 224 (0.031) 0.002 0.020 + +Locus 11 : Ac139 +8 alleles +13.4% missing data + 327 (0.527) 0.515 0.736 + 329 (0.225) 0.368 0.144 + 331 (0.076) 0.071 0.027 + 328 (0.046) 0.037 0.009 + 341 (0.029) 0.002 0.012 + 337 (0.040) 0.003 0.048 + 323 (0.029) 0.003 0.012 + 339 (0.029) 0.002 0.012 + +Locus 12 : Ac306 +6 alleles +4.7% missing data + 165 (0.674) 0.761 0.800 + 177 (0.107) 0.054 0.097 + 173 (0.102) 0.118 0.041 + 169 (0.050) 0.059 0.008 + 171 (0.028) 0.005 0.007 + 179 (0.040) 0.003 0.047 + +Locus 13 : Ap15 +7 alleles +6.0% missing data + 202 (0.754) 0.955 0.805 + 212 (0.035) 0.018 0.004 + 204 (0.053) 0.010 0.038 + 208 (0.047) 0.005 0.062 + 220 (0.054) 0.007 0.068 + 219 (0.028) 0.002 0.011 + 210 (0.029) 0.002 0.011 + +Locus 14 : Ap68 +9 alleles +4.7% missing data + 158 (0.303) 0.434 0.302 + 160 (0.084) 0.096 0.033 + 156 (0.271) 0.294 0.335 + 162 (0.051) 0.021 0.020 + 154 (0.076) 0.105 0.025 + 152 (0.107) 0.030 0.228 + 164 (0.053) 0.016 0.028 + 170 (0.027) 0.003 0.010 + 166 (0.031) 0.002 0.020 + +Locus 15 : Ap85 +10 alleles +3.4% missing data + 202 (0.324) 0.325 0.484 + 186 (0.205) 0.413 0.129 + 204 (0.069) 0.027 0.055 + 188 (0.088) 0.120 0.035 + 194 (0.075) 0.067 0.034 + 196 (0.068) 0.014 0.108 + 200 (0.068) 0.018 0.085 + 192 (0.037) 0.007 0.014 + 190 (0.026) 0.007 0.004 + 198 (0.038) 0.003 0.054 + +Locus 16 : Ap90 +13 alleles +0.7% missing data + 131 (0.349) 0.511 0.505 + 135 (0.085) 0.054 0.077 + 133 (0.197) 0.277 0.226 + 129 (0.103) 0.100 0.087 + 137 (0.047) 0.021 0.017 + 141 (0.025) 0.006 0.004 + 143 (0.028) 0.012 0.004 + 151 (0.036) 0.007 0.012 + 155 (0.025) 0.006 0.004 + 145 (0.025) 0.002 0.011 + 130 (0.028) 0.002 0.020 + 139 (0.025) 0.002 0.011 + 153 (0.028) 0.002 0.020 + +Locus 17 : Ap223 +7 alleles +2.0% missing data + 183 (0.654) 0.654 0.864 + 187 (0.106) 0.258 0.027 + 189 (0.035) 0.017 0.004 + 173 (0.082) 0.041 0.050 + 182 (0.038) 0.016 0.008 + 180 (0.038) 0.006 0.016 + 179 (0.048) 0.008 0.031 + +Locus 18 : Ap224 +7 alleles +4.0% missing data + 283 (0.094) 0.186 0.023 + 287 (0.424) 0.461 0.470 + 281 (0.130) 0.166 0.063 + 289 (0.244) 0.145 0.388 + 291 (0.042) 0.033 0.006 + 285 (0.028) 0.007 0.004 + 279 (0.039) 0.003 0.046 + +Locus 19 : Ap226 +5 alleles +17.4% missing data + 237 (0.350) 0.346 0.372 + 239 (0.485) 0.477 0.568 + 247 (0.103) 0.168 0.035 + 235 (0.031) 0.007 0.006 + 241 (0.031) 0.002 0.019 + +Locus 20 : Ap249 +9 alleles +1.3% missing data + 209 (0.553) 0.655 0.685 + 211 (0.052) 0.045 0.012 + 217 (0.087) 0.102 0.033 + 219 (0.092) 0.150 0.030 + 215 (0.107) 0.027 0.217 + 208 (0.027) 0.006 0.004 + 225 (0.027) 0.006 0.004 + 223 (0.027) 0.007 0.003 + 213 (0.027) 0.002 0.011 + +Locus 21 : Ap273 +4 alleles +1.3% missing data + 106 (0.851) 0.939 0.944 + 108 (0.065) 0.028 0.026 + 104 (0.041) 0.027 0.006 + 102 (0.044) 0.006 0.024 + +Locus 22 : Ap274 +2 alleles +2.0% missing data + 120 (0.926) 0.986 0.914 + 122 (0.074) 0.014 0.086 + +Locus 23 : Ap288 +5 alleles +0.0% missing data + 123 (0.753) 0.706 0.929 + 131 (0.155) 0.263 0.060 + 139 (0.036) 0.017 0.004 + 121 (0.029) 0.007 0.004 + 124 (0.029) 0.007 0.004 + +Locus 24 : At163 +7 alleles +0.0% missing data + 128 (0.693) 0.695 0.887 + 134 (0.163) 0.280 0.072 + 130 (0.033) 0.011 0.005 + 136 (0.028) 0.007 0.003 + 140 (0.028) 0.002 0.011 + 146 (0.028) 0.002 0.011 + 142 (0.028) 0.002 0.011 + +Locus 25 : At188 +13 alleles +1.3% missing data + 189 (0.559) 0.734 0.866 + 205 (0.036) 0.033 0.004 + 207 (0.039) 0.048 0.005 + 219 (0.029) 0.012 0.004 + 209 (0.040) 0.037 0.006 + 217 (0.038) 0.026 0.007 + 215 (0.029) 0.012 0.004 + 199 (0.075) 0.041 0.056 + 212 (0.033) 0.016 0.006 + 213 (0.038) 0.027 0.006 + 211 (0.026) 0.006 0.004 + 191 (0.026) 0.007 0.003 + 187 (0.031) 0.002 0.028 + +Values of parameters used in structure: +DATAFILE=, OUTFILE=, NUMINDS=149, NUMLOCI=25, MISSING=-9, LABEL=1, POPDATA=0, POPFLAG=1, PHENOTYPE=0, EXTRACOLS=1, MAXPOPS=2, BURNIN=100000, NUMREPS=1000000, USEPOPINFO=0, INFERALPHA=1, INFERLAMBDA=0, POPSPECIFICLAMBDA=0, POPALPHAS=0, COMPUTEPROB=1, NOADMIX=0, ADMBURNIN=2500, UPDATEFREQ=1, PRINTLIKES=0, INTERMEDSAVE=0, PRINTKLD=0, PRINTNET=0, PRINTLAMBDA=0, ANCESTDIST=0, NUMBOXES=1000, ANCESTPINT=0.90000, GENSBACK=2, MIGRPRIOR=0.05000, PRINTQHAT=0, PRINTQSUM=0, ALPHA=1.0000, FREQSCORR=1, FPRIORMEAN=0.0100, FPRIORSD=0.0500, ONEFST=0, LAMBDA=1.0000, UNIFPRIORALPHA=1, ALPHAMAX=10.0000, ALPHAPRIORA=1.0000, ALPHAPRIORB=2.0000, ALPHAPROPSD=0.0250, STARTATPOPINFO=0, RANDOMIZE=1, LINKAGE=0, METROFREQ=10, REPORTHITRATE=0, MARKOVPHASE=-1, PHASED=0, PLOIDY=2, PHASEINFO=0 LOCPRIOR=0, LOCPRIORINIT=1.000000, LOCDATA=0, LOCISPOP=0, LOCPRIORSTEP=0.100000, MAXLOCPRIOR=20.000000, SEED=1335106980, +[STRAT parameters]: NUMSIMSTATS=1000, PHENOTYPECOL=-9, POOLFREQ=10, LOCUSxONLY=0, EMERROR=0.00100, MISSINGPHENO=-9, \ No newline at end of file diff --git a/inst/files/structure/structure_03 b/inst/files/structure/structure_03 new file mode 100644 index 0000000..0abc37e --- /dev/null +++ b/inst/files/structure/structure_03 @@ -0,0 +1,532 @@ + + +---------------------------------------------------- +STRUCTURE by Pritchard, Stephens and Donnelly (2000) + and Falush, Stephens and Pritchard (2003) + Code by Pritchard, Falush and Hubisz + Version 2.3.2.1 (Oct 2009) +---------------------------------------------------- + + + +Command line arguments: +Input File: + +Run parameters: + 149 individuals + 25 loci + 3 populations assumed + 100000 Burn-in period + 1000000 Reps + + +-------------------------------------------- +Overall proportion of membership of the +sample in each of the 3 clusters + +Inferred Clusters + 1 2 3 +0.313 0.343 0.344 + +-------------------------------------------- + +Allele-freq. divergence among pops (Net nucleotide distance), +computed using point estimates of P. + + 1 2 3 + 1 - 0.0137 0.0316 + 2 0.0137 - 0.0286 + 3 0.0316 0.0286 - + +Average distances (expected heterozygosity) between individuals in same cluster: +cluster 1 : 0.5386 +cluster 2 : 0.4834 +cluster 3 : 0.4572 + +-------------------------------------------- +Estimated Ln Prob of Data = -7475.8 +Mean value of ln likelihood = -7268.8 +Variance of ln likelihood = 414.1 +Mean value of alpha = 0.1201 + +Mean value of Fst_1 = 0.0526 +Mean value of Fst_2 = 0.0880 +Mean value of Fst_3 = 0.0718 + + +Inferred ancestry of individuals: + Label (%Miss) : Inferred clusters + 1 I13825 (0) : 0.911 0.067 0.023 + 2 I13826 (0) : 0.891 0.089 0.019 + 3 I13827 (20) : 0.044 0.931 0.025 + 4 I13828 (0) : 0.919 0.058 0.023 + 5 I13829 (8) : 0.099 0.879 0.022 + 6 I13830 (0) : 0.858 0.126 0.016 + 7 I13831 (0) : 0.239 0.734 0.026 + 8 I13832 (16) : 0.170 0.791 0.040 + 9 I13833 (0) : 0.075 0.897 0.028 + 10 I13834 (0) : 0.052 0.934 0.014 + 11 I13835 (0) : 0.365 0.617 0.018 + 12 I13836 (0) : 0.068 0.914 0.018 + 13 I13377 (0) : 0.073 0.868 0.059 + 14 I13378 (0) : 0.738 0.227 0.035 + 15 I13379 (0) : 0.444 0.526 0.030 + 16 I13380 (0) : 0.045 0.836 0.119 + 17 I13381 (0) : 0.179 0.745 0.076 + 18 I13382 (0) : 0.028 0.959 0.013 + 19 I13383 (0) : 0.380 0.566 0.054 + 20 I13384 (0) : 0.136 0.829 0.035 + 21 I13385 (0) : 0.045 0.941 0.013 + 22 I13386 (0) : 0.023 0.962 0.015 + 23 I13387 (0) : 0.764 0.209 0.026 + 24 I13388 (0) : 0.876 0.053 0.072 + 25 I13389 (0) : 0.096 0.813 0.091 + 26 I13390 (0) : 0.037 0.934 0.029 + 27 I13391 (0) : 0.375 0.504 0.120 + 28 I13392 (0) : 0.679 0.276 0.045 + 29 I13393 (0) : 0.035 0.776 0.190 + 30 I13394 (4) : 0.197 0.387 0.415 + 31 I13395 (0) : 0.323 0.325 0.352 + 32 I13396 (0) : 0.875 0.038 0.087 + 33 I13397 (0) : 0.685 0.294 0.021 + 34 I13398 (0) : 0.779 0.207 0.013 + 35 I13399 (4) : 0.208 0.741 0.050 + 36 I13400 (0) : 0.283 0.621 0.096 + 37 I13401 (0) : 0.131 0.475 0.394 + 38 I13402 (0) : 0.880 0.070 0.050 + 39 I13403 (0) : 0.715 0.184 0.100 + 40 I13404 (0) : 0.293 0.688 0.019 + 41 I13405 (0) : 0.021 0.961 0.018 + 42 I13406 (16) : 0.712 0.262 0.026 + 43 I13407 (0) : 0.710 0.268 0.022 + 44 I13408 (0) : 0.087 0.892 0.021 + 45 I13409 (0) : 0.836 0.091 0.073 + 46 I13410 (0) : 0.123 0.863 0.015 + 47 I13411 (0) : 0.115 0.873 0.012 + 48 I13412 (0) : 0.204 0.501 0.296 + 49 I13413 (0) : 0.834 0.118 0.047 + 50 I13414 (0) : 0.795 0.182 0.023 + 51 I13415 (4) : 0.204 0.735 0.061 + 52 I13416 (4) : 0.527 0.382 0.092 + 53 I13417 (4) : 0.125 0.779 0.097 + 54 I13418 (0) : 0.170 0.742 0.088 + 55 I13419 (0) : 0.329 0.649 0.022 + 56 I13420 (0) : 0.393 0.459 0.148 + 57 I13421 (0) : 0.071 0.779 0.149 + 58 I13422 (0) : 0.231 0.531 0.238 + 59 I13423 (0) : 0.507 0.350 0.143 + 60 I13424 (0) : 0.106 0.858 0.036 + 61 I13425 (4) : 0.272 0.671 0.057 + 62 I13426 (4) : 0.245 0.183 0.573 + 63 I13870 (0) : 0.545 0.282 0.173 + 64 I13871 (16) : 0.674 0.294 0.032 + 65 I13872 (0) : 0.936 0.044 0.019 + 66 I13873 (4) : 0.799 0.109 0.092 + 67 I13874 (0) : 0.840 0.093 0.067 + 68 I13875 (8) : 0.847 0.107 0.046 + 69 I13876 (0) : 0.597 0.165 0.238 + 70 I13877 (20) : 0.128 0.813 0.059 + 71 I13878 (28) : 0.525 0.452 0.023 + 72 I13879 (4) : 0.179 0.807 0.014 + 73 I13880 (4) : 0.949 0.037 0.014 + 74 I13881 (0) : 0.597 0.340 0.063 + 75 I13882 (0) : 0.861 0.112 0.027 + 76 I13883 (4) : 0.932 0.028 0.041 + 77 I13884 (16) : 0.722 0.221 0.057 + 78 I13885 (20) : 0.155 0.826 0.019 + 79 I13886 (8) : 0.677 0.305 0.018 + 80 I13887 (0) : 0.878 0.037 0.085 + 81 I13888 (0) : 0.686 0.252 0.062 + 82 I13889 (0) : 0.050 0.123 0.827 + 83 I13890 (32) : 0.187 0.203 0.610 + 84 I13891 (0) : 0.675 0.292 0.033 + 85 I13892 (0) : 0.131 0.481 0.388 + 86 I13893 (8) : 0.499 0.402 0.099 + 87 I13894 (0) : 0.966 0.017 0.017 + 88 I13895 (4) : 0.305 0.420 0.275 + 89 I13896 (0) : 0.785 0.076 0.138 + 90 I13897 (0) : 0.763 0.226 0.012 + 91 I13898 (4) : 0.763 0.203 0.034 + 92 I13899 (0) : 0.949 0.040 0.011 + 93 I13900 (32) : 0.817 0.104 0.079 + 94 I13837 (0) : 0.024 0.946 0.030 + 95 I13838 (0) : 0.149 0.095 0.756 + 96 I13839 (0) : 0.075 0.851 0.073 + 97 I13840 (0) : 0.209 0.680 0.110 + 98 I13841 (0) : 0.055 0.471 0.474 + 99 I13842 (0) : 0.028 0.774 0.199 +100 I13843 (4) : 0.103 0.252 0.645 +101 I13844 (16) : 0.135 0.743 0.122 +102 I13845 (0) : 0.074 0.908 0.018 +103 I13846 (0) : 0.045 0.921 0.034 +104 I13847 (0) : 0.386 0.205 0.408 +105 I13848 (0) : 0.382 0.241 0.377 +106 I13849 (0) : 0.891 0.044 0.065 +107 I13850 (0) : 0.265 0.223 0.512 +108 I12577 (4) : 0.031 0.030 0.939 +109 I12578 (4) : 0.051 0.034 0.914 +110 I12579 (8) : 0.018 0.040 0.941 +111 I12580 (8) : 0.023 0.034 0.943 +112 I12581 (4) : 0.143 0.256 0.601 +113 I12582 (4) : 0.036 0.029 0.935 +114 I12583 (8) : 0.105 0.116 0.779 +115 I12584 (4) : 0.109 0.032 0.859 +116 I12585 (4) : 0.020 0.017 0.962 +117 I12586 (4) : 0.027 0.024 0.950 +118 I12587 (8) : 0.017 0.024 0.959 +119 I12588 (4) : 0.017 0.019 0.964 +120 I12589 (0) : 0.041 0.033 0.926 +121 I12590 (0) : 0.050 0.044 0.906 +122 I12591 (12) : 0.011 0.011 0.977 +123 I12592 (4) : 0.024 0.030 0.946 +124 I12593 (4) : 0.024 0.013 0.963 +125 I12594 (8) : 0.019 0.018 0.963 +126 I12595 (0) : 0.026 0.038 0.937 +127 I12596 (0) : 0.016 0.019 0.966 +128 I12597 (4) : 0.094 0.054 0.853 +129 I12598 (0) : 0.066 0.088 0.846 +130 I12599 (0) : 0.110 0.035 0.855 +131 I12600 (4) : 0.036 0.027 0.937 +132 I12601 (8) : 0.026 0.024 0.950 +133 I12602 (12) : 0.026 0.025 0.950 +134 I12603 (0) : 0.031 0.033 0.936 +135 I12604 (4) : 0.055 0.031 0.914 +136 I12605 (4) : 0.064 0.021 0.915 +137 I12606 (8) : 0.021 0.018 0.961 +138 I12607 (4) : 0.057 0.021 0.922 +139 I12608 (8) : 0.047 0.031 0.923 +140 I12609 (8) : 0.030 0.022 0.948 +141 I12610 (52) : 0.029 0.045 0.927 +142 I12611 (0) : 0.020 0.015 0.965 +143 I12612 (0) : 0.022 0.018 0.960 +144 I12613 (0) : 0.013 0.021 0.966 +145 I12614 (4) : 0.028 0.080 0.892 +146 I12615 (0) : 0.057 0.060 0.883 +147 I12616 (4) : 0.033 0.077 0.890 +148 I12617 (8) : 0.019 0.011 0.970 +149 I12618 (48) : 0.021 0.022 0.957 + + +Estimated Allele Frequencies in each cluster +First column gives estimated ancestral frequencies + + +Locus 1 : A8 +7 alleles +4.0% missing data + 177 (0.483) 0.520 0.435 0.595 + 179 (0.106) 0.075 0.133 0.057 + 175 (0.114) 0.194 0.240 0.015 + 173 (0.051) 0.037 0.068 0.008 + 181 (0.172) 0.130 0.103 0.289 + 165 (0.044) 0.021 0.009 0.031 + 183 (0.029) 0.023 0.012 0.004 + +Locus 2 : A14 +5 alleles +0.0% missing data + 112 (0.187) 0.350 0.213 0.041 + 110 (0.706) 0.602 0.771 0.817 + 114 (0.031) 0.027 0.006 0.004 + 118 (0.047) 0.014 0.006 0.102 + 116 (0.030) 0.006 0.004 0.036 + +Locus 3 : A24 +5 alleles +2.7% missing data + 104 (0.386) 0.468 0.300 0.373 + 106 (0.532) 0.487 0.686 0.565 + 101 (0.022) 0.007 0.007 0.003 + 108 (0.028) 0.031 0.003 0.004 + 96 (0.031) 0.006 0.004 0.056 + +Locus 4 : A29 +29 alleles +6.7% missing data + 143 (0.037) 0.078 0.040 0.007 + 149 (0.044) 0.043 0.017 0.061 + 147 (0.032) 0.033 0.007 0.029 + 153 (0.055) 0.034 0.109 0.086 + 169 (0.041) 0.083 0.009 0.037 + 151 (0.036) 0.010 0.087 0.038 + 145 (0.030) 0.029 0.006 0.024 + 157 (0.068) 0.108 0.053 0.120 + 155 (0.081) 0.126 0.085 0.150 + 159 (0.057) 0.123 0.040 0.045 + 161 (0.032) 0.025 0.091 0.008 + 141 (0.031) 0.014 0.050 0.013 + 139 (0.017) 0.003 0.019 0.002 + 144 (0.025) 0.013 0.067 0.004 + 171 (0.042) 0.023 0.073 0.042 + 163 (0.064) 0.084 0.088 0.067 + 167 (0.047) 0.046 0.029 0.056 + 173 (0.025) 0.008 0.039 0.010 + 142 (0.015) 0.010 0.003 0.002 + 177 (0.028) 0.011 0.010 0.039 + 175 (0.024) 0.008 0.012 0.018 + 165 (0.043) 0.049 0.019 0.042 + 146 (0.022) 0.012 0.031 0.003 + 137 (0.022) 0.011 0.004 0.014 + 183 (0.018) 0.004 0.002 0.021 + 179 (0.018) 0.004 0.003 0.020 + 191 (0.016) 0.003 0.002 0.011 + 185 (0.015) 0.003 0.002 0.010 + 180 (0.017) 0.003 0.002 0.022 + +Locus 5 : A43 +7 alleles +1.3% missing data + 123 (0.156) 0.159 0.091 0.163 + 141 (0.021) 0.012 0.003 0.003 + 137 (0.688) 0.797 0.842 0.686 + 139 (0.061) 0.017 0.056 0.066 + 124 (0.031) 0.007 0.004 0.063 + 143 (0.021) 0.005 0.002 0.010 + 128 (0.021) 0.004 0.002 0.011 + +Locus 6 : A79 +13 alleles +3.4% missing data + 103 (0.218) 0.290 0.283 0.200 + 97 (0.113) 0.196 0.074 0.063 + 101 (0.096) 0.076 0.222 0.046 + 107 (0.100) 0.064 0.186 0.079 + 109 (0.095) 0.091 0.067 0.087 + 105 (0.176) 0.187 0.107 0.366 + 111 (0.047) 0.034 0.012 0.036 + 113 (0.020) 0.012 0.002 0.003 + 91 (0.029) 0.007 0.004 0.074 + 99 (0.038) 0.010 0.025 0.026 + 115 (0.029) 0.013 0.012 0.013 + 117 (0.020) 0.011 0.003 0.003 + 121 (0.020) 0.009 0.003 0.004 + +Locus 7 : A88 +9 alleles +6.0% missing data + 133 (0.022) 0.013 0.003 0.003 + 149 (0.518) 0.531 0.474 0.770 + 137 (0.091) 0.119 0.111 0.021 + 147 (0.195) 0.221 0.376 0.085 + 141 (0.085) 0.088 0.020 0.083 + 152 (0.022) 0.006 0.009 0.003 + 143 (0.021) 0.012 0.003 0.003 + 151 (0.022) 0.004 0.002 0.011 + 144 (0.025) 0.006 0.003 0.020 + +Locus 8 : A113 +12 alleles +7.4% missing data + 214 (0.551) 0.661 0.770 0.718 + 226 (0.078) 0.104 0.034 0.043 + 218 (0.020) 0.004 0.010 0.003 + 220 (0.064) 0.023 0.038 0.131 + 216 (0.057) 0.033 0.023 0.043 + 230 (0.040) 0.020 0.070 0.008 + 234 (0.031) 0.036 0.008 0.005 + 232 (0.037) 0.029 0.015 0.008 + 228 (0.048) 0.051 0.013 0.021 + 224 (0.020) 0.009 0.005 0.003 + 222 (0.032) 0.025 0.003 0.013 + 208 (0.021) 0.004 0.010 0.003 + +Locus 9 : Ac11 +9 alleles +4.7% missing data + 111 (0.139) 0.247 0.144 0.044 + 117 (0.274) 0.296 0.403 0.218 + 115 (0.256) 0.266 0.329 0.232 + 113 (0.151) 0.128 0.078 0.253 + 119 (0.063) 0.021 0.027 0.150 + 121 (0.032) 0.007 0.006 0.054 + 123 (0.034) 0.021 0.005 0.016 + 127 (0.031) 0.009 0.006 0.024 + 125 (0.021) 0.005 0.003 0.009 + +Locus 10 : Ac88 +8 alleles +0.7% missing data + 214 (0.731) 0.749 0.892 0.884 + 216 (0.032) 0.023 0.012 0.004 + 220 (0.118) 0.198 0.084 0.039 + 230 (0.029) 0.014 0.003 0.011 + 221 (0.021) 0.004 0.002 0.011 + 212 (0.024) 0.004 0.002 0.020 + 217 (0.021) 0.004 0.002 0.011 + 224 (0.024) 0.004 0.003 0.020 + +Locus 11 : Ac139 +8 alleles +13.4% missing data + 327 (0.517) 0.477 0.558 0.743 + 329 (0.268) 0.377 0.342 0.141 + 331 (0.078) 0.104 0.037 0.027 + 328 (0.040) 0.021 0.052 0.006 + 341 (0.022) 0.005 0.003 0.011 + 337 (0.030) 0.006 0.004 0.050 + 323 (0.022) 0.005 0.003 0.010 + 339 (0.023) 0.005 0.003 0.011 + +Locus 12 : Ac306 +6 alleles +4.7% missing data + 165 (0.697) 0.720 0.792 0.809 + 177 (0.097) 0.072 0.050 0.091 + 173 (0.110) 0.168 0.063 0.041 + 169 (0.045) 0.022 0.090 0.007 + 171 (0.022) 0.012 0.002 0.003 + 179 (0.029) 0.006 0.003 0.049 + +Locus 13 : Ap15 +7 alleles +6.0% missing data + 202 (0.811) 0.920 0.970 0.808 + 212 (0.028) 0.033 0.003 0.003 + 204 (0.041) 0.015 0.010 0.037 + 208 (0.035) 0.008 0.007 0.062 + 220 (0.041) 0.015 0.005 0.069 + 219 (0.022) 0.004 0.003 0.011 + 210 (0.022) 0.005 0.003 0.010 + +Locus 14 : Ap68 +9 alleles +4.7% missing data + 158 (0.362) 0.570 0.287 0.303 + 160 (0.081) 0.052 0.136 0.031 + 156 (0.265) 0.202 0.381 0.341 + 162 (0.041) 0.041 0.007 0.014 + 154 (0.080) 0.070 0.133 0.023 + 152 (0.080) 0.025 0.043 0.234 + 164 (0.044) 0.030 0.007 0.025 + 170 (0.021) 0.005 0.004 0.008 + 166 (0.024) 0.005 0.003 0.020 + +Locus 15 : Ap85 +10 alleles +3.4% missing data + 202 (0.334) 0.381 0.281 0.490 + 186 (0.246) 0.320 0.470 0.129 + 204 (0.060) 0.033 0.026 0.054 + 188 (0.095) 0.101 0.132 0.033 + 194 (0.078) 0.079 0.055 0.033 + 196 (0.054) 0.021 0.014 0.110 + 200 (0.056) 0.037 0.010 0.082 + 192 (0.028) 0.013 0.005 0.011 + 190 (0.021) 0.010 0.004 0.003 + 198 (0.028) 0.005 0.003 0.056 + +Locus 16 : Ap90 +13 alleles +0.7% missing data + 131 (0.388) 0.468 0.534 0.518 + 135 (0.080) 0.077 0.034 0.079 + 133 (0.225) 0.316 0.237 0.222 + 129 (0.095) 0.060 0.139 0.084 + 137 (0.038) 0.011 0.031 0.017 + 141 (0.019) 0.011 0.002 0.003 + 143 (0.025) 0.016 0.008 0.003 + 151 (0.028) 0.015 0.003 0.010 + 155 (0.020) 0.011 0.003 0.003 + 145 (0.019) 0.004 0.002 0.011 + 130 (0.022) 0.004 0.002 0.020 + 139 (0.020) 0.003 0.002 0.011 + 153 (0.022) 0.004 0.002 0.020 + +Locus 17 : Ap223 +7 alleles +2.0% missing data + 183 (0.654) 0.645 0.675 0.867 + 187 (0.146) 0.240 0.249 0.031 + 189 (0.027) 0.007 0.026 0.003 + 173 (0.073) 0.062 0.023 0.050 + 182 (0.032) 0.017 0.016 0.006 + 180 (0.029) 0.011 0.005 0.013 + 179 (0.037) 0.017 0.004 0.029 + +Locus 18 : Ap224 +7 alleles +4.0% missing data + 283 (0.120) 0.176 0.177 0.027 + 287 (0.440) 0.487 0.444 0.464 + 281 (0.140) 0.141 0.183 0.062 + 289 (0.207) 0.130 0.170 0.391 + 291 (0.043) 0.052 0.016 0.006 + 285 (0.022) 0.008 0.007 0.003 + 279 (0.029) 0.005 0.003 0.047 + +Locus 19 : Ap226 +5 alleles +17.4% missing data + 237 (0.347) 0.346 0.355 0.359 + 239 (0.479) 0.472 0.479 0.577 + 247 (0.128) 0.172 0.153 0.041 + 235 (0.023) 0.005 0.010 0.005 + 241 (0.023) 0.004 0.003 0.018 + +Locus 20 : Ap249 +9 alleles +1.3% missing data + 209 (0.582) 0.615 0.691 0.688 + 211 (0.053) 0.038 0.053 0.010 + 217 (0.097) 0.117 0.085 0.032 + 219 (0.109) 0.179 0.113 0.028 + 215 (0.075) 0.020 0.041 0.223 + 208 (0.021) 0.012 0.002 0.003 + 225 (0.021) 0.009 0.005 0.003 + 223 (0.021) 0.005 0.009 0.003 + 213 (0.021) 0.004 0.002 0.010 + +Locus 21 : Ap273 +4 alleles +1.3% missing data + 106 (0.869) 0.926 0.944 0.946 + 108 (0.057) 0.037 0.022 0.025 + 104 (0.039) 0.024 0.030 0.005 + 102 (0.034) 0.013 0.004 0.023 + +Locus 22 : Ap274 +2 alleles +2.0% missing data + 120 (0.945) 0.976 0.991 0.914 + 122 (0.055) 0.024 0.009 0.086 + +Locus 23 : Ap288 +5 alleles +0.0% missing data + 123 (0.736) 0.680 0.749 0.927 + 131 (0.190) 0.270 0.237 0.064 + 139 (0.030) 0.028 0.006 0.004 + 121 (0.022) 0.011 0.003 0.003 + 124 (0.022) 0.010 0.004 0.003 + +Locus 24 : At163 +7 alleles +0.0% missing data + 128 (0.683) 0.604 0.790 0.892 + 134 (0.204) 0.357 0.188 0.073 + 130 (0.026) 0.020 0.004 0.004 + 136 (0.021) 0.005 0.009 0.003 + 140 (0.022) 0.005 0.003 0.009 + 146 (0.021) 0.005 0.003 0.009 + 142 (0.022) 0.004 0.003 0.010 + +Locus 25 : At188 +13 alleles +1.3% missing data + 189 (0.616) 0.710 0.752 0.877 + 205 (0.031) 0.058 0.005 0.004 + 207 (0.036) 0.016 0.076 0.004 + 219 (0.027) 0.015 0.010 0.004 + 209 (0.035) 0.015 0.057 0.005 + 217 (0.037) 0.032 0.022 0.005 + 215 (0.023) 0.006 0.018 0.003 + 199 (0.068) 0.068 0.018 0.055 + 212 (0.028) 0.019 0.013 0.005 + 213 (0.034) 0.042 0.012 0.004 + 211 (0.020) 0.010 0.004 0.003 + 191 (0.020) 0.004 0.010 0.002 + 187 (0.024) 0.004 0.003 0.028 + +Values of parameters used in structure: +DATAFILE=, OUTFILE=, NUMINDS=149, NUMLOCI=25, MISSING=-9, LABEL=1, POPDATA=0, POPFLAG=1, PHENOTYPE=0, EXTRACOLS=1, MAXPOPS=3, BURNIN=100000, NUMREPS=1000000, USEPOPINFO=0, INFERALPHA=1, INFERLAMBDA=0, POPSPECIFICLAMBDA=0, POPALPHAS=0, COMPUTEPROB=1, NOADMIX=0, ADMBURNIN=2500, UPDATEFREQ=1, PRINTLIKES=0, INTERMEDSAVE=0, PRINTKLD=0, PRINTNET=0, PRINTLAMBDA=0, ANCESTDIST=0, NUMBOXES=1000, ANCESTPINT=0.90000, GENSBACK=2, MIGRPRIOR=0.05000, PRINTQHAT=0, PRINTQSUM=0, ALPHA=1.0000, FREQSCORR=1, FPRIORMEAN=0.0100, FPRIORSD=0.0500, ONEFST=0, LAMBDA=1.0000, UNIFPRIORALPHA=1, ALPHAMAX=10.0000, ALPHAPRIORA=1.0000, ALPHAPRIORB=2.0000, ALPHAPROPSD=0.0250, STARTATPOPINFO=0, RANDOMIZE=1, LINKAGE=0, METROFREQ=10, REPORTHITRATE=0, MARKOVPHASE=-1, PHASED=0, PLOIDY=2, PHASEINFO=0 LOCPRIOR=0, LOCPRIORINIT=1.000000, LOCDATA=0, LOCISPOP=0, LOCPRIORSTEP=0.100000, MAXLOCPRIOR=20.000000, SEED=1335108395, +[STRAT parameters]: NUMSIMSTATS=1000, PHENOTYPECOL=-9, POOLFREQ=10, LOCUSxONLY=0, EMERROR=0.00100, MISSINGPHENO=-9, \ No newline at end of file diff --git a/inst/files/structure/structure_04 b/inst/files/structure/structure_04 new file mode 100644 index 0000000..46d34cb --- /dev/null +++ b/inst/files/structure/structure_04 @@ -0,0 +1,532 @@ + + +---------------------------------------------------- +STRUCTURE by Pritchard, Stephens and Donnelly (2000) + and Falush, Stephens and Pritchard (2003) + Code by Pritchard, Falush and Hubisz + Version 2.3.2.1 (Oct 2009) +---------------------------------------------------- + + + +Command line arguments: +Input File: + +Run parameters: + 149 individuals + 25 loci + 3 populations assumed + 100000 Burn-in period + 1000000 Reps + + +-------------------------------------------- +Overall proportion of membership of the +sample in each of the 3 clusters + +Inferred Clusters + 1 2 3 +0.345 0.343 0.312 + +-------------------------------------------- + +Allele-freq. divergence among pops (Net nucleotide distance), +computed using point estimates of P. + + 1 2 3 + 1 - 0.0286 0.0318 + 2 0.0286 - 0.0138 + 3 0.0318 0.0138 - + +Average distances (expected heterozygosity) between individuals in same cluster: +cluster 1 : 0.4572 +cluster 2 : 0.4833 +cluster 3 : 0.5387 + +-------------------------------------------- +Estimated Ln Prob of Data = -7475.7 +Mean value of ln likelihood = -7268.9 +Variance of ln likelihood = 413.6 +Mean value of alpha = 0.1218 + +Mean value of Fst_1 = 0.0718 +Mean value of Fst_2 = 0.0883 +Mean value of Fst_3 = 0.0530 + + +Inferred ancestry of individuals: + Label (%Miss) : Inferred clusters + 1 I13825 (0) : 0.024 0.070 0.906 + 2 I13826 (0) : 0.020 0.090 0.891 + 3 I13827 (20) : 0.025 0.930 0.045 + 4 I13828 (0) : 0.024 0.058 0.918 + 5 I13829 (8) : 0.022 0.879 0.099 + 6 I13830 (0) : 0.016 0.124 0.859 + 7 I13831 (0) : 0.027 0.732 0.241 + 8 I13832 (16) : 0.040 0.788 0.172 + 9 I13833 (0) : 0.029 0.895 0.076 + 10 I13834 (0) : 0.014 0.935 0.052 + 11 I13835 (0) : 0.018 0.627 0.354 + 12 I13836 (0) : 0.018 0.911 0.070 + 13 I13377 (0) : 0.059 0.867 0.074 + 14 I13378 (0) : 0.036 0.241 0.723 + 15 I13379 (0) : 0.030 0.531 0.439 + 16 I13380 (0) : 0.121 0.833 0.046 + 17 I13381 (0) : 0.075 0.745 0.180 + 18 I13382 (0) : 0.013 0.958 0.028 + 19 I13383 (0) : 0.057 0.564 0.379 + 20 I13384 (0) : 0.036 0.822 0.142 + 21 I13385 (0) : 0.014 0.941 0.046 + 22 I13386 (0) : 0.015 0.961 0.024 + 23 I13387 (0) : 0.027 0.206 0.767 + 24 I13388 (0) : 0.075 0.053 0.872 + 25 I13389 (0) : 0.091 0.814 0.095 + 26 I13390 (0) : 0.029 0.933 0.038 + 27 I13391 (0) : 0.123 0.510 0.368 + 28 I13392 (0) : 0.046 0.277 0.677 + 29 I13393 (0) : 0.186 0.779 0.034 + 30 I13394 (4) : 0.413 0.392 0.196 + 31 I13395 (0) : 0.355 0.327 0.318 + 32 I13396 (0) : 0.089 0.040 0.871 + 33 I13397 (0) : 0.021 0.303 0.677 + 34 I13398 (0) : 0.014 0.205 0.781 + 35 I13399 (4) : 0.051 0.746 0.203 + 36 I13400 (0) : 0.098 0.626 0.275 + 37 I13401 (0) : 0.398 0.476 0.126 + 38 I13402 (0) : 0.052 0.073 0.875 + 39 I13403 (0) : 0.103 0.189 0.709 + 40 I13404 (0) : 0.019 0.683 0.297 + 41 I13405 (0) : 0.018 0.961 0.021 + 42 I13406 (16) : 0.027 0.258 0.715 + 43 I13407 (0) : 0.023 0.278 0.699 + 44 I13408 (0) : 0.022 0.890 0.088 + 45 I13409 (0) : 0.074 0.095 0.830 + 46 I13410 (0) : 0.016 0.856 0.129 + 47 I13411 (0) : 0.012 0.873 0.115 + 48 I13412 (0) : 0.298 0.497 0.205 + 49 I13413 (0) : 0.049 0.120 0.831 + 50 I13414 (0) : 0.024 0.172 0.804 + 51 I13415 (4) : 0.062 0.735 0.203 + 52 I13416 (4) : 0.092 0.377 0.531 + 53 I13417 (4) : 0.101 0.772 0.127 + 54 I13418 (0) : 0.089 0.737 0.174 + 55 I13419 (0) : 0.023 0.647 0.330 + 56 I13420 (0) : 0.153 0.457 0.391 + 57 I13421 (0) : 0.151 0.778 0.071 + 58 I13422 (0) : 0.243 0.525 0.232 + 59 I13423 (0) : 0.144 0.352 0.505 + 60 I13424 (0) : 0.036 0.858 0.105 + 61 I13425 (4) : 0.057 0.674 0.268 + 62 I13426 (4) : 0.573 0.189 0.238 + 63 I13870 (0) : 0.176 0.283 0.541 + 64 I13871 (16) : 0.034 0.295 0.671 + 65 I13872 (0) : 0.020 0.043 0.937 + 66 I13873 (4) : 0.092 0.112 0.797 + 67 I13874 (0) : 0.068 0.093 0.839 + 68 I13875 (8) : 0.047 0.106 0.847 + 69 I13876 (0) : 0.243 0.162 0.595 + 70 I13877 (20) : 0.060 0.808 0.132 + 71 I13878 (28) : 0.024 0.441 0.535 + 72 I13879 (4) : 0.014 0.801 0.185 + 73 I13880 (4) : 0.015 0.036 0.950 + 74 I13881 (0) : 0.063 0.347 0.590 + 75 I13882 (0) : 0.027 0.113 0.860 + 76 I13883 (4) : 0.042 0.028 0.930 + 77 I13884 (16) : 0.059 0.219 0.722 + 78 I13885 (20) : 0.020 0.821 0.159 + 79 I13886 (8) : 0.019 0.309 0.673 + 80 I13887 (0) : 0.088 0.039 0.873 + 81 I13888 (0) : 0.061 0.242 0.697 + 82 I13889 (0) : 0.826 0.124 0.050 + 83 I13890 (32) : 0.611 0.202 0.187 + 84 I13891 (0) : 0.033 0.283 0.684 + 85 I13892 (0) : 0.384 0.490 0.126 + 86 I13893 (8) : 0.101 0.413 0.486 + 87 I13894 (0) : 0.018 0.017 0.966 + 88 I13895 (4) : 0.277 0.421 0.302 + 89 I13896 (0) : 0.141 0.077 0.781 + 90 I13897 (0) : 0.012 0.224 0.764 + 91 I13898 (4) : 0.034 0.205 0.760 + 92 I13899 (0) : 0.011 0.040 0.949 + 93 I13900 (32) : 0.080 0.111 0.809 + 94 I13837 (0) : 0.030 0.946 0.023 + 95 I13838 (0) : 0.759 0.093 0.148 + 96 I13839 (0) : 0.075 0.849 0.075 + 97 I13840 (0) : 0.112 0.679 0.209 + 98 I13841 (0) : 0.466 0.479 0.055 + 99 I13842 (0) : 0.200 0.772 0.027 +100 I13843 (4) : 0.637 0.258 0.105 +101 I13844 (16) : 0.125 0.743 0.133 +102 I13845 (0) : 0.018 0.908 0.073 +103 I13846 (0) : 0.035 0.921 0.045 +104 I13847 (0) : 0.414 0.204 0.382 +105 I13848 (0) : 0.383 0.237 0.381 +106 I13849 (0) : 0.067 0.046 0.888 +107 I13850 (0) : 0.514 0.227 0.259 +108 I12577 (4) : 0.938 0.031 0.031 +109 I12578 (4) : 0.915 0.033 0.052 +110 I12579 (8) : 0.941 0.041 0.018 +111 I12580 (8) : 0.943 0.034 0.023 +112 I12581 (4) : 0.598 0.258 0.145 +113 I12582 (4) : 0.935 0.029 0.036 +114 I12583 (8) : 0.778 0.117 0.105 +115 I12584 (4) : 0.861 0.031 0.108 +116 I12585 (4) : 0.962 0.017 0.020 +117 I12586 (4) : 0.949 0.024 0.027 +118 I12587 (8) : 0.958 0.024 0.018 +119 I12588 (4) : 0.964 0.019 0.017 +120 I12589 (0) : 0.926 0.034 0.041 +121 I12590 (0) : 0.905 0.045 0.050 +122 I12591 (12) : 0.977 0.011 0.011 +123 I12592 (4) : 0.945 0.030 0.025 +124 I12593 (4) : 0.963 0.013 0.023 +125 I12594 (8) : 0.963 0.017 0.019 +126 I12595 (0) : 0.937 0.037 0.025 +127 I12596 (0) : 0.966 0.018 0.016 +128 I12597 (4) : 0.854 0.055 0.092 +129 I12598 (0) : 0.845 0.090 0.065 +130 I12599 (0) : 0.854 0.035 0.110 +131 I12600 (4) : 0.937 0.027 0.035 +132 I12601 (8) : 0.950 0.024 0.026 +133 I12602 (12) : 0.950 0.025 0.026 +134 I12603 (0) : 0.936 0.033 0.031 +135 I12604 (4) : 0.914 0.031 0.055 +136 I12605 (4) : 0.915 0.021 0.064 +137 I12606 (8) : 0.961 0.019 0.020 +138 I12607 (4) : 0.924 0.021 0.056 +139 I12608 (8) : 0.923 0.031 0.046 +140 I12609 (8) : 0.948 0.022 0.030 +141 I12610 (52) : 0.927 0.044 0.029 +142 I12611 (0) : 0.965 0.015 0.020 +143 I12612 (0) : 0.959 0.019 0.022 +144 I12613 (0) : 0.965 0.022 0.013 +145 I12614 (4) : 0.891 0.081 0.028 +146 I12615 (0) : 0.885 0.060 0.056 +147 I12616 (4) : 0.889 0.078 0.033 +148 I12617 (8) : 0.969 0.011 0.019 +149 I12618 (48) : 0.957 0.023 0.021 + + +Estimated Allele Frequencies in each cluster +First column gives estimated ancestral frequencies + + +Locus 1 : A8 +7 alleles +4.0% missing data + 177 (0.483) 0.595 0.436 0.519 + 179 (0.107) 0.057 0.132 0.076 + 175 (0.113) 0.015 0.239 0.195 + 173 (0.051) 0.008 0.068 0.036 + 181 (0.173) 0.289 0.103 0.129 + 165 (0.044) 0.031 0.009 0.021 + 183 (0.030) 0.004 0.012 0.024 + +Locus 2 : A14 +5 alleles +0.0% missing data + 112 (0.187) 0.041 0.212 0.351 + 110 (0.705) 0.817 0.771 0.601 + 114 (0.031) 0.004 0.006 0.027 + 118 (0.047) 0.102 0.006 0.014 + 116 (0.030) 0.036 0.004 0.006 + +Locus 3 : A24 +5 alleles +2.7% missing data + 104 (0.386) 0.372 0.300 0.468 + 106 (0.532) 0.565 0.685 0.487 + 101 (0.022) 0.003 0.007 0.007 + 108 (0.028) 0.004 0.003 0.031 + 96 (0.031) 0.056 0.004 0.006 + +Locus 4 : A29 +29 alleles +6.7% missing data + 143 (0.037) 0.007 0.039 0.079 + 149 (0.043) 0.061 0.018 0.043 + 147 (0.032) 0.029 0.007 0.034 + 153 (0.055) 0.086 0.109 0.034 + 169 (0.040) 0.036 0.009 0.083 + 151 (0.035) 0.038 0.087 0.010 + 145 (0.030) 0.024 0.006 0.029 + 157 (0.069) 0.120 0.053 0.108 + 155 (0.083) 0.150 0.086 0.126 + 159 (0.057) 0.045 0.040 0.123 + 161 (0.033) 0.008 0.091 0.025 + 141 (0.030) 0.013 0.051 0.014 + 139 (0.017) 0.002 0.019 0.003 + 144 (0.025) 0.004 0.067 0.013 + 171 (0.041) 0.042 0.073 0.022 + 163 (0.065) 0.067 0.088 0.084 + 167 (0.046) 0.056 0.029 0.046 + 173 (0.025) 0.010 0.039 0.008 + 142 (0.015) 0.002 0.003 0.010 + 177 (0.029) 0.039 0.010 0.011 + 175 (0.024) 0.018 0.012 0.008 + 165 (0.041) 0.042 0.019 0.049 + 146 (0.022) 0.003 0.031 0.012 + 137 (0.022) 0.013 0.004 0.010 + 183 (0.017) 0.021 0.002 0.004 + 179 (0.018) 0.020 0.003 0.004 + 191 (0.016) 0.011 0.002 0.003 + 185 (0.015) 0.010 0.002 0.003 + 180 (0.017) 0.022 0.002 0.003 + +Locus 5 : A43 +7 alleles +1.3% missing data + 123 (0.157) 0.163 0.091 0.159 + 141 (0.021) 0.003 0.003 0.012 + 137 (0.687) 0.686 0.841 0.798 + 139 (0.061) 0.066 0.056 0.017 + 124 (0.031) 0.063 0.004 0.006 + 143 (0.021) 0.010 0.002 0.005 + 128 (0.021) 0.011 0.002 0.004 + +Locus 6 : A79 +13 alleles +3.4% missing data + 103 (0.216) 0.199 0.284 0.290 + 97 (0.113) 0.063 0.074 0.196 + 101 (0.096) 0.046 0.223 0.076 + 107 (0.100) 0.079 0.185 0.065 + 109 (0.096) 0.087 0.068 0.091 + 105 (0.176) 0.366 0.106 0.187 + 111 (0.047) 0.036 0.012 0.034 + 113 (0.019) 0.003 0.002 0.011 + 91 (0.030) 0.074 0.004 0.007 + 99 (0.038) 0.026 0.025 0.010 + 115 (0.029) 0.013 0.013 0.013 + 117 (0.020) 0.003 0.003 0.011 + 121 (0.020) 0.004 0.003 0.009 + +Locus 7 : A88 +9 alleles +6.0% missing data + 133 (0.021) 0.003 0.003 0.013 + 149 (0.518) 0.770 0.474 0.530 + 137 (0.091) 0.021 0.111 0.120 + 147 (0.195) 0.085 0.376 0.221 + 141 (0.084) 0.084 0.020 0.089 + 152 (0.022) 0.003 0.009 0.006 + 143 (0.021) 0.003 0.003 0.012 + 151 (0.022) 0.011 0.003 0.004 + 144 (0.025) 0.020 0.003 0.006 + +Locus 8 : A113 +12 alleles +7.4% missing data + 214 (0.551) 0.718 0.770 0.661 + 226 (0.078) 0.043 0.034 0.104 + 218 (0.020) 0.003 0.010 0.004 + 220 (0.064) 0.131 0.038 0.022 + 216 (0.057) 0.043 0.023 0.033 + 230 (0.040) 0.008 0.070 0.020 + 234 (0.032) 0.005 0.008 0.036 + 232 (0.037) 0.008 0.015 0.029 + 228 (0.048) 0.021 0.013 0.051 + 224 (0.020) 0.003 0.005 0.009 + 222 (0.032) 0.013 0.003 0.025 + 208 (0.020) 0.003 0.010 0.004 + +Locus 9 : Ac11 +9 alleles +4.7% missing data + 111 (0.138) 0.044 0.144 0.247 + 117 (0.274) 0.218 0.403 0.297 + 115 (0.256) 0.232 0.329 0.266 + 113 (0.151) 0.254 0.078 0.128 + 119 (0.063) 0.150 0.026 0.020 + 121 (0.032) 0.054 0.006 0.007 + 123 (0.034) 0.016 0.005 0.021 + 127 (0.030) 0.024 0.006 0.009 + 125 (0.021) 0.009 0.003 0.005 + +Locus 10 : Ac88 +8 alleles +0.7% missing data + 214 (0.731) 0.884 0.892 0.748 + 216 (0.032) 0.004 0.012 0.023 + 220 (0.118) 0.039 0.083 0.199 + 230 (0.029) 0.011 0.003 0.014 + 221 (0.021) 0.011 0.002 0.004 + 212 (0.024) 0.020 0.002 0.004 + 217 (0.021) 0.011 0.002 0.004 + 224 (0.024) 0.020 0.003 0.004 + +Locus 11 : Ac139 +8 alleles +13.4% missing data + 327 (0.517) 0.743 0.559 0.475 + 329 (0.268) 0.141 0.341 0.378 + 331 (0.078) 0.027 0.036 0.104 + 328 (0.040) 0.006 0.052 0.021 + 341 (0.023) 0.011 0.003 0.005 + 337 (0.030) 0.049 0.004 0.006 + 323 (0.022) 0.010 0.003 0.005 + 339 (0.022) 0.011 0.003 0.005 + +Locus 12 : Ac306 +6 alleles +4.7% missing data + 165 (0.696) 0.809 0.793 0.718 + 177 (0.098) 0.091 0.050 0.072 + 173 (0.110) 0.041 0.062 0.169 + 169 (0.046) 0.007 0.090 0.023 + 171 (0.022) 0.003 0.002 0.012 + 179 (0.029) 0.049 0.003 0.006 + +Locus 13 : Ap15 +7 alleles +6.0% missing data + 202 (0.811) 0.808 0.970 0.921 + 212 (0.028) 0.003 0.003 0.033 + 204 (0.041) 0.037 0.010 0.015 + 208 (0.035) 0.062 0.007 0.008 + 220 (0.041) 0.069 0.005 0.015 + 219 (0.022) 0.011 0.003 0.004 + 210 (0.022) 0.010 0.003 0.005 + +Locus 14 : Ap68 +9 alleles +4.7% missing data + 158 (0.362) 0.303 0.287 0.571 + 160 (0.081) 0.031 0.136 0.052 + 156 (0.266) 0.341 0.380 0.202 + 162 (0.041) 0.014 0.007 0.041 + 154 (0.080) 0.023 0.134 0.069 + 152 (0.080) 0.234 0.042 0.025 + 164 (0.044) 0.025 0.008 0.030 + 170 (0.021) 0.008 0.004 0.005 + 166 (0.024) 0.020 0.003 0.005 + +Locus 15 : Ap85 +10 alleles +3.4% missing data + 202 (0.334) 0.490 0.280 0.381 + 186 (0.245) 0.129 0.470 0.320 + 204 (0.060) 0.054 0.026 0.033 + 188 (0.095) 0.033 0.133 0.100 + 194 (0.079) 0.034 0.055 0.079 + 196 (0.054) 0.110 0.014 0.021 + 200 (0.056) 0.082 0.010 0.037 + 192 (0.028) 0.011 0.005 0.013 + 190 (0.021) 0.003 0.004 0.010 + 198 (0.028) 0.055 0.003 0.005 + +Locus 16 : Ap90 +13 alleles +0.7% missing data + 131 (0.388) 0.518 0.533 0.469 + 135 (0.081) 0.079 0.034 0.077 + 133 (0.226) 0.222 0.238 0.316 + 129 (0.095) 0.084 0.140 0.060 + 137 (0.037) 0.017 0.031 0.011 + 141 (0.020) 0.003 0.003 0.011 + 143 (0.025) 0.003 0.008 0.016 + 151 (0.027) 0.010 0.003 0.015 + 155 (0.019) 0.003 0.003 0.011 + 145 (0.019) 0.011 0.002 0.004 + 130 (0.022) 0.020 0.002 0.004 + 139 (0.020) 0.011 0.002 0.003 + 153 (0.022) 0.020 0.002 0.004 + +Locus 17 : Ap223 +7 alleles +2.0% missing data + 183 (0.654) 0.867 0.676 0.645 + 187 (0.146) 0.031 0.249 0.241 + 189 (0.027) 0.003 0.026 0.007 + 173 (0.073) 0.050 0.023 0.062 + 182 (0.033) 0.006 0.016 0.017 + 180 (0.029) 0.013 0.005 0.011 + 179 (0.038) 0.029 0.004 0.017 + +Locus 18 : Ap224 +7 alleles +4.0% missing data + 283 (0.120) 0.027 0.177 0.177 + 287 (0.440) 0.464 0.444 0.487 + 281 (0.139) 0.062 0.183 0.141 + 289 (0.207) 0.391 0.171 0.129 + 291 (0.043) 0.006 0.016 0.052 + 285 (0.022) 0.003 0.007 0.008 + 279 (0.029) 0.047 0.003 0.005 + +Locus 19 : Ap226 +5 alleles +17.4% missing data + 237 (0.346) 0.358 0.356 0.346 + 239 (0.479) 0.578 0.479 0.472 + 247 (0.128) 0.042 0.152 0.173 + 235 (0.023) 0.005 0.010 0.005 + 241 (0.023) 0.018 0.003 0.004 + +Locus 20 : Ap249 +9 alleles +1.3% missing data + 209 (0.582) 0.688 0.690 0.615 + 211 (0.052) 0.010 0.053 0.038 + 217 (0.097) 0.033 0.085 0.117 + 219 (0.109) 0.028 0.113 0.179 + 215 (0.075) 0.223 0.041 0.020 + 208 (0.021) 0.003 0.003 0.012 + 225 (0.021) 0.003 0.005 0.009 + 223 (0.021) 0.003 0.009 0.005 + 213 (0.021) 0.010 0.002 0.004 + +Locus 21 : Ap273 +4 alleles +1.3% missing data + 106 (0.869) 0.946 0.944 0.926 + 108 (0.058) 0.025 0.022 0.037 + 104 (0.039) 0.005 0.030 0.023 + 102 (0.034) 0.023 0.004 0.013 + +Locus 22 : Ap274 +2 alleles +2.0% missing data + 120 (0.944) 0.914 0.990 0.976 + 122 (0.056) 0.086 0.010 0.024 + +Locus 23 : Ap288 +5 alleles +0.0% missing data + 123 (0.736) 0.927 0.750 0.679 + 131 (0.190) 0.064 0.236 0.271 + 139 (0.030) 0.004 0.006 0.028 + 121 (0.022) 0.003 0.003 0.011 + 124 (0.022) 0.003 0.004 0.010 + +Locus 24 : At163 +7 alleles +0.0% missing data + 128 (0.683) 0.892 0.790 0.604 + 134 (0.204) 0.073 0.189 0.357 + 130 (0.026) 0.004 0.004 0.020 + 136 (0.022) 0.003 0.009 0.005 + 140 (0.022) 0.009 0.003 0.005 + 146 (0.022) 0.009 0.003 0.005 + 142 (0.022) 0.010 0.003 0.004 + +Locus 25 : At188 +13 alleles +1.3% missing data + 189 (0.614) 0.877 0.752 0.710 + 205 (0.031) 0.004 0.005 0.058 + 207 (0.036) 0.005 0.076 0.016 + 219 (0.027) 0.004 0.010 0.015 + 209 (0.035) 0.005 0.057 0.015 + 217 (0.037) 0.005 0.023 0.031 + 215 (0.023) 0.003 0.018 0.006 + 199 (0.068) 0.055 0.018 0.068 + 212 (0.028) 0.005 0.013 0.019 + 213 (0.035) 0.005 0.012 0.042 + 211 (0.020) 0.003 0.004 0.010 + 191 (0.020) 0.002 0.010 0.004 + 187 (0.024) 0.028 0.003 0.004 + +Values of parameters used in structure: +DATAFILE=, OUTFILE=, NUMINDS=149, NUMLOCI=25, MISSING=-9, LABEL=1, POPDATA=0, POPFLAG=1, PHENOTYPE=0, EXTRACOLS=1, MAXPOPS=3, BURNIN=100000, NUMREPS=1000000, USEPOPINFO=0, INFERALPHA=1, INFERLAMBDA=0, POPSPECIFICLAMBDA=0, POPALPHAS=0, COMPUTEPROB=1, NOADMIX=0, ADMBURNIN=2500, UPDATEFREQ=1, PRINTLIKES=0, INTERMEDSAVE=0, PRINTKLD=0, PRINTNET=0, PRINTLAMBDA=0, ANCESTDIST=0, NUMBOXES=1000, ANCESTPINT=0.90000, GENSBACK=2, MIGRPRIOR=0.05000, PRINTQHAT=0, PRINTQSUM=0, ALPHA=1.0000, FREQSCORR=1, FPRIORMEAN=0.0100, FPRIORSD=0.0500, ONEFST=0, LAMBDA=1.0000, UNIFPRIORALPHA=1, ALPHAMAX=10.0000, ALPHAPRIORA=1.0000, ALPHAPRIORB=2.0000, ALPHAPROPSD=0.0250, STARTATPOPINFO=0, RANDOMIZE=1, LINKAGE=0, METROFREQ=10, REPORTHITRATE=0, MARKOVPHASE=-1, PHASED=0, PLOIDY=2, PHASEINFO=0 LOCPRIOR=0, LOCPRIORINIT=1.000000, LOCDATA=0, LOCISPOP=0, LOCPRIORSTEP=0.100000, MAXLOCPRIOR=20.000000, SEED=1335110290, +[STRAT parameters]: NUMSIMSTATS=1000, PHENOTYPECOL=-9, POOLFREQ=10, LOCUSxONLY=0, EMERROR=0.00100, MISSINGPHENO=-9, \ No newline at end of file diff --git a/inst/files/structure/structure_05 b/inst/files/structure/structure_05 new file mode 100644 index 0000000..e2a3994 --- /dev/null +++ b/inst/files/structure/structure_05 @@ -0,0 +1,535 @@ + + +---------------------------------------------------- +STRUCTURE by Pritchard, Stephens and Donnelly (2000) + and Falush, Stephens and Pritchard (2003) + Code by Pritchard, Falush and Hubisz + Version 2.3.2.1 (Oct 2009) +---------------------------------------------------- + + + +Command line arguments: +Input File: + +Run parameters: + 149 individuals + 25 loci + 4 populations assumed + 100000 Burn-in period + 1000000 Reps + + +-------------------------------------------- +Overall proportion of membership of the +sample in each of the 4 clusters + +Inferred Clusters + 1 2 3 4 +0.244 0.297 0.189 0.271 + +-------------------------------------------- + +Allele-freq. divergence among pops (Net nucleotide distance), +computed using point estimates of P. + + 1 2 3 4 + 1 - 0.0509 0.0145 0.0237 + 2 0.0509 - 0.0243 0.0394 + 3 0.0145 0.0243 - 0.0160 + 4 0.0237 0.0394 0.0160 - + +Average distances (expected heterozygosity) between individuals in same cluster: +cluster 1 : 0.5190 +cluster 2 : 0.4270 +cluster 3 : 0.5745 +cluster 4 : 0.4606 + +-------------------------------------------- +Estimated Ln Prob of Data = -7687.5 +Mean value of ln likelihood = -7260.2 +Variance of ln likelihood = 854.7 +Mean value of alpha = 0.2130 + +Mean value of Fst_1 = 0.1081 +Mean value of Fst_2 = 0.1160 +Mean value of Fst_3 = 0.0040 +Mean value of Fst_4 = 0.1282 + + +Inferred ancestry of individuals: + Label (%Miss) : Inferred clusters + 1 I13825 (0) : 0.417 0.034 0.465 0.085 + 2 I13826 (0) : 0.821 0.034 0.073 0.071 + 3 I13827 (20) : 0.076 0.037 0.067 0.819 + 4 I13828 (0) : 0.730 0.034 0.160 0.076 + 5 I13829 (8) : 0.152 0.033 0.071 0.743 + 6 I13830 (0) : 0.821 0.030 0.067 0.082 + 7 I13831 (0) : 0.276 0.048 0.108 0.568 + 8 I13832 (16) : 0.118 0.050 0.254 0.578 + 9 I13833 (0) : 0.106 0.049 0.058 0.787 + 10 I13834 (0) : 0.127 0.022 0.036 0.814 + 11 I13835 (0) : 0.117 0.023 0.415 0.445 + 12 I13836 (0) : 0.115 0.028 0.136 0.722 + 13 I13377 (0) : 0.053 0.062 0.126 0.760 + 14 I13378 (0) : 0.201 0.038 0.552 0.209 + 15 I13379 (0) : 0.526 0.049 0.096 0.328 + 16 I13380 (0) : 0.044 0.138 0.072 0.745 + 17 I13381 (0) : 0.099 0.083 0.379 0.439 + 18 I13382 (0) : 0.061 0.026 0.036 0.877 + 19 I13383 (0) : 0.176 0.051 0.427 0.346 + 20 I13384 (0) : 0.306 0.052 0.115 0.527 + 21 I13385 (0) : 0.069 0.022 0.044 0.865 + 22 I13386 (0) : 0.056 0.028 0.067 0.849 + 23 I13387 (0) : 0.576 0.038 0.181 0.205 + 24 I13388 (0) : 0.441 0.068 0.436 0.055 + 25 I13389 (0) : 0.100 0.126 0.082 0.692 + 26 I13390 (0) : 0.108 0.051 0.052 0.789 + 27 I13391 (0) : 0.136 0.120 0.431 0.313 + 28 I13392 (0) : 0.266 0.054 0.443 0.236 + 29 I13393 (0) : 0.042 0.171 0.151 0.637 + 30 I13394 (4) : 0.123 0.370 0.273 0.234 + 31 I13395 (0) : 0.181 0.348 0.206 0.265 + 32 I13396 (0) : 0.575 0.136 0.244 0.045 + 33 I13397 (0) : 0.329 0.033 0.410 0.228 + 34 I13398 (0) : 0.739 0.022 0.048 0.191 + 35 I13399 (4) : 0.090 0.042 0.528 0.340 + 36 I13400 (0) : 0.160 0.096 0.264 0.481 + 37 I13401 (0) : 0.091 0.295 0.219 0.394 + 38 I13402 (0) : 0.390 0.065 0.438 0.107 + 39 I13403 (0) : 0.655 0.146 0.062 0.137 + 40 I13404 (0) : 0.481 0.029 0.059 0.431 + 41 I13405 (0) : 0.038 0.032 0.036 0.895 + 42 I13406 (16) : 0.483 0.035 0.364 0.118 + 43 I13407 (0) : 0.555 0.038 0.151 0.256 + 44 I13408 (0) : 0.133 0.031 0.069 0.767 + 45 I13409 (0) : 0.438 0.067 0.421 0.073 + 46 I13410 (0) : 0.244 0.023 0.087 0.645 + 47 I13411 (0) : 0.236 0.018 0.054 0.691 + 48 I13412 (0) : 0.288 0.269 0.140 0.304 + 49 I13413 (0) : 0.582 0.071 0.268 0.079 + 50 I13414 (0) : 0.683 0.035 0.165 0.118 + 51 I13415 (4) : 0.215 0.083 0.080 0.622 + 52 I13416 (4) : 0.485 0.137 0.131 0.247 + 53 I13417 (4) : 0.182 0.147 0.058 0.613 + 54 I13418 (0) : 0.316 0.143 0.082 0.459 + 55 I13419 (0) : 0.172 0.029 0.427 0.373 + 56 I13420 (0) : 0.513 0.213 0.065 0.209 + 57 I13421 (0) : 0.106 0.253 0.054 0.587 + 58 I13422 (0) : 0.275 0.252 0.108 0.365 + 59 I13423 (0) : 0.189 0.099 0.420 0.292 + 60 I13424 (0) : 0.106 0.056 0.140 0.698 + 61 I13425 (4) : 0.206 0.085 0.140 0.569 + 62 I13426 (4) : 0.161 0.414 0.275 0.151 + 63 I13870 (0) : 0.530 0.213 0.103 0.154 + 64 I13871 (16) : 0.558 0.049 0.208 0.185 + 65 I13872 (0) : 0.778 0.024 0.156 0.043 + 66 I13873 (4) : 0.652 0.119 0.139 0.090 + 67 I13874 (0) : 0.552 0.067 0.302 0.078 + 68 I13875 (8) : 0.716 0.077 0.112 0.095 + 69 I13876 (0) : 0.220 0.115 0.588 0.077 + 70 I13877 (20) : 0.174 0.095 0.130 0.600 + 71 I13878 (28) : 0.590 0.035 0.065 0.310 + 72 I13879 (4) : 0.322 0.020 0.054 0.604 + 73 I13880 (4) : 0.871 0.026 0.064 0.039 + 74 I13881 (0) : 0.347 0.081 0.419 0.153 + 75 I13882 (0) : 0.705 0.048 0.121 0.126 + 76 I13883 (4) : 0.743 0.073 0.148 0.036 + 77 I13884 (16) : 0.163 0.041 0.668 0.128 + 78 I13885 (20) : 0.115 0.024 0.375 0.485 + 79 I13886 (8) : 0.530 0.032 0.133 0.305 + 80 I13887 (0) : 0.142 0.066 0.760 0.031 + 81 I13888 (0) : 0.376 0.056 0.443 0.125 + 82 I13889 (0) : 0.057 0.660 0.139 0.144 + 83 I13890 (32) : 0.151 0.424 0.231 0.194 + 84 I13891 (0) : 0.659 0.045 0.118 0.177 + 85 I13892 (0) : 0.147 0.357 0.131 0.366 + 86 I13893 (8) : 0.095 0.043 0.680 0.181 + 87 I13894 (0) : 0.865 0.035 0.075 0.025 + 88 I13895 (4) : 0.167 0.131 0.394 0.308 + 89 I13896 (0) : 0.586 0.210 0.143 0.061 + 90 I13897 (0) : 0.693 0.019 0.052 0.237 + 91 I13898 (4) : 0.676 0.063 0.102 0.159 + 92 I13899 (0) : 0.901 0.017 0.044 0.038 + 93 I13900 (32) : 0.282 0.087 0.537 0.094 + 94 I13837 (0) : 0.049 0.056 0.048 0.848 + 95 I13838 (0) : 0.196 0.614 0.108 0.082 + 96 I13839 (0) : 0.109 0.123 0.082 0.687 + 97 I13840 (0) : 0.230 0.190 0.061 0.519 + 98 I13841 (0) : 0.077 0.464 0.074 0.386 + 99 I13842 (0) : 0.032 0.269 0.058 0.640 +100 I13843 (4) : 0.139 0.578 0.096 0.187 +101 I13844 (16) : 0.103 0.129 0.211 0.557 +102 I13845 (0) : 0.111 0.029 0.067 0.793 +103 I13846 (0) : 0.074 0.053 0.121 0.752 +104 I13847 (0) : 0.357 0.359 0.153 0.132 +105 I13848 (0) : 0.275 0.257 0.302 0.166 +106 I13849 (0) : 0.607 0.101 0.237 0.055 +107 I13850 (0) : 0.144 0.505 0.164 0.187 +108 I12577 (4) : 0.036 0.812 0.109 0.043 +109 I12578 (4) : 0.066 0.755 0.134 0.045 +110 I12579 (8) : 0.025 0.688 0.220 0.066 +111 I12580 (8) : 0.037 0.869 0.039 0.055 +112 I12581 (4) : 0.059 0.231 0.504 0.206 +113 I12582 (4) : 0.056 0.836 0.070 0.038 +114 I12583 (8) : 0.055 0.300 0.558 0.086 +115 I12584 (4) : 0.066 0.583 0.318 0.033 +116 I12585 (4) : 0.033 0.879 0.063 0.025 +117 I12586 (4) : 0.044 0.871 0.052 0.033 +118 I12587 (8) : 0.027 0.908 0.029 0.036 +119 I12588 (4) : 0.022 0.838 0.109 0.030 +120 I12589 (0) : 0.067 0.814 0.074 0.045 +121 I12590 (0) : 0.071 0.683 0.179 0.067 +122 I12591 (12) : 0.017 0.923 0.042 0.019 +123 I12592 (4) : 0.045 0.789 0.116 0.051 +124 I12593 (4) : 0.041 0.859 0.080 0.021 +125 I12594 (8) : 0.031 0.897 0.043 0.029 +126 I12595 (0) : 0.027 0.572 0.354 0.047 +127 I12596 (0) : 0.020 0.895 0.056 0.029 +128 I12597 (4) : 0.040 0.415 0.494 0.051 +129 I12598 (0) : 0.055 0.541 0.342 0.061 +130 I12599 (0) : 0.151 0.598 0.209 0.042 +131 I12600 (4) : 0.066 0.849 0.047 0.038 +132 I12601 (8) : 0.037 0.833 0.100 0.031 +133 I12602 (12) : 0.040 0.826 0.092 0.042 +134 I12603 (0) : 0.041 0.658 0.255 0.046 +135 I12604 (4) : 0.088 0.761 0.113 0.038 +136 I12605 (4) : 0.060 0.786 0.122 0.032 +137 I12606 (8) : 0.025 0.851 0.094 0.030 +138 I12607 (4) : 0.046 0.613 0.311 0.030 +139 I12608 (8) : 0.054 0.686 0.212 0.049 +140 I12609 (8) : 0.030 0.875 0.062 0.034 +141 I12610 (52) : 0.044 0.766 0.113 0.077 +142 I12611 (0) : 0.036 0.894 0.046 0.024 +143 I12612 (0) : 0.033 0.873 0.064 0.030 +144 I12613 (0) : 0.019 0.890 0.051 0.040 +145 I12614 (4) : 0.055 0.761 0.073 0.110 +146 I12615 (0) : 0.070 0.659 0.184 0.087 +147 I12616 (4) : 0.035 0.515 0.365 0.086 +148 I12617 (8) : 0.029 0.924 0.030 0.017 +149 I12618 (48) : 0.030 0.840 0.095 0.034 + + +Estimated Allele Frequencies in each cluster +First column gives estimated ancestral frequencies + + +Locus 1 : A8 +7 alleles +4.0% missing data + 177 (0.522) 0.489 0.595 0.527 0.442 + 179 (0.091) 0.077 0.054 0.087 0.142 + 175 (0.100) 0.254 0.011 0.100 0.247 + 173 (0.046) 0.024 0.006 0.046 0.081 + 181 (0.171) 0.128 0.305 0.170 0.075 + 165 (0.040) 0.014 0.027 0.039 0.006 + 183 (0.031) 0.013 0.003 0.031 0.007 + +Locus 2 : A14 +5 alleles +0.0% missing data + 112 (0.204) 0.388 0.029 0.209 0.201 + 110 (0.702) 0.583 0.821 0.701 0.788 + 114 (0.031) 0.016 0.004 0.031 0.004 + 118 (0.035) 0.009 0.113 0.033 0.004 + 116 (0.028) 0.004 0.033 0.027 0.003 + +Locus 3 : A24 +5 alleles +2.7% missing data + 104 (0.414) 0.466 0.369 0.419 0.273 + 106 (0.514) 0.502 0.566 0.513 0.717 + 101 (0.018) 0.003 0.002 0.017 0.004 + 108 (0.027) 0.025 0.003 0.027 0.003 + 96 (0.027) 0.004 0.060 0.025 0.003 + +Locus 4 : A29 +29 alleles +6.7% missing data + 143 (0.032) 0.102 0.005 0.031 0.035 + 149 (0.053) 0.024 0.055 0.054 0.019 + 147 (0.029) 0.034 0.032 0.028 0.004 + 153 (0.057) 0.026 0.088 0.057 0.128 + 169 (0.035) 0.104 0.031 0.034 0.006 + 151 (0.037) 0.008 0.026 0.037 0.108 + 145 (0.028) 0.025 0.027 0.027 0.005 + 157 (0.065) 0.126 0.146 0.067 0.034 + 155 (0.097) 0.116 0.183 0.101 0.071 + 159 (0.052) 0.158 0.045 0.053 0.026 + 161 (0.034) 0.014 0.006 0.033 0.109 + 141 (0.029) 0.011 0.007 0.028 0.058 + 139 (0.016) 0.003 0.002 0.014 0.020 + 144 (0.022) 0.012 0.003 0.021 0.081 + 171 (0.050) 0.022 0.032 0.053 0.069 + 163 (0.078) 0.071 0.058 0.082 0.098 + 167 (0.046) 0.039 0.067 0.046 0.020 + 173 (0.024) 0.012 0.006 0.023 0.038 + 142 (0.013) 0.007 0.002 0.012 0.002 + 177 (0.024) 0.005 0.046 0.023 0.007 + 175 (0.022) 0.004 0.017 0.023 0.006 + 165 (0.044) 0.047 0.041 0.044 0.015 + 146 (0.020) 0.014 0.002 0.019 0.030 + 137 (0.019) 0.003 0.011 0.019 0.002 + 183 (0.017) 0.003 0.017 0.016 0.002 + 179 (0.018) 0.003 0.013 0.018 0.003 + 191 (0.013) 0.002 0.005 0.013 0.001 + 185 (0.013) 0.002 0.005 0.012 0.001 + 180 (0.015) 0.002 0.022 0.014 0.001 + +Locus 5 : A43 +7 alleles +1.3% missing data + 123 (0.217) 0.090 0.154 0.223 0.082 + 141 (0.017) 0.005 0.002 0.016 0.002 + 137 (0.653) 0.882 0.688 0.654 0.862 + 139 (0.050) 0.014 0.080 0.047 0.048 + 124 (0.030) 0.004 0.065 0.028 0.003 + 143 (0.017) 0.002 0.004 0.016 0.002 + 128 (0.017) 0.002 0.008 0.016 0.002 + +Locus 6 : A79 +13 alleles +3.4% missing data + 103 (0.237) 0.311 0.176 0.240 0.304 + 97 (0.128) 0.208 0.055 0.132 0.059 + 101 (0.093) 0.064 0.034 0.095 0.264 + 107 (0.099) 0.075 0.074 0.097 0.195 + 109 (0.100) 0.076 0.087 0.101 0.068 + 105 (0.160) 0.205 0.422 0.159 0.064 + 111 (0.050) 0.025 0.028 0.050 0.009 + 113 (0.016) 0.005 0.002 0.015 0.002 + 91 (0.024) 0.004 0.083 0.023 0.003 + 99 (0.031) 0.010 0.026 0.029 0.022 + 115 (0.028) 0.007 0.009 0.028 0.008 + 117 (0.016) 0.006 0.002 0.015 0.002 + 121 (0.016) 0.003 0.002 0.016 0.002 + +Locus 7 : A88 +9 alleles +6.0% missing data + 133 (0.017) 0.005 0.002 0.017 0.002 + 149 (0.525) 0.536 0.813 0.528 0.453 + 137 (0.101) 0.137 0.014 0.102 0.094 + 147 (0.200) 0.228 0.062 0.201 0.425 + 141 (0.080) 0.080 0.088 0.078 0.016 + 152 (0.017) 0.003 0.002 0.017 0.003 + 143 (0.018) 0.004 0.002 0.017 0.002 + 151 (0.018) 0.002 0.006 0.017 0.002 + 144 (0.025) 0.004 0.010 0.024 0.003 + +Locus 8 : A113 +12 alleles +7.4% missing data + 214 (0.588) 0.676 0.747 0.596 0.808 + 226 (0.057) 0.142 0.029 0.056 0.018 + 218 (0.017) 0.003 0.002 0.015 0.009 + 220 (0.061) 0.017 0.143 0.060 0.031 + 216 (0.059) 0.020 0.035 0.058 0.021 + 230 (0.041) 0.015 0.006 0.041 0.076 + 234 (0.032) 0.031 0.004 0.032 0.007 + 232 (0.030) 0.033 0.005 0.029 0.010 + 228 (0.052) 0.041 0.015 0.052 0.008 + 224 (0.017) 0.004 0.002 0.016 0.002 + 222 (0.031) 0.016 0.010 0.030 0.003 + 208 (0.016) 0.003 0.002 0.015 0.008 + +Locus 9 : Ac11 +9 alleles +4.7% missing data + 111 (0.125) 0.306 0.031 0.126 0.128 + 117 (0.310) 0.284 0.194 0.314 0.441 + 115 (0.252) 0.275 0.235 0.252 0.339 + 113 (0.159) 0.103 0.274 0.160 0.064 + 119 (0.047) 0.013 0.178 0.044 0.014 + 121 (0.026) 0.004 0.061 0.024 0.003 + 123 (0.033) 0.006 0.012 0.033 0.003 + 127 (0.031) 0.006 0.013 0.030 0.005 + 125 (0.017) 0.002 0.003 0.017 0.002 + +Locus 10 : Ac88 +8 alleles +0.7% missing data + 214 (0.757) 0.725 0.923 0.761 0.926 + 216 (0.029) 0.020 0.003 0.028 0.006 + 220 (0.113) 0.239 0.026 0.115 0.058 + 230 (0.025) 0.006 0.004 0.024 0.002 + 221 (0.017) 0.002 0.008 0.016 0.002 + 212 (0.020) 0.003 0.019 0.019 0.002 + 217 (0.017) 0.002 0.005 0.016 0.002 + 224 (0.023) 0.003 0.012 0.022 0.002 + +Locus 11 : Ac139 +8 alleles +13.4% missing data + 327 (0.504) 0.428 0.803 0.506 0.587 + 329 (0.293) 0.436 0.103 0.297 0.326 + 331 (0.073) 0.110 0.019 0.072 0.032 + 328 (0.044) 0.012 0.005 0.044 0.046 + 341 (0.019) 0.003 0.008 0.018 0.002 + 337 (0.028) 0.004 0.051 0.027 0.003 + 323 (0.019) 0.003 0.004 0.018 0.002 + 339 (0.019) 0.003 0.006 0.018 0.002 + +Locus 12 : Ac306 +6 alleles +4.7% missing data + 165 (0.738) 0.705 0.808 0.743 0.818 + 177 (0.080) 0.066 0.104 0.078 0.038 + 173 (0.095) 0.209 0.031 0.095 0.036 + 169 (0.043) 0.015 0.005 0.042 0.103 + 171 (0.017) 0.003 0.002 0.017 0.002 + 179 (0.026) 0.003 0.050 0.025 0.003 + +Locus 13 : Ap15 +7 alleles +6.0% missing data + 202 (0.816) 0.944 0.830 0.823 0.974 + 212 (0.027) 0.028 0.003 0.026 0.003 + 204 (0.043) 0.008 0.027 0.042 0.008 + 208 (0.040) 0.006 0.056 0.038 0.007 + 220 (0.038) 0.008 0.070 0.037 0.004 + 219 (0.018) 0.003 0.008 0.016 0.002 + 210 (0.018) 0.003 0.006 0.017 0.002 + +Locus 14 : Ap68 +9 alleles +4.7% missing data + 158 (0.389) 0.626 0.291 0.394 0.253 + 160 (0.088) 0.035 0.023 0.089 0.148 + 156 (0.228) 0.236 0.360 0.223 0.393 + 162 (0.044) 0.030 0.009 0.043 0.006 + 154 (0.093) 0.036 0.017 0.096 0.155 + 152 (0.075) 0.017 0.262 0.073 0.034 + 164 (0.043) 0.015 0.022 0.043 0.005 + 170 (0.017) 0.002 0.003 0.017 0.003 + 166 (0.022) 0.003 0.015 0.021 0.002 + +Locus 15 : Ap85 +10 alleles +3.4% missing data + 202 (0.314) 0.389 0.547 0.311 0.259 + 186 (0.251) 0.377 0.104 0.258 0.494 + 204 (0.066) 0.025 0.037 0.066 0.026 + 188 (0.111) 0.076 0.024 0.113 0.147 + 194 (0.077) 0.083 0.027 0.075 0.048 + 196 (0.052) 0.013 0.116 0.050 0.012 + 200 (0.064) 0.018 0.078 0.065 0.008 + 192 (0.024) 0.007 0.005 0.024 0.003 + 190 (0.017) 0.008 0.002 0.016 0.003 + 198 (0.024) 0.003 0.061 0.022 0.002 + +Locus 16 : Ap90 +13 alleles +0.7% missing data + 131 (0.355) 0.526 0.545 0.355 0.564 + 135 (0.065) 0.080 0.089 0.063 0.025 + 133 (0.300) 0.307 0.204 0.310 0.216 + 129 (0.098) 0.042 0.088 0.098 0.150 + 137 (0.035) 0.008 0.012 0.034 0.029 + 141 (0.016) 0.005 0.002 0.015 0.002 + 143 (0.022) 0.009 0.002 0.022 0.004 + 151 (0.023) 0.010 0.004 0.022 0.002 + 155 (0.016) 0.004 0.002 0.015 0.002 + 145 (0.016) 0.002 0.009 0.015 0.002 + 130 (0.019) 0.003 0.018 0.018 0.002 + 139 (0.016) 0.002 0.009 0.015 0.001 + 153 (0.020) 0.003 0.017 0.019 0.002 + +Locus 17 : Ap223 +7 alleles +2.0% missing data + 183 (0.691) 0.612 0.897 0.695 0.676 + 187 (0.134) 0.286 0.021 0.137 0.265 + 189 (0.025) 0.005 0.002 0.024 0.026 + 173 (0.063) 0.070 0.041 0.061 0.016 + 182 (0.031) 0.010 0.005 0.030 0.010 + 180 (0.025) 0.005 0.006 0.024 0.004 + 179 (0.031) 0.012 0.028 0.030 0.003 + +Locus 18 : Ap224 +7 alleles +4.0% missing data + 283 (0.112) 0.199 0.019 0.113 0.187 + 287 (0.470) 0.482 0.457 0.474 0.439 + 281 (0.132) 0.156 0.048 0.132 0.188 + 289 (0.207) 0.103 0.421 0.205 0.167 + 291 (0.038) 0.054 0.004 0.037 0.013 + 285 (0.017) 0.003 0.002 0.017 0.003 + 279 (0.024) 0.003 0.050 0.022 0.002 + +Locus 19 : Ap226 +5 alleles +17.4% missing data + 237 (0.385) 0.323 0.345 0.387 0.358 + 239 (0.460) 0.451 0.610 0.461 0.494 + 247 (0.117) 0.219 0.030 0.117 0.139 + 235 (0.019) 0.003 0.003 0.018 0.008 + 241 (0.019) 0.003 0.011 0.017 0.002 + +Locus 20 : Ap249 +9 alleles +1.3% missing data + 209 (0.617) 0.586 0.702 0.623 0.731 + 211 (0.055) 0.015 0.008 0.055 0.060 + 217 (0.081) 0.145 0.019 0.079 0.079 + 219 (0.104) 0.227 0.018 0.105 0.088 + 215 (0.075) 0.013 0.243 0.074 0.032 + 208 (0.017) 0.005 0.002 0.016 0.002 + 225 (0.017) 0.004 0.002 0.016 0.002 + 223 (0.017) 0.003 0.002 0.016 0.004 + 213 (0.017) 0.002 0.005 0.016 0.002 + +Locus 21 : Ap273 +4 alleles +1.3% missing data + 106 (0.875) 0.950 0.953 0.878 0.961 + 108 (0.052) 0.032 0.021 0.051 0.015 + 104 (0.044) 0.012 0.005 0.045 0.021 + 102 (0.028) 0.006 0.021 0.026 0.003 + +Locus 22 : Ap274 +2 alleles +2.0% missing data + 120 (0.946) 0.984 0.916 0.947 0.993 + 122 (0.054) 0.016 0.084 0.053 0.007 + +Locus 23 : Ap288 +5 alleles +0.0% missing data + 123 (0.775) 0.620 0.952 0.780 0.764 + 131 (0.161) 0.344 0.042 0.159 0.226 + 139 (0.029) 0.020 0.003 0.028 0.004 + 121 (0.017) 0.008 0.002 0.016 0.002 + 124 (0.017) 0.007 0.002 0.017 0.003 + +Locus 24 : At163 +7 alleles +0.0% missing data + 128 (0.713) 0.559 0.933 0.714 0.814 + 134 (0.193) 0.421 0.053 0.196 0.173 + 130 (0.024) 0.010 0.003 0.024 0.003 + 136 (0.017) 0.003 0.002 0.017 0.004 + 140 (0.017) 0.002 0.003 0.017 0.002 + 146 (0.017) 0.002 0.003 0.017 0.002 + 142 (0.017) 0.002 0.004 0.016 0.002 + +Locus 25 : At188 +13 alleles +1.3% missing data + 189 (0.634) 0.770 0.898 0.641 0.754 + 205 (0.031) 0.060 0.003 0.030 0.005 + 207 (0.030) 0.012 0.003 0.028 0.091 + 219 (0.023) 0.008 0.002 0.023 0.006 + 209 (0.033) 0.013 0.004 0.031 0.063 + 217 (0.042) 0.014 0.004 0.044 0.016 + 215 (0.020) 0.008 0.002 0.019 0.014 + 199 (0.064) 0.066 0.052 0.063 0.013 + 212 (0.028) 0.010 0.005 0.028 0.010 + 213 (0.037) 0.030 0.004 0.037 0.013 + 211 (0.017) 0.003 0.002 0.016 0.002 + 191 (0.016) 0.003 0.002 0.015 0.009 + 187 (0.026) 0.003 0.021 0.024 0.003 + +Values of parameters used in structure: +DATAFILE=, OUTFILE=, NUMINDS=149, NUMLOCI=25, MISSING=-9, LABEL=1, POPDATA=0, POPFLAG=1, PHENOTYPE=0, EXTRACOLS=1, MAXPOPS=4, BURNIN=100000, NUMREPS=1000000, USEPOPINFO=0, INFERALPHA=1, INFERLAMBDA=0, POPSPECIFICLAMBDA=0, POPALPHAS=0, COMPUTEPROB=1, NOADMIX=0, ADMBURNIN=2500, UPDATEFREQ=1, PRINTLIKES=0, INTERMEDSAVE=0, PRINTKLD=0, PRINTNET=0, PRINTLAMBDA=0, ANCESTDIST=0, NUMBOXES=1000, ANCESTPINT=0.90000, GENSBACK=2, MIGRPRIOR=0.05000, PRINTQHAT=0, PRINTQSUM=0, ALPHA=1.0000, FREQSCORR=1, FPRIORMEAN=0.0100, FPRIORSD=0.0500, ONEFST=0, LAMBDA=1.0000, UNIFPRIORALPHA=1, ALPHAMAX=10.0000, ALPHAPRIORA=1.0000, ALPHAPRIORB=2.0000, ALPHAPROPSD=0.0250, STARTATPOPINFO=0, RANDOMIZE=1, LINKAGE=0, METROFREQ=10, REPORTHITRATE=0, MARKOVPHASE=-1, PHASED=0, PLOIDY=2, PHASEINFO=0 LOCPRIOR=0, LOCPRIORINIT=1.000000, LOCDATA=0, LOCISPOP=0, LOCPRIORSTEP=0.100000, MAXLOCPRIOR=20.000000, SEED=1335116168, +[STRAT parameters]: NUMSIMSTATS=1000, PHENOTYPECOL=-9, POOLFREQ=10, LOCUSxONLY=0, EMERROR=0.00100, MISSINGPHENO=-9, \ No newline at end of file diff --git a/inst/files/structure/structure_06 b/inst/files/structure/structure_06 new file mode 100644 index 0000000..f68cd23 --- /dev/null +++ b/inst/files/structure/structure_06 @@ -0,0 +1,538 @@ + + +---------------------------------------------------- +STRUCTURE by Pritchard, Stephens and Donnelly (2000) + and Falush, Stephens and Pritchard (2003) + Code by Pritchard, Falush and Hubisz + Version 2.3.2.1 (Oct 2009) +---------------------------------------------------- + + + +Command line arguments: +Input File: + +Run parameters: + 149 individuals + 25 loci + 5 populations assumed + 100000 Burn-in period + 1000000 Reps + + +-------------------------------------------- +Overall proportion of membership of the +sample in each of the 5 clusters + +Inferred Clusters + 1 2 3 4 5 +0.159 0.204 0.211 0.213 0.213 + +-------------------------------------------- + +Allele-freq. divergence among pops (Net nucleotide distance), +computed using point estimates of P. + + 1 2 3 4 5 + 1 - 0.0160 0.0086 0.0087 0.0083 + 2 0.0160 - 0.0263 0.0279 0.0230 + 3 0.0086 0.0263 - 0.0007 0.0004 + 4 0.0087 0.0279 0.0007 - 0.0017 + 5 0.0083 0.0230 0.0004 0.0017 - + +Average distances (expected heterozygosity) between individuals in same cluster: +cluster 1 : 0.5819 +cluster 2 : 0.5208 +cluster 3 : 0.4696 +cluster 4 : 0.4695 +cluster 5 : 0.4764 + +-------------------------------------------- +Estimated Ln Prob of Data = -7692.4 +Mean value of ln likelihood = -7210.5 +Variance of ln likelihood = 963.9 +Mean value of alpha = 0.2308 + +Mean value of Fst_1 = 0.0005 +Mean value of Fst_2 = 0.1319 +Mean value of Fst_3 = 0.1522 +Mean value of Fst_4 = 0.1490 +Mean value of Fst_5 = 0.1507 + + +Inferred ancestry of individuals: + Label (%Miss) : Inferred clusters + 1 I13825 (0) : 0.421 0.340 0.072 0.089 0.077 + 2 I13826 (0) : 0.072 0.690 0.059 0.093 0.087 + 3 I13827 (20) : 0.067 0.084 0.293 0.181 0.375 + 4 I13828 (0) : 0.141 0.589 0.076 0.106 0.088 + 5 I13829 (8) : 0.076 0.172 0.261 0.193 0.298 + 6 I13830 (0) : 0.061 0.673 0.069 0.098 0.099 + 7 I13831 (0) : 0.068 0.218 0.260 0.203 0.250 + 8 I13832 (16) : 0.190 0.102 0.251 0.194 0.264 + 9 I13833 (0) : 0.047 0.110 0.300 0.202 0.341 + 10 I13834 (0) : 0.038 0.143 0.283 0.172 0.363 + 11 I13835 (0) : 0.256 0.108 0.223 0.181 0.232 + 12 I13836 (0) : 0.142 0.119 0.259 0.158 0.323 + 13 I13377 (0) : 0.087 0.074 0.302 0.219 0.319 + 14 I13378 (0) : 0.337 0.148 0.181 0.162 0.172 + 15 I13379 (0) : 0.069 0.418 0.173 0.150 0.191 + 16 I13380 (0) : 0.067 0.057 0.304 0.222 0.350 + 17 I13381 (0) : 0.205 0.102 0.252 0.221 0.220 + 18 I13382 (0) : 0.036 0.091 0.310 0.235 0.328 + 19 I13383 (0) : 0.280 0.150 0.203 0.183 0.184 + 20 I13384 (0) : 0.107 0.267 0.226 0.173 0.228 + 21 I13385 (0) : 0.052 0.087 0.301 0.187 0.373 + 22 I13386 (0) : 0.068 0.077 0.301 0.209 0.345 + 23 I13387 (0) : 0.167 0.503 0.098 0.106 0.127 + 24 I13388 (0) : 0.421 0.331 0.077 0.091 0.080 + 25 I13389 (0) : 0.051 0.097 0.304 0.218 0.330 + 26 I13390 (0) : 0.054 0.136 0.289 0.200 0.320 + 27 I13391 (0) : 0.267 0.113 0.221 0.178 0.222 + 28 I13392 (0) : 0.300 0.218 0.164 0.143 0.175 + 29 I13393 (0) : 0.079 0.069 0.306 0.278 0.268 + 30 I13394 (4) : 0.177 0.104 0.246 0.245 0.228 + 31 I13395 (0) : 0.132 0.145 0.246 0.235 0.241 + 32 I13396 (0) : 0.212 0.447 0.103 0.134 0.104 + 33 I13397 (0) : 0.270 0.280 0.156 0.126 0.168 + 34 I13398 (0) : 0.040 0.620 0.097 0.108 0.134 + 35 I13399 (4) : 0.365 0.088 0.196 0.145 0.205 + 36 I13400 (0) : 0.149 0.136 0.255 0.192 0.267 + 37 I13401 (0) : 0.195 0.088 0.234 0.225 0.257 + 38 I13402 (0) : 0.338 0.265 0.137 0.136 0.124 + 39 I13403 (0) : 0.056 0.488 0.143 0.163 0.150 + 40 I13404 (0) : 0.053 0.433 0.171 0.131 0.212 + 41 I13405 (0) : 0.040 0.061 0.319 0.197 0.383 + 42 I13406 (16) : 0.331 0.408 0.079 0.091 0.092 + 43 I13407 (0) : 0.099 0.435 0.156 0.140 0.170 + 44 I13408 (0) : 0.056 0.139 0.287 0.212 0.306 + 45 I13409 (0) : 0.386 0.356 0.077 0.095 0.086 + 46 I13410 (0) : 0.075 0.243 0.248 0.191 0.243 + 47 I13411 (0) : 0.057 0.249 0.238 0.158 0.298 + 48 I13412 (0) : 0.132 0.230 0.207 0.203 0.229 + 49 I13413 (0) : 0.240 0.439 0.096 0.117 0.108 + 50 I13414 (0) : 0.152 0.548 0.089 0.103 0.108 + 51 I13415 (4) : 0.065 0.173 0.264 0.186 0.311 + 52 I13416 (4) : 0.103 0.330 0.186 0.182 0.199 + 53 I13417 (4) : 0.056 0.167 0.265 0.206 0.305 + 54 I13418 (0) : 0.070 0.241 0.236 0.201 0.252 + 55 I13419 (0) : 0.416 0.146 0.144 0.110 0.183 + 56 I13420 (0) : 0.064 0.397 0.170 0.179 0.189 + 57 I13421 (0) : 0.052 0.103 0.300 0.264 0.281 + 58 I13422 (0) : 0.103 0.210 0.228 0.219 0.240 + 59 I13423 (0) : 0.267 0.143 0.207 0.193 0.190 + 60 I13424 (0) : 0.112 0.114 0.280 0.194 0.300 + 61 I13425 (4) : 0.144 0.180 0.231 0.174 0.271 + 62 I13426 (4) : 0.209 0.122 0.230 0.244 0.195 + 63 I13870 (0) : 0.092 0.420 0.156 0.170 0.162 + 64 I13871 (16) : 0.184 0.402 0.134 0.142 0.138 + 65 I13872 (0) : 0.154 0.666 0.040 0.078 0.062 + 66 I13873 (4) : 0.111 0.459 0.143 0.152 0.135 + 67 I13874 (0) : 0.295 0.444 0.072 0.095 0.093 + 68 I13875 (8) : 0.106 0.553 0.102 0.126 0.113 + 69 I13876 (0) : 0.542 0.177 0.091 0.097 0.093 + 70 I13877 (20) : 0.092 0.151 0.273 0.231 0.253 + 71 I13878 (28) : 0.059 0.503 0.138 0.128 0.172 + 72 I13879 (4) : 0.050 0.281 0.229 0.158 0.283 + 73 I13880 (4) : 0.059 0.736 0.046 0.088 0.071 + 74 I13881 (0) : 0.384 0.282 0.110 0.102 0.122 + 75 I13882 (0) : 0.108 0.564 0.099 0.116 0.113 + 76 I13883 (4) : 0.135 0.625 0.062 0.104 0.075 + 77 I13884 (16) : 0.589 0.141 0.092 0.080 0.097 + 78 I13885 (20) : 0.323 0.119 0.198 0.151 0.208 + 79 I13886 (8) : 0.101 0.445 0.150 0.124 0.180 + 80 I13887 (0) : 0.701 0.111 0.061 0.066 0.060 + 81 I13888 (0) : 0.357 0.300 0.114 0.114 0.114 + 82 I13889 (0) : 0.107 0.054 0.267 0.314 0.257 + 83 I13890 (32) : 0.182 0.122 0.233 0.248 0.216 + 84 I13891 (0) : 0.114 0.524 0.108 0.113 0.141 + 85 I13892 (0) : 0.095 0.122 0.276 0.255 0.252 + 86 I13893 (8) : 0.479 0.089 0.158 0.126 0.148 + 87 I13894 (0) : 0.064 0.758 0.037 0.083 0.058 + 88 I13895 (4) : 0.272 0.126 0.215 0.186 0.201 + 89 I13896 (0) : 0.114 0.480 0.124 0.158 0.125 + 90 I13897 (0) : 0.045 0.555 0.121 0.119 0.160 + 91 I13898 (4) : 0.081 0.494 0.141 0.137 0.148 + 92 I13899 (0) : 0.035 0.785 0.036 0.080 0.064 + 93 I13900 (32) : 0.471 0.216 0.102 0.105 0.106 + 94 I13837 (0) : 0.049 0.061 0.315 0.200 0.375 + 95 I13838 (0) : 0.104 0.160 0.232 0.285 0.218 + 96 I13839 (0) : 0.079 0.107 0.276 0.194 0.344 + 97 I13840 (0) : 0.053 0.171 0.267 0.234 0.275 + 98 I13841 (0) : 0.060 0.085 0.300 0.305 0.249 + 99 I13842 (0) : 0.064 0.046 0.308 0.256 0.326 +100 I13843 (4) : 0.072 0.109 0.286 0.305 0.227 +101 I13844 (16) : 0.159 0.103 0.260 0.221 0.257 +102 I13845 (0) : 0.065 0.119 0.283 0.214 0.319 +103 I13846 (0) : 0.121 0.098 0.289 0.194 0.297 +104 I13847 (0) : 0.143 0.284 0.178 0.208 0.187 +105 I13848 (0) : 0.186 0.182 0.214 0.231 0.187 +106 I13849 (0) : 0.199 0.420 0.123 0.146 0.112 +107 I13850 (0) : 0.105 0.119 0.270 0.285 0.220 +108 I12577 (4) : 0.112 0.035 0.272 0.337 0.243 +109 I12578 (4) : 0.110 0.057 0.256 0.332 0.245 +110 I12579 (8) : 0.207 0.029 0.250 0.300 0.214 +111 I12580 (8) : 0.040 0.038 0.297 0.365 0.261 +112 I12581 (4) : 0.342 0.060 0.206 0.203 0.189 +113 I12582 (4) : 0.074 0.053 0.279 0.349 0.246 +114 I12583 (8) : 0.518 0.048 0.137 0.163 0.134 +115 I12584 (4) : 0.307 0.057 0.201 0.253 0.182 +116 I12585 (4) : 0.072 0.035 0.287 0.360 0.246 +117 I12586 (4) : 0.050 0.040 0.298 0.363 0.248 +118 I12587 (8) : 0.031 0.029 0.307 0.376 0.258 +119 I12588 (4) : 0.122 0.022 0.273 0.343 0.241 +120 I12589 (0) : 0.078 0.061 0.270 0.343 0.247 +121 I12590 (0) : 0.163 0.068 0.247 0.302 0.220 +122 I12591 (12) : 0.045 0.018 0.289 0.379 0.269 +123 I12592 (4) : 0.112 0.040 0.257 0.338 0.252 +124 I12593 (4) : 0.081 0.040 0.268 0.356 0.256 +125 I12594 (8) : 0.047 0.032 0.291 0.369 0.260 +126 I12595 (0) : 0.309 0.029 0.214 0.259 0.188 +127 I12596 (0) : 0.061 0.021 0.286 0.370 0.262 +128 I12597 (4) : 0.457 0.035 0.174 0.192 0.142 +129 I12598 (0) : 0.327 0.048 0.199 0.241 0.184 +130 I12599 (0) : 0.204 0.128 0.213 0.264 0.191 +131 I12600 (4) : 0.051 0.066 0.285 0.353 0.244 +132 I12601 (8) : 0.112 0.038 0.274 0.342 0.234 +133 I12602 (12) : 0.090 0.038 0.279 0.347 0.246 +134 I12603 (0) : 0.265 0.039 0.225 0.274 0.197 +135 I12604 (4) : 0.120 0.083 0.255 0.319 0.223 +136 I12605 (4) : 0.118 0.057 0.265 0.331 0.230 +137 I12606 (8) : 0.092 0.026 0.275 0.355 0.253 +138 I12607 (4) : 0.291 0.044 0.202 0.266 0.196 +139 I12608 (8) : 0.193 0.051 0.241 0.295 0.220 +140 I12609 (8) : 0.063 0.030 0.282 0.365 0.260 +141 I12610 (52) : 0.111 0.045 0.274 0.334 0.236 +142 I12611 (0) : 0.051 0.036 0.285 0.370 0.259 +143 I12612 (0) : 0.067 0.033 0.288 0.363 0.249 +144 I12613 (0) : 0.054 0.020 0.286 0.372 0.268 +145 I12614 (4) : 0.073 0.054 0.286 0.333 0.253 +146 I12615 (0) : 0.179 0.063 0.240 0.292 0.227 +147 I12616 (4) : 0.371 0.035 0.187 0.231 0.177 +148 I12617 (8) : 0.032 0.029 0.294 0.379 0.265 +149 I12618 (48) : 0.097 0.030 0.281 0.351 0.241 + + +Estimated Allele Frequencies in each cluster +First column gives estimated ancestral frequencies + + +Locus 1 : A8 +7 alleles +4.0% missing data + 177 (0.508) 0.509 0.485 0.529 0.548 0.499 + 179 (0.093) 0.092 0.085 0.091 0.077 0.102 + 175 (0.105) 0.104 0.267 0.131 0.108 0.163 + 173 (0.045) 0.045 0.024 0.047 0.036 0.049 + 181 (0.178) 0.179 0.113 0.177 0.204 0.164 + 165 (0.041) 0.040 0.013 0.016 0.020 0.015 + 183 (0.030) 0.030 0.012 0.008 0.008 0.008 + +Locus 2 : A14 +5 alleles +0.0% missing data + 112 (0.202) 0.202 0.404 0.142 0.138 0.150 + 110 (0.701) 0.701 0.568 0.791 0.780 0.790 + 114 (0.032) 0.032 0.016 0.006 0.006 0.006 + 118 (0.036) 0.035 0.008 0.045 0.058 0.041 + 116 (0.030) 0.029 0.004 0.015 0.018 0.013 + +Locus 3 : A24 +5 alleles +2.7% missing data + 104 (0.408) 0.409 0.465 0.335 0.350 0.328 + 106 (0.519) 0.519 0.506 0.630 0.609 0.640 + 101 (0.018) 0.017 0.003 0.004 0.004 0.004 + 108 (0.029) 0.029 0.022 0.006 0.007 0.006 + 96 (0.027) 0.027 0.004 0.025 0.031 0.022 + +Locus 4 : A29 +29 alleles +6.7% missing data + 143 (0.034) 0.033 0.108 0.022 0.023 0.027 + 149 (0.050) 0.051 0.022 0.035 0.042 0.035 + 147 (0.029) 0.029 0.034 0.016 0.021 0.016 + 153 (0.055) 0.055 0.027 0.097 0.085 0.111 + 169 (0.037) 0.037 0.106 0.019 0.027 0.021 + 151 (0.037) 0.037 0.015 0.069 0.061 0.061 + 145 (0.028) 0.028 0.023 0.016 0.019 0.015 + 157 (0.067) 0.067 0.119 0.089 0.103 0.079 + 155 (0.094) 0.094 0.109 0.124 0.135 0.117 + 159 (0.051) 0.051 0.163 0.043 0.051 0.042 + 161 (0.033) 0.033 0.016 0.061 0.047 0.065 + 141 (0.029) 0.029 0.012 0.032 0.022 0.037 + 139 (0.016) 0.016 0.004 0.010 0.007 0.012 + 144 (0.025) 0.025 0.017 0.039 0.028 0.044 + 171 (0.048) 0.049 0.023 0.054 0.048 0.054 + 163 (0.074) 0.074 0.066 0.092 0.083 0.085 + 167 (0.046) 0.046 0.031 0.044 0.052 0.042 + 173 (0.024) 0.024 0.014 0.022 0.016 0.023 + 142 (0.013) 0.013 0.007 0.002 0.003 0.003 + 177 (0.023) 0.023 0.005 0.022 0.026 0.021 + 175 (0.022) 0.022 0.005 0.011 0.012 0.010 + 165 (0.045) 0.045 0.043 0.028 0.033 0.029 + 146 (0.020) 0.020 0.017 0.015 0.011 0.017 + 137 (0.019) 0.020 0.003 0.006 0.007 0.006 + 183 (0.017) 0.017 0.003 0.008 0.009 0.007 + 179 (0.018) 0.018 0.003 0.008 0.009 0.007 + 191 (0.013) 0.013 0.002 0.003 0.004 0.003 + 185 (0.013) 0.013 0.002 0.003 0.003 0.003 + 180 (0.016) 0.016 0.002 0.009 0.012 0.008 + +Locus 5 : A43 +7 alleles +1.3% missing data + 123 (0.205) 0.207 0.081 0.139 0.145 0.121 + 141 (0.017) 0.017 0.004 0.002 0.002 0.002 + 137 (0.665) 0.664 0.891 0.759 0.745 0.794 + 139 (0.046) 0.046 0.015 0.065 0.066 0.053 + 124 (0.032) 0.031 0.005 0.027 0.034 0.023 + 143 (0.017) 0.017 0.002 0.003 0.003 0.003 + 128 (0.018) 0.017 0.002 0.004 0.005 0.004 + +Locus 6 : A79 +13 alleles +3.4% missing data + 103 (0.237) 0.237 0.312 0.262 0.251 0.255 + 97 (0.130) 0.131 0.214 0.067 0.072 0.071 + 101 (0.089) 0.089 0.065 0.149 0.109 0.172 + 107 (0.097) 0.097 0.077 0.139 0.122 0.138 + 109 (0.098) 0.098 0.072 0.079 0.082 0.078 + 105 (0.164) 0.164 0.204 0.208 0.257 0.198 + 111 (0.048) 0.048 0.023 0.022 0.026 0.021 + 113 (0.017) 0.017 0.004 0.002 0.002 0.002 + 91 (0.025) 0.025 0.004 0.034 0.042 0.029 + 99 (0.033) 0.033 0.010 0.022 0.021 0.022 + 115 (0.028) 0.028 0.007 0.012 0.011 0.010 + 117 (0.017) 0.016 0.006 0.002 0.002 0.002 + 121 (0.017) 0.017 0.003 0.002 0.002 0.002 + +Locus 7 : A88 +9 alleles +6.0% missing data + 133 (0.018) 0.018 0.005 0.002 0.003 0.002 + 149 (0.521) 0.522 0.542 0.605 0.654 0.575 + 137 (0.104) 0.104 0.141 0.063 0.054 0.071 + 147 (0.195) 0.195 0.217 0.268 0.214 0.290 + 141 (0.082) 0.082 0.083 0.045 0.058 0.046 + 152 (0.018) 0.018 0.003 0.004 0.003 0.003 + 143 (0.018) 0.018 0.004 0.002 0.003 0.002 + 151 (0.018) 0.018 0.002 0.004 0.004 0.004 + 144 (0.025) 0.025 0.004 0.006 0.007 0.005 + +Locus 8 : A113 +12 alleles +7.4% missing data + 214 (0.579) 0.580 0.671 0.779 0.765 0.770 + 226 (0.061) 0.060 0.143 0.028 0.034 0.032 + 218 (0.017) 0.017 0.003 0.005 0.004 0.006 + 220 (0.061) 0.060 0.016 0.073 0.086 0.071 + 216 (0.058) 0.059 0.020 0.025 0.029 0.027 + 230 (0.043) 0.043 0.020 0.041 0.030 0.044 + 234 (0.033) 0.033 0.030 0.008 0.009 0.009 + 232 (0.031) 0.030 0.034 0.009 0.010 0.010 + 228 (0.051) 0.051 0.040 0.017 0.019 0.016 + 224 (0.017) 0.017 0.004 0.003 0.002 0.003 + 222 (0.032) 0.032 0.016 0.007 0.008 0.007 + 208 (0.017) 0.017 0.003 0.005 0.004 0.005 + +Locus 9 : Ac11 +9 alleles +4.7% missing data + 111 (0.129) 0.129 0.316 0.092 0.090 0.108 + 117 (0.296) 0.296 0.285 0.343 0.312 0.336 + 115 (0.257) 0.257 0.272 0.292 0.272 0.300 + 113 (0.158) 0.158 0.096 0.154 0.180 0.144 + 119 (0.050) 0.050 0.013 0.073 0.093 0.071 + 121 (0.027) 0.026 0.004 0.025 0.032 0.023 + 123 (0.034) 0.034 0.006 0.008 0.009 0.007 + 127 (0.032) 0.032 0.006 0.010 0.010 0.008 + 125 (0.018) 0.018 0.002 0.002 0.003 0.002 + +Locus 10 : Ac88 +8 alleles +0.7% missing data + 214 (0.751) 0.751 0.709 0.917 0.905 0.911 + 216 (0.029) 0.029 0.020 0.007 0.008 0.007 + 220 (0.114) 0.114 0.255 0.050 0.056 0.057 + 230 (0.026) 0.026 0.005 0.004 0.004 0.004 + 221 (0.018) 0.017 0.002 0.004 0.005 0.004 + 212 (0.021) 0.020 0.003 0.008 0.011 0.008 + 217 (0.018) 0.018 0.002 0.003 0.004 0.003 + 224 (0.024) 0.024 0.003 0.006 0.008 0.006 + +Locus 11 : Ac139 +8 alleles +13.4% missing data + 327 (0.502) 0.502 0.413 0.675 0.693 0.639 + 329 (0.295) 0.295 0.447 0.230 0.206 0.267 + 331 (0.074) 0.074 0.113 0.029 0.032 0.034 + 328 (0.041) 0.041 0.013 0.033 0.029 0.029 + 341 (0.019) 0.019 0.003 0.005 0.005 0.004 + 337 (0.029) 0.029 0.004 0.021 0.027 0.019 + 323 (0.019) 0.019 0.003 0.003 0.004 0.003 + 339 (0.019) 0.019 0.003 0.004 0.004 0.004 + +Locus 12 : Ac306 +6 alleles +4.7% missing data + 165 (0.729) 0.730 0.698 0.811 0.809 0.809 + 177 (0.081) 0.080 0.065 0.072 0.080 0.059 + 173 (0.099) 0.099 0.214 0.043 0.050 0.048 + 169 (0.045) 0.045 0.017 0.052 0.033 0.063 + 171 (0.018) 0.018 0.003 0.002 0.002 0.002 + 179 (0.028) 0.027 0.004 0.020 0.026 0.019 + +Locus 13 : Ap15 +7 alleles +6.0% missing data + 202 (0.811) 0.812 0.943 0.917 0.895 0.919 + 212 (0.028) 0.028 0.028 0.004 0.005 0.005 + 204 (0.044) 0.044 0.009 0.016 0.018 0.015 + 208 (0.041) 0.041 0.006 0.025 0.033 0.025 + 220 (0.039) 0.039 0.008 0.029 0.038 0.028 + 219 (0.018) 0.018 0.003 0.004 0.005 0.004 + 210 (0.019) 0.018 0.003 0.004 0.005 0.004 + +Locus 14 : Ap68 +9 alleles +4.7% missing data + 158 (0.392) 0.393 0.630 0.296 0.316 0.300 + 160 (0.083) 0.083 0.036 0.096 0.083 0.090 + 156 (0.239) 0.239 0.230 0.355 0.343 0.371 + 162 (0.044) 0.045 0.030 0.009 0.011 0.010 + 154 (0.084) 0.084 0.038 0.096 0.071 0.100 + 152 (0.073) 0.073 0.017 0.121 0.145 0.105 + 164 (0.043) 0.043 0.014 0.015 0.017 0.014 + 170 (0.018) 0.018 0.002 0.004 0.004 0.003 + 166 (0.023) 0.023 0.003 0.007 0.009 0.007 + +Locus 15 : Ap85 +10 alleles +3.4% missing data + 202 (0.319) 0.319 0.393 0.373 0.409 0.361 + 186 (0.247) 0.247 0.371 0.334 0.280 0.349 + 204 (0.062) 0.062 0.024 0.036 0.039 0.033 + 188 (0.106) 0.106 0.077 0.098 0.081 0.100 + 194 (0.078) 0.078 0.087 0.038 0.038 0.043 + 196 (0.054) 0.054 0.014 0.052 0.066 0.047 + 200 (0.064) 0.065 0.017 0.038 0.048 0.036 + 192 (0.025) 0.025 0.006 0.005 0.005 0.005 + 190 (0.017) 0.017 0.008 0.003 0.003 0.003 + 198 (0.026) 0.026 0.003 0.024 0.031 0.022 + +Locus 16 : Ap90 +13 alleles +0.7% missing data + 131 (0.364) 0.364 0.536 0.521 0.514 0.553 + 135 (0.066) 0.066 0.080 0.052 0.061 0.050 + 133 (0.288) 0.290 0.295 0.243 0.247 0.228 + 129 (0.095) 0.095 0.044 0.127 0.117 0.114 + 137 (0.035) 0.034 0.009 0.021 0.017 0.021 + 141 (0.017) 0.017 0.004 0.002 0.002 0.002 + 143 (0.023) 0.023 0.009 0.004 0.004 0.004 + 151 (0.024) 0.024 0.010 0.004 0.004 0.004 + 155 (0.016) 0.016 0.003 0.002 0.002 0.002 + 145 (0.016) 0.016 0.002 0.004 0.005 0.004 + 130 (0.020) 0.019 0.003 0.008 0.010 0.007 + 139 (0.016) 0.016 0.002 0.004 0.006 0.004 + 153 (0.021) 0.020 0.003 0.008 0.009 0.007 + +Locus 17 : Ap223 +7 alleles +2.0% missing data + 183 (0.686) 0.687 0.600 0.777 0.804 0.746 + 187 (0.134) 0.133 0.296 0.156 0.122 0.183 + 189 (0.026) 0.026 0.006 0.013 0.009 0.016 + 173 (0.065) 0.065 0.072 0.027 0.033 0.029 + 182 (0.032) 0.032 0.010 0.008 0.007 0.008 + 180 (0.025) 0.025 0.005 0.006 0.006 0.005 + 179 (0.032) 0.032 0.011 0.014 0.017 0.012 + +Locus 18 : Ap224 +7 alleles +4.0% missing data + 283 (0.110) 0.110 0.198 0.116 0.095 0.132 + 287 (0.468) 0.469 0.475 0.464 0.468 0.448 + 281 (0.135) 0.135 0.167 0.123 0.109 0.135 + 289 (0.206) 0.206 0.097 0.266 0.289 0.250 + 291 (0.038) 0.037 0.057 0.010 0.011 0.013 + 285 (0.018) 0.018 0.003 0.003 0.003 0.003 + 279 (0.025) 0.025 0.003 0.019 0.026 0.019 + +Locus 19 : Ap226 +5 alleles +17.4% missing data + 237 (0.380) 0.381 0.330 0.353 0.348 0.350 + 239 (0.459) 0.459 0.437 0.545 0.559 0.528 + 247 (0.122) 0.122 0.227 0.091 0.082 0.111 + 235 (0.019) 0.019 0.003 0.005 0.004 0.006 + 241 (0.020) 0.019 0.003 0.006 0.007 0.005 + +Locus 20 : Ap249 +9 alleles +1.3% missing data + 209 (0.610) 0.611 0.570 0.719 0.708 0.714 + 211 (0.055) 0.055 0.017 0.037 0.029 0.038 + 217 (0.084) 0.083 0.154 0.050 0.047 0.061 + 219 (0.104) 0.103 0.230 0.069 0.067 0.074 + 215 (0.078) 0.078 0.015 0.113 0.137 0.100 + 208 (0.017) 0.017 0.004 0.003 0.003 0.003 + 225 (0.017) 0.017 0.004 0.002 0.002 0.002 + 223 (0.017) 0.017 0.003 0.003 0.003 0.003 + 213 (0.018) 0.018 0.002 0.003 0.004 0.003 + +Locus 21 : Ap273 +4 alleles +1.3% missing data + 106 (0.877) 0.877 0.954 0.950 0.949 0.952 + 108 (0.050) 0.050 0.028 0.024 0.025 0.021 + 104 (0.044) 0.044 0.012 0.016 0.013 0.017 + 102 (0.029) 0.029 0.006 0.010 0.013 0.010 + +Locus 22 : Ap274 +2 alleles +2.0% missing data + 120 (0.943) 0.943 0.985 0.960 0.950 0.964 + 122 (0.057) 0.057 0.015 0.040 0.050 0.036 + +Locus 23 : Ap288 +5 alleles +0.0% missing data + 123 (0.768) 0.769 0.601 0.851 0.868 0.819 + 131 (0.165) 0.165 0.365 0.137 0.120 0.170 + 139 (0.030) 0.030 0.020 0.006 0.006 0.006 + 121 (0.018) 0.018 0.008 0.003 0.003 0.003 + 124 (0.018) 0.018 0.006 0.003 0.003 0.003 + +Locus 24 : At163 +7 alleles +0.0% missing data + 128 (0.709) 0.710 0.543 0.854 0.858 0.835 + 134 (0.194) 0.194 0.439 0.130 0.125 0.149 + 130 (0.025) 0.025 0.009 0.005 0.006 0.005 + 136 (0.018) 0.018 0.003 0.003 0.003 0.003 + 140 (0.018) 0.018 0.002 0.002 0.003 0.002 + 146 (0.018) 0.018 0.002 0.002 0.003 0.002 + 142 (0.018) 0.018 0.002 0.003 0.003 0.003 + +Locus 25 : At188 +13 alleles +1.3% missing data + 189 (0.626) 0.627 0.766 0.817 0.838 0.799 + 205 (0.032) 0.031 0.064 0.006 0.009 0.008 + 207 (0.030) 0.030 0.013 0.043 0.027 0.056 + 219 (0.024) 0.024 0.007 0.006 0.005 0.006 + 209 (0.035) 0.035 0.015 0.032 0.022 0.036 + 217 (0.040) 0.040 0.014 0.016 0.013 0.015 + 215 (0.021) 0.020 0.009 0.009 0.007 0.008 + 199 (0.067) 0.067 0.063 0.033 0.041 0.032 + 212 (0.027) 0.027 0.009 0.011 0.009 0.011 + 213 (0.037) 0.037 0.031 0.011 0.010 0.012 + 211 (0.017) 0.017 0.003 0.002 0.002 0.002 + 191 (0.017) 0.017 0.003 0.005 0.004 0.005 + 187 (0.027) 0.027 0.004 0.010 0.012 0.009 + +Values of parameters used in structure: +DATAFILE=, OUTFILE=, NUMINDS=149, NUMLOCI=25, MISSING=-9, LABEL=1, POPDATA=0, POPFLAG=1, PHENOTYPE=0, EXTRACOLS=1, MAXPOPS=5, BURNIN=100000, NUMREPS=1000000, USEPOPINFO=0, INFERALPHA=1, INFERLAMBDA=0, POPSPECIFICLAMBDA=0, POPALPHAS=0, COMPUTEPROB=1, NOADMIX=0, ADMBURNIN=2500, UPDATEFREQ=1, PRINTLIKES=0, INTERMEDSAVE=0, PRINTKLD=0, PRINTNET=0, PRINTLAMBDA=0, ANCESTDIST=0, NUMBOXES=1000, ANCESTPINT=0.90000, GENSBACK=2, MIGRPRIOR=0.05000, PRINTQHAT=0, PRINTQSUM=0, ALPHA=1.0000, FREQSCORR=1, FPRIORMEAN=0.0100, FPRIORSD=0.0500, ONEFST=0, LAMBDA=1.0000, UNIFPRIORALPHA=1, ALPHAMAX=10.0000, ALPHAPRIORA=1.0000, ALPHAPRIORB=2.0000, ALPHAPROPSD=0.0250, STARTATPOPINFO=0, RANDOMIZE=1, LINKAGE=0, METROFREQ=10, REPORTHITRATE=0, MARKOVPHASE=-1, PHASED=0, PLOIDY=2, PHASEINFO=0 LOCPRIOR=0, LOCPRIORINIT=1.000000, LOCDATA=0, LOCISPOP=0, LOCPRIORSTEP=0.100000, MAXLOCPRIOR=20.000000, SEED=1335118428, +[STRAT parameters]: NUMSIMSTATS=1000, PHENOTYPECOL=-9, POOLFREQ=10, LOCUSxONLY=0, EMERROR=0.00100, MISSINGPHENO=-9, \ No newline at end of file diff --git a/inst/files/structure/structure_07 b/inst/files/structure/structure_07 new file mode 100644 index 0000000..32a063b --- /dev/null +++ b/inst/files/structure/structure_07 @@ -0,0 +1,541 @@ + + +---------------------------------------------------- +STRUCTURE by Pritchard, Stephens and Donnelly (2000) + and Falush, Stephens and Pritchard (2003) + Code by Pritchard, Falush and Hubisz + Version 2.3.2.1 (Oct 2009) +---------------------------------------------------- + + + +Command line arguments: +Input File: + +Run parameters: + 149 individuals + 25 loci + 6 populations assumed + 100000 Burn-in period + 1000000 Reps + + +-------------------------------------------- +Overall proportion of membership of the +sample in each of the 6 clusters + +Inferred Clusters + 1 2 3 4 5 6 +0.178 0.169 0.167 0.174 0.141 0.171 + +-------------------------------------------- + +Allele-freq. divergence among pops (Net nucleotide distance), +computed using point estimates of P. + + 1 2 3 4 5 6 + 1 - 0.0188 0.0122 0.0326 0.0154 0.0282 + 2 0.0188 - 0.0072 0.0025 0.0076 0.0022 + 3 0.0122 0.0072 - 0.0169 0.0123 0.0156 + 4 0.0326 0.0025 0.0169 - 0.0129 0.0007 + 5 0.0154 0.0076 0.0123 0.0129 - 0.0124 + 6 0.0282 0.0022 0.0156 0.0007 0.0124 - + +Average distances (expected heterozygosity) between individuals in same cluster: +cluster 1 : 0.5213 +cluster 2 : 0.4793 +cluster 3 : 0.4806 +cluster 4 : 0.4567 +cluster 5 : 0.5899 +cluster 6 : 0.4623 + +-------------------------------------------- +Estimated Ln Prob of Data = -7970.6 +Mean value of ln likelihood = -7160.4 +Variance of ln likelihood = 1620.5 +Mean value of alpha = 0.2811 + +Mean value of Fst_1 = 0.1788 +Mean value of Fst_2 = 0.2039 +Mean value of Fst_3 = 0.2097 +Mean value of Fst_4 = 0.1993 +Mean value of Fst_5 = 0.0018 +Mean value of Fst_6 = 0.2162 + + +Inferred ancestry of individuals: + Label (%Miss) : Inferred clusters + 1 I13825 (0) : 0.270 0.110 0.101 0.072 0.365 0.082 + 2 I13826 (0) : 0.495 0.126 0.129 0.067 0.075 0.109 + 3 I13827 (20) : 0.184 0.142 0.378 0.109 0.067 0.119 + 4 I13828 (0) : 0.424 0.133 0.128 0.079 0.130 0.105 + 5 I13829 (8) : 0.207 0.172 0.301 0.136 0.076 0.108 + 6 I13830 (0) : 0.471 0.133 0.161 0.065 0.064 0.106 + 7 I13831 (0) : 0.185 0.226 0.239 0.164 0.064 0.121 + 8 I13832 (16) : 0.154 0.160 0.278 0.124 0.179 0.105 + 9 I13833 (0) : 0.164 0.195 0.309 0.166 0.052 0.115 + 10 I13834 (0) : 0.229 0.145 0.372 0.109 0.044 0.101 + 11 I13835 (0) : 0.138 0.187 0.249 0.139 0.192 0.095 + 12 I13836 (0) : 0.201 0.130 0.339 0.098 0.135 0.096 + 13 I13377 (0) : 0.122 0.217 0.276 0.179 0.083 0.123 + 14 I13378 (0) : 0.126 0.197 0.193 0.153 0.230 0.102 + 15 I13379 (0) : 0.313 0.188 0.191 0.127 0.066 0.115 + 16 I13380 (0) : 0.132 0.176 0.307 0.166 0.070 0.150 + 17 I13381 (0) : 0.113 0.195 0.229 0.149 0.190 0.125 + 18 I13382 (0) : 0.169 0.186 0.362 0.132 0.039 0.112 + 19 I13383 (0) : 0.139 0.191 0.205 0.139 0.210 0.116 + 20 I13384 (0) : 0.233 0.180 0.239 0.121 0.106 0.120 + 21 I13385 (0) : 0.185 0.155 0.374 0.124 0.059 0.102 + 22 I13386 (0) : 0.182 0.155 0.388 0.104 0.069 0.102 + 23 I13387 (0) : 0.389 0.131 0.153 0.078 0.148 0.101 + 24 I13388 (0) : 0.245 0.111 0.100 0.084 0.362 0.099 + 25 I13389 (0) : 0.139 0.206 0.264 0.181 0.055 0.155 + 26 I13390 (0) : 0.193 0.175 0.333 0.128 0.056 0.115 + 27 I13391 (0) : 0.118 0.188 0.188 0.167 0.221 0.117 + 28 I13392 (0) : 0.190 0.174 0.190 0.138 0.206 0.103 + 29 I13393 (0) : 0.091 0.238 0.247 0.207 0.072 0.145 + 30 I13394 (4) : 0.102 0.188 0.164 0.205 0.147 0.194 + 31 I13395 (0) : 0.139 0.190 0.164 0.212 0.116 0.180 + 32 I13396 (0) : 0.296 0.148 0.098 0.127 0.185 0.146 + 33 I13397 (0) : 0.235 0.152 0.175 0.108 0.233 0.098 + 34 I13398 (0) : 0.470 0.129 0.190 0.066 0.041 0.105 + 35 I13399 (4) : 0.110 0.161 0.188 0.126 0.323 0.091 + 36 I13400 (0) : 0.145 0.204 0.228 0.171 0.130 0.122 + 37 I13401 (0) : 0.091 0.178 0.163 0.188 0.145 0.235 + 38 I13402 (0) : 0.187 0.155 0.135 0.125 0.290 0.107 + 39 I13403 (0) : 0.319 0.175 0.136 0.146 0.056 0.168 + 40 I13404 (0) : 0.353 0.155 0.235 0.094 0.054 0.109 + 41 I13405 (0) : 0.165 0.172 0.366 0.143 0.049 0.105 + 42 I13406 (16) : 0.314 0.118 0.114 0.076 0.285 0.094 + 43 I13407 (0) : 0.310 0.187 0.170 0.127 0.090 0.116 + 44 I13408 (0) : 0.159 0.213 0.292 0.169 0.055 0.112 + 45 I13409 (0) : 0.265 0.116 0.096 0.087 0.330 0.107 + 46 I13410 (0) : 0.213 0.216 0.245 0.147 0.070 0.109 + 47 I13411 (0) : 0.270 0.147 0.332 0.092 0.062 0.098 + 48 I13412 (0) : 0.199 0.171 0.199 0.167 0.107 0.158 + 49 I13413 (0) : 0.311 0.143 0.132 0.099 0.200 0.115 + 50 I13414 (0) : 0.400 0.131 0.161 0.068 0.139 0.101 + 51 I13415 (4) : 0.198 0.165 0.282 0.141 0.063 0.151 + 52 I13416 (4) : 0.241 0.171 0.206 0.142 0.091 0.148 + 53 I13417 (4) : 0.177 0.168 0.256 0.160 0.051 0.188 + 54 I13418 (0) : 0.219 0.161 0.273 0.141 0.058 0.148 + 55 I13419 (0) : 0.180 0.101 0.221 0.073 0.347 0.078 + 56 I13420 (0) : 0.291 0.154 0.186 0.146 0.059 0.163 + 57 I13421 (0) : 0.127 0.200 0.234 0.202 0.052 0.185 + 58 I13422 (0) : 0.179 0.180 0.191 0.177 0.090 0.182 + 59 I13423 (0) : 0.153 0.158 0.208 0.126 0.229 0.126 + 60 I13424 (0) : 0.157 0.199 0.268 0.157 0.108 0.111 + 61 I13425 (4) : 0.209 0.144 0.267 0.125 0.135 0.120 + 62 I13426 (4) : 0.110 0.176 0.138 0.220 0.161 0.195 + 63 I13870 (0) : 0.293 0.160 0.137 0.155 0.078 0.176 + 64 I13871 (16) : 0.285 0.158 0.170 0.110 0.169 0.108 + 65 I13872 (0) : 0.479 0.114 0.099 0.057 0.152 0.099 + 66 I13873 (4) : 0.308 0.182 0.138 0.129 0.094 0.148 + 67 I13874 (0) : 0.336 0.115 0.121 0.081 0.237 0.110 + 68 I13875 (8) : 0.371 0.150 0.133 0.108 0.106 0.132 + 69 I13876 (0) : 0.155 0.105 0.092 0.089 0.454 0.106 + 70 I13877 (20) : 0.164 0.198 0.249 0.147 0.095 0.147 + 71 I13878 (28) : 0.393 0.136 0.215 0.086 0.058 0.112 + 72 I13879 (4) : 0.289 0.148 0.314 0.098 0.049 0.102 + 73 I13880 (4) : 0.517 0.129 0.121 0.061 0.064 0.108 + 74 I13881 (0) : 0.216 0.116 0.122 0.096 0.338 0.112 + 75 I13882 (0) : 0.409 0.141 0.138 0.091 0.104 0.117 + 76 I13883 (4) : 0.435 0.128 0.087 0.096 0.129 0.125 + 77 I13884 (16) : 0.135 0.095 0.110 0.076 0.506 0.077 + 78 I13885 (20) : 0.147 0.153 0.226 0.103 0.285 0.087 + 79 I13886 (8) : 0.350 0.150 0.192 0.098 0.100 0.111 + 80 I13887 (0) : 0.097 0.079 0.055 0.078 0.613 0.078 + 81 I13888 (0) : 0.222 0.147 0.134 0.095 0.301 0.101 + 82 I13889 (0) : 0.062 0.203 0.113 0.262 0.103 0.258 + 83 I13890 (32) : 0.115 0.177 0.149 0.220 0.145 0.194 + 84 I13891 (0) : 0.385 0.129 0.200 0.081 0.102 0.103 + 85 I13892 (0) : 0.120 0.202 0.182 0.207 0.087 0.201 + 86 I13893 (8) : 0.103 0.146 0.145 0.114 0.398 0.094 + 87 I13894 (0) : 0.537 0.124 0.088 0.068 0.069 0.114 + 88 I13895 (4) : 0.124 0.181 0.182 0.152 0.220 0.141 + 89 I13896 (0) : 0.322 0.150 0.099 0.150 0.098 0.180 + 90 I13897 (0) : 0.434 0.131 0.222 0.066 0.047 0.099 + 91 I13898 (4) : 0.334 0.182 0.156 0.122 0.078 0.128 + 92 I13899 (0) : 0.564 0.123 0.112 0.055 0.039 0.105 + 93 I13900 (32) : 0.167 0.115 0.112 0.098 0.409 0.099 + 94 I13837 (0) : 0.163 0.163 0.361 0.137 0.057 0.119 + 95 I13838 (0) : 0.126 0.186 0.099 0.245 0.098 0.246 + 96 I13839 (0) : 0.174 0.153 0.323 0.138 0.072 0.139 + 97 I13840 (0) : 0.162 0.187 0.243 0.177 0.054 0.177 + 98 I13841 (0) : 0.093 0.194 0.167 0.245 0.052 0.249 + 99 I13842 (0) : 0.105 0.187 0.249 0.207 0.068 0.185 +100 I13843 (4) : 0.098 0.190 0.153 0.238 0.062 0.259 +101 I13844 (16) : 0.121 0.190 0.227 0.181 0.142 0.139 +102 I13845 (0) : 0.189 0.164 0.349 0.119 0.066 0.112 +103 I13846 (0) : 0.150 0.180 0.288 0.137 0.123 0.122 +104 I13847 (0) : 0.209 0.167 0.124 0.190 0.124 0.187 +105 I13848 (0) : 0.138 0.191 0.159 0.187 0.143 0.183 +106 I13849 (0) : 0.279 0.163 0.110 0.132 0.176 0.141 +107 I13850 (0) : 0.098 0.203 0.142 0.235 0.083 0.239 +108 I12577 (4) : 0.045 0.191 0.073 0.294 0.119 0.279 +109 I12578 (4) : 0.047 0.203 0.086 0.276 0.092 0.295 +110 I12579 (8) : 0.041 0.178 0.086 0.270 0.193 0.232 +111 I12580 (8) : 0.050 0.199 0.081 0.328 0.046 0.297 +112 I12581 (4) : 0.071 0.179 0.162 0.177 0.252 0.160 +113 I12582 (4) : 0.056 0.196 0.070 0.317 0.078 0.283 +114 I12583 (8) : 0.049 0.136 0.096 0.151 0.378 0.190 +115 I12584 (4) : 0.056 0.153 0.072 0.211 0.280 0.228 +116 I12585 (4) : 0.042 0.180 0.073 0.302 0.080 0.322 +117 I12586 (4) : 0.050 0.195 0.074 0.341 0.054 0.286 +118 I12587 (8) : 0.043 0.191 0.082 0.315 0.035 0.334 +119 I12588 (4) : 0.034 0.188 0.057 0.327 0.129 0.266 +120 I12589 (0) : 0.056 0.191 0.096 0.260 0.077 0.319 +121 I12590 (0) : 0.068 0.188 0.077 0.284 0.142 0.241 +122 I12591 (12) : 0.023 0.220 0.059 0.336 0.053 0.309 +123 I12592 (4) : 0.043 0.199 0.088 0.277 0.098 0.295 +124 I12593 (4) : 0.037 0.213 0.062 0.311 0.076 0.301 +125 I12594 (8) : 0.042 0.209 0.056 0.351 0.053 0.289 +126 I12595 (0) : 0.035 0.160 0.090 0.217 0.283 0.214 +127 I12596 (0) : 0.030 0.213 0.059 0.339 0.065 0.294 +128 I12597 (4) : 0.044 0.130 0.076 0.196 0.368 0.186 +129 I12598 (0) : 0.051 0.155 0.096 0.194 0.256 0.248 +130 I12599 (0) : 0.100 0.177 0.082 0.234 0.187 0.221 +131 I12600 (4) : 0.067 0.183 0.077 0.307 0.050 0.316 +132 I12601 (8) : 0.046 0.170 0.070 0.290 0.136 0.288 +133 I12602 (12) : 0.045 0.198 0.072 0.320 0.092 0.272 +134 I12603 (0) : 0.047 0.157 0.070 0.251 0.254 0.222 +135 I12604 (4) : 0.077 0.176 0.069 0.290 0.119 0.269 +136 I12605 (4) : 0.060 0.184 0.068 0.295 0.126 0.267 +137 I12606 (8) : 0.031 0.211 0.077 0.298 0.088 0.295 +138 I12607 (4) : 0.041 0.169 0.073 0.226 0.233 0.258 +139 I12608 (8) : 0.050 0.192 0.092 0.245 0.156 0.265 +140 I12609 (8) : 0.035 0.204 0.078 0.300 0.071 0.311 +141 I12610 (52) : 0.057 0.189 0.095 0.291 0.105 0.264 +142 I12611 (0) : 0.037 0.197 0.083 0.285 0.057 0.341 +143 I12612 (0) : 0.042 0.185 0.072 0.302 0.082 0.317 +144 I12613 (0) : 0.027 0.213 0.085 0.292 0.062 0.322 +145 I12614 (4) : 0.069 0.191 0.131 0.264 0.085 0.260 +146 I12615 (0) : 0.062 0.178 0.115 0.223 0.155 0.267 +147 I12616 (4) : 0.045 0.148 0.090 0.186 0.327 0.203 +148 I12617 (8) : 0.037 0.209 0.055 0.360 0.040 0.300 +149 I12618 (48) : 0.042 0.189 0.062 0.324 0.099 0.284 + + +Estimated Allele Frequencies in each cluster +First column gives estimated ancestral frequencies + + +Locus 1 : A8 +7 alleles +4.0% missing data + 177 (0.505) 0.460 0.548 0.451 0.574 0.507 0.569 + 179 (0.096) 0.107 0.075 0.120 0.064 0.095 0.063 + 175 (0.096) 0.287 0.116 0.253 0.057 0.096 0.085 + 173 (0.046) 0.030 0.045 0.055 0.035 0.046 0.024 + 181 (0.183) 0.095 0.185 0.100 0.241 0.183 0.231 + 165 (0.042) 0.011 0.019 0.010 0.022 0.041 0.022 + 183 (0.032) 0.011 0.011 0.010 0.007 0.032 0.007 + +Locus 2 : A14 +5 alleles +0.0% missing data + 112 (0.198) 0.373 0.180 0.209 0.108 0.199 0.123 + 110 (0.695) 0.599 0.754 0.768 0.786 0.695 0.795 + 114 (0.034) 0.014 0.008 0.007 0.006 0.035 0.007 + 118 (0.040) 0.009 0.045 0.010 0.078 0.039 0.057 + 116 (0.033) 0.005 0.013 0.006 0.022 0.033 0.019 + +Locus 3 : A24 +5 alleles +2.7% missing data + 104 (0.399) 0.427 0.369 0.316 0.372 0.401 0.370 + 106 (0.519) 0.548 0.594 0.665 0.578 0.518 0.588 + 101 (0.019) 0.003 0.004 0.004 0.004 0.019 0.003 + 108 (0.030) 0.017 0.009 0.007 0.007 0.030 0.007 + 96 (0.032) 0.005 0.023 0.007 0.039 0.031 0.031 + +Locus 4 : A29 +29 alleles +6.7% missing data + 143 (0.033) 0.098 0.030 0.042 0.016 0.033 0.024 + 149 (0.049) 0.019 0.041 0.024 0.046 0.050 0.047 + 147 (0.030) 0.028 0.021 0.010 0.025 0.029 0.022 + 153 (0.051) 0.048 0.087 0.109 0.083 0.051 0.109 + 169 (0.038) 0.089 0.034 0.020 0.028 0.038 0.037 + 151 (0.036) 0.026 0.060 0.076 0.053 0.036 0.037 + 145 (0.029) 0.018 0.020 0.012 0.023 0.029 0.020 + 157 (0.064) 0.098 0.098 0.059 0.120 0.065 0.126 + 155 (0.094) 0.096 0.132 0.084 0.159 0.096 0.145 + 159 (0.049) 0.142 0.058 0.048 0.049 0.049 0.067 + 161 (0.031) 0.043 0.039 0.096 0.025 0.031 0.027 + 141 (0.031) 0.025 0.022 0.047 0.017 0.031 0.016 + 139 (0.017) 0.008 0.006 0.015 0.005 0.017 0.005 + 144 (0.026) 0.030 0.031 0.053 0.022 0.026 0.017 + 171 (0.048) 0.033 0.052 0.055 0.043 0.048 0.039 + 163 (0.072) 0.067 0.089 0.100 0.080 0.073 0.067 + 167 (0.045) 0.025 0.048 0.031 0.055 0.045 0.054 + 173 (0.024) 0.020 0.017 0.030 0.011 0.024 0.013 + 142 (0.014) 0.006 0.003 0.003 0.002 0.014 0.002 + 177 (0.024) 0.006 0.022 0.009 0.032 0.024 0.026 + 175 (0.023) 0.005 0.011 0.008 0.013 0.023 0.012 + 165 (0.044) 0.036 0.033 0.026 0.036 0.044 0.037 + 146 (0.021) 0.019 0.013 0.023 0.009 0.021 0.008 + 137 (0.021) 0.003 0.006 0.004 0.008 0.021 0.007 + 183 (0.018) 0.003 0.007 0.003 0.010 0.018 0.009 + 179 (0.019) 0.003 0.008 0.005 0.010 0.019 0.009 + 191 (0.014) 0.002 0.003 0.002 0.003 0.014 0.004 + 185 (0.014) 0.002 0.003 0.002 0.003 0.014 0.004 + 180 (0.017) 0.002 0.008 0.003 0.013 0.017 0.012 + +Locus 5 : A43 +7 alleles +1.3% missing data + 123 (0.204) 0.080 0.139 0.118 0.148 0.207 0.135 + 141 (0.019) 0.004 0.003 0.002 0.002 0.019 0.002 + 137 (0.653) 0.884 0.776 0.818 0.735 0.653 0.756 + 139 (0.050) 0.022 0.050 0.048 0.064 0.049 0.062 + 124 (0.036) 0.006 0.025 0.008 0.042 0.035 0.036 + 143 (0.019) 0.002 0.003 0.002 0.003 0.019 0.003 + 128 (0.019) 0.002 0.004 0.002 0.005 0.018 0.005 + +Locus 6 : A79 +13 alleles +3.4% missing data + 103 (0.231) 0.302 0.268 0.292 0.231 0.231 0.233 + 97 (0.126) 0.193 0.090 0.076 0.072 0.128 0.080 + 101 (0.090) 0.120 0.111 0.209 0.083 0.090 0.076 + 107 (0.099) 0.107 0.106 0.184 0.085 0.098 0.088 + 109 (0.099) 0.067 0.087 0.070 0.091 0.100 0.076 + 105 (0.161) 0.157 0.243 0.108 0.314 0.161 0.335 + 111 (0.048) 0.018 0.026 0.018 0.027 0.048 0.030 + 113 (0.018) 0.004 0.003 0.002 0.002 0.017 0.002 + 91 (0.029) 0.005 0.032 0.008 0.055 0.029 0.045 + 99 (0.035) 0.012 0.019 0.018 0.023 0.034 0.020 + 115 (0.029) 0.007 0.011 0.009 0.011 0.029 0.010 + 117 (0.018) 0.005 0.003 0.003 0.003 0.017 0.003 + 121 (0.018) 0.003 0.003 0.002 0.002 0.018 0.002 + +Locus 7 : A88 +9 alleles +6.0% missing data + 133 (0.020) 0.004 0.003 0.003 0.002 0.019 0.002 + 149 (0.512) 0.496 0.643 0.459 0.722 0.513 0.714 + 137 (0.104) 0.141 0.068 0.091 0.042 0.104 0.052 + 147 (0.189) 0.276 0.212 0.403 0.150 0.190 0.148 + 141 (0.090) 0.071 0.057 0.032 0.065 0.090 0.067 + 152 (0.019) 0.003 0.004 0.003 0.003 0.019 0.003 + 143 (0.020) 0.003 0.003 0.003 0.003 0.020 0.003 + 151 (0.019) 0.002 0.004 0.003 0.005 0.019 0.004 + 144 (0.027) 0.004 0.006 0.004 0.008 0.027 0.007 + +Locus 8 : A113 +12 alleles +7.4% missing data + 214 (0.554) 0.697 0.749 0.790 0.753 0.557 0.758 + 226 (0.063) 0.121 0.045 0.043 0.032 0.062 0.043 + 218 (0.019) 0.004 0.004 0.007 0.003 0.018 0.003 + 220 (0.067) 0.017 0.077 0.034 0.102 0.066 0.088 + 216 (0.060) 0.019 0.028 0.020 0.032 0.060 0.032 + 230 (0.047) 0.031 0.035 0.052 0.026 0.047 0.021 + 234 (0.036) 0.026 0.012 0.012 0.008 0.036 0.009 + 232 (0.032) 0.029 0.012 0.013 0.009 0.032 0.010 + 228 (0.052) 0.034 0.022 0.016 0.020 0.052 0.021 + 224 (0.019) 0.004 0.003 0.003 0.003 0.018 0.003 + 222 (0.034) 0.013 0.009 0.005 0.009 0.034 0.009 + 208 (0.019) 0.004 0.004 0.005 0.004 0.018 0.003 + +Locus 9 : Ac11 +9 alleles +4.7% missing data + 111 (0.127) 0.291 0.119 0.142 0.071 0.127 0.097 + 117 (0.293) 0.310 0.321 0.399 0.276 0.294 0.247 + 115 (0.244) 0.286 0.272 0.329 0.253 0.244 0.299 + 113 (0.162) 0.081 0.166 0.085 0.215 0.163 0.204 + 119 (0.055) 0.014 0.077 0.024 0.120 0.054 0.097 + 121 (0.031) 0.005 0.025 0.007 0.041 0.030 0.032 + 123 (0.036) 0.006 0.008 0.005 0.009 0.037 0.010 + 127 (0.033) 0.006 0.010 0.007 0.012 0.033 0.010 + 125 (0.019) 0.002 0.003 0.002 0.003 0.019 0.003 + +Locus 10 : Ac88 +8 alleles +0.7% missing data + 214 (0.742) 0.742 0.883 0.901 0.911 0.743 0.889 + 216 (0.032) 0.017 0.009 0.009 0.006 0.031 0.007 + 220 (0.113) 0.226 0.081 0.073 0.050 0.114 0.070 + 230 (0.027) 0.005 0.005 0.004 0.005 0.027 0.005 + 221 (0.019) 0.002 0.004 0.002 0.005 0.018 0.005 + 212 (0.024) 0.003 0.008 0.004 0.011 0.023 0.013 + 217 (0.019) 0.002 0.003 0.002 0.003 0.018 0.004 + 224 (0.025) 0.003 0.007 0.004 0.008 0.025 0.009 + +Locus 11 : Ac139 +8 alleles +13.4% missing data + 327 (0.499) 0.413 0.665 0.542 0.748 0.500 0.710 + 329 (0.284) 0.453 0.232 0.358 0.159 0.286 0.197 + 331 (0.075) 0.103 0.039 0.044 0.025 0.075 0.036 + 328 (0.044) 0.018 0.031 0.040 0.020 0.043 0.016 + 341 (0.021) 0.003 0.005 0.003 0.006 0.021 0.006 + 337 (0.035) 0.005 0.021 0.007 0.033 0.034 0.028 + 323 (0.021) 0.003 0.004 0.003 0.004 0.020 0.004 + 339 (0.021) 0.003 0.004 0.003 0.004 0.020 0.004 + +Locus 12 : Ac306 +6 alleles +4.7% missing data + 165 (0.725) 0.710 0.805 0.801 0.814 0.727 0.787 + 177 (0.077) 0.052 0.073 0.042 0.090 0.076 0.100 + 173 (0.099) 0.188 0.068 0.064 0.043 0.099 0.060 + 169 (0.046) 0.044 0.031 0.084 0.020 0.046 0.022 + 171 (0.019) 0.002 0.002 0.002 0.002 0.019 0.002 + 179 (0.033) 0.004 0.021 0.007 0.030 0.032 0.028 + +Locus 13 : Ap15 +7 alleles +6.0% missing data + 202 (0.802) 0.949 0.906 0.953 0.883 0.804 0.875 + 212 (0.030) 0.024 0.008 0.006 0.005 0.030 0.006 + 204 (0.047) 0.009 0.016 0.011 0.020 0.048 0.019 + 208 (0.040) 0.005 0.029 0.013 0.036 0.039 0.045 + 220 (0.041) 0.007 0.033 0.010 0.046 0.040 0.044 + 219 (0.020) 0.003 0.004 0.003 0.005 0.020 0.006 + 210 (0.020) 0.003 0.004 0.003 0.004 0.019 0.005 + +Locus 14 : Ap68 +9 alleles +4.7% missing data + 158 (0.379) 0.567 0.343 0.338 0.308 0.381 0.362 + 160 (0.079) 0.047 0.089 0.113 0.070 0.079 0.050 + 156 (0.247) 0.265 0.326 0.366 0.331 0.245 0.341 + 162 (0.047) 0.026 0.013 0.011 0.011 0.047 0.013 + 154 (0.081) 0.057 0.086 0.115 0.067 0.082 0.045 + 152 (0.078) 0.022 0.115 0.040 0.180 0.077 0.157 + 164 (0.046) 0.012 0.017 0.010 0.019 0.046 0.017 + 170 (0.019) 0.003 0.004 0.003 0.004 0.019 0.004 + 166 (0.024) 0.003 0.008 0.004 0.010 0.024 0.011 + +Locus 15 : Ap85 +10 alleles +3.4% missing data + 202 (0.313) 0.352 0.393 0.276 0.461 0.312 0.492 + 186 (0.238) 0.409 0.305 0.459 0.215 0.239 0.207 + 204 (0.064) 0.022 0.036 0.031 0.039 0.064 0.035 + 188 (0.098) 0.087 0.095 0.127 0.073 0.099 0.055 + 194 (0.082) 0.085 0.041 0.051 0.033 0.081 0.041 + 196 (0.064) 0.015 0.053 0.022 0.076 0.063 0.070 + 200 (0.065) 0.014 0.044 0.017 0.057 0.066 0.055 + 192 (0.027) 0.005 0.006 0.004 0.005 0.027 0.006 + 190 (0.019) 0.007 0.003 0.004 0.003 0.018 0.003 + 198 (0.032) 0.004 0.023 0.008 0.037 0.031 0.036 + +Locus 16 : Ap90 +13 alleles +0.7% missing data + 131 (0.354) 0.553 0.513 0.547 0.510 0.354 0.562 + 135 (0.069) 0.071 0.056 0.036 0.073 0.068 0.068 + 133 (0.276) 0.268 0.272 0.239 0.257 0.280 0.220 + 129 (0.100) 0.064 0.104 0.133 0.097 0.100 0.092 + 137 (0.037) 0.012 0.018 0.021 0.018 0.036 0.014 + 141 (0.017) 0.004 0.003 0.002 0.002 0.017 0.002 + 143 (0.025) 0.008 0.005 0.005 0.004 0.025 0.004 + 151 (0.025) 0.008 0.005 0.004 0.004 0.025 0.005 + 155 (0.018) 0.003 0.003 0.002 0.002 0.018 0.002 + 145 (0.017) 0.002 0.004 0.002 0.005 0.017 0.006 + 130 (0.022) 0.003 0.007 0.003 0.012 0.021 0.010 + 139 (0.018) 0.002 0.005 0.002 0.006 0.017 0.006 + 153 (0.022) 0.003 0.006 0.003 0.010 0.022 0.009 + +Locus 17 : Ap223 +7 alleles +2.0% missing data + 183 (0.676) 0.594 0.773 0.692 0.828 0.678 0.816 + 187 (0.133) 0.309 0.154 0.242 0.095 0.134 0.104 + 189 (0.028) 0.011 0.009 0.019 0.007 0.028 0.006 + 173 (0.068) 0.062 0.036 0.027 0.035 0.067 0.042 + 182 (0.034) 0.010 0.008 0.009 0.007 0.034 0.008 + 180 (0.027) 0.005 0.006 0.005 0.006 0.027 0.006 + 179 (0.033) 0.009 0.014 0.006 0.021 0.032 0.018 + +Locus 18 : Ap224 +7 alleles +4.0% missing data + 283 (0.114) 0.206 0.113 0.175 0.074 0.114 0.077 + 287 (0.468) 0.462 0.468 0.452 0.478 0.470 0.424 + 281 (0.139) 0.179 0.115 0.179 0.079 0.139 0.089 + 289 (0.192) 0.095 0.263 0.166 0.327 0.192 0.365 + 291 (0.039) 0.051 0.016 0.018 0.010 0.039 0.013 + 285 (0.019) 0.003 0.003 0.003 0.002 0.019 0.002 + 279 (0.028) 0.003 0.022 0.007 0.031 0.027 0.030 + +Locus 19 : Ap226 +5 alleles +17.4% missing data + 237 (0.382) 0.347 0.334 0.362 0.345 0.383 0.327 + 239 (0.459) 0.420 0.561 0.472 0.585 0.459 0.581 + 247 (0.117) 0.226 0.095 0.157 0.058 0.117 0.081 + 235 (0.021) 0.004 0.004 0.006 0.004 0.021 0.004 + 241 (0.021) 0.003 0.006 0.003 0.008 0.021 0.007 + +Locus 20 : Ap249 +9 alleles +1.3% missing data + 209 (0.589) 0.594 0.697 0.727 0.697 0.591 0.702 + 211 (0.058) 0.025 0.031 0.047 0.025 0.058 0.020 + 217 (0.086) 0.144 0.060 0.075 0.041 0.085 0.051 + 219 (0.104) 0.205 0.091 0.099 0.057 0.105 0.069 + 215 (0.088) 0.020 0.107 0.041 0.167 0.087 0.146 + 208 (0.019) 0.003 0.003 0.003 0.003 0.018 0.003 + 225 (0.019) 0.003 0.003 0.003 0.002 0.019 0.002 + 223 (0.019) 0.003 0.003 0.004 0.003 0.018 0.002 + 213 (0.019) 0.002 0.003 0.003 0.004 0.018 0.005 + +Locus 21 : Ap273 +4 alleles +1.3% missing data + 106 (0.869) 0.955 0.949 0.953 0.951 0.870 0.955 + 108 (0.054) 0.025 0.025 0.023 0.023 0.053 0.021 + 104 (0.047) 0.015 0.015 0.019 0.011 0.047 0.010 + 102 (0.030) 0.005 0.011 0.005 0.015 0.029 0.014 + +Locus 22 : Ap274 +2 alleles +2.0% missing data + 120 (0.944) 0.988 0.955 0.979 0.947 0.945 0.933 + 122 (0.056) 0.012 0.045 0.021 0.053 0.055 0.067 + +Locus 23 : Ap288 +5 alleles +0.0% missing data + 123 (0.772) 0.603 0.843 0.746 0.905 0.774 0.870 + 131 (0.157) 0.368 0.141 0.239 0.084 0.156 0.118 + 139 (0.031) 0.018 0.009 0.008 0.006 0.031 0.006 + 121 (0.020) 0.006 0.003 0.003 0.002 0.019 0.003 + 124 (0.020) 0.005 0.004 0.003 0.003 0.019 0.003 + +Locus 24 : At163 +7 alleles +0.0% missing data + 128 (0.710) 0.578 0.816 0.790 0.876 0.711 0.850 + 134 (0.186) 0.405 0.165 0.193 0.107 0.187 0.133 + 130 (0.026) 0.008 0.007 0.006 0.006 0.026 0.005 + 136 (0.020) 0.003 0.003 0.004 0.003 0.019 0.003 + 140 (0.019) 0.002 0.003 0.002 0.003 0.019 0.003 + 146 (0.019) 0.002 0.003 0.002 0.003 0.019 0.003 + 142 (0.020) 0.002 0.003 0.002 0.003 0.019 0.004 + +Locus 25 : At188 +13 alleles +1.3% missing data + 189 (0.602) 0.751 0.824 0.770 0.853 0.603 0.858 + 205 (0.034) 0.055 0.014 0.012 0.007 0.034 0.012 + 207 (0.030) 0.039 0.023 0.077 0.014 0.029 0.017 + 219 (0.026) 0.007 0.006 0.006 0.005 0.026 0.005 + 209 (0.038) 0.025 0.025 0.042 0.020 0.038 0.015 + 217 (0.040) 0.013 0.018 0.017 0.014 0.041 0.010 + 215 (0.023) 0.009 0.009 0.010 0.006 0.022 0.005 + 199 (0.074) 0.053 0.041 0.025 0.045 0.073 0.043 + 212 (0.029) 0.009 0.011 0.011 0.009 0.029 0.007 + 213 (0.039) 0.029 0.013 0.015 0.009 0.040 0.010 + 211 (0.018) 0.003 0.002 0.002 0.002 0.018 0.002 + 191 (0.018) 0.004 0.004 0.006 0.003 0.018 0.003 + 187 (0.030) 0.004 0.010 0.005 0.014 0.029 0.012 + +Values of parameters used in structure: +DATAFILE=, OUTFILE=, NUMINDS=149, NUMLOCI=25, MISSING=-9, LABEL=1, POPDATA=0, POPFLAG=1, PHENOTYPE=0, EXTRACOLS=1, MAXPOPS=6, BURNIN=100000, NUMREPS=1000000, USEPOPINFO=0, INFERALPHA=1, INFERLAMBDA=0, POPSPECIFICLAMBDA=0, POPALPHAS=0, COMPUTEPROB=1, NOADMIX=0, ADMBURNIN=2500, UPDATEFREQ=1, PRINTLIKES=0, INTERMEDSAVE=0, PRINTKLD=0, PRINTNET=0, PRINTLAMBDA=0, ANCESTDIST=0, NUMBOXES=1000, ANCESTPINT=0.90000, GENSBACK=2, MIGRPRIOR=0.05000, PRINTQHAT=0, PRINTQSUM=0, ALPHA=1.0000, FREQSCORR=1, FPRIORMEAN=0.0100, FPRIORSD=0.0500, ONEFST=0, LAMBDA=1.0000, UNIFPRIORALPHA=1, ALPHAMAX=10.0000, ALPHAPRIORA=1.0000, ALPHAPRIORB=2.0000, ALPHAPROPSD=0.0250, STARTATPOPINFO=0, RANDOMIZE=1, LINKAGE=0, METROFREQ=10, REPORTHITRATE=0, MARKOVPHASE=-1, PHASED=0, PLOIDY=2, PHASEINFO=0 LOCPRIOR=0, LOCPRIORINIT=1.000000, LOCDATA=0, LOCISPOP=0, LOCPRIORSTEP=0.100000, MAXLOCPRIOR=20.000000, SEED=1335121138, +[STRAT parameters]: NUMSIMSTATS=1000, PHENOTYPECOL=-9, POOLFREQ=10, LOCUSxONLY=0, EMERROR=0.00100, MISSINGPHENO=-9, \ No newline at end of file diff --git a/inst/files/structure/structure_08 b/inst/files/structure/structure_08 new file mode 100644 index 0000000..50e76da --- /dev/null +++ b/inst/files/structure/structure_08 @@ -0,0 +1,544 @@ + + +---------------------------------------------------- +STRUCTURE by Pritchard, Stephens and Donnelly (2000) + and Falush, Stephens and Pritchard (2003) + Code by Pritchard, Falush and Hubisz + Version 2.3.2.1 (Oct 2009) +---------------------------------------------------- + + + +Command line arguments: +Input File: + +Run parameters: + 149 individuals + 25 loci + 7 populations assumed + 100000 Burn-in period + 1000000 Reps + + +-------------------------------------------- +Overall proportion of membership of the +sample in each of the 7 clusters + +Inferred Clusters + 1 2 3 4 5 6 7 +0.148 0.148 0.149 0.147 0.131 0.146 0.132 + +-------------------------------------------- + +Allele-freq. divergence among pops (Net nucleotide distance), +computed using point estimates of P. + + 1 2 3 4 5 6 7 + 1 - 0.0008 0.0051 0.0070 0.0055 0.0011 0.0055 + 2 0.0008 - 0.0057 0.0062 0.0041 0.0014 0.0043 + 3 0.0051 0.0057 - 0.0231 0.0174 0.0099 0.0185 + 4 0.0070 0.0062 0.0231 - 0.0027 0.0037 0.0017 + 5 0.0055 0.0041 0.0174 0.0027 - 0.0030 0.0003 + 6 0.0011 0.0014 0.0099 0.0037 0.0030 - 0.0024 + 7 0.0055 0.0043 0.0185 0.0017 0.0003 0.0024 - + +Average distances (expected heterozygosity) between individuals in same cluster: +cluster 1 : 0.4809 +cluster 2 : 0.5015 +cluster 3 : 0.4595 +cluster 4 : 0.5042 +cluster 5 : 0.5568 +cluster 6 : 0.4924 +cluster 7 : 0.5413 + +-------------------------------------------- +Estimated Ln Prob of Data = -8656.8 +Mean value of ln likelihood = -7144.2 +Variance of ln likelihood = 3025.1 +Mean value of alpha = 0.2280 + +Mean value of Fst_1 = 0.2006 +Mean value of Fst_2 = 0.1754 +Mean value of Fst_3 = 0.1866 +Mean value of Fst_4 = 0.1919 +Mean value of Fst_5 = 0.0656 +Mean value of Fst_6 = 0.1890 +Mean value of Fst_7 = 0.0993 + + +Inferred ancestry of individuals: + Label (%Miss) : Inferred clusters + 1 I13825 (0) : 0.086 0.138 0.080 0.134 0.234 0.119 0.208 + 2 I13826 (0) : 0.113 0.188 0.053 0.220 0.115 0.143 0.168 + 3 I13827 (20) : 0.171 0.131 0.075 0.232 0.163 0.103 0.124 + 4 I13828 (0) : 0.105 0.171 0.063 0.192 0.134 0.151 0.184 + 5 I13829 (8) : 0.156 0.121 0.052 0.223 0.139 0.159 0.149 + 6 I13830 (0) : 0.111 0.175 0.049 0.237 0.124 0.149 0.156 + 7 I13831 (0) : 0.148 0.107 0.066 0.226 0.113 0.196 0.144 + 8 I13832 (16) : 0.146 0.112 0.070 0.181 0.169 0.157 0.165 + 9 I13833 (0) : 0.173 0.118 0.058 0.230 0.131 0.161 0.129 + 10 I13834 (0) : 0.175 0.132 0.042 0.248 0.155 0.118 0.130 + 11 I13835 (0) : 0.132 0.102 0.066 0.171 0.167 0.169 0.192 + 12 I13836 (0) : 0.159 0.125 0.057 0.213 0.188 0.103 0.154 + 13 I13377 (0) : 0.167 0.100 0.074 0.210 0.126 0.183 0.140 + 14 I13378 (0) : 0.124 0.100 0.086 0.155 0.173 0.166 0.196 + 15 I13379 (0) : 0.135 0.140 0.060 0.227 0.115 0.167 0.155 + 16 I13380 (0) : 0.185 0.133 0.108 0.191 0.131 0.135 0.118 + 17 I13381 (0) : 0.134 0.105 0.079 0.175 0.135 0.198 0.174 + 18 I13382 (0) : 0.158 0.104 0.038 0.229 0.124 0.198 0.149 + 19 I13383 (0) : 0.126 0.104 0.079 0.168 0.161 0.178 0.184 + 20 I13384 (0) : 0.133 0.123 0.067 0.216 0.137 0.164 0.160 + 21 I13385 (0) : 0.178 0.124 0.048 0.235 0.155 0.129 0.132 + 22 I13386 (0) : 0.159 0.113 0.045 0.230 0.152 0.153 0.148 + 23 I13387 (0) : 0.113 0.162 0.060 0.198 0.151 0.141 0.174 + 24 I13388 (0) : 0.088 0.135 0.100 0.122 0.248 0.112 0.196 + 25 I13389 (0) : 0.177 0.126 0.109 0.210 0.107 0.156 0.114 + 26 I13390 (0) : 0.155 0.118 0.055 0.229 0.138 0.158 0.147 + 27 I13391 (0) : 0.135 0.116 0.110 0.158 0.163 0.148 0.169 + 28 I13392 (0) : 0.123 0.121 0.089 0.158 0.172 0.151 0.185 + 29 I13393 (0) : 0.157 0.106 0.079 0.185 0.096 0.230 0.148 + 30 I13394 (4) : 0.152 0.139 0.169 0.129 0.124 0.159 0.128 + 31 I13395 (0) : 0.156 0.151 0.170 0.144 0.112 0.153 0.114 + 32 I13396 (0) : 0.117 0.160 0.127 0.145 0.149 0.135 0.168 + 33 I13397 (0) : 0.117 0.130 0.087 0.170 0.178 0.142 0.176 + 34 I13398 (0) : 0.123 0.183 0.042 0.241 0.117 0.144 0.150 + 35 I13399 (4) : 0.115 0.096 0.094 0.154 0.223 0.132 0.185 + 36 I13400 (0) : 0.146 0.115 0.089 0.184 0.138 0.169 0.159 + 37 I13401 (0) : 0.186 0.148 0.216 0.111 0.117 0.120 0.102 + 38 I13402 (0) : 0.108 0.122 0.102 0.138 0.191 0.139 0.200 + 39 I13403 (0) : 0.144 0.172 0.117 0.181 0.091 0.157 0.138 + 40 I13404 (0) : 0.136 0.144 0.049 0.246 0.128 0.148 0.150 + 41 I13405 (0) : 0.182 0.117 0.051 0.241 0.141 0.141 0.127 + 42 I13406 (16) : 0.093 0.146 0.079 0.149 0.207 0.122 0.203 + 43 I13407 (0) : 0.130 0.141 0.068 0.210 0.114 0.166 0.170 + 44 I13408 (0) : 0.162 0.110 0.049 0.223 0.121 0.189 0.146 + 45 I13409 (0) : 0.095 0.145 0.101 0.128 0.227 0.111 0.192 + 46 I13410 (0) : 0.140 0.106 0.044 0.227 0.120 0.199 0.163 + 47 I13411 (0) : 0.147 0.132 0.042 0.247 0.155 0.130 0.148 + 48 I13412 (0) : 0.148 0.156 0.134 0.163 0.131 0.137 0.131 + 49 I13413 (0) : 0.108 0.140 0.092 0.173 0.173 0.136 0.179 + 50 I13414 (0) : 0.109 0.165 0.059 0.208 0.151 0.141 0.168 + 51 I13415 (4) : 0.169 0.140 0.109 0.205 0.129 0.126 0.122 + 52 I13416 (4) : 0.146 0.147 0.105 0.186 0.125 0.152 0.140 + 53 I13417 (4) : 0.180 0.152 0.152 0.184 0.114 0.120 0.100 + 54 I13418 (0) : 0.146 0.141 0.094 0.208 0.124 0.157 0.130 + 55 I13419 (0) : 0.109 0.116 0.067 0.158 0.262 0.097 0.191 + 56 I13420 (0) : 0.148 0.170 0.120 0.189 0.109 0.138 0.126 + 57 I13421 (0) : 0.164 0.134 0.130 0.171 0.093 0.190 0.119 + 58 I13422 (0) : 0.168 0.152 0.144 0.156 0.114 0.142 0.123 + 59 I13423 (0) : 0.124 0.116 0.092 0.154 0.162 0.171 0.180 + 60 I13424 (0) : 0.155 0.106 0.069 0.213 0.139 0.171 0.148 + 61 I13425 (4) : 0.146 0.135 0.087 0.188 0.166 0.129 0.149 + 62 I13426 (4) : 0.142 0.149 0.178 0.106 0.139 0.151 0.136 + 63 I13870 (0) : 0.143 0.170 0.140 0.174 0.107 0.143 0.123 + 64 I13871 (16) : 0.115 0.136 0.077 0.183 0.158 0.156 0.176 + 65 I13872 (0) : 0.097 0.184 0.056 0.202 0.142 0.135 0.184 + 66 I13873 (4) : 0.131 0.152 0.096 0.193 0.112 0.156 0.160 + 67 I13874 (0) : 0.104 0.155 0.084 0.162 0.198 0.118 0.178 + 68 I13875 (8) : 0.120 0.170 0.092 0.185 0.123 0.147 0.162 + 69 I13876 (0) : 0.086 0.117 0.122 0.100 0.287 0.092 0.197 + 70 I13877 (20) : 0.142 0.115 0.079 0.198 0.113 0.203 0.151 + 71 I13878 (28) : 0.137 0.167 0.052 0.232 0.125 0.134 0.153 + 72 I13879 (4) : 0.161 0.141 0.042 0.245 0.137 0.133 0.142 + 73 I13880 (4) : 0.105 0.189 0.048 0.233 0.114 0.153 0.158 + 74 I13881 (0) : 0.101 0.135 0.111 0.129 0.241 0.104 0.178 + 75 I13882 (0) : 0.116 0.170 0.072 0.193 0.125 0.153 0.171 + 76 I13883 (4) : 0.108 0.185 0.089 0.180 0.128 0.143 0.167 + 77 I13884 (16) : 0.080 0.109 0.101 0.096 0.306 0.091 0.217 + 78 I13885 (20) : 0.113 0.101 0.067 0.166 0.214 0.145 0.194 + 79 I13886 (8) : 0.127 0.149 0.068 0.219 0.138 0.146 0.154 + 80 I13887 (0) : 0.069 0.106 0.123 0.063 0.329 0.082 0.229 + 81 I13888 (0) : 0.105 0.123 0.087 0.166 0.196 0.136 0.186 + 82 I13889 (0) : 0.196 0.163 0.258 0.085 0.082 0.137 0.079 + 83 I13890 (32) : 0.149 0.150 0.177 0.116 0.129 0.151 0.127 + 84 I13891 (0) : 0.123 0.165 0.055 0.219 0.144 0.132 0.163 + 85 I13892 (0) : 0.157 0.139 0.162 0.158 0.102 0.167 0.115 + 86 I13893 (8) : 0.103 0.099 0.110 0.129 0.224 0.130 0.206 + 87 I13894 (0) : 0.105 0.202 0.058 0.219 0.101 0.147 0.168 + 88 I13895 (4) : 0.131 0.115 0.118 0.147 0.165 0.152 0.173 + 89 I13896 (0) : 0.133 0.186 0.144 0.156 0.104 0.146 0.130 + 90 I13897 (0) : 0.128 0.166 0.042 0.240 0.122 0.145 0.157 + 91 I13898 (4) : 0.133 0.151 0.073 0.213 0.111 0.160 0.159 + 92 I13899 (0) : 0.107 0.200 0.038 0.244 0.098 0.151 0.162 + 93 I13900 (32) : 0.094 0.122 0.113 0.114 0.257 0.108 0.193 + 94 I13837 (0) : 0.176 0.124 0.070 0.228 0.149 0.127 0.126 + 95 I13838 (0) : 0.172 0.175 0.248 0.093 0.085 0.140 0.087 + 96 I13839 (0) : 0.171 0.136 0.101 0.211 0.152 0.110 0.119 + 97 I13840 (0) : 0.165 0.142 0.131 0.186 0.107 0.159 0.111 + 98 I13841 (0) : 0.163 0.158 0.194 0.124 0.069 0.199 0.093 + 99 I13842 (0) : 0.180 0.137 0.148 0.165 0.113 0.151 0.106 +100 I13843 (4) : 0.160 0.156 0.196 0.125 0.071 0.197 0.096 +101 I13844 (16) : 0.151 0.115 0.104 0.163 0.149 0.160 0.159 +102 I13845 (0) : 0.158 0.115 0.051 0.225 0.140 0.165 0.146 +103 I13846 (0) : 0.151 0.114 0.074 0.198 0.148 0.159 0.156 +104 I13847 (0) : 0.147 0.168 0.173 0.131 0.120 0.136 0.124 +105 I13848 (0) : 0.149 0.138 0.143 0.129 0.129 0.158 0.153 +106 I13849 (0) : 0.117 0.151 0.110 0.145 0.144 0.147 0.186 +107 I13850 (0) : 0.159 0.151 0.195 0.120 0.083 0.177 0.115 +108 I12577 (4) : 0.171 0.181 0.287 0.059 0.083 0.147 0.073 +109 I12578 (4) : 0.204 0.169 0.294 0.065 0.070 0.129 0.069 +110 I12579 (8) : 0.153 0.164 0.248 0.060 0.129 0.141 0.105 +111 I12580 (8) : 0.183 0.191 0.312 0.062 0.041 0.169 0.042 +112 I12581 (4) : 0.140 0.118 0.149 0.111 0.182 0.135 0.165 +113 I12582 (4) : 0.179 0.190 0.299 0.060 0.061 0.153 0.058 +114 I12583 (8) : 0.142 0.132 0.201 0.061 0.227 0.094 0.143 +115 I12584 (4) : 0.149 0.147 0.248 0.057 0.169 0.110 0.120 +116 I12585 (4) : 0.180 0.184 0.326 0.051 0.056 0.154 0.047 +117 I12586 (4) : 0.175 0.198 0.302 0.060 0.042 0.178 0.046 +118 I12587 (8) : 0.184 0.190 0.335 0.056 0.030 0.171 0.033 +119 I12588 (4) : 0.165 0.195 0.300 0.046 0.075 0.156 0.062 +120 I12589 (0) : 0.207 0.171 0.322 0.063 0.058 0.130 0.050 +121 I12590 (0) : 0.159 0.178 0.261 0.068 0.098 0.148 0.088 +122 I12591 (12) : 0.210 0.194 0.340 0.047 0.035 0.143 0.031 +123 I12592 (4) : 0.210 0.176 0.304 0.057 0.070 0.124 0.058 +124 I12593 (4) : 0.206 0.188 0.318 0.052 0.054 0.135 0.047 +125 I12594 (8) : 0.180 0.204 0.324 0.052 0.039 0.165 0.037 +126 I12595 (0) : 0.149 0.144 0.227 0.059 0.172 0.116 0.132 +127 I12596 (0) : 0.193 0.198 0.324 0.049 0.044 0.153 0.039 +128 I12597 (4) : 0.117 0.144 0.198 0.052 0.223 0.109 0.157 +129 I12598 (0) : 0.172 0.146 0.256 0.059 0.152 0.108 0.106 +130 I12599 (0) : 0.153 0.163 0.228 0.077 0.135 0.130 0.114 +131 I12600 (4) : 0.178 0.192 0.322 0.060 0.043 0.164 0.042 +132 I12601 (8) : 0.161 0.175 0.298 0.053 0.087 0.151 0.074 +133 I12602 (12) : 0.172 0.189 0.293 0.059 0.067 0.157 0.064 +134 I12603 (0) : 0.139 0.164 0.251 0.053 0.153 0.125 0.115 +135 I12604 (4) : 0.164 0.187 0.277 0.061 0.086 0.149 0.076 +136 I12605 (4) : 0.163 0.181 0.287 0.058 0.082 0.152 0.077 +137 I12606 (8) : 0.208 0.179 0.308 0.054 0.059 0.135 0.057 +138 I12607 (4) : 0.183 0.156 0.271 0.049 0.132 0.108 0.101 +139 I12608 (8) : 0.182 0.159 0.260 0.065 0.110 0.125 0.100 +140 I12609 (8) : 0.198 0.179 0.323 0.055 0.051 0.146 0.047 +141 I12610 (52) : 0.169 0.174 0.268 0.071 0.083 0.155 0.080 +142 I12611 (0) : 0.213 0.177 0.347 0.052 0.040 0.135 0.036 +143 I12612 (0) : 0.180 0.179 0.329 0.051 0.055 0.157 0.050 +144 I12613 (0) : 0.219 0.179 0.332 0.053 0.043 0.134 0.040 +145 I12614 (4) : 0.167 0.165 0.235 0.100 0.074 0.177 0.083 +146 I12615 (0) : 0.187 0.155 0.259 0.073 0.108 0.124 0.093 +147 I12616 (4) : 0.143 0.137 0.213 0.061 0.202 0.106 0.138 +148 I12617 (8) : 0.186 0.206 0.334 0.049 0.030 0.167 0.029 +149 I12618 (48) : 0.169 0.193 0.308 0.050 0.065 0.158 0.056 + + +Estimated Allele Frequencies in each cluster +First column gives estimated ancestral frequencies + + +Locus 1 : A8 +7 alleles +4.0% missing data + 177 (0.515) 0.535 0.528 0.583 0.474 0.479 0.536 0.498 + 179 (0.092) 0.084 0.083 0.059 0.103 0.102 0.082 0.099 + 175 (0.095) 0.127 0.135 0.042 0.242 0.169 0.150 0.172 + 173 (0.047) 0.039 0.028 0.020 0.049 0.047 0.045 0.048 + 181 (0.185) 0.188 0.197 0.261 0.108 0.151 0.159 0.139 + 165 (0.039) 0.019 0.020 0.026 0.011 0.029 0.016 0.024 + 183 (0.028) 0.009 0.010 0.008 0.013 0.022 0.012 0.021 + +Locus 2 : A14 +5 alleles +0.0% missing data + 112 (0.198) 0.161 0.187 0.082 0.278 0.218 0.222 0.255 + 110 (0.705) 0.773 0.731 0.806 0.695 0.712 0.719 0.690 + 114 (0.031) 0.008 0.011 0.010 0.010 0.023 0.010 0.019 + 118 (0.036) 0.044 0.054 0.078 0.012 0.026 0.038 0.020 + 116 (0.030) 0.014 0.017 0.024 0.006 0.021 0.013 0.016 + +Locus 3 : A24 +5 alleles +2.7% missing data + 104 (0.402) 0.356 0.384 0.373 0.375 0.383 0.371 0.391 + 106 (0.523) 0.609 0.572 0.572 0.603 0.562 0.593 0.562 + 101 (0.017) 0.004 0.004 0.005 0.004 0.012 0.005 0.010 + 108 (0.028) 0.008 0.012 0.010 0.011 0.022 0.011 0.021 + 96 (0.030) 0.024 0.028 0.041 0.007 0.021 0.020 0.016 + +Locus 4 : A29 +29 alleles +6.7% missing data + 143 (0.033) 0.031 0.042 0.014 0.062 0.043 0.040 0.050 + 149 (0.048) 0.041 0.036 0.051 0.025 0.039 0.034 0.036 + 147 (0.029) 0.020 0.027 0.028 0.018 0.024 0.021 0.022 + 153 (0.050) 0.103 0.084 0.120 0.075 0.065 0.062 0.054 + 169 (0.040) 0.034 0.049 0.032 0.048 0.040 0.038 0.045 + 151 (0.037) 0.053 0.035 0.024 0.060 0.043 0.073 0.053 + 145 (0.028) 0.018 0.021 0.024 0.016 0.023 0.019 0.021 + 157 (0.070) 0.096 0.108 0.129 0.082 0.071 0.098 0.072 + 155 (0.097) 0.126 0.133 0.159 0.096 0.092 0.122 0.096 + 159 (0.052) 0.058 0.080 0.052 0.087 0.058 0.073 0.072 + 161 (0.031) 0.046 0.036 0.016 0.061 0.049 0.052 0.051 + 141 (0.028) 0.025 0.022 0.014 0.034 0.036 0.022 0.030 + 139 (0.016) 0.008 0.007 0.005 0.010 0.015 0.007 0.013 + 144 (0.026) 0.032 0.021 0.011 0.043 0.035 0.034 0.034 + 171 (0.048) 0.046 0.036 0.036 0.050 0.047 0.050 0.050 + 163 (0.077) 0.080 0.069 0.058 0.087 0.080 0.086 0.090 + 167 (0.045) 0.048 0.046 0.057 0.030 0.038 0.041 0.037 + 173 (0.024) 0.018 0.015 0.011 0.024 0.025 0.018 0.025 + 142 (0.013) 0.003 0.005 0.004 0.004 0.010 0.004 0.008 + 177 (0.024) 0.021 0.023 0.033 0.009 0.018 0.018 0.015 + 175 (0.022) 0.010 0.011 0.014 0.008 0.017 0.010 0.014 + 165 (0.045) 0.034 0.037 0.040 0.030 0.040 0.031 0.037 + 146 (0.021) 0.013 0.013 0.007 0.020 0.023 0.014 0.021 + 137 (0.019) 0.007 0.008 0.011 0.004 0.014 0.006 0.010 + 183 (0.017) 0.008 0.009 0.013 0.004 0.012 0.007 0.010 + 179 (0.018) 0.007 0.008 0.011 0.004 0.013 0.007 0.011 + 191 (0.013) 0.003 0.004 0.006 0.002 0.009 0.003 0.007 + 185 (0.013) 0.004 0.004 0.006 0.002 0.010 0.003 0.007 + 180 (0.015) 0.009 0.010 0.016 0.003 0.011 0.008 0.008 + +Locus 5 : A43 +7 alleles +1.3% missing data + 123 (0.199) 0.129 0.127 0.145 0.108 0.162 0.142 0.162 + 141 (0.016) 0.003 0.004 0.004 0.003 0.012 0.003 0.009 + 137 (0.671) 0.784 0.778 0.734 0.836 0.737 0.762 0.749 + 139 (0.045) 0.050 0.050 0.058 0.040 0.041 0.063 0.043 + 124 (0.035) 0.027 0.031 0.046 0.008 0.024 0.022 0.019 + 143 (0.017) 0.004 0.005 0.006 0.002 0.012 0.003 0.009 + 128 (0.017) 0.004 0.006 0.008 0.003 0.012 0.004 0.009 + +Locus 6 : A79 +13 alleles +3.4% missing data + 103 (0.240) 0.254 0.248 0.200 0.297 0.256 0.284 0.280 + 97 (0.128) 0.083 0.109 0.072 0.126 0.122 0.103 0.134 + 101 (0.092) 0.124 0.094 0.059 0.159 0.135 0.111 0.123 + 107 (0.094) 0.109 0.096 0.067 0.141 0.118 0.132 0.125 + 109 (0.098) 0.079 0.077 0.083 0.076 0.088 0.083 0.086 + 105 (0.168) 0.255 0.267 0.381 0.140 0.145 0.197 0.137 + 111 (0.046) 0.026 0.026 0.032 0.019 0.035 0.024 0.032 + 113 (0.016) 0.003 0.004 0.005 0.003 0.012 0.003 0.009 + 91 (0.027) 0.032 0.038 0.058 0.008 0.019 0.028 0.015 + 99 (0.032) 0.020 0.021 0.024 0.016 0.027 0.017 0.022 + 115 (0.027) 0.009 0.010 0.012 0.010 0.020 0.011 0.018 + 117 (0.016) 0.003 0.005 0.005 0.003 0.012 0.004 0.009 + 121 (0.016) 0.003 0.004 0.004 0.003 0.011 0.003 0.008 + +Locus 7 : A88 +9 alleles +6.0% missing data + 133 (0.017) 0.003 0.005 0.005 0.003 0.012 0.004 0.010 + 149 (0.530) 0.628 0.631 0.748 0.508 0.499 0.594 0.507 + 137 (0.101) 0.069 0.077 0.042 0.109 0.104 0.078 0.109 + 147 (0.192) 0.225 0.194 0.102 0.316 0.260 0.251 0.270 + 141 (0.083) 0.059 0.071 0.077 0.050 0.069 0.055 0.063 + 152 (0.018) 0.003 0.004 0.005 0.004 0.013 0.004 0.010 + 143 (0.017) 0.003 0.004 0.005 0.003 0.012 0.003 0.009 + 151 (0.017) 0.004 0.005 0.006 0.003 0.012 0.004 0.009 + 144 (0.024) 0.006 0.008 0.010 0.004 0.018 0.006 0.014 + +Locus 8 : A113 +12 alleles +7.4% missing data + 214 (0.578) 0.755 0.721 0.730 0.744 0.638 0.753 0.670 + 226 (0.063) 0.044 0.061 0.035 0.076 0.066 0.054 0.069 + 218 (0.017) 0.005 0.005 0.005 0.006 0.013 0.004 0.010 + 220 (0.066) 0.075 0.074 0.105 0.034 0.052 0.058 0.045 + 216 (0.056) 0.030 0.030 0.038 0.021 0.044 0.025 0.036 + 230 (0.046) 0.032 0.026 0.018 0.043 0.048 0.036 0.045 + 234 (0.033) 0.011 0.016 0.011 0.016 0.027 0.014 0.025 + 232 (0.031) 0.012 0.017 0.011 0.019 0.027 0.015 0.024 + 228 (0.048) 0.021 0.026 0.023 0.025 0.038 0.025 0.039 + 224 (0.017) 0.003 0.004 0.005 0.003 0.012 0.003 0.009 + 222 (0.029) 0.009 0.013 0.013 0.008 0.022 0.010 0.019 + 208 (0.017) 0.004 0.005 0.005 0.005 0.013 0.005 0.010 + +Locus 9 : Ac11 +9 alleles +4.7% missing data + 111 (0.130) 0.116 0.141 0.065 0.203 0.156 0.140 0.171 + 117 (0.301) 0.310 0.272 0.211 0.357 0.320 0.351 0.347 + 115 (0.248) 0.283 0.276 0.290 0.298 0.278 0.269 0.270 + 113 (0.161) 0.167 0.170 0.234 0.093 0.130 0.139 0.121 + 119 (0.053) 0.078 0.085 0.123 0.025 0.040 0.058 0.031 + 121 (0.027) 0.025 0.030 0.043 0.008 0.019 0.021 0.014 + 123 (0.032) 0.009 0.011 0.014 0.006 0.023 0.008 0.018 + 127 (0.030) 0.009 0.011 0.014 0.007 0.022 0.010 0.018 + 125 (0.017) 0.003 0.004 0.006 0.002 0.012 0.003 0.009 + +Locus 10 : Ac88 +8 alleles +0.7% missing data + 214 (0.755) 0.885 0.846 0.889 0.831 0.787 0.865 0.797 + 216 (0.029) 0.008 0.012 0.009 0.012 0.023 0.011 0.021 + 220 (0.115) 0.076 0.107 0.053 0.140 0.118 0.097 0.128 + 230 (0.025) 0.005 0.007 0.008 0.004 0.018 0.005 0.014 + 221 (0.017) 0.004 0.006 0.007 0.002 0.012 0.004 0.009 + 212 (0.020) 0.010 0.010 0.016 0.004 0.014 0.007 0.010 + 217 (0.017) 0.004 0.005 0.006 0.002 0.012 0.003 0.009 + 224 (0.023) 0.008 0.008 0.011 0.004 0.017 0.006 0.012 + +Locus 11 : Ac139 +8 alleles +13.4% missing data + 327 (0.521) 0.655 0.621 0.738 0.513 0.500 0.620 0.512 + 329 (0.286) 0.247 0.264 0.159 0.371 0.336 0.261 0.334 + 331 (0.070) 0.039 0.054 0.033 0.064 0.068 0.049 0.068 + 328 (0.037) 0.025 0.019 0.012 0.034 0.034 0.038 0.039 + 341 (0.019) 0.005 0.006 0.008 0.003 0.014 0.005 0.010 + 337 (0.031) 0.021 0.025 0.036 0.008 0.022 0.019 0.017 + 323 (0.019) 0.005 0.005 0.007 0.003 0.013 0.004 0.010 + 339 (0.019) 0.004 0.005 0.007 0.003 0.013 0.004 0.010 + +Locus 12 : Ac306 +6 alleles +4.7% missing data + 165 (0.739) 0.794 0.768 0.789 0.765 0.747 0.793 0.760 + 177 (0.073) 0.072 0.080 0.105 0.050 0.061 0.075 0.060 + 173 (0.097) 0.066 0.090 0.048 0.119 0.101 0.082 0.106 + 169 (0.043) 0.043 0.034 0.016 0.056 0.058 0.032 0.049 + 171 (0.017) 0.003 0.004 0.005 0.002 0.012 0.003 0.009 + 179 (0.030) 0.023 0.023 0.036 0.007 0.021 0.015 0.016 + +Locus 13 : Ap15 +7 alleles +6.0% missing data + 202 (0.819) 0.895 0.890 0.844 0.950 0.868 0.922 0.893 + 212 (0.027) 0.007 0.014 0.008 0.012 0.021 0.011 0.021 + 204 (0.044) 0.016 0.019 0.025 0.011 0.032 0.016 0.026 + 208 (0.036) 0.036 0.031 0.053 0.010 0.026 0.020 0.020 + 220 (0.038) 0.036 0.035 0.054 0.010 0.027 0.023 0.021 + 219 (0.018) 0.005 0.006 0.009 0.003 0.013 0.004 0.009 + 210 (0.018) 0.005 0.005 0.007 0.003 0.013 0.004 0.009 + +Locus 14 : Ap68 +9 alleles +4.7% missing data + 158 (0.383) 0.345 0.397 0.338 0.425 0.395 0.379 0.410 + 160 (0.081) 0.076 0.052 0.037 0.091 0.084 0.098 0.093 + 156 (0.254) 0.344 0.317 0.332 0.313 0.282 0.300 0.280 + 162 (0.042) 0.013 0.019 0.017 0.016 0.033 0.016 0.030 + 154 (0.082) 0.078 0.056 0.038 0.097 0.088 0.084 0.089 + 152 (0.077) 0.115 0.126 0.194 0.040 0.060 0.095 0.050 + 164 (0.041) 0.015 0.018 0.022 0.012 0.030 0.017 0.027 + 170 (0.017) 0.004 0.005 0.006 0.003 0.012 0.004 0.009 + 166 (0.022) 0.010 0.010 0.015 0.004 0.016 0.006 0.012 + +Locus 15 : Ap85 +10 alleles +3.4% missing data + 202 (0.320) 0.406 0.437 0.529 0.308 0.308 0.358 0.302 + 186 (0.246) 0.291 0.257 0.143 0.432 0.324 0.350 0.350 + 204 (0.061) 0.035 0.034 0.037 0.028 0.048 0.034 0.047 + 188 (0.100) 0.087 0.073 0.043 0.112 0.104 0.101 0.112 + 194 (0.078) 0.045 0.056 0.040 0.060 0.072 0.046 0.070 + 196 (0.061) 0.055 0.058 0.084 0.022 0.046 0.046 0.039 + 200 (0.064) 0.045 0.046 0.066 0.019 0.047 0.033 0.039 + 192 (0.024) 0.006 0.007 0.009 0.006 0.018 0.006 0.014 + 190 (0.017) 0.004 0.006 0.005 0.005 0.013 0.004 0.010 + 198 (0.030) 0.026 0.027 0.044 0.008 0.021 0.020 0.016 + +Locus 16 : Ap90 +13 alleles +0.7% missing data + 131 (0.366) 0.544 0.534 0.555 0.531 0.437 0.481 0.437 + 135 (0.066) 0.057 0.073 0.076 0.051 0.060 0.060 0.054 + 133 (0.288) 0.241 0.239 0.211 0.267 0.271 0.275 0.295 + 129 (0.096) 0.101 0.085 0.076 0.104 0.096 0.126 0.106 + 137 (0.035) 0.017 0.016 0.016 0.018 0.029 0.018 0.026 + 141 (0.016) 0.003 0.004 0.004 0.003 0.012 0.003 0.009 + 143 (0.022) 0.005 0.007 0.007 0.006 0.017 0.006 0.014 + 151 (0.023) 0.005 0.008 0.007 0.005 0.017 0.006 0.014 + 155 (0.016) 0.003 0.004 0.004 0.003 0.011 0.003 0.009 + 145 (0.016) 0.004 0.006 0.008 0.002 0.011 0.004 0.008 + 130 (0.020) 0.008 0.010 0.014 0.003 0.014 0.007 0.010 + 139 (0.016) 0.005 0.006 0.009 0.002 0.011 0.004 0.008 + 153 (0.020) 0.007 0.009 0.013 0.003 0.014 0.007 0.011 + +Locus 17 : Ap223 +7 alleles +2.0% missing data + 183 (0.689) 0.763 0.746 0.841 0.661 0.666 0.753 0.679 + 187 (0.135) 0.157 0.158 0.063 0.264 0.193 0.171 0.200 + 189 (0.026) 0.011 0.011 0.007 0.014 0.024 0.010 0.019 + 173 (0.064) 0.040 0.048 0.045 0.039 0.054 0.036 0.050 + 182 (0.031) 0.009 0.011 0.011 0.009 0.024 0.009 0.019 + 180 (0.024) 0.006 0.007 0.009 0.005 0.018 0.007 0.015 + 179 (0.031) 0.014 0.018 0.024 0.008 0.022 0.014 0.018 + +Locus 18 : Ap224 +7 alleles +4.0% missing data + 283 (0.112) 0.113 0.113 0.054 0.181 0.144 0.128 0.148 + 287 (0.481) 0.448 0.456 0.417 0.462 0.467 0.485 0.491 + 281 (0.134) 0.118 0.114 0.069 0.172 0.156 0.134 0.156 + 289 (0.192) 0.276 0.263 0.407 0.146 0.168 0.214 0.149 + 291 (0.038) 0.016 0.026 0.012 0.029 0.034 0.020 0.034 + 285 (0.017) 0.003 0.004 0.005 0.003 0.013 0.003 0.009 + 279 (0.026) 0.025 0.024 0.037 0.006 0.018 0.015 0.013 + +Locus 19 : Ap226 +5 alleles +17.4% missing data + 237 (0.378) 0.340 0.347 0.323 0.348 0.373 0.352 0.366 + 239 (0.466) 0.549 0.522 0.600 0.469 0.450 0.525 0.467 + 247 (0.118) 0.100 0.117 0.061 0.175 0.149 0.114 0.146 + 235 (0.019) 0.005 0.006 0.006 0.005 0.015 0.004 0.011 + 241 (0.019) 0.006 0.007 0.010 0.003 0.013 0.005 0.010 + +Locus 20 : Ap249 +9 alleles +1.3% missing data + 209 (0.605) 0.695 0.660 0.700 0.665 0.630 0.686 0.636 + 211 (0.056) 0.030 0.026 0.020 0.036 0.052 0.033 0.048 + 217 (0.082) 0.064 0.078 0.039 0.100 0.089 0.068 0.093 + 219 (0.105) 0.086 0.102 0.047 0.147 0.116 0.109 0.130 + 215 (0.086) 0.111 0.117 0.173 0.039 0.065 0.090 0.056 + 208 (0.017) 0.003 0.004 0.005 0.003 0.012 0.004 0.010 + 225 (0.017) 0.003 0.004 0.005 0.003 0.012 0.003 0.009 + 223 (0.017) 0.003 0.004 0.004 0.004 0.012 0.004 0.010 + 213 (0.017) 0.004 0.005 0.007 0.002 0.012 0.003 0.009 + +Locus 21 : Ap273 +4 alleles +1.3% missing data + 106 (0.881) 0.951 0.946 0.943 0.953 0.906 0.946 0.918 + 108 (0.049) 0.023 0.025 0.024 0.024 0.039 0.028 0.038 + 104 (0.042) 0.014 0.015 0.014 0.018 0.035 0.016 0.030 + 102 (0.028) 0.012 0.014 0.019 0.005 0.020 0.010 0.015 + +Locus 22 : Ap274 +2 alleles +2.0% missing data + 120 (0.950) 0.949 0.954 0.921 0.981 0.963 0.966 0.969 + 122 (0.050) 0.051 0.046 0.079 0.019 0.037 0.034 0.031 + +Locus 23 : Ap288 +5 alleles +0.0% missing data + 123 (0.775) 0.832 0.795 0.902 0.710 0.737 0.809 0.741 + 131 (0.162) 0.153 0.182 0.080 0.271 0.215 0.172 0.219 + 139 (0.029) 0.008 0.012 0.009 0.011 0.022 0.010 0.020 + 121 (0.017) 0.003 0.005 0.005 0.004 0.013 0.004 0.010 + 124 (0.017) 0.003 0.005 0.005 0.004 0.013 0.004 0.010 + +Locus 24 : At163 +7 alleles +0.0% missing data + 128 (0.710) 0.821 0.774 0.873 0.706 0.709 0.782 0.707 + 134 (0.197) 0.160 0.201 0.098 0.277 0.224 0.197 0.241 + 130 (0.024) 0.006 0.008 0.008 0.007 0.018 0.008 0.015 + 136 (0.017) 0.003 0.004 0.005 0.004 0.013 0.004 0.010 + 140 (0.017) 0.003 0.004 0.005 0.002 0.012 0.003 0.009 + 146 (0.017) 0.003 0.004 0.005 0.002 0.012 0.003 0.009 + 142 (0.017) 0.003 0.004 0.006 0.002 0.012 0.003 0.009 + +Locus 25 : At188 +13 alleles +1.3% missing data + 189 (0.633) 0.822 0.801 0.845 0.772 0.669 0.810 0.706 + 205 (0.031) 0.014 0.025 0.010 0.028 0.029 0.020 0.031 + 207 (0.027) 0.035 0.028 0.011 0.049 0.048 0.023 0.037 + 219 (0.023) 0.006 0.007 0.007 0.007 0.018 0.007 0.015 + 209 (0.035) 0.026 0.021 0.013 0.034 0.038 0.026 0.034 + 217 (0.038) 0.014 0.014 0.013 0.018 0.030 0.018 0.030 + 215 (0.021) 0.007 0.007 0.006 0.011 0.017 0.010 0.015 + 199 (0.069) 0.039 0.049 0.049 0.039 0.057 0.043 0.054 + 212 (0.026) 0.010 0.010 0.010 0.011 0.020 0.011 0.018 + 213 (0.037) 0.013 0.017 0.012 0.019 0.031 0.016 0.028 + 211 (0.016) 0.002 0.004 0.004 0.002 0.012 0.003 0.009 + 191 (0.016) 0.004 0.005 0.004 0.005 0.013 0.005 0.010 + 187 (0.027) 0.010 0.012 0.017 0.005 0.019 0.009 0.015 + +Values of parameters used in structure: +DATAFILE=, OUTFILE=, NUMINDS=149, NUMLOCI=25, MISSING=-9, LABEL=1, POPDATA=0, POPFLAG=1, PHENOTYPE=0, EXTRACOLS=1, MAXPOPS=7, BURNIN=100000, NUMREPS=1000000, USEPOPINFO=0, INFERALPHA=1, INFERLAMBDA=0, POPSPECIFICLAMBDA=0, POPALPHAS=0, COMPUTEPROB=1, NOADMIX=0, ADMBURNIN=2500, UPDATEFREQ=1, PRINTLIKES=0, INTERMEDSAVE=0, PRINTKLD=0, PRINTNET=0, PRINTLAMBDA=0, ANCESTDIST=0, NUMBOXES=1000, ANCESTPINT=0.90000, GENSBACK=2, MIGRPRIOR=0.05000, PRINTQHAT=0, PRINTQSUM=0, ALPHA=1.0000, FREQSCORR=1, FPRIORMEAN=0.0100, FPRIORSD=0.0500, ONEFST=0, LAMBDA=1.0000, UNIFPRIORALPHA=1, ALPHAMAX=10.0000, ALPHAPRIORA=1.0000, ALPHAPRIORB=2.0000, ALPHAPROPSD=0.0250, STARTATPOPINFO=0, RANDOMIZE=1, LINKAGE=0, METROFREQ=10, REPORTHITRATE=0, MARKOVPHASE=-1, PHASED=0, PLOIDY=2, PHASEINFO=0 LOCPRIOR=0, LOCPRIORINIT=1.000000, LOCDATA=0, LOCISPOP=0, LOCPRIORSTEP=0.100000, MAXLOCPRIOR=20.000000, SEED=1335124338, +[STRAT parameters]: NUMSIMSTATS=1000, PHENOTYPECOL=-9, POOLFREQ=10, LOCUSxONLY=0, EMERROR=0.00100, MISSINGPHENO=-9, \ No newline at end of file diff --git a/inst/files/structure/structure_09 b/inst/files/structure/structure_09 new file mode 100644 index 0000000..f147b95 --- /dev/null +++ b/inst/files/structure/structure_09 @@ -0,0 +1,529 @@ + + +---------------------------------------------------- +STRUCTURE by Pritchard, Stephens and Donnelly (2000) + and Falush, Stephens and Pritchard (2003) + Code by Pritchard, Falush and Hubisz + Version 2.3.2.1 (Oct 2009) +---------------------------------------------------- + + + +Command line arguments: +Input File: + +Run parameters: + 149 individuals + 25 loci + 2 populations assumed + 100000 Burn-in period + 1000000 Reps + + +-------------------------------------------- +Overall proportion of membership of the +sample in each of the 2 clusters + +Inferred Clusters + 1 2 +0.372 0.628 + +-------------------------------------------- + +Allele-freq. divergence among pops (Net nucleotide distance), +computed using point estimates of P. + + 1 2 + 1 - 0.0284 + 2 0.0284 - + +Average distances (expected heterozygosity) between individuals in same cluster: +cluster 1 : 0.4621 +cluster 2 : 0.5131 + +-------------------------------------------- +Estimated Ln Prob of Data = -7510.1 +Mean value of ln likelihood = -7387.4 +Variance of ln likelihood = 245.3 +Mean value of alpha = 0.1330 + +Mean value of Fst_1 = 0.0679 +Mean value of Fst_2 = 0.0723 + + +Inferred ancestry of individuals: + Label (%Miss) : Inferred clusters + 1 I13825 (0) : 0.037 0.963 + 2 I13826 (0) : 0.024 0.976 + 3 I13827 (20) : 0.040 0.960 + 4 I13828 (0) : 0.026 0.974 + 5 I13829 (8) : 0.027 0.973 + 6 I13830 (0) : 0.019 0.981 + 7 I13831 (0) : 0.026 0.974 + 8 I13832 (16) : 0.044 0.956 + 9 I13833 (0) : 0.030 0.970 + 10 I13834 (0) : 0.016 0.984 + 11 I13835 (0) : 0.022 0.978 + 12 I13836 (0) : 0.024 0.976 + 13 I13377 (0) : 0.057 0.943 + 14 I13378 (0) : 0.050 0.950 + 15 I13379 (0) : 0.030 0.970 + 16 I13380 (0) : 0.125 0.875 + 17 I13381 (0) : 0.094 0.906 + 18 I13382 (0) : 0.020 0.980 + 19 I13383 (0) : 0.060 0.940 + 20 I13384 (0) : 0.040 0.960 + 21 I13385 (0) : 0.017 0.983 + 22 I13386 (0) : 0.022 0.978 + 23 I13387 (0) : 0.036 0.964 + 24 I13388 (0) : 0.187 0.813 + 25 I13389 (0) : 0.114 0.886 + 26 I13390 (0) : 0.041 0.959 + 27 I13391 (0) : 0.130 0.870 + 28 I13392 (0) : 0.058 0.942 + 29 I13393 (0) : 0.407 0.593 + 30 I13394 (4) : 0.464 0.536 + 31 I13395 (0) : 0.349 0.651 + 32 I13396 (0) : 0.178 0.822 + 33 I13397 (0) : 0.024 0.976 + 34 I13398 (0) : 0.015 0.985 + 35 I13399 (4) : 0.070 0.930 + 36 I13400 (0) : 0.103 0.897 + 37 I13401 (0) : 0.457 0.543 + 38 I13402 (0) : 0.089 0.911 + 39 I13403 (0) : 0.089 0.911 + 40 I13404 (0) : 0.019 0.981 + 41 I13405 (0) : 0.029 0.971 + 42 I13406 (16) : 0.031 0.969 + 43 I13407 (0) : 0.024 0.976 + 44 I13408 (0) : 0.029 0.971 + 45 I13409 (0) : 0.136 0.864 + 46 I13410 (0) : 0.018 0.982 + 47 I13411 (0) : 0.013 0.987 + 48 I13412 (0) : 0.288 0.712 + 49 I13413 (0) : 0.063 0.937 + 50 I13414 (0) : 0.026 0.974 + 51 I13415 (4) : 0.062 0.938 + 52 I13416 (4) : 0.082 0.918 + 53 I13417 (4) : 0.104 0.896 + 54 I13418 (0) : 0.090 0.910 + 55 I13419 (0) : 0.025 0.975 + 56 I13420 (0) : 0.130 0.870 + 57 I13421 (0) : 0.175 0.825 + 58 I13422 (0) : 0.187 0.813 + 59 I13423 (0) : 0.186 0.814 + 60 I13424 (0) : 0.039 0.961 + 61 I13425 (4) : 0.061 0.939 + 62 I13426 (4) : 0.629 0.371 + 63 I13870 (0) : 0.163 0.837 + 64 I13871 (16) : 0.038 0.962 + 65 I13872 (0) : 0.027 0.973 + 66 I13873 (4) : 0.107 0.893 + 67 I13874 (0) : 0.125 0.875 + 68 I13875 (8) : 0.056 0.944 + 69 I13876 (0) : 0.316 0.684 + 70 I13877 (20) : 0.067 0.933 + 71 I13878 (28) : 0.022 0.978 + 72 I13879 (4) : 0.014 0.986 + 73 I13880 (4) : 0.021 0.979 + 74 I13881 (0) : 0.084 0.916 + 75 I13882 (0) : 0.028 0.972 + 76 I13883 (4) : 0.092 0.908 + 77 I13884 (16) : 0.103 0.897 + 78 I13885 (20) : 0.027 0.973 + 79 I13886 (8) : 0.018 0.982 + 80 I13887 (0) : 0.400 0.600 + 81 I13888 (0) : 0.091 0.909 + 82 I13889 (0) : 0.858 0.142 + 83 I13890 (32) : 0.676 0.324 + 84 I13891 (0) : 0.040 0.960 + 85 I13892 (0) : 0.510 0.490 + 86 I13893 (8) : 0.141 0.859 + 87 I13894 (0) : 0.036 0.964 + 88 I13895 (4) : 0.304 0.696 + 89 I13896 (0) : 0.163 0.837 + 90 I13897 (0) : 0.012 0.988 + 91 I13898 (4) : 0.034 0.966 + 92 I13899 (0) : 0.013 0.987 + 93 I13900 (32) : 0.154 0.846 + 94 I13837 (0) : 0.043 0.957 + 95 I13838 (0) : 0.768 0.232 + 96 I13839 (0) : 0.073 0.927 + 97 I13840 (0) : 0.092 0.908 + 98 I13841 (0) : 0.659 0.341 + 99 I13842 (0) : 0.325 0.675 +100 I13843 (4) : 0.725 0.275 +101 I13844 (16) : 0.157 0.843 +102 I13845 (0) : 0.026 0.974 +103 I13846 (0) : 0.061 0.939 +104 I13847 (0) : 0.355 0.645 +105 I13848 (0) : 0.430 0.570 +106 I13849 (0) : 0.100 0.900 +107 I13850 (0) : 0.562 0.438 +108 I12577 (4) : 0.969 0.031 +109 I12578 (4) : 0.939 0.061 +110 I12579 (8) : 0.975 0.025 +111 I12580 (8) : 0.967 0.033 +112 I12581 (4) : 0.723 0.277 +113 I12582 (4) : 0.962 0.038 +114 I12583 (8) : 0.903 0.097 +115 I12584 (4) : 0.944 0.056 +116 I12585 (4) : 0.980 0.020 +117 I12586 (4) : 0.973 0.027 +118 I12587 (8) : 0.978 0.022 +119 I12588 (4) : 0.982 0.018 +120 I12589 (0) : 0.956 0.044 +121 I12590 (0) : 0.947 0.053 +122 I12591 (12) : 0.988 0.012 +123 I12592 (4) : 0.970 0.030 +124 I12593 (4) : 0.982 0.018 +125 I12594 (8) : 0.980 0.020 +126 I12595 (0) : 0.972 0.028 +127 I12596 (0) : 0.983 0.017 +128 I12597 (4) : 0.930 0.070 +129 I12598 (0) : 0.895 0.105 +130 I12599 (0) : 0.907 0.093 +131 I12600 (4) : 0.963 0.037 +132 I12601 (8) : 0.974 0.026 +133 I12602 (12) : 0.972 0.028 +134 I12603 (0) : 0.969 0.031 +135 I12604 (4) : 0.949 0.051 +136 I12605 (4) : 0.965 0.035 +137 I12606 (8) : 0.979 0.021 +138 I12607 (4) : 0.971 0.029 +139 I12608 (8) : 0.961 0.039 +140 I12609 (8) : 0.976 0.024 +141 I12610 (52) : 0.962 0.038 +142 I12611 (0) : 0.981 0.019 +143 I12612 (0) : 0.977 0.023 +144 I12613 (0) : 0.982 0.018 +145 I12614 (4) : 0.944 0.056 +146 I12615 (0) : 0.925 0.075 +147 I12616 (4) : 0.936 0.064 +148 I12617 (8) : 0.984 0.016 +149 I12618 (48) : 0.978 0.022 + + +Estimated Allele Frequencies in each cluster +First column gives estimated ancestral frequencies + + +Locus 1 : A8 +7 alleles +4.0% missing data + 177 (0.477) 0.603 0.466 + 179 (0.110) 0.057 0.105 + 175 (0.075) 0.010 0.232 + 173 (0.052) 0.010 0.054 + 181 (0.196) 0.283 0.112 + 165 (0.056) 0.032 0.013 + 183 (0.036) 0.005 0.018 + +Locus 2 : A14 +5 alleles +0.0% missing data + 112 (0.133) 0.035 0.294 + 110 (0.724) 0.825 0.678 + 114 (0.037) 0.006 0.016 + 118 (0.066) 0.098 0.008 + 116 (0.040) 0.036 0.003 + +Locus 3 : A24 +5 alleles +2.7% missing data + 104 (0.364) 0.375 0.380 + 106 (0.529) 0.562 0.593 + 101 (0.029) 0.004 0.007 + 108 (0.036) 0.005 0.017 + 96 (0.043) 0.054 0.003 + +Locus 4 : A29 +29 alleles +6.7% missing data + 143 (0.027) 0.005 0.063 + 149 (0.043) 0.060 0.029 + 147 (0.035) 0.028 0.020 + 153 (0.055) 0.084 0.073 + 169 (0.043) 0.037 0.047 + 151 (0.045) 0.050 0.045 + 145 (0.034) 0.024 0.017 + 157 (0.060) 0.117 0.081 + 155 (0.067) 0.145 0.107 + 159 (0.049) 0.043 0.085 + 161 (0.031) 0.009 0.061 + 141 (0.032) 0.013 0.033 + 139 (0.020) 0.003 0.011 + 144 (0.025) 0.004 0.042 + 171 (0.044) 0.044 0.048 + 163 (0.054) 0.066 0.088 + 167 (0.044) 0.052 0.038 + 173 (0.030) 0.011 0.023 + 142 (0.018) 0.003 0.006 + 177 (0.031) 0.038 0.008 + 175 (0.027) 0.019 0.008 + 165 (0.041) 0.044 0.032 + 146 (0.022) 0.003 0.022 + 137 (0.025) 0.015 0.005 + 183 (0.020) 0.020 0.002 + 179 (0.020) 0.020 0.002 + 191 (0.018) 0.011 0.001 + 185 (0.018) 0.011 0.002 + 180 (0.020) 0.021 0.001 + +Locus 5 : A43 +7 alleles +1.3% missing data + 123 (0.161) 0.166 0.120 + 141 (0.028) 0.004 0.007 + 137 (0.630) 0.679 0.832 + 139 (0.084) 0.069 0.034 + 124 (0.043) 0.060 0.003 + 143 (0.028) 0.011 0.002 + 128 (0.027) 0.011 0.002 + +Locus 6 : A79 +13 alleles +3.4% missing data + 103 (0.184) 0.203 0.289 + 97 (0.100) 0.067 0.136 + 101 (0.093) 0.047 0.157 + 107 (0.104) 0.083 0.127 + 109 (0.092) 0.085 0.079 + 105 (0.177) 0.349 0.145 + 111 (0.055) 0.037 0.021 + 113 (0.025) 0.005 0.005 + 91 (0.039) 0.071 0.004 + 99 (0.048) 0.026 0.016 + 115 (0.035) 0.016 0.010 + 117 (0.025) 0.004 0.006 + 121 (0.025) 0.006 0.005 + +Locus 7 : A88 +9 alleles +6.0% missing data + 133 (0.028) 0.004 0.007 + 149 (0.515) 0.764 0.493 + 137 (0.076) 0.020 0.119 + 147 (0.169) 0.085 0.313 + 141 (0.098) 0.085 0.051 + 152 (0.028) 0.004 0.007 + 143 (0.028) 0.005 0.006 + 151 (0.028) 0.012 0.002 + 144 (0.032) 0.021 0.002 + +Locus 8 : A113 +12 alleles +7.4% missing data + 214 (0.488) 0.711 0.725 + 226 (0.077) 0.042 0.069 + 218 (0.026) 0.004 0.006 + 220 (0.084) 0.126 0.030 + 216 (0.062) 0.043 0.026 + 230 (0.044) 0.009 0.047 + 234 (0.035) 0.006 0.022 + 232 (0.038) 0.009 0.021 + 228 (0.054) 0.022 0.031 + 224 (0.026) 0.005 0.006 + 222 (0.041) 0.020 0.010 + 208 (0.026) 0.004 0.006 + +Locus 9 : Ac11 +9 alleles +4.7% missing data + 111 (0.110) 0.042 0.204 + 117 (0.249) 0.222 0.356 + 115 (0.240) 0.237 0.298 + 113 (0.164) 0.247 0.099 + 119 (0.087) 0.142 0.023 + 121 (0.044) 0.052 0.005 + 123 (0.040) 0.022 0.008 + 127 (0.039) 0.025 0.006 + 125 (0.027) 0.011 0.002 + +Locus 10 : Ac88 +8 alleles +0.7% missing data + 214 (0.709) 0.880 0.824 + 216 (0.034) 0.004 0.017 + 220 (0.102) 0.038 0.145 + 230 (0.037) 0.015 0.006 + 221 (0.027) 0.011 0.002 + 212 (0.031) 0.020 0.002 + 217 (0.028) 0.011 0.002 + 224 (0.031) 0.020 0.002 + +Locus 11 : Ac139 +8 alleles +13.4% missing data + 327 (0.527) 0.737 0.514 + 329 (0.225) 0.144 0.368 + 331 (0.076) 0.027 0.071 + 328 (0.046) 0.009 0.037 + 341 (0.029) 0.012 0.002 + 337 (0.040) 0.048 0.003 + 323 (0.029) 0.011 0.003 + 339 (0.029) 0.012 0.002 + +Locus 12 : Ac306 +6 alleles +4.7% missing data + 165 (0.674) 0.800 0.761 + 177 (0.106) 0.097 0.054 + 173 (0.102) 0.041 0.118 + 169 (0.050) 0.008 0.059 + 171 (0.028) 0.007 0.005 + 179 (0.040) 0.047 0.003 + +Locus 13 : Ap15 +7 alleles +6.0% missing data + 202 (0.755) 0.806 0.956 + 212 (0.035) 0.004 0.018 + 204 (0.052) 0.038 0.010 + 208 (0.047) 0.061 0.005 + 220 (0.054) 0.068 0.007 + 219 (0.028) 0.011 0.002 + 210 (0.029) 0.011 0.002 + +Locus 14 : Ap68 +9 alleles +4.7% missing data + 158 (0.302) 0.302 0.434 + 160 (0.083) 0.033 0.096 + 156 (0.272) 0.336 0.293 + 162 (0.051) 0.020 0.021 + 154 (0.075) 0.025 0.105 + 152 (0.106) 0.227 0.029 + 164 (0.053) 0.028 0.016 + 170 (0.027) 0.010 0.003 + 166 (0.030) 0.020 0.002 + +Locus 15 : Ap85 +10 alleles +3.4% missing data + 202 (0.324) 0.485 0.324 + 186 (0.205) 0.129 0.414 + 204 (0.069) 0.055 0.027 + 188 (0.088) 0.034 0.120 + 194 (0.076) 0.034 0.067 + 196 (0.068) 0.108 0.014 + 200 (0.068) 0.085 0.017 + 192 (0.037) 0.014 0.007 + 190 (0.026) 0.004 0.007 + 198 (0.038) 0.053 0.003 + +Locus 16 : Ap90 +13 alleles +0.7% missing data + 131 (0.348) 0.505 0.512 + 135 (0.084) 0.077 0.054 + 133 (0.199) 0.227 0.277 + 129 (0.103) 0.088 0.100 + 137 (0.047) 0.017 0.021 + 141 (0.025) 0.004 0.006 + 143 (0.028) 0.004 0.012 + 151 (0.036) 0.012 0.007 + 155 (0.025) 0.004 0.006 + 145 (0.025) 0.011 0.002 + 130 (0.028) 0.020 0.002 + 139 (0.025) 0.011 0.002 + 153 (0.028) 0.020 0.002 + +Locus 17 : Ap223 +7 alleles +2.0% missing data + 183 (0.654) 0.864 0.653 + 187 (0.106) 0.027 0.259 + 189 (0.035) 0.004 0.017 + 173 (0.082) 0.050 0.041 + 182 (0.038) 0.008 0.016 + 180 (0.038) 0.015 0.006 + 179 (0.047) 0.031 0.008 + +Locus 18 : Ap224 +7 alleles +4.0% missing data + 283 (0.094) 0.023 0.186 + 287 (0.424) 0.471 0.461 + 281 (0.130) 0.063 0.166 + 289 (0.244) 0.388 0.144 + 291 (0.042) 0.006 0.034 + 285 (0.028) 0.004 0.007 + 279 (0.039) 0.046 0.003 + +Locus 19 : Ap226 +5 alleles +17.4% missing data + 237 (0.349) 0.372 0.346 + 239 (0.486) 0.569 0.476 + 247 (0.102) 0.034 0.169 + 235 (0.031) 0.006 0.007 + 241 (0.031) 0.019 0.002 + +Locus 20 : Ap249 +9 alleles +1.3% missing data + 209 (0.553) 0.685 0.655 + 211 (0.052) 0.012 0.045 + 217 (0.087) 0.032 0.103 + 219 (0.093) 0.030 0.150 + 215 (0.106) 0.217 0.027 + 208 (0.027) 0.004 0.006 + 225 (0.027) 0.004 0.006 + 223 (0.027) 0.004 0.007 + 213 (0.027) 0.011 0.002 + +Locus 21 : Ap273 +4 alleles +1.3% missing data + 106 (0.851) 0.944 0.939 + 108 (0.065) 0.026 0.028 + 104 (0.041) 0.006 0.027 + 102 (0.043) 0.024 0.006 + +Locus 22 : Ap274 +2 alleles +2.0% missing data + 120 (0.926) 0.914 0.987 + 122 (0.074) 0.086 0.013 + +Locus 23 : Ap288 +5 alleles +0.0% missing data + 123 (0.753) 0.929 0.705 + 131 (0.155) 0.059 0.264 + 139 (0.036) 0.004 0.017 + 121 (0.029) 0.004 0.007 + 124 (0.029) 0.004 0.007 + +Locus 24 : At163 +7 alleles +0.0% missing data + 128 (0.694) 0.887 0.695 + 134 (0.162) 0.072 0.281 + 130 (0.033) 0.005 0.011 + 136 (0.028) 0.003 0.007 + 140 (0.028) 0.011 0.002 + 146 (0.028) 0.011 0.002 + 142 (0.028) 0.011 0.002 + +Locus 25 : At188 +13 alleles +1.3% missing data + 189 (0.558) 0.865 0.734 + 205 (0.036) 0.004 0.033 + 207 (0.040) 0.005 0.048 + 219 (0.030) 0.004 0.012 + 209 (0.040) 0.006 0.037 + 217 (0.038) 0.007 0.026 + 215 (0.029) 0.004 0.012 + 199 (0.076) 0.056 0.041 + 212 (0.034) 0.006 0.016 + 213 (0.038) 0.007 0.027 + 211 (0.025) 0.004 0.006 + 191 (0.025) 0.003 0.007 + 187 (0.032) 0.027 0.002 + +Values of parameters used in structure: +DATAFILE=, OUTFILE=, NUMINDS=149, NUMLOCI=25, MISSING=-9, LABEL=1, POPDATA=0, POPFLAG=1, PHENOTYPE=0, EXTRACOLS=1, MAXPOPS=2, BURNIN=100000, NUMREPS=1000000, USEPOPINFO=0, INFERALPHA=1, INFERLAMBDA=0, POPSPECIFICLAMBDA=0, POPALPHAS=0, COMPUTEPROB=1, NOADMIX=0, ADMBURNIN=2500, UPDATEFREQ=1, PRINTLIKES=0, INTERMEDSAVE=0, PRINTKLD=0, PRINTNET=0, PRINTLAMBDA=0, ANCESTDIST=0, NUMBOXES=1000, ANCESTPINT=0.90000, GENSBACK=2, MIGRPRIOR=0.05000, PRINTQHAT=0, PRINTQSUM=0, ALPHA=1.0000, FREQSCORR=1, FPRIORMEAN=0.0100, FPRIORSD=0.0500, ONEFST=0, LAMBDA=1.0000, UNIFPRIORALPHA=1, ALPHAMAX=10.0000, ALPHAPRIORA=1.0000, ALPHAPRIORB=2.0000, ALPHAPROPSD=0.0250, STARTATPOPINFO=0, RANDOMIZE=1, LINKAGE=0, METROFREQ=10, REPORTHITRATE=0, MARKOVPHASE=-1, PHASED=0, PLOIDY=2, PHASEINFO=0 LOCPRIOR=0, LOCPRIORINIT=1.000000, LOCDATA=0, LOCISPOP=0, LOCPRIORSTEP=0.100000, MAXLOCPRIOR=20.000000, SEED=1342785531, +[STRAT parameters]: NUMSIMSTATS=1000, PHENOTYPECOL=-9, POOLFREQ=10, LOCUSxONLY=0, EMERROR=0.00100, MISSINGPHENO=-9, \ No newline at end of file diff --git a/inst/files/structure/structure_10 b/inst/files/structure/structure_10 new file mode 100644 index 0000000..886e693 --- /dev/null +++ b/inst/files/structure/structure_10 @@ -0,0 +1,532 @@ + + +---------------------------------------------------- +STRUCTURE by Pritchard, Stephens and Donnelly (2000) + and Falush, Stephens and Pritchard (2003) + Code by Pritchard, Falush and Hubisz + Version 2.3.2.1 (Oct 2009) +---------------------------------------------------- + + + +Command line arguments: +Input File: + +Run parameters: + 149 individuals + 25 loci + 3 populations assumed + 100000 Burn-in period + 1000000 Reps + + +-------------------------------------------- +Overall proportion of membership of the +sample in each of the 3 clusters + +Inferred Clusters + 1 2 3 +0.313 0.343 0.344 + +-------------------------------------------- + +Allele-freq. divergence among pops (Net nucleotide distance), +computed using point estimates of P. + + 1 2 3 + 1 - 0.0138 0.0317 + 2 0.0138 - 0.0287 + 3 0.0317 0.0287 - + +Average distances (expected heterozygosity) between individuals in same cluster: +cluster 1 : 0.5387 +cluster 2 : 0.4831 +cluster 3 : 0.4572 + +-------------------------------------------- +Estimated Ln Prob of Data = -7476.5 +Mean value of ln likelihood = -7268.7 +Variance of ln likelihood = 415.4 +Mean value of alpha = 0.1212 + +Mean value of Fst_1 = 0.0528 +Mean value of Fst_2 = 0.0883 +Mean value of Fst_3 = 0.0719 + + +Inferred ancestry of individuals: + Label (%Miss) : Inferred clusters + 1 I13825 (0) : 0.908 0.068 0.024 + 2 I13826 (0) : 0.892 0.089 0.019 + 3 I13827 (20) : 0.042 0.933 0.025 + 4 I13828 (0) : 0.918 0.059 0.023 + 5 I13829 (8) : 0.101 0.877 0.022 + 6 I13830 (0) : 0.858 0.125 0.017 + 7 I13831 (0) : 0.242 0.732 0.027 + 8 I13832 (16) : 0.168 0.792 0.040 + 9 I13833 (0) : 0.077 0.895 0.029 + 10 I13834 (0) : 0.054 0.932 0.014 + 11 I13835 (0) : 0.372 0.609 0.019 + 12 I13836 (0) : 0.067 0.914 0.018 + 13 I13377 (0) : 0.071 0.871 0.058 + 14 I13378 (0) : 0.743 0.222 0.035 + 15 I13379 (0) : 0.441 0.529 0.030 + 16 I13380 (0) : 0.045 0.835 0.120 + 17 I13381 (0) : 0.186 0.740 0.074 + 18 I13382 (0) : 0.028 0.959 0.013 + 19 I13383 (0) : 0.390 0.555 0.055 + 20 I13384 (0) : 0.140 0.826 0.035 + 21 I13385 (0) : 0.046 0.940 0.014 + 22 I13386 (0) : 0.024 0.961 0.015 + 23 I13387 (0) : 0.767 0.207 0.026 + 24 I13388 (0) : 0.872 0.054 0.075 + 25 I13389 (0) : 0.096 0.813 0.091 + 26 I13390 (0) : 0.038 0.933 0.029 + 27 I13391 (0) : 0.378 0.500 0.122 + 28 I13392 (0) : 0.692 0.262 0.045 + 29 I13393 (0) : 0.036 0.772 0.192 + 30 I13394 (4) : 0.197 0.385 0.417 + 31 I13395 (0) : 0.315 0.329 0.355 + 32 I13396 (0) : 0.875 0.038 0.087 + 33 I13397 (0) : 0.681 0.299 0.020 + 34 I13398 (0) : 0.774 0.212 0.013 + 35 I13399 (4) : 0.208 0.741 0.051 + 36 I13400 (0) : 0.293 0.611 0.096 + 37 I13401 (0) : 0.134 0.470 0.396 + 38 I13402 (0) : 0.880 0.070 0.050 + 39 I13403 (0) : 0.719 0.181 0.100 + 40 I13404 (0) : 0.293 0.689 0.019 + 41 I13405 (0) : 0.020 0.961 0.019 + 42 I13406 (16) : 0.722 0.252 0.026 + 43 I13407 (0) : 0.723 0.255 0.022 + 44 I13408 (0) : 0.089 0.889 0.022 + 45 I13409 (0) : 0.832 0.095 0.073 + 46 I13410 (0) : 0.130 0.854 0.015 + 47 I13411 (0) : 0.113 0.875 0.012 + 48 I13412 (0) : 0.202 0.500 0.298 + 49 I13413 (0) : 0.830 0.121 0.048 + 50 I13414 (0) : 0.799 0.178 0.023 + 51 I13415 (4) : 0.198 0.741 0.061 + 52 I13416 (4) : 0.522 0.388 0.090 + 53 I13417 (4) : 0.119 0.781 0.099 + 54 I13418 (0) : 0.167 0.745 0.088 + 55 I13419 (0) : 0.323 0.654 0.022 + 56 I13420 (0) : 0.383 0.467 0.151 + 57 I13421 (0) : 0.069 0.781 0.150 + 58 I13422 (0) : 0.232 0.528 0.240 + 59 I13423 (0) : 0.507 0.352 0.141 + 60 I13424 (0) : 0.105 0.858 0.036 + 61 I13425 (4) : 0.265 0.677 0.058 + 62 I13426 (4) : 0.243 0.185 0.573 + 63 I13870 (0) : 0.548 0.279 0.173 + 64 I13871 (16) : 0.663 0.304 0.033 + 65 I13872 (0) : 0.936 0.045 0.019 + 66 I13873 (4) : 0.801 0.107 0.091 + 67 I13874 (0) : 0.842 0.091 0.067 + 68 I13875 (8) : 0.847 0.107 0.046 + 69 I13876 (0) : 0.597 0.163 0.240 + 70 I13877 (20) : 0.129 0.811 0.059 + 71 I13878 (28) : 0.528 0.449 0.023 + 72 I13879 (4) : 0.179 0.807 0.014 + 73 I13880 (4) : 0.949 0.037 0.014 + 74 I13881 (0) : 0.593 0.344 0.062 + 75 I13882 (0) : 0.860 0.113 0.027 + 76 I13883 (4) : 0.931 0.028 0.041 + 77 I13884 (16) : 0.721 0.221 0.057 + 78 I13885 (20) : 0.161 0.820 0.019 + 79 I13886 (8) : 0.677 0.305 0.018 + 80 I13887 (0) : 0.879 0.037 0.084 + 81 I13888 (0) : 0.708 0.233 0.060 + 82 I13889 (0) : 0.051 0.122 0.827 + 83 I13890 (32) : 0.191 0.199 0.610 + 84 I13891 (0) : 0.687 0.281 0.033 + 85 I13892 (0) : 0.132 0.482 0.386 + 86 I13893 (8) : 0.496 0.405 0.099 + 87 I13894 (0) : 0.966 0.016 0.017 + 88 I13895 (4) : 0.302 0.422 0.276 + 89 I13896 (0) : 0.789 0.075 0.135 + 90 I13897 (0) : 0.754 0.234 0.012 + 91 I13898 (4) : 0.774 0.192 0.034 + 92 I13899 (0) : 0.948 0.041 0.011 + 93 I13900 (32) : 0.813 0.109 0.079 + 94 I13837 (0) : 0.024 0.947 0.030 + 95 I13838 (0) : 0.150 0.093 0.757 + 96 I13839 (0) : 0.072 0.856 0.072 + 97 I13840 (0) : 0.206 0.683 0.110 + 98 I13841 (0) : 0.055 0.471 0.474 + 99 I13842 (0) : 0.028 0.770 0.202 +100 I13843 (4) : 0.105 0.252 0.643 +101 I13844 (16) : 0.131 0.744 0.124 +102 I13845 (0) : 0.071 0.911 0.018 +103 I13846 (0) : 0.045 0.921 0.033 +104 I13847 (0) : 0.384 0.206 0.410 +105 I13848 (0) : 0.381 0.236 0.382 +106 I13849 (0) : 0.890 0.045 0.065 +107 I13850 (0) : 0.272 0.218 0.510 +108 I12577 (4) : 0.031 0.031 0.939 +109 I12578 (4) : 0.052 0.034 0.914 +110 I12579 (8) : 0.018 0.041 0.941 +111 I12580 (8) : 0.023 0.034 0.943 +112 I12581 (4) : 0.148 0.250 0.602 +113 I12582 (4) : 0.036 0.029 0.935 +114 I12583 (8) : 0.105 0.119 0.776 +115 I12584 (4) : 0.112 0.031 0.857 +116 I12585 (4) : 0.020 0.017 0.962 +117 I12586 (4) : 0.027 0.024 0.949 +118 I12587 (8) : 0.018 0.024 0.958 +119 I12588 (4) : 0.018 0.019 0.963 +120 I12589 (0) : 0.042 0.033 0.925 +121 I12590 (0) : 0.051 0.044 0.905 +122 I12591 (12) : 0.011 0.011 0.977 +123 I12592 (4) : 0.025 0.030 0.946 +124 I12593 (4) : 0.025 0.013 0.962 +125 I12594 (8) : 0.020 0.018 0.963 +126 I12595 (0) : 0.026 0.038 0.936 +127 I12596 (0) : 0.016 0.019 0.965 +128 I12597 (4) : 0.094 0.053 0.852 +129 I12598 (0) : 0.065 0.090 0.845 +130 I12599 (0) : 0.113 0.035 0.852 +131 I12600 (4) : 0.036 0.026 0.937 +132 I12601 (8) : 0.026 0.024 0.949 +133 I12602 (12) : 0.026 0.025 0.950 +134 I12603 (0) : 0.032 0.033 0.936 +135 I12604 (4) : 0.056 0.030 0.914 +136 I12605 (4) : 0.065 0.021 0.914 +137 I12606 (8) : 0.021 0.019 0.961 +138 I12607 (4) : 0.056 0.021 0.923 +139 I12608 (8) : 0.047 0.031 0.922 +140 I12609 (8) : 0.031 0.022 0.948 +141 I12610 (52) : 0.028 0.045 0.927 +142 I12611 (0) : 0.020 0.015 0.965 +143 I12612 (0) : 0.022 0.019 0.959 +144 I12613 (0) : 0.013 0.021 0.965 +145 I12614 (4) : 0.029 0.081 0.890 +146 I12615 (0) : 0.056 0.060 0.883 +147 I12616 (4) : 0.033 0.078 0.889 +148 I12617 (8) : 0.019 0.011 0.970 +149 I12618 (48) : 0.021 0.022 0.957 + + +Estimated Allele Frequencies in each cluster +First column gives estimated ancestral frequencies + + +Locus 1 : A8 +7 alleles +4.0% missing data + 177 (0.483) 0.520 0.435 0.595 + 179 (0.106) 0.075 0.133 0.057 + 175 (0.114) 0.193 0.241 0.015 + 173 (0.051) 0.038 0.067 0.008 + 181 (0.173) 0.129 0.103 0.289 + 165 (0.044) 0.021 0.009 0.031 + 183 (0.029) 0.024 0.011 0.004 + +Locus 2 : A14 +5 alleles +0.0% missing data + 112 (0.187) 0.351 0.212 0.041 + 110 (0.705) 0.601 0.772 0.817 + 114 (0.031) 0.027 0.006 0.004 + 118 (0.047) 0.014 0.006 0.102 + 116 (0.030) 0.006 0.004 0.036 + +Locus 3 : A24 +5 alleles +2.7% missing data + 104 (0.386) 0.469 0.299 0.372 + 106 (0.532) 0.486 0.687 0.565 + 101 (0.022) 0.007 0.007 0.003 + 108 (0.029) 0.031 0.003 0.004 + 96 (0.031) 0.006 0.004 0.056 + +Locus 4 : A29 +29 alleles +6.7% missing data + 143 (0.038) 0.078 0.040 0.007 + 149 (0.044) 0.043 0.017 0.061 + 147 (0.033) 0.034 0.007 0.029 + 153 (0.055) 0.034 0.110 0.086 + 169 (0.040) 0.083 0.009 0.036 + 151 (0.036) 0.010 0.087 0.038 + 145 (0.030) 0.029 0.006 0.024 + 157 (0.069) 0.107 0.053 0.121 + 155 (0.082) 0.127 0.085 0.150 + 159 (0.057) 0.123 0.040 0.044 + 161 (0.033) 0.025 0.091 0.008 + 141 (0.030) 0.014 0.050 0.013 + 139 (0.016) 0.003 0.019 0.002 + 144 (0.025) 0.013 0.067 0.004 + 171 (0.041) 0.022 0.073 0.042 + 163 (0.064) 0.084 0.088 0.067 + 167 (0.046) 0.046 0.029 0.056 + 173 (0.025) 0.008 0.039 0.010 + 142 (0.016) 0.010 0.003 0.002 + 177 (0.028) 0.011 0.010 0.039 + 175 (0.024) 0.008 0.012 0.018 + 165 (0.041) 0.049 0.019 0.042 + 146 (0.022) 0.012 0.031 0.003 + 137 (0.022) 0.010 0.004 0.013 + 183 (0.017) 0.004 0.002 0.021 + 179 (0.018) 0.004 0.003 0.020 + 191 (0.015) 0.003 0.002 0.011 + 185 (0.015) 0.003 0.002 0.010 + 180 (0.017) 0.003 0.002 0.022 + +Locus 5 : A43 +7 alleles +1.3% missing data + 123 (0.157) 0.160 0.091 0.162 + 141 (0.021) 0.012 0.003 0.003 + 137 (0.688) 0.797 0.842 0.686 + 139 (0.061) 0.017 0.057 0.066 + 124 (0.031) 0.006 0.004 0.063 + 143 (0.021) 0.005 0.002 0.010 + 128 (0.021) 0.004 0.002 0.011 + +Locus 6 : A79 +13 alleles +3.4% missing data + 103 (0.218) 0.291 0.283 0.200 + 97 (0.113) 0.197 0.073 0.063 + 101 (0.096) 0.075 0.223 0.046 + 107 (0.099) 0.064 0.186 0.079 + 109 (0.096) 0.091 0.067 0.087 + 105 (0.176) 0.187 0.106 0.366 + 111 (0.047) 0.034 0.012 0.036 + 113 (0.019) 0.011 0.002 0.003 + 91 (0.030) 0.007 0.004 0.074 + 99 (0.038) 0.010 0.025 0.026 + 115 (0.029) 0.013 0.012 0.013 + 117 (0.020) 0.011 0.003 0.003 + 121 (0.020) 0.009 0.003 0.004 + +Locus 7 : A88 +9 alleles +6.0% missing data + 133 (0.021) 0.013 0.003 0.003 + 149 (0.519) 0.531 0.473 0.770 + 137 (0.091) 0.119 0.111 0.021 + 147 (0.195) 0.221 0.376 0.085 + 141 (0.085) 0.088 0.020 0.084 + 152 (0.021) 0.006 0.009 0.003 + 143 (0.022) 0.012 0.003 0.003 + 151 (0.021) 0.004 0.002 0.011 + 144 (0.025) 0.006 0.003 0.020 + +Locus 8 : A113 +12 alleles +7.4% missing data + 214 (0.550) 0.661 0.770 0.718 + 226 (0.077) 0.104 0.034 0.043 + 218 (0.021) 0.004 0.010 0.003 + 220 (0.065) 0.023 0.038 0.131 + 216 (0.056) 0.033 0.024 0.043 + 230 (0.041) 0.020 0.070 0.008 + 234 (0.032) 0.036 0.008 0.005 + 232 (0.038) 0.029 0.015 0.008 + 228 (0.048) 0.051 0.013 0.021 + 224 (0.021) 0.009 0.005 0.003 + 222 (0.032) 0.025 0.003 0.013 + 208 (0.020) 0.004 0.010 0.003 + +Locus 9 : Ac11 +9 alleles +4.7% missing data + 111 (0.138) 0.247 0.144 0.043 + 117 (0.274) 0.297 0.403 0.218 + 115 (0.255) 0.266 0.329 0.232 + 113 (0.152) 0.128 0.078 0.254 + 119 (0.063) 0.020 0.027 0.150 + 121 (0.033) 0.007 0.006 0.054 + 123 (0.034) 0.021 0.005 0.016 + 127 (0.030) 0.009 0.006 0.024 + 125 (0.021) 0.005 0.003 0.009 + +Locus 10 : Ac88 +8 alleles +0.7% missing data + 214 (0.731) 0.749 0.892 0.884 + 216 (0.032) 0.023 0.012 0.004 + 220 (0.117) 0.198 0.083 0.038 + 230 (0.029) 0.014 0.003 0.011 + 221 (0.021) 0.004 0.002 0.011 + 212 (0.024) 0.004 0.002 0.020 + 217 (0.021) 0.004 0.002 0.011 + 224 (0.024) 0.004 0.003 0.020 + +Locus 11 : Ac139 +8 alleles +13.4% missing data + 327 (0.516) 0.477 0.558 0.743 + 329 (0.268) 0.377 0.342 0.141 + 331 (0.078) 0.103 0.037 0.027 + 328 (0.040) 0.021 0.051 0.006 + 341 (0.023) 0.005 0.003 0.011 + 337 (0.030) 0.006 0.004 0.050 + 323 (0.023) 0.005 0.003 0.010 + 339 (0.023) 0.005 0.003 0.011 + +Locus 12 : Ac306 +6 alleles +4.7% missing data + 165 (0.697) 0.719 0.793 0.809 + 177 (0.098) 0.072 0.049 0.091 + 173 (0.109) 0.169 0.062 0.041 + 169 (0.045) 0.022 0.091 0.007 + 171 (0.022) 0.012 0.002 0.003 + 179 (0.029) 0.006 0.003 0.049 + +Locus 13 : Ap15 +7 alleles +6.0% missing data + 202 (0.810) 0.920 0.970 0.808 + 212 (0.028) 0.033 0.003 0.003 + 204 (0.042) 0.015 0.010 0.037 + 208 (0.035) 0.008 0.007 0.063 + 220 (0.041) 0.015 0.005 0.069 + 219 (0.022) 0.004 0.003 0.011 + 210 (0.022) 0.005 0.003 0.010 + +Locus 14 : Ap68 +9 alleles +4.7% missing data + 158 (0.361) 0.569 0.287 0.303 + 160 (0.081) 0.052 0.136 0.031 + 156 (0.266) 0.202 0.381 0.341 + 162 (0.041) 0.041 0.007 0.014 + 154 (0.081) 0.070 0.133 0.024 + 152 (0.080) 0.025 0.042 0.235 + 164 (0.044) 0.030 0.007 0.025 + 170 (0.021) 0.005 0.004 0.008 + 166 (0.024) 0.004 0.003 0.020 + +Locus 15 : Ap85 +10 alleles +3.4% missing data + 202 (0.334) 0.380 0.281 0.490 + 186 (0.245) 0.319 0.470 0.129 + 204 (0.061) 0.033 0.026 0.054 + 188 (0.095) 0.102 0.131 0.033 + 194 (0.079) 0.079 0.055 0.034 + 196 (0.054) 0.021 0.014 0.110 + 200 (0.056) 0.037 0.010 0.082 + 192 (0.028) 0.014 0.005 0.011 + 190 (0.021) 0.010 0.004 0.003 + 198 (0.028) 0.005 0.003 0.056 + +Locus 16 : Ap90 +13 alleles +0.7% missing data + 131 (0.388) 0.468 0.534 0.518 + 135 (0.081) 0.077 0.034 0.079 + 133 (0.223) 0.316 0.236 0.222 + 129 (0.096) 0.060 0.140 0.084 + 137 (0.038) 0.011 0.031 0.017 + 141 (0.020) 0.011 0.003 0.003 + 143 (0.025) 0.016 0.008 0.003 + 151 (0.028) 0.015 0.003 0.010 + 155 (0.020) 0.011 0.003 0.003 + 145 (0.020) 0.004 0.002 0.011 + 130 (0.022) 0.004 0.002 0.020 + 139 (0.020) 0.003 0.002 0.011 + 153 (0.022) 0.004 0.002 0.020 + +Locus 17 : Ap223 +7 alleles +2.0% missing data + 183 (0.655) 0.645 0.676 0.867 + 187 (0.146) 0.241 0.249 0.031 + 189 (0.027) 0.007 0.027 0.003 + 173 (0.073) 0.062 0.023 0.050 + 182 (0.032) 0.017 0.016 0.006 + 180 (0.029) 0.011 0.005 0.013 + 179 (0.038) 0.017 0.004 0.029 + +Locus 18 : Ap224 +7 alleles +4.0% missing data + 283 (0.120) 0.175 0.178 0.027 + 287 (0.440) 0.488 0.443 0.464 + 281 (0.139) 0.141 0.183 0.062 + 289 (0.207) 0.130 0.171 0.391 + 291 (0.043) 0.052 0.016 0.006 + 285 (0.022) 0.008 0.007 0.003 + 279 (0.029) 0.005 0.003 0.047 + +Locus 19 : Ap226 +5 alleles +17.4% missing data + 237 (0.347) 0.345 0.356 0.359 + 239 (0.478) 0.473 0.478 0.577 + 247 (0.128) 0.172 0.153 0.042 + 235 (0.023) 0.005 0.010 0.005 + 241 (0.023) 0.004 0.003 0.018 + +Locus 20 : Ap249 +9 alleles +1.3% missing data + 209 (0.582) 0.614 0.692 0.688 + 211 (0.053) 0.038 0.053 0.010 + 217 (0.097) 0.118 0.084 0.032 + 219 (0.110) 0.180 0.112 0.028 + 215 (0.075) 0.020 0.041 0.223 + 208 (0.021) 0.012 0.002 0.003 + 225 (0.021) 0.009 0.005 0.003 + 223 (0.021) 0.005 0.009 0.003 + 213 (0.021) 0.004 0.002 0.010 + +Locus 21 : Ap273 +4 alleles +1.3% missing data + 106 (0.869) 0.927 0.944 0.946 + 108 (0.057) 0.037 0.022 0.025 + 104 (0.039) 0.024 0.030 0.005 + 102 (0.034) 0.013 0.004 0.023 + +Locus 22 : Ap274 +2 alleles +2.0% missing data + 120 (0.944) 0.976 0.991 0.914 + 122 (0.056) 0.024 0.009 0.086 + +Locus 23 : Ap288 +5 alleles +0.0% missing data + 123 (0.737) 0.680 0.749 0.928 + 131 (0.190) 0.270 0.237 0.063 + 139 (0.030) 0.028 0.006 0.004 + 121 (0.022) 0.011 0.003 0.003 + 124 (0.022) 0.010 0.004 0.003 + +Locus 24 : At163 +7 alleles +0.0% missing data + 128 (0.684) 0.604 0.790 0.892 + 134 (0.204) 0.356 0.188 0.073 + 130 (0.026) 0.020 0.004 0.004 + 136 (0.022) 0.005 0.009 0.003 + 140 (0.022) 0.005 0.003 0.009 + 146 (0.021) 0.005 0.003 0.009 + 142 (0.022) 0.004 0.003 0.010 + +Locus 25 : At188 +13 alleles +1.3% missing data + 189 (0.615) 0.711 0.752 0.877 + 205 (0.031) 0.058 0.005 0.004 + 207 (0.036) 0.015 0.076 0.004 + 219 (0.027) 0.015 0.010 0.004 + 209 (0.036) 0.015 0.057 0.005 + 217 (0.037) 0.032 0.022 0.005 + 215 (0.023) 0.006 0.018 0.003 + 199 (0.068) 0.068 0.018 0.055 + 212 (0.029) 0.019 0.013 0.005 + 213 (0.035) 0.042 0.013 0.005 + 211 (0.020) 0.010 0.004 0.003 + 191 (0.020) 0.004 0.010 0.002 + 187 (0.024) 0.004 0.003 0.028 + +Values of parameters used in structure: +DATAFILE=, OUTFILE=, NUMINDS=149, NUMLOCI=25, MISSING=-9, LABEL=1, POPDATA=0, POPFLAG=1, PHENOTYPE=0, EXTRACOLS=1, MAXPOPS=3, BURNIN=100000, NUMREPS=1000000, USEPOPINFO=0, INFERALPHA=1, INFERLAMBDA=0, POPSPECIFICLAMBDA=0, POPALPHAS=0, COMPUTEPROB=1, NOADMIX=0, ADMBURNIN=2500, UPDATEFREQ=1, PRINTLIKES=0, INTERMEDSAVE=0, PRINTKLD=0, PRINTNET=0, PRINTLAMBDA=0, ANCESTDIST=0, NUMBOXES=1000, ANCESTPINT=0.90000, GENSBACK=2, MIGRPRIOR=0.05000, PRINTQHAT=0, PRINTQSUM=0, ALPHA=1.0000, FREQSCORR=1, FPRIORMEAN=0.0100, FPRIORSD=0.0500, ONEFST=0, LAMBDA=1.0000, UNIFPRIORALPHA=1, ALPHAMAX=10.0000, ALPHAPRIORA=1.0000, ALPHAPRIORB=2.0000, ALPHAPROPSD=0.0250, STARTATPOPINFO=0, RANDOMIZE=1, LINKAGE=0, METROFREQ=10, REPORTHITRATE=0, MARKOVPHASE=-1, PHASED=0, PLOIDY=2, PHASEINFO=0 LOCPRIOR=0, LOCPRIORINIT=1.000000, LOCDATA=0, LOCISPOP=0, LOCPRIORSTEP=0.100000, MAXLOCPRIOR=20.000000, SEED=1342787006, +[STRAT parameters]: NUMSIMSTATS=1000, PHENOTYPECOL=-9, POOLFREQ=10, LOCUSxONLY=0, EMERROR=0.00100, MISSINGPHENO=-9, \ No newline at end of file diff --git a/inst/files/structure/structure_11 b/inst/files/structure/structure_11 new file mode 100644 index 0000000..2f8b97b --- /dev/null +++ b/inst/files/structure/structure_11 @@ -0,0 +1,535 @@ + + +---------------------------------------------------- +STRUCTURE by Pritchard, Stephens and Donnelly (2000) + and Falush, Stephens and Pritchard (2003) + Code by Pritchard, Falush and Hubisz + Version 2.3.2.1 (Oct 2009) +---------------------------------------------------- + + + +Command line arguments: +Input File: + +Run parameters: + 149 individuals + 25 loci + 4 populations assumed + 100000 Burn-in period + 1000000 Reps + + +-------------------------------------------- +Overall proportion of membership of the +sample in each of the 4 clusters + +Inferred Clusters + 1 2 3 4 +0.296 0.244 0.271 0.188 + +-------------------------------------------- + +Allele-freq. divergence among pops (Net nucleotide distance), +computed using point estimates of P. + + 1 2 3 4 + 1 - 0.0525 0.0402 0.0252 + 2 0.0525 - 0.0246 0.0154 + 3 0.0402 0.0246 - 0.0168 + 4 0.0252 0.0154 0.0168 - + +Average distances (expected heterozygosity) between individuals in same cluster: +cluster 1 : 0.4245 +cluster 2 : 0.5175 +cluster 3 : 0.4592 +cluster 4 : 0.5785 + +-------------------------------------------- +Estimated Ln Prob of Data = -7599.0 +Mean value of ln likelihood = -7264.7 +Variance of ln likelihood = 668.7 +Mean value of alpha = 0.2225 + +Mean value of Fst_1 = 0.1200 +Mean value of Fst_2 = 0.1119 +Mean value of Fst_3 = 0.1311 +Mean value of Fst_4 = 0.0004 + + +Inferred ancestry of individuals: + Label (%Miss) : Inferred clusters + 1 I13825 (0) : 0.035 0.387 0.091 0.487 + 2 I13826 (0) : 0.036 0.824 0.071 0.069 + 3 I13827 (20) : 0.039 0.079 0.811 0.071 + 4 I13828 (0) : 0.036 0.716 0.084 0.165 + 5 I13829 (8) : 0.034 0.155 0.739 0.071 + 6 I13830 (0) : 0.031 0.830 0.081 0.058 + 7 I13831 (0) : 0.050 0.290 0.577 0.082 + 8 I13832 (16) : 0.052 0.113 0.581 0.253 + 9 I13833 (0) : 0.050 0.107 0.794 0.049 + 10 I13834 (0) : 0.024 0.133 0.807 0.036 + 11 I13835 (0) : 0.024 0.117 0.459 0.400 + 12 I13836 (0) : 0.029 0.121 0.706 0.144 + 13 I13377 (0) : 0.065 0.053 0.771 0.112 + 14 I13378 (0) : 0.040 0.202 0.216 0.541 + 15 I13379 (0) : 0.052 0.541 0.327 0.079 + 16 I13380 (0) : 0.145 0.044 0.740 0.071 + 17 I13381 (0) : 0.087 0.096 0.428 0.388 + 18 I13382 (0) : 0.028 0.065 0.872 0.035 + 19 I13383 (0) : 0.053 0.168 0.345 0.434 + 20 I13384 (0) : 0.055 0.315 0.521 0.109 + 21 I13385 (0) : 0.023 0.071 0.861 0.046 + 22 I13386 (0) : 0.030 0.059 0.843 0.068 + 23 I13387 (0) : 0.038 0.571 0.208 0.184 + 24 I13388 (0) : 0.071 0.435 0.057 0.437 + 25 I13389 (0) : 0.130 0.102 0.704 0.064 + 26 I13390 (0) : 0.052 0.114 0.783 0.050 + 27 I13391 (0) : 0.126 0.136 0.314 0.424 + 28 I13392 (0) : 0.058 0.261 0.245 0.436 + 29 I13393 (0) : 0.179 0.040 0.643 0.138 + 30 I13394 (4) : 0.381 0.122 0.239 0.258 + 31 I13395 (0) : 0.357 0.184 0.272 0.186 + 32 I13396 (0) : 0.143 0.578 0.048 0.231 + 33 I13397 (0) : 0.035 0.335 0.239 0.391 + 34 I13398 (0) : 0.023 0.738 0.198 0.041 + 35 I13399 (4) : 0.045 0.092 0.349 0.515 + 36 I13400 (0) : 0.101 0.166 0.495 0.237 + 37 I13401 (0) : 0.297 0.092 0.386 0.225 + 38 I13402 (0) : 0.068 0.383 0.113 0.436 + 39 I13403 (0) : 0.153 0.653 0.139 0.055 + 40 I13404 (0) : 0.030 0.493 0.423 0.054 + 41 I13405 (0) : 0.033 0.039 0.891 0.036 + 42 I13406 (16) : 0.038 0.475 0.113 0.375 + 43 I13407 (0) : 0.040 0.577 0.257 0.127 + 44 I13408 (0) : 0.032 0.132 0.775 0.061 + 45 I13409 (0) : 0.069 0.422 0.075 0.434 + 46 I13410 (0) : 0.024 0.257 0.641 0.077 + 47 I13411 (0) : 0.019 0.234 0.695 0.052 + 48 I13412 (0) : 0.271 0.286 0.298 0.144 + 49 I13413 (0) : 0.073 0.581 0.080 0.266 + 50 I13414 (0) : 0.036 0.680 0.123 0.160 + 51 I13415 (4) : 0.085 0.219 0.622 0.074 + 52 I13416 (4) : 0.143 0.490 0.252 0.116 + 53 I13417 (4) : 0.153 0.183 0.608 0.056 + 54 I13418 (0) : 0.150 0.323 0.446 0.080 + 55 I13419 (0) : 0.030 0.164 0.359 0.447 + 56 I13420 (0) : 0.221 0.523 0.194 0.062 + 57 I13421 (0) : 0.266 0.108 0.572 0.054 + 58 I13422 (0) : 0.255 0.276 0.361 0.108 + 59 I13423 (0) : 0.099 0.184 0.296 0.421 + 60 I13424 (0) : 0.060 0.110 0.703 0.126 + 61 I13425 (4) : 0.091 0.213 0.560 0.136 + 62 I13426 (4) : 0.414 0.160 0.154 0.271 + 63 I13870 (0) : 0.220 0.543 0.148 0.088 + 64 I13871 (16) : 0.051 0.547 0.188 0.214 + 65 I13872 (0) : 0.025 0.767 0.046 0.162 + 66 I13873 (4) : 0.124 0.657 0.093 0.125 + 67 I13874 (0) : 0.068 0.541 0.078 0.313 + 68 I13875 (8) : 0.081 0.719 0.100 0.100 + 69 I13876 (0) : 0.117 0.216 0.079 0.587 + 70 I13877 (20) : 0.100 0.182 0.591 0.127 + 71 I13878 (28) : 0.037 0.593 0.308 0.061 + 72 I13879 (4) : 0.021 0.330 0.601 0.048 + 73 I13880 (4) : 0.027 0.879 0.040 0.054 + 74 I13881 (0) : 0.085 0.344 0.151 0.419 + 75 I13882 (0) : 0.050 0.712 0.130 0.108 + 76 I13883 (4) : 0.077 0.737 0.038 0.148 + 77 I13884 (16) : 0.043 0.150 0.127 0.680 + 78 I13885 (20) : 0.026 0.109 0.470 0.395 + 79 I13886 (8) : 0.033 0.546 0.303 0.118 + 80 I13887 (0) : 0.069 0.133 0.032 0.766 + 81 I13888 (0) : 0.057 0.365 0.126 0.452 + 82 I13889 (0) : 0.650 0.058 0.148 0.144 + 83 I13890 (32) : 0.419 0.152 0.198 0.231 + 84 I13891 (0) : 0.046 0.656 0.181 0.117 + 85 I13892 (0) : 0.364 0.154 0.367 0.116 + 86 I13893 (8) : 0.046 0.093 0.191 0.670 + 87 I13894 (0) : 0.037 0.868 0.027 0.068 + 88 I13895 (4) : 0.131 0.170 0.316 0.382 + 89 I13896 (0) : 0.218 0.593 0.062 0.127 + 90 I13897 (0) : 0.019 0.685 0.248 0.048 + 91 I13898 (4) : 0.066 0.691 0.160 0.083 + 92 I13899 (0) : 0.018 0.908 0.041 0.034 + 93 I13900 (32) : 0.087 0.272 0.097 0.544 + 94 I13837 (0) : 0.058 0.049 0.846 0.047 + 95 I13838 (0) : 0.608 0.201 0.082 0.109 + 96 I13839 (0) : 0.129 0.111 0.681 0.079 + 97 I13840 (0) : 0.199 0.234 0.514 0.054 + 98 I13841 (0) : 0.478 0.079 0.371 0.072 + 99 I13842 (0) : 0.283 0.032 0.632 0.053 +100 I13843 (4) : 0.585 0.144 0.181 0.089 +101 I13844 (16) : 0.135 0.097 0.566 0.203 +102 I13845 (0) : 0.031 0.111 0.791 0.067 +103 I13846 (0) : 0.055 0.078 0.744 0.123 +104 I13847 (0) : 0.358 0.350 0.133 0.159 +105 I13848 (0) : 0.264 0.270 0.170 0.296 +106 I13849 (0) : 0.106 0.603 0.057 0.234 +107 I13850 (0) : 0.517 0.145 0.190 0.147 +108 I12577 (4) : 0.807 0.037 0.045 0.112 +109 I12578 (4) : 0.753 0.069 0.048 0.130 +110 I12579 (8) : 0.675 0.025 0.071 0.229 +111 I12580 (8) : 0.865 0.038 0.058 0.039 +112 I12581 (4) : 0.226 0.053 0.220 0.501 +113 I12582 (4) : 0.830 0.058 0.039 0.074 +114 I12583 (8) : 0.278 0.049 0.090 0.583 +115 I12584 (4) : 0.577 0.062 0.035 0.326 +116 I12585 (4) : 0.874 0.035 0.026 0.065 +117 I12586 (4) : 0.865 0.045 0.035 0.055 +118 I12587 (8) : 0.906 0.028 0.037 0.029 +119 I12588 (4) : 0.826 0.022 0.032 0.119 +120 I12589 (0) : 0.805 0.069 0.046 0.080 +121 I12590 (0) : 0.674 0.071 0.071 0.184 +122 I12591 (12) : 0.919 0.017 0.019 0.044 +123 I12592 (4) : 0.778 0.047 0.054 0.122 +124 I12593 (4) : 0.852 0.042 0.022 0.084 +125 I12594 (8) : 0.892 0.033 0.030 0.045 +126 I12595 (0) : 0.560 0.025 0.048 0.367 +127 I12596 (0) : 0.890 0.020 0.031 0.059 +128 I12597 (4) : 0.406 0.035 0.052 0.508 +129 I12598 (0) : 0.517 0.051 0.062 0.371 +130 I12599 (0) : 0.577 0.151 0.044 0.228 +131 I12600 (4) : 0.843 0.070 0.039 0.048 +132 I12601 (8) : 0.825 0.038 0.032 0.105 +133 I12602 (12) : 0.819 0.041 0.044 0.097 +134 I12603 (0) : 0.642 0.043 0.047 0.268 +135 I12604 (4) : 0.749 0.089 0.039 0.123 +136 I12605 (4) : 0.781 0.062 0.034 0.123 +137 I12606 (8) : 0.847 0.025 0.031 0.097 +138 I12607 (4) : 0.594 0.045 0.030 0.330 +139 I12608 (8) : 0.672 0.054 0.051 0.223 +140 I12609 (8) : 0.871 0.031 0.035 0.062 +141 I12610 (52) : 0.762 0.044 0.079 0.114 +142 I12611 (0) : 0.889 0.037 0.025 0.048 +143 I12612 (0) : 0.866 0.034 0.032 0.068 +144 I12613 (0) : 0.884 0.020 0.042 0.054 +145 I12614 (4) : 0.756 0.056 0.112 0.076 +146 I12615 (0) : 0.641 0.070 0.089 0.200 +147 I12616 (4) : 0.499 0.034 0.087 0.380 +148 I12617 (8) : 0.920 0.031 0.018 0.031 +149 I12618 (48) : 0.833 0.031 0.035 0.100 + + +Estimated Allele Frequencies in each cluster +First column gives estimated ancestral frequencies + + +Locus 1 : A8 +7 alleles +4.0% missing data + 177 (0.519) 0.595 0.488 0.445 0.520 + 179 (0.092) 0.054 0.076 0.141 0.092 + 175 (0.098) 0.010 0.257 0.246 0.098 + 173 (0.045) 0.005 0.024 0.083 0.045 + 181 (0.174) 0.306 0.128 0.073 0.174 + 165 (0.041) 0.026 0.014 0.006 0.041 + 183 (0.031) 0.003 0.013 0.007 0.031 + +Locus 2 : A14 +5 alleles +0.0% missing data + 112 (0.206) 0.029 0.392 0.200 0.207 + 110 (0.699) 0.822 0.580 0.788 0.699 + 114 (0.032) 0.004 0.015 0.005 0.032 + 118 (0.035) 0.113 0.008 0.004 0.034 + 116 (0.028) 0.033 0.004 0.003 0.028 + +Locus 3 : A24 +5 alleles +2.7% missing data + 104 (0.419) 0.368 0.467 0.272 0.420 + 106 (0.509) 0.567 0.502 0.718 0.509 + 101 (0.017) 0.002 0.003 0.004 0.017 + 108 (0.028) 0.003 0.025 0.003 0.028 + 96 (0.027) 0.060 0.003 0.003 0.026 + +Locus 4 : A29 +29 alleles +6.7% missing data + 143 (0.033) 0.005 0.102 0.035 0.033 + 149 (0.053) 0.055 0.023 0.019 0.054 + 147 (0.028) 0.032 0.034 0.004 0.028 + 153 (0.057) 0.088 0.026 0.129 0.057 + 169 (0.035) 0.031 0.104 0.006 0.035 + 151 (0.036) 0.025 0.007 0.109 0.036 + 145 (0.028) 0.027 0.026 0.005 0.028 + 157 (0.065) 0.148 0.128 0.033 0.065 + 155 (0.098) 0.185 0.117 0.070 0.098 + 159 (0.050) 0.045 0.161 0.025 0.050 + 161 (0.033) 0.006 0.013 0.110 0.033 + 141 (0.028) 0.007 0.010 0.058 0.028 + 139 (0.015) 0.002 0.003 0.019 0.015 + 144 (0.022) 0.003 0.011 0.081 0.021 + 171 (0.052) 0.032 0.023 0.070 0.053 + 163 (0.080) 0.059 0.071 0.099 0.081 + 167 (0.046) 0.067 0.038 0.019 0.046 + 173 (0.024) 0.005 0.012 0.038 0.024 + 142 (0.013) 0.002 0.007 0.002 0.013 + 177 (0.023) 0.047 0.004 0.006 0.023 + 175 (0.023) 0.017 0.004 0.006 0.023 + 165 (0.043) 0.041 0.048 0.014 0.043 + 146 (0.020) 0.002 0.014 0.030 0.020 + 137 (0.019) 0.011 0.003 0.002 0.019 + 183 (0.017) 0.016 0.003 0.002 0.016 + 179 (0.018) 0.013 0.003 0.003 0.017 + 191 (0.013) 0.005 0.002 0.001 0.013 + 185 (0.013) 0.004 0.002 0.001 0.013 + 180 (0.015) 0.022 0.002 0.001 0.015 + +Locus 5 : A43 +7 alleles +1.3% missing data + 123 (0.222) 0.154 0.088 0.083 0.224 + 141 (0.017) 0.001 0.004 0.002 0.017 + 137 (0.648) 0.688 0.886 0.863 0.647 + 139 (0.050) 0.081 0.014 0.046 0.049 + 124 (0.030) 0.064 0.004 0.003 0.030 + 143 (0.017) 0.004 0.002 0.002 0.017 + 128 (0.017) 0.008 0.002 0.002 0.017 + +Locus 6 : A79 +13 alleles +3.4% missing data + 103 (0.238) 0.175 0.312 0.305 0.239 + 97 (0.129) 0.054 0.211 0.059 0.130 + 101 (0.091) 0.033 0.063 0.269 0.091 + 107 (0.098) 0.074 0.075 0.193 0.098 + 109 (0.101) 0.087 0.076 0.068 0.101 + 105 (0.158) 0.426 0.206 0.061 0.158 + 111 (0.051) 0.028 0.025 0.009 0.051 + 113 (0.016) 0.002 0.005 0.001 0.016 + 91 (0.025) 0.083 0.003 0.003 0.024 + 99 (0.032) 0.026 0.010 0.022 0.032 + 115 (0.028) 0.009 0.007 0.008 0.028 + 117 (0.016) 0.002 0.006 0.002 0.016 + 121 (0.016) 0.002 0.003 0.002 0.016 + +Locus 7 : A88 +9 alleles +6.0% missing data + 133 (0.018) 0.002 0.004 0.002 0.018 + 149 (0.521) 0.817 0.537 0.453 0.521 + 137 (0.101) 0.014 0.139 0.093 0.101 + 147 (0.205) 0.061 0.227 0.427 0.205 + 141 (0.079) 0.088 0.080 0.016 0.079 + 152 (0.017) 0.002 0.002 0.003 0.017 + 143 (0.017) 0.002 0.004 0.002 0.017 + 151 (0.017) 0.006 0.002 0.002 0.017 + 144 (0.025) 0.009 0.004 0.002 0.025 + +Locus 8 : A113 +12 alleles +7.4% missing data + 214 (0.588) 0.748 0.677 0.809 0.589 + 226 (0.057) 0.028 0.144 0.017 0.057 + 218 (0.017) 0.002 0.003 0.009 0.017 + 220 (0.061) 0.143 0.016 0.030 0.060 + 216 (0.058) 0.035 0.019 0.021 0.058 + 230 (0.041) 0.005 0.015 0.076 0.040 + 234 (0.031) 0.004 0.031 0.007 0.031 + 232 (0.030) 0.005 0.032 0.010 0.030 + 228 (0.052) 0.015 0.041 0.008 0.052 + 224 (0.017) 0.002 0.004 0.002 0.017 + 222 (0.031) 0.010 0.015 0.003 0.031 + 208 (0.016) 0.002 0.003 0.007 0.016 + +Locus 9 : Ac11 +9 alleles +4.7% missing data + 111 (0.127) 0.030 0.309 0.127 0.127 + 117 (0.308) 0.193 0.282 0.445 0.308 + 115 (0.250) 0.236 0.277 0.338 0.250 + 113 (0.162) 0.274 0.102 0.065 0.163 + 119 (0.047) 0.179 0.012 0.013 0.046 + 121 (0.025) 0.061 0.004 0.003 0.025 + 123 (0.032) 0.012 0.006 0.003 0.032 + 127 (0.031) 0.012 0.006 0.005 0.031 + 125 (0.017) 0.002 0.002 0.002 0.017 + +Locus 10 : Ac88 +8 alleles +0.7% missing data + 214 (0.755) 0.926 0.724 0.927 0.755 + 216 (0.029) 0.003 0.020 0.006 0.029 + 220 (0.115) 0.026 0.242 0.057 0.115 + 230 (0.025) 0.004 0.006 0.002 0.025 + 221 (0.017) 0.007 0.002 0.002 0.017 + 212 (0.020) 0.019 0.002 0.002 0.020 + 217 (0.017) 0.004 0.002 0.002 0.017 + 224 (0.023) 0.011 0.003 0.002 0.022 + +Locus 11 : Ac139 +8 alleles +13.4% missing data + 327 (0.498) 0.808 0.425 0.588 0.498 + 329 (0.297) 0.100 0.441 0.326 0.298 + 331 (0.073) 0.018 0.110 0.031 0.073 + 328 (0.047) 0.005 0.012 0.045 0.047 + 341 (0.019) 0.008 0.003 0.002 0.019 + 337 (0.028) 0.051 0.004 0.003 0.027 + 323 (0.019) 0.004 0.003 0.002 0.019 + 339 (0.019) 0.006 0.003 0.002 0.019 + +Locus 12 : Ac306 +6 alleles +4.7% missing data + 165 (0.740) 0.808 0.703 0.821 0.741 + 177 (0.078) 0.105 0.065 0.036 0.078 + 173 (0.095) 0.031 0.211 0.036 0.095 + 169 (0.043) 0.005 0.014 0.103 0.043 + 171 (0.018) 0.002 0.003 0.002 0.018 + 179 (0.026) 0.050 0.003 0.003 0.026 + +Locus 13 : Ap15 +7 alleles +6.0% missing data + 202 (0.813) 0.833 0.946 0.974 0.814 + 212 (0.028) 0.003 0.027 0.003 0.028 + 204 (0.043) 0.027 0.008 0.008 0.043 + 208 (0.041) 0.055 0.006 0.006 0.041 + 220 (0.039) 0.069 0.008 0.004 0.038 + 219 (0.018) 0.008 0.003 0.002 0.018 + 210 (0.018) 0.006 0.003 0.002 0.018 + +Locus 14 : Ap68 +9 alleles +4.7% missing data + 158 (0.399) 0.289 0.630 0.253 0.399 + 160 (0.088) 0.022 0.033 0.151 0.088 + 156 (0.221) 0.361 0.237 0.390 0.220 + 162 (0.044) 0.008 0.029 0.006 0.044 + 154 (0.094) 0.017 0.035 0.158 0.095 + 152 (0.070) 0.264 0.016 0.033 0.070 + 164 (0.044) 0.022 0.015 0.005 0.044 + 170 (0.018) 0.003 0.002 0.003 0.018 + 166 (0.022) 0.015 0.003 0.002 0.022 + +Locus 15 : Ap85 +10 alleles +3.4% missing data + 202 (0.310) 0.551 0.389 0.254 0.310 + 186 (0.254) 0.102 0.382 0.497 0.254 + 204 (0.067) 0.037 0.024 0.026 0.067 + 188 (0.110) 0.023 0.075 0.149 0.110 + 194 (0.077) 0.026 0.083 0.047 0.077 + 196 (0.052) 0.115 0.012 0.011 0.052 + 200 (0.065) 0.078 0.017 0.008 0.065 + 192 (0.025) 0.005 0.006 0.003 0.025 + 190 (0.017) 0.002 0.008 0.003 0.017 + 198 (0.024) 0.061 0.003 0.002 0.024 + +Locus 16 : Ap90 +13 alleles +0.7% missing data + 131 (0.355) 0.545 0.528 0.563 0.355 + 135 (0.062) 0.090 0.081 0.024 0.062 + 133 (0.305) 0.204 0.308 0.218 0.306 + 129 (0.096) 0.090 0.040 0.150 0.096 + 137 (0.035) 0.011 0.007 0.029 0.035 + 141 (0.016) 0.002 0.004 0.002 0.016 + 143 (0.022) 0.002 0.009 0.004 0.022 + 151 (0.023) 0.004 0.009 0.002 0.023 + 155 (0.016) 0.002 0.003 0.002 0.016 + 145 (0.015) 0.008 0.002 0.001 0.015 + 130 (0.019) 0.017 0.003 0.002 0.019 + 139 (0.015) 0.009 0.002 0.001 0.015 + 153 (0.019) 0.016 0.002 0.002 0.019 + +Locus 17 : Ap223 +7 alleles +2.0% missing data + 183 (0.694) 0.900 0.609 0.676 0.695 + 187 (0.131) 0.020 0.291 0.266 0.131 + 189 (0.025) 0.002 0.005 0.026 0.025 + 173 (0.064) 0.040 0.070 0.015 0.064 + 182 (0.031) 0.004 0.010 0.009 0.031 + 180 (0.025) 0.006 0.005 0.004 0.025 + 179 (0.031) 0.028 0.011 0.003 0.030 + +Locus 18 : Ap224 +7 alleles +4.0% missing data + 283 (0.108) 0.018 0.200 0.190 0.108 + 287 (0.470) 0.457 0.483 0.438 0.471 + 281 (0.134) 0.047 0.157 0.188 0.134 + 289 (0.206) 0.422 0.100 0.166 0.207 + 291 (0.038) 0.004 0.054 0.013 0.038 + 285 (0.018) 0.002 0.003 0.003 0.018 + 279 (0.025) 0.050 0.003 0.002 0.024 + +Locus 19 : Ap226 +5 alleles +17.4% missing data + 237 (0.386) 0.346 0.321 0.359 0.387 + 239 (0.463) 0.611 0.450 0.494 0.463 + 247 (0.113) 0.029 0.223 0.138 0.113 + 235 (0.019) 0.003 0.003 0.007 0.018 + 241 (0.019) 0.011 0.003 0.002 0.019 + +Locus 20 : Ap249 +9 alleles +1.3% missing data + 209 (0.620) 0.703 0.582 0.734 0.621 + 211 (0.053) 0.008 0.014 0.061 0.053 + 217 (0.082) 0.018 0.146 0.078 0.082 + 219 (0.101) 0.017 0.232 0.087 0.101 + 215 (0.075) 0.244 0.012 0.031 0.075 + 208 (0.017) 0.002 0.005 0.002 0.017 + 225 (0.017) 0.002 0.004 0.002 0.017 + 223 (0.017) 0.002 0.003 0.004 0.017 + 213 (0.017) 0.004 0.002 0.002 0.017 + +Locus 21 : Ap273 +4 alleles +1.3% missing data + 106 (0.875) 0.954 0.951 0.962 0.875 + 108 (0.052) 0.021 0.032 0.015 0.052 + 104 (0.045) 0.004 0.011 0.021 0.045 + 102 (0.028) 0.021 0.006 0.003 0.028 + +Locus 22 : Ap274 +2 alleles +2.0% missing data + 120 (0.945) 0.917 0.985 0.993 0.945 + 122 (0.055) 0.083 0.015 0.007 0.055 + +Locus 23 : Ap288 +5 alleles +0.0% missing data + 123 (0.777) 0.954 0.618 0.766 0.778 + 131 (0.159) 0.040 0.347 0.225 0.159 + 139 (0.029) 0.003 0.020 0.004 0.029 + 121 (0.017) 0.002 0.008 0.002 0.017 + 124 (0.017) 0.002 0.006 0.003 0.017 + +Locus 24 : At163 +7 alleles +0.0% missing data + 128 (0.713) 0.936 0.555 0.815 0.713 + 134 (0.193) 0.052 0.426 0.173 0.193 + 130 (0.025) 0.003 0.010 0.003 0.025 + 136 (0.017) 0.001 0.002 0.004 0.017 + 140 (0.017) 0.002 0.002 0.002 0.017 + 146 (0.018) 0.002 0.002 0.002 0.018 + 142 (0.017) 0.004 0.002 0.002 0.017 + +Locus 25 : At188 +13 alleles +1.3% missing data + 189 (0.634) 0.900 0.772 0.755 0.635 + 205 (0.031) 0.003 0.060 0.005 0.031 + 207 (0.029) 0.003 0.011 0.092 0.029 + 219 (0.024) 0.002 0.007 0.006 0.024 + 209 (0.032) 0.004 0.012 0.064 0.032 + 217 (0.042) 0.004 0.015 0.016 0.043 + 215 (0.020) 0.002 0.008 0.014 0.020 + 199 (0.064) 0.051 0.067 0.013 0.064 + 212 (0.029) 0.005 0.010 0.010 0.029 + 213 (0.037) 0.004 0.031 0.013 0.037 + 211 (0.016) 0.001 0.002 0.002 0.016 + 191 (0.016) 0.002 0.003 0.008 0.016 + 187 (0.025) 0.021 0.003 0.003 0.025 + +Values of parameters used in structure: +DATAFILE=, OUTFILE=, NUMINDS=149, NUMLOCI=25, MISSING=-9, LABEL=1, POPDATA=0, POPFLAG=1, PHENOTYPE=0, EXTRACOLS=1, MAXPOPS=4, BURNIN=100000, NUMREPS=1000000, USEPOPINFO=0, INFERALPHA=1, INFERLAMBDA=0, POPSPECIFICLAMBDA=0, POPALPHAS=0, COMPUTEPROB=1, NOADMIX=0, ADMBURNIN=2500, UPDATEFREQ=1, PRINTLIKES=0, INTERMEDSAVE=0, PRINTKLD=0, PRINTNET=0, PRINTLAMBDA=0, ANCESTDIST=0, NUMBOXES=1000, ANCESTPINT=0.90000, GENSBACK=2, MIGRPRIOR=0.05000, PRINTQHAT=0, PRINTQSUM=0, ALPHA=1.0000, FREQSCORR=1, FPRIORMEAN=0.0100, FPRIORSD=0.0500, ONEFST=0, LAMBDA=1.0000, UNIFPRIORALPHA=1, ALPHAMAX=10.0000, ALPHAPRIORA=1.0000, ALPHAPRIORB=2.0000, ALPHAPROPSD=0.0250, STARTATPOPINFO=0, RANDOMIZE=1, LINKAGE=0, METROFREQ=10, REPORTHITRATE=0, MARKOVPHASE=-1, PHASED=0, PLOIDY=2, PHASEINFO=0 LOCPRIOR=0, LOCPRIORINIT=1.000000, LOCDATA=0, LOCISPOP=0, LOCPRIORSTEP=0.100000, MAXLOCPRIOR=20.000000, SEED=1342788936, +[STRAT parameters]: NUMSIMSTATS=1000, PHENOTYPECOL=-9, POOLFREQ=10, LOCUSxONLY=0, EMERROR=0.00100, MISSINGPHENO=-9, \ No newline at end of file diff --git a/inst/files/structure/structure_12 b/inst/files/structure/structure_12 new file mode 100644 index 0000000..e1e22d4 --- /dev/null +++ b/inst/files/structure/structure_12 @@ -0,0 +1,538 @@ + + +---------------------------------------------------- +STRUCTURE by Pritchard, Stephens and Donnelly (2000) + and Falush, Stephens and Pritchard (2003) + Code by Pritchard, Falush and Hubisz + Version 2.3.2.1 (Oct 2009) +---------------------------------------------------- + + + +Command line arguments: +Input File: + +Run parameters: + 149 individuals + 25 loci + 5 populations assumed + 100000 Burn-in period + 1000000 Reps + + +-------------------------------------------- +Overall proportion of membership of the +sample in each of the 5 clusters + +Inferred Clusters + 1 2 3 4 5 +0.209 0.212 0.217 0.164 0.199 + +-------------------------------------------- + +Allele-freq. divergence among pops (Net nucleotide distance), +computed using point estimates of P. + + 1 2 3 4 5 + 1 - 0.0017 0.0035 0.0076 0.0061 + 2 0.0017 - 0.0019 0.0081 0.0105 + 3 0.0035 0.0019 - 0.0039 0.0066 + 4 0.0076 0.0081 0.0039 - 0.0058 + 5 0.0061 0.0105 0.0066 0.0058 - + +Average distances (expected heterozygosity) between individuals in same cluster: +cluster 1 : 0.4789 +cluster 2 : 0.4750 +cluster 3 : 0.5047 +cluster 4 : 0.5760 +cluster 5 : 0.5099 + +-------------------------------------------- +Estimated Ln Prob of Data = -7828.5 +Mean value of ln likelihood = -7205.4 +Variance of ln likelihood = 1246.2 +Mean value of alpha = 0.2182 + +Mean value of Fst_1 = 0.1461 +Mean value of Fst_2 = 0.1448 +Mean value of Fst_3 = 0.1215 +Mean value of Fst_4 = 0.0160 +Mean value of Fst_5 = 0.1368 + + +Inferred ancestry of individuals: + Label (%Miss) : Inferred clusters + 1 I13825 (0) : 0.085 0.096 0.201 0.405 0.212 + 2 I13826 (0) : 0.101 0.104 0.270 0.145 0.379 + 3 I13827 (20) : 0.374 0.170 0.080 0.064 0.312 + 4 I13828 (0) : 0.100 0.113 0.257 0.194 0.336 + 5 I13829 (8) : 0.300 0.211 0.130 0.083 0.276 + 6 I13830 (0) : 0.112 0.115 0.259 0.136 0.378 + 7 I13831 (0) : 0.243 0.234 0.169 0.096 0.258 + 8 I13832 (16) : 0.262 0.211 0.125 0.178 0.224 + 9 I13833 (0) : 0.325 0.197 0.131 0.055 0.292 + 10 I13834 (0) : 0.360 0.168 0.094 0.046 0.331 + 11 I13835 (0) : 0.213 0.202 0.152 0.240 0.193 + 12 I13836 (0) : 0.329 0.162 0.090 0.129 0.290 + 13 I13377 (0) : 0.303 0.207 0.141 0.089 0.260 + 14 I13378 (0) : 0.162 0.168 0.179 0.317 0.174 + 15 I13379 (0) : 0.190 0.162 0.211 0.117 0.321 + 16 I13380 (0) : 0.342 0.204 0.123 0.061 0.269 + 17 I13381 (0) : 0.224 0.287 0.142 0.183 0.164 + 18 I13382 (0) : 0.334 0.286 0.095 0.038 0.247 + 19 I13383 (0) : 0.186 0.229 0.160 0.252 0.173 + 20 I13384 (0) : 0.235 0.223 0.155 0.127 0.261 + 21 I13385 (0) : 0.368 0.178 0.089 0.052 0.313 + 22 I13386 (0) : 0.352 0.242 0.072 0.064 0.270 + 23 I13387 (0) : 0.133 0.115 0.224 0.208 0.322 + 24 I13388 (0) : 0.087 0.101 0.201 0.411 0.201 + 25 I13389 (0) : 0.317 0.198 0.144 0.063 0.278 + 26 I13390 (0) : 0.325 0.233 0.108 0.061 0.274 + 27 I13391 (0) : 0.212 0.170 0.171 0.251 0.196 + 28 I13392 (0) : 0.164 0.145 0.185 0.298 0.208 + 29 I13393 (0) : 0.265 0.338 0.158 0.077 0.163 + 30 I13394 (4) : 0.221 0.232 0.218 0.175 0.154 + 31 I13395 (0) : 0.230 0.230 0.219 0.141 0.180 + 32 I13396 (0) : 0.113 0.134 0.241 0.246 0.266 + 33 I13397 (0) : 0.170 0.123 0.182 0.274 0.250 + 34 I13398 (0) : 0.151 0.111 0.241 0.109 0.388 + 35 I13399 (4) : 0.195 0.140 0.150 0.330 0.186 + 36 I13400 (0) : 0.243 0.190 0.169 0.162 0.236 + 37 I13401 (0) : 0.241 0.197 0.174 0.187 0.201 + 38 I13402 (0) : 0.126 0.135 0.206 0.334 0.200 + 39 I13403 (0) : 0.154 0.181 0.252 0.106 0.306 + 40 I13404 (0) : 0.220 0.158 0.187 0.098 0.336 + 41 I13405 (0) : 0.377 0.185 0.090 0.039 0.309 + 42 I13406 (16) : 0.098 0.105 0.210 0.334 0.253 + 43 I13407 (0) : 0.165 0.159 0.221 0.151 0.305 + 44 I13408 (0) : 0.292 0.228 0.150 0.068 0.263 + 45 I13409 (0) : 0.091 0.099 0.205 0.382 0.223 + 46 I13410 (0) : 0.239 0.252 0.157 0.096 0.257 + 47 I13411 (0) : 0.301 0.165 0.129 0.078 0.328 + 48 I13412 (0) : 0.228 0.210 0.203 0.142 0.218 + 49 I13413 (0) : 0.115 0.127 0.219 0.276 0.263 + 50 I13414 (0) : 0.116 0.127 0.233 0.198 0.327 + 51 I13415 (4) : 0.318 0.170 0.132 0.082 0.298 + 52 I13416 (4) : 0.206 0.182 0.207 0.134 0.272 + 53 I13417 (4) : 0.315 0.194 0.143 0.067 0.281 + 54 I13418 (0) : 0.269 0.240 0.149 0.090 0.252 + 55 I13419 (0) : 0.187 0.120 0.118 0.385 0.191 + 56 I13420 (0) : 0.204 0.185 0.223 0.104 0.283 + 57 I13421 (0) : 0.293 0.300 0.154 0.055 0.197 + 58 I13422 (0) : 0.240 0.207 0.199 0.117 0.238 + 59 I13423 (0) : 0.195 0.227 0.153 0.251 0.174 + 60 I13424 (0) : 0.286 0.197 0.138 0.122 0.258 + 61 I13425 (4) : 0.275 0.168 0.139 0.151 0.267 + 62 I13426 (4) : 0.197 0.241 0.226 0.209 0.128 + 63 I13870 (0) : 0.168 0.188 0.237 0.135 0.272 + 64 I13871 (16) : 0.142 0.158 0.216 0.210 0.273 + 65 I13872 (0) : 0.077 0.088 0.267 0.207 0.360 + 66 I13873 (4) : 0.139 0.182 0.234 0.161 0.284 + 67 I13874 (0) : 0.096 0.104 0.212 0.320 0.268 + 68 I13875 (8) : 0.126 0.134 0.251 0.159 0.330 + 69 I13876 (0) : 0.090 0.100 0.162 0.519 0.128 + 70 I13877 (20) : 0.266 0.299 0.129 0.093 0.213 + 71 I13878 (28) : 0.193 0.131 0.212 0.113 0.351 + 72 I13879 (4) : 0.288 0.165 0.138 0.075 0.334 + 73 I13880 (4) : 0.086 0.101 0.280 0.139 0.394 + 74 I13881 (0) : 0.126 0.112 0.179 0.371 0.212 + 75 I13882 (0) : 0.120 0.128 0.248 0.166 0.338 + 76 I13883 (4) : 0.088 0.112 0.270 0.193 0.337 + 77 I13884 (16) : 0.096 0.081 0.149 0.547 0.127 + 78 I13885 (20) : 0.203 0.195 0.117 0.301 0.184 + 79 I13886 (8) : 0.187 0.131 0.205 0.147 0.330 + 80 I13887 (0) : 0.056 0.069 0.154 0.640 0.081 + 81 I13888 (0) : 0.120 0.159 0.183 0.341 0.197 + 82 I13889 (0) : 0.228 0.267 0.281 0.099 0.124 + 83 I13890 (32) : 0.212 0.239 0.236 0.174 0.138 + 84 I13891 (0) : 0.151 0.127 0.223 0.161 0.338 + 85 I13892 (0) : 0.255 0.261 0.190 0.104 0.190 + 86 I13893 (8) : 0.137 0.118 0.150 0.454 0.141 + 87 I13894 (0) : 0.076 0.093 0.288 0.146 0.397 + 88 I13895 (4) : 0.196 0.180 0.168 0.270 0.186 + 89 I13896 (0) : 0.132 0.168 0.260 0.160 0.280 + 90 I13897 (0) : 0.175 0.114 0.225 0.110 0.376 + 91 I13898 (4) : 0.150 0.171 0.227 0.138 0.315 + 92 I13899 (0) : 0.080 0.091 0.288 0.123 0.417 + 93 I13900 (32) : 0.107 0.104 0.174 0.452 0.163 + 94 I13837 (0) : 0.368 0.191 0.093 0.048 0.300 + 95 I13838 (0) : 0.204 0.270 0.294 0.108 0.124 + 96 I13839 (0) : 0.343 0.182 0.112 0.077 0.286 + 97 I13840 (0) : 0.278 0.242 0.169 0.068 0.243 + 98 I13841 (0) : 0.272 0.339 0.187 0.061 0.140 + 99 I13842 (0) : 0.324 0.245 0.159 0.061 0.210 +100 I13843 (4) : 0.247 0.340 0.205 0.075 0.133 +101 I13844 (16) : 0.252 0.222 0.167 0.152 0.206 +102 I13845 (0) : 0.325 0.244 0.102 0.067 0.262 +103 I13846 (0) : 0.306 0.233 0.109 0.112 0.240 +104 I13847 (0) : 0.181 0.201 0.255 0.162 0.202 +105 I13848 (0) : 0.189 0.222 0.213 0.186 0.191 +106 I13849 (0) : 0.118 0.151 0.240 0.226 0.265 +107 I13850 (0) : 0.224 0.303 0.223 0.110 0.140 +108 I12577 (4) : 0.224 0.307 0.317 0.103 0.049 +109 I12578 (4) : 0.211 0.277 0.310 0.102 0.100 +110 I12579 (8) : 0.205 0.274 0.291 0.174 0.056 +111 I12580 (8) : 0.247 0.339 0.330 0.037 0.046 +112 I12581 (4) : 0.178 0.182 0.188 0.312 0.140 +113 I12582 (4) : 0.228 0.319 0.328 0.069 0.056 +114 I12583 (8) : 0.121 0.154 0.169 0.466 0.091 +115 I12584 (4) : 0.161 0.240 0.256 0.272 0.072 +116 I12585 (4) : 0.229 0.336 0.326 0.064 0.045 +117 I12586 (4) : 0.237 0.346 0.329 0.046 0.042 +118 I12587 (8) : 0.241 0.362 0.327 0.029 0.041 +119 I12588 (4) : 0.226 0.314 0.326 0.104 0.031 +120 I12589 (0) : 0.218 0.310 0.314 0.073 0.084 +121 I12590 (0) : 0.207 0.277 0.296 0.152 0.068 +122 I12591 (12) : 0.231 0.336 0.347 0.039 0.047 +123 I12592 (4) : 0.215 0.280 0.315 0.097 0.093 +124 I12593 (4) : 0.218 0.306 0.337 0.072 0.068 +125 I12594 (8) : 0.241 0.338 0.344 0.043 0.034 +126 I12595 (0) : 0.169 0.235 0.256 0.264 0.076 +127 I12596 (0) : 0.232 0.329 0.341 0.054 0.044 +128 I12597 (4) : 0.145 0.193 0.203 0.407 0.051 +129 I12598 (0) : 0.163 0.225 0.237 0.287 0.088 +130 I12599 (0) : 0.181 0.241 0.288 0.184 0.106 +131 I12600 (4) : 0.235 0.339 0.323 0.050 0.054 +132 I12601 (8) : 0.225 0.312 0.319 0.101 0.042 +133 I12602 (12) : 0.230 0.318 0.326 0.078 0.048 +134 I12603 (0) : 0.192 0.252 0.281 0.224 0.050 +135 I12604 (4) : 0.212 0.297 0.313 0.112 0.066 +136 I12605 (4) : 0.215 0.307 0.319 0.108 0.052 +137 I12606 (8) : 0.214 0.303 0.331 0.080 0.072 +138 I12607 (4) : 0.165 0.222 0.270 0.260 0.084 +139 I12608 (8) : 0.193 0.254 0.284 0.178 0.091 +140 I12609 (8) : 0.232 0.326 0.330 0.058 0.054 +141 I12610 (52) : 0.227 0.301 0.306 0.098 0.067 +142 I12611 (0) : 0.224 0.331 0.333 0.046 0.065 +143 I12612 (0) : 0.233 0.337 0.330 0.059 0.040 +144 I12613 (0) : 0.223 0.323 0.334 0.047 0.073 +145 I12614 (4) : 0.240 0.324 0.283 0.067 0.086 +146 I12615 (0) : 0.203 0.250 0.276 0.159 0.111 +147 I12616 (4) : 0.163 0.200 0.236 0.316 0.084 +148 I12617 (8) : 0.245 0.351 0.349 0.029 0.027 +149 I12618 (48) : 0.228 0.327 0.325 0.086 0.035 + + +Estimated Allele Frequencies in each cluster +First column gives estimated ancestral frequencies + + +Locus 1 : A8 +7 alleles +4.0% missing data + 177 (0.508) 0.496 0.539 0.551 0.508 0.478 + 179 (0.093) 0.105 0.077 0.071 0.090 0.102 + 175 (0.107) 0.169 0.123 0.121 0.126 0.236 + 173 (0.045) 0.046 0.035 0.030 0.044 0.046 + 181 (0.176) 0.160 0.197 0.195 0.168 0.115 + 165 (0.040) 0.015 0.018 0.022 0.036 0.013 + 183 (0.029) 0.008 0.011 0.011 0.027 0.010 + +Locus 2 : A14 +5 alleles +0.0% missing data + 112 (0.202) 0.157 0.166 0.203 0.227 0.286 + 110 (0.701) 0.785 0.757 0.713 0.686 0.689 + 114 (0.031) 0.007 0.007 0.012 0.030 0.012 + 118 (0.036) 0.038 0.054 0.054 0.031 0.008 + 116 (0.030) 0.013 0.017 0.019 0.026 0.005 + +Locus 3 : A24 +5 alleles +2.7% missing data + 104 (0.402) 0.330 0.360 0.400 0.413 0.383 + 106 (0.525) 0.638 0.600 0.553 0.521 0.595 + 101 (0.018) 0.004 0.004 0.005 0.016 0.004 + 108 (0.028) 0.007 0.008 0.014 0.027 0.014 + 96 (0.027) 0.021 0.029 0.029 0.024 0.004 + +Locus 4 : A29 +29 alleles +6.7% missing data + 143 (0.033) 0.030 0.026 0.046 0.042 0.068 + 149 (0.051) 0.033 0.036 0.041 0.049 0.028 + 147 (0.029) 0.016 0.021 0.029 0.029 0.020 + 153 (0.056) 0.108 0.074 0.059 0.052 0.082 + 169 (0.036) 0.023 0.028 0.055 0.044 0.061 + 151 (0.037) 0.060 0.068 0.041 0.034 0.041 + 145 (0.028) 0.015 0.019 0.024 0.027 0.016 + 157 (0.068) 0.081 0.111 0.109 0.075 0.081 + 155 (0.095) 0.113 0.140 0.135 0.098 0.096 + 159 (0.052) 0.048 0.057 0.081 0.065 0.101 + 161 (0.033) 0.066 0.052 0.023 0.031 0.051 + 141 (0.029) 0.037 0.021 0.015 0.026 0.032 + 139 (0.016) 0.012 0.008 0.005 0.014 0.010 + 144 (0.025) 0.043 0.028 0.018 0.024 0.039 + 171 (0.050) 0.052 0.044 0.039 0.048 0.046 + 163 (0.073) 0.085 0.081 0.079 0.075 0.081 + 167 (0.046) 0.040 0.048 0.049 0.044 0.033 + 173 (0.024) 0.024 0.019 0.013 0.022 0.022 + 142 (0.014) 0.003 0.003 0.005 0.012 0.005 + 177 (0.023) 0.019 0.024 0.024 0.021 0.007 + 175 (0.022) 0.010 0.011 0.012 0.020 0.007 + 165 (0.043) 0.030 0.030 0.039 0.044 0.035 + 146 (0.021) 0.017 0.012 0.012 0.020 0.020 + 137 (0.019) 0.006 0.007 0.008 0.017 0.004 + 183 (0.016) 0.007 0.009 0.010 0.014 0.003 + 179 (0.018) 0.007 0.008 0.009 0.016 0.004 + 191 (0.014) 0.003 0.004 0.004 0.012 0.003 + 185 (0.013) 0.003 0.003 0.004 0.012 0.003 + 180 (0.015) 0.008 0.011 0.012 0.013 0.002 + +Locus 5 : A43 +7 alleles +1.3% missing data + 123 (0.201) 0.119 0.146 0.142 0.191 0.095 + 141 (0.017) 0.002 0.003 0.004 0.016 0.004 + 137 (0.669) 0.793 0.738 0.766 0.694 0.862 + 139 (0.047) 0.056 0.074 0.044 0.041 0.028 + 124 (0.031) 0.022 0.032 0.032 0.028 0.006 + 143 (0.017) 0.003 0.003 0.005 0.015 0.003 + 128 (0.017) 0.004 0.005 0.006 0.015 0.002 + +Locus 6 : A79 +13 alleles +3.4% missing data + 103 (0.235) 0.259 0.263 0.258 0.245 0.293 + 97 (0.131) 0.073 0.076 0.121 0.145 0.140 + 101 (0.093) 0.172 0.095 0.074 0.090 0.155 + 107 (0.098) 0.142 0.137 0.085 0.093 0.117 + 109 (0.099) 0.077 0.078 0.086 0.096 0.073 + 105 (0.162) 0.190 0.247 0.267 0.165 0.160 + 111 (0.047) 0.020 0.024 0.029 0.044 0.022 + 113 (0.016) 0.002 0.003 0.004 0.015 0.004 + 91 (0.025) 0.027 0.041 0.038 0.022 0.004 + 99 (0.032) 0.022 0.021 0.019 0.029 0.016 + 115 (0.028) 0.010 0.011 0.011 0.026 0.009 + 117 (0.016) 0.002 0.003 0.005 0.015 0.004 + 121 (0.016) 0.002 0.002 0.004 0.014 0.003 + +Locus 7 : A88 +9 alleles +6.0% missing data + 133 (0.018) 0.003 0.003 0.005 0.016 0.004 + 149 (0.522) 0.570 0.638 0.647 0.524 0.518 + 137 (0.104) 0.074 0.061 0.075 0.109 0.114 + 147 (0.197) 0.293 0.226 0.173 0.201 0.292 + 141 (0.082) 0.045 0.056 0.076 0.081 0.057 + 152 (0.018) 0.004 0.003 0.005 0.016 0.004 + 143 (0.018) 0.003 0.003 0.005 0.016 0.003 + 151 (0.018) 0.004 0.004 0.006 0.015 0.003 + 144 (0.024) 0.006 0.007 0.009 0.022 0.004 + +Locus 8 : A113 +12 alleles +7.4% missing data + 214 (0.577) 0.773 0.771 0.706 0.591 0.720 + 226 (0.062) 0.035 0.040 0.068 0.070 0.084 + 218 (0.017) 0.006 0.004 0.004 0.015 0.006 + 220 (0.062) 0.063 0.076 0.078 0.056 0.034 + 216 (0.059) 0.026 0.024 0.031 0.055 0.025 + 230 (0.043) 0.043 0.031 0.023 0.040 0.041 + 234 (0.032) 0.010 0.009 0.017 0.032 0.020 + 232 (0.031) 0.011 0.010 0.019 0.031 0.023 + 228 (0.050) 0.017 0.018 0.030 0.050 0.029 + 224 (0.017) 0.003 0.003 0.005 0.016 0.004 + 222 (0.032) 0.007 0.008 0.014 0.030 0.011 + 208 (0.017) 0.005 0.005 0.004 0.015 0.005 + +Locus 9 : Ac11 +9 alleles +4.7% missing data + 111 (0.131) 0.114 0.104 0.147 0.153 0.220 + 117 (0.294) 0.337 0.316 0.289 0.294 0.338 + 115 (0.263) 0.308 0.276 0.247 0.265 0.301 + 113 (0.155) 0.137 0.168 0.176 0.149 0.099 + 119 (0.048) 0.065 0.086 0.083 0.042 0.020 + 121 (0.027) 0.021 0.029 0.030 0.023 0.006 + 123 (0.033) 0.007 0.008 0.011 0.030 0.006 + 127 (0.031) 0.009 0.010 0.012 0.028 0.007 + 125 (0.018) 0.003 0.003 0.004 0.016 0.003 + +Locus 10 : Ac88 +8 alleles +0.7% missing data + 214 (0.752) 0.905 0.898 0.831 0.749 0.810 + 216 (0.029) 0.008 0.010 0.013 0.028 0.014 + 220 (0.116) 0.063 0.064 0.118 0.132 0.157 + 230 (0.025) 0.004 0.005 0.007 0.023 0.005 + 221 (0.017) 0.004 0.004 0.006 0.015 0.002 + 212 (0.020) 0.007 0.009 0.011 0.018 0.004 + 217 (0.017) 0.003 0.004 0.005 0.015 0.003 + 224 (0.023) 0.006 0.006 0.009 0.020 0.005 + +Locus 11 : Ac139 +8 alleles +13.4% missing data + 327 (0.506) 0.627 0.679 0.620 0.495 0.502 + 329 (0.292) 0.276 0.212 0.258 0.312 0.385 + 331 (0.073) 0.036 0.033 0.058 0.078 0.075 + 328 (0.040) 0.030 0.038 0.020 0.036 0.023 + 341 (0.019) 0.005 0.005 0.007 0.017 0.003 + 337 (0.031) 0.019 0.025 0.026 0.027 0.005 + 323 (0.019) 0.003 0.004 0.005 0.017 0.004 + 339 (0.019) 0.004 0.004 0.006 0.017 0.003 + +Locus 12 : Ac306 +6 alleles +4.7% missing data + 165 (0.729) 0.801 0.796 0.776 0.728 0.755 + 177 (0.082) 0.063 0.088 0.075 0.079 0.053 + 173 (0.100) 0.053 0.059 0.101 0.114 0.128 + 169 (0.043) 0.063 0.032 0.019 0.040 0.054 + 171 (0.018) 0.002 0.002 0.004 0.016 0.003 + 179 (0.028) 0.017 0.023 0.025 0.024 0.007 + +Locus 13 : Ap15 +7 alleles +6.0% missing data + 202 (0.814) 0.925 0.908 0.886 0.831 0.940 + 212 (0.028) 0.005 0.006 0.015 0.028 0.017 + 204 (0.043) 0.015 0.017 0.020 0.039 0.011 + 208 (0.040) 0.022 0.028 0.030 0.036 0.013 + 220 (0.039) 0.025 0.032 0.037 0.035 0.013 + 219 (0.018) 0.004 0.005 0.006 0.016 0.003 + 210 (0.018) 0.004 0.004 0.006 0.016 0.004 + +Locus 14 : Ap68 +9 alleles +4.7% missing data + 158 (0.390) 0.315 0.328 0.415 0.421 0.459 + 160 (0.082) 0.086 0.090 0.062 0.077 0.073 + 156 (0.240) 0.369 0.334 0.286 0.234 0.309 + 162 (0.043) 0.010 0.012 0.020 0.042 0.021 + 154 (0.084) 0.096 0.066 0.058 0.081 0.089 + 152 (0.076) 0.100 0.143 0.122 0.068 0.028 + 164 (0.043) 0.014 0.016 0.021 0.040 0.013 + 170 (0.018) 0.004 0.004 0.005 0.016 0.004 + 166 (0.023) 0.007 0.008 0.010 0.020 0.005 + +Locus 15 : Ap85 +10 alleles +3.4% missing data + 202 (0.320) 0.364 0.407 0.415 0.326 0.340 + 186 (0.249) 0.355 0.294 0.265 0.267 0.401 + 204 (0.061) 0.033 0.035 0.040 0.056 0.031 + 188 (0.105) 0.096 0.086 0.076 0.104 0.102 + 194 (0.079) 0.046 0.039 0.054 0.079 0.068 + 196 (0.053) 0.044 0.062 0.060 0.048 0.019 + 200 (0.064) 0.033 0.041 0.048 0.059 0.021 + 192 (0.025) 0.005 0.006 0.008 0.022 0.006 + 190 (0.018) 0.003 0.003 0.006 0.016 0.006 + 198 (0.026) 0.020 0.028 0.029 0.023 0.006 + +Locus 16 : Ap90 +13 alleles +0.7% missing data + 131 (0.368) 0.552 0.503 0.493 0.386 0.553 + 135 (0.066) 0.051 0.063 0.073 0.067 0.054 + 133 (0.282) 0.226 0.250 0.275 0.290 0.261 + 129 (0.097) 0.114 0.127 0.085 0.090 0.083 + 137 (0.035) 0.021 0.016 0.016 0.031 0.018 + 141 (0.017) 0.002 0.002 0.004 0.015 0.004 + 143 (0.023) 0.005 0.005 0.007 0.022 0.007 + 151 (0.024) 0.004 0.005 0.008 0.022 0.007 + 155 (0.016) 0.002 0.002 0.004 0.015 0.003 + 145 (0.016) 0.004 0.005 0.006 0.014 0.002 + 130 (0.020) 0.007 0.009 0.011 0.017 0.003 + 139 (0.016) 0.004 0.005 0.007 0.014 0.003 + 153 (0.020) 0.007 0.008 0.010 0.018 0.003 + +Locus 17 : Ap223 +7 alleles +2.0% missing data + 183 (0.684) 0.741 0.800 0.753 0.676 0.643 + 187 (0.135) 0.186 0.128 0.151 0.155 0.268 + 189 (0.027) 0.016 0.010 0.008 0.024 0.014 + 173 (0.065) 0.030 0.031 0.051 0.065 0.050 + 182 (0.031) 0.009 0.007 0.010 0.029 0.011 + 180 (0.025) 0.006 0.007 0.008 0.023 0.006 + 179 (0.032) 0.013 0.017 0.020 0.029 0.009 + +Locus 18 : Ap224 +7 alleles +4.0% missing data + 283 (0.111) 0.136 0.092 0.113 0.122 0.187 + 287 (0.468) 0.448 0.471 0.482 0.472 0.452 + 281 (0.137) 0.137 0.118 0.111 0.139 0.164 + 289 (0.205) 0.245 0.283 0.239 0.191 0.149 + 291 (0.037) 0.014 0.012 0.027 0.039 0.036 + 285 (0.018) 0.003 0.003 0.004 0.016 0.003 + 279 (0.024) 0.016 0.022 0.025 0.021 0.007 + +Locus 19 : Ap226 +5 alleles +17.4% missing data + 237 (0.378) 0.354 0.347 0.342 0.374 0.346 + 239 (0.462) 0.518 0.553 0.533 0.459 0.467 + 247 (0.120) 0.117 0.089 0.112 0.133 0.178 + 235 (0.020) 0.006 0.005 0.005 0.017 0.006 + 241 (0.019) 0.005 0.006 0.008 0.017 0.003 + +Locus 20 : Ap249 +9 alleles +1.3% missing data + 209 (0.610) 0.713 0.695 0.655 0.608 0.649 + 211 (0.055) 0.038 0.030 0.024 0.051 0.034 + 217 (0.082) 0.063 0.049 0.077 0.089 0.115 + 219 (0.105) 0.080 0.082 0.108 0.120 0.156 + 215 (0.079) 0.094 0.130 0.117 0.071 0.032 + 208 (0.017) 0.003 0.003 0.005 0.016 0.004 + 225 (0.018) 0.003 0.003 0.004 0.016 0.004 + 223 (0.017) 0.004 0.004 0.004 0.015 0.003 + 213 (0.017) 0.003 0.003 0.005 0.015 0.003 + +Locus 21 : Ap273 +4 alleles +1.3% missing data + 106 (0.878) 0.952 0.948 0.942 0.888 0.952 + 108 (0.050) 0.022 0.028 0.029 0.047 0.024 + 104 (0.043) 0.017 0.013 0.014 0.040 0.018 + 102 (0.029) 0.009 0.011 0.015 0.026 0.006 + +Locus 22 : Ap274 +2 alleles +2.0% missing data + 120 (0.944) 0.966 0.953 0.955 0.949 0.979 + 122 (0.056) 0.034 0.047 0.045 0.051 0.021 + +Locus 23 : Ap288 +5 alleles +0.0% missing data + 123 (0.768) 0.809 0.856 0.802 0.750 0.690 + 131 (0.167) 0.178 0.130 0.174 0.190 0.286 + 139 (0.030) 0.006 0.007 0.013 0.029 0.014 + 121 (0.017) 0.003 0.003 0.006 0.016 0.005 + 124 (0.018) 0.003 0.004 0.005 0.016 0.005 + +Locus 24 : At163 +7 alleles +0.0% missing data + 128 (0.710) 0.826 0.847 0.760 0.691 0.675 + 134 (0.194) 0.158 0.135 0.215 0.223 0.305 + 130 (0.025) 0.005 0.006 0.009 0.024 0.008 + 136 (0.018) 0.003 0.004 0.004 0.015 0.003 + 140 (0.018) 0.002 0.003 0.004 0.015 0.003 + 146 (0.017) 0.002 0.003 0.004 0.015 0.003 + 142 (0.018) 0.003 0.003 0.005 0.016 0.003 + +Locus 25 : At188 +13 alleles +1.3% missing data + 189 (0.633) 0.797 0.838 0.807 0.651 0.760 + 205 (0.031) 0.009 0.010 0.027 0.035 0.035 + 207 (0.029) 0.056 0.024 0.013 0.026 0.048 + 219 (0.024) 0.006 0.006 0.007 0.022 0.007 + 209 (0.034) 0.036 0.021 0.017 0.031 0.033 + 217 (0.039) 0.015 0.014 0.016 0.037 0.016 + 215 (0.021) 0.009 0.010 0.008 0.019 0.009 + 199 (0.066) 0.032 0.041 0.054 0.065 0.044 + 212 (0.027) 0.011 0.009 0.011 0.025 0.012 + 213 (0.036) 0.013 0.010 0.018 0.036 0.023 + 211 (0.017) 0.002 0.002 0.004 0.015 0.003 + 191 (0.017) 0.006 0.005 0.004 0.015 0.005 + 187 (0.026) 0.009 0.011 0.014 0.023 0.005 + +Values of parameters used in structure: +DATAFILE=, OUTFILE=, NUMINDS=149, NUMLOCI=25, MISSING=-9, LABEL=1, POPDATA=0, POPFLAG=1, PHENOTYPE=0, EXTRACOLS=1, MAXPOPS=5, BURNIN=100000, NUMREPS=1000000, USEPOPINFO=0, INFERALPHA=1, INFERLAMBDA=0, POPSPECIFICLAMBDA=0, POPALPHAS=0, COMPUTEPROB=1, NOADMIX=0, ADMBURNIN=2500, UPDATEFREQ=1, PRINTLIKES=0, INTERMEDSAVE=0, PRINTKLD=0, PRINTNET=0, PRINTLAMBDA=0, ANCESTDIST=0, NUMBOXES=1000, ANCESTPINT=0.90000, GENSBACK=2, MIGRPRIOR=0.05000, PRINTQHAT=0, PRINTQSUM=0, ALPHA=1.0000, FREQSCORR=1, FPRIORMEAN=0.0100, FPRIORSD=0.0500, ONEFST=0, LAMBDA=1.0000, UNIFPRIORALPHA=1, ALPHAMAX=10.0000, ALPHAPRIORA=1.0000, ALPHAPRIORB=2.0000, ALPHAPROPSD=0.0250, STARTATPOPINFO=0, RANDOMIZE=1, LINKAGE=0, METROFREQ=10, REPORTHITRATE=0, MARKOVPHASE=-1, PHASED=0, PLOIDY=2, PHASEINFO=0 LOCPRIOR=0, LOCPRIORINIT=1.000000, LOCDATA=0, LOCISPOP=0, LOCPRIORSTEP=0.100000, MAXLOCPRIOR=20.000000, SEED=1342791227, +[STRAT parameters]: NUMSIMSTATS=1000, PHENOTYPECOL=-9, POOLFREQ=10, LOCUSxONLY=0, EMERROR=0.00100, MISSINGPHENO=-9, \ No newline at end of file diff --git a/inst/files/structure/structure_13 b/inst/files/structure/structure_13 new file mode 100644 index 0000000..c80ff6a --- /dev/null +++ b/inst/files/structure/structure_13 @@ -0,0 +1,541 @@ + + +---------------------------------------------------- +STRUCTURE by Pritchard, Stephens and Donnelly (2000) + and Falush, Stephens and Pritchard (2003) + Code by Pritchard, Falush and Hubisz + Version 2.3.2.1 (Oct 2009) +---------------------------------------------------- + + + +Command line arguments: +Input File: + +Run parameters: + 149 individuals + 25 loci + 6 populations assumed + 100000 Burn-in period + 1000000 Reps + + +-------------------------------------------- +Overall proportion of membership of the +sample in each of the 6 clusters + +Inferred Clusters + 1 2 3 4 5 6 +0.169 0.175 0.182 0.167 0.158 0.150 + +-------------------------------------------- + +Allele-freq. divergence among pops (Net nucleotide distance), +computed using point estimates of P. + + 1 2 3 4 5 6 + 1 - 0.0019 0.0015 0.0064 0.0045 0.0066 + 2 0.0019 - 0.0004 0.0041 0.0014 0.0029 + 3 0.0015 0.0004 - 0.0044 0.0018 0.0036 + 4 0.0064 0.0041 0.0044 - 0.0023 0.0033 + 5 0.0045 0.0014 0.0018 0.0023 - 0.0004 + 6 0.0066 0.0029 0.0036 0.0033 0.0004 - + +Average distances (expected heterozygosity) between individuals in same cluster: +cluster 1 : 0.4756 +cluster 2 : 0.4997 +cluster 3 : 0.4966 +cluster 4 : 0.4887 +cluster 5 : 0.5322 +cluster 6 : 0.5538 + +-------------------------------------------- +Estimated Ln Prob of Data = -8023.3 +Mean value of ln likelihood = -7158.0 +Variance of ln likelihood = 1730.6 +Mean value of alpha = 0.2483 + +Mean value of Fst_1 = 0.1894 +Mean value of Fst_2 = 0.1756 +Mean value of Fst_3 = 0.1765 +Mean value of Fst_4 = 0.1802 +Mean value of Fst_5 = 0.1192 +Mean value of Fst_6 = 0.0745 + + +Inferred ancestry of individuals: + Label (%Miss) : Inferred clusters + 1 I13825 (0) : 0.106 0.148 0.123 0.130 0.222 0.271 + 2 I13826 (0) : 0.122 0.230 0.210 0.124 0.178 0.135 + 3 I13827 (20) : 0.114 0.132 0.178 0.276 0.167 0.134 + 4 I13828 (0) : 0.124 0.208 0.183 0.140 0.185 0.160 + 5 I13829 (8) : 0.128 0.156 0.148 0.270 0.162 0.137 + 6 I13830 (0) : 0.127 0.213 0.211 0.136 0.174 0.138 + 7 I13831 (0) : 0.149 0.154 0.138 0.254 0.164 0.141 + 8 I13832 (16) : 0.136 0.137 0.128 0.241 0.179 0.179 + 9 I13833 (0) : 0.127 0.141 0.148 0.300 0.154 0.130 + 10 I13834 (0) : 0.105 0.147 0.177 0.281 0.161 0.129 + 11 I13835 (0) : 0.133 0.128 0.100 0.262 0.181 0.197 + 12 I13836 (0) : 0.100 0.134 0.160 0.254 0.176 0.176 + 13 I13377 (0) : 0.147 0.130 0.135 0.279 0.162 0.146 + 14 I13378 (0) : 0.136 0.124 0.097 0.233 0.184 0.226 + 15 I13379 (0) : 0.136 0.185 0.171 0.202 0.168 0.139 + 16 I13380 (0) : 0.152 0.140 0.169 0.257 0.155 0.126 + 17 I13381 (0) : 0.166 0.151 0.110 0.224 0.176 0.173 + 18 I13382 (0) : 0.155 0.149 0.134 0.297 0.160 0.105 + 19 I13383 (0) : 0.145 0.136 0.117 0.220 0.183 0.200 + 20 I13384 (0) : 0.144 0.160 0.155 0.214 0.174 0.154 + 21 I13385 (0) : 0.110 0.139 0.162 0.297 0.160 0.133 + 22 I13386 (0) : 0.130 0.134 0.152 0.288 0.169 0.128 + 23 I13387 (0) : 0.115 0.192 0.180 0.155 0.186 0.171 + 24 I13388 (0) : 0.114 0.144 0.134 0.112 0.219 0.276 + 25 I13389 (0) : 0.160 0.141 0.160 0.252 0.157 0.131 + 26 I13390 (0) : 0.142 0.143 0.158 0.266 0.162 0.130 + 27 I13391 (0) : 0.139 0.128 0.121 0.212 0.181 0.219 + 28 I13392 (0) : 0.130 0.141 0.121 0.217 0.179 0.212 + 29 I13393 (0) : 0.187 0.168 0.119 0.263 0.148 0.114 + 30 I13394 (4) : 0.181 0.166 0.154 0.182 0.157 0.161 + 31 I13395 (0) : 0.168 0.180 0.180 0.181 0.148 0.144 + 32 I13396 (0) : 0.150 0.187 0.171 0.122 0.178 0.192 + 33 I13397 (0) : 0.116 0.142 0.129 0.195 0.190 0.228 + 34 I13398 (0) : 0.117 0.216 0.216 0.157 0.170 0.124 + 35 I13399 (4) : 0.116 0.105 0.098 0.206 0.207 0.267 + 36 I13400 (0) : 0.143 0.140 0.128 0.250 0.167 0.172 + 37 I13401 (0) : 0.214 0.144 0.178 0.153 0.162 0.150 + 38 I13402 (0) : 0.130 0.137 0.111 0.175 0.197 0.250 + 39 I13403 (0) : 0.167 0.215 0.197 0.148 0.159 0.114 + 40 I13404 (0) : 0.125 0.183 0.190 0.194 0.169 0.139 + 41 I13405 (0) : 0.114 0.134 0.161 0.305 0.155 0.131 + 42 I13406 (16) : 0.110 0.172 0.144 0.131 0.212 0.232 + 43 I13407 (0) : 0.136 0.186 0.161 0.199 0.169 0.148 + 44 I13408 (0) : 0.137 0.147 0.132 0.300 0.152 0.132 + 45 I13409 (0) : 0.122 0.155 0.140 0.116 0.216 0.251 + 46 I13410 (0) : 0.143 0.163 0.137 0.255 0.165 0.138 + 47 I13411 (0) : 0.115 0.151 0.180 0.253 0.163 0.138 + 48 I13412 (0) : 0.164 0.173 0.195 0.176 0.153 0.138 + 49 I13413 (0) : 0.130 0.174 0.159 0.143 0.197 0.196 + 50 I13414 (0) : 0.126 0.192 0.185 0.139 0.187 0.170 + 51 I13415 (4) : 0.138 0.155 0.175 0.237 0.162 0.133 + 52 I13416 (4) : 0.160 0.170 0.177 0.187 0.163 0.143 + 53 I13417 (4) : 0.163 0.162 0.188 0.211 0.158 0.117 + 54 I13418 (0) : 0.155 0.178 0.179 0.211 0.157 0.119 + 55 I13419 (0) : 0.088 0.115 0.122 0.184 0.224 0.267 + 56 I13420 (0) : 0.157 0.204 0.205 0.159 0.156 0.120 + 57 I13421 (0) : 0.192 0.184 0.159 0.212 0.150 0.103 + 58 I13422 (0) : 0.184 0.165 0.198 0.174 0.154 0.125 + 59 I13423 (0) : 0.155 0.152 0.115 0.194 0.186 0.199 + 60 I13424 (0) : 0.133 0.135 0.135 0.262 0.169 0.167 + 61 I13425 (4) : 0.124 0.150 0.163 0.219 0.177 0.166 + 62 I13426 (4) : 0.181 0.187 0.161 0.159 0.151 0.160 + 63 I13870 (0) : 0.162 0.215 0.197 0.138 0.159 0.129 + 64 I13871 (16) : 0.133 0.170 0.155 0.174 0.189 0.180 + 65 I13872 (0) : 0.114 0.219 0.196 0.107 0.192 0.171 + 66 I13873 (4) : 0.157 0.195 0.175 0.157 0.170 0.145 + 67 I13874 (0) : 0.122 0.174 0.167 0.123 0.205 0.209 + 68 I13875 (8) : 0.139 0.208 0.192 0.139 0.177 0.146 + 69 I13876 (0) : 0.108 0.123 0.113 0.110 0.230 0.317 + 70 I13877 (20) : 0.177 0.169 0.135 0.221 0.171 0.127 + 71 I13878 (28) : 0.119 0.203 0.199 0.181 0.168 0.131 + 72 I13879 (4) : 0.113 0.168 0.178 0.247 0.161 0.133 + 73 I13880 (4) : 0.125 0.231 0.217 0.113 0.177 0.137 + 74 I13881 (0) : 0.114 0.142 0.133 0.137 0.211 0.262 + 75 I13882 (0) : 0.133 0.208 0.184 0.146 0.177 0.152 + 76 I13883 (4) : 0.131 0.229 0.198 0.107 0.183 0.154 + 77 I13884 (16) : 0.087 0.103 0.085 0.135 0.245 0.346 + 78 I13885 (20) : 0.122 0.127 0.109 0.212 0.204 0.226 + 79 I13886 (8) : 0.125 0.182 0.175 0.187 0.175 0.156 + 80 I13887 (0) : 0.085 0.095 0.069 0.094 0.263 0.393 + 81 I13888 (0) : 0.121 0.150 0.135 0.149 0.205 0.240 + 82 I13889 (0) : 0.248 0.168 0.237 0.124 0.119 0.104 + 83 I13890 (32) : 0.176 0.191 0.178 0.168 0.143 0.144 + 84 I13891 (0) : 0.123 0.196 0.194 0.164 0.172 0.152 + 85 I13892 (0) : 0.192 0.173 0.166 0.187 0.151 0.130 + 86 I13893 (8) : 0.117 0.096 0.089 0.168 0.218 0.313 + 87 I13894 (0) : 0.124 0.245 0.218 0.105 0.177 0.130 + 88 I13895 (4) : 0.158 0.126 0.132 0.190 0.183 0.212 + 89 I13896 (0) : 0.164 0.221 0.195 0.120 0.162 0.137 + 90 I13897 (0) : 0.112 0.199 0.206 0.186 0.170 0.127 + 91 I13898 (4) : 0.144 0.202 0.174 0.172 0.169 0.139 + 92 I13899 (0) : 0.121 0.246 0.227 0.112 0.174 0.121 + 93 I13900 (32) : 0.111 0.124 0.115 0.129 0.225 0.295 + 94 I13837 (0) : 0.125 0.134 0.168 0.284 0.159 0.130 + 95 I13838 (0) : 0.215 0.210 0.234 0.113 0.124 0.104 + 96 I13839 (0) : 0.134 0.141 0.188 0.243 0.160 0.134 + 97 I13840 (0) : 0.177 0.165 0.173 0.217 0.156 0.113 + 98 I13841 (0) : 0.228 0.219 0.160 0.164 0.137 0.091 + 99 I13842 (0) : 0.174 0.164 0.171 0.229 0.147 0.115 +100 I13843 (4) : 0.236 0.213 0.166 0.152 0.138 0.096 +101 I13844 (16) : 0.160 0.142 0.134 0.237 0.164 0.162 +102 I13845 (0) : 0.137 0.148 0.148 0.280 0.165 0.122 +103 I13846 (0) : 0.142 0.139 0.137 0.248 0.172 0.162 +104 I13847 (0) : 0.177 0.195 0.209 0.134 0.149 0.136 +105 I13848 (0) : 0.191 0.157 0.153 0.181 0.158 0.159 +106 I13849 (0) : 0.154 0.183 0.164 0.137 0.183 0.179 +107 I13850 (0) : 0.222 0.197 0.158 0.165 0.140 0.119 +108 I12577 (4) : 0.231 0.208 0.247 0.102 0.115 0.096 +109 I12578 (4) : 0.279 0.167 0.258 0.099 0.111 0.085 +110 I12579 (8) : 0.205 0.194 0.209 0.120 0.132 0.140 +111 I12580 (8) : 0.238 0.241 0.261 0.109 0.089 0.062 +112 I12581 (4) : 0.173 0.124 0.126 0.186 0.176 0.215 +113 I12582 (4) : 0.234 0.227 0.260 0.100 0.103 0.077 +114 I12583 (8) : 0.185 0.119 0.127 0.109 0.204 0.257 +115 I12584 (4) : 0.203 0.164 0.186 0.094 0.159 0.194 +116 I12585 (4) : 0.247 0.225 0.251 0.097 0.103 0.076 +117 I12586 (4) : 0.229 0.249 0.257 0.105 0.095 0.064 +118 I12587 (8) : 0.257 0.242 0.245 0.105 0.093 0.058 +119 I12588 (4) : 0.218 0.232 0.255 0.092 0.107 0.096 +120 I12589 (0) : 0.270 0.188 0.251 0.101 0.109 0.080 +121 I12590 (0) : 0.206 0.213 0.227 0.112 0.124 0.118 +122 I12591 (12) : 0.281 0.208 0.293 0.082 0.087 0.048 +123 I12592 (4) : 0.283 0.167 0.278 0.089 0.107 0.076 +124 I12593 (4) : 0.281 0.187 0.292 0.080 0.099 0.061 +125 I12594 (8) : 0.237 0.247 0.280 0.093 0.088 0.056 +126 I12595 (0) : 0.212 0.149 0.184 0.110 0.157 0.188 +127 I12596 (0) : 0.258 0.219 0.285 0.087 0.094 0.057 +128 I12597 (4) : 0.155 0.166 0.137 0.106 0.191 0.246 +129 I12598 (0) : 0.231 0.142 0.187 0.102 0.164 0.174 +130 I12599 (0) : 0.210 0.182 0.223 0.103 0.142 0.142 +131 I12600 (4) : 0.231 0.251 0.250 0.102 0.096 0.069 +132 I12601 (8) : 0.223 0.225 0.238 0.097 0.112 0.104 +133 I12602 (12) : 0.226 0.229 0.252 0.107 0.101 0.084 +134 I12603 (0) : 0.183 0.197 0.210 0.093 0.142 0.174 +135 I12604 (4) : 0.215 0.229 0.239 0.099 0.116 0.104 +136 I12605 (4) : 0.216 0.226 0.241 0.100 0.113 0.104 +137 I12606 (8) : 0.279 0.177 0.273 0.093 0.107 0.072 +138 I12607 (4) : 0.247 0.149 0.223 0.084 0.146 0.151 +139 I12608 (8) : 0.254 0.159 0.228 0.104 0.131 0.124 +140 I12609 (8) : 0.270 0.201 0.262 0.098 0.098 0.071 +141 I12610 (52) : 0.224 0.212 0.231 0.120 0.115 0.098 +142 I12611 (0) : 0.290 0.190 0.266 0.092 0.100 0.062 +143 I12612 (0) : 0.240 0.230 0.252 0.101 0.099 0.078 +144 I12613 (0) : 0.298 0.176 0.277 0.093 0.098 0.058 +145 I12614 (4) : 0.234 0.203 0.222 0.136 0.117 0.090 +146 I12615 (0) : 0.248 0.154 0.221 0.116 0.134 0.127 +147 I12616 (4) : 0.202 0.135 0.184 0.100 0.170 0.208 +148 I12617 (8) : 0.247 0.250 0.284 0.090 0.081 0.049 +149 I12618 (48) : 0.218 0.243 0.254 0.096 0.101 0.088 + + +Estimated Allele Frequencies in each cluster +First column gives estimated ancestral frequencies + + +Locus 1 : A8 +7 alleles +4.0% missing data + 177 (0.505) 0.555 0.529 0.506 0.501 0.506 0.502 + 179 (0.096) 0.069 0.083 0.086 0.102 0.092 0.097 + 175 (0.100) 0.108 0.146 0.159 0.191 0.159 0.144 + 173 (0.046) 0.030 0.030 0.026 0.060 0.042 0.049 + 181 (0.182) 0.208 0.185 0.193 0.122 0.159 0.157 + 165 (0.040) 0.023 0.017 0.020 0.013 0.024 0.028 + 183 (0.030) 0.009 0.010 0.008 0.012 0.018 0.023 + +Locus 2 : A14 +5 alleles +0.0% missing data + 112 (0.198) 0.150 0.214 0.183 0.215 0.225 0.221 + 110 (0.700) 0.778 0.707 0.737 0.749 0.713 0.706 + 114 (0.033) 0.008 0.010 0.008 0.010 0.018 0.024 + 118 (0.038) 0.049 0.052 0.055 0.018 0.028 0.028 + 116 (0.031) 0.015 0.017 0.016 0.008 0.016 0.021 + +Locus 3 : A24 +5 alleles +2.7% missing data + 104 (0.402) 0.359 0.396 0.371 0.349 0.384 0.397 + 106 (0.520) 0.602 0.561 0.588 0.624 0.571 0.548 + 101 (0.018) 0.004 0.004 0.003 0.006 0.009 0.012 + 108 (0.030) 0.009 0.012 0.010 0.010 0.018 0.023 + 96 (0.030) 0.026 0.028 0.028 0.011 0.019 0.021 + +Locus 4 : A29 +29 alleles +6.7% missing data + 143 (0.033) 0.027 0.048 0.046 0.039 0.045 0.041 + 149 (0.049) 0.048 0.032 0.038 0.030 0.038 0.041 + 147 (0.030) 0.022 0.027 0.026 0.014 0.023 0.025 + 153 (0.053) 0.097 0.067 0.088 0.087 0.073 0.063 + 169 (0.038) 0.035 0.052 0.051 0.025 0.044 0.040 + 151 (0.037) 0.050 0.043 0.030 0.080 0.045 0.043 + 145 (0.028) 0.020 0.021 0.021 0.015 0.021 0.023 + 157 (0.066) 0.106 0.117 0.107 0.068 0.087 0.075 + 155 (0.093) 0.130 0.139 0.131 0.100 0.105 0.100 + 159 (0.051) 0.062 0.089 0.076 0.053 0.072 0.062 + 161 (0.033) 0.039 0.035 0.036 0.072 0.046 0.040 + 141 (0.030) 0.018 0.020 0.023 0.038 0.028 0.030 + 139 (0.017) 0.006 0.006 0.007 0.012 0.012 0.014 + 144 (0.026) 0.022 0.024 0.024 0.048 0.031 0.032 + 171 (0.047) 0.045 0.034 0.038 0.056 0.046 0.051 + 163 (0.073) 0.075 0.071 0.064 0.106 0.077 0.083 + 167 (0.045) 0.054 0.039 0.048 0.033 0.041 0.040 + 173 (0.025) 0.016 0.015 0.016 0.025 0.022 0.024 + 142 (0.014) 0.003 0.004 0.004 0.004 0.007 0.010 + 177 (0.025) 0.024 0.021 0.024 0.012 0.017 0.018 + 175 (0.023) 0.011 0.011 0.009 0.010 0.014 0.017 + 165 (0.045) 0.037 0.034 0.039 0.026 0.037 0.040 + 146 (0.021) 0.011 0.013 0.013 0.020 0.018 0.020 + 137 (0.020) 0.007 0.007 0.007 0.005 0.010 0.013 + 183 (0.018) 0.008 0.009 0.009 0.005 0.009 0.012 + 179 (0.019) 0.008 0.007 0.007 0.006 0.010 0.013 + 191 (0.014) 0.004 0.003 0.003 0.003 0.006 0.009 + 185 (0.014) 0.004 0.003 0.003 0.003 0.006 0.009 + 180 (0.016) 0.010 0.010 0.010 0.005 0.009 0.011 + +Locus 5 : A43 +7 alleles +1.3% missing data + 123 (0.199) 0.141 0.123 0.110 0.137 0.147 0.171 + 141 (0.018) 0.003 0.003 0.003 0.004 0.008 0.012 + 137 (0.664) 0.756 0.781 0.806 0.795 0.758 0.727 + 139 (0.048) 0.061 0.054 0.044 0.045 0.048 0.043 + 124 (0.034) 0.030 0.030 0.030 0.013 0.022 0.024 + 143 (0.018) 0.004 0.003 0.003 0.003 0.008 0.012 + 128 (0.018) 0.005 0.005 0.005 0.004 0.008 0.011 + +Locus 6 : A79 +13 alleles +3.4% missing data + 103 (0.233) 0.251 0.260 0.239 0.295 0.265 0.256 + 97 (0.127) 0.079 0.120 0.105 0.091 0.122 0.127 + 101 (0.093) 0.087 0.088 0.109 0.175 0.117 0.118 + 107 (0.097) 0.109 0.102 0.098 0.147 0.114 0.109 + 109 (0.097) 0.080 0.076 0.077 0.082 0.083 0.091 + 105 (0.165) 0.289 0.253 0.273 0.134 0.186 0.160 + 111 (0.047) 0.030 0.023 0.025 0.022 0.031 0.036 + 113 (0.017) 0.003 0.003 0.003 0.003 0.008 0.012 + 91 (0.028) 0.034 0.039 0.038 0.014 0.021 0.021 + 99 (0.033) 0.019 0.020 0.021 0.019 0.023 0.025 + 115 (0.028) 0.010 0.010 0.008 0.012 0.016 0.021 + 117 (0.017) 0.003 0.004 0.003 0.003 0.008 0.011 + 121 (0.017) 0.003 0.003 0.003 0.003 0.008 0.011 + +Locus 7 : A88 +9 alleles +6.0% missing data + 133 (0.018) 0.003 0.004 0.003 0.004 0.009 0.012 + 149 (0.518) 0.666 0.628 0.631 0.518 0.552 0.528 + 137 (0.105) 0.058 0.082 0.076 0.085 0.098 0.105 + 147 (0.189) 0.189 0.201 0.202 0.337 0.236 0.230 + 141 (0.087) 0.065 0.066 0.072 0.039 0.067 0.070 + 152 (0.019) 0.003 0.003 0.003 0.005 0.009 0.013 + 143 (0.019) 0.003 0.003 0.003 0.004 0.009 0.012 + 151 (0.019) 0.005 0.005 0.004 0.004 0.009 0.012 + 144 (0.026) 0.007 0.007 0.007 0.006 0.013 0.017 + +Locus 8 : A113 +12 alleles +7.4% missing data + 214 (0.566) 0.745 0.739 0.723 0.770 0.682 0.642 + 226 (0.064) 0.045 0.067 0.064 0.043 0.065 0.065 + 218 (0.018) 0.004 0.004 0.004 0.006 0.009 0.012 + 220 (0.065) 0.085 0.062 0.080 0.042 0.055 0.052 + 216 (0.057) 0.033 0.025 0.031 0.022 0.036 0.043 + 230 (0.046) 0.026 0.026 0.026 0.051 0.039 0.045 + 234 (0.034) 0.011 0.015 0.014 0.013 0.022 0.027 + 232 (0.032) 0.012 0.017 0.016 0.014 0.022 0.026 + 228 (0.051) 0.023 0.025 0.024 0.020 0.034 0.041 + 224 (0.018) 0.003 0.003 0.003 0.004 0.008 0.012 + 222 (0.033) 0.010 0.012 0.010 0.008 0.018 0.023 + 208 (0.017) 0.004 0.004 0.004 0.006 0.009 0.012 + +Locus 9 : Ac11 +9 alleles +4.7% missing data + 111 (0.129) 0.105 0.157 0.147 0.139 0.160 0.151 + 117 (0.295) 0.285 0.285 0.267 0.394 0.311 0.320 + 115 (0.250) 0.288 0.273 0.275 0.295 0.285 0.269 + 113 (0.158) 0.183 0.161 0.169 0.110 0.136 0.140 + 119 (0.054) 0.087 0.075 0.091 0.032 0.047 0.042 + 121 (0.029) 0.028 0.027 0.030 0.011 0.019 0.020 + 123 (0.034) 0.010 0.009 0.009 0.007 0.017 0.023 + 127 (0.032) 0.010 0.010 0.009 0.009 0.017 0.022 + 125 (0.018) 0.004 0.003 0.003 0.003 0.008 0.012 + +Locus 10 : Ac88 +8 alleles +0.7% missing data + 214 (0.744) 0.883 0.843 0.851 0.884 0.811 0.786 + 216 (0.030) 0.009 0.012 0.009 0.011 0.018 0.022 + 220 (0.116) 0.072 0.118 0.108 0.083 0.119 0.121 + 230 (0.026) 0.005 0.006 0.005 0.005 0.012 0.018 + 221 (0.018) 0.005 0.005 0.005 0.003 0.008 0.011 + 212 (0.022) 0.012 0.008 0.011 0.005 0.011 0.014 + 217 (0.018) 0.004 0.004 0.003 0.003 0.008 0.012 + 224 (0.024) 0.009 0.006 0.008 0.005 0.012 0.015 + +Locus 11 : Ac139 +8 alleles +13.4% missing data + 327 (0.504) 0.680 0.614 0.608 0.584 0.552 0.517 + 329 (0.290) 0.218 0.270 0.285 0.309 0.304 0.319 + 331 (0.073) 0.038 0.057 0.054 0.046 0.065 0.067 + 328 (0.041) 0.025 0.022 0.016 0.039 0.033 0.036 + 341 (0.020) 0.006 0.005 0.005 0.004 0.010 0.013 + 337 (0.032) 0.024 0.023 0.025 0.011 0.019 0.022 + 323 (0.020) 0.005 0.004 0.004 0.004 0.009 0.013 + 339 (0.020) 0.004 0.005 0.004 0.004 0.009 0.013 + +Locus 12 : Ac306 +6 alleles +4.7% missing data + 165 (0.727) 0.795 0.762 0.775 0.806 0.754 0.747 + 177 (0.077) 0.087 0.086 0.068 0.051 0.072 0.069 + 173 (0.100) 0.063 0.101 0.093 0.068 0.102 0.104 + 169 (0.046) 0.026 0.030 0.037 0.062 0.045 0.048 + 171 (0.019) 0.003 0.003 0.002 0.003 0.008 0.012 + 179 (0.031) 0.026 0.018 0.025 0.009 0.018 0.021 + +Locus 13 : Ap15 +7 alleles +6.0% missing data + 202 (0.807) 0.879 0.911 0.891 0.943 0.887 0.866 + 212 (0.029) 0.008 0.013 0.011 0.008 0.018 0.022 + 204 (0.046) 0.018 0.018 0.017 0.014 0.024 0.033 + 208 (0.039) 0.042 0.022 0.032 0.014 0.026 0.028 + 220 (0.040) 0.043 0.027 0.039 0.013 0.027 0.027 + 219 (0.019) 0.006 0.005 0.005 0.004 0.009 0.012 + 210 (0.019) 0.005 0.004 0.004 0.004 0.009 0.012 + +Locus 14 : Ap68 +9 alleles +4.7% missing data + 158 (0.381) 0.356 0.410 0.393 0.344 0.406 0.396 + 160 (0.079) 0.070 0.058 0.047 0.117 0.078 0.084 + 156 (0.247) 0.343 0.301 0.337 0.323 0.291 0.268 + 162 (0.045) 0.015 0.018 0.016 0.013 0.027 0.033 + 154 (0.083) 0.058 0.055 0.053 0.122 0.078 0.092 + 152 (0.079) 0.125 0.130 0.126 0.057 0.074 0.067 + 164 (0.044) 0.017 0.017 0.016 0.014 0.024 0.033 + 170 (0.019) 0.004 0.004 0.003 0.005 0.009 0.012 + 166 (0.023) 0.011 0.007 0.010 0.005 0.012 0.015 + +Locus 15 : Ap85 +10 alleles +3.4% missing data + 202 (0.316) 0.438 0.433 0.430 0.295 0.355 0.319 + 186 (0.244) 0.252 0.282 0.277 0.415 0.317 0.315 + 204 (0.061) 0.039 0.031 0.030 0.037 0.041 0.049 + 188 (0.100) 0.071 0.076 0.064 0.133 0.094 0.104 + 194 (0.080) 0.041 0.055 0.053 0.049 0.065 0.071 + 196 (0.060) 0.064 0.052 0.059 0.028 0.044 0.044 + 200 (0.064) 0.054 0.036 0.048 0.023 0.042 0.047 + 192 (0.026) 0.007 0.006 0.006 0.006 0.013 0.018 + 190 (0.018) 0.004 0.005 0.004 0.004 0.009 0.012 + 198 (0.030) 0.031 0.024 0.029 0.011 0.019 0.021 + +Locus 16 : Ap90 +13 alleles +0.7% missing data + 131 (0.363) 0.536 0.523 0.562 0.504 0.475 0.425 + 135 (0.068) 0.059 0.075 0.071 0.041 0.060 0.062 + 133 (0.276) 0.239 0.252 0.230 0.274 0.265 0.280 + 129 (0.098) 0.105 0.089 0.078 0.123 0.099 0.099 + 137 (0.035) 0.016 0.015 0.015 0.023 0.024 0.029 + 141 (0.017) 0.003 0.003 0.003 0.003 0.008 0.011 + 143 (0.024) 0.005 0.006 0.005 0.006 0.013 0.017 + 151 (0.025) 0.005 0.007 0.006 0.005 0.012 0.017 + 155 (0.017) 0.003 0.003 0.002 0.003 0.008 0.011 + 145 (0.017) 0.005 0.005 0.005 0.003 0.008 0.011 + 130 (0.021) 0.009 0.009 0.009 0.005 0.010 0.013 + 139 (0.017) 0.006 0.005 0.005 0.003 0.008 0.010 + 153 (0.022) 0.008 0.009 0.008 0.005 0.010 0.014 + +Locus 17 : Ap223 +7 alleles +2.0% missing data + 183 (0.680) 0.798 0.742 0.739 0.710 0.700 0.681 + 187 (0.136) 0.121 0.170 0.172 0.218 0.185 0.181 + 189 (0.028) 0.008 0.009 0.010 0.017 0.017 0.021 + 173 (0.066) 0.042 0.045 0.048 0.029 0.049 0.053 + 182 (0.033) 0.008 0.009 0.008 0.010 0.018 0.023 + 180 (0.026) 0.007 0.007 0.005 0.006 0.013 0.018 + 179 (0.032) 0.016 0.018 0.017 0.010 0.018 0.022 + +Locus 18 : Ap224 +7 alleles +4.0% missing data + 283 (0.113) 0.089 0.118 0.122 0.163 0.136 0.136 + 287 (0.471) 0.442 0.469 0.448 0.472 0.460 0.473 + 281 (0.137) 0.108 0.119 0.121 0.154 0.142 0.144 + 289 (0.194) 0.313 0.248 0.256 0.180 0.205 0.183 + 291 (0.039) 0.015 0.026 0.023 0.019 0.030 0.034 + 285 (0.018) 0.003 0.003 0.003 0.004 0.009 0.012 + 279 (0.027) 0.029 0.017 0.027 0.008 0.017 0.017 + +Locus 19 : Ap226 +5 alleles +17.4% missing data + 237 (0.376) 0.335 0.349 0.339 0.358 0.355 0.367 + 239 (0.461) 0.565 0.516 0.521 0.501 0.489 0.470 + 247 (0.122) 0.090 0.124 0.129 0.131 0.136 0.136 + 235 (0.020) 0.004 0.005 0.005 0.006 0.010 0.014 + 241 (0.020) 0.007 0.007 0.006 0.004 0.010 0.013 + +Locus 20 : Ap249 +9 alleles +1.3% missing data + 209 (0.597) 0.701 0.651 0.670 0.706 0.645 0.632 + 211 (0.057) 0.026 0.025 0.023 0.046 0.041 0.050 + 217 (0.085) 0.053 0.082 0.077 0.075 0.086 0.088 + 219 (0.104) 0.078 0.118 0.099 0.104 0.120 0.116 + 215 (0.084) 0.127 0.110 0.120 0.054 0.075 0.068 + 208 (0.018) 0.003 0.003 0.003 0.004 0.009 0.012 + 225 (0.018) 0.003 0.003 0.003 0.004 0.008 0.012 + 223 (0.018) 0.003 0.004 0.003 0.005 0.009 0.012 + 213 (0.018) 0.005 0.004 0.004 0.003 0.008 0.011 + +Locus 21 : Ap273 +4 alleles +1.3% missing data + 106 (0.873) 0.948 0.951 0.953 0.948 0.924 0.906 + 108 (0.052) 0.025 0.025 0.022 0.025 0.035 0.040 + 104 (0.045) 0.013 0.013 0.012 0.021 0.027 0.035 + 102 (0.030) 0.014 0.011 0.014 0.007 0.015 0.019 + +Locus 22 : Ap274 +2 alleles +2.0% missing data + 120 (0.946) 0.939 0.963 0.955 0.976 0.960 0.960 + 122 (0.054) 0.061 0.037 0.045 0.024 0.040 0.040 + +Locus 23 : Ap288 +5 alleles +0.0% missing data + 123 (0.769) 0.857 0.785 0.784 0.779 0.762 0.759 + 131 (0.162) 0.128 0.195 0.199 0.202 0.202 0.194 + 139 (0.031) 0.008 0.011 0.009 0.010 0.018 0.023 + 121 (0.019) 0.004 0.004 0.004 0.004 0.009 0.013 + 124 (0.019) 0.004 0.004 0.004 0.004 0.009 0.012 + +Locus 24 : At163 +7 alleles +0.0% missing data + 128 (0.705) 0.834 0.762 0.777 0.782 0.732 0.711 + 134 (0.195) 0.145 0.218 0.206 0.196 0.222 0.223 + 130 (0.026) 0.006 0.007 0.005 0.008 0.013 0.018 + 136 (0.019) 0.003 0.004 0.003 0.005 0.009 0.012 + 140 (0.019) 0.004 0.003 0.003 0.003 0.008 0.012 + 146 (0.018) 0.004 0.003 0.003 0.003 0.008 0.012 + 142 (0.018) 0.004 0.003 0.003 0.003 0.008 0.012 + +Locus 25 : At188 +13 alleles +1.3% missing data + 189 (0.616) 0.840 0.812 0.813 0.773 0.731 0.683 + 205 (0.033) 0.013 0.026 0.023 0.015 0.028 0.029 + 207 (0.030) 0.019 0.023 0.034 0.053 0.036 0.035 + 219 (0.025) 0.006 0.006 0.005 0.008 0.013 0.017 + 209 (0.037) 0.018 0.020 0.021 0.041 0.031 0.035 + 217 (0.040) 0.013 0.013 0.010 0.022 0.025 0.032 + 215 (0.022) 0.007 0.008 0.007 0.011 0.014 0.017 + 199 (0.069) 0.044 0.048 0.048 0.030 0.052 0.057 + 212 (0.027) 0.009 0.009 0.008 0.014 0.016 0.022 + 213 (0.038) 0.012 0.017 0.015 0.017 0.025 0.032 + 211 (0.018) 0.003 0.003 0.002 0.003 0.008 0.012 + 191 (0.017) 0.004 0.004 0.004 0.006 0.009 0.012 + 187 (0.028) 0.012 0.011 0.011 0.007 0.014 0.018 + +Values of parameters used in structure: +DATAFILE=, OUTFILE=, NUMINDS=149, NUMLOCI=25, MISSING=-9, LABEL=1, POPDATA=0, POPFLAG=1, PHENOTYPE=0, EXTRACOLS=1, MAXPOPS=6, BURNIN=100000, NUMREPS=1000000, USEPOPINFO=0, INFERALPHA=1, INFERLAMBDA=0, POPSPECIFICLAMBDA=0, POPALPHAS=0, COMPUTEPROB=1, NOADMIX=0, ADMBURNIN=2500, UPDATEFREQ=1, PRINTLIKES=0, INTERMEDSAVE=0, PRINTKLD=0, PRINTNET=0, PRINTLAMBDA=0, ANCESTDIST=0, NUMBOXES=1000, ANCESTPINT=0.90000, GENSBACK=2, MIGRPRIOR=0.05000, PRINTQHAT=0, PRINTQSUM=0, ALPHA=1.0000, FREQSCORR=1, FPRIORMEAN=0.0100, FPRIORSD=0.0500, ONEFST=0, LAMBDA=1.0000, UNIFPRIORALPHA=1, ALPHAMAX=10.0000, ALPHAPRIORA=1.0000, ALPHAPRIORB=2.0000, ALPHAPROPSD=0.0250, STARTATPOPINFO=0, RANDOMIZE=1, LINKAGE=0, METROFREQ=10, REPORTHITRATE=0, MARKOVPHASE=-1, PHASED=0, PLOIDY=2, PHASEINFO=0 LOCPRIOR=0, LOCPRIORINIT=1.000000, LOCDATA=0, LOCISPOP=0, LOCPRIORSTEP=0.100000, MAXLOCPRIOR=20.000000, SEED=1342793987, +[STRAT parameters]: NUMSIMSTATS=1000, PHENOTYPECOL=-9, POOLFREQ=10, LOCUSxONLY=0, EMERROR=0.00100, MISSINGPHENO=-9, \ No newline at end of file diff --git a/inst/files/structure/structure_14 b/inst/files/structure/structure_14 new file mode 100644 index 0000000..b3de195 --- /dev/null +++ b/inst/files/structure/structure_14 @@ -0,0 +1,544 @@ + + +---------------------------------------------------- +STRUCTURE by Pritchard, Stephens and Donnelly (2000) + and Falush, Stephens and Pritchard (2003) + Code by Pritchard, Falush and Hubisz + Version 2.3.2.1 (Oct 2009) +---------------------------------------------------- + + + +Command line arguments: +Input File: + +Run parameters: + 149 individuals + 25 loci + 7 populations assumed + 100000 Burn-in period + 1000000 Reps + + +-------------------------------------------- +Overall proportion of membership of the +sample in each of the 7 clusters + +Inferred Clusters + 1 2 3 4 5 6 7 +0.123 0.136 0.149 0.152 0.150 0.148 0.142 + +-------------------------------------------- + +Allele-freq. divergence among pops (Net nucleotide distance), +computed using point estimates of P. + + 1 2 3 4 5 6 7 + 1 - 0.0019 0.0047 0.0080 0.0075 0.0039 0.0027 + 2 0.0019 - 0.0007 0.0059 0.0057 0.0026 0.0006 + 3 0.0047 0.0007 - 0.0060 0.0055 0.0027 0.0008 + 4 0.0080 0.0059 0.0060 - 0.0006 0.0069 0.0035 + 5 0.0075 0.0057 0.0055 0.0006 - 0.0057 0.0033 + 6 0.0039 0.0026 0.0027 0.0069 0.0057 - 0.0015 + 7 0.0027 0.0006 0.0008 0.0035 0.0033 0.0015 - + +Average distances (expected heterozygosity) between individuals in same cluster: +cluster 1 : 0.5683 +cluster 2 : 0.5236 +cluster 3 : 0.4954 +cluster 4 : 0.4693 +cluster 5 : 0.4764 +cluster 6 : 0.5116 +cluster 7 : 0.5070 + +-------------------------------------------- +Estimated Ln Prob of Data = -8571.2 +Mean value of ln likelihood = -7137.5 +Variance of ln likelihood = 2867.4 +Mean value of alpha = 0.2095 + +Mean value of Fst_1 = 0.0193 +Mean value of Fst_2 = 0.1197 +Mean value of Fst_3 = 0.1847 +Mean value of Fst_4 = 0.1970 +Mean value of Fst_5 = 0.1925 +Mean value of Fst_6 = 0.1752 +Mean value of Fst_7 = 0.1620 + + +Inferred ancestry of individuals: + Label (%Miss) : Inferred clusters + 1 I13825 (0) : 0.273 0.156 0.114 0.078 0.079 0.164 0.136 + 2 I13826 (0) : 0.079 0.111 0.172 0.082 0.103 0.290 0.163 + 3 I13827 (20) : 0.075 0.205 0.262 0.109 0.116 0.082 0.152 + 4 I13828 (0) : 0.121 0.127 0.156 0.086 0.098 0.249 0.163 + 5 I13829 (8) : 0.088 0.170 0.215 0.132 0.111 0.129 0.155 + 6 I13830 (0) : 0.066 0.126 0.177 0.083 0.099 0.283 0.165 + 7 I13831 (0) : 0.080 0.161 0.181 0.134 0.131 0.158 0.156 + 8 I13832 (16) : 0.153 0.179 0.181 0.133 0.102 0.100 0.154 + 9 I13833 (0) : 0.077 0.182 0.226 0.132 0.127 0.109 0.147 + 10 I13834 (0) : 0.064 0.199 0.262 0.108 0.112 0.102 0.152 + 11 I13835 (0) : 0.173 0.179 0.149 0.127 0.105 0.113 0.154 + 12 I13836 (0) : 0.123 0.201 0.235 0.099 0.101 0.090 0.150 + 13 I13377 (0) : 0.098 0.166 0.203 0.134 0.141 0.113 0.146 + 14 I13378 (0) : 0.201 0.179 0.137 0.108 0.110 0.124 0.141 + 15 I13379 (0) : 0.082 0.142 0.175 0.104 0.125 0.220 0.152 + 16 I13380 (0) : 0.083 0.171 0.226 0.137 0.149 0.093 0.142 + 17 I13381 (0) : 0.132 0.160 0.136 0.170 0.107 0.110 0.185 + 18 I13382 (0) : 0.053 0.164 0.227 0.164 0.113 0.105 0.174 + 19 I13383 (0) : 0.168 0.171 0.132 0.133 0.107 0.121 0.169 + 20 I13384 (0) : 0.108 0.160 0.171 0.119 0.116 0.165 0.161 + 21 I13385 (0) : 0.075 0.199 0.261 0.117 0.113 0.087 0.148 + 22 I13386 (0) : 0.074 0.190 0.245 0.137 0.103 0.086 0.166 + 23 I13387 (0) : 0.136 0.134 0.167 0.084 0.099 0.226 0.155 + 24 I13388 (0) : 0.276 0.161 0.105 0.079 0.084 0.161 0.135 + 25 I13389 (0) : 0.075 0.158 0.207 0.134 0.163 0.121 0.142 + 26 I13390 (0) : 0.076 0.176 0.216 0.127 0.123 0.119 0.163 + 27 I13391 (0) : 0.195 0.171 0.149 0.109 0.124 0.111 0.140 + 28 I13392 (0) : 0.206 0.169 0.140 0.103 0.104 0.133 0.145 + 29 I13393 (0) : 0.068 0.142 0.150 0.212 0.126 0.114 0.187 + 30 I13394 (4) : 0.143 0.139 0.133 0.164 0.156 0.128 0.138 + 31 I13395 (0) : 0.116 0.138 0.144 0.175 0.151 0.135 0.141 + 32 I13396 (0) : 0.170 0.131 0.128 0.102 0.121 0.206 0.142 + 33 I13397 (0) : 0.202 0.165 0.148 0.091 0.100 0.145 0.148 + 34 I13398 (0) : 0.052 0.128 0.201 0.083 0.104 0.268 0.164 + 35 I13399 (4) : 0.256 0.184 0.142 0.091 0.099 0.102 0.126 + 36 I13400 (0) : 0.141 0.168 0.168 0.125 0.129 0.128 0.142 + 37 I13401 (0) : 0.122 0.125 0.144 0.143 0.208 0.134 0.124 + 38 I13402 (0) : 0.236 0.167 0.123 0.090 0.105 0.146 0.133 + 39 I13403 (0) : 0.068 0.112 0.159 0.131 0.142 0.231 0.157 + 40 I13404 (0) : 0.071 0.149 0.194 0.095 0.119 0.211 0.160 + 41 I13405 (0) : 0.069 0.192 0.257 0.123 0.123 0.085 0.151 + 42 I13406 (16) : 0.241 0.153 0.119 0.075 0.081 0.186 0.147 + 43 I13407 (0) : 0.102 0.140 0.157 0.103 0.125 0.217 0.156 + 44 I13408 (0) : 0.079 0.168 0.202 0.149 0.119 0.126 0.158 + 45 I13409 (0) : 0.275 0.148 0.110 0.077 0.093 0.168 0.128 + 46 I13410 (0) : 0.083 0.159 0.174 0.137 0.117 0.163 0.168 + 47 I13411 (0) : 0.071 0.184 0.233 0.102 0.107 0.143 0.160 + 48 I13412 (0) : 0.109 0.142 0.162 0.143 0.144 0.145 0.154 + 49 I13413 (0) : 0.179 0.151 0.134 0.087 0.104 0.202 0.143 + 50 I13414 (0) : 0.121 0.140 0.159 0.087 0.093 0.240 0.160 + 51 I13415 (4) : 0.076 0.170 0.221 0.121 0.136 0.125 0.149 + 52 I13416 (4) : 0.103 0.147 0.174 0.120 0.133 0.169 0.154 + 53 I13417 (4) : 0.063 0.154 0.212 0.139 0.157 0.131 0.144 + 54 I13418 (0) : 0.067 0.158 0.189 0.157 0.123 0.143 0.163 + 55 I13419 (0) : 0.268 0.197 0.159 0.080 0.072 0.095 0.129 + 56 I13420 (0) : 0.069 0.129 0.181 0.134 0.137 0.196 0.153 + 57 I13421 (0) : 0.059 0.134 0.173 0.199 0.150 0.122 0.163 + 58 I13422 (0) : 0.096 0.129 0.170 0.138 0.175 0.148 0.146 + 59 I13423 (0) : 0.165 0.158 0.138 0.151 0.105 0.121 0.163 + 60 I13424 (0) : 0.115 0.167 0.195 0.124 0.128 0.123 0.148 + 61 I13425 (4) : 0.131 0.180 0.197 0.114 0.111 0.120 0.147 + 62 I13426 (4) : 0.159 0.140 0.114 0.185 0.142 0.126 0.135 + 63 I13870 (0) : 0.088 0.119 0.146 0.143 0.142 0.214 0.147 + 64 I13871 (16) : 0.156 0.147 0.152 0.103 0.100 0.190 0.153 + 65 I13872 (0) : 0.127 0.119 0.153 0.072 0.092 0.283 0.154 + 66 I13873 (4) : 0.102 0.129 0.147 0.109 0.136 0.223 0.153 + 67 I13874 (0) : 0.203 0.131 0.136 0.084 0.099 0.207 0.140 + 68 I13875 (8) : 0.109 0.125 0.158 0.100 0.115 0.236 0.156 + 69 I13876 (0) : 0.342 0.168 0.085 0.081 0.085 0.121 0.119 + 70 I13877 (20) : 0.081 0.143 0.162 0.177 0.121 0.132 0.183 + 71 I13878 (28) : 0.068 0.141 0.203 0.093 0.108 0.226 0.160 + 72 I13879 (4) : 0.068 0.172 0.235 0.107 0.109 0.150 0.158 + 73 I13880 (4) : 0.062 0.112 0.170 0.077 0.102 0.316 0.161 + 74 I13881 (0) : 0.275 0.162 0.115 0.088 0.089 0.143 0.128 + 75 I13882 (0) : 0.110 0.127 0.159 0.094 0.106 0.244 0.160 + 76 I13883 (4) : 0.119 0.114 0.144 0.094 0.105 0.270 0.154 + 77 I13884 (16) : 0.379 0.182 0.090 0.069 0.067 0.098 0.114 + 78 I13885 (20) : 0.226 0.173 0.145 0.109 0.091 0.105 0.151 + 79 I13886 (8) : 0.105 0.149 0.178 0.092 0.113 0.210 0.153 + 80 I13887 (0) : 0.420 0.189 0.063 0.063 0.063 0.092 0.111 + 81 I13888 (0) : 0.221 0.164 0.119 0.098 0.091 0.151 0.156 + 82 I13889 (0) : 0.091 0.094 0.135 0.180 0.244 0.134 0.122 + 83 I13890 (32) : 0.135 0.136 0.120 0.196 0.153 0.124 0.136 + 84 I13891 (0) : 0.103 0.145 0.181 0.092 0.098 0.229 0.152 + 85 I13892 (0) : 0.093 0.135 0.152 0.169 0.166 0.140 0.145 + 86 I13893 (8) : 0.276 0.181 0.121 0.082 0.101 0.108 0.131 + 87 I13894 (0) : 0.071 0.098 0.165 0.077 0.105 0.325 0.160 + 88 I13895 (4) : 0.181 0.161 0.143 0.112 0.132 0.128 0.142 + 89 I13896 (0) : 0.101 0.110 0.140 0.135 0.141 0.228 0.146 + 90 I13897 (0) : 0.055 0.140 0.217 0.086 0.105 0.235 0.162 + 91 I13898 (4) : 0.093 0.136 0.158 0.105 0.126 0.223 0.158 + 92 I13899 (0) : 0.047 0.095 0.179 0.074 0.103 0.342 0.160 + 93 I13900 (32) : 0.315 0.170 0.103 0.083 0.087 0.121 0.122 + 94 I13837 (0) : 0.074 0.197 0.250 0.123 0.123 0.085 0.148 + 95 I13838 (0) : 0.095 0.103 0.119 0.209 0.196 0.148 0.130 + 96 I13839 (0) : 0.077 0.188 0.237 0.118 0.136 0.095 0.150 + 97 I13840 (0) : 0.066 0.148 0.191 0.155 0.153 0.137 0.149 + 98 I13841 (0) : 0.051 0.107 0.127 0.256 0.171 0.132 0.156 + 99 I13842 (0) : 0.077 0.153 0.192 0.175 0.156 0.102 0.144 +100 I13843 (4) : 0.056 0.103 0.122 0.248 0.175 0.139 0.156 +101 I13844 (16) : 0.143 0.161 0.161 0.139 0.129 0.119 0.148 +102 I13845 (0) : 0.073 0.172 0.234 0.147 0.109 0.109 0.157 +103 I13846 (0) : 0.123 0.170 0.188 0.130 0.121 0.111 0.158 +104 I13847 (0) : 0.122 0.121 0.136 0.156 0.155 0.168 0.142 +105 I13848 (0) : 0.144 0.136 0.132 0.140 0.154 0.145 0.150 +106 I13849 (0) : 0.159 0.135 0.131 0.102 0.122 0.196 0.155 +107 I13850 (0) : 0.084 0.117 0.123 0.210 0.177 0.145 0.144 +108 I12577 (4) : 0.097 0.094 0.107 0.245 0.216 0.116 0.124 +109 I12578 (4) : 0.074 0.079 0.125 0.184 0.279 0.137 0.122 +110 I12579 (8) : 0.156 0.118 0.095 0.232 0.177 0.104 0.119 +111 I12580 (8) : 0.038 0.083 0.105 0.296 0.228 0.120 0.130 +112 I12581 (4) : 0.221 0.152 0.118 0.123 0.144 0.109 0.133 +113 I12582 (4) : 0.067 0.089 0.105 0.265 0.220 0.127 0.129 +114 I12583 (8) : 0.294 0.135 0.082 0.122 0.161 0.103 0.103 +115 I12584 (4) : 0.219 0.123 0.086 0.166 0.180 0.115 0.111 +116 I12585 (4) : 0.060 0.080 0.098 0.280 0.238 0.126 0.118 +117 I12586 (4) : 0.041 0.089 0.102 0.301 0.214 0.120 0.132 +118 I12587 (8) : 0.030 0.073 0.102 0.305 0.236 0.135 0.119 +119 I12588 (4) : 0.090 0.096 0.094 0.276 0.210 0.108 0.127 +120 I12589 (0) : 0.061 0.072 0.117 0.222 0.267 0.150 0.110 +121 I12590 (0) : 0.115 0.109 0.102 0.240 0.188 0.120 0.127 +122 I12591 (12) : 0.038 0.062 0.114 0.246 0.285 0.126 0.128 +123 I12592 (4) : 0.071 0.072 0.128 0.185 0.295 0.129 0.120 +124 I12593 (4) : 0.056 0.065 0.121 0.212 0.288 0.130 0.128 +125 I12594 (8) : 0.041 0.078 0.104 0.295 0.231 0.116 0.135 +126 I12595 (0) : 0.216 0.123 0.096 0.162 0.181 0.107 0.115 +127 I12596 (0) : 0.049 0.073 0.113 0.258 0.254 0.122 0.130 +128 I12597 (4) : 0.272 0.149 0.072 0.174 0.126 0.096 0.112 +129 I12598 (0) : 0.186 0.104 0.101 0.155 0.221 0.127 0.106 +130 I12599 (0) : 0.161 0.114 0.106 0.176 0.187 0.130 0.127 +131 I12600 (4) : 0.042 0.084 0.102 0.302 0.216 0.137 0.117 +132 I12601 (8) : 0.098 0.101 0.089 0.270 0.206 0.117 0.119 +133 I12602 (12) : 0.074 0.092 0.100 0.274 0.214 0.112 0.132 +134 I12603 (0) : 0.188 0.132 0.084 0.221 0.163 0.099 0.114 +135 I12604 (4) : 0.098 0.101 0.097 0.257 0.196 0.129 0.122 +136 I12605 (4) : 0.098 0.100 0.095 0.259 0.201 0.121 0.126 +137 I12606 (8) : 0.066 0.074 0.124 0.202 0.281 0.129 0.124 +138 I12607 (4) : 0.158 0.098 0.107 0.155 0.247 0.124 0.111 +139 I12608 (8) : 0.122 0.100 0.115 0.170 0.241 0.128 0.124 +140 I12609 (8) : 0.056 0.075 0.115 0.242 0.262 0.129 0.121 +141 I12610 (52) : 0.091 0.106 0.109 0.254 0.198 0.117 0.123 +142 I12611 (0) : 0.044 0.063 0.113 0.235 0.291 0.146 0.109 +143 I12612 (0) : 0.059 0.087 0.097 0.282 0.229 0.128 0.117 +144 I12613 (0) : 0.044 0.062 0.127 0.210 0.305 0.135 0.116 +145 I12614 (4) : 0.071 0.100 0.119 0.247 0.204 0.117 0.142 +146 I12615 (0) : 0.122 0.100 0.119 0.170 0.243 0.131 0.116 +147 I12616 (4) : 0.249 0.132 0.095 0.138 0.175 0.098 0.113 +148 I12617 (8) : 0.030 0.073 0.100 0.304 0.242 0.116 0.136 +149 I12618 (48) : 0.073 0.097 0.096 0.293 0.204 0.116 0.121 + + +Estimated Allele Frequencies in each cluster +First column gives estimated ancestral frequencies + + +Locus 1 : A8 +7 alleles +4.0% missing data + 177 (0.517) 0.516 0.494 0.481 0.554 0.557 0.523 0.510 + 179 (0.096) 0.097 0.100 0.104 0.077 0.071 0.078 0.091 + 175 (0.097) 0.109 0.175 0.204 0.104 0.099 0.180 0.166 + 173 (0.046) 0.048 0.047 0.046 0.031 0.031 0.033 0.038 + 181 (0.180) 0.171 0.146 0.140 0.209 0.210 0.159 0.162 + 165 (0.038) 0.035 0.021 0.015 0.017 0.024 0.017 0.019 + 183 (0.027) 0.025 0.017 0.009 0.009 0.008 0.011 0.014 + +Locus 2 : A14 +5 alleles +0.0% missing data + 112 (0.206) 0.212 0.207 0.211 0.146 0.145 0.271 0.221 + 110 (0.701) 0.703 0.732 0.747 0.761 0.779 0.677 0.717 + 114 (0.029) 0.027 0.016 0.009 0.007 0.007 0.011 0.012 + 118 (0.036) 0.032 0.028 0.025 0.065 0.053 0.030 0.036 + 116 (0.028) 0.025 0.017 0.008 0.021 0.015 0.011 0.013 + +Locus 3 : A24 +5 alleles +2.7% missing data + 104 (0.401) 0.401 0.371 0.350 0.363 0.362 0.415 0.371 + 106 (0.525) 0.531 0.586 0.624 0.590 0.599 0.551 0.591 + 101 (0.017) 0.015 0.009 0.004 0.004 0.003 0.004 0.006 + 108 (0.028) 0.026 0.016 0.010 0.007 0.008 0.014 0.013 + 96 (0.029) 0.026 0.019 0.012 0.036 0.028 0.016 0.019 + +Locus 4 : A29 +29 alleles +6.7% missing data + 143 (0.033) 0.034 0.039 0.049 0.025 0.027 0.063 0.044 + 149 (0.047) 0.045 0.035 0.032 0.034 0.051 0.034 0.033 + 147 (0.029) 0.027 0.021 0.017 0.025 0.022 0.026 0.023 + 153 (0.049) 0.053 0.079 0.095 0.080 0.107 0.064 0.076 + 169 (0.040) 0.039 0.032 0.037 0.029 0.039 0.067 0.043 + 151 (0.037) 0.039 0.054 0.053 0.065 0.042 0.036 0.055 + 145 (0.028) 0.027 0.020 0.016 0.020 0.020 0.020 0.020 + 157 (0.069) 0.068 0.078 0.079 0.120 0.103 0.114 0.091 + 155 (0.100) 0.101 0.106 0.104 0.147 0.130 0.118 0.118 + 159 (0.052) 0.055 0.056 0.067 0.061 0.060 0.108 0.072 + 161 (0.032) 0.036 0.059 0.063 0.045 0.031 0.028 0.048 + 141 (0.028) 0.030 0.037 0.035 0.020 0.019 0.016 0.026 + 139 (0.016) 0.015 0.014 0.012 0.006 0.005 0.005 0.010 + 144 (0.025) 0.028 0.036 0.043 0.025 0.022 0.023 0.031 + 171 (0.049) 0.051 0.047 0.051 0.037 0.046 0.040 0.044 + 163 (0.077) 0.081 0.086 0.084 0.075 0.072 0.073 0.080 + 167 (0.045) 0.043 0.037 0.038 0.043 0.056 0.038 0.043 + 173 (0.024) 0.024 0.023 0.022 0.015 0.016 0.017 0.020 + 142 (0.013) 0.012 0.007 0.004 0.003 0.003 0.005 0.005 + 177 (0.024) 0.022 0.016 0.014 0.026 0.025 0.015 0.018 + 175 (0.022) 0.021 0.014 0.008 0.012 0.011 0.009 0.011 + 165 (0.046) 0.044 0.035 0.032 0.029 0.038 0.037 0.035 + 146 (0.021) 0.021 0.021 0.018 0.011 0.011 0.014 0.016 + 137 (0.018) 0.016 0.009 0.005 0.007 0.007 0.006 0.007 + 183 (0.017) 0.015 0.009 0.005 0.010 0.008 0.006 0.007 + 179 (0.018) 0.017 0.010 0.006 0.009 0.008 0.006 0.008 + 191 (0.013) 0.012 0.006 0.003 0.003 0.004 0.003 0.004 + 185 (0.012) 0.011 0.006 0.003 0.003 0.004 0.003 0.004 + 180 (0.015) 0.013 0.009 0.005 0.013 0.010 0.007 0.007 + +Locus 5 : A43 +7 alleles +1.3% missing data + 123 (0.192) 0.186 0.148 0.111 0.142 0.132 0.114 0.135 + 141 (0.016) 0.015 0.007 0.003 0.003 0.003 0.004 0.005 + 137 (0.681) 0.698 0.761 0.825 0.732 0.777 0.818 0.779 + 139 (0.045) 0.042 0.047 0.041 0.075 0.050 0.037 0.051 + 124 (0.034) 0.031 0.022 0.015 0.038 0.030 0.020 0.021 + 143 (0.016) 0.014 0.007 0.003 0.003 0.004 0.003 0.004 + 128 (0.016) 0.014 0.008 0.003 0.006 0.004 0.004 0.005 + +Locus 6 : A79 +13 alleles +3.4% missing data + 103 (0.243) 0.249 0.265 0.270 0.252 0.240 0.278 0.274 + 97 (0.127) 0.130 0.108 0.097 0.075 0.083 0.147 0.109 + 101 (0.093) 0.103 0.149 0.171 0.087 0.096 0.082 0.116 + 107 (0.093) 0.096 0.130 0.131 0.122 0.091 0.092 0.125 + 109 (0.098) 0.097 0.084 0.079 0.076 0.082 0.078 0.078 + 105 (0.170) 0.162 0.155 0.178 0.275 0.304 0.239 0.203 + 111 (0.045) 0.042 0.029 0.021 0.023 0.031 0.026 0.025 + 113 (0.016) 0.014 0.007 0.003 0.003 0.003 0.004 0.005 + 91 (0.026) 0.023 0.021 0.017 0.050 0.037 0.022 0.025 + 99 (0.032) 0.030 0.024 0.018 0.021 0.019 0.016 0.020 + 115 (0.026) 0.025 0.016 0.010 0.009 0.009 0.010 0.012 + 117 (0.016) 0.014 0.007 0.003 0.003 0.003 0.004 0.005 + 121 (0.016) 0.014 0.007 0.003 0.002 0.003 0.003 0.004 + +Locus 7 : A88 +9 alleles +6.0% missing data + 133 (0.017) 0.015 0.008 0.003 0.003 0.003 0.004 0.005 + 149 (0.527) 0.525 0.522 0.537 0.662 0.678 0.608 0.577 + 137 (0.103) 0.105 0.092 0.090 0.053 0.061 0.102 0.087 + 147 (0.194) 0.210 0.285 0.302 0.205 0.172 0.197 0.248 + 141 (0.083) 0.078 0.057 0.052 0.059 0.069 0.071 0.061 + 152 (0.017) 0.016 0.008 0.004 0.003 0.003 0.004 0.005 + 143 (0.017) 0.015 0.008 0.003 0.003 0.003 0.004 0.005 + 151 (0.017) 0.015 0.008 0.003 0.005 0.004 0.004 0.005 + 144 (0.024) 0.021 0.011 0.005 0.007 0.007 0.006 0.008 + +Locus 8 : A113 +12 alleles +7.4% missing data + 214 (0.585) 0.604 0.704 0.748 0.777 0.738 0.710 0.729 + 226 (0.065) 0.065 0.056 0.054 0.039 0.045 0.089 0.060 + 218 (0.016) 0.015 0.010 0.006 0.004 0.004 0.004 0.006 + 220 (0.064) 0.061 0.048 0.054 0.077 0.092 0.052 0.058 + 216 (0.054) 0.050 0.033 0.025 0.025 0.035 0.026 0.029 + 230 (0.046) 0.047 0.046 0.042 0.026 0.026 0.027 0.035 + 234 (0.033) 0.031 0.020 0.015 0.009 0.011 0.019 0.017 + 232 (0.030) 0.028 0.020 0.016 0.010 0.012 0.022 0.018 + 228 (0.046) 0.044 0.030 0.023 0.017 0.023 0.032 0.026 + 224 (0.017) 0.015 0.008 0.003 0.003 0.003 0.004 0.005 + 222 (0.029) 0.027 0.016 0.008 0.009 0.009 0.013 0.012 + 208 (0.016) 0.015 0.009 0.005 0.004 0.004 0.004 0.006 + +Locus 9 : Ac11 +9 alleles +4.7% missing data + 111 (0.134) 0.140 0.143 0.156 0.092 0.109 0.206 0.154 + 117 (0.305) 0.314 0.338 0.340 0.298 0.274 0.285 0.326 + 115 (0.246) 0.251 0.290 0.301 0.278 0.277 0.280 0.278 + 113 (0.160) 0.154 0.130 0.123 0.180 0.189 0.142 0.136 + 119 (0.052) 0.047 0.043 0.047 0.096 0.098 0.049 0.060 + 121 (0.026) 0.023 0.018 0.015 0.034 0.030 0.017 0.021 + 123 (0.032) 0.029 0.016 0.007 0.009 0.010 0.009 0.011 + 127 (0.029) 0.027 0.015 0.008 0.011 0.010 0.009 0.011 + 125 (0.017) 0.016 0.007 0.003 0.003 0.003 0.004 0.004 + +Locus 10 : Ac88 +8 alleles +0.7% missing data + 214 (0.757) 0.769 0.838 0.868 0.903 0.878 0.797 0.847 + 216 (0.028) 0.026 0.017 0.010 0.008 0.007 0.014 0.014 + 220 (0.115) 0.116 0.098 0.100 0.059 0.078 0.162 0.107 + 230 (0.025) 0.023 0.012 0.005 0.005 0.005 0.006 0.008 + 221 (0.016) 0.014 0.008 0.003 0.005 0.004 0.004 0.005 + 212 (0.020) 0.017 0.010 0.006 0.009 0.014 0.008 0.008 + 217 (0.016) 0.014 0.007 0.003 0.003 0.004 0.004 0.005 + 224 (0.022) 0.020 0.010 0.005 0.007 0.009 0.006 0.008 + +Locus 11 : Ac139 +8 alleles +13.4% missing data + 327 (0.521) 0.523 0.550 0.570 0.696 0.680 0.560 0.580 + 329 (0.288) 0.296 0.315 0.326 0.196 0.222 0.320 0.294 + 331 (0.069) 0.068 0.055 0.053 0.034 0.039 0.072 0.055 + 328 (0.036) 0.036 0.036 0.027 0.031 0.019 0.020 0.035 + 341 (0.019) 0.017 0.009 0.004 0.006 0.005 0.005 0.006 + 337 (0.031) 0.028 0.018 0.013 0.030 0.026 0.014 0.020 + 323 (0.018) 0.016 0.008 0.004 0.004 0.005 0.004 0.005 + 339 (0.018) 0.016 0.009 0.003 0.005 0.004 0.004 0.005 + +Locus 12 : Ac306 +6 alleles +4.7% missing data + 165 (0.734) 0.741 0.770 0.785 0.795 0.797 0.748 0.773 + 177 (0.073) 0.070 0.060 0.053 0.096 0.077 0.076 0.070 + 173 (0.103) 0.103 0.087 0.084 0.055 0.067 0.134 0.093 + 169 (0.042) 0.044 0.059 0.061 0.029 0.027 0.022 0.042 + 171 (0.017) 0.016 0.008 0.003 0.002 0.003 0.003 0.004 + 179 (0.031) 0.027 0.016 0.014 0.023 0.030 0.016 0.017 + +Locus 13 : Ap15 +7 alleles +6.0% missing data + 202 (0.824) 0.840 0.904 0.927 0.904 0.867 0.911 0.911 + 212 (0.026) 0.025 0.014 0.010 0.007 0.007 0.017 0.013 + 204 (0.044) 0.041 0.024 0.013 0.019 0.017 0.015 0.018 + 208 (0.035) 0.031 0.021 0.020 0.028 0.049 0.024 0.021 + 220 (0.036) 0.033 0.021 0.022 0.033 0.049 0.024 0.026 + 219 (0.017) 0.015 0.008 0.004 0.005 0.006 0.005 0.005 + 210 (0.017) 0.016 0.008 0.004 0.004 0.005 0.004 0.005 + +Locus 14 : Ap68 +9 alleles +4.7% missing data + 158 (0.384) 0.385 0.376 0.374 0.332 0.350 0.475 0.391 + 160 (0.081) 0.083 0.088 0.084 0.075 0.062 0.059 0.080 + 156 (0.252) 0.259 0.305 0.342 0.324 0.350 0.280 0.313 + 162 (0.042) 0.039 0.023 0.015 0.012 0.014 0.021 0.020 + 154 (0.085) 0.091 0.093 0.095 0.059 0.061 0.056 0.076 + 152 (0.075) 0.070 0.072 0.067 0.169 0.129 0.081 0.087 + 164 (0.041) 0.039 0.024 0.014 0.017 0.017 0.016 0.018 + 170 (0.017) 0.016 0.008 0.003 0.003 0.004 0.004 0.005 + 166 (0.022) 0.019 0.010 0.006 0.008 0.013 0.008 0.008 + +Locus 15 : Ap85 +10 alleles +3.4% missing data + 202 (0.314) 0.309 0.321 0.343 0.443 0.440 0.406 0.369 + 186 (0.256) 0.277 0.354 0.382 0.259 0.244 0.319 0.326 + 204 (0.062) 0.059 0.041 0.031 0.032 0.037 0.032 0.036 + 188 (0.102) 0.107 0.110 0.100 0.078 0.069 0.077 0.096 + 194 (0.078) 0.076 0.062 0.055 0.038 0.042 0.061 0.055 + 196 (0.060) 0.055 0.040 0.035 0.066 0.067 0.041 0.047 + 200 (0.059) 0.054 0.035 0.030 0.042 0.059 0.034 0.037 + 192 (0.023) 0.021 0.012 0.005 0.005 0.006 0.007 0.008 + 190 (0.016) 0.015 0.008 0.004 0.003 0.003 0.006 0.006 + 198 (0.029) 0.026 0.018 0.014 0.032 0.034 0.017 0.020 + +Locus 16 : Ap90 +13 alleles +0.7% missing data + 131 (0.374) 0.390 0.474 0.554 0.514 0.554 0.526 0.507 + 135 (0.063) 0.060 0.056 0.050 0.072 0.062 0.069 0.060 + 133 (0.288) 0.291 0.267 0.244 0.235 0.235 0.271 0.260 + 129 (0.097) 0.097 0.107 0.100 0.117 0.091 0.079 0.107 + 137 (0.033) 0.032 0.025 0.020 0.015 0.015 0.014 0.018 + 141 (0.016) 0.014 0.007 0.003 0.003 0.003 0.004 0.004 + 143 (0.022) 0.020 0.012 0.006 0.004 0.005 0.007 0.008 + 151 (0.022) 0.020 0.011 0.005 0.005 0.005 0.008 0.008 + 155 (0.015) 0.014 0.007 0.003 0.002 0.002 0.003 0.004 + 145 (0.015) 0.014 0.007 0.003 0.006 0.005 0.004 0.005 + 130 (0.019) 0.017 0.010 0.005 0.011 0.009 0.006 0.008 + 139 (0.016) 0.014 0.007 0.004 0.005 0.006 0.004 0.005 + 153 (0.020) 0.017 0.010 0.004 0.010 0.008 0.006 0.007 + +Locus 17 : Ap223 +7 alleles +2.0% missing data + 183 (0.689) 0.685 0.695 0.695 0.813 0.786 0.700 0.731 + 187 (0.140) 0.156 0.198 0.226 0.113 0.131 0.210 0.179 + 189 (0.024) 0.023 0.019 0.015 0.009 0.008 0.008 0.012 + 173 (0.062) 0.059 0.042 0.038 0.032 0.046 0.053 0.042 + 182 (0.030) 0.028 0.017 0.009 0.007 0.008 0.010 0.012 + 180 (0.024) 0.022 0.012 0.005 0.007 0.006 0.007 0.009 + 179 (0.030) 0.027 0.018 0.010 0.020 0.016 0.014 0.015 + +Locus 18 : Ap224 +7 alleles +4.0% missing data + 283 (0.114) 0.121 0.145 0.165 0.086 0.094 0.142 0.131 + 287 (0.476) 0.478 0.471 0.449 0.466 0.435 0.455 0.469 + 281 (0.137) 0.140 0.148 0.150 0.103 0.104 0.138 0.140 + 289 (0.196) 0.189 0.188 0.194 0.309 0.315 0.213 0.215 + 291 (0.036) 0.035 0.026 0.023 0.012 0.015 0.034 0.024 + 285 (0.017) 0.016 0.008 0.003 0.003 0.003 0.003 0.005 + 279 (0.024) 0.021 0.013 0.014 0.022 0.035 0.015 0.017 + +Locus 19 : Ap226 +5 alleles +17.4% missing data + 237 (0.379) 0.378 0.365 0.349 0.352 0.329 0.331 0.352 + 239 (0.465) 0.466 0.477 0.496 0.554 0.570 0.507 0.504 + 247 (0.120) 0.124 0.139 0.145 0.082 0.090 0.152 0.131 + 235 (0.018) 0.016 0.010 0.006 0.004 0.004 0.004 0.006 + 241 (0.018) 0.016 0.009 0.004 0.007 0.006 0.005 0.006 + +Locus 20 : Ap249 +9 alleles +1.3% missing data + 209 (0.604) 0.611 0.668 0.691 0.696 0.694 0.634 0.668 + 211 (0.054) 0.053 0.045 0.037 0.026 0.024 0.025 0.035 + 217 (0.085) 0.087 0.081 0.083 0.048 0.058 0.103 0.078 + 219 (0.107) 0.112 0.106 0.108 0.075 0.078 0.147 0.115 + 215 (0.084) 0.078 0.070 0.068 0.143 0.134 0.076 0.085 + 208 (0.017) 0.015 0.008 0.003 0.003 0.003 0.004 0.005 + 225 (0.016) 0.015 0.008 0.003 0.003 0.003 0.004 0.005 + 223 (0.016) 0.014 0.008 0.003 0.003 0.003 0.003 0.005 + 213 (0.016) 0.014 0.007 0.003 0.004 0.005 0.004 0.004 + +Locus 21 : Ap273 +4 alleles +1.3% missing data + 106 (0.882) 0.890 0.927 0.952 0.951 0.951 0.951 0.940 + 108 (0.049) 0.046 0.033 0.022 0.025 0.022 0.025 0.030 + 104 (0.042) 0.040 0.027 0.017 0.012 0.012 0.014 0.019 + 102 (0.027) 0.024 0.013 0.009 0.012 0.015 0.010 0.011 + +Locus 22 : Ap274 +2 alleles +2.0% missing data + 120 (0.951) 0.956 0.969 0.970 0.952 0.934 0.961 0.965 + 122 (0.049) 0.044 0.031 0.030 0.048 0.066 0.039 0.035 + +Locus 23 : Ap288 +5 alleles +0.0% missing data + 123 (0.773) 0.768 0.763 0.757 0.865 0.854 0.739 0.779 + 131 (0.165) 0.175 0.205 0.226 0.122 0.133 0.238 0.197 + 139 (0.028) 0.026 0.016 0.009 0.007 0.007 0.013 0.013 + 121 (0.016) 0.015 0.008 0.004 0.003 0.003 0.005 0.006 + 124 (0.018) 0.016 0.009 0.004 0.003 0.003 0.005 0.006 + +Locus 24 : At163 +7 alleles +0.0% missing data + 128 (0.710) 0.711 0.754 0.764 0.854 0.829 0.694 0.764 + 134 (0.200) 0.208 0.203 0.218 0.129 0.152 0.285 0.209 + 130 (0.023) 0.021 0.012 0.006 0.005 0.006 0.008 0.009 + 136 (0.016) 0.015 0.008 0.003 0.003 0.003 0.004 0.005 + 140 (0.017) 0.015 0.007 0.003 0.003 0.003 0.003 0.004 + 146 (0.017) 0.015 0.007 0.003 0.003 0.003 0.003 0.004 + 142 (0.017) 0.015 0.007 0.003 0.003 0.004 0.003 0.004 + +Locus 25 : At188 +13 alleles +1.3% missing data + 189 (0.640) 0.652 0.725 0.779 0.846 0.841 0.802 0.780 + 205 (0.030) 0.029 0.021 0.021 0.011 0.014 0.036 0.023 + 207 (0.028) 0.031 0.051 0.055 0.021 0.021 0.016 0.034 + 219 (0.022) 0.021 0.012 0.006 0.005 0.005 0.007 0.008 + 209 (0.036) 0.036 0.037 0.034 0.020 0.019 0.019 0.027 + 217 (0.037) 0.036 0.025 0.016 0.012 0.013 0.015 0.018 + 215 (0.020) 0.019 0.013 0.009 0.007 0.006 0.009 0.010 + 199 (0.068) 0.064 0.045 0.037 0.042 0.044 0.052 0.047 + 212 (0.025) 0.025 0.016 0.011 0.008 0.008 0.009 0.012 + 213 (0.036) 0.035 0.024 0.017 0.010 0.012 0.020 0.019 + 211 (0.016) 0.014 0.007 0.003 0.002 0.002 0.003 0.004 + 191 (0.016) 0.015 0.009 0.005 0.004 0.003 0.004 0.006 + 187 (0.026) 0.024 0.014 0.007 0.012 0.011 0.008 0.010 + +Values of parameters used in structure: +DATAFILE=, OUTFILE=, NUMINDS=149, NUMLOCI=25, MISSING=-9, LABEL=1, POPDATA=0, POPFLAG=1, PHENOTYPE=0, EXTRACOLS=1, MAXPOPS=7, BURNIN=100000, NUMREPS=1000000, USEPOPINFO=0, INFERALPHA=1, INFERLAMBDA=0, POPSPECIFICLAMBDA=0, POPALPHAS=0, COMPUTEPROB=1, NOADMIX=0, ADMBURNIN=2500, UPDATEFREQ=1, PRINTLIKES=0, INTERMEDSAVE=0, PRINTKLD=0, PRINTNET=0, PRINTLAMBDA=0, ANCESTDIST=0, NUMBOXES=1000, ANCESTPINT=0.90000, GENSBACK=2, MIGRPRIOR=0.05000, PRINTQHAT=0, PRINTQSUM=0, ALPHA=1.0000, FREQSCORR=1, FPRIORMEAN=0.0100, FPRIORSD=0.0500, ONEFST=0, LAMBDA=1.0000, UNIFPRIORALPHA=1, ALPHAMAX=10.0000, ALPHAPRIORA=1.0000, ALPHAPRIORB=2.0000, ALPHAPROPSD=0.0250, STARTATPOPINFO=0, RANDOMIZE=1, LINKAGE=0, METROFREQ=10, REPORTHITRATE=0, MARKOVPHASE=-1, PHASED=0, PLOIDY=2, PHASEINFO=0 LOCPRIOR=0, LOCPRIORINIT=1.000000, LOCDATA=0, LOCISPOP=0, LOCPRIORSTEP=0.100000, MAXLOCPRIOR=20.000000, SEED=1342797202, +[STRAT parameters]: NUMSIMSTATS=1000, PHENOTYPECOL=-9, POOLFREQ=10, LOCUSxONLY=0, EMERROR=0.00100, MISSINGPHENO=-9, \ No newline at end of file diff --git a/inst/files/structure/structure_15 b/inst/files/structure/structure_15 new file mode 100644 index 0000000..b309e1e --- /dev/null +++ b/inst/files/structure/structure_15 @@ -0,0 +1,535 @@ + + +---------------------------------------------------- +STRUCTURE by Pritchard, Stephens and Donnelly (2000) + and Falush, Stephens and Pritchard (2003) + Code by Pritchard, Falush and Hubisz + Version 2.3.2.1 (Oct 2009) +---------------------------------------------------- + + + +Command line arguments: +Input File: + +Run parameters: + 149 individuals + 25 loci + 4 populations assumed + 100000 Burn-in period + 1000000 Reps + + +-------------------------------------------- +Overall proportion of membership of the +sample in each of the 4 clusters + +Inferred Clusters + 1 2 3 4 +0.221 0.242 0.297 0.239 + +-------------------------------------------- + +Allele-freq. divergence among pops (Net nucleotide distance), +computed using point estimates of P. + + 1 2 3 4 + 1 - 0.0135 0.0266 0.0008 + 2 0.0135 - 0.0501 0.0161 + 3 0.0266 0.0501 - 0.0297 + 4 0.0008 0.0161 0.0297 - + +Average distances (expected heterozygosity) between individuals in same cluster: +cluster 1 : 0.5389 +cluster 2 : 0.5197 +cluster 3 : 0.4277 +cluster 4 : 0.5112 + +-------------------------------------------- +Estimated Ln Prob of Data = -7665.9 +Mean value of ln likelihood = -7258.4 +Variance of ln likelihood = 815.1 +Mean value of alpha = 0.2082 + +Mean value of Fst_1 = 0.0511 +Mean value of Fst_2 = 0.1058 +Mean value of Fst_3 = 0.1152 +Mean value of Fst_4 = 0.0802 + + +Inferred ancestry of individuals: + Label (%Miss) : Inferred clusters + 1 I13825 (0) : 0.324 0.419 0.033 0.224 + 2 I13826 (0) : 0.080 0.820 0.033 0.067 + 3 I13827 (20) : 0.372 0.069 0.037 0.522 + 4 I13828 (0) : 0.140 0.720 0.033 0.107 + 5 I13829 (8) : 0.343 0.147 0.032 0.478 + 6 I13830 (0) : 0.081 0.814 0.029 0.076 + 7 I13831 (0) : 0.279 0.275 0.046 0.399 + 8 I13832 (16) : 0.384 0.115 0.049 0.453 + 9 I13833 (0) : 0.342 0.105 0.048 0.505 + 10 I13834 (0) : 0.349 0.122 0.022 0.507 + 11 I13835 (0) : 0.413 0.120 0.023 0.443 + 12 I13836 (0) : 0.380 0.111 0.027 0.481 + 13 I13377 (0) : 0.362 0.053 0.062 0.522 + 14 I13378 (0) : 0.396 0.218 0.038 0.348 + 15 I13379 (0) : 0.183 0.523 0.049 0.245 + 16 I13380 (0) : 0.338 0.043 0.139 0.481 + 17 I13381 (0) : 0.401 0.099 0.083 0.417 + 18 I13382 (0) : 0.368 0.057 0.025 0.550 + 19 I13383 (0) : 0.395 0.168 0.051 0.387 + 20 I13384 (0) : 0.277 0.302 0.051 0.370 + 21 I13385 (0) : 0.374 0.065 0.021 0.540 + 22 I13386 (0) : 0.380 0.051 0.027 0.542 + 23 I13387 (0) : 0.196 0.579 0.037 0.188 + 24 I13388 (0) : 0.291 0.441 0.068 0.199 + 25 I13389 (0) : 0.314 0.099 0.124 0.464 + 26 I13390 (0) : 0.343 0.104 0.050 0.503 + 27 I13391 (0) : 0.368 0.142 0.120 0.369 + 28 I13392 (0) : 0.352 0.265 0.056 0.327 + 29 I13393 (0) : 0.331 0.041 0.173 0.455 + 30 I13394 (4) : 0.246 0.126 0.369 0.260 + 31 I13395 (0) : 0.220 0.183 0.345 0.252 + 32 I13396 (0) : 0.158 0.583 0.135 0.123 + 33 I13397 (0) : 0.327 0.329 0.033 0.310 + 34 I13398 (0) : 0.116 0.726 0.022 0.136 + 35 I13399 (4) : 0.438 0.097 0.041 0.423 + 36 I13400 (0) : 0.328 0.159 0.096 0.416 + 37 I13401 (0) : 0.288 0.089 0.296 0.327 + 38 I13402 (0) : 0.297 0.398 0.064 0.241 + 39 I13403 (0) : 0.096 0.651 0.145 0.108 + 40 I13404 (0) : 0.211 0.469 0.028 0.291 + 41 I13405 (0) : 0.376 0.035 0.031 0.557 + 42 I13406 (16) : 0.278 0.484 0.035 0.203 + 43 I13407 (0) : 0.183 0.559 0.037 0.220 + 44 I13408 (0) : 0.344 0.125 0.030 0.501 + 45 I13409 (0) : 0.292 0.440 0.067 0.202 + 46 I13410 (0) : 0.303 0.242 0.023 0.432 + 47 I13411 (0) : 0.312 0.219 0.018 0.451 + 48 I13412 (0) : 0.209 0.277 0.272 0.242 + 49 I13413 (0) : 0.199 0.575 0.069 0.157 + 50 I13414 (0) : 0.157 0.673 0.034 0.136 + 51 I13415 (4) : 0.302 0.210 0.080 0.408 + 52 I13416 (4) : 0.180 0.480 0.136 0.204 + 53 I13417 (4) : 0.286 0.174 0.145 0.396 + 54 I13418 (0) : 0.242 0.304 0.140 0.314 + 55 I13419 (0) : 0.427 0.164 0.028 0.381 + 56 I13420 (0) : 0.133 0.509 0.213 0.145 + 57 I13421 (0) : 0.269 0.102 0.254 0.375 + 58 I13422 (0) : 0.211 0.272 0.250 0.267 + 59 I13423 (0) : 0.370 0.186 0.098 0.346 + 60 I13424 (0) : 0.348 0.106 0.055 0.491 + 61 I13425 (4) : 0.314 0.200 0.085 0.400 + 62 I13426 (4) : 0.220 0.163 0.410 0.207 + 63 I13870 (0) : 0.125 0.530 0.210 0.136 + 64 I13871 (16) : 0.205 0.553 0.048 0.194 + 65 I13872 (0) : 0.128 0.764 0.024 0.084 + 66 I13873 (4) : 0.116 0.653 0.118 0.113 + 67 I13874 (0) : 0.225 0.546 0.067 0.163 + 68 I13875 (8) : 0.105 0.721 0.074 0.099 + 69 I13876 (0) : 0.384 0.220 0.115 0.281 + 70 I13877 (20) : 0.317 0.172 0.093 0.418 + 71 I13878 (28) : 0.177 0.577 0.035 0.211 + 72 I13879 (4) : 0.279 0.312 0.020 0.389 + 73 I13880 (4) : 0.060 0.869 0.025 0.045 + 74 I13881 (0) : 0.314 0.354 0.082 0.249 + 75 I13882 (0) : 0.128 0.698 0.046 0.128 + 76 I13883 (4) : 0.108 0.745 0.072 0.075 + 77 I13884 (16) : 0.457 0.159 0.041 0.344 + 78 I13885 (20) : 0.423 0.117 0.024 0.435 + 79 I13886 (8) : 0.201 0.522 0.031 0.246 + 80 I13887 (0) : 0.464 0.156 0.066 0.313 + 81 I13888 (0) : 0.324 0.370 0.054 0.252 + 82 I13889 (0) : 0.137 0.057 0.663 0.143 + 83 I13890 (32) : 0.212 0.152 0.430 0.207 + 84 I13891 (0) : 0.160 0.638 0.045 0.157 + 85 I13892 (0) : 0.217 0.149 0.350 0.284 + 86 I13893 (8) : 0.468 0.103 0.044 0.386 + 87 I13894 (0) : 0.063 0.861 0.034 0.042 + 88 I13895 (4) : 0.343 0.172 0.132 0.353 + 89 I13896 (0) : 0.113 0.588 0.205 0.094 + 90 I13897 (0) : 0.137 0.685 0.018 0.160 + 91 I13898 (4) : 0.122 0.676 0.061 0.140 + 92 I13899 (0) : 0.047 0.899 0.017 0.037 + 93 I13900 (32) : 0.358 0.290 0.086 0.266 + 94 I13837 (0) : 0.365 0.045 0.055 0.535 + 95 I13838 (0) : 0.098 0.195 0.617 0.090 + 96 I13839 (0) : 0.327 0.099 0.122 0.453 + 97 I13840 (0) : 0.247 0.226 0.188 0.339 + 98 I13841 (0) : 0.199 0.077 0.465 0.259 + 99 I13842 (0) : 0.286 0.031 0.273 0.409 +100 I13843 (4) : 0.133 0.138 0.576 0.153 +101 I13844 (16) : 0.343 0.103 0.129 0.425 +102 I13845 (0) : 0.361 0.103 0.029 0.507 +103 I13846 (0) : 0.366 0.075 0.051 0.507 +104 I13847 (0) : 0.152 0.350 0.360 0.139 +105 I13848 (0) : 0.243 0.273 0.258 0.226 +106 I13849 (0) : 0.163 0.611 0.101 0.125 +107 I13850 (0) : 0.169 0.148 0.502 0.182 +108 I12577 (4) : 0.083 0.036 0.815 0.067 +109 I12578 (4) : 0.095 0.065 0.762 0.078 +110 I12579 (8) : 0.160 0.025 0.692 0.123 +111 I12580 (8) : 0.044 0.036 0.871 0.048 +112 I12581 (4) : 0.375 0.059 0.234 0.332 +113 I12582 (4) : 0.056 0.055 0.840 0.049 +114 I12583 (8) : 0.373 0.056 0.302 0.270 +115 I12584 (4) : 0.206 0.065 0.591 0.137 +116 I12585 (4) : 0.048 0.033 0.881 0.038 +117 I12586 (4) : 0.046 0.043 0.872 0.039 +118 I12587 (8) : 0.031 0.026 0.910 0.033 +119 I12588 (4) : 0.080 0.022 0.841 0.057 +120 I12589 (0) : 0.063 0.067 0.815 0.056 +121 I12590 (0) : 0.135 0.069 0.687 0.109 +122 I12591 (12) : 0.032 0.017 0.926 0.026 +123 I12592 (4) : 0.085 0.044 0.799 0.072 +124 I12593 (4) : 0.055 0.040 0.864 0.041 +125 I12594 (8) : 0.036 0.031 0.900 0.032 +126 I12595 (0) : 0.230 0.027 0.580 0.162 +127 I12596 (0) : 0.045 0.020 0.897 0.038 +128 I12597 (4) : 0.321 0.041 0.417 0.221 +129 I12598 (0) : 0.230 0.056 0.546 0.167 +130 I12599 (0) : 0.143 0.148 0.600 0.109 +131 I12600 (4) : 0.044 0.065 0.851 0.040 +132 I12601 (8) : 0.073 0.037 0.835 0.055 +133 I12602 (12) : 0.072 0.039 0.830 0.059 +134 I12603 (0) : 0.171 0.042 0.671 0.116 +135 I12604 (4) : 0.085 0.086 0.764 0.065 +136 I12605 (4) : 0.087 0.060 0.788 0.065 +137 I12606 (8) : 0.067 0.025 0.855 0.053 +138 I12607 (4) : 0.200 0.047 0.624 0.130 +139 I12608 (8) : 0.144 0.054 0.690 0.112 +140 I12609 (8) : 0.049 0.030 0.876 0.044 +141 I12610 (52) : 0.095 0.043 0.770 0.092 +142 I12611 (0) : 0.037 0.035 0.896 0.031 +143 I12612 (0) : 0.050 0.033 0.876 0.041 +144 I12613 (0) : 0.045 0.019 0.893 0.043 +145 I12614 (4) : 0.087 0.053 0.765 0.094 +146 I12615 (0) : 0.145 0.069 0.663 0.123 +147 I12616 (4) : 0.249 0.035 0.534 0.181 +148 I12617 (8) : 0.024 0.029 0.925 0.021 +149 I12618 (48) : 0.071 0.030 0.845 0.054 + + +Estimated Allele Frequencies in each cluster +First column gives estimated ancestral frequencies + + +Locus 1 : A8 +7 alleles +4.0% missing data + 177 (0.519) 0.489 0.492 0.595 0.477 + 179 (0.091) 0.110 0.077 0.055 0.118 + 175 (0.103) 0.163 0.249 0.011 0.190 + 173 (0.046) 0.058 0.025 0.006 0.068 + 181 (0.171) 0.133 0.130 0.304 0.112 + 165 (0.040) 0.026 0.014 0.027 0.019 + 183 (0.031) 0.022 0.013 0.003 0.016 + +Locus 2 : A14 +5 alleles +0.0% missing data + 112 (0.205) 0.207 0.388 0.030 0.204 + 110 (0.700) 0.732 0.584 0.820 0.755 + 114 (0.032) 0.021 0.016 0.004 0.015 + 118 (0.035) 0.022 0.009 0.113 0.014 + 116 (0.028) 0.017 0.004 0.033 0.011 + +Locus 3 : A24 +5 alleles +2.7% missing data + 104 (0.413) 0.362 0.466 0.368 0.331 + 106 (0.516) 0.593 0.502 0.567 0.637 + 101 (0.018) 0.012 0.003 0.002 0.009 + 108 (0.028) 0.018 0.025 0.003 0.012 + 96 (0.026) 0.016 0.004 0.060 0.011 + +Locus 4 : A29 +29 alleles +6.7% missing data + 143 (0.033) 0.035 0.101 0.005 0.033 + 149 (0.053) 0.040 0.025 0.055 0.033 + 147 (0.029) 0.019 0.034 0.032 0.013 + 153 (0.056) 0.085 0.026 0.088 0.100 + 169 (0.035) 0.024 0.104 0.032 0.017 + 151 (0.037) 0.064 0.008 0.026 0.080 + 145 (0.028) 0.018 0.026 0.027 0.013 + 157 (0.067) 0.055 0.125 0.145 0.048 + 155 (0.095) 0.087 0.117 0.182 0.083 + 159 (0.053) 0.044 0.157 0.045 0.037 + 161 (0.034) 0.063 0.014 0.006 0.080 + 141 (0.028) 0.039 0.010 0.007 0.046 + 139 (0.015) 0.017 0.003 0.002 0.017 + 144 (0.023) 0.044 0.012 0.003 0.057 + 171 (0.051) 0.058 0.023 0.033 0.064 + 163 (0.078) 0.087 0.072 0.059 0.093 + 167 (0.046) 0.036 0.039 0.067 0.030 + 173 (0.023) 0.029 0.012 0.006 0.032 + 142 (0.014) 0.009 0.007 0.002 0.006 + 177 (0.023) 0.016 0.005 0.046 0.012 + 175 (0.023) 0.016 0.005 0.017 0.012 + 165 (0.042) 0.032 0.047 0.041 0.026 + 146 (0.020) 0.024 0.013 0.002 0.026 + 137 (0.019) 0.012 0.003 0.011 0.009 + 183 (0.016) 0.010 0.003 0.017 0.007 + 179 (0.018) 0.012 0.003 0.013 0.008 + 191 (0.013) 0.008 0.002 0.005 0.006 + 185 (0.013) 0.008 0.002 0.005 0.006 + 180 (0.015) 0.009 0.002 0.023 0.006 + +Locus 5 : A43 +7 alleles +1.3% missing data + 123 (0.215) 0.165 0.092 0.154 0.138 + 141 (0.017) 0.011 0.005 0.002 0.007 + 137 (0.654) 0.738 0.879 0.688 0.782 + 139 (0.050) 0.048 0.014 0.080 0.046 + 124 (0.029) 0.018 0.004 0.065 0.013 + 143 (0.017) 0.011 0.003 0.004 0.007 + 128 (0.017) 0.010 0.002 0.008 0.007 + +Locus 6 : A79 +13 alleles +3.4% missing data + 103 (0.237) 0.264 0.311 0.176 0.280 + 97 (0.130) 0.105 0.207 0.055 0.089 + 101 (0.092) 0.159 0.063 0.034 0.199 + 107 (0.100) 0.136 0.074 0.074 0.155 + 109 (0.099) 0.086 0.077 0.087 0.081 + 105 (0.158) 0.123 0.206 0.421 0.099 + 111 (0.049) 0.033 0.026 0.028 0.025 + 113 (0.016) 0.010 0.005 0.002 0.007 + 91 (0.025) 0.016 0.004 0.083 0.010 + 99 (0.032) 0.027 0.010 0.026 0.025 + 115 (0.028) 0.020 0.007 0.009 0.016 + 117 (0.016) 0.010 0.006 0.002 0.007 + 121 (0.016) 0.010 0.003 0.002 0.007 + +Locus 7 : A88 +9 alleles +6.0% missing data + 133 (0.017) 0.011 0.005 0.002 0.008 + 149 (0.523) 0.495 0.538 0.812 0.484 + 137 (0.100) 0.099 0.138 0.014 0.096 + 147 (0.204) 0.292 0.225 0.063 0.339 + 141 (0.078) 0.054 0.081 0.088 0.039 + 152 (0.017) 0.012 0.003 0.002 0.009 + 143 (0.018) 0.011 0.004 0.002 0.008 + 151 (0.018) 0.011 0.002 0.006 0.007 + 144 (0.025) 0.016 0.005 0.010 0.011 + +Locus 8 : A113 +12 alleles +7.4% missing data + 214 (0.587) 0.678 0.675 0.746 0.726 + 226 (0.058) 0.043 0.140 0.029 0.033 + 218 (0.017) 0.013 0.003 0.002 0.011 + 220 (0.060) 0.048 0.017 0.143 0.042 + 216 (0.058) 0.043 0.020 0.035 0.035 + 230 (0.040) 0.053 0.015 0.006 0.062 + 234 (0.032) 0.022 0.031 0.004 0.016 + 232 (0.030) 0.022 0.033 0.005 0.017 + 228 (0.052) 0.035 0.042 0.015 0.026 + 224 (0.017) 0.011 0.005 0.002 0.007 + 222 (0.032) 0.020 0.016 0.010 0.014 + 208 (0.017) 0.013 0.003 0.002 0.011 + +Locus 9 : Ac11 +9 alleles +4.7% missing data + 111 (0.126) 0.129 0.305 0.031 0.127 + 117 (0.306) 0.359 0.283 0.195 0.391 + 115 (0.256) 0.290 0.274 0.235 0.306 + 113 (0.158) 0.120 0.105 0.273 0.103 + 119 (0.048) 0.034 0.013 0.178 0.025 + 121 (0.025) 0.016 0.004 0.061 0.010 + 123 (0.033) 0.021 0.007 0.012 0.015 + 127 (0.031) 0.020 0.006 0.013 0.015 + 125 (0.017) 0.011 0.002 0.003 0.008 + +Locus 10 : Ac88 +8 alleles +0.7% missing data + 214 (0.754) 0.822 0.726 0.922 0.862 + 216 (0.029) 0.020 0.020 0.003 0.015 + 220 (0.115) 0.095 0.237 0.027 0.081 + 230 (0.025) 0.016 0.006 0.004 0.011 + 221 (0.017) 0.010 0.002 0.008 0.007 + 212 (0.020) 0.012 0.003 0.019 0.008 + 217 (0.017) 0.011 0.002 0.005 0.007 + 224 (0.023) 0.014 0.003 0.012 0.010 + +Locus 11 : Ac139 +8 alleles +13.4% missing data + 327 (0.503) 0.533 0.432 0.801 0.555 + 329 (0.293) 0.311 0.432 0.104 0.317 + 331 (0.072) 0.057 0.110 0.019 0.046 + 328 (0.046) 0.046 0.012 0.005 0.045 + 341 (0.019) 0.012 0.003 0.008 0.008 + 337 (0.028) 0.017 0.004 0.052 0.011 + 323 (0.019) 0.012 0.003 0.005 0.008 + 339 (0.019) 0.012 0.003 0.006 0.008 + +Locus 12 : Ac306 +6 alleles +4.7% missing data + 165 (0.736) 0.768 0.704 0.809 0.791 + 177 (0.081) 0.063 0.067 0.103 0.053 + 173 (0.096) 0.074 0.207 0.032 0.060 + 169 (0.043) 0.067 0.014 0.005 0.078 + 171 (0.018) 0.011 0.003 0.002 0.008 + 179 (0.027) 0.016 0.004 0.050 0.011 + +Locus 13 : Ap15 +7 alleles +6.0% missing data + 202 (0.818) 0.883 0.943 0.829 0.918 + 212 (0.027) 0.018 0.027 0.003 0.012 + 204 (0.042) 0.028 0.009 0.027 0.021 + 208 (0.038) 0.025 0.006 0.057 0.018 + 220 (0.038) 0.024 0.009 0.070 0.016 + 219 (0.018) 0.011 0.003 0.008 0.007 + 210 (0.018) 0.011 0.003 0.006 0.008 + +Locus 14 : Ap68 +9 alleles +4.7% missing data + 158 (0.398) 0.349 0.624 0.290 0.311 + 160 (0.087) 0.110 0.036 0.023 0.125 + 156 (0.224) 0.287 0.235 0.360 0.323 + 162 (0.043) 0.029 0.031 0.009 0.020 + 154 (0.092) 0.116 0.036 0.017 0.135 + 152 (0.074) 0.057 0.017 0.261 0.048 + 164 (0.043) 0.027 0.016 0.022 0.020 + 170 (0.018) 0.011 0.003 0.003 0.008 + 166 (0.022) 0.014 0.003 0.015 0.009 + +Locus 15 : Ap85 +10 alleles +3.4% missing data + 202 (0.311) 0.294 0.389 0.545 0.275 + 186 (0.255) 0.348 0.376 0.104 0.407 + 204 (0.065) 0.050 0.026 0.038 0.041 + 188 (0.111) 0.124 0.077 0.024 0.135 + 194 (0.078) 0.067 0.082 0.027 0.058 + 196 (0.051) 0.035 0.013 0.116 0.026 + 200 (0.063) 0.042 0.018 0.078 0.030 + 192 (0.025) 0.016 0.007 0.005 0.011 + 190 (0.017) 0.011 0.008 0.002 0.008 + 198 (0.024) 0.015 0.003 0.061 0.010 + +Locus 16 : Ap90 +13 alleles +0.7% missing data + 131 (0.357) 0.442 0.523 0.544 0.483 + 135 (0.065) 0.049 0.080 0.089 0.039 + 133 (0.296) 0.268 0.308 0.204 0.255 + 129 (0.098) 0.117 0.042 0.088 0.130 + 137 (0.035) 0.032 0.008 0.012 0.031 + 141 (0.016) 0.010 0.005 0.002 0.007 + 143 (0.023) 0.015 0.010 0.002 0.011 + 151 (0.024) 0.015 0.010 0.004 0.010 + 155 (0.016) 0.010 0.004 0.002 0.007 + 145 (0.016) 0.010 0.002 0.009 0.006 + 130 (0.019) 0.011 0.003 0.018 0.007 + 139 (0.016) 0.010 0.002 0.010 0.006 + 153 (0.020) 0.012 0.003 0.017 0.008 + +Locus 17 : Ap223 +7 alleles +2.0% missing data + 183 (0.691) 0.686 0.614 0.896 0.685 + 187 (0.134) 0.187 0.284 0.021 0.216 + 189 (0.025) 0.025 0.005 0.002 0.024 + 173 (0.063) 0.044 0.070 0.041 0.033 + 182 (0.031) 0.023 0.010 0.005 0.017 + 180 (0.025) 0.016 0.005 0.006 0.012 + 179 (0.031) 0.019 0.012 0.028 0.013 + +Locus 18 : Ap224 +7 alleles +4.0% missing data + 283 (0.112) 0.142 0.198 0.019 0.159 + 287 (0.471) 0.460 0.483 0.457 0.454 + 281 (0.134) 0.155 0.155 0.049 0.167 + 289 (0.204) 0.189 0.103 0.419 0.181 + 291 (0.038) 0.028 0.054 0.004 0.022 + 285 (0.017) 0.012 0.003 0.002 0.008 + 279 (0.024) 0.014 0.003 0.050 0.009 + +Locus 19 : Ap226 +5 alleles +17.4% missing data + 237 (0.384) 0.376 0.324 0.346 0.368 + 239 (0.461) 0.470 0.453 0.609 0.482 + 247 (0.117) 0.128 0.217 0.030 0.130 + 235 (0.019) 0.014 0.003 0.003 0.011 + 241 (0.019) 0.012 0.003 0.011 0.008 + +Locus 20 : Ap249 +9 alleles +1.3% missing data + 209 (0.617) 0.662 0.585 0.702 0.692 + 211 (0.053) 0.056 0.016 0.008 0.058 + 217 (0.083) 0.082 0.144 0.020 0.078 + 219 (0.102) 0.099 0.227 0.018 0.094 + 215 (0.076) 0.058 0.014 0.243 0.047 + 208 (0.017) 0.011 0.005 0.002 0.007 + 225 (0.017) 0.011 0.004 0.002 0.008 + 223 (0.017) 0.012 0.003 0.002 0.009 + 213 (0.017) 0.011 0.002 0.005 0.007 + +Locus 21 : Ap273 +4 alleles +1.3% missing data + 106 (0.876) 0.911 0.949 0.953 0.930 + 108 (0.052) 0.037 0.033 0.021 0.028 + 104 (0.044) 0.035 0.012 0.004 0.030 + 102 (0.028) 0.017 0.006 0.022 0.012 + +Locus 22 : Ap274 +2 alleles +2.0% missing data + 120 (0.946) 0.965 0.984 0.916 0.975 + 122 (0.054) 0.035 0.016 0.084 0.025 + +Locus 23 : Ap288 +5 alleles +0.0% missing data + 123 (0.772) 0.767 0.624 0.952 0.771 + 131 (0.164) 0.192 0.340 0.042 0.201 + 139 (0.029) 0.019 0.021 0.003 0.013 + 121 (0.017) 0.011 0.008 0.002 0.007 + 124 (0.017) 0.011 0.007 0.002 0.008 + +Locus 24 : At163 +7 alleles +0.0% missing data + 128 (0.710) 0.750 0.560 0.933 0.774 + 134 (0.196) 0.189 0.420 0.053 0.184 + 130 (0.024) 0.016 0.011 0.003 0.011 + 136 (0.018) 0.012 0.003 0.002 0.009 + 140 (0.018) 0.011 0.002 0.003 0.008 + 146 (0.018) 0.011 0.002 0.003 0.008 + 142 (0.017) 0.010 0.002 0.004 0.007 + +Locus 25 : At188 +13 alleles +1.3% missing data + 189 (0.635) 0.685 0.768 0.897 0.713 + 205 (0.031) 0.021 0.060 0.003 0.014 + 207 (0.030) 0.054 0.011 0.003 0.066 + 219 (0.024) 0.017 0.008 0.002 0.013 + 209 (0.032) 0.043 0.013 0.004 0.050 + 217 (0.042) 0.032 0.015 0.004 0.027 + 215 (0.020) 0.017 0.008 0.002 0.016 + 199 (0.064) 0.043 0.067 0.052 0.032 + 212 (0.028) 0.021 0.010 0.005 0.018 + 213 (0.037) 0.027 0.030 0.004 0.022 + 211 (0.016) 0.010 0.003 0.001 0.007 + 191 (0.017) 0.013 0.003 0.002 0.011 + 187 (0.024) 0.015 0.003 0.021 0.011 + +Values of parameters used in structure: +DATAFILE=, OUTFILE=, NUMINDS=149, NUMLOCI=25, MISSING=-9, LABEL=1, POPDATA=0, POPFLAG=1, PHENOTYPE=0, EXTRACOLS=1, MAXPOPS=4, BURNIN=100000, NUMREPS=1000000, USEPOPINFO=0, INFERALPHA=1, INFERLAMBDA=0, POPSPECIFICLAMBDA=0, POPALPHAS=0, COMPUTEPROB=1, NOADMIX=0, ADMBURNIN=2500, UPDATEFREQ=1, PRINTLIKES=0, INTERMEDSAVE=0, PRINTKLD=0, PRINTNET=0, PRINTLAMBDA=0, ANCESTDIST=0, NUMBOXES=1000, ANCESTPINT=0.90000, GENSBACK=2, MIGRPRIOR=0.05000, PRINTQHAT=0, PRINTQSUM=0, ALPHA=1.0000, FREQSCORR=1, FPRIORMEAN=0.0100, FPRIORSD=0.0500, ONEFST=0, LAMBDA=1.0000, UNIFPRIORALPHA=1, ALPHAMAX=10.0000, ALPHAPRIORA=1.0000, ALPHAPRIORB=2.0000, ALPHAPROPSD=0.0250, STARTATPOPINFO=0, RANDOMIZE=1, LINKAGE=0, METROFREQ=10, REPORTHITRATE=0, MARKOVPHASE=-1, PHASED=0, PLOIDY=2, PHASEINFO=0 LOCPRIOR=0, LOCPRIORINIT=1.000000, LOCDATA=0, LOCISPOP=0, LOCPRIORSTEP=0.100000, MAXLOCPRIOR=20.000000, SEED=1342967587, +[STRAT parameters]: NUMSIMSTATS=1000, PHENOTYPECOL=-9, POOLFREQ=10, LOCUSxONLY=0, EMERROR=0.00100, MISSINGPHENO=-9, \ No newline at end of file diff --git a/inst/files/structure/structure_16 b/inst/files/structure/structure_16 new file mode 100644 index 0000000..03b7540 --- /dev/null +++ b/inst/files/structure/structure_16 @@ -0,0 +1,538 @@ + + +---------------------------------------------------- +STRUCTURE by Pritchard, Stephens and Donnelly (2000) + and Falush, Stephens and Pritchard (2003) + Code by Pritchard, Falush and Hubisz + Version 2.3.2.1 (Oct 2009) +---------------------------------------------------- + + + +Command line arguments: +Input File: + +Run parameters: + 149 individuals + 25 loci + 5 populations assumed + 100000 Burn-in period + 1000000 Reps + + +-------------------------------------------- +Overall proportion of membership of the +sample in each of the 5 clusters + +Inferred Clusters + 1 2 3 4 5 +0.210 0.192 0.164 0.232 0.202 + +-------------------------------------------- + +Allele-freq. divergence among pops (Net nucleotide distance), +computed using point estimates of P. + + 1 2 3 4 5 + 1 - 0.0057 0.0043 0.0029 0.0055 + 2 0.0057 - 0.0096 0.0141 0.0064 + 3 0.0043 0.0096 - 0.0061 0.0071 + 4 0.0029 0.0141 0.0061 - 0.0057 + 5 0.0055 0.0064 0.0071 0.0057 - + +Average distances (expected heterozygosity) between individuals in same cluster: +cluster 1 : 0.5068 +cluster 2 : 0.4731 +cluster 3 : 0.5752 +cluster 4 : 0.5045 +cluster 5 : 0.4812 + +-------------------------------------------- +Estimated Ln Prob of Data = -7709.8 +Mean value of ln likelihood = -7208.7 +Variance of ln likelihood = 1002.3 +Mean value of alpha = 0.2266 + +Mean value of Fst_1 = 0.1404 +Mean value of Fst_2 = 0.1511 +Mean value of Fst_3 = 0.0176 +Mean value of Fst_4 = 0.1342 +Mean value of Fst_5 = 0.1360 + + +Inferred ancestry of individuals: + Label (%Miss) : Inferred clusters + 1 I13825 (0) : 0.190 0.093 0.410 0.190 0.117 + 2 I13826 (0) : 0.347 0.070 0.138 0.388 0.056 + 3 I13827 (20) : 0.237 0.444 0.080 0.058 0.182 + 4 I13828 (0) : 0.299 0.098 0.190 0.328 0.085 + 5 I13829 (8) : 0.232 0.368 0.102 0.101 0.196 + 6 I13830 (0) : 0.344 0.091 0.128 0.377 0.061 + 7 I13831 (0) : 0.195 0.392 0.091 0.122 0.201 + 8 I13832 (16) : 0.188 0.343 0.185 0.070 0.213 + 9 I13833 (0) : 0.196 0.469 0.068 0.067 0.200 + 10 I13834 (0) : 0.245 0.439 0.062 0.082 0.171 + 11 I13835 (0) : 0.146 0.334 0.240 0.060 0.220 + 12 I13836 (0) : 0.224 0.388 0.150 0.070 0.168 + 13 I13377 (0) : 0.165 0.476 0.095 0.052 0.213 + 14 I13378 (0) : 0.126 0.288 0.307 0.085 0.193 + 15 I13379 (0) : 0.260 0.268 0.105 0.232 0.134 + 16 I13380 (0) : 0.212 0.413 0.081 0.082 0.212 + 17 I13381 (0) : 0.175 0.295 0.199 0.075 0.255 + 18 I13382 (0) : 0.235 0.406 0.066 0.053 0.239 + 19 I13383 (0) : 0.157 0.271 0.261 0.093 0.217 + 20 I13384 (0) : 0.237 0.303 0.130 0.153 0.176 + 21 I13385 (0) : 0.227 0.464 0.071 0.049 0.189 + 22 I13386 (0) : 0.238 0.412 0.088 0.048 0.214 + 23 I13387 (0) : 0.281 0.140 0.203 0.283 0.093 + 24 I13388 (0) : 0.190 0.078 0.400 0.204 0.127 + 25 I13389 (0) : 0.192 0.454 0.061 0.088 0.205 + 26 I13390 (0) : 0.237 0.405 0.078 0.083 0.197 + 27 I13391 (0) : 0.146 0.320 0.237 0.094 0.203 + 28 I13392 (0) : 0.160 0.250 0.280 0.133 0.177 + 29 I13393 (0) : 0.175 0.355 0.101 0.081 0.288 + 30 I13394 (4) : 0.164 0.233 0.172 0.181 0.250 + 31 I13395 (0) : 0.189 0.228 0.135 0.219 0.230 + 32 I13396 (0) : 0.247 0.094 0.235 0.297 0.127 + 33 I13397 (0) : 0.187 0.242 0.259 0.159 0.153 + 34 I13398 (0) : 0.343 0.137 0.105 0.344 0.071 + 35 I13399 (4) : 0.120 0.318 0.322 0.056 0.185 + 36 I13400 (0) : 0.163 0.384 0.148 0.097 0.208 + 37 I13401 (0) : 0.183 0.254 0.180 0.164 0.219 + 38 I13402 (0) : 0.164 0.186 0.325 0.157 0.167 + 39 I13403 (0) : 0.295 0.135 0.109 0.325 0.136 + 40 I13404 (0) : 0.289 0.257 0.097 0.242 0.115 + 41 I13405 (0) : 0.210 0.501 0.059 0.037 0.193 + 42 I13406 (16) : 0.230 0.105 0.319 0.237 0.108 + 43 I13407 (0) : 0.248 0.242 0.135 0.241 0.134 + 44 I13408 (0) : 0.192 0.431 0.082 0.077 0.218 + 45 I13409 (0) : 0.199 0.086 0.374 0.221 0.120 + 46 I13410 (0) : 0.213 0.362 0.102 0.126 0.197 + 47 I13411 (0) : 0.268 0.360 0.084 0.139 0.149 + 48 I13412 (0) : 0.235 0.201 0.144 0.231 0.189 + 49 I13413 (0) : 0.243 0.120 0.252 0.264 0.121 + 50 I13414 (0) : 0.302 0.108 0.190 0.308 0.093 + 51 I13415 (4) : 0.239 0.373 0.083 0.122 0.184 + 52 I13416 (4) : 0.249 0.230 0.130 0.225 0.166 + 53 I13417 (4) : 0.245 0.333 0.076 0.153 0.192 + 54 I13418 (0) : 0.259 0.268 0.095 0.178 0.200 + 55 I13419 (0) : 0.169 0.209 0.379 0.088 0.154 + 56 I13420 (0) : 0.292 0.155 0.102 0.298 0.153 + 57 I13421 (0) : 0.220 0.310 0.074 0.138 0.257 + 58 I13422 (0) : 0.234 0.241 0.120 0.213 0.191 + 59 I13423 (0) : 0.183 0.235 0.251 0.106 0.226 + 60 I13424 (0) : 0.181 0.428 0.121 0.072 0.198 + 61 I13425 (4) : 0.222 0.321 0.153 0.129 0.176 + 62 I13426 (4) : 0.164 0.171 0.199 0.212 0.254 + 63 I13870 (0) : 0.274 0.133 0.125 0.318 0.151 + 64 I13871 (16) : 0.246 0.181 0.204 0.232 0.136 + 65 I13872 (0) : 0.322 0.048 0.205 0.371 0.054 + 66 I13873 (4) : 0.267 0.155 0.149 0.287 0.142 + 67 I13874 (0) : 0.247 0.077 0.307 0.266 0.102 + 68 I13875 (8) : 0.300 0.115 0.155 0.328 0.101 + 69 I13876 (0) : 0.129 0.085 0.480 0.145 0.161 + 70 I13877 (20) : 0.222 0.316 0.115 0.102 0.244 + 71 I13878 (28) : 0.313 0.194 0.110 0.283 0.101 + 72 I13879 (4) : 0.266 0.350 0.081 0.154 0.150 + 73 I13880 (4) : 0.355 0.059 0.130 0.410 0.045 + 74 I13881 (0) : 0.189 0.130 0.354 0.189 0.138 + 75 I13882 (0) : 0.301 0.123 0.153 0.324 0.099 + 76 I13883 (4) : 0.311 0.050 0.191 0.371 0.077 + 77 I13884 (16) : 0.105 0.125 0.519 0.091 0.160 + 78 I13885 (20) : 0.162 0.272 0.304 0.066 0.195 + 79 I13886 (8) : 0.270 0.229 0.139 0.247 0.115 + 80 I13887 (0) : 0.075 0.063 0.615 0.089 0.158 + 81 I13888 (0) : 0.188 0.139 0.333 0.185 0.155 + 82 I13889 (0) : 0.186 0.148 0.098 0.313 0.255 + 83 I13890 (32) : 0.174 0.178 0.175 0.229 0.243 + 84 I13891 (0) : 0.306 0.143 0.156 0.299 0.097 + 85 I13892 (0) : 0.192 0.292 0.104 0.168 0.243 + 86 I13893 (8) : 0.101 0.217 0.439 0.061 0.182 + 87 I13894 (0) : 0.355 0.037 0.139 0.426 0.043 + 88 I13895 (4) : 0.158 0.268 0.263 0.108 0.203 + 89 I13896 (0) : 0.276 0.086 0.153 0.344 0.141 + 90 I13897 (0) : 0.334 0.176 0.104 0.303 0.083 + 91 I13898 (4) : 0.277 0.185 0.129 0.286 0.122 + 92 I13899 (0) : 0.370 0.046 0.116 0.434 0.034 + 93 I13900 (32) : 0.149 0.118 0.429 0.152 0.152 + 94 I13837 (0) : 0.213 0.475 0.064 0.050 0.199 + 95 I13838 (0) : 0.210 0.079 0.108 0.358 0.244 + 96 I13839 (0) : 0.237 0.382 0.091 0.107 0.184 + 97 I13840 (0) : 0.229 0.321 0.078 0.156 0.217 + 98 I13841 (0) : 0.201 0.232 0.079 0.189 0.299 + 99 I13842 (0) : 0.198 0.355 0.074 0.129 0.244 +100 I13843 (4) : 0.198 0.195 0.085 0.222 0.300 +101 I13844 (16) : 0.172 0.346 0.161 0.094 0.228 +102 I13845 (0) : 0.242 0.377 0.088 0.074 0.218 +103 I13846 (0) : 0.207 0.388 0.132 0.062 0.211 +104 I13847 (0) : 0.233 0.118 0.154 0.310 0.186 +105 I13848 (0) : 0.182 0.237 0.186 0.167 0.228 +106 I13849 (0) : 0.247 0.126 0.230 0.263 0.134 +107 I13850 (0) : 0.184 0.212 0.113 0.211 0.279 +108 I12577 (4) : 0.178 0.060 0.102 0.372 0.288 +109 I12578 (4) : 0.193 0.082 0.107 0.362 0.256 +110 I12579 (8) : 0.147 0.094 0.180 0.304 0.276 +111 I12580 (8) : 0.188 0.062 0.040 0.398 0.313 +112 I12581 (4) : 0.122 0.235 0.301 0.112 0.230 +113 I12582 (4) : 0.190 0.052 0.070 0.396 0.291 +114 I12583 (8) : 0.105 0.092 0.446 0.147 0.209 +115 I12584 (4) : 0.150 0.054 0.262 0.288 0.245 +116 I12585 (4) : 0.182 0.041 0.066 0.401 0.311 +117 I12586 (4) : 0.183 0.059 0.050 0.390 0.317 +118 I12587 (8) : 0.183 0.051 0.031 0.405 0.330 +119 I12588 (4) : 0.171 0.042 0.108 0.383 0.296 +120 I12589 (0) : 0.196 0.053 0.073 0.395 0.284 +121 I12590 (0) : 0.170 0.076 0.149 0.335 0.270 +122 I12591 (12) : 0.202 0.027 0.042 0.434 0.296 +123 I12592 (4) : 0.201 0.059 0.104 0.381 0.255 +124 I12593 (4) : 0.203 0.033 0.077 0.418 0.270 +125 I12594 (8) : 0.192 0.036 0.044 0.420 0.309 +126 I12595 (0) : 0.135 0.095 0.267 0.254 0.250 +127 I12596 (0) : 0.194 0.037 0.055 0.416 0.298 +128 I12597 (4) : 0.103 0.075 0.402 0.180 0.240 +129 I12598 (0) : 0.152 0.065 0.274 0.266 0.243 +130 I12599 (0) : 0.181 0.069 0.188 0.331 0.230 +131 I12600 (4) : 0.189 0.044 0.051 0.405 0.310 +132 I12601 (8) : 0.171 0.050 0.103 0.375 0.301 +133 I12602 (12) : 0.180 0.061 0.082 0.378 0.299 +134 I12603 (0) : 0.145 0.059 0.234 0.305 0.257 +135 I12604 (4) : 0.183 0.050 0.114 0.376 0.277 +136 I12605 (4) : 0.177 0.048 0.109 0.377 0.288 +137 I12606 (8) : 0.195 0.054 0.083 0.392 0.275 +138 I12607 (4) : 0.160 0.049 0.261 0.300 0.229 +139 I12608 (8) : 0.169 0.085 0.183 0.312 0.251 +140 I12609 (8) : 0.191 0.049 0.060 0.405 0.296 +141 I12610 (52) : 0.172 0.097 0.102 0.339 0.289 +142 I12611 (0) : 0.196 0.038 0.048 0.421 0.297 +143 I12612 (0) : 0.181 0.042 0.062 0.403 0.313 +144 I12613 (0) : 0.201 0.050 0.049 0.413 0.286 +145 I12614 (4) : 0.188 0.120 0.073 0.322 0.296 +146 I12615 (0) : 0.176 0.104 0.162 0.307 0.252 +147 I12616 (4) : 0.135 0.089 0.313 0.237 0.226 +148 I12617 (8) : 0.195 0.026 0.030 0.433 0.315 +149 I12618 (48) : 0.174 0.045 0.090 0.387 0.305 + + +Estimated Allele Frequencies in each cluster +First column gives estimated ancestral frequencies + + +Locus 1 : A8 +7 alleles +4.0% missing data + 177 (0.510) 0.489 0.494 0.508 0.533 0.545 + 179 (0.095) 0.094 0.112 0.094 0.069 0.080 + 175 (0.104) 0.209 0.189 0.123 0.147 0.110 + 173 (0.045) 0.029 0.077 0.042 0.013 0.040 + 181 (0.177) 0.153 0.107 0.168 0.209 0.194 + 165 (0.040) 0.016 0.011 0.036 0.021 0.020 + 183 (0.029) 0.009 0.011 0.028 0.008 0.012 + +Locus 2 : A14 +5 alleles +0.0% missing data + 112 (0.201) 0.251 0.195 0.223 0.229 0.146 + 110 (0.702) 0.697 0.786 0.690 0.680 0.774 + 114 (0.032) 0.010 0.008 0.030 0.010 0.010 + 118 (0.036) 0.032 0.006 0.031 0.063 0.051 + 116 (0.030) 0.010 0.005 0.026 0.018 0.019 + +Locus 3 : A24 +5 alleles +2.7% missing data + 104 (0.407) 0.381 0.321 0.410 0.420 0.356 + 106 (0.519) 0.587 0.661 0.523 0.532 0.601 + 101 (0.018) 0.003 0.005 0.016 0.002 0.006 + 108 (0.029) 0.013 0.008 0.027 0.013 0.009 + 96 (0.028) 0.017 0.005 0.024 0.033 0.029 + +Locus 4 : A29 +29 alleles +6.7% missing data + 143 (0.033) 0.062 0.030 0.041 0.060 0.021 + 149 (0.051) 0.031 0.031 0.048 0.037 0.039 + 147 (0.029) 0.025 0.007 0.028 0.035 0.020 + 153 (0.056) 0.075 0.107 0.054 0.057 0.084 + 169 (0.037) 0.058 0.012 0.043 0.074 0.022 + 151 (0.037) 0.038 0.086 0.039 0.016 0.065 + 145 (0.028) 0.019 0.011 0.027 0.026 0.019 + 157 (0.069) 0.100 0.051 0.073 0.134 0.098 + 155 (0.095) 0.115 0.086 0.097 0.150 0.130 + 159 (0.051) 0.093 0.041 0.061 0.106 0.050 + 161 (0.032) 0.046 0.081 0.034 0.011 0.052 + 141 (0.029) 0.024 0.046 0.027 0.009 0.025 + 139 (0.016) 0.008 0.014 0.015 0.003 0.009 + 144 (0.026) 0.028 0.062 0.025 0.009 0.029 + 171 (0.049) 0.037 0.073 0.046 0.024 0.047 + 163 (0.072) 0.071 0.113 0.074 0.054 0.089 + 167 (0.046) 0.041 0.033 0.045 0.048 0.047 + 173 (0.024) 0.019 0.029 0.023 0.009 0.019 + 142 (0.013) 0.004 0.003 0.012 0.004 0.004 + 177 (0.024) 0.016 0.009 0.021 0.026 0.024 + 175 (0.022) 0.008 0.010 0.020 0.009 0.014 + 165 (0.045) 0.037 0.023 0.044 0.043 0.031 + 146 (0.021) 0.016 0.022 0.020 0.010 0.013 + 137 (0.019) 0.005 0.004 0.017 0.007 0.009 + 183 (0.017) 0.006 0.003 0.015 0.010 0.010 + 179 (0.018) 0.006 0.006 0.016 0.008 0.010 + 191 (0.014) 0.003 0.003 0.012 0.003 0.005 + 185 (0.013) 0.003 0.002 0.011 0.003 0.004 + 180 (0.015) 0.006 0.002 0.013 0.012 0.012 + +Locus 5 : A43 +7 alleles +1.3% missing data + 123 (0.206) 0.104 0.127 0.195 0.109 0.158 + 141 (0.018) 0.003 0.003 0.016 0.003 0.004 + 137 (0.663) 0.827 0.811 0.687 0.804 0.724 + 139 (0.047) 0.042 0.048 0.045 0.040 0.070 + 124 (0.031) 0.018 0.006 0.028 0.035 0.032 + 143 (0.018) 0.003 0.002 0.015 0.003 0.005 + 128 (0.017) 0.003 0.003 0.015 0.005 0.006 + +Locus 6 : A79 +13 alleles +3.4% missing data + 103 (0.237) 0.274 0.299 0.250 0.239 0.260 + 97 (0.131) 0.126 0.078 0.137 0.140 0.076 + 101 (0.092) 0.113 0.228 0.091 0.045 0.111 + 107 (0.096) 0.117 0.159 0.099 0.068 0.131 + 109 (0.099) 0.072 0.083 0.095 0.079 0.082 + 105 (0.162) 0.219 0.087 0.163 0.326 0.228 + 111 (0.048) 0.022 0.021 0.045 0.025 0.027 + 113 (0.016) 0.003 0.002 0.015 0.003 0.004 + 91 (0.025) 0.021 0.005 0.022 0.045 0.039 + 99 (0.033) 0.018 0.020 0.030 0.017 0.022 + 115 (0.028) 0.008 0.013 0.025 0.007 0.013 + 117 (0.016) 0.004 0.002 0.015 0.004 0.004 + 121 (0.017) 0.003 0.002 0.015 0.002 0.004 + +Locus 7 : A88 +9 alleles +6.0% missing data + 133 (0.018) 0.003 0.003 0.016 0.003 0.004 + 149 (0.522) 0.567 0.504 0.523 0.673 0.625 + 137 (0.104) 0.098 0.088 0.107 0.081 0.061 + 147 (0.196) 0.252 0.367 0.206 0.136 0.232 + 141 (0.081) 0.066 0.023 0.079 0.090 0.053 + 152 (0.018) 0.003 0.005 0.016 0.002 0.005 + 143 (0.018) 0.003 0.003 0.016 0.003 0.005 + 151 (0.018) 0.003 0.003 0.015 0.004 0.006 + 144 (0.025) 0.005 0.004 0.022 0.007 0.009 + +Locus 8 : A113 +12 alleles +7.4% missing data + 214 (0.578) 0.726 0.784 0.597 0.698 0.760 + 226 (0.062) 0.079 0.027 0.068 0.091 0.033 + 218 (0.017) 0.005 0.007 0.015 0.003 0.006 + 220 (0.060) 0.053 0.040 0.055 0.081 0.074 + 216 (0.059) 0.025 0.023 0.054 0.028 0.029 + 230 (0.043) 0.029 0.064 0.041 0.011 0.034 + 234 (0.033) 0.018 0.011 0.032 0.018 0.011 + 232 (0.030) 0.020 0.011 0.030 0.021 0.011 + 228 (0.051) 0.026 0.018 0.049 0.029 0.021 + 224 (0.017) 0.003 0.003 0.015 0.003 0.004 + 222 (0.032) 0.011 0.005 0.029 0.014 0.011 + 208 (0.017) 0.004 0.006 0.015 0.002 0.006 + +Locus 9 : Ac11 +9 alleles +4.7% missing data + 111 (0.130) 0.191 0.127 0.147 0.183 0.090 + 117 (0.297) 0.300 0.423 0.302 0.230 0.325 + 115 (0.258) 0.288 0.318 0.261 0.248 0.282 + 113 (0.157) 0.130 0.094 0.149 0.187 0.166 + 119 (0.049) 0.056 0.016 0.044 0.099 0.079 + 121 (0.027) 0.018 0.005 0.023 0.033 0.029 + 123 (0.033) 0.007 0.006 0.030 0.009 0.012 + 127 (0.032) 0.007 0.008 0.028 0.009 0.013 + 125 (0.017) 0.002 0.003 0.015 0.002 0.005 + +Locus 10 : Ac88 +8 alleles +0.7% missing data + 214 (0.749) 0.827 0.909 0.753 0.806 0.896 + 216 (0.029) 0.013 0.009 0.028 0.012 0.010 + 220 (0.117) 0.137 0.066 0.127 0.150 0.056 + 230 (0.025) 0.005 0.004 0.023 0.005 0.007 + 221 (0.017) 0.003 0.002 0.015 0.005 0.006 + 212 (0.020) 0.007 0.003 0.018 0.011 0.010 + 217 (0.018) 0.003 0.003 0.015 0.003 0.005 + 224 (0.024) 0.005 0.004 0.021 0.007 0.009 + +Locus 11 : Ac139 +8 alleles +13.4% missing data + 327 (0.506) 0.549 0.599 0.501 0.597 0.673 + 329 (0.293) 0.335 0.308 0.307 0.284 0.214 + 331 (0.073) 0.068 0.036 0.076 0.069 0.033 + 328 (0.040) 0.023 0.042 0.039 0.008 0.035 + 341 (0.019) 0.004 0.003 0.017 0.005 0.007 + 337 (0.029) 0.015 0.005 0.025 0.028 0.026 + 323 (0.020) 0.003 0.003 0.017 0.004 0.006 + 339 (0.019) 0.003 0.003 0.017 0.004 0.006 + +Locus 12 : Ac306 +6 alleles +4.7% missing data + 165 (0.728) 0.759 0.817 0.730 0.749 0.800 + 177 (0.083) 0.065 0.047 0.080 0.080 0.084 + 173 (0.100) 0.117 0.050 0.109 0.131 0.050 + 169 (0.045) 0.042 0.078 0.043 0.010 0.039 + 171 (0.018) 0.002 0.002 0.016 0.002 0.004 + 179 (0.027) 0.015 0.004 0.023 0.028 0.022 + +Locus 13 : Ap15 +7 alleles +6.0% missing data + 202 (0.811) 0.920 0.960 0.830 0.883 0.899 + 212 (0.028) 0.015 0.005 0.028 0.016 0.007 + 204 (0.044) 0.013 0.012 0.040 0.017 0.021 + 208 (0.040) 0.020 0.010 0.036 0.032 0.029 + 220 (0.040) 0.025 0.007 0.035 0.041 0.031 + 219 (0.018) 0.004 0.003 0.016 0.006 0.006 + 210 (0.018) 0.004 0.003 0.016 0.004 0.006 + +Locus 14 : Ap68 +9 alleles +4.7% missing data + 158 (0.390) 0.439 0.299 0.411 0.471 0.321 + 160 (0.083) 0.059 0.135 0.081 0.025 0.091 + 156 (0.240) 0.322 0.353 0.241 0.290 0.325 + 162 (0.044) 0.019 0.010 0.042 0.020 0.014 + 154 (0.084) 0.059 0.149 0.081 0.023 0.080 + 152 (0.076) 0.079 0.034 0.068 0.142 0.134 + 164 (0.043) 0.014 0.012 0.039 0.017 0.020 + 170 (0.018) 0.003 0.004 0.016 0.003 0.005 + 166 (0.023) 0.006 0.004 0.020 0.009 0.009 + +Locus 15 : Ap85 +10 alleles +3.4% missing data + 202 (0.318) 0.397 0.260 0.324 0.477 0.391 + 186 (0.249) 0.334 0.467 0.266 0.231 0.292 + 204 (0.061) 0.028 0.040 0.057 0.027 0.041 + 188 (0.104) 0.079 0.141 0.104 0.048 0.092 + 194 (0.079) 0.063 0.045 0.078 0.059 0.042 + 196 (0.053) 0.039 0.017 0.048 0.065 0.059 + 200 (0.066) 0.032 0.017 0.060 0.049 0.043 + 192 (0.025) 0.006 0.005 0.023 0.006 0.008 + 190 (0.018) 0.005 0.003 0.016 0.005 0.005 + 198 (0.026) 0.017 0.005 0.022 0.032 0.028 + +Locus 16 : Ap90 +13 alleles +0.7% missing data + 131 (0.364) 0.553 0.512 0.384 0.549 0.489 + 135 (0.067) 0.066 0.029 0.066 0.088 0.059 + 133 (0.287) 0.244 0.272 0.291 0.246 0.253 + 129 (0.095) 0.087 0.133 0.094 0.058 0.125 + 137 (0.034) 0.013 0.029 0.031 0.009 0.020 + 141 (0.016) 0.003 0.002 0.014 0.003 0.004 + 143 (0.023) 0.006 0.005 0.021 0.006 0.007 + 151 (0.024) 0.006 0.004 0.022 0.007 0.007 + 155 (0.016) 0.003 0.003 0.015 0.003 0.004 + 145 (0.017) 0.003 0.002 0.014 0.005 0.006 + 130 (0.020) 0.006 0.003 0.017 0.010 0.010 + 139 (0.016) 0.004 0.002 0.014 0.006 0.006 + 153 (0.020) 0.005 0.003 0.018 0.010 0.010 + +Locus 17 : Ap223 +7 alleles +2.0% missing data + 183 (0.685) 0.698 0.697 0.682 0.740 0.793 + 187 (0.136) 0.214 0.242 0.151 0.163 0.125 + 189 (0.026) 0.011 0.019 0.024 0.004 0.012 + 173 (0.065) 0.049 0.021 0.064 0.060 0.032 + 182 (0.031) 0.009 0.010 0.029 0.008 0.010 + 180 (0.025) 0.006 0.006 0.023 0.005 0.009 + 179 (0.031) 0.013 0.006 0.028 0.020 0.018 + +Locus 18 : Ap224 +7 alleles +4.0% missing data + 283 (0.110) 0.149 0.178 0.119 0.112 0.096 + 287 (0.467) 0.455 0.467 0.471 0.459 0.470 + 281 (0.138) 0.147 0.160 0.142 0.110 0.114 + 289 (0.204) 0.199 0.174 0.192 0.256 0.282 + 291 (0.038) 0.031 0.014 0.039 0.033 0.013 + 285 (0.018) 0.003 0.003 0.016 0.002 0.005 + 279 (0.025) 0.016 0.004 0.022 0.028 0.021 + +Locus 19 : Ap226 +5 alleles +17.4% missing data + 237 (0.380) 0.339 0.364 0.376 0.327 0.356 + 239 (0.461) 0.493 0.503 0.461 0.526 0.546 + 247 (0.120) 0.159 0.123 0.129 0.137 0.084 + 235 (0.019) 0.005 0.007 0.017 0.003 0.006 + 241 (0.019) 0.004 0.003 0.017 0.007 0.008 + +Locus 20 : Ap249 +9 alleles +1.3% missing data + 209 (0.608) 0.652 0.730 0.610 0.627 0.703 + 211 (0.057) 0.027 0.053 0.053 0.011 0.036 + 217 (0.084) 0.097 0.070 0.089 0.091 0.049 + 219 (0.104) 0.136 0.094 0.115 0.130 0.072 + 215 (0.078) 0.075 0.040 0.071 0.129 0.122 + 208 (0.017) 0.003 0.004 0.015 0.003 0.005 + 225 (0.017) 0.003 0.003 0.015 0.003 0.004 + 223 (0.018) 0.003 0.004 0.016 0.002 0.005 + 213 (0.017) 0.003 0.002 0.015 0.004 0.005 + +Locus 21 : Ap273 +4 alleles +1.3% missing data + 106 (0.877) 0.952 0.949 0.887 0.954 0.941 + 108 (0.050) 0.025 0.024 0.047 0.024 0.028 + 104 (0.044) 0.014 0.023 0.041 0.008 0.018 + 102 (0.029) 0.009 0.004 0.025 0.014 0.013 + +Locus 22 : Ap274 +2 alleles +2.0% missing data + 120 (0.945) 0.968 0.983 0.950 0.951 0.953 + 122 (0.055) 0.032 0.017 0.050 0.049 0.047 + +Locus 23 : Ap288 +5 alleles +0.0% missing data + 123 (0.769) 0.730 0.794 0.756 0.764 0.859 + 131 (0.165) 0.249 0.191 0.184 0.215 0.123 + 139 (0.030) 0.012 0.008 0.028 0.012 0.009 + 121 (0.018) 0.005 0.003 0.016 0.005 0.004 + 124 (0.018) 0.004 0.004 0.016 0.004 0.005 + +Locus 24 : At163 +7 alleles +0.0% missing data + 128 (0.706) 0.722 0.800 0.696 0.726 0.847 + 134 (0.197) 0.261 0.180 0.218 0.257 0.126 + 130 (0.025) 0.006 0.007 0.023 0.006 0.008 + 136 (0.018) 0.003 0.004 0.016 0.002 0.005 + 140 (0.018) 0.002 0.002 0.016 0.002 0.004 + 146 (0.018) 0.002 0.003 0.016 0.002 0.005 + 142 (0.018) 0.003 0.003 0.016 0.003 0.005 + +Locus 25 : At188 +13 alleles +1.3% missing data + 189 (0.628) 0.794 0.763 0.648 0.829 0.812 + 205 (0.032) 0.031 0.008 0.034 0.036 0.009 + 207 (0.030) 0.036 0.067 0.029 0.007 0.030 + 219 (0.024) 0.006 0.007 0.022 0.005 0.008 + 209 (0.035) 0.023 0.050 0.033 0.009 0.026 + 217 (0.039) 0.012 0.024 0.037 0.008 0.018 + 215 (0.021) 0.008 0.012 0.019 0.005 0.009 + 199 (0.067) 0.048 0.022 0.066 0.060 0.040 + 212 (0.027) 0.009 0.016 0.025 0.006 0.012 + 213 (0.037) 0.019 0.016 0.035 0.018 0.013 + 211 (0.017) 0.002 0.003 0.015 0.002 0.004 + 191 (0.017) 0.005 0.007 0.015 0.002 0.006 + 187 (0.026) 0.007 0.005 0.023 0.012 0.013 + +Values of parameters used in structure: +DATAFILE=, OUTFILE=, NUMINDS=149, NUMLOCI=25, MISSING=-9, LABEL=1, POPDATA=0, POPFLAG=1, PHENOTYPE=0, EXTRACOLS=1, MAXPOPS=5, BURNIN=100000, NUMREPS=1000000, USEPOPINFO=0, INFERALPHA=1, INFERLAMBDA=0, POPSPECIFICLAMBDA=0, POPALPHAS=0, COMPUTEPROB=1, NOADMIX=0, ADMBURNIN=2500, UPDATEFREQ=1, PRINTLIKES=0, INTERMEDSAVE=0, PRINTKLD=0, PRINTNET=0, PRINTLAMBDA=0, ANCESTDIST=0, NUMBOXES=1000, ANCESTPINT=0.90000, GENSBACK=2, MIGRPRIOR=0.05000, PRINTQHAT=0, PRINTQSUM=0, ALPHA=1.0000, FREQSCORR=1, FPRIORMEAN=0.0100, FPRIORSD=0.0500, ONEFST=0, LAMBDA=1.0000, UNIFPRIORALPHA=1, ALPHAMAX=10.0000, ALPHAPRIORA=1.0000, ALPHAPRIORB=2.0000, ALPHAPROPSD=0.0250, STARTATPOPINFO=0, RANDOMIZE=1, LINKAGE=0, METROFREQ=10, REPORTHITRATE=0, MARKOVPHASE=-1, PHASED=0, PLOIDY=2, PHASEINFO=0 LOCPRIOR=0, LOCPRIORINIT=1.000000, LOCDATA=0, LOCISPOP=0, LOCPRIORSTEP=0.100000, MAXLOCPRIOR=20.000000, SEED=1342974377, +[STRAT parameters]: NUMSIMSTATS=1000, PHENOTYPECOL=-9, POOLFREQ=10, LOCUSxONLY=0, EMERROR=0.00100, MISSINGPHENO=-9, \ No newline at end of file diff --git a/inst/files/structure/structure_17 b/inst/files/structure/structure_17 new file mode 100644 index 0000000..63070bb --- /dev/null +++ b/inst/files/structure/structure_17 @@ -0,0 +1,541 @@ + + +---------------------------------------------------- +STRUCTURE by Pritchard, Stephens and Donnelly (2000) + and Falush, Stephens and Pritchard (2003) + Code by Pritchard, Falush and Hubisz + Version 2.3.2.1 (Oct 2009) +---------------------------------------------------- + + + +Command line arguments: +Input File: + +Run parameters: + 149 individuals + 25 loci + 6 populations assumed + 100000 Burn-in period + 1000000 Reps + + +-------------------------------------------- +Overall proportion of membership of the +sample in each of the 6 clusters + +Inferred Clusters + 1 2 3 4 5 6 +0.169 0.160 0.165 0.167 0.161 0.178 + +-------------------------------------------- + +Allele-freq. divergence among pops (Net nucleotide distance), +computed using point estimates of P. + + 1 2 3 4 5 6 + 1 - 0.0037 0.0056 0.0074 0.0039 0.0035 + 2 0.0037 - 0.0038 0.0104 0.0072 0.0025 + 3 0.0056 0.0038 - 0.0212 0.0161 0.0024 + 4 0.0074 0.0104 0.0212 - 0.0035 0.0160 + 5 0.0039 0.0072 0.0161 0.0035 - 0.0103 + 6 0.0035 0.0025 0.0024 0.0160 0.0103 - + +Average distances (expected heterozygosity) between individuals in same cluster: +cluster 1 : 0.4845 +cluster 2 : 0.5360 +cluster 3 : 0.4700 +cluster 4 : 0.5268 +cluster 5 : 0.5331 +cluster 6 : 0.4723 + +-------------------------------------------- +Estimated Ln Prob of Data = -7963.6 +Mean value of ln likelihood = -7164.9 +Variance of ln likelihood = 1597.3 +Mean value of alpha = 0.2581 + +Mean value of Fst_1 = 0.2087 +Mean value of Fst_2 = 0.0877 +Mean value of Fst_3 = 0.1833 +Mean value of Fst_4 = 0.1486 +Mean value of Fst_5 = 0.1272 +Mean value of Fst_6 = 0.1823 + + +Inferred ancestry of individuals: + Label (%Miss) : Inferred clusters + 1 I13825 (0) : 0.121 0.222 0.095 0.256 0.231 0.075 + 2 I13826 (0) : 0.189 0.090 0.061 0.386 0.215 0.060 + 3 I13827 (20) : 0.249 0.102 0.156 0.084 0.246 0.163 + 4 I13828 (0) : 0.168 0.115 0.066 0.359 0.212 0.079 + 5 I13829 (8) : 0.224 0.110 0.103 0.179 0.208 0.177 + 6 I13830 (0) : 0.187 0.089 0.068 0.344 0.239 0.073 + 7 I13831 (0) : 0.197 0.104 0.093 0.236 0.175 0.195 + 8 I13832 (16) : 0.196 0.154 0.119 0.139 0.218 0.174 + 9 I13833 (0) : 0.217 0.109 0.114 0.159 0.188 0.213 + 10 I13834 (0) : 0.243 0.087 0.123 0.139 0.239 0.169 + 11 I13835 (0) : 0.164 0.161 0.098 0.192 0.196 0.190 + 12 I13836 (0) : 0.225 0.126 0.128 0.125 0.249 0.147 + 13 I13377 (0) : 0.192 0.125 0.115 0.163 0.179 0.227 + 14 I13378 (0) : 0.129 0.178 0.105 0.219 0.183 0.185 + 15 I13379 (0) : 0.188 0.100 0.079 0.298 0.188 0.146 + 16 I13380 (0) : 0.221 0.129 0.160 0.094 0.185 0.213 + 17 I13381 (0) : 0.199 0.170 0.105 0.164 0.192 0.170 + 18 I13382 (0) : 0.247 0.090 0.100 0.137 0.233 0.192 + 19 I13383 (0) : 0.158 0.180 0.101 0.197 0.192 0.172 + 20 I13384 (0) : 0.207 0.119 0.103 0.212 0.214 0.144 + 21 I13385 (0) : 0.244 0.099 0.124 0.114 0.233 0.186 + 22 I13386 (0) : 0.247 0.097 0.124 0.103 0.260 0.170 + 23 I13387 (0) : 0.173 0.128 0.073 0.320 0.218 0.087 + 24 I13388 (0) : 0.119 0.229 0.125 0.218 0.228 0.080 + 25 I13389 (0) : 0.220 0.115 0.153 0.143 0.166 0.203 + 26 I13390 (0) : 0.235 0.094 0.118 0.145 0.237 0.173 + 27 I13391 (0) : 0.146 0.183 0.133 0.176 0.178 0.184 + 28 I13392 (0) : 0.142 0.168 0.111 0.227 0.190 0.161 + 29 I13393 (0) : 0.210 0.132 0.108 0.166 0.157 0.226 + 30 I13394 (4) : 0.164 0.163 0.201 0.135 0.140 0.197 + 31 I13395 (0) : 0.172 0.148 0.195 0.144 0.144 0.196 + 32 I13396 (0) : 0.160 0.158 0.135 0.269 0.178 0.100 + 33 I13397 (0) : 0.156 0.176 0.105 0.229 0.206 0.127 + 34 I13398 (0) : 0.201 0.079 0.068 0.344 0.231 0.078 + 35 I13399 (4) : 0.134 0.216 0.122 0.162 0.213 0.153 + 36 I13400 (0) : 0.173 0.140 0.120 0.202 0.168 0.198 + 37 I13401 (0) : 0.180 0.184 0.217 0.106 0.124 0.189 + 38 I13402 (0) : 0.132 0.195 0.116 0.227 0.196 0.133 + 39 I13403 (0) : 0.195 0.105 0.122 0.289 0.162 0.127 + 40 I13404 (0) : 0.218 0.085 0.083 0.269 0.229 0.115 + 41 I13405 (0) : 0.244 0.101 0.125 0.108 0.221 0.201 + 42 I13406 (16) : 0.147 0.186 0.090 0.288 0.217 0.073 + 43 I13407 (0) : 0.181 0.107 0.076 0.326 0.176 0.135 + 44 I13408 (0) : 0.207 0.110 0.087 0.192 0.179 0.225 + 45 I13409 (0) : 0.125 0.208 0.120 0.249 0.214 0.084 + 46 I13410 (0) : 0.205 0.104 0.068 0.257 0.187 0.180 + 47 I13411 (0) : 0.222 0.094 0.107 0.174 0.253 0.150 + 48 I13412 (0) : 0.175 0.141 0.162 0.159 0.183 0.180 + 49 I13413 (0) : 0.150 0.157 0.108 0.277 0.205 0.103 + 50 I13414 (0) : 0.177 0.122 0.076 0.310 0.237 0.078 + 51 I13415 (4) : 0.238 0.109 0.158 0.142 0.192 0.160 + 52 I13416 (4) : 0.181 0.127 0.138 0.200 0.194 0.159 + 53 I13417 (4) : 0.240 0.122 0.190 0.118 0.165 0.166 + 54 I13418 (0) : 0.227 0.102 0.162 0.149 0.214 0.145 + 55 I13419 (0) : 0.148 0.222 0.130 0.137 0.257 0.106 + 56 I13420 (0) : 0.200 0.116 0.153 0.215 0.178 0.137 + 57 I13421 (0) : 0.242 0.115 0.178 0.126 0.152 0.185 + 58 I13422 (0) : 0.168 0.145 0.162 0.162 0.158 0.205 + 59 I13423 (0) : 0.185 0.184 0.128 0.157 0.203 0.143 + 60 I13424 (0) : 0.198 0.120 0.112 0.181 0.195 0.194 + 61 I13425 (4) : 0.199 0.139 0.146 0.153 0.215 0.149 + 62 I13426 (4) : 0.163 0.167 0.217 0.139 0.135 0.179 + 63 I13870 (0) : 0.196 0.114 0.163 0.242 0.162 0.123 + 64 I13871 (16) : 0.165 0.146 0.094 0.259 0.212 0.124 + 65 I13872 (0) : 0.166 0.125 0.054 0.389 0.217 0.049 + 66 I13873 (4) : 0.183 0.114 0.104 0.309 0.168 0.123 + 67 I13874 (0) : 0.145 0.169 0.109 0.271 0.222 0.084 + 68 I13875 (8) : 0.177 0.119 0.103 0.312 0.193 0.097 + 69 I13876 (0) : 0.104 0.271 0.153 0.161 0.223 0.087 + 70 I13877 (20) : 0.242 0.119 0.121 0.172 0.189 0.157 + 71 I13878 (28) : 0.209 0.089 0.085 0.291 0.224 0.102 + 72 I13879 (4) : 0.231 0.086 0.100 0.203 0.234 0.146 + 73 I13880 (4) : 0.184 0.088 0.052 0.399 0.221 0.056 + 74 I13881 (0) : 0.139 0.217 0.144 0.188 0.221 0.091 + 75 I13882 (0) : 0.181 0.113 0.076 0.344 0.198 0.089 + 76 I13883 (4) : 0.172 0.123 0.089 0.358 0.192 0.065 + 77 I13884 (16) : 0.097 0.286 0.132 0.155 0.245 0.085 + 78 I13885 (20) : 0.168 0.191 0.102 0.163 0.239 0.137 + 79 I13886 (8) : 0.193 0.109 0.092 0.283 0.211 0.112 + 80 I13887 (0) : 0.072 0.336 0.150 0.141 0.234 0.067 + 81 I13888 (0) : 0.144 0.204 0.100 0.236 0.214 0.102 + 82 I13889 (0) : 0.119 0.200 0.223 0.085 0.082 0.292 + 83 I13890 (32) : 0.158 0.163 0.204 0.137 0.137 0.201 + 84 I13891 (0) : 0.185 0.109 0.087 0.286 0.238 0.095 + 85 I13892 (0) : 0.207 0.131 0.203 0.141 0.134 0.184 + 86 I13893 (8) : 0.114 0.250 0.128 0.165 0.210 0.133 + 87 I13894 (0) : 0.182 0.091 0.049 0.433 0.198 0.046 + 88 I13895 (4) : 0.150 0.179 0.144 0.170 0.182 0.175 + 89 I13896 (0) : 0.187 0.125 0.159 0.276 0.151 0.102 + 90 I13897 (0) : 0.198 0.078 0.075 0.311 0.242 0.096 + 91 I13898 (4) : 0.188 0.103 0.084 0.332 0.175 0.117 + 92 I13899 (0) : 0.190 0.074 0.036 0.438 0.217 0.046 + 93 I13900 (32) : 0.110 0.253 0.143 0.173 0.222 0.098 + 94 I13837 (0) : 0.237 0.105 0.149 0.095 0.226 0.188 + 95 I13838 (0) : 0.148 0.175 0.232 0.124 0.091 0.230 + 96 I13839 (0) : 0.222 0.120 0.168 0.093 0.218 0.180 + 97 I13840 (0) : 0.222 0.118 0.170 0.142 0.166 0.183 + 98 I13841 (0) : 0.250 0.129 0.244 0.104 0.111 0.162 + 99 I13842 (0) : 0.214 0.137 0.193 0.093 0.151 0.212 +100 I13843 (4) : 0.241 0.133 0.250 0.109 0.106 0.162 +101 I13844 (16) : 0.178 0.148 0.132 0.164 0.174 0.206 +102 I13845 (0) : 0.238 0.105 0.118 0.131 0.233 0.175 +103 I13846 (0) : 0.227 0.129 0.125 0.136 0.215 0.168 +104 I13847 (0) : 0.153 0.162 0.182 0.183 0.142 0.178 +105 I13848 (0) : 0.153 0.161 0.160 0.183 0.146 0.198 +106 I13849 (0) : 0.150 0.154 0.112 0.290 0.170 0.125 +107 I13850 (0) : 0.212 0.137 0.232 0.140 0.105 0.175 +108 I12577 (4) : 0.123 0.205 0.270 0.065 0.065 0.272 +109 I12578 (4) : 0.102 0.212 0.239 0.072 0.061 0.315 +110 I12579 (8) : 0.121 0.218 0.239 0.076 0.097 0.249 +111 I12580 (8) : 0.158 0.168 0.302 0.054 0.045 0.272 +112 I12581 (4) : 0.128 0.211 0.163 0.137 0.162 0.199 +113 I12582 (4) : 0.137 0.186 0.284 0.067 0.052 0.274 +114 I12583 (8) : 0.112 0.265 0.222 0.083 0.170 0.148 +115 I12584 (4) : 0.116 0.247 0.235 0.081 0.121 0.200 +116 I12585 (4) : 0.168 0.184 0.311 0.050 0.046 0.242 +117 I12586 (4) : 0.157 0.166 0.303 0.062 0.046 0.265 +118 I12587 (8) : 0.193 0.162 0.327 0.047 0.036 0.235 +119 I12588 (4) : 0.122 0.207 0.293 0.050 0.059 0.269 +120 I12589 (0) : 0.156 0.188 0.275 0.062 0.057 0.262 +121 I12590 (0) : 0.123 0.200 0.251 0.090 0.085 0.252 +122 I12591 (12) : 0.101 0.210 0.277 0.037 0.029 0.347 +123 I12592 (4) : 0.086 0.225 0.235 0.053 0.061 0.340 +124 I12593 (4) : 0.085 0.219 0.252 0.054 0.042 0.348 +125 I12594 (8) : 0.125 0.183 0.301 0.050 0.038 0.304 +126 I12595 (0) : 0.100 0.252 0.212 0.079 0.125 0.232 +127 I12596 (0) : 0.109 0.203 0.277 0.042 0.040 0.329 +128 I12597 (4) : 0.119 0.258 0.244 0.081 0.156 0.141 +129 I12598 (0) : 0.123 0.242 0.235 0.072 0.124 0.205 +130 I12599 (0) : 0.109 0.216 0.204 0.122 0.107 0.242 +131 I12600 (4) : 0.186 0.159 0.318 0.064 0.046 0.227 +132 I12601 (8) : 0.153 0.198 0.289 0.059 0.064 0.237 +133 I12602 (12) : 0.130 0.191 0.284 0.062 0.057 0.276 +134 I12603 (0) : 0.112 0.236 0.253 0.070 0.112 0.217 +135 I12604 (4) : 0.146 0.191 0.279 0.086 0.070 0.228 +136 I12605 (4) : 0.137 0.195 0.273 0.077 0.066 0.253 +137 I12606 (8) : 0.092 0.220 0.240 0.055 0.049 0.345 +138 I12607 (4) : 0.080 0.256 0.228 0.070 0.098 0.268 +139 I12608 (8) : 0.108 0.219 0.229 0.080 0.087 0.278 +140 I12609 (8) : 0.139 0.199 0.280 0.048 0.043 0.291 +141 I12610 (52) : 0.143 0.181 0.262 0.078 0.076 0.259 +142 I12611 (0) : 0.151 0.197 0.283 0.046 0.036 0.287 +143 I12612 (0) : 0.169 0.182 0.299 0.050 0.046 0.253 +144 I12613 (0) : 0.109 0.212 0.255 0.044 0.040 0.339 +145 I12614 (4) : 0.168 0.170 0.251 0.078 0.089 0.243 +146 I12615 (0) : 0.129 0.212 0.228 0.080 0.098 0.253 +147 I12616 (4) : 0.091 0.269 0.206 0.073 0.145 0.216 +148 I12617 (8) : 0.135 0.182 0.317 0.044 0.028 0.295 +149 I12618 (48) : 0.140 0.187 0.297 0.056 0.054 0.267 + + +Estimated Allele Frequencies in each cluster +First column gives estimated ancestral frequencies + + +Locus 1 : A8 +7 alleles +4.0% missing data + 177 (0.509) 0.518 0.532 0.545 0.521 0.448 0.543 + 179 (0.095) 0.096 0.081 0.073 0.086 0.114 0.077 + 175 (0.097) 0.180 0.092 0.088 0.199 0.238 0.103 + 173 (0.046) 0.036 0.040 0.023 0.046 0.046 0.046 + 181 (0.181) 0.150 0.203 0.241 0.117 0.117 0.199 + 165 (0.040) 0.011 0.033 0.022 0.016 0.019 0.023 + 183 (0.031) 0.010 0.020 0.008 0.016 0.017 0.008 + +Locus 2 : A14 +5 alleles +0.0% missing data + 112 (0.200) 0.209 0.166 0.089 0.358 0.249 0.133 + 110 (0.697) 0.746 0.738 0.809 0.606 0.705 0.786 + 114 (0.033) 0.008 0.020 0.010 0.015 0.017 0.006 + 118 (0.039) 0.026 0.051 0.069 0.013 0.017 0.058 + 116 (0.031) 0.011 0.024 0.023 0.008 0.013 0.016 + +Locus 3 : A24 +5 alleles +2.7% missing data + 104 (0.404) 0.367 0.380 0.366 0.445 0.365 0.337 + 106 (0.518) 0.605 0.559 0.583 0.522 0.597 0.622 + 101 (0.018) 0.004 0.011 0.005 0.006 0.009 0.004 + 108 (0.030) 0.009 0.019 0.009 0.019 0.017 0.007 + 96 (0.030) 0.015 0.031 0.037 0.008 0.012 0.029 + +Locus 4 : A29 +29 alleles +6.7% missing data + 143 (0.034) 0.045 0.029 0.018 0.080 0.055 0.021 + 149 (0.049) 0.025 0.050 0.043 0.029 0.030 0.048 + 147 (0.030) 0.018 0.027 0.025 0.026 0.021 0.020 + 153 (0.051) 0.102 0.073 0.108 0.034 0.074 0.086 + 169 (0.037) 0.036 0.036 0.025 0.081 0.041 0.026 + 151 (0.037) 0.054 0.043 0.030 0.045 0.049 0.068 + 145 (0.029) 0.016 0.025 0.023 0.021 0.018 0.019 + 157 (0.066) 0.107 0.083 0.130 0.091 0.070 0.081 + 155 (0.095) 0.116 0.118 0.147 0.107 0.088 0.132 + 159 (0.052) 0.082 0.052 0.054 0.125 0.070 0.036 + 161 (0.033) 0.057 0.031 0.034 0.030 0.066 0.047 + 141 (0.029) 0.028 0.024 0.023 0.018 0.037 0.025 + 139 (0.017) 0.010 0.011 0.008 0.006 0.015 0.007 + 144 (0.026) 0.035 0.023 0.018 0.028 0.041 0.033 + 171 (0.049) 0.040 0.047 0.038 0.041 0.050 0.054 + 163 (0.071) 0.080 0.072 0.062 0.085 0.084 0.092 + 167 (0.046) 0.032 0.054 0.050 0.032 0.033 0.057 + 173 (0.025) 0.021 0.019 0.014 0.017 0.028 0.016 + 142 (0.014) 0.003 0.008 0.004 0.006 0.007 0.002 + 177 (0.025) 0.012 0.027 0.029 0.010 0.012 0.028 + 175 (0.023) 0.009 0.017 0.014 0.009 0.012 0.011 + 165 (0.044) 0.028 0.042 0.038 0.034 0.035 0.036 + 146 (0.021) 0.016 0.016 0.010 0.017 0.022 0.013 + 137 (0.020) 0.004 0.014 0.009 0.005 0.009 0.008 + 183 (0.018) 0.005 0.014 0.012 0.005 0.008 0.009 + 179 (0.019) 0.005 0.014 0.010 0.006 0.009 0.009 + 191 (0.014) 0.002 0.009 0.005 0.003 0.006 0.004 + 185 (0.014) 0.002 0.009 0.005 0.003 0.006 0.004 + 180 (0.016) 0.007 0.014 0.015 0.004 0.007 0.010 + +Locus 5 : A43 +7 alleles +1.3% missing data + 123 (0.203) 0.117 0.172 0.142 0.122 0.131 0.147 + 141 (0.018) 0.003 0.011 0.004 0.005 0.008 0.002 + 137 (0.659) 0.794 0.709 0.730 0.828 0.792 0.764 + 139 (0.049) 0.062 0.051 0.070 0.027 0.040 0.046 + 124 (0.034) 0.018 0.035 0.041 0.010 0.014 0.032 + 143 (0.018) 0.002 0.011 0.005 0.004 0.007 0.003 + 128 (0.018) 0.003 0.012 0.007 0.004 0.007 0.005 + +Locus 6 : A79 +13 alleles +3.4% missing data + 103 (0.230) 0.280 0.231 0.211 0.314 0.274 0.250 + 97 (0.130) 0.099 0.104 0.068 0.191 0.116 0.068 + 101 (0.092) 0.129 0.093 0.092 0.090 0.161 0.128 + 107 (0.097) 0.134 0.094 0.096 0.091 0.148 0.110 + 109 (0.099) 0.067 0.093 0.079 0.080 0.080 0.091 + 105 (0.164) 0.214 0.235 0.321 0.160 0.124 0.248 + 111 (0.047) 0.019 0.039 0.028 0.026 0.026 0.028 + 113 (0.017) 0.002 0.010 0.004 0.005 0.007 0.002 + 91 (0.028) 0.023 0.035 0.052 0.009 0.011 0.039 + 99 (0.034) 0.018 0.028 0.026 0.013 0.022 0.021 + 115 (0.029) 0.010 0.019 0.013 0.012 0.014 0.010 + 117 (0.017) 0.003 0.010 0.004 0.006 0.008 0.003 + 121 (0.017) 0.002 0.010 0.004 0.004 0.007 0.002 + +Locus 7 : A88 +9 alleles +6.0% missing data + 133 (0.019) 0.003 0.011 0.005 0.006 0.008 0.003 + 149 (0.519) 0.586 0.603 0.692 0.547 0.469 0.636 + 137 (0.104) 0.086 0.077 0.048 0.130 0.109 0.052 + 147 (0.189) 0.265 0.177 0.165 0.229 0.322 0.231 + 141 (0.086) 0.046 0.081 0.065 0.068 0.058 0.061 + 152 (0.019) 0.003 0.011 0.005 0.005 0.008 0.003 + 143 (0.019) 0.003 0.011 0.005 0.005 0.008 0.003 + 151 (0.019) 0.003 0.012 0.006 0.004 0.007 0.004 + 144 (0.026) 0.005 0.017 0.010 0.007 0.011 0.007 + +Locus 8 : A113 +12 alleles +7.4% missing data + 214 (0.562) 0.786 0.642 0.749 0.688 0.692 0.740 + 226 (0.064) 0.055 0.052 0.035 0.103 0.071 0.032 + 218 (0.018) 0.005 0.011 0.006 0.004 0.010 0.004 + 220 (0.065) 0.038 0.086 0.086 0.032 0.036 0.102 + 216 (0.059) 0.019 0.048 0.034 0.024 0.032 0.034 + 230 (0.047) 0.034 0.037 0.024 0.034 0.048 0.035 + 234 (0.034) 0.013 0.022 0.011 0.025 0.023 0.009 + 232 (0.032) 0.015 0.022 0.012 0.026 0.024 0.009 + 228 (0.051) 0.020 0.037 0.021 0.039 0.031 0.020 + 224 (0.018) 0.003 0.011 0.005 0.005 0.008 0.003 + 222 (0.033) 0.008 0.021 0.012 0.015 0.016 0.008 + 208 (0.018) 0.005 0.011 0.005 0.005 0.009 0.004 + +Locus 9 : Ac11 +9 alleles +4.7% missing data + 111 (0.129) 0.152 0.109 0.074 0.256 0.181 0.083 + 117 (0.296) 0.316 0.289 0.235 0.335 0.345 0.340 + 115 (0.246) 0.335 0.250 0.307 0.251 0.299 0.239 + 113 (0.161) 0.125 0.181 0.208 0.107 0.101 0.183 + 119 (0.054) 0.040 0.084 0.107 0.020 0.027 0.101 + 121 (0.029) 0.015 0.032 0.037 0.008 0.012 0.032 + 123 (0.035) 0.006 0.023 0.013 0.009 0.014 0.009 + 127 (0.032) 0.008 0.021 0.014 0.010 0.015 0.010 + 125 (0.018) 0.002 0.011 0.005 0.004 0.007 0.003 + +Locus 10 : Ac88 +8 alleles +0.7% missing data + 214 (0.742) 0.872 0.813 0.900 0.755 0.812 0.906 + 216 (0.031) 0.010 0.019 0.009 0.017 0.019 0.007 + 220 (0.119) 0.099 0.094 0.049 0.202 0.124 0.053 + 230 (0.026) 0.004 0.016 0.008 0.007 0.011 0.004 + 221 (0.018) 0.003 0.011 0.007 0.004 0.007 0.005 + 212 (0.022) 0.005 0.018 0.012 0.005 0.009 0.012 + 217 (0.018) 0.002 0.011 0.005 0.004 0.007 0.004 + 224 (0.025) 0.004 0.017 0.010 0.005 0.010 0.009 + +Locus 11 : Ac139 +8 alleles +13.4% missing data + 327 (0.503) 0.608 0.601 0.704 0.487 0.475 0.688 + 329 (0.289) 0.288 0.244 0.195 0.372 0.382 0.216 + 331 (0.072) 0.051 0.053 0.033 0.091 0.069 0.028 + 328 (0.042) 0.030 0.033 0.015 0.028 0.036 0.029 + 341 (0.020) 0.004 0.013 0.007 0.005 0.008 0.005 + 337 (0.032) 0.013 0.031 0.033 0.008 0.013 0.026 + 323 (0.020) 0.003 0.012 0.006 0.005 0.008 0.004 + 339 (0.020) 0.003 0.012 0.007 0.005 0.008 0.004 + +Locus 12 : Ac306 +6 alleles +4.7% missing data + 165 (0.727) 0.764 0.768 0.783 0.737 0.754 0.832 + 177 (0.077) 0.090 0.074 0.106 0.059 0.053 0.053 + 173 (0.099) 0.085 0.078 0.046 0.166 0.107 0.044 + 169 (0.046) 0.049 0.036 0.033 0.026 0.066 0.039 + 171 (0.019) 0.002 0.011 0.005 0.004 0.008 0.002 + 179 (0.032) 0.010 0.033 0.027 0.008 0.012 0.030 + +Locus 13 : Ap15 +7 alleles +6.0% missing data + 202 (0.808) 0.939 0.836 0.874 0.931 0.912 0.882 + 212 (0.029) 0.010 0.018 0.007 0.023 0.018 0.004 + 204 (0.046) 0.013 0.033 0.024 0.014 0.021 0.018 + 208 (0.039) 0.019 0.042 0.041 0.011 0.016 0.037 + 220 (0.039) 0.013 0.047 0.040 0.012 0.016 0.049 + 219 (0.019) 0.004 0.012 0.007 0.004 0.008 0.005 + 210 (0.019) 0.003 0.012 0.006 0.004 0.008 0.005 + +Locus 14 : Ap68 +9 alleles +4.7% missing data + 158 (0.383) 0.400 0.355 0.336 0.519 0.408 0.288 + 160 (0.081) 0.074 0.074 0.043 0.077 0.088 0.097 + 156 (0.243) 0.329 0.295 0.344 0.239 0.307 0.347 + 162 (0.045) 0.014 0.030 0.015 0.026 0.025 0.011 + 154 (0.082) 0.074 0.074 0.048 0.075 0.092 0.094 + 152 (0.079) 0.090 0.112 0.175 0.035 0.041 0.130 + 164 (0.044) 0.012 0.031 0.021 0.017 0.021 0.017 + 170 (0.018) 0.003 0.011 0.005 0.005 0.008 0.004 + 166 (0.023) 0.004 0.018 0.012 0.005 0.009 0.012 + +Locus 15 : Ap85 +10 alleles +3.4% missing data + 202 (0.315) 0.413 0.374 0.491 0.337 0.294 0.365 + 186 (0.244) 0.338 0.235 0.202 0.376 0.404 0.295 + 204 (0.061) 0.027 0.050 0.034 0.034 0.038 0.044 + 188 (0.101) 0.088 0.086 0.053 0.109 0.105 0.100 + 194 (0.080) 0.052 0.061 0.043 0.075 0.068 0.035 + 196 (0.062) 0.034 0.070 0.071 0.024 0.030 0.067 + 200 (0.064) 0.022 0.064 0.054 0.024 0.029 0.056 + 192 (0.026) 0.005 0.016 0.008 0.008 0.011 0.005 + 190 (0.018) 0.004 0.011 0.005 0.007 0.009 0.003 + 198 (0.030) 0.017 0.033 0.038 0.008 0.012 0.030 + +Locus 16 : Ap90 +13 alleles +0.7% missing data + 131 (0.358) 0.560 0.446 0.546 0.474 0.492 0.505 + 135 (0.068) 0.060 0.065 0.078 0.064 0.054 0.051 + 133 (0.278) 0.225 0.261 0.204 0.322 0.257 0.270 + 129 (0.100) 0.107 0.098 0.092 0.080 0.103 0.113 + 137 (0.037) 0.016 0.027 0.017 0.016 0.024 0.020 + 141 (0.017) 0.003 0.010 0.004 0.005 0.008 0.002 + 143 (0.024) 0.005 0.015 0.007 0.009 0.012 0.004 + 151 (0.025) 0.005 0.015 0.007 0.009 0.012 0.004 + 155 (0.017) 0.002 0.010 0.004 0.004 0.007 0.002 + 145 (0.017) 0.003 0.011 0.007 0.004 0.007 0.005 + 130 (0.021) 0.005 0.015 0.013 0.005 0.008 0.009 + 139 (0.017) 0.003 0.011 0.007 0.003 0.006 0.006 + 153 (0.022) 0.005 0.015 0.012 0.005 0.009 0.008 + +Locus 17 : Ap223 +7 alleles +2.0% missing data + 183 (0.678) 0.736 0.740 0.813 0.641 0.650 0.791 + 187 (0.137) 0.192 0.125 0.096 0.259 0.240 0.133 + 189 (0.027) 0.013 0.018 0.010 0.010 0.020 0.011 + 173 (0.066) 0.033 0.055 0.038 0.058 0.046 0.037 + 182 (0.033) 0.008 0.021 0.011 0.012 0.017 0.008 + 180 (0.026) 0.006 0.017 0.009 0.007 0.012 0.006 + 179 (0.033) 0.012 0.025 0.023 0.012 0.015 0.016 + +Locus 18 : Ap224 +7 alleles +4.0% missing data + 283 (0.114) 0.134 0.101 0.075 0.173 0.172 0.108 + 287 (0.474) 0.430 0.467 0.426 0.497 0.460 0.483 + 281 (0.136) 0.137 0.115 0.087 0.158 0.177 0.111 + 289 (0.191) 0.266 0.248 0.368 0.116 0.140 0.251 + 291 (0.039) 0.022 0.026 0.012 0.045 0.032 0.010 + 285 (0.018) 0.003 0.011 0.005 0.004 0.008 0.003 + 279 (0.027) 0.008 0.032 0.027 0.007 0.011 0.033 + +Locus 19 : Ap226 +5 alleles +17.4% missing data + 237 (0.379) 0.345 0.356 0.347 0.341 0.368 0.344 + 239 (0.461) 0.515 0.518 0.555 0.474 0.440 0.564 + 247 (0.120) 0.132 0.100 0.082 0.175 0.174 0.080 + 235 (0.020) 0.005 0.012 0.006 0.005 0.010 0.004 + 241 (0.020) 0.004 0.014 0.009 0.005 0.008 0.007 + +Locus 20 : Ap249 +9 alleles +1.3% missing data + 209 (0.598) 0.693 0.646 0.708 0.590 0.659 0.710 + 211 (0.057) 0.032 0.041 0.025 0.031 0.046 0.033 + 217 (0.083) 0.078 0.067 0.042 0.130 0.093 0.047 + 219 (0.103) 0.112 0.084 0.052 0.194 0.127 0.062 + 215 (0.085) 0.074 0.118 0.154 0.036 0.043 0.134 + 208 (0.019) 0.003 0.011 0.005 0.005 0.008 0.003 + 225 (0.018) 0.003 0.010 0.005 0.005 0.008 0.002 + 223 (0.018) 0.003 0.011 0.004 0.005 0.008 0.003 + 213 (0.018) 0.002 0.012 0.006 0.004 0.007 0.004 + +Locus 21 : Ap273 +4 alleles +1.3% missing data + 106 (0.871) 0.956 0.909 0.946 0.944 0.926 0.946 + 108 (0.053) 0.023 0.038 0.023 0.030 0.033 0.024 + 104 (0.046) 0.015 0.030 0.015 0.018 0.028 0.014 + 102 (0.030) 0.006 0.023 0.016 0.008 0.012 0.015 + +Locus 22 : Ap274 +2 alleles +2.0% missing data + 120 (0.945) 0.964 0.942 0.939 0.979 0.974 0.951 + 122 (0.055) 0.036 0.058 0.061 0.021 0.026 0.049 + +Locus 23 : Ap288 +5 alleles +0.0% missing data + 123 (0.770) 0.780 0.820 0.870 0.682 0.706 0.871 + 131 (0.162) 0.204 0.139 0.113 0.286 0.258 0.117 + 139 (0.030) 0.009 0.019 0.008 0.019 0.017 0.006 + 121 (0.019) 0.004 0.011 0.005 0.007 0.009 0.003 + 124 (0.019) 0.004 0.011 0.005 0.006 0.009 0.003 + +Locus 24 : At163 +7 alleles +0.0% missing data + 128 (0.705) 0.779 0.778 0.863 0.622 0.701 0.860 + 134 (0.196) 0.205 0.163 0.110 0.352 0.256 0.122 + 130 (0.026) 0.006 0.016 0.007 0.011 0.012 0.006 + 136 (0.018) 0.003 0.010 0.005 0.005 0.008 0.003 + 140 (0.019) 0.002 0.011 0.005 0.004 0.007 0.003 + 146 (0.018) 0.002 0.011 0.005 0.004 0.007 0.003 + 142 (0.018) 0.002 0.011 0.005 0.004 0.007 0.004 + +Locus 25 : At188 +13 alleles +1.3% missing data + 189 (0.613) 0.811 0.723 0.827 0.756 0.708 0.825 + 205 (0.033) 0.020 0.022 0.009 0.048 0.030 0.007 + 207 (0.030) 0.041 0.025 0.029 0.017 0.058 0.030 + 219 (0.025) 0.006 0.015 0.007 0.009 0.013 0.005 + 209 (0.036) 0.028 0.028 0.019 0.023 0.037 0.028 + 217 (0.040) 0.013 0.028 0.013 0.022 0.023 0.017 + 215 (0.023) 0.009 0.015 0.006 0.012 0.014 0.007 + 199 (0.069) 0.035 0.058 0.043 0.055 0.046 0.041 + 212 (0.028) 0.009 0.019 0.010 0.013 0.016 0.011 + 213 (0.039) 0.015 0.026 0.012 0.028 0.026 0.010 + 211 (0.018) 0.002 0.010 0.004 0.004 0.007 0.002 + 191 (0.017) 0.005 0.011 0.005 0.005 0.010 0.004 + 187 (0.028) 0.007 0.021 0.015 0.007 0.012 0.013 + +Values of parameters used in structure: +DATAFILE=, OUTFILE=, NUMINDS=149, NUMLOCI=25, MISSING=-9, LABEL=1, POPDATA=0, POPFLAG=1, PHENOTYPE=0, EXTRACOLS=1, MAXPOPS=6, BURNIN=100000, NUMREPS=1000000, USEPOPINFO=0, INFERALPHA=1, INFERLAMBDA=0, POPSPECIFICLAMBDA=0, POPALPHAS=0, COMPUTEPROB=1, NOADMIX=0, ADMBURNIN=2500, UPDATEFREQ=1, PRINTLIKES=0, INTERMEDSAVE=0, PRINTKLD=0, PRINTNET=0, PRINTLAMBDA=0, ANCESTDIST=0, NUMBOXES=1000, ANCESTPINT=0.90000, GENSBACK=2, MIGRPRIOR=0.05000, PRINTQHAT=0, PRINTQSUM=0, ALPHA=1.0000, FREQSCORR=1, FPRIORMEAN=0.0100, FPRIORSD=0.0500, ONEFST=0, LAMBDA=1.0000, UNIFPRIORALPHA=1, ALPHAMAX=10.0000, ALPHAPRIORA=1.0000, ALPHAPRIORB=2.0000, ALPHAPROPSD=0.0250, STARTATPOPINFO=0, RANDOMIZE=1, LINKAGE=0, METROFREQ=10, REPORTHITRATE=0, MARKOVPHASE=-1, PHASED=0, PLOIDY=2, PHASEINFO=0 LOCPRIOR=0, LOCPRIORINIT=1.000000, LOCDATA=0, LOCISPOP=0, LOCPRIORSTEP=0.100000, MAXLOCPRIOR=20.000000, SEED=1342982542, +[STRAT parameters]: NUMSIMSTATS=1000, PHENOTYPECOL=-9, POOLFREQ=10, LOCUSxONLY=0, EMERROR=0.00100, MISSINGPHENO=-9, \ No newline at end of file diff --git a/inst/files/structuregrplabels-rep.txt b/inst/files/structuregrplabels-rep.txt new file mode 100644 index 0000000..7e52587 --- /dev/null +++ b/inst/files/structuregrplabels-rep.txt @@ -0,0 +1,149 @@ +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop C +Pop C +Pop C +Pop C +Pop C +Pop C +Pop C +Pop C +Pop C +Pop C +Pop C +Pop C +Pop C +Pop C +Pop C +Pop C +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A diff --git a/inst/files/structuregrplabels.txt b/inst/files/structuregrplabels.txt new file mode 100644 index 0000000..935e4d2 --- /dev/null +++ b/inst/files/structuregrplabels.txt @@ -0,0 +1,149 @@ +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B diff --git a/inst/files/structuregrplabels2.txt b/inst/files/structuregrplabels2.txt new file mode 100644 index 0000000..da1e33a --- /dev/null +++ b/inst/files/structuregrplabels2.txt @@ -0,0 +1,149 @@ +Loc1 +Loc1 +Loc1 +Loc1 +Loc1 +Loc1 +Loc1 +Loc1 +Loc1 +Loc1 +Loc1 +Loc1 +Loc1 +Loc1 +Loc1 +Loc1 +Loc1 +Loc1 +Loc1 +Loc1 +Loc1 +Loc1 +Loc1 +Loc1 +Loc2 +Loc2 +Loc2 +Loc2 +Loc2 +Loc2 +Loc2 +Loc2 +Loc2 +Loc2 +Loc2 +Loc2 +Loc2 +Loc2 +Loc2 +Loc2 +Loc2 +Loc2 +Loc2 +Loc2 +Loc2 +Loc2 +Loc2 +Loc2 +Loc2 +Loc2 +Loc2 +Loc2 +Loc2 +Loc2 +Loc2 +Loc2 +Loc3 +Loc3 +Loc3 +Loc3 +Loc3 +Loc3 +Loc3 +Loc3 +Loc3 +Loc3 +Loc3 +Loc3 +Loc3 +Loc3 +Loc3 +Loc3 +Loc3 +Loc3 +Loc3 +Loc3 +Loc3 +Loc3 +Loc3 +Loc3 +Loc3 +Loc3 +Loc3 +Loc3 +Loc3 +Loc3 +Loc3 +Loc3 +Loc3 +Loc3 +Loc3 +Loc3 +Loc3 +Loc3 +Loc3 +Loc3 +Loc3 +Loc3 +Loc3 +Loc3 +Loc3 +Loc3 +Loc3 +Loc3 +Loc3 +Loc3 +Loc3 +Loc3 +Loc3 +Loc3 +Loc3 +Loc3 +Loc3 +Loc3 +Loc3 +Loc3 +Loc3 +Loc4 +Loc4 +Loc4 +Loc4 +Loc4 +Loc4 +Loc4 +Loc4 +Loc4 +Loc4 +Loc4 +Loc4 +Loc4 +Loc4 +Loc4 +Loc4 +Loc4 +Loc4 +Loc4 +Loc4 +Loc4 +Loc4 +Loc4 +Loc4 +Loc4 +Loc4 +Loc4 +Loc4 +Loc4 +Loc4 +Loc4 +Loc4 diff --git a/inst/files/structureindlabels.txt b/inst/files/structureindlabels.txt new file mode 100644 index 0000000..c5778a9 --- /dev/null +++ b/inst/files/structureindlabels.txt @@ -0,0 +1,149 @@ +I13825 +I13826 +I13827 +I13828 +I13829 +I13830 +I13831 +I13832 +I13833 +I13834 +I13835 +I13836 +I13377 +I13378 +I13379 +I13380 +I13381 +I13382 +I13383 +I13384 +I13385 +I13386 +I13387 +I13388 +I13389 +I13390 +I13391 +I13392 +I13393 +I13394 +I13395 +I13396 +I13397 +I13398 +I13399 +I13400 +I13401 +I13402 +I13403 +I13404 +I13405 +I13406 +I13407 +I13408 +I13409 +I13410 +I13411 +I13412 +I13413 +I13414 +I13415 +I13416 +I13417 +I13418 +I13419 +I13420 +I13421 +I13422 +I13423 +I13424 +I13425 +I13426 +I13870 +I13871 +I13872 +I13873 +I13874 +I13875 +I13876 +I13877 +I13878 +I13879 +I13880 +I13881 +I13882 +I13883 +I13884 +I13885 +I13886 +I13887 +I13888 +I13889 +I13890 +I13891 +I13892 +I13893 +I13894 +I13895 +I13896 +I13897 +I13898 +I13899 +I13900 +I13837 +I13838 +I13839 +I13840 +I13841 +I13842 +I13843 +I13844 +I13845 +I13846 +I13847 +I13848 +I13849 +I13850 +I12577 +I12578 +I12579 +I12580 +I12581 +I12582 +I12583 +I12584 +I12585 +I12586 +I12587 +I12588 +I12589 +I12590 +I12591 +I12592 +I12593 +I12594 +I12595 +I12596 +I12597 +I12598 +I12599 +I12600 +I12601 +I12602 +I12603 +I12604 +I12605 +I12606 +I12607 +I12608 +I12609 +I12610 +I12611 +I12612 +I12613 +I12614 +I12615 +I12616 +I12617 +I12618 diff --git a/inst/files/structureindlabelslong.txt b/inst/files/structureindlabelslong.txt new file mode 100644 index 0000000..671e533 --- /dev/null +++ b/inst/files/structureindlabelslong.txt @@ -0,0 +1,149 @@ +this_is_a_real_long_label_13825 +this_is_a_real_long_label_13826 +this_is_a_real_long_label_13827 +this_is_a_real_long_label_13828 +this_is_a_real_long_label_13829 +this_is_a_real_long_label_13830 +this_is_a_real_long_label_13831 +this_is_a_real_long_label_13832 +this_is_a_real_long_label_13833 +this_is_a_real_long_label_13834 +this_is_a_real_long_label_13835 +this_is_a_real_long_label_13836 +this_is_a_real_long_label_13377 +this_is_a_real_long_label_13378 +this_is_a_real_long_label_13379 +this_is_a_real_long_label_13380 +this_is_a_real_long_label_13381 +this_is_a_real_long_label_13382 +this_is_a_real_long_label_13383 +this_is_a_real_long_label_13384 +this_is_a_real_long_label_13385 +this_is_a_real_long_label_13386 +this_is_a_real_long_label_13387 +this_is_a_real_long_label_13388 +this_is_a_real_long_label_13389 +this_is_a_real_long_label_13390 +this_is_a_real_long_label_13391 +this_is_a_real_long_label_13392 +this_is_a_real_long_label_13393 +this_is_a_real_long_label_13394 +this_is_a_real_long_label_13395 +this_is_a_real_long_label_13396 +this_is_a_real_long_label_13397 +this_is_a_real_long_label_13398 +this_is_a_real_long_label_13399 +this_is_a_real_long_label_13400 +this_is_a_real_long_label_13401 +this_is_a_real_long_label_13402 +this_is_a_real_long_label_13403 +this_is_a_real_long_label_13404 +this_is_a_real_long_label_13405 +this_is_a_real_long_label_13406 +this_is_a_real_long_label_13407 +this_is_a_real_long_label_13408 +this_is_a_real_long_label_13409 +this_is_a_real_long_label_13410 +this_is_a_real_long_label_13411 +this_is_a_real_long_label_13412 +this_is_a_real_long_label_13413 +this_is_a_real_long_label_13414 +this_is_a_real_long_label_13415 +this_is_a_real_long_label_13416 +this_is_a_real_long_label_13417 +this_is_a_real_long_label_13418 +this_is_a_real_long_label_13419 +this_is_a_real_long_label_13420 +this_is_a_real_long_label_13421 +this_is_a_real_long_label_13422 +this_is_a_real_long_label_13423 +this_is_a_real_long_label_13424 +this_is_a_real_long_label_13425 +this_is_a_real_long_label_13426 +this_is_a_real_long_label_13870 +this_is_a_real_long_label_13871 +this_is_a_real_long_label_13872 +this_is_a_real_long_label_13873 +this_is_a_real_long_label_13874 +this_is_a_real_long_label_13875 +this_is_a_real_long_label_13876 +this_is_a_real_long_label_13877 +this_is_a_real_long_label_13878 +this_is_a_real_long_label_13879 +this_is_a_real_long_label_13880 +this_is_a_real_long_label_13881 +this_is_a_real_long_label_13882 +this_is_a_real_long_label_13883 +this_is_a_real_long_label_13884 +this_is_a_real_long_label_13885 +this_is_a_real_long_label_13886 +this_is_a_real_long_label_13887 +this_is_a_real_long_label_13888 +this_is_a_real_long_label_13889 +this_is_a_real_long_label_13890 +this_is_a_real_long_label_13891 +this_is_a_real_long_label_13892 +this_is_a_real_long_label_13893 +this_is_a_real_long_label_13894 +this_is_a_real_long_label_13895 +this_is_a_real_long_label_13896 +this_is_a_real_long_label_13897 +this_is_a_real_long_label_13898 +this_is_a_real_long_label_13899 +this_is_a_real_long_label_13900 +this_is_a_real_long_label_13837 +this_is_a_real_long_label_13838 +this_is_a_real_long_label_13839 +this_is_a_real_long_label_13840 +this_is_a_real_long_label_13841 +this_is_a_real_long_label_13842 +this_is_a_real_long_label_13843 +this_is_a_real_long_label_13844 +this_is_a_real_long_label_13845 +this_is_a_real_long_label_13846 +this_is_a_real_long_label_13847 +this_is_a_real_long_label_13848 +this_is_a_real_long_label_13849 +this_is_a_real_long_label_13850 +this_is_a_real_long_label_12577 +this_is_a_real_long_label_12578 +this_is_a_real_long_label_12579 +this_is_a_real_long_label_12580 +this_is_a_real_long_label_12581 +this_is_a_real_long_label_12582 +this_is_a_real_long_label_12583 +this_is_a_real_long_label_12584 +this_is_a_real_long_label_12585 +this_is_a_real_long_label_12586 +this_is_a_real_long_label_12587 +this_is_a_real_long_label_12588 +this_is_a_real_long_label_12589 +this_is_a_real_long_label_12590 +this_is_a_real_long_label_12591 +this_is_a_real_long_label_12592 +this_is_a_real_long_label_12593 +this_is_a_real_long_label_12594 +this_is_a_real_long_label_12595 +this_is_a_real_long_label_12596 +this_is_a_real_long_label_12597 +this_is_a_real_long_label_12598 +this_is_a_real_long_label_12599 +this_is_a_real_long_label_12600 +this_is_a_real_long_label_12601 +this_is_a_real_long_label_12602 +this_is_a_real_long_label_12603 +this_is_a_real_long_label_12604 +this_is_a_real_long_label_12605 +this_is_a_real_long_label_12606 +this_is_a_real_long_label_12607 +this_is_a_real_long_label_12608 +this_is_a_real_long_label_12609 +this_is_a_real_long_label_12610 +this_is_a_real_long_label_12611 +this_is_a_real_long_label_12612 +this_is_a_real_long_label_12613 +this_is_a_real_long_label_12614 +this_is_a_real_long_label_12615 +this_is_a_real_long_label_12616 +this_is_a_real_long_label_12617 +this_is_a_real_long_label_12618 diff --git a/inst/files/tess/tess_01.txt b/inst/files/tess/tess_01.txt new file mode 100644 index 0000000..109ff14 --- /dev/null +++ b/inst/files/tess/tess_01.txt @@ -0,0 +1,434 @@ +Estimated Clustering Probabilities for Samples +Sample ***Cluster 01*** ***Cluster 02*** +000001: 0.062785000000000 0.937215000000000 1 +000002: 0.020135000000000 0.979865000000000 1 +000003: 0.006845000000000 0.993155000000000 1 +000004: 0.057385000000000 0.942615000000000 1 +000005: 0.022340000000000 0.977660000000000 1 +000006: 0.017525000000000 0.982475000000000 1 +000007: 0.522840000000000 0.477160000000000 1 +000008: 0.043065000000000 0.956935000000000 1 +000009: 0.028680000000000 0.971320000000000 1 +000010: 0.062985000000000 0.937015000000000 1 +000011: 0.149370000000000 0.850630000000000 1 +000012: 0.013425000000000 0.986575000000000 1 +000013: 0.025140000000000 0.974860000000000 1 +000014: 0.032960000000000 0.967040000000000 1 +000015: 0.038680000000000 0.961320000000000 1 +000016: 0.006170000000000 0.993830000000000 1 +000017: 0.026240000000000 0.973760000000000 1 +000018: 0.022830000000000 0.977170000000000 1 +000019: 0.156455000000000 0.843545000000000 1 +000020: 0.048540000000000 0.951460000000000 1 +000021: 0.122090000000000 0.877910000000000 1 +000022: 0.494555000000000 0.505445000000000 1 +000023: 0.004500000000000 0.995500000000000 1 +000024: 0.006055000000000 0.993945000000000 1 +000025: 0.009955000000000 0.990045000000000 1 +000026: 0.026170000000000 0.973830000000000 1 +000027: 0.010650000000000 0.989350000000000 1 +000028: 0.009140000000000 0.990860000000000 1 +000029: 0.014675000000000 0.985325000000000 1 +000030: 0.024395000000000 0.975605000000000 1 +000031: 0.022615000000000 0.977385000000000 1 +000032: 0.004725000000000 0.995275000000000 1 +000033: 0.026070000000000 0.973930000000000 1 +000034: 0.007525000000000 0.992475000000000 1 +000035: 0.024340000000000 0.975660000000000 1 +000036: 0.015955000000000 0.984045000000000 1 +000037: 0.014055000000000 0.985945000000000 1 +000038: 0.011195000000000 0.988805000000000 1 +000039: 0.006430000000000 0.993570000000000 1 +000040: 0.003580000000000 0.996420000000000 1 +000041: 0.008860000000000 0.991140000000000 1 +000042: 0.006180000000000 0.993820000000000 1 +000043: 0.007300000000000 0.992700000000000 1 +000044: 0.005880000000000 0.994120000000000 1 +000045: 0.048885000000000 0.951115000000000 1 +000046: 0.022035000000000 0.977965000000000 1 +000047: 0.086350000000000 0.913650000000000 1 +000048: 0.107455000000000 0.892545000000000 1 +000049: 0.278380000000000 0.721620000000000 1 +000050: 0.114950000000000 0.885050000000000 1 +000051: 0.157325000000000 0.842675000000000 1 +000052: 0.015780000000000 0.984220000000000 1 +000053: 0.015240000000000 0.984760000000000 1 +000054: 0.086225000000000 0.913775000000000 1 +000055: 0.025310000000000 0.974690000000000 1 +000056: 0.030990000000000 0.969010000000000 1 +000057: 0.029965000000000 0.970035000000000 1 +000058: 0.009300000000000 0.990700000000000 1 +000059: 0.120635000000000 0.879365000000000 1 +000060: 0.156725000000000 0.843275000000000 1 +000061: 0.017815000000000 0.982185000000000 1 +000062: 0.110335000000000 0.889665000000000 1 +000063: 0.042680000000000 0.957320000000000 1 +000064: 0.140690000000000 0.859310000000000 1 +000065: 0.061455000000000 0.938545000000000 1 +000066: 0.022190000000000 0.977810000000000 1 +000067: 0.013460000000000 0.986540000000000 1 +000068: 0.027930000000000 0.972070000000000 1 +000069: 0.006235000000000 0.993765000000000 1 +000070: 0.012955000000000 0.987045000000000 1 +000071: 0.004775000000000 0.995225000000000 1 +000072: 0.006945000000000 0.993055000000000 1 +000073: 0.005000000000000 0.995000000000000 1 +000074: 0.010995000000000 0.989005000000000 1 +000075: 0.006995000000000 0.993005000000000 1 + + + +Estimated Allele Frequencies +Cluster 01 +Locus 001 +Allele 092 0.109795836949125 +Allele 094 0.120101850759899 +Allele 096 0.083345269095729 +Allele 098 0.112604562345767 +Allele 100 0.151835934699853 +Allele 102 0.076085360746509 +Allele 104 0.090813542138441 +Allele 106 0.185390220159350 +Allele 108 0.070027423105328 + +Locus 002 +Allele 118 0.064614900684296 +Allele 122 0.070448308748881 +Allele 124 0.075340063514001 +Allele 126 0.182965044391451 +Allele 127 0.066881898872523 +Allele 128 0.079959140960099 +Allele 130 0.066416809339111 +Allele 132 0.096096580396959 +Allele 134 0.056914059748312 +Allele 135 0.096405344826238 +Allele 137 0.080778889547009 +Allele 151 0.063178958971120 + +Locus 003 +Allele 130 0.052150348646969 +Allele 133 0.056640663140276 +Allele 136 0.058745378121435 +Allele 138 0.104590820848390 +Allele 139 0.068180502968343 +Allele 141 0.073947776468032 +Allele 143 0.049430231084304 +Allele 145 0.109002183044404 +Allele 146 0.073004487848507 +Allele 147 0.060261857831006 +Allele 148 0.084307889641829 +Allele 150 0.059352606281293 +Allele 152 0.096735184114739 +Allele 156 0.053650069960473 + +Locus 004 +Allele 093 0.049522252784376 +Allele 095 0.049833601317015 +Allele 096 0.045042906910595 +Allele 097 0.058160849446192 +Allele 099 0.069301147963041 +Allele 100 0.055890040162314 +Allele 101 0.075007761863232 +Allele 103 0.157177215525489 +Allele 105 0.046161992664255 +Allele 107 0.047212621954946 +Allele 109 0.044623565876632 +Allele 110 0.046989708034579 +Allele 113 0.060457740619920 +Allele 121 0.054514444950950 +Allele 123 0.043492400977826 +Allele 125 0.048664811670139 +Allele 131 0.047946937278499 + +Locus 005 +Allele 218 0.039384712822010 +Allele 220 0.063948111796719 +Allele 222 0.048964691352031 +Allele 224 0.055699528943944 +Allele 226 0.050869496958549 +Allele 228 0.049747388855039 +Allele 230 0.067717956594112 +Allele 232 0.061286288236355 +Allele 234 0.065513196607824 +Allele 236 0.074127923977923 +Allele 238 0.047367316817678 +Allele 240 0.047027463764174 +Allele 242 0.039545608255921 +Allele 244 0.040584490080765 +Allele 246 0.044877593284153 +Allele 248 0.040149723415360 +Allele 250 0.045800498124368 +Allele 252 0.040816615677869 +Allele 254 0.038230248087190 +Allele 256 0.038341146348016 + +Locus 006 +Allele 094 0.065530434058765 +Allele 096 0.067244088362870 +Allele 098 0.064573628828187 +Allele 100 0.049515764688743 +Allele 102 0.066641608956412 +Allele 104 0.133224393550546 +Allele 106 0.074195615945223 +Allele 108 0.056286410629798 +Allele 110 0.122630865784744 +Allele 112 0.075456643247450 +Allele 114 0.052401230016884 +Allele 124 0.068974871609593 +Allele 126 0.052441500432881 +Allele 149 0.050882943887905 + +Locus 007 +Allele 202 0.052128342116498 +Allele 204 0.047523278834130 +Allele 206 0.046355428830892 +Allele 208 0.077586465521092 +Allele 210 0.057665298577338 +Allele 212 0.058755282907148 +Allele 214 0.062277234077095 +Allele 216 0.062203403798486 +Allele 218 0.053028639860094 +Allele 220 0.057519677238984 +Allele 222 0.068962713635479 +Allele 224 0.079180351240761 +Allele 226 0.104726362693220 +Allele 228 0.051478713743537 +Allele 233 0.065226061679084 +Allele 238 0.055382745246161 + +Locus 008 +Allele 121 0.099623640992555 +Allele 123 0.192288820218250 +Allele 125 0.069228860329803 +Allele 127 0.062351152675025 +Allele 129 0.072324917612380 +Allele 131 0.085612343210650 +Allele 133 0.113369626756613 +Allele 135 0.074288648256259 +Allele 137 0.109975080142387 +Allele 151 0.058068563741939 +Allele 161 0.062868346064139 + +Locus 009 +Allele 161 0.063871965780604 +Allele 165 0.066393915580085 +Allele 167 0.098478217452421 +Allele 169 0.081927537202794 +Allele 171 0.099296085064290 +Allele 173 0.112659602281827 +Allele 175 0.091402252551673 +Allele 177 0.076465003003056 +Allele 179 0.065880352087277 +Allele 181 0.079934906546721 +Allele 183 0.092796722857372 +Allele 185 0.070893439591880 + +Locus 010 +Allele 108 0.043104963337324 +Allele 115 0.044137730171208 +Allele 121 0.040854842606595 +Allele 123 0.054010904869639 +Allele 125 0.046109433816263 +Allele 127 0.042330641566283 +Allele 129 0.061545391382182 +Allele 131 0.044004896074096 +Allele 133 0.066658722696083 +Allele 135 0.044632964290673 +Allele 137 0.073112801242615 +Allele 139 0.053844990127258 +Allele 141 0.047486889748589 +Allele 143 0.041920881004391 +Allele 145 0.038777124522753 +Allele 147 0.076079331302112 +Allele 149 0.044262037402547 +Allele 152 0.046472999367444 +Allele 155 0.043852497468402 +Allele 157 0.046799957003543 + + +Cluster 02 +Locus 001 +Allele 092 0.041193276556533 +Allele 094 0.395144946911050 +Allele 096 0.064794487338457 +Allele 098 0.202395225235983 +Allele 100 0.082981193113124 +Allele 102 0.092430167637767 +Allele 104 0.077012316230059 +Allele 106 0.024835665553462 +Allele 108 0.019212721423564 + +Locus 002 +Allele 118 0.017827679069179 +Allele 122 0.030122707412040 +Allele 124 0.211368735204638 +Allele 126 0.116956784683555 +Allele 127 0.011305395407616 +Allele 128 0.099142523504611 +Allele 130 0.076183758198818 +Allele 132 0.234736258950273 +Allele 134 0.012614641212867 +Allele 135 0.104302397990782 +Allele 137 0.073856647608372 +Allele 151 0.011582470757248 + +Locus 003 +Allele 130 0.024809556503734 +Allele 133 0.011487649415007 +Allele 136 0.133179683553644 +Allele 138 0.100146494429615 +Allele 139 0.138035895848371 +Allele 141 0.034685221499087 +Allele 143 0.012517162684747 +Allele 145 0.080620840127108 +Allele 146 0.111029518007100 +Allele 147 0.011229899076749 +Allele 148 0.147572084084236 +Allele 150 0.081488205636691 +Allele 152 0.095038625539080 +Allele 156 0.018159163594832 + +Locus 004 +Allele 093 0.048941017099610 +Allele 095 0.074205960498735 +Allele 096 0.012154488624049 +Allele 097 0.185926939580927 +Allele 099 0.051815797933593 +Allele 100 0.085595528643852 +Allele 101 0.151417611228739 +Allele 103 0.124275880540258 +Allele 105 0.049755317332106 +Allele 107 0.093497340355496 +Allele 109 0.024636468665319 +Allele 110 0.024148911276987 +Allele 113 0.015908471333541 +Allele 121 0.016563860560708 +Allele 123 0.018693726680292 +Allele 125 0.011159085623158 +Allele 131 0.011303594022632 + +Locus 005 +Allele 218 0.011880295422684 +Allele 220 0.093864622463892 +Allele 222 0.133568478114304 +Allele 224 0.132376145472688 +Allele 226 0.095916673682503 +Allele 228 0.047161826740898 +Allele 230 0.043430560275940 +Allele 232 0.063246696512200 +Allele 234 0.068252220242271 +Allele 236 0.054396321257407 +Allele 238 0.078168151718398 +Allele 240 0.041259621109049 +Allele 242 0.036650749274989 +Allele 244 0.011837092223415 +Allele 246 0.017429217834601 +Allele 248 0.011648085509409 +Allele 250 0.016812751446518 +Allele 252 0.017855117779715 +Allele 254 0.012238931996469 +Allele 256 0.012006440922647 + +Locus 006 +Allele 094 0.107086772041385 +Allele 096 0.171616529131661 +Allele 098 0.042835856328734 +Allele 100 0.012791481200671 +Allele 102 0.101406088619585 +Allele 104 0.233006652218114 +Allele 106 0.145254427929545 +Allele 108 0.069989432569112 +Allele 110 0.047035283365795 +Allele 112 0.021794857921904 +Allele 114 0.012379848483715 +Allele 124 0.010016437364633 +Allele 126 0.012286122709826 +Allele 149 0.012500210115319 + +Locus 007 +Allele 202 0.011647734815164 +Allele 204 0.025371168978339 +Allele 206 0.012505953224124 +Allele 208 0.137101404224382 +Allele 210 0.043007025953324 +Allele 212 0.185627077137002 +Allele 214 0.106684158877979 +Allele 216 0.113664017035805 +Allele 218 0.063144782273374 +Allele 220 0.056046637551509 +Allele 222 0.060487646840381 +Allele 224 0.110870119574624 +Allele 226 0.035200153428450 +Allele 228 0.018245210432408 +Allele 233 0.009176960651107 +Allele 238 0.011219949002029 + +Locus 008 +Allele 121 0.084232668130734 +Allele 123 0.070167063181606 +Allele 125 0.059022330095836 +Allele 127 0.014610774560535 +Allele 129 0.058752465292432 +Allele 131 0.269307200408079 +Allele 133 0.151120228159728 +Allele 135 0.187765966218539 +Allele 137 0.075680187725162 +Allele 151 0.015030756949116 +Allele 161 0.014310359278234 + +Locus 009 +Allele 161 0.015055183448564 +Allele 165 0.030658885203611 +Allele 167 0.056895702832535 +Allele 169 0.098924853062480 +Allele 171 0.278565688735583 +Allele 173 0.189012664922660 +Allele 175 0.105927190208999 +Allele 177 0.108806309965940 +Allele 179 0.014918043798640 +Allele 181 0.044453392775551 +Allele 183 0.026594053586836 +Allele 185 0.030188031458602 + +Locus 010 +Allele 108 0.029972707480745 +Allele 115 0.011121131764291 +Allele 121 0.011692508489830 +Allele 123 0.046692969069866 +Allele 125 0.098203793937466 +Allele 127 0.073916883712045 +Allele 129 0.083201286536221 +Allele 131 0.092766633070359 +Allele 133 0.162568370849537 +Allele 135 0.105230782482448 +Allele 137 0.080209375999473 +Allele 139 0.027810700287702 +Allele 141 0.042031806297936 +Allele 143 0.011429084706929 +Allele 145 0.030782424277544 +Allele 147 0.017714155724794 +Allele 149 0.029704342029300 +Allele 152 0.016879799457544 +Allele 155 0.011218359661638 +Allele 157 0.016852884164330 + + + +Estimated Mixing Proportions +0.053963933333333 +0.946036066666667 + + + +Estimated sigma: +k: 0 1.000000000000000 +k: 1 1.000000000000000 + + + +Estimated tau: +k: 0 10.000000000000000 +k: 1 10.000000000000000 + + + diff --git a/inst/files/tess/tess_02.txt b/inst/files/tess/tess_02.txt new file mode 100644 index 0000000..b01bbb8 --- /dev/null +++ b/inst/files/tess/tess_02.txt @@ -0,0 +1,604 @@ +Estimated Clustering Probabilities for Samples +Sample ***Cluster 01*** ***Cluster 02*** ***Cluster 03*** +000001: 0.926330000000000 0.057885000000000 0.015785000000000 1 +000002: 0.682480000000000 0.307585000000000 0.009935000000000 1 +000003: 0.935345000000000 0.059910000000000 0.004745000000000 1 +000004: 0.877755000000000 0.108125000000000 0.014120000000000 1 +000005: 0.855695000000000 0.128085000000000 0.016220000000000 1 +000006: 0.940490000000000 0.053025000000000 0.006485000000000 1 +000007: 0.479200000000000 0.393205000000000 0.127595000000000 1 +000008: 0.674830000000000 0.311105000000000 0.014065000000000 1 +000009: 0.715590000000000 0.263975000000000 0.020435000000000 1 +000010: 0.760645000000000 0.191240000000000 0.048115000000000 1 +000011: 0.736425000000000 0.215840000000000 0.047735000000000 1 +000012: 0.799770000000000 0.191755000000000 0.008475000000000 1 +000013: 0.746380000000000 0.233435000000000 0.020185000000000 1 +000014: 0.913990000000000 0.067570000000000 0.018440000000000 1 +000015: 0.813655000000000 0.167695000000000 0.018650000000000 1 +000016: 0.961345000000000 0.034485000000000 0.004170000000000 1 +000017: 0.664755000000000 0.317515000000000 0.017730000000000 1 +000018: 0.835900000000000 0.140730000000000 0.023370000000000 1 +000019: 0.784935000000000 0.120195000000000 0.094870000000000 1 +000020: 0.813735000000000 0.142155000000000 0.044110000000000 1 +000021: 0.669755000000000 0.274390000000000 0.055855000000000 1 +000022: 0.696605000000000 0.136065000000000 0.167330000000000 1 +000023: 0.959930000000000 0.035815000000000 0.004255000000000 1 +000024: 0.765655000000000 0.225335000000000 0.009010000000000 1 +000025: 0.934280000000000 0.057075000000000 0.008645000000000 1 +000026: 0.721295000000000 0.261755000000000 0.016950000000000 1 +000027: 0.909340000000000 0.079875000000000 0.010785000000000 1 +000028: 0.963815000000000 0.031780000000000 0.004405000000000 1 +000029: 0.912960000000000 0.068685000000000 0.018355000000000 1 +000030: 0.641330000000000 0.321560000000000 0.037110000000000 1 +000031: 0.584810000000000 0.408210000000000 0.006980000000000 1 +000032: 0.777540000000000 0.215080000000000 0.007380000000000 1 +000033: 0.528710000000000 0.457225000000000 0.014065000000000 1 +000034: 0.550240000000000 0.442820000000000 0.006940000000000 1 +000035: 0.796835000000000 0.180400000000000 0.022765000000000 1 +000036: 0.931815000000000 0.050930000000000 0.017255000000000 1 +000037: 0.915155000000000 0.075070000000000 0.009775000000000 1 +000038: 0.685855000000000 0.307150000000000 0.006995000000000 1 +000039: 0.662430000000000 0.321105000000000 0.016465000000000 1 +000040: 0.731645000000000 0.264210000000000 0.004145000000000 1 +000041: 0.916960000000000 0.076265000000000 0.006775000000000 1 +000042: 0.672360000000000 0.322630000000000 0.005010000000000 1 +000043: 0.892960000000000 0.102485000000000 0.004555000000000 1 +000044: 0.752315000000000 0.244275000000000 0.003410000000000 1 +000045: 0.910620000000000 0.064775000000000 0.024605000000000 1 +000046: 0.888450000000000 0.102210000000000 0.009340000000000 1 +000047: 0.900920000000000 0.073475000000000 0.025605000000000 1 +000048: 0.690555000000000 0.270850000000000 0.038595000000000 1 +000049: 0.629020000000000 0.293970000000000 0.077010000000000 1 +000050: 0.924890000000000 0.047760000000000 0.027350000000000 1 +000051: 0.856255000000000 0.087500000000000 0.056245000000000 1 +000052: 0.945840000000000 0.043995000000000 0.010165000000000 1 +000053: 0.898200000000000 0.091260000000000 0.010540000000000 1 +000054: 0.889730000000000 0.068030000000000 0.042240000000000 1 +000055: 0.764175000000000 0.220515000000000 0.015310000000000 1 +000056: 0.933695000000000 0.052070000000000 0.014235000000000 1 +000057: 0.936780000000000 0.044045000000000 0.019175000000000 1 +000058: 0.949515000000000 0.041625000000000 0.008860000000000 1 +000059: 0.892755000000000 0.063405000000000 0.043840000000000 1 +000060: 0.671810000000000 0.261960000000000 0.066230000000000 1 +000061: 0.944390000000000 0.042755000000000 0.012855000000000 1 +000062: 0.683955000000000 0.269325000000000 0.046720000000000 1 +000063: 0.885265000000000 0.089080000000000 0.025655000000000 1 +000064: 0.845370000000000 0.087840000000000 0.066790000000000 1 +000065: 0.943995000000000 0.027945000000000 0.028060000000000 1 +000066: 0.970395000000000 0.016390000000000 0.013215000000000 1 +000067: 0.915600000000000 0.080305000000000 0.004095000000000 1 +000068: 0.963830000000000 0.024145000000000 0.012025000000000 1 +000069: 0.982020000000000 0.010825000000000 0.007155000000000 1 +000070: 0.946585000000000 0.045520000000000 0.007895000000000 1 +000071: 0.979385000000000 0.016760000000000 0.003855000000000 1 +000072: 0.712255000000000 0.279540000000000 0.008205000000000 1 +000073: 0.655345000000000 0.340465000000000 0.004190000000000 1 +000074: 0.706595000000000 0.283935000000000 0.009470000000000 1 +000075: 0.870720000000000 0.120915000000000 0.008365000000000 1 + + + +Estimated Allele Frequencies +Cluster 01 +Locus 001 +Allele 092 0.041570365834075 +Allele 094 0.405975651371289 +Allele 096 0.051038174339831 +Allele 098 0.219547211558997 +Allele 100 0.090570164928721 +Allele 102 0.070134523948938 +Allele 104 0.080800065381430 +Allele 106 0.023757736338933 +Allele 108 0.016606106297786 + +Locus 002 +Allele 118 0.021322619822431 +Allele 122 0.035204808346632 +Allele 124 0.184128591258992 +Allele 126 0.132418439940422 +Allele 127 0.012912324433132 +Allele 128 0.111571132359968 +Allele 130 0.082950385492457 +Allele 132 0.219286560386878 +Allele 134 0.014113786562441 +Allele 135 0.098971875318322 +Allele 137 0.073618054327406 +Allele 151 0.013501421750919 + +Locus 003 +Allele 130 0.027463723659546 +Allele 133 0.013425895086851 +Allele 136 0.135645731303690 +Allele 138 0.095445076117670 +Allele 139 0.157135238258571 +Allele 141 0.026899056148886 +Allele 143 0.013845991971361 +Allele 145 0.092673292767169 +Allele 146 0.093010557242215 +Allele 147 0.012836923456282 +Allele 148 0.147909252202408 +Allele 150 0.067293454706280 +Allele 152 0.097663459982251 +Allele 156 0.018752347096822 + +Locus 004 +Allele 093 0.049971605736202 +Allele 095 0.079906209368105 +Allele 096 0.011141639760955 +Allele 097 0.194103726933669 +Allele 099 0.049145187118157 +Allele 100 0.063187827539141 +Allele 101 0.159861054578185 +Allele 103 0.133468535275978 +Allele 105 0.047388944785007 +Allele 107 0.093018500348684 +Allele 109 0.017578140876856 +Allele 110 0.024283805307460 +Allele 113 0.016814683014554 +Allele 121 0.015602311588769 +Allele 123 0.017822071338175 +Allele 125 0.013340651127828 +Allele 131 0.013365105302276 + +Locus 005 +Allele 218 0.010215079847038 +Allele 220 0.083327340304860 +Allele 222 0.131228621755742 +Allele 224 0.128840529529744 +Allele 226 0.097393708114914 +Allele 228 0.051932297880812 +Allele 230 0.039591847775219 +Allele 232 0.064158249061206 +Allele 234 0.067188946885844 +Allele 236 0.060064687624028 +Allele 238 0.087549530696595 +Allele 240 0.041611661994962 +Allele 242 0.037824217652151 +Allele 244 0.012316435396807 +Allele 246 0.018317843760700 +Allele 248 0.013394154841796 +Allele 250 0.015276742775152 +Allele 252 0.017903847700205 +Allele 254 0.011006809820751 +Allele 256 0.010857446581475 + +Locus 006 +Allele 094 0.092131597214950 +Allele 096 0.163215660632995 +Allele 098 0.046212254843407 +Allele 100 0.013583911076957 +Allele 102 0.109198859367387 +Allele 104 0.273184089949993 +Allele 106 0.107101726948626 +Allele 108 0.078241331065033 +Allele 110 0.037668125369144 +Allele 112 0.027269508382863 +Allele 114 0.013171455397045 +Allele 124 0.010979170244888 +Allele 126 0.014152511268317 +Allele 149 0.013889798238395 + +Locus 007 +Allele 202 0.012709513815848 +Allele 204 0.023484208876039 +Allele 206 0.014354607789112 +Allele 208 0.155727428596984 +Allele 210 0.046299956140677 +Allele 212 0.196560607916168 +Allele 214 0.099349215318793 +Allele 216 0.099695809443672 +Allele 218 0.059910587839233 +Allele 220 0.059833922101664 +Allele 222 0.065152979921838 +Allele 224 0.085440042493607 +Allele 226 0.037704387861364 +Allele 228 0.020026057510343 +Allele 233 0.012256164369585 +Allele 238 0.011494510005073 + +Locus 008 +Allele 121 0.088074107184861 +Allele 123 0.069247889849360 +Allele 125 0.052902649477842 +Allele 127 0.013129372995587 +Allele 129 0.067993007487003 +Allele 131 0.215557950610502 +Allele 133 0.174108837483356 +Allele 135 0.206828527239901 +Allele 137 0.083008947301541 +Allele 151 0.013474993830999 +Allele 161 0.015673716539049 + +Locus 009 +Allele 161 0.013781316508692 +Allele 165 0.032807221265144 +Allele 167 0.052257639613151 +Allele 169 0.106834947506253 +Allele 171 0.270890877309745 +Allele 173 0.209664528558231 +Allele 175 0.091354388368239 +Allele 177 0.117997869386843 +Allele 179 0.016961108136460 +Allele 181 0.039065275504097 +Allele 183 0.024131285886126 +Allele 185 0.024253541957022 + +Locus 010 +Allele 108 0.028223637722624 +Allele 115 0.011146024781235 +Allele 121 0.013281622420009 +Allele 123 0.052137104689493 +Allele 125 0.109634155501797 +Allele 127 0.086205770193138 +Allele 129 0.078144175829430 +Allele 131 0.096589073973063 +Allele 133 0.144376114347973 +Allele 135 0.080854866803931 +Allele 137 0.090347823960322 +Allele 139 0.029198151898877 +Allele 141 0.038321540570909 +Allele 143 0.011757721910233 +Allele 145 0.030831417425297 +Allele 147 0.022067544637542 +Allele 149 0.028006367732710 +Allele 152 0.017182876943117 +Allele 155 0.011257960002118 +Allele 157 0.020436048656182 + + +Cluster 02 +Locus 001 +Allele 092 0.087820043494914 +Allele 094 0.183322288696724 +Allele 096 0.114920464266161 +Allele 098 0.104925489864672 +Allele 100 0.102090442391229 +Allele 102 0.138941794880725 +Allele 104 0.085304524235494 +Allele 106 0.115220351812298 +Allele 108 0.067454600357784 + +Locus 002 +Allele 118 0.048256540692714 +Allele 122 0.050636422593886 +Allele 124 0.171629409269222 +Allele 126 0.105737836287532 +Allele 127 0.049578328714743 +Allele 128 0.067190475042542 +Allele 130 0.060911514880725 +Allele 132 0.162004355253111 +Allele 134 0.045838088368258 +Allele 135 0.109359723555937 +Allele 137 0.080604291361239 +Allele 151 0.048253013980092 + +Locus 003 +Allele 130 0.043686162542312 +Allele 133 0.043462004055582 +Allele 136 0.081724732226425 +Allele 138 0.100724807192453 +Allele 139 0.058064411517058 +Allele 141 0.075334812101885 +Allele 143 0.041320765576918 +Allele 145 0.065662160291859 +Allele 146 0.120232472597122 +Allele 147 0.045017512991903 +Allele 148 0.099490116288233 +Allele 150 0.092665765948863 +Allele 152 0.085439274955156 +Allele 156 0.047175001714233 + +Locus 004 +Allele 093 0.049440875495234 +Allele 095 0.048472391843628 +Allele 096 0.040419820530762 +Allele 097 0.081586524520546 +Allele 099 0.064839869644653 +Allele 100 0.111688614941679 +Allele 101 0.078717955942037 +Allele 103 0.098917431308622 +Allele 105 0.054345474132383 +Allele 107 0.062866059452626 +Allele 109 0.059558285852691 +Allele 110 0.042725889567196 +Allele 113 0.045264915871386 +Allele 121 0.045013697686036 +Allele 123 0.041886588788726 +Allele 125 0.037057497788583 +Allele 131 0.037198106633215 + +Locus 005 +Allele 218 0.039209376136470 +Allele 220 0.087496533892745 +Allele 222 0.074824862786805 +Allele 224 0.078592738435323 +Allele 226 0.061092282227477 +Allele 228 0.039054232708615 +Allele 230 0.063262049270767 +Allele 232 0.058595783320512 +Allele 234 0.062686603278804 +Allele 236 0.052021569957532 +Allele 238 0.040716253210786 +Allele 240 0.047387353425007 +Allele 242 0.039236400836921 +Allele 244 0.033049525686809 +Allele 246 0.037083744021685 +Allele 248 0.033154849699462 +Allele 250 0.042894644369084 +Allele 252 0.036326556918520 +Allele 254 0.035608660289399 +Allele 256 0.037705979527276 + +Locus 006 +Allele 094 0.106356926888550 +Allele 096 0.111055023507243 +Allele 098 0.053994250077765 +Allele 100 0.042462526204655 +Allele 102 0.065233883003275 +Allele 104 0.072988144165674 +Allele 106 0.169751621726281 +Allele 108 0.050546691943656 +Allele 110 0.102125873687653 +Allele 112 0.047631607192932 +Allele 114 0.043743553649415 +Allele 124 0.050758695589522 +Allele 126 0.041415639954185 +Allele 149 0.041935562409193 + +Locus 007 +Allele 202 0.039677041467607 +Allele 204 0.048609988635010 +Allele 206 0.037133245311555 +Allele 208 0.057506759740385 +Allele 210 0.050682208647651 +Allele 212 0.074781658138514 +Allele 214 0.094653176960304 +Allele 216 0.097654349525204 +Allele 218 0.065116685625784 +Allele 220 0.051916942369619 +Allele 222 0.057425418452164 +Allele 224 0.130421376535783 +Allele 226 0.067905434835235 +Allele 228 0.040219092876772 +Allele 233 0.041839570565621 +Allele 238 0.044457050312793 + +Locus 008 +Allele 121 0.083681945828463 +Allele 123 0.125897144852358 +Allele 125 0.085156253724417 +Allele 127 0.057579584858682 +Allele 129 0.058487214258865 +Allele 131 0.234296282504232 +Allele 133 0.079350859061708 +Allele 135 0.083206413296170 +Allele 137 0.083364665084371 +Allele 151 0.056850096761027 +Allele 161 0.052129539769704 + +Locus 009 +Allele 161 0.056757255535154 +Allele 165 0.055281808572908 +Allele 167 0.086813330410998 +Allele 169 0.072679397092074 +Allele 171 0.171413966233419 +Allele 173 0.087896341115652 +Allele 175 0.118797924207788 +Allele 177 0.068085392545824 +Allele 179 0.050871990212942 +Allele 181 0.081585066187139 +Allele 183 0.075820619359343 +Allele 185 0.073996908526758 + +Locus 010 +Allele 108 0.044090935922028 +Allele 115 0.037255883764688 +Allele 121 0.032799195135954 +Allele 123 0.042641404503754 +Allele 125 0.045220429138090 +Allele 127 0.034464554333670 +Allele 129 0.071807031653901 +Allele 131 0.054174751474299 +Allele 133 0.115549801350183 +Allele 135 0.105891141194861 +Allele 137 0.053515025093873 +Allele 139 0.039353332459766 +Allele 141 0.051941268294904 +Allele 143 0.033942201338813 +Allele 145 0.040858210938708 +Allele 147 0.043379248136879 +Allele 149 0.044943968333415 +Allele 152 0.038161279329193 +Allele 155 0.036270880281086 +Allele 157 0.033739457321937 + + +Cluster 03 +Locus 001 +Allele 092 0.112938470098911 +Allele 094 0.114134260270495 +Allele 096 0.102246546991962 +Allele 098 0.114044052738846 +Allele 100 0.130098744010488 +Allele 102 0.101299488704848 +Allele 104 0.108717931503582 +Allele 106 0.125536215208731 +Allele 108 0.090984290472138 + +Locus 002 +Allele 118 0.072176310795783 +Allele 122 0.076256065990864 +Allele 124 0.084199520420166 +Allele 126 0.115452840540623 +Allele 127 0.076111502887112 +Allele 128 0.084705709991354 +Allele 130 0.079734762384259 +Allele 132 0.084511165832830 +Allele 134 0.070376634535980 +Allele 135 0.089926876582921 +Allele 137 0.091700375600742 +Allele 151 0.074848234437366 + +Locus 003 +Allele 130 0.062452272883050 +Allele 133 0.064398282549918 +Allele 136 0.067569679663760 +Allele 138 0.083469366275913 +Allele 139 0.071153101774265 +Allele 141 0.073092463967996 +Allele 143 0.060702220238317 +Allele 145 0.079121312847715 +Allele 146 0.074230572699166 +Allele 147 0.067319179354184 +Allele 148 0.077628471764108 +Allele 150 0.073509692104125 +Allele 152 0.079958972460184 +Allele 156 0.065394411417299 + +Locus 004 +Allele 093 0.055262057822350 +Allele 095 0.057932453472535 +Allele 096 0.051763357409561 +Allele 097 0.058327398208561 +Allele 099 0.063651556958719 +Allele 100 0.058420788842124 +Allele 101 0.064500528165002 +Allele 103 0.092106915540442 +Allele 105 0.052597457692279 +Allele 107 0.055513054417399 +Allele 109 0.057386140906874 +Allele 110 0.054653861860990 +Allele 113 0.059472147162859 +Allele 121 0.058406907836113 +Allele 123 0.053381731081695 +Allele 125 0.053731066492425 +Allele 131 0.052892576130072 + +Locus 005 +Allele 218 0.044801352368565 +Allele 220 0.051185414325398 +Allele 222 0.050488502117495 +Allele 224 0.052201897072400 +Allele 226 0.050392118362352 +Allele 228 0.051397397584080 +Allele 230 0.054640692733324 +Allele 232 0.056966048306179 +Allele 234 0.059248483834318 +Allele 236 0.057105122428825 +Allele 238 0.050839197430434 +Allele 240 0.049132564322828 +Allele 242 0.045821868884533 +Allele 244 0.046749349778077 +Allele 246 0.047204249477221 +Allele 248 0.047080011719064 +Allele 250 0.047328391440812 +Allele 252 0.046586236756865 +Allele 254 0.044252980168428 +Allele 256 0.046578120888802 + +Locus 006 +Allele 094 0.071287077338721 +Allele 096 0.072652119781235 +Allele 098 0.069485736602022 +Allele 100 0.061732665807907 +Allele 102 0.072613090186218 +Allele 104 0.095964871006617 +Allele 106 0.078611217706716 +Allele 108 0.065502045069197 +Allele 110 0.086713482335297 +Allele 112 0.070231514944277 +Allele 114 0.063884737858075 +Allele 124 0.066719598017300 +Allele 126 0.063941464956014 +Allele 149 0.060660378390407 + +Locus 007 +Allele 202 0.060279226792171 +Allele 204 0.056079526142819 +Allele 206 0.055362843296826 +Allele 208 0.068228532463320 +Allele 210 0.061801362766764 +Allele 212 0.064976943093357 +Allele 214 0.064932399512503 +Allele 216 0.062243237664555 +Allele 218 0.059821677580373 +Allele 220 0.062420909726025 +Allele 222 0.065542341104455 +Allele 224 0.064182808754168 +Allele 226 0.075281600999652 +Allele 228 0.057923351369124 +Allele 233 0.062849466673253 +Allele 238 0.058073772060636 + +Locus 008 +Allele 121 0.092663161740701 +Allele 123 0.121371205491578 +Allele 125 0.087895474745701 +Allele 127 0.075582809224203 +Allele 129 0.084389627608563 +Allele 131 0.092963076942283 +Allele 133 0.098249158904288 +Allele 135 0.084804037893991 +Allele 137 0.105022477067932 +Allele 151 0.077988295439032 +Allele 161 0.079070674941726 + +Locus 009 +Allele 161 0.075905564786750 +Allele 165 0.075793073332392 +Allele 167 0.091855359288631 +Allele 169 0.084272557792474 +Allele 171 0.091015736304738 +Allele 173 0.094345247691328 +Allele 175 0.085781854895970 +Allele 177 0.084908386312001 +Allele 179 0.072924938214093 +Allele 181 0.080531383253845 +Allele 183 0.083568715391391 +Allele 185 0.079097182736388 + +Locus 010 +Allele 108 0.047999533956549 +Allele 115 0.047131107381407 +Allele 121 0.045841498056877 +Allele 123 0.050631009433762 +Allele 125 0.048806431549055 +Allele 127 0.047118535267856 +Allele 129 0.051586512940044 +Allele 131 0.048493428868149 +Allele 133 0.055340535365991 +Allele 135 0.048703473538607 +Allele 137 0.053842122967485 +Allele 139 0.059630946879571 +Allele 141 0.050259689300105 +Allele 143 0.047569573029227 +Allele 145 0.045615030095545 +Allele 147 0.060534479062198 +Allele 149 0.049639189677978 +Allele 152 0.046587603643529 +Allele 155 0.047227026632640 +Allele 157 0.047442272353424 + + + +Estimated Mixing Proportions +0.815770133333333 +0.160385266666667 +0.023844600000000 + + + +Estimated sigma: +k: 0 1.000000000000000 +k: 1 1.000000000000000 +k: 2 1.000000000000000 + + + +Estimated tau: +k: 0 10.000000000000000 +k: 1 10.000000000000000 +k: 2 10.000000000000000 + + + diff --git a/inst/files/tess/tess_03.txt b/inst/files/tess/tess_03.txt new file mode 100644 index 0000000..8252189 --- /dev/null +++ b/inst/files/tess/tess_03.txt @@ -0,0 +1,774 @@ +Estimated Clustering Probabilities for Samples +Sample ***Cluster 01*** ***Cluster 02*** ***Cluster 03*** ***Cluster 04*** +000001: 0.955705000000000 0.023290000000000 0.010225000000000 0.010780000000000 1 +000002: 0.970250000000000 0.009780000000000 0.011555000000000 0.008415000000000 1 +000003: 0.988065000000000 0.004500000000000 0.004015000000000 0.003420000000000 1 +000004: 0.956495000000000 0.016455000000000 0.011880000000000 0.015170000000000 1 +000005: 0.975235000000000 0.010725000000000 0.007525000000000 0.006515000000000 1 +000006: 0.984600000000000 0.007280000000000 0.005150000000000 0.002970000000000 1 +000007: 0.662400000000000 0.171935000000000 0.096505000000000 0.069160000000000 1 +000008: 0.953795000000000 0.017610000000000 0.017365000000000 0.011230000000000 1 +000009: 0.947975000000000 0.014595000000000 0.022330000000000 0.015100000000000 1 +000010: 0.871835000000000 0.059255000000000 0.024305000000000 0.044605000000000 1 +000011: 0.894005000000000 0.049685000000000 0.024755000000000 0.031555000000000 1 +000012: 0.977285000000000 0.009810000000000 0.006085000000000 0.006820000000000 1 +000013: 0.942240000000000 0.022565000000000 0.012215000000000 0.022980000000000 1 +000014: 0.947730000000000 0.030070000000000 0.012020000000000 0.010180000000000 1 +000015: 0.956865000000000 0.018370000000000 0.012210000000000 0.012555000000000 1 +000016: 0.988305000000000 0.004275000000000 0.004155000000000 0.003265000000000 1 +000017: 0.925050000000000 0.038375000000000 0.017735000000000 0.018840000000000 1 +000018: 0.919855000000000 0.035305000000000 0.018225000000000 0.026615000000000 1 +000019: 0.564580000000000 0.329155000000000 0.018835000000000 0.087430000000000 1 +000020: 0.778205000000000 0.108265000000000 0.006135000000000 0.107395000000000 1 +000021: 0.820950000000000 0.113005000000000 0.013575000000000 0.052470000000000 1 +000022: 0.511920000000000 0.372590000000000 0.018025000000000 0.097465000000000 1 +000023: 0.983605000000000 0.010075000000000 0.001605000000000 0.004715000000000 1 +000024: 0.965540000000000 0.021285000000000 0.003270000000000 0.009905000000000 1 +000025: 0.974070000000000 0.016685000000000 0.002805000000000 0.006440000000000 1 +000026: 0.948345000000000 0.023420000000000 0.010710000000000 0.017525000000000 1 +000027: 0.949370000000000 0.024450000000000 0.011645000000000 0.014535000000000 1 +000028: 0.979710000000000 0.010200000000000 0.004130000000000 0.005960000000000 1 +000029: 0.921990000000000 0.022930000000000 0.032440000000000 0.022640000000000 1 +000030: 0.885585000000000 0.032595000000000 0.045510000000000 0.036310000000000 1 +000031: 0.967930000000000 0.010835000000000 0.009970000000000 0.011265000000000 1 +000032: 0.985540000000000 0.004815000000000 0.005455000000000 0.004190000000000 1 +000033: 0.940185000000000 0.013145000000000 0.021650000000000 0.025020000000000 1 +000034: 0.963735000000000 0.006250000000000 0.016340000000000 0.013675000000000 1 +000035: 0.956795000000000 0.012500000000000 0.013490000000000 0.017215000000000 1 +000036: 0.940980000000000 0.017040000000000 0.022710000000000 0.019270000000000 1 +000037: 0.972195000000000 0.009990000000000 0.010835000000000 0.006980000000000 1 +000038: 0.981735000000000 0.003055000000000 0.010665000000000 0.004545000000000 1 +000039: 0.971005000000000 0.006650000000000 0.016790000000000 0.005555000000000 1 +000040: 0.987380000000000 0.002990000000000 0.005655000000000 0.003975000000000 1 +000041: 0.987855000000000 0.003515000000000 0.005265000000000 0.003365000000000 1 +000042: 0.991800000000000 0.002690000000000 0.003940000000000 0.001570000000000 1 +000043: 0.985485000000000 0.004530000000000 0.006025000000000 0.003960000000000 1 +000044: 0.984470000000000 0.004800000000000 0.006375000000000 0.004355000000000 1 +000045: 0.917025000000000 0.035990000000000 0.024245000000000 0.022740000000000 1 +000046: 0.978760000000000 0.008740000000000 0.006855000000000 0.005645000000000 1 +000047: 0.918060000000000 0.030410000000000 0.028090000000000 0.023440000000000 1 +000048: 0.908525000000000 0.025610000000000 0.038330000000000 0.027535000000000 1 +000049: 0.777225000000000 0.070740000000000 0.078860000000000 0.073175000000000 1 +000050: 0.898780000000000 0.052275000000000 0.031945000000000 0.017000000000000 1 +000051: 0.855605000000000 0.052475000000000 0.061310000000000 0.030610000000000 1 +000052: 0.972265000000000 0.009335000000000 0.008475000000000 0.009925000000000 1 +000053: 0.973980000000000 0.011230000000000 0.005605000000000 0.009185000000000 1 +000054: 0.895810000000000 0.037245000000000 0.030860000000000 0.036085000000000 1 +000055: 0.944470000000000 0.019380000000000 0.019640000000000 0.016510000000000 1 +000056: 0.955700000000000 0.018580000000000 0.012855000000000 0.012865000000000 1 +000057: 0.924785000000000 0.036545000000000 0.020675000000000 0.017995000000000 1 +000058: 0.974025000000000 0.010130000000000 0.007770000000000 0.008075000000000 1 +000059: 0.901480000000000 0.041965000000000 0.028315000000000 0.028240000000000 1 +000060: 0.829025000000000 0.060805000000000 0.040000000000000 0.070170000000000 1 +000061: 0.937760000000000 0.030930000000000 0.010225000000000 0.021085000000000 1 +000062: 0.792850000000000 0.119565000000000 0.032560000000000 0.055025000000000 1 +000063: 0.904355000000000 0.053740000000000 0.011330000000000 0.030575000000000 1 +000064: 0.831070000000000 0.071360000000000 0.050180000000000 0.047390000000000 1 +000065: 0.832325000000000 0.124045000000000 0.012075000000000 0.031555000000000 1 +000066: 0.887160000000000 0.086790000000000 0.006475000000000 0.019575000000000 1 +000067: 0.973310000000000 0.014200000000000 0.004050000000000 0.008440000000000 1 +000068: 0.917850000000000 0.040620000000000 0.011910000000000 0.029620000000000 1 +000069: 0.978590000000000 0.008935000000000 0.005360000000000 0.007115000000000 1 +000070: 0.963800000000000 0.013895000000000 0.007115000000000 0.015190000000000 1 +000071: 0.978020000000000 0.009835000000000 0.005215000000000 0.006930000000000 1 +000072: 0.978475000000000 0.005615000000000 0.008790000000000 0.007120000000000 1 +000073: 0.980590000000000 0.004490000000000 0.008870000000000 0.006050000000000 1 +000074: 0.950055000000000 0.011995000000000 0.022745000000000 0.015205000000000 1 +000075: 0.971085000000000 0.007535000000000 0.012945000000000 0.008435000000000 1 + + + +Estimated Allele Frequencies +Cluster 01 +Locus 001 +Allele 092 0.040108554611014 +Allele 094 0.401586129242885 +Allele 096 0.062321803261995 +Allele 098 0.200441033460974 +Allele 100 0.081407852232587 +Allele 102 0.092259660433905 +Allele 104 0.074593622787285 +Allele 106 0.028732621653324 +Allele 108 0.018548722316029 + +Locus 002 +Allele 118 0.017716220204917 +Allele 122 0.030180158594178 +Allele 124 0.212070025461366 +Allele 126 0.121854479519218 +Allele 127 0.010428138625849 +Allele 128 0.099018326739128 +Allele 130 0.075936867301427 +Allele 132 0.239907136435167 +Allele 134 0.011570507128993 +Allele 135 0.103368687925994 +Allele 137 0.066712475096687 +Allele 151 0.011236976967075 + +Locus 003 +Allele 130 0.024168171170407 +Allele 133 0.011075387642230 +Allele 136 0.134325793981698 +Allele 138 0.101546983802528 +Allele 139 0.138673769730887 +Allele 141 0.033285935638299 +Allele 143 0.011630039694974 +Allele 145 0.082577792747991 +Allele 146 0.110911635890706 +Allele 147 0.010408800918958 +Allele 148 0.148226745588540 +Allele 150 0.079669418913063 +Allele 152 0.095978930858523 +Allele 156 0.017520593421195 + +Locus 004 +Allele 093 0.049133735219267 +Allele 095 0.073049205022888 +Allele 096 0.011532345397148 +Allele 097 0.187956663457259 +Allele 099 0.051948945664038 +Allele 100 0.086793744269821 +Allele 101 0.153630963033314 +Allele 103 0.125519582645606 +Allele 105 0.049582171851280 +Allele 107 0.094378166243936 +Allele 109 0.022533823941602 +Allele 110 0.024356750261549 +Allele 113 0.014589416247822 +Allele 121 0.015376051402950 +Allele 123 0.017240679081163 +Allele 125 0.011156106070962 +Allele 131 0.011221650189396 + +Locus 005 +Allele 218 0.011729758268348 +Allele 220 0.097100723873848 +Allele 222 0.135483229662037 +Allele 224 0.132975553105457 +Allele 226 0.097762154696245 +Allele 228 0.044348008190638 +Allele 230 0.044631836495491 +Allele 232 0.063504973917684 +Allele 234 0.066179849089570 +Allele 236 0.055825082381455 +Allele 238 0.079213682405182 +Allele 240 0.040622030056251 +Allele 242 0.036424674423670 +Allele 244 0.009808667678075 +Allele 246 0.017224966052254 +Allele 248 0.011145901261600 +Allele 250 0.015603490214788 +Allele 252 0.017109075551485 +Allele 254 0.012143276559009 +Allele 256 0.011163066116913 + +Locus 006 +Allele 094 0.105191233453980 +Allele 096 0.173356043184489 +Allele 098 0.042348697778101 +Allele 100 0.012311530970041 +Allele 102 0.101393929599986 +Allele 104 0.235302648029483 +Allele 106 0.144813770170653 +Allele 108 0.068788525859801 +Allele 110 0.049034312537799 +Allele 112 0.022591265710838 +Allele 114 0.011537697161458 +Allele 124 0.010403448881205 +Allele 126 0.010533641042627 +Allele 149 0.012393255619539 + +Locus 007 +Allele 202 0.008813177013327 +Allele 204 0.024363963946223 +Allele 206 0.011693890581910 +Allele 208 0.140381301096945 +Allele 210 0.039159464982013 +Allele 212 0.185551742741611 +Allele 214 0.108316485852427 +Allele 216 0.114646534562713 +Allele 218 0.063670626245623 +Allele 220 0.054110571885971 +Allele 222 0.060609728639030 +Allele 224 0.113597137128733 +Allele 226 0.036541539797695 +Allele 228 0.017975214446075 +Allele 233 0.008934703413459 +Allele 238 0.011633917666246 + +Locus 008 +Allele 121 0.084890706953635 +Allele 123 0.074352441609644 +Allele 125 0.053739273507208 +Allele 127 0.014508495260032 +Allele 129 0.057794070301220 +Allele 131 0.271596935997128 +Allele 133 0.150494683010639 +Allele 135 0.189311113099157 +Allele 137 0.075719109037381 +Allele 151 0.014511493180565 +Allele 161 0.013081678043392 + +Locus 009 +Allele 161 0.014005313681283 +Allele 165 0.030779931304849 +Allele 167 0.053184340596214 +Allele 169 0.097409180326294 +Allele 171 0.281941649328400 +Allele 173 0.191836968177223 +Allele 175 0.107488571179021 +Allele 177 0.107849548532832 +Allele 179 0.014545766738058 +Allele 181 0.044869859035437 +Allele 183 0.027856262610093 +Allele 185 0.028232608490295 + +Locus 010 +Allele 108 0.030460595953904 +Allele 115 0.009950426286644 +Allele 121 0.011381319905051 +Allele 123 0.047170110754328 +Allele 125 0.098279739004298 +Allele 127 0.075031032023183 +Allele 129 0.085877070751716 +Allele 131 0.093795077233142 +Allele 133 0.165651498771051 +Allele 135 0.106537377383759 +Allele 137 0.082980300603477 +Allele 139 0.020058078859378 +Allele 141 0.041162485226837 +Allele 143 0.010872579938961 +Allele 145 0.030096129052681 +Allele 147 0.017042582000834 +Allele 149 0.030008492136677 +Allele 152 0.017254714455685 +Allele 155 0.010251269737336 +Allele 157 0.016139119921055 + + +Cluster 02 +Locus 001 +Allele 092 0.104934267798894 +Allele 094 0.124764176588192 +Allele 096 0.090692725687741 +Allele 098 0.129186986294003 +Allele 100 0.158579189257893 +Allele 102 0.085877692802314 +Allele 104 0.110230975966629 +Allele 106 0.115504582524995 +Allele 108 0.080229403079336 + +Locus 002 +Allele 118 0.066852784497074 +Allele 122 0.067463216358785 +Allele 124 0.077717868739846 +Allele 126 0.126367300206697 +Allele 127 0.068000623071501 +Allele 128 0.087777299555508 +Allele 130 0.071200184563664 +Allele 132 0.080452313487939 +Allele 134 0.064781530347602 +Allele 135 0.098917952030810 +Allele 137 0.126203100813013 +Allele 151 0.064265826327559 + +Locus 003 +Allele 130 0.059928630128923 +Allele 133 0.058014361743496 +Allele 136 0.061715483535140 +Allele 138 0.080612399248765 +Allele 139 0.070760941166029 +Allele 141 0.075237792714932 +Allele 143 0.059342638190187 +Allele 145 0.088422320639415 +Allele 146 0.076239685488096 +Allele 147 0.060059286620077 +Allele 148 0.090151003630642 +Allele 150 0.071385801960909 +Allele 152 0.088663126117135 +Allele 156 0.059466528816255 + +Locus 004 +Allele 093 0.051028986051902 +Allele 095 0.058825757577810 +Allele 096 0.049763399218745 +Allele 097 0.058125911482528 +Allele 099 0.059848316658620 +Allele 100 0.050716336036072 +Allele 101 0.072409445342017 +Allele 103 0.135171528216030 +Allele 105 0.050709765338937 +Allele 107 0.051732721458645 +Allele 109 0.050997086927831 +Allele 110 0.049440973501488 +Allele 113 0.060050859280805 +Allele 121 0.054943972742370 +Allele 123 0.048749782071698 +Allele 125 0.048715583572416 +Allele 131 0.048769574522085 + +Locus 005 +Allele 218 0.040512429624111 +Allele 220 0.049125426728646 +Allele 222 0.047070608371379 +Allele 224 0.062203212908370 +Allele 226 0.046074969732668 +Allele 228 0.061028667548746 +Allele 230 0.058249861844197 +Allele 232 0.058750762078115 +Allele 234 0.067675110139617 +Allele 236 0.063461666989823 +Allele 238 0.046623731816229 +Allele 240 0.045412793530142 +Allele 242 0.042749439935093 +Allele 244 0.050341754731003 +Allele 246 0.042100450991233 +Allele 248 0.043815876180247 +Allele 250 0.049047847643866 +Allele 252 0.041887005310958 +Allele 254 0.040509652191139 +Allele 256 0.043358731704418 + +Locus 006 +Allele 094 0.082121320565134 +Allele 096 0.066958806742702 +Allele 098 0.067968217549047 +Allele 100 0.054721997229729 +Allele 102 0.066275502694848 +Allele 104 0.126845593466303 +Allele 106 0.076497580581460 +Allele 108 0.067811346077793 +Allele 110 0.082605683947674 +Allele 112 0.065271088554606 +Allele 114 0.058876413409796 +Allele 124 0.060049053958939 +Allele 126 0.067358208609088 +Allele 149 0.056639186612881 + +Locus 007 +Allele 202 0.068942281700125 +Allele 204 0.052891529664621 +Allele 206 0.052937243864503 +Allele 208 0.061924134657653 +Allele 210 0.074500244475872 +Allele 212 0.068098159746782 +Allele 214 0.058879901116526 +Allele 216 0.058988978460001 +Allele 218 0.053921736023863 +Allele 220 0.069090760072166 +Allele 222 0.064772971000620 +Allele 224 0.063322236117412 +Allele 226 0.081794004254566 +Allele 228 0.051762651513164 +Allele 233 0.067637350373976 +Allele 238 0.050535816958148 + +Locus 008 +Allele 121 0.085958244770361 +Allele 123 0.142799153751805 +Allele 125 0.094291312955559 +Allele 127 0.069333429562150 +Allele 129 0.081981738901233 +Allele 131 0.090471187430166 +Allele 133 0.121167235584117 +Allele 135 0.077471396057736 +Allele 137 0.089884432023658 +Allele 151 0.067551516814475 +Allele 161 0.079090352148742 + +Locus 009 +Allele 161 0.074092576880633 +Allele 165 0.070265689909580 +Allele 167 0.098612616177378 +Allele 169 0.097660194469492 +Allele 171 0.091206935877574 +Allele 173 0.104293066955020 +Allele 175 0.077988110141851 +Allele 177 0.080149675369672 +Allele 179 0.069308973335685 +Allele 181 0.075479401178658 +Allele 183 0.080026381755258 +Allele 185 0.080916377949198 + +Locus 010 +Allele 108 0.042435177372088 +Allele 115 0.048742053847349 +Allele 121 0.043141133813758 +Allele 123 0.047700402030165 +Allele 125 0.050350739278068 +Allele 127 0.043074429418675 +Allele 129 0.048712644844607 +Allele 131 0.043100153803127 +Allele 133 0.057260179418383 +Allele 135 0.043628616177499 +Allele 137 0.056906235936092 +Allele 139 0.088117610762878 +Allele 141 0.047786116238894 +Allele 143 0.044137073317670 +Allele 145 0.043263295609747 +Allele 147 0.073310442802059 +Allele 149 0.043563648654567 +Allele 152 0.042458674467798 +Allele 155 0.047697774211368 +Allele 157 0.044613597995209 + + +Cluster 03 +Locus 001 +Allele 092 0.112533653229288 +Allele 094 0.115830591315555 +Allele 096 0.108373883681895 +Allele 098 0.116095371608180 +Allele 100 0.108360767851195 +Allele 102 0.103032242711618 +Allele 104 0.110331774453241 +Allele 106 0.130975640211819 +Allele 108 0.094466074937211 + +Locus 002 +Allele 118 0.076969778092671 +Allele 122 0.079324990588736 +Allele 124 0.089716996962543 +Allele 126 0.099963230160580 +Allele 127 0.079204398753550 +Allele 128 0.083864899574499 +Allele 130 0.081042767552752 +Allele 132 0.088722915060188 +Allele 134 0.073568225207996 +Allele 135 0.084594515348725 +Allele 137 0.086504974267688 +Allele 151 0.076522308430074 + +Locus 003 +Allele 130 0.065944384506739 +Allele 133 0.066660193470540 +Allele 136 0.071999257327702 +Allele 138 0.083920646652871 +Allele 139 0.073772539395073 +Allele 141 0.071328352003945 +Allele 143 0.064564363502922 +Allele 145 0.074568567649043 +Allele 146 0.074403048612943 +Allele 147 0.069304654127504 +Allele 148 0.074671033529538 +Allele 150 0.070247673463793 +Allele 152 0.073935891845499 +Allele 156 0.064679393911886 + +Locus 004 +Allele 093 0.058185833647632 +Allele 095 0.056967985835057 +Allele 096 0.054181516396374 +Allele 097 0.059082569604487 +Allele 099 0.061553224918807 +Allele 100 0.061064633578584 +Allele 101 0.061924267067878 +Allele 103 0.068641332860290 +Allele 105 0.055254695929406 +Allele 107 0.056595576362745 +Allele 109 0.061879220092503 +Allele 110 0.055887071148629 +Allele 113 0.061465771702897 +Allele 121 0.058628871062145 +Allele 123 0.058570723364957 +Allele 125 0.055548159371923 +Allele 131 0.054568547055686 + +Locus 005 +Allele 218 0.048362879196234 +Allele 220 0.052179551456886 +Allele 222 0.051192784572611 +Allele 224 0.049157304887038 +Allele 226 0.051912422082059 +Allele 228 0.049252980046356 +Allele 230 0.052155107832336 +Allele 232 0.051127919697100 +Allele 234 0.054518564539170 +Allele 236 0.052378255042094 +Allele 238 0.050759261323133 +Allele 240 0.051427335770391 +Allele 242 0.048128837140434 +Allele 244 0.045159179113030 +Allele 246 0.049129190699686 +Allele 248 0.047545392503691 +Allele 250 0.050991337200426 +Allele 252 0.049510485409298 +Allele 254 0.046333675570249 +Allele 256 0.048777535917778 + +Locus 006 +Allele 094 0.073454145225206 +Allele 096 0.073087515338012 +Allele 098 0.070276803032272 +Allele 100 0.065266346938957 +Allele 102 0.074695539207377 +Allele 104 0.074655751799102 +Allele 106 0.077993970534211 +Allele 108 0.067687283508614 +Allele 110 0.083640087034072 +Allele 112 0.073961187545001 +Allele 114 0.065263217062817 +Allele 124 0.071068553565515 +Allele 126 0.064233262933047 +Allele 149 0.064716336275797 + +Locus 007 +Allele 202 0.057551213727100 +Allele 204 0.058977447194035 +Allele 206 0.056749241941319 +Allele 208 0.069668928196359 +Allele 210 0.064285134779192 +Allele 212 0.063446417856349 +Allele 214 0.065082394186301 +Allele 216 0.063175870968695 +Allele 218 0.062988320087798 +Allele 220 0.062839119700740 +Allele 222 0.065198163520671 +Allele 224 0.064989331447923 +Allele 226 0.067047043818900 +Allele 228 0.060272186503611 +Allele 233 0.057327103870163 +Allele 238 0.060402082200844 + +Locus 008 +Allele 121 0.094331745123623 +Allele 123 0.105637989593499 +Allele 125 0.087722524257106 +Allele 127 0.080008516102335 +Allele 129 0.089398385204571 +Allele 131 0.091420500040831 +Allele 133 0.094454138330221 +Allele 135 0.088586083992200 +Allele 137 0.104786204367657 +Allele 151 0.082148826268926 +Allele 161 0.081505086719032 + +Locus 009 +Allele 161 0.076573466243298 +Allele 165 0.077161297980504 +Allele 167 0.091476195925195 +Allele 169 0.081957796499079 +Allele 171 0.089328397714836 +Allele 173 0.086594504950919 +Allele 175 0.088128445589296 +Allele 177 0.083628237635631 +Allele 179 0.075922952047036 +Allele 181 0.082823264385807 +Allele 183 0.083533670615166 +Allele 185 0.082871770413234 + +Locus 010 +Allele 108 0.048403902156600 +Allele 115 0.047719463455114 +Allele 121 0.047135340256083 +Allele 123 0.053749233611564 +Allele 125 0.051048134693856 +Allele 127 0.049253387207262 +Allele 129 0.051675572859411 +Allele 131 0.050215042540722 +Allele 133 0.052330349197988 +Allele 135 0.050164061742671 +Allele 137 0.055622618712791 +Allele 139 0.049777254484764 +Allele 141 0.050395826104002 +Allele 143 0.047430052612016 +Allele 145 0.048449099718733 +Allele 147 0.047881045630655 +Allele 149 0.050307045579108 +Allele 152 0.050367651129978 +Allele 155 0.046986547165849 +Allele 157 0.051088371140832 + + +Cluster 04 +Locus 001 +Allele 092 0.111127514052583 +Allele 094 0.114480002584449 +Allele 096 0.109133693587497 +Allele 098 0.129168296803696 +Allele 100 0.120079026560190 +Allele 102 0.098520674328380 +Allele 104 0.107549661442828 +Allele 106 0.114092668393364 +Allele 108 0.095848462247012 + +Locus 002 +Allele 118 0.072354274513497 +Allele 122 0.078037555494859 +Allele 124 0.087632497502051 +Allele 126 0.107678596703993 +Allele 127 0.075875075083015 +Allele 128 0.085162353352597 +Allele 130 0.079307627898071 +Allele 132 0.083626229194105 +Allele 134 0.073660851427244 +Allele 135 0.087354280771185 +Allele 137 0.094356864598913 +Allele 151 0.074953793460472 + +Locus 003 +Allele 130 0.065818105406796 +Allele 133 0.065412991870046 +Allele 136 0.066746546566848 +Allele 138 0.084651825030917 +Allele 139 0.072788770639362 +Allele 141 0.072992290829459 +Allele 143 0.063910753470616 +Allele 145 0.073899906010658 +Allele 146 0.074406839318271 +Allele 147 0.065398191782278 +Allele 148 0.078430026955233 +Allele 150 0.076383950561516 +Allele 152 0.075430698540503 +Allele 156 0.063729103017497 + +Locus 004 +Allele 093 0.055242030916725 +Allele 095 0.060747536071568 +Allele 096 0.053628386965924 +Allele 097 0.059963645720157 +Allele 099 0.062775817467747 +Allele 100 0.058711332736246 +Allele 101 0.062612541691701 +Allele 103 0.083425997848272 +Allele 105 0.056730498904270 +Allele 107 0.056101374192545 +Allele 109 0.056397778572778 +Allele 110 0.053400266405129 +Allele 113 0.059600802793032 +Allele 121 0.059744438574846 +Allele 123 0.054527853048203 +Allele 125 0.053308819346587 +Allele 131 0.053080878744269 + +Locus 005 +Allele 218 0.045299755157920 +Allele 220 0.049124532065908 +Allele 222 0.049757067017009 +Allele 224 0.053361958346797 +Allele 226 0.049476653059243 +Allele 228 0.052027568921549 +Allele 230 0.053659702027721 +Allele 232 0.052610687196331 +Allele 234 0.061498593584780 +Allele 236 0.054956246525770 +Allele 238 0.048431655673055 +Allele 240 0.051628526169475 +Allele 242 0.046306887478259 +Allele 244 0.049971205103150 +Allele 246 0.047468479017364 +Allele 248 0.046047884762261 +Allele 250 0.049353919603760 +Allele 252 0.047207224758158 +Allele 254 0.044925010681090 +Allele 256 0.046886442850401 + +Locus 006 +Allele 094 0.074594673030225 +Allele 096 0.075431987378495 +Allele 098 0.069146308348182 +Allele 100 0.063034843444204 +Allele 102 0.073552987029039 +Allele 104 0.087912746926881 +Allele 106 0.078889138668773 +Allele 108 0.069529437934864 +Allele 110 0.080988903474055 +Allele 112 0.066915656001548 +Allele 114 0.064259789373979 +Allele 124 0.068062507140904 +Allele 126 0.065263755108299 +Allele 149 0.062417266140550 + +Locus 007 +Allele 202 0.059780649563392 +Allele 204 0.057609262332209 +Allele 206 0.059854949139156 +Allele 208 0.067099496007677 +Allele 210 0.065168511454284 +Allele 212 0.068913085353231 +Allele 214 0.062334550002467 +Allele 216 0.066254087991239 +Allele 218 0.059523893063426 +Allele 220 0.062447881357781 +Allele 222 0.065585184143770 +Allele 224 0.064479351979140 +Allele 226 0.068310278692953 +Allele 228 0.056747321043956 +Allele 233 0.059174409795565 +Allele 238 0.056717088079753 + +Locus 008 +Allele 121 0.098635748287812 +Allele 123 0.107770709221073 +Allele 125 0.101516050945840 +Allele 127 0.076307934156414 +Allele 129 0.086198165058918 +Allele 131 0.093419895802614 +Allele 133 0.091911351622796 +Allele 135 0.084110318871762 +Allele 137 0.100037560069573 +Allele 151 0.077348326600330 +Allele 161 0.082743939362867 + +Locus 009 +Allele 161 0.076213478925103 +Allele 165 0.075103995868309 +Allele 167 0.099381527784328 +Allele 169 0.085907336008597 +Allele 171 0.093719477981618 +Allele 173 0.090275958614306 +Allele 175 0.080862223262146 +Allele 177 0.084176164560038 +Allele 179 0.074353669454743 +Allele 181 0.079101047357488 +Allele 183 0.080462029532936 +Allele 185 0.080443090650388 + +Locus 010 +Allele 108 0.047096770348486 +Allele 115 0.049510453380706 +Allele 121 0.046802212479947 +Allele 123 0.052245754663440 +Allele 125 0.049463815880109 +Allele 127 0.047503310898458 +Allele 129 0.049414235283319 +Allele 131 0.048259813694038 +Allele 133 0.059011392983760 +Allele 135 0.047957181390361 +Allele 137 0.051994272280947 +Allele 139 0.059027374460027 +Allele 141 0.052198738413139 +Allele 143 0.048050933865218 +Allele 145 0.046691932053950 +Allele 147 0.054403981502413 +Allele 149 0.046806433533254 +Allele 152 0.046513749534037 +Allele 155 0.048182201173212 +Allele 157 0.048865442181177 + + + +Estimated Mixing Proportions +0.922952866666667 +0.038084600000000 +0.017277066666667 +0.021685466666667 + + + +Estimated sigma: +k: 0 1.000000000000000 +k: 1 1.000000000000000 +k: 2 1.000000000000000 +k: 3 1.000000000000000 + + + +Estimated tau: +k: 0 10.000000000000000 +k: 1 10.000000000000000 +k: 2 10.000000000000000 +k: 3 10.000000000000000 + + + diff --git a/inst/files/tess/tess_04.txt b/inst/files/tess/tess_04.txt new file mode 100644 index 0000000..9fd7ac9 --- /dev/null +++ b/inst/files/tess/tess_04.txt @@ -0,0 +1,944 @@ +Estimated Clustering Probabilities for Samples +Sample ***Cluster 01*** ***Cluster 02*** ***Cluster 03*** ***Cluster 04*** ***Cluster 05*** +000001: 0.787660000000000 0.035545000000000 0.021665000000000 0.148980000000000 0.006150000000000 1 +000002: 0.817585000000000 0.095465000000000 0.022575000000000 0.054130000000000 0.010245000000000 1 +000003: 0.935455000000000 0.025210000000000 0.007015000000000 0.030660000000000 0.001660000000000 1 +000004: 0.767805000000000 0.064570000000000 0.029915000000000 0.131635000000000 0.006075000000000 1 +000005: 0.836550000000000 0.023065000000000 0.042845000000000 0.095180000000000 0.002360000000000 1 +000006: 0.916895000000000 0.012525000000000 0.011800000000000 0.056220000000000 0.002560000000000 1 +000007: 0.414585000000000 0.107505000000000 0.150730000000000 0.322700000000000 0.004480000000000 1 +000008: 0.723070000000000 0.097715000000000 0.070690000000000 0.103095000000000 0.005430000000000 1 +000009: 0.762105000000000 0.042930000000000 0.130130000000000 0.062035000000000 0.002800000000000 1 +000010: 0.700740000000000 0.071655000000000 0.056360000000000 0.161935000000000 0.009310000000000 1 +000011: 0.586635000000000 0.054310000000000 0.054970000000000 0.296680000000000 0.007405000000000 1 +000012: 0.865345000000000 0.064235000000000 0.016240000000000 0.049420000000000 0.004760000000000 1 +000013: 0.742435000000000 0.086295000000000 0.025555000000000 0.138560000000000 0.007155000000000 1 +000014: 0.847705000000000 0.031365000000000 0.016500000000000 0.098125000000000 0.006305000000000 1 +000015: 0.814595000000000 0.063985000000000 0.020000000000000 0.093790000000000 0.007630000000000 1 +000016: 0.937370000000000 0.021225000000000 0.010020000000000 0.029015000000000 0.002370000000000 1 +000017: 0.748705000000000 0.086540000000000 0.030325000000000 0.125095000000000 0.009335000000000 1 +000018: 0.800610000000000 0.053275000000000 0.031685000000000 0.102520000000000 0.011910000000000 1 +000019: 0.574400000000000 0.056205000000000 0.024215000000000 0.330255000000000 0.014925000000000 1 +000020: 0.732615000000000 0.074540000000000 0.035340000000000 0.141665000000000 0.015840000000000 1 +000021: 0.503500000000000 0.174230000000000 0.022075000000000 0.285750000000000 0.014445000000000 1 +000022: 0.395820000000000 0.270670000000000 0.033610000000000 0.280365000000000 0.019535000000000 1 +000023: 0.922555000000000 0.008115000000000 0.002015000000000 0.065815000000000 0.001500000000000 1 +000024: 0.809655000000000 0.067335000000000 0.007700000000000 0.110700000000000 0.004610000000000 1 +000025: 0.869160000000000 0.038795000000000 0.007870000000000 0.079160000000000 0.005015000000000 1 +000026: 0.778535000000000 0.108365000000000 0.012665000000000 0.094500000000000 0.005935000000000 1 +000027: 0.895745000000000 0.044455000000000 0.008870000000000 0.042595000000000 0.008335000000000 1 +000028: 0.908325000000000 0.042380000000000 0.005220000000000 0.041770000000000 0.002305000000000 1 +000029: 0.868345000000000 0.078020000000000 0.006740000000000 0.031870000000000 0.015025000000000 1 +000030: 0.562750000000000 0.397610000000000 0.009310000000000 0.020535000000000 0.009795000000000 1 +000031: 0.511225000000000 0.468060000000000 0.005765000000000 0.013875000000000 0.001075000000000 1 +000032: 0.773375000000000 0.198245000000000 0.010645000000000 0.015295000000000 0.002440000000000 1 +000033: 0.419985000000000 0.550890000000000 0.015080000000000 0.010195000000000 0.003850000000000 1 +000034: 0.401690000000000 0.585635000000000 0.005240000000000 0.005285000000000 0.002150000000000 1 +000035: 0.719160000000000 0.231900000000000 0.010600000000000 0.032000000000000 0.006340000000000 1 +000036: 0.838430000000000 0.064685000000000 0.025690000000000 0.060065000000000 0.011130000000000 1 +000037: 0.866880000000000 0.053490000000000 0.016175000000000 0.058465000000000 0.004990000000000 1 +000038: 0.888505000000000 0.056145000000000 0.025365000000000 0.027445000000000 0.002540000000000 1 +000039: 0.849665000000000 0.126890000000000 0.006785000000000 0.010825000000000 0.005835000000000 1 +000040: 0.936230000000000 0.036545000000000 0.002460000000000 0.021080000000000 0.003685000000000 1 +000041: 0.940560000000000 0.034055000000000 0.010030000000000 0.013065000000000 0.002290000000000 1 +000042: 0.753860000000000 0.222330000000000 0.008965000000000 0.013600000000000 0.001245000000000 1 +000043: 0.896105000000000 0.034175000000000 0.013355000000000 0.054600000000000 0.001765000000000 1 +000044: 0.895730000000000 0.055500000000000 0.023825000000000 0.022680000000000 0.002265000000000 1 +000045: 0.744490000000000 0.008810000000000 0.101545000000000 0.139980000000000 0.005175000000000 1 +000046: 0.819225000000000 0.003525000000000 0.023335000000000 0.152060000000000 0.001855000000000 1 +000047: 0.854465000000000 0.010190000000000 0.049865000000000 0.081295000000000 0.004185000000000 1 +000048: 0.595100000000000 0.000515000000000 0.393050000000000 0.011060000000000 0.000275000000000 1 +000049: 0.595900000000000 0.024860000000000 0.142800000000000 0.232720000000000 0.003720000000000 1 +000050: 0.612745000000000 0.014675000000000 0.100440000000000 0.269185000000000 0.002955000000000 1 +000051: 0.709530000000000 0.025255000000000 0.117545000000000 0.143400000000000 0.004270000000000 1 +000052: 0.867065000000000 0.004685000000000 0.032370000000000 0.094960000000000 0.000920000000000 1 +000053: 0.887065000000000 0.018265000000000 0.020470000000000 0.070735000000000 0.003465000000000 1 +000054: 0.668190000000000 0.017880000000000 0.163935000000000 0.142560000000000 0.007435000000000 1 +000055: 0.716825000000000 0.024995000000000 0.081275000000000 0.170090000000000 0.006815000000000 1 +000056: 0.812025000000000 0.014975000000000 0.043445000000000 0.123760000000000 0.005795000000000 1 +000057: 0.656825000000000 0.006890000000000 0.034025000000000 0.296610000000000 0.005650000000000 1 +000058: 0.873575000000000 0.005165000000000 0.016310000000000 0.102345000000000 0.002605000000000 1 +000059: 0.572085000000000 0.022730000000000 0.039660000000000 0.359160000000000 0.006365000000000 1 +000060: 0.564520000000000 0.072335000000000 0.063200000000000 0.289110000000000 0.010835000000000 1 +000061: 0.869835000000000 0.020690000000000 0.032750000000000 0.066020000000000 0.010705000000000 1 +000062: 0.577630000000000 0.136195000000000 0.051195000000000 0.212715000000000 0.022265000000000 1 +000063: 0.665770000000000 0.027180000000000 0.028125000000000 0.268480000000000 0.010445000000000 1 +000064: 0.500445000000000 0.042015000000000 0.092590000000000 0.345610000000000 0.019340000000000 1 +000065: 0.466745000000000 0.023915000000000 0.003565000000000 0.498015000000000 0.007760000000000 1 +000066: 0.769470000000000 0.037415000000000 0.005950000000000 0.181610000000000 0.005555000000000 1 +000067: 0.856160000000000 0.027240000000000 0.003685000000000 0.108950000000000 0.003965000000000 1 +000068: 0.832130000000000 0.031305000000000 0.004875000000000 0.122325000000000 0.009365000000000 1 +000069: 0.914005000000000 0.013695000000000 0.004350000000000 0.060940000000000 0.007010000000000 1 +000070: 0.837785000000000 0.027755000000000 0.006190000000000 0.117055000000000 0.011215000000000 1 +000071: 0.936495000000000 0.012705000000000 0.003520000000000 0.042920000000000 0.004360000000000 1 +000072: 0.906210000000000 0.056205000000000 0.004510000000000 0.029120000000000 0.003955000000000 1 +000073: 0.276935000000000 0.721920000000000 0.000435000000000 0.000370000000000 0.000340000000000 1 +000074: 0.723590000000000 0.240885000000000 0.005445000000000 0.025530000000000 0.004550000000000 1 +000075: 0.840400000000000 0.107435000000000 0.010435000000000 0.032995000000000 0.008735000000000 1 + + + +Estimated Allele Frequencies +Cluster 01 +Locus 001 +Allele 092 0.028283644159051 +Allele 094 0.433772971030676 +Allele 096 0.051579769624336 +Allele 098 0.216215077689902 +Allele 100 0.086111670885622 +Allele 102 0.079478513452439 +Allele 104 0.062996323082260 +Allele 106 0.022164379126625 +Allele 108 0.019397650949088 + +Locus 002 +Allele 118 0.017647685801028 +Allele 122 0.029294702098378 +Allele 124 0.216962814926117 +Allele 126 0.115658295385519 +Allele 127 0.010295376536545 +Allele 128 0.093962296122081 +Allele 130 0.079856212958373 +Allele 132 0.257926018207615 +Allele 134 0.013478201901568 +Allele 135 0.083358136714658 +Allele 137 0.070332991307592 +Allele 151 0.011227268040525 + +Locus 003 +Allele 130 0.024957016142363 +Allele 133 0.011813191177055 +Allele 136 0.149235651057441 +Allele 138 0.107036450094309 +Allele 139 0.152047704366029 +Allele 141 0.027897465213292 +Allele 143 0.013925641151885 +Allele 145 0.086529091255984 +Allele 146 0.095719588471939 +Allele 147 0.010283732304383 +Allele 148 0.139241829705286 +Allele 150 0.078622698273735 +Allele 152 0.084251839170950 +Allele 156 0.018438101615351 + +Locus 004 +Allele 093 0.051754342436259 +Allele 095 0.080893818081768 +Allele 096 0.012634997185536 +Allele 097 0.208293591539757 +Allele 099 0.046018236821332 +Allele 100 0.059024756908380 +Allele 101 0.135289424815207 +Allele 103 0.135009278262535 +Allele 105 0.052068399199807 +Allele 107 0.102579713698451 +Allele 109 0.015118042122797 +Allele 110 0.026432120351744 +Allele 113 0.014615232901101 +Allele 121 0.014896138990170 +Allele 123 0.018721625778449 +Allele 125 0.013373516738541 +Allele 131 0.013276764168166 + +Locus 005 +Allele 218 0.009990518102715 +Allele 220 0.091451187791735 +Allele 222 0.149658059737548 +Allele 224 0.126952105043867 +Allele 226 0.103293668729178 +Allele 228 0.043029299207375 +Allele 230 0.040019155423134 +Allele 232 0.059481171896597 +Allele 234 0.064542960298966 +Allele 236 0.057292978655520 +Allele 238 0.080465996972422 +Allele 240 0.040609479837892 +Allele 242 0.040774181712856 +Allele 244 0.011949796592463 +Allele 246 0.016926497988095 +Allele 248 0.011403763389104 +Allele 250 0.014811756399966 +Allele 252 0.018388986818262 +Allele 254 0.008134745126991 +Allele 256 0.010823690275314 + +Locus 006 +Allele 094 0.106624744823052 +Allele 096 0.197390200298799 +Allele 098 0.037356451930948 +Allele 100 0.013655455858787 +Allele 102 0.113537143750050 +Allele 104 0.237450499453150 +Allele 106 0.101922262805560 +Allele 108 0.078810408868470 +Allele 110 0.043331622062638 +Allele 112 0.021091079417518 +Allele 114 0.013100310929294 +Allele 124 0.011032843809649 +Allele 126 0.010801985905681 +Allele 149 0.013894990086403 + +Locus 007 +Allele 202 0.011458591631832 +Allele 204 0.023572323515092 +Allele 206 0.013808639985987 +Allele 208 0.148614121188677 +Allele 210 0.033794786269565 +Allele 212 0.208672152318774 +Allele 214 0.090485627937008 +Allele 216 0.119410333681662 +Allele 218 0.068354129271954 +Allele 220 0.061848639639761 +Allele 222 0.050398320896776 +Allele 224 0.099640199314483 +Allele 226 0.031962394332809 +Allele 228 0.017915099087795 +Allele 233 0.010199448748720 +Allele 238 0.009865192179106 + +Locus 008 +Allele 121 0.083152263391760 +Allele 123 0.069927123451411 +Allele 125 0.046053055097731 +Allele 127 0.012256979063059 +Allele 129 0.062811658122223 +Allele 131 0.267015923308387 +Allele 133 0.160477315055526 +Allele 135 0.207911817528720 +Allele 137 0.060753488128524 +Allele 151 0.016044045735750 +Allele 161 0.013596331116909 + +Locus 009 +Allele 161 0.015732647415355 +Allele 165 0.034369278252859 +Allele 167 0.049803274752013 +Allele 169 0.102869232480907 +Allele 171 0.263949858262823 +Allele 173 0.194869409761370 +Allele 175 0.111819501246298 +Allele 177 0.122026634380207 +Allele 179 0.016252456570436 +Allele 181 0.039172362199441 +Allele 183 0.021733960535507 +Allele 185 0.027401384142785 + +Locus 010 +Allele 108 0.031216956644514 +Allele 115 0.010745578175468 +Allele 121 0.011869145494145 +Allele 123 0.048613692262781 +Allele 125 0.103487194493423 +Allele 127 0.085316884636360 +Allele 129 0.086702884127289 +Allele 131 0.105092310015576 +Allele 133 0.144618173965837 +Allele 135 0.093411643356716 +Allele 137 0.079073804275810 +Allele 139 0.020809973748873 +Allele 141 0.042094372447917 +Allele 143 0.011960084936125 +Allele 145 0.030920606478697 +Allele 147 0.015707405122746 +Allele 149 0.031009841505283 +Allele 152 0.018789066412856 +Allele 155 0.010503368825095 +Allele 157 0.018057013074490 + + +Cluster 02 +Locus 001 +Allele 092 0.094207282149325 +Allele 094 0.147055892944522 +Allele 096 0.144081409125143 +Allele 098 0.092033120716839 +Allele 100 0.113543556810254 +Allele 102 0.179634040927553 +Allele 104 0.097277355070813 +Allele 106 0.066177935919060 +Allele 108 0.065989406336491 + +Locus 002 +Allele 118 0.047808021966192 +Allele 122 0.051522959241806 +Allele 124 0.168361505259810 +Allele 126 0.072105142439032 +Allele 127 0.047636572698555 +Allele 128 0.057822745391700 +Allele 130 0.051112098899908 +Allele 132 0.128676897662038 +Allele 134 0.047387513345293 +Allele 135 0.196518664217984 +Allele 137 0.084392477013586 +Allele 151 0.046655401864096 + +Locus 003 +Allele 130 0.044511731691805 +Allele 133 0.041530722540264 +Allele 136 0.053003992232535 +Allele 138 0.066654579383299 +Allele 139 0.059997555342093 +Allele 141 0.058808444066886 +Allele 143 0.043769170581686 +Allele 145 0.065371092633645 +Allele 146 0.145664119275084 +Allele 147 0.042181532236425 +Allele 148 0.085598571896174 +Allele 150 0.112998033109566 +Allele 152 0.134026391973025 +Allele 156 0.045884063037516 + +Locus 004 +Allele 093 0.053697976060221 +Allele 095 0.044141177624463 +Allele 096 0.039275372342438 +Allele 097 0.057256406180777 +Allele 099 0.042610858329408 +Allele 100 0.162610932911289 +Allele 101 0.076510420226304 +Allele 103 0.081912775481414 +Allele 105 0.059281345977781 +Allele 107 0.044553379026015 +Allele 109 0.090782507597161 +Allele 110 0.042740189528996 +Allele 113 0.040969313580721 +Allele 121 0.041706543625029 +Allele 123 0.049418311755835 +Allele 125 0.036557017488470 +Allele 131 0.035975472263678 + +Locus 005 +Allele 218 0.049369114926057 +Allele 220 0.078973289556770 +Allele 222 0.046218255799740 +Allele 224 0.080910616432568 +Allele 226 0.045975821535336 +Allele 228 0.039793922954760 +Allele 230 0.061941371450653 +Allele 232 0.071763862823770 +Allele 234 0.052839799353091 +Allele 236 0.045639982158599 +Allele 238 0.046714860037257 +Allele 240 0.056187513594468 +Allele 242 0.038217127096951 +Allele 244 0.035330677239057 +Allele 246 0.033151695649362 +Allele 248 0.032725633885128 +Allele 250 0.038045919028845 +Allele 252 0.037067157609164 +Allele 254 0.062007232788261 +Allele 256 0.047126146080164 + +Locus 006 +Allele 094 0.079365572262340 +Allele 096 0.074751412378578 +Allele 098 0.044845101946671 +Allele 100 0.046526164429795 +Allele 102 0.071621670495346 +Allele 104 0.070408789081423 +Allele 106 0.276271545573585 +Allele 108 0.051891200913331 +Allele 110 0.070833100836102 +Allele 112 0.042323228796384 +Allele 114 0.043571165998898 +Allele 124 0.040753597583681 +Allele 126 0.042409623852929 +Allele 149 0.044427825850936 + +Locus 007 +Allele 202 0.040378852859008 +Allele 204 0.050002171695297 +Allele 206 0.040833849588110 +Allele 208 0.049505086535662 +Allele 210 0.052745724360647 +Allele 212 0.078758997393505 +Allele 214 0.109049818763988 +Allele 216 0.088358599374045 +Allele 218 0.057823398859820 +Allele 220 0.052547626449309 +Allele 222 0.055539854038427 +Allele 224 0.130384570814845 +Allele 226 0.064598885052633 +Allele 228 0.044226244926639 +Allele 233 0.047142299975850 +Allele 238 0.038104019312215 + +Locus 008 +Allele 121 0.069817657106389 +Allele 123 0.097613069540168 +Allele 125 0.137159607277938 +Allele 127 0.083655202291886 +Allele 129 0.066777080582598 +Allele 131 0.187087248444977 +Allele 133 0.081100411753530 +Allele 135 0.085381100697669 +Allele 137 0.072616626299909 +Allele 151 0.063402251749126 +Allele 161 0.055389744255810 + +Locus 009 +Allele 161 0.058026467969086 +Allele 165 0.058179588184413 +Allele 167 0.064176782768854 +Allele 169 0.081241673668325 +Allele 171 0.221332643259958 +Allele 173 0.080261705927446 +Allele 175 0.104590699645702 +Allele 177 0.063756736289879 +Allele 179 0.052986041105157 +Allele 181 0.078948075688453 +Allele 183 0.057404201858773 +Allele 185 0.079095383633950 + +Locus 010 +Allele 108 0.038226485303101 +Allele 115 0.035863544134134 +Allele 121 0.032142392512712 +Allele 123 0.034895176337302 +Allele 125 0.048660352510446 +Allele 127 0.036361805101451 +Allele 129 0.062714040113506 +Allele 131 0.045413428065275 +Allele 133 0.135661329105667 +Allele 135 0.125337003078994 +Allele 137 0.039543656992498 +Allele 139 0.038318573576449 +Allele 141 0.036934688429573 +Allele 143 0.034453716200029 +Allele 145 0.050686486078897 +Allele 147 0.058280634771545 +Allele 149 0.037975318525463 +Allele 152 0.035482521680175 +Allele 155 0.038493306235888 +Allele 157 0.034555541246894 + + +Cluster 03 +Locus 001 +Allele 092 0.106360060906541 +Allele 094 0.125566772802378 +Allele 096 0.090727813805641 +Allele 098 0.151270489243973 +Allele 100 0.095286179407676 +Allele 102 0.092825990318414 +Allele 104 0.108732417381877 +Allele 106 0.149535710824100 +Allele 108 0.079694565309399 + +Locus 002 +Allele 118 0.074192550703221 +Allele 122 0.079131200144637 +Allele 124 0.091069233912310 +Allele 126 0.113975054362503 +Allele 127 0.071834217155147 +Allele 128 0.079976893825315 +Allele 130 0.083212565791072 +Allele 132 0.118603531395613 +Allele 134 0.067645233199705 +Allele 135 0.077993187152926 +Allele 137 0.076676944329117 +Allele 151 0.065689388028434 + +Locus 003 +Allele 130 0.056845088843383 +Allele 133 0.068018921037471 +Allele 136 0.089290784811717 +Allele 138 0.089378744455633 +Allele 139 0.073792293907340 +Allele 141 0.096511697892786 +Allele 143 0.054347782324435 +Allele 145 0.074887024278979 +Allele 146 0.071538347959749 +Allele 147 0.062298845064174 +Allele 148 0.073621778793302 +Allele 150 0.063726403788462 +Allele 152 0.068585635501432 +Allele 156 0.057156651341138 + +Locus 004 +Allele 093 0.052576984101698 +Allele 095 0.055023438880774 +Allele 096 0.048482197688518 +Allele 097 0.066746077192759 +Allele 099 0.067458566028161 +Allele 100 0.108578076688363 +Allele 101 0.063487913580406 +Allele 103 0.071944077956133 +Allele 105 0.051325725143900 +Allele 107 0.054251896852274 +Allele 109 0.046811343554065 +Allele 110 0.050270992132223 +Allele 113 0.058943874411738 +Allele 121 0.055819456848027 +Allele 123 0.045954820995001 +Allele 125 0.050691739208464 +Allele 131 0.051632818737495 + +Locus 005 +Allele 218 0.040793286907028 +Allele 220 0.053086416395797 +Allele 222 0.059225847626483 +Allele 224 0.052134220253466 +Allele 226 0.052939954040929 +Allele 228 0.047931621151201 +Allele 230 0.052564953893757 +Allele 232 0.051538128503071 +Allele 234 0.062018909530954 +Allele 236 0.054380979639479 +Allele 238 0.048836382937293 +Allele 240 0.047575118416345 +Allele 242 0.043952467231898 +Allele 244 0.042448836376721 +Allele 246 0.066207260430536 +Allele 248 0.043451780161960 +Allele 250 0.052558255250396 +Allele 252 0.049080515440032 +Allele 254 0.039254419945309 +Allele 256 0.040020645867345 + +Locus 006 +Allele 094 0.078864362445555 +Allele 096 0.074395447187892 +Allele 098 0.067807321684430 +Allele 100 0.057050083933930 +Allele 102 0.073036041806744 +Allele 104 0.081363141537374 +Allele 106 0.092068257526657 +Allele 108 0.064924156570072 +Allele 110 0.089017125770900 +Allele 112 0.081118731700819 +Allele 114 0.058330836948815 +Allele 124 0.070101076317564 +Allele 126 0.055360503076848 +Allele 149 0.056562913492399 + +Locus 007 +Allele 202 0.049285399764930 +Allele 204 0.056924965264406 +Allele 206 0.048986241793247 +Allele 208 0.073555503052340 +Allele 210 0.058433525736216 +Allele 212 0.066019465908083 +Allele 214 0.073631562953411 +Allele 216 0.064083301499160 +Allele 218 0.060562849152001 +Allele 220 0.054463976196824 +Allele 222 0.066182097426602 +Allele 224 0.064983911248640 +Allele 226 0.067881838491122 +Allele 228 0.060082659656904 +Allele 233 0.050786894611780 +Allele 238 0.084135807244333 + +Locus 008 +Allele 121 0.089225275773615 +Allele 123 0.107219226258662 +Allele 125 0.076706571842999 +Allele 127 0.064438097349105 +Allele 129 0.076449244468297 +Allele 131 0.103207582578436 +Allele 133 0.112246886171783 +Allele 135 0.087118556124430 +Allele 137 0.147250609087093 +Allele 151 0.066099805518512 +Allele 161 0.070038144827067 + +Locus 009 +Allele 161 0.064017822486842 +Allele 165 0.065209546222300 +Allele 167 0.095440991620616 +Allele 169 0.068599864116151 +Allele 171 0.088820917733247 +Allele 173 0.085200029390827 +Allele 175 0.084774511628750 +Allele 177 0.083886169384244 +Allele 179 0.066477756451347 +Allele 181 0.111790344000246 +Allele 183 0.120581201900145 +Allele 185 0.065200845065286 + +Locus 010 +Allele 108 0.044508631344133 +Allele 115 0.042683449202241 +Allele 121 0.047199034361807 +Allele 123 0.063190037548998 +Allele 125 0.049079391000154 +Allele 127 0.046993675012607 +Allele 129 0.051571594746909 +Allele 131 0.062045672724382 +Allele 133 0.053246876945086 +Allele 135 0.046891329725552 +Allele 137 0.056835565921297 +Allele 139 0.046140272064506 +Allele 141 0.071298967728486 +Allele 143 0.044753778654698 +Allele 145 0.042163391982873 +Allele 147 0.043738635138165 +Allele 149 0.048958649895384 +Allele 152 0.050122928520329 +Allele 155 0.041055941064452 +Allele 157 0.047522176417942 + + +Cluster 04 +Locus 001 +Allele 092 0.116860070644228 +Allele 094 0.204763911591353 +Allele 096 0.081487234557261 +Allele 098 0.118771068317842 +Allele 100 0.107061934061799 +Allele 102 0.070447501298137 +Allele 104 0.128442069162696 +Allele 106 0.112462793359296 +Allele 108 0.059703417007390 + +Locus 002 +Allele 118 0.059274544991434 +Allele 122 0.060840380696356 +Allele 124 0.077184252281918 +Allele 126 0.163337303797186 +Allele 127 0.055497871667226 +Allele 128 0.132718923376707 +Allele 130 0.077525629064148 +Allele 132 0.083248053309082 +Allele 134 0.047440164692369 +Allele 135 0.094464872879974 +Allele 137 0.091975085023296 +Allele 151 0.056492918220305 + +Locus 003 +Allele 130 0.051065808551441 +Allele 133 0.043157540435778 +Allele 136 0.067935044618555 +Allele 138 0.089059791226005 +Allele 139 0.087209308464846 +Allele 141 0.065435592196118 +Allele 143 0.042390923544801 +Allele 145 0.084286127936583 +Allele 146 0.079852053836816 +Allele 147 0.050615146255036 +Allele 148 0.137472502091449 +Allele 150 0.062033245708813 +Allele 152 0.089631727682949 +Allele 156 0.049855187450809 + +Locus 004 +Allele 093 0.043562288074665 +Allele 095 0.056790154048292 +Allele 096 0.038341056568971 +Allele 097 0.076655984749708 +Allele 099 0.079745895905970 +Allele 100 0.041932436411787 +Allele 101 0.158649499081878 +Allele 103 0.119036370155704 +Allele 105 0.041692712393574 +Allele 107 0.059075635235732 +Allele 109 0.034559437494352 +Allele 110 0.040204750110979 +Allele 113 0.048320009880528 +Allele 121 0.050985100211331 +Allele 123 0.036515288672398 +Allele 125 0.036338710659220 +Allele 131 0.037594670344911 + +Locus 005 +Allele 218 0.030513213269204 +Allele 220 0.058342571369277 +Allele 222 0.058032306381974 +Allele 224 0.092880986440567 +Allele 226 0.056837620406061 +Allele 228 0.073487313485647 +Allele 230 0.057973230821892 +Allele 232 0.051980717228913 +Allele 234 0.075936704069429 +Allele 236 0.060114031283227 +Allele 238 0.059782467119732 +Allele 240 0.042174397671355 +Allele 242 0.036430442997058 +Allele 244 0.036146756605440 +Allele 246 0.031987186248165 +Allele 248 0.040279467717057 +Allele 250 0.041319724318635 +Allele 252 0.033926671572166 +Allele 254 0.031026823010867 +Allele 256 0.030827367983335 + +Locus 006 +Allele 094 0.076894994114097 +Allele 096 0.066247454134067 +Allele 098 0.082782629648022 +Allele 100 0.040683289283071 +Allele 102 0.058031879773964 +Allele 104 0.181880431206813 +Allele 106 0.090442361030167 +Allele 108 0.058788750327848 +Allele 110 0.092222876115028 +Allele 112 0.060905922767283 +Allele 114 0.043732188116791 +Allele 124 0.048722445306695 +Allele 126 0.056429174742572 +Allele 149 0.042235603433582 + +Locus 007 +Allele 202 0.048528374520223 +Allele 204 0.043381080426530 +Allele 206 0.039529264496079 +Allele 208 0.086590056604875 +Allele 210 0.085589407575202 +Allele 212 0.082077689763663 +Allele 214 0.082655535440642 +Allele 216 0.064042034743173 +Allele 218 0.047000771516821 +Allele 220 0.052841475009526 +Allele 222 0.097593680248602 +Allele 224 0.071909437945864 +Allele 226 0.074400195464659 +Allele 228 0.040764649677252 +Allele 233 0.045980063802116 +Allele 238 0.037116282764772 + +Locus 008 +Allele 121 0.108177929812706 +Allele 123 0.137035406181202 +Allele 125 0.067464914520067 +Allele 127 0.049323350911379 +Allele 129 0.073405427866143 +Allele 131 0.122965890874856 +Allele 133 0.130264659897582 +Allele 135 0.082996869540455 +Allele 137 0.119439121479320 +Allele 151 0.049277217703511 +Allele 161 0.059649211212781 + +Locus 009 +Allele 161 0.052145491715199 +Allele 165 0.053668632306579 +Allele 167 0.100084596296406 +Allele 169 0.108055499092290 +Allele 171 0.138157330118802 +Allele 173 0.170034919529826 +Allele 175 0.068800795349315 +Allele 177 0.077490975545546 +Allele 179 0.051663578195947 +Allele 181 0.059097042401450 +Allele 183 0.064194858574154 +Allele 185 0.056606280874486 + +Locus 010 +Allele 108 0.042091998876189 +Allele 115 0.038020704994226 +Allele 121 0.036317470105293 +Allele 123 0.048777895452877 +Allele 125 0.070201793383298 +Allele 127 0.042282133313253 +Allele 129 0.055295407749006 +Allele 131 0.039894438295236 +Allele 133 0.104382217340535 +Allele 135 0.043980415173742 +Allele 137 0.088690475769165 +Allele 139 0.074830722944362 +Allele 141 0.040795161952511 +Allele 143 0.036676655921837 +Allele 145 0.034101099453983 +Allele 147 0.048649607021035 +Allele 149 0.041866185812476 +Allele 152 0.035848760696383 +Allele 155 0.039695438621365 +Allele 157 0.037601417123229 + + +Cluster 05 +Locus 001 +Allele 092 0.112278440279104 +Allele 094 0.112386107221679 +Allele 096 0.112431899701373 +Allele 098 0.112875693561490 +Allele 100 0.117495790459528 +Allele 102 0.108327666216061 +Allele 104 0.111133521572419 +Allele 106 0.105469744139944 +Allele 108 0.107601136848402 + +Locus 002 +Allele 118 0.081549586150101 +Allele 122 0.083892506157281 +Allele 124 0.084236588704157 +Allele 126 0.085508745524335 +Allele 127 0.082120644834126 +Allele 128 0.083999027769045 +Allele 130 0.082554987496523 +Allele 132 0.083605543352617 +Allele 134 0.081585322340469 +Allele 135 0.085051521692355 +Allele 137 0.086252976132441 +Allele 151 0.079642549846552 + +Locus 003 +Allele 130 0.070857207536798 +Allele 133 0.067545035320512 +Allele 136 0.070973159108267 +Allele 138 0.070707935116467 +Allele 139 0.073814701909824 +Allele 141 0.073990626065653 +Allele 143 0.069609934157006 +Allele 145 0.071372155805999 +Allele 146 0.072632397075533 +Allele 147 0.069849427044994 +Allele 148 0.072078485614766 +Allele 150 0.074790892538442 +Allele 152 0.072441265936979 +Allele 156 0.069336776768762 + +Locus 004 +Allele 093 0.058350402042384 +Allele 095 0.060537100903388 +Allele 096 0.057938868635627 +Allele 097 0.060931551134316 +Allele 099 0.059192722142974 +Allele 100 0.057883568517900 +Allele 101 0.059870766692703 +Allele 103 0.062029994215978 +Allele 105 0.059272347380887 +Allele 107 0.058608832362052 +Allele 109 0.058415393687363 +Allele 110 0.058526458310798 +Allele 113 0.058473523508576 +Allele 121 0.058049280732857 +Allele 123 0.058242089033634 +Allele 125 0.056753055002445 +Allele 131 0.056924045696118 + +Locus 005 +Allele 218 0.048726021261940 +Allele 220 0.050878780246945 +Allele 222 0.049850439059634 +Allele 224 0.051008649739849 +Allele 226 0.050170532880235 +Allele 228 0.050028168568800 +Allele 230 0.050686047489717 +Allele 232 0.051857862050807 +Allele 234 0.051156870812825 +Allele 236 0.049633107583635 +Allele 238 0.050579198691771 +Allele 240 0.050652300250604 +Allele 242 0.049766051309321 +Allele 244 0.049685887392741 +Allele 246 0.049561583263089 +Allele 248 0.048823490209579 +Allele 250 0.050173004082378 +Allele 252 0.049925828353211 +Allele 254 0.048001414207782 +Allele 256 0.048834762545139 + +Locus 006 +Allele 094 0.074059969679713 +Allele 096 0.071600116824124 +Allele 098 0.071759579381185 +Allele 100 0.070219858438103 +Allele 102 0.072659080355449 +Allele 104 0.076883518256662 +Allele 106 0.073327314765491 +Allele 108 0.072308968770569 +Allele 110 0.073321643351095 +Allele 112 0.068530612977999 +Allele 114 0.070780056026183 +Allele 124 0.067853387379947 +Allele 126 0.068438212644970 +Allele 149 0.068257681148510 + +Locus 007 +Allele 202 0.061797427390827 +Allele 204 0.062459087067540 +Allele 206 0.060846148085605 +Allele 208 0.063636527616597 +Allele 210 0.062514889582884 +Allele 212 0.065271612322516 +Allele 214 0.063520223454477 +Allele 216 0.064009063389824 +Allele 218 0.061880723294733 +Allele 220 0.063172969445863 +Allele 222 0.062925672616605 +Allele 224 0.062160601729212 +Allele 226 0.062625078326420 +Allele 228 0.061548375788218 +Allele 233 0.061906628469502 +Allele 238 0.059724971419178 + +Locus 008 +Allele 121 0.091346247553294 +Allele 123 0.094395797282227 +Allele 125 0.093239140401031 +Allele 127 0.085291527582607 +Allele 129 0.091288814954737 +Allele 131 0.091922192807793 +Allele 133 0.092567310571108 +Allele 135 0.091026036474389 +Allele 137 0.092476357991618 +Allele 151 0.086818677272356 +Allele 161 0.089627897108839 + +Locus 009 +Allele 161 0.081189239339670 +Allele 165 0.081643451253800 +Allele 167 0.088331412192477 +Allele 169 0.084672494235126 +Allele 171 0.084515695638099 +Allele 173 0.085801989655399 +Allele 175 0.083131519007583 +Allele 177 0.084447185068034 +Allele 179 0.079669293804784 +Allele 181 0.082540785941031 +Allele 183 0.081185875237079 +Allele 185 0.082871058626918 + +Locus 010 +Allele 108 0.049113325921766 +Allele 115 0.050914997543373 +Allele 121 0.048813497335215 +Allele 123 0.048995359821657 +Allele 125 0.050861875030238 +Allele 127 0.049373211209661 +Allele 129 0.050477658263182 +Allele 131 0.049070442381368 +Allele 133 0.051633523017424 +Allele 135 0.050118652282395 +Allele 137 0.050820221548459 +Allele 139 0.051200511218498 +Allele 141 0.050571444046892 +Allele 143 0.048935257309244 +Allele 145 0.050961647586440 +Allele 147 0.051427847566656 +Allele 149 0.049362065571808 +Allele 152 0.048077779370984 +Allele 155 0.049869271829278 +Allele 157 0.049401411145463 + + + +Estimated Mixing Proportions +0.747225200000000 +0.092253133333333 +0.037140266666667 +0.116998866666667 +0.006382533333333 + + + +Estimated sigma: +k: 0 1.000000000000000 +k: 1 1.000000000000000 +k: 2 1.000000000000000 +k: 3 1.000000000000000 +k: 4 1.000000000000000 + + + +Estimated tau: +k: 0 10.000000000000000 +k: 1 10.000000000000000 +k: 2 10.000000000000000 +k: 3 10.000000000000000 +k: 4 10.000000000000000 + + + diff --git a/inst/files/tess/tess_05.txt b/inst/files/tess/tess_05.txt new file mode 100644 index 0000000..156ac1c --- /dev/null +++ b/inst/files/tess/tess_05.txt @@ -0,0 +1,1114 @@ +Estimated Clustering Probabilities for Samples +Sample ***Cluster 01*** ***Cluster 02*** ***Cluster 03*** ***Cluster 04*** ***Cluster 05*** ***Cluster 06*** +000001: 0.071640000000000 0.007995000000000 0.058830000000000 0.161185000000000 0.038865000000000 0.661485000000000 1 +000002: 0.319855000000000 0.004580000000000 0.259815000000000 0.060895000000000 0.012920000000000 0.341935000000000 1 +000003: 0.117710000000000 0.003480000000000 0.011810000000000 0.812375000000000 0.009945000000000 0.044680000000000 1 +000004: 0.157545000000000 0.015465000000000 0.044860000000000 0.120235000000000 0.022990000000000 0.638905000000000 1 +000005: 0.092900000000000 0.006835000000000 0.019110000000000 0.793970000000000 0.011590000000000 0.075595000000000 1 +000006: 0.163720000000000 0.010415000000000 0.020050000000000 0.242505000000000 0.018405000000000 0.544905000000000 1 +000007: 0.225065000000000 0.026495000000000 0.106540000000000 0.132690000000000 0.064515000000000 0.444695000000000 1 +000008: 0.605735000000000 0.023645000000000 0.026285000000000 0.145160000000000 0.059050000000000 0.140125000000000 1 +000009: 0.193830000000000 0.022690000000000 0.033325000000000 0.658310000000000 0.031810000000000 0.060035000000000 1 +000010: 0.208760000000000 0.009090000000000 0.014615000000000 0.105270000000000 0.021170000000000 0.641095000000000 1 +000011: 0.218015000000000 0.009435000000000 0.019900000000000 0.195475000000000 0.043055000000000 0.514120000000000 1 +000012: 0.541540000000000 0.007535000000000 0.014335000000000 0.231915000000000 0.024905000000000 0.179770000000000 1 +000013: 0.382355000000000 0.009025000000000 0.025440000000000 0.205300000000000 0.029095000000000 0.348785000000000 1 +000014: 0.161320000000000 0.013510000000000 0.027605000000000 0.285175000000000 0.054845000000000 0.457545000000000 1 +000015: 0.279615000000000 0.007200000000000 0.090410000000000 0.104335000000000 0.027875000000000 0.490565000000000 1 +000016: 0.171145000000000 0.007195000000000 0.011400000000000 0.149800000000000 0.017320000000000 0.643140000000000 1 +000017: 0.544770000000000 0.012320000000000 0.021165000000000 0.113470000000000 0.041695000000000 0.266580000000000 1 +000018: 0.225060000000000 0.036100000000000 0.038550000000000 0.112805000000000 0.054630000000000 0.532855000000000 1 +000019: 0.062840000000000 0.005950000000000 0.007280000000000 0.124330000000000 0.017995000000000 0.781605000000000 1 +000020: 0.220960000000000 0.008360000000000 0.011320000000000 0.093110000000000 0.021830000000000 0.644420000000000 1 +000021: 0.213970000000000 0.016695000000000 0.027660000000000 0.126180000000000 0.038735000000000 0.576760000000000 1 +000022: 0.051425000000000 0.018025000000000 0.069680000000000 0.174305000000000 0.085640000000000 0.600925000000000 1 +000023: 0.068130000000000 0.004030000000000 0.004325000000000 0.795000000000000 0.009200000000000 0.119315000000000 1 +000024: 0.330350000000000 0.008585000000000 0.013515000000000 0.301010000000000 0.022970000000000 0.323570000000000 1 +000025: 0.101760000000000 0.007715000000000 0.005430000000000 0.148660000000000 0.011420000000000 0.725015000000000 1 +000026: 0.489055000000000 0.008165000000000 0.020550000000000 0.113440000000000 0.023290000000000 0.345500000000000 1 +000027: 0.388630000000000 0.007845000000000 0.016670000000000 0.203690000000000 0.049190000000000 0.333975000000000 1 +000028: 0.135525000000000 0.006615000000000 0.010155000000000 0.123270000000000 0.012915000000000 0.711520000000000 1 +000029: 0.184030000000000 0.013555000000000 0.013890000000000 0.161605000000000 0.033310000000000 0.593610000000000 1 +000030: 0.592460000000000 0.003210000000000 0.012280000000000 0.073695000000000 0.013300000000000 0.305055000000000 1 +000031: 0.841595000000000 0.003590000000000 0.005970000000000 0.110575000000000 0.009900000000000 0.028370000000000 1 +000032: 0.548415000000000 0.021070000000000 0.051545000000000 0.086090000000000 0.250815000000000 0.042065000000000 1 +000033: 0.880230000000000 0.004735000000000 0.034750000000000 0.039910000000000 0.016930000000000 0.023445000000000 1 +000034: 0.893050000000000 0.005535000000000 0.007815000000000 0.049635000000000 0.015990000000000 0.027975000000000 1 +000035: 0.620650000000000 0.004430000000000 0.077280000000000 0.136470000000000 0.086660000000000 0.074510000000000 1 +000036: 0.104920000000000 0.014425000000000 0.018290000000000 0.619405000000000 0.033250000000000 0.209710000000000 1 +000037: 0.096850000000000 0.006290000000000 0.040750000000000 0.307635000000000 0.009590000000000 0.538885000000000 1 +000038: 0.391745000000000 0.007620000000000 0.018585000000000 0.533915000000000 0.012210000000000 0.035925000000000 1 +000039: 0.277255000000000 0.006780000000000 0.113010000000000 0.578920000000000 0.012325000000000 0.011710000000000 1 +000040: 0.683850000000000 0.004935000000000 0.026985000000000 0.234235000000000 0.032760000000000 0.017235000000000 1 +000041: 0.097755000000000 0.039650000000000 0.021825000000000 0.724740000000000 0.038760000000000 0.077270000000000 1 +000042: 0.501730000000000 0.010600000000000 0.113850000000000 0.265650000000000 0.013380000000000 0.094790000000000 1 +000043: 0.067640000000000 0.004740000000000 0.004090000000000 0.894140000000000 0.007225000000000 0.022165000000000 1 +000044: 0.661815000000000 0.010605000000000 0.007095000000000 0.229650000000000 0.013735000000000 0.077100000000000 1 +000045: 0.094945000000000 0.013265000000000 0.014975000000000 0.482125000000000 0.043685000000000 0.351005000000000 1 +000046: 0.098625000000000 0.008875000000000 0.010550000000000 0.410355000000000 0.032405000000000 0.439190000000000 1 +000047: 0.092780000000000 0.030920000000000 0.022745000000000 0.574825000000000 0.043635000000000 0.235095000000000 1 +000048: 0.275955000000000 0.030835000000000 0.038900000000000 0.452705000000000 0.036195000000000 0.165410000000000 1 +000049: 0.160070000000000 0.030250000000000 0.033370000000000 0.239530000000000 0.033090000000000 0.503690000000000 1 +000050: 0.037120000000000 0.032655000000000 0.041585000000000 0.257385000000000 0.027170000000000 0.604085000000000 1 +000051: 0.072080000000000 0.029815000000000 0.016220000000000 0.744425000000000 0.025945000000000 0.111515000000000 1 +000052: 0.248575000000000 0.015695000000000 0.013160000000000 0.358360000000000 0.018195000000000 0.346015000000000 1 +000053: 0.074340000000000 0.005130000000000 0.007670000000000 0.219470000000000 0.021670000000000 0.671720000000000 1 +000054: 0.117825000000000 0.024845000000000 0.025850000000000 0.489380000000000 0.034240000000000 0.307860000000000 1 +000055: 0.337450000000000 0.010430000000000 0.008225000000000 0.229505000000000 0.039270000000000 0.375120000000000 1 +000056: 0.073755000000000 0.009265000000000 0.014220000000000 0.623510000000000 0.023415000000000 0.255835000000000 1 +000057: 0.055920000000000 0.012265000000000 0.006195000000000 0.467360000000000 0.330965000000000 0.127295000000000 1 +000058: 0.129310000000000 0.005920000000000 0.005270000000000 0.308360000000000 0.020030000000000 0.531110000000000 1 +000059: 0.057020000000000 0.045655000000000 0.017555000000000 0.603845000000000 0.082475000000000 0.193450000000000 1 +000060: 0.134490000000000 0.022055000000000 0.027860000000000 0.161360000000000 0.037980000000000 0.616255000000000 1 +000061: 0.098750000000000 0.007330000000000 0.008220000000000 0.240800000000000 0.018625000000000 0.626275000000000 1 +000062: 0.355825000000000 0.016145000000000 0.022015000000000 0.200970000000000 0.073620000000000 0.331425000000000 1 +000063: 0.069915000000000 0.032910000000000 0.007255000000000 0.652410000000000 0.038450000000000 0.199060000000000 1 +000064: 0.055015000000000 0.058175000000000 0.021870000000000 0.580950000000000 0.093000000000000 0.190990000000000 1 +000065: 0.036005000000000 0.010575000000000 0.004725000000000 0.143630000000000 0.018565000000000 0.786500000000000 1 +000066: 0.031140000000000 0.002265000000000 0.002085000000000 0.062415000000000 0.004645000000000 0.897450000000000 1 +000067: 0.190765000000000 0.005945000000000 0.005880000000000 0.504030000000000 0.020085000000000 0.273295000000000 1 +000068: 0.079115000000000 0.009400000000000 0.008080000000000 0.274005000000000 0.030085000000000 0.599315000000000 1 +000069: 0.075115000000000 0.005290000000000 0.004315000000000 0.792160000000000 0.017600000000000 0.105520000000000 1 +000070: 0.114445000000000 0.006795000000000 0.015125000000000 0.534955000000000 0.036075000000000 0.292605000000000 1 +000071: 0.074865000000000 0.004955000000000 0.006360000000000 0.443965000000000 0.016715000000000 0.453140000000000 1 +000072: 0.936135000000000 0.000825000000000 0.000480000000000 0.047845000000000 0.000445000000000 0.014270000000000 1 +000073: 0.924500000000000 0.000720000000000 0.001180000000000 0.046395000000000 0.001885000000000 0.025320000000000 1 +000074: 0.687760000000000 0.010935000000000 0.008240000000000 0.259605000000000 0.018205000000000 0.015255000000000 1 +000075: 0.263955000000000 0.004055000000000 0.010290000000000 0.656240000000000 0.013335000000000 0.052125000000000 1 + + + +Estimated Allele Frequencies +Cluster 01 +Locus 001 +Allele 092 0.052860198446585 +Allele 094 0.319975167208048 +Allele 096 0.122324028610369 +Allele 098 0.129399073345568 +Allele 100 0.077764939728289 +Allele 102 0.143781115071884 +Allele 104 0.067256666927868 +Allele 106 0.049374469314265 +Allele 108 0.037264341347125 + +Locus 002 +Allele 118 0.022081103156606 +Allele 122 0.025915989608452 +Allele 124 0.335494755019173 +Allele 126 0.052804991225412 +Allele 127 0.020276449254472 +Allele 128 0.038013319966708 +Allele 130 0.038360776619057 +Allele 132 0.211290246104047 +Allele 134 0.021097214231049 +Allele 135 0.158319457405097 +Allele 137 0.055933361775660 +Allele 151 0.020412335634265 + +Locus 003 +Allele 130 0.022745055195507 +Allele 133 0.021454992586487 +Allele 136 0.104135568161684 +Allele 138 0.111775696453269 +Allele 139 0.045250385751555 +Allele 141 0.049832826672835 +Allele 143 0.026251798296563 +Allele 145 0.037335706737380 +Allele 146 0.169903786360024 +Allele 147 0.020463914192838 +Allele 148 0.112674734632014 +Allele 150 0.143207061758003 +Allele 152 0.106343163490112 +Allele 156 0.028625309711729 + +Locus 004 +Allele 093 0.059355418350500 +Allele 095 0.039971831156035 +Allele 096 0.027571067440086 +Allele 097 0.098970443118115 +Allele 099 0.038807927425117 +Allele 100 0.159868870035686 +Allele 101 0.118303127975181 +Allele 103 0.089182084055300 +Allele 105 0.074716985744254 +Allele 107 0.077427937945085 +Allele 109 0.061174748608659 +Allele 110 0.029548587428954 +Allele 113 0.025630599662870 +Allele 121 0.023896704782297 +Allele 123 0.035096755768266 +Allele 125 0.020350158771635 +Allele 131 0.020126751731959 + +Locus 005 +Allele 218 0.031314685987964 +Allele 220 0.118460901016291 +Allele 222 0.106295965212760 +Allele 224 0.115802951001185 +Allele 226 0.093110269636932 +Allele 228 0.025929467343338 +Allele 230 0.050839065535196 +Allele 232 0.076913967711996 +Allele 234 0.043716531255542 +Allele 236 0.039425681735869 +Allele 238 0.034736462888868 +Allele 240 0.042405617323635 +Allele 242 0.049068876652114 +Allele 244 0.020095210198544 +Allele 246 0.022553884551461 +Allele 248 0.018193616947592 +Allele 250 0.025706897040848 +Allele 252 0.023724899443286 +Allele 254 0.034086676286145 +Allele 256 0.027618372230434 + +Locus 006 +Allele 094 0.148051431125862 +Allele 096 0.237886505607735 +Allele 098 0.030563592053947 +Allele 100 0.023804834863925 +Allele 102 0.049893423854143 +Allele 104 0.052552641905765 +Allele 106 0.231151245067101 +Allele 108 0.060852506246669 +Allele 110 0.059857217282223 +Allele 112 0.021784583212968 +Allele 114 0.022281622833001 +Allele 124 0.020986879696869 +Allele 126 0.019783080625156 +Allele 149 0.020550435624634 + +Locus 007 +Allele 202 0.020066573153422 +Allele 204 0.036705046616355 +Allele 206 0.020782386896996 +Allele 208 0.035752987063997 +Allele 210 0.040134064525251 +Allele 212 0.115265188037276 +Allele 214 0.127838304772578 +Allele 216 0.090002246137834 +Allele 218 0.103871699638795 +Allele 220 0.040587507212527 +Allele 222 0.047788305334519 +Allele 224 0.208621866955664 +Allele 226 0.044358025126103 +Allele 228 0.025564304398383 +Allele 233 0.019817415108979 +Allele 238 0.022844079021324 + +Locus 008 +Allele 121 0.048212851946609 +Allele 123 0.074168140368532 +Allele 125 0.109099018209305 +Allele 127 0.043810929683730 +Allele 129 0.036292101044000 +Allele 131 0.395169329853113 +Allele 133 0.060246142458875 +Allele 135 0.128422739574765 +Allele 137 0.048728100219616 +Allele 151 0.030039149869289 +Allele 161 0.025811496772166 + +Locus 009 +Allele 161 0.037829556132068 +Allele 165 0.033494904633968 +Allele 167 0.055424164116172 +Allele 169 0.052216892336168 +Allele 171 0.370619189608504 +Allele 173 0.069572587785924 +Allele 175 0.113858270672992 +Allele 177 0.052590207744496 +Allele 179 0.027641873088250 +Allele 181 0.074499460162724 +Allele 183 0.051092327243986 +Allele 185 0.061160566474750 + +Locus 010 +Allele 108 0.033174071238663 +Allele 115 0.022333685701339 +Allele 121 0.019322664888337 +Allele 123 0.037958979612688 +Allele 125 0.047879398516308 +Allele 127 0.027159101419907 +Allele 129 0.085339277732045 +Allele 131 0.052505924431917 +Allele 133 0.186411580047162 +Allele 135 0.180588533937246 +Allele 137 0.036707013977580 +Allele 139 0.021031632097628 +Allele 141 0.044087733366332 +Allele 143 0.020243508276320 +Allele 145 0.050703885638219 +Allele 147 0.028115630783391 +Allele 149 0.041701241292004 +Allele 152 0.024140211924428 +Allele 155 0.020636352182122 +Allele 157 0.019959572936362 + + +Cluster 02 +Locus 001 +Allele 092 0.113790397393786 +Allele 094 0.118423234670202 +Allele 096 0.109309957122076 +Allele 098 0.112509266176299 +Allele 100 0.109378604015569 +Allele 102 0.106072230419142 +Allele 104 0.118910219545488 +Allele 106 0.112725504700038 +Allele 108 0.098880585957398 + +Locus 002 +Allele 118 0.078834452017432 +Allele 122 0.081480075118889 +Allele 124 0.086716312401014 +Allele 126 0.094624112131338 +Allele 127 0.078203811104946 +Allele 128 0.088547566308124 +Allele 130 0.084125587083180 +Allele 132 0.090754625174490 +Allele 134 0.075586970326936 +Allele 135 0.083287654243795 +Allele 137 0.079624235460033 +Allele 151 0.078214598629824 + +Locus 003 +Allele 130 0.067219357186415 +Allele 133 0.066195510493107 +Allele 136 0.075068779393533 +Allele 138 0.077500890429078 +Allele 139 0.075941446205306 +Allele 141 0.072259407178590 +Allele 143 0.064729157679190 +Allele 145 0.075104086068011 +Allele 146 0.072386592709463 +Allele 147 0.068567078364087 +Allele 148 0.076497990082198 +Allele 150 0.069781501284237 +Allele 152 0.072893054686586 +Allele 156 0.065855148240198 + +Locus 004 +Allele 093 0.057913882056019 +Allele 095 0.058853518788819 +Allele 096 0.053917192323066 +Allele 097 0.063164681375163 +Allele 099 0.060315528803836 +Allele 100 0.059695945359797 +Allele 101 0.069279406135503 +Allele 103 0.066089545988005 +Allele 105 0.057579228061827 +Allele 107 0.057555055092504 +Allele 109 0.054249105450078 +Allele 110 0.057939338562848 +Allele 113 0.058680039051882 +Allele 121 0.056204534795202 +Allele 123 0.056636797021612 +Allele 125 0.055598966938662 +Allele 131 0.056327234195175 + +Locus 005 +Allele 218 0.045887359268515 +Allele 220 0.050937096437454 +Allele 222 0.054732330335990 +Allele 224 0.051235358719741 +Allele 226 0.053504726230222 +Allele 228 0.049454528982036 +Allele 230 0.051553274876457 +Allele 232 0.051322299282284 +Allele 234 0.052376809829629 +Allele 236 0.052976296031562 +Allele 238 0.053626301995570 +Allele 240 0.050400075427982 +Allele 242 0.048505049526667 +Allele 244 0.046721374936261 +Allele 246 0.049504383506946 +Allele 248 0.047626727851913 +Allele 250 0.049072953464707 +Allele 252 0.048661248364967 +Allele 254 0.045722056920084 +Allele 256 0.046179748011012 + +Locus 006 +Allele 094 0.071269621859996 +Allele 096 0.073837192087760 +Allele 098 0.069740365250574 +Allele 100 0.064977797558493 +Allele 102 0.079803098371711 +Allele 104 0.081653258380092 +Allele 106 0.074466896775128 +Allele 108 0.072019038626899 +Allele 110 0.072656773432471 +Allele 112 0.072512713089862 +Allele 114 0.068393061965652 +Allele 124 0.067989413134646 +Allele 126 0.066083340802396 +Allele 149 0.064597428664320 + +Locus 007 +Allele 202 0.057189879473102 +Allele 204 0.062801709088815 +Allele 206 0.057834203757273 +Allele 208 0.067046402598100 +Allele 210 0.061689054540643 +Allele 212 0.065975845685742 +Allele 214 0.069263265324065 +Allele 216 0.062886362941950 +Allele 218 0.063443030658682 +Allele 220 0.060573753672373 +Allele 222 0.069026692572441 +Allele 224 0.062382579069076 +Allele 226 0.061736338380177 +Allele 228 0.060144260761230 +Allele 233 0.057969591618273 +Allele 238 0.060037029858057 + +Locus 008 +Allele 121 0.090421039295110 +Allele 123 0.093800734585216 +Allele 125 0.085701886108243 +Allele 127 0.080085257385043 +Allele 129 0.100056826981908 +Allele 131 0.095488772169669 +Allele 133 0.092933940907665 +Allele 135 0.091741896143397 +Allele 137 0.102963577051253 +Allele 151 0.081499755780654 +Allele 161 0.085306313591842 + +Locus 009 +Allele 161 0.077030414508661 +Allele 165 0.078513088942400 +Allele 167 0.088550178400492 +Allele 169 0.080525540418928 +Allele 171 0.094555653609711 +Allele 173 0.093134353779906 +Allele 175 0.087663794037863 +Allele 177 0.082505734423639 +Allele 179 0.076241945292458 +Allele 181 0.082015971069756 +Allele 183 0.081635583142479 +Allele 185 0.077627742373707 + +Locus 010 +Allele 108 0.048440528536511 +Allele 115 0.047356158421143 +Allele 121 0.047262315812359 +Allele 123 0.052057208908085 +Allele 125 0.049516112502327 +Allele 127 0.049264605770737 +Allele 129 0.052899974677292 +Allele 131 0.052828872213927 +Allele 133 0.052942546979442 +Allele 135 0.053375606311004 +Allele 137 0.056617155567322 +Allele 139 0.047863579311433 +Allele 141 0.052204270931525 +Allele 143 0.047061566677355 +Allele 145 0.048429905972191 +Allele 147 0.048002865360438 +Allele 149 0.049970267136003 +Allele 152 0.048692669172663 +Allele 155 0.046472383172955 +Allele 157 0.048741406565287 + + +Cluster 03 +Locus 001 +Allele 092 0.104906108189853 +Allele 094 0.108360799815777 +Allele 096 0.099438471906538 +Allele 098 0.099064227936240 +Allele 100 0.116007657089466 +Allele 102 0.160971058336265 +Allele 104 0.101427283547129 +Allele 106 0.105780297636086 +Allele 108 0.104044095542646 + +Locus 002 +Allele 118 0.071129051153378 +Allele 122 0.079104760614343 +Allele 124 0.085151701131399 +Allele 126 0.094306761424492 +Allele 127 0.069249719736065 +Allele 128 0.091072393322788 +Allele 130 0.076000606335757 +Allele 132 0.132758154756016 +Allele 134 0.069240905148797 +Allele 135 0.083669172087758 +Allele 137 0.079317322265010 +Allele 151 0.068999452024197 + +Locus 003 +Allele 130 0.060184505294431 +Allele 133 0.060351710686295 +Allele 136 0.070587990193402 +Allele 138 0.072741775147564 +Allele 139 0.071281370643492 +Allele 141 0.082075972514089 +Allele 143 0.059325393412886 +Allele 145 0.085105710089879 +Allele 146 0.091992349401539 +Allele 147 0.061919198787420 +Allele 148 0.072252000248657 +Allele 150 0.072203349512332 +Allele 152 0.076722788402784 +Allele 156 0.063255885665231 + +Locus 004 +Allele 093 0.055163386339658 +Allele 095 0.061386834082057 +Allele 096 0.051709048579233 +Allele 097 0.082125975536823 +Allele 099 0.055274428247433 +Allele 100 0.063736095169879 +Allele 101 0.068996182430494 +Allele 103 0.084286948605145 +Allele 105 0.053665575531989 +Allele 107 0.053415704888193 +Allele 109 0.051329687810604 +Allele 110 0.060392229953596 +Allele 113 0.052350137737417 +Allele 121 0.052115288939150 +Allele 123 0.051202090295931 +Allele 125 0.051692480415245 +Allele 131 0.051157905437154 + +Locus 005 +Allele 218 0.045207488929376 +Allele 220 0.059613591768677 +Allele 222 0.050036555983370 +Allele 224 0.063701890212361 +Allele 226 0.065012586837405 +Allele 228 0.045987548026275 +Allele 230 0.051356515619972 +Allele 232 0.053834985579737 +Allele 234 0.057051956964119 +Allele 236 0.052716641443968 +Allele 238 0.049342904838117 +Allele 240 0.047876704077732 +Allele 242 0.046617833729120 +Allele 244 0.044251247542827 +Allele 246 0.045012889404182 +Allele 248 0.043417401211093 +Allele 250 0.046728405641713 +Allele 252 0.045708364899335 +Allele 254 0.043220482652630 +Allele 256 0.043304004637990 + +Locus 006 +Allele 094 0.067993273277212 +Allele 096 0.104844685802239 +Allele 098 0.065531183442320 +Allele 100 0.060896684906747 +Allele 102 0.073897800507768 +Allele 104 0.078713935884405 +Allele 106 0.073025177757488 +Allele 108 0.063305800174014 +Allele 110 0.098786994729489 +Allele 112 0.067156563105425 +Allele 114 0.062363825052190 +Allele 124 0.061953541994397 +Allele 126 0.059893237298488 +Allele 149 0.061637296067817 + +Locus 007 +Allele 202 0.053387345637663 +Allele 204 0.058046076286409 +Allele 206 0.053599703724881 +Allele 208 0.066097669980682 +Allele 210 0.056204562097475 +Allele 212 0.073486096802247 +Allele 214 0.064027727862689 +Allele 216 0.080775164120837 +Allele 218 0.059479120916080 +Allele 220 0.070522617119454 +Allele 222 0.062211892415315 +Allele 224 0.064729215314826 +Allele 226 0.070835349187094 +Allele 228 0.055530875801676 +Allele 233 0.055299514889699 +Allele 238 0.055767067842974 + +Locus 008 +Allele 121 0.087677885986447 +Allele 123 0.106623917335411 +Allele 125 0.084892993118427 +Allele 127 0.073040113353038 +Allele 129 0.081216462101789 +Allele 131 0.135834151200608 +Allele 133 0.100490948221429 +Allele 135 0.086877016270098 +Allele 137 0.086119310345661 +Allele 151 0.083930089109281 +Allele 161 0.073297112957808 + +Locus 009 +Allele 161 0.071358277064291 +Allele 165 0.076735315761079 +Allele 167 0.079710570313680 +Allele 169 0.093835717417824 +Allele 171 0.088448058156244 +Allele 173 0.087887585865775 +Allele 175 0.114848127152098 +Allele 177 0.079962729063348 +Allele 179 0.071457334095983 +Allele 181 0.077868621211658 +Allele 183 0.077186438113605 +Allele 185 0.080701225784413 + +Locus 010 +Allele 108 0.050626031219793 +Allele 115 0.044751509352470 +Allele 121 0.043370781547272 +Allele 123 0.048331703497871 +Allele 125 0.050028091107263 +Allele 127 0.046824360037300 +Allele 129 0.073064784198801 +Allele 131 0.048617000346969 +Allele 133 0.049212281408735 +Allele 135 0.069810600019010 +Allele 137 0.054417715465541 +Allele 139 0.044047939387532 +Allele 141 0.049543312580147 +Allele 143 0.044077749671674 +Allele 145 0.050775392862991 +Allele 147 0.054531870349632 +Allele 149 0.045565170991301 +Allele 152 0.044513806764074 +Allele 155 0.044054470352591 +Allele 157 0.043835428839033 + + +Cluster 04 +Locus 001 +Allele 092 0.044121401382861 +Allele 094 0.395015757481541 +Allele 096 0.029211379013098 +Allele 098 0.246430832088596 +Allele 100 0.078304653879011 +Allele 102 0.069318482995407 +Allele 104 0.088172366155573 +Allele 106 0.028964509456132 +Allele 108 0.020460617547782 + +Locus 002 +Allele 118 0.022928592641566 +Allele 122 0.036281294818373 +Allele 124 0.143712437312922 +Allele 126 0.117321617061984 +Allele 127 0.025578693551070 +Allele 128 0.089698218725782 +Allele 130 0.108973907887512 +Allele 132 0.302125048348063 +Allele 134 0.020836515076464 +Allele 135 0.064481433495337 +Allele 137 0.041690782012276 +Allele 151 0.026371459068653 + +Locus 003 +Allele 130 0.052709395416872 +Allele 133 0.024039085187842 +Allele 136 0.207485924140683 +Allele 138 0.072936942287190 +Allele 139 0.069086351591417 +Allele 141 0.028129652864007 +Allele 143 0.019528990024106 +Allele 145 0.124914184989101 +Allele 146 0.045456950134097 +Allele 147 0.024787784013148 +Allele 148 0.178526653782075 +Allele 150 0.041484747412094 +Allele 152 0.087329555095282 +Allele 156 0.023583783062086 + +Locus 004 +Allele 093 0.077976568349168 +Allele 095 0.086824907073664 +Allele 096 0.017656983026708 +Allele 097 0.135581059697188 +Allele 099 0.061902285793747 +Allele 100 0.068962860864600 +Allele 101 0.111794831190950 +Allele 103 0.062994433614135 +Allele 105 0.045919349720927 +Allele 107 0.163575359217319 +Allele 109 0.018322118342031 +Allele 110 0.028223607463966 +Allele 113 0.030117359055016 +Allele 121 0.019700076927003 +Allele 123 0.022127111707857 +Allele 125 0.023811517543187 +Allele 131 0.024509570412534 + +Locus 005 +Allele 218 0.015162358933394 +Allele 220 0.058306837331098 +Allele 222 0.174611922388044 +Allele 224 0.054889696456035 +Allele 226 0.102643746170186 +Allele 228 0.021356597354779 +Allele 230 0.053841193492294 +Allele 232 0.033736851528133 +Allele 234 0.049117333739316 +Allele 236 0.072972319667586 +Allele 238 0.147881055247535 +Allele 240 0.029370554968215 +Allele 242 0.036790872061510 +Allele 244 0.016057013694597 +Allele 246 0.027862777694003 +Allele 248 0.020672864522609 +Allele 250 0.026674062974405 +Allele 252 0.026515796874240 +Allele 254 0.015524012285998 +Allele 256 0.016012132616024 + +Locus 006 +Allele 094 0.068917065622328 +Allele 096 0.060486099184700 +Allele 098 0.050272870077102 +Allele 100 0.026748286169581 +Allele 102 0.125144303474882 +Allele 104 0.374700235937641 +Allele 106 0.111273217609722 +Allele 108 0.039841034539723 +Allele 110 0.030223303976865 +Allele 112 0.033501580353452 +Allele 114 0.018051970216132 +Allele 124 0.020348941434163 +Allele 126 0.018991808295976 +Allele 149 0.021499283107734 + +Locus 007 +Allele 202 0.018101514778065 +Allele 204 0.021641759328579 +Allele 206 0.019835905537973 +Allele 208 0.220271277340752 +Allele 210 0.038908497779975 +Allele 212 0.075440664217480 +Allele 214 0.110309140812347 +Allele 216 0.143255895749969 +Allele 218 0.052225246316835 +Allele 220 0.068229173771601 +Allele 222 0.066601725425681 +Allele 224 0.053598973355656 +Allele 226 0.035370415096332 +Allele 228 0.034538307882958 +Allele 233 0.018910522141120 +Allele 238 0.022760980464677 + +Locus 008 +Allele 121 0.079736975991121 +Allele 123 0.050907276787414 +Allele 125 0.036928727142935 +Allele 127 0.020888922067350 +Allele 129 0.078315585918437 +Allele 131 0.154994787459821 +Allele 133 0.090600969219478 +Allele 135 0.280963384342271 +Allele 137 0.148189615092432 +Allele 151 0.028751618259202 +Allele 161 0.029722137719540 + +Locus 009 +Allele 161 0.021784539109375 +Allele 165 0.056415936166160 +Allele 167 0.046751162869343 +Allele 169 0.034811987104753 +Allele 171 0.190832402877675 +Allele 173 0.257493972731352 +Allele 175 0.137294622757663 +Allele 177 0.093899404313389 +Allele 179 0.031008354915030 +Allele 181 0.058649867506970 +Allele 183 0.034057596648298 +Allele 185 0.037000152999992 + +Locus 010 +Allele 108 0.051758790570844 +Allele 115 0.017991443164590 +Allele 121 0.021949087606833 +Allele 123 0.052968773895689 +Allele 125 0.057627706031179 +Allele 127 0.123251624705078 +Allele 129 0.058054724413703 +Allele 131 0.133225068103640 +Allele 133 0.075522097333950 +Allele 135 0.062313140125887 +Allele 137 0.093078846508845 +Allele 139 0.020835737640401 +Allele 141 0.044359879438144 +Allele 143 0.016767369563432 +Allele 145 0.022056390348810 +Allele 147 0.021129894308524 +Allele 149 0.045741658950566 +Allele 152 0.035067239935378 +Allele 155 0.016786297211109 +Allele 157 0.029514230143398 + + +Cluster 05 +Locus 001 +Allele 092 0.102518557904706 +Allele 094 0.159305795761434 +Allele 096 0.097785911282308 +Allele 098 0.108107449360730 +Allele 100 0.114645068823640 +Allele 102 0.109919968452694 +Allele 104 0.131533815522656 +Allele 106 0.094840310133385 +Allele 108 0.081343122758446 + +Locus 002 +Allele 118 0.065675896893629 +Allele 122 0.074335437967469 +Allele 124 0.094332169273882 +Allele 126 0.098069176100847 +Allele 127 0.068292825207619 +Allele 128 0.097876214283286 +Allele 130 0.097883596836368 +Allele 132 0.107447238138641 +Allele 134 0.063720230478743 +Allele 135 0.084503828743923 +Allele 137 0.080231799467134 +Allele 151 0.067631586608458 + +Locus 003 +Allele 130 0.060371995826403 +Allele 133 0.056216996462489 +Allele 136 0.123948982247652 +Allele 138 0.071327964246706 +Allele 139 0.071323213183027 +Allele 141 0.068374478028988 +Allele 143 0.058135100415452 +Allele 145 0.075375470300046 +Allele 146 0.083844041262501 +Allele 147 0.058934742549828 +Allele 148 0.073874420369767 +Allele 150 0.066472587417862 +Allele 152 0.071883550293552 +Allele 156 0.059916457395727 + +Locus 004 +Allele 093 0.057215054965721 +Allele 095 0.058196673965074 +Allele 096 0.049755230598381 +Allele 097 0.076031765934307 +Allele 099 0.056863994092198 +Allele 100 0.054661321697307 +Allele 101 0.089258762820739 +Allele 103 0.085060765532154 +Allele 105 0.053782050150427 +Allele 107 0.066234112439233 +Allele 109 0.048620524577419 +Allele 110 0.054597457706006 +Allele 113 0.053020142916046 +Allele 121 0.049068137329108 +Allele 123 0.050871331816459 +Allele 125 0.048215102658246 +Allele 131 0.048547570801176 + +Locus 005 +Allele 218 0.041879614840367 +Allele 220 0.063753240149186 +Allele 222 0.067690092902951 +Allele 224 0.051708054228257 +Allele 226 0.051621992720919 +Allele 228 0.045439987856865 +Allele 230 0.052804238491713 +Allele 232 0.063739721572368 +Allele 234 0.047904246089760 +Allele 236 0.052778990010599 +Allele 238 0.055249995291527 +Allele 240 0.048329131033288 +Allele 242 0.044593803901287 +Allele 244 0.041922421821372 +Allele 246 0.044810476913251 +Allele 248 0.052579500373811 +Allele 250 0.045422119541745 +Allele 252 0.044788595862280 +Allele 254 0.041114243828204 +Allele 256 0.041869532570250 + +Locus 006 +Allele 094 0.075925176026351 +Allele 096 0.087028493287510 +Allele 098 0.100314833929566 +Allele 100 0.056769582236172 +Allele 102 0.069051798114691 +Allele 104 0.111855581979495 +Allele 106 0.074008521165158 +Allele 108 0.063802764664289 +Allele 110 0.070046484386698 +Allele 112 0.062966300055256 +Allele 114 0.059522465087130 +Allele 124 0.057272248036527 +Allele 126 0.056005418946587 +Allele 149 0.055430332084568 + +Locus 007 +Allele 202 0.049998237591738 +Allele 204 0.070187968740251 +Allele 206 0.051776474291974 +Allele 208 0.064662805675058 +Allele 210 0.071723959910841 +Allele 212 0.066680133530166 +Allele 214 0.077941830971429 +Allele 216 0.058096593322262 +Allele 218 0.059289003786376 +Allele 220 0.061554131003261 +Allele 222 0.078650816747117 +Allele 224 0.064329356744776 +Allele 226 0.067371373619128 +Allele 228 0.053225967408732 +Allele 233 0.053229641262282 +Allele 238 0.051281705394611 + +Locus 008 +Allele 121 0.082995120407308 +Allele 123 0.098535253374726 +Allele 125 0.083835827230637 +Allele 127 0.068801521540587 +Allele 129 0.091830152028637 +Allele 131 0.094855169814853 +Allele 133 0.105926322017669 +Allele 135 0.143222587481841 +Allele 137 0.092079169086345 +Allele 151 0.067998919628857 +Allele 161 0.069919957388539 + +Locus 009 +Allele 161 0.068801299610914 +Allele 165 0.068490071926429 +Allele 167 0.078139905383295 +Allele 169 0.072106259150391 +Allele 171 0.175234902619440 +Allele 173 0.088447394990183 +Allele 175 0.081751937848003 +Allele 177 0.080414792323659 +Allele 179 0.067538069527455 +Allele 181 0.072908837211543 +Allele 183 0.074166632221241 +Allele 185 0.071999897187446 + +Locus 010 +Allele 108 0.047483119757368 +Allele 115 0.044321649638877 +Allele 121 0.042818511712539 +Allele 123 0.047446187968274 +Allele 125 0.048387940589569 +Allele 127 0.046651226323536 +Allele 129 0.051692054248906 +Allele 131 0.050235343291474 +Allele 133 0.054779005703694 +Allele 135 0.056311796738971 +Allele 137 0.080672233568054 +Allele 139 0.043496185687736 +Allele 141 0.050160739180008 +Allele 143 0.042401678130074 +Allele 145 0.063351529748083 +Allele 147 0.055086343919168 +Allele 149 0.045370044181755 +Allele 152 0.042733699842671 +Allele 155 0.041936887231204 +Allele 157 0.044663822538037 + + +Cluster 06 +Locus 001 +Allele 092 0.051237182505948 +Allele 094 0.358208782125071 +Allele 096 0.067486038747254 +Allele 098 0.186190989869120 +Allele 100 0.120848007638993 +Allele 102 0.059400130446481 +Allele 104 0.072824175905351 +Allele 106 0.053438675857257 +Allele 108 0.030366016904523 + +Locus 002 +Allele 118 0.038441004360712 +Allele 122 0.048038692758398 +Allele 124 0.114730003054551 +Allele 126 0.179071043573727 +Allele 127 0.020679599833235 +Allele 128 0.142849879904221 +Allele 130 0.071310275856367 +Allele 132 0.108505653911388 +Allele 134 0.027724207374421 +Allele 135 0.099173128629127 +Allele 137 0.128487684235823 +Allele 151 0.020988826508031 + +Locus 003 +Allele 130 0.022344470782892 +Allele 133 0.021198443526735 +Allele 136 0.038248515651731 +Allele 138 0.113686979231373 +Allele 139 0.242821467186678 +Allele 141 0.040866748398856 +Allele 143 0.021582986243732 +Allele 145 0.078187229904687 +Allele 146 0.093147714635111 +Allele 147 0.019167632250406 +Allele 148 0.119636307205452 +Allele 150 0.066363479571887 +Allele 152 0.094080092397606 +Allele 156 0.028667933012856 + +Locus 004 +Allele 093 0.021690949590200 +Allele 095 0.078292108184528 +Allele 096 0.019144694132102 +Allele 097 0.211418041651480 +Allele 099 0.059044268264162 +Allele 100 0.031596373372864 +Allele 101 0.148929857175120 +Allele 103 0.194237014583320 +Allele 105 0.040178399523292 +Allele 107 0.026551518921796 +Allele 109 0.025923841421876 +Allele 110 0.028562293357901 +Allele 113 0.021578525646616 +Allele 121 0.032930555196477 +Allele 123 0.023043296386402 +Allele 125 0.018560253688991 +Allele 131 0.018318008902870 + +Locus 005 +Allele 218 0.015613312834047 +Allele 220 0.076213761926796 +Allele 222 0.058532037150889 +Allele 224 0.167956321407223 +Allele 226 0.057112159804806 +Allele 228 0.094708861381533 +Allele 230 0.037259206794767 +Allele 232 0.071741732607034 +Allele 234 0.099567908660046 +Allele 236 0.054345853222134 +Allele 238 0.031339568008749 +Allele 240 0.057373081022843 +Allele 242 0.034052874914509 +Allele 244 0.023836805652762 +Allele 246 0.022853718569640 +Allele 248 0.016850837344412 +Allele 250 0.020551944257951 +Allele 252 0.023329666399334 +Allele 254 0.015981615364183 +Allele 256 0.020778732676340 + +Locus 006 +Allele 094 0.087890952602263 +Allele 096 0.154979306626713 +Allele 098 0.046461777212069 +Allele 100 0.019269326579297 +Allele 102 0.105761217360173 +Allele 104 0.183589314018205 +Allele 106 0.080806191395089 +Allele 108 0.108148056129751 +Allele 110 0.070926208729934 +Allele 112 0.037773377972464 +Allele 114 0.024570560938945 +Allele 124 0.024844814212286 +Allele 126 0.029170490418550 +Allele 149 0.025808405804262 + +Locus 007 +Allele 202 0.028301412331897 +Allele 204 0.029270052597954 +Allele 206 0.024934123849256 +Allele 208 0.110009809616621 +Allele 210 0.056577422387926 +Allele 212 0.274458144198472 +Allele 214 0.057531831528647 +Allele 216 0.073898897702711 +Allele 218 0.040142353170187 +Allele 220 0.058171292978441 +Allele 222 0.059131822619611 +Allele 224 0.067442978119105 +Allele 226 0.053701281241561 +Allele 228 0.021121958762637 +Allele 233 0.025738310674085 +Allele 238 0.019568308220888 + +Locus 008 +Allele 121 0.127524130066687 +Allele 123 0.126867409833730 +Allele 125 0.054431170715863 +Allele 127 0.021931616907446 +Allele 129 0.063843795462566 +Allele 131 0.176641196107513 +Allele 133 0.262765636973069 +Allele 135 0.082600438811529 +Allele 137 0.036496008737401 +Allele 151 0.021537868829980 +Allele 161 0.025360727554217 + +Locus 009 +Allele 161 0.025165941307271 +Allele 165 0.031179592039088 +Allele 167 0.083987352425835 +Allele 169 0.196115715295880 +Allele 171 0.172476348195484 +Allele 173 0.173632159464896 +Allele 175 0.054680798563296 +Allele 177 0.147458731174494 +Allele 179 0.025048648271952 +Allele 181 0.030763719290285 +Allele 183 0.033463647970130 +Allele 185 0.026027346001388 + +Locus 010 +Allele 108 0.018135861791608 +Allele 115 0.020121266148177 +Allele 121 0.020113305896580 +Allele 123 0.051092999127458 +Allele 125 0.151773996121479 +Allele 127 0.053532359238210 +Allele 129 0.075106946478642 +Allele 131 0.064057334759312 +Allele 133 0.161583965015045 +Allele 135 0.038357107801298 +Allele 137 0.079115361289198 +Allele 139 0.062033099775648 +Allele 141 0.038757686990438 +Allele 143 0.024394082246739 +Allele 145 0.024669136099581 +Allele 147 0.033840109064650 +Allele 149 0.018352046542254 +Allele 152 0.017201211477180 +Allele 155 0.023132570763885 +Allele 157 0.024629553372619 + + + +Estimated Mixing Proportions +0.269877066666667 +0.013212800000000 +0.027054800000000 +0.319240133333333 +0.036396066666667 +0.334219133333333 + + + +Estimated sigma: +k: 0 1.000000000000000 +k: 1 1.000000000000000 +k: 2 1.000000000000000 +k: 3 1.000000000000000 +k: 4 1.000000000000000 +k: 5 1.000000000000000 + + + +Estimated tau: +k: 0 10.000000000000000 +k: 1 10.000000000000000 +k: 2 10.000000000000000 +k: 3 10.000000000000000 +k: 4 10.000000000000000 +k: 5 10.000000000000000 + + + diff --git a/inst/files/tess/tess_06.txt b/inst/files/tess/tess_06.txt new file mode 100644 index 0000000..d74bedf --- /dev/null +++ b/inst/files/tess/tess_06.txt @@ -0,0 +1,1284 @@ +Estimated Clustering Probabilities for Samples +Sample ***Cluster 01*** ***Cluster 02*** ***Cluster 03*** ***Cluster 04*** ***Cluster 05*** ***Cluster 06*** ***Cluster 07*** +000001: 0.002655000000000 0.212270000000000 0.053820000000000 0.012310000000000 0.005690000000000 0.095220000000000 0.618035000000000 1 +000002: 0.004565000000000 0.441800000000000 0.168610000000000 0.012845000000000 0.006835000000000 0.164985000000000 0.200360000000000 1 +000003: 0.001225000000000 0.891075000000000 0.046415000000000 0.003355000000000 0.001900000000000 0.022345000000000 0.033685000000000 1 +000004: 0.004990000000000 0.476350000000000 0.069380000000000 0.012710000000000 0.008315000000000 0.022090000000000 0.406165000000000 1 +000005: 0.000560000000000 0.929540000000000 0.015635000000000 0.002980000000000 0.002355000000000 0.006340000000000 0.042590000000000 1 +000006: 0.002390000000000 0.681470000000000 0.015560000000000 0.004795000000000 0.003725000000000 0.021685000000000 0.270375000000000 1 +000007: 0.008490000000000 0.338300000000000 0.229585000000000 0.076070000000000 0.053050000000000 0.046655000000000 0.247850000000000 1 +000008: 0.006850000000000 0.117540000000000 0.747985000000000 0.038350000000000 0.005200000000000 0.020345000000000 0.063730000000000 1 +000009: 0.012095000000000 0.455060000000000 0.241530000000000 0.048345000000000 0.008395000000000 0.137410000000000 0.097165000000000 1 +000010: 0.028315000000000 0.274620000000000 0.366060000000000 0.265950000000000 0.002695000000000 0.015995000000000 0.046365000000000 1 +000011: 0.003125000000000 0.100730000000000 0.062690000000000 0.015575000000000 0.205840000000000 0.012160000000000 0.599880000000000 1 +000012: 0.004055000000000 0.598300000000000 0.204320000000000 0.010125000000000 0.002975000000000 0.044190000000000 0.136035000000000 1 +000013: 0.006405000000000 0.374230000000000 0.182365000000000 0.097490000000000 0.007920000000000 0.028910000000000 0.302680000000000 1 +000014: 0.005675000000000 0.453770000000000 0.043540000000000 0.037510000000000 0.004250000000000 0.016635000000000 0.438620000000000 1 +000015: 0.003600000000000 0.686300000000000 0.086860000000000 0.026315000000000 0.005575000000000 0.036845000000000 0.154505000000000 1 +000016: 0.000530000000000 0.848495000000000 0.038285000000000 0.004255000000000 0.002480000000000 0.003660000000000 0.102295000000000 1 +000017: 0.001170000000000 0.601035000000000 0.333375000000000 0.010000000000000 0.002415000000000 0.013675000000000 0.038330000000000 1 +000018: 0.005125000000000 0.691710000000000 0.141525000000000 0.019010000000000 0.003465000000000 0.036660000000000 0.102505000000000 1 +000019: 0.010695000000000 0.531345000000000 0.090585000000000 0.084760000000000 0.001885000000000 0.039095000000000 0.241635000000000 1 +000020: 0.006460000000000 0.650905000000000 0.077205000000000 0.033460000000000 0.018960000000000 0.020205000000000 0.192805000000000 1 +000021: 0.003555000000000 0.142315000000000 0.383620000000000 0.046405000000000 0.003585000000000 0.087590000000000 0.332930000000000 1 +000022: 0.002810000000000 0.361215000000000 0.256475000000000 0.038830000000000 0.002655000000000 0.011645000000000 0.326370000000000 1 +000023: 0.001360000000000 0.618980000000000 0.069175000000000 0.006410000000000 0.001070000000000 0.009260000000000 0.293745000000000 1 +000024: 0.003785000000000 0.443625000000000 0.203315000000000 0.016635000000000 0.003895000000000 0.060355000000000 0.268390000000000 1 +000025: 0.001885000000000 0.569330000000000 0.180185000000000 0.007050000000000 0.003035000000000 0.009790000000000 0.228725000000000 1 +000026: 0.002705000000000 0.249560000000000 0.510180000000000 0.010185000000000 0.002140000000000 0.059390000000000 0.165840000000000 1 +000027: 0.000145000000000 0.961700000000000 0.008405000000000 0.000410000000000 0.000265000000000 0.008495000000000 0.020580000000000 1 +000028: 0.001990000000000 0.772135000000000 0.065735000000000 0.005855000000000 0.005210000000000 0.019025000000000 0.130050000000000 1 +000029: 0.002355000000000 0.703645000000000 0.116280000000000 0.008980000000000 0.004105000000000 0.029665000000000 0.134970000000000 1 +000030: 0.003445000000000 0.119590000000000 0.767995000000000 0.003940000000000 0.002600000000000 0.042925000000000 0.059505000000000 1 +000031: 0.000015000000000 0.004795000000000 0.001540000000000 0.000005000000000 0.000000000000000 0.993410000000000 0.000235000000000 1 +000032: 0.000640000000000 0.636800000000000 0.275345000000000 0.001665000000000 0.003045000000000 0.065135000000000 0.017370000000000 1 +000033: 0.001140000000000 0.063915000000000 0.839185000000000 0.002075000000000 0.000970000000000 0.076150000000000 0.016565000000000 1 +000034: 0.001275000000000 0.080545000000000 0.836375000000000 0.001985000000000 0.003630000000000 0.064540000000000 0.011650000000000 1 +000035: 0.003975000000000 0.585605000000000 0.290060000000000 0.007435000000000 0.003060000000000 0.057540000000000 0.052325000000000 1 +000036: 0.005850000000000 0.779050000000000 0.125795000000000 0.004625000000000 0.010750000000000 0.030020000000000 0.043910000000000 1 +000037: 0.002655000000000 0.712410000000000 0.089435000000000 0.005180000000000 0.002665000000000 0.043220000000000 0.144435000000000 1 +000038: 0.003135000000000 0.844610000000000 0.066435000000000 0.002200000000000 0.002445000000000 0.054655000000000 0.026520000000000 1 +000039: 0.007820000000000 0.458640000000000 0.262140000000000 0.002705000000000 0.006055000000000 0.233465000000000 0.029175000000000 1 +000040: 0.002610000000000 0.571375000000000 0.180125000000000 0.004000000000000 0.003575000000000 0.196915000000000 0.041400000000000 1 +000041: 0.006400000000000 0.784645000000000 0.053845000000000 0.004705000000000 0.004955000000000 0.087555000000000 0.057895000000000 1 +000042: 0.001220000000000 0.359700000000000 0.354655000000000 0.001535000000000 0.001435000000000 0.266215000000000 0.015240000000000 1 +000043: 0.002675000000000 0.725940000000000 0.108585000000000 0.004290000000000 0.003595000000000 0.073610000000000 0.081305000000000 1 +000044: 0.004015000000000 0.139840000000000 0.599955000000000 0.006330000000000 0.004350000000000 0.058760000000000 0.186750000000000 1 +000045: 0.018820000000000 0.493320000000000 0.036960000000000 0.020530000000000 0.021765000000000 0.128690000000000 0.279915000000000 1 +000046: 0.019520000000000 0.453695000000000 0.027085000000000 0.026425000000000 0.009670000000000 0.086505000000000 0.377100000000000 1 +000047: 0.044585000000000 0.608070000000000 0.057780000000000 0.040825000000000 0.052215000000000 0.022225000000000 0.174300000000000 1 +000048: 0.010035000000000 0.405275000000000 0.091925000000000 0.042170000000000 0.010600000000000 0.372765000000000 0.067230000000000 1 +000049: 0.009970000000000 0.599820000000000 0.074540000000000 0.033330000000000 0.018430000000000 0.047925000000000 0.215985000000000 1 +000050: 0.010890000000000 0.237695000000000 0.017620000000000 0.019710000000000 0.012300000000000 0.050850000000000 0.650935000000000 1 +000051: 0.027480000000000 0.465475000000000 0.062070000000000 0.032125000000000 0.023490000000000 0.133050000000000 0.256310000000000 1 +000052: 0.004275000000000 0.375805000000000 0.062095000000000 0.007950000000000 0.006250000000000 0.028550000000000 0.515075000000000 1 +000053: 0.012010000000000 0.274630000000000 0.245105000000000 0.020335000000000 0.002630000000000 0.024870000000000 0.420420000000000 1 +000054: 0.008340000000000 0.302585000000000 0.083310000000000 0.044880000000000 0.004580000000000 0.025500000000000 0.530805000000000 1 +000055: 0.015100000000000 0.379475000000000 0.116995000000000 0.057615000000000 0.006155000000000 0.029015000000000 0.395645000000000 1 +000056: 0.030730000000000 0.082315000000000 0.015580000000000 0.086110000000000 0.000765000000000 0.054915000000000 0.729585000000000 1 +000057: 0.013990000000000 0.456595000000000 0.061790000000000 0.061210000000000 0.003255000000000 0.003775000000000 0.399385000000000 1 +000058: 0.007630000000000 0.794725000000000 0.044395000000000 0.027660000000000 0.005130000000000 0.009070000000000 0.111390000000000 1 +000059: 0.006915000000000 0.094110000000000 0.020465000000000 0.020900000000000 0.001645000000000 0.007310000000000 0.848655000000000 1 +000060: 0.007150000000000 0.138010000000000 0.106060000000000 0.038355000000000 0.002820000000000 0.023970000000000 0.683635000000000 1 +000061: 0.005420000000000 0.728675000000000 0.068810000000000 0.045065000000000 0.003545000000000 0.009795000000000 0.138690000000000 1 +000062: 0.004040000000000 0.122120000000000 0.252235000000000 0.009880000000000 0.001810000000000 0.010975000000000 0.598940000000000 1 +000063: 0.007810000000000 0.109430000000000 0.033650000000000 0.033640000000000 0.002465000000000 0.005640000000000 0.807365000000000 1 +000064: 0.026860000000000 0.103015000000000 0.093480000000000 0.078300000000000 0.004515000000000 0.015370000000000 0.678460000000000 1 +000065: 0.000955000000000 0.045915000000000 0.012980000000000 0.005190000000000 0.002615000000000 0.012735000000000 0.919610000000000 1 +000066: 0.002405000000000 0.070945000000000 0.019550000000000 0.013345000000000 0.001465000000000 0.008565000000000 0.883725000000000 1 +000067: 0.001305000000000 0.701625000000000 0.042335000000000 0.005705000000000 0.001755000000000 0.018935000000000 0.228340000000000 1 +000068: 0.000995000000000 0.182850000000000 0.061205000000000 0.003050000000000 0.000905000000000 0.019385000000000 0.731610000000000 1 +000069: 0.001580000000000 0.884520000000000 0.027400000000000 0.003765000000000 0.001295000000000 0.007210000000000 0.074230000000000 1 +000070: 0.003115000000000 0.587675000000000 0.056685000000000 0.006040000000000 0.002965000000000 0.021630000000000 0.321890000000000 1 +000071: 0.000440000000000 0.934770000000000 0.013775000000000 0.001895000000000 0.000730000000000 0.004145000000000 0.044245000000000 1 +000072: 0.002020000000000 0.593285000000000 0.310460000000000 0.004940000000000 0.003190000000000 0.061265000000000 0.024840000000000 1 +000073: 0.002405000000000 0.261575000000000 0.404810000000000 0.003380000000000 0.001735000000000 0.217965000000000 0.108130000000000 1 +000074: 0.004060000000000 0.494225000000000 0.298720000000000 0.004365000000000 0.006510000000000 0.142775000000000 0.049345000000000 1 +000075: 0.006440000000000 0.445025000000000 0.387910000000000 0.005205000000000 0.003150000000000 0.091905000000000 0.060365000000000 1 + + + +Estimated Allele Frequencies +Cluster 01 +Locus 001 +Allele 092 0.109926522840528 +Allele 094 0.114679975793078 +Allele 096 0.106452562953521 +Allele 098 0.122262999492008 +Allele 100 0.115350181933398 +Allele 102 0.107078004901212 +Allele 104 0.112520321888918 +Allele 106 0.108166804528040 +Allele 108 0.103562625669297 + +Locus 002 +Allele 118 0.080606668860060 +Allele 122 0.080566046142954 +Allele 124 0.083875721763745 +Allele 126 0.088579397389572 +Allele 127 0.082494284514805 +Allele 128 0.082188023571273 +Allele 130 0.089753680901908 +Allele 132 0.087392751631447 +Allele 134 0.079097938093333 +Allele 135 0.084072219386881 +Allele 137 0.082028722586228 +Allele 151 0.079344545157793 + +Locus 003 +Allele 130 0.069364262330965 +Allele 133 0.068878142969063 +Allele 136 0.070684375877616 +Allele 138 0.074920154055635 +Allele 139 0.072914816351910 +Allele 141 0.069337659709527 +Allele 143 0.066561518890525 +Allele 145 0.071600494584309 +Allele 146 0.075462418231939 +Allele 147 0.070182265482205 +Allele 148 0.075560574957944 +Allele 150 0.072289280237043 +Allele 152 0.072798704499139 +Allele 156 0.069445331822179 + +Locus 004 +Allele 093 0.059076489525706 +Allele 095 0.058256428497259 +Allele 096 0.055499224573323 +Allele 097 0.059204618906232 +Allele 099 0.059961618582574 +Allele 100 0.057676653609530 +Allele 101 0.059488566361832 +Allele 103 0.060210902296120 +Allele 105 0.060354728579249 +Allele 107 0.060329247739801 +Allele 109 0.056410937738564 +Allele 110 0.057616325696137 +Allele 113 0.058926119227981 +Allele 121 0.058766105283092 +Allele 123 0.056236587217325 +Allele 125 0.060579842116735 +Allele 131 0.061405604048540 + +Locus 005 +Allele 218 0.047371243957245 +Allele 220 0.052278693992134 +Allele 222 0.051058471576408 +Allele 224 0.051102804030135 +Allele 226 0.050879011463115 +Allele 228 0.050177320575487 +Allele 230 0.049893533841547 +Allele 232 0.049592649886784 +Allele 234 0.052353013120196 +Allele 236 0.051156269534546 +Allele 238 0.052066373240193 +Allele 240 0.051706345170479 +Allele 242 0.048840658009895 +Allele 244 0.048015459367952 +Allele 246 0.049070270329252 +Allele 248 0.050103222821620 +Allele 250 0.049302931015551 +Allele 252 0.048645352254816 +Allele 254 0.048558595418492 +Allele 256 0.047827780394156 + +Locus 006 +Allele 094 0.073185178806069 +Allele 096 0.071155930985500 +Allele 098 0.075229938696668 +Allele 100 0.068878426291577 +Allele 102 0.076786420210837 +Allele 104 0.073169648273196 +Allele 106 0.075158015602782 +Allele 108 0.069087733900504 +Allele 110 0.071806609219030 +Allele 112 0.072673072723495 +Allele 114 0.067919709785183 +Allele 124 0.068804719670007 +Allele 126 0.067880709785781 +Allele 149 0.068263886049371 + +Locus 007 +Allele 202 0.060149603443301 +Allele 204 0.061285341678947 +Allele 206 0.059672601957805 +Allele 208 0.064647124225580 +Allele 210 0.062378429239149 +Allele 212 0.063863168430243 +Allele 214 0.062372836223688 +Allele 216 0.063151692349745 +Allele 218 0.066970256824604 +Allele 220 0.064362714967427 +Allele 222 0.063656065050326 +Allele 224 0.063388498840222 +Allele 226 0.061754640790115 +Allele 228 0.062655415901661 +Allele 233 0.059676740804615 +Allele 238 0.060014869272573 + +Locus 008 +Allele 121 0.089742277022798 +Allele 123 0.091000020467917 +Allele 125 0.089205015858598 +Allele 127 0.085340063462674 +Allele 129 0.092017799612890 +Allele 131 0.095522471841732 +Allele 133 0.093577966137020 +Allele 135 0.094038975380107 +Allele 137 0.096799661678695 +Allele 151 0.086131662240899 +Allele 161 0.086624086296673 + +Locus 009 +Allele 161 0.079753768596936 +Allele 165 0.079337474771243 +Allele 167 0.083049981300399 +Allele 169 0.083115139858936 +Allele 171 0.087327908865199 +Allele 173 0.090279612240222 +Allele 175 0.081803948995891 +Allele 177 0.086411054109558 +Allele 179 0.085403941105990 +Allele 181 0.082724930150695 +Allele 183 0.081676621228857 +Allele 185 0.079115618776073 + +Locus 010 +Allele 108 0.049607960526110 +Allele 115 0.047918357220021 +Allele 121 0.050907729288406 +Allele 123 0.050613310971762 +Allele 125 0.049854816060268 +Allele 127 0.050730361760545 +Allele 129 0.049267723482895 +Allele 131 0.052505797390781 +Allele 133 0.049666341530553 +Allele 135 0.051224705530625 +Allele 137 0.052291824690194 +Allele 139 0.049498699628150 +Allele 141 0.050711122046114 +Allele 143 0.050424287223349 +Allele 145 0.047768606925839 +Allele 147 0.048883409328553 +Allele 149 0.050028666736867 +Allele 152 0.049409741157243 +Allele 155 0.048409440037722 +Allele 157 0.050277098464003 + + +Cluster 02 +Locus 001 +Allele 092 0.023213633401773 +Allele 094 0.445289134387911 +Allele 096 0.045111751930830 +Allele 098 0.232253140231317 +Allele 100 0.079353603124003 +Allele 102 0.072528698435661 +Allele 104 0.060309345076436 +Allele 106 0.023194478039583 +Allele 108 0.018746215372484 + +Locus 002 +Allele 118 0.019945969455832 +Allele 122 0.026250859076801 +Allele 124 0.215762462258070 +Allele 126 0.108646959347732 +Allele 127 0.013122769781017 +Allele 128 0.046644852691369 +Allele 130 0.112457139669373 +Allele 132 0.299096424221958 +Allele 134 0.018929143738856 +Allele 135 0.061488398598971 +Allele 137 0.064138759276635 +Allele 151 0.013516261883386 + +Locus 003 +Allele 130 0.025816023939257 +Allele 133 0.014212244258307 +Allele 136 0.182961763111893 +Allele 138 0.117179038766874 +Allele 139 0.164277103387081 +Allele 141 0.026241347308172 +Allele 143 0.023721896724453 +Allele 145 0.098968821559029 +Allele 146 0.084228710409959 +Allele 147 0.012851418110298 +Allele 148 0.085481636007139 +Allele 150 0.073494633363017 +Allele 152 0.071484988991204 +Allele 156 0.019080374063317 + +Locus 004 +Allele 093 0.068002904321929 +Allele 095 0.080152186560489 +Allele 096 0.016871783115045 +Allele 097 0.214941600378018 +Allele 099 0.047501921004596 +Allele 100 0.054631899166831 +Allele 101 0.053897247037651 +Allele 103 0.176764891743644 +Allele 105 0.039633670923116 +Allele 107 0.113471776791169 +Allele 109 0.012880245218642 +Allele 110 0.034902281875718 +Allele 113 0.015957364425612 +Allele 121 0.013947623320687 +Allele 123 0.023508050236003 +Allele 125 0.016269971745993 +Allele 131 0.016664582134856 + +Locus 005 +Allele 218 0.011951393744121 +Allele 220 0.070011146224286 +Allele 222 0.171364764622539 +Allele 224 0.083811362796229 +Allele 226 0.106036352641097 +Allele 228 0.028423690775978 +Allele 230 0.042854873786554 +Allele 232 0.043873048891003 +Allele 234 0.067764010249793 +Allele 236 0.082981653078644 +Allele 238 0.072726151273913 +Allele 240 0.045022580703621 +Allele 242 0.052478664225698 +Allele 244 0.016833922807319 +Allele 246 0.025350246245335 +Allele 248 0.014927903845235 +Allele 250 0.015169874049708 +Allele 252 0.022870881219555 +Allele 254 0.013334149961818 +Allele 256 0.012213328857554 + +Locus 006 +Allele 094 0.127284550240942 +Allele 096 0.253489313857811 +Allele 098 0.031854548657702 +Allele 100 0.016028081354300 +Allele 102 0.131088826386320 +Allele 104 0.241487869862360 +Allele 106 0.038684927097693 +Allele 108 0.042502503281004 +Allele 110 0.027666869229489 +Allele 112 0.019717653460174 +Allele 114 0.018795197112019 +Allele 124 0.018530473668249 +Allele 126 0.012934178755917 +Allele 149 0.019935007036023 + +Locus 007 +Allele 202 0.017391208493960 +Allele 204 0.029980043588879 +Allele 206 0.013910725769259 +Allele 208 0.179899558697848 +Allele 210 0.024585200155269 +Allele 212 0.256278124882559 +Allele 214 0.066231303957624 +Allele 216 0.116489750993973 +Allele 218 0.040514376165416 +Allele 220 0.080104080497620 +Allele 222 0.033253380557166 +Allele 224 0.063072702159882 +Allele 226 0.028667133719841 +Allele 228 0.018714559143973 +Allele 233 0.015565648614110 +Allele 238 0.015342202602619 + +Locus 008 +Allele 121 0.087102451227462 +Allele 123 0.070419012131643 +Allele 125 0.056232182496391 +Allele 127 0.014735236567968 +Allele 129 0.068911745891897 +Allele 131 0.180105012887659 +Allele 133 0.144278631322839 +Allele 135 0.290076955860954 +Allele 137 0.053170916614410 +Allele 151 0.019199349920132 +Allele 161 0.015768505078644 + +Locus 009 +Allele 161 0.023601267736408 +Allele 165 0.049984178394257 +Allele 167 0.055080689223252 +Allele 169 0.062004565992158 +Allele 171 0.246745555717377 +Allele 173 0.165734896091444 +Allele 175 0.132011974996057 +Allele 177 0.144320588195441 +Allele 179 0.017082872348620 +Allele 181 0.054316208230377 +Allele 183 0.021751691404150 +Allele 185 0.027365511670458 + +Locus 010 +Allele 108 0.034519959268178 +Allele 115 0.012951795612387 +Allele 121 0.016163911406589 +Allele 123 0.040816230227055 +Allele 125 0.058135259773637 +Allele 127 0.113086752690241 +Allele 129 0.079836565654145 +Allele 131 0.110628041901509 +Allele 133 0.113028362505848 +Allele 135 0.078260356973707 +Allele 137 0.085473039169370 +Allele 139 0.023710147225048 +Allele 141 0.048312078071191 +Allele 143 0.013632979753228 +Allele 145 0.049572421879027 +Allele 147 0.024508235761731 +Allele 149 0.041519702466808 +Allele 152 0.025951993914873 +Allele 155 0.013210515696898 +Allele 157 0.016681650048529 + + +Cluster 03 +Locus 001 +Allele 092 0.077502693918032 +Allele 094 0.176930707244430 +Allele 096 0.147673610017821 +Allele 098 0.069628696415677 +Allele 100 0.138779975299223 +Allele 102 0.200703641836682 +Allele 104 0.057479796874615 +Allele 106 0.077079651642223 +Allele 108 0.054221226751298 + +Locus 002 +Allele 118 0.033483982271157 +Allele 122 0.033397052090392 +Allele 124 0.333290771524924 +Allele 126 0.060302930492912 +Allele 127 0.028925326805275 +Allele 128 0.041705531770307 +Allele 130 0.039579048966842 +Allele 132 0.086519895697641 +Allele 134 0.029398123619200 +Allele 135 0.164039055104917 +Allele 137 0.121381036080941 +Allele 151 0.027977245575492 + +Locus 003 +Allele 130 0.031233334634975 +Allele 133 0.027631915076263 +Allele 136 0.094448194095948 +Allele 138 0.092164459710754 +Allele 139 0.065181379221334 +Allele 141 0.063833564598226 +Allele 143 0.025912384693571 +Allele 145 0.052404827608027 +Allele 146 0.184848290147773 +Allele 147 0.027918316053976 +Allele 148 0.057779656052870 +Allele 150 0.135633230940558 +Allele 152 0.109775330025289 +Allele 156 0.031235117140435 + +Locus 004 +Allele 093 0.045799242270326 +Allele 095 0.035914082192208 +Allele 096 0.035044150195490 +Allele 097 0.116056344145598 +Allele 099 0.036291863846516 +Allele 100 0.137411042159701 +Allele 101 0.105381810022552 +Allele 103 0.085161397579378 +Allele 105 0.056004758249105 +Allele 107 0.066547093824900 +Allele 109 0.088558096676570 +Allele 110 0.030846024151210 +Allele 113 0.032981493850120 +Allele 121 0.038978107033818 +Allele 123 0.036295887157461 +Allele 125 0.026507232531195 +Allele 131 0.026221374113852 + +Locus 005 +Allele 218 0.040724696679011 +Allele 220 0.125861386587727 +Allele 222 0.084374199426964 +Allele 224 0.057703095441828 +Allele 226 0.050398437920640 +Allele 228 0.035394712426357 +Allele 230 0.045127748335394 +Allele 232 0.116998370849687 +Allele 234 0.058962180293466 +Allele 236 0.033255539300346 +Allele 238 0.054654583397871 +Allele 240 0.051559306623149 +Allele 242 0.036608283457241 +Allele 244 0.024546789111914 +Allele 246 0.024556590802800 +Allele 248 0.023893306425888 +Allele 250 0.033931656062372 +Allele 252 0.030647971941628 +Allele 254 0.031547172018229 +Allele 256 0.039253972897488 + +Locus 006 +Allele 094 0.120438313685904 +Allele 096 0.080780186727023 +Allele 098 0.033324957095261 +Allele 100 0.036024788621941 +Allele 102 0.074256975421020 +Allele 104 0.042660474958933 +Allele 106 0.316624672402058 +Allele 108 0.060674678494213 +Allele 110 0.095488787320104 +Allele 112 0.028492125275743 +Allele 114 0.030232504480731 +Allele 124 0.027456303551990 +Allele 126 0.025745435579203 +Allele 149 0.027799796385878 + +Locus 007 +Allele 202 0.027382525873026 +Allele 204 0.039362365248543 +Allele 206 0.025681840686113 +Allele 208 0.041840378382689 +Allele 210 0.035904722576813 +Allele 212 0.078136324065439 +Allele 214 0.155270438621412 +Allele 216 0.101319795837337 +Allele 218 0.103016794409594 +Allele 220 0.042086683310587 +Allele 222 0.048499109918565 +Allele 224 0.154415167212879 +Allele 226 0.050956348503604 +Allele 228 0.036891904726502 +Allele 233 0.032774681092580 +Allele 238 0.026460919534316 + +Locus 008 +Allele 121 0.045881821469018 +Allele 123 0.094378452879327 +Allele 125 0.107410989658485 +Allele 127 0.029451514165455 +Allele 129 0.040144791081766 +Allele 131 0.396247609908455 +Allele 133 0.052560609673844 +Allele 135 0.104869137129723 +Allele 137 0.059428362584515 +Allele 151 0.038686448988001 +Allele 161 0.030940262461412 + +Locus 009 +Allele 161 0.044531063019825 +Allele 165 0.040032641481314 +Allele 167 0.047287363956740 +Allele 169 0.078433269713975 +Allele 171 0.312768303821675 +Allele 173 0.103634301932684 +Allele 175 0.070747005081267 +Allele 177 0.072896296263418 +Allele 179 0.032238902228620 +Allele 181 0.071837375487856 +Allele 183 0.061186358435868 +Allele 185 0.064407118576756 + +Locus 010 +Allele 108 0.032319246442563 +Allele 115 0.027853698323231 +Allele 121 0.023369033944952 +Allele 123 0.040757952640835 +Allele 125 0.071423976639148 +Allele 127 0.032982577887094 +Allele 129 0.111298539435169 +Allele 131 0.070994043698758 +Allele 133 0.109262325887745 +Allele 135 0.146514861110952 +Allele 137 0.039893386568326 +Allele 139 0.035573182496270 +Allele 141 0.036488271523591 +Allele 143 0.030837351120588 +Allele 145 0.031384977738432 +Allele 147 0.044539131779983 +Allele 149 0.031674477411634 +Allele 152 0.026206412256798 +Allele 155 0.031370693916479 +Allele 157 0.025255859177450 + + +Cluster 04 +Locus 001 +Allele 092 0.104631729274462 +Allele 094 0.128973428632415 +Allele 096 0.109889720925623 +Allele 098 0.121533415345908 +Allele 100 0.125241149429020 +Allele 102 0.095528922182871 +Allele 104 0.101780379460466 +Allele 106 0.125468431852571 +Allele 108 0.086952822896661 + +Locus 002 +Allele 118 0.070434453880081 +Allele 122 0.074603016848696 +Allele 124 0.091262996074738 +Allele 126 0.094232591632678 +Allele 127 0.075673783808474 +Allele 128 0.083596018652832 +Allele 130 0.098033219428096 +Allele 132 0.103865129818200 +Allele 134 0.073785732979727 +Allele 135 0.076314557480656 +Allele 137 0.086994534225192 +Allele 151 0.071203965170630 + +Locus 003 +Allele 130 0.063548563643990 +Allele 133 0.063631252884648 +Allele 136 0.077385277742163 +Allele 138 0.084285662301233 +Allele 139 0.087812151466370 +Allele 141 0.068800620251758 +Allele 143 0.058112824592094 +Allele 145 0.066602202884695 +Allele 146 0.074562096991380 +Allele 147 0.064308259061409 +Allele 148 0.072997385434017 +Allele 150 0.083238728364140 +Allele 152 0.065457481308852 +Allele 156 0.069257493073249 + +Locus 004 +Allele 093 0.052992572587020 +Allele 095 0.057813550748188 +Allele 096 0.050547257006360 +Allele 097 0.059830451316222 +Allele 099 0.062182300659411 +Allele 100 0.059460594565333 +Allele 101 0.065664834261874 +Allele 103 0.081029392188443 +Allele 105 0.059985494730741 +Allele 107 0.062350720889993 +Allele 109 0.050153507299164 +Allele 110 0.054700401780180 +Allele 113 0.053178122677321 +Allele 121 0.071027273735664 +Allele 123 0.050849837653672 +Allele 125 0.054132305158210 +Allele 131 0.054101382742207 + +Locus 005 +Allele 218 0.043181534465138 +Allele 220 0.050782497385216 +Allele 222 0.055105344679808 +Allele 224 0.057620206561670 +Allele 226 0.049773656379330 +Allele 228 0.059865839716488 +Allele 230 0.049989963150725 +Allele 232 0.050000150101729 +Allele 234 0.066076755274822 +Allele 236 0.049584244964838 +Allele 238 0.052058858848190 +Allele 240 0.048638861661723 +Allele 242 0.045476535498009 +Allele 244 0.045637798868133 +Allele 246 0.045604164831367 +Allele 248 0.049790674529307 +Allele 250 0.047255443751071 +Allele 252 0.048025631015973 +Allele 254 0.043230055587349 +Allele 256 0.042301782729115 + +Locus 006 +Allele 094 0.076115483533884 +Allele 096 0.075950001341796 +Allele 098 0.080968183389555 +Allele 100 0.058405764497382 +Allele 102 0.067945125879074 +Allele 104 0.080209569133471 +Allele 106 0.108663519071251 +Allele 108 0.063331348688234 +Allele 110 0.077845820721901 +Allele 112 0.065982369935581 +Allele 114 0.061467253925294 +Allele 124 0.063845623886086 +Allele 126 0.059361244961687 +Allele 149 0.059908691034805 + +Locus 007 +Allele 202 0.058690091994146 +Allele 204 0.058246681161960 +Allele 206 0.052900548714184 +Allele 208 0.061700472769089 +Allele 210 0.059384474482630 +Allele 212 0.085610305952422 +Allele 214 0.064295911716295 +Allele 216 0.061761353661291 +Allele 218 0.065988260252234 +Allele 220 0.064041580860262 +Allele 222 0.064953224728279 +Allele 224 0.062545214835578 +Allele 226 0.072648560434772 +Allele 228 0.057072879145218 +Allele 233 0.054113172454178 +Allele 238 0.056047266837461 + +Locus 008 +Allele 121 0.091184311932563 +Allele 123 0.102186659840136 +Allele 125 0.081083624174932 +Allele 127 0.072959130569551 +Allele 129 0.087970882978435 +Allele 131 0.129677867867225 +Allele 133 0.090379411661840 +Allele 135 0.087761632123448 +Allele 137 0.104169925857530 +Allele 151 0.073641589514329 +Allele 161 0.078984963480009 + +Locus 009 +Allele 161 0.069522163136102 +Allele 165 0.071517125566931 +Allele 167 0.091193119170636 +Allele 169 0.079419423558131 +Allele 171 0.085703045851731 +Allele 173 0.115154330363578 +Allele 175 0.078259612752250 +Allele 177 0.104346669447564 +Allele 179 0.077187975052786 +Allele 181 0.076027751186806 +Allele 183 0.082073148644538 +Allele 185 0.069595635268947 + +Locus 010 +Allele 108 0.044596349048522 +Allele 115 0.042409649258352 +Allele 121 0.044547772740805 +Allele 123 0.050444888074482 +Allele 125 0.054965637627449 +Allele 127 0.047459011553919 +Allele 129 0.052219942488720 +Allele 131 0.051997098228877 +Allele 133 0.050085665529094 +Allele 135 0.052178729698421 +Allele 137 0.055037012046619 +Allele 139 0.069433371054616 +Allele 141 0.053339534688113 +Allele 143 0.057824248071095 +Allele 145 0.042314571163609 +Allele 147 0.047837573186648 +Allele 149 0.047828737621534 +Allele 152 0.044326685222670 +Allele 155 0.045864246318437 +Allele 157 0.045289276378020 + + +Cluster 05 +Locus 001 +Allele 092 0.100910602878763 +Allele 094 0.116456562795552 +Allele 096 0.103982297362311 +Allele 098 0.111042746570337 +Allele 100 0.107438521146096 +Allele 102 0.103098236464380 +Allele 104 0.106685071120238 +Allele 106 0.151699240758697 +Allele 108 0.098686720903625 + +Locus 002 +Allele 118 0.079155083365142 +Allele 122 0.080049114572719 +Allele 124 0.082803489019107 +Allele 126 0.103209955592960 +Allele 127 0.077415276564891 +Allele 128 0.092327584921194 +Allele 130 0.082580891459354 +Allele 132 0.083562382399636 +Allele 134 0.078378896938238 +Allele 135 0.083313435592923 +Allele 137 0.080102952976605 +Allele 151 0.077100936597232 + +Locus 003 +Allele 130 0.067710629549674 +Allele 133 0.066805908548135 +Allele 136 0.069760254700190 +Allele 138 0.075047508488090 +Allele 139 0.069083549572414 +Allele 141 0.067749162790251 +Allele 143 0.065997103075545 +Allele 145 0.073157378204194 +Allele 146 0.085611655250847 +Allele 147 0.066090438945521 +Allele 148 0.073042823701376 +Allele 150 0.069332334535240 +Allele 152 0.082847596262265 +Allele 156 0.067763656376258 + +Locus 004 +Allele 093 0.056418476694116 +Allele 095 0.058136280381146 +Allele 096 0.056250807566411 +Allele 097 0.058916809502185 +Allele 099 0.068710009016884 +Allele 100 0.058121948955090 +Allele 101 0.062976699143077 +Allele 103 0.061106366197921 +Allele 105 0.056946215948501 +Allele 107 0.057793361607151 +Allele 109 0.055148142699368 +Allele 110 0.057072654415877 +Allele 113 0.056826006273473 +Allele 121 0.056628230940621 +Allele 123 0.057224681679259 +Allele 125 0.060999337201773 +Allele 131 0.060723971777147 + +Locus 005 +Allele 218 0.046787021691868 +Allele 220 0.061242089528778 +Allele 222 0.049998933646203 +Allele 224 0.050220873203237 +Allele 226 0.050092132785076 +Allele 228 0.057782074455236 +Allele 230 0.050559085945756 +Allele 232 0.048284665027872 +Allele 234 0.051502659634114 +Allele 236 0.051355170779026 +Allele 238 0.048588462077016 +Allele 240 0.051940170884978 +Allele 242 0.047251822078751 +Allele 244 0.048450031906265 +Allele 246 0.047735994217022 +Allele 248 0.047931501143620 +Allele 250 0.046852407314412 +Allele 252 0.049021517016585 +Allele 254 0.047222271270006 +Allele 256 0.047181115394180 + +Locus 006 +Allele 094 0.068072710559507 +Allele 096 0.071185415648484 +Allele 098 0.085022419321786 +Allele 100 0.066717121921492 +Allele 102 0.076519199617971 +Allele 104 0.077362609948476 +Allele 106 0.069501686739977 +Allele 108 0.068122824375085 +Allele 110 0.075289479732987 +Allele 112 0.071387344985247 +Allele 114 0.066894395995742 +Allele 124 0.069034252284869 +Allele 126 0.067672535763138 +Allele 149 0.067218003105239 + +Locus 007 +Allele 202 0.057790547965636 +Allele 204 0.058497778490642 +Allele 206 0.058240534826301 +Allele 208 0.061482788475598 +Allele 210 0.061296486322277 +Allele 212 0.061319379396731 +Allele 214 0.059652299543575 +Allele 216 0.061684335205539 +Allele 218 0.064494438376517 +Allele 220 0.062729650563170 +Allele 222 0.061750600426377 +Allele 224 0.075665620312126 +Allele 226 0.079587271386199 +Allele 228 0.057583581723510 +Allele 233 0.058298081498205 +Allele 238 0.059926605487595 + +Locus 008 +Allele 121 0.086778434400097 +Allele 123 0.093453580829395 +Allele 125 0.091405680975437 +Allele 127 0.082159981483178 +Allele 129 0.085154141284795 +Allele 131 0.123626182475314 +Allele 133 0.089261716497888 +Allele 135 0.090366086466793 +Allele 137 0.090311541901910 +Allele 151 0.083029238889213 +Allele 161 0.084453414795980 + +Locus 009 +Allele 161 0.077845932543825 +Allele 165 0.079443274965226 +Allele 167 0.082902615020713 +Allele 169 0.078697883154068 +Allele 171 0.085298836876488 +Allele 173 0.092687671179869 +Allele 175 0.082877236897958 +Allele 177 0.081232417161503 +Allele 179 0.076330477824428 +Allele 181 0.080742487652852 +Allele 183 0.104664154998949 +Allele 185 0.077277011724121 + +Locus 010 +Allele 108 0.048688548928673 +Allele 115 0.047076676706298 +Allele 121 0.049667790836341 +Allele 123 0.050061571566065 +Allele 125 0.049379450602864 +Allele 127 0.050453259590347 +Allele 129 0.050578290939955 +Allele 131 0.049351439403635 +Allele 133 0.055034694608784 +Allele 135 0.048904114809110 +Allele 137 0.063634098854449 +Allele 139 0.048009821790130 +Allele 141 0.050135718179669 +Allele 143 0.048513549084527 +Allele 145 0.048144489383624 +Allele 147 0.048215767388603 +Allele 149 0.048272484794740 +Allele 152 0.049333851336080 +Allele 155 0.047954669267953 +Allele 157 0.048589711928149 + + +Cluster 06 +Locus 001 +Allele 092 0.071708317534915 +Allele 094 0.143241553656723 +Allele 096 0.078004554696390 +Allele 098 0.207753901289592 +Allele 100 0.074445344954660 +Allele 102 0.136764533851028 +Allele 104 0.147712796483316 +Allele 106 0.067535322669944 +Allele 108 0.072833674863430 + +Locus 002 +Allele 118 0.051918596424369 +Allele 122 0.056228287636375 +Allele 124 0.085966331911350 +Allele 126 0.075089831513735 +Allele 127 0.047307749825065 +Allele 128 0.061794053955350 +Allele 130 0.061645691569427 +Allele 132 0.248145740766638 +Allele 134 0.047282164227105 +Allele 135 0.150804076501977 +Allele 137 0.066636368455644 +Allele 151 0.047181107212963 + +Locus 003 +Allele 130 0.048134158423012 +Allele 133 0.043899388559281 +Allele 136 0.078101363284594 +Allele 138 0.065652748504680 +Allele 139 0.051542873678705 +Allele 141 0.075511823458979 +Allele 143 0.042572503364738 +Allele 145 0.077376597867988 +Allele 146 0.067200089566391 +Allele 147 0.043481120700594 +Allele 148 0.205496330293263 +Allele 150 0.077214171901071 +Allele 152 0.079348056160360 +Allele 156 0.044468774236342 + +Locus 004 +Allele 093 0.056384374919593 +Allele 095 0.058079254368021 +Allele 096 0.037765901105136 +Allele 097 0.062286124156039 +Allele 099 0.043977196478693 +Allele 100 0.159946499495332 +Allele 101 0.060605275215486 +Allele 103 0.066944854605203 +Allele 105 0.102013215079861 +Allele 107 0.053695498087605 +Allele 109 0.043262010257642 +Allele 110 0.046525866970695 +Allele 113 0.044993747362423 +Allele 121 0.039079258888885 +Allele 123 0.046315442421675 +Allele 125 0.039243620568403 +Allele 131 0.038881860019309 + +Locus 005 +Allele 218 0.037054480763984 +Allele 220 0.060199691170746 +Allele 222 0.059661877494523 +Allele 224 0.118962378145356 +Allele 226 0.056544797361280 +Allele 228 0.036895676308342 +Allele 230 0.080572682182438 +Allele 232 0.043056421134164 +Allele 234 0.064412841790655 +Allele 236 0.038637453588310 +Allele 238 0.046513305613132 +Allele 240 0.039352722531253 +Allele 242 0.040389565521674 +Allele 244 0.035270602636100 +Allele 246 0.048015882460570 +Allele 248 0.034491040238917 +Allele 250 0.039791423575542 +Allele 252 0.040237847443496 +Allele 254 0.043566069376713 +Allele 256 0.036373240662804 + +Locus 006 +Allele 094 0.057955991279073 +Allele 096 0.092146897605407 +Allele 098 0.050588516049629 +Allele 100 0.049113296619884 +Allele 102 0.073635514607436 +Allele 104 0.056346597991802 +Allele 106 0.239993453403329 +Allele 108 0.054373503101258 +Allele 110 0.077498918397018 +Allele 112 0.064013755599953 +Allele 114 0.046045242921752 +Allele 124 0.047321189413757 +Allele 126 0.044846517838112 +Allele 149 0.046120605171590 + +Locus 007 +Allele 202 0.041339339978119 +Allele 204 0.047663623802592 +Allele 206 0.040957371112216 +Allele 208 0.070494867582212 +Allele 210 0.053448357122442 +Allele 212 0.074439406387385 +Allele 214 0.054158884562676 +Allele 216 0.093553072515761 +Allele 218 0.053052892286491 +Allele 220 0.054497725369668 +Allele 222 0.052765187811452 +Allele 224 0.171626330341129 +Allele 226 0.047442665139602 +Allele 228 0.046614557642940 +Allele 233 0.040427704718963 +Allele 238 0.057518013626351 + +Locus 008 +Allele 121 0.065673739404708 +Allele 123 0.088985111452779 +Allele 125 0.068455336269630 +Allele 127 0.103381132996361 +Allele 129 0.066046539165629 +Allele 131 0.220009139988045 +Allele 133 0.102017467740743 +Allele 135 0.077118048546601 +Allele 137 0.089413348671848 +Allele 151 0.067494670664819 +Allele 161 0.051405465098836 + +Locus 009 +Allele 161 0.050361276516522 +Allele 165 0.056925075670063 +Allele 167 0.058281497742710 +Allele 169 0.063358940309871 +Allele 171 0.141296783178178 +Allele 173 0.086482630056551 +Allele 175 0.191688265124363 +Allele 177 0.065311737494088 +Allele 179 0.054157004159300 +Allele 181 0.086721547329122 +Allele 183 0.072732112108707 +Allele 185 0.072683130310525 + +Locus 010 +Allele 108 0.049519125543168 +Allele 115 0.033140113848429 +Allele 121 0.039775796088610 +Allele 123 0.043618506420157 +Allele 125 0.046079423609855 +Allele 127 0.038370538527746 +Allele 129 0.052152083178946 +Allele 131 0.063240870994244 +Allele 133 0.100722408834648 +Allele 135 0.118720945456007 +Allele 137 0.041921375309392 +Allele 139 0.038171931610002 +Allele 141 0.066618414784052 +Allele 143 0.033288772901071 +Allele 145 0.039581518310883 +Allele 147 0.035960577224445 +Allele 149 0.038366253610962 +Allele 152 0.043036343061903 +Allele 155 0.037420025584632 +Allele 157 0.040294975100849 + + +Cluster 07 +Locus 001 +Allele 092 0.084668580084810 +Allele 094 0.376400642729551 +Allele 096 0.059637113606618 +Allele 098 0.172763246540094 +Allele 100 0.087832070573399 +Allele 102 0.033030918886236 +Allele 104 0.109523945245830 +Allele 106 0.047675646331453 +Allele 108 0.028467836002010 + +Locus 002 +Allele 118 0.037518649262818 +Allele 122 0.062212984346654 +Allele 124 0.054356296055984 +Allele 126 0.197475596310642 +Allele 127 0.031801990315967 +Allele 128 0.232372124727390 +Allele 130 0.045532872009305 +Allele 132 0.114979840066932 +Allele 134 0.023382562362755 +Allele 135 0.102809934971790 +Allele 137 0.061765540472037 +Allele 151 0.035791609097728 + +Locus 003 +Allele 130 0.043759674117037 +Allele 133 0.029204907671370 +Allele 136 0.045786324588611 +Allele 138 0.083098059830538 +Allele 139 0.129125398573331 +Allele 141 0.042766473354587 +Allele 143 0.019727129527796 +Allele 145 0.083451128639359 +Allele 146 0.073361171511167 +Allele 147 0.031648397042789 +Allele 148 0.229733927028642 +Allele 150 0.034741152554401 +Allele 152 0.118971904111978 +Allele 156 0.034624351448394 + +Locus 004 +Allele 093 0.027043349518447 +Allele 095 0.078134738863336 +Allele 096 0.019149020881108 +Allele 097 0.127545108032182 +Allele 099 0.081917445483357 +Allele 100 0.033032783432866 +Allele 101 0.296416499978595 +Allele 103 0.075548600106846 +Allele 105 0.037580720042506 +Allele 107 0.055969817139608 +Allele 109 0.019474242401951 +Allele 110 0.023394838291847 +Allele 113 0.034651601268126 +Allele 121 0.029163042394350 +Allele 123 0.020450525947534 +Allele 125 0.020572838732757 +Allele 131 0.019954827484583 + +Locus 005 +Allele 218 0.017347535963084 +Allele 220 0.072079033030366 +Allele 222 0.060927328648290 +Allele 224 0.178672454283352 +Allele 226 0.085226073057246 +Allele 228 0.086758260001729 +Allele 230 0.042866292075921 +Allele 232 0.052345598378099 +Allele 234 0.058561671910318 +Allele 236 0.046197645792179 +Allele 238 0.087900812837626 +Allele 240 0.036446884712344 +Allele 242 0.022775274815968 +Allele 244 0.021059109722527 +Allele 246 0.019083681039450 +Allele 248 0.023840933675147 +Allele 250 0.029792626699521 +Allele 252 0.021233308864938 +Allele 254 0.018926849404821 +Allele 256 0.017958625087077 + +Locus 006 +Allele 094 0.055523179556433 +Allele 096 0.054375744942307 +Allele 098 0.076820885349215 +Allele 100 0.020044869943714 +Allele 102 0.057456737486810 +Allele 104 0.332551313067557 +Allele 106 0.055918794817330 +Allele 108 0.128408229805570 +Allele 110 0.065883562460571 +Allele 112 0.049236431942836 +Allele 114 0.021288900229245 +Allele 124 0.023457330217933 +Allele 126 0.036684721664793 +Allele 149 0.022349298515688 + +Locus 007 +Allele 202 0.023626773340780 +Allele 204 0.026738453451820 +Allele 206 0.032632764470120 +Allele 208 0.115866706002596 +Allele 210 0.091069626849783 +Allele 212 0.092334534171944 +Allele 214 0.113695015498705 +Allele 216 0.072444454493351 +Allele 218 0.063099685824507 +Allele 220 0.032589622324945 +Allele 222 0.121389230504982 +Allele 224 0.075905864776200 +Allele 226 0.064836088081435 +Allele 228 0.029288095357499 +Allele 233 0.024101054741114 +Allele 238 0.020382030110218 + +Locus 008 +Allele 121 0.131302085020387 +Allele 123 0.103769596019844 +Allele 125 0.043329028204111 +Allele 127 0.023596629548458 +Allele 129 0.073997701580968 +Allele 131 0.143511956791639 +Allele 133 0.228790254114716 +Allele 135 0.055760973595758 +Allele 137 0.131086291225824 +Allele 151 0.023851496385251 +Allele 161 0.041003987513045 + +Locus 009 +Allele 161 0.022317294868948 +Allele 165 0.030396350200488 +Allele 167 0.088687616499536 +Allele 169 0.172244957171836 +Allele 171 0.202978123520475 +Allele 173 0.238025710747865 +Allele 175 0.043074746727968 +Allele 177 0.069199054887788 +Allele 179 0.034530243199651 +Allele 181 0.029182981582118 +Allele 183 0.034397058527070 +Allele 185 0.034965862066259 + +Locus 010 +Allele 108 0.031681124183616 +Allele 115 0.027329714797333 +Allele 121 0.021009704885938 +Allele 123 0.067006176822830 +Allele 125 0.149406095426941 +Allele 127 0.039227148578901 +Allele 129 0.052070546155359 +Allele 131 0.047621303465601 +Allele 133 0.187113513334188 +Allele 135 0.041449557110408 +Allele 137 0.099154660561325 +Allele 139 0.041383409622246 +Allele 141 0.027787330544082 +Allele 143 0.017349814339581 +Allele 145 0.018404026108408 +Allele 147 0.027570615734308 +Allele 149 0.027748776274376 +Allele 152 0.020881005379917 +Allele 155 0.021631765345218 +Allele 157 0.034173711329422 + + + +Estimated Mixing Proportions +0.006716333333333 +0.459627466666667 +0.174239333333333 +0.024180533333333 +0.008711533333333 +0.068556200000000 +0.257968600000000 + + + +Estimated sigma: +k: 0 1.000000000000000 +k: 1 1.000000000000000 +k: 2 1.000000000000000 +k: 3 1.000000000000000 +k: 4 1.000000000000000 +k: 5 1.000000000000000 +k: 6 1.000000000000000 + + + +Estimated tau: +k: 0 10.000000000000000 +k: 1 10.000000000000000 +k: 2 10.000000000000000 +k: 3 10.000000000000000 +k: 4 10.000000000000000 +k: 5 10.000000000000000 +k: 6 10.000000000000000 + + + diff --git a/inst/files/tess/tess_07.txt b/inst/files/tess/tess_07.txt new file mode 100644 index 0000000..eb06927 --- /dev/null +++ b/inst/files/tess/tess_07.txt @@ -0,0 +1,1454 @@ +Estimated Clustering Probabilities for Samples +Sample ***Cluster 01*** ***Cluster 02*** ***Cluster 03*** ***Cluster 04*** ***Cluster 05*** ***Cluster 06*** ***Cluster 07*** ***Cluster 08*** +000001: 0.661455000000000 0.060990000000000 0.003800000000000 0.012715000000000 0.007520000000000 0.015240000000000 0.171930000000000 0.066350000000000 1 +000002: 0.067795000000000 0.009770000000000 0.002985000000000 0.007335000000000 0.006730000000000 0.007975000000000 0.855020000000000 0.042390000000000 1 +000003: 0.752610000000000 0.002275000000000 0.001135000000000 0.002950000000000 0.114640000000000 0.002285000000000 0.113790000000000 0.010315000000000 1 +000004: 0.399830000000000 0.065100000000000 0.007720000000000 0.022610000000000 0.008475000000000 0.021105000000000 0.392370000000000 0.082790000000000 1 +000005: 0.614410000000000 0.013430000000000 0.035360000000000 0.007220000000000 0.008330000000000 0.020730000000000 0.230185000000000 0.070335000000000 1 +000006: 0.325075000000000 0.020100000000000 0.005080000000000 0.009640000000000 0.005740000000000 0.012550000000000 0.583870000000000 0.037945000000000 1 +000007: 0.288875000000000 0.090480000000000 0.008260000000000 0.072500000000000 0.010425000000000 0.103985000000000 0.352805000000000 0.072670000000000 1 +000008: 0.156355000000000 0.025230000000000 0.003845000000000 0.005265000000000 0.003640000000000 0.020765000000000 0.756955000000000 0.027945000000000 1 +000009: 0.080005000000000 0.041320000000000 0.004670000000000 0.002650000000000 0.001870000000000 0.013520000000000 0.825335000000000 0.030630000000000 1 +000010: 0.104160000000000 0.027155000000000 0.004635000000000 0.008035000000000 0.005800000000000 0.037980000000000 0.740510000000000 0.071725000000000 1 +000011: 0.351490000000000 0.066955000000000 0.014890000000000 0.035820000000000 0.010885000000000 0.079750000000000 0.278865000000000 0.161345000000000 1 +000012: 0.687275000000000 0.028815000000000 0.016635000000000 0.011490000000000 0.009175000000000 0.129510000000000 0.072155000000000 0.044945000000000 1 +000013: 0.327860000000000 0.049140000000000 0.009165000000000 0.078390000000000 0.014135000000000 0.065400000000000 0.256590000000000 0.199320000000000 1 +000014: 0.486920000000000 0.058130000000000 0.005255000000000 0.042890000000000 0.020350000000000 0.068185000000000 0.139215000000000 0.179055000000000 1 +000015: 0.118150000000000 0.079010000000000 0.003535000000000 0.013280000000000 0.010970000000000 0.009695000000000 0.711740000000000 0.053620000000000 1 +000016: 0.090930000000000 0.005870000000000 0.001220000000000 0.002825000000000 0.003395000000000 0.007555000000000 0.852775000000000 0.035430000000000 1 +000017: 0.105505000000000 0.009300000000000 0.003340000000000 0.044615000000000 0.098845000000000 0.009635000000000 0.708335000000000 0.020425000000000 1 +000018: 0.199125000000000 0.013715000000000 0.006885000000000 0.012245000000000 0.010270000000000 0.019560000000000 0.677930000000000 0.060270000000000 1 +000019: 0.228075000000000 0.452980000000000 0.003540000000000 0.001285000000000 0.010245000000000 0.110930000000000 0.123555000000000 0.069390000000000 1 +000020: 0.061200000000000 0.022445000000000 0.009355000000000 0.003215000000000 0.006025000000000 0.037635000000000 0.800155000000000 0.059970000000000 1 +000021: 0.245930000000000 0.057175000000000 0.009205000000000 0.051420000000000 0.017170000000000 0.095210000000000 0.357910000000000 0.165980000000000 1 +000022: 0.834570000000000 0.007775000000000 0.005120000000000 0.006010000000000 0.012025000000000 0.041900000000000 0.063135000000000 0.029465000000000 1 +000023: 0.739680000000000 0.002210000000000 0.001200000000000 0.001390000000000 0.002885000000000 0.010850000000000 0.210705000000000 0.031080000000000 1 +000024: 0.041355000000000 0.001835000000000 0.000935000000000 0.001285000000000 0.006365000000000 0.016770000000000 0.912030000000000 0.019425000000000 1 +000025: 0.192845000000000 0.006840000000000 0.005670000000000 0.004290000000000 0.037150000000000 0.027415000000000 0.585490000000000 0.140300000000000 1 +000026: 0.071955000000000 0.002825000000000 0.003155000000000 0.003620000000000 0.007435000000000 0.007155000000000 0.874490000000000 0.029365000000000 1 +000027: 0.228195000000000 0.005135000000000 0.006470000000000 0.013700000000000 0.011600000000000 0.011880000000000 0.647130000000000 0.075890000000000 1 +000028: 0.132080000000000 0.005270000000000 0.004725000000000 0.004385000000000 0.009475000000000 0.011675000000000 0.766625000000000 0.065765000000000 1 +000029: 0.337680000000000 0.006940000000000 0.061720000000000 0.006075000000000 0.007310000000000 0.008315000000000 0.424985000000000 0.146975000000000 1 +000030: 0.101100000000000 0.002880000000000 0.007990000000000 0.007185000000000 0.013020000000000 0.006590000000000 0.799435000000000 0.061800000000000 1 +000031: 0.081775000000000 0.003445000000000 0.003675000000000 0.008740000000000 0.005645000000000 0.004435000000000 0.865695000000000 0.026590000000000 1 +000032: 0.193240000000000 0.003115000000000 0.004035000000000 0.006400000000000 0.006120000000000 0.004660000000000 0.765035000000000 0.017395000000000 1 +000033: 0.048225000000000 0.003185000000000 0.003035000000000 0.013265000000000 0.026995000000000 0.003360000000000 0.878675000000000 0.023260000000000 1 +000034: 0.019745000000000 0.002020000000000 0.001925000000000 0.005735000000000 0.003530000000000 0.001870000000000 0.951690000000000 0.013485000000000 1 +000035: 0.512065000000000 0.002475000000000 0.001410000000000 0.003435000000000 0.011910000000000 0.003350000000000 0.453580000000000 0.011775000000000 1 +000036: 0.159280000000000 0.009265000000000 0.004440000000000 0.003785000000000 0.026495000000000 0.004915000000000 0.754985000000000 0.036835000000000 1 +000037: 0.529700000000000 0.028075000000000 0.007560000000000 0.014675000000000 0.017560000000000 0.010425000000000 0.323875000000000 0.068130000000000 1 +000038: 0.250360000000000 0.002670000000000 0.005930000000000 0.012885000000000 0.003870000000000 0.001635000000000 0.663370000000000 0.059280000000000 1 +000039: 0.149490000000000 0.003705000000000 0.006720000000000 0.019755000000000 0.007555000000000 0.002500000000000 0.735670000000000 0.074605000000000 1 +000040: 0.121305000000000 0.001185000000000 0.004175000000000 0.010185000000000 0.001330000000000 0.000935000000000 0.783530000000000 0.077355000000000 1 +000041: 0.013565000000000 0.000255000000000 0.000345000000000 0.001040000000000 0.000445000000000 0.000820000000000 0.361210000000000 0.622320000000000 1 +000042: 0.100205000000000 0.005860000000000 0.001385000000000 0.006615000000000 0.004770000000000 0.001385000000000 0.855470000000000 0.024310000000000 1 +000043: 0.735975000000000 0.007955000000000 0.005690000000000 0.012900000000000 0.012420000000000 0.004960000000000 0.192220000000000 0.027880000000000 1 +000044: 0.218020000000000 0.004255000000000 0.001985000000000 0.006020000000000 0.003380000000000 0.004265000000000 0.705915000000000 0.056160000000000 1 +000045: 0.614100000000000 0.051660000000000 0.009680000000000 0.008280000000000 0.005960000000000 0.031405000000000 0.198565000000000 0.080350000000000 1 +000046: 0.611515000000000 0.032975000000000 0.004980000000000 0.002700000000000 0.002725000000000 0.011840000000000 0.265070000000000 0.068195000000000 1 +000047: 0.790180000000000 0.189930000000000 0.000540000000000 0.000265000000000 0.000310000000000 0.001760000000000 0.009605000000000 0.007410000000000 1 +000048: 0.210815000000000 0.041890000000000 0.045925000000000 0.035960000000000 0.010000000000000 0.040480000000000 0.552690000000000 0.062240000000000 1 +000049: 0.201360000000000 0.082315000000000 0.012400000000000 0.022605000000000 0.009630000000000 0.053385000000000 0.352130000000000 0.266175000000000 1 +000050: 0.281030000000000 0.124080000000000 0.010715000000000 0.018025000000000 0.012660000000000 0.039590000000000 0.203820000000000 0.310080000000000 1 +000051: 0.582125000000000 0.077940000000000 0.010220000000000 0.006740000000000 0.010435000000000 0.089860000000000 0.100350000000000 0.122330000000000 1 +000052: 0.330570000000000 0.024300000000000 0.010775000000000 0.007200000000000 0.005880000000000 0.017600000000000 0.336745000000000 0.266930000000000 1 +000053: 0.149270000000000 0.037780000000000 0.003710000000000 0.002940000000000 0.006155000000000 0.016160000000000 0.674900000000000 0.109085000000000 1 +000054: 0.453095000000000 0.113635000000000 0.003280000000000 0.009905000000000 0.018755000000000 0.035180000000000 0.166570000000000 0.199580000000000 1 +000055: 0.204490000000000 0.056390000000000 0.006210000000000 0.006520000000000 0.033140000000000 0.028515000000000 0.484455000000000 0.180280000000000 1 +000056: 0.540075000000000 0.032600000000000 0.007115000000000 0.006595000000000 0.008555000000000 0.019320000000000 0.122395000000000 0.263345000000000 1 +000057: 0.521950000000000 0.068780000000000 0.004460000000000 0.002600000000000 0.009720000000000 0.033415000000000 0.212950000000000 0.146125000000000 1 +000058: 0.314640000000000 0.046065000000000 0.006685000000000 0.003025000000000 0.010080000000000 0.026060000000000 0.423075000000000 0.170370000000000 1 +000059: 0.369160000000000 0.107045000000000 0.005255000000000 0.003610000000000 0.007925000000000 0.059680000000000 0.105300000000000 0.342025000000000 1 +000060: 0.230390000000000 0.115790000000000 0.007800000000000 0.010465000000000 0.014380000000000 0.061370000000000 0.291000000000000 0.268805000000000 1 +000061: 0.407480000000000 0.070155000000000 0.047450000000000 0.004310000000000 0.021120000000000 0.069030000000000 0.282930000000000 0.097525000000000 1 +000062: 0.033670000000000 0.005985000000000 0.005190000000000 0.000530000000000 0.004900000000000 0.525200000000000 0.412845000000000 0.011680000000000 1 +000063: 0.523155000000000 0.040225000000000 0.005560000000000 0.002170000000000 0.021730000000000 0.042160000000000 0.166730000000000 0.198270000000000 1 +000064: 0.071430000000000 0.020925000000000 0.003490000000000 0.001155000000000 0.004705000000000 0.046030000000000 0.043855000000000 0.808410000000000 1 +000065: 0.140840000000000 0.016640000000000 0.012720000000000 0.003465000000000 0.017680000000000 0.046935000000000 0.181060000000000 0.580660000000000 1 +000066: 0.139620000000000 0.015645000000000 0.012260000000000 0.003480000000000 0.010000000000000 0.078500000000000 0.327760000000000 0.412735000000000 1 +000067: 0.689310000000000 0.004100000000000 0.003715000000000 0.003605000000000 0.006765000000000 0.012105000000000 0.159265000000000 0.121135000000000 1 +000068: 0.332180000000000 0.009700000000000 0.006890000000000 0.007260000000000 0.013980000000000 0.010290000000000 0.124395000000000 0.495305000000000 1 +000069: 0.954150000000000 0.000895000000000 0.000725000000000 0.000875000000000 0.004490000000000 0.001505000000000 0.028025000000000 0.009335000000000 1 +000070: 0.486575000000000 0.005445000000000 0.005595000000000 0.002235000000000 0.022470000000000 0.018670000000000 0.118230000000000 0.340780000000000 1 +000071: 0.560825000000000 0.003585000000000 0.003870000000000 0.002500000000000 0.007845000000000 0.007435000000000 0.359740000000000 0.054200000000000 1 +000072: 0.228535000000000 0.002185000000000 0.003975000000000 0.012350000000000 0.004360000000000 0.005680000000000 0.714360000000000 0.028555000000000 1 +000073: 0.037710000000000 0.000770000000000 0.000815000000000 0.000875000000000 0.000690000000000 0.002055000000000 0.929795000000000 0.027290000000000 1 +000074: 0.099850000000000 0.007085000000000 0.006700000000000 0.009945000000000 0.007270000000000 0.004460000000000 0.766965000000000 0.097725000000000 1 +000075: 0.336630000000000 0.004115000000000 0.004335000000000 0.005980000000000 0.005275000000000 0.004525000000000 0.565960000000000 0.073180000000000 1 + + + +Estimated Allele Frequencies +Cluster 01 +Locus 001 +Allele 092 0.030098193676737 +Allele 094 0.335538933146174 +Allele 096 0.040297425618595 +Allele 098 0.288700222187635 +Allele 100 0.152906076291385 +Allele 102 0.048739335532038 +Allele 104 0.047503216588364 +Allele 106 0.036353864224941 +Allele 108 0.019862732734130 + +Locus 002 +Allele 118 0.023003845910317 +Allele 122 0.051796483972883 +Allele 124 0.094506839659776 +Allele 126 0.168923783293354 +Allele 127 0.018195382554374 +Allele 128 0.087876210711011 +Allele 130 0.121850214265436 +Allele 132 0.242456667266290 +Allele 134 0.022218709191037 +Allele 135 0.103026136771652 +Allele 137 0.044962380195602 +Allele 151 0.021183346208269 + +Locus 003 +Allele 130 0.043949834578795 +Allele 133 0.022672609996408 +Allele 136 0.158449815084019 +Allele 138 0.058263917894697 +Allele 139 0.109973835432259 +Allele 141 0.024884341832878 +Allele 143 0.020194269256908 +Allele 145 0.137586522150043 +Allele 146 0.063657821224429 +Allele 147 0.017211850682525 +Allele 148 0.155143288805114 +Allele 150 0.044068166710125 +Allele 152 0.116859813664643 +Allele 156 0.027083912687159 + +Locus 004 +Allele 093 0.096453938939525 +Allele 095 0.099013284245223 +Allele 096 0.017515328112232 +Allele 097 0.145000437348327 +Allele 099 0.052492504727750 +Allele 100 0.038175408347847 +Allele 101 0.122280048947974 +Allele 103 0.109398595958923 +Allele 105 0.035681390511966 +Allele 107 0.131696024452793 +Allele 109 0.018523063653961 +Allele 110 0.018669394077833 +Allele 113 0.023318053399173 +Allele 121 0.020184997806793 +Allele 123 0.021818611633801 +Allele 125 0.025263787559888 +Allele 131 0.024515130275992 + +Locus 005 +Allele 218 0.015932502488174 +Allele 220 0.071363888198606 +Allele 222 0.116423215440112 +Allele 224 0.103800611709546 +Allele 226 0.098623468738626 +Allele 228 0.026573909475456 +Allele 230 0.036464358480566 +Allele 232 0.060355992179871 +Allele 234 0.038141827663187 +Allele 236 0.092971595109467 +Allele 238 0.104680202805338 +Allele 240 0.039968584072788 +Allele 242 0.060842290139907 +Allele 244 0.016063657141489 +Allele 246 0.025875579006449 +Allele 248 0.021671360947125 +Allele 250 0.016649783034255 +Allele 252 0.021158072026218 +Allele 254 0.015629556443793 +Allele 256 0.016809544899028 + +Locus 006 +Allele 094 0.054721694089547 +Allele 096 0.115327125938080 +Allele 098 0.055241549221226 +Allele 100 0.020757090313012 +Allele 102 0.052209389801516 +Allele 104 0.459699918901828 +Allele 106 0.042773293753881 +Allele 108 0.050037194060107 +Allele 110 0.029965548610174 +Allele 112 0.039081481971587 +Allele 114 0.019600451230227 +Allele 124 0.018648659939693 +Allele 126 0.018105799368592 +Allele 149 0.023830802800531 + +Locus 007 +Allele 202 0.018647860796076 +Allele 204 0.025026823051639 +Allele 206 0.020686746603888 +Allele 208 0.198344635009007 +Allele 210 0.038295033118491 +Allele 212 0.067262826145749 +Allele 214 0.091085877030557 +Allele 216 0.087210116075765 +Allele 218 0.080308980978914 +Allele 220 0.092428630717739 +Allele 222 0.047755260041265 +Allele 224 0.085104053116460 +Allele 226 0.070478913147298 +Allele 228 0.028149970002493 +Allele 233 0.029551664024183 +Allele 238 0.019662610140477 + +Locus 008 +Allele 121 0.118349958152270 +Allele 123 0.090588235415941 +Allele 125 0.030765089174233 +Allele 127 0.020526601290446 +Allele 129 0.036190080236937 +Allele 131 0.110960544174146 +Allele 133 0.170598533007505 +Allele 135 0.314590259614212 +Allele 137 0.060474177535840 +Allele 151 0.021491036032209 +Allele 161 0.025465485366260 + +Locus 009 +Allele 161 0.023258369699536 +Allele 165 0.062114992397345 +Allele 167 0.046586223563174 +Allele 169 0.058945051363067 +Allele 171 0.241133008408801 +Allele 173 0.267473890830796 +Allele 175 0.072821629306158 +Allele 177 0.070587000504109 +Allele 179 0.029792180512639 +Allele 181 0.067613584837139 +Allele 183 0.034476870061017 +Allele 185 0.025197198516218 + +Locus 010 +Allele 108 0.032609324683071 +Allele 115 0.015457613991305 +Allele 121 0.023928724921527 +Allele 123 0.055355257926728 +Allele 125 0.084439212139224 +Allele 127 0.137260577403684 +Allele 129 0.055154057453570 +Allele 131 0.050722816904988 +Allele 133 0.117096950807883 +Allele 135 0.053598339527292 +Allele 137 0.116959423056246 +Allele 139 0.021812473851475 +Allele 141 0.031445043071945 +Allele 143 0.016729831004728 +Allele 145 0.030921907485516 +Allele 147 0.051847970460419 +Allele 149 0.031111638118630 +Allele 152 0.027486036692060 +Allele 155 0.018552782373001 +Allele 157 0.027510018126709 + + +Cluster 02 +Locus 001 +Allele 092 0.114606192991637 +Allele 094 0.162521193814962 +Allele 096 0.099084286576848 +Allele 098 0.154043770380337 +Allele 100 0.099797612477392 +Allele 102 0.082376578816341 +Allele 104 0.095870791092402 +Allele 106 0.115176883682248 +Allele 108 0.076522690167834 + +Locus 002 +Allele 118 0.070766722703107 +Allele 122 0.078965692146158 +Allele 124 0.071857815141754 +Allele 126 0.121982881269578 +Allele 127 0.060348519722943 +Allele 128 0.090375980769790 +Allele 130 0.077045132259289 +Allele 132 0.083240260717829 +Allele 134 0.066755120352394 +Allele 135 0.070559622715147 +Allele 137 0.137571101025502 +Allele 151 0.070531151176507 + +Locus 003 +Allele 130 0.057209923286729 +Allele 133 0.063394994399721 +Allele 136 0.068940037071320 +Allele 138 0.074074917450227 +Allele 139 0.077156734469664 +Allele 141 0.060320261655702 +Allele 143 0.053139366931834 +Allele 145 0.071632460499635 +Allele 146 0.117539946789708 +Allele 147 0.053787346382083 +Allele 148 0.108190749682569 +Allele 150 0.061605911563810 +Allele 152 0.070172819537817 +Allele 156 0.062834530279180 + +Locus 004 +Allele 093 0.050303763892992 +Allele 095 0.054671731853188 +Allele 096 0.047020813187464 +Allele 097 0.064139091274402 +Allele 099 0.068809833096865 +Allele 100 0.056336503905698 +Allele 101 0.069145908167195 +Allele 103 0.101816105481598 +Allele 105 0.052656587291184 +Allele 107 0.055548803885135 +Allele 109 0.046310168102498 +Allele 110 0.054866482875477 +Allele 113 0.050123944496601 +Allele 121 0.054784358833407 +Allele 123 0.046319510924125 +Allele 125 0.063267118008777 +Allele 131 0.063879274723393 + +Locus 005 +Allele 218 0.040784467842053 +Allele 220 0.051670399826865 +Allele 222 0.049761904691442 +Allele 224 0.077894697685181 +Allele 226 0.057231981393352 +Allele 228 0.045472346535080 +Allele 230 0.046903925489421 +Allele 232 0.046346886864227 +Allele 234 0.079662909832584 +Allele 236 0.053336560471161 +Allele 238 0.046851168428972 +Allele 240 0.063093507376151 +Allele 242 0.044732982186437 +Allele 244 0.041571364607584 +Allele 246 0.042510257962239 +Allele 248 0.044111410387771 +Allele 250 0.043905283860335 +Allele 252 0.043856419311966 +Allele 254 0.039952828652526 +Allele 256 0.040348696594655 + +Locus 006 +Allele 094 0.093898704523046 +Allele 096 0.084015456986168 +Allele 098 0.076167540131042 +Allele 100 0.054198457699777 +Allele 102 0.086705780624207 +Allele 104 0.091470303654701 +Allele 106 0.068438852381606 +Allele 108 0.062842756957571 +Allele 110 0.079143052245500 +Allele 112 0.074945960815657 +Allele 114 0.055483144954213 +Allele 124 0.060887651463525 +Allele 126 0.055512299236843 +Allele 149 0.056290038326144 + +Locus 007 +Allele 202 0.075897853484538 +Allele 204 0.052313619066978 +Allele 206 0.048926881072648 +Allele 208 0.068045631752091 +Allele 210 0.057170522467470 +Allele 212 0.060491333551772 +Allele 214 0.067666968760369 +Allele 216 0.060004277661472 +Allele 218 0.067407544732601 +Allele 220 0.089060115197255 +Allele 222 0.073101093469594 +Allele 224 0.060574930889370 +Allele 226 0.061640277616351 +Allele 228 0.056555750700292 +Allele 233 0.049366702529758 +Allele 238 0.051776497047443 + +Locus 008 +Allele 121 0.105936307458480 +Allele 123 0.104611381613129 +Allele 125 0.072114205810498 +Allele 127 0.067734098526967 +Allele 129 0.080721246319959 +Allele 131 0.099575704924648 +Allele 133 0.109765291680423 +Allele 135 0.088727426811428 +Allele 137 0.129443399457420 +Allele 151 0.067894280676149 +Allele 161 0.073476656720897 + +Locus 009 +Allele 161 0.066260264369514 +Allele 165 0.071254296438355 +Allele 167 0.096014042262724 +Allele 169 0.085575128781977 +Allele 171 0.103112785340264 +Allele 173 0.106953656582324 +Allele 175 0.080577026000716 +Allele 177 0.098788885211267 +Allele 179 0.068750299396221 +Allele 181 0.077590322475509 +Allele 183 0.079466457503439 +Allele 185 0.065656835637690 + +Locus 010 +Allele 108 0.045640903645261 +Allele 115 0.040280939018532 +Allele 121 0.043190833125079 +Allele 123 0.053968371952308 +Allele 125 0.056500689656468 +Allele 127 0.050930635291306 +Allele 129 0.055423419072310 +Allele 131 0.045376485676642 +Allele 133 0.057306157672839 +Allele 135 0.046168235497173 +Allele 137 0.067286849523583 +Allele 139 0.093927063906987 +Allele 141 0.046178155672600 +Allele 143 0.041645706303744 +Allele 145 0.041021041608892 +Allele 147 0.040741073368250 +Allele 149 0.042318485184682 +Allele 152 0.044127754974376 +Allele 155 0.042842448101598 +Allele 157 0.045124750747368 + + +Cluster 03 +Locus 001 +Allele 092 0.104665561828387 +Allele 094 0.118031438424618 +Allele 096 0.114761225893911 +Allele 098 0.122990593850425 +Allele 100 0.107772368978217 +Allele 102 0.111337186803969 +Allele 104 0.108623778848360 +Allele 106 0.107966550295495 +Allele 108 0.103851295076616 + +Locus 002 +Allele 118 0.077978340809217 +Allele 122 0.080550419954602 +Allele 124 0.084997903886715 +Allele 126 0.082944053307181 +Allele 127 0.077534110650849 +Allele 128 0.085096453102899 +Allele 130 0.085924626017738 +Allele 132 0.097677864025136 +Allele 134 0.082080195174756 +Allele 135 0.083935169466384 +Allele 137 0.082691792877759 +Allele 151 0.078589070726765 + +Locus 003 +Allele 130 0.069099692740643 +Allele 133 0.067665284714796 +Allele 136 0.074594901274263 +Allele 138 0.073398014174483 +Allele 139 0.077663009617360 +Allele 141 0.071064844804603 +Allele 143 0.068332832561524 +Allele 145 0.070338936657767 +Allele 146 0.070487361840071 +Allele 147 0.066963612593410 +Allele 148 0.074029256401956 +Allele 150 0.076352918887683 +Allele 152 0.071652715555205 +Allele 156 0.068356618176237 + +Locus 004 +Allele 093 0.057774272724249 +Allele 095 0.059197814193829 +Allele 096 0.055135490606511 +Allele 097 0.064271567269648 +Allele 099 0.062479741239619 +Allele 100 0.061452307779156 +Allele 101 0.060151705203843 +Allele 103 0.059935652960328 +Allele 105 0.059341322613335 +Allele 107 0.059218335497348 +Allele 109 0.057270244914596 +Allele 110 0.057050288923814 +Allele 113 0.057077631559363 +Allele 121 0.057215903974545 +Allele 123 0.060735275718369 +Allele 125 0.055364836592908 +Allele 131 0.056327608228541 + +Locus 005 +Allele 218 0.048416964260701 +Allele 220 0.050006384886905 +Allele 222 0.050966720162997 +Allele 224 0.051794484366610 +Allele 226 0.049935859363351 +Allele 228 0.050017864574699 +Allele 230 0.052441043338566 +Allele 232 0.050591328653828 +Allele 234 0.050282893941902 +Allele 236 0.050716185528138 +Allele 238 0.049424512810119 +Allele 240 0.054176708818763 +Allele 242 0.051720476815346 +Allele 244 0.047882009861260 +Allele 246 0.050502381746229 +Allele 248 0.047865726595501 +Allele 250 0.048359875149614 +Allele 252 0.050697510615307 +Allele 254 0.047045368776514 +Allele 256 0.047155699733650 + +Locus 006 +Allele 094 0.071873319179925 +Allele 096 0.074357212285054 +Allele 098 0.069738698152554 +Allele 100 0.066883272176367 +Allele 102 0.070464831180504 +Allele 104 0.078800549309729 +Allele 106 0.071580011061341 +Allele 108 0.077813287619559 +Allele 110 0.071376000894800 +Allele 112 0.070723152075587 +Allele 114 0.067740862127104 +Allele 124 0.069194459674200 +Allele 126 0.070130688441650 +Allele 149 0.069323655821628 + +Locus 007 +Allele 202 0.059227106672819 +Allele 204 0.060107733698663 +Allele 206 0.059767451253287 +Allele 208 0.062766634002912 +Allele 210 0.062622048019094 +Allele 212 0.072390302796530 +Allele 214 0.064337510255753 +Allele 216 0.061268863119073 +Allele 218 0.062650398425554 +Allele 220 0.062979214087682 +Allele 222 0.062512840066427 +Allele 224 0.063852821289253 +Allele 226 0.062402422700116 +Allele 228 0.059743888011030 +Allele 233 0.060723833915168 +Allele 238 0.062646931686638 + +Locus 008 +Allele 121 0.092923192682704 +Allele 123 0.091955728211674 +Allele 125 0.089718993897862 +Allele 127 0.084727482057921 +Allele 129 0.092940473402674 +Allele 131 0.091100274802987 +Allele 133 0.103044279506138 +Allele 135 0.095272075961631 +Allele 137 0.087048389089175 +Allele 151 0.085555398973305 +Allele 161 0.085713711413928 + +Locus 009 +Allele 161 0.078487792192376 +Allele 165 0.080904749177958 +Allele 167 0.082816922344837 +Allele 169 0.085193239945075 +Allele 171 0.081987801809670 +Allele 173 0.088096565846869 +Allele 175 0.083733601448591 +Allele 177 0.085100144572387 +Allele 179 0.079754831412719 +Allele 181 0.090022399374551 +Allele 183 0.084259408554569 +Allele 185 0.079642543320399 + +Locus 010 +Allele 108 0.052103691129728 +Allele 115 0.047898636979758 +Allele 121 0.048827361815913 +Allele 123 0.049471879076016 +Allele 125 0.052634517015124 +Allele 127 0.049406424159541 +Allele 129 0.051158236308762 +Allele 131 0.051965211185894 +Allele 133 0.051489189700454 +Allele 135 0.049210216992494 +Allele 137 0.051070601971843 +Allele 139 0.049902821184837 +Allele 141 0.052209055790613 +Allele 143 0.048418486296554 +Allele 145 0.049104080312410 +Allele 147 0.048637913419894 +Allele 149 0.051347224740408 +Allele 152 0.048427838483331 +Allele 155 0.047434241932130 +Allele 157 0.049282371504298 + + +Cluster 04 +Locus 001 +Allele 092 0.112327699754212 +Allele 094 0.116984781816149 +Allele 096 0.122003148738199 +Allele 098 0.106834602814091 +Allele 100 0.107009275064932 +Allele 102 0.109529133192088 +Allele 104 0.104331037435105 +Allele 106 0.121579551220213 +Allele 108 0.099400769965009 + +Locus 002 +Allele 118 0.077388322689293 +Allele 122 0.079593735341682 +Allele 124 0.086605987489658 +Allele 126 0.090704076019888 +Allele 127 0.074749845758395 +Allele 128 0.093201172993919 +Allele 130 0.080475845643597 +Allele 132 0.097922355917108 +Allele 134 0.075425266146903 +Allele 135 0.080926342708975 +Allele 137 0.086937269742217 +Allele 151 0.076069779548366 + +Locus 003 +Allele 130 0.066407547815598 +Allele 133 0.066008504958375 +Allele 136 0.072446552351478 +Allele 138 0.081726746928168 +Allele 139 0.070702225853711 +Allele 141 0.077700304113997 +Allele 143 0.067722052808421 +Allele 145 0.074836554553851 +Allele 146 0.069942160814781 +Allele 147 0.066123428166214 +Allele 148 0.070392831261857 +Allele 150 0.070554686431558 +Allele 152 0.070614041504127 +Allele 156 0.074822362437865 + +Locus 004 +Allele 093 0.057765772119417 +Allele 095 0.059496107712134 +Allele 096 0.058012193566093 +Allele 097 0.060820541340540 +Allele 099 0.059255188032782 +Allele 100 0.066427108147741 +Allele 101 0.063145969002271 +Allele 103 0.065651620447903 +Allele 105 0.057136480649816 +Allele 107 0.061633814671348 +Allele 109 0.056057434754073 +Allele 110 0.055935136755467 +Allele 113 0.055633936684943 +Allele 121 0.056880824799599 +Allele 123 0.056001799473723 +Allele 125 0.054524027206411 +Allele 131 0.055622044635740 + +Locus 005 +Allele 218 0.047419152988723 +Allele 220 0.052800592976065 +Allele 222 0.054178050360100 +Allele 224 0.054874216480903 +Allele 226 0.054736819361056 +Allele 228 0.050464463094385 +Allele 230 0.055309676084281 +Allele 232 0.049229574361556 +Allele 234 0.050581051412908 +Allele 236 0.053345236215564 +Allele 238 0.049027444838889 +Allele 240 0.048135399498369 +Allele 242 0.048834015232494 +Allele 244 0.047299929803245 +Allele 246 0.049512122676940 +Allele 248 0.046654823427237 +Allele 250 0.047041729060694 +Allele 252 0.047184545570911 +Allele 254 0.046248241105906 +Allele 256 0.047122915449775 + +Locus 006 +Allele 094 0.075639044258747 +Allele 096 0.083519619395685 +Allele 098 0.072318898448933 +Allele 100 0.067915894198252 +Allele 102 0.068846949262726 +Allele 104 0.072403335801777 +Allele 106 0.072063585055126 +Allele 108 0.070749039260917 +Allele 110 0.077981056380601 +Allele 112 0.068948980242221 +Allele 114 0.066597817942387 +Allele 124 0.068683169233414 +Allele 126 0.066552414883756 +Allele 149 0.067780195635459 + +Locus 007 +Allele 202 0.058490460126912 +Allele 204 0.059523848847136 +Allele 206 0.059100787872341 +Allele 208 0.061388683287017 +Allele 210 0.059303596191224 +Allele 212 0.062669337631376 +Allele 214 0.067722872664547 +Allele 216 0.062073869146443 +Allele 218 0.063157945877345 +Allele 220 0.062497536610868 +Allele 222 0.063980553379548 +Allele 224 0.069863939698224 +Allele 226 0.069884965450449 +Allele 228 0.059779219053641 +Allele 233 0.058910288916947 +Allele 238 0.061652095245983 + +Locus 008 +Allele 121 0.097376616837862 +Allele 123 0.115403417173979 +Allele 125 0.085670477779051 +Allele 127 0.083612419508375 +Allele 129 0.086988046050099 +Allele 131 0.096860100804509 +Allele 133 0.094548298942534 +Allele 135 0.085838418801125 +Allele 137 0.086108575151680 +Allele 151 0.084976391261489 +Allele 161 0.082617237689297 + +Locus 009 +Allele 161 0.082526605260110 +Allele 165 0.081034582729368 +Allele 167 0.080960371780615 +Allele 169 0.085482888124579 +Allele 171 0.083157475487014 +Allele 173 0.095677659454558 +Allele 175 0.083670254439971 +Allele 177 0.080591789926056 +Allele 179 0.077086569167336 +Allele 181 0.084032873072938 +Allele 183 0.085032505106013 +Allele 185 0.080746425451443 + +Locus 010 +Allele 108 0.048791917601659 +Allele 115 0.046225763192630 +Allele 121 0.047307221142313 +Allele 123 0.049764832488830 +Allele 125 0.054849760253209 +Allele 127 0.048514703504482 +Allele 129 0.051287867620776 +Allele 131 0.049292400775997 +Allele 133 0.054828871049016 +Allele 135 0.056492354684326 +Allele 137 0.056666681037105 +Allele 139 0.047120424830513 +Allele 141 0.049811638100088 +Allele 143 0.048231355886859 +Allele 145 0.048665604683677 +Allele 147 0.046962954132789 +Allele 149 0.049364718691840 +Allele 152 0.047971368902231 +Allele 155 0.049822418855282 +Allele 157 0.048027142566378 + + +Cluster 05 +Locus 001 +Allele 092 0.106545039224512 +Allele 094 0.133571934464985 +Allele 096 0.107391435964770 +Allele 098 0.113183741161405 +Allele 100 0.117718623343340 +Allele 102 0.108902888406114 +Allele 104 0.112447361266778 +Allele 106 0.100480975494762 +Allele 108 0.099758000673335 + +Locus 002 +Allele 118 0.082310962653929 +Allele 122 0.081580559585415 +Allele 124 0.095846073370310 +Allele 126 0.080664117191355 +Allele 127 0.074059437670508 +Allele 128 0.086111877123744 +Allele 130 0.080561767507433 +Allele 132 0.092431724701194 +Allele 134 0.076633614104798 +Allele 135 0.082468539209947 +Allele 137 0.092701032011942 +Allele 151 0.074630294869426 + +Locus 003 +Allele 130 0.069116532155508 +Allele 133 0.066565171615408 +Allele 136 0.083716020014648 +Allele 138 0.074425133272156 +Allele 139 0.075510347325423 +Allele 141 0.076390313261146 +Allele 143 0.066404297433670 +Allele 145 0.072312176534058 +Allele 146 0.071970344789846 +Allele 147 0.064688510622895 +Allele 148 0.071865627125703 +Allele 150 0.069123343090257 +Allele 152 0.071423049613011 +Allele 156 0.066489133146270 + +Locus 004 +Allele 093 0.057323296197267 +Allele 095 0.064330152325629 +Allele 096 0.063575652551750 +Allele 097 0.065168451455383 +Allele 099 0.061318130568733 +Allele 100 0.060732357850274 +Allele 101 0.060101178348351 +Allele 103 0.058801609878749 +Allele 105 0.058664185328343 +Allele 107 0.065218523132617 +Allele 109 0.055520812389722 +Allele 110 0.056084710043786 +Allele 113 0.054381314602183 +Allele 121 0.056115416585633 +Allele 123 0.055119510310019 +Allele 125 0.053412346425433 +Allele 131 0.054132352006129 + +Locus 005 +Allele 218 0.047912479037064 +Allele 220 0.051412135127244 +Allele 222 0.055503216041464 +Allele 224 0.051233871259043 +Allele 226 0.052755892099087 +Allele 228 0.049729186128295 +Allele 230 0.050386058051302 +Allele 232 0.052059704572151 +Allele 234 0.052278847371347 +Allele 236 0.062006901391503 +Allele 238 0.050238793216402 +Allele 240 0.048754915354518 +Allele 242 0.049016090481428 +Allele 244 0.046674538569931 +Allele 246 0.047481027998428 +Allele 248 0.046262104453702 +Allele 250 0.046827647236481 +Allele 252 0.046842000858675 +Allele 254 0.045442569083728 +Allele 256 0.047182021668207 + +Locus 006 +Allele 094 0.090504683000120 +Allele 096 0.073630661947961 +Allele 098 0.070400355910941 +Allele 100 0.065394219000024 +Allele 102 0.075746044639318 +Allele 104 0.083450315615510 +Allele 106 0.070370426759882 +Allele 108 0.068578606243947 +Allele 110 0.069953408483969 +Allele 112 0.067661002776271 +Allele 114 0.065197931011748 +Allele 124 0.065702445692660 +Allele 126 0.066411291241384 +Allele 149 0.066998607676266 + +Locus 007 +Allele 202 0.057272542307333 +Allele 204 0.061870570314072 +Allele 206 0.058399784228946 +Allele 208 0.064931230689886 +Allele 210 0.060843655319933 +Allele 212 0.063496044030905 +Allele 214 0.069799030183385 +Allele 216 0.066684535416352 +Allele 218 0.060951818591594 +Allele 220 0.070296767010710 +Allele 222 0.061993032094402 +Allele 224 0.068749822117351 +Allele 226 0.060554710903341 +Allele 228 0.059046497877244 +Allele 233 0.057766251719622 +Allele 238 0.057343707194924 + +Locus 008 +Allele 121 0.092376565868176 +Allele 123 0.091417350598049 +Allele 125 0.090440292268313 +Allele 127 0.082179271124094 +Allele 129 0.085520648600870 +Allele 131 0.096077576753518 +Allele 133 0.092594600078902 +Allele 135 0.109526193993897 +Allele 137 0.092522219146786 +Allele 151 0.082066554681080 +Allele 161 0.085278726886316 + +Locus 009 +Allele 161 0.088503164727573 +Allele 165 0.085457731395041 +Allele 167 0.087406658862262 +Allele 169 0.084705912838974 +Allele 171 0.085923871523647 +Allele 173 0.091485187938410 +Allele 175 0.078770763709304 +Allele 177 0.087845159021118 +Allele 179 0.076078984786917 +Allele 181 0.079589656399166 +Allele 183 0.077734031506650 +Allele 185 0.076498877290938 + +Locus 010 +Allele 108 0.047410343148683 +Allele 115 0.047523548513609 +Allele 121 0.046168399703500 +Allele 123 0.049626257192087 +Allele 125 0.052399722957529 +Allele 127 0.049784105568043 +Allele 129 0.051519185468772 +Allele 131 0.056903260535342 +Allele 133 0.055487528702209 +Allele 135 0.055005996438935 +Allele 137 0.057041809793013 +Allele 139 0.049443990816850 +Allele 141 0.047797996076142 +Allele 143 0.046670738490071 +Allele 145 0.049014489719644 +Allele 147 0.047825273956569 +Allele 149 0.047371350756736 +Allele 152 0.047021899746286 +Allele 155 0.047096451188863 +Allele 157 0.048887651227118 + + +Cluster 06 +Locus 001 +Allele 092 0.098651027339178 +Allele 094 0.150521116499503 +Allele 096 0.097190697407351 +Allele 098 0.113959053449650 +Allele 100 0.159817549557358 +Allele 102 0.086142970547989 +Allele 104 0.098788801917662 +Allele 106 0.118305510122654 +Allele 108 0.076623273158654 + +Locus 002 +Allele 118 0.068677745631342 +Allele 122 0.069448347190687 +Allele 124 0.098986278398442 +Allele 126 0.103982776602005 +Allele 127 0.066318937945193 +Allele 128 0.098838095673509 +Allele 130 0.075060680334968 +Allele 132 0.112999476387455 +Allele 134 0.070017709370377 +Allele 135 0.078616379854960 +Allele 137 0.089486529777357 +Allele 151 0.067567042833704 + +Locus 003 +Allele 130 0.059394332868144 +Allele 133 0.058032752588574 +Allele 136 0.066913570703980 +Allele 138 0.073974534357219 +Allele 139 0.072306511170079 +Allele 141 0.104317477108736 +Allele 143 0.054116600815073 +Allele 145 0.065440708435005 +Allele 146 0.068254125501373 +Allele 147 0.056852746945823 +Allele 148 0.074469540101355 +Allele 150 0.066454934639045 +Allele 152 0.115326596269850 +Allele 156 0.064145568495748 + +Locus 004 +Allele 093 0.056419821474423 +Allele 095 0.060656016920760 +Allele 096 0.047279749517615 +Allele 097 0.076550811147101 +Allele 099 0.065948922030749 +Allele 100 0.055020201324240 +Allele 101 0.075411516324181 +Allele 103 0.072185942032642 +Allele 105 0.052380559183458 +Allele 107 0.053915023532295 +Allele 109 0.047386088099930 +Allele 110 0.048141672157920 +Allele 113 0.092540274043625 +Allele 121 0.055032889045904 +Allele 123 0.047481605667778 +Allele 125 0.046770018016788 +Allele 131 0.046878889480589 + +Locus 005 +Allele 218 0.039625146342816 +Allele 220 0.048976930983523 +Allele 222 0.051075722480883 +Allele 224 0.058710518380516 +Allele 226 0.050616417710133 +Allele 228 0.056572153348241 +Allele 230 0.078976564322184 +Allele 232 0.045998398294629 +Allele 234 0.055044334999605 +Allele 236 0.046726472230445 +Allele 238 0.046664921782643 +Allele 240 0.047573616963445 +Allele 242 0.051104599822760 +Allele 244 0.042895679488030 +Allele 246 0.043485629204006 +Allele 248 0.042032957138613 +Allele 250 0.070663745613828 +Allele 252 0.041529066009785 +Allele 254 0.040712805373227 +Allele 256 0.041014319510687 + +Locus 006 +Allele 094 0.104929992516361 +Allele 096 0.077482283704815 +Allele 098 0.072287257292972 +Allele 100 0.053077904378581 +Allele 102 0.067010084977684 +Allele 104 0.120484320708172 +Allele 106 0.069124486368589 +Allele 108 0.066798761806047 +Allele 110 0.075931080913351 +Allele 112 0.064950122928783 +Allele 114 0.056141158451806 +Allele 124 0.058134879686851 +Allele 126 0.057694011754494 +Allele 149 0.055953654511493 + +Locus 007 +Allele 202 0.054859697727177 +Allele 204 0.052671409920226 +Allele 206 0.049053556115285 +Allele 208 0.066212222704360 +Allele 210 0.099474793722327 +Allele 212 0.062642107698265 +Allele 214 0.062380512919948 +Allele 216 0.056104183149815 +Allele 218 0.060328175502227 +Allele 220 0.060844662441811 +Allele 222 0.065801265519819 +Allele 224 0.088378382494001 +Allele 226 0.067283475618269 +Allele 228 0.051136601395148 +Allele 233 0.050788628707293 +Allele 238 0.052040324364029 + +Locus 008 +Allele 121 0.087212112377396 +Allele 123 0.111248343176483 +Allele 125 0.074533224968782 +Allele 127 0.067389158000969 +Allele 129 0.079915802334692 +Allele 131 0.102135779508646 +Allele 133 0.151016168175095 +Allele 135 0.087960694708003 +Allele 137 0.099208705114977 +Allele 151 0.066169042962413 +Allele 161 0.073210968672545 + +Locus 009 +Allele 161 0.063924265450864 +Allele 165 0.065863656884119 +Allele 167 0.085124397364912 +Allele 169 0.090670267574251 +Allele 171 0.101459641461653 +Allele 173 0.100113295948460 +Allele 175 0.076292276017696 +Allele 177 0.080956849064468 +Allele 179 0.065168414795099 +Allele 181 0.083309674936421 +Allele 183 0.078345393758020 +Allele 185 0.108771866744037 + +Locus 010 +Allele 108 0.044481124450141 +Allele 115 0.071270031984322 +Allele 121 0.042017590422820 +Allele 123 0.047880803569649 +Allele 125 0.055713858777919 +Allele 127 0.044351489463928 +Allele 129 0.051045562802772 +Allele 131 0.043925171209919 +Allele 133 0.082927030753518 +Allele 135 0.051942368972611 +Allele 137 0.053220799058509 +Allele 139 0.055786229372216 +Allele 141 0.045018302572290 +Allele 143 0.043863052518876 +Allele 145 0.041905234768697 +Allele 147 0.044002556657760 +Allele 149 0.043972875993579 +Allele 152 0.045127476015830 +Allele 155 0.046280030315759 +Allele 157 0.045268410318883 + + +Cluster 07 +Locus 001 +Allele 092 0.037411353090694 +Allele 094 0.393350111488914 +Allele 096 0.081107667253886 +Allele 098 0.133993087506583 +Allele 100 0.050581586320266 +Allele 102 0.147066898704463 +Allele 104 0.089277204668544 +Allele 106 0.032364018034824 +Allele 108 0.034848072931823 + +Locus 002 +Allele 118 0.019000387805215 +Allele 122 0.017490485865221 +Allele 124 0.318987089001879 +Allele 126 0.076512384051648 +Allele 127 0.012735159119779 +Allele 128 0.043875733635603 +Allele 130 0.048343978751943 +Allele 132 0.235596933148892 +Allele 134 0.014416886131399 +Allele 135 0.118879762756884 +Allele 137 0.080966535584383 +Allele 151 0.013194664147155 + +Locus 003 +Allele 130 0.014927187740656 +Allele 133 0.013158830353458 +Allele 136 0.127007313369016 +Allele 138 0.122679581606834 +Allele 139 0.129467403081310 +Allele 141 0.043187400904708 +Allele 143 0.018168970332509 +Allele 145 0.043983952191482 +Allele 146 0.150310236865344 +Allele 147 0.012582718722915 +Allele 148 0.106971539052977 +Allele 150 0.121551622457628 +Allele 152 0.081419401594938 +Allele 156 0.014583841726225 + +Locus 004 +Allele 093 0.023781631809071 +Allele 095 0.046385685612102 +Allele 096 0.017576393953075 +Allele 097 0.207907860821185 +Allele 099 0.043121434073699 +Allele 100 0.127845207977262 +Allele 101 0.095102953365234 +Allele 103 0.149255867664825 +Allele 105 0.064307634934019 +Allele 107 0.070848384935037 +Allele 109 0.041185157179906 +Allele 110 0.030205176668679 +Allele 113 0.013843064860990 +Allele 121 0.020824543880853 +Allele 123 0.024181226406963 +Allele 125 0.011744121834275 +Allele 131 0.011883654022824 + +Locus 005 +Allele 218 0.020181989732971 +Allele 220 0.116582097004664 +Allele 222 0.125679015739466 +Allele 224 0.126025322128767 +Allele 226 0.085092338219588 +Allele 228 0.048281658917649 +Allele 230 0.038397878420306 +Allele 232 0.070965257402916 +Allele 234 0.083993040237699 +Allele 236 0.032105644979444 +Allele 238 0.049759771393268 +Allele 240 0.041059873088277 +Allele 242 0.022523905459175 +Allele 244 0.019361290830911 +Allele 246 0.019957263184248 +Allele 248 0.013142112276927 +Allele 250 0.022185076166347 +Allele 252 0.023982135353711 +Allele 254 0.021622063336122 +Allele 256 0.019102266127541 + +Locus 006 +Allele 094 0.132023315470761 +Allele 096 0.212307841364113 +Allele 098 0.032861551736985 +Allele 100 0.017985372951632 +Allele 102 0.121584875636755 +Allele 104 0.033521850973082 +Allele 106 0.234285404077504 +Allele 108 0.063413316199392 +Allele 110 0.073802700333253 +Allele 112 0.015413621942175 +Allele 114 0.019038578949722 +Allele 124 0.014989245397489 +Allele 126 0.013596093291020 +Allele 149 0.015176231676119 + +Locus 007 +Allele 202 0.012820405112425 +Allele 204 0.034098391358509 +Allele 206 0.013178820295044 +Allele 208 0.069282844318865 +Allele 210 0.030791156768233 +Allele 212 0.265172535381988 +Allele 214 0.100383131819691 +Allele 216 0.143041644350167 +Allele 218 0.050138657685366 +Allele 220 0.027518502736516 +Allele 222 0.047247740159123 +Allele 224 0.136733506529584 +Allele 226 0.021596599272086 +Allele 228 0.018663306656426 +Allele 233 0.012782354257066 +Allele 238 0.016550403298910 + +Locus 008 +Allele 121 0.037289848943466 +Allele 123 0.069064046967589 +Allele 125 0.098536179706049 +Allele 127 0.026788181009149 +Allele 129 0.025832748714127 +Allele 131 0.424020380299585 +Allele 133 0.108473572227867 +Allele 135 0.104371810053857 +Allele 137 0.064711533692640 +Allele 151 0.024560665157473 +Allele 161 0.016351033228198 + +Locus 009 +Allele 161 0.022339587017406 +Allele 165 0.021264938176298 +Allele 167 0.058916809178750 +Allele 169 0.106434150031764 +Allele 171 0.320021252231460 +Allele 173 0.060588396148640 +Allele 175 0.141329893604241 +Allele 177 0.141274569101511 +Allele 179 0.016009942311158 +Allele 181 0.037610358059130 +Allele 183 0.033338950816521 +Allele 185 0.040871153323122 + +Locus 010 +Allele 108 0.031290774887391 +Allele 115 0.013207650233768 +Allele 121 0.012886847359174 +Allele 123 0.029153590732853 +Allele 125 0.076236223174458 +Allele 127 0.030928056158557 +Allele 129 0.108053021906259 +Allele 131 0.113715519488275 +Allele 133 0.172879718508275 +Allele 135 0.136854573733293 +Allele 137 0.051163393305336 +Allele 139 0.020179029988584 +Allele 141 0.057145876009446 +Allele 143 0.017925677404335 +Allele 145 0.040278668222323 +Allele 147 0.015039119380796 +Allele 149 0.027984388859936 +Allele 152 0.018233898888553 +Allele 155 0.013691932632719 +Allele 157 0.013152039125669 + + +Cluster 08 +Locus 001 +Allele 092 0.108600074320319 +Allele 094 0.338320501060808 +Allele 096 0.077198372010632 +Allele 098 0.144929446139326 +Allele 100 0.050352066872297 +Allele 102 0.054244352748836 +Allele 104 0.126622908151424 +Allele 106 0.060036459382345 +Allele 108 0.039695819314012 + +Locus 002 +Allele 118 0.049924971736925 +Allele 122 0.057574272804225 +Allele 124 0.061634201674435 +Allele 126 0.140571666034928 +Allele 127 0.058514889662540 +Allele 128 0.236449766031225 +Allele 130 0.064076744253868 +Allele 132 0.102939333013375 +Allele 134 0.037727285830473 +Allele 135 0.077151938639818 +Allele 137 0.069562766259915 +Allele 151 0.043872164058275 + +Locus 003 +Allele 130 0.050626663463826 +Allele 133 0.036961763708464 +Allele 136 0.048943347881504 +Allele 138 0.113440068620649 +Allele 139 0.152260541450400 +Allele 141 0.039534217302334 +Allele 143 0.034057343873260 +Allele 145 0.087521047773003 +Allele 146 0.054431741930305 +Allele 147 0.054939166061196 +Allele 148 0.171092019930330 +Allele 150 0.045422330960473 +Allele 152 0.067033628128583 +Allele 156 0.043736118915672 + +Locus 004 +Allele 093 0.037737035650334 +Allele 095 0.072595397568610 +Allele 096 0.028723747609842 +Allele 097 0.083692769730915 +Allele 099 0.069127007358090 +Allele 100 0.043440294243755 +Allele 101 0.253347148900856 +Allele 103 0.073904507242687 +Allele 105 0.046425440623966 +Allele 107 0.042840577731616 +Allele 109 0.032435729331295 +Allele 110 0.051558537737444 +Allele 113 0.031362584087860 +Allele 121 0.039343625640800 +Allele 123 0.036506459696294 +Allele 125 0.028395349287853 +Allele 131 0.028563787557786 + +Locus 005 +Allele 218 0.027059011169187 +Allele 220 0.054061853461452 +Allele 222 0.100313268441927 +Allele 224 0.096437677198579 +Allele 226 0.066938029344195 +Allele 228 0.081000697741326 +Allele 230 0.066740990524233 +Allele 232 0.053345722514093 +Allele 234 0.057109976256368 +Allele 236 0.042217950318884 +Allele 238 0.076127249404903 +Allele 240 0.041629450171605 +Allele 242 0.032258263043391 +Allele 244 0.028406863255812 +Allele 246 0.030159047629019 +Allele 248 0.030790876182261 +Allele 250 0.027500678311892 +Allele 252 0.031861334048540 +Allele 254 0.027655667196225 +Allele 256 0.028385393786106 + +Locus 006 +Allele 094 0.070984559496786 +Allele 096 0.077033766840484 +Allele 098 0.056434967808114 +Allele 100 0.037017917629561 +Allele 102 0.109663149249480 +Allele 104 0.185653795101414 +Allele 106 0.078555470111226 +Allele 108 0.118109400617366 +Allele 110 0.056465602956731 +Allele 112 0.047908635136258 +Allele 114 0.034962338890692 +Allele 124 0.041448738448331 +Allele 126 0.050336833034523 +Allele 149 0.035424824679034 + +Locus 007 +Allele 202 0.031215257889306 +Allele 204 0.037323998035571 +Allele 206 0.045617783529337 +Allele 208 0.140096851349849 +Allele 210 0.074825339515467 +Allele 212 0.107713932546208 +Allele 214 0.105379271888940 +Allele 216 0.053876539401553 +Allele 218 0.053440131019376 +Allele 220 0.040435726063180 +Allele 222 0.109248145514644 +Allele 224 0.047054161833464 +Allele 226 0.051029276602314 +Allele 228 0.039371941466499 +Allele 233 0.031164704784737 +Allele 238 0.032206938559555 + +Locus 008 +Allele 121 0.125785532353636 +Allele 123 0.087473870706590 +Allele 125 0.051292213765791 +Allele 127 0.038889510916527 +Allele 129 0.209320438290530 +Allele 131 0.070951152774616 +Allele 133 0.129806971117718 +Allele 135 0.065540998036951 +Allele 137 0.133749250774797 +Allele 151 0.040649689887176 +Allele 161 0.046540371375668 + +Locus 009 +Allele 161 0.036604453257698 +Allele 165 0.039318646046528 +Allele 167 0.088456668087967 +Allele 169 0.129040855472575 +Allele 171 0.106993399191927 +Allele 173 0.269354961775274 +Allele 175 0.082130503834730 +Allele 177 0.067699762264364 +Allele 179 0.047134399434735 +Allele 181 0.044465461098910 +Allele 183 0.044843376706796 +Allele 185 0.043957512828496 + +Locus 010 +Allele 108 0.043451490807866 +Allele 115 0.026205070518762 +Allele 121 0.028970168239664 +Allele 123 0.075816174515073 +Allele 125 0.110993257246084 +Allele 127 0.045410820179364 +Allele 129 0.044308032930206 +Allele 131 0.077571115311322 +Allele 133 0.096610173864586 +Allele 135 0.062550861907689 +Allele 137 0.051406574689470 +Allele 139 0.050882341179483 +Allele 141 0.034998045523475 +Allele 143 0.029216887124031 +Allele 145 0.031100847957646 +Allele 147 0.027920870832371 +Allele 149 0.054523709916941 +Allele 152 0.031664696279029 +Allele 155 0.031808024354558 +Allele 157 0.044590836622379 + + + +Estimated Mixing Proportions +0.314828866666667 +0.036389200000000 +0.007771333333333 +0.011065866666667 +0.012580200000000 +0.033619533333333 +0.456779666666667 +0.126965333333333 + + + +Estimated sigma: +k: 0 1.000000000000000 +k: 1 1.000000000000000 +k: 2 1.000000000000000 +k: 3 1.000000000000000 +k: 4 1.000000000000000 +k: 5 1.000000000000000 +k: 6 1.000000000000000 +k: 7 1.000000000000000 + + + +Estimated tau: +k: 0 10.000000000000000 +k: 1 10.000000000000000 +k: 2 10.000000000000000 +k: 3 10.000000000000000 +k: 4 10.000000000000000 +k: 5 10.000000000000000 +k: 6 10.000000000000000 +k: 7 10.000000000000000 + + + diff --git a/inst/files/tess/tess_08.txt b/inst/files/tess/tess_08.txt new file mode 100644 index 0000000..6430c4d --- /dev/null +++ b/inst/files/tess/tess_08.txt @@ -0,0 +1,434 @@ +Estimated Clustering Probabilities for Samples +Sample ***Cluster 01*** ***Cluster 02*** +000001: 0.023274000000000 0.976726000000000 1 +000002: 0.012941000000000 0.987059000000000 1 +000003: 0.005657500000000 0.994342500000000 1 +000004: 0.032876000000000 0.967124000000000 1 +000005: 0.016765500000000 0.983234500000000 1 +000006: 0.008466000000000 0.991534000000000 1 +000007: 0.290259000000000 0.709741000000000 1 +000008: 0.025965000000000 0.974035000000000 1 +000009: 0.031239000000000 0.968761000000000 1 +000010: 0.041414000000000 0.958586000000000 1 +000011: 0.079210000000000 0.920790000000000 1 +000012: 0.007966000000000 0.992034000000000 1 +000013: 0.027895000000000 0.972105000000000 1 +000014: 0.022102000000000 0.977898000000000 1 +000015: 0.022983000000000 0.977017000000000 1 +000016: 0.003942000000000 0.996058000000000 1 +000017: 0.017515000000000 0.982485000000000 1 +000018: 0.021065500000000 0.978934500000000 1 +000019: 0.102470000000000 0.897530000000000 1 +000020: 0.043616000000000 0.956384000000000 1 +000021: 0.082868000000000 0.917132000000000 1 +000022: 0.226759000000000 0.773241000000000 1 +000023: 0.004699500000000 0.995300500000000 1 +000024: 0.007406000000000 0.992594000000000 1 +000025: 0.008294500000000 0.991705500000000 1 +000026: 0.017229000000000 0.982771000000000 1 +000027: 0.011508000000000 0.988492000000000 1 +000028: 0.006210500000000 0.993789500000000 1 +000029: 0.011468500000000 0.988531500000000 1 +000030: 0.019265500000000 0.980734500000000 1 +000031: 0.006805000000000 0.993195000000000 1 +000032: 0.004432500000000 0.995567500000000 1 +000033: 0.013675000000000 0.986325000000000 1 +000034: 0.006581500000000 0.993418500000000 1 +000035: 0.016418500000000 0.983581500000000 1 +000036: 0.009070000000000 0.990930000000000 1 +000037: 0.011416500000000 0.988583500000000 1 +000038: 0.010838500000000 0.989161500000000 1 +000039: 0.008496500000000 0.991503500000000 1 +000040: 0.004946000000000 0.995054000000000 1 +000041: 0.012455000000000 0.987545000000000 1 +000042: 0.012523000000000 0.987477000000000 1 +000043: 0.008206500000000 0.991793500000000 1 +000044: 0.006300000000000 0.993700000000000 1 +000045: 0.044849000000000 0.955151000000000 1 +000046: 0.014452500000000 0.985547500000000 1 +000047: 0.056939000000000 0.943061000000000 1 +000048: 0.072207500000000 0.927792500000000 1 +000049: 0.209332000000000 0.790668000000000 1 +000050: 0.085497500000000 0.914502500000000 1 +000051: 0.102352000000000 0.897648000000000 1 +000052: 0.017294000000000 0.982706000000000 1 +000053: 0.013477000000000 0.986523000000000 1 +000054: 0.075819500000000 0.924180500000000 1 +000055: 0.035095500000000 0.964904500000000 1 +000056: 0.029497000000000 0.970503000000000 1 +000057: 0.048464500000000 0.951535500000000 1 +000058: 0.014327000000000 0.985673000000000 1 +000059: 0.108774500000000 0.891225500000000 1 +000060: 0.143939500000000 0.856060500000000 1 +000061: 0.019454500000000 0.980545500000000 1 +000062: 0.077577000000000 0.922423000000000 1 +000063: 0.046772000000000 0.953228000000000 1 +000064: 0.178795500000000 0.821204500000000 1 +000065: 0.044477000000000 0.955523000000000 1 +000066: 0.021526500000000 0.978473500000000 1 +000067: 0.005752000000000 0.994248000000000 1 +000068: 0.013397500000000 0.986602500000000 1 +000069: 0.004631500000000 0.995368500000000 1 +000070: 0.008163000000000 0.991837000000000 1 +000071: 0.004021000000000 0.995979000000000 1 +000072: 0.004850000000000 0.995150000000000 1 +000073: 0.005509500000000 0.994490500000000 1 +000074: 0.009498000000000 0.990502000000000 1 +000075: 0.006671000000000 0.993329000000000 1 + + + +Estimated Allele Frequencies +Cluster 01 +Locus 001 +Allele 092 0.121085210699183 +Allele 094 0.121825999599505 +Allele 096 0.095859454352596 +Allele 098 0.111683199269423 +Allele 100 0.122561209652237 +Allele 102 0.088334162869266 +Allele 104 0.105494330399024 +Allele 106 0.152881379877404 +Allele 108 0.080275053281363 + +Locus 002 +Allele 118 0.069823394287490 +Allele 122 0.071834925666624 +Allele 124 0.079121831777663 +Allele 126 0.149000452823660 +Allele 127 0.078950269241602 +Allele 128 0.085777071640893 +Allele 130 0.071825408918024 +Allele 132 0.089568987911619 +Allele 134 0.065484282132185 +Allele 135 0.084496534177593 +Allele 137 0.081902245531336 +Allele 151 0.072214595891316 + +Locus 003 +Allele 130 0.059434000038944 +Allele 133 0.063517545793595 +Allele 136 0.064576162819495 +Allele 138 0.096451696691375 +Allele 139 0.072117214518041 +Allele 141 0.071390603393428 +Allele 143 0.055869977101278 +Allele 145 0.087101518423523 +Allele 146 0.072675634128341 +Allele 147 0.070287665520105 +Allele 148 0.081371312298990 +Allele 150 0.063790705141652 +Allele 152 0.081703093044956 +Allele 156 0.059712871086274 + +Locus 004 +Allele 093 0.052443743671058 +Allele 095 0.052637695387834 +Allele 096 0.048186076112685 +Allele 097 0.057288682120145 +Allele 099 0.071311633269785 +Allele 100 0.056969302778689 +Allele 101 0.077724754397933 +Allele 103 0.110955639534410 +Allele 105 0.049890684339000 +Allele 107 0.051842818630043 +Allele 109 0.049650048649416 +Allele 110 0.050428796366522 +Allele 113 0.060095917201738 +Allele 121 0.057801987393699 +Allele 123 0.048042931454418 +Allele 125 0.052470336739650 +Allele 131 0.052258951952973 + +Locus 005 +Allele 218 0.042217008137908 +Allele 220 0.055281821298397 +Allele 222 0.052754946126988 +Allele 224 0.052613092000116 +Allele 226 0.051218990470738 +Allele 228 0.048745174781740 +Allele 230 0.058928700150514 +Allele 232 0.054004161609196 +Allele 234 0.065221352738768 +Allele 236 0.062955745843142 +Allele 238 0.053130658194716 +Allele 240 0.049742273356768 +Allele 242 0.042686409350706 +Allele 244 0.044199957557062 +Allele 246 0.045668893104986 +Allele 248 0.045036694785404 +Allele 250 0.048393613213637 +Allele 252 0.043616532311112 +Allele 254 0.041361808420648 +Allele 256 0.042222166547451 + +Locus 006 +Allele 094 0.068114000841937 +Allele 096 0.072239231426665 +Allele 098 0.069188312697392 +Allele 100 0.056071055545062 +Allele 102 0.068565978925168 +Allele 104 0.107157722381788 +Allele 106 0.075704721833062 +Allele 108 0.061468817556288 +Allele 110 0.106365139756145 +Allele 112 0.072294856497592 +Allele 114 0.057612352182750 +Allele 124 0.069123054047275 +Allele 126 0.059097368405710 +Allele 149 0.056997387903162 + +Locus 007 +Allele 202 0.056362289775020 +Allele 204 0.052974147332122 +Allele 206 0.050195676095665 +Allele 208 0.078471718168342 +Allele 210 0.061466027211925 +Allele 212 0.059610660507327 +Allele 214 0.062717819193073 +Allele 216 0.065958780170964 +Allele 218 0.055642293431624 +Allele 220 0.058569715303207 +Allele 222 0.074990270437168 +Allele 224 0.067042617662783 +Allele 226 0.083248512760822 +Allele 228 0.055570225638534 +Allele 233 0.060999574586556 +Allele 238 0.056179671724868 + +Locus 008 +Allele 121 0.101732596518375 +Allele 123 0.144034915336754 +Allele 125 0.076295683635188 +Allele 127 0.068096318776578 +Allele 129 0.083011496828005 +Allele 131 0.083920745839078 +Allele 133 0.100689384039409 +Allele 135 0.079285227267131 +Allele 137 0.120591151018016 +Allele 151 0.068140061962372 +Allele 161 0.074202418779091 + +Locus 009 +Allele 161 0.068066511269012 +Allele 165 0.070222014008857 +Allele 167 0.104052167617065 +Allele 169 0.082000924449691 +Allele 171 0.093494064028581 +Allele 173 0.109020199050906 +Allele 175 0.086935848284350 +Allele 177 0.077678879372131 +Allele 179 0.070691377765683 +Allele 181 0.078639243806501 +Allele 183 0.084969004343254 +Allele 185 0.074229766003971 + +Locus 010 +Allele 108 0.046119430063084 +Allele 115 0.046378875474613 +Allele 121 0.044553344643459 +Allele 123 0.054887666333652 +Allele 125 0.047867301096731 +Allele 127 0.044971776232827 +Allele 129 0.055456332986157 +Allele 131 0.045990981210722 +Allele 133 0.063232325820025 +Allele 135 0.047979628695120 +Allele 137 0.062967578478940 +Allele 139 0.055272869772013 +Allele 141 0.047642321439026 +Allele 143 0.044132790818307 +Allele 145 0.042612966534511 +Allele 147 0.060967392872702 +Allele 149 0.049926456266705 +Allele 152 0.046966673281957 +Allele 155 0.045300515761930 +Allele 157 0.046772772217523 + + +Cluster 02 +Locus 001 +Allele 092 0.041025833118816 +Allele 094 0.391278177494289 +Allele 096 0.063466572565136 +Allele 098 0.201085947676313 +Allele 100 0.086745439317740 +Allele 102 0.091078556101514 +Allele 104 0.076003842775259 +Allele 106 0.030087784698138 +Allele 108 0.019227846252800 + +Locus 002 +Allele 118 0.017987999855263 +Allele 122 0.030362782828023 +Allele 124 0.209012314116049 +Allele 126 0.121950159224107 +Allele 127 0.010546834633812 +Allele 128 0.098806900765708 +Allele 130 0.075467535535479 +Allele 132 0.233040436687880 +Allele 134 0.012262916842353 +Allele 135 0.105440041632663 +Allele 137 0.073823338807238 +Allele 151 0.011298739071424 + +Locus 003 +Allele 130 0.024527990995522 +Allele 133 0.011346375526821 +Allele 136 0.131215969929136 +Allele 138 0.101045906411455 +Allele 139 0.136496434131236 +Allele 141 0.035365106984574 +Allele 143 0.012301862155531 +Allele 145 0.083347670304444 +Allele 146 0.110927806535173 +Allele 147 0.010480996189914 +Allele 148 0.147365574271702 +Allele 150 0.080651575953705 +Allele 152 0.096853360405807 +Allele 156 0.018073370204981 + +Locus 004 +Allele 093 0.048728071302380 +Allele 095 0.073297631508606 +Allele 096 0.012033406034309 +Allele 097 0.184472689169068 +Allele 099 0.051341211985354 +Allele 100 0.085217518078817 +Allele 101 0.149643408939185 +Allele 103 0.131583958858966 +Allele 105 0.049024668374712 +Allele 107 0.092215162888074 +Allele 109 0.024248415827937 +Allele 110 0.024140203757509 +Allele 113 0.016444801157042 +Allele 121 0.016477430287749 +Allele 123 0.018280347926904 +Allele 125 0.011433626999168 +Allele 131 0.011417446904223 + +Locus 005 +Allele 218 0.011869409325829 +Allele 220 0.094650163734482 +Allele 222 0.131695911648400 +Allele 224 0.131574813268717 +Allele 226 0.095444031243840 +Allele 228 0.046993731790902 +Allele 230 0.045257081484370 +Allele 232 0.064625503874420 +Allele 234 0.068339676218079 +Allele 236 0.056806850781758 +Allele 238 0.077034303172244 +Allele 240 0.040868066090180 +Allele 242 0.036141122720749 +Allele 244 0.011467170147812 +Allele 246 0.017357458655126 +Allele 248 0.011397868353868 +Allele 250 0.016837176809315 +Allele 252 0.017683510015456 +Allele 254 0.012059046930121 +Allele 256 0.011897103734336 + +Locus 006 +Allele 094 0.106608622033759 +Allele 096 0.170132447087134 +Allele 098 0.042525343518851 +Allele 100 0.012522667801034 +Allele 102 0.100213130026593 +Allele 104 0.234798656302604 +Allele 106 0.143702388266889 +Allele 108 0.069279652484186 +Allele 110 0.049662176309007 +Allele 112 0.022998277375359 +Allele 114 0.012346054742947 +Allele 124 0.010634983676874 +Allele 126 0.012132752733236 +Allele 149 0.012442847641529 + +Locus 007 +Allele 202 0.011550090299546 +Allele 204 0.024828797525942 +Allele 206 0.012484544674403 +Allele 208 0.135839900204345 +Allele 210 0.042647976674027 +Allele 212 0.183758010939750 +Allele 214 0.106491421092706 +Allele 216 0.112285802278933 +Allele 218 0.062774540107413 +Allele 220 0.055999894411895 +Allele 222 0.059559803704371 +Allele 224 0.112226085249057 +Allele 226 0.038969448971911 +Allele 228 0.018089893653642 +Allele 233 0.010841888425162 +Allele 238 0.011651901786893 + +Locus 008 +Allele 121 0.084124440774722 +Allele 123 0.077725122601157 +Allele 125 0.058416881413901 +Allele 127 0.014781410724871 +Allele 129 0.057511712339062 +Allele 131 0.267044632837881 +Allele 133 0.152009028670656 +Allele 135 0.185426565084651 +Allele 137 0.074277150814527 +Allele 151 0.014747524044707 +Allele 161 0.013935530693866 + +Locus 009 +Allele 161 0.015186420269922 +Allele 165 0.030479814267211 +Allele 167 0.056421132984275 +Allele 169 0.099195803718109 +Allele 171 0.277707988481803 +Allele 173 0.188655484863727 +Allele 175 0.106174212408733 +Allele 177 0.108027264483229 +Allele 179 0.014741179604277 +Allele 181 0.045005863368749 +Allele 183 0.028409685702680 +Allele 185 0.029995149847293 + +Locus 010 +Allele 108 0.029713213126277 +Allele 115 0.011233192050088 +Allele 121 0.011540962440569 +Allele 123 0.046563152620476 +Allele 125 0.097355889441991 +Allele 127 0.073258479057436 +Allele 129 0.083537147668163 +Allele 131 0.091676855131341 +Allele 133 0.162007524170266 +Allele 135 0.103435012877915 +Allele 137 0.081928576972960 +Allele 139 0.027975051610747 +Allele 141 0.041784172281727 +Allele 143 0.011628668697235 +Allele 145 0.030463361344895 +Allele 147 0.020835176904397 +Allele 149 0.029125793447131 +Allele 152 0.017322739506044 +Allele 155 0.011325912396066 +Allele 157 0.017289118254274 + + + +Estimated Mixing Proportions +0.038518780000000 +0.961481220000000 + + + +Estimated sigma: +k: 0 1.000000000000000 +k: 1 1.000000000000000 + + + +Estimated psi: +k: 0 0.599999999999828 +k: 1 0.599999999999828 + + + diff --git a/inst/files/tess/tess_09.txt b/inst/files/tess/tess_09.txt new file mode 100644 index 0000000..dd889c9 --- /dev/null +++ b/inst/files/tess/tess_09.txt @@ -0,0 +1,604 @@ +Estimated Clustering Probabilities for Samples +Sample ***Cluster 01*** ***Cluster 02*** ***Cluster 03*** +000001: 0.013275000000000 0.974972500000000 0.011752500000000 1 +000002: 0.007244000000000 0.984878000000000 0.007878000000000 1 +000003: 0.003949000000000 0.992516000000000 0.003535000000000 1 +000004: 0.015657500000000 0.968584000000000 0.015758500000000 1 +000005: 0.011497500000000 0.978134000000000 0.010368500000000 1 +000006: 0.005593000000000 0.989786500000000 0.004620500000000 1 +000007: 0.112590000000000 0.780073500000000 0.107336500000000 1 +000008: 0.018929000000000 0.964234500000000 0.016836500000000 1 +000009: 0.030394500000000 0.944510500000000 0.025095000000000 1 +000010: 0.028521000000000 0.949241000000000 0.022238000000000 1 +000011: 0.040202000000000 0.929208500000000 0.030589500000000 1 +000012: 0.006784500000000 0.987544500000000 0.005671000000000 1 +000013: 0.017036500000000 0.968391000000000 0.014572500000000 1 +000014: 0.017205000000000 0.969804000000000 0.012991000000000 1 +000015: 0.014535500000000 0.971316000000000 0.014148500000000 1 +000016: 0.003092500000000 0.994204000000000 0.002703500000000 1 +000017: 0.012738500000000 0.974668000000000 0.012593500000000 1 +000018: 0.016248500000000 0.968888500000000 0.014863000000000 1 +000019: 0.086250500000000 0.847501000000000 0.066248500000000 1 +000020: 0.036080500000000 0.935907500000000 0.028012000000000 1 +000021: 0.061045000000000 0.895059500000000 0.043895500000000 1 +000022: 0.136480000000000 0.759121000000000 0.104399000000000 1 +000023: 0.004354500000000 0.992320500000000 0.003325000000000 1 +000024: 0.006528500000000 0.987930000000000 0.005541500000000 1 +000025: 0.008996500000000 0.983538500000000 0.007465000000000 1 +000026: 0.009709500000000 0.979946500000000 0.010344000000000 1 +000027: 0.008827000000000 0.983134500000000 0.008038500000000 1 +000028: 0.003926500000000 0.992546000000000 0.003527500000000 1 +000029: 0.009380000000000 0.981988000000000 0.008632000000000 1 +000030: 0.013283000000000 0.971237000000000 0.015480000000000 1 +000031: 0.005435500000000 0.989149000000000 0.005415500000000 1 +000032: 0.003354500000000 0.993477500000000 0.003168000000000 1 +000033: 0.009406000000000 0.981618500000000 0.008975500000000 1 +000034: 0.004393500000000 0.990983000000000 0.004623500000000 1 +000035: 0.008683000000000 0.982083500000000 0.009233500000000 1 +000036: 0.006840500000000 0.986268500000000 0.006891000000000 1 +000037: 0.007362000000000 0.984895000000000 0.007743000000000 1 +000038: 0.009124500000000 0.981175000000000 0.009700500000000 1 +000039: 0.008275500000000 0.981806000000000 0.009918500000000 1 +000040: 0.003120000000000 0.993243500000000 0.003636500000000 1 +000041: 0.007784500000000 0.984364000000000 0.007851500000000 1 +000042: 0.005877000000000 0.988291000000000 0.005832000000000 1 +000043: 0.006122500000000 0.987800000000000 0.006077500000000 1 +000044: 0.004918000000000 0.990405500000000 0.004676500000000 1 +000045: 0.039304500000000 0.926736000000000 0.033959500000000 1 +000046: 0.014702500000000 0.973863500000000 0.011434000000000 1 +000047: 0.047141500000000 0.913893000000000 0.038965500000000 1 +000048: 0.062304000000000 0.877852000000000 0.059844000000000 1 +000049: 0.074745500000000 0.843030500000000 0.082224000000000 1 +000050: 0.063102500000000 0.885538000000000 0.051359500000000 1 +000051: 0.084205000000000 0.851280000000000 0.064515000000000 1 +000052: 0.016326500000000 0.968951500000000 0.014722000000000 1 +000053: 0.011085000000000 0.980194000000000 0.008721000000000 1 +000054: 0.070252000000000 0.878324500000000 0.051423500000000 1 +000055: 0.021251500000000 0.960448000000000 0.018300500000000 1 +000056: 0.023316000000000 0.956778500000000 0.019905500000000 1 +000057: 0.040387000000000 0.928933000000000 0.030680000000000 1 +000058: 0.012600000000000 0.976171500000000 0.011228500000000 1 +000059: 0.093765000000000 0.846149000000000 0.060086000000000 1 +000060: 0.056809500000000 0.888820000000000 0.054370500000000 1 +000061: 0.018015000000000 0.967230500000000 0.014754500000000 1 +000062: 0.072050500000000 0.875250000000000 0.052699500000000 1 +000063: 0.031964000000000 0.941637500000000 0.026398500000000 1 +000064: 0.141371500000000 0.754763500000000 0.103865000000000 1 +000065: 0.042288000000000 0.931086000000000 0.026626000000000 1 +000066: 0.023562000000000 0.963674500000000 0.012763500000000 1 +000067: 0.004287500000000 0.992079000000000 0.003633500000000 1 +000068: 0.013241500000000 0.976086500000000 0.010672000000000 1 +000069: 0.004075000000000 0.991951000000000 0.003974000000000 1 +000070: 0.006950000000000 0.986620000000000 0.006430000000000 1 +000071: 0.003965500000000 0.992835000000000 0.003199500000000 1 +000072: 0.003029000000000 0.993690500000000 0.003280500000000 1 +000073: 0.003457000000000 0.992752500000000 0.003790500000000 1 +000074: 0.007935000000000 0.983662500000000 0.008402500000000 1 +000075: 0.005605500000000 0.988996500000000 0.005398000000000 1 + + + +Estimated Allele Frequencies +Cluster 01 +Locus 001 +Allele 092 0.124865076409309 +Allele 094 0.116052563049216 +Allele 096 0.096441469022509 +Allele 098 0.117992720339091 +Allele 100 0.121394593874818 +Allele 102 0.095643911080986 +Allele 104 0.112624977757140 +Allele 106 0.126683210400768 +Allele 108 0.088301478066165 + +Locus 002 +Allele 118 0.075881327834813 +Allele 122 0.076641134756369 +Allele 124 0.077641342213884 +Allele 126 0.121077556172154 +Allele 127 0.082124268139986 +Allele 128 0.085277450680368 +Allele 130 0.077212790662048 +Allele 132 0.084644533246479 +Allele 134 0.070786463749447 +Allele 135 0.085019521613246 +Allele 137 0.085869001246330 +Allele 151 0.077824609684876 + +Locus 003 +Allele 130 0.063810246407607 +Allele 133 0.067418712496167 +Allele 136 0.068152722612116 +Allele 138 0.078088645165639 +Allele 139 0.074727197507508 +Allele 141 0.075617819309981 +Allele 143 0.060660004932125 +Allele 145 0.077451383753108 +Allele 146 0.070968268050209 +Allele 147 0.072199427650875 +Allele 148 0.080649217120792 +Allele 150 0.066870188340010 +Allele 152 0.080229681819271 +Allele 156 0.063156484834589 + +Locus 004 +Allele 093 0.054940816340650 +Allele 095 0.056563690905710 +Allele 096 0.051639631916241 +Allele 097 0.059741588381756 +Allele 099 0.062679575702785 +Allele 100 0.058990279536969 +Allele 101 0.076283607105407 +Allele 103 0.082663536390719 +Allele 105 0.052942164540993 +Allele 107 0.054645697347311 +Allele 109 0.052503380353240 +Allele 110 0.052969095225833 +Allele 113 0.063399384905493 +Allele 121 0.057471914872401 +Allele 123 0.051463711624321 +Allele 125 0.055426714977250 +Allele 131 0.055675209872920 + +Locus 005 +Allele 218 0.043987913061326 +Allele 220 0.050093747910004 +Allele 222 0.052880299979595 +Allele 224 0.052636626680545 +Allele 226 0.053351497226686 +Allele 228 0.050516768612336 +Allele 230 0.054242889806026 +Allele 232 0.052570088530968 +Allele 234 0.057372662331714 +Allele 236 0.055811962916219 +Allele 238 0.053430543902556 +Allele 240 0.049298433656030 +Allele 242 0.045266336272569 +Allele 244 0.047059127026533 +Allele 246 0.048488646408872 +Allele 248 0.047272239877403 +Allele 250 0.051220314695648 +Allele 252 0.046300087096000 +Allele 254 0.043770850256144 +Allele 256 0.044428963752824 + +Locus 006 +Allele 094 0.071043547384714 +Allele 096 0.068863557063709 +Allele 098 0.072530484588040 +Allele 100 0.060291011925693 +Allele 102 0.071572455343047 +Allele 104 0.099456293987345 +Allele 106 0.076947238672106 +Allele 108 0.066591303972710 +Allele 110 0.082190068781854 +Allele 112 0.074991618879747 +Allele 114 0.061968151453902 +Allele 124 0.068228450605374 +Allele 126 0.064651110464736 +Allele 149 0.060674706877026 + +Locus 007 +Allele 202 0.059935826027120 +Allele 204 0.056078505004871 +Allele 206 0.054195101869714 +Allele 208 0.070044822924128 +Allele 210 0.066276668031591 +Allele 212 0.061010975632554 +Allele 214 0.064451198548253 +Allele 216 0.060164652793734 +Allele 218 0.058511868976583 +Allele 220 0.061204351693931 +Allele 222 0.075375264900128 +Allele 224 0.062025197557837 +Allele 226 0.070935421833640 +Allele 228 0.058728209000538 +Allele 233 0.061393418375172 +Allele 238 0.059668516830203 + +Locus 008 +Allele 121 0.089517791867792 +Allele 123 0.113546963425836 +Allele 125 0.083013396944636 +Allele 127 0.074116858126152 +Allele 129 0.087501868311475 +Allele 131 0.086783489863356 +Allele 133 0.101275078056686 +Allele 135 0.084728077841728 +Allele 137 0.125792221325047 +Allele 151 0.074698172647698 +Allele 161 0.079026081589592 + +Locus 009 +Allele 161 0.072179226073506 +Allele 165 0.072779780991964 +Allele 167 0.091570955286957 +Allele 169 0.081755190350956 +Allele 171 0.093915882300166 +Allele 173 0.103962895565015 +Allele 175 0.082329453071055 +Allele 177 0.080788606084288 +Allele 179 0.074685062878345 +Allele 181 0.081699442615597 +Allele 183 0.085063838080311 +Allele 185 0.079269666701837 + +Locus 010 +Allele 108 0.048416892162207 +Allele 115 0.048746967738988 +Allele 121 0.046914204150140 +Allele 123 0.053004071806519 +Allele 125 0.049276177595209 +Allele 127 0.047266473132321 +Allele 129 0.051325624173896 +Allele 131 0.047602004519831 +Allele 133 0.053161092959162 +Allele 135 0.048142586273300 +Allele 137 0.055954635076716 +Allele 139 0.057427329128775 +Allele 141 0.050108502385826 +Allele 143 0.045521781001248 +Allele 145 0.044215305695871 +Allele 147 0.057024451499625 +Allele 149 0.050392410223812 +Allele 152 0.049333433086277 +Allele 155 0.046959246095259 +Allele 157 0.049206811295017 + + +Cluster 02 +Locus 001 +Allele 092 0.038807086022118 +Allele 094 0.394695364058600 +Allele 096 0.064027470422019 +Allele 098 0.200635270674173 +Allele 100 0.086287646953818 +Allele 102 0.091162273329189 +Allele 104 0.074564488946199 +Allele 106 0.030745762751341 +Allele 108 0.019074636842544 + +Locus 002 +Allele 118 0.017273753860876 +Allele 122 0.030022628320376 +Allele 124 0.210626472812369 +Allele 126 0.122518610580035 +Allele 127 0.009639424371759 +Allele 128 0.098992462339505 +Allele 130 0.074841170794730 +Allele 132 0.234803331105432 +Allele 134 0.011911244597580 +Allele 135 0.105682471807628 +Allele 137 0.073114895150137 +Allele 151 0.010573534259570 + +Locus 003 +Allele 130 0.024308727532536 +Allele 133 0.010637199993106 +Allele 136 0.131380177294169 +Allele 138 0.102734948039910 +Allele 139 0.136345372477507 +Allele 141 0.034105914324697 +Allele 143 0.012196017989201 +Allele 145 0.084216964764432 +Allele 146 0.111553008269049 +Allele 147 0.009595500977876 +Allele 148 0.147615271962808 +Allele 150 0.080793614772815 +Allele 152 0.096601899959795 +Allele 156 0.017915381642088 + +Locus 004 +Allele 093 0.048615456435284 +Allele 095 0.073005227254980 +Allele 096 0.011923337969950 +Allele 097 0.185167388798170 +Allele 099 0.052302147323346 +Allele 100 0.084845623785124 +Allele 101 0.149105940971765 +Allele 103 0.133881284864419 +Allele 105 0.049053410040124 +Allele 107 0.092557445880507 +Allele 109 0.024082446210965 +Allele 110 0.024026727443678 +Allele 113 0.015037460282532 +Allele 121 0.016494636505409 +Allele 123 0.018180410007989 +Allele 125 0.010896954057390 +Allele 131 0.010824102168369 + +Locus 005 +Allele 218 0.011874557184510 +Allele 220 0.095957017445477 +Allele 222 0.132016041436957 +Allele 224 0.131947654368644 +Allele 226 0.095365202099761 +Allele 228 0.046734323589335 +Allele 230 0.045509015045765 +Allele 232 0.064397620346815 +Allele 234 0.068889944064206 +Allele 236 0.057251883500139 +Allele 238 0.076823010156850 +Allele 240 0.041009135452395 +Allele 242 0.036139229683068 +Allele 244 0.011106555897603 +Allele 246 0.016770375401217 +Allele 248 0.010981141939221 +Allele 250 0.015968775354025 +Allele 252 0.017337995229065 +Allele 254 0.012088816807683 +Allele 256 0.011831704997264 + +Locus 006 +Allele 094 0.106464149372734 +Allele 096 0.171393979911185 +Allele 098 0.041784970382899 +Allele 100 0.012516329757420 +Allele 102 0.099887748207055 +Allele 104 0.234854859504830 +Allele 106 0.143991924345775 +Allele 108 0.069046736928963 +Allele 110 0.051423645996354 +Allele 112 0.021825252698391 +Allele 114 0.012167584431025 +Allele 124 0.010532355120801 +Allele 126 0.011678570767083 +Allele 149 0.012431892575478 + +Locus 007 +Allele 202 0.010858560850867 +Allele 204 0.024760301853165 +Allele 206 0.012364604015908 +Allele 208 0.137024780505455 +Allele 210 0.041520889705010 +Allele 212 0.184864689699660 +Allele 214 0.106475818783743 +Allele 216 0.113872954502654 +Allele 218 0.062674164502475 +Allele 220 0.055610449744260 +Allele 222 0.058229614244391 +Allele 224 0.113384057143151 +Allele 226 0.039519950520696 +Allele 228 0.017546794365403 +Allele 233 0.010462583040474 +Allele 238 0.010829786522692 + +Locus 008 +Allele 121 0.085948431927200 +Allele 123 0.079583800936942 +Allele 125 0.058040937300589 +Allele 127 0.014769606614047 +Allele 129 0.056772038983722 +Allele 131 0.268531371360500 +Allele 133 0.151812902575437 +Allele 135 0.186069242602749 +Allele 137 0.070362994614061 +Allele 151 0.014634933799036 +Allele 161 0.013473739285717 + +Locus 009 +Allele 161 0.015102604330148 +Allele 165 0.030667883053342 +Allele 167 0.056997962044007 +Allele 169 0.099570783254045 +Allele 171 0.278653790739316 +Allele 173 0.188904291869373 +Allele 175 0.107156221421411 +Allele 177 0.107677845669658 +Allele 179 0.014382480484715 +Allele 181 0.044175259874705 +Allele 183 0.027432684662332 +Allele 185 0.029278192596957 + +Locus 010 +Allele 108 0.029351094839218 +Allele 115 0.010555236603636 +Allele 121 0.011089618691549 +Allele 123 0.046449055804471 +Allele 125 0.097512382413422 +Allele 127 0.073412729417044 +Allele 129 0.084489069500992 +Allele 131 0.091855643231405 +Allele 133 0.164896326315773 +Allele 135 0.104147603371347 +Allele 137 0.082729075010939 +Allele 139 0.026705642609824 +Allele 141 0.041188267860206 +Allele 143 0.011462480800523 +Allele 145 0.030573805890253 +Allele 147 0.020501481154962 +Allele 149 0.028708707292858 +Allele 152 0.016716565102015 +Allele 155 0.011017832017639 +Allele 157 0.016637382071927 + + +Cluster 03 +Locus 001 +Allele 092 0.121398870040308 +Allele 094 0.114021469299776 +Allele 096 0.100516976757846 +Allele 098 0.117007453061219 +Allele 100 0.117170203023205 +Allele 102 0.098326607415167 +Allele 104 0.111672486374047 +Allele 106 0.128269146034721 +Allele 108 0.091616787993710 + +Locus 002 +Allele 118 0.076776310399725 +Allele 122 0.078025014919657 +Allele 124 0.080247087538312 +Allele 126 0.113452959997067 +Allele 127 0.081436139251337 +Allele 128 0.084390668559680 +Allele 130 0.078957432281033 +Allele 132 0.086129229013196 +Allele 134 0.072989275559085 +Allele 135 0.084124291914430 +Allele 137 0.085950708564419 +Allele 151 0.077520882002060 + +Locus 003 +Allele 130 0.064971956073415 +Allele 133 0.067959578376043 +Allele 136 0.069433019938897 +Allele 138 0.080892730526571 +Allele 139 0.073141508334869 +Allele 141 0.074872051948719 +Allele 143 0.061990237946297 +Allele 145 0.077378784380590 +Allele 146 0.071624377081395 +Allele 147 0.071676204980044 +Allele 148 0.077105496366343 +Allele 150 0.067913578492620 +Allele 152 0.076751127958341 +Allele 156 0.064289347595856 + +Locus 004 +Allele 093 0.055651463118240 +Allele 095 0.056703636569500 +Allele 096 0.052338475206261 +Allele 097 0.059025594012486 +Allele 099 0.063070032386754 +Allele 100 0.060105390776755 +Allele 101 0.069725325052623 +Allele 103 0.079721787976338 +Allele 105 0.054056824548702 +Allele 107 0.055525334793602 +Allele 109 0.054385194918884 +Allele 110 0.054423306767447 +Allele 113 0.062406030849881 +Allele 121 0.057757762727110 +Allele 123 0.052856699852120 +Allele 125 0.056012968830935 +Allele 131 0.056234171612358 + +Locus 005 +Allele 218 0.045261598535810 +Allele 220 0.050537998940949 +Allele 222 0.052532084145116 +Allele 224 0.051552971964876 +Allele 226 0.051488292540334 +Allele 228 0.049499931804227 +Allele 230 0.053765415129169 +Allele 232 0.052171700407122 +Allele 234 0.057106308129415 +Allele 236 0.055845419027120 +Allele 238 0.052089413706304 +Allele 240 0.049707244547470 +Allele 242 0.046298289783965 +Allele 244 0.047232010676332 +Allele 246 0.049219223375981 +Allele 248 0.047500390648119 +Allele 250 0.050412360266889 +Allele 252 0.047288119876795 +Allele 254 0.044678481836978 +Allele 256 0.045812744657030 + +Locus 006 +Allele 094 0.071668183804375 +Allele 096 0.070346954410189 +Allele 098 0.071352118256572 +Allele 100 0.062244772541661 +Allele 102 0.071315272255293 +Allele 104 0.089643713813239 +Allele 106 0.075091381344312 +Allele 108 0.067156928945284 +Allele 110 0.084058199822147 +Allele 112 0.075445546394947 +Allele 114 0.063462694178304 +Allele 124 0.070057438242231 +Allele 126 0.065263310425051 +Allele 149 0.062893485566394 + +Locus 007 +Allele 202 0.060038170886271 +Allele 204 0.057178814212858 +Allele 206 0.055336392279670 +Allele 208 0.069509696672446 +Allele 210 0.064511749857326 +Allele 212 0.060753642832708 +Allele 214 0.063471972849225 +Allele 216 0.062139993117206 +Allele 218 0.059881268955319 +Allele 220 0.061599744379609 +Allele 222 0.071684888789338 +Allele 224 0.062462038585712 +Allele 226 0.070532904941616 +Allele 228 0.058968524355397 +Allele 233 0.060874240768270 +Allele 238 0.061055956517031 + +Locus 008 +Allele 121 0.092699933050176 +Allele 123 0.112552784314946 +Allele 125 0.084040379935260 +Allele 127 0.076956426553491 +Allele 129 0.088636013825308 +Allele 131 0.087594173236420 +Allele 133 0.098240802897281 +Allele 135 0.085568319338023 +Allele 137 0.115282408604925 +Allele 151 0.077719172929504 +Allele 161 0.080709585314666 + +Locus 009 +Allele 161 0.074255902544787 +Allele 165 0.075185021316940 +Allele 167 0.092169550886098 +Allele 169 0.081570248147749 +Allele 171 0.089559828632370 +Allele 173 0.096598267205119 +Allele 175 0.084218461537987 +Allele 177 0.081113604038504 +Allele 179 0.076263369462078 +Allele 181 0.083096529288497 +Allele 183 0.085882552716263 +Allele 185 0.080086664223604 + +Locus 010 +Allele 108 0.048192680496695 +Allele 115 0.048379751319229 +Allele 121 0.047514874099594 +Allele 123 0.053332501092746 +Allele 125 0.049099998549370 +Allele 127 0.047794354459010 +Allele 129 0.051283723506049 +Allele 131 0.048789956739964 +Allele 133 0.053027499858643 +Allele 135 0.048800219357660 +Allele 137 0.055000651559079 +Allele 139 0.055194875917116 +Allele 141 0.050414509855266 +Allele 143 0.046291322661988 +Allele 145 0.045510356595249 +Allele 147 0.055279709588625 +Allele 149 0.050169583231029 +Allele 152 0.049379948863207 +Allele 155 0.047230660605067 +Allele 157 0.049312821644414 + + + +Estimated Mixing Proportions +0.026188626666667 +0.952080313333333 +0.021731060000000 + + + +Estimated sigma: +k: 0 1.000000000000000 +k: 1 1.000000000000000 +k: 2 1.000000000000000 + + + +Estimated psi: +k: 0 0.599999999999828 +k: 1 0.599999999999828 +k: 2 0.599999999999828 + + + diff --git a/inst/files/tess/tess_10.txt b/inst/files/tess/tess_10.txt new file mode 100644 index 0000000..de260c6 --- /dev/null +++ b/inst/files/tess/tess_10.txt @@ -0,0 +1,774 @@ +Estimated Clustering Probabilities for Samples +Sample ***Cluster 01*** ***Cluster 02*** ***Cluster 03*** ***Cluster 04*** +000001: 0.009484500000000 0.011469500000000 0.969730500000000 0.009315500000000 1 +000002: 0.007812500000000 0.007337500000000 0.977771500000000 0.007078500000000 1 +000003: 0.003687000000000 0.003711500000000 0.989209000000000 0.003392500000000 1 +000004: 0.013829000000000 0.015447000000000 0.959405500000000 0.011318500000000 1 +000005: 0.010243500000000 0.010735000000000 0.969065000000000 0.009956500000000 1 +000006: 0.005160500000000 0.005732500000000 0.984766500000000 0.004340500000000 1 +000007: 0.085316500000000 0.091396500000000 0.745909000000000 0.077378000000000 1 +000008: 0.017367000000000 0.017649000000000 0.950747000000000 0.014237000000000 1 +000009: 0.026040000000000 0.025448000000000 0.926699500000000 0.021812500000000 1 +000010: 0.024717500000000 0.024186000000000 0.931707000000000 0.019389500000000 1 +000011: 0.029947000000000 0.029576500000000 0.912791000000000 0.027685500000000 1 +000012: 0.005960000000000 0.007087000000000 0.981704500000000 0.005248500000000 1 +000013: 0.013908000000000 0.014045500000000 0.959569500000000 0.012477000000000 1 +000014: 0.013755000000000 0.015483500000000 0.957173000000000 0.013588500000000 1 +000015: 0.013041500000000 0.013393500000000 0.961304500000000 0.012260500000000 1 +000016: 0.003093000000000 0.003068000000000 0.991008500000000 0.002830500000000 1 +000017: 0.012155500000000 0.012820500000000 0.964209500000000 0.010814500000000 1 +000018: 0.015624000000000 0.015042500000000 0.955480500000000 0.013853000000000 1 +000019: 0.060209500000000 0.055751500000000 0.826978000000000 0.057061000000000 1 +000020: 0.027116500000000 0.028282000000000 0.917308500000000 0.027293000000000 1 +000021: 0.038501000000000 0.044444500000000 0.878922500000000 0.038132000000000 1 +000022: 0.079112500000000 0.081712000000000 0.770110000000000 0.069065500000000 1 +000023: 0.003784000000000 0.003791000000000 0.989158500000000 0.003266500000000 1 +000024: 0.006048000000000 0.006168500000000 0.982031500000000 0.005752000000000 1 +000025: 0.008058000000000 0.008776000000000 0.975301500000000 0.007864500000000 1 +000026: 0.009312500000000 0.009000500000000 0.972930000000000 0.008757000000000 1 +000027: 0.009628500000000 0.009287500000000 0.973589500000000 0.007494500000000 1 +000028: 0.004289000000000 0.005071000000000 0.987380000000000 0.003260000000000 1 +000029: 0.013064500000000 0.010052000000000 0.967960500000000 0.008923000000000 1 +000030: 0.015774000000000 0.015769500000000 0.952194000000000 0.016262500000000 1 +000031: 0.005314000000000 0.005978000000000 0.983701000000000 0.005007000000000 1 +000032: 0.003453000000000 0.003370000000000 0.989984000000000 0.003193000000000 1 +000033: 0.009536000000000 0.010423000000000 0.970192500000000 0.009848500000000 1 +000034: 0.005565000000000 0.004961500000000 0.984362500000000 0.005111000000000 1 +000035: 0.009177500000000 0.008885000000000 0.974502000000000 0.007435500000000 1 +000036: 0.006715500000000 0.007230000000000 0.978332000000000 0.007722500000000 1 +000037: 0.007799500000000 0.008352500000000 0.976951500000000 0.006896500000000 1 +000038: 0.010058500000000 0.010461500000000 0.969548000000000 0.009932000000000 1 +000039: 0.010624000000000 0.009953500000000 0.967478500000000 0.011944000000000 1 +000040: 0.004544000000000 0.003764500000000 0.987153000000000 0.004538500000000 1 +000041: 0.007232500000000 0.007460000000000 0.977497500000000 0.007810000000000 1 +000042: 0.004965500000000 0.004645000000000 0.985352000000000 0.005037500000000 1 +000043: 0.007248000000000 0.005690500000000 0.980512500000000 0.006549000000000 1 +000044: 0.005174000000000 0.004879500000000 0.985594500000000 0.004352000000000 1 +000045: 0.033037000000000 0.035119500000000 0.903192000000000 0.028651500000000 1 +000046: 0.012391500000000 0.012693500000000 0.964515500000000 0.010399500000000 1 +000047: 0.034890500000000 0.036623500000000 0.896833000000000 0.031653000000000 1 +000048: 0.052627000000000 0.057368000000000 0.845098500000000 0.044906500000000 1 +000049: 0.058252000000000 0.061923500000000 0.826310500000000 0.053514000000000 1 +000050: 0.050513000000000 0.050213500000000 0.857076500000000 0.042197000000000 1 +000051: 0.064422500000000 0.063327500000000 0.821022000000000 0.051228000000000 1 +000052: 0.015415500000000 0.017380000000000 0.953723500000000 0.013481000000000 1 +000053: 0.008968000000000 0.009381500000000 0.973889500000000 0.007761000000000 1 +000054: 0.049380000000000 0.048148000000000 0.861844500000000 0.040627500000000 1 +000055: 0.017821000000000 0.016921000000000 0.949387500000000 0.015870500000000 1 +000056: 0.018146000000000 0.019218500000000 0.945031000000000 0.017604500000000 1 +000057: 0.033219500000000 0.036065000000000 0.900926500000000 0.029789000000000 1 +000058: 0.011744500000000 0.011438000000000 0.966330000000000 0.010487500000000 1 +000059: 0.057100500000000 0.057086000000000 0.836156500000000 0.049657000000000 1 +000060: 0.041691000000000 0.043669000000000 0.875615000000000 0.039025000000000 1 +000061: 0.015197500000000 0.016121500000000 0.954156500000000 0.014524500000000 1 +000062: 0.050604000000000 0.054258500000000 0.848574500000000 0.046563000000000 1 +000063: 0.024816500000000 0.024689000000000 0.928002000000000 0.022492500000000 1 +000064: 0.090744000000000 0.092442000000000 0.732072500000000 0.084741500000000 1 +000065: 0.030063500000000 0.030903500000000 0.912452000000000 0.026581000000000 1 +000066: 0.019654500000000 0.019744000000000 0.945618500000000 0.014983000000000 1 +000067: 0.004020500000000 0.005040000000000 0.987457500000000 0.003482000000000 1 +000068: 0.012737000000000 0.013388000000000 0.961916000000000 0.011959000000000 1 +000069: 0.004797000000000 0.005435500000000 0.985613000000000 0.004154500000000 1 +000070: 0.008280000000000 0.007792000000000 0.976580500000000 0.007347500000000 1 +000071: 0.004102000000000 0.003709000000000 0.988808500000000 0.003380500000000 1 +000072: 0.003505000000000 0.003838000000000 0.989131500000000 0.003525500000000 1 +000073: 0.004105000000000 0.003967000000000 0.987760500000000 0.004167500000000 1 +000074: 0.008827000000000 0.009454500000000 0.973614500000000 0.008104000000000 1 +000075: 0.006162500000000 0.006025000000000 0.982089000000000 0.005723500000000 1 + + + +Estimated Allele Frequencies +Cluster 01 +Locus 001 +Allele 092 0.120348159533939 +Allele 094 0.115096917696415 +Allele 096 0.101563056368591 +Allele 098 0.118585053478684 +Allele 100 0.114641629838007 +Allele 102 0.099446058546340 +Allele 104 0.112065231565619 +Allele 106 0.125754084506808 +Allele 108 0.092499808465596 + +Locus 002 +Allele 118 0.078603315066877 +Allele 122 0.078577891566185 +Allele 124 0.080227951194550 +Allele 126 0.108216631678650 +Allele 127 0.080809166060044 +Allele 128 0.085190135262401 +Allele 130 0.080747459880546 +Allele 132 0.086228997404958 +Allele 134 0.073507679673464 +Allele 135 0.084217813970756 +Allele 137 0.086183437641372 +Allele 151 0.077489520600194 + +Locus 003 +Allele 130 0.065807953076309 +Allele 133 0.067494545285296 +Allele 136 0.070160624099649 +Allele 138 0.078187109434731 +Allele 139 0.074605723370347 +Allele 141 0.074303061289033 +Allele 143 0.063357891147410 +Allele 145 0.075807191079909 +Allele 146 0.071555858056407 +Allele 147 0.070244538642913 +Allele 148 0.077671506267764 +Allele 150 0.069012326675514 +Allele 152 0.076545598955466 +Allele 156 0.065246072619253 + +Locus 004 +Allele 093 0.056737535314122 +Allele 095 0.057799891731189 +Allele 096 0.053205306935777 +Allele 097 0.060044890978695 +Allele 099 0.062048618416950 +Allele 100 0.059797763200672 +Allele 101 0.068603199440204 +Allele 103 0.074481635271829 +Allele 105 0.054457916038244 +Allele 107 0.056760403732749 +Allele 109 0.055200197609229 +Allele 110 0.054845701861749 +Allele 113 0.062630944459592 +Allele 121 0.058123635857655 +Allele 123 0.053678187771220 +Allele 125 0.055736860729891 +Allele 131 0.055847310650231 + +Locus 005 +Allele 218 0.045340118264832 +Allele 220 0.050575397015582 +Allele 222 0.052256770259759 +Allele 224 0.051709313035286 +Allele 226 0.052054033031417 +Allele 228 0.050678596043657 +Allele 230 0.052991555424662 +Allele 232 0.051538838943430 +Allele 234 0.055697732375529 +Allele 236 0.053662167673611 +Allele 238 0.051802997641144 +Allele 240 0.049823091327217 +Allele 242 0.046613032312157 +Allele 244 0.047484069567433 +Allele 246 0.049295338406524 +Allele 248 0.048243619053780 +Allele 250 0.050989460964767 +Allele 252 0.048045438370014 +Allele 254 0.045370694157507 +Allele 256 0.045827736131693 + +Locus 006 +Allele 094 0.072495895672363 +Allele 096 0.069981345061321 +Allele 098 0.073079814996969 +Allele 100 0.063043156299719 +Allele 102 0.072259136895436 +Allele 104 0.086873952959887 +Allele 106 0.075608011961793 +Allele 108 0.068646651831777 +Allele 110 0.081098556857471 +Allele 112 0.075276162045567 +Allele 114 0.064248567329374 +Allele 124 0.068598482152342 +Allele 126 0.065595169771014 +Allele 149 0.063195096164969 + +Locus 007 +Allele 202 0.060156203157687 +Allele 204 0.057832779513051 +Allele 206 0.056074494410895 +Allele 208 0.068009629631705 +Allele 210 0.065353549255656 +Allele 212 0.061941273365330 +Allele 214 0.064285629824115 +Allele 216 0.061695968145295 +Allele 218 0.060329102020193 +Allele 220 0.061835930862584 +Allele 222 0.071721550095323 +Allele 224 0.061985081984513 +Allele 226 0.068339355106396 +Allele 228 0.059687038268158 +Allele 233 0.059974433958809 +Allele 238 0.060777980400292 + +Locus 008 +Allele 121 0.090227428515903 +Allele 123 0.107025248354389 +Allele 125 0.085133813679660 +Allele 127 0.078083016203828 +Allele 129 0.088570415632402 +Allele 131 0.088707358291542 +Allele 133 0.099213207757790 +Allele 135 0.087027811555105 +Allele 137 0.115279210992764 +Allele 151 0.078962962372603 +Allele 161 0.081769526644015 + +Locus 009 +Allele 161 0.074753641856838 +Allele 165 0.075860927795639 +Allele 167 0.090682571809457 +Allele 169 0.082666340052379 +Allele 171 0.090067585913332 +Allele 173 0.095801808215100 +Allele 175 0.082957678324819 +Allele 177 0.081507813111607 +Allele 179 0.076573293935820 +Allele 181 0.082872421123025 +Allele 183 0.085736965933557 +Allele 185 0.080518951928425 + +Locus 010 +Allele 108 0.048742213643949 +Allele 115 0.048406219846817 +Allele 121 0.047679452412089 +Allele 123 0.052649837597027 +Allele 125 0.049669623776875 +Allele 127 0.048114969676128 +Allele 129 0.050977574840738 +Allele 131 0.048681695845139 +Allele 133 0.051803005195059 +Allele 135 0.048617291827094 +Allele 137 0.054802757326573 +Allele 139 0.055492656195461 +Allele 141 0.050793022318254 +Allele 143 0.046808764465385 +Allele 145 0.046295372969033 +Allele 147 0.053632805614574 +Allele 149 0.049937649213396 +Allele 152 0.049925717073662 +Allele 155 0.047266850320191 +Allele 157 0.049702519842556 + + +Cluster 02 +Locus 001 +Allele 092 0.120509686984814 +Allele 094 0.115076358881358 +Allele 096 0.100792122273995 +Allele 098 0.117321133541194 +Allele 100 0.116273716324223 +Allele 102 0.099416301054822 +Allele 104 0.112128445075619 +Allele 106 0.125850158809866 +Allele 108 0.092632077054110 + +Locus 002 +Allele 118 0.077994444549856 +Allele 122 0.078403197820937 +Allele 124 0.080570065574037 +Allele 126 0.108227659897506 +Allele 127 0.080663595915714 +Allele 128 0.085257372621446 +Allele 130 0.080804663920445 +Allele 132 0.086375223258954 +Allele 134 0.074153141587499 +Allele 135 0.084273211358193 +Allele 137 0.085727835877805 +Allele 151 0.077549587617606 + +Locus 003 +Allele 130 0.065566718192204 +Allele 133 0.067426484262115 +Allele 136 0.070480070394367 +Allele 138 0.078841627642835 +Allele 139 0.073337307168182 +Allele 141 0.075927015296084 +Allele 143 0.062896895295168 +Allele 145 0.076127104811700 +Allele 146 0.071044183740021 +Allele 147 0.070573977874131 +Allele 148 0.077281620640342 +Allele 150 0.069026886335713 +Allele 152 0.076363932849350 +Allele 156 0.065106175497792 + +Locus 004 +Allele 093 0.056631746911860 +Allele 095 0.057812138479579 +Allele 096 0.053488339687553 +Allele 097 0.059909411196704 +Allele 099 0.061888016914214 +Allele 100 0.059942441209504 +Allele 101 0.069191348602027 +Allele 103 0.074064867935577 +Allele 105 0.054703035885390 +Allele 107 0.056453542969500 +Allele 109 0.054722337151400 +Allele 110 0.054702963425292 +Allele 113 0.062135316519749 +Allele 121 0.057996700169329 +Allele 123 0.053714094700584 +Allele 125 0.056165940835025 +Allele 131 0.056477757406713 + +Locus 005 +Allele 218 0.045620051800044 +Allele 220 0.050513245631889 +Allele 222 0.052622693394307 +Allele 224 0.052123007124071 +Allele 226 0.051457575521799 +Allele 228 0.050558999029510 +Allele 230 0.053651413325013 +Allele 232 0.051684265120793 +Allele 234 0.055682230541198 +Allele 236 0.053923886720567 +Allele 238 0.051320728678385 +Allele 240 0.049585160141180 +Allele 242 0.046545772894613 +Allele 244 0.047424393864252 +Allele 246 0.049480165285168 +Allele 248 0.048122101282845 +Allele 250 0.051107474715718 +Allele 252 0.047656197998264 +Allele 254 0.045080137612542 +Allele 256 0.045840499317839 + +Locus 006 +Allele 094 0.071754189101534 +Allele 096 0.070262632416583 +Allele 098 0.072936565506474 +Allele 100 0.062990768193458 +Allele 102 0.072280673331026 +Allele 104 0.086450626046252 +Allele 106 0.076052202664673 +Allele 108 0.068667386580891 +Allele 110 0.081190346204176 +Allele 112 0.074376458972098 +Allele 114 0.064603258665575 +Allele 124 0.069513211523939 +Allele 126 0.065790719043831 +Allele 149 0.063130961749492 + +Locus 007 +Allele 202 0.059317057724500 +Allele 204 0.057853155773691 +Allele 206 0.056072692837797 +Allele 208 0.068337183367420 +Allele 210 0.065670699115459 +Allele 212 0.061967190640754 +Allele 214 0.063933397194866 +Allele 216 0.061602464363939 +Allele 218 0.060611105370916 +Allele 220 0.061443639955184 +Allele 222 0.071378979659911 +Allele 224 0.062452176749830 +Allele 226 0.068390421540886 +Allele 228 0.059680473477682 +Allele 233 0.060296282093720 +Allele 238 0.060993080133444 + +Locus 008 +Allele 121 0.091261567306131 +Allele 123 0.108549335620927 +Allele 125 0.085949051391534 +Allele 127 0.077411637010798 +Allele 129 0.088729442626363 +Allele 131 0.087751689989897 +Allele 133 0.098863858166100 +Allele 135 0.086732956561844 +Allele 137 0.114166753285426 +Allele 151 0.078760803708229 +Allele 161 0.081822904332750 + +Locus 009 +Allele 161 0.074874372308683 +Allele 165 0.075040647883863 +Allele 167 0.089978233267756 +Allele 169 0.081704437305931 +Allele 171 0.090008025326341 +Allele 173 0.096216627497460 +Allele 175 0.083391604402699 +Allele 177 0.081656439806058 +Allele 179 0.076564428925387 +Allele 181 0.083718627190219 +Allele 183 0.085776024167671 +Allele 185 0.081070531917928 + +Locus 010 +Allele 108 0.048426938410221 +Allele 115 0.049007555941891 +Allele 121 0.047766850595433 +Allele 123 0.052903638834251 +Allele 125 0.049571458365586 +Allele 127 0.048183761284604 +Allele 129 0.050785809616898 +Allele 131 0.049037131617855 +Allele 133 0.052324693045602 +Allele 135 0.048893289404498 +Allele 137 0.055057191265799 +Allele 139 0.054321852507284 +Allele 141 0.050985102715715 +Allele 143 0.046559975422973 +Allele 145 0.046012811463860 +Allele 147 0.054028339113176 +Allele 149 0.049826902888649 +Allele 152 0.049312341052352 +Allele 155 0.047674994520758 +Allele 157 0.049319361932594 + + +Cluster 03 +Locus 001 +Allele 092 0.037806929541897 +Allele 094 0.397563436928490 +Allele 096 0.063921542352453 +Allele 098 0.201113459430041 +Allele 100 0.086421394711884 +Allele 102 0.091298200845328 +Allele 104 0.073988124679203 +Allele 106 0.028964511150029 +Allele 108 0.018922400360672 + +Locus 002 +Allele 118 0.016705823355876 +Allele 122 0.029638041761061 +Allele 124 0.211883517164902 +Allele 126 0.122911183341104 +Allele 127 0.009294214978836 +Allele 128 0.098580294633360 +Allele 130 0.074648581466706 +Allele 132 0.236151055946708 +Allele 134 0.011567404915534 +Allele 135 0.105836008977764 +Allele 137 0.072544082802004 +Allele 151 0.010239790656146 + +Locus 003 +Allele 130 0.023925006634948 +Allele 133 0.010367425576889 +Allele 136 0.131845143941260 +Allele 138 0.102722441158857 +Allele 139 0.136822111730458 +Allele 141 0.033341444674427 +Allele 143 0.012051900368863 +Allele 145 0.084400978036359 +Allele 146 0.112091781138493 +Allele 147 0.009257142807583 +Allele 148 0.147998919334311 +Allele 150 0.080685670167507 +Allele 152 0.096857787688500 +Allele 156 0.017632246741546 + +Locus 004 +Allele 093 0.048486410267212 +Allele 095 0.073016454835454 +Allele 096 0.011833627008754 +Allele 097 0.186226610979691 +Allele 099 0.052039160546095 +Allele 100 0.084852630855552 +Allele 101 0.149712394207813 +Allele 103 0.134571442583419 +Allele 105 0.049134209695577 +Allele 107 0.092776223374755 +Allele 109 0.023781499412429 +Allele 110 0.023737758027893 +Allele 113 0.014436695281302 +Allele 121 0.016092303723246 +Allele 123 0.018017298341983 +Allele 125 0.010639291976611 +Allele 131 0.010645988882211 + +Locus 005 +Allele 218 0.011784719959860 +Allele 220 0.096383727798384 +Allele 222 0.132661117251069 +Allele 224 0.132488813584022 +Allele 226 0.095771015411892 +Allele 228 0.046391764733087 +Allele 230 0.045242751119125 +Allele 232 0.064733413006058 +Allele 234 0.068807337530692 +Allele 236 0.057387269402447 +Allele 238 0.077091983349375 +Allele 240 0.040940100888876 +Allele 242 0.036204731036743 +Allele 244 0.010872216308193 +Allele 246 0.016437089826204 +Allele 248 0.010584345817709 +Allele 250 0.015415356982923 +Allele 252 0.017118905173163 +Allele 254 0.012037619570554 +Allele 256 0.011645721249624 + +Locus 006 +Allele 094 0.106669969988650 +Allele 096 0.172448681403658 +Allele 098 0.040905015544941 +Allele 100 0.012448630172597 +Allele 102 0.099998718580186 +Allele 104 0.236971068837525 +Allele 106 0.144063949521615 +Allele 108 0.068790567948608 +Allele 110 0.050736039120612 +Allele 112 0.021120137512625 +Allele 114 0.011978555896446 +Allele 124 0.010189907474135 +Allele 126 0.011415732936926 +Allele 149 0.012263025061472 + +Locus 007 +Allele 202 0.010562879582142 +Allele 204 0.024605970839522 +Allele 206 0.012168563342419 +Allele 208 0.137414136003733 +Allele 210 0.040642019764368 +Allele 212 0.186309420652105 +Allele 214 0.106692812321659 +Allele 216 0.114566430057333 +Allele 218 0.062457476886016 +Allele 220 0.055506659453893 +Allele 222 0.057605668260412 +Allele 224 0.113974251441943 +Allele 226 0.039331483610596 +Allele 228 0.017344204736615 +Allele 233 0.010416992314342 +Allele 238 0.010401030732911 + +Locus 008 +Allele 121 0.086135397728632 +Allele 123 0.078947315873770 +Allele 125 0.057546118864494 +Allele 127 0.014548642606777 +Allele 129 0.056440249355703 +Allele 131 0.270769112292282 +Allele 133 0.151648821396296 +Allele 135 0.187372166044072 +Allele 137 0.069070571101086 +Allele 151 0.014283456200753 +Allele 161 0.013238148536132 + +Locus 009 +Allele 161 0.014878380276653 +Allele 165 0.030453875932472 +Allele 167 0.056343710425963 +Allele 169 0.099505206394834 +Allele 171 0.280692956330958 +Allele 173 0.189823253426758 +Allele 175 0.107398242254077 +Allele 177 0.107888231034350 +Allele 179 0.014232857942215 +Allele 181 0.043571111521969 +Allele 183 0.026516792594167 +Allele 185 0.028695381865582 + +Locus 010 +Allele 108 0.029255572231242 +Allele 115 0.010341748834056 +Allele 121 0.010791706009049 +Allele 123 0.046184038924676 +Allele 125 0.098027689734082 +Allele 127 0.073762141122910 +Allele 129 0.084883023285035 +Allele 131 0.092348969295175 +Allele 133 0.165994585402888 +Allele 135 0.104760856733180 +Allele 137 0.082744760364500 +Allele 139 0.025907083772634 +Allele 141 0.040820640679924 +Allele 143 0.011312896336803 +Allele 145 0.030501729435594 +Allele 147 0.020453000155464 +Allele 149 0.028458806413033 +Allele 152 0.016270416140961 +Allele 155 0.010894484744472 +Allele 157 0.016285850384325 + + +Cluster 04 +Locus 001 +Allele 092 0.119959280297570 +Allele 094 0.113852782453893 +Allele 096 0.102111930411213 +Allele 098 0.115541707695551 +Allele 100 0.114887523890691 +Allele 102 0.101709652041763 +Allele 104 0.112851009927381 +Allele 106 0.124012984317642 +Allele 108 0.095073128964299 + +Locus 002 +Allele 118 0.078379451273933 +Allele 122 0.078820770166428 +Allele 124 0.080704194478686 +Allele 126 0.104786852969717 +Allele 127 0.081409833843237 +Allele 128 0.085529835759125 +Allele 130 0.081121426448060 +Allele 132 0.085579882846798 +Allele 134 0.075086380448856 +Allele 135 0.083673198998745 +Allele 137 0.086578801178397 +Allele 151 0.078329371588016 + +Locus 003 +Allele 130 0.066264668503082 +Allele 133 0.067930580998581 +Allele 136 0.070139244548546 +Allele 138 0.077692575696012 +Allele 139 0.073332392058900 +Allele 141 0.075134130494241 +Allele 143 0.063909273635648 +Allele 145 0.075198752656109 +Allele 146 0.071406140483462 +Allele 147 0.071647220039548 +Allele 148 0.077070246696291 +Allele 150 0.069189944244594 +Allele 152 0.075184292038583 +Allele 156 0.065900537906405 + +Locus 004 +Allele 093 0.056109424609680 +Allele 095 0.057874548903962 +Allele 096 0.053604185181446 +Allele 097 0.059487768790773 +Allele 099 0.061979083039545 +Allele 100 0.059787137138718 +Allele 101 0.068721312888911 +Allele 103 0.072688221612873 +Allele 105 0.055339167751014 +Allele 107 0.056552033237394 +Allele 109 0.055859581553484 +Allele 110 0.055288503244589 +Allele 113 0.061516216027719 +Allele 121 0.057755632141905 +Allele 123 0.054301855136657 +Allele 125 0.056558948443508 +Allele 131 0.056576380297818 + +Locus 005 +Allele 218 0.045960322575970 +Allele 220 0.050428781375968 +Allele 222 0.051940807683526 +Allele 224 0.051812694490059 +Allele 226 0.051637973989270 +Allele 228 0.050688073494883 +Allele 230 0.053131098431451 +Allele 232 0.051523305413187 +Allele 234 0.055370282388247 +Allele 236 0.053127135998949 +Allele 238 0.051784990488265 +Allele 240 0.049341104683315 +Allele 242 0.046886809890612 +Allele 244 0.048140081097193 +Allele 246 0.048828650065343 +Allele 248 0.048544796038450 +Allele 250 0.050863682915517 +Allele 252 0.047493413224509 +Allele 254 0.045896913047071 +Allele 256 0.046599082708214 + +Locus 006 +Allele 094 0.072376371482719 +Allele 096 0.070310968109772 +Allele 098 0.072979226955527 +Allele 100 0.064130841471334 +Allele 102 0.072313669628767 +Allele 104 0.085160315040322 +Allele 106 0.075758034235092 +Allele 108 0.068242723586501 +Allele 110 0.080384932339363 +Allele 112 0.074023158591011 +Allele 114 0.064584917561453 +Allele 124 0.068898425382317 +Allele 126 0.066628646341872 +Allele 149 0.064207769273952 + +Locus 007 +Allele 202 0.060330118388856 +Allele 204 0.057743673882000 +Allele 206 0.056715644774980 +Allele 208 0.067800119163965 +Allele 210 0.065163834138077 +Allele 212 0.062046771312778 +Allele 214 0.063598330717481 +Allele 216 0.061515123855721 +Allele 218 0.060964183939777 +Allele 220 0.062411454710311 +Allele 222 0.070510702819256 +Allele 224 0.062902910904273 +Allele 226 0.067874105286697 +Allele 228 0.059650025373617 +Allele 233 0.060365239610375 +Allele 238 0.060407761121840 + +Locus 008 +Allele 121 0.090475805265453 +Allele 123 0.106725629937390 +Allele 125 0.086917595337722 +Allele 127 0.078975235594075 +Allele 129 0.089448628000581 +Allele 131 0.089098595791940 +Allele 133 0.096751196081170 +Allele 135 0.087646356505163 +Allele 137 0.111008332212878 +Allele 151 0.080469672886988 +Allele 161 0.082482952386643 + +Locus 009 +Allele 161 0.075473889225538 +Allele 165 0.076261095510394 +Allele 167 0.089688159449721 +Allele 169 0.082348471288919 +Allele 171 0.089651398671016 +Allele 173 0.094727861882558 +Allele 175 0.083226986669194 +Allele 177 0.082263908759418 +Allele 179 0.077089841538919 +Allele 181 0.082777156429577 +Allele 183 0.084653367140818 +Allele 185 0.081837863433931 + +Locus 010 +Allele 108 0.049243222168591 +Allele 115 0.049030541849594 +Allele 121 0.047776234328698 +Allele 123 0.052109566031171 +Allele 125 0.049573137904617 +Allele 127 0.048156132581210 +Allele 129 0.050770776110117 +Allele 131 0.048723640726390 +Allele 133 0.051744501374877 +Allele 135 0.049003839186992 +Allele 137 0.054054366961577 +Allele 139 0.054808388280640 +Allele 141 0.050782015364518 +Allele 143 0.046754036420117 +Allele 145 0.046682117593890 +Allele 147 0.053244610427534 +Allele 149 0.050662867983400 +Allele 152 0.049449520396172 +Allele 155 0.048113294277791 +Allele 157 0.049317190032105 + + + +Estimated Mixing Proportions +0.020409100000000 +0.020948980000000 +0.940321020000000 +0.018320900000000 + + + +Estimated sigma: +k: 0 1.000000000000000 +k: 1 1.000000000000000 +k: 2 1.000000000000000 +k: 3 1.000000000000000 + + + +Estimated psi: +k: 0 0.599999999999828 +k: 1 0.599999999999828 +k: 2 0.599999999999828 +k: 3 0.599999999999828 + + + diff --git a/inst/files/tess/tess_11.txt b/inst/files/tess/tess_11.txt new file mode 100644 index 0000000..d2fbf2b --- /dev/null +++ b/inst/files/tess/tess_11.txt @@ -0,0 +1,944 @@ +Estimated Clustering Probabilities for Samples +Sample ***Cluster 01*** ***Cluster 02*** ***Cluster 03*** ***Cluster 04*** ***Cluster 05*** +000001: 0.005893500000000 0.971344500000000 0.007557500000000 0.008262000000000 0.006942500000000 1 +000002: 0.004952500000000 0.974772000000000 0.006939000000000 0.007025500000000 0.006311000000000 1 +000003: 0.002871000000000 0.986871000000000 0.003570500000000 0.003337500000000 0.003350000000000 1 +000004: 0.009096500000000 0.959312000000000 0.010894000000000 0.010985500000000 0.009712000000000 1 +000005: 0.006896000000000 0.965586000000000 0.009081000000000 0.009857500000000 0.008579500000000 1 +000006: 0.002806000000000 0.984957000000000 0.003904000000000 0.004064000000000 0.004269000000000 1 +000007: 0.042390000000000 0.776902500000000 0.060873000000000 0.061647500000000 0.058187000000000 1 +000008: 0.011106500000000 0.948884500000000 0.013521000000000 0.014150000000000 0.012338000000000 1 +000009: 0.018541500000000 0.920212500000000 0.021126500000000 0.021777500000000 0.018342000000000 1 +000010: 0.015009500000000 0.929775000000000 0.018681000000000 0.019152000000000 0.017382500000000 1 +000011: 0.015034500000000 0.917177000000000 0.022636000000000 0.025011000000000 0.020141500000000 1 +000012: 0.004757500000000 0.978854500000000 0.005172000000000 0.005825500000000 0.005390500000000 1 +000013: 0.008975500000000 0.955996000000000 0.010874000000000 0.012561000000000 0.011593500000000 1 +000014: 0.008668000000000 0.958535000000000 0.010707500000000 0.010719000000000 0.011370500000000 1 +000015: 0.008165000000000 0.959524000000000 0.010622500000000 0.011066500000000 0.010622000000000 1 +000016: 0.002140500000000 0.989820000000000 0.002687000000000 0.002586000000000 0.002766500000000 1 +000017: 0.009118000000000 0.959453000000000 0.010139500000000 0.010475500000000 0.010814000000000 1 +000018: 0.009702500000000 0.952314500000000 0.012622500000000 0.012822000000000 0.012538500000000 1 +000019: 0.044227000000000 0.821806000000000 0.045714500000000 0.043364500000000 0.044888000000000 1 +000020: 0.020343500000000 0.908128500000000 0.023707000000000 0.022968500000000 0.024852500000000 1 +000021: 0.023945500000000 0.887402500000000 0.030508500000000 0.028588500000000 0.029555000000000 1 +000022: 0.048926500000000 0.784773000000000 0.052887500000000 0.054887500000000 0.058525500000000 1 +000023: 0.003250000000000 0.986341500000000 0.003554500000000 0.003237500000000 0.003616500000000 1 +000024: 0.005018000000000 0.978089500000000 0.005469000000000 0.005832000000000 0.005591500000000 1 +000025: 0.006699500000000 0.971011500000000 0.007266000000000 0.006675500000000 0.008347500000000 1 +000026: 0.006671500000000 0.969516500000000 0.007721000000000 0.007690500000000 0.008400500000000 1 +000027: 0.007088500000000 0.968407500000000 0.008297000000000 0.008048000000000 0.008159000000000 1 +000028: 0.002637000000000 0.987856500000000 0.003093500000000 0.003026000000000 0.003387000000000 1 +000029: 0.009161500000000 0.961269500000000 0.010174000000000 0.008391000000000 0.011004000000000 1 +000030: 0.011475500000000 0.946733000000000 0.014281000000000 0.012761000000000 0.014749500000000 1 +000031: 0.004122000000000 0.980250000000000 0.004982500000000 0.005329500000000 0.005316000000000 1 +000032: 0.002766500000000 0.986757500000000 0.003506000000000 0.003402500000000 0.003567500000000 1 +000033: 0.006748500000000 0.966338000000000 0.009052500000000 0.008767500000000 0.009093500000000 1 +000034: 0.003877000000000 0.981577500000000 0.004648500000000 0.004786000000000 0.005111000000000 1 +000035: 0.004924000000000 0.974452000000000 0.006798500000000 0.006893500000000 0.006932000000000 1 +000036: 0.004646000000000 0.977338500000000 0.006029500000000 0.005654000000000 0.006332000000000 1 +000037: 0.005363000000000 0.975092500000000 0.006622500000000 0.006326500000000 0.006595500000000 1 +000038: 0.006790000000000 0.964201500000000 0.009668500000000 0.009627500000000 0.009712500000000 1 +000039: 0.008007500000000 0.958259000000000 0.010834000000000 0.011119000000000 0.011780500000000 1 +000040: 0.002965500000000 0.983861000000000 0.004283500000000 0.004427500000000 0.004462500000000 1 +000041: 0.005702000000000 0.971951500000000 0.008302000000000 0.006578000000000 0.007466500000000 1 +000042: 0.003418000000000 0.981826500000000 0.005050000000000 0.004936500000000 0.004769000000000 1 +000043: 0.004682000000000 0.977075000000000 0.006214500000000 0.006095000000000 0.005933500000000 1 +000044: 0.003609500000000 0.982777000000000 0.004616000000000 0.004643000000000 0.004354500000000 1 +000045: 0.023522500000000 0.898146000000000 0.027130500000000 0.028794500000000 0.022406500000000 1 +000046: 0.008733500000000 0.961563500000000 0.010453000000000 0.010564000000000 0.008686000000000 1 +000047: 0.024987500000000 0.889772500000000 0.029259500000000 0.031353000000000 0.024627500000000 1 +000048: 0.039641000000000 0.830917000000000 0.045437500000000 0.045666500000000 0.038338000000000 1 +000049: 0.034172000000000 0.832933000000000 0.044661000000000 0.048311000000000 0.039923000000000 1 +000050: 0.029393000000000 0.856698500000000 0.038574000000000 0.039496000000000 0.035838500000000 1 +000051: 0.044727500000000 0.806418000000000 0.048682000000000 0.052297500000000 0.047875000000000 1 +000052: 0.011713500000000 0.950954000000000 0.013001000000000 0.013276000000000 0.011055500000000 1 +000053: 0.005955000000000 0.973744500000000 0.006659000000000 0.007349000000000 0.006292500000000 1 +000054: 0.029601000000000 0.860989500000000 0.037130000000000 0.038221500000000 0.034058000000000 1 +000055: 0.010704500000000 0.945729000000000 0.014063500000000 0.014856000000000 0.014647000000000 1 +000056: 0.011842500000000 0.944847000000000 0.014297000000000 0.015636500000000 0.013377000000000 1 +000057: 0.025170000000000 0.895871000000000 0.026575500000000 0.028855500000000 0.023528000000000 1 +000058: 0.008881000000000 0.962022500000000 0.009826500000000 0.010697500000000 0.008572500000000 1 +000059: 0.031602000000000 0.844318500000000 0.042949500000000 0.043917500000000 0.037212500000000 1 +000060: 0.023110000000000 0.877942000000000 0.034292500000000 0.034114000000000 0.030541500000000 1 +000061: 0.011408500000000 0.949700500000000 0.013510000000000 0.012561500000000 0.012819500000000 1 +000062: 0.037503000000000 0.839587500000000 0.040551000000000 0.042905000000000 0.039453500000000 1 +000063: 0.016964000000000 0.921461000000000 0.021266500000000 0.021095500000000 0.019213000000000 1 +000064: 0.055338500000000 0.743626000000000 0.069279500000000 0.069048000000000 0.062708000000000 1 +000065: 0.021435000000000 0.912061000000000 0.023827000000000 0.018404500000000 0.024272500000000 1 +000066: 0.012638500000000 0.949310500000000 0.012959500000000 0.009958500000000 0.015133000000000 1 +000067: 0.003689000000000 0.983738000000000 0.004044000000000 0.003689500000000 0.004839500000000 1 +000068: 0.010387000000000 0.956372500000000 0.011326500000000 0.009697500000000 0.012216500000000 1 +000069: 0.004423000000000 0.982464500000000 0.004653500000000 0.003865500000000 0.004593500000000 1 +000070: 0.007008500000000 0.970478500000000 0.008059000000000 0.006348000000000 0.008106000000000 1 +000071: 0.003270000000000 0.986216500000000 0.003615500000000 0.003107500000000 0.003790500000000 1 +000072: 0.002844500000000 0.986414500000000 0.003465500000000 0.003351000000000 0.003924500000000 1 +000073: 0.003368000000000 0.984379000000000 0.003693000000000 0.004329500000000 0.004230500000000 1 +000074: 0.006795500000000 0.968591000000000 0.008208500000000 0.008061000000000 0.008344000000000 1 +000075: 0.004861500000000 0.976283000000000 0.006394000000000 0.005931000000000 0.006530500000000 1 + + + +Estimated Allele Frequencies +Cluster 01 +Locus 001 +Allele 092 0.116634414221220 +Allele 094 0.114203174725991 +Allele 096 0.103462320299765 +Allele 098 0.117817365588619 +Allele 100 0.115121545559491 +Allele 102 0.103476108006095 +Allele 104 0.113007036318698 +Allele 106 0.117952179744596 +Allele 108 0.098325855535526 + +Locus 002 +Allele 118 0.079920409334796 +Allele 122 0.079881892691091 +Allele 124 0.081487991233089 +Allele 126 0.096387311614152 +Allele 127 0.081868024797968 +Allele 128 0.085531407240769 +Allele 130 0.082208149070264 +Allele 132 0.084712003735144 +Allele 134 0.077230667311559 +Allele 135 0.085041436797552 +Allele 137 0.086566388507307 +Allele 151 0.079164317666309 + +Locus 003 +Allele 130 0.068109680960037 +Allele 133 0.068234948133899 +Allele 136 0.071566972255275 +Allele 138 0.075407355898964 +Allele 139 0.072859906478514 +Allele 141 0.074542492796536 +Allele 143 0.065954970092887 +Allele 145 0.073483386447526 +Allele 146 0.071102784093699 +Allele 147 0.071007072937728 +Allele 148 0.076002176465790 +Allele 150 0.069895226751253 +Allele 152 0.074707947751905 +Allele 156 0.067125078935982 + +Locus 004 +Allele 093 0.057728904442786 +Allele 095 0.058700071095867 +Allele 096 0.054863159838875 +Allele 097 0.059249052715037 +Allele 099 0.060945925806044 +Allele 100 0.059871269596139 +Allele 101 0.064195034800833 +Allele 103 0.067129380875133 +Allele 105 0.056369457885051 +Allele 107 0.057488939124724 +Allele 109 0.056455565976169 +Allele 110 0.056015411311704 +Allele 113 0.062108081388419 +Allele 121 0.058321456862478 +Allele 123 0.056071963377186 +Allele 125 0.057233265122341 +Allele 131 0.057253059781208 + +Locus 005 +Allele 218 0.046662903616893 +Allele 220 0.049801400378916 +Allele 222 0.051945374869394 +Allele 224 0.051379914146461 +Allele 226 0.051172314695896 +Allele 228 0.050488888725019 +Allele 230 0.051739419838172 +Allele 232 0.051249328099252 +Allele 234 0.053504713476593 +Allele 236 0.052216211209629 +Allele 238 0.050774508549509 +Allele 240 0.049666114203327 +Allele 242 0.047822997640562 +Allele 244 0.048699185920146 +Allele 246 0.049799748091043 +Allele 248 0.049339687813479 +Allele 250 0.051224991947921 +Allele 252 0.048653855319704 +Allele 254 0.046851834190568 +Allele 256 0.047006607267515 + +Locus 006 +Allele 094 0.072805518590577 +Allele 096 0.070440971457145 +Allele 098 0.073432867307334 +Allele 100 0.065657243628936 +Allele 102 0.072640386163082 +Allele 104 0.080601736059697 +Allele 106 0.073832988956407 +Allele 108 0.070127315108248 +Allele 110 0.075840227843971 +Allele 112 0.074565574864386 +Allele 114 0.066712201831812 +Allele 124 0.069341851388683 +Allele 126 0.068165251306113 +Allele 149 0.065835865493608 + +Locus 007 +Allele 202 0.061231469069970 +Allele 204 0.058774664987370 +Allele 206 0.058459406667878 +Allele 208 0.066097949011240 +Allele 210 0.065556110436030 +Allele 212 0.062240825124858 +Allele 214 0.063377702130527 +Allele 216 0.061509640820156 +Allele 218 0.061354249172617 +Allele 220 0.062275114585954 +Allele 222 0.068331211716886 +Allele 224 0.062167529367426 +Allele 226 0.065034195635461 +Allele 228 0.060585744884579 +Allele 233 0.061409269222774 +Allele 238 0.061594917166275 + +Locus 008 +Allele 121 0.090683493770917 +Allele 123 0.099498757051911 +Allele 125 0.088307530203259 +Allele 127 0.081359124121505 +Allele 129 0.090036398819468 +Allele 131 0.090026034651086 +Allele 133 0.096703546687984 +Allele 135 0.089718005525720 +Allele 137 0.106125534149004 +Allele 151 0.082580038088462 +Allele 161 0.084961536930683 + +Locus 009 +Allele 161 0.077891155987707 +Allele 165 0.077962271195678 +Allele 167 0.087725342642758 +Allele 169 0.082965044339730 +Allele 171 0.087105990824300 +Allele 173 0.090122596208711 +Allele 175 0.083515264504109 +Allele 177 0.082870528849061 +Allele 179 0.078791483759760 +Allele 181 0.084165764730873 +Allele 183 0.084732899501943 +Allele 185 0.082151657455368 + +Locus 010 +Allele 108 0.048721772226490 +Allele 115 0.049154542909329 +Allele 121 0.048380262348676 +Allele 123 0.052084823470215 +Allele 125 0.049638509063711 +Allele 127 0.048876930047605 +Allele 129 0.049869866838763 +Allele 131 0.049510490914097 +Allele 133 0.050799108689269 +Allele 135 0.049166242862127 +Allele 137 0.052404202430132 +Allele 139 0.054776271137760 +Allele 141 0.051060712963279 +Allele 143 0.047504421205755 +Allele 145 0.047172135818451 +Allele 147 0.052734026740206 +Allele 149 0.049912896782275 +Allele 152 0.050017313319054 +Allele 155 0.048277529143404 +Allele 157 0.049937941089400 + + +Cluster 02 +Locus 001 +Allele 092 0.037614037322982 +Allele 094 0.398817509965667 +Allele 096 0.063624515788589 +Allele 098 0.200627717868013 +Allele 100 0.086508757404667 +Allele 102 0.091083283468469 +Allele 104 0.073764074704811 +Allele 106 0.029387015611633 +Allele 108 0.018573087865173 + +Locus 002 +Allele 118 0.016315970260030 +Allele 122 0.029328890165268 +Allele 124 0.211920281152315 +Allele 126 0.124014631619232 +Allele 127 0.009198786228056 +Allele 128 0.098662891879244 +Allele 130 0.074176222750643 +Allele 132 0.236264378889951 +Allele 134 0.011447446406725 +Allele 135 0.105964995066717 +Allele 137 0.072564649047732 +Allele 151 0.010140856534091 + +Locus 003 +Allele 130 0.023627922573752 +Allele 133 0.010334470678391 +Allele 136 0.131545391713127 +Allele 138 0.103009447206327 +Allele 139 0.136868661602334 +Allele 141 0.033073546561976 +Allele 143 0.011876249038801 +Allele 145 0.084585101829695 +Allele 146 0.111868623610190 +Allele 147 0.009224299303220 +Allele 148 0.148534768819209 +Allele 150 0.080605421927730 +Allele 152 0.097348773950380 +Allele 156 0.017497321184866 + +Locus 004 +Allele 093 0.048158958561580 +Allele 095 0.072802158815922 +Allele 096 0.011613135131740 +Allele 097 0.186397412591156 +Allele 099 0.051942394906948 +Allele 100 0.084828729023688 +Allele 101 0.150945837632446 +Allele 103 0.136282808042756 +Allele 105 0.049035493399014 +Allele 107 0.092572685989881 +Allele 109 0.023456849264587 +Allele 110 0.023570963898889 +Allele 113 0.013909487182220 +Allele 121 0.015918420299467 +Allele 123 0.017695466465394 +Allele 125 0.010437470814130 +Allele 131 0.010431727980180 + +Locus 005 +Allele 218 0.011611531086540 +Allele 220 0.096541190343139 +Allele 222 0.132893231386412 +Allele 224 0.133180581972275 +Allele 226 0.095778266162546 +Allele 228 0.046540304636687 +Allele 230 0.045512452837417 +Allele 232 0.064769526736989 +Allele 234 0.068854073133342 +Allele 236 0.057557610286561 +Allele 238 0.077307732641484 +Allele 240 0.040731370497993 +Allele 242 0.036003326025586 +Allele 244 0.010668996015049 +Allele 246 0.016120330049741 +Allele 248 0.010463355697779 +Allele 250 0.015166626075364 +Allele 252 0.016875986128763 +Allele 254 0.011908133670508 +Allele 256 0.011515374615826 + +Locus 006 +Allele 094 0.106331371414148 +Allele 096 0.172524190025881 +Allele 098 0.040593331463721 +Allele 100 0.012243998601108 +Allele 102 0.099774337228095 +Allele 104 0.238387699688111 +Allele 106 0.144308686073208 +Allele 108 0.068766868037788 +Allele 110 0.051278377144434 +Allele 112 0.020615349078468 +Allele 114 0.011840726197430 +Allele 124 0.010095756039467 +Allele 126 0.011130606562312 +Allele 149 0.012108702445832 + +Locus 007 +Allele 202 0.010304517039585 +Allele 204 0.024405730713827 +Allele 206 0.011972457681004 +Allele 208 0.137760252992337 +Allele 210 0.040441166272087 +Allele 212 0.186617571937594 +Allele 214 0.106719893073914 +Allele 216 0.114581190511815 +Allele 218 0.062485909865379 +Allele 220 0.055231878843054 +Allele 222 0.057867598853626 +Allele 224 0.114233089661328 +Allele 226 0.039854839502452 +Allele 228 0.017070019516674 +Allele 233 0.010324987942563 +Allele 238 0.010128895592765 + +Locus 008 +Allele 121 0.086178988297285 +Allele 123 0.080504451637936 +Allele 125 0.057136199194649 +Allele 127 0.014444434699758 +Allele 129 0.056045007582751 +Allele 131 0.270619319505764 +Allele 133 0.152231578389764 +Allele 135 0.186828480115308 +Allele 137 0.069057879711272 +Allele 151 0.013983343438513 +Allele 161 0.012970317426996 + +Locus 009 +Allele 161 0.014638873943568 +Allele 165 0.030291534600602 +Allele 167 0.056199494849911 +Allele 169 0.099913995219223 +Allele 171 0.281436914237413 +Allele 173 0.190873337018149 +Allele 175 0.107193884922058 +Allele 177 0.108137191592215 +Allele 179 0.013996390276467 +Allele 181 0.042986102530667 +Allele 183 0.026144451401368 +Allele 185 0.028187829408360 + +Locus 010 +Allele 108 0.029118663596081 +Allele 115 0.010177886614407 +Allele 121 0.010669342328140 +Allele 123 0.046169601767268 +Allele 125 0.098348913687120 +Allele 127 0.073684408693174 +Allele 129 0.085168060637938 +Allele 131 0.092327449366855 +Allele 133 0.166594165397913 +Allele 135 0.105113210040981 +Allele 137 0.083272837098249 +Allele 139 0.025565925515119 +Allele 141 0.040559283352577 +Allele 143 0.011238484353207 +Allele 145 0.030387409961701 +Allele 147 0.020519051121452 +Allele 149 0.028398837028643 +Allele 152 0.015890019416304 +Allele 155 0.010840496008608 +Allele 157 0.015955954014257 + + +Cluster 03 +Locus 001 +Allele 092 0.118848385375675 +Allele 094 0.113833589124030 +Allele 096 0.102966110152822 +Allele 098 0.116849579209256 +Allele 100 0.113424954123089 +Allele 102 0.103012406883104 +Allele 104 0.112800813028541 +Allele 106 0.121611080418547 +Allele 108 0.096653081684931 + +Locus 002 +Allele 118 0.079110079882796 +Allele 122 0.080163379955103 +Allele 124 0.081020480386187 +Allele 126 0.101453004628773 +Allele 127 0.081062234015895 +Allele 128 0.085703412321487 +Allele 130 0.081957124421867 +Allele 132 0.085554340848590 +Allele 134 0.075619603802642 +Allele 135 0.084217967267085 +Allele 137 0.085075956177911 +Allele 151 0.079062416291663 + +Locus 003 +Allele 130 0.067910668778904 +Allele 133 0.068360614622630 +Allele 136 0.070759235323074 +Allele 138 0.076716178638455 +Allele 139 0.073496994329480 +Allele 141 0.074846821758971 +Allele 143 0.065011536853623 +Allele 145 0.074555164228489 +Allele 146 0.071145231631556 +Allele 147 0.070606971159229 +Allele 148 0.076170645512461 +Allele 150 0.069907165632993 +Allele 152 0.074678979756447 +Allele 156 0.065833791773687 + +Locus 004 +Allele 093 0.056959783399905 +Allele 095 0.058439683311026 +Allele 096 0.054314977435607 +Allele 097 0.059810631592863 +Allele 099 0.061885831832857 +Allele 100 0.059791110146262 +Allele 101 0.066160967625603 +Allele 103 0.069107553653136 +Allele 105 0.055872546107316 +Allele 107 0.057391742611460 +Allele 109 0.056012312377604 +Allele 110 0.055707381884893 +Allele 113 0.061641894338032 +Allele 121 0.058407686361384 +Allele 123 0.054684918859421 +Allele 125 0.056824657523498 +Allele 131 0.056986320939135 + +Locus 005 +Allele 218 0.046647545788288 +Allele 220 0.050089394839051 +Allele 222 0.051900853243419 +Allele 224 0.051310167298154 +Allele 226 0.051380391407897 +Allele 228 0.050322703400670 +Allele 230 0.052254923922991 +Allele 232 0.051045571549752 +Allele 234 0.054833923587976 +Allele 236 0.052652651987570 +Allele 238 0.051468399621643 +Allele 240 0.050259317106475 +Allele 242 0.047770926144337 +Allele 244 0.048095757671749 +Allele 246 0.049424341165323 +Allele 248 0.048306794864536 +Allele 250 0.050894179499233 +Allele 252 0.048284540076417 +Allele 254 0.045965959359413 +Allele 256 0.047091657465107 + +Locus 006 +Allele 094 0.072327098143017 +Allele 096 0.070918391786790 +Allele 098 0.073086868267582 +Allele 100 0.064760996061907 +Allele 102 0.072269949208381 +Allele 104 0.081322514312105 +Allele 106 0.074366699221138 +Allele 108 0.069473073578969 +Allele 110 0.078827737229697 +Allele 112 0.074495058174129 +Allele 114 0.066120124503609 +Allele 124 0.069320581380085 +Allele 126 0.067471338718234 +Allele 149 0.065239569414356 + +Locus 007 +Allele 202 0.060375265084419 +Allele 204 0.058854590059671 +Allele 206 0.057705179992937 +Allele 208 0.066988209184319 +Allele 210 0.065166216095171 +Allele 212 0.061893986124218 +Allele 214 0.063827609601393 +Allele 216 0.062105986994189 +Allele 218 0.060786760794858 +Allele 220 0.062234594515358 +Allele 222 0.069421002326152 +Allele 224 0.061986654830439 +Allele 226 0.066271089905680 +Allele 228 0.060062887543554 +Allele 233 0.060600532731577 +Allele 238 0.061719434216063 + +Locus 008 +Allele 121 0.090621379076399 +Allele 123 0.102117446937695 +Allele 125 0.087411670214620 +Allele 127 0.080064370714270 +Allele 129 0.090674213048904 +Allele 131 0.089550667670454 +Allele 133 0.096713223725108 +Allele 135 0.088783953574868 +Allele 137 0.109382752288583 +Allele 151 0.081067383570650 +Allele 161 0.083612939178451 + +Locus 009 +Allele 161 0.076141135705135 +Allele 165 0.077157278476505 +Allele 167 0.089248739080435 +Allele 169 0.082783148014545 +Allele 171 0.088181471687481 +Allele 173 0.092228849234867 +Allele 175 0.083561262069754 +Allele 177 0.082445343267330 +Allele 179 0.077723355611124 +Allele 181 0.083804153447603 +Allele 183 0.084843922797005 +Allele 185 0.081881340608220 + +Locus 010 +Allele 108 0.049041205993505 +Allele 115 0.048740245020654 +Allele 121 0.048193332343054 +Allele 123 0.052026685341610 +Allele 125 0.049576501605825 +Allele 127 0.048675428855937 +Allele 129 0.050549681840692 +Allele 131 0.049517319884449 +Allele 133 0.051250303241680 +Allele 135 0.048847810618394 +Allele 137 0.053184823655614 +Allele 139 0.054886134398776 +Allele 141 0.051165055836225 +Allele 143 0.047165613918866 +Allele 145 0.046960576075328 +Allele 147 0.052534688735002 +Allele 149 0.050128674807159 +Allele 152 0.049909500221941 +Allele 155 0.047803638152254 +Allele 157 0.049842779453035 + + +Cluster 04 +Locus 001 +Allele 092 0.119144452198456 +Allele 094 0.113663570331453 +Allele 096 0.102968752036908 +Allele 098 0.117094715125712 +Allele 100 0.113875733750938 +Allele 102 0.102294886004936 +Allele 104 0.112744410116143 +Allele 106 0.121902200564144 +Allele 108 0.096311279871306 + +Locus 002 +Allele 118 0.079215638872405 +Allele 122 0.079727791325014 +Allele 124 0.081583405515113 +Allele 126 0.102415283805088 +Allele 127 0.081325801452613 +Allele 128 0.085487331455003 +Allele 130 0.081772110732692 +Allele 132 0.085552581032877 +Allele 134 0.075436202491643 +Allele 135 0.083455403794214 +Allele 137 0.085208488533890 +Allele 151 0.078819960989445 + +Locus 003 +Allele 130 0.067105577519957 +Allele 133 0.068360480651227 +Allele 136 0.071222693274195 +Allele 138 0.076946796375295 +Allele 139 0.073130574688712 +Allele 141 0.074913701946592 +Allele 143 0.064628226977377 +Allele 145 0.074445906097947 +Allele 146 0.071298540055112 +Allele 147 0.070908413776975 +Allele 148 0.076240570110325 +Allele 150 0.069702289850895 +Allele 152 0.074403926515310 +Allele 156 0.066692302160086 + +Locus 004 +Allele 093 0.057337676396205 +Allele 095 0.058285953496281 +Allele 096 0.054284405750891 +Allele 097 0.059574817884556 +Allele 099 0.062242611661556 +Allele 100 0.059764337260735 +Allele 101 0.065548281155902 +Allele 103 0.069173002695417 +Allele 105 0.055598858462756 +Allele 107 0.057422389635345 +Allele 109 0.055616486454580 +Allele 110 0.055661101808461 +Allele 113 0.062217089042275 +Allele 121 0.058497425991503 +Allele 123 0.054466833420494 +Allele 125 0.057291020714381 +Allele 131 0.057017708168663 + +Locus 005 +Allele 218 0.046786232172161 +Allele 220 0.050071142033965 +Allele 222 0.052121704921559 +Allele 224 0.051012691180296 +Allele 226 0.052086947635695 +Allele 228 0.049938716317430 +Allele 230 0.052439875735484 +Allele 232 0.050904718586825 +Allele 234 0.054540388862121 +Allele 236 0.053016507555489 +Allele 238 0.051297223735026 +Allele 240 0.049786803369793 +Allele 242 0.047520745256144 +Allele 244 0.047938452723145 +Allele 246 0.049819264758755 +Allele 248 0.048564937086211 +Allele 250 0.051039806164429 +Allele 252 0.048047056065982 +Allele 254 0.046118222212203 +Allele 256 0.046948563627286 + +Locus 006 +Allele 094 0.071942482929643 +Allele 096 0.071060077540656 +Allele 098 0.073672637052557 +Allele 100 0.064893796711468 +Allele 102 0.072462253782610 +Allele 104 0.082265496772227 +Allele 106 0.074936432224144 +Allele 108 0.068671298902629 +Allele 110 0.078645994019968 +Allele 112 0.074739232175748 +Allele 114 0.065687014161113 +Allele 124 0.069526173488337 +Allele 126 0.066652033973643 +Allele 149 0.064845076265256 + +Locus 007 +Allele 202 0.060458256284950 +Allele 204 0.059049342105526 +Allele 206 0.057283163273160 +Allele 208 0.067128570060861 +Allele 210 0.065105515968144 +Allele 212 0.061351702964089 +Allele 214 0.064011311478214 +Allele 216 0.062311913791642 +Allele 218 0.061265556220753 +Allele 220 0.062209641229567 +Allele 222 0.068974071690617 +Allele 224 0.062268626140237 +Allele 226 0.066681940185463 +Allele 228 0.060104878114403 +Allele 233 0.060660510811668 +Allele 238 0.061134999680707 + +Locus 008 +Allele 121 0.091163483600424 +Allele 123 0.102687582413744 +Allele 125 0.087308222642688 +Allele 127 0.080007280288792 +Allele 129 0.088897817181197 +Allele 131 0.090365828443274 +Allele 133 0.096163534862479 +Allele 135 0.088335744679502 +Allele 137 0.110158983754786 +Allele 151 0.081424346285629 +Allele 161 0.083487175847482 + +Locus 009 +Allele 161 0.076022992550159 +Allele 165 0.077116546002389 +Allele 167 0.089209030829609 +Allele 169 0.081284370969102 +Allele 171 0.088283557643470 +Allele 173 0.092195678679117 +Allele 175 0.084065640328169 +Allele 177 0.081565818205719 +Allele 179 0.078285673846930 +Allele 181 0.084374376228929 +Allele 183 0.085534136914397 +Allele 185 0.082062177802013 + +Locus 010 +Allele 108 0.049178618931232 +Allele 115 0.049120128569312 +Allele 121 0.048342103633482 +Allele 123 0.052583121844616 +Allele 125 0.049204759479630 +Allele 127 0.048451790561814 +Allele 129 0.050318501543843 +Allele 131 0.048850827031453 +Allele 133 0.051316808221266 +Allele 135 0.048942508196049 +Allele 137 0.053980622245896 +Allele 139 0.053940498349953 +Allele 141 0.051267776324918 +Allele 143 0.047360987768608 +Allele 145 0.046681215622610 +Allele 147 0.052238758033769 +Allele 149 0.050236346605985 +Allele 152 0.050162610338531 +Allele 155 0.047871186461251 +Allele 157 0.049950830235788 + + +Cluster 05 +Locus 001 +Allele 092 0.117998747574061 +Allele 094 0.112968412315215 +Allele 096 0.104241873645089 +Allele 098 0.117515516130226 +Allele 100 0.115417195425035 +Allele 102 0.103184342690045 +Allele 104 0.111869478121288 +Allele 106 0.120118034283592 +Allele 108 0.096686399815450 + +Locus 002 +Allele 118 0.079834320762632 +Allele 122 0.079883531865090 +Allele 124 0.081941555333713 +Allele 126 0.099487861173631 +Allele 127 0.080262845255862 +Allele 128 0.085337912678696 +Allele 130 0.081655540402518 +Allele 132 0.085520453025712 +Allele 134 0.076345346586519 +Allele 135 0.084737861480982 +Allele 137 0.086142290791455 +Allele 151 0.078850480643190 + +Locus 003 +Allele 130 0.067624828493864 +Allele 133 0.068275351059415 +Allele 136 0.070804159140114 +Allele 138 0.076084384818299 +Allele 139 0.073785170972660 +Allele 141 0.074086223687711 +Allele 143 0.065335672991235 +Allele 145 0.074335366300098 +Allele 146 0.071094837984376 +Allele 147 0.070442277230110 +Allele 148 0.076159782439379 +Allele 150 0.070068941995855 +Allele 152 0.075003850043018 +Allele 156 0.066899152843867 + +Locus 004 +Allele 093 0.057703439738236 +Allele 095 0.058826334367435 +Allele 096 0.054738917156772 +Allele 097 0.059532194193582 +Allele 099 0.061178844780864 +Allele 100 0.059543763450529 +Allele 101 0.065705744732658 +Allele 103 0.069217823596828 +Allele 105 0.056383637572049 +Allele 107 0.057168505638820 +Allele 109 0.056507736871861 +Allele 110 0.055970445454297 +Allele 113 0.061826100624411 +Allele 121 0.057950094131435 +Allele 123 0.055187842530319 +Allele 125 0.056170892061680 +Allele 131 0.056387683098227 + +Locus 005 +Allele 218 0.046978931016820 +Allele 220 0.050237046689944 +Allele 222 0.051536395224279 +Allele 224 0.051441099070452 +Allele 226 0.051559375338145 +Allele 228 0.050868891632203 +Allele 230 0.052639656310005 +Allele 232 0.051402762820091 +Allele 234 0.054034471025846 +Allele 236 0.052375230359805 +Allele 238 0.050933063021047 +Allele 240 0.049655493306062 +Allele 242 0.047464661596178 +Allele 244 0.048339220110345 +Allele 246 0.049286395314705 +Allele 248 0.048271784508679 +Allele 250 0.051194659134980 +Allele 252 0.048358421719655 +Allele 254 0.046234796766575 +Allele 256 0.047187645034183 + +Locus 006 +Allele 094 0.072979719301982 +Allele 096 0.070596030914106 +Allele 098 0.072314461880045 +Allele 100 0.065096166540351 +Allele 102 0.072538048483201 +Allele 104 0.081659974002132 +Allele 106 0.074544515611141 +Allele 108 0.069882061119255 +Allele 110 0.078355510155237 +Allele 112 0.074608215503476 +Allele 114 0.065874575955622 +Allele 124 0.068785353947194 +Allele 126 0.067483530225769 +Allele 149 0.065281836360488 + +Locus 007 +Allele 202 0.060666798401705 +Allele 204 0.058822236945721 +Allele 206 0.057956176749429 +Allele 208 0.066685848051512 +Allele 210 0.065116351055798 +Allele 212 0.062333346756971 +Allele 214 0.064119734712227 +Allele 216 0.061575205980116 +Allele 218 0.061030141925559 +Allele 220 0.062305200322539 +Allele 222 0.068493656461620 +Allele 224 0.062224569216810 +Allele 226 0.066332311316493 +Allele 228 0.060532530663904 +Allele 233 0.061103768726767 +Allele 238 0.060702122712828 + +Locus 008 +Allele 121 0.090016575798557 +Allele 123 0.103134924953533 +Allele 125 0.088373544186216 +Allele 127 0.081196824660511 +Allele 129 0.089947278766777 +Allele 131 0.089924712557965 +Allele 133 0.096347897629968 +Allele 135 0.088091134315931 +Allele 137 0.107479179998121 +Allele 151 0.082035640286516 +Allele 161 0.083452286845902 + +Locus 009 +Allele 161 0.077425896331225 +Allele 165 0.076965766015471 +Allele 167 0.089706660890191 +Allele 169 0.083822564317610 +Allele 171 0.087602893481821 +Allele 173 0.092203622654837 +Allele 175 0.083166507479231 +Allele 177 0.081962005864856 +Allele 179 0.077512464949429 +Allele 181 0.083062852876389 +Allele 183 0.084788969711334 +Allele 185 0.081779795427607 + +Locus 010 +Allele 108 0.049305079085412 +Allele 115 0.049112355199272 +Allele 121 0.048046154707873 +Allele 123 0.051180658587055 +Allele 125 0.049640206651487 +Allele 127 0.048766137719316 +Allele 129 0.050431427600867 +Allele 131 0.048870825228710 +Allele 133 0.051219525751195 +Allele 135 0.049167760244398 +Allele 137 0.053140865726122 +Allele 139 0.054350232991149 +Allele 141 0.050862121620918 +Allele 143 0.047169823322893 +Allele 145 0.047064619804327 +Allele 147 0.053328420524696 +Allele 149 0.050240293058788 +Allele 152 0.049908961265697 +Allele 155 0.048229843266891 +Allele 157 0.049964687642936 + + + +Estimated Mixing Proportions +0.013451746666667 +0.938225793333334 +0.016303140000000 +0.016415220000000 +0.015604100000000 + + + +Estimated sigma: +k: 0 1.000000000000000 +k: 1 1.000000000000000 +k: 2 1.000000000000000 +k: 3 1.000000000000000 +k: 4 1.000000000000000 + + + +Estimated psi: +k: 0 0.599999999999828 +k: 1 0.599999999999828 +k: 2 0.599999999999828 +k: 3 0.599999999999828 +k: 4 0.599999999999828 + + + diff --git a/inst/files/tess/tess_12.txt b/inst/files/tess/tess_12.txt new file mode 100644 index 0000000..0169547 --- /dev/null +++ b/inst/files/tess/tess_12.txt @@ -0,0 +1,1114 @@ +Estimated Clustering Probabilities for Samples +Sample ***Cluster 01*** ***Cluster 02*** ***Cluster 03*** ***Cluster 04*** ***Cluster 05*** ***Cluster 06*** +000001: 0.006543000000000 0.007226000000000 0.006819500000000 0.966442000000000 0.005917500000000 0.007052000000000 1 +000002: 0.006603500000000 0.007063500000000 0.006108000000000 0.969008000000000 0.005485000000000 0.005732000000000 1 +000003: 0.003512000000000 0.003387500000000 0.003272500000000 0.983788500000000 0.002945000000000 0.003094500000000 1 +000004: 0.010055000000000 0.010376000000000 0.008909000000000 0.952022500000000 0.009033500000000 0.009604000000000 1 +000005: 0.008434000000000 0.008597500000000 0.006935000000000 0.959134000000000 0.007708500000000 0.009191000000000 1 +000006: 0.003693000000000 0.003666500000000 0.003346500000000 0.982359500000000 0.003213000000000 0.003721500000000 1 +000007: 0.040918000000000 0.049813000000000 0.039793500000000 0.772482000000000 0.042035000000000 0.054958500000000 1 +000008: 0.011631500000000 0.011901000000000 0.010256000000000 0.941455000000000 0.011895000000000 0.012861500000000 1 +000009: 0.018413000000000 0.017709000000000 0.016856500000000 0.909137000000000 0.018804000000000 0.019080500000000 1 +000010: 0.016087000000000 0.018104500000000 0.012892500000000 0.922269000000000 0.015311500000000 0.015335500000000 1 +000011: 0.017414000000000 0.019873000000000 0.013881000000000 0.911722500000000 0.017112500000000 0.019997000000000 1 +000012: 0.004821500000000 0.005679000000000 0.003934500000000 0.976440500000000 0.004307500000000 0.004817000000000 1 +000013: 0.010965500000000 0.012189000000000 0.008499000000000 0.948094500000000 0.009471000000000 0.010781000000000 1 +000014: 0.010577500000000 0.012138000000000 0.008204000000000 0.950222000000000 0.009530500000000 0.009328000000000 1 +000015: 0.010045500000000 0.010718000000000 0.008618000000000 0.952396500000000 0.008674500000000 0.009547500000000 1 +000016: 0.002822500000000 0.002799000000000 0.002492000000000 0.987069500000000 0.002249000000000 0.002568000000000 1 +000017: 0.009793000000000 0.011067500000000 0.009259500000000 0.952210000000000 0.008254500000000 0.009415500000000 1 +000018: 0.011446000000000 0.013371000000000 0.010408500000000 0.942922500000000 0.010420000000000 0.011432000000000 1 +000019: 0.035823500000000 0.044947500000000 0.030766000000000 0.816210000000000 0.035453000000000 0.036800000000000 1 +000020: 0.019833000000000 0.025558500000000 0.016908500000000 0.897901000000000 0.019317000000000 0.020482000000000 1 +000021: 0.024736000000000 0.030980500000000 0.020347500000000 0.881263000000000 0.020873000000000 0.021800000000000 1 +000022: 0.038454500000000 0.048034500000000 0.033553500000000 0.799984500000000 0.034542500000000 0.045430500000000 1 +000023: 0.003262500000000 0.004115500000000 0.003050000000000 0.983590000000000 0.002790500000000 0.003191500000000 1 +000024: 0.005422000000000 0.007330000000000 0.004731500000000 0.972567000000000 0.004922000000000 0.005027500000000 1 +000025: 0.007587500000000 0.009267500000000 0.007042500000000 0.962239000000000 0.006413500000000 0.007450000000000 1 +000026: 0.007683500000000 0.009249000000000 0.007050500000000 0.962763500000000 0.006288000000000 0.006965500000000 1 +000027: 0.008058500000000 0.009003500000000 0.007568000000000 0.961167500000000 0.006735000000000 0.007467500000000 1 +000028: 0.003144500000000 0.003499500000000 0.003099500000000 0.984749500000000 0.002534000000000 0.002973000000000 1 +000029: 0.010958000000000 0.011420500000000 0.010779000000000 0.948759500000000 0.009021000000000 0.009062000000000 1 +000030: 0.017456000000000 0.014487500000000 0.015563500000000 0.930072500000000 0.011125000000000 0.011295500000000 1 +000031: 0.005343000000000 0.005555500000000 0.005220000000000 0.975415500000000 0.004149500000000 0.004316500000000 1 +000032: 0.004071500000000 0.003792500000000 0.003263000000000 0.982877500000000 0.002863000000000 0.003132500000000 1 +000033: 0.009124000000000 0.008764500000000 0.008467500000000 0.959053500000000 0.007242500000000 0.007348000000000 1 +000034: 0.005413500000000 0.004553500000000 0.005014500000000 0.977476000000000 0.003723500000000 0.003819000000000 1 +000035: 0.007112500000000 0.007587500000000 0.006906000000000 0.966915000000000 0.005278000000000 0.006201000000000 1 +000036: 0.006005500000000 0.006802500000000 0.005732500000000 0.970758000000000 0.004621000000000 0.006080500000000 1 +000037: 0.006764500000000 0.006709500000000 0.005908000000000 0.969359000000000 0.005298500000000 0.005960500000000 1 +000038: 0.009416000000000 0.008303000000000 0.008703000000000 0.957228500000000 0.008010000000000 0.008339500000000 1 +000039: 0.014808500000000 0.010089000000000 0.013486500000000 0.942997500000000 0.007991000000000 0.010627500000000 1 +000040: 0.006199000000000 0.004095500000000 0.004902500000000 0.977364500000000 0.003721500000000 0.003717000000000 1 +000041: 0.007845000000000 0.006821500000000 0.008777500000000 0.964122000000000 0.005933000000000 0.006501000000000 1 +000042: 0.004544000000000 0.004521000000000 0.004448000000000 0.978780500000000 0.003794500000000 0.003912000000000 1 +000043: 0.006461500000000 0.006003500000000 0.006079000000000 0.971006000000000 0.005067500000000 0.005382500000000 1 +000044: 0.004885000000000 0.004545500000000 0.004239000000000 0.978587000000000 0.003947500000000 0.003796000000000 1 +000045: 0.021747000000000 0.024365000000000 0.019157500000000 0.887183500000000 0.022750500000000 0.024796500000000 1 +000046: 0.008222500000000 0.010169000000000 0.007152000000000 0.955752000000000 0.009363000000000 0.009341500000000 1 +000047: 0.023259000000000 0.024152000000000 0.019112500000000 0.881516000000000 0.027285000000000 0.024675500000000 1 +000048: 0.034432500000000 0.035304000000000 0.031717500000000 0.817820000000000 0.041683000000000 0.039043000000000 1 +000049: 0.031734000000000 0.036766000000000 0.029289500000000 0.826582000000000 0.034957000000000 0.040671500000000 1 +000050: 0.030095500000000 0.031464500000000 0.027878500000000 0.845188500000000 0.031152500000000 0.034220500000000 1 +000051: 0.041383000000000 0.040518000000000 0.036906500000000 0.792570500000000 0.041652500000000 0.046969500000000 1 +000052: 0.010838000000000 0.011229500000000 0.010113500000000 0.943729500000000 0.011419000000000 0.012670500000000 1 +000053: 0.005613000000000 0.007071500000000 0.004776500000000 0.969967000000000 0.006013000000000 0.006559000000000 1 +000054: 0.030142500000000 0.031793500000000 0.025872500000000 0.844396500000000 0.033627000000000 0.034168000000000 1 +000055: 0.011609500000000 0.014310500000000 0.010220000000000 0.938636000000000 0.012249500000000 0.012974500000000 1 +000056: 0.012841000000000 0.013373000000000 0.010197500000000 0.936864500000000 0.013035000000000 0.013689000000000 1 +000057: 0.021749000000000 0.023668500000000 0.017442500000000 0.891945500000000 0.022451500000000 0.022743000000000 1 +000058: 0.008571000000000 0.010282500000000 0.006832000000000 0.955014000000000 0.009623000000000 0.009677500000000 1 +000059: 0.032483000000000 0.035114500000000 0.026309500000000 0.838601000000000 0.034452000000000 0.033040000000000 1 +000060: 0.026753000000000 0.031871500000000 0.020796000000000 0.866391500000000 0.024982500000000 0.029205500000000 1 +000061: 0.011888000000000 0.013500000000000 0.010406000000000 0.939604500000000 0.012385000000000 0.012216500000000 1 +000062: 0.034409500000000 0.038173500000000 0.029304500000000 0.826977500000000 0.034107500000000 0.037027500000000 1 +000063: 0.017495500000000 0.021445500000000 0.013887000000000 0.911993500000000 0.017552500000000 0.017626000000000 1 +000064: 0.051690000000000 0.054641500000000 0.042915000000000 0.736730000000000 0.058085000000000 0.055938500000000 1 +000065: 0.020166000000000 0.024855000000000 0.017141000000000 0.902738500000000 0.016425000000000 0.018674500000000 1 +000066: 0.011377500000000 0.015215500000000 0.012301500000000 0.941523500000000 0.009282500000000 0.010299500000000 1 +000067: 0.004597000000000 0.005092500000000 0.004159000000000 0.979204000000000 0.003581000000000 0.003366500000000 1 +000068: 0.011991500000000 0.013980500000000 0.011710000000000 0.944015000000000 0.009178500000000 0.009124500000000 1 +000069: 0.005035000000000 0.005059500000000 0.005126500000000 0.977271500000000 0.003739000000000 0.003768500000000 1 +000070: 0.008116500000000 0.009302000000000 0.008082000000000 0.962237000000000 0.006123000000000 0.006139500000000 1 +000071: 0.003948000000000 0.004386000000000 0.003670500000000 0.981770000000000 0.002936000000000 0.003289500000000 1 +000072: 0.003979000000000 0.003832500000000 0.003405000000000 0.982907500000000 0.002811000000000 0.003065000000000 1 +000073: 0.005246000000000 0.004078000000000 0.004071500000000 0.979944000000000 0.003278500000000 0.003382000000000 1 +000074: 0.009929500000000 0.008889000000000 0.009711000000000 0.957646500000000 0.006859000000000 0.006965000000000 1 +000075: 0.007282500000000 0.006730000000000 0.006523000000000 0.969196500000000 0.005151000000000 0.005117000000000 1 + + + +Estimated Allele Frequencies +Cluster 01 +Locus 001 +Allele 092 0.116385019530884 +Allele 094 0.113888066347871 +Allele 096 0.106177441726139 +Allele 098 0.116812181106730 +Allele 100 0.113670684620799 +Allele 102 0.105925778125163 +Allele 104 0.110987933234489 +Allele 106 0.117360033867082 +Allele 108 0.098792861440842 + +Locus 002 +Allele 118 0.080210309341411 +Allele 122 0.080691417238511 +Allele 124 0.083147270636887 +Allele 126 0.095568845369813 +Allele 127 0.080214121416085 +Allele 128 0.085630584384119 +Allele 130 0.082083273610159 +Allele 132 0.086253126797095 +Allele 134 0.077151585485655 +Allele 135 0.084134001818507 +Allele 137 0.085853009831307 +Allele 151 0.079062454070452 + +Locus 003 +Allele 130 0.068588157554422 +Allele 133 0.068528259981785 +Allele 136 0.071150882996740 +Allele 138 0.075214924198982 +Allele 139 0.072988482341209 +Allele 141 0.073972212623051 +Allele 143 0.066082541178224 +Allele 145 0.073008786021409 +Allele 146 0.071715999822793 +Allele 147 0.070284354369150 +Allele 148 0.076072894420329 +Allele 150 0.070818366268036 +Allele 152 0.073804494020674 +Allele 156 0.067769644203197 + +Locus 004 +Allele 093 0.057716414563395 +Allele 095 0.058845412762769 +Allele 096 0.054984940514453 +Allele 097 0.059690768406811 +Allele 099 0.060938899538981 +Allele 100 0.059841512367035 +Allele 101 0.064356381683832 +Allele 103 0.065321167460258 +Allele 105 0.056956394551518 +Allele 107 0.057490454000977 +Allele 109 0.057395359164721 +Allele 110 0.056776789387537 +Allele 113 0.061298938417227 +Allele 121 0.058398903973717 +Allele 123 0.056112986483827 +Allele 125 0.056921428407807 +Allele 131 0.056953248315136 + +Locus 005 +Allele 218 0.047424244895629 +Allele 220 0.050106218741022 +Allele 222 0.051806800395715 +Allele 224 0.051208083188896 +Allele 226 0.051692043710198 +Allele 228 0.050371494957074 +Allele 230 0.051719264519499 +Allele 232 0.051062511978516 +Allele 234 0.053203053151870 +Allele 236 0.051785209038622 +Allele 238 0.051044150223314 +Allele 240 0.050013420720214 +Allele 242 0.048234681288446 +Allele 244 0.048633048856799 +Allele 246 0.049334185023431 +Allele 248 0.048447431230728 +Allele 250 0.050499112597373 +Allele 252 0.048682750658257 +Allele 254 0.047042126632208 +Allele 256 0.047690168192184 + +Locus 006 +Allele 094 0.072405767803654 +Allele 096 0.071525370815303 +Allele 098 0.072930330525634 +Allele 100 0.066294006644925 +Allele 102 0.073285896937830 +Allele 104 0.079160165721076 +Allele 106 0.075147031919499 +Allele 108 0.070454805150069 +Allele 110 0.076309021703079 +Allele 112 0.073433320874865 +Allele 114 0.066651535562405 +Allele 124 0.069046706324316 +Allele 126 0.067665994355747 +Allele 149 0.065690045661597 + +Locus 007 +Allele 202 0.060408912079897 +Allele 204 0.059505403279329 +Allele 206 0.058453584864575 +Allele 208 0.065895061247044 +Allele 210 0.065104529488928 +Allele 212 0.062518629666825 +Allele 214 0.064125964047969 +Allele 216 0.062020819369386 +Allele 218 0.061853069692155 +Allele 220 0.062584951525544 +Allele 222 0.067827174567345 +Allele 224 0.062276815632777 +Allele 226 0.064924568355239 +Allele 228 0.061027411842912 +Allele 233 0.060338235223053 +Allele 238 0.061134869117024 + +Locus 008 +Allele 121 0.090951171583684 +Allele 123 0.098356022595583 +Allele 125 0.088337905309305 +Allele 127 0.081862697362953 +Allele 129 0.090298063121881 +Allele 131 0.090391958820268 +Allele 133 0.095286086127961 +Allele 135 0.090159195287677 +Allele 137 0.105528376205006 +Allele 151 0.084101015368506 +Allele 161 0.084727508217171 + +Locus 009 +Allele 161 0.077479480677158 +Allele 165 0.078144893930522 +Allele 167 0.087416183477648 +Allele 169 0.083160919131789 +Allele 171 0.087135178964978 +Allele 173 0.090527356010716 +Allele 175 0.083832075805793 +Allele 177 0.082389308325921 +Allele 179 0.078410822802911 +Allele 181 0.083789913190411 +Allele 183 0.084717168048571 +Allele 185 0.082996699633580 + +Locus 010 +Allele 108 0.049630109506005 +Allele 115 0.049108914828748 +Allele 121 0.048424482287555 +Allele 123 0.051343933219396 +Allele 125 0.049895771216644 +Allele 127 0.049101927340776 +Allele 129 0.050369573570172 +Allele 131 0.049761712343351 +Allele 133 0.050871478993245 +Allele 135 0.049263994886366 +Allele 137 0.052421760895011 +Allele 139 0.053419092365028 +Allele 141 0.050956257298659 +Allele 143 0.047544857115130 +Allele 145 0.047946349192507 +Allele 147 0.051232856088508 +Allele 149 0.050214943475725 +Allele 152 0.050096890844637 +Allele 155 0.048288674210930 +Allele 157 0.050106420321608 + + +Cluster 02 +Locus 001 +Allele 092 0.116398250965795 +Allele 094 0.113070714959788 +Allele 096 0.105685632200454 +Allele 098 0.117742580995792 +Allele 100 0.113759448371314 +Allele 102 0.104247149691904 +Allele 104 0.112320322869671 +Allele 106 0.118298870616946 +Allele 108 0.098477029328339 + +Locus 002 +Allele 118 0.079814941728369 +Allele 122 0.080206618939597 +Allele 124 0.082224996162816 +Allele 126 0.098233713762768 +Allele 127 0.079818902924657 +Allele 128 0.086313285623418 +Allele 130 0.082125557944295 +Allele 132 0.085139143617488 +Allele 134 0.076629329578392 +Allele 135 0.084352699799046 +Allele 137 0.086698641344095 +Allele 151 0.078442168575060 + +Locus 003 +Allele 130 0.068541323684105 +Allele 133 0.067704903169217 +Allele 136 0.071024609882168 +Allele 138 0.075744053802160 +Allele 139 0.073305181424317 +Allele 141 0.075107533437258 +Allele 143 0.065395406309829 +Allele 145 0.073641869510751 +Allele 146 0.071432552753221 +Allele 147 0.069472243068709 +Allele 148 0.076327194283625 +Allele 150 0.070650180641526 +Allele 152 0.074067086732855 +Allele 156 0.067585861300262 + +Locus 004 +Allele 093 0.057772127383021 +Allele 095 0.059243103023988 +Allele 096 0.054653176942113 +Allele 097 0.059431919024042 +Allele 099 0.061864387741947 +Allele 100 0.059437933579512 +Allele 101 0.065123213041816 +Allele 103 0.067337328748133 +Allele 105 0.056134444767135 +Allele 107 0.057663292343539 +Allele 109 0.056859637614225 +Allele 110 0.056443022598303 +Allele 113 0.061144253326315 +Allele 121 0.058285478394449 +Allele 123 0.055675848522858 +Allele 125 0.056524829200451 +Allele 131 0.056406003748152 + +Locus 005 +Allele 218 0.046990120358780 +Allele 220 0.049893119894901 +Allele 222 0.051587473069395 +Allele 224 0.051597640131757 +Allele 226 0.051108422209106 +Allele 228 0.050980418437923 +Allele 230 0.052303287787622 +Allele 232 0.051410338251264 +Allele 234 0.054024196070755 +Allele 236 0.052194922622063 +Allele 238 0.050557027617968 +Allele 240 0.050199638958661 +Allele 242 0.047857863749285 +Allele 244 0.048578899408415 +Allele 246 0.049195735706599 +Allele 248 0.048713289679039 +Allele 250 0.050455227230293 +Allele 252 0.048447361030123 +Allele 254 0.046673294381859 +Allele 256 0.047231723404187 + +Locus 006 +Allele 094 0.072656569849558 +Allele 096 0.070986701525798 +Allele 098 0.072990974828110 +Allele 100 0.065512440235631 +Allele 102 0.072294484951065 +Allele 104 0.080858861448795 +Allele 106 0.074586888054277 +Allele 108 0.070465327060694 +Allele 110 0.077874624261829 +Allele 112 0.073054466771375 +Allele 114 0.066350002553799 +Allele 124 0.068515124066248 +Allele 126 0.068046711997693 +Allele 149 0.065806822395125 + +Locus 007 +Allele 202 0.060802095370661 +Allele 204 0.059558811953032 +Allele 206 0.058227199671962 +Allele 208 0.066118640763788 +Allele 210 0.065339822861194 +Allele 212 0.062481736245278 +Allele 214 0.064082499635298 +Allele 216 0.062408168907701 +Allele 218 0.061355597422245 +Allele 220 0.062421541415136 +Allele 222 0.067809550181088 +Allele 224 0.062134104671045 +Allele 226 0.065665078633387 +Allele 228 0.060349519902453 +Allele 233 0.060821818551092 +Allele 238 0.060423813814637 + +Locus 008 +Allele 121 0.091730821229414 +Allele 123 0.101040719673981 +Allele 125 0.089020873392743 +Allele 127 0.081634963890209 +Allele 129 0.090241578227283 +Allele 131 0.089968761520158 +Allele 133 0.095951212226264 +Allele 135 0.089176567671511 +Allele 137 0.104460549860573 +Allele 151 0.082488589693400 +Allele 161 0.084285362614465 + +Locus 009 +Allele 161 0.077732352595608 +Allele 165 0.077867825768904 +Allele 167 0.088860350286277 +Allele 169 0.083409437830426 +Allele 171 0.087653075632499 +Allele 173 0.090877794758273 +Allele 175 0.082930848633133 +Allele 177 0.083021450217289 +Allele 179 0.077972671400859 +Allele 181 0.083190134603953 +Allele 183 0.084126293095915 +Allele 185 0.082357765176861 + +Locus 010 +Allele 108 0.049072404008121 +Allele 115 0.049151756133760 +Allele 121 0.048197253195076 +Allele 123 0.051621318735026 +Allele 125 0.049908475148447 +Allele 127 0.048736712078939 +Allele 129 0.050152685253403 +Allele 131 0.048949867117495 +Allele 133 0.052088866946802 +Allele 135 0.048987113404427 +Allele 137 0.052603553047906 +Allele 139 0.054809050644399 +Allele 141 0.050897728809962 +Allele 143 0.047448876411133 +Allele 145 0.047683036452727 +Allele 147 0.052023693020718 +Allele 149 0.049603989389613 +Allele 152 0.049728059174252 +Allele 155 0.048350309101655 +Allele 157 0.049985251926139 + + +Cluster 03 +Locus 001 +Allele 092 0.114687852968100 +Allele 094 0.112940583546324 +Allele 096 0.106672862174980 +Allele 098 0.116192385057390 +Allele 100 0.112564421518671 +Allele 102 0.106264104837390 +Allele 104 0.112061933828132 +Allele 106 0.117814533305720 +Allele 108 0.100801322763295 + +Locus 002 +Allele 118 0.080700706978521 +Allele 122 0.080896507689404 +Allele 124 0.082685567746718 +Allele 126 0.093666448087049 +Allele 127 0.080773103090842 +Allele 128 0.085170278357322 +Allele 130 0.082459767914031 +Allele 132 0.086320938839302 +Allele 134 0.077887211386477 +Allele 135 0.084717517721453 +Allele 137 0.085636171902473 +Allele 151 0.079085780286408 + +Locus 003 +Allele 130 0.068565400328924 +Allele 133 0.068673555026959 +Allele 136 0.071034385165498 +Allele 138 0.075285079800937 +Allele 139 0.073432321606397 +Allele 141 0.073997315772055 +Allele 143 0.066781506941141 +Allele 145 0.073629448839775 +Allele 146 0.071652966237093 +Allele 147 0.070124165837375 +Allele 148 0.075062442243197 +Allele 150 0.070993085708698 +Allele 152 0.073311961677838 +Allele 156 0.067456364814114 + +Locus 004 +Allele 093 0.058366396286852 +Allele 095 0.059024595693375 +Allele 096 0.055455140710141 +Allele 097 0.060122927393010 +Allele 099 0.060139205350366 +Allele 100 0.059836870260741 +Allele 101 0.062810474030995 +Allele 103 0.065107405278937 +Allele 105 0.056918720308298 +Allele 107 0.057761495119382 +Allele 109 0.058048681353347 +Allele 110 0.057237183610167 +Allele 113 0.060746306442757 +Allele 121 0.057958272049153 +Allele 123 0.056700758168725 +Allele 125 0.056730830362262 +Allele 131 0.057034737581488 + +Locus 005 +Allele 218 0.047679309076648 +Allele 220 0.050040935554342 +Allele 222 0.051327552700907 +Allele 224 0.051228448198222 +Allele 226 0.051160907886812 +Allele 228 0.050482708046778 +Allele 230 0.051880659719400 +Allele 232 0.051127860532525 +Allele 234 0.053049452271770 +Allele 236 0.051533532008815 +Allele 238 0.050811167215316 +Allele 240 0.049679822002949 +Allele 242 0.048154520448996 +Allele 244 0.048708754970874 +Allele 246 0.049975151127205 +Allele 248 0.048628029498479 +Allele 250 0.050714712776759 +Allele 252 0.048827190559079 +Allele 254 0.047016482312473 +Allele 256 0.047972803091648 + +Locus 006 +Allele 094 0.072424238130753 +Allele 096 0.071017091630582 +Allele 098 0.072359335948348 +Allele 100 0.066370139012366 +Allele 102 0.072990458936482 +Allele 104 0.077688498811186 +Allele 106 0.074849513008131 +Allele 108 0.071166780077080 +Allele 110 0.075702390396163 +Allele 112 0.073790874413513 +Allele 114 0.067129607021054 +Allele 124 0.069260081709441 +Allele 126 0.068497333435820 +Allele 149 0.066753657469078 + +Locus 007 +Allele 202 0.060877629690268 +Allele 204 0.060105000145721 +Allele 206 0.059340512096336 +Allele 208 0.065718565245933 +Allele 210 0.064685687462098 +Allele 212 0.062871454515966 +Allele 214 0.063621465633072 +Allele 216 0.061932091782032 +Allele 218 0.061477816504964 +Allele 220 0.062533630191891 +Allele 222 0.066983888882528 +Allele 224 0.062448381484540 +Allele 226 0.064390086640773 +Allele 228 0.060988279428249 +Allele 233 0.060617397250435 +Allele 238 0.061408113045195 + +Locus 008 +Allele 121 0.090744499165390 +Allele 123 0.097862368022300 +Allele 125 0.088967784630406 +Allele 127 0.082910699708845 +Allele 129 0.090779036405333 +Allele 131 0.089905835577313 +Allele 133 0.096014366016350 +Allele 135 0.089820360254585 +Allele 137 0.104103214298000 +Allele 151 0.084062192437552 +Allele 161 0.084829643483928 + +Locus 009 +Allele 161 0.078125397674565 +Allele 165 0.079413929804499 +Allele 167 0.086657101229049 +Allele 169 0.083106363590186 +Allele 171 0.086821606745780 +Allele 173 0.088723116632399 +Allele 175 0.084548317784710 +Allele 177 0.082387161466110 +Allele 179 0.078974535185845 +Allele 181 0.083419096922914 +Allele 183 0.084271576505981 +Allele 185 0.083551796457958 + +Locus 010 +Allele 108 0.049379111326151 +Allele 115 0.049032045163222 +Allele 121 0.048621353272776 +Allele 123 0.051651237687505 +Allele 125 0.049884138122071 +Allele 127 0.049321580806873 +Allele 129 0.050031711281399 +Allele 131 0.049779889337768 +Allele 133 0.050928946851414 +Allele 135 0.049550675190384 +Allele 137 0.052179113435331 +Allele 139 0.052891972662839 +Allele 141 0.050985943295992 +Allele 143 0.047533570538109 +Allele 145 0.048318484480307 +Allele 147 0.051550293361073 +Allele 149 0.050137026117944 +Allele 152 0.050024472467381 +Allele 155 0.048278947297701 +Allele 157 0.049919487303765 + + +Cluster 04 +Locus 001 +Allele 092 0.037148535960040 +Allele 094 0.400627838764025 +Allele 096 0.063020310958798 +Allele 098 0.200998324642032 +Allele 100 0.086751102525385 +Allele 102 0.090831966589404 +Allele 104 0.073455114631697 +Allele 106 0.028799257207104 +Allele 108 0.018367548721512 + +Locus 002 +Allele 118 0.016033271423786 +Allele 122 0.029056957291679 +Allele 124 0.212602305276542 +Allele 126 0.124602201293519 +Allele 127 0.009157578193553 +Allele 128 0.098328172553315 +Allele 130 0.074154775476462 +Allele 132 0.236695647969580 +Allele 134 0.011189179536890 +Allele 135 0.106001018727686 +Allele 137 0.072153520543004 +Allele 151 0.010025371713983 + +Locus 003 +Allele 130 0.023320544089390 +Allele 133 0.010086175346301 +Allele 136 0.132027589237015 +Allele 138 0.103009028736259 +Allele 139 0.136832803392622 +Allele 141 0.032606479679320 +Allele 143 0.011722791570222 +Allele 145 0.085007149035753 +Allele 146 0.112319391969659 +Allele 147 0.009108221996036 +Allele 148 0.148534002647448 +Allele 150 0.080489553137554 +Allele 152 0.097684728828965 +Allele 156 0.017251540333458 + +Locus 004 +Allele 093 0.047943170061785 +Allele 095 0.072689542057524 +Allele 096 0.011550018830597 +Allele 097 0.187065580544718 +Allele 099 0.051667860306736 +Allele 100 0.084881282492322 +Allele 101 0.151520416745894 +Allele 103 0.137321271486713 +Allele 105 0.048802751059711 +Allele 107 0.092810605508574 +Allele 109 0.023039966325866 +Allele 110 0.023294615464079 +Allele 113 0.013616775185112 +Allele 121 0.015664218779439 +Allele 123 0.017477947366839 +Allele 125 0.010318803370992 +Allele 131 0.010335174413102 + +Locus 005 +Allele 218 0.011588549003909 +Allele 220 0.096897399882027 +Allele 222 0.133221617974455 +Allele 224 0.133660853851889 +Allele 226 0.095938114768991 +Allele 228 0.046464330688195 +Allele 230 0.045337163186370 +Allele 232 0.064870860185706 +Allele 234 0.068767194965061 +Allele 236 0.057735748911728 +Allele 238 0.077400605030633 +Allele 240 0.040553792357129 +Allele 242 0.035938484279830 +Allele 244 0.010539229726517 +Allele 246 0.015946709939597 +Allele 248 0.010450634814289 +Allele 250 0.014978407215235 +Allele 252 0.016594961475541 +Allele 254 0.011796813374254 +Allele 256 0.011318528368646 + +Locus 006 +Allele 094 0.106602545498460 +Allele 096 0.173005876993399 +Allele 098 0.040327643028089 +Allele 100 0.012092939137567 +Allele 102 0.099576121799227 +Allele 104 0.239518374547595 +Allele 106 0.144549094317209 +Allele 108 0.068385880577945 +Allele 110 0.050915648874227 +Allele 112 0.020377754513703 +Allele 114 0.011613502473565 +Allele 124 0.010013951869649 +Allele 126 0.010969854227416 +Allele 149 0.012050812141951 + +Locus 007 +Allele 202 0.010213565210936 +Allele 204 0.024207575802177 +Allele 206 0.011765601568318 +Allele 208 0.138195112239287 +Allele 210 0.039964742784425 +Allele 212 0.187155050608319 +Allele 214 0.106909992718253 +Allele 216 0.114652486857707 +Allele 218 0.062347800219688 +Allele 220 0.055067575315970 +Allele 222 0.057863406481601 +Allele 224 0.114558215764505 +Allele 226 0.039891949015309 +Allele 228 0.016832517788272 +Allele 233 0.010381355716788 +Allele 238 0.009993051908443 + +Locus 008 +Allele 121 0.085845680725724 +Allele 123 0.080546390314859 +Allele 125 0.056802454956854 +Allele 127 0.014307907614335 +Allele 129 0.055650513342275 +Allele 131 0.272175129098553 +Allele 133 0.152393328912749 +Allele 135 0.187467605969930 +Allele 137 0.068333088877623 +Allele 151 0.013677192228622 +Allele 161 0.012800707958478 + +Locus 009 +Allele 161 0.014539882717757 +Allele 165 0.030122731900174 +Allele 167 0.055770182971715 +Allele 169 0.099719006904376 +Allele 171 0.282971241750308 +Allele 173 0.191599617978715 +Allele 175 0.107324494560388 +Allele 177 0.107811593310931 +Allele 179 0.013959104454524 +Allele 181 0.042789004822089 +Allele 183 0.025793666634518 +Allele 185 0.027599471994507 + +Locus 010 +Allele 108 0.028875403519884 +Allele 115 0.010024893718198 +Allele 121 0.010507721898888 +Allele 123 0.045915505755862 +Allele 125 0.098612185090860 +Allele 127 0.073777024444667 +Allele 129 0.085508418874959 +Allele 131 0.092446277331487 +Allele 133 0.167501473153870 +Allele 135 0.105433771728015 +Allele 137 0.083330277064194 +Allele 139 0.025338315654108 +Allele 141 0.040350598277062 +Allele 143 0.011106487366341 +Allele 145 0.030234516352182 +Allele 147 0.020672627143168 +Allele 149 0.028356979208483 +Allele 152 0.015727876050374 +Allele 155 0.010685908333241 +Allele 157 0.015593739034159 + + +Cluster 05 +Locus 001 +Allele 092 0.117467933965593 +Allele 094 0.112915741326391 +Allele 096 0.104783428358805 +Allele 098 0.117302377960244 +Allele 100 0.112063196138010 +Allele 102 0.103741709438605 +Allele 104 0.113109211832575 +Allele 106 0.119700682805995 +Allele 108 0.098915718173784 + +Locus 002 +Allele 118 0.080400553089342 +Allele 122 0.080376212633386 +Allele 124 0.081835860867110 +Allele 126 0.097043194940221 +Allele 127 0.081944541973212 +Allele 128 0.085278085407903 +Allele 130 0.082546147300266 +Allele 132 0.085161485676078 +Allele 134 0.077189375967464 +Allele 135 0.083380597746072 +Allele 137 0.085200902199606 +Allele 151 0.079643042199342 + +Locus 003 +Allele 130 0.068298010976405 +Allele 133 0.069371299860396 +Allele 136 0.071784454764709 +Allele 138 0.075271098485301 +Allele 139 0.073854884264266 +Allele 141 0.074358237846637 +Allele 143 0.065614645748869 +Allele 145 0.072861001329064 +Allele 146 0.071240837025932 +Allele 147 0.071316125397894 +Allele 148 0.075240750816954 +Allele 150 0.069981344002527 +Allele 152 0.073287051641505 +Allele 156 0.067520257839538 + +Locus 004 +Allele 093 0.057694330790847 +Allele 095 0.059080866410836 +Allele 096 0.055269746026429 +Allele 097 0.059620441970270 +Allele 099 0.061388797120837 +Allele 100 0.060323085261820 +Allele 101 0.064253595591314 +Allele 103 0.065667153289395 +Allele 105 0.056511845787107 +Allele 107 0.057520828512428 +Allele 109 0.056268045806528 +Allele 110 0.056024161093526 +Allele 113 0.061286318483285 +Allele 121 0.058317723793932 +Allele 123 0.055575040774174 +Allele 125 0.057617249647304 +Allele 131 0.057580769639960 + +Locus 005 +Allele 218 0.046976191941606 +Allele 220 0.049855680985222 +Allele 222 0.051848009374840 +Allele 224 0.050859892420812 +Allele 226 0.051703589072221 +Allele 228 0.050135553697493 +Allele 230 0.051393589509430 +Allele 232 0.050599670755291 +Allele 234 0.053313730459098 +Allele 236 0.051841986314691 +Allele 238 0.051243471974888 +Allele 240 0.050329512752014 +Allele 242 0.048075345741047 +Allele 244 0.048607669846337 +Allele 246 0.050130807154852 +Allele 248 0.049054308886629 +Allele 250 0.051116398611329 +Allele 252 0.048783888714306 +Allele 254 0.046630532130222 +Allele 256 0.047500169657671 + +Locus 006 +Allele 094 0.072202755879472 +Allele 096 0.070720952181037 +Allele 098 0.073581738064464 +Allele 100 0.066232190168328 +Allele 102 0.072811755554824 +Allele 104 0.078913029189903 +Allele 106 0.074449123964354 +Allele 108 0.070004598132504 +Allele 110 0.076336671691607 +Allele 112 0.074126599328724 +Allele 114 0.066652048543537 +Allele 124 0.069629201226446 +Allele 126 0.068396185179762 +Allele 149 0.065943150895036 + +Locus 007 +Allele 202 0.061150925122583 +Allele 204 0.059640123736164 +Allele 206 0.058156440560907 +Allele 208 0.065639752373996 +Allele 210 0.064706947247682 +Allele 212 0.062187216809814 +Allele 214 0.063725536063812 +Allele 216 0.062061716009577 +Allele 218 0.062135683283878 +Allele 220 0.061972664977894 +Allele 222 0.068123985162201 +Allele 224 0.062389897433060 +Allele 226 0.064982785358787 +Allele 228 0.060953913886656 +Allele 233 0.060388929364520 +Allele 238 0.061783482608468 + +Locus 008 +Allele 121 0.090706342648465 +Allele 123 0.097961567339879 +Allele 125 0.087998125847745 +Allele 127 0.081925071162904 +Allele 129 0.090822782470151 +Allele 131 0.090107394451439 +Allele 133 0.095300365768870 +Allele 135 0.089066871195761 +Allele 137 0.107818389562571 +Allele 151 0.082976491912574 +Allele 161 0.085316597639645 + +Locus 009 +Allele 161 0.077347215253294 +Allele 165 0.078317638311317 +Allele 167 0.088017739756679 +Allele 169 0.082063465363404 +Allele 171 0.087401647050725 +Allele 173 0.090295899070184 +Allele 175 0.083551227505970 +Allele 177 0.082747596481576 +Allele 179 0.078592132994685 +Allele 181 0.084248533838707 +Allele 183 0.085804005922132 +Allele 185 0.081612898451332 + +Locus 010 +Allele 108 0.049247585497100 +Allele 115 0.049273556953127 +Allele 121 0.048551568910423 +Allele 123 0.051929969191614 +Allele 125 0.049658488149906 +Allele 127 0.049085109062872 +Allele 129 0.050233908953246 +Allele 131 0.049532023955666 +Allele 133 0.050559581385180 +Allele 135 0.049254356823906 +Allele 137 0.052522276707847 +Allele 139 0.053434168095954 +Allele 141 0.051812790988069 +Allele 143 0.048239512994586 +Allele 145 0.047124372509049 +Allele 147 0.051089916086774 +Allele 149 0.050503138934647 +Allele 152 0.050121029880517 +Allele 155 0.048017357001915 +Allele 157 0.049809287917601 + + +Cluster 06 +Locus 001 +Allele 092 0.117110894856946 +Allele 094 0.112166153321328 +Allele 096 0.104329336128517 +Allele 098 0.117048910125218 +Allele 100 0.113212340871630 +Allele 102 0.103458844942846 +Allele 104 0.112512097162980 +Allele 106 0.121869307435106 +Allele 108 0.098292115155425 + +Locus 002 +Allele 118 0.080580029073336 +Allele 122 0.080518666377302 +Allele 124 0.081898149211719 +Allele 126 0.098833277960108 +Allele 127 0.080909324093164 +Allele 128 0.085274558780654 +Allele 130 0.082274325853319 +Allele 132 0.085451103380688 +Allele 134 0.076837314937673 +Allele 135 0.083782071692413 +Allele 137 0.084724550347209 +Allele 151 0.078916628292416 + +Locus 003 +Allele 130 0.067759333416405 +Allele 133 0.069513189950331 +Allele 136 0.071018970588118 +Allele 138 0.076519930100449 +Allele 139 0.073230356712550 +Allele 141 0.073737765727212 +Allele 143 0.065786409128326 +Allele 145 0.073861764210359 +Allele 146 0.071258401491628 +Allele 147 0.070608445220931 +Allele 148 0.075509558901199 +Allele 150 0.069967804073868 +Allele 152 0.074097236396357 +Allele 156 0.067130834082265 + +Locus 004 +Allele 093 0.057419713195751 +Allele 095 0.058962360155047 +Allele 096 0.054895626534563 +Allele 097 0.059653489021902 +Allele 099 0.061783949111206 +Allele 100 0.059509789690226 +Allele 101 0.064039475684468 +Allele 103 0.068343970839983 +Allele 105 0.056052826847530 +Allele 107 0.057552301008079 +Allele 109 0.056210051092078 +Allele 110 0.056126961726076 +Allele 113 0.062108929233159 +Allele 121 0.058581721091261 +Allele 123 0.055480748433929 +Allele 125 0.056710920808951 +Allele 131 0.056567165525795 + +Locus 005 +Allele 218 0.046851062422643 +Allele 220 0.050656380340432 +Allele 222 0.051637989706844 +Allele 224 0.051110529883855 +Allele 226 0.051405693312363 +Allele 228 0.050219881267583 +Allele 230 0.052037827039497 +Allele 232 0.050755200579194 +Allele 234 0.054115839031414 +Allele 236 0.052258592551754 +Allele 238 0.050928364290070 +Allele 240 0.049981957147657 +Allele 242 0.047908655753356 +Allele 244 0.048265659742620 +Allele 246 0.049600871706163 +Allele 248 0.048754404043272 +Allele 250 0.051181721985098 +Allele 252 0.048621073014302 +Allele 254 0.046458548744390 +Allele 256 0.047249747437494 + +Locus 006 +Allele 094 0.072295306756271 +Allele 096 0.070292461652303 +Allele 098 0.073123544162714 +Allele 100 0.065589391793758 +Allele 102 0.073011612098238 +Allele 104 0.079617417317981 +Allele 106 0.073960976843214 +Allele 108 0.069537770552870 +Allele 110 0.078450100653294 +Allele 112 0.074742722598994 +Allele 114 0.066383368043303 +Allele 124 0.069919961024084 +Allele 126 0.067563439686208 +Allele 149 0.065511926816769 + +Locus 007 +Allele 202 0.060641445949993 +Allele 204 0.059292159700036 +Allele 206 0.058126779938391 +Allele 208 0.066825741403800 +Allele 210 0.065382277874977 +Allele 212 0.061902327148652 +Allele 214 0.063955392799913 +Allele 216 0.061984192913184 +Allele 218 0.060958216249896 +Allele 220 0.062628299728150 +Allele 222 0.067720903571931 +Allele 224 0.062396721519789 +Allele 226 0.066097844047630 +Allele 228 0.060366643917831 +Allele 233 0.060652214716468 +Allele 238 0.061068838519362 + +Locus 008 +Allele 121 0.091249646791774 +Allele 123 0.100600355328894 +Allele 125 0.087866927380119 +Allele 127 0.081099634704342 +Allele 129 0.089848852471805 +Allele 131 0.090180002805415 +Allele 133 0.096168801880581 +Allele 135 0.089482283498883 +Allele 137 0.106944979300890 +Allele 151 0.082636593269908 +Allele 161 0.083921922567393 + +Locus 009 +Allele 161 0.077011895412368 +Allele 165 0.077643618101345 +Allele 167 0.088812603779261 +Allele 169 0.082808443137417 +Allele 171 0.087576190948993 +Allele 173 0.089797865492316 +Allele 175 0.083012996798395 +Allele 177 0.082815477044686 +Allele 179 0.078267094398124 +Allele 181 0.084170861474132 +Allele 183 0.085654589071740 +Allele 185 0.082428364341221 + +Locus 010 +Allele 108 0.048952969682896 +Allele 115 0.049250791718888 +Allele 121 0.048809527854651 +Allele 123 0.052320129734610 +Allele 125 0.049703240334835 +Allele 127 0.048734267705216 +Allele 129 0.050452255851457 +Allele 131 0.049260943237850 +Allele 133 0.050912870038857 +Allele 135 0.049337098966091 +Allele 137 0.053330372603399 +Allele 139 0.053331576586163 +Allele 141 0.050947446187149 +Allele 143 0.047679932941943 +Allele 145 0.047390164511208 +Allele 147 0.051735976007185 +Allele 149 0.050124985842985 +Allele 152 0.049967687720621 +Allele 155 0.047704206251605 +Allele 157 0.050053556222393 + + + +Estimated Mixing Proportions +0.013904180000000 +0.015231360000000 +0.012243733333333 +0.931177340000000 +0.013229513333333 +0.014213873333333 + + + +Estimated sigma: +k: 0 1.000000000000000 +k: 1 1.000000000000000 +k: 2 1.000000000000000 +k: 3 1.000000000000000 +k: 4 1.000000000000000 +k: 5 1.000000000000000 + + + +Estimated psi: +k: 0 0.599999999999828 +k: 1 0.599999999999828 +k: 2 0.599999999999828 +k: 3 0.599999999999828 +k: 4 0.599999999999828 +k: 5 0.599999999999828 + + + diff --git a/inst/files/tess/tess_13.txt b/inst/files/tess/tess_13.txt new file mode 100644 index 0000000..8a83055 --- /dev/null +++ b/inst/files/tess/tess_13.txt @@ -0,0 +1,1284 @@ +Estimated Clustering Probabilities for Samples +Sample ***Cluster 01*** ***Cluster 02*** ***Cluster 03*** ***Cluster 04*** ***Cluster 05*** ***Cluster 06*** ***Cluster 07*** +000001: 0.005081000000000 0.005512000000000 0.006962000000000 0.007198000000000 0.006862500000000 0.962802000000000 0.005582500000000 1 +000002: 0.005653000000000 0.005363500000000 0.005697500000000 0.006237000000000 0.006199500000000 0.965624500000000 0.005225000000000 1 +000003: 0.002851500000000 0.003073000000000 0.003367500000000 0.003456000000000 0.003430500000000 0.980986000000000 0.002835500000000 1 +000004: 0.008250000000000 0.008147000000000 0.008934000000000 0.010434000000000 0.009576000000000 0.946594500000000 0.008064500000000 1 +000005: 0.006749500000000 0.008095500000000 0.007753500000000 0.008065500000000 0.008363000000000 0.954513000000000 0.006460000000000 1 +000006: 0.003045500000000 0.003075000000000 0.003137000000000 0.003659500000000 0.003725500000000 0.980269500000000 0.003088000000000 1 +000007: 0.037524500000000 0.038618000000000 0.038374000000000 0.048497000000000 0.047997500000000 0.753082000000000 0.035907000000000 1 +000008: 0.009738500000000 0.011528000000000 0.010767500000000 0.012719500000000 0.012277500000000 0.933231500000000 0.009737500000000 1 +000009: 0.013784500000000 0.016362000000000 0.015403500000000 0.017270000000000 0.018726000000000 0.903723500000000 0.014730500000000 1 +000010: 0.013445000000000 0.012898500000000 0.013671500000000 0.016599500000000 0.016354500000000 0.914023000000000 0.013008000000000 1 +000011: 0.015816000000000 0.014909000000000 0.016315500000000 0.020810000000000 0.017634500000000 0.900214000000000 0.014301000000000 1 +000012: 0.004296000000000 0.003753000000000 0.004444000000000 0.005387500000000 0.005222000000000 0.972267500000000 0.004630000000000 1 +000013: 0.009474500000000 0.007748000000000 0.009696000000000 0.011973000000000 0.011213000000000 0.940262500000000 0.009633000000000 1 +000014: 0.009709500000000 0.008105500000000 0.008992500000000 0.010888000000000 0.010881500000000 0.941448500000000 0.009974500000000 1 +000015: 0.007578000000000 0.008209000000000 0.009102000000000 0.011146500000000 0.009632500000000 0.945409500000000 0.008922500000000 1 +000016: 0.002450000000000 0.002179500000000 0.002182000000000 0.002921500000000 0.002670000000000 0.985270000000000 0.002327000000000 1 +000017: 0.008280000000000 0.007437000000000 0.008339500000000 0.009712000000000 0.009270000000000 0.947762000000000 0.009199500000000 1 +000018: 0.010230500000000 0.008783500000000 0.009497500000000 0.012616000000000 0.011031000000000 0.936484000000000 0.011357500000000 1 +000019: 0.035882500000000 0.021612000000000 0.029891000000000 0.044721500000000 0.037096000000000 0.794708500000000 0.036088500000000 1 +000020: 0.023027000000000 0.013163000000000 0.017092000000000 0.024350500000000 0.021899000000000 0.879127500000000 0.021341000000000 1 +000021: 0.022415500000000 0.015582500000000 0.020334500000000 0.025841000000000 0.025400000000000 0.864868000000000 0.025558500000000 1 +000022: 0.035598500000000 0.026171000000000 0.032389000000000 0.040531500000000 0.040581000000000 0.776129000000000 0.048600000000000 1 +000023: 0.003289000000000 0.002260500000000 0.002864500000000 0.003617500000000 0.003444000000000 0.981132500000000 0.003392000000000 1 +000024: 0.005252500000000 0.003436500000000 0.004911000000000 0.005802500000000 0.005335500000000 0.969788000000000 0.005474000000000 1 +000025: 0.007498000000000 0.004859500000000 0.006263000000000 0.007224500000000 0.007171000000000 0.959437500000000 0.007546500000000 1 +000026: 0.007032500000000 0.005330500000000 0.007058000000000 0.007463000000000 0.007850500000000 0.957890000000000 0.007375500000000 1 +000027: 0.007352000000000 0.005781500000000 0.006680000000000 0.007509500000000 0.008719500000000 0.956474000000000 0.007483500000000 1 +000028: 0.002844500000000 0.002442000000000 0.002644000000000 0.003174000000000 0.003177500000000 0.982602000000000 0.003116000000000 1 +000029: 0.009169500000000 0.008437000000000 0.009200000000000 0.009246000000000 0.010398500000000 0.943182000000000 0.010367000000000 1 +000030: 0.011415000000000 0.012181500000000 0.012567500000000 0.010326000000000 0.013200500000000 0.927595500000000 0.012714000000000 1 +000031: 0.004604500000000 0.004568000000000 0.005211500000000 0.004517500000000 0.004973000000000 0.971832500000000 0.004293000000000 1 +000032: 0.003026000000000 0.003171000000000 0.003270500000000 0.003250000000000 0.003641000000000 0.980784500000000 0.002857000000000 1 +000033: 0.007392000000000 0.008197500000000 0.007720500000000 0.008360000000000 0.008601500000000 0.952387500000000 0.007341000000000 1 +000034: 0.003720000000000 0.004492000000000 0.004709000000000 0.004537500000000 0.005185000000000 0.972987000000000 0.004369500000000 1 +000035: 0.005140500000000 0.005453000000000 0.005896000000000 0.007038000000000 0.007212000000000 0.963466000000000 0.005794500000000 1 +000036: 0.004846500000000 0.004114000000000 0.005607500000000 0.005994500000000 0.006863000000000 0.966932500000000 0.005642000000000 1 +000037: 0.005465000000000 0.005548000000000 0.007035000000000 0.006025500000000 0.006448000000000 0.964253000000000 0.005225500000000 1 +000038: 0.007974000000000 0.009995500000000 0.009069500000000 0.007933000000000 0.008512500000000 0.950154500000000 0.006361000000000 1 +000039: 0.009738500000000 0.014702000000000 0.012550000000000 0.010017500000000 0.010004500000000 0.934415500000000 0.008572000000000 1 +000040: 0.004195000000000 0.005785500000000 0.005234000000000 0.004814000000000 0.003946500000000 0.972518500000000 0.003506500000000 1 +000041: 0.006262000000000 0.007704000000000 0.008351500000000 0.006724000000000 0.007234500000000 0.958922500000000 0.004801500000000 1 +000042: 0.003868500000000 0.004645000000000 0.005372000000000 0.004509500000000 0.004308500000000 0.974155000000000 0.003141500000000 1 +000043: 0.005090500000000 0.006461500000000 0.007013500000000 0.005774000000000 0.005730000000000 0.965726000000000 0.004204500000000 1 +000044: 0.003829000000000 0.004903500000000 0.004722000000000 0.003708000000000 0.004283000000000 0.975528500000000 0.003026000000000 1 +000045: 0.018922000000000 0.019538500000000 0.019727500000000 0.022871000000000 0.024341000000000 0.875029500000000 0.019570500000000 1 +000046: 0.007617500000000 0.007607000000000 0.007915000000000 0.009588000000000 0.009386500000000 0.949994500000000 0.007891500000000 1 +000047: 0.019301000000000 0.020889500000000 0.020420000000000 0.025377500000000 0.024939000000000 0.869130000000000 0.019943000000000 1 +000048: 0.029804000000000 0.033551000000000 0.032387500000000 0.035628500000000 0.038073000000000 0.801398500000000 0.029157500000000 1 +000049: 0.029257000000000 0.032152500000000 0.029710000000000 0.036924500000000 0.035042000000000 0.810300000000000 0.026614000000000 1 +000050: 0.025210000000000 0.027460000000000 0.027871500000000 0.030428500000000 0.032784500000000 0.828783000000000 0.027462500000000 1 +000051: 0.032500500000000 0.038621500000000 0.035066000000000 0.039565000000000 0.039522000000000 0.783295000000000 0.031430000000000 1 +000052: 0.010334500000000 0.011005500000000 0.010738500000000 0.011147500000000 0.012720000000000 0.934618500000000 0.009435500000000 1 +000053: 0.005274000000000 0.004720000000000 0.005368000000000 0.007097500000000 0.006898500000000 0.964633500000000 0.006008500000000 1 +000054: 0.023646000000000 0.025289500000000 0.025044000000000 0.029728500000000 0.031995000000000 0.838317000000000 0.025980000000000 1 +000055: 0.010911500000000 0.010045500000000 0.010059500000000 0.013878000000000 0.012162000000000 0.932560500000000 0.010383000000000 1 +000056: 0.010534500000000 0.010152000000000 0.011275000000000 0.014204000000000 0.013474500000000 0.928957000000000 0.011403000000000 1 +000057: 0.018561500000000 0.018536000000000 0.018793000000000 0.022796000000000 0.025096500000000 0.877287500000000 0.018929500000000 1 +000058: 0.007861000000000 0.007593500000000 0.007404500000000 0.009736500000000 0.009674500000000 0.949419000000000 0.008311000000000 1 +000059: 0.024446000000000 0.025313500000000 0.027498500000000 0.033365000000000 0.035130500000000 0.825114000000000 0.029132500000000 1 +000060: 0.022619500000000 0.019524500000000 0.023032000000000 0.028703000000000 0.024751500000000 0.860754500000000 0.020615000000000 1 +000061: 0.010939500000000 0.008281500000000 0.009882000000000 0.013081500000000 0.012521500000000 0.934050000000000 0.011244000000000 1 +000062: 0.030930500000000 0.023048000000000 0.028663500000000 0.035285500000000 0.032899500000000 0.816131500000000 0.033041500000000 1 +000063: 0.016562500000000 0.012079500000000 0.014549000000000 0.019963000000000 0.018070500000000 0.902181500000000 0.016594000000000 1 +000064: 0.040742500000000 0.040974500000000 0.043579500000000 0.053682000000000 0.055291500000000 0.720304000000000 0.045426000000000 1 +000065: 0.019609500000000 0.011384000000000 0.016677000000000 0.022842000000000 0.019018000000000 0.890030000000000 0.020439500000000 1 +000066: 0.012062000000000 0.006066000000000 0.010798000000000 0.011667500000000 0.011879500000000 0.934584500000000 0.012942500000000 1 +000067: 0.003500500000000 0.002869000000000 0.003763000000000 0.004243500000000 0.004412500000000 0.977058500000000 0.004153000000000 1 +000068: 0.009408000000000 0.008028500000000 0.009997000000000 0.010122000000000 0.010849500000000 0.940878000000000 0.010717000000000 1 +000069: 0.004390500000000 0.003298500000000 0.004289500000000 0.004616500000000 0.004720000000000 0.973970500000000 0.004714500000000 1 +000070: 0.006590000000000 0.005745000000000 0.007172500000000 0.006858000000000 0.007229500000000 0.958956000000000 0.007449000000000 1 +000071: 0.003039500000000 0.003008000000000 0.003823500000000 0.003585000000000 0.004013500000000 0.978597500000000 0.003933000000000 1 +000072: 0.003100000000000 0.004259000000000 0.003383000000000 0.003233000000000 0.003812000000000 0.978996000000000 0.003217000000000 1 +000073: 0.003188000000000 0.004176500000000 0.004157500000000 0.003751500000000 0.003960500000000 0.977558500000000 0.003207500000000 1 +000074: 0.007300500000000 0.007847500000000 0.007967500000000 0.007398500000000 0.007318000000000 0.955768500000000 0.006399500000000 1 +000075: 0.005581000000000 0.005927000000000 0.006260000000000 0.005557000000000 0.005734000000000 0.966041000000000 0.004900000000000 1 + + + +Estimated Allele Frequencies +Cluster 01 +Locus 001 +Allele 092 0.115196565607340 +Allele 094 0.112826637627513 +Allele 096 0.106356372524787 +Allele 098 0.116989080926762 +Allele 100 0.113622686487423 +Allele 102 0.105261976220423 +Allele 104 0.112515701691951 +Allele 106 0.117124554348507 +Allele 108 0.100106424565290 + +Locus 002 +Allele 118 0.080357284374965 +Allele 122 0.080695494391507 +Allele 124 0.082799858963745 +Allele 126 0.094853797384627 +Allele 127 0.080275261525051 +Allele 128 0.086001135110277 +Allele 130 0.082477894711318 +Allele 132 0.084932578083151 +Allele 134 0.077969259753427 +Allele 135 0.084062511931666 +Allele 137 0.086278009818547 +Allele 151 0.079296913951718 + +Locus 003 +Allele 130 0.069009775803690 +Allele 133 0.068530747438646 +Allele 136 0.071161978871878 +Allele 138 0.075334225341859 +Allele 139 0.073256254889251 +Allele 141 0.074097876798589 +Allele 143 0.066755509045641 +Allele 145 0.072952425691628 +Allele 146 0.071226879011350 +Allele 147 0.070076083657623 +Allele 148 0.074946872723599 +Allele 150 0.071153667566189 +Allele 152 0.073437720591304 +Allele 156 0.068059982568754 + +Locus 004 +Allele 093 0.057862259543174 +Allele 095 0.059284926425403 +Allele 096 0.055508380130158 +Allele 097 0.059832855659806 +Allele 099 0.061390380998513 +Allele 100 0.059487854663864 +Allele 101 0.063443586262543 +Allele 103 0.065554326148855 +Allele 105 0.056845487168102 +Allele 107 0.057921602128113 +Allele 109 0.056733387160149 +Allele 110 0.056917698807710 +Allele 113 0.060958544323310 +Allele 121 0.058288510968772 +Allele 123 0.056259535323530 +Allele 125 0.056799437821369 +Allele 131 0.056911226466632 + +Locus 005 +Allele 218 0.047426629293235 +Allele 220 0.049965829502341 +Allele 222 0.051299508085652 +Allele 224 0.051197400096943 +Allele 226 0.050777062492146 +Allele 228 0.050831599270549 +Allele 230 0.051616551396598 +Allele 232 0.050686641365592 +Allele 234 0.053567514196031 +Allele 236 0.051838596585983 +Allele 238 0.050502337259249 +Allele 240 0.050020316051611 +Allele 242 0.048428606237411 +Allele 244 0.049122456142748 +Allele 246 0.049540595169204 +Allele 248 0.048642299531070 +Allele 250 0.050662832036408 +Allele 252 0.048629084118151 +Allele 254 0.047344333739347 +Allele 256 0.047899807429730 + +Locus 006 +Allele 094 0.072773619273596 +Allele 096 0.070995708252440 +Allele 098 0.072943517096392 +Allele 100 0.066693708048494 +Allele 102 0.072944364556470 +Allele 104 0.078570520896649 +Allele 106 0.073775158315720 +Allele 108 0.070717457660804 +Allele 110 0.075821895727463 +Allele 112 0.072790321829426 +Allele 114 0.067475263542852 +Allele 124 0.069120165746592 +Allele 126 0.068681261940438 +Allele 149 0.066697037112667 + +Locus 007 +Allele 202 0.061065612212378 +Allele 204 0.059899873462325 +Allele 206 0.058930373173966 +Allele 208 0.065271344221787 +Allele 210 0.065069308123936 +Allele 212 0.062803983364467 +Allele 214 0.063376537393224 +Allele 216 0.062443795436148 +Allele 218 0.061914686225924 +Allele 220 0.063106644535780 +Allele 222 0.066698546347318 +Allele 224 0.062223947069783 +Allele 226 0.064696683882366 +Allele 228 0.060540328217351 +Allele 233 0.060851801450274 +Allele 238 0.061106534882972 + +Locus 008 +Allele 121 0.091251667178794 +Allele 123 0.099433193736762 +Allele 125 0.089909237373899 +Allele 127 0.082652645945078 +Allele 129 0.090590447494169 +Allele 131 0.090551761758000 +Allele 133 0.096017645831779 +Allele 135 0.089186814089580 +Allele 137 0.100927249651190 +Allele 151 0.084048996928924 +Allele 161 0.085430340011820 + +Locus 009 +Allele 161 0.078309795194133 +Allele 165 0.079238052699617 +Allele 167 0.088519999465883 +Allele 169 0.083899334777449 +Allele 171 0.086491818511275 +Allele 173 0.089108126113252 +Allele 175 0.083283806329258 +Allele 177 0.082373548148034 +Allele 179 0.078582695484729 +Allele 181 0.083059682436062 +Allele 183 0.083989628177935 +Allele 185 0.083143512662370 + +Locus 010 +Allele 108 0.049265552167982 +Allele 115 0.049340997513761 +Allele 121 0.048522238186992 +Allele 123 0.051089497885626 +Allele 125 0.049733518419775 +Allele 127 0.049320147283549 +Allele 129 0.049906462264820 +Allele 131 0.049413393355318 +Allele 133 0.051267341800005 +Allele 135 0.049406677772626 +Allele 137 0.052170680128543 +Allele 139 0.054406110776705 +Allele 141 0.050840771233993 +Allele 143 0.047882966679674 +Allele 145 0.047997681489176 +Allele 147 0.051787153019408 +Allele 149 0.049594008613359 +Allele 152 0.049608417974868 +Allele 155 0.048573734317087 +Allele 157 0.049872649116732 + + +Cluster 02 +Locus 001 +Allele 092 0.114914287374741 +Allele 094 0.113571437564430 +Allele 096 0.106589077321874 +Allele 098 0.116196788946335 +Allele 100 0.110853334599583 +Allele 102 0.106879526236175 +Allele 104 0.111052521412425 +Allele 106 0.119592346335140 +Allele 108 0.100350680209293 + +Locus 002 +Allele 118 0.081268537394865 +Allele 122 0.081292943708290 +Allele 124 0.082861941757136 +Allele 126 0.094433079420816 +Allele 127 0.080880817922766 +Allele 128 0.084753839489183 +Allele 130 0.083180675904172 +Allele 132 0.085862977895320 +Allele 134 0.077496951191854 +Allele 135 0.083869066416688 +Allele 137 0.083998626632177 +Allele 151 0.080100542266730 + +Locus 003 +Allele 130 0.069074109646949 +Allele 133 0.069119273012313 +Allele 136 0.071680308227538 +Allele 138 0.075377386549342 +Allele 139 0.072832220226156 +Allele 141 0.073032683945440 +Allele 143 0.066642401542022 +Allele 145 0.073127813935700 +Allele 146 0.071726922763050 +Allele 147 0.070031690187978 +Allele 148 0.075051057075857 +Allele 150 0.071014397708074 +Allele 152 0.073588857924984 +Allele 156 0.067700877254598 + +Locus 004 +Allele 093 0.058184854736408 +Allele 095 0.058825584245197 +Allele 096 0.055746373755200 +Allele 097 0.059533755286194 +Allele 099 0.060684763062305 +Allele 100 0.060359014451220 +Allele 101 0.062724806454917 +Allele 103 0.064036965302711 +Allele 105 0.057183476820972 +Allele 107 0.058221406690834 +Allele 109 0.057501135674691 +Allele 110 0.057281660143421 +Allele 113 0.060667656729914 +Allele 121 0.058282967125622 +Allele 123 0.056099203765913 +Allele 125 0.057161499513222 +Allele 131 0.057504876241258 + +Locus 005 +Allele 218 0.047915570343835 +Allele 220 0.050541920036165 +Allele 222 0.051368900532446 +Allele 224 0.050756278718714 +Allele 226 0.051738125876105 +Allele 228 0.049576540241016 +Allele 230 0.051412052913664 +Allele 232 0.050251988921688 +Allele 234 0.052880587151726 +Allele 236 0.051268385811530 +Allele 238 0.050907127565123 +Allele 240 0.049821486579809 +Allele 242 0.048661587136743 +Allele 244 0.048439578829219 +Allele 246 0.050272190436322 +Allele 248 0.048549532145628 +Allele 250 0.050487599418607 +Allele 252 0.049496200807224 +Allele 254 0.047480603115710 +Allele 256 0.048173743418724 + +Locus 006 +Allele 094 0.072011847837453 +Allele 096 0.071190046031050 +Allele 098 0.072540609924321 +Allele 100 0.067254110065882 +Allele 102 0.073383506988553 +Allele 104 0.076805925870303 +Allele 106 0.074276130567559 +Allele 108 0.070340549407729 +Allele 110 0.075973842492938 +Allele 112 0.074276042665382 +Allele 114 0.067290454318999 +Allele 124 0.069692443558264 +Allele 126 0.068023476875872 +Allele 149 0.066941013395698 + +Locus 007 +Allele 202 0.060190912843048 +Allele 204 0.060311759547363 +Allele 206 0.059124940007461 +Allele 208 0.065931809917866 +Allele 210 0.064219329779772 +Allele 212 0.062114513864084 +Allele 214 0.063623733665720 +Allele 216 0.062548115544843 +Allele 218 0.062272627418978 +Allele 220 0.062619217939163 +Allele 222 0.066850545227049 +Allele 224 0.062678008110281 +Allele 226 0.064529912373837 +Allele 228 0.061267307062100 +Allele 233 0.060009161262227 +Allele 238 0.061708105436207 + +Locus 008 +Allele 121 0.090843910741318 +Allele 123 0.097105747709786 +Allele 125 0.088404576544825 +Allele 127 0.083284048080942 +Allele 129 0.090327724003741 +Allele 131 0.090730881177807 +Allele 133 0.094638332386377 +Allele 135 0.090165502115610 +Allele 137 0.104083661129836 +Allele 151 0.085429046615017 +Allele 161 0.084986569494741 + +Locus 009 +Allele 161 0.078209076028817 +Allele 165 0.079687671906975 +Allele 167 0.086288408921281 +Allele 169 0.082426049676547 +Allele 171 0.087025529684365 +Allele 173 0.088202302700041 +Allele 175 0.084602087304954 +Allele 177 0.082153210815439 +Allele 179 0.079102560883535 +Allele 181 0.084452381947455 +Allele 183 0.085105194331464 +Allele 185 0.082745525799128 + +Locus 010 +Allele 108 0.050160443218814 +Allele 115 0.048828095997670 +Allele 121 0.048876105840666 +Allele 123 0.051791993676425 +Allele 125 0.049566523700420 +Allele 127 0.049324930917775 +Allele 129 0.050624364391564 +Allele 131 0.050086816042284 +Allele 133 0.050284265924288 +Allele 135 0.049645090607399 +Allele 137 0.051880637958139 +Allele 139 0.051497827467590 +Allele 141 0.051112629213790 +Allele 143 0.048153202958734 +Allele 145 0.047912509150400 +Allele 147 0.050406430847172 +Allele 149 0.050590119882255 +Allele 152 0.050786143398714 +Allele 155 0.048201761144048 +Allele 157 0.050270107661850 + + +Cluster 03 +Locus 001 +Allele 092 0.115482315922773 +Allele 094 0.113586243139164 +Allele 096 0.106653117296050 +Allele 098 0.115920612338173 +Allele 100 0.113031435157547 +Allele 102 0.106086595495618 +Allele 104 0.111548941051707 +Allele 106 0.117805617681058 +Allele 108 0.099885121917907 + +Locus 002 +Allele 118 0.080364426592146 +Allele 122 0.080874013925099 +Allele 124 0.082471568601670 +Allele 126 0.094792935769458 +Allele 127 0.080678918157114 +Allele 128 0.086054833455402 +Allele 130 0.082436150163810 +Allele 132 0.086148088983573 +Allele 134 0.077334991986039 +Allele 135 0.084187360276129 +Allele 137 0.085290014123781 +Allele 151 0.079366697965783 + +Locus 003 +Allele 130 0.068936834548416 +Allele 133 0.068770696761085 +Allele 136 0.071181601573614 +Allele 138 0.075111964190595 +Allele 139 0.072747551247146 +Allele 141 0.074138970029272 +Allele 143 0.066380562294266 +Allele 145 0.073455895029082 +Allele 146 0.071118349792081 +Allele 147 0.070428254691319 +Allele 148 0.075114928998911 +Allele 150 0.071069144839053 +Allele 152 0.073333415354724 +Allele 156 0.068211830650434 + +Locus 004 +Allele 093 0.057697828448408 +Allele 095 0.059145258580331 +Allele 096 0.055205808100469 +Allele 097 0.059412284603308 +Allele 099 0.060747657569562 +Allele 100 0.060404027535903 +Allele 101 0.063904315133290 +Allele 103 0.065116068942300 +Allele 105 0.057047075915669 +Allele 107 0.058053789131714 +Allele 109 0.057143660638459 +Allele 110 0.057047746395400 +Allele 113 0.060604443467878 +Allele 121 0.058049439401792 +Allele 123 0.056313544716294 +Allele 125 0.057063399327416 +Allele 131 0.057043652091806 + +Locus 005 +Allele 218 0.047687086192804 +Allele 220 0.050374196663862 +Allele 222 0.051345864399141 +Allele 224 0.051235220091589 +Allele 226 0.051478087567163 +Allele 228 0.050630391068417 +Allele 230 0.051580310871636 +Allele 232 0.050695359140980 +Allele 234 0.052883463221051 +Allele 236 0.051389906520037 +Allele 238 0.050842980057615 +Allele 240 0.050075506387804 +Allele 242 0.048276093367165 +Allele 244 0.048565711656482 +Allele 246 0.049913185914766 +Allele 248 0.048553108506930 +Allele 250 0.050614619606057 +Allele 252 0.048665064621856 +Allele 254 0.047337697173246 +Allele 256 0.047856146971394 + +Locus 006 +Allele 094 0.072299805570810 +Allele 096 0.071281453323694 +Allele 098 0.072722023097219 +Allele 100 0.066888826382048 +Allele 102 0.072982484247141 +Allele 104 0.078182354675500 +Allele 106 0.074262347764551 +Allele 108 0.071110006462748 +Allele 110 0.075932177696997 +Allele 112 0.073695722812216 +Allele 114 0.066984347165273 +Allele 124 0.069137773336845 +Allele 126 0.067999466929637 +Allele 149 0.066521210535319 + +Locus 007 +Allele 202 0.060681527122367 +Allele 204 0.059979535746548 +Allele 206 0.059101268991396 +Allele 208 0.065812789971020 +Allele 210 0.064900891936501 +Allele 212 0.062577875867402 +Allele 214 0.063486564535033 +Allele 216 0.062237045270025 +Allele 218 0.061932885132612 +Allele 220 0.062736238066804 +Allele 222 0.066800407153478 +Allele 224 0.062672358713027 +Allele 226 0.064593594229383 +Allele 228 0.060833539617775 +Allele 233 0.060264549621024 +Allele 238 0.061388928025605 + +Locus 008 +Allele 121 0.091115573990849 +Allele 123 0.098084206054074 +Allele 125 0.089052709365647 +Allele 127 0.082707417160323 +Allele 129 0.091106837283892 +Allele 131 0.090003164454665 +Allele 133 0.095447964070682 +Allele 135 0.090037053139878 +Allele 137 0.102813563258718 +Allele 151 0.084378149804776 +Allele 161 0.085253361416500 + +Locus 009 +Allele 161 0.077566495472610 +Allele 165 0.079180345794843 +Allele 167 0.087262352850088 +Allele 169 0.082928338652706 +Allele 171 0.086771322046891 +Allele 173 0.089219912914107 +Allele 175 0.084232871785646 +Allele 177 0.082905269544876 +Allele 179 0.078796084591967 +Allele 181 0.083324775387748 +Allele 183 0.084891072867644 +Allele 185 0.082921158090876 + +Locus 010 +Allele 108 0.050126845109613 +Allele 115 0.048775680153604 +Allele 121 0.048574270191763 +Allele 123 0.051321949937941 +Allele 125 0.050013638538692 +Allele 127 0.048863118725265 +Allele 129 0.050344767047725 +Allele 131 0.049760550960678 +Allele 133 0.051159111613880 +Allele 135 0.049488740956077 +Allele 137 0.052622773479882 +Allele 139 0.052687047231153 +Allele 141 0.050985352529716 +Allele 143 0.047729703683595 +Allele 145 0.047987846546623 +Allele 147 0.050934955766055 +Allele 149 0.050199294100470 +Allele 152 0.050125782701743 +Allele 155 0.048377033801049 +Allele 157 0.049921536924476 + + +Cluster 04 +Locus 001 +Allele 092 0.117690125420753 +Allele 094 0.113692257341475 +Allele 096 0.105231366655084 +Allele 098 0.117809592335980 +Allele 100 0.112398316151463 +Allele 102 0.103552986026317 +Allele 104 0.111893664062991 +Allele 106 0.119676721236714 +Allele 108 0.098054970769223 + +Locus 002 +Allele 118 0.079821333478203 +Allele 122 0.079975951140889 +Allele 124 0.081376554983428 +Allele 126 0.097798033706611 +Allele 127 0.080307840914477 +Allele 128 0.086186144510080 +Allele 130 0.082636419210123 +Allele 132 0.085264687939470 +Allele 134 0.076846464583889 +Allele 135 0.084009483680652 +Allele 137 0.087008591957521 +Allele 151 0.078768493894657 + +Locus 003 +Allele 130 0.068137832387608 +Allele 133 0.068167431518912 +Allele 136 0.071058427128617 +Allele 138 0.076013394292758 +Allele 139 0.073233173958629 +Allele 141 0.073673354746281 +Allele 143 0.065590084946870 +Allele 145 0.073641739420447 +Allele 146 0.072177414910897 +Allele 147 0.070059046672750 +Allele 148 0.076283802597725 +Allele 150 0.070279062279278 +Allele 152 0.074317053164359 +Allele 156 0.067368181974866 + +Locus 004 +Allele 093 0.057519568985921 +Allele 095 0.058954420524653 +Allele 096 0.055248391349338 +Allele 097 0.059787634828162 +Allele 099 0.061660417250951 +Allele 100 0.059241291141316 +Allele 101 0.064168285670226 +Allele 103 0.067275400146906 +Allele 105 0.056807912713094 +Allele 107 0.057133178009586 +Allele 109 0.056146165895383 +Allele 110 0.056835357505502 +Allele 113 0.061350485844079 +Allele 121 0.058411756658921 +Allele 123 0.055362041870544 +Allele 125 0.057226089450079 +Allele 131 0.056871602155339 + +Locus 005 +Allele 218 0.046985771755354 +Allele 220 0.050478165374664 +Allele 222 0.051532921546332 +Allele 224 0.051409618888549 +Allele 226 0.050890092465447 +Allele 228 0.050870748892445 +Allele 230 0.051922435847080 +Allele 232 0.050480086671728 +Allele 234 0.054055531041445 +Allele 236 0.052362360288360 +Allele 238 0.051262661939007 +Allele 240 0.050167514493792 +Allele 242 0.047973518218861 +Allele 244 0.048650326549396 +Allele 246 0.049482167066953 +Allele 248 0.048753660999525 +Allele 250 0.050723454116945 +Allele 252 0.048425500469735 +Allele 254 0.046607811868248 +Allele 256 0.046965651506129 + +Locus 006 +Allele 094 0.072764657868202 +Allele 096 0.071229854700344 +Allele 098 0.073208656974323 +Allele 100 0.065305875523616 +Allele 102 0.072769652537477 +Allele 104 0.080138398748466 +Allele 106 0.074346544581959 +Allele 108 0.070121693137847 +Allele 110 0.077159996865456 +Allele 112 0.073515231279871 +Allele 114 0.066126308333538 +Allele 124 0.069205298582170 +Allele 126 0.068422505237698 +Allele 149 0.065685325629034 + +Locus 007 +Allele 202 0.061345435576781 +Allele 204 0.059657333179446 +Allele 206 0.058359560190127 +Allele 208 0.065973407563604 +Allele 210 0.065386534327378 +Allele 212 0.062508409742297 +Allele 214 0.063324453933942 +Allele 216 0.062161607409693 +Allele 218 0.061623290303973 +Allele 220 0.063074398055720 +Allele 222 0.068061626393665 +Allele 224 0.062253349964841 +Allele 226 0.065744951107950 +Allele 228 0.060086914694482 +Allele 233 0.059950730104725 +Allele 238 0.060487997451376 + +Locus 008 +Allele 121 0.091677796824966 +Allele 123 0.100687834777268 +Allele 125 0.089336376607626 +Allele 127 0.081029114983192 +Allele 129 0.089314743692327 +Allele 131 0.090278566569442 +Allele 133 0.095152391459697 +Allele 135 0.089316889824730 +Allele 137 0.105698956310333 +Allele 151 0.082695394440445 +Allele 161 0.084811934509970 + +Locus 009 +Allele 161 0.077174158097902 +Allele 165 0.078347179763687 +Allele 167 0.089069660571108 +Allele 169 0.082607686905734 +Allele 171 0.087353803689102 +Allele 173 0.090873255886082 +Allele 175 0.083134430194173 +Allele 177 0.082959518593778 +Allele 179 0.078394029433721 +Allele 181 0.083601953333873 +Allele 183 0.085071062128027 +Allele 185 0.081413261402814 + +Locus 010 +Allele 108 0.049109982170561 +Allele 115 0.049065955240229 +Allele 121 0.048256589192145 +Allele 123 0.051377725317883 +Allele 125 0.049658765436154 +Allele 127 0.048967177036940 +Allele 129 0.050513161565311 +Allele 131 0.049271845707019 +Allele 133 0.051475237168551 +Allele 135 0.049352732554474 +Allele 137 0.052856997459869 +Allele 139 0.055150162252024 +Allele 141 0.051012080655365 +Allele 143 0.047494751226559 +Allele 145 0.047497414654819 +Allele 147 0.051292770418274 +Allele 149 0.050116260087511 +Allele 152 0.049329642258884 +Allele 155 0.048370123125464 +Allele 157 0.049830626471962 + + +Cluster 05 +Locus 001 +Allele 092 0.118050465471623 +Allele 094 0.112631627736395 +Allele 096 0.104579327441213 +Allele 098 0.118033117100944 +Allele 100 0.112195730027942 +Allele 102 0.104119329965460 +Allele 104 0.112444089029876 +Allele 106 0.119885555699537 +Allele 108 0.098060757527005 + +Locus 002 +Allele 118 0.080020947634382 +Allele 122 0.080777078690239 +Allele 124 0.081830631171615 +Allele 126 0.097054967863036 +Allele 127 0.080777970216265 +Allele 128 0.086402474545788 +Allele 130 0.082719755630586 +Allele 132 0.085178120611985 +Allele 134 0.076501448292091 +Allele 135 0.083985003571929 +Allele 137 0.085528810851221 +Allele 151 0.079222790920862 + +Locus 003 +Allele 130 0.068062048491132 +Allele 133 0.068602577685268 +Allele 136 0.071716550827282 +Allele 138 0.075516933652450 +Allele 139 0.073231289462440 +Allele 141 0.073891395214285 +Allele 143 0.065985466480822 +Allele 145 0.073838013554863 +Allele 146 0.071524374162107 +Allele 147 0.070330827401814 +Allele 148 0.074922502770030 +Allele 150 0.070712490074820 +Allele 152 0.074042667407721 +Allele 156 0.067622862814964 + +Locus 004 +Allele 093 0.057302257411176 +Allele 095 0.058896027531504 +Allele 096 0.054935311732524 +Allele 097 0.059699222836841 +Allele 099 0.060961395130990 +Allele 100 0.060205237234652 +Allele 101 0.064809536069345 +Allele 103 0.066975352129152 +Allele 105 0.057011124998814 +Allele 107 0.057603033975019 +Allele 109 0.056569995962726 +Allele 110 0.056707176624959 +Allele 113 0.060831097470323 +Allele 121 0.057872858931397 +Allele 123 0.055494126639312 +Allele 125 0.057089246316416 +Allele 131 0.057036999004849 + +Locus 005 +Allele 218 0.047141738660583 +Allele 220 0.050427698273398 +Allele 222 0.051474334315395 +Allele 224 0.051062686739937 +Allele 226 0.051478421859510 +Allele 228 0.050661889201424 +Allele 230 0.051559528568383 +Allele 232 0.051405098579030 +Allele 234 0.054096854181885 +Allele 236 0.051866227889214 +Allele 238 0.051064255765934 +Allele 240 0.050057127055647 +Allele 242 0.047867860362489 +Allele 244 0.048434495560579 +Allele 246 0.049480491245553 +Allele 248 0.048981567437581 +Allele 250 0.050494929126576 +Allele 252 0.048604430716335 +Allele 254 0.046609488731023 +Allele 256 0.047230875729523 + +Locus 006 +Allele 094 0.072032765251556 +Allele 096 0.070783349683645 +Allele 098 0.073432617697813 +Allele 100 0.065513846002845 +Allele 102 0.073250038318647 +Allele 104 0.079678926532531 +Allele 106 0.074768463032108 +Allele 108 0.070526679276770 +Allele 110 0.076851660390701 +Allele 112 0.073587899592358 +Allele 114 0.066591315222615 +Allele 124 0.069632341920075 +Allele 126 0.067790859842496 +Allele 149 0.065559237235836 + +Locus 007 +Allele 202 0.060372325756940 +Allele 204 0.059396045429951 +Allele 206 0.057936140868723 +Allele 208 0.065505373527461 +Allele 210 0.065454042613026 +Allele 212 0.062266699981929 +Allele 214 0.064092485597981 +Allele 216 0.061813848344803 +Allele 218 0.062005680680625 +Allele 220 0.062687689392292 +Allele 222 0.068649418132792 +Allele 224 0.061954163397851 +Allele 226 0.065462701091221 +Allele 228 0.060809443540610 +Allele 233 0.060661720389143 +Allele 238 0.060932221254652 + +Locus 008 +Allele 121 0.090365479325537 +Allele 123 0.100365927788885 +Allele 125 0.088522250920936 +Allele 127 0.081632911991408 +Allele 129 0.090905384709077 +Allele 131 0.089708048386508 +Allele 133 0.095911693529245 +Allele 135 0.089268389776116 +Allele 137 0.107328791026156 +Allele 151 0.082174100167529 +Allele 161 0.083817022378602 + +Locus 009 +Allele 161 0.076952949320142 +Allele 165 0.078115542990228 +Allele 167 0.087860540801832 +Allele 169 0.082585915627385 +Allele 171 0.088023576819540 +Allele 173 0.090419703597098 +Allele 175 0.083426995659549 +Allele 177 0.083621250979275 +Allele 179 0.078246098862111 +Allele 181 0.083820142939805 +Allele 183 0.085101484614500 +Allele 185 0.081825797788535 + +Locus 010 +Allele 108 0.049158121327064 +Allele 115 0.048965087990126 +Allele 121 0.048387618286334 +Allele 123 0.052149860293674 +Allele 125 0.050069264267738 +Allele 127 0.049048093899562 +Allele 129 0.050509671177151 +Allele 131 0.049487394221834 +Allele 133 0.050881868659493 +Allele 135 0.049023476629258 +Allele 137 0.052947458883090 +Allele 139 0.053853858220019 +Allele 141 0.051161028824319 +Allele 143 0.047482146977638 +Allele 145 0.047550437796173 +Allele 147 0.051618772801000 +Allele 149 0.050108979719819 +Allele 152 0.049587974832503 +Allele 155 0.048277828435477 +Allele 157 0.049731056757724 + + +Cluster 06 +Locus 001 +Allele 092 0.036267903018900 +Allele 094 0.403255253384204 +Allele 096 0.062895093231025 +Allele 098 0.201416794715678 +Allele 100 0.086376972944628 +Allele 102 0.090946191679869 +Allele 104 0.072981039450382 +Allele 106 0.027682577934597 +Allele 108 0.018178173640722 + +Locus 002 +Allele 118 0.015721123167040 +Allele 122 0.028877749779771 +Allele 124 0.213517561342959 +Allele 126 0.124015966229949 +Allele 127 0.009002701806445 +Allele 128 0.098252844860611 +Allele 130 0.073743621876039 +Allele 132 0.237769743213127 +Allele 134 0.011177165818359 +Allele 135 0.106052396874854 +Allele 137 0.072012119426644 +Allele 151 0.009857005604199 + +Locus 003 +Allele 130 0.023113584145231 +Allele 133 0.009984236659968 +Allele 136 0.132491188474954 +Allele 138 0.102947355454339 +Allele 139 0.137512818368130 +Allele 141 0.032301031890565 +Allele 143 0.011717196833816 +Allele 145 0.084907538472101 +Allele 146 0.112325725931435 +Allele 147 0.008932044098290 +Allele 148 0.148930794204377 +Allele 150 0.080429154918215 +Allele 152 0.097381492147955 +Allele 156 0.017025838400618 + +Locus 004 +Allele 093 0.048098054812309 +Allele 095 0.072680281946126 +Allele 096 0.011529838274400 +Allele 097 0.187993737948682 +Allele 099 0.051592069510714 +Allele 100 0.084925711776612 +Allele 101 0.151792428580221 +Allele 103 0.137088040320467 +Allele 105 0.048842194661291 +Allele 107 0.092887270505185 +Allele 109 0.023004488447201 +Allele 110 0.023025580748881 +Allele 113 0.013436632127235 +Allele 121 0.015506778006870 +Allele 123 0.017394430591604 +Allele 125 0.010141756448204 +Allele 131 0.010060705293997 + +Locus 005 +Allele 218 0.011543684950662 +Allele 220 0.097031049443418 +Allele 222 0.133696497363056 +Allele 224 0.134154215523891 +Allele 226 0.096015679183242 +Allele 228 0.046393972284256 +Allele 230 0.045138855288312 +Allele 232 0.064955249975195 +Allele 234 0.068720731661915 +Allele 236 0.057655079618417 +Allele 238 0.077431476731100 +Allele 240 0.040553542783219 +Allele 242 0.035963838117952 +Allele 244 0.010320557127213 +Allele 246 0.015781913168150 +Allele 248 0.010292589504258 +Allele 250 0.014751777098811 +Allele 252 0.016525363483359 +Allele 254 0.011803965965737 +Allele 256 0.011269960727838 + +Locus 006 +Allele 094 0.106561429388909 +Allele 096 0.173505774723175 +Allele 098 0.039859989137388 +Allele 100 0.012009982775935 +Allele 102 0.099672210332619 +Allele 104 0.240175700191375 +Allele 106 0.144994744894331 +Allele 108 0.068385917845371 +Allele 110 0.050699115797300 +Allele 112 0.020007342917516 +Allele 114 0.011577702477053 +Allele 124 0.009795175940258 +Allele 126 0.010791924985055 +Allele 149 0.011962988593718 + +Locus 007 +Allele 202 0.010044766482614 +Allele 204 0.024056415701419 +Allele 206 0.011772732535615 +Allele 208 0.138668897622138 +Allele 210 0.039653425577698 +Allele 212 0.188021235215305 +Allele 214 0.107043294723935 +Allele 216 0.115131636493091 +Allele 218 0.062323899308969 +Allele 220 0.054989014686050 +Allele 222 0.057374057640067 +Allele 224 0.114856480300766 +Allele 226 0.039403351993841 +Allele 228 0.016737972850413 +Allele 233 0.010148594940817 +Allele 238 0.009774223927266 + +Locus 008 +Allele 121 0.086011490018096 +Allele 123 0.079671375300318 +Allele 125 0.056300037248542 +Allele 127 0.014274054757639 +Allele 129 0.055253781426850 +Allele 131 0.273290973442095 +Allele 133 0.152855506948261 +Allele 135 0.188140743988402 +Allele 137 0.068037722837672 +Allele 151 0.013555053686715 +Allele 161 0.012609260345414 + +Locus 009 +Allele 161 0.014499532121887 +Allele 165 0.030016673700832 +Allele 167 0.055213511850170 +Allele 169 0.100076232849685 +Allele 171 0.283789391781659 +Allele 173 0.192200115511139 +Allele 175 0.107515452915086 +Allele 177 0.108103720389000 +Allele 179 0.013720268789831 +Allele 181 0.042396326714861 +Allele 183 0.025133913041562 +Allele 185 0.027334860334281 + +Locus 010 +Allele 108 0.028567565512107 +Allele 115 0.009906707294749 +Allele 121 0.010382682828004 +Allele 123 0.045763757745433 +Allele 125 0.098742322189652 +Allele 127 0.074029077281428 +Allele 129 0.085646149823429 +Allele 131 0.093066127724661 +Allele 133 0.168535952714309 +Allele 135 0.105994707852009 +Allele 137 0.083190767957486 +Allele 139 0.024668899366110 +Allele 141 0.040109489018623 +Allele 143 0.011025312008191 +Allele 145 0.030294139544743 +Allele 147 0.020269911163771 +Allele 149 0.028108733978911 +Allele 152 0.015551441087337 +Allele 155 0.010583242785642 +Allele 157 0.015563012123403 + + +Cluster 07 +Locus 001 +Allele 092 0.116314685699665 +Allele 094 0.112916376041208 +Allele 096 0.106475143000489 +Allele 098 0.115522548060108 +Allele 100 0.115827148991757 +Allele 102 0.105114193382755 +Allele 104 0.112503054060391 +Allele 106 0.115475343921745 +Allele 108 0.099851506841880 + +Locus 002 +Allele 118 0.080770173527774 +Allele 122 0.080922137557580 +Allele 124 0.081755615634909 +Allele 126 0.094882151402769 +Allele 127 0.080666985303384 +Allele 128 0.085700137064818 +Allele 130 0.082277452978004 +Allele 132 0.084632417595862 +Allele 134 0.077628167800815 +Allele 135 0.084814425416882 +Allele 137 0.086308498157118 +Allele 151 0.079641837560087 + +Locus 003 +Allele 130 0.068953124285987 +Allele 133 0.068468471363386 +Allele 136 0.070620201648179 +Allele 138 0.074128881732064 +Allele 139 0.073652407168406 +Allele 141 0.074902684017730 +Allele 143 0.066422071699558 +Allele 145 0.073477264611383 +Allele 146 0.070989599903400 +Allele 147 0.070067740208458 +Allele 148 0.074778563650093 +Allele 150 0.070840329461326 +Allele 152 0.074406843170645 +Allele 156 0.068291817079387 + +Locus 004 +Allele 093 0.057801647796146 +Allele 095 0.059311753742999 +Allele 096 0.055587435800979 +Allele 097 0.060054574728131 +Allele 099 0.060306963050319 +Allele 100 0.059178849693200 +Allele 101 0.063777382609906 +Allele 103 0.066493502197216 +Allele 105 0.056831765766084 +Allele 107 0.057714581382452 +Allele 109 0.057278028148572 +Allele 110 0.056973883312301 +Allele 113 0.060658363115209 +Allele 121 0.057991747118613 +Allele 123 0.056177777424152 +Allele 125 0.057051970947279 +Allele 131 0.056809773166437 + +Locus 005 +Allele 218 0.047367786464616 +Allele 220 0.050009954772455 +Allele 222 0.051136074765474 +Allele 224 0.050796231836838 +Allele 226 0.051199465529382 +Allele 228 0.050715641081042 +Allele 230 0.051342370752801 +Allele 232 0.051515969936841 +Allele 234 0.053284538208683 +Allele 236 0.051962466145440 +Allele 238 0.050689437464411 +Allele 240 0.049759571988801 +Allele 242 0.048480721465320 +Allele 244 0.048780003194271 +Allele 246 0.049502216688324 +Allele 248 0.048891642400820 +Allele 250 0.050843019028845 +Allele 252 0.048788835376900 +Allele 254 0.047006750136111 +Allele 256 0.047927302762624 + +Locus 006 +Allele 094 0.072436022689613 +Allele 096 0.070708602993555 +Allele 098 0.072969932855880 +Allele 100 0.066449219346561 +Allele 102 0.072540092352515 +Allele 104 0.080017981158592 +Allele 106 0.074421605022049 +Allele 108 0.070843757687687 +Allele 110 0.074975423406820 +Allele 112 0.073054764043078 +Allele 114 0.067333039381711 +Allele 124 0.069225188103012 +Allele 126 0.068637822247815 +Allele 149 0.066386548711113 + +Locus 007 +Allele 202 0.061097187528789 +Allele 204 0.059454719307570 +Allele 206 0.058872986822574 +Allele 208 0.064915959973270 +Allele 210 0.065607457168594 +Allele 212 0.062636017223142 +Allele 214 0.063972639463163 +Allele 216 0.061398571642466 +Allele 218 0.061728046178701 +Allele 220 0.062674808792946 +Allele 222 0.067283011139421 +Allele 224 0.062009815813969 +Allele 226 0.065203774165548 +Allele 228 0.060667800940208 +Allele 233 0.061894372848807 +Allele 238 0.060582830990836 + +Locus 008 +Allele 121 0.090488704033546 +Allele 123 0.099234823986251 +Allele 125 0.089693012829975 +Allele 127 0.082911631696435 +Allele 129 0.090347237217498 +Allele 131 0.089967328997324 +Allele 133 0.096343610847961 +Allele 135 0.089466909960131 +Allele 137 0.102596801429667 +Allele 151 0.083802072126942 +Allele 161 0.085147866874275 + +Locus 009 +Allele 161 0.078053268311704 +Allele 165 0.079175673672655 +Allele 167 0.087015489347322 +Allele 169 0.083748454299329 +Allele 171 0.087634402315921 +Allele 173 0.089446777546390 +Allele 175 0.083154584282780 +Allele 177 0.082590816578610 +Allele 179 0.079613234430914 +Allele 181 0.083199546443897 +Allele 183 0.083831342316192 +Allele 185 0.082536410454286 + +Locus 010 +Allele 108 0.049460739048729 +Allele 115 0.049309870618257 +Allele 121 0.048368758789131 +Allele 123 0.051547049265970 +Allele 125 0.049938647290862 +Allele 127 0.049062243959056 +Allele 129 0.050072404528657 +Allele 131 0.049059738969388 +Allele 133 0.050987334302931 +Allele 135 0.049383446080592 +Allele 137 0.052160661444146 +Allele 139 0.054035274618478 +Allele 141 0.050833197566979 +Allele 143 0.047684358437301 +Allele 145 0.047693793216993 +Allele 147 0.052919590947225 +Allele 149 0.049913297321204 +Allele 152 0.049476105424750 +Allele 155 0.048351455912761 +Allele 157 0.049742032256586 + + + +Estimated Mixing Proportions +0.011915080000000 +0.011250500000000 +0.012180893333333 +0.014260353333333 +0.014133386666667 +0.923942180000000 +0.012317606666667 + + + +Estimated sigma: +k: 0 1.000000000000000 +k: 1 1.000000000000000 +k: 2 1.000000000000000 +k: 3 1.000000000000000 +k: 4 1.000000000000000 +k: 5 1.000000000000000 +k: 6 1.000000000000000 + + + +Estimated psi: +k: 0 0.599999999999828 +k: 1 0.599999999999828 +k: 2 0.599999999999828 +k: 3 0.599999999999828 +k: 4 0.599999999999828 +k: 5 0.599999999999828 +k: 6 0.599999999999828 + + + diff --git a/inst/files/tess/tess_14.txt b/inst/files/tess/tess_14.txt new file mode 100644 index 0000000..fb55769 --- /dev/null +++ b/inst/files/tess/tess_14.txt @@ -0,0 +1,1454 @@ +Estimated Clustering Probabilities for Samples +Sample ***Cluster 01*** ***Cluster 02*** ***Cluster 03*** ***Cluster 04*** ***Cluster 05*** ***Cluster 06*** ***Cluster 07*** ***Cluster 08*** +000001: 0.005482500000000 0.961102500000000 0.004925000000000 0.006497500000000 0.004594000000000 0.005187500000000 0.007021000000000 0.005190000000000 1 +000002: 0.005582000000000 0.961427000000000 0.004747500000000 0.006770500000000 0.004176000000000 0.005378500000000 0.007070000000000 0.004848500000000 1 +000003: 0.003061500000000 0.978998000000000 0.002403000000000 0.003499500000000 0.002376500000000 0.002853500000000 0.003944500000000 0.002863500000000 1 +000004: 0.008861500000000 0.940010000000000 0.008270500000000 0.009841000000000 0.007106000000000 0.007847000000000 0.010172500000000 0.007891500000000 1 +000005: 0.007246000000000 0.952253500000000 0.006548500000000 0.006961500000000 0.005957000000000 0.006989500000000 0.008095500000000 0.005948500000000 1 +000006: 0.003263000000000 0.977890000000000 0.002871000000000 0.003231500000000 0.002638500000000 0.003277500000000 0.003817500000000 0.003011000000000 1 +000007: 0.033185500000000 0.769670000000000 0.034501500000000 0.032974500000000 0.026033000000000 0.032995000000000 0.037484500000000 0.033156000000000 1 +000008: 0.010120000000000 0.930935500000000 0.010416000000000 0.009298500000000 0.008683500000000 0.009674500000000 0.011458000000000 0.009414000000000 1 +000009: 0.015810000000000 0.894308000000000 0.015177500000000 0.013180000000000 0.013817500000000 0.015139500000000 0.017490000000000 0.015077500000000 1 +000010: 0.013632500000000 0.909089500000000 0.014231500000000 0.013514000000000 0.010772000000000 0.012998000000000 0.014383500000000 0.011379000000000 1 +000011: 0.014701500000000 0.901362000000000 0.014595500000000 0.014526500000000 0.012401500000000 0.014313500000000 0.015255500000000 0.012844000000000 1 +000012: 0.004560500000000 0.970351500000000 0.004313500000000 0.004371500000000 0.003672500000000 0.004223000000000 0.004351500000000 0.004156000000000 1 +000013: 0.009115000000000 0.937656000000000 0.009734500000000 0.009710500000000 0.007623500000000 0.008163000000000 0.009509000000000 0.008488500000000 1 +000014: 0.008315500000000 0.941498500000000 0.008637000000000 0.009492000000000 0.007110500000000 0.007811000000000 0.008824000000000 0.008311500000000 1 +000015: 0.007442500000000 0.946454000000000 0.007301000000000 0.007984500000000 0.006798000000000 0.007486000000000 0.009447500000000 0.007086500000000 1 +000016: 0.002300500000000 0.983201500000000 0.002163000000000 0.003083000000000 0.001920000000000 0.002324000000000 0.002909000000000 0.002099000000000 1 +000017: 0.007979500000000 0.943401500000000 0.007812500000000 0.008687500000000 0.007249000000000 0.007901000000000 0.009593000000000 0.007376000000000 1 +000018: 0.009578000000000 0.932663000000000 0.008919000000000 0.011073500000000 0.008184500000000 0.009324000000000 0.011348500000000 0.008909500000000 1 +000019: 0.032462500000000 0.790613000000000 0.035268500000000 0.030669000000000 0.028600500000000 0.028970000000000 0.024470500000000 0.028946000000000 1 +000020: 0.018347500000000 0.876511500000000 0.020321500000000 0.017376000000000 0.017276500000000 0.018581500000000 0.014545500000000 0.017040000000000 1 +000021: 0.019232500000000 0.870620500000000 0.021313500000000 0.019937000000000 0.017289000000000 0.017177000000000 0.016367500000000 0.018063000000000 1 +000022: 0.031037000000000 0.799474000000000 0.032555000000000 0.026827000000000 0.028515500000000 0.026449000000000 0.028952500000000 0.026190000000000 1 +000023: 0.003134500000000 0.978774500000000 0.003044500000000 0.003379500000000 0.002767500000000 0.002778500000000 0.003321000000000 0.002800000000000 1 +000024: 0.004857500000000 0.966671000000000 0.004925500000000 0.005220000000000 0.004395000000000 0.004671000000000 0.004653000000000 0.004607000000000 1 +000025: 0.006670500000000 0.954661500000000 0.006455500000000 0.008073500000000 0.005765500000000 0.006111000000000 0.006373000000000 0.005889500000000 1 +000026: 0.006854000000000 0.951939500000000 0.006156500000000 0.007187000000000 0.005910500000000 0.006293000000000 0.009452500000000 0.006207000000000 1 +000027: 0.006786500000000 0.951586500000000 0.006703500000000 0.007893500000000 0.005755000000000 0.006994000000000 0.008002000000000 0.006279000000000 1 +000028: 0.002714500000000 0.978926000000000 0.002412000000000 0.004176500000000 0.002600500000000 0.003056500000000 0.003752500000000 0.002361500000000 1 +000029: 0.007741500000000 0.929739500000000 0.006818500000000 0.014644000000000 0.007738500000000 0.011025000000000 0.012830000000000 0.009463000000000 1 +000030: 0.010051000000000 0.912428000000000 0.008109500000000 0.016522500000000 0.010331000000000 0.013942000000000 0.019375000000000 0.009241000000000 1 +000031: 0.004071000000000 0.967790000000000 0.003616500000000 0.005543500000000 0.003497000000000 0.004726000000000 0.006317000000000 0.004439000000000 1 +000032: 0.002767500000000 0.977021000000000 0.002446500000000 0.004643000000000 0.002569000000000 0.003340000000000 0.004539500000000 0.002673500000000 1 +000033: 0.006648000000000 0.946639500000000 0.006237000000000 0.008753500000000 0.006591500000000 0.007016500000000 0.010926000000000 0.007188000000000 1 +000034: 0.003851500000000 0.968143000000000 0.003459500000000 0.006150500000000 0.003584000000000 0.004191000000000 0.006905000000000 0.003715500000000 1 +000035: 0.005944500000000 0.956238000000000 0.004491000000000 0.008830500000000 0.005060000000000 0.006104000000000 0.007997500000000 0.005334500000000 1 +000036: 0.005193000000000 0.961873000000000 0.004903500000000 0.006930000000000 0.004513500000000 0.005085500000000 0.006929500000000 0.004572000000000 1 +000037: 0.005806500000000 0.962631500000000 0.004220000000000 0.006143000000000 0.004240500000000 0.005126000000000 0.006936000000000 0.004896500000000 1 +000038: 0.006530500000000 0.944659000000000 0.005690500000000 0.010839000000000 0.005910500000000 0.008814500000000 0.010278000000000 0.007278000000000 1 +000039: 0.006892500000000 0.921173000000000 0.005804500000000 0.022175000000000 0.008932500000000 0.010688000000000 0.013416000000000 0.010918500000000 1 +000040: 0.003145500000000 0.966697000000000 0.002510000000000 0.007860500000000 0.003772500000000 0.005046500000000 0.007030000000000 0.003938000000000 1 +000041: 0.005874000000000 0.952057500000000 0.004148500000000 0.011997500000000 0.004785500000000 0.006278500000000 0.009353500000000 0.005505000000000 1 +000042: 0.004021500000000 0.970059000000000 0.003004500000000 0.005854500000000 0.002885500000000 0.004461500000000 0.006214500000000 0.003499000000000 1 +000043: 0.005273000000000 0.960538000000000 0.003938500000000 0.007653000000000 0.004381500000000 0.005174000000000 0.008245500000000 0.004796500000000 1 +000044: 0.004395000000000 0.970290000000000 0.002986500000000 0.005692000000000 0.003246000000000 0.004004000000000 0.005854500000000 0.003532000000000 1 +000045: 0.019127500000000 0.872190000000000 0.021032500000000 0.016091000000000 0.018411000000000 0.016959500000000 0.019009000000000 0.017179500000000 1 +000046: 0.007657000000000 0.948991000000000 0.007782000000000 0.006798000000000 0.007327500000000 0.006713500000000 0.007506500000000 0.007224500000000 1 +000047: 0.020910000000000 0.868344500000000 0.020029000000000 0.015942500000000 0.018183500000000 0.018456000000000 0.019389500000000 0.018745000000000 1 +000048: 0.031536000000000 0.790077000000000 0.033072500000000 0.027420000000000 0.027361500000000 0.028164500000000 0.032315000000000 0.030053500000000 1 +000049: 0.028911500000000 0.803411500000000 0.028620000000000 0.026997000000000 0.025873500000000 0.027873000000000 0.031815500000000 0.026498000000000 1 +000050: 0.025921500000000 0.824231500000000 0.025253500000000 0.023738500000000 0.021836500000000 0.025126000000000 0.027841500000000 0.026051000000000 1 +000051: 0.031990500000000 0.773645000000000 0.034272500000000 0.026463000000000 0.031975000000000 0.031366000000000 0.037385500000000 0.032902500000000 1 +000052: 0.009914000000000 0.934120000000000 0.009538000000000 0.008494500000000 0.009370500000000 0.008508500000000 0.010507500000000 0.009547000000000 1 +000053: 0.005471500000000 0.963636500000000 0.005768500000000 0.005142500000000 0.004973000000000 0.004705000000000 0.005223500000000 0.005079500000000 1 +000054: 0.024117000000000 0.833117500000000 0.026770500000000 0.019765000000000 0.024507000000000 0.022692500000000 0.024472000000000 0.024558500000000 1 +000055: 0.010905000000000 0.929489500000000 0.010567000000000 0.009920500000000 0.009686000000000 0.010130000000000 0.009825500000000 0.009476500000000 1 +000056: 0.010574000000000 0.928108500000000 0.011097500000000 0.010090000000000 0.009590000000000 0.009753500000000 0.010708500000000 0.010078000000000 1 +000057: 0.019723500000000 0.875609000000000 0.020324500000000 0.016980500000000 0.017349000000000 0.017368500000000 0.015855500000000 0.016789500000000 1 +000058: 0.007608500000000 0.947656500000000 0.008410500000000 0.006944500000000 0.007580000000000 0.007277500000000 0.007544000000000 0.006978500000000 1 +000059: 0.022711000000000 0.830351500000000 0.030905000000000 0.021495500000000 0.023068500000000 0.025098000000000 0.022616500000000 0.023754000000000 1 +000060: 0.021962500000000 0.856480000000000 0.022924000000000 0.022011500000000 0.018640500000000 0.019325500000000 0.019649000000000 0.019007000000000 1 +000061: 0.010495000000000 0.929460000000000 0.011082500000000 0.010406500000000 0.009225500000000 0.009957500000000 0.009274500000000 0.010098500000000 1 +000062: 0.030080500000000 0.808743000000000 0.031864000000000 0.024553000000000 0.026856500000000 0.026476500000000 0.023975000000000 0.027451500000000 1 +000063: 0.014260000000000 0.898681000000000 0.016235500000000 0.014752000000000 0.014615500000000 0.014357500000000 0.013122000000000 0.013976500000000 1 +000064: 0.038082000000000 0.732562500000000 0.045910000000000 0.034665000000000 0.035294000000000 0.038692000000000 0.036579500000000 0.038215000000000 1 +000065: 0.015491000000000 0.887929500000000 0.017457000000000 0.017900000000000 0.014404500000000 0.014880500000000 0.014417000000000 0.017520500000000 1 +000066: 0.008886500000000 0.930489000000000 0.010722500000000 0.012526000000000 0.010121000000000 0.008397500000000 0.008678500000000 0.010179000000000 1 +000067: 0.003812500000000 0.971511000000000 0.003404500000000 0.005016500000000 0.003532000000000 0.003959500000000 0.004981500000000 0.003782500000000 1 +000068: 0.009281500000000 0.930926000000000 0.008831000000000 0.012436000000000 0.008525000000000 0.009735500000000 0.011446000000000 0.008819000000000 1 +000069: 0.004867500000000 0.969477000000000 0.003549500000000 0.004708500000000 0.003408000000000 0.004266000000000 0.005463000000000 0.004260500000000 1 +000070: 0.006034500000000 0.953506500000000 0.006117000000000 0.008890000000000 0.005320000000000 0.006656500000000 0.007562500000000 0.005913000000000 1 +000071: 0.003320000000000 0.975137500000000 0.002951500000000 0.004300500000000 0.003184500000000 0.003315000000000 0.004480000000000 0.003311000000000 1 +000072: 0.004153000000000 0.972844500000000 0.002313000000000 0.005312500000000 0.002647000000000 0.003628000000000 0.005768500000000 0.003333500000000 1 +000073: 0.003191500000000 0.971458500000000 0.002815000000000 0.006436500000000 0.003063500000000 0.003898000000000 0.005748000000000 0.003389000000000 1 +000074: 0.006111500000000 0.945112000000000 0.005331500000000 0.009565500000000 0.006544500000000 0.008690500000000 0.011179000000000 0.007465500000000 1 +000075: 0.004243000000000 0.953084000000000 0.003927500000000 0.008548500000000 0.004317500000000 0.005723000000000 0.015265000000000 0.004891500000000 1 + + + +Estimated Allele Frequencies +Cluster 01 +Locus 001 +Allele 092 0.114673054557870 +Allele 094 0.113338988126621 +Allele 096 0.106169662619679 +Allele 098 0.115825182703946 +Allele 100 0.113255962725029 +Allele 102 0.106055600473567 +Allele 104 0.111910463081781 +Allele 106 0.117283854977272 +Allele 108 0.101487230734230 + +Locus 002 +Allele 118 0.081218214162194 +Allele 122 0.080942320262304 +Allele 124 0.082582750084224 +Allele 126 0.093258988473685 +Allele 127 0.080704515106582 +Allele 128 0.085768926003759 +Allele 130 0.083175593555675 +Allele 132 0.085247959664985 +Allele 134 0.077930060027372 +Allele 135 0.084207233822045 +Allele 137 0.085919558377345 +Allele 151 0.079043880459830 + +Locus 003 +Allele 130 0.068909515786421 +Allele 133 0.069046656331084 +Allele 136 0.071857381263820 +Allele 138 0.074730435355826 +Allele 139 0.072637093133881 +Allele 141 0.073821850394026 +Allele 143 0.066607787783901 +Allele 145 0.072878819317142 +Allele 146 0.071427528028353 +Allele 147 0.070239545158704 +Allele 148 0.074949029583361 +Allele 150 0.070766243237682 +Allele 152 0.073781885693989 +Allele 156 0.068346228931811 + +Locus 004 +Allele 093 0.057763842521637 +Allele 095 0.059228108999276 +Allele 096 0.055516403915668 +Allele 097 0.059549741328956 +Allele 099 0.060908097377382 +Allele 100 0.059630129906038 +Allele 101 0.062737763777858 +Allele 103 0.064245497360815 +Allele 105 0.057198325355332 +Allele 107 0.058493379135536 +Allele 109 0.057045246580001 +Allele 110 0.056730865377011 +Allele 113 0.061334693188865 +Allele 121 0.058462895532479 +Allele 123 0.056128746028922 +Allele 125 0.057878599245131 +Allele 131 0.057147664369087 + +Locus 005 +Allele 218 0.047736108600308 +Allele 220 0.049943654252366 +Allele 222 0.050832886529115 +Allele 224 0.050881694695580 +Allele 226 0.051019366812094 +Allele 228 0.050535212432207 +Allele 230 0.051463148948032 +Allele 232 0.050743927345321 +Allele 234 0.053344326310902 +Allele 236 0.051583388479188 +Allele 238 0.050245815439492 +Allele 240 0.050228586449669 +Allele 242 0.048586437368793 +Allele 244 0.048936512186230 +Allele 246 0.049694329337314 +Allele 248 0.049187269651639 +Allele 250 0.050735028210822 +Allele 252 0.049381500214885 +Allele 254 0.047101643883594 +Allele 256 0.047819162852446 + +Locus 006 +Allele 094 0.072402217059640 +Allele 096 0.071599662056918 +Allele 098 0.072995939209109 +Allele 100 0.066540497923730 +Allele 102 0.072660636410449 +Allele 104 0.077223827969164 +Allele 106 0.073794782272942 +Allele 108 0.070698274306723 +Allele 110 0.075371002516778 +Allele 112 0.073718886436525 +Allele 114 0.067399529931065 +Allele 124 0.069662405865585 +Allele 126 0.068820422340622 +Allele 149 0.067111915700751 + +Locus 007 +Allele 202 0.060927230726497 +Allele 204 0.060199852474021 +Allele 206 0.059172987158711 +Allele 208 0.065530473656581 +Allele 210 0.064901551969070 +Allele 212 0.062603414250688 +Allele 214 0.063237552175067 +Allele 216 0.062212956555385 +Allele 218 0.061848899776928 +Allele 220 0.062586821175184 +Allele 222 0.066797424758395 +Allele 224 0.062355294212826 +Allele 226 0.064659618971584 +Allele 228 0.061183558368537 +Allele 233 0.060491121097257 +Allele 238 0.061291242673267 + +Locus 008 +Allele 121 0.091993034349539 +Allele 123 0.096887721721009 +Allele 125 0.089712759978540 +Allele 127 0.083161194941527 +Allele 129 0.090067792968744 +Allele 131 0.090907080177185 +Allele 133 0.095228299863376 +Allele 135 0.090550772677966 +Allele 137 0.102025868003657 +Allele 151 0.083728799334407 +Allele 161 0.085736675984050 + +Locus 009 +Allele 161 0.078408148577112 +Allele 165 0.079842212644437 +Allele 167 0.088083653611150 +Allele 169 0.083390196267138 +Allele 171 0.085969692296465 +Allele 173 0.088111752665403 +Allele 175 0.083384621183092 +Allele 177 0.082481631709405 +Allele 179 0.078984429437842 +Allele 181 0.083925469253386 +Allele 183 0.085081095822068 +Allele 185 0.082337096532501 + +Locus 010 +Allele 108 0.049023715075928 +Allele 115 0.049255365442167 +Allele 121 0.048688981392053 +Allele 123 0.051574514350125 +Allele 125 0.049881527681364 +Allele 127 0.049469861757151 +Allele 129 0.049774864522794 +Allele 131 0.049569029874439 +Allele 133 0.051189327586117 +Allele 135 0.049013839315162 +Allele 137 0.052124006293406 +Allele 139 0.053495284766279 +Allele 141 0.051129008659737 +Allele 143 0.048011798268576 +Allele 145 0.048016448238792 +Allele 147 0.051308876526341 +Allele 149 0.050146315702115 +Allele 152 0.049956682779078 +Allele 155 0.048377926499528 +Allele 157 0.049992625268848 + + +Cluster 02 +Locus 001 +Allele 092 0.036530514392736 +Allele 094 0.403594145510764 +Allele 096 0.062502614689429 +Allele 098 0.201344036821630 +Allele 100 0.086865654280941 +Allele 102 0.090404745121872 +Allele 104 0.073055596340239 +Allele 106 0.027731390219414 +Allele 108 0.017971302622968 + +Locus 002 +Allele 118 0.015484576772815 +Allele 122 0.028543332480080 +Allele 124 0.213502979399701 +Allele 126 0.125080797232127 +Allele 127 0.009054068602259 +Allele 128 0.098092234593772 +Allele 130 0.073886543389902 +Allele 132 0.238056338516289 +Allele 134 0.011005169992321 +Allele 135 0.105869760490119 +Allele 137 0.071581974508898 +Allele 151 0.009842224021714 + +Locus 003 +Allele 130 0.022813044052750 +Allele 133 0.009855282286604 +Allele 136 0.132415956202441 +Allele 138 0.103004886098493 +Allele 139 0.137575354734894 +Allele 141 0.032108891428582 +Allele 143 0.011508607556667 +Allele 145 0.085112611506503 +Allele 146 0.112514341587390 +Allele 147 0.009025186965155 +Allele 148 0.149119582447014 +Allele 150 0.080109056733411 +Allele 152 0.097890537154660 +Allele 156 0.016946661245436 + +Locus 004 +Allele 093 0.047677050820486 +Allele 095 0.072689329898299 +Allele 096 0.011427874570707 +Allele 097 0.188041960052497 +Allele 099 0.051483975371253 +Allele 100 0.084796983563476 +Allele 101 0.152585426547191 +Allele 103 0.138183248559790 +Allele 105 0.048685553147143 +Allele 107 0.093001636990981 +Allele 109 0.022494293578349 +Allele 110 0.023121396031561 +Allele 113 0.013192220705747 +Allele 121 0.015374902307288 +Allele 123 0.017074849685059 +Allele 125 0.010088347930364 +Allele 131 0.010080950239814 + +Locus 005 +Allele 218 0.011397286611517 +Allele 220 0.097323679876016 +Allele 222 0.133950615717491 +Allele 224 0.134326705881836 +Allele 226 0.096429956976234 +Allele 228 0.046291614629302 +Allele 230 0.045396016199413 +Allele 232 0.065031337189086 +Allele 234 0.068654250864775 +Allele 236 0.057795308025380 +Allele 238 0.077687594757222 +Allele 240 0.040398062625113 +Allele 242 0.035878318256706 +Allele 244 0.010192852629796 +Allele 246 0.015510326485148 +Allele 248 0.010233104777966 +Allele 250 0.014592826364021 +Allele 252 0.016192363297862 +Allele 254 0.011682802535355 +Allele 256 0.011034976299765 + +Locus 006 +Allele 094 0.106476263751469 +Allele 096 0.173637952224668 +Allele 098 0.039887651846896 +Allele 100 0.011702839377474 +Allele 102 0.099472535961767 +Allele 104 0.241464999469823 +Allele 106 0.144927602600836 +Allele 108 0.068203921628254 +Allele 110 0.050837069876033 +Allele 112 0.019663256885832 +Allele 114 0.011459846263252 +Allele 124 0.009674997841659 +Allele 126 0.010676901663928 +Allele 149 0.011914160608112 + +Locus 007 +Allele 202 0.009904849304794 +Allele 204 0.024022157142939 +Allele 206 0.011553478522348 +Allele 208 0.138969209648168 +Allele 210 0.039414265830309 +Allele 212 0.188026317343213 +Allele 214 0.107100759076359 +Allele 216 0.115142052233131 +Allele 218 0.062188771473936 +Allele 220 0.054810117976196 +Allele 222 0.057618137575568 +Allele 224 0.115141973931158 +Allele 226 0.039683422801784 +Allele 228 0.016353852892546 +Allele 233 0.010357595043617 +Allele 238 0.009713039203935 + +Locus 008 +Allele 121 0.085527391396431 +Allele 123 0.080702484277185 +Allele 125 0.056262387390469 +Allele 127 0.014212889816911 +Allele 129 0.055101548667880 +Allele 131 0.273533117774929 +Allele 133 0.152908894877962 +Allele 135 0.188227258410080 +Allele 137 0.067901461541725 +Allele 151 0.013178116773001 +Allele 161 0.012444449073427 + +Locus 009 +Allele 161 0.014403024942514 +Allele 165 0.029753928067817 +Allele 167 0.054976028055562 +Allele 169 0.099802632622958 +Allele 171 0.284948652587971 +Allele 173 0.193055299245830 +Allele 175 0.107175981333746 +Allele 177 0.108277385634560 +Allele 179 0.013621989699271 +Allele 181 0.042242340570014 +Allele 183 0.025032135254742 +Allele 185 0.026710601985020 + +Locus 010 +Allele 108 0.028447706204141 +Allele 115 0.009832205902250 +Allele 121 0.010377445881780 +Allele 123 0.045644464341119 +Allele 125 0.098742095970314 +Allele 127 0.074125676539370 +Allele 129 0.086013703249374 +Allele 131 0.092860548862894 +Allele 133 0.168731945271225 +Allele 135 0.106101394667135 +Allele 137 0.083907282654042 +Allele 139 0.024477430745169 +Allele 141 0.039884781941752 +Allele 143 0.010993469660785 +Allele 145 0.030093180397497 +Allele 147 0.020439944623746 +Allele 149 0.028153212616234 +Allele 152 0.015309607187170 +Allele 155 0.010600326724916 +Allele 157 0.015263576559086 + + +Cluster 03 +Locus 001 +Allele 092 0.117199088363928 +Allele 094 0.112916055151440 +Allele 096 0.106270190018705 +Allele 098 0.116814505438707 +Allele 100 0.111733454314978 +Allele 102 0.104494762737098 +Allele 104 0.112505080613575 +Allele 106 0.117506293862893 +Allele 108 0.100560569498673 + +Locus 002 +Allele 118 0.080729247222057 +Allele 122 0.080850558341288 +Allele 124 0.082503060027423 +Allele 126 0.094557513014396 +Allele 127 0.081214038607665 +Allele 128 0.085610305109441 +Allele 130 0.082690613312584 +Allele 132 0.084613660695366 +Allele 134 0.077894729915954 +Allele 135 0.083642324351571 +Allele 137 0.085937805297112 +Allele 151 0.079756144105144 + +Locus 003 +Allele 130 0.068919717140279 +Allele 133 0.069232195508953 +Allele 136 0.071341305864017 +Allele 138 0.074568368438044 +Allele 139 0.073047369735429 +Allele 141 0.074161421265411 +Allele 143 0.066458049949361 +Allele 145 0.072973624185851 +Allele 146 0.071973028176220 +Allele 147 0.070624612631626 +Allele 148 0.074730633101534 +Allele 150 0.070176023098969 +Allele 152 0.073677324379701 +Allele 156 0.068116326524607 + +Locus 004 +Allele 093 0.057694935116706 +Allele 095 0.058806836661554 +Allele 096 0.055870378485516 +Allele 097 0.059558295255610 +Allele 099 0.061086402760301 +Allele 100 0.059962074544395 +Allele 101 0.063800425083763 +Allele 103 0.064748578043427 +Allele 105 0.056879265702584 +Allele 107 0.058054593314244 +Allele 109 0.056452784977670 +Allele 110 0.056522402905891 +Allele 113 0.061151302869455 +Allele 121 0.058721622279800 +Allele 123 0.055772314830470 +Allele 125 0.057463377378308 +Allele 131 0.057454409790305 + +Locus 005 +Allele 218 0.047385556188241 +Allele 220 0.049612282056625 +Allele 222 0.051073316942386 +Allele 224 0.051150198880323 +Allele 226 0.050690384258125 +Allele 228 0.050611203438744 +Allele 230 0.051272937733160 +Allele 232 0.050861303162593 +Allele 234 0.053534104469538 +Allele 236 0.051533251852384 +Allele 238 0.050843636726291 +Allele 240 0.050096219036571 +Allele 242 0.048340052596867 +Allele 244 0.049245092236630 +Allele 246 0.049865265090163 +Allele 248 0.048913217561294 +Allele 250 0.051181954853833 +Allele 252 0.048828573049827 +Allele 254 0.047390835660312 +Allele 256 0.047570614206098 + +Locus 006 +Allele 094 0.072438162710164 +Allele 096 0.070750599142916 +Allele 098 0.073831886698329 +Allele 100 0.066616061907985 +Allele 102 0.072544293106853 +Allele 104 0.078296518594002 +Allele 106 0.073504236419328 +Allele 108 0.070580110156593 +Allele 110 0.075751407980307 +Allele 112 0.073364905958237 +Allele 114 0.067233952271435 +Allele 124 0.069781559239188 +Allele 126 0.068664665788839 +Allele 149 0.066641640025827 + +Locus 007 +Allele 202 0.061417563528283 +Allele 204 0.059945960356660 +Allele 206 0.058706437396632 +Allele 208 0.065617873753411 +Allele 210 0.065493452131480 +Allele 212 0.062320176338823 +Allele 214 0.063549809236437 +Allele 216 0.061920797476825 +Allele 218 0.061480446870326 +Allele 220 0.062831248868335 +Allele 222 0.067468626404198 +Allele 224 0.061914731218865 +Allele 226 0.064322003194315 +Allele 228 0.060862696365015 +Allele 233 0.060494031932054 +Allele 238 0.061654144928342 + +Locus 008 +Allele 121 0.091775453088689 +Allele 123 0.096854853646575 +Allele 125 0.089307699546113 +Allele 127 0.083063503605890 +Allele 129 0.090122315227468 +Allele 131 0.089936442042900 +Allele 133 0.094852510348800 +Allele 135 0.089744330464780 +Allele 137 0.105060961055878 +Allele 151 0.083308563449061 +Allele 161 0.085973367523847 + +Locus 009 +Allele 161 0.077987137569916 +Allele 165 0.078883485821451 +Allele 167 0.087718513443933 +Allele 169 0.082491052510434 +Allele 171 0.086591556904506 +Allele 173 0.089374628143573 +Allele 175 0.083006346708678 +Allele 177 0.083253333110621 +Allele 179 0.079490242156036 +Allele 181 0.083945796864955 +Allele 183 0.085200664434567 +Allele 185 0.082057242331332 + +Locus 010 +Allele 108 0.049269797452639 +Allele 115 0.049403296881887 +Allele 121 0.048647315432408 +Allele 123 0.051712869687476 +Allele 125 0.049835211315482 +Allele 127 0.049122203211812 +Allele 129 0.050271651854584 +Allele 131 0.049319743404505 +Allele 133 0.050959100951364 +Allele 135 0.049051174604887 +Allele 137 0.052140554154521 +Allele 139 0.053818176398264 +Allele 141 0.051096694699495 +Allele 143 0.048175499357280 +Allele 145 0.048011546877120 +Allele 147 0.051049911292800 +Allele 149 0.049664777514528 +Allele 152 0.049664331018102 +Allele 155 0.048740941588453 +Allele 157 0.050045202302394 + + +Cluster 04 +Locus 001 +Allele 092 0.113156000398434 +Allele 094 0.114822661041067 +Allele 096 0.107587413343403 +Allele 098 0.114875548856164 +Allele 100 0.110822080638021 +Allele 102 0.109096854647041 +Allele 104 0.111376532900407 +Allele 106 0.116935833331636 +Allele 108 0.101327074843823 + +Locus 002 +Allele 118 0.080691421884075 +Allele 122 0.081306781574583 +Allele 124 0.083728323900724 +Allele 126 0.091712191532326 +Allele 127 0.079763555895628 +Allele 128 0.086093550594992 +Allele 130 0.082515570272711 +Allele 132 0.087232372901070 +Allele 134 0.077871242514462 +Allele 135 0.084583525415722 +Allele 137 0.086094465376606 +Allele 151 0.078406998137100 + +Locus 003 +Allele 130 0.069549713093767 +Allele 133 0.067948373922098 +Allele 136 0.071509410390795 +Allele 138 0.074931765801380 +Allele 139 0.073304395154171 +Allele 141 0.073024174056065 +Allele 143 0.066981033316017 +Allele 145 0.073315317922378 +Allele 146 0.071567956487435 +Allele 147 0.069351440077019 +Allele 148 0.074973062988779 +Allele 150 0.072555820834277 +Allele 152 0.073187960293025 +Allele 156 0.067799575662793 + +Locus 004 +Allele 093 0.058209733441776 +Allele 095 0.059248071212587 +Allele 096 0.055499986842403 +Allele 097 0.059825993239375 +Allele 099 0.060587654291683 +Allele 100 0.060333869044028 +Allele 101 0.062733721670064 +Allele 103 0.064070982643618 +Allele 105 0.057799341247894 +Allele 107 0.058287218009967 +Allele 109 0.058625477540676 +Allele 110 0.057565336926688 +Allele 113 0.059400667350083 +Allele 121 0.057923168728126 +Allele 123 0.056978568915563 +Allele 125 0.056427600425415 +Allele 131 0.056482608470052 + +Locus 005 +Allele 218 0.047582205962794 +Allele 220 0.050610473063819 +Allele 222 0.050962734048381 +Allele 224 0.051383470036770 +Allele 226 0.050975165311335 +Allele 228 0.050472830188025 +Allele 230 0.051615155235796 +Allele 232 0.050709929414006 +Allele 234 0.052990480711166 +Allele 236 0.051160923003269 +Allele 238 0.050891605134857 +Allele 240 0.050158917401939 +Allele 242 0.048599228356323 +Allele 244 0.048512642238626 +Allele 246 0.049652524406999 +Allele 248 0.048461891372295 +Allele 250 0.050076592964762 +Allele 252 0.048889275678774 +Allele 254 0.047870126591516 +Allele 256 0.048423828878548 + +Locus 006 +Allele 094 0.072398114977971 +Allele 096 0.071559442604792 +Allele 098 0.072346696655410 +Allele 100 0.067887059619552 +Allele 102 0.073558260547081 +Allele 104 0.077030918560293 +Allele 106 0.074456954707523 +Allele 108 0.071127704459468 +Allele 110 0.075524182150274 +Allele 112 0.072262135249688 +Allele 114 0.067629517339593 +Allele 124 0.069051186368816 +Allele 126 0.068187245421508 +Allele 149 0.066980581338033 + +Locus 007 +Allele 202 0.060441907848949 +Allele 204 0.060196862017416 +Allele 206 0.059864099062272 +Allele 208 0.064837019870881 +Allele 210 0.064266237543475 +Allele 212 0.063795760876317 +Allele 214 0.063390192050471 +Allele 216 0.063103130084327 +Allele 218 0.061888970353491 +Allele 220 0.063566624072685 +Allele 222 0.066134672938209 +Allele 224 0.062646691130033 +Allele 226 0.064058473105078 +Allele 228 0.060819365215714 +Allele 233 0.060276970802403 +Allele 238 0.060713023028279 + +Locus 008 +Allele 121 0.091841552961205 +Allele 123 0.097304255486173 +Allele 125 0.089517401107669 +Allele 127 0.083733259456839 +Allele 129 0.091707754124858 +Allele 131 0.090470698074196 +Allele 133 0.095001542140347 +Allele 135 0.089700611541350 +Allele 137 0.098773861028543 +Allele 151 0.087573157681056 +Allele 161 0.084375906397770 + +Locus 009 +Allele 161 0.078484549896725 +Allele 165 0.079653104652673 +Allele 167 0.087023092447792 +Allele 169 0.083639803392324 +Allele 171 0.085987754143930 +Allele 173 0.088254148457365 +Allele 175 0.084747707845665 +Allele 177 0.082502133176196 +Allele 179 0.078776911343478 +Allele 181 0.082350509793894 +Allele 183 0.083696389590605 +Allele 185 0.084883895259349 + +Locus 010 +Allele 108 0.050657635303432 +Allele 115 0.048728057358449 +Allele 121 0.048177899810335 +Allele 123 0.050825856556617 +Allele 125 0.050268462057793 +Allele 127 0.048988889502910 +Allele 129 0.050065800255450 +Allele 131 0.050085618740124 +Allele 133 0.051341274004477 +Allele 135 0.049920318209796 +Allele 137 0.051882931475234 +Allele 139 0.052954683261919 +Allele 141 0.050910153646317 +Allele 143 0.047987782405834 +Allele 145 0.048517666934858 +Allele 147 0.050789958401770 +Allele 149 0.049964874734484 +Allele 152 0.049982975413323 +Allele 155 0.048286984098653 +Allele 157 0.049662177828225 + + +Cluster 05 +Locus 001 +Allele 092 0.115019986652793 +Allele 094 0.112416440983384 +Allele 096 0.106709036809186 +Allele 098 0.117953703403446 +Allele 100 0.112767737870972 +Allele 102 0.105978768017756 +Allele 104 0.112231110894223 +Allele 106 0.115952523803949 +Allele 108 0.100970691564293 + +Locus 002 +Allele 118 0.080743767512157 +Allele 122 0.081005211557610 +Allele 124 0.082803480319588 +Allele 126 0.092708234044934 +Allele 127 0.080943112862376 +Allele 128 0.085771601150351 +Allele 130 0.083172983747830 +Allele 132 0.084844715854051 +Allele 134 0.078597698538928 +Allele 135 0.084267624604415 +Allele 137 0.085296559543669 +Allele 151 0.079845010264089 + +Locus 003 +Allele 130 0.069410156412473 +Allele 133 0.069775130692744 +Allele 136 0.071175108062235 +Allele 138 0.074438987827635 +Allele 139 0.072596867477780 +Allele 141 0.073382895440616 +Allele 143 0.067280372765651 +Allele 145 0.072801276000169 +Allele 146 0.071653960016217 +Allele 147 0.070304742243600 +Allele 148 0.074815585570991 +Allele 150 0.071027412618783 +Allele 152 0.073191838649536 +Allele 156 0.068145666221569 + +Locus 004 +Allele 093 0.058166675283971 +Allele 095 0.059268287453241 +Allele 096 0.056104971798278 +Allele 097 0.059680335934522 +Allele 099 0.061048256735907 +Allele 100 0.059675354950275 +Allele 101 0.062187904093381 +Allele 103 0.063236250268588 +Allele 105 0.057280982741424 +Allele 107 0.057840350362530 +Allele 109 0.057481285751246 +Allele 110 0.057173404183824 +Allele 113 0.060705587374434 +Allele 121 0.058056889032577 +Allele 123 0.056465083846153 +Allele 125 0.057667533784403 +Allele 131 0.057960846405247 + +Locus 005 +Allele 218 0.047891590364972 +Allele 220 0.049786152605645 +Allele 222 0.050972135929271 +Allele 224 0.050724414719069 +Allele 226 0.051057614978187 +Allele 228 0.050573741015609 +Allele 230 0.050922959963422 +Allele 232 0.050841355782391 +Allele 234 0.052859873618785 +Allele 236 0.051618295589281 +Allele 238 0.050350665209702 +Allele 240 0.050244031773809 +Allele 242 0.048258206082249 +Allele 244 0.049124281046379 +Allele 246 0.049817445805280 +Allele 248 0.049362595515698 +Allele 250 0.050930151356956 +Allele 252 0.049232562745247 +Allele 254 0.047392938983112 +Allele 256 0.048038986914940 + +Locus 006 +Allele 094 0.072519919030960 +Allele 096 0.071272689515193 +Allele 098 0.072770463099188 +Allele 100 0.067153469617586 +Allele 102 0.073041976744795 +Allele 104 0.077117207414715 +Allele 106 0.074151087870784 +Allele 108 0.071016570174976 +Allele 110 0.074662349804985 +Allele 112 0.072934276585701 +Allele 114 0.067590039258215 +Allele 124 0.069973424170422 +Allele 126 0.068789826234286 +Allele 149 0.067006700478195 + +Locus 007 +Allele 202 0.061268216752207 +Allele 204 0.060307471680975 +Allele 206 0.059786905405780 +Allele 208 0.065263504424750 +Allele 210 0.064938091969076 +Allele 212 0.062501363848534 +Allele 214 0.063377697703250 +Allele 216 0.062416882392977 +Allele 218 0.061946465745357 +Allele 220 0.062611077438571 +Allele 222 0.066198673512846 +Allele 224 0.062018928148877 +Allele 226 0.064027345199902 +Allele 228 0.061051053593097 +Allele 233 0.061038327419508 +Allele 238 0.061247994764296 + +Locus 008 +Allele 121 0.091454713441657 +Allele 123 0.095700492097160 +Allele 125 0.089793439146136 +Allele 127 0.084086763700686 +Allele 129 0.090523634556624 +Allele 131 0.090459698828623 +Allele 133 0.095003015411616 +Allele 135 0.089869164058971 +Allele 137 0.101595818644316 +Allele 151 0.085300474279023 +Allele 161 0.086212785835190 + +Locus 009 +Allele 161 0.078613855831473 +Allele 165 0.079090204832625 +Allele 167 0.087595253675693 +Allele 169 0.082768342903085 +Allele 171 0.086890406646402 +Allele 173 0.086720694782108 +Allele 175 0.084729999393984 +Allele 177 0.083217085212775 +Allele 179 0.079854702394478 +Allele 181 0.083755364641113 +Allele 183 0.083853061846440 +Allele 185 0.082911027839826 + +Locus 010 +Allele 108 0.049445287865320 +Allele 115 0.049496613627967 +Allele 121 0.048958594973764 +Allele 123 0.051491736057620 +Allele 125 0.050194551597818 +Allele 127 0.049353417539834 +Allele 129 0.049448367713754 +Allele 131 0.049375331385293 +Allele 133 0.050623054325146 +Allele 135 0.049385279958990 +Allele 137 0.051827025448523 +Allele 139 0.053131532965009 +Allele 141 0.051000644777343 +Allele 143 0.047970579785644 +Allele 145 0.048084461132753 +Allele 147 0.051177360468890 +Allele 149 0.049918989858006 +Allele 152 0.050008962602153 +Allele 155 0.048819508457618 +Allele 157 0.050288699458557 + + +Cluster 06 +Locus 001 +Allele 092 0.115485883711649 +Allele 094 0.112717184358785 +Allele 096 0.106969699681446 +Allele 098 0.116978614784969 +Allele 100 0.111435782576341 +Allele 102 0.106267634438076 +Allele 104 0.111290154015320 +Allele 106 0.118120937367745 +Allele 108 0.100734109065666 + +Locus 002 +Allele 118 0.080733881699975 +Allele 122 0.081086544008632 +Allele 124 0.082852416345851 +Allele 126 0.093275588337293 +Allele 127 0.080427335376005 +Allele 128 0.085237314518809 +Allele 130 0.082990173230028 +Allele 132 0.085662198963152 +Allele 134 0.078573497152937 +Allele 135 0.084239743830057 +Allele 137 0.085713438482867 +Allele 151 0.079207868054394 + +Locus 003 +Allele 130 0.069645364374098 +Allele 133 0.068655827770310 +Allele 136 0.071375476603272 +Allele 138 0.074781210932522 +Allele 139 0.073058070431927 +Allele 141 0.073054699020017 +Allele 143 0.067426521670787 +Allele 145 0.072733684024926 +Allele 146 0.071812330436259 +Allele 147 0.070184168200408 +Allele 148 0.074595769421697 +Allele 150 0.070945267533386 +Allele 152 0.073467109009235 +Allele 156 0.068264500571153 + +Locus 004 +Allele 093 0.058323448858566 +Allele 095 0.058805609847872 +Allele 096 0.055703274138049 +Allele 097 0.059774585839570 +Allele 099 0.060974790223381 +Allele 100 0.059801678951841 +Allele 101 0.062702697868185 +Allele 103 0.064303652373861 +Allele 105 0.057183424877374 +Allele 107 0.057980302620157 +Allele 109 0.057621536248442 +Allele 110 0.056810396836482 +Allele 113 0.060869103682032 +Allele 121 0.058127175323538 +Allele 123 0.057121714702608 +Allele 125 0.057043501967050 +Allele 131 0.056853105640991 + +Locus 005 +Allele 218 0.047701438371973 +Allele 220 0.050067688406330 +Allele 222 0.051129099223666 +Allele 224 0.050481925273677 +Allele 226 0.051242325228153 +Allele 228 0.050211977212660 +Allele 230 0.051233372489064 +Allele 232 0.050573597293680 +Allele 234 0.053324007648622 +Allele 236 0.051338468939583 +Allele 238 0.050979895411046 +Allele 240 0.050112364443841 +Allele 242 0.048406544795405 +Allele 244 0.048965772498495 +Allele 246 0.049908334433233 +Allele 248 0.048751125750721 +Allele 250 0.050323280819790 +Allele 252 0.049213640974178 +Allele 254 0.047574920524697 +Allele 256 0.048460220261185 + +Locus 006 +Allele 094 0.073258578622300 +Allele 096 0.071595319623206 +Allele 098 0.072224742241858 +Allele 100 0.066696854665280 +Allele 102 0.072775285147587 +Allele 104 0.077001441693488 +Allele 106 0.074467763257987 +Allele 108 0.070754196148321 +Allele 110 0.075415000586322 +Allele 112 0.073374142991753 +Allele 114 0.067605031250531 +Allele 124 0.069710687624591 +Allele 126 0.068530951428258 +Allele 149 0.066590004718522 + +Locus 007 +Allele 202 0.061044022227240 +Allele 204 0.060497969220581 +Allele 206 0.059196326803666 +Allele 208 0.065157329104393 +Allele 210 0.064625572624041 +Allele 212 0.062569702365707 +Allele 214 0.064038118991699 +Allele 216 0.062681085386620 +Allele 218 0.061772307739811 +Allele 220 0.062656757553900 +Allele 222 0.066564423127071 +Allele 224 0.062168157669241 +Allele 226 0.064367745607068 +Allele 228 0.060902458097303 +Allele 233 0.060541606153307 +Allele 238 0.061216417328354 + +Locus 008 +Allele 121 0.090739799726608 +Allele 123 0.096326252233163 +Allele 125 0.089566197026293 +Allele 127 0.083647356897897 +Allele 129 0.091337125476887 +Allele 131 0.090325366514681 +Allele 133 0.094511586892717 +Allele 135 0.089925494430737 +Allele 137 0.102398167590825 +Allele 151 0.085527061492299 +Allele 161 0.085695591717891 + +Locus 009 +Allele 161 0.078296263592775 +Allele 165 0.079295140429448 +Allele 167 0.087756584213484 +Allele 169 0.082818940282446 +Allele 171 0.086596550149408 +Allele 173 0.088044190057606 +Allele 175 0.084187097262239 +Allele 177 0.082643145621524 +Allele 179 0.079621529252292 +Allele 181 0.083223014583494 +Allele 183 0.084345922083668 +Allele 185 0.083171622471617 + +Locus 010 +Allele 108 0.049842098514770 +Allele 115 0.049141938875855 +Allele 121 0.048431933061938 +Allele 123 0.051408569185533 +Allele 125 0.049989916577556 +Allele 127 0.049437253446898 +Allele 129 0.049932199714797 +Allele 131 0.049799684784507 +Allele 133 0.050621777695359 +Allele 135 0.049655026696012 +Allele 137 0.052089346955426 +Allele 139 0.052861781217010 +Allele 141 0.050771656291502 +Allele 143 0.048247527753974 +Allele 145 0.048373137057123 +Allele 147 0.050577795136083 +Allele 149 0.050368102801477 +Allele 152 0.050023463683810 +Allele 155 0.048396713320787 +Allele 157 0.050030077229586 + + +Cluster 07 +Locus 001 +Allele 092 0.113651059975543 +Allele 094 0.113243765712940 +Allele 096 0.107537927945103 +Allele 098 0.116816264436744 +Allele 100 0.112251030551457 +Allele 102 0.107158398924163 +Allele 104 0.110727794586823 +Allele 106 0.118135027501400 +Allele 108 0.100478730365826 + +Locus 002 +Allele 118 0.080883798614714 +Allele 122 0.081261892144026 +Allele 124 0.084987953518425 +Allele 126 0.093257660495593 +Allele 127 0.079687118231270 +Allele 128 0.084930194522614 +Allele 130 0.082532335086067 +Allele 132 0.086807807201915 +Allele 134 0.077284193604915 +Allele 135 0.084776356893916 +Allele 137 0.084977643338593 +Allele 151 0.078613046347955 + +Locus 003 +Allele 130 0.068785935620895 +Allele 133 0.068400165259021 +Allele 136 0.071883763691030 +Allele 138 0.075696605522263 +Allele 139 0.073198543174107 +Allele 141 0.073214422676221 +Allele 143 0.066823171450064 +Allele 145 0.073664056573904 +Allele 146 0.071746949883513 +Allele 147 0.068688210335424 +Allele 148 0.074832000741567 +Allele 150 0.071316107685359 +Allele 152 0.073886090263699 +Allele 156 0.067863977122934 + +Locus 004 +Allele 093 0.058479400020070 +Allele 095 0.058521289714419 +Allele 096 0.055721638645110 +Allele 097 0.059733457738263 +Allele 099 0.060384949637600 +Allele 100 0.060481787966498 +Allele 101 0.062195897521669 +Allele 103 0.064428952792011 +Allele 105 0.058098828522120 +Allele 107 0.058234216713385 +Allele 109 0.058867022960379 +Allele 110 0.057168732588303 +Allele 113 0.060286291184689 +Allele 121 0.057514748382322 +Allele 123 0.056874772772258 +Allele 125 0.056246146727979 +Allele 131 0.056761866112922 + +Locus 005 +Allele 218 0.047761535687400 +Allele 220 0.050422394154369 +Allele 222 0.051267921912485 +Allele 224 0.050965956587556 +Allele 226 0.051274471527138 +Allele 228 0.050217461607615 +Allele 230 0.051419815931266 +Allele 232 0.050890449196261 +Allele 234 0.052957928512183 +Allele 236 0.051721448659944 +Allele 238 0.051567452324579 +Allele 240 0.049999623849501 +Allele 242 0.048183560230374 +Allele 244 0.047877747133295 +Allele 246 0.050049989263161 +Allele 248 0.048420891296191 +Allele 250 0.050207975992306 +Allele 252 0.049069143835763 +Allele 254 0.047234814837576 +Allele 256 0.048489417461040 + +Locus 006 +Allele 094 0.072671556577011 +Allele 096 0.071908390551658 +Allele 098 0.071784343576428 +Allele 100 0.068294462715485 +Allele 102 0.073025406800696 +Allele 104 0.076468031622339 +Allele 106 0.075352205099379 +Allele 108 0.070744351241358 +Allele 110 0.075370759799061 +Allele 112 0.074239020160701 +Allele 114 0.067101632243588 +Allele 124 0.069362118313654 +Allele 126 0.067302387259483 +Allele 149 0.066375334039157 + +Locus 007 +Allele 202 0.059995164140969 +Allele 204 0.059779009426609 +Allele 206 0.059213776231389 +Allele 208 0.066029914885308 +Allele 210 0.063810432545376 +Allele 212 0.062767280210726 +Allele 214 0.064123365252978 +Allele 216 0.062937564933309 +Allele 218 0.062199009804613 +Allele 220 0.062835279088334 +Allele 222 0.065924991572552 +Allele 224 0.062760639239099 +Allele 226 0.064705586050661 +Allele 228 0.061929920478302 +Allele 233 0.059968284944158 +Allele 238 0.061019781195618 + +Locus 008 +Allele 121 0.091420894855502 +Allele 123 0.097439280516083 +Allele 125 0.088493268839672 +Allele 127 0.083077365046343 +Allele 129 0.091304228242539 +Allele 131 0.090922102558250 +Allele 133 0.094894864131324 +Allele 135 0.090915991406903 +Allele 137 0.102102765676830 +Allele 151 0.085020913700815 +Allele 161 0.084408325025739 + +Locus 009 +Allele 161 0.078197899309634 +Allele 165 0.079818379256640 +Allele 167 0.086524005171682 +Allele 169 0.082892170246623 +Allele 171 0.086578362597431 +Allele 173 0.088234931686985 +Allele 175 0.084935278088611 +Allele 177 0.082481246013689 +Allele 179 0.079058058437771 +Allele 181 0.083558996156149 +Allele 183 0.084763288889047 +Allele 185 0.082957384145735 + +Locus 010 +Allele 108 0.050010760422127 +Allele 115 0.048443708655433 +Allele 121 0.048459861990689 +Allele 123 0.051911076428828 +Allele 125 0.049892391109681 +Allele 127 0.049661736659432 +Allele 129 0.050386968241559 +Allele 131 0.050239683149124 +Allele 133 0.050334979280817 +Allele 135 0.049476283952074 +Allele 137 0.051719053700543 +Allele 139 0.051933250372032 +Allele 141 0.050967106592204 +Allele 143 0.047897298702937 +Allele 145 0.048584513642486 +Allele 147 0.051105788487479 +Allele 149 0.050135202659553 +Allele 152 0.050764984126394 +Allele 155 0.047704896396560 +Allele 157 0.050370455430047 + + +Cluster 08 +Locus 001 +Allele 092 0.115839671408792 +Allele 094 0.113276977736798 +Allele 096 0.106762679211871 +Allele 098 0.116494102029099 +Allele 100 0.112497067642344 +Allele 102 0.105809224740087 +Allele 104 0.111714626958662 +Allele 106 0.116890422841647 +Allele 108 0.100715227430698 + +Locus 002 +Allele 118 0.081057128894192 +Allele 122 0.080983194621615 +Allele 124 0.082232220757920 +Allele 126 0.093031485742912 +Allele 127 0.081023844110370 +Allele 128 0.085129055396242 +Allele 130 0.082424266803722 +Allele 132 0.085953644940551 +Allele 134 0.078664056635366 +Allele 135 0.084164918101069 +Allele 137 0.085284901128677 +Allele 151 0.080051282867363 + +Locus 003 +Allele 130 0.068748296899301 +Allele 133 0.068967579764539 +Allele 136 0.071381728377823 +Allele 138 0.075056901195713 +Allele 139 0.072989774054059 +Allele 141 0.073741006625963 +Allele 143 0.066763840179471 +Allele 145 0.072722280239061 +Allele 146 0.071584704958830 +Allele 147 0.070353226539303 +Allele 148 0.074665501062486 +Allele 150 0.070818876371214 +Allele 152 0.073807861925195 +Allele 156 0.068398421807045 + +Locus 004 +Allele 093 0.058554010671472 +Allele 095 0.059456697676797 +Allele 096 0.055465513508165 +Allele 097 0.059571380838199 +Allele 099 0.060819983576499 +Allele 100 0.059715709560317 +Allele 101 0.062957858115899 +Allele 103 0.063785427521394 +Allele 105 0.057286181608162 +Allele 107 0.058026790308366 +Allele 109 0.056700558617852 +Allele 110 0.056791420807612 +Allele 113 0.061071480804291 +Allele 121 0.058368580875635 +Allele 123 0.056839909620114 +Allele 125 0.057280056942271 +Allele 131 0.057308438946956 + +Locus 005 +Allele 218 0.047605578337484 +Allele 220 0.050151728658433 +Allele 222 0.051313036326210 +Allele 224 0.051053117485655 +Allele 226 0.051538382489131 +Allele 228 0.050529037529317 +Allele 230 0.051188243907509 +Allele 232 0.050436693469459 +Allele 234 0.052928945205918 +Allele 236 0.051286826148333 +Allele 238 0.050745350318408 +Allele 240 0.049886835921616 +Allele 242 0.048417997072410 +Allele 244 0.048901437843769 +Allele 246 0.050006911993018 +Allele 248 0.048423767181319 +Allele 250 0.050844276855138 +Allele 252 0.049127816522254 +Allele 254 0.047557808904725 +Allele 256 0.048056207829896 + +Locus 006 +Allele 094 0.072994808470662 +Allele 096 0.071404769820865 +Allele 098 0.072799409791874 +Allele 100 0.067119843764931 +Allele 102 0.072797841632456 +Allele 104 0.076599050576799 +Allele 106 0.073603758179458 +Allele 108 0.070627484918498 +Allele 110 0.075328205940779 +Allele 112 0.073515712799271 +Allele 114 0.067624694295194 +Allele 124 0.069706721542746 +Allele 126 0.068955174394181 +Allele 149 0.066922523872285 + +Locus 007 +Allele 202 0.060900541411457 +Allele 204 0.060315514006328 +Allele 206 0.059087392009221 +Allele 208 0.065067123283612 +Allele 210 0.065218618426950 +Allele 212 0.062457575158928 +Allele 214 0.063046018775548 +Allele 216 0.062826563845600 +Allele 218 0.061791400756498 +Allele 220 0.062889843117466 +Allele 222 0.066642053218079 +Allele 224 0.062348248591271 +Allele 226 0.064188157144943 +Allele 228 0.061249244947132 +Allele 233 0.060341403615228 +Allele 238 0.061630301691743 + +Locus 008 +Allele 121 0.090958354309168 +Allele 123 0.096759538327373 +Allele 125 0.089219876594002 +Allele 127 0.083488420459483 +Allele 129 0.089985470683496 +Allele 131 0.090313170148086 +Allele 133 0.094994824936718 +Allele 135 0.089864003317523 +Allele 137 0.102576236311520 +Allele 151 0.085530420132959 +Allele 161 0.086309684779671 + +Locus 009 +Allele 161 0.078768720802056 +Allele 165 0.079212323013882 +Allele 167 0.086482207573251 +Allele 169 0.083152889347127 +Allele 171 0.086396762872881 +Allele 173 0.088782395428159 +Allele 175 0.083526222632504 +Allele 177 0.082862967245237 +Allele 179 0.079574529278687 +Allele 181 0.083696002328633 +Allele 183 0.084412093505140 +Allele 185 0.083132885972444 + +Locus 010 +Allele 108 0.049516055885743 +Allele 115 0.049395441524991 +Allele 121 0.048976735509803 +Allele 123 0.051374372423159 +Allele 125 0.050058227345211 +Allele 127 0.049458944082558 +Allele 129 0.049940691454898 +Allele 131 0.049638016725474 +Allele 133 0.050954567168107 +Allele 135 0.049316486739896 +Allele 137 0.051910168028612 +Allele 139 0.053069871038089 +Allele 141 0.050931834430593 +Allele 143 0.048091981011350 +Allele 145 0.048172989978163 +Allele 147 0.050505491427163 +Allele 149 0.050050833095232 +Allele 152 0.050128318492748 +Allele 155 0.048494032243025 +Allele 157 0.050014941395182 + + + +Estimated Mixing Proportions +0.011358560000000 +0.920405446666667 +0.011573180000000 +0.011999733333333 +0.010250933333333 +0.011095220000000 +0.012464226666667 +0.010852700000000 + + + +Estimated sigma: +k: 0 1.000000000000000 +k: 1 1.000000000000000 +k: 2 1.000000000000000 +k: 3 1.000000000000000 +k: 4 1.000000000000000 +k: 5 1.000000000000000 +k: 6 1.000000000000000 +k: 7 1.000000000000000 + + + +Estimated psi: +k: 0 0.599999999999828 +k: 1 0.599999999999828 +k: 2 0.599999999999828 +k: 3 0.599999999999828 +k: 4 0.599999999999828 +k: 5 0.599999999999828 +k: 6 0.599999999999828 +k: 7 0.599999999999828 + + + diff --git a/inst/files/tess/tess_15.txt b/inst/files/tess/tess_15.txt new file mode 100644 index 0000000..7de70a2 --- /dev/null +++ b/inst/files/tess/tess_15.txt @@ -0,0 +1,568 @@ +Estimated Clustering Probabilities for Samples +Sample ***Cluster 01*** ***Cluster 02*** +000001: 0.999150000000000 0.000850000000000 1 +000002: 0.999990000000000 0.000010000000000 1 +000003: 1.000000000000000 0.000000000000000 1 +000004: 0.999600000000000 0.000400000000000 1 +000005: 0.998230000000000 0.001770000000000 1 +000006: 1.000000000000000 0.000000000000000 1 +000007: 0.958390000000000 0.041610000000000 1 +000008: 0.999890000000000 0.000110000000000 1 +000009: 0.999200000000000 0.000800000000000 1 +000010: 0.997520000000000 0.002480000000000 1 +000011: 0.999700000000000 0.000300000000000 1 +000012: 1.000000000000000 0.000000000000000 1 +000013: 1.000000000000000 0.000000000000000 1 +000014: 0.999990000000000 0.000010000000000 1 +000015: 0.991040000000000 0.008960000000000 1 +000016: 1.000000000000000 0.000000000000000 1 +000017: 0.998540000000000 0.001460000000000 1 +000018: 0.999120000000000 0.000880000000000 1 +000019: 0.965280000000000 0.034720000000000 1 +000020: 0.993010000000000 0.006990000000000 1 +000021: 0.992130000000000 0.007870000000000 1 +000022: 0.285970000000000 0.714030000000000 1 +000023: 1.000000000000000 0.000000000000000 1 +000024: 0.999980000000000 0.000020000000000 1 +000025: 0.999900000000000 0.000100000000000 1 +000026: 0.999930000000000 0.000070000000000 1 +000027: 0.999950000000000 0.000050000000000 1 +000028: 0.999970000000000 0.000030000000000 1 +000029: 0.994000000000000 0.006000000000000 1 +000030: 0.883970000000000 0.116030000000000 1 +000031: 0.988830000000000 0.011170000000000 1 +000032: 0.999940000000000 0.000060000000000 1 +000033: 0.991900000000000 0.008100000000000 1 +000034: 0.993440000000000 0.006560000000000 1 +000035: 0.988340000000000 0.011660000000000 1 +000036: 0.998630000000000 0.001370000000000 1 +000037: 1.000000000000000 0.000000000000000 1 +000038: 0.999600000000000 0.000400000000000 1 +000039: 0.998950000000000 0.001050000000000 1 +000040: 0.999900000000000 0.000100000000000 1 +000041: 0.999610000000000 0.000390000000000 1 +000042: 0.999960000000000 0.000040000000000 1 +000043: 0.999980000000000 0.000020000000000 1 +000044: 0.998720000000000 0.001280000000000 1 +000045: 0.929090000000000 0.070910000000000 1 +000046: 0.999980000000000 0.000020000000000 1 +000047: 0.998650000000000 0.001350000000000 1 +000048: 0.992810000000000 0.007190000000000 1 +000049: 0.973520000000000 0.026480000000000 1 +000050: 0.996440000000000 0.003560000000000 1 +000051: 0.790910000000000 0.209090000000000 1 +000052: 0.992930000000000 0.007070000000000 1 +000053: 1.000000000000000 0.000000000000000 1 +000054: 0.999090000000000 0.000910000000000 1 +000055: 0.999970000000000 0.000030000000000 1 +000056: 0.999220000000000 0.000780000000000 1 +000057: 0.997050000000000 0.002950000000000 1 +000058: 0.999980000000000 0.000020000000000 1 +000059: 0.782820000000000 0.217180000000000 1 +000060: 0.981210000000000 0.018790000000000 1 +000061: 0.999910000000000 0.000090000000000 1 +000062: 0.996520000000000 0.003480000000000 1 +000063: 0.998550000000000 0.001450000000000 1 +000064: 0.689880000000000 0.310120000000000 1 +000065: 0.990730000000000 0.009270000000000 1 +000066: 0.995210000000000 0.004790000000000 1 +000067: 0.999650000000000 0.000350000000000 1 +000068: 0.999970000000000 0.000030000000000 1 +000069: 0.959250000000000 0.040750000000000 1 +000070: 0.997240000000000 0.002760000000000 1 +000071: 0.999720000000000 0.000280000000000 1 +000072: 0.997690000000000 0.002310000000000 1 +000073: 0.995750000000000 0.004250000000000 1 +000074: 0.999260000000000 0.000740000000000 1 +000075: 0.996070000000000 0.003930000000000 1 + + + +Estimated Allele Frequencies +Cluster 01 +Locus 001 +Allele 092 0.041771507143763 +Allele 094 0.387541422279836 +Allele 096 0.161959653724329 +Allele 098 0.088679036756157 +Allele 100 0.026928539956823 +Allele 102 0.083045731572843 +Allele 104 0.107919810162276 +Allele 106 0.050725389656020 +Allele 108 0.025782659846201 +Allele 110 0.025646248901751 + +Locus 002 +Allele 094 0.105964863613492 +Allele 096 0.075715783120919 +Allele 098 0.149959402130328 +Allele 100 0.064771476565221 +Allele 102 0.106499282583464 +Allele 104 0.193057186433063 +Allele 106 0.128926530363054 +Allele 108 0.063176590947736 +Allele 110 0.037573671518461 +Allele 112 0.023972885354398 +Allele 114 0.012640471611555 +Allele 124 0.012486316912656 +Allele 126 0.012599837675823 +Allele 149 0.012655701169826 + +Locus 003 +Allele 118 0.018248289804173 +Allele 122 0.030540694364427 +Allele 124 0.181591652523058 +Allele 126 0.094143819843686 +Allele 128 0.060826657244376 +Allele 130 0.035792020471586 +Allele 132 0.060637510296316 +Allele 137 0.012021784137693 +Allele 202 0.012023415313724 +Allele 204 0.024394922206047 +Allele 206 0.012194358854291 +Allele 208 0.117594114335229 +Allele 210 0.036439129376854 +Allele 212 0.097238845292475 +Allele 214 0.071054069370235 +Allele 216 0.042579728153119 +Allele 218 0.048667027304770 +Allele 220 0.012122917890284 +Allele 224 0.024059041052699 +Allele 226 0.007830002164958 + +Locus 004 +Allele 124 0.023937572727324 +Allele 126 0.029751380749929 +Allele 127 0.010088781625336 +Allele 128 0.041661688147428 +Allele 130 0.041732008569531 +Allele 132 0.167203069145931 +Allele 134 0.011910672749095 +Allele 135 0.095132841426341 +Allele 137 0.064836373905109 +Allele 151 0.010619843855770 +Allele 208 0.016384396834759 +Allele 210 0.011576321591478 +Allele 212 0.083682285550333 +Allele 214 0.035889436929652 +Allele 216 0.071554090335481 +Allele 218 0.017233392347221 +Allele 220 0.047677371996045 +Allele 222 0.056484298719039 +Allele 224 0.089515144671229 +Allele 226 0.035569577927106 +Allele 228 0.017905399662355 +Allele 233 0.007732076752051 +Allele 238 0.011921973781459 + +Locus 005 +Allele 121 0.058492166599127 +Allele 123 0.053625451632542 +Allele 125 0.038902937778932 +Allele 127 0.012972610714862 +Allele 129 0.030488026419653 +Allele 130 0.026130033068109 +Allele 131 0.123765425891929 +Allele 133 0.071167151846147 +Allele 135 0.057106082587627 +Allele 136 0.117045851820373 +Allele 137 0.024637270057489 +Allele 138 0.096155287794326 +Allele 139 0.095628218984205 +Allele 141 0.026049484465360 +Allele 145 0.034485470536739 +Allele 146 0.071157097209345 +Allele 148 0.049172275112048 +Allele 150 0.013019157481188 + +Locus 006 +Allele 121 0.025346432253426 +Allele 123 0.024943623534006 +Allele 125 0.018998044410290 +Allele 129 0.025431948983935 +Allele 131 0.114224254522551 +Allele 133 0.071572910682013 +Allele 135 0.107377576401531 +Allele 136 0.025432210999116 +Allele 137 0.046153460452047 +Allele 138 0.018930910537527 +Allele 139 0.050150818812395 +Allele 141 0.018932035232671 +Allele 143 0.012696313631160 +Allele 145 0.056472093402617 +Allele 146 0.050764653076383 +Allele 147 0.010673093982528 +Allele 148 0.107389950385551 +Allele 150 0.075985445539864 +Allele 151 0.012737931090363 +Allele 152 0.094012152285835 +Allele 156 0.019079733048632 +Allele 161 0.012694406735559 + +Locus 007 +Allele 093 0.050328454771796 +Allele 095 0.070751432164322 +Allele 096 0.013003402296298 +Allele 097 0.149351054175034 +Allele 099 0.038691124644171 +Allele 100 0.058268085576322 +Allele 101 0.041900939005493 +Allele 103 0.053248061171112 +Allele 105 0.019398988260524 +Allele 107 0.025934902406404 +Allele 109 0.012188293419737 +Allele 110 0.012926699613561 +Allele 125 0.012959213617895 +Allele 161 0.013002765000220 +Allele 165 0.025956013672751 +Allele 167 0.045078412072118 +Allele 169 0.064046210924944 +Allele 171 0.139249785904090 +Allele 173 0.075733808405983 +Allele 175 0.045459186859713 +Allele 177 0.019523029303240 +Allele 181 0.013000136734274 + +Locus 008 +Allele 095 0.012801370469952 +Allele 097 0.050467730320482 +Allele 099 0.025644600545116 +Allele 100 0.038309080951549 +Allele 101 0.118276141513921 +Allele 103 0.090863947985946 +Allele 105 0.038349886212246 +Allele 107 0.076916031414154 +Allele 109 0.018459727783483 +Allele 110 0.019194481128750 +Allele 113 0.017805167918568 +Allele 121 0.019095772475784 +Allele 123 0.019165682216622 +Allele 131 0.012795347380690 +Allele 167 0.012824079978785 +Allele 169 0.025504297279712 +Allele 171 0.093599864641461 +Allele 173 0.087637983252442 +Allele 175 0.049839411502793 +Allele 177 0.076858653233873 +Allele 179 0.012810059354801 +Allele 181 0.031558629652847 +Allele 183 0.025571190791140 +Allele 185 0.025650861994882 + +Locus 009 +Allele 108 0.027391979771432 +Allele 115 0.011456463009451 +Allele 121 0.011027606737089 +Allele 123 0.040072456345249 +Allele 125 0.085382418813068 +Allele 127 0.039940533016549 +Allele 129 0.045589866638943 +Allele 131 0.045958877818001 +Allele 133 0.091410709313581 +Allele 135 0.026860449625787 +Allele 137 0.017253190769568 +Allele 139 0.017076223681090 +Allele 145 0.017152242432943 +Allele 147 0.007339997807752 +Allele 149 0.011511917554887 +Allele 152 0.010273843502709 +Allele 218 0.011480848009377 +Allele 220 0.085819403748988 +Allele 222 0.107887399881269 +Allele 224 0.085222333339695 +Allele 226 0.038643018111989 +Allele 228 0.022993555932894 +Allele 230 0.017210082067630 +Allele 232 0.023833296672129 +Allele 234 0.034163174181099 +Allele 236 0.017222259569055 +Allele 238 0.021147008724181 +Allele 240 0.017204271331420 +Allele 250 0.011474571592178 + +Locus 010 +Allele 123 0.010655532372659 +Allele 125 0.010986908369216 +Allele 127 0.032867157091138 +Allele 129 0.037381676016679 +Allele 131 0.043463710193580 +Allele 133 0.065900538376778 +Allele 135 0.071719577542783 +Allele 137 0.065918455092404 +Allele 139 0.016292918609741 +Allele 141 0.038522199408598 +Allele 143 0.011041472774974 +Allele 145 0.016586703853000 +Allele 147 0.012538157977333 +Allele 149 0.020360443021008 +Allele 152 0.011051250254749 +Allele 155 0.010986053086701 +Allele 157 0.015392765348837 +Allele 220 0.011044418213426 +Allele 222 0.020333546228600 +Allele 224 0.044175985662767 +Allele 226 0.054030348019958 +Allele 228 0.027529734935382 +Allele 230 0.032766261041715 +Allele 232 0.038697089668779 +Allele 234 0.038017118323424 +Allele 236 0.040072818660926 +Allele 238 0.053933357617699 +Allele 240 0.027360770894091 +Allele 242 0.032831602473368 +Allele 244 0.011030607233792 +Allele 246 0.016503469776727 +Allele 248 0.011026041245903 +Allele 250 0.011068249553989 +Allele 252 0.016514650790376 +Allele 254 0.010994763857481 +Allele 256 0.010403646411424 + + +Cluster 02 +Locus 001 +Allele 092 0.109037340148124 +Allele 094 0.088585925842492 +Allele 096 0.079470593883882 +Allele 098 0.093612645675709 +Allele 100 0.133009315123365 +Allele 102 0.088962052027546 +Allele 104 0.165294637238336 +Allele 106 0.087218079536272 +Allele 108 0.075779354644551 +Allele 110 0.079030055879719 + +Locus 002 +Allele 094 0.068828573322450 +Allele 096 0.059634579857473 +Allele 098 0.070913342200783 +Allele 100 0.099161097791003 +Allele 102 0.065242470577700 +Allele 104 0.131748524867320 +Allele 106 0.087856133199922 +Allele 108 0.058231330932417 +Allele 110 0.060327090415997 +Allele 112 0.067620874038081 +Allele 114 0.057335790538616 +Allele 124 0.058480816178965 +Allele 126 0.057398576920938 +Allele 149 0.057220799158334 + +Locus 003 +Allele 118 0.042673478414226 +Allele 122 0.042620934692803 +Allele 124 0.049948160994813 +Allele 126 0.102848721809708 +Allele 128 0.042942015076869 +Allele 130 0.046556667372327 +Allele 132 0.044047793921610 +Allele 137 0.043828212296820 +Allele 202 0.043881525418793 +Allele 204 0.042608386493729 +Allele 206 0.042431235442088 +Allele 208 0.068402269424761 +Allele 210 0.043058368413392 +Allele 212 0.043829631369333 +Allele 214 0.055833677986771 +Allele 216 0.042620073689315 +Allele 218 0.042974567720417 +Allele 220 0.042634129464553 +Allele 224 0.044508494686121 +Allele 226 0.071751655311556 + +Locus 004 +Allele 124 0.037740507980709 +Allele 126 0.039027090047448 +Allele 127 0.048340690770772 +Allele 128 0.038570076103890 +Allele 130 0.037903452652230 +Allele 132 0.040061207902047 +Allele 134 0.037358845353973 +Allele 135 0.076751615330193 +Allele 137 0.043264137653169 +Allele 151 0.044982805850605 +Allele 208 0.046089498551418 +Allele 210 0.039894543830714 +Allele 212 0.038358124705187 +Allele 214 0.037800337276469 +Allele 216 0.039615417878936 +Allele 218 0.041950112262504 +Allele 220 0.038893452519406 +Allele 222 0.056368414908622 +Allele 224 0.038719920758082 +Allele 226 0.039479200955794 +Allele 228 0.037463149868032 +Allele 233 0.063441183775532 +Allele 238 0.037926213064269 + +Locus 005 +Allele 121 0.048590068121530 +Allele 123 0.080958964521823 +Allele 125 0.048179089882432 +Allele 127 0.047153636965604 +Allele 129 0.059861777926292 +Allele 130 0.046949734616257 +Allele 131 0.047821026947759 +Allele 133 0.050021609852755 +Allele 135 0.057227934101743 +Allele 136 0.049065134042425 +Allele 137 0.055861017692184 +Allele 138 0.058739630052512 +Allele 139 0.060648771412573 +Allele 141 0.047036011062231 +Allele 145 0.079320280601842 +Allele 146 0.050267725344138 +Allele 148 0.065483730234321 +Allele 150 0.046813856621578 + +Locus 006 +Allele 121 0.039862345246371 +Allele 123 0.041991782358742 +Allele 125 0.039710133302559 +Allele 129 0.039344858669306 +Allele 131 0.040389493627973 +Allele 133 0.067693093561251 +Allele 135 0.043796179647885 +Allele 136 0.039472262844878 +Allele 137 0.065572020816352 +Allele 138 0.040570750465139 +Allele 139 0.043779983565454 +Allele 141 0.039567615564277 +Allele 143 0.039387951299410 +Allele 145 0.043358014661171 +Allele 146 0.040024619629344 +Allele 147 0.050506910815257 +Allele 148 0.042412946518096 +Allele 150 0.040612394859553 +Allele 151 0.039216010206745 +Allele 152 0.083953821810711 +Allele 156 0.039334923161637 +Allele 161 0.039441887367888 + +Locus 007 +Allele 093 0.050025958118790 +Allele 095 0.043910771539246 +Allele 096 0.040589370743892 +Allele 097 0.041259055485689 +Allele 099 0.042130097549259 +Allele 100 0.041237085712337 +Allele 101 0.059860086325794 +Allele 103 0.071617582970195 +Allele 105 0.040905087142453 +Allele 107 0.040690756509855 +Allele 109 0.044606082214908 +Allele 110 0.040621541793014 +Allele 125 0.040250467932687 +Allele 161 0.040347977775061 +Allele 165 0.040460877295518 +Allele 167 0.042181674586939 +Allele 169 0.045071716283271 +Allele 171 0.060035344157965 +Allele 173 0.052430870363198 +Allele 175 0.040532228546200 +Allele 177 0.040480465056100 +Allele 181 0.040754901897629 + +Locus 008 +Allele 095 0.037372722708301 +Allele 097 0.041213390836622 +Allele 099 0.037239678488912 +Allele 100 0.038439649150780 +Allele 101 0.056042371811871 +Allele 103 0.068207475426446 +Allele 105 0.037087514171970 +Allele 107 0.037563013980023 +Allele 109 0.041579997876777 +Allele 110 0.037697710786451 +Allele 113 0.044597065488341 +Allele 121 0.038034466970383 +Allele 123 0.037605595892842 +Allele 131 0.037439017789484 +Allele 167 0.037372454122320 +Allele 169 0.038025731379288 +Allele 171 0.049950132138565 +Allele 173 0.048650073439521 +Allele 175 0.045711584521826 +Allele 177 0.037452608925588 +Allele 179 0.037473598373844 +Allele 181 0.040022074284314 +Allele 183 0.037603022578646 +Allele 185 0.037619048856886 + +Locus 009 +Allele 108 0.036622569624390 +Allele 115 0.030863971786814 +Allele 121 0.032725765565265 +Allele 123 0.031566041133682 +Allele 125 0.034542552264739 +Allele 127 0.031762900705647 +Allele 129 0.032387038099988 +Allele 131 0.030894902776564 +Allele 133 0.032239210610359 +Allele 135 0.039509994424522 +Allele 137 0.030608050485838 +Allele 139 0.031700363597972 +Allele 145 0.030982372693274 +Allele 147 0.052082250484813 +Allele 149 0.030528294277594 +Allele 152 0.036561786867723 +Allele 218 0.030868207307487 +Allele 220 0.032070707420619 +Allele 222 0.036995533084321 +Allele 224 0.034914804434502 +Allele 226 0.038197084081933 +Allele 228 0.030931958837068 +Allele 230 0.030814815552925 +Allele 232 0.055751706567599 +Allele 234 0.032106427248823 +Allele 236 0.030580055785406 +Allele 238 0.039537984980040 +Allele 240 0.030975200560826 +Allele 250 0.030677448739268 + +Locus 010 +Allele 123 0.026819112491488 +Allele 125 0.025479303049425 +Allele 127 0.026256976670300 +Allele 129 0.030549166510734 +Allele 131 0.028017206207422 +Allele 133 0.026571174963378 +Allele 135 0.025840055140129 +Allele 137 0.026395882984999 +Allele 139 0.026216374061554 +Allele 141 0.025693304034708 +Allele 143 0.025176220445625 +Allele 145 0.025188024191240 +Allele 147 0.043145821804902 +Allele 149 0.032726851484464 +Allele 152 0.025097387322128 +Allele 155 0.025372468513929 +Allele 157 0.030066214098449 +Allele 220 0.025380030430433 +Allele 222 0.032701483768603 +Allele 224 0.025218743961144 +Allele 226 0.030575177269937 +Allele 228 0.025520043778519 +Allele 230 0.026696854132362 +Allele 232 0.025373833695755 +Allele 234 0.027836288092741 +Allele 236 0.043476360890596 +Allele 238 0.030664997050776 +Allele 240 0.025929685719021 +Allele 242 0.026110195177002 +Allele 244 0.025437474261121 +Allele 246 0.025257855531420 +Allele 248 0.025164232134549 +Allele 250 0.025307411573824 +Allele 252 0.025504390261986 +Allele 254 0.025224534509350 +Allele 256 0.028008863785989 + + + +Estimated Mixing Proportions +0.974150933333333 +0.025849066666667 + + + diff --git a/inst/files/tess/tess_16.txt b/inst/files/tess/tess_16.txt new file mode 100644 index 0000000..bdae93e --- /dev/null +++ b/inst/files/tess/tess_16.txt @@ -0,0 +1,809 @@ +Estimated Clustering Probabilities for Samples +Sample ***Cluster 01*** ***Cluster 02*** ***Cluster 03*** +000001: 0.001020000000000 0.000570000000000 0.998410000000000 1 +000002: 0.000190000000000 0.000070000000000 0.999740000000000 1 +000003: 0.000010000000000 0.000000000000000 0.999990000000000 1 +000004: 0.000270000000000 0.001710000000000 0.998020000000000 1 +000005: 0.001510000000000 0.000860000000000 0.997630000000000 1 +000006: 0.000040000000000 0.000000000000000 0.999960000000000 1 +000007: 0.027760000000000 0.035760000000000 0.936480000000000 1 +000008: 0.000070000000000 0.000020000000000 0.999910000000000 1 +000009: 0.000700000000000 0.001770000000000 0.997530000000000 1 +000010: 0.002320000000000 0.004190000000000 0.993490000000000 1 +000011: 0.000000000000000 0.000100000000000 0.999900000000000 1 +000012: 0.000000000000000 0.000040000000000 0.999960000000000 1 +000013: 0.000000000000000 0.000000000000000 1.000000000000000 1 +000014: 0.000070000000000 0.000040000000000 0.999890000000000 1 +000015: 0.006500000000000 0.009020000000000 0.984480000000000 1 +000016: 0.000000000000000 0.000000000000000 1.000000000000000 1 +000017: 0.000760000000000 0.000910000000000 0.998330000000000 1 +000018: 0.001770000000000 0.000990000000000 0.997240000000000 1 +000019: 0.027130000000000 0.028860000000000 0.944010000000000 1 +000020: 0.011250000000000 0.020870000000000 0.967880000000000 1 +000021: 0.005930000000000 0.006460000000000 0.987610000000000 1 +000022: 0.424710000000000 0.387160000000000 0.188130000000000 1 +000023: 0.000000000000000 0.000000000000000 1.000000000000000 1 +000024: 0.000000000000000 0.000000000000000 1.000000000000000 1 +000025: 0.000020000000000 0.000070000000000 0.999910000000000 1 +000026: 0.000250000000000 0.000020000000000 0.999730000000000 1 +000027: 0.000000000000000 0.000000000000000 1.000000000000000 1 +000028: 0.000080000000000 0.000000000000000 0.999920000000000 1 +000029: 0.007450000000000 0.005170000000000 0.987380000000000 1 +000030: 0.107950000000000 0.101510000000000 0.790540000000000 1 +000031: 0.004970000000000 0.006700000000000 0.988330000000000 1 +000032: 0.000080000000000 0.000000000000000 0.999920000000000 1 +000033: 0.002620000000000 0.002670000000000 0.994710000000000 1 +000034: 0.001110000000000 0.000170000000000 0.998720000000000 1 +000035: 0.007250000000000 0.006140000000000 0.986610000000000 1 +000036: 0.002570000000000 0.002510000000000 0.994920000000000 1 +000037: 0.000010000000000 0.000000000000000 0.999990000000000 1 +000038: 0.000360000000000 0.000990000000000 0.998650000000000 1 +000039: 0.000750000000000 0.000780000000000 0.998470000000000 1 +000040: 0.000000000000000 0.000000000000000 1.000000000000000 1 +000041: 0.000340000000000 0.000750000000000 0.998910000000000 1 +000042: 0.000000000000000 0.000000000000000 1.000000000000000 1 +000043: 0.000020000000000 0.000000000000000 0.999980000000000 1 +000044: 0.001680000000000 0.001360000000000 0.996960000000000 1 +000045: 0.052680000000000 0.052590000000000 0.894730000000000 1 +000046: 0.000050000000000 0.000030000000000 0.999920000000000 1 +000047: 0.001700000000000 0.001990000000000 0.996310000000000 1 +000048: 0.009220000000000 0.008720000000000 0.982060000000000 1 +000049: 0.029260000000000 0.050340000000000 0.920400000000000 1 +000050: 0.002980000000000 0.002070000000000 0.994950000000000 1 +000051: 0.157310000000000 0.151460000000000 0.691230000000000 1 +000052: 0.007670000000000 0.012990000000000 0.979340000000000 1 +000053: 0.000050000000000 0.000000000000000 0.999950000000000 1 +000054: 0.001500000000000 0.001930000000000 0.996570000000000 1 +000055: 0.000000000000000 0.000280000000000 0.999720000000000 1 +000056: 0.001040000000000 0.000690000000000 0.998270000000000 1 +000057: 0.004470000000000 0.005220000000000 0.990310000000000 1 +000058: 0.000020000000000 0.000130000000000 0.999850000000000 1 +000059: 0.120310000000000 0.128930000000000 0.750760000000000 1 +000060: 0.016790000000000 0.032070000000000 0.951140000000000 1 +000061: 0.000170000000000 0.000000000000000 0.999830000000000 1 +000062: 0.001150000000000 0.002660000000000 0.996190000000000 1 +000063: 0.001950000000000 0.001470000000000 0.996580000000000 1 +000064: 0.194720000000000 0.199680000000000 0.605600000000000 1 +000065: 0.006030000000000 0.005020000000000 0.988950000000000 1 +000066: 0.003790000000000 0.001960000000000 0.994250000000000 1 +000067: 0.000700000000000 0.000410000000000 0.998890000000000 1 +000068: 0.000500000000000 0.000390000000000 0.999110000000000 1 +000069: 0.028480000000000 0.025280000000000 0.946240000000000 1 +000070: 0.001760000000000 0.001790000000000 0.996450000000000 1 +000071: 0.000090000000000 0.000130000000000 0.999780000000000 1 +000072: 0.001710000000000 0.002820000000000 0.995470000000000 1 +000073: 0.001620000000000 0.000950000000000 0.997430000000000 1 +000074: 0.001260000000000 0.002280000000000 0.996460000000000 1 +000075: 0.003300000000000 0.003000000000000 0.993700000000000 1 + + + +Estimated Allele Frequencies +Cluster 01 +Locus 001 +Allele 092 0.103796864840980 +Allele 094 0.094648616094992 +Allele 096 0.086987466622895 +Allele 098 0.098015181602006 +Allele 100 0.121720479129642 +Allele 102 0.093574167295998 +Allele 104 0.139912844182901 +Allele 106 0.093327949422164 +Allele 108 0.082883901328886 +Allele 110 0.085132529479536 + +Locus 002 +Allele 094 0.068633742679846 +Allele 096 0.063115597481203 +Allele 098 0.073208179548626 +Allele 100 0.087456711224524 +Allele 102 0.069512152266585 +Allele 104 0.108716504009231 +Allele 106 0.084179372743604 +Allele 108 0.062885864750055 +Allele 110 0.063799616875533 +Allele 112 0.070161475496263 +Allele 114 0.061840782569714 +Allele 124 0.063073347083387 +Allele 126 0.061970495935049 +Allele 149 0.061446157336381 + +Locus 003 +Allele 118 0.044919598209257 +Allele 122 0.045103338612478 +Allele 124 0.052340780031646 +Allele 126 0.083399502920465 +Allele 128 0.045160436772165 +Allele 130 0.047813075725931 +Allele 132 0.046338790179600 +Allele 137 0.045897434575344 +Allele 202 0.045839309462009 +Allele 204 0.044811451617008 +Allele 206 0.044723077246476 +Allele 208 0.063811804902744 +Allele 210 0.045525936135458 +Allele 212 0.046184391322504 +Allele 214 0.054381456092060 +Allele 216 0.044726060877831 +Allele 218 0.045312915694453 +Allele 220 0.044944990451072 +Allele 224 0.045821790991961 +Allele 226 0.062943858179537 + +Locus 004 +Allele 124 0.039541945635789 +Allele 126 0.040913925810149 +Allele 127 0.046271624122088 +Allele 128 0.040234810700189 +Allele 130 0.039446939015318 +Allele 132 0.041355988722203 +Allele 134 0.039498009476427 +Allele 135 0.064933244089609 +Allele 137 0.044852908549432 +Allele 151 0.043471898423995 +Allele 208 0.046032397505157 +Allele 210 0.041401990624549 +Allele 212 0.040377908262951 +Allele 214 0.039587226776749 +Allele 216 0.041583641503068 +Allele 218 0.043569087809339 +Allele 220 0.040386486997204 +Allele 222 0.051025628875482 +Allele 224 0.040103281930345 +Allele 226 0.040704674106409 +Allele 228 0.039589835850028 +Allele 233 0.055369325297231 +Allele 238 0.039747219916287 + +Locus 005 +Allele 121 0.051559206947467 +Allele 123 0.070582936654973 +Allele 125 0.050621701910211 +Allele 127 0.050045612096009 +Allele 129 0.058161153721843 +Allele 130 0.049810526825096 +Allele 131 0.050711883695123 +Allele 133 0.052404746651214 +Allele 135 0.058125814095222 +Allele 136 0.051459163273554 +Allele 137 0.054721314852303 +Allele 138 0.060345947506561 +Allele 139 0.059011901931697 +Allele 141 0.049841729107976 +Allele 145 0.069352773718800 +Allele 146 0.052089957682560 +Allele 148 0.061801329935711 +Allele 150 0.049352299393683 + +Locus 006 +Allele 121 0.041905834979659 +Allele 123 0.043665186148139 +Allele 125 0.041917925533911 +Allele 129 0.041255188313029 +Allele 131 0.041911129176535 +Allele 133 0.058741458819831 +Allele 135 0.044903194633531 +Allele 136 0.041397118674657 +Allele 137 0.058799892951133 +Allele 138 0.042719912313174 +Allele 139 0.045888042847482 +Allele 141 0.041620101132367 +Allele 143 0.041240600458164 +Allele 145 0.044409347151528 +Allele 146 0.041621986020806 +Allele 147 0.048228909203926 +Allele 148 0.043789762662390 +Allele 150 0.042668472999392 +Allele 151 0.041379576624599 +Allele 152 0.069254889104409 +Allele 156 0.041251714974108 +Allele 161 0.041429755277225 + +Locus 007 +Allele 093 0.048803449632889 +Allele 095 0.044810147907026 +Allele 096 0.042160420309223 +Allele 097 0.042692878768113 +Allele 099 0.043667646039231 +Allele 100 0.042273691486607 +Allele 101 0.053873636608513 +Allele 103 0.061605293880051 +Allele 105 0.042207136070743 +Allele 107 0.042023072295877 +Allele 109 0.046341104580648 +Allele 110 0.041860286243929 +Allele 125 0.041981748286458 +Allele 161 0.041943361397780 +Allele 165 0.041899117533718 +Allele 167 0.044213611778957 +Allele 169 0.046299601004655 +Allele 171 0.055294408082680 +Allele 173 0.049451585384902 +Allele 175 0.042173764714351 +Allele 177 0.041971846788501 +Allele 181 0.042452191205148 + +Locus 008 +Allele 095 0.038631624729025 +Allele 097 0.041501733328795 +Allele 099 0.038591965934675 +Allele 100 0.039473193828274 +Allele 101 0.050523455156392 +Allele 103 0.058367092648905 +Allele 105 0.038496047912330 +Allele 107 0.038990764528285 +Allele 109 0.042629739245736 +Allele 110 0.038906416374791 +Allele 113 0.044250812750097 +Allele 121 0.039345897674216 +Allele 123 0.039104232379408 +Allele 131 0.038625965314164 +Allele 167 0.038631179291466 +Allele 169 0.039256372164062 +Allele 171 0.047785038322009 +Allele 173 0.046014076674042 +Allele 175 0.045386598730863 +Allele 177 0.038885499035933 +Allele 179 0.038536711812801 +Allele 181 0.040574875774931 +Allele 183 0.038858927608335 +Allele 185 0.038631778780467 + +Locus 009 +Allele 108 0.035229562384432 +Allele 115 0.031817233953752 +Allele 121 0.033372481565111 +Allele 123 0.032956666128977 +Allele 125 0.035579555011371 +Allele 127 0.032676465831407 +Allele 129 0.032991524108366 +Allele 131 0.032245343983613 +Allele 133 0.033210528847227 +Allele 135 0.037522074148859 +Allele 137 0.031949925268380 +Allele 139 0.032545084803937 +Allele 145 0.032014511489692 +Allele 147 0.044751340462700 +Allele 149 0.031933389517969 +Allele 152 0.036511444248124 +Allele 218 0.031822421737285 +Allele 220 0.032885132298854 +Allele 222 0.037085749288700 +Allele 224 0.035067023021682 +Allele 226 0.036311635613428 +Allele 228 0.032093200203408 +Allele 230 0.031935220641136 +Allele 232 0.048302286614858 +Allele 234 0.033612243875286 +Allele 236 0.031988191992175 +Allele 238 0.037600002877392 +Allele 240 0.032133243173709 +Allele 250 0.031856516908172 + +Locus 010 +Allele 123 0.027236963603328 +Allele 125 0.026213960914314 +Allele 127 0.026793096886126 +Allele 129 0.029183978465385 +Allele 131 0.028833186998657 +Allele 133 0.027326559134622 +Allele 135 0.026263975524821 +Allele 137 0.027047274171125 +Allele 139 0.026858562722255 +Allele 141 0.026559256419718 +Allele 143 0.025992539418825 +Allele 145 0.026022021210562 +Allele 147 0.036858558699057 +Allele 149 0.030709239924956 +Allele 152 0.026169273122869 +Allele 155 0.026092850040818 +Allele 157 0.029854052116667 +Allele 220 0.026044682606791 +Allele 222 0.030717978187765 +Allele 224 0.026129174482256 +Allele 226 0.030244018981651 +Allele 228 0.026166082130377 +Allele 230 0.027083289407469 +Allele 232 0.025987109365521 +Allele 234 0.027992664987704 +Allele 236 0.037301985449689 +Allele 238 0.029202499457638 +Allele 240 0.026537603130441 +Allele 242 0.026721873876643 +Allele 244 0.026273006799314 +Allele 246 0.026220112852231 +Allele 248 0.026146814618776 +Allele 250 0.026155912034004 +Allele 252 0.026237320495520 +Allele 254 0.026154029845115 +Allele 256 0.028668491916989 + + +Cluster 02 +Locus 001 +Allele 092 0.104398121366849 +Allele 094 0.097440087320870 +Allele 096 0.088816360991219 +Allele 098 0.097874812104710 +Allele 100 0.118257647767380 +Allele 102 0.092791018675290 +Allele 104 0.137702151135466 +Allele 106 0.093069292544755 +Allele 108 0.083149151139386 +Allele 110 0.086501356954077 + +Locus 002 +Allele 094 0.069105912194915 +Allele 096 0.064207641825802 +Allele 098 0.074295108965154 +Allele 100 0.084984271008598 +Allele 102 0.068835605095336 +Allele 104 0.107365323980651 +Allele 106 0.086260508121277 +Allele 108 0.062773990142700 +Allele 110 0.065106041233708 +Allele 112 0.069198063274741 +Allele 114 0.061201076653498 +Allele 124 0.063880410406290 +Allele 126 0.061435869419628 +Allele 149 0.061350177677701 + +Locus 003 +Allele 118 0.044752575546452 +Allele 122 0.044913809754059 +Allele 124 0.053170998363839 +Allele 126 0.083119804457950 +Allele 128 0.045414606126855 +Allele 130 0.047887622463631 +Allele 132 0.046023348739600 +Allele 137 0.045710498078767 +Allele 202 0.046074389968146 +Allele 204 0.044389591953509 +Allele 206 0.044654776967951 +Allele 208 0.064864894629696 +Allele 210 0.045316726536733 +Allele 212 0.046857265628991 +Allele 214 0.054175656829793 +Allele 216 0.044907622891921 +Allele 218 0.045567686852375 +Allele 220 0.044830470464106 +Allele 224 0.046282410398712 +Allele 226 0.061085243346914 + +Locus 004 +Allele 124 0.039596746699043 +Allele 126 0.042002564503973 +Allele 127 0.046641827499250 +Allele 128 0.040895705007701 +Allele 130 0.039795557092700 +Allele 132 0.041815010766776 +Allele 134 0.039282280098199 +Allele 135 0.062943963173396 +Allele 137 0.044242303635874 +Allele 151 0.043766964070088 +Allele 208 0.045541730822723 +Allele 210 0.041232689915427 +Allele 212 0.039959443725169 +Allele 214 0.039603407480771 +Allele 216 0.043192485598182 +Allele 218 0.043072367041194 +Allele 220 0.040565928246064 +Allele 222 0.051884926039218 +Allele 224 0.039920185452549 +Allele 226 0.041139331563051 +Allele 228 0.039423579026992 +Allele 233 0.053641332246251 +Allele 238 0.039839670295405 + +Locus 005 +Allele 121 0.053044245951463 +Allele 123 0.069109827635513 +Allele 125 0.050619761492834 +Allele 127 0.049911902490594 +Allele 129 0.058308338691616 +Allele 130 0.050043626711637 +Allele 131 0.050634951155277 +Allele 133 0.052463087842792 +Allele 135 0.057533066143862 +Allele 136 0.051272033453676 +Allele 137 0.054900558879906 +Allele 138 0.062074131039958 +Allele 139 0.058896563579722 +Allele 141 0.049736955032128 +Allele 145 0.067090365997491 +Allele 146 0.052764399230876 +Allele 148 0.061895214474834 +Allele 150 0.049700970195821 + +Locus 006 +Allele 121 0.042469903370942 +Allele 123 0.044861550071723 +Allele 125 0.042200752420351 +Allele 129 0.041308822201395 +Allele 131 0.041817156199672 +Allele 133 0.057082700178250 +Allele 135 0.044555879859552 +Allele 136 0.041423776281379 +Allele 137 0.058903742776802 +Allele 138 0.042950076911564 +Allele 139 0.045543219697285 +Allele 141 0.041376362152126 +Allele 143 0.041312601564166 +Allele 145 0.044452541598666 +Allele 146 0.041707743466116 +Allele 147 0.048414123592866 +Allele 148 0.044719306286150 +Allele 150 0.042957141934167 +Allele 151 0.041125263546927 +Allele 152 0.068104941886047 +Allele 156 0.041243674782480 +Allele 161 0.041468719221375 + +Locus 007 +Allele 093 0.048291183779742 +Allele 095 0.045329829239350 +Allele 096 0.041940224192517 +Allele 097 0.042553891714025 +Allele 099 0.044857219684418 +Allele 100 0.042448130847686 +Allele 101 0.054008450557641 +Allele 103 0.060206758437292 +Allele 105 0.042142179963740 +Allele 107 0.041816777321018 +Allele 109 0.046031271993290 +Allele 110 0.042006758704062 +Allele 125 0.041810042015032 +Allele 161 0.041857765885105 +Allele 165 0.041536639655644 +Allele 167 0.045883034286066 +Allele 169 0.045921834156210 +Allele 171 0.055544766716539 +Allele 173 0.049638996349211 +Allele 175 0.041976044005125 +Allele 177 0.041759139767793 +Allele 181 0.042439060728496 + +Locus 008 +Allele 095 0.038497942057526 +Allele 097 0.041388926356104 +Allele 099 0.038513970313848 +Allele 100 0.039512445342498 +Allele 101 0.050929661736790 +Allele 103 0.058012609023021 +Allele 105 0.038209309334208 +Allele 107 0.039183670563424 +Allele 109 0.042104251795609 +Allele 110 0.038941068011999 +Allele 113 0.043862919152875 +Allele 121 0.039923319609141 +Allele 123 0.038778097967666 +Allele 131 0.038666088647394 +Allele 167 0.038429612122807 +Allele 169 0.039616611053052 +Allele 171 0.048072756325612 +Allele 173 0.046296110128711 +Allele 175 0.045864055100386 +Allele 177 0.038869806236425 +Allele 179 0.038483144772537 +Allele 181 0.040243781689154 +Allele 183 0.038887978904683 +Allele 185 0.038711863754528 + +Locus 009 +Allele 108 0.035437597378562 +Allele 115 0.031832101508102 +Allele 121 0.033281866490370 +Allele 123 0.033693664032736 +Allele 125 0.035116453114700 +Allele 127 0.032511633713515 +Allele 129 0.033200275685524 +Allele 131 0.032148094648858 +Allele 133 0.033910538549769 +Allele 135 0.037639024885337 +Allele 137 0.031916469329448 +Allele 139 0.032840279118768 +Allele 145 0.031874763235106 +Allele 147 0.043547496647008 +Allele 149 0.031988326154663 +Allele 152 0.036401658958684 +Allele 218 0.031938842069430 +Allele 220 0.033133392276030 +Allele 222 0.036786557727210 +Allele 224 0.035059976146054 +Allele 226 0.036527073013109 +Allele 228 0.032045417029459 +Allele 230 0.031969418358724 +Allele 232 0.046864937652097 +Allele 234 0.034893799545276 +Allele 236 0.031840187858148 +Allele 238 0.037668099416119 +Allele 240 0.032017796127636 +Allele 250 0.031914259329558 + +Locus 010 +Allele 123 0.027229318160539 +Allele 125 0.026310120992981 +Allele 127 0.026704124370124 +Allele 129 0.029358488136134 +Allele 131 0.028688235841124 +Allele 133 0.028116110266849 +Allele 135 0.026326748607575 +Allele 137 0.027268070960411 +Allele 139 0.026651234717147 +Allele 141 0.026841126511555 +Allele 143 0.026069427737078 +Allele 145 0.025978640475615 +Allele 147 0.035889591077183 +Allele 149 0.030816349031198 +Allele 152 0.025981402002852 +Allele 155 0.026195835658843 +Allele 157 0.029745186695381 +Allele 220 0.025962507238126 +Allele 222 0.030931190192265 +Allele 224 0.025996163104063 +Allele 226 0.030293185342046 +Allele 228 0.026170004707618 +Allele 230 0.027278544201701 +Allele 232 0.025980532324343 +Allele 234 0.027992931156250 +Allele 236 0.036983550811727 +Allele 238 0.029200960161117 +Allele 240 0.026856306348445 +Allele 242 0.026546008352878 +Allele 244 0.026345823146058 +Allele 246 0.026180618737960 +Allele 248 0.026170255083985 +Allele 250 0.026122255425403 +Allele 252 0.026179517232026 +Allele 254 0.026012770852947 +Allele 256 0.028626864338452 + + +Cluster 03 +Locus 001 +Allele 092 0.041262319944463 +Allele 094 0.390166203713116 +Allele 096 0.162530482726280 +Allele 098 0.088431319139170 +Allele 100 0.025950200661200 +Allele 102 0.083077515296684 +Allele 104 0.106905995069622 +Allele 106 0.050292674529127 +Allele 108 0.025949230906086 +Allele 110 0.025434058014248 + +Locus 002 +Allele 094 0.106490365145047 +Allele 096 0.076024340918695 +Allele 098 0.150152866731324 +Allele 100 0.064576401479259 +Allele 102 0.106893307800164 +Allele 104 0.192829536941264 +Allele 106 0.128207698696989 +Allele 108 0.063412554846944 +Allele 110 0.037533658869370 +Allele 112 0.023449021769757 +Allele 114 0.012745971564696 +Allele 124 0.012233448603954 +Allele 126 0.012683122485078 +Allele 149 0.012767704147459 + +Locus 003 +Allele 118 0.018435593882270 +Allele 122 0.030664133117358 +Allele 124 0.181893468934061 +Allele 126 0.092498456694478 +Allele 128 0.061281733275604 +Allele 130 0.035882251209498 +Allele 132 0.061104395322243 +Allele 137 0.011919546583863 +Allele 202 0.011988802857842 +Allele 204 0.024593839405532 +Allele 206 0.012296340101488 +Allele 208 0.116568283361322 +Allele 210 0.036690026847367 +Allele 212 0.097899589633524 +Allele 214 0.070732136840423 +Allele 216 0.042935921320423 +Allele 218 0.048949079717608 +Allele 220 0.012200945658239 +Allele 224 0.024147335226610 +Allele 226 0.007318120010246 + +Locus 004 +Allele 124 0.024070116365399 +Allele 126 0.029487265611695 +Allele 127 0.009667986483544 +Allele 128 0.041804876005609 +Allele 130 0.042144181703439 +Allele 132 0.168160339604790 +Allele 134 0.012066043818836 +Allele 135 0.094389555590150 +Allele 137 0.064662684416718 +Allele 151 0.010527995066716 +Allele 208 0.015878720531271 +Allele 210 0.011406268507441 +Allele 212 0.084251319555606 +Allele 214 0.036144540788126 +Allele 216 0.071436568411180 +Allele 218 0.016836129579986 +Allele 220 0.047900769103594 +Allele 222 0.056014668565305 +Allele 224 0.090273830756515 +Allele 226 0.035685786379024 +Allele 228 0.018060584188185 +Allele 233 0.007158841378920 +Allele 238 0.011970927587950 + +Locus 005 +Allele 121 0.058244724989502 +Allele 123 0.053374055185071 +Allele 125 0.039108008353042 +Allele 127 0.013069091089497 +Allele 129 0.030213500081569 +Allele 130 0.026186511113440 +Allele 131 0.124625644843340 +Allele 133 0.071473296862140 +Allele 135 0.056617876906044 +Allele 136 0.117708938411637 +Allele 137 0.024550906134165 +Allele 138 0.095286851519249 +Allele 139 0.095783112867745 +Allele 141 0.026173202628048 +Allele 145 0.034036413107547 +Allele 146 0.071622781695886 +Allele 148 0.048716916766923 +Allele 150 0.013208167445153 + +Locus 006 +Allele 121 0.025348198577349 +Allele 123 0.024647873060515 +Allele 125 0.018915520267001 +Allele 129 0.025606491689221 +Allele 131 0.115123446325629 +Allele 133 0.071483172708784 +Allele 135 0.107616970860085 +Allele 136 0.025546724603380 +Allele 137 0.045017348241680 +Allele 138 0.018698710376701 +Allele 139 0.049813209301683 +Allele 141 0.019170949400315 +Allele 143 0.012827114610443 +Allele 145 0.056496501472634 +Allele 146 0.051231128507222 +Allele 147 0.010239058889071 +Allele 148 0.107910923287411 +Allele 150 0.076327610472768 +Allele 151 0.012777477550475 +Allele 152 0.093185173713335 +Allele 156 0.019208881374561 +Allele 161 0.012807514709737 + +Locus 007 +Allele 093 0.049827622515516 +Allele 095 0.070915926969413 +Allele 096 0.013087577376190 +Allele 097 0.150390102522638 +Allele 099 0.038403055790515 +Allele 100 0.058716833502350 +Allele 101 0.041421126792308 +Allele 103 0.052724069792755 +Allele 105 0.019509063194667 +Allele 107 0.026107125861653 +Allele 109 0.011708384176903 +Allele 110 0.013019840652269 +Allele 125 0.013088428252608 +Allele 161 0.013096398929983 +Allele 165 0.026258961799259 +Allele 167 0.044763646668364 +Allele 169 0.063786068532258 +Allele 171 0.139051744692043 +Allele 173 0.075833014912282 +Allele 175 0.045652637440423 +Allele 177 0.019619015051280 +Allele 181 0.013019354574321 + +Locus 008 +Allele 095 0.012941750017913 +Allele 097 0.050582823323022 +Allele 099 0.025869046931042 +Allele 100 0.038508426785031 +Allele 101 0.118027379617678 +Allele 103 0.090062168646512 +Allele 105 0.038735315123557 +Allele 107 0.077401580537141 +Allele 109 0.018005102437898 +Allele 110 0.019339924109253 +Allele 113 0.017317050488312 +Allele 121 0.019035926250868 +Allele 123 0.019323285106314 +Allele 131 0.012925297643978 +Allele 167 0.012913790898036 +Allele 169 0.025562839576473 +Allele 171 0.093410688365482 +Allele 173 0.087707465234853 +Allele 175 0.049019226036849 +Allele 177 0.077325747918853 +Allele 179 0.012912733982882 +Allele 181 0.031480088461473 +Allele 183 0.025789446131022 +Allele 185 0.025802896375560 + +Locus 009 +Allele 108 0.027487877556954 +Allele 115 0.011558451697479 +Allele 121 0.010978232814493 +Allele 123 0.039987725225302 +Allele 125 0.085561985964399 +Allele 127 0.040174293037426 +Allele 129 0.045821297739292 +Allele 131 0.046032508626177 +Allele 133 0.091896442221048 +Allele 135 0.026631111377179 +Allele 137 0.017280676078035 +Allele 139 0.016992763393737 +Allele 145 0.017255291085344 +Allele 147 0.006890902754655 +Allele 149 0.011622596796613 +Allele 152 0.009759642234141 +Allele 218 0.011582528633544 +Allele 220 0.086400246042255 +Allele 222 0.107976140663355 +Allele 224 0.085578321336309 +Allele 226 0.038518707713678 +Allele 228 0.023136728139944 +Allele 230 0.017300767969752 +Allele 232 0.022930776168485 +Allele 234 0.033702146052806 +Allele 236 0.017308005237596 +Allele 238 0.020787792164856 +Allele 240 0.017322617057628 +Allele 250 0.011523424217514 + +Locus 010 +Allele 123 0.010536974253178 +Allele 125 0.011018348410898 +Allele 127 0.033024586316187 +Allele 129 0.037458761296605 +Allele 131 0.043274819121713 +Allele 133 0.065938836464644 +Allele 135 0.072216137540665 +Allele 137 0.066211625768557 +Allele 139 0.016299357461809 +Allele 141 0.038662031384744 +Allele 143 0.011100939147578 +Allele 145 0.016664710607993 +Allele 147 0.012079246959204 +Allele 149 0.020014852752176 +Allele 152 0.011107504366160 +Allele 155 0.011027970441023 +Allele 157 0.014959399780447 +Allele 220 0.011133501819753 +Allele 222 0.020033667132425 +Allele 224 0.044438703073513 +Allele 226 0.053643528012897 +Allele 228 0.027715143980754 +Allele 230 0.032858073371350 +Allele 232 0.038962725095351 +Allele 234 0.038010050409865 +Allele 236 0.039506508139849 +Allele 238 0.054116298048640 +Allele 240 0.027514098573465 +Allele 242 0.033087453588062 +Allele 244 0.010959138292835 +Allele 246 0.016600871299257 +Allele 248 0.011075147041176 +Allele 250 0.011093969246167 +Allele 252 0.016604372528638 +Allele 254 0.011117222579449 +Allele 256 0.009933425692972 + + + +Estimated Mixing Proportions +0.017357333333333 +0.017673600000000 +0.964969066666667 + + + diff --git a/inst/files/tess/tess_17.txt b/inst/files/tess/tess_17.txt new file mode 100644 index 0000000..66ac4f3 --- /dev/null +++ b/inst/files/tess/tess_17.txt @@ -0,0 +1,1050 @@ +Estimated Clustering Probabilities for Samples +Sample ***Cluster 01*** ***Cluster 02*** ***Cluster 03*** ***Cluster 04*** +000001: 0.000600000000000 0.998640000000000 0.000510000000000 0.000250000000000 1 +000002: 0.000010000000000 0.999980000000000 0.000000000000000 0.000010000000000 1 +000003: 0.000000000000000 0.999960000000000 0.000040000000000 0.000000000000000 1 +000004: 0.001450000000000 0.997560000000000 0.000640000000000 0.000350000000000 1 +000005: 0.001040000000000 0.996540000000000 0.001140000000000 0.001280000000000 1 +000006: 0.000050000000000 0.999950000000000 0.000000000000000 0.000000000000000 1 +000007: 0.028540000000000 0.910230000000000 0.030770000000000 0.030460000000000 1 +000008: 0.000000000000000 0.999970000000000 0.000030000000000 0.000000000000000 1 +000009: 0.001270000000000 0.996780000000000 0.001290000000000 0.000660000000000 1 +000010: 0.005720000000000 0.982630000000000 0.005200000000000 0.006450000000000 1 +000011: 0.000720000000000 0.998630000000000 0.000080000000000 0.000570000000000 1 +000012: 0.000000000000000 1.000000000000000 0.000000000000000 0.000000000000000 1 +000013: 0.000000000000000 1.000000000000000 0.000000000000000 0.000000000000000 1 +000014: 0.000020000000000 0.999880000000000 0.000000000000000 0.000100000000000 1 +000015: 0.007770000000000 0.975670000000000 0.007540000000000 0.009020000000000 1 +000016: 0.000000000000000 1.000000000000000 0.000000000000000 0.000000000000000 1 +000017: 0.000420000000000 0.997410000000000 0.001040000000000 0.001130000000000 1 +000018: 0.002000000000000 0.997220000000000 0.000370000000000 0.000410000000000 1 +000019: 0.026190000000000 0.913170000000000 0.037740000000000 0.022900000000000 1 +000020: 0.019120000000000 0.964260000000000 0.008830000000000 0.007790000000000 1 +000021: 0.007310000000000 0.981560000000000 0.004970000000000 0.006160000000000 1 +000022: 0.273480000000000 0.132420000000000 0.290570000000000 0.303530000000000 1 +000023: 0.000010000000000 0.999990000000000 0.000000000000000 0.000000000000000 1 +000024: 0.000000000000000 1.000000000000000 0.000000000000000 0.000000000000000 1 +000025: 0.000000000000000 0.999810000000000 0.000020000000000 0.000170000000000 1 +000026: 0.000070000000000 0.999620000000000 0.000250000000000 0.000060000000000 1 +000027: 0.000000000000000 1.000000000000000 0.000000000000000 0.000000000000000 1 +000028: 0.000000000000000 0.999990000000000 0.000010000000000 0.000000000000000 1 +000029: 0.005980000000000 0.984010000000000 0.004740000000000 0.005270000000000 1 +000030: 0.101940000000000 0.679480000000000 0.108530000000000 0.110050000000000 1 +000031: 0.010280000000000 0.980130000000000 0.004660000000000 0.004930000000000 1 +000032: 0.000050000000000 0.999950000000000 0.000000000000000 0.000000000000000 1 +000033: 0.007940000000000 0.988570000000000 0.001060000000000 0.002430000000000 1 +000034: 0.005820000000000 0.993240000000000 0.000290000000000 0.000650000000000 1 +000035: 0.007850000000000 0.982060000000000 0.004070000000000 0.006020000000000 1 +000036: 0.003280000000000 0.992980000000000 0.001530000000000 0.002210000000000 1 +000037: 0.000000000000000 0.999970000000000 0.000030000000000 0.000000000000000 1 +000038: 0.001890000000000 0.995240000000000 0.002180000000000 0.000690000000000 1 +000039: 0.001180000000000 0.997510000000000 0.000640000000000 0.000670000000000 1 +000040: 0.000060000000000 0.999890000000000 0.000000000000000 0.000050000000000 1 +000041: 0.000480000000000 0.998530000000000 0.000380000000000 0.000610000000000 1 +000042: 0.000070000000000 0.999930000000000 0.000000000000000 0.000000000000000 1 +000043: 0.000080000000000 0.999890000000000 0.000000000000000 0.000030000000000 1 +000044: 0.002240000000000 0.992110000000000 0.003090000000000 0.002560000000000 1 +000045: 0.046830000000000 0.869240000000000 0.035060000000000 0.048870000000000 1 +000046: 0.000000000000000 0.999960000000000 0.000040000000000 0.000000000000000 1 +000047: 0.000640000000000 0.997760000000000 0.001000000000000 0.000600000000000 1 +000048: 0.004970000000000 0.976360000000000 0.010120000000000 0.008550000000000 1 +000049: 0.041430000000000 0.895170000000000 0.035240000000000 0.028160000000000 1 +000050: 0.002420000000000 0.993570000000000 0.001750000000000 0.002260000000000 1 +000051: 0.107660000000000 0.640180000000000 0.116810000000000 0.135350000000000 1 +000052: 0.006170000000000 0.975880000000000 0.007250000000000 0.010700000000000 1 +000053: 0.000000000000000 1.000000000000000 0.000000000000000 0.000000000000000 1 +000054: 0.000590000000000 0.996330000000000 0.002350000000000 0.000730000000000 1 +000055: 0.000200000000000 0.999700000000000 0.000060000000000 0.000040000000000 1 +000056: 0.000660000000000 0.998620000000000 0.000250000000000 0.000470000000000 1 +000057: 0.004930000000000 0.988490000000000 0.002960000000000 0.003620000000000 1 +000058: 0.000020000000000 0.999980000000000 0.000000000000000 0.000000000000000 1 +000059: 0.104610000000000 0.698170000000000 0.093430000000000 0.103790000000000 1 +000060: 0.026060000000000 0.934880000000000 0.021540000000000 0.017520000000000 1 +000061: 0.000350000000000 0.999550000000000 0.000080000000000 0.000020000000000 1 +000062: 0.001400000000000 0.993370000000000 0.003800000000000 0.001430000000000 1 +000063: 0.003040000000000 0.995970000000000 0.000100000000000 0.000890000000000 1 +000064: 0.160540000000000 0.503030000000000 0.162070000000000 0.174360000000000 1 +000065: 0.007260000000000 0.980350000000000 0.007900000000000 0.004490000000000 1 +000066: 0.004300000000000 0.988820000000000 0.004470000000000 0.002410000000000 1 +000067: 0.000440000000000 0.998910000000000 0.000400000000000 0.000250000000000 1 +000068: 0.000200000000000 0.998870000000000 0.000330000000000 0.000600000000000 1 +000069: 0.024520000000000 0.945490000000000 0.014180000000000 0.015810000000000 1 +000070: 0.001050000000000 0.996390000000000 0.001510000000000 0.001050000000000 1 +000071: 0.000300000000000 0.999360000000000 0.000280000000000 0.000060000000000 1 +000072: 0.003950000000000 0.990400000000000 0.003800000000000 0.001850000000000 1 +000073: 0.004670000000000 0.993490000000000 0.001060000000000 0.000780000000000 1 +000074: 0.000920000000000 0.994820000000000 0.001070000000000 0.003190000000000 1 +000075: 0.004480000000000 0.988730000000000 0.001960000000000 0.004830000000000 1 + + + +Estimated Allele Frequencies +Cluster 01 +Locus 001 +Allele 092 0.104148358305151 +Allele 094 0.100263518057360 +Allele 096 0.091529119929460 +Allele 098 0.097766894327086 +Allele 100 0.113883188519014 +Allele 102 0.092940815995780 +Allele 104 0.128542400703612 +Allele 106 0.096592451435536 +Allele 108 0.085460825571574 +Allele 110 0.088872427155427 + +Locus 002 +Allele 094 0.070162775910037 +Allele 096 0.065910640137412 +Allele 098 0.072739673073230 +Allele 100 0.080182849258033 +Allele 102 0.071459856223163 +Allele 104 0.099481803823573 +Allele 106 0.085831062323887 +Allele 108 0.064077647154914 +Allele 110 0.066284422513325 +Allele 112 0.068782722637575 +Allele 114 0.062949369320792 +Allele 124 0.065165978364551 +Allele 126 0.063456444006742 +Allele 149 0.063514755252763 + +Locus 003 +Allele 118 0.045783101895776 +Allele 122 0.045780043192782 +Allele 124 0.053841636299111 +Allele 126 0.074559068489538 +Allele 128 0.046407898905107 +Allele 130 0.048780098670085 +Allele 132 0.046864101797172 +Allele 137 0.046854640684834 +Allele 202 0.046927587186140 +Allele 204 0.045757994749963 +Allele 206 0.045574359677086 +Allele 208 0.062111251345935 +Allele 210 0.046434872463254 +Allele 212 0.047464798119115 +Allele 214 0.054405083583244 +Allele 216 0.045892207669822 +Allele 218 0.046162846643630 +Allele 220 0.046045801387338 +Allele 224 0.047392594673001 +Allele 226 0.056960012567065 + +Locus 004 +Allele 124 0.040583950544753 +Allele 126 0.042182729712278 +Allele 127 0.045618513514379 +Allele 128 0.041246247273378 +Allele 130 0.040507982770159 +Allele 132 0.042199378740522 +Allele 134 0.039946147618537 +Allele 135 0.058254752001775 +Allele 137 0.045319099929182 +Allele 151 0.043742378097260 +Allele 208 0.044878601199310 +Allele 210 0.041710005101722 +Allele 212 0.041222324532713 +Allele 214 0.040345576959815 +Allele 216 0.043443890104440 +Allele 218 0.044075636393925 +Allele 220 0.041072041955843 +Allele 222 0.050386925765241 +Allele 224 0.041015419613859 +Allele 226 0.041351512394552 +Allele 228 0.040315860605897 +Allele 233 0.050332953580329 +Allele 238 0.040248071590130 + +Locus 005 +Allele 121 0.053709161382205 +Allele 123 0.064692748157081 +Allele 125 0.052395998657783 +Allele 127 0.050939424852646 +Allele 129 0.057959506585602 +Allele 130 0.050675796653916 +Allele 131 0.052066122175801 +Allele 133 0.053037925667734 +Allele 135 0.056574939172189 +Allele 136 0.052423682285288 +Allele 137 0.055299317964494 +Allele 138 0.061938195149801 +Allele 139 0.058884042388949 +Allele 141 0.051058191828999 +Allele 145 0.063629402251395 +Allele 146 0.053564071277902 +Allele 148 0.060472977065337 +Allele 150 0.050678496482876 + +Locus 006 +Allele 121 0.043202050879743 +Allele 123 0.044851843124153 +Allele 125 0.043013643738550 +Allele 129 0.042033485298028 +Allele 131 0.043270806666934 +Allele 133 0.053638448331082 +Allele 135 0.045044311257114 +Allele 136 0.042282166485118 +Allele 137 0.055969813575263 +Allele 138 0.043575451568900 +Allele 139 0.046155739993640 +Allele 141 0.042088281921216 +Allele 143 0.042118362388870 +Allele 145 0.044868672363244 +Allele 146 0.042729140577213 +Allele 147 0.047819515881071 +Allele 148 0.045206532759070 +Allele 150 0.043871494552264 +Allele 151 0.042085234917214 +Allele 152 0.062015799004125 +Allele 156 0.042170238413622 +Allele 161 0.041988966303564 + +Locus 007 +Allele 093 0.047462511497335 +Allele 095 0.045329667499166 +Allele 096 0.042358970181056 +Allele 097 0.043714743324330 +Allele 099 0.044863067197383 +Allele 100 0.043218641803214 +Allele 101 0.052266031193503 +Allele 103 0.055843966465735 +Allele 105 0.042927790914981 +Allele 107 0.042865008422810 +Allele 109 0.046337701448081 +Allele 110 0.042616448048179 +Allele 125 0.042530899489763 +Allele 161 0.042202977611976 +Allele 165 0.042508196280579 +Allele 167 0.045848375601355 +Allele 169 0.046834099471629 +Allele 171 0.053469237741174 +Allele 173 0.049202486217799 +Allele 175 0.042572634205287 +Allele 177 0.042345946167548 +Allele 181 0.042680599217121 + +Locus 008 +Allele 095 0.039079901376771 +Allele 097 0.041300159967498 +Allele 099 0.038876774912982 +Allele 100 0.039996867708781 +Allele 101 0.049334261258994 +Allele 103 0.053864829124975 +Allele 105 0.039194669643542 +Allele 107 0.039768155586066 +Allele 109 0.042894610544775 +Allele 110 0.039502102106053 +Allele 113 0.042879549366708 +Allele 121 0.040292150378707 +Allele 123 0.039275471688479 +Allele 131 0.039048924246983 +Allele 167 0.039040303155000 +Allele 169 0.039970143118810 +Allele 171 0.047857792492504 +Allele 173 0.045335923890500 +Allele 175 0.044592494307310 +Allele 177 0.039413159367794 +Allele 179 0.039185264251195 +Allele 181 0.040991514303484 +Allele 183 0.039245811861395 +Allele 185 0.039059165340693 + +Locus 009 +Allele 108 0.035278159898168 +Allele 115 0.032343555247342 +Allele 121 0.033426196770764 +Allele 123 0.033896839248701 +Allele 125 0.035876247108396 +Allele 127 0.033119136490711 +Allele 129 0.033511953859950 +Allele 131 0.032599673142506 +Allele 133 0.034441804403933 +Allele 135 0.036843318578762 +Allele 137 0.032474145355615 +Allele 139 0.033206668455236 +Allele 145 0.032429145736307 +Allele 147 0.040731975371933 +Allele 149 0.032281393406439 +Allele 152 0.035413665756322 +Allele 218 0.032409211528129 +Allele 220 0.033541624613318 +Allele 222 0.036092993947494 +Allele 224 0.035323241722178 +Allele 226 0.036293672896573 +Allele 228 0.032652877390632 +Allele 230 0.032264063839903 +Allele 232 0.043960692914597 +Allele 234 0.034971167450868 +Allele 236 0.032414273643927 +Allele 238 0.037168523793801 +Allele 240 0.032634196992852 +Allele 250 0.032399580434641 + +Locus 010 +Allele 123 0.027500354543393 +Allele 125 0.026409360944263 +Allele 127 0.026986806907237 +Allele 129 0.028991813493653 +Allele 131 0.028874624739235 +Allele 133 0.028204237536947 +Allele 135 0.026941564656374 +Allele 137 0.027435139039678 +Allele 139 0.026956571492211 +Allele 141 0.027147196448264 +Allele 143 0.026502487042402 +Allele 145 0.026330496948639 +Allele 147 0.033245904408468 +Allele 149 0.030263746625500 +Allele 152 0.026337806900054 +Allele 155 0.026484195628636 +Allele 157 0.028760193277304 +Allele 220 0.026594684925848 +Allele 222 0.030254957758773 +Allele 224 0.026384000089480 +Allele 226 0.029256433856738 +Allele 228 0.026726835445026 +Allele 230 0.027436252894089 +Allele 232 0.026307313919740 +Allele 234 0.028156505360293 +Allele 236 0.034319469012484 +Allele 238 0.029268778328386 +Allele 240 0.027131083397187 +Allele 242 0.026972584940999 +Allele 244 0.026773813916133 +Allele 246 0.026302559573632 +Allele 248 0.026525144928114 +Allele 250 0.026391213728006 +Allele 252 0.026568774991597 +Allele 254 0.026296508766335 +Allele 256 0.028960583534883 + + +Cluster 02 +Locus 001 +Allele 092 0.040569507728928 +Allele 094 0.391736785790058 +Allele 096 0.163585517160238 +Allele 098 0.088603265054149 +Allele 100 0.025122294506133 +Allele 102 0.083097930841521 +Allele 104 0.106250484632191 +Allele 106 0.049608382902949 +Allele 108 0.026065316946566 +Allele 110 0.025360514437267 + +Locus 002 +Allele 094 0.106722244678286 +Allele 096 0.076413914213293 +Allele 098 0.150539216421267 +Allele 100 0.064656175374493 +Allele 102 0.106679940541498 +Allele 104 0.192449510235398 +Allele 106 0.126945675653127 +Allele 108 0.064015772606490 +Allele 110 0.037537178890052 +Allele 112 0.023369916784043 +Allele 114 0.012842180565424 +Allele 124 0.012201445824661 +Allele 126 0.012804331683283 +Allele 149 0.012822496528685 + +Locus 003 +Allele 118 0.018572130078588 +Allele 122 0.030923968719114 +Allele 124 0.182208387774697 +Allele 126 0.091364352440936 +Allele 128 0.061613972927857 +Allele 130 0.035804104445903 +Allele 132 0.061418396740956 +Allele 137 0.011840172302310 +Allele 202 0.011878507548002 +Allele 204 0.024795380430623 +Allele 206 0.012375087026348 +Allele 208 0.116137433444999 +Allele 210 0.036779686486497 +Allele 212 0.098203685222398 +Allele 214 0.070276638943616 +Allele 216 0.043273900012719 +Allele 218 0.049252341876168 +Allele 220 0.012260817817010 +Allele 224 0.024036534145640 +Allele 226 0.006984501615622 + +Locus 004 +Allele 124 0.024219360684101 +Allele 126 0.029461346140947 +Allele 127 0.009114024788630 +Allele 128 0.042030768892762 +Allele 130 0.042424647636578 +Allele 132 0.169341948311509 +Allele 134 0.012144701468688 +Allele 135 0.093994768688960 +Allele 137 0.064180037144286 +Allele 151 0.010314130836600 +Allele 208 0.015643647077302 +Allele 210 0.011278843871083 +Allele 212 0.084626040203375 +Allele 214 0.036350230740890 +Allele 216 0.071574067021027 +Allele 218 0.016257955663907 +Allele 220 0.047996899256574 +Allele 222 0.055486445480162 +Allele 224 0.090756299590987 +Allele 226 0.035785162691606 +Allele 228 0.018136674241021 +Allele 233 0.006888187711122 +Allele 238 0.011993811857887 + +Locus 005 +Allele 121 0.058441467023299 +Allele 123 0.053069710792638 +Allele 125 0.039155840417551 +Allele 127 0.013115633356203 +Allele 129 0.029755355058811 +Allele 130 0.026476632261868 +Allele 131 0.125322370674971 +Allele 133 0.071669936692240 +Allele 135 0.056551617525828 +Allele 136 0.118523556313908 +Allele 137 0.024413010112733 +Allele 138 0.094555350502755 +Allele 139 0.095566202805032 +Allele 141 0.026367870712029 +Allele 145 0.034104312862860 +Allele 146 0.071494936359172 +Allele 148 0.048146593885084 +Allele 150 0.013269602643014 + +Locus 006 +Allele 121 0.025326489958933 +Allele 123 0.024343879504813 +Allele 125 0.018995784598053 +Allele 129 0.025778899230993 +Allele 131 0.115637222491371 +Allele 133 0.071570096763954 +Allele 135 0.108146114883442 +Allele 136 0.025733221479627 +Allele 137 0.043964743974134 +Allele 138 0.018703281974685 +Allele 139 0.049457077450120 +Allele 141 0.019163746456229 +Allele 143 0.012913955977865 +Allele 145 0.056573109047768 +Allele 146 0.051342892450010 +Allele 147 0.009642739426446 +Allele 148 0.108204494179019 +Allele 150 0.076716181796323 +Allele 151 0.012858153706120 +Allele 152 0.092658450752074 +Allele 156 0.019370990344899 +Allele 161 0.012898473553120 + +Locus 007 +Allele 093 0.049876124564346 +Allele 095 0.071138227824155 +Allele 096 0.013192703436236 +Allele 097 0.151174930959504 +Allele 099 0.038357241819251 +Allele 100 0.059042606627953 +Allele 101 0.040561432998053 +Allele 103 0.052330864821495 +Allele 105 0.019647225863947 +Allele 107 0.026279758030291 +Allele 109 0.011059875740145 +Allele 110 0.013056151454739 +Allele 125 0.013189229933848 +Allele 161 0.013202266782082 +Allele 165 0.026346609697510 +Allele 167 0.044694298392528 +Allele 169 0.063586696232702 +Allele 171 0.138856789605898 +Allele 173 0.075512512376351 +Allele 175 0.046070726968847 +Allele 177 0.019785012771085 +Allele 181 0.013038713099035 + +Locus 008 +Allele 095 0.013015784191598 +Allele 097 0.050781306957869 +Allele 099 0.026075554395506 +Allele 100 0.038660695296520 +Allele 101 0.117838988113560 +Allele 103 0.089718930440283 +Allele 105 0.039096857673185 +Allele 107 0.077772849641848 +Allele 109 0.017384896665774 +Allele 110 0.019310506619813 +Allele 113 0.017087170367969 +Allele 121 0.019013306225951 +Allele 123 0.019409435700776 +Allele 131 0.012987475692377 +Allele 167 0.013079711232591 +Allele 169 0.025501602469184 +Allele 171 0.092760440190151 +Allele 173 0.087525473179063 +Allele 175 0.048853818165030 +Allele 177 0.077747902433449 +Allele 179 0.012987070836804 +Allele 181 0.031608136762426 +Allele 183 0.025864702619181 +Allele 185 0.025917384129091 + +Locus 009 +Allele 108 0.027320622449544 +Allele 115 0.011626670926365 +Allele 121 0.010867061498014 +Allele 123 0.039949460829258 +Allele 125 0.085250131302920 +Allele 127 0.040467688539069 +Allele 129 0.045931103107022 +Allele 131 0.046384080020108 +Allele 133 0.092295260035152 +Allele 135 0.026195373575891 +Allele 137 0.017382000895476 +Allele 139 0.016879880265461 +Allele 145 0.017389790872942 +Allele 147 0.006585258383447 +Allele 149 0.011663182202827 +Allele 152 0.009542070577237 +Allele 218 0.011606318084092 +Allele 220 0.086846890763229 +Allele 222 0.108235948662311 +Allele 224 0.085707130743316 +Allele 226 0.038498478875608 +Allele 228 0.023196286852477 +Allele 230 0.017445972954106 +Allele 232 0.022177298357567 +Allele 234 0.033716370616591 +Allele 236 0.017452946151627 +Allele 238 0.020352232251056 +Allele 240 0.017394028786600 +Allele 250 0.011640461420686 + +Locus 010 +Allele 123 0.010474602718360 +Allele 125 0.011065404018147 +Allele 127 0.033223359837528 +Allele 129 0.037353611219949 +Allele 131 0.042989527018861 +Allele 133 0.066192800725072 +Allele 135 0.072474666752916 +Allele 137 0.066555264364208 +Allele 139 0.016224184444075 +Allele 141 0.038870492935218 +Allele 143 0.011123054426573 +Allele 145 0.016774174888668 +Allele 147 0.011846637976403 +Allele 149 0.019534766220700 +Allele 152 0.011157885723785 +Allele 155 0.011073648707734 +Allele 157 0.014751431646030 +Allele 220 0.011079732102906 +Allele 222 0.019500668221627 +Allele 224 0.044893996614020 +Allele 226 0.053699402455641 +Allele 228 0.027859415302084 +Allele 230 0.032833632653743 +Allele 232 0.039190902753622 +Allele 234 0.037856589450436 +Allele 236 0.039326553409508 +Allele 238 0.054066556069473 +Allele 240 0.027585097473045 +Allele 242 0.033225760653627 +Allele 244 0.010983887641639 +Allele 246 0.016691561712803 +Allele 248 0.011151900805418 +Allele 250 0.011181335959725 +Allele 252 0.016668858243231 +Allele 254 0.011136347530074 +Allele 256 0.009382287323150 + + +Cluster 03 +Locus 001 +Allele 092 0.103399631114623 +Allele 094 0.100106736583715 +Allele 096 0.089937488365632 +Allele 098 0.097436906982342 +Allele 100 0.115344869831193 +Allele 102 0.093793920186946 +Allele 104 0.127794410164572 +Allele 106 0.097475714187980 +Allele 108 0.086052497687956 +Allele 110 0.088657824895040 + +Locus 002 +Allele 094 0.069647961560594 +Allele 096 0.065108099787052 +Allele 098 0.073555219164606 +Allele 100 0.081011878221133 +Allele 102 0.070797612681508 +Allele 104 0.099285543434652 +Allele 106 0.085044635503108 +Allele 108 0.064208528843364 +Allele 110 0.066047628954632 +Allele 112 0.069830098913582 +Allele 114 0.063191351767030 +Allele 124 0.065173847929396 +Allele 126 0.063703344031623 +Allele 149 0.063394249207718 + +Locus 003 +Allele 118 0.045988435885396 +Allele 122 0.045994243305316 +Allele 124 0.053390552112819 +Allele 126 0.075569946419904 +Allele 128 0.046389790420910 +Allele 130 0.047615946080910 +Allele 132 0.046709600014874 +Allele 137 0.047216895554388 +Allele 202 0.047326712589552 +Allele 204 0.045518967094166 +Allele 206 0.045824238113846 +Allele 208 0.061563816957132 +Allele 210 0.046305779123120 +Allele 212 0.047333811184262 +Allele 214 0.054321372799520 +Allele 216 0.045737312726990 +Allele 218 0.046354819793118 +Allele 220 0.045613554111420 +Allele 224 0.047161297180003 +Allele 226 0.058062908532355 + +Locus 004 +Allele 124 0.040350278385984 +Allele 126 0.042005238758610 +Allele 127 0.046141574985085 +Allele 128 0.041372772004518 +Allele 130 0.040447603893713 +Allele 132 0.042342515940715 +Allele 134 0.040219207406470 +Allele 135 0.058005493955464 +Allele 137 0.046089233995223 +Allele 151 0.043261816951302 +Allele 208 0.045042088621804 +Allele 210 0.041217618024535 +Allele 212 0.040990127377547 +Allele 214 0.040115073506322 +Allele 216 0.042853925613405 +Allele 218 0.044283896747771 +Allele 220 0.041468125959368 +Allele 222 0.049570669820464 +Allele 224 0.040858103926276 +Allele 226 0.041458713418586 +Allele 228 0.040313442372380 +Allele 233 0.051158716280576 +Allele 238 0.040433762053880 + +Locus 005 +Allele 121 0.053495726953184 +Allele 123 0.065713834593511 +Allele 125 0.051217633533549 +Allele 127 0.050628947743938 +Allele 129 0.058161408540543 +Allele 130 0.050806480563870 +Allele 131 0.051857838269916 +Allele 133 0.052702988965575 +Allele 135 0.057215607197702 +Allele 136 0.052352195791535 +Allele 137 0.054806283496166 +Allele 138 0.061463501449790 +Allele 139 0.059107651628434 +Allele 141 0.050879084799698 +Allele 145 0.064305202762572 +Allele 146 0.054108310352574 +Allele 148 0.060576752034507 +Allele 150 0.050600551322936 + +Locus 006 +Allele 121 0.043097820568901 +Allele 123 0.044801563982107 +Allele 125 0.043209777035950 +Allele 129 0.042071223762347 +Allele 131 0.042833267783972 +Allele 133 0.054506534351761 +Allele 135 0.044025065760873 +Allele 136 0.042381841994276 +Allele 137 0.056164115355173 +Allele 138 0.043353547328979 +Allele 139 0.046719751941034 +Allele 141 0.042520916919416 +Allele 143 0.042227635834011 +Allele 145 0.044697789981370 +Allele 146 0.042161526036672 +Allele 147 0.048105860320711 +Allele 148 0.045214254908861 +Allele 150 0.043451803331452 +Allele 151 0.042207250067508 +Allele 152 0.062128384678409 +Allele 156 0.042102078317913 +Allele 161 0.042017989738306 + +Locus 007 +Allele 093 0.047579175134162 +Allele 095 0.044814202911049 +Allele 096 0.042670476083749 +Allele 097 0.043415019477945 +Allele 099 0.044799494507377 +Allele 100 0.042902110197413 +Allele 101 0.052555967549724 +Allele 103 0.057155661188736 +Allele 105 0.042586304065563 +Allele 107 0.042328176587945 +Allele 109 0.046720471734638 +Allele 110 0.042746749888252 +Allele 125 0.042669052403187 +Allele 161 0.042516137448623 +Allele 165 0.042303937583311 +Allele 167 0.044857968602387 +Allele 169 0.047215734986623 +Allele 171 0.052956544553162 +Allele 173 0.049103540620343 +Allele 175 0.042648310189483 +Allele 177 0.042532290452994 +Allele 181 0.042922673833333 + +Locus 008 +Allele 095 0.038908117796496 +Allele 097 0.040836900058852 +Allele 099 0.039104721995240 +Allele 100 0.039840627759758 +Allele 101 0.049253359299804 +Allele 103 0.054711735398671 +Allele 105 0.038958680417899 +Allele 107 0.039510727336325 +Allele 109 0.043062782613906 +Allele 110 0.039441548582340 +Allele 113 0.043329528741503 +Allele 121 0.040153602791834 +Allele 123 0.039483751841521 +Allele 131 0.039211684407648 +Allele 167 0.039145157802540 +Allele 169 0.039978736426656 +Allele 171 0.047348315697110 +Allele 173 0.045276052727842 +Allele 175 0.044716494609507 +Allele 177 0.039438672276729 +Allele 179 0.039089890432747 +Allele 181 0.040520616791725 +Allele 183 0.039396734565279 +Allele 185 0.039281559628067 + +Locus 009 +Allele 108 0.035097727612370 +Allele 115 0.032395792148620 +Allele 121 0.033266248735495 +Allele 123 0.033661400699052 +Allele 125 0.036205076043174 +Allele 127 0.032819138671763 +Allele 129 0.033497490241538 +Allele 131 0.032691972988134 +Allele 133 0.033726271478321 +Allele 135 0.037050582234677 +Allele 137 0.032336841732950 +Allele 139 0.033761306981124 +Allele 145 0.032472165857210 +Allele 147 0.041291844013244 +Allele 149 0.032331829004345 +Allele 152 0.035720689953563 +Allele 218 0.032252524074256 +Allele 220 0.033221370329582 +Allele 222 0.036354591269739 +Allele 224 0.035324560088816 +Allele 226 0.035958792331998 +Allele 228 0.032655118398817 +Allele 230 0.032471879338482 +Allele 232 0.044843765343920 +Allele 234 0.034223127993745 +Allele 236 0.032282620162704 +Allele 238 0.037218949388368 +Allele 240 0.032544423267655 +Allele 250 0.032321899616339 + +Locus 010 +Allele 123 0.027231739169276 +Allele 125 0.026538398150509 +Allele 127 0.026824344454687 +Allele 129 0.028628605022512 +Allele 131 0.029013100036599 +Allele 133 0.028166196552634 +Allele 135 0.026535939176689 +Allele 137 0.027365436832300 +Allele 139 0.027476067881699 +Allele 141 0.026706805302187 +Allele 143 0.026397017186336 +Allele 145 0.026475384678834 +Allele 147 0.033863615973019 +Allele 149 0.030464696069444 +Allele 152 0.026341587822473 +Allele 155 0.026540446968063 +Allele 157 0.029139436079514 +Allele 220 0.026429059283523 +Allele 222 0.030534800982856 +Allele 224 0.026469880477458 +Allele 226 0.029633726940492 +Allele 228 0.026525379717464 +Allele 230 0.027331378131074 +Allele 232 0.026414347451617 +Allele 234 0.028215975724199 +Allele 236 0.034527500879293 +Allele 238 0.028838726846295 +Allele 240 0.026907177667252 +Allele 242 0.026770053545401 +Allele 244 0.026530196034012 +Allele 246 0.026476523069251 +Allele 248 0.026447611771249 +Allele 250 0.026342555810816 +Allele 252 0.026465006244043 +Allele 254 0.026353430946686 +Allele 256 0.029077851120241 + + +Cluster 04 +Locus 001 +Allele 092 0.103979635950282 +Allele 094 0.096490061726961 +Allele 096 0.089455774805001 +Allele 098 0.098628625453339 +Allele 100 0.116261257528414 +Allele 102 0.094257512432951 +Allele 104 0.130864810023924 +Allele 106 0.096571356827517 +Allele 108 0.085090873371349 +Allele 110 0.088400091880265 + +Locus 002 +Allele 094 0.069592509423704 +Allele 096 0.064423684844562 +Allele 098 0.073956258067209 +Allele 100 0.081218373562793 +Allele 102 0.071039361350668 +Allele 104 0.100924863844667 +Allele 106 0.085753338257998 +Allele 108 0.063790965150726 +Allele 110 0.065177484005733 +Allele 112 0.070476529023366 +Allele 114 0.062679714646393 +Allele 124 0.064612682420020 +Allele 126 0.063223997140879 +Allele 149 0.063130238261281 + +Locus 003 +Allele 118 0.045518699229104 +Allele 122 0.045724496192923 +Allele 124 0.053414692097350 +Allele 126 0.077520593779278 +Allele 128 0.046090770021429 +Allele 130 0.048396828315746 +Allele 132 0.046606923862010 +Allele 137 0.046559675109370 +Allele 202 0.046289511878981 +Allele 204 0.045425224469964 +Allele 206 0.045603935761255 +Allele 208 0.062712770730002 +Allele 210 0.045857284351008 +Allele 212 0.046913350055621 +Allele 214 0.054814848077555 +Allele 216 0.045505761085207 +Allele 218 0.046316166256722 +Allele 220 0.045500506159671 +Allele 224 0.046786384216085 +Allele 226 0.058441578350720 + +Locus 004 +Allele 124 0.040324972055295 +Allele 126 0.041286994588526 +Allele 127 0.046333216499393 +Allele 128 0.041018142059009 +Allele 130 0.040315598472590 +Allele 132 0.042229261110295 +Allele 134 0.040107040137263 +Allele 135 0.059380741624170 +Allele 137 0.045518943987434 +Allele 151 0.043763631673135 +Allele 208 0.045452943905372 +Allele 210 0.041638831357536 +Allele 212 0.040869827165524 +Allele 214 0.040224103196442 +Allele 216 0.041975507386835 +Allele 218 0.044142104989360 +Allele 220 0.040800188309118 +Allele 222 0.050766705991989 +Allele 224 0.040541436556856 +Allele 226 0.041349525711947 +Allele 228 0.040088650351734 +Allele 233 0.051513617332690 +Allele 238 0.040358015537488 + +Locus 005 +Allele 121 0.052260020780534 +Allele 123 0.065894036633401 +Allele 125 0.051113049565715 +Allele 127 0.050879191735861 +Allele 129 0.058440985258873 +Allele 130 0.050728045260466 +Allele 131 0.051846220425755 +Allele 133 0.053107616950355 +Allele 135 0.057437539931446 +Allele 136 0.052118387052163 +Allele 137 0.054781173952375 +Allele 138 0.061933197484299 +Allele 139 0.059384687778534 +Allele 141 0.050782241626268 +Allele 145 0.064390096172808 +Allele 146 0.053017032855656 +Allele 148 0.061363592567079 +Allele 150 0.050522883968409 + +Locus 006 +Allele 121 0.042786821765434 +Allele 123 0.044469386030439 +Allele 125 0.042764405532230 +Allele 129 0.041989573150117 +Allele 131 0.042574296232469 +Allele 133 0.054294052998280 +Allele 135 0.044732812441137 +Allele 136 0.042274103690404 +Allele 137 0.057570379792966 +Allele 138 0.043095140334666 +Allele 139 0.046388602959452 +Allele 141 0.042240355484039 +Allele 143 0.041857783872531 +Allele 145 0.045138440230154 +Allele 146 0.042504973531370 +Allele 147 0.048451889450268 +Allele 148 0.044378829759263 +Allele 150 0.043132819253083 +Allele 151 0.041956467573523 +Allele 152 0.063731098010797 +Allele 156 0.041845947064831 +Allele 161 0.041821820842547 + +Locus 007 +Allele 093 0.048418297603626 +Allele 095 0.045110529565757 +Allele 096 0.042474295727282 +Allele 097 0.042968957051653 +Allele 099 0.043980511060601 +Allele 100 0.042980696056695 +Allele 101 0.052790076146132 +Allele 103 0.056879137265230 +Allele 105 0.042591056947382 +Allele 107 0.042541675845317 +Allele 109 0.046796004392547 +Allele 110 0.042639416970844 +Allele 125 0.041999634505391 +Allele 161 0.042391109498141 +Allele 165 0.042385214227455 +Allele 167 0.044288199127069 +Allele 169 0.047067117817875 +Allele 171 0.054694521895725 +Allele 173 0.049487298143077 +Allele 175 0.042577218749772 +Allele 177 0.042549554041556 +Allele 181 0.042389477360875 + +Locus 008 +Allele 095 0.038613123085763 +Allele 097 0.041374746997628 +Allele 099 0.039008475579740 +Allele 100 0.039706898736145 +Allele 101 0.049424988049269 +Allele 103 0.054164891982887 +Allele 105 0.038890446864615 +Allele 107 0.039250639688127 +Allele 109 0.043185647967734 +Allele 110 0.039292082526327 +Allele 113 0.043786243339643 +Allele 121 0.039946013634178 +Allele 123 0.039407218408121 +Allele 131 0.039158274671690 +Allele 167 0.038988070649957 +Allele 169 0.039765710507149 +Allele 171 0.047779733849742 +Allele 173 0.045699059502277 +Allele 175 0.044962444951627 +Allele 177 0.039274252314941 +Allele 179 0.039126065203963 +Allele 181 0.040765155894101 +Allele 183 0.039308155778744 +Allele 185 0.039121659815634 + +Locus 009 +Allele 108 0.035223122712781 +Allele 115 0.032274944172931 +Allele 121 0.033764367551790 +Allele 123 0.033415540202001 +Allele 125 0.036222683435490 +Allele 127 0.032716093014218 +Allele 129 0.033263564757426 +Allele 131 0.032624028844672 +Allele 133 0.033488677886422 +Allele 135 0.037552631118978 +Allele 137 0.032253978339788 +Allele 139 0.033164423895619 +Allele 145 0.032442983020396 +Allele 147 0.041587826904571 +Allele 149 0.032075857374311 +Allele 152 0.036273685648519 +Allele 218 0.032412117323911 +Allele 220 0.033203141607696 +Allele 222 0.036545700832509 +Allele 224 0.035129675269018 +Allele 226 0.036017627037383 +Allele 228 0.032298353995019 +Allele 230 0.032498765362282 +Allele 232 0.045316264056901 +Allele 234 0.033673128574587 +Allele 236 0.032297599839688 +Allele 238 0.037567813706179 +Allele 240 0.032518149441152 +Allele 250 0.032177254073763 + +Locus 010 +Allele 123 0.027616924054611 +Allele 125 0.026499722131650 +Allele 127 0.026732931519620 +Allele 129 0.029137296821651 +Allele 131 0.029160578739695 +Allele 133 0.027499152175970 +Allele 135 0.026506373436809 +Allele 137 0.027169074777233 +Allele 139 0.026910356703746 +Allele 141 0.026714230286123 +Allele 143 0.026446055835628 +Allele 145 0.026186028157294 +Allele 147 0.034077461501365 +Allele 149 0.030655006967457 +Allele 152 0.026184884302906 +Allele 155 0.026405437984552 +Allele 157 0.029503250679892 +Allele 220 0.026426488609953 +Allele 222 0.030640221784973 +Allele 224 0.026248796627603 +Allele 226 0.030326545607483 +Allele 228 0.026440138348294 +Allele 230 0.027463643882681 +Allele 232 0.026221434393997 +Allele 234 0.028321106134698 +Allele 236 0.034651237328570 +Allele 238 0.028910803979848 +Allele 240 0.026694788287586 +Allele 242 0.026781482491324 +Allele 244 0.026412038976845 +Allele 246 0.026546439240154 +Allele 248 0.026424951012769 +Allele 250 0.026259261983843 +Allele 252 0.026289138444307 +Allele 254 0.026336889554836 +Allele 256 0.029199827234037 + + + +Estimated Mixing Proportions +0.014527200000000 +0.956762666666667 +0.014041466666667 +0.014668666666667 + + + diff --git a/inst/files/tess/tess_18.txt b/inst/files/tess/tess_18.txt new file mode 100644 index 0000000..fe27ed8 --- /dev/null +++ b/inst/files/tess/tess_18.txt @@ -0,0 +1,1291 @@ +Estimated Clustering Probabilities for Samples +Sample ***Cluster 01*** ***Cluster 02*** ***Cluster 03*** ***Cluster 04*** ***Cluster 05*** +000001: 0.000450000000000 0.998710000000000 0.000760000000000 0.000020000000000 0.000060000000000 1 +000002: 0.000000000000000 0.999880000000000 0.000000000000000 0.000000000000000 0.000120000000000 1 +000003: 0.000040000000000 0.999960000000000 0.000000000000000 0.000000000000000 0.000000000000000 1 +000004: 0.000510000000000 0.998080000000000 0.000310000000000 0.000240000000000 0.000860000000000 1 +000005: 0.001170000000000 0.994360000000000 0.000900000000000 0.002380000000000 0.001190000000000 1 +000006: 0.000000000000000 1.000000000000000 0.000000000000000 0.000000000000000 0.000000000000000 1 +000007: 0.033740000000000 0.868850000000000 0.033630000000000 0.027660000000000 0.036120000000000 1 +000008: 0.000000000000000 0.999810000000000 0.000000000000000 0.000000000000000 0.000190000000000 1 +000009: 0.000620000000000 0.993640000000000 0.001680000000000 0.001860000000000 0.002200000000000 1 +000010: 0.005230000000000 0.975170000000000 0.007670000000000 0.008290000000000 0.003640000000000 1 +000011: 0.000060000000000 0.998550000000000 0.000850000000000 0.000270000000000 0.000270000000000 1 +000012: 0.000000000000000 1.000000000000000 0.000000000000000 0.000000000000000 0.000000000000000 1 +000013: 0.000000000000000 1.000000000000000 0.000000000000000 0.000000000000000 0.000000000000000 1 +000014: 0.000000000000000 0.999970000000000 0.000000000000000 0.000000000000000 0.000030000000000 1 +000015: 0.007890000000000 0.968140000000000 0.008960000000000 0.006620000000000 0.008390000000000 1 +000016: 0.000000000000000 1.000000000000000 0.000000000000000 0.000000000000000 0.000000000000000 1 +000017: 0.001570000000000 0.996140000000000 0.000770000000000 0.000630000000000 0.000890000000000 1 +000018: 0.000440000000000 0.995500000000000 0.001790000000000 0.000800000000000 0.001470000000000 1 +000019: 0.025630000000000 0.880040000000000 0.027080000000000 0.031390000000000 0.035860000000000 1 +000020: 0.016640000000000 0.937360000000000 0.013960000000000 0.010290000000000 0.021750000000000 1 +000021: 0.006560000000000 0.972470000000000 0.008490000000000 0.005840000000000 0.006640000000000 1 +000022: 0.232610000000000 0.107820000000000 0.192270000000000 0.256330000000000 0.210970000000000 1 +000023: 0.000000000000000 0.999940000000000 0.000000000000000 0.000060000000000 0.000000000000000 1 +000024: 0.000020000000000 0.999980000000000 0.000000000000000 0.000000000000000 0.000000000000000 1 +000025: 0.000000000000000 0.999930000000000 0.000070000000000 0.000000000000000 0.000000000000000 1 +000026: 0.000000000000000 0.999460000000000 0.000370000000000 0.000020000000000 0.000150000000000 1 +000027: 0.000000000000000 0.999950000000000 0.000050000000000 0.000000000000000 0.000000000000000 1 +000028: 0.000000000000000 0.999940000000000 0.000000000000000 0.000050000000000 0.000010000000000 1 +000029: 0.004880000000000 0.973850000000000 0.008030000000000 0.005650000000000 0.007590000000000 1 +000030: 0.086760000000000 0.646820000000000 0.099990000000000 0.063700000000000 0.102730000000000 1 +000031: 0.004010000000000 0.974260000000000 0.005500000000000 0.004610000000000 0.011620000000000 1 +000032: 0.000000000000000 0.999920000000000 0.000050000000000 0.000030000000000 0.000000000000000 1 +000033: 0.001060000000000 0.985450000000000 0.002280000000000 0.002160000000000 0.009050000000000 1 +000034: 0.000320000000000 0.991920000000000 0.000030000000000 0.000090000000000 0.007640000000000 1 +000035: 0.004800000000000 0.975540000000000 0.004780000000000 0.008420000000000 0.006460000000000 1 +000036: 0.001660000000000 0.994160000000000 0.001460000000000 0.002140000000000 0.000580000000000 1 +000037: 0.000000000000000 1.000000000000000 0.000000000000000 0.000000000000000 0.000000000000000 1 +000038: 0.000940000000000 0.995860000000000 0.001440000000000 0.000870000000000 0.000890000000000 1 +000039: 0.001220000000000 0.995420000000000 0.001260000000000 0.000110000000000 0.001990000000000 1 +000040: 0.000000000000000 0.999940000000000 0.000040000000000 0.000000000000000 0.000020000000000 1 +000041: 0.000120000000000 0.997260000000000 0.001200000000000 0.000590000000000 0.000830000000000 1 +000042: 0.000000000000000 0.999430000000000 0.000000000000000 0.000000000000000 0.000570000000000 1 +000043: 0.000000000000000 0.999800000000000 0.000000000000000 0.000140000000000 0.000060000000000 1 +000044: 0.001400000000000 0.993140000000000 0.001790000000000 0.001510000000000 0.002160000000000 1 +000045: 0.037360000000000 0.863490000000000 0.031780000000000 0.034310000000000 0.033060000000000 1 +000046: 0.000000000000000 0.999910000000000 0.000000000000000 0.000030000000000 0.000060000000000 1 +000047: 0.001090000000000 0.996740000000000 0.000700000000000 0.000410000000000 0.001060000000000 1 +000048: 0.008470000000000 0.967770000000000 0.008710000000000 0.005850000000000 0.009200000000000 1 +000049: 0.047330000000000 0.833810000000000 0.032990000000000 0.031830000000000 0.054040000000000 1 +000050: 0.000340000000000 0.995210000000000 0.002270000000000 0.000970000000000 0.001210000000000 1 +000051: 0.114190000000000 0.560720000000000 0.104320000000000 0.111340000000000 0.109430000000000 1 +000052: 0.011200000000000 0.960350000000000 0.006750000000000 0.009620000000000 0.012080000000000 1 +000053: 0.000000000000000 1.000000000000000 0.000000000000000 0.000000000000000 0.000000000000000 1 +000054: 0.000980000000000 0.989300000000000 0.002430000000000 0.001720000000000 0.005570000000000 1 +000055: 0.000120000000000 0.999370000000000 0.000230000000000 0.000190000000000 0.000090000000000 1 +000056: 0.000220000000000 0.997970000000000 0.000510000000000 0.000610000000000 0.000690000000000 1 +000057: 0.003070000000000 0.983990000000000 0.003050000000000 0.003760000000000 0.006130000000000 1 +000058: 0.000180000000000 0.999500000000000 0.000280000000000 0.000000000000000 0.000040000000000 1 +000059: 0.081730000000000 0.624710000000000 0.112930000000000 0.082460000000000 0.098170000000000 1 +000060: 0.029400000000000 0.886920000000000 0.022370000000000 0.024190000000000 0.037120000000000 1 +000061: 0.000180000000000 0.999050000000000 0.000370000000000 0.000000000000000 0.000400000000000 1 +000062: 0.001690000000000 0.991410000000000 0.003040000000000 0.000900000000000 0.002960000000000 1 +000063: 0.000390000000000 0.996970000000000 0.001520000000000 0.000580000000000 0.000540000000000 1 +000064: 0.125750000000000 0.414900000000000 0.168570000000000 0.127750000000000 0.163030000000000 1 +000065: 0.001950000000000 0.977820000000000 0.006200000000000 0.005820000000000 0.008210000000000 1 +000066: 0.001530000000000 0.987650000000000 0.004680000000000 0.001790000000000 0.004350000000000 1 +000067: 0.000340000000000 0.997220000000000 0.000730000000000 0.001130000000000 0.000580000000000 1 +000068: 0.000150000000000 0.999300000000000 0.000160000000000 0.000280000000000 0.000110000000000 1 +000069: 0.016460000000000 0.937880000000000 0.012360000000000 0.021530000000000 0.011770000000000 1 +000070: 0.001970000000000 0.991020000000000 0.002290000000000 0.002990000000000 0.001730000000000 1 +000071: 0.000240000000000 0.999150000000000 0.000440000000000 0.000170000000000 0.000000000000000 1 +000072: 0.003280000000000 0.988840000000000 0.002490000000000 0.002090000000000 0.003300000000000 1 +000073: 0.000850000000000 0.988890000000000 0.001630000000000 0.001830000000000 0.006800000000000 1 +000074: 0.003910000000000 0.992200000000000 0.001180000000000 0.001450000000000 0.001260000000000 1 +000075: 0.002210000000000 0.986410000000000 0.003340000000000 0.002400000000000 0.005640000000000 1 + + + +Estimated Allele Frequencies +Cluster 01 +Locus 001 +Allele 092 0.102353977196108 +Allele 094 0.100736510298131 +Allele 096 0.093108171388250 +Allele 098 0.099247585687932 +Allele 100 0.110675846841480 +Allele 102 0.094807912596366 +Allele 104 0.122845729497730 +Allele 106 0.096903444761799 +Allele 108 0.087778159654208 +Allele 110 0.091542662077998 + +Locus 002 +Allele 094 0.069809705908348 +Allele 096 0.066518521594509 +Allele 098 0.074435131458664 +Allele 100 0.078418955017304 +Allele 102 0.070834503473685 +Allele 104 0.094067764301366 +Allele 106 0.083808847301085 +Allele 108 0.065005286955103 +Allele 110 0.067688427437311 +Allele 112 0.070710141965637 +Allele 114 0.064089694471317 +Allele 124 0.066431797357394 +Allele 126 0.063959393260897 +Allele 149 0.064221829497380 + +Locus 003 +Allele 118 0.046245267243293 +Allele 122 0.046350203384115 +Allele 124 0.053609403011828 +Allele 126 0.072448554707188 +Allele 128 0.046134578588025 +Allele 130 0.048333661351451 +Allele 132 0.047321282840597 +Allele 137 0.047084305401677 +Allele 202 0.046798103311341 +Allele 204 0.046256581747009 +Allele 206 0.046027049151034 +Allele 208 0.061418188394490 +Allele 210 0.046584129660784 +Allele 212 0.048094365105647 +Allele 214 0.053691578290724 +Allele 216 0.046486879969833 +Allele 218 0.046799892386860 +Allele 220 0.046335617342812 +Allele 224 0.047690835738459 +Allele 226 0.056289522372835 + +Locus 004 +Allele 124 0.040842438671478 +Allele 126 0.042968601883013 +Allele 127 0.045118567919095 +Allele 128 0.041939078614184 +Allele 130 0.041004975822520 +Allele 132 0.042582781603909 +Allele 134 0.040565061204086 +Allele 135 0.056102137538296 +Allele 137 0.045212755333941 +Allele 151 0.043221505316993 +Allele 208 0.045029878731202 +Allele 210 0.041789252702781 +Allele 212 0.041056853230029 +Allele 214 0.040681736311699 +Allele 216 0.043818505731560 +Allele 218 0.044161310716008 +Allele 220 0.041518385322373 +Allele 222 0.048658779449364 +Allele 224 0.041133124248269 +Allele 226 0.041795842730585 +Allele 228 0.040708990704208 +Allele 233 0.049120370456070 +Allele 238 0.040969065758340 + +Locus 005 +Allele 121 0.054625757898563 +Allele 123 0.064046873067214 +Allele 125 0.052079195837565 +Allele 127 0.051423349406377 +Allele 129 0.057357900580419 +Allele 130 0.051215250122011 +Allele 131 0.052095328633096 +Allele 133 0.053092979122336 +Allele 135 0.057626426881707 +Allele 136 0.052550611181756 +Allele 137 0.054732961715024 +Allele 138 0.061828642719497 +Allele 139 0.057951052692399 +Allele 141 0.051603805809662 +Allele 145 0.062115615118317 +Allele 146 0.054110157353242 +Allele 148 0.060218120067153 +Allele 150 0.051325971793661 + +Locus 006 +Allele 121 0.043558614062608 +Allele 123 0.045668186853846 +Allele 125 0.043232255901435 +Allele 129 0.042554251958461 +Allele 131 0.042953263981244 +Allele 133 0.052462390188304 +Allele 135 0.044739958781484 +Allele 136 0.042594551476679 +Allele 137 0.054856958237453 +Allele 138 0.044321122673108 +Allele 139 0.046089437254799 +Allele 141 0.042700853077408 +Allele 143 0.042503400008836 +Allele 145 0.045167329947664 +Allele 146 0.042641739878644 +Allele 147 0.047152995529634 +Allele 148 0.045340017662802 +Allele 150 0.044197433174475 +Allele 151 0.042473971012053 +Allele 152 0.059763971806664 +Allele 156 0.042535232310753 +Allele 161 0.042492064221644 + +Locus 007 +Allele 093 0.047992128089133 +Allele 095 0.045438075051172 +Allele 096 0.042716097914514 +Allele 097 0.043291453168132 +Allele 099 0.045789213204066 +Allele 100 0.043095716994403 +Allele 101 0.050618878809481 +Allele 103 0.055165615616825 +Allele 105 0.042906534985943 +Allele 107 0.043144167821781 +Allele 109 0.046112408772152 +Allele 110 0.043153737168216 +Allele 125 0.042991062982379 +Allele 161 0.043007498364671 +Allele 165 0.042704398651411 +Allele 167 0.045847953269991 +Allele 169 0.046542321675564 +Allele 171 0.052803951133865 +Allele 173 0.047928804441748 +Allele 175 0.042912890469383 +Allele 177 0.042841332827473 +Allele 181 0.042995758587695 + +Locus 008 +Allele 095 0.039112067781912 +Allele 097 0.041312413117357 +Allele 099 0.039166223612177 +Allele 100 0.039791655558533 +Allele 101 0.047724418385100 +Allele 103 0.052984769931454 +Allele 105 0.039265851015363 +Allele 107 0.039623307056027 +Allele 109 0.042563153303630 +Allele 110 0.039797305037425 +Allele 113 0.043328893409413 +Allele 121 0.040661597001622 +Allele 123 0.039746889948703 +Allele 131 0.039427754871302 +Allele 167 0.039402696665719 +Allele 169 0.040446797547666 +Allele 171 0.046755363610820 +Allele 173 0.044356037560259 +Allele 175 0.045294577256618 +Allele 177 0.039717569798775 +Allele 179 0.039717932805322 +Allele 181 0.040719263201540 +Allele 183 0.039609626094184 +Allele 185 0.039473835429081 + +Locus 009 +Allele 108 0.034996959186380 +Allele 115 0.032555999047547 +Allele 121 0.033611118412612 +Allele 123 0.034305213358811 +Allele 125 0.035349817513706 +Allele 127 0.033240251940860 +Allele 129 0.033746803168171 +Allele 131 0.032777854237821 +Allele 133 0.034525002694040 +Allele 135 0.036399073422261 +Allele 137 0.032621264649467 +Allele 139 0.033711689978222 +Allele 145 0.032682139036831 +Allele 147 0.039692669409333 +Allele 149 0.032573111896833 +Allele 152 0.035868433893486 +Allele 218 0.032571234000211 +Allele 220 0.033688313717649 +Allele 222 0.036361397619967 +Allele 224 0.035196182794881 +Allele 226 0.036111908724104 +Allele 228 0.032735038839802 +Allele 230 0.032619294875745 +Allele 232 0.042560420471771 +Allele 234 0.035461816992564 +Allele 236 0.032711601292213 +Allele 238 0.036115306103757 +Allele 240 0.032724238420728 +Allele 250 0.032485844300227 + +Locus 010 +Allele 123 0.027438018780761 +Allele 125 0.026634680868235 +Allele 127 0.026850965363421 +Allele 129 0.028653910804137 +Allele 131 0.028757780516783 +Allele 133 0.028537684386420 +Allele 135 0.026776076212254 +Allele 137 0.027524778638680 +Allele 139 0.026988312004507 +Allele 141 0.027214744634595 +Allele 143 0.026611812093058 +Allele 145 0.026376510192717 +Allele 147 0.032518940584908 +Allele 149 0.029736365110669 +Allele 152 0.026559273291504 +Allele 155 0.026715632743412 +Allele 157 0.029273678609644 +Allele 220 0.026608807239305 +Allele 222 0.029646240133834 +Allele 224 0.026677081876165 +Allele 226 0.029877506360588 +Allele 228 0.026649769185420 +Allele 230 0.027641376861676 +Allele 232 0.026620646769692 +Allele 234 0.028102923885812 +Allele 236 0.033620801414253 +Allele 238 0.028741019223289 +Allele 240 0.027274557250381 +Allele 242 0.026828688626854 +Allele 244 0.026867389134049 +Allele 246 0.026667280902016 +Allele 248 0.026485205174213 +Allele 250 0.026602499271742 +Allele 252 0.026539019084230 +Allele 254 0.026523087125238 +Allele 256 0.028856935645541 + + +Cluster 02 +Locus 001 +Allele 092 0.039625212368731 +Allele 094 0.393377779814863 +Allele 096 0.164104304476790 +Allele 098 0.088460231219868 +Allele 100 0.024929714432999 +Allele 102 0.083375473806857 +Allele 104 0.105570623188907 +Allele 106 0.049355763223824 +Allele 108 0.026229884703143 +Allele 110 0.024971012764016 + +Locus 002 +Allele 094 0.107024526714766 +Allele 096 0.076680114000396 +Allele 098 0.150688157777851 +Allele 100 0.064722215229346 +Allele 102 0.107025671119892 +Allele 104 0.192434521092318 +Allele 106 0.126285435095557 +Allele 108 0.064285018877023 +Allele 110 0.037248298885213 +Allele 112 0.023016603526542 +Allele 114 0.012940971427584 +Allele 124 0.011881806054003 +Allele 126 0.012826879039805 +Allele 149 0.012939781159706 + +Locus 003 +Allele 118 0.018746184904937 +Allele 122 0.031096946703126 +Allele 124 0.182581967899863 +Allele 126 0.089905349126948 +Allele 128 0.062081781931758 +Allele 130 0.036116838914370 +Allele 132 0.061579669039878 +Allele 137 0.011741134587608 +Allele 202 0.011722220584299 +Allele 204 0.024833018282753 +Allele 206 0.012452447298032 +Allele 208 0.115081152197927 +Allele 210 0.037059711988256 +Allele 212 0.098569130706066 +Allele 214 0.070050993179188 +Allele 216 0.043678818157184 +Allele 218 0.049501973564213 +Allele 220 0.012317442225026 +Allele 224 0.023965301734900 +Allele 226 0.006917916973666 + +Locus 004 +Allele 124 0.024281173069598 +Allele 126 0.029127859515252 +Allele 127 0.008629717959642 +Allele 128 0.041924237960512 +Allele 130 0.042642818251019 +Allele 132 0.170122635191347 +Allele 134 0.012256621119564 +Allele 135 0.093792547736486 +Allele 137 0.064232988987579 +Allele 151 0.009907187343554 +Allele 208 0.015232662075953 +Allele 210 0.011397687678795 +Allele 212 0.085108210315888 +Allele 214 0.036682307240773 +Allele 216 0.071224148335308 +Allele 218 0.016194181032929 +Allele 220 0.048193273472254 +Allele 222 0.054747441126857 +Allele 224 0.091457852396184 +Allele 226 0.035741575918919 +Allele 228 0.018242821225023 +Allele 233 0.006819197493092 +Allele 238 0.012040854553469 + +Locus 005 +Allele 121 0.058169678701545 +Allele 123 0.053048021303057 +Allele 125 0.039251376134159 +Allele 127 0.013161271720001 +Allele 129 0.029212191804955 +Allele 130 0.026621877733334 +Allele 131 0.126295631289730 +Allele 133 0.072238859851057 +Allele 135 0.056409600197259 +Allele 136 0.119218239046141 +Allele 137 0.024061446882751 +Allele 138 0.094094675572383 +Allele 139 0.095429823319180 +Allele 141 0.026448880745511 +Allele 145 0.034093746538291 +Allele 146 0.071442064069074 +Allele 148 0.047513581080467 +Allele 150 0.013289034011101 + +Locus 006 +Allele 121 0.025232150409500 +Allele 123 0.023818908841820 +Allele 125 0.018860504560986 +Allele 129 0.026088308369046 +Allele 131 0.116505049302604 +Allele 133 0.071657159476330 +Allele 135 0.108780985154031 +Allele 136 0.025917817865093 +Allele 137 0.042564261722944 +Allele 138 0.018424415009528 +Allele 139 0.049571672153023 +Allele 141 0.019259526579818 +Allele 143 0.013015322224734 +Allele 145 0.056641742504496 +Allele 146 0.051819827149785 +Allele 147 0.009173906121621 +Allele 148 0.108388315861492 +Allele 150 0.076829081928823 +Allele 151 0.012944845156890 +Allele 152 0.092001914651752 +Allele 156 0.019536337862778 +Allele 161 0.012967947092907 + +Locus 007 +Allele 093 0.049688491403856 +Allele 095 0.071342489554698 +Allele 096 0.013242585681705 +Allele 097 0.152069421947055 +Allele 099 0.037834348520912 +Allele 100 0.059300618975946 +Allele 101 0.039740153271484 +Allele 103 0.052041941243607 +Allele 105 0.019680565231466 +Allele 107 0.026442510819259 +Allele 109 0.010941995019515 +Allele 110 0.013139142114580 +Allele 125 0.013258687703366 +Allele 161 0.013251060929950 +Allele 165 0.026600985903692 +Allele 167 0.044235110676724 +Allele 169 0.063845246708998 +Allele 171 0.138717708186072 +Allele 173 0.075345797898825 +Allele 175 0.046351188055353 +Allele 177 0.019911768636313 +Allele 181 0.013018181516624 + +Locus 008 +Allele 095 0.013102576646973 +Allele 097 0.050953130964846 +Allele 099 0.026167705470050 +Allele 100 0.038805218861514 +Allele 101 0.117451973969205 +Allele 103 0.088984182571780 +Allele 105 0.039328526170490 +Allele 107 0.078325069565864 +Allele 109 0.017295036084942 +Allele 110 0.019417028639867 +Allele 113 0.016710520705232 +Allele 121 0.018729181836210 +Allele 123 0.019391798857241 +Allele 131 0.013114125093591 +Allele 167 0.013090076428517 +Allele 169 0.025484077737755 +Allele 171 0.092428954032322 +Allele 173 0.087478751786909 +Allele 175 0.048319408467677 +Allele 177 0.078382086406530 +Allele 179 0.013118202987277 +Allele 181 0.031732334541689 +Allele 183 0.026049510095796 +Allele 185 0.026140522077723 + +Locus 009 +Allele 108 0.027110772520289 +Allele 115 0.011668208724931 +Allele 121 0.010964344408660 +Allele 123 0.039776578643214 +Allele 125 0.085824665467761 +Allele 127 0.040725049900339 +Allele 129 0.045873863014921 +Allele 131 0.046723310919520 +Allele 133 0.092384295937654 +Allele 135 0.025879687438035 +Allele 137 0.017526034254812 +Allele 139 0.016769637060949 +Allele 145 0.017478181829663 +Allele 147 0.006528093161093 +Allele 149 0.011718724667668 +Allele 152 0.009138637017010 +Allele 218 0.011674348444348 +Allele 220 0.087310502627711 +Allele 222 0.108471482884549 +Allele 224 0.085715601182176 +Allele 226 0.038161305091928 +Allele 228 0.023313476517206 +Allele 230 0.017503083578412 +Allele 232 0.021892883450050 +Allele 234 0.033194063646989 +Allele 236 0.017587750815501 +Allele 238 0.019991289207033 +Allele 240 0.017404342977853 +Allele 250 0.011689784609726 + +Locus 010 +Allele 123 0.010490047430274 +Allele 125 0.011040571961087 +Allele 127 0.033354965350170 +Allele 129 0.037125763330447 +Allele 131 0.043168983868873 +Allele 133 0.065881730026427 +Allele 135 0.073034691147281 +Allele 137 0.066721271974636 +Allele 139 0.016079427870494 +Allele 141 0.038889263139350 +Allele 143 0.011142107950468 +Allele 145 0.016918550921219 +Allele 147 0.011785320560054 +Allele 149 0.019179397217087 +Allele 152 0.011282781773566 +Allele 155 0.011137521339901 +Allele 157 0.014419106267627 +Allele 220 0.011197891037957 +Allele 222 0.019166401902132 +Allele 224 0.045074372346959 +Allele 226 0.053361162603802 +Allele 228 0.028001909050851 +Allele 230 0.032781839149879 +Allele 232 0.039430966442341 +Allele 234 0.037907996087994 +Allele 236 0.039059239638172 +Allele 238 0.054042607068283 +Allele 240 0.027526291225545 +Allele 242 0.033436686662977 +Allele 244 0.010941623977291 +Allele 246 0.016725220144303 +Allele 248 0.011226412883454 +Allele 250 0.011211207075493 +Allele 252 0.016722488382557 +Allele 254 0.011232190322684 +Allele 256 0.009301991868367 + + +Cluster 03 +Locus 001 +Allele 092 0.107105918251000 +Allele 094 0.099681259568595 +Allele 096 0.091924680667852 +Allele 098 0.098115573055428 +Allele 100 0.108724834224123 +Allele 102 0.094506559424804 +Allele 104 0.123536825613754 +Allele 106 0.098631812985035 +Allele 108 0.087259640440466 +Allele 110 0.090512895768941 + +Locus 002 +Allele 094 0.071205507215276 +Allele 096 0.065943765498472 +Allele 098 0.073528476213651 +Allele 100 0.076241858309824 +Allele 102 0.071922518502863 +Allele 104 0.095400951013860 +Allele 106 0.086298695937773 +Allele 108 0.065055083108854 +Allele 110 0.066661329080272 +Allele 112 0.069847139150166 +Allele 114 0.064055745597743 +Allele 124 0.065851735732759 +Allele 126 0.064304759638847 +Allele 149 0.063682434999643 + +Locus 003 +Allele 118 0.046388747007119 +Allele 122 0.046338222310803 +Allele 124 0.053735324113498 +Allele 126 0.072495886054181 +Allele 128 0.046809712514299 +Allele 130 0.047959428235253 +Allele 132 0.047199156769243 +Allele 137 0.047243415239855 +Allele 202 0.047145729439644 +Allele 204 0.046114842557961 +Allele 206 0.046095822674335 +Allele 208 0.061126996025051 +Allele 210 0.046746087413623 +Allele 212 0.048050036112572 +Allele 214 0.055188989692231 +Allele 216 0.046341986850934 +Allele 218 0.046689465209681 +Allele 220 0.046272213625073 +Allele 224 0.048007583897543 +Allele 226 0.054050354257105 + +Locus 004 +Allele 124 0.040622750099964 +Allele 126 0.042265629068883 +Allele 127 0.046596029359822 +Allele 128 0.041388284015675 +Allele 130 0.041156261662267 +Allele 132 0.042863126177810 +Allele 134 0.040429998785298 +Allele 135 0.054055187797025 +Allele 137 0.045684248696901 +Allele 151 0.044495528194541 +Allele 208 0.044573743586022 +Allele 210 0.041532464182330 +Allele 212 0.041606435668421 +Allele 214 0.040701651095662 +Allele 216 0.043273411863116 +Allele 218 0.044399312163946 +Allele 220 0.041332052610697 +Allele 222 0.051306817056963 +Allele 224 0.041083384612272 +Allele 226 0.041888186827673 +Allele 228 0.040519515832084 +Allele 233 0.047597935293784 +Allele 238 0.040628045348841 + +Locus 005 +Allele 121 0.053609476433749 +Allele 123 0.061964992704592 +Allele 125 0.052002311147898 +Allele 127 0.051382696340371 +Allele 129 0.059111203471124 +Allele 130 0.051307991321205 +Allele 131 0.052414929762236 +Allele 133 0.053056300985053 +Allele 135 0.056600691816422 +Allele 136 0.052473330405619 +Allele 137 0.056167571645201 +Allele 138 0.061871910861042 +Allele 139 0.060102922977720 +Allele 141 0.051437422691991 +Allele 145 0.060164652756482 +Allele 146 0.053844826987267 +Allele 148 0.061177249835875 +Allele 150 0.051309517856156 + +Locus 006 +Allele 121 0.043097474699075 +Allele 123 0.045235381375915 +Allele 125 0.043387037770744 +Allele 129 0.042433639093683 +Allele 131 0.043430497741559 +Allele 133 0.050692100330050 +Allele 135 0.044518683933045 +Allele 136 0.042655886266939 +Allele 137 0.056579839372392 +Allele 138 0.043576785732986 +Allele 139 0.046746194252497 +Allele 141 0.042851055114163 +Allele 143 0.042538168023700 +Allele 145 0.045131183355323 +Allele 146 0.042735437654829 +Allele 147 0.048750244726494 +Allele 148 0.045143997746041 +Allele 150 0.044363874387719 +Allele 151 0.042391703138554 +Allele 152 0.059080155377439 +Allele 156 0.042389281218702 +Allele 161 0.042271378688152 + +Locus 007 +Allele 093 0.047198524029758 +Allele 095 0.045065801426634 +Allele 096 0.042513812839596 +Allele 097 0.043596132231909 +Allele 099 0.044566033544291 +Allele 100 0.043315573643992 +Allele 101 0.053582829943838 +Allele 103 0.053261171554927 +Allele 105 0.042977001350730 +Allele 107 0.042669137468161 +Allele 109 0.046754629304562 +Allele 110 0.042722894626428 +Allele 125 0.042683779623274 +Allele 161 0.042833891115234 +Allele 165 0.042561132739876 +Allele 167 0.045628350917311 +Allele 169 0.047037752448429 +Allele 171 0.052920333533794 +Allele 173 0.049968522242802 +Allele 175 0.042686245765165 +Allele 177 0.042602210347446 +Allele 181 0.042854239301843 + +Locus 008 +Allele 095 0.039203894422470 +Allele 097 0.040899550194016 +Allele 099 0.039516046640580 +Allele 100 0.039961120296422 +Allele 101 0.050238468984873 +Allele 103 0.050756385007557 +Allele 105 0.039332497725149 +Allele 107 0.039827072445643 +Allele 109 0.042917441084375 +Allele 110 0.039434099254647 +Allele 113 0.042708661710639 +Allele 121 0.040331786370738 +Allele 123 0.039392404347254 +Allele 131 0.039273691882578 +Allele 167 0.039211655660913 +Allele 169 0.040095275148265 +Allele 171 0.048068093766912 +Allele 173 0.045929121410002 +Allele 175 0.044405165552383 +Allele 177 0.039822178675156 +Allele 179 0.039150977141858 +Allele 181 0.040401785636337 +Allele 183 0.039629822492092 +Allele 185 0.039492804149136 + +Locus 009 +Allele 108 0.035810649020804 +Allele 115 0.032622131647108 +Allele 121 0.033398459409839 +Allele 123 0.033602686446463 +Allele 125 0.036293583968932 +Allele 127 0.033025308819143 +Allele 129 0.033787983670446 +Allele 131 0.032889464290510 +Allele 133 0.034225602949385 +Allele 135 0.037440545456407 +Allele 137 0.032743815681453 +Allele 139 0.033331784836632 +Allele 145 0.032768990539725 +Allele 147 0.038494742412515 +Allele 149 0.032555559391299 +Allele 152 0.035693662731948 +Allele 218 0.032560176297632 +Allele 220 0.033521807788941 +Allele 222 0.036324170843237 +Allele 224 0.035061064070286 +Allele 226 0.036264199047142 +Allele 228 0.032816199157282 +Allele 230 0.032552132938136 +Allele 232 0.041485931622507 +Allele 234 0.034838584147368 +Allele 236 0.032675834174476 +Allele 238 0.037717638041461 +Allele 240 0.032813584804519 +Allele 250 0.032683705794401 + +Locus 010 +Allele 123 0.027141665389971 +Allele 125 0.026520890266495 +Allele 127 0.026816244081785 +Allele 129 0.029499964834138 +Allele 131 0.028984387005620 +Allele 133 0.028094471030801 +Allele 135 0.026836254804913 +Allele 137 0.027420833327597 +Allele 139 0.027298568295954 +Allele 141 0.027195088672399 +Allele 143 0.026725492639671 +Allele 145 0.026528839951894 +Allele 147 0.031317894461715 +Allele 149 0.030672508147228 +Allele 152 0.026426854829960 +Allele 155 0.026711075956683 +Allele 157 0.029054327587093 +Allele 220 0.026600017150199 +Allele 222 0.030675766386345 +Allele 224 0.026594635927412 +Allele 226 0.029313330160791 +Allele 228 0.026858656880651 +Allele 230 0.027761781134152 +Allele 232 0.026474515904779 +Allele 234 0.028193135156706 +Allele 236 0.032059665154503 +Allele 238 0.029480353747574 +Allele 240 0.027068255640903 +Allele 242 0.026729267442415 +Allele 244 0.026967170905939 +Allele 246 0.026621247531354 +Allele 248 0.026563707202937 +Allele 250 0.026497917727037 +Allele 252 0.026818261388774 +Allele 254 0.026466352635377 +Allele 256 0.029010600638236 + + +Cluster 04 +Locus 001 +Allele 092 0.101793588813745 +Allele 094 0.100522365085932 +Allele 096 0.091463576129529 +Allele 098 0.099205013896727 +Allele 100 0.111589751572565 +Allele 102 0.095440792594921 +Allele 104 0.125299282251458 +Allele 106 0.095620619470800 +Allele 108 0.088126530232733 +Allele 110 0.090938479951593 + +Locus 002 +Allele 094 0.069601723637868 +Allele 096 0.066343511382769 +Allele 098 0.074437551285840 +Allele 100 0.080703888738611 +Allele 102 0.069605198578248 +Allele 104 0.096126932494764 +Allele 106 0.081205582479152 +Allele 108 0.065240722255006 +Allele 110 0.067274173773309 +Allele 112 0.070130981169813 +Allele 114 0.064148314956201 +Allele 124 0.066008069736701 +Allele 126 0.064351687192930 +Allele 149 0.064821662318794 + +Locus 003 +Allele 118 0.046222179303201 +Allele 122 0.046632734622199 +Allele 124 0.051987968715048 +Allele 126 0.072812236455288 +Allele 128 0.046728135463563 +Allele 130 0.048722049374561 +Allele 132 0.047396647176582 +Allele 137 0.047584126744334 +Allele 202 0.047567981797186 +Allele 204 0.046271047942017 +Allele 206 0.046139914401879 +Allele 208 0.060607913244958 +Allele 210 0.046801473549111 +Allele 212 0.047741727774480 +Allele 214 0.052383992940761 +Allele 216 0.046275982000119 +Allele 218 0.046790557423757 +Allele 220 0.046420281916231 +Allele 224 0.047623592323922 +Allele 226 0.057289456830803 + +Locus 004 +Allele 124 0.040744613029646 +Allele 126 0.042130025557015 +Allele 127 0.045346890620412 +Allele 128 0.041864244439770 +Allele 130 0.041047240394749 +Allele 132 0.042314027426273 +Allele 134 0.040429004142792 +Allele 135 0.057342109782770 +Allele 137 0.044552546387272 +Allele 151 0.043360354892462 +Allele 208 0.045528987962312 +Allele 210 0.041766970975739 +Allele 212 0.041487379504365 +Allele 214 0.040852371737476 +Allele 216 0.043007174147834 +Allele 218 0.042940310831563 +Allele 220 0.041753176073671 +Allele 222 0.049007961098712 +Allele 224 0.040839046924767 +Allele 226 0.041872690316399 +Allele 228 0.040823372588022 +Allele 233 0.050258483163516 +Allele 238 0.040731018002458 + +Locus 005 +Allele 121 0.054089918250366 +Allele 123 0.064681221859270 +Allele 125 0.052154512064447 +Allele 127 0.051446136518826 +Allele 129 0.057011828593817 +Allele 130 0.051350279781432 +Allele 131 0.052211854348583 +Allele 133 0.053110761061231 +Allele 135 0.057840737160690 +Allele 136 0.052793351133576 +Allele 137 0.054926583053032 +Allele 138 0.059537722436889 +Allele 139 0.057909133544161 +Allele 141 0.051422608186103 +Allele 145 0.063468345984055 +Allele 146 0.054425787021917 +Allele 148 0.060297867877291 +Allele 150 0.051321351124315 + +Locus 006 +Allele 121 0.043318895563853 +Allele 123 0.044665403056807 +Allele 125 0.043099143160620 +Allele 129 0.042715470529939 +Allele 131 0.043522677457278 +Allele 133 0.052951454430289 +Allele 135 0.045136251608431 +Allele 136 0.042322536070079 +Allele 137 0.054568413829673 +Allele 138 0.043769445568849 +Allele 139 0.045063056922968 +Allele 141 0.042831233533592 +Allele 143 0.042457910308861 +Allele 145 0.044936732306399 +Allele 146 0.042862455053458 +Allele 147 0.047291369822878 +Allele 148 0.045827692116449 +Allele 150 0.044094967792161 +Allele 151 0.042446836214364 +Allele 152 0.060960432146966 +Allele 156 0.042540544863370 +Allele 161 0.042617077642716 + +Locus 007 +Allele 093 0.048193688300931 +Allele 095 0.045064216228218 +Allele 096 0.042771344804941 +Allele 097 0.043691194003426 +Allele 099 0.045183852958372 +Allele 100 0.042860488779271 +Allele 101 0.051188431806734 +Allele 103 0.056000887791926 +Allele 105 0.043368902762563 +Allele 107 0.042933114362326 +Allele 109 0.045333726471371 +Allele 110 0.042916754801474 +Allele 125 0.042925799666945 +Allele 161 0.042847411453381 +Allele 165 0.043071984057534 +Allele 167 0.045502709705323 +Allele 169 0.045674809346945 +Allele 171 0.052898960725454 +Allele 173 0.048448142680283 +Allele 175 0.042955316253841 +Allele 177 0.042872464466070 +Allele 181 0.043295798572672 + +Locus 008 +Allele 095 0.039380118813252 +Allele 097 0.041642789605782 +Allele 099 0.039740562790765 +Allele 100 0.039786004407456 +Allele 101 0.047839300256066 +Allele 103 0.053341284066549 +Allele 105 0.039645187575728 +Allele 107 0.040014444901161 +Allele 109 0.041597233862661 +Allele 110 0.039743398097683 +Allele 113 0.043156921718695 +Allele 121 0.040439548061943 +Allele 123 0.039812424691826 +Allele 131 0.039352124267672 +Allele 167 0.039473748104832 +Allele 169 0.040449892434846 +Allele 171 0.045924202571928 +Allele 173 0.044658472285488 +Allele 175 0.044713424625869 +Allele 177 0.039948114891956 +Allele 179 0.039344555003326 +Allele 181 0.040816322332058 +Allele 183 0.039611421414758 +Allele 185 0.039568503217697 + +Locus 009 +Allele 108 0.035110337877602 +Allele 115 0.032397082954929 +Allele 121 0.033610759846001 +Allele 123 0.033889120253060 +Allele 125 0.034963430470315 +Allele 127 0.033275028305085 +Allele 129 0.033662374533117 +Allele 131 0.032895966691248 +Allele 133 0.034004449131942 +Allele 135 0.036259672807334 +Allele 137 0.032587189914271 +Allele 139 0.033898646448919 +Allele 145 0.032951536801477 +Allele 147 0.040582075121587 +Allele 149 0.032626575629670 +Allele 152 0.036067172279461 +Allele 218 0.032836330611659 +Allele 220 0.033581352608464 +Allele 222 0.036198827542790 +Allele 224 0.035242942059845 +Allele 226 0.035691576446622 +Allele 228 0.032917269353871 +Allele 230 0.032523791584865 +Allele 232 0.042814106173590 +Allele 234 0.034668229965382 +Allele 236 0.032648618277086 +Allele 238 0.036553205650721 +Allele 240 0.032810627270910 +Allele 250 0.032731703388175 + +Locus 010 +Allele 123 0.027402699860522 +Allele 125 0.026778195269695 +Allele 127 0.027182329332207 +Allele 129 0.028642181937352 +Allele 131 0.028251889857923 +Allele 133 0.028308697644288 +Allele 135 0.026704079042555 +Allele 137 0.027309098701439 +Allele 139 0.027442509099229 +Allele 141 0.026934311300411 +Allele 143 0.026693727483359 +Allele 145 0.026458640474338 +Allele 147 0.033148466289501 +Allele 149 0.029699090559908 +Allele 152 0.026505011924023 +Allele 155 0.026592174326987 +Allele 157 0.029354942701116 +Allele 220 0.026718320474136 +Allele 222 0.029539076224385 +Allele 224 0.026633298113707 +Allele 226 0.029783577640669 +Allele 228 0.026837834972830 +Allele 230 0.027501234643669 +Allele 232 0.026423752562411 +Allele 234 0.028408150620985 +Allele 236 0.033947572251107 +Allele 238 0.028876668333567 +Allele 240 0.027181439023403 +Allele 242 0.026981024868172 +Allele 244 0.026635910456994 +Allele 246 0.026530056534323 +Allele 248 0.026658870515350 +Allele 250 0.026597699264129 +Allele 252 0.026657789952369 +Allele 254 0.026530034782919 +Allele 256 0.028149642960023 + + +Cluster 05 +Locus 001 +Allele 092 0.104150324040209 +Allele 094 0.103829559374375 +Allele 096 0.093497878326579 +Allele 098 0.097727910487354 +Allele 100 0.109478805592468 +Allele 102 0.093681755402086 +Allele 104 0.122908733286937 +Allele 106 0.097663313508014 +Allele 108 0.086826638677993 +Allele 110 0.090235081303988 + +Locus 002 +Allele 094 0.069398125797368 +Allele 096 0.066711527721074 +Allele 098 0.075138629251893 +Allele 100 0.076379035255943 +Allele 102 0.071186776916940 +Allele 104 0.095258609560987 +Allele 106 0.087212289199820 +Allele 108 0.065042683373417 +Allele 110 0.067184434742484 +Allele 112 0.069705901999594 +Allele 114 0.063270721043186 +Allele 124 0.065898356281778 +Allele 126 0.063812348188146 +Allele 149 0.063800560667369 + +Locus 003 +Allele 118 0.045925000076952 +Allele 122 0.045897753773509 +Allele 124 0.055124289380501 +Allele 126 0.073124782521085 +Allele 128 0.046243852353528 +Allele 130 0.047707628040022 +Allele 132 0.047657666284637 +Allele 137 0.047286997833807 +Allele 202 0.047217215706716 +Allele 204 0.045946887720425 +Allele 206 0.045587301995865 +Allele 208 0.062424737746154 +Allele 210 0.046524423683927 +Allele 212 0.047955881663158 +Allele 214 0.054959454842578 +Allele 216 0.045928941940862 +Allele 218 0.046445114909399 +Allele 220 0.045769901243122 +Allele 224 0.047501228996398 +Allele 226 0.054770939287359 + +Locus 004 +Allele 124 0.040291020482112 +Allele 126 0.043181949985064 +Allele 127 0.045920603510834 +Allele 128 0.041825117293522 +Allele 130 0.040648899665049 +Allele 132 0.042574625943414 +Allele 134 0.040311265052294 +Allele 135 0.055370114254320 +Allele 137 0.045740523243834 +Allele 151 0.043652674414396 +Allele 208 0.044701648089672 +Allele 210 0.041701770444205 +Allele 212 0.041186491642469 +Allele 214 0.040320781284968 +Allele 216 0.044375447566429 +Allele 218 0.044145745823208 +Allele 220 0.041572449305426 +Allele 222 0.050452550526574 +Allele 224 0.041312544267501 +Allele 226 0.041483080865187 +Allele 228 0.040413034899357 +Allele 233 0.048186525819303 +Allele 238 0.040631135620862 + +Locus 005 +Allele 121 0.054450770682723 +Allele 123 0.062472812037020 +Allele 125 0.052330402222097 +Allele 127 0.051364546426860 +Allele 129 0.058425191802116 +Allele 130 0.050832638702964 +Allele 131 0.052150997890403 +Allele 133 0.052803958056915 +Allele 135 0.056797333995713 +Allele 136 0.052236128732928 +Allele 137 0.055075540433956 +Allele 138 0.063025345606553 +Allele 139 0.059186704587054 +Allele 141 0.051157278044996 +Allele 145 0.060708811559670 +Allele 146 0.055082822467556 +Allele 148 0.060972227184507 +Allele 150 0.050926489565970 + +Locus 006 +Allele 121 0.043596712843697 +Allele 123 0.045739888900406 +Allele 125 0.043413475351681 +Allele 129 0.041942983156875 +Allele 131 0.043550676721949 +Allele 133 0.051454690279035 +Allele 135 0.044481078701913 +Allele 136 0.042466278063677 +Allele 137 0.056421701973780 +Allele 138 0.043885707751373 +Allele 139 0.046562727696488 +Allele 141 0.042405516864204 +Allele 143 0.042228501383761 +Allele 145 0.044920688166085 +Allele 146 0.042928030662726 +Allele 147 0.048070530924500 +Allele 148 0.046339500318165 +Allele 150 0.044090562644230 +Allele 151 0.042012943273362 +Allele 152 0.059344696844003 +Allele 156 0.042099699708626 +Allele 161 0.042043407769465 + +Locus 007 +Allele 093 0.047264961842092 +Allele 095 0.045128165711923 +Allele 096 0.042635329185991 +Allele 097 0.043370819407887 +Allele 099 0.045829854792592 +Allele 100 0.043546381456422 +Allele 101 0.052553370278766 +Allele 103 0.054009522778936 +Allele 105 0.043123310201533 +Allele 107 0.042535120143798 +Allele 109 0.046258223890502 +Allele 110 0.042954595008630 +Allele 125 0.042337745278337 +Allele 161 0.042390411956426 +Allele 165 0.042211658619785 +Allele 167 0.046698359466367 +Allele 169 0.046854185309940 +Allele 171 0.053549470473413 +Allele 173 0.049033538301957 +Allele 175 0.042648974732130 +Allele 177 0.042281218890064 +Allele 181 0.042784782272512 + +Locus 008 +Allele 095 0.039066789795235 +Allele 097 0.040576703286438 +Allele 099 0.039027384059709 +Allele 100 0.040175271371508 +Allele 101 0.049288519073622 +Allele 103 0.052802029532109 +Allele 105 0.039052740893015 +Allele 107 0.039676656542965 +Allele 109 0.043169784338832 +Allele 110 0.039485621667433 +Allele 113 0.042946717798668 +Allele 121 0.040596297382606 +Allele 123 0.039589827253063 +Allele 131 0.038966715929431 +Allele 167 0.039091484450722 +Allele 169 0.040382443029375 +Allele 171 0.047759234095947 +Allele 173 0.045323608084540 +Allele 175 0.045430633050672 +Allele 177 0.039523547958989 +Allele 179 0.039188397547352 +Allele 181 0.040370782641286 +Allele 183 0.039326512065844 +Allele 185 0.039182298150639 + +Locus 009 +Allele 108 0.035289715533210 +Allele 115 0.032630842397279 +Allele 121 0.033289415633555 +Allele 123 0.034447281315002 +Allele 125 0.036073316160371 +Allele 127 0.032760157246847 +Allele 129 0.034016832758536 +Allele 131 0.032799478155943 +Allele 133 0.035061474419171 +Allele 135 0.037098428370021 +Allele 137 0.032543147816489 +Allele 139 0.033492067091850 +Allele 145 0.032594381013694 +Allele 147 0.038742178885150 +Allele 149 0.032348279427124 +Allele 152 0.035611054795558 +Allele 218 0.032604042081922 +Allele 220 0.033665462535331 +Allele 222 0.036377929425696 +Allele 224 0.035679876461559 +Allele 226 0.036039571004021 +Allele 228 0.032336866074846 +Allele 230 0.032352786424991 +Allele 232 0.041822436039320 +Allele 234 0.035662722165092 +Allele 236 0.032252011316403 +Allele 238 0.037377758691503 +Allele 240 0.032491569253505 +Allele 250 0.032538917506009 + +Locus 010 +Allele 123 0.027241638745498 +Allele 125 0.026729674665366 +Allele 127 0.026921661716757 +Allele 129 0.029021878299604 +Allele 131 0.028857062147149 +Allele 133 0.028977381215989 +Allele 135 0.026990518513666 +Allele 137 0.027459238973841 +Allele 139 0.027489341138433 +Allele 141 0.027225795313041 +Allele 143 0.026469991637867 +Allele 145 0.026474633713964 +Allele 147 0.031804363477436 +Allele 149 0.030463435600295 +Allele 152 0.026290599788712 +Allele 155 0.026442638470152 +Allele 157 0.028903839052580 +Allele 220 0.026558437552959 +Allele 222 0.030357457636960 +Allele 224 0.026256823453245 +Allele 226 0.029655620116347 +Allele 228 0.026488374476948 +Allele 230 0.027750543491595 +Allele 232 0.026477148088501 +Allele 234 0.028190127832632 +Allele 236 0.032870270841023 +Allele 238 0.029091373559844 +Allele 240 0.027312282327207 +Allele 242 0.026805111863258 +Allele 244 0.026962588207837 +Allele 246 0.026578450484205 +Allele 248 0.026372162874590 +Allele 250 0.026459498217628 +Allele 252 0.026705303434655 +Allele 254 0.026404480665724 +Allele 256 0.028940252404491 + + + +Estimated Mixing Proportions +0.012492400000000 +0.948198533333334 +0.012877066666667 +0.012276933333333 +0.014155066666667 + + + diff --git a/inst/files/tess/tess_19.txt b/inst/files/tess/tess_19.txt new file mode 100644 index 0000000..82a442f --- /dev/null +++ b/inst/files/tess/tess_19.txt @@ -0,0 +1,1532 @@ +Estimated Clustering Probabilities for Samples +Sample ***Cluster 01*** ***Cluster 02*** ***Cluster 03*** ***Cluster 04*** ***Cluster 05*** ***Cluster 06*** +000001: 0.000250000000000 0.000840000000000 0.000040000000000 0.998170000000000 0.000060000000000 0.000640000000000 1 +000002: 0.025230000000000 0.000000000000000 0.000000000000000 0.974770000000000 0.000000000000000 0.000000000000000 1 +000003: 0.000000000000000 0.000060000000000 0.000000000000000 0.999940000000000 0.000000000000000 0.000000000000000 1 +000004: 0.035440000000000 0.000750000000000 0.001080000000000 0.962010000000000 0.000000000000000 0.000720000000000 1 +000005: 0.000950000000000 0.000760000000000 0.001270000000000 0.995060000000000 0.000040000000000 0.001920000000000 1 +000006: 0.000000000000000 0.000000000000000 0.000000000000000 1.000000000000000 0.000000000000000 0.000000000000000 1 +000007: 0.090070000000000 0.032140000000000 0.028650000000000 0.785600000000000 0.030470000000000 0.033070000000000 1 +000008: 0.021740000000000 0.000000000000000 0.000000000000000 0.977910000000000 0.000260000000000 0.000090000000000 1 +000009: 0.001040000000000 0.001190000000000 0.000970000000000 0.991920000000000 0.003750000000000 0.001130000000000 1 +000010: 0.039980000000000 0.006980000000000 0.004420000000000 0.937080000000000 0.007060000000000 0.004480000000000 1 +000011: 0.050730000000000 0.000320000000000 0.000000000000000 0.948930000000000 0.000020000000000 0.000000000000000 1 +000012: 0.000430000000000 0.000000000000000 0.000030000000000 0.999520000000000 0.000020000000000 0.000000000000000 1 +000013: 0.008290000000000 0.000000000000000 0.000000000000000 0.991710000000000 0.000000000000000 0.000000000000000 1 +000014: 0.000070000000000 0.000000000000000 0.000000000000000 0.999920000000000 0.000010000000000 0.000000000000000 1 +000015: 0.019550000000000 0.009260000000000 0.007170000000000 0.949780000000000 0.006090000000000 0.008150000000000 1 +000016: 0.000080000000000 0.000000000000000 0.000000000000000 0.999920000000000 0.000000000000000 0.000000000000000 1 +000017: 0.006570000000000 0.001890000000000 0.000720000000000 0.988840000000000 0.000440000000000 0.001540000000000 1 +000018: 0.001050000000000 0.001280000000000 0.001590000000000 0.994960000000000 0.000510000000000 0.000610000000000 1 +000019: 0.048440000000000 0.030500000000000 0.026090000000000 0.834250000000000 0.029990000000000 0.030730000000000 1 +000020: 0.060910000000000 0.014770000000000 0.010030000000000 0.890590000000000 0.011000000000000 0.012700000000000 1 +000021: 0.054000000000000 0.006580000000000 0.004630000000000 0.920350000000000 0.006050000000000 0.008390000000000 1 +000022: 0.174330000000000 0.202550000000000 0.200030000000000 0.072150000000000 0.140330000000000 0.210610000000000 1 +000023: 0.000000000000000 0.000000000000000 0.000000000000000 1.000000000000000 0.000000000000000 0.000000000000000 1 +000024: 0.000270000000000 0.000000000000000 0.000000000000000 0.999710000000000 0.000000000000000 0.000020000000000 1 +000025: 0.000530000000000 0.000000000000000 0.000280000000000 0.999120000000000 0.000000000000000 0.000070000000000 1 +000026: 0.010400000000000 0.000120000000000 0.000000000000000 0.988120000000000 0.001200000000000 0.000160000000000 1 +000027: 0.000000000000000 0.000000000000000 0.000000000000000 0.999980000000000 0.000020000000000 0.000000000000000 1 +000028: 0.000440000000000 0.000000000000000 0.000000000000000 0.999500000000000 0.000000000000000 0.000060000000000 1 +000029: 0.007380000000000 0.005440000000000 0.006930000000000 0.969200000000000 0.005970000000000 0.005080000000000 1 +000030: 0.105780000000000 0.098830000000000 0.081380000000000 0.553930000000000 0.088180000000000 0.071900000000000 1 +000031: 0.066570000000000 0.004130000000000 0.004700000000000 0.913840000000000 0.002620000000000 0.008140000000000 1 +000032: 0.000070000000000 0.000310000000000 0.000150000000000 0.999470000000000 0.000000000000000 0.000000000000000 1 +000033: 0.065990000000000 0.001010000000000 0.003590000000000 0.922130000000000 0.002320000000000 0.004960000000000 1 +000034: 0.062380000000000 0.000150000000000 0.000620000000000 0.934660000000000 0.000300000000000 0.001890000000000 1 +000035: 0.028950000000000 0.006510000000000 0.005670000000000 0.950930000000000 0.004170000000000 0.003770000000000 1 +000036: 0.002270000000000 0.003380000000000 0.002630000000000 0.988820000000000 0.001860000000000 0.001040000000000 1 +000037: 0.000420000000000 0.000000000000000 0.000000000000000 0.999580000000000 0.000000000000000 0.000000000000000 1 +000038: 0.001240000000000 0.001400000000000 0.001010000000000 0.993130000000000 0.000790000000000 0.002430000000000 1 +000039: 0.001210000000000 0.001960000000000 0.001100000000000 0.994490000000000 0.000600000000000 0.000640000000000 1 +000040: 0.000030000000000 0.000000000000000 0.000000000000000 0.999780000000000 0.000060000000000 0.000130000000000 1 +000041: 0.001620000000000 0.000100000000000 0.000360000000000 0.997390000000000 0.000300000000000 0.000230000000000 1 +000042: 0.057660000000000 0.000000000000000 0.000000000000000 0.942250000000000 0.000090000000000 0.000000000000000 1 +000043: 0.000090000000000 0.000000000000000 0.000000000000000 0.999910000000000 0.000000000000000 0.000000000000000 1 +000044: 0.001580000000000 0.002370000000000 0.001540000000000 0.991830000000000 0.001040000000000 0.001640000000000 1 +000045: 0.032780000000000 0.039400000000000 0.034440000000000 0.831120000000000 0.028230000000000 0.034030000000000 1 +000046: 0.000000000000000 0.000000000000000 0.000000000000000 0.999940000000000 0.000000000000000 0.000060000000000 1 +000047: 0.001140000000000 0.002980000000000 0.000090000000000 0.993390000000000 0.001520000000000 0.000880000000000 1 +000048: 0.013740000000000 0.007320000000000 0.007260000000000 0.952660000000000 0.010570000000000 0.008450000000000 1 +000049: 0.097550000000000 0.046500000000000 0.026410000000000 0.761120000000000 0.033390000000000 0.035030000000000 1 +000050: 0.002720000000000 0.003960000000000 0.002100000000000 0.986830000000000 0.002320000000000 0.002070000000000 1 +000051: 0.103550000000000 0.088850000000000 0.102330000000000 0.487840000000000 0.101600000000000 0.115830000000000 1 +000052: 0.008090000000000 0.008000000000000 0.006980000000000 0.953190000000000 0.009350000000000 0.014390000000000 1 +000053: 0.001510000000000 0.000000000000000 0.000000000000000 0.998490000000000 0.000000000000000 0.000000000000000 1 +000054: 0.001310000000000 0.002110000000000 0.001110000000000 0.991660000000000 0.002040000000000 0.001770000000000 1 +000055: 0.001210000000000 0.000000000000000 0.000000000000000 0.997160000000000 0.000400000000000 0.001230000000000 1 +000056: 0.000210000000000 0.000410000000000 0.000250000000000 0.998750000000000 0.000120000000000 0.000260000000000 1 +000057: 0.003250000000000 0.003140000000000 0.002310000000000 0.983170000000000 0.005110000000000 0.003020000000000 1 +000058: 0.000050000000000 0.000240000000000 0.000140000000000 0.999300000000000 0.000000000000000 0.000270000000000 1 +000059: 0.083400000000000 0.074350000000000 0.056740000000000 0.613610000000000 0.074210000000000 0.097690000000000 1 +000060: 0.088630000000000 0.036150000000000 0.017810000000000 0.803480000000000 0.023760000000000 0.030170000000000 1 +000061: 0.000160000000000 0.000390000000000 0.000010000000000 0.998840000000000 0.000550000000000 0.000050000000000 1 +000062: 0.004110000000000 0.002280000000000 0.001640000000000 0.988280000000000 0.002040000000000 0.001650000000000 1 +000063: 0.000670000000000 0.003100000000000 0.000260000000000 0.993740000000000 0.001080000000000 0.001150000000000 1 +000064: 0.116030000000000 0.132430000000000 0.092740000000000 0.397860000000000 0.121240000000000 0.139700000000000 1 +000065: 0.006460000000000 0.003270000000000 0.006430000000000 0.972530000000000 0.006690000000000 0.004620000000000 1 +000066: 0.004350000000000 0.001150000000000 0.004360000000000 0.985350000000000 0.003910000000000 0.000880000000000 1 +000067: 0.016670000000000 0.000840000000000 0.000880000000000 0.979280000000000 0.000750000000000 0.001580000000000 1 +000068: 0.001000000000000 0.000730000000000 0.000790000000000 0.996870000000000 0.000180000000000 0.000430000000000 1 +000069: 0.013060000000000 0.012780000000000 0.008560000000000 0.944280000000000 0.009990000000000 0.011330000000000 1 +000070: 0.001130000000000 0.002290000000000 0.000870000000000 0.992280000000000 0.001830000000000 0.001600000000000 1 +000071: 0.000240000000000 0.000270000000000 0.000040000000000 0.999420000000000 0.000030000000000 0.000000000000000 1 +000072: 0.003460000000000 0.001160000000000 0.001470000000000 0.987190000000000 0.002200000000000 0.004520000000000 1 +000073: 0.065030000000000 0.001140000000000 0.000870000000000 0.929400000000000 0.001470000000000 0.002090000000000 1 +000074: 0.004400000000000 0.001020000000000 0.001050000000000 0.989180000000000 0.001600000000000 0.002750000000000 1 +000075: 0.006090000000000 0.003330000000000 0.002650000000000 0.980580000000000 0.003710000000000 0.003640000000000 1 + + + +Estimated Allele Frequencies +Cluster 01 +Locus 001 +Allele 092 0.101293892240797 +Allele 094 0.110099376518517 +Allele 096 0.098284961554805 +Allele 098 0.099642880893633 +Allele 100 0.104056850426311 +Allele 102 0.095070492157553 +Allele 104 0.114310444806362 +Allele 106 0.101171410981303 +Allele 108 0.084513279765839 +Allele 110 0.091556410654879 + +Locus 002 +Allele 094 0.069378333967792 +Allele 096 0.068770555347840 +Allele 098 0.073972844857622 +Allele 100 0.073846148034578 +Allele 102 0.074298915308570 +Allele 104 0.091935232626441 +Allele 106 0.093180349173696 +Allele 108 0.065086788126027 +Allele 110 0.070070422861472 +Allele 112 0.067613448419571 +Allele 114 0.061954583195588 +Allele 124 0.065461756775252 +Allele 126 0.062695540323868 +Allele 149 0.061735080981683 + +Locus 003 +Allele 118 0.045060524027356 +Allele 122 0.045724961513592 +Allele 124 0.059813243506141 +Allele 126 0.072277824450595 +Allele 128 0.046015542722887 +Allele 130 0.046598154730426 +Allele 132 0.049173736443527 +Allele 137 0.046214812654283 +Allele 202 0.045955911363144 +Allele 204 0.044734131660346 +Allele 206 0.044750850929545 +Allele 208 0.062345740861634 +Allele 210 0.045539361838709 +Allele 212 0.052019607594170 +Allele 214 0.056124472329104 +Allele 216 0.044961499417467 +Allele 218 0.045029790109744 +Allele 220 0.045568691735578 +Allele 224 0.049844297588004 +Allele 226 0.052246844523748 + +Locus 004 +Allele 124 0.039731400225651 +Allele 126 0.043368174994230 +Allele 127 0.043407541458255 +Allele 128 0.042847512348101 +Allele 130 0.040342168632732 +Allele 132 0.045206168275583 +Allele 134 0.039663213708084 +Allele 135 0.058562147860278 +Allele 137 0.046147621550733 +Allele 151 0.042214497719062 +Allele 208 0.043323459350719 +Allele 210 0.040561435872259 +Allele 212 0.040935587191811 +Allele 214 0.039513081162398 +Allele 216 0.048775369871654 +Allele 218 0.043026826297639 +Allele 220 0.040958307385856 +Allele 222 0.048930757325144 +Allele 224 0.043766643194192 +Allele 226 0.043385210336067 +Allele 228 0.039721910813220 +Allele 233 0.045844175690623 +Allele 238 0.039766788735708 + +Locus 005 +Allele 121 0.056477669175002 +Allele 123 0.062120152116939 +Allele 125 0.054841880579140 +Allele 127 0.051180572773175 +Allele 129 0.055166423743194 +Allele 130 0.049716685789293 +Allele 131 0.055457589180139 +Allele 133 0.051570937160723 +Allele 135 0.055118372336902 +Allele 136 0.051760018983250 +Allele 137 0.053490053850155 +Allele 138 0.064055087484232 +Allele 139 0.057328303832416 +Allele 141 0.051636360443124 +Allele 145 0.059912670566942 +Allele 146 0.059204857284636 +Allele 148 0.059835107343689 +Allele 150 0.051127257357045 + +Locus 006 +Allele 121 0.044666744499431 +Allele 123 0.047347585793773 +Allele 125 0.042840921603633 +Allele 129 0.041247994585465 +Allele 131 0.049679246448409 +Allele 133 0.049479655552479 +Allele 135 0.044404323395909 +Allele 136 0.041480524604953 +Allele 137 0.052665763546646 +Allele 138 0.043845531121939 +Allele 139 0.045035527703377 +Allele 141 0.041846664321474 +Allele 143 0.041105363056107 +Allele 145 0.045188694761397 +Allele 146 0.044296612716185 +Allele 147 0.045475174286624 +Allele 148 0.047414085916382 +Allele 150 0.046345975198830 +Allele 151 0.041459126421221 +Allele 152 0.061392660941727 +Allele 156 0.041468222168828 +Allele 161 0.041313601355209 + +Locus 007 +Allele 093 0.046918091842463 +Allele 095 0.044440115485599 +Allele 096 0.041837013705844 +Allele 097 0.045339060549173 +Allele 099 0.047525461167503 +Allele 100 0.047464462799846 +Allele 101 0.049446884516594 +Allele 103 0.053587249075574 +Allele 105 0.043170653925482 +Allele 107 0.041550743327993 +Allele 109 0.045272758335070 +Allele 110 0.042371285122672 +Allele 125 0.041522496588965 +Allele 161 0.041583171685687 +Allele 165 0.042222395619187 +Allele 167 0.047728343885057 +Allele 169 0.046285577719720 +Allele 171 0.056052855535849 +Allele 173 0.050576061459927 +Allele 175 0.041713460502975 +Allele 177 0.041396795810920 +Allele 181 0.041995061337900 + +Locus 008 +Allele 095 0.038713825881818 +Allele 097 0.039970485168862 +Allele 099 0.038330027839045 +Allele 100 0.041721870427205 +Allele 101 0.050380766394037 +Allele 103 0.054616542191546 +Allele 105 0.038552021304980 +Allele 107 0.039005871746502 +Allele 109 0.043017830670945 +Allele 110 0.038951364115979 +Allele 113 0.042038174009549 +Allele 121 0.041348401498033 +Allele 123 0.038720768466387 +Allele 131 0.038216397005479 +Allele 167 0.038297751844596 +Allele 169 0.041273663744395 +Allele 171 0.048697571821015 +Allele 173 0.043832960483363 +Allele 175 0.047320401592713 +Allele 177 0.039435114307684 +Allele 179 0.038225471767356 +Allele 181 0.040725004820174 +Allele 183 0.040025084156943 +Allele 185 0.038582628741392 + +Locus 009 +Allele 108 0.034060441344885 +Allele 115 0.031691689753314 +Allele 121 0.032643182260743 +Allele 123 0.034147113533147 +Allele 125 0.035736829434561 +Allele 127 0.032063293364102 +Allele 129 0.037003654473037 +Allele 131 0.032187165995805 +Allele 133 0.041159152493777 +Allele 135 0.035155141362278 +Allele 137 0.032040606548041 +Allele 139 0.033731730723729 +Allele 145 0.032185435825844 +Allele 147 0.037108338413628 +Allele 149 0.031801242954895 +Allele 152 0.034534839670838 +Allele 218 0.032812335507906 +Allele 220 0.036151251384740 +Allele 222 0.035955246736392 +Allele 224 0.038901658835987 +Allele 226 0.034913095602189 +Allele 228 0.032566449183964 +Allele 230 0.031867656251793 +Allele 232 0.040355693789805 +Allele 234 0.038119868284624 +Allele 236 0.031855942586391 +Allele 238 0.035553419187294 +Allele 240 0.031807224891674 +Allele 250 0.031890299604616 + +Locus 010 +Allele 123 0.026485421047616 +Allele 125 0.026148243739264 +Allele 127 0.026414436020867 +Allele 129 0.028361787642854 +Allele 131 0.028501880202900 +Allele 133 0.031024675397810 +Allele 135 0.031375028741332 +Allele 137 0.028660196871708 +Allele 139 0.027002854934796 +Allele 141 0.027337512518119 +Allele 143 0.026552891531671 +Allele 145 0.025899371025970 +Allele 147 0.030676108461847 +Allele 149 0.028820324131291 +Allele 152 0.026005548518400 +Allele 155 0.026782871764017 +Allele 157 0.028470452946747 +Allele 220 0.027008928144431 +Allele 222 0.028861725314430 +Allele 224 0.026046492857997 +Allele 226 0.029733099181117 +Allele 228 0.026855063688011 +Allele 230 0.029452679821914 +Allele 232 0.026311399988408 +Allele 234 0.029226571315275 +Allele 236 0.032836619875686 +Allele 238 0.028301999524497 +Allele 240 0.028468901831310 +Allele 242 0.026241476671086 +Allele 244 0.026945092102789 +Allele 246 0.026189042039215 +Allele 248 0.025873464489159 +Allele 250 0.025869386641543 +Allele 252 0.026034277431228 +Allele 254 0.026910672739298 +Allele 256 0.028313500845398 + + +Cluster 02 +Locus 001 +Allele 092 0.103009241392329 +Allele 094 0.102455696361900 +Allele 096 0.093260955414671 +Allele 098 0.097368252926304 +Allele 100 0.110364353027604 +Allele 102 0.094591270669299 +Allele 104 0.121296111067372 +Allele 106 0.098348331316444 +Allele 108 0.087664191304251 +Allele 110 0.091641596519825 + +Locus 002 +Allele 094 0.069267734392679 +Allele 096 0.066924408034281 +Allele 098 0.073405695682943 +Allele 100 0.076989872111086 +Allele 102 0.072507902197897 +Allele 104 0.093436220489536 +Allele 106 0.084571479889197 +Allele 108 0.065042933565704 +Allele 110 0.067487358708330 +Allele 112 0.070131942337046 +Allele 114 0.064395634678469 +Allele 124 0.067000213607276 +Allele 126 0.064526568591402 +Allele 149 0.064312035714151 + +Locus 003 +Allele 118 0.046381012979359 +Allele 122 0.046603574505760 +Allele 124 0.054438193456552 +Allele 126 0.070384576511629 +Allele 128 0.046740812169219 +Allele 130 0.048315470918904 +Allele 132 0.047409734394772 +Allele 137 0.047421288849951 +Allele 202 0.047354574229614 +Allele 204 0.046302800542105 +Allele 206 0.046454832740305 +Allele 208 0.061365127285508 +Allele 210 0.046512099457698 +Allele 212 0.048121207068974 +Allele 214 0.053781528107216 +Allele 216 0.046395432234467 +Allele 218 0.046843228998628 +Allele 220 0.046523020904149 +Allele 224 0.047843076245948 +Allele 226 0.054808408399241 + +Locus 004 +Allele 124 0.040746995210408 +Allele 126 0.043201193039500 +Allele 127 0.045404010126243 +Allele 128 0.042278467530754 +Allele 130 0.041028306751785 +Allele 132 0.043096590362602 +Allele 134 0.040695778992607 +Allele 135 0.054397839153351 +Allele 137 0.046067646914983 +Allele 151 0.043278519102176 +Allele 208 0.044259211118906 +Allele 210 0.042193155246709 +Allele 212 0.041161920753216 +Allele 214 0.040772066278582 +Allele 216 0.044050614059852 +Allele 218 0.044212122750493 +Allele 220 0.041498055317570 +Allele 222 0.048758192158964 +Allele 224 0.041082921881313 +Allele 226 0.042173447346092 +Allele 228 0.040678177139308 +Allele 233 0.048175740204752 +Allele 238 0.040789028559832 + +Locus 005 +Allele 121 0.054957095536834 +Allele 123 0.062617933632496 +Allele 125 0.052134616056245 +Allele 127 0.051484223057285 +Allele 129 0.057455023400681 +Allele 130 0.051481197749743 +Allele 131 0.052919586813028 +Allele 133 0.053649298349339 +Allele 135 0.056418439430049 +Allele 136 0.052718325629198 +Allele 137 0.054804959699443 +Allele 138 0.062466577628561 +Allele 139 0.058658152400878 +Allele 141 0.051819833102712 +Allele 145 0.061139496209295 +Allele 146 0.055048073900088 +Allele 148 0.059003181771311 +Allele 150 0.051223985632816 + +Locus 006 +Allele 121 0.043771120756529 +Allele 123 0.045901603104490 +Allele 125 0.043370641411281 +Allele 129 0.042669739823219 +Allele 131 0.043230432935898 +Allele 133 0.051499839778411 +Allele 135 0.045026031821856 +Allele 136 0.042586674048624 +Allele 137 0.054032398820179 +Allele 138 0.044126934689425 +Allele 139 0.046713645911296 +Allele 141 0.043075605064753 +Allele 143 0.042553743286631 +Allele 145 0.045494202829449 +Allele 146 0.042721580400985 +Allele 147 0.047393536121361 +Allele 148 0.046124358277238 +Allele 150 0.044343743187770 +Allele 151 0.042719940889636 +Allele 152 0.057329053119288 +Allele 156 0.042576385473460 +Allele 161 0.042738788248220 + +Locus 007 +Allele 093 0.047013860482701 +Allele 095 0.045282879666356 +Allele 096 0.043040762736708 +Allele 097 0.043677608748480 +Allele 099 0.046223407877325 +Allele 100 0.043100520279563 +Allele 101 0.050980365811200 +Allele 103 0.053984843460779 +Allele 105 0.042940557908420 +Allele 107 0.043162762619643 +Allele 109 0.046656155076259 +Allele 110 0.043197353630014 +Allele 125 0.042978491525771 +Allele 161 0.042790492257346 +Allele 165 0.042799418058103 +Allele 167 0.046666499349999 +Allele 169 0.046571044636950 +Allele 171 0.051648275230332 +Allele 173 0.048535723356038 +Allele 175 0.042964859405340 +Allele 177 0.042842477583918 +Allele 181 0.042941640298756 + +Locus 008 +Allele 095 0.039236820653248 +Allele 097 0.041459331888864 +Allele 099 0.039326419237449 +Allele 100 0.039948060900159 +Allele 101 0.047384035301034 +Allele 103 0.052126291254052 +Allele 105 0.039555049294669 +Allele 107 0.040030631118511 +Allele 109 0.043055700026115 +Allele 110 0.039729442252136 +Allele 113 0.042641241487596 +Allele 121 0.040653049866920 +Allele 123 0.039651470618521 +Allele 131 0.039380372257682 +Allele 167 0.039481723705068 +Allele 169 0.040751222414144 +Allele 171 0.046939916325202 +Allele 173 0.044530621387907 +Allele 175 0.044484464120644 +Allele 177 0.040024661109584 +Allele 179 0.039418065597196 +Allele 181 0.040769539741774 +Allele 183 0.039726632972872 +Allele 185 0.039695236468650 + +Locus 009 +Allele 108 0.034974280028153 +Allele 115 0.032701926176262 +Allele 121 0.033909323496420 +Allele 123 0.034215457203577 +Allele 125 0.036122081423317 +Allele 127 0.033048930042549 +Allele 129 0.034167702010192 +Allele 131 0.033092859480245 +Allele 133 0.034543188476056 +Allele 135 0.036407989884892 +Allele 137 0.032788838614060 +Allele 139 0.033769199576148 +Allele 145 0.032664631068223 +Allele 147 0.038550576388884 +Allele 149 0.032582728575161 +Allele 152 0.035380218573978 +Allele 218 0.032613723485330 +Allele 220 0.033701842615736 +Allele 222 0.035838768582915 +Allele 224 0.035501402552167 +Allele 226 0.035385828627100 +Allele 228 0.032821131115369 +Allele 230 0.032821587014279 +Allele 232 0.042050591203432 +Allele 234 0.035629265449931 +Allele 236 0.032766961608344 +Allele 238 0.036622284643429 +Allele 240 0.032701215540931 +Allele 250 0.032625466542921 + +Locus 010 +Allele 123 0.027439474390191 +Allele 125 0.026837036260581 +Allele 127 0.026928134799750 +Allele 129 0.028491687941235 +Allele 131 0.029085552750433 +Allele 133 0.028694234997283 +Allele 135 0.026865348967842 +Allele 137 0.027892479761999 +Allele 139 0.027475251051398 +Allele 141 0.027113055304456 +Allele 143 0.026578697207640 +Allele 145 0.026424872957031 +Allele 147 0.031744708877793 +Allele 149 0.029872198839033 +Allele 152 0.026520527628868 +Allele 155 0.026548470244379 +Allele 157 0.028575837588594 +Allele 220 0.026622331651896 +Allele 222 0.029837768815499 +Allele 224 0.026786920418628 +Allele 226 0.029347937805222 +Allele 228 0.026641625518254 +Allele 230 0.027488185161413 +Allele 232 0.026800871005247 +Allele 234 0.028448925085503 +Allele 236 0.032829070593782 +Allele 238 0.028680318660564 +Allele 240 0.027471221752718 +Allele 242 0.026864618312234 +Allele 244 0.026895586013820 +Allele 246 0.026765653093373 +Allele 248 0.026620210696330 +Allele 250 0.026598371073050 +Allele 252 0.026727757111751 +Allele 254 0.026558535164976 +Allele 256 0.028926522497235 + + +Cluster 03 +Locus 001 +Allele 092 0.099798128474913 +Allele 094 0.100356703059607 +Allele 096 0.093185619303486 +Allele 098 0.100258064033072 +Allele 100 0.110800553697021 +Allele 102 0.096566801720284 +Allele 104 0.118573484415405 +Allele 106 0.098350558553769 +Allele 108 0.089943249937386 +Allele 110 0.092166836805060 + +Locus 002 +Allele 094 0.068941019089502 +Allele 096 0.067005255289859 +Allele 098 0.075090594752170 +Allele 100 0.077253399675373 +Allele 102 0.071222790953198 +Allele 104 0.090066391087082 +Allele 106 0.081505855154045 +Allele 108 0.066492578308465 +Allele 110 0.067824780778449 +Allele 112 0.071273933620576 +Allele 114 0.065577355174443 +Allele 124 0.066754912088454 +Allele 126 0.065599989425641 +Allele 149 0.065391144602743 + +Locus 003 +Allele 118 0.046728828252204 +Allele 122 0.046840171967900 +Allele 124 0.052813024149104 +Allele 126 0.068407372943089 +Allele 128 0.047171651462114 +Allele 130 0.048703648510314 +Allele 132 0.047960802001026 +Allele 137 0.047814022363032 +Allele 202 0.048035202963407 +Allele 204 0.046857482533128 +Allele 206 0.046894171442809 +Allele 208 0.058603121218228 +Allele 210 0.047513181343079 +Allele 212 0.048177725236264 +Allele 214 0.052895448410489 +Allele 216 0.046861075772772 +Allele 218 0.047045641380393 +Allele 220 0.046999458725863 +Allele 224 0.048241690903914 +Allele 226 0.055436278420868 + +Locus 004 +Allele 124 0.041047351073493 +Allele 126 0.042599548872098 +Allele 127 0.044292966915544 +Allele 128 0.041931786104068 +Allele 130 0.041434538655693 +Allele 132 0.043015734525563 +Allele 134 0.040722389239066 +Allele 135 0.055233207290142 +Allele 137 0.045315426179524 +Allele 151 0.042957987516753 +Allele 208 0.045212961162110 +Allele 210 0.042092706622146 +Allele 212 0.041953557533888 +Allele 214 0.041114631594361 +Allele 216 0.042995015794455 +Allele 218 0.044232395061240 +Allele 220 0.041916446974560 +Allele 222 0.047144446286306 +Allele 224 0.041435670259675 +Allele 226 0.042318503475153 +Allele 228 0.040939863900885 +Allele 233 0.048815721652742 +Allele 238 0.041277143310535 + +Locus 005 +Allele 121 0.054041825163401 +Allele 123 0.063011834147497 +Allele 125 0.052881983070479 +Allele 127 0.052067231147093 +Allele 129 0.056565697233064 +Allele 130 0.051898437107973 +Allele 131 0.053009581817983 +Allele 133 0.053639372372912 +Allele 135 0.057310909873207 +Allele 136 0.052882756754478 +Allele 137 0.054430856947181 +Allele 138 0.060916981225114 +Allele 139 0.057239515148232 +Allele 141 0.051984550677496 +Allele 145 0.061803980482788 +Allele 146 0.054572776720656 +Allele 148 0.059884256132357 +Allele 150 0.051857453978083 + +Locus 006 +Allele 121 0.043490519683438 +Allele 123 0.045494402382144 +Allele 125 0.043774322442664 +Allele 129 0.043032134938852 +Allele 131 0.043526840527196 +Allele 133 0.051911049040423 +Allele 135 0.044916691213239 +Allele 136 0.043182612832216 +Allele 137 0.052821361254943 +Allele 138 0.043709625206054 +Allele 139 0.046313880162477 +Allele 141 0.043142481978603 +Allele 143 0.042948201142546 +Allele 145 0.045649810553875 +Allele 146 0.043491699374154 +Allele 147 0.046236917729373 +Allele 148 0.045405275608341 +Allele 150 0.044198290661356 +Allele 151 0.043013573198597 +Allele 152 0.057667952689098 +Allele 156 0.042962485025449 +Allele 161 0.043109872354960 + +Locus 007 +Allele 093 0.047586146912114 +Allele 095 0.045569784842188 +Allele 096 0.043013828312196 +Allele 097 0.043868615718112 +Allele 099 0.044897047140475 +Allele 100 0.043703446685739 +Allele 101 0.049076354401875 +Allele 103 0.053763935248313 +Allele 105 0.043346169740890 +Allele 107 0.043590258414646 +Allele 109 0.046528071286633 +Allele 110 0.043703507063038 +Allele 125 0.043207167192880 +Allele 161 0.043058994617383 +Allele 165 0.043498143068828 +Allele 167 0.045368919141046 +Allele 169 0.047002323530007 +Allele 171 0.051622991890998 +Allele 173 0.047448733236300 +Allele 175 0.043232612498828 +Allele 177 0.043464743387242 +Allele 181 0.043448205670267 + +Locus 008 +Allele 095 0.039971163566087 +Allele 097 0.041462374026155 +Allele 099 0.039794116596165 +Allele 100 0.040587599514135 +Allele 101 0.045959479956176 +Allele 103 0.051149996378169 +Allele 105 0.039625547058375 +Allele 107 0.040056356883714 +Allele 109 0.042850634610619 +Allele 110 0.039850993800486 +Allele 113 0.043404511220711 +Allele 121 0.040706941966706 +Allele 123 0.040176611892084 +Allele 131 0.039348766405243 +Allele 167 0.039705826225103 +Allele 169 0.040425390462419 +Allele 171 0.045793892960148 +Allele 173 0.043622506914758 +Allele 175 0.044480545578961 +Allele 177 0.040292024588085 +Allele 179 0.039574500423847 +Allele 181 0.041411687560039 +Allele 183 0.039825619113217 +Allele 185 0.039922912298599 + +Locus 009 +Allele 108 0.034480915735655 +Allele 115 0.032956070542681 +Allele 121 0.033881072998965 +Allele 123 0.033852996644800 +Allele 125 0.035875371594824 +Allele 127 0.033138260870305 +Allele 129 0.034138080338647 +Allele 131 0.033152343796747 +Allele 133 0.034026690439366 +Allele 135 0.035527153868767 +Allele 137 0.033017988466724 +Allele 139 0.034037433110247 +Allele 145 0.033028383408734 +Allele 147 0.039208090746025 +Allele 149 0.033022398837685 +Allele 152 0.035891054770365 +Allele 218 0.032849816788054 +Allele 220 0.033901395818783 +Allele 222 0.036326012123541 +Allele 224 0.035376853922603 +Allele 226 0.035077561954630 +Allele 228 0.033103528045611 +Allele 230 0.033054925945546 +Allele 232 0.041931610727373 +Allele 234 0.034477736476870 +Allele 236 0.032904186491236 +Allele 238 0.035682201360935 +Allele 240 0.033055071107544 +Allele 250 0.033024793066734 + +Locus 010 +Allele 123 0.027780054158348 +Allele 125 0.026981484537279 +Allele 127 0.026948700937564 +Allele 129 0.028259472205942 +Allele 131 0.028730178252580 +Allele 133 0.027915882115184 +Allele 135 0.026865864008182 +Allele 137 0.027567482766758 +Allele 139 0.027436387591109 +Allele 141 0.027060109945360 +Allele 143 0.026852759275491 +Allele 145 0.026721975385137 +Allele 147 0.031975896825853 +Allele 149 0.029002093661114 +Allele 152 0.026932213378445 +Allele 155 0.026805256998538 +Allele 157 0.029297772253021 +Allele 220 0.026720934176272 +Allele 222 0.029068567250146 +Allele 224 0.026698631174228 +Allele 226 0.029646056146383 +Allele 228 0.027041287513871 +Allele 230 0.027690939955056 +Allele 232 0.026779315734198 +Allele 234 0.028411827651086 +Allele 236 0.032428991399981 +Allele 238 0.028463782636937 +Allele 240 0.027093766451279 +Allele 242 0.026978841927107 +Allele 244 0.026860996180709 +Allele 246 0.026948295893438 +Allele 248 0.026650195494798 +Allele 250 0.026777429941809 +Allele 252 0.026847303200393 +Allele 254 0.026904832103850 +Allele 256 0.028854420872557 + + +Cluster 04 +Locus 001 +Allele 092 0.039008702928001 +Allele 094 0.396577419258993 +Allele 096 0.164087887863459 +Allele 098 0.087779960505372 +Allele 100 0.024354816162342 +Allele 102 0.083198971285086 +Allele 104 0.107034455947046 +Allele 106 0.047280245360844 +Allele 108 0.026625435877603 +Allele 110 0.024052104811253 + +Locus 002 +Allele 094 0.108299605091386 +Allele 096 0.076456898665504 +Allele 098 0.151900786586924 +Allele 100 0.065543093265872 +Allele 102 0.106328756173174 +Allele 104 0.193640656608723 +Allele 106 0.123094232679808 +Allele 108 0.064861801077224 +Allele 110 0.036031729086518 +Allele 112 0.022863059575912 +Allele 114 0.013166137292615 +Allele 124 0.011537688525801 +Allele 126 0.013014443667704 +Allele 149 0.013261111702834 + +Locus 003 +Allele 118 0.019014717588218 +Allele 122 0.031350631564717 +Allele 124 0.182326879273340 +Allele 126 0.088257511700234 +Allele 128 0.062811304069588 +Allele 130 0.036585856515447 +Allele 132 0.061474599904992 +Allele 137 0.011621158189165 +Allele 202 0.011635636533346 +Allele 204 0.025291217781385 +Allele 206 0.012630031050377 +Allele 208 0.114980860474306 +Allele 210 0.037622189585502 +Allele 212 0.098304369031980 +Allele 214 0.069255607607025 +Allele 216 0.044392434474383 +Allele 218 0.050376337197933 +Allele 220 0.012340097399533 +Allele 224 0.022952857067918 +Allele 226 0.006775702990612 + +Locus 004 +Allele 124 0.024697390941108 +Allele 126 0.028832078241470 +Allele 127 0.008687663029425 +Allele 128 0.041498610500935 +Allele 130 0.043064086541004 +Allele 132 0.171441575312725 +Allele 134 0.012511389876196 +Allele 135 0.092227528100921 +Allele 137 0.063844436912109 +Allele 151 0.010050803870071 +Allele 208 0.015139082863222 +Allele 210 0.011349969665815 +Allele 212 0.086272340639989 +Allele 214 0.037280906837281 +Allele 216 0.069681970235032 +Allele 218 0.015724357766856 +Allele 220 0.048782672806209 +Allele 222 0.054802481375419 +Allele 224 0.091542227153988 +Allele 226 0.035090830839466 +Allele 228 0.018595155191601 +Allele 233 0.006702671401800 +Allele 238 0.012179769897357 + +Locus 005 +Allele 121 0.057476440570993 +Allele 123 0.052741174333288 +Allele 125 0.038384990821552 +Allele 127 0.012883245066641 +Allele 129 0.029667662514084 +Allele 130 0.027055918550588 +Allele 131 0.126596721508723 +Allele 133 0.073167798219391 +Allele 135 0.056763485312649 +Allele 136 0.121073235745096 +Allele 137 0.024441140776822 +Allele 138 0.092962190080284 +Allele 139 0.096593709505327 +Allele 141 0.026306764338037 +Allele 145 0.033476516409049 +Allele 146 0.070206088977525 +Allele 148 0.047162697594188 +Allele 150 0.013040219675765 + +Locus 006 +Allele 121 0.024631665387728 +Allele 123 0.022774249748775 +Allele 125 0.018756970383203 +Allele 129 0.026487465082132 +Allele 131 0.115481708116248 +Allele 133 0.072450402155845 +Allele 135 0.110210633911227 +Allele 136 0.026265708432602 +Allele 137 0.042709630904211 +Allele 138 0.018178508679613 +Allele 139 0.049925050218270 +Allele 141 0.019480036655755 +Allele 143 0.013159000498786 +Allele 145 0.056725074564909 +Allele 146 0.051494045660819 +Allele 147 0.009228488883779 +Allele 148 0.108528168632527 +Allele 150 0.076618965168560 +Allele 151 0.013198102068942 +Allele 152 0.090736201395753 +Allele 156 0.019815202619903 +Allele 161 0.013144720830412 + +Locus 007 +Allele 093 0.049519497164947 +Allele 095 0.071934916997158 +Allele 096 0.013442184027261 +Allele 097 0.153651239926851 +Allele 099 0.037013253237313 +Allele 100 0.058312637883837 +Allele 101 0.040226751495703 +Allele 103 0.051422355568652 +Allele 105 0.019473547576970 +Allele 107 0.026918646549028 +Allele 109 0.010490160766362 +Allele 110 0.013122238910455 +Allele 125 0.013494922267885 +Allele 161 0.013424471759792 +Allele 165 0.026777986500770 +Allele 167 0.043290722962611 +Allele 169 0.064056054839784 +Allele 171 0.138169777679727 +Allele 173 0.074702912407057 +Allele 175 0.047203621995338 +Allele 177 0.020124004933698 +Allele 181 0.013228094548799 + +Locus 008 +Allele 095 0.013197295259603 +Allele 097 0.051599846080472 +Allele 099 0.026700575599228 +Allele 100 0.038329005682753 +Allele 101 0.117497970973945 +Allele 103 0.087469578430830 +Allele 105 0.039961633083251 +Allele 107 0.079522434384181 +Allele 109 0.016533067844709 +Allele 110 0.019559959801157 +Allele 113 0.016519321116139 +Allele 121 0.018145734661811 +Allele 123 0.019752528264641 +Allele 131 0.013305737993849 +Allele 167 0.013321010336911 +Allele 169 0.024950986585673 +Allele 171 0.092030192701071 +Allele 173 0.088164317236399 +Allele 175 0.046982064192952 +Allele 177 0.079321869010983 +Allele 179 0.013335495271448 +Allele 181 0.031647590859961 +Allele 183 0.025721003578061 +Allele 185 0.026430781049971 + +Locus 009 +Allele 108 0.027460641271670 +Allele 115 0.011878773199817 +Allele 121 0.010942254314656 +Allele 123 0.039957869015981 +Allele 125 0.086256762793061 +Allele 127 0.041429431502942 +Allele 129 0.044918798341310 +Allele 131 0.047437423053781 +Allele 133 0.090623123145264 +Allele 135 0.026202202198888 +Allele 137 0.017816214355394 +Allele 139 0.016532767753023 +Allele 145 0.017593117618610 +Allele 147 0.006459672084561 +Allele 149 0.011870769755657 +Allele 152 0.008874834324676 +Allele 218 0.011423616523418 +Allele 220 0.087214499044325 +Allele 222 0.109513218447585 +Allele 224 0.084945814037313 +Allele 226 0.038694692147834 +Allele 228 0.023390459608982 +Allele 230 0.017821544924710 +Allele 232 0.021291757748538 +Allele 234 0.031920770525053 +Allele 236 0.017808015322894 +Allele 238 0.020133512430261 +Allele 240 0.017711925556501 +Allele 250 0.011875518953292 + +Locus 010 +Allele 123 0.010521462769485 +Allele 125 0.011227663720708 +Allele 127 0.033945452083120 +Allele 129 0.037522608712020 +Allele 131 0.043148557102005 +Allele 133 0.065385151981061 +Allele 135 0.071948605594587 +Allele 137 0.066919311352485 +Allele 139 0.016033412937755 +Allele 141 0.039067279766411 +Allele 143 0.011083904929969 +Allele 145 0.017197002278823 +Allele 147 0.011574720471506 +Allele 149 0.019360711289577 +Allele 152 0.011413983079410 +Allele 155 0.010931995268941 +Allele 157 0.014202251363799 +Allele 220 0.010948548602618 +Allele 222 0.019422944557358 +Allele 224 0.045783071441081 +Allele 226 0.053436403105493 +Allele 228 0.028018348061643 +Allele 230 0.032025098720806 +Allele 232 0.039811640800015 +Allele 234 0.037270051373940 +Allele 236 0.038814047997224 +Allele 238 0.054548170405785 +Allele 240 0.027077487714957 +Allele 242 0.034062056917252 +Allele 244 0.010708456525635 +Allele 246 0.016966858267782 +Allele 248 0.011360830382526 +Allele 250 0.011393238745430 +Allele 252 0.016958966123936 +Allele 254 0.011013971044406 +Allele 256 0.008895734510453 + + +Cluster 05 +Locus 001 +Allele 092 0.102717359286393 +Allele 094 0.102982988980806 +Allele 096 0.093867086777549 +Allele 098 0.099678562579856 +Allele 100 0.106394265139969 +Allele 102 0.096538829920070 +Allele 104 0.115863352376203 +Allele 106 0.099385281131204 +Allele 108 0.090055852191501 +Allele 110 0.092516421616444 + +Locus 002 +Allele 094 0.070127361803102 +Allele 096 0.066719956296663 +Allele 098 0.075378438573951 +Allele 100 0.074307828550308 +Allele 102 0.071510705696493 +Allele 104 0.089115339775909 +Allele 106 0.083781474651823 +Allele 108 0.066142903891083 +Allele 110 0.068101272178478 +Allele 112 0.071118702561030 +Allele 114 0.065662794510588 +Allele 124 0.066781418750420 +Allele 126 0.065662708033478 +Allele 149 0.065589094726670 + +Locus 003 +Allele 118 0.046979666972026 +Allele 122 0.046811268756448 +Allele 124 0.053702393519905 +Allele 126 0.067789169151160 +Allele 128 0.047376341609994 +Allele 130 0.048126785014991 +Allele 132 0.047729999721454 +Allele 137 0.048262219996836 +Allele 202 0.047983411137044 +Allele 204 0.046642500945690 +Allele 206 0.046942503128321 +Allele 208 0.059824275767690 +Allele 210 0.047366338051966 +Allele 212 0.048431321102709 +Allele 214 0.054078317797567 +Allele 216 0.046998447061342 +Allele 218 0.047128349888617 +Allele 220 0.046900124706154 +Allele 224 0.048201541105991 +Allele 226 0.052725024564096 + +Locus 004 +Allele 124 0.041294298310069 +Allele 126 0.042559035614616 +Allele 127 0.045452434898353 +Allele 128 0.042028784605185 +Allele 130 0.041319187327268 +Allele 132 0.043048137553030 +Allele 134 0.041045376976957 +Allele 135 0.052284546373610 +Allele 137 0.045901694968155 +Allele 151 0.043721182703044 +Allele 208 0.044991665042548 +Allele 210 0.042151195188311 +Allele 212 0.041902175038639 +Allele 214 0.041050223502337 +Allele 216 0.043639902374043 +Allele 218 0.044312009183825 +Allele 220 0.042087862098904 +Allele 222 0.048538884844943 +Allele 224 0.041352034854438 +Allele 226 0.042066135693402 +Allele 228 0.041219439722000 +Allele 233 0.046467227737894 +Allele 238 0.041566565388426 + +Locus 005 +Allele 121 0.054429925806592 +Allele 123 0.060330079880693 +Allele 125 0.052736409606045 +Allele 127 0.052041207220580 +Allele 129 0.057258725295801 +Allele 130 0.052453583455084 +Allele 131 0.053190481998351 +Allele 133 0.053868831500643 +Allele 135 0.057414549795687 +Allele 136 0.053523661210285 +Allele 137 0.055642621838125 +Allele 138 0.061202901545818 +Allele 139 0.058763268172405 +Allele 141 0.052192002549735 +Allele 145 0.057981808369818 +Allele 146 0.054717258541474 +Allele 148 0.060199572959925 +Allele 150 0.052053110252938 + +Locus 006 +Allele 121 0.043914041863007 +Allele 123 0.045819778123688 +Allele 125 0.043614676989424 +Allele 129 0.042780373000598 +Allele 131 0.043296608753650 +Allele 133 0.049351025901745 +Allele 135 0.044666455078973 +Allele 136 0.043092117643200 +Allele 137 0.054318463386673 +Allele 138 0.044344474121141 +Allele 139 0.046905145670943 +Allele 141 0.043299187482267 +Allele 143 0.042911070282710 +Allele 145 0.045387411699999 +Allele 146 0.043270433013964 +Allele 147 0.047557879834226 +Allele 148 0.046181771553494 +Allele 150 0.044373885827575 +Allele 151 0.043059743430320 +Allele 152 0.055987634280804 +Allele 156 0.042966848393075 +Allele 161 0.042900973668522 + +Locus 007 +Allele 093 0.047792232070245 +Allele 095 0.045143790989999 +Allele 096 0.042916388333774 +Allele 097 0.044160702535660 +Allele 099 0.045259264285311 +Allele 100 0.043751132378162 +Allele 101 0.051024917762108 +Allele 103 0.051729847064946 +Allele 105 0.043283695489463 +Allele 107 0.043261199748508 +Allele 109 0.046620086236607 +Allele 110 0.043491593406743 +Allele 125 0.043111732207901 +Allele 161 0.043009973777139 +Allele 165 0.042868512460397 +Allele 167 0.045633600256156 +Allele 169 0.046895659031526 +Allele 171 0.052101327726989 +Allele 173 0.048241963606168 +Allele 175 0.043317915798511 +Allele 177 0.042877975690810 +Allele 181 0.043506489142878 + +Locus 008 +Allele 095 0.039652148277244 +Allele 097 0.040991735403891 +Allele 099 0.039641167683106 +Allele 100 0.040261023168451 +Allele 101 0.047402935281536 +Allele 103 0.048991872514952 +Allele 105 0.039628429185696 +Allele 107 0.039899159344726 +Allele 109 0.043020747687029 +Allele 110 0.039979952151303 +Allele 113 0.043298568928050 +Allele 121 0.040623925537927 +Allele 123 0.040035148559463 +Allele 131 0.039503303167296 +Allele 167 0.039605720819482 +Allele 169 0.040820103892140 +Allele 171 0.046713940187592 +Allele 173 0.044766176125887 +Allele 175 0.044621176748126 +Allele 177 0.040550579709442 +Allele 179 0.039479420480478 +Allele 181 0.040769840338940 +Allele 183 0.039961071634996 +Allele 185 0.039781853172249 + +Locus 009 +Allele 108 0.035078154970876 +Allele 115 0.032990669274720 +Allele 121 0.033806741400137 +Allele 123 0.034296483181974 +Allele 125 0.036053492233916 +Allele 127 0.033099525589545 +Allele 129 0.034070002819773 +Allele 131 0.033381355466059 +Allele 133 0.034122144033859 +Allele 135 0.036356992791290 +Allele 137 0.033096761474444 +Allele 139 0.033867896597382 +Allele 145 0.033048072870068 +Allele 147 0.037301927981441 +Allele 149 0.032892560175408 +Allele 152 0.035825945481765 +Allele 218 0.032805883106255 +Allele 220 0.033812893597331 +Allele 222 0.036594412807368 +Allele 224 0.035370671359480 +Allele 226 0.035693056991175 +Allele 228 0.033085467963088 +Allele 230 0.032808064292276 +Allele 232 0.040040051856097 +Allele 234 0.035030164081893 +Allele 236 0.032828006343823 +Allele 238 0.036620973721452 +Allele 240 0.033084609768593 +Allele 250 0.032937017768511 + +Locus 010 +Allele 123 0.027446981780249 +Allele 125 0.026844578791520 +Allele 127 0.027096695357337 +Allele 129 0.028667912230940 +Allele 131 0.028971791874382 +Allele 133 0.028306923375901 +Allele 135 0.026774387008910 +Allele 137 0.027866079802362 +Allele 139 0.027566342266557 +Allele 141 0.027406606109010 +Allele 143 0.026958078748042 +Allele 145 0.026636405628275 +Allele 147 0.030318809079812 +Allele 149 0.029752928607172 +Allele 152 0.026586138122232 +Allele 155 0.026755089763759 +Allele 157 0.029199749173725 +Allele 220 0.026773428619906 +Allele 222 0.029711787027782 +Allele 224 0.026686908879243 +Allele 226 0.029528089747655 +Allele 228 0.026922242085974 +Allele 230 0.027749642200450 +Allele 232 0.026898627401475 +Allele 234 0.028407357035556 +Allele 236 0.031096402915626 +Allele 238 0.028790710028860 +Allele 240 0.027317213696694 +Allele 242 0.026948995843110 +Allele 244 0.027086891312983 +Allele 246 0.026971901048126 +Allele 248 0.026827462961376 +Allele 250 0.026663611782180 +Allele 252 0.026817598954498 +Allele 254 0.026679441180319 +Allele 256 0.028966189558003 + + +Cluster 06 +Locus 001 +Allele 092 0.105012465655240 +Allele 094 0.101099930129454 +Allele 096 0.092122537277379 +Allele 098 0.099164024987732 +Allele 100 0.107946996723924 +Allele 102 0.095443338426042 +Allele 104 0.123369574119294 +Allele 106 0.096472299452447 +Allele 108 0.088151327700977 +Allele 110 0.091217505527518 + +Locus 002 +Allele 094 0.070497292302619 +Allele 096 0.066610118311581 +Allele 098 0.074960500839346 +Allele 100 0.077186216720502 +Allele 102 0.070067347984637 +Allele 104 0.094633418391494 +Allele 106 0.083389259529207 +Allele 108 0.065586531193437 +Allele 110 0.067643455695083 +Allele 112 0.070462367222186 +Allele 114 0.064056899628352 +Allele 124 0.066332476869825 +Allele 126 0.064267215247809 +Allele 149 0.064306900063921 + +Locus 003 +Allele 118 0.046398654070145 +Allele 122 0.046399357332741 +Allele 124 0.052646645786175 +Allele 126 0.073032119210106 +Allele 128 0.046559461551184 +Allele 130 0.048170574701559 +Allele 132 0.047168936223444 +Allele 137 0.047309216697853 +Allele 202 0.047477568984547 +Allele 204 0.046238589941191 +Allele 206 0.046392114695998 +Allele 208 0.061459252383581 +Allele 210 0.046592796330257 +Allele 212 0.047630464874229 +Allele 214 0.053864294819396 +Allele 216 0.046176348749770 +Allele 218 0.046974148333590 +Allele 220 0.046463373758602 +Allele 224 0.047901726557477 +Allele 226 0.055144354998156 + +Locus 004 +Allele 124 0.040771531790442 +Allele 126 0.042297395730142 +Allele 127 0.045356704368662 +Allele 128 0.042162279737118 +Allele 130 0.040579086133959 +Allele 132 0.042822753089056 +Allele 134 0.040618016375999 +Allele 135 0.055502805241135 +Allele 137 0.044827443651884 +Allele 151 0.044179341183888 +Allele 208 0.045066982080161 +Allele 210 0.041918417317513 +Allele 212 0.041289361304154 +Allele 214 0.040929868269749 +Allele 216 0.043409508776908 +Allele 218 0.043169988701353 +Allele 220 0.041504427573950 +Allele 222 0.050335414747223 +Allele 224 0.041453702118471 +Allele 226 0.041637541130065 +Allele 228 0.040744377998543 +Allele 233 0.048688223752038 +Allele 238 0.040734828927586 + +Locus 005 +Allele 121 0.054376255443879 +Allele 123 0.062768920256202 +Allele 125 0.052285781809786 +Allele 127 0.051697048257281 +Allele 129 0.057669573036991 +Allele 130 0.051263552428139 +Allele 131 0.052376931684466 +Allele 133 0.053192589427508 +Allele 135 0.057523622751471 +Allele 136 0.052545474418816 +Allele 137 0.055627618710881 +Allele 138 0.060228051997077 +Allele 139 0.058308532685614 +Allele 141 0.051375215548752 +Allele 145 0.061280238158517 +Allele 146 0.054848549240491 +Allele 148 0.061500429599709 +Allele 150 0.051131614544421 + +Locus 006 +Allele 121 0.043532577694052 +Allele 123 0.045310580557399 +Allele 125 0.043301178219914 +Allele 129 0.042563112507251 +Allele 131 0.043274371043472 +Allele 133 0.051402398717541 +Allele 135 0.044626144674990 +Allele 136 0.042697752513573 +Allele 137 0.055862204953043 +Allele 138 0.043800161861174 +Allele 139 0.045482507413141 +Allele 141 0.042585410256167 +Allele 143 0.042370421287767 +Allele 145 0.044880240013794 +Allele 146 0.042905721417830 +Allele 147 0.047955971427478 +Allele 148 0.046351949509332 +Allele 150 0.043974098113464 +Allele 151 0.042554406148404 +Allele 152 0.059460123488886 +Allele 156 0.042662103246453 +Allele 161 0.042446564934877 + +Locus 007 +Allele 093 0.047939398517531 +Allele 095 0.045045052891221 +Allele 096 0.042609638666613 +Allele 097 0.043819640685540 +Allele 099 0.045186433255045 +Allele 100 0.043131901116232 +Allele 101 0.051994505896901 +Allele 103 0.054212636449181 +Allele 105 0.042977672990498 +Allele 107 0.043070103334800 +Allele 109 0.045712056923006 +Allele 110 0.043103932736858 +Allele 125 0.042936795590159 +Allele 161 0.042846956251760 +Allele 165 0.042791930950333 +Allele 167 0.045544164553366 +Allele 169 0.045860044737287 +Allele 171 0.053819373578542 +Allele 173 0.048549560486468 +Allele 175 0.043119022202314 +Allele 177 0.042865687626385 +Allele 181 0.042863490559957 + +Locus 008 +Allele 095 0.039332510626682 +Allele 097 0.041113826002736 +Allele 099 0.039495578841250 +Allele 100 0.040194147585850 +Allele 101 0.048668807543402 +Allele 103 0.051575833995966 +Allele 105 0.039310787723438 +Allele 107 0.039930509838919 +Allele 109 0.041985654084657 +Allele 110 0.039544031842794 +Allele 113 0.043502272744573 +Allele 121 0.040587616593665 +Allele 123 0.039647139545033 +Allele 131 0.039167542660345 +Allele 167 0.039409893959549 +Allele 169 0.040633053035932 +Allele 171 0.046944132572208 +Allele 173 0.044896691597041 +Allele 175 0.044908739786000 +Allele 177 0.039702183726055 +Allele 179 0.039472468613588 +Allele 181 0.040666912098437 +Allele 183 0.039628114211000 +Allele 185 0.039681550770879 + +Locus 009 +Allele 108 0.035496652697627 +Allele 115 0.032542044842170 +Allele 121 0.033527185047490 +Allele 123 0.034033787903757 +Allele 125 0.035044211366516 +Allele 127 0.032878302641328 +Allele 129 0.033911352527593 +Allele 131 0.032874150829431 +Allele 133 0.034597360732624 +Allele 135 0.036545024300659 +Allele 137 0.032614816873594 +Allele 139 0.033625885880211 +Allele 145 0.032855383662178 +Allele 147 0.039121559933057 +Allele 149 0.032447159316425 +Allele 152 0.036100422752888 +Allele 218 0.032748434216251 +Allele 220 0.033751705248694 +Allele 222 0.036607459197937 +Allele 224 0.035560817007855 +Allele 226 0.036416870419149 +Allele 228 0.032927632751001 +Allele 230 0.032703476111499 +Allele 232 0.041288552352793 +Allele 234 0.034694856408694 +Allele 236 0.032596710587209 +Allele 238 0.036983203793931 +Allele 240 0.032844273119346 +Allele 250 0.032660707478096 + +Locus 010 +Allele 123 0.027241875078471 +Allele 125 0.026642109209514 +Allele 127 0.026958288775845 +Allele 129 0.029111399431393 +Allele 131 0.028300982426124 +Allele 133 0.028281880356942 +Allele 135 0.027072494987091 +Allele 137 0.027521230762956 +Allele 139 0.027421740093047 +Allele 141 0.027072992030462 +Allele 143 0.026537286779637 +Allele 145 0.026696172103513 +Allele 147 0.031691142149593 +Allele 149 0.030220113466390 +Allele 152 0.026480876211310 +Allele 155 0.026724113179379 +Allele 157 0.029462912728901 +Allele 220 0.026468703839670 +Allele 222 0.030083246318057 +Allele 224 0.026449018836789 +Allele 226 0.030084297888745 +Allele 228 0.026703960729553 +Allele 230 0.027732238806624 +Allele 232 0.026552701623371 +Allele 234 0.028192866573279 +Allele 236 0.032779142919847 +Allele 238 0.029102613962294 +Allele 240 0.027475282532030 +Allele 242 0.026836696117141 +Allele 244 0.026838099188336 +Allele 246 0.026774300622299 +Allele 248 0.026623606116061 +Allele 250 0.026479629175185 +Allele 252 0.026606267562721 +Allele 254 0.026429786762533 +Allele 256 0.028349930654899 + + + +Estimated Mixing Proportions +0.023147066666667 +0.012202266666667 +0.010363600000000 +0.931172533333334 +0.010606800000000 +0.012507733333333 + + + diff --git a/inst/files/tess/tess_20.txt b/inst/files/tess/tess_20.txt new file mode 100644 index 0000000..1997852 --- /dev/null +++ b/inst/files/tess/tess_20.txt @@ -0,0 +1,1773 @@ +Estimated Clustering Probabilities for Samples +Sample ***Cluster 01*** ***Cluster 02*** ***Cluster 03*** ***Cluster 04*** ***Cluster 05*** ***Cluster 06*** ***Cluster 07*** +000001: 0.000340000000000 0.000340000000000 0.000020000000000 0.000990000000000 0.000470000000000 0.000380000000000 0.997460000000000 1 +000002: 0.000000000000000 0.000000000000000 0.000000000000000 0.000000000000000 0.004590000000000 0.000000000000000 0.995410000000000 1 +000003: 0.000020000000000 0.000000000000000 0.000000000000000 0.000000000000000 0.000000000000000 0.000000000000000 0.999980000000000 1 +000004: 0.000060000000000 0.000080000000000 0.000550000000000 0.000000000000000 0.010480000000000 0.000060000000000 0.988770000000000 1 +000005: 0.000740000000000 0.000400000000000 0.002880000000000 0.002320000000000 0.001380000000000 0.001150000000000 0.991130000000000 1 +000006: 0.000040000000000 0.000000000000000 0.000000000000000 0.000000000000000 0.000000000000000 0.000000000000000 0.999960000000000 1 +000007: 0.023210000000000 0.030480000000000 0.022560000000000 0.024340000000000 0.037530000000000 0.030630000000000 0.831250000000000 1 +000008: 0.000000000000000 0.000060000000000 0.000000000000000 0.000000000000000 0.006320000000000 0.000000000000000 0.993620000000000 1 +000009: 0.000940000000000 0.001020000000000 0.001560000000000 0.000910000000000 0.003750000000000 0.000980000000000 0.990840000000000 1 +000010: 0.007510000000000 0.002470000000000 0.007160000000000 0.005220000000000 0.018350000000000 0.005750000000000 0.953540000000000 1 +000011: 0.000870000000000 0.000000000000000 0.000690000000000 0.000060000000000 0.016080000000000 0.000000000000000 0.982300000000000 1 +000012: 0.000000000000000 0.000000000000000 0.000000000000000 0.000000000000000 0.000000000000000 0.000000000000000 1.000000000000000 1 +000013: 0.000000000000000 0.000000000000000 0.000000000000000 0.000000000000000 0.000470000000000 0.000000000000000 0.999530000000000 1 +000014: 0.000000000000000 0.000000000000000 0.000060000000000 0.000000000000000 0.000000000000000 0.000000000000000 0.999940000000000 1 +000015: 0.009880000000000 0.006520000000000 0.008260000000000 0.007560000000000 0.009850000000000 0.007200000000000 0.950730000000000 1 +000016: 0.000000000000000 0.000000000000000 0.000000000000000 0.000000000000000 0.000000000000000 0.000000000000000 1.000000000000000 1 +000017: 0.000610000000000 0.002140000000000 0.000580000000000 0.000580000000000 0.003430000000000 0.001600000000000 0.991060000000000 1 +000018: 0.001030000000000 0.000350000000000 0.000430000000000 0.002290000000000 0.001780000000000 0.001910000000000 0.992210000000000 1 +000019: 0.031980000000000 0.026990000000000 0.024850000000000 0.029270000000000 0.035650000000000 0.024820000000000 0.826440000000000 1 +000020: 0.019990000000000 0.018470000000000 0.009160000000000 0.012510000000000 0.027930000000000 0.015760000000000 0.896180000000000 1 +000021: 0.008660000000000 0.005010000000000 0.001850000000000 0.005680000000000 0.018710000000000 0.010760000000000 0.949330000000000 1 +000022: 0.159680000000000 0.162930000000000 0.116010000000000 0.168360000000000 0.117400000000000 0.194610000000000 0.081010000000000 1 +000023: 0.000090000000000 0.000000000000000 0.000000000000000 0.000000000000000 0.000000000000000 0.000000000000000 0.999910000000000 1 +000024: 0.000000000000000 0.000000000000000 0.000000000000000 0.000140000000000 0.000060000000000 0.000000000000000 0.999800000000000 1 +000025: 0.000000000000000 0.000000000000000 0.000000000000000 0.000050000000000 0.000980000000000 0.000050000000000 0.998920000000000 1 +000026: 0.000000000000000 0.000510000000000 0.000520000000000 0.000480000000000 0.002200000000000 0.000040000000000 0.996250000000000 1 +000027: 0.000110000000000 0.000000000000000 0.000000000000000 0.000000000000000 0.000210000000000 0.000070000000000 0.999610000000000 1 +000028: 0.000000000000000 0.000010000000000 0.000000000000000 0.000000000000000 0.000070000000000 0.000010000000000 0.999910000000000 1 +000029: 0.004940000000000 0.004980000000000 0.006100000000000 0.009830000000000 0.004990000000000 0.003280000000000 0.965880000000000 1 +000030: 0.074080000000000 0.082840000000000 0.076780000000000 0.059650000000000 0.085990000000000 0.074790000000000 0.545870000000000 1 +000031: 0.004290000000000 0.004170000000000 0.002830000000000 0.006030000000000 0.026140000000000 0.004110000000000 0.952430000000000 1 +000032: 0.000000000000000 0.000000000000000 0.000030000000000 0.000070000000000 0.000120000000000 0.000150000000000 0.999630000000000 1 +000033: 0.002280000000000 0.002380000000000 0.001910000000000 0.003930000000000 0.023960000000000 0.000720000000000 0.964820000000000 1 +000034: 0.000000000000000 0.000280000000000 0.000160000000000 0.000470000000000 0.022080000000000 0.000250000000000 0.976760000000000 1 +000035: 0.004250000000000 0.005500000000000 0.003240000000000 0.007030000000000 0.013720000000000 0.005950000000000 0.960310000000000 1 +000036: 0.002190000000000 0.001910000000000 0.001810000000000 0.002220000000000 0.003660000000000 0.001280000000000 0.986930000000000 1 +000037: 0.000000000000000 0.000000000000000 0.000000000000000 0.000000000000000 0.000000000000000 0.000000000000000 1.000000000000000 1 +000038: 0.001380000000000 0.000830000000000 0.002820000000000 0.000870000000000 0.002780000000000 0.002750000000000 0.988570000000000 1 +000039: 0.003110000000000 0.000840000000000 0.000960000000000 0.000460000000000 0.001210000000000 0.002360000000000 0.991060000000000 1 +000040: 0.000000000000000 0.000000000000000 0.000000000000000 0.000000000000000 0.000090000000000 0.000000000000000 0.999910000000000 1 +000041: 0.001540000000000 0.001960000000000 0.001740000000000 0.000600000000000 0.000380000000000 0.000660000000000 0.993120000000000 1 +000042: 0.000000000000000 0.000000000000000 0.000000000000000 0.000000000000000 0.018950000000000 0.000000000000000 0.981050000000000 1 +000043: 0.000000000000000 0.000040000000000 0.000010000000000 0.000000000000000 0.000000000000000 0.000000000000000 0.999950000000000 1 +000044: 0.001600000000000 0.002210000000000 0.003030000000000 0.002430000000000 0.002340000000000 0.002840000000000 0.985550000000000 1 +000045: 0.013420000000000 0.037930000000000 0.029230000000000 0.027630000000000 0.025170000000000 0.033850000000000 0.832770000000000 1 +000046: 0.000000000000000 0.000000000000000 0.000000000000000 0.000000000000000 0.000000000000000 0.000000000000000 1.000000000000000 1 +000047: 0.000670000000000 0.000320000000000 0.001200000000000 0.000810000000000 0.000610000000000 0.000220000000000 0.996170000000000 1 +000048: 0.011440000000000 0.008460000000000 0.010140000000000 0.010750000000000 0.013120000000000 0.010160000000000 0.935930000000000 1 +000049: 0.042930000000000 0.050670000000000 0.026110000000000 0.031050000000000 0.051280000000000 0.036720000000000 0.761240000000000 1 +000050: 0.003670000000000 0.000500000000000 0.001480000000000 0.001320000000000 0.003100000000000 0.003960000000000 0.985970000000000 1 +000051: 0.097600000000000 0.098760000000000 0.072780000000000 0.110930000000000 0.088650000000000 0.075010000000000 0.456270000000000 1 +000052: 0.008300000000000 0.010250000000000 0.012470000000000 0.011350000000000 0.007240000000000 0.013650000000000 0.936740000000000 1 +000053: 0.000000000000000 0.000000000000000 0.000000000000000 0.000000000000000 0.000400000000000 0.000000000000000 0.999600000000000 1 +000054: 0.001650000000000 0.000820000000000 0.002920000000000 0.002080000000000 0.000690000000000 0.003870000000000 0.987970000000000 1 +000055: 0.000110000000000 0.000580000000000 0.000000000000000 0.000040000000000 0.000720000000000 0.000150000000000 0.998400000000000 1 +000056: 0.000270000000000 0.000260000000000 0.000310000000000 0.000470000000000 0.000270000000000 0.000250000000000 0.998170000000000 1 +000057: 0.004550000000000 0.001230000000000 0.004550000000000 0.002360000000000 0.001380000000000 0.002340000000000 0.983590000000000 1 +000058: 0.000100000000000 0.000000000000000 0.000000000000000 0.000000000000000 0.000000000000000 0.000000000000000 0.999900000000000 1 +000059: 0.079790000000000 0.065400000000000 0.067600000000000 0.087640000000000 0.068030000000000 0.092150000000000 0.539390000000000 1 +000060: 0.030940000000000 0.030700000000000 0.019900000000000 0.024050000000000 0.050750000000000 0.026850000000000 0.816810000000000 1 +000061: 0.000620000000000 0.000340000000000 0.000380000000000 0.001100000000000 0.000230000000000 0.000200000000000 0.997130000000000 1 +000062: 0.002490000000000 0.004470000000000 0.003410000000000 0.000310000000000 0.003550000000000 0.001720000000000 0.984050000000000 1 +000063: 0.002410000000000 0.000190000000000 0.001660000000000 0.001130000000000 0.000940000000000 0.003110000000000 0.990560000000000 1 +000064: 0.118520000000000 0.100540000000000 0.103670000000000 0.136000000000000 0.096750000000000 0.138170000000000 0.306350000000000 1 +000065: 0.007550000000000 0.009250000000000 0.003530000000000 0.007250000000000 0.003060000000000 0.003530000000000 0.965830000000000 1 +000066: 0.004100000000000 0.009670000000000 0.002450000000000 0.005740000000000 0.000710000000000 0.001120000000000 0.976210000000000 1 +000067: 0.000690000000000 0.000750000000000 0.000060000000000 0.000260000000000 0.002630000000000 0.000190000000000 0.995420000000000 1 +000068: 0.000950000000000 0.000530000000000 0.000920000000000 0.000950000000000 0.000740000000000 0.000850000000000 0.995060000000000 1 +000069: 0.010360000000000 0.016460000000000 0.011680000000000 0.017100000000000 0.008440000000000 0.014930000000000 0.921030000000000 1 +000070: 0.002040000000000 0.001950000000000 0.002990000000000 0.001560000000000 0.001190000000000 0.002010000000000 0.988260000000000 1 +000071: 0.000110000000000 0.000170000000000 0.000400000000000 0.000090000000000 0.000000000000000 0.000240000000000 0.998990000000000 1 +000072: 0.001890000000000 0.003240000000000 0.002080000000000 0.002320000000000 0.003360000000000 0.003230000000000 0.983880000000000 1 +000073: 0.001040000000000 0.001630000000000 0.000460000000000 0.000530000000000 0.022430000000000 0.001430000000000 0.972480000000000 1 +000074: 0.003310000000000 0.000890000000000 0.004760000000000 0.000900000000000 0.001760000000000 0.001530000000000 0.986850000000000 1 +000075: 0.004110000000000 0.003880000000000 0.005010000000000 0.002090000000000 0.001960000000000 0.005860000000000 0.977090000000000 1 + + + +Estimated Allele Frequencies +Cluster 01 +Locus 001 +Allele 092 0.103150970734204 +Allele 094 0.104191951404844 +Allele 096 0.094948788182696 +Allele 098 0.098571654622225 +Allele 100 0.106779627153616 +Allele 102 0.096310288428423 +Allele 104 0.116667148049697 +Allele 106 0.097303079915332 +Allele 108 0.089938830994726 +Allele 110 0.092137660514239 + +Locus 002 +Allele 094 0.070694699578479 +Allele 096 0.067538569747826 +Allele 098 0.075527110829331 +Allele 100 0.075192421193202 +Allele 102 0.071587455357945 +Allele 104 0.089574310510827 +Allele 106 0.081426111452135 +Allele 108 0.066076837637868 +Allele 110 0.067890444323048 +Allele 112 0.070741671262725 +Allele 114 0.065454243103391 +Allele 124 0.067480478856087 +Allele 126 0.065575446523249 +Allele 149 0.065240199623886 + +Locus 003 +Allele 118 0.046696890824320 +Allele 122 0.046675440934295 +Allele 124 0.053654661213755 +Allele 126 0.068450748318712 +Allele 128 0.047488694287339 +Allele 130 0.047758236437255 +Allele 132 0.047919329158591 +Allele 137 0.048192655151278 +Allele 202 0.047991816373874 +Allele 204 0.046913022791705 +Allele 206 0.046657470188064 +Allele 208 0.059601157500721 +Allele 210 0.047417539050388 +Allele 212 0.048917023029091 +Allele 214 0.053583743916815 +Allele 216 0.047076107385298 +Allele 218 0.047173612160173 +Allele 220 0.046782526194036 +Allele 224 0.047845575918953 +Allele 226 0.053203749165342 + +Locus 004 +Allele 124 0.041305258144401 +Allele 126 0.042805964839951 +Allele 127 0.045339958457258 +Allele 128 0.042562598422132 +Allele 130 0.041543017365428 +Allele 132 0.043124231337847 +Allele 134 0.041001314204939 +Allele 135 0.052259210789653 +Allele 137 0.045374643699631 +Allele 151 0.043649513874740 +Allele 208 0.044770594047986 +Allele 210 0.041429337186838 +Allele 212 0.041984627576076 +Allele 214 0.041028656598394 +Allele 216 0.044321690587826 +Allele 218 0.043766655514111 +Allele 220 0.042283738952301 +Allele 222 0.048830262129729 +Allele 224 0.041333538535083 +Allele 226 0.042019482426266 +Allele 228 0.041021611579822 +Allele 233 0.046770666800596 +Allele 238 0.041473426928992 + +Locus 005 +Allele 121 0.055223343219403 +Allele 123 0.060768091012908 +Allele 125 0.052806695631357 +Allele 127 0.052133433966949 +Allele 129 0.057480476532382 +Allele 130 0.051956038226702 +Allele 131 0.053436946190774 +Allele 133 0.053379570288169 +Allele 135 0.056804881288721 +Allele 136 0.053325320542576 +Allele 137 0.055244224584610 +Allele 138 0.060263409449238 +Allele 139 0.058360068456758 +Allele 141 0.052030854545068 +Allele 145 0.059102278924451 +Allele 146 0.055209159914872 +Allele 148 0.060590268980770 +Allele 150 0.051884938244293 + +Locus 006 +Allele 121 0.043934432527730 +Allele 123 0.045645767145286 +Allele 125 0.043795575938823 +Allele 129 0.042985516097100 +Allele 131 0.043830856443096 +Allele 133 0.050360861948407 +Allele 135 0.044376168324945 +Allele 136 0.043080498740039 +Allele 137 0.054124198889611 +Allele 138 0.044164481873115 +Allele 139 0.046135117875510 +Allele 141 0.043424074705623 +Allele 143 0.042891120104069 +Allele 145 0.044739749284042 +Allele 146 0.043117677398719 +Allele 147 0.047205778723669 +Allele 148 0.045996599041600 +Allele 150 0.044770846507811 +Allele 151 0.043047328731343 +Allele 152 0.056771213602010 +Allele 156 0.042828972248926 +Allele 161 0.042773163848527 + +Locus 007 +Allele 093 0.047406500357473 +Allele 095 0.044829870284035 +Allele 096 0.043201259589262 +Allele 097 0.043860585758387 +Allele 099 0.045852912568872 +Allele 100 0.043581797434447 +Allele 101 0.050718479914530 +Allele 103 0.052259553249692 +Allele 105 0.043367296793131 +Allele 107 0.043148086369790 +Allele 109 0.046202309139149 +Allele 110 0.043447253554071 +Allele 125 0.042952784137728 +Allele 161 0.043134526557665 +Allele 165 0.043126311140832 +Allele 167 0.046726100197707 +Allele 169 0.046521374250344 +Allele 171 0.051432942229339 +Allele 173 0.048314526381287 +Allele 175 0.043305212636529 +Allele 177 0.043170047198106 +Allele 181 0.043440270257624 + +Locus 008 +Allele 095 0.039544707585423 +Allele 097 0.040577680747587 +Allele 099 0.039451922286736 +Allele 100 0.040394432092279 +Allele 101 0.047631676524671 +Allele 103 0.050014977217885 +Allele 105 0.039557630834229 +Allele 107 0.040270963210107 +Allele 109 0.042233166606608 +Allele 110 0.040027878082500 +Allele 113 0.043148678520100 +Allele 121 0.040692702829616 +Allele 123 0.039978162399031 +Allele 131 0.039667598675486 +Allele 167 0.039636297237232 +Allele 169 0.040746484041694 +Allele 171 0.046652943762545 +Allele 173 0.044788068188840 +Allele 175 0.044826140548572 +Allele 177 0.040105742805723 +Allele 179 0.039846812641428 +Allele 181 0.040190284474526 +Allele 183 0.040136915096151 +Allele 185 0.039878133591032 + +Locus 009 +Allele 108 0.035088826728903 +Allele 115 0.032991561508263 +Allele 121 0.033233681382928 +Allele 123 0.034356197525182 +Allele 125 0.035706459220876 +Allele 127 0.033171183380147 +Allele 129 0.033817370442160 +Allele 131 0.033357244904912 +Allele 133 0.034946802058006 +Allele 135 0.036333717806080 +Allele 137 0.032887339770612 +Allele 139 0.033909277374661 +Allele 145 0.032866180082580 +Allele 147 0.037640286233732 +Allele 149 0.032742000025253 +Allele 152 0.035835626687508 +Allele 218 0.032861652121886 +Allele 220 0.033902677961177 +Allele 222 0.036468013211768 +Allele 224 0.035172565572507 +Allele 226 0.035722122017806 +Allele 228 0.033033810397992 +Allele 230 0.033092076700280 +Allele 232 0.040008059460670 +Allele 234 0.035573738743165 +Allele 236 0.032947489629989 +Allele 238 0.036419322907709 +Allele 240 0.033077984863626 +Allele 250 0.032836731279621 + +Locus 010 +Allele 123 0.026976845989774 +Allele 125 0.026870754858211 +Allele 127 0.027097717022062 +Allele 129 0.028679136970503 +Allele 131 0.028640681423158 +Allele 133 0.028478208304991 +Allele 135 0.027038405861939 +Allele 137 0.027461521930841 +Allele 139 0.027579116801528 +Allele 141 0.027475473701737 +Allele 143 0.026852632007856 +Allele 145 0.026592537337280 +Allele 147 0.030866832273504 +Allele 149 0.029558666179415 +Allele 152 0.026653112479491 +Allele 155 0.027011599663782 +Allele 157 0.029107214445766 +Allele 220 0.026695462946317 +Allele 222 0.029545200613696 +Allele 224 0.026674812926882 +Allele 226 0.029741842003991 +Allele 228 0.027147914874625 +Allele 230 0.027573825638433 +Allele 232 0.026725280310486 +Allele 234 0.027976210369060 +Allele 236 0.031863461383127 +Allele 238 0.028955723094760 +Allele 240 0.027385636240905 +Allele 242 0.027045279838255 +Allele 244 0.027172368478075 +Allele 246 0.026829019628962 +Allele 248 0.026674410881245 +Allele 250 0.026757186853246 +Allele 252 0.026814473241640 +Allele 254 0.026847514640063 +Allele 256 0.028633918784394 + + +Cluster 02 +Locus 001 +Allele 092 0.100878779260535 +Allele 094 0.104225473817373 +Allele 096 0.094360486798893 +Allele 098 0.099591115474467 +Allele 100 0.107552863857132 +Allele 102 0.095959194186248 +Allele 104 0.116656494759297 +Allele 106 0.097681182922514 +Allele 108 0.090212994651305 +Allele 110 0.092881414272238 + +Locus 002 +Allele 094 0.070015327426463 +Allele 096 0.067282567455496 +Allele 098 0.074686387956437 +Allele 100 0.075542088168478 +Allele 102 0.071610885247884 +Allele 104 0.089430002523384 +Allele 106 0.083117609626759 +Allele 108 0.066170069056794 +Allele 110 0.068317075622736 +Allele 112 0.070679192670842 +Allele 114 0.064953161478492 +Allele 124 0.067810422591834 +Allele 126 0.065458359674829 +Allele 149 0.064926850499568 + +Locus 003 +Allele 118 0.046339034618933 +Allele 122 0.046849813809189 +Allele 124 0.054637765042115 +Allele 126 0.067510070671373 +Allele 128 0.047433494752466 +Allele 130 0.048569908251092 +Allele 132 0.047819779762634 +Allele 137 0.047696754661076 +Allele 202 0.047777875264141 +Allele 204 0.046733331655354 +Allele 206 0.046682211118951 +Allele 208 0.060245781725711 +Allele 210 0.047659769880250 +Allele 212 0.048031715282562 +Allele 214 0.053296761359565 +Allele 216 0.046782629882422 +Allele 218 0.047140238814220 +Allele 220 0.046845597254633 +Allele 224 0.048174129812140 +Allele 226 0.053773336381175 + +Locus 004 +Allele 124 0.041240195199726 +Allele 126 0.043079777639983 +Allele 127 0.044510979407449 +Allele 128 0.042232285335371 +Allele 130 0.041087058298820 +Allele 132 0.043166999286854 +Allele 134 0.040627412501890 +Allele 135 0.054110353392815 +Allele 137 0.045372192456010 +Allele 151 0.043190311800600 +Allele 208 0.045061843020286 +Allele 210 0.042222767650270 +Allele 212 0.041820081978365 +Allele 214 0.041033245713399 +Allele 216 0.044387000048346 +Allele 218 0.043865291062531 +Allele 220 0.042028139158652 +Allele 222 0.047513410065893 +Allele 224 0.041664728455586 +Allele 226 0.042392584622110 +Allele 228 0.041099768909988 +Allele 233 0.047082181900223 +Allele 238 0.041211392094831 + +Locus 005 +Allele 121 0.055409762837164 +Allele 123 0.061079816201357 +Allele 125 0.052688812503888 +Allele 127 0.051986968960558 +Allele 129 0.056793888461276 +Allele 130 0.051780040245494 +Allele 131 0.052776664081835 +Allele 133 0.053854997489298 +Allele 135 0.057663457076313 +Allele 136 0.052964899287464 +Allele 137 0.054631703241497 +Allele 138 0.062620968584346 +Allele 139 0.057417176866105 +Allele 141 0.052354088587084 +Allele 145 0.059455616775640 +Allele 146 0.054896179536472 +Allele 148 0.059865348896585 +Allele 150 0.051759610367627 + +Locus 006 +Allele 121 0.043939428288659 +Allele 123 0.045668967448527 +Allele 125 0.043760579721192 +Allele 129 0.043050210782087 +Allele 131 0.043549207399785 +Allele 133 0.050556798489453 +Allele 135 0.045168120451486 +Allele 136 0.043039918661599 +Allele 137 0.052752750292032 +Allele 138 0.044553585346949 +Allele 139 0.046480170117667 +Allele 141 0.043035042210385 +Allele 143 0.042711586876766 +Allele 145 0.045722394723221 +Allele 146 0.043179364268781 +Allele 147 0.046543610699459 +Allele 148 0.046028573153226 +Allele 150 0.044507682934368 +Allele 151 0.042978715555252 +Allele 152 0.057257572666333 +Allele 156 0.042756951552380 +Allele 161 0.042758768360392 + +Locus 007 +Allele 093 0.047726498204579 +Allele 095 0.045864907274233 +Allele 096 0.042950588346945 +Allele 097 0.043504603295443 +Allele 099 0.046126030139399 +Allele 100 0.043584993999990 +Allele 101 0.049843099080226 +Allele 103 0.051991005013957 +Allele 105 0.043353936252285 +Allele 107 0.043312939219730 +Allele 109 0.046341272005970 +Allele 110 0.043404525689391 +Allele 125 0.043040005996439 +Allele 161 0.043090348933841 +Allele 165 0.043128339868061 +Allele 167 0.046667892222876 +Allele 169 0.047118987801054 +Allele 171 0.052026526733104 +Allele 173 0.047307801873888 +Allele 175 0.043235609009360 +Allele 177 0.043008218218897 +Allele 181 0.043371870820332 + +Locus 008 +Allele 095 0.039652517053336 +Allele 097 0.041732596532502 +Allele 099 0.039590126685841 +Allele 100 0.040444706483278 +Allele 101 0.046912212351493 +Allele 103 0.050363135432197 +Allele 105 0.039666513775702 +Allele 107 0.040229861475141 +Allele 109 0.042745495886715 +Allele 110 0.039930149602294 +Allele 113 0.043205993480532 +Allele 121 0.040760422989700 +Allele 123 0.039755505307391 +Allele 131 0.039588940963247 +Allele 167 0.039760801158879 +Allele 169 0.040904394115409 +Allele 171 0.045965003648630 +Allele 173 0.043955217976836 +Allele 175 0.044978536479472 +Allele 177 0.040013717310761 +Allele 179 0.039553149614980 +Allele 181 0.040914314521805 +Allele 183 0.039680861106997 +Allele 185 0.039695826046864 + +Locus 009 +Allele 108 0.034870190475793 +Allele 115 0.033000368128778 +Allele 121 0.033784680337939 +Allele 123 0.034722240434171 +Allele 125 0.036156959401458 +Allele 127 0.033415991192790 +Allele 129 0.033973276810331 +Allele 131 0.033388357246624 +Allele 133 0.034545919458691 +Allele 135 0.035986848645435 +Allele 137 0.032820574546666 +Allele 139 0.033760210298375 +Allele 145 0.032937954022193 +Allele 147 0.037933185676286 +Allele 149 0.032827573239768 +Allele 152 0.035689030647495 +Allele 218 0.032918794966228 +Allele 220 0.033714797917225 +Allele 222 0.036193088899777 +Allele 224 0.035323270323020 +Allele 226 0.035466395967238 +Allele 228 0.033123642044102 +Allele 230 0.033013952215921 +Allele 232 0.040529228357505 +Allele 234 0.035600054302815 +Allele 236 0.032792049100086 +Allele 238 0.035892319408046 +Allele 240 0.032889198145222 +Allele 250 0.032729847790025 + +Locus 010 +Allele 123 0.027646510529348 +Allele 125 0.026871195805788 +Allele 127 0.027227312258435 +Allele 129 0.028466292736059 +Allele 131 0.028815641596624 +Allele 133 0.029201719977721 +Allele 135 0.026890348560975 +Allele 137 0.027490130228885 +Allele 139 0.027576977705573 +Allele 141 0.027396173689547 +Allele 143 0.026546913646271 +Allele 145 0.026757197129164 +Allele 147 0.030749069930513 +Allele 149 0.029243601415039 +Allele 152 0.026614658192090 +Allele 155 0.026891162058383 +Allele 157 0.029395717538340 +Allele 220 0.026720355203135 +Allele 222 0.029161271528240 +Allele 224 0.026770180239648 +Allele 226 0.029458795618767 +Allele 228 0.026972876284360 +Allele 230 0.027666827046189 +Allele 232 0.026574002407530 +Allele 234 0.028263754536750 +Allele 236 0.031960141118807 +Allele 238 0.028459952681214 +Allele 240 0.027319458800431 +Allele 242 0.027150263168608 +Allele 244 0.027132731628866 +Allele 246 0.026818623584480 +Allele 248 0.026852114273993 +Allele 250 0.026719852509591 +Allele 252 0.026774736917861 +Allele 254 0.026737491828950 +Allele 256 0.028705947623828 + + +Cluster 03 +Locus 001 +Allele 092 0.102557488018007 +Allele 094 0.104352416605588 +Allele 096 0.094926780524972 +Allele 098 0.098425434019538 +Allele 100 0.105354080955060 +Allele 102 0.095790541016874 +Allele 104 0.114671859956708 +Allele 106 0.099028828273009 +Allele 108 0.091478164766589 +Allele 110 0.093414405863654 + +Locus 002 +Allele 094 0.071415484170144 +Allele 096 0.067923089301790 +Allele 098 0.074111605580543 +Allele 100 0.073981356410832 +Allele 102 0.071734104592133 +Allele 104 0.086745243092964 +Allele 106 0.081720077694693 +Allele 108 0.067601111600876 +Allele 110 0.068634265757244 +Allele 112 0.070107177408416 +Allele 114 0.066130276928100 +Allele 124 0.067553402779609 +Allele 126 0.066192117936078 +Allele 149 0.066150686746579 + +Locus 003 +Allele 118 0.046979740774838 +Allele 122 0.047622936596881 +Allele 124 0.053699018821134 +Allele 126 0.064216253645002 +Allele 128 0.047734600537027 +Allele 130 0.049275561081587 +Allele 132 0.048140526422306 +Allele 137 0.048018268717353 +Allele 202 0.048195329659972 +Allele 204 0.047136251180155 +Allele 206 0.047104169504486 +Allele 208 0.058349474865682 +Allele 210 0.047920261718478 +Allele 212 0.048695542738882 +Allele 214 0.053900038115454 +Allele 216 0.047143248875643 +Allele 218 0.048082748830511 +Allele 220 0.047389514362545 +Allele 224 0.048193688877629 +Allele 226 0.052202824674439 + +Locus 004 +Allele 124 0.041817995494516 +Allele 126 0.042689703624530 +Allele 127 0.045123197953214 +Allele 128 0.042603012817762 +Allele 130 0.041895844923791 +Allele 132 0.043119863840107 +Allele 134 0.041339767658994 +Allele 135 0.050646690425474 +Allele 137 0.045303361544991 +Allele 151 0.043654967158614 +Allele 208 0.044561896914298 +Allele 210 0.042563254643137 +Allele 212 0.042112129605867 +Allele 214 0.041474850522534 +Allele 216 0.043379878279938 +Allele 218 0.044365637538405 +Allele 220 0.042215588656815 +Allele 222 0.048506244761236 +Allele 224 0.041849852176104 +Allele 226 0.042328582976113 +Allele 228 0.041295568595122 +Allele 233 0.045604716160524 +Allele 238 0.041547393727914 + +Locus 005 +Allele 121 0.054658540211420 +Allele 123 0.059100067788627 +Allele 125 0.053097108961412 +Allele 127 0.052485125097192 +Allele 129 0.057265810261222 +Allele 130 0.053021938915580 +Allele 131 0.054024663984574 +Allele 133 0.053971807849899 +Allele 135 0.056937338105735 +Allele 136 0.053665754675371 +Allele 137 0.055490416332520 +Allele 138 0.060810466812924 +Allele 139 0.058390854919282 +Allele 141 0.052646374579663 +Allele 145 0.057603853198901 +Allele 146 0.054824874591588 +Allele 148 0.059547876671251 +Allele 150 0.052457127042840 + +Locus 006 +Allele 121 0.044123666615794 +Allele 123 0.045307160418542 +Allele 125 0.044069675267985 +Allele 129 0.043208941970623 +Allele 131 0.043981743755113 +Allele 133 0.048552844569397 +Allele 135 0.045309899792704 +Allele 136 0.043781907293929 +Allele 137 0.052613414678702 +Allele 138 0.044230008488884 +Allele 139 0.046498043288924 +Allele 141 0.043774809568567 +Allele 143 0.043373076819143 +Allele 145 0.045313423559035 +Allele 146 0.043580150929108 +Allele 147 0.047133145652972 +Allele 148 0.046382149196216 +Allele 150 0.044684012360181 +Allele 151 0.043438908313910 +Allele 152 0.053827498829420 +Allele 156 0.043415879390644 +Allele 161 0.043399639240202 + +Locus 007 +Allele 093 0.046896814841258 +Allele 095 0.045645954709863 +Allele 096 0.043652065393430 +Allele 097 0.044193809850228 +Allele 099 0.045280657881640 +Allele 100 0.044006355731342 +Allele 101 0.050178248641774 +Allele 103 0.050332263788949 +Allele 105 0.043535589434414 +Allele 107 0.043485315855102 +Allele 109 0.046464906526892 +Allele 110 0.043418095680062 +Allele 125 0.043246956797369 +Allele 161 0.043370187358462 +Allele 165 0.043488345247001 +Allele 167 0.045870227351345 +Allele 169 0.046733489343431 +Allele 171 0.051258231678924 +Allele 173 0.047866256993116 +Allele 175 0.043503658566747 +Allele 177 0.043670941487101 +Allele 181 0.043901626841550 + +Locus 008 +Allele 095 0.039975194195894 +Allele 097 0.041305455774068 +Allele 099 0.040173246502172 +Allele 100 0.040591194661387 +Allele 101 0.047073675836243 +Allele 103 0.047502243202376 +Allele 105 0.039987887163250 +Allele 107 0.040544937359743 +Allele 109 0.042819936279774 +Allele 110 0.040291213295973 +Allele 113 0.042586154078352 +Allele 121 0.040736297666048 +Allele 123 0.040121106639243 +Allele 131 0.039905004660125 +Allele 167 0.039752256785289 +Allele 169 0.040798316902945 +Allele 171 0.046276577644370 +Allele 173 0.044210933836213 +Allele 175 0.043403672359805 +Allele 177 0.040267876610059 +Allele 179 0.039871957199071 +Allele 181 0.041164125739174 +Allele 183 0.040360678752140 +Allele 185 0.040280056856285 + +Locus 009 +Allele 108 0.034969347228351 +Allele 115 0.033475220869562 +Allele 121 0.034093122694600 +Allele 123 0.034508121895469 +Allele 125 0.035898527979197 +Allele 127 0.033518853424949 +Allele 129 0.034063816366789 +Allele 131 0.033415784195249 +Allele 133 0.034248678500527 +Allele 135 0.036365247685145 +Allele 137 0.032903407076570 +Allele 139 0.033986095894498 +Allele 145 0.032987419270105 +Allele 147 0.036607099216133 +Allele 149 0.032990109967304 +Allele 152 0.035211707629733 +Allele 218 0.033257888264802 +Allele 220 0.033872862510832 +Allele 222 0.035961299792477 +Allele 224 0.035233421026820 +Allele 226 0.035771049691800 +Allele 228 0.033374135474503 +Allele 230 0.033315859377834 +Allele 232 0.039361225456478 +Allele 234 0.034802930126170 +Allele 236 0.033017424115270 +Allele 238 0.036343556520395 +Allele 240 0.033348121582522 +Allele 250 0.033097666165915 + +Locus 010 +Allele 123 0.027514109060397 +Allele 125 0.027296953665813 +Allele 127 0.027298236963449 +Allele 129 0.028768581688574 +Allele 131 0.028884703357703 +Allele 133 0.028198430939897 +Allele 135 0.027074722716899 +Allele 137 0.027700522315219 +Allele 139 0.027564134431669 +Allele 141 0.027242097090656 +Allele 143 0.027042446331445 +Allele 145 0.026794798086880 +Allele 147 0.029772751652028 +Allele 149 0.029545431400430 +Allele 152 0.027103196168085 +Allele 155 0.026783569125008 +Allele 157 0.028732437411686 +Allele 220 0.026749072203090 +Allele 222 0.029610461609585 +Allele 224 0.026816183761764 +Allele 226 0.029243370982498 +Allele 228 0.026938138400982 +Allele 230 0.027521165009021 +Allele 232 0.026918706411478 +Allele 234 0.028430457210362 +Allele 236 0.030346421981500 +Allele 238 0.028754299698766 +Allele 240 0.027445382117149 +Allele 242 0.027158491026684 +Allele 244 0.027013240448673 +Allele 246 0.027187200379157 +Allele 248 0.026915445756642 +Allele 250 0.026958158683480 +Allele 252 0.026924755362880 +Allele 254 0.026949297122585 +Allele 256 0.028802629427865 + + +Cluster 04 +Locus 001 +Allele 092 0.104789789902124 +Allele 094 0.101934391795949 +Allele 096 0.093789684488370 +Allele 098 0.099885757269514 +Allele 100 0.105272458528018 +Allele 102 0.096689643404411 +Allele 104 0.120995370692491 +Allele 106 0.095875751895716 +Allele 108 0.089479402911449 +Allele 110 0.091287749111960 + +Locus 002 +Allele 094 0.070550772177638 +Allele 096 0.066747311291531 +Allele 098 0.075843756820178 +Allele 100 0.075693831954683 +Allele 102 0.070372376399250 +Allele 104 0.092499998169152 +Allele 106 0.081446877335962 +Allele 108 0.066420352677600 +Allele 110 0.067884825886040 +Allele 112 0.070935529794811 +Allele 114 0.064914709752192 +Allele 124 0.066691077515427 +Allele 126 0.065164203380202 +Allele 149 0.064834376845333 + +Locus 003 +Allele 118 0.046695172987514 +Allele 122 0.046862183295016 +Allele 124 0.052120665079007 +Allele 126 0.069948019339610 +Allele 128 0.047195827889320 +Allele 130 0.048368282185692 +Allele 132 0.048220207706259 +Allele 137 0.047753185723672 +Allele 202 0.047696970133443 +Allele 204 0.046638558849733 +Allele 206 0.046593421537742 +Allele 208 0.061166638202485 +Allele 210 0.047194631136198 +Allele 212 0.048522235595965 +Allele 214 0.052864090316373 +Allele 216 0.046661295247124 +Allele 218 0.047257839719936 +Allele 220 0.046690048948335 +Allele 224 0.047904418646133 +Allele 226 0.053646307460444 + +Locus 004 +Allele 124 0.041222860823765 +Allele 126 0.042417686943514 +Allele 127 0.045793683085689 +Allele 128 0.042014450730582 +Allele 130 0.041058804274469 +Allele 132 0.042643996328089 +Allele 134 0.041019536670288 +Allele 135 0.054063428958536 +Allele 137 0.044731820632229 +Allele 151 0.044216484401905 +Allele 208 0.045370353588099 +Allele 210 0.041841133821712 +Allele 212 0.042323546324504 +Allele 214 0.040960733307503 +Allele 216 0.043060497209997 +Allele 218 0.043119760209849 +Allele 220 0.042010804632418 +Allele 222 0.049456934955985 +Allele 224 0.041427934791325 +Allele 226 0.042069511114899 +Allele 228 0.040782429766543 +Allele 233 0.047229511062248 +Allele 238 0.041164096365853 + +Locus 005 +Allele 121 0.054222057498798 +Allele 123 0.060676888962613 +Allele 125 0.052401109849795 +Allele 127 0.051625432622414 +Allele 129 0.058421814370930 +Allele 130 0.051702840058802 +Allele 131 0.052685026281626 +Allele 133 0.053694747001410 +Allele 135 0.058024574030498 +Allele 136 0.053547127724153 +Allele 137 0.055604180271285 +Allele 138 0.059832438149092 +Allele 139 0.059205941897489 +Allele 141 0.051855709089888 +Allele 145 0.059308584016414 +Allele 146 0.054597572862291 +Allele 148 0.060992446265184 +Allele 150 0.051601509047316 + +Locus 006 +Allele 121 0.043470000938505 +Allele 123 0.045092464880141 +Allele 125 0.043591392490976 +Allele 129 0.042635558294996 +Allele 131 0.043463397438641 +Allele 133 0.050288132568055 +Allele 135 0.045031573300508 +Allele 136 0.042926468781887 +Allele 137 0.055811980048354 +Allele 138 0.044024565156719 +Allele 139 0.045438634813865 +Allele 141 0.043134111582863 +Allele 143 0.042677213566137 +Allele 145 0.044823974027825 +Allele 146 0.043059977437352 +Allele 147 0.047916707951834 +Allele 148 0.045973985723821 +Allele 150 0.044734302647439 +Allele 151 0.042777314634805 +Allele 152 0.057752460774089 +Allele 156 0.042597842754919 +Allele 161 0.042777940186269 + +Locus 007 +Allele 093 0.048044292433323 +Allele 095 0.045272434994102 +Allele 096 0.042869487894669 +Allele 097 0.044087534358301 +Allele 099 0.045180549169688 +Allele 100 0.043766297771315 +Allele 101 0.051784180594854 +Allele 103 0.052144431901666 +Allele 105 0.043303015613418 +Allele 107 0.042999788986240 +Allele 109 0.045471313890014 +Allele 110 0.043497062270973 +Allele 125 0.042884117754232 +Allele 161 0.043025789456666 +Allele 165 0.042902970627202 +Allele 167 0.045803143483138 +Allele 169 0.046040843646138 +Allele 171 0.052750618444040 +Allele 173 0.048818024141519 +Allele 175 0.043148447240627 +Allele 177 0.042909507246508 +Allele 181 0.043296148081366 + +Locus 008 +Allele 095 0.039711837681866 +Allele 097 0.041392833625912 +Allele 099 0.039701550219235 +Allele 100 0.040303596835609 +Allele 101 0.048563144591232 +Allele 103 0.049811089124883 +Allele 105 0.039604337105469 +Allele 107 0.039783524319825 +Allele 109 0.041753988953280 +Allele 110 0.039729879733749 +Allele 113 0.043598717099130 +Allele 121 0.040457947018244 +Allele 123 0.039957903116807 +Allele 131 0.039596278331614 +Allele 167 0.039562539645659 +Allele 169 0.040601282753045 +Allele 171 0.046056889000679 +Allele 173 0.044949466103265 +Allele 175 0.044959112651327 +Allele 177 0.040056477794456 +Allele 179 0.039559411762462 +Allele 181 0.040808326507988 +Allele 183 0.040030512206329 +Allele 185 0.039449353817936 + +Locus 009 +Allele 108 0.035435259673931 +Allele 115 0.032520522807334 +Allele 121 0.033557237159025 +Allele 123 0.034329187174703 +Allele 125 0.035322052651953 +Allele 127 0.033354637329376 +Allele 129 0.033646651293877 +Allele 131 0.033171156297067 +Allele 133 0.034173828117773 +Allele 135 0.036950468052770 +Allele 137 0.032867829717135 +Allele 139 0.033826626696136 +Allele 145 0.032798147056968 +Allele 147 0.037789694868114 +Allele 149 0.032812463191783 +Allele 152 0.036153168431034 +Allele 218 0.032793622152093 +Allele 220 0.033719800267706 +Allele 222 0.036877538266618 +Allele 224 0.035462916110951 +Allele 226 0.036354568520513 +Allele 228 0.032969329510785 +Allele 230 0.032846751696713 +Allele 232 0.040081155221463 +Allele 234 0.034769419426712 +Allele 236 0.032860519706176 +Allele 238 0.036765637118469 +Allele 240 0.033154382495979 +Allele 250 0.032635428986845 + +Locus 010 +Allele 123 0.027165593951210 +Allele 125 0.026905375383718 +Allele 127 0.027041431643710 +Allele 129 0.029056410705806 +Allele 131 0.028275573771464 +Allele 133 0.028266729689255 +Allele 135 0.027082587319278 +Allele 137 0.027465704307676 +Allele 139 0.027524100363854 +Allele 141 0.027457537865989 +Allele 143 0.026700057774415 +Allele 145 0.026599585693873 +Allele 147 0.031163665766816 +Allele 149 0.030162443033851 +Allele 152 0.026551594424355 +Allele 155 0.026715772362755 +Allele 157 0.029249360672620 +Allele 220 0.026867208580879 +Allele 222 0.030016422364158 +Allele 224 0.026636632661388 +Allele 226 0.030050912019730 +Allele 228 0.026937151455642 +Allele 230 0.027594715932676 +Allele 232 0.026750515128020 +Allele 234 0.028168361564420 +Allele 236 0.031736434940024 +Allele 238 0.028989717806518 +Allele 240 0.027097464079136 +Allele 242 0.027004644783806 +Allele 244 0.026867277301836 +Allele 246 0.026904841918962 +Allele 248 0.026760588794001 +Allele 250 0.026697706018183 +Allele 252 0.026874449958973 +Allele 254 0.026571219966166 +Allele 256 0.028090209994838 + + +Cluster 05 +Locus 001 +Allele 092 0.102026042136810 +Allele 094 0.107024861394273 +Allele 096 0.096073811846834 +Allele 098 0.100041094300917 +Allele 100 0.104163152721594 +Allele 102 0.096763577217687 +Allele 104 0.111248428930140 +Allele 106 0.099627986892778 +Allele 108 0.089673817410284 +Allele 110 0.093357227148682 + +Locus 002 +Allele 094 0.070373221713790 +Allele 096 0.069294221478971 +Allele 098 0.074103654842022 +Allele 100 0.073134379893338 +Allele 102 0.073564046888786 +Allele 104 0.086534642941207 +Allele 106 0.084898782090687 +Allele 108 0.066276598277293 +Allele 110 0.069159563187446 +Allele 112 0.070062027490772 +Allele 114 0.065347050142223 +Allele 124 0.067307790132957 +Allele 126 0.065313261473106 +Allele 149 0.064630759447403 + +Locus 003 +Allele 118 0.046916610640026 +Allele 122 0.046890478275978 +Allele 124 0.055900877187756 +Allele 126 0.065920643252496 +Allele 128 0.046887492393193 +Allele 130 0.047743707259772 +Allele 132 0.048979899971084 +Allele 137 0.048002664360566 +Allele 202 0.047590423312416 +Allele 204 0.046530713549493 +Allele 206 0.046454158982008 +Allele 208 0.059858714674907 +Allele 210 0.046796672644228 +Allele 212 0.049918100674477 +Allele 214 0.054691820469290 +Allele 216 0.046742083681232 +Allele 218 0.047132074563819 +Allele 220 0.046828099490688 +Allele 224 0.048513415691087 +Allele 226 0.051701348925480 + +Locus 004 +Allele 124 0.041102462323489 +Allele 126 0.043137698532300 +Allele 127 0.044163357059696 +Allele 128 0.043181242019646 +Allele 130 0.041128160942754 +Allele 132 0.043670517659254 +Allele 134 0.040689516802349 +Allele 135 0.052755009004239 +Allele 137 0.045978804816764 +Allele 151 0.043299117589705 +Allele 208 0.044392476625357 +Allele 210 0.041598658593331 +Allele 212 0.041748801863169 +Allele 214 0.041067670969874 +Allele 216 0.045841662942651 +Allele 218 0.044043319528655 +Allele 220 0.042032208329461 +Allele 222 0.047603003638116 +Allele 224 0.042735837735113 +Allele 226 0.042546253905986 +Allele 228 0.040787630626560 +Allele 233 0.045196390207478 +Allele 238 0.041300198284052 + +Locus 005 +Allele 121 0.055862922937362 +Allele 123 0.059020076737945 +Allele 125 0.054094302722265 +Allele 127 0.052318800635219 +Allele 129 0.056131183919708 +Allele 130 0.051796309213022 +Allele 131 0.054732420855244 +Allele 133 0.053078503426743 +Allele 135 0.056525858776309 +Allele 136 0.053238286117387 +Allele 137 0.054626361355508 +Allele 138 0.061845022872667 +Allele 139 0.057448653164564 +Allele 141 0.052439138441927 +Allele 145 0.057692304894842 +Allele 146 0.057149663466089 +Allele 148 0.059674292425897 +Allele 150 0.052325898037304 + +Locus 006 +Allele 121 0.044622768028122 +Allele 123 0.045705663307335 +Allele 125 0.043691943536715 +Allele 129 0.042833645428798 +Allele 131 0.046151849203802 +Allele 133 0.048254297913779 +Allele 135 0.044901718852867 +Allele 136 0.042840920228643 +Allele 137 0.052489640491139 +Allele 138 0.044240866078116 +Allele 139 0.046213571683195 +Allele 141 0.043358115952647 +Allele 143 0.042623195894920 +Allele 145 0.045245513190460 +Allele 146 0.043929415606112 +Allele 147 0.046442532063017 +Allele 148 0.046780001227167 +Allele 150 0.045545590055086 +Allele 151 0.042791182655027 +Allele 152 0.055846347857706 +Allele 156 0.042632253028943 +Allele 161 0.042858967716405 + +Locus 007 +Allele 093 0.046951479215562 +Allele 095 0.045018429380216 +Allele 096 0.042822609748171 +Allele 097 0.044827239262452 +Allele 099 0.046646400324060 +Allele 100 0.045357055790376 +Allele 101 0.049363407364414 +Allele 103 0.050405141930484 +Allele 105 0.043592684657546 +Allele 107 0.043041063643648 +Allele 109 0.046044530821371 +Allele 110 0.043149813333564 +Allele 125 0.042886161588129 +Allele 161 0.042815055784677 +Allele 165 0.043358244758018 +Allele 167 0.046946617832618 +Allele 169 0.046601478670882 +Allele 171 0.052414862276571 +Allele 173 0.048213311504927 +Allele 175 0.043078713444100 +Allele 177 0.043011934193660 +Allele 181 0.043453764474555 + +Locus 008 +Allele 095 0.039684421776790 +Allele 097 0.040639561731264 +Allele 099 0.039582460744721 +Allele 100 0.041045320637336 +Allele 101 0.046820808597672 +Allele 103 0.049287769705504 +Allele 105 0.039383431644112 +Allele 107 0.039958669688625 +Allele 109 0.043173350167495 +Allele 110 0.039817347948553 +Allele 113 0.042813880401958 +Allele 121 0.041422988880186 +Allele 123 0.039909325078467 +Allele 131 0.039473402531701 +Allele 167 0.039568787086449 +Allele 169 0.041263213020351 +Allele 171 0.046782586288718 +Allele 173 0.043646549990161 +Allele 175 0.045136408428511 +Allele 177 0.040097893298244 +Allele 179 0.039278371908958 +Allele 181 0.041047332320676 +Allele 183 0.040376340116503 +Allele 185 0.039789778007045 + +Locus 009 +Allele 108 0.034710545500297 +Allele 115 0.032839855985873 +Allele 121 0.033528602348128 +Allele 123 0.034370270840734 +Allele 125 0.035579569203311 +Allele 127 0.033021443514081 +Allele 129 0.034841568655454 +Allele 131 0.033294983989270 +Allele 133 0.036922766564807 +Allele 135 0.035609736121846 +Allele 137 0.032737262991496 +Allele 139 0.034072906714898 +Allele 145 0.032964198837045 +Allele 147 0.036306602421865 +Allele 149 0.032768907065796 +Allele 152 0.035336013902455 +Allele 218 0.033203686895815 +Allele 220 0.034610591653027 +Allele 222 0.035985995919558 +Allele 224 0.036386827843609 +Allele 226 0.035479085826651 +Allele 228 0.033096816530510 +Allele 230 0.032819641248034 +Allele 232 0.039302114625000 +Allele 234 0.036441134019611 +Allele 236 0.032565490882745 +Allele 238 0.035386690360039 +Allele 240 0.032921425924692 +Allele 250 0.032895263613353 + +Locus 010 +Allele 123 0.027201880503484 +Allele 125 0.026914940215951 +Allele 127 0.026938444879506 +Allele 129 0.028439412459183 +Allele 131 0.028684535236505 +Allele 133 0.029131972216394 +Allele 135 0.028513599703756 +Allele 137 0.027720928586511 +Allele 139 0.027377932887971 +Allele 141 0.027639163308447 +Allele 143 0.026995169359547 +Allele 145 0.026438645815662 +Allele 147 0.029685944382827 +Allele 149 0.029156167232772 +Allele 152 0.026549637574530 +Allele 155 0.026813031748570 +Allele 157 0.028911909006591 +Allele 220 0.026934547599416 +Allele 222 0.029045070536284 +Allele 224 0.026598932505370 +Allele 226 0.029389048687523 +Allele 228 0.026918327733577 +Allele 230 0.028122228591886 +Allele 232 0.026698209989404 +Allele 234 0.028693383251532 +Allele 236 0.031061990706842 +Allele 238 0.028630413868234 +Allele 240 0.028057312546364 +Allele 242 0.026873694762056 +Allele 244 0.027140257742189 +Allele 246 0.026955434643882 +Allele 248 0.026595157702429 +Allele 250 0.026625237968909 +Allele 252 0.026777074422389 +Allele 254 0.027071006121149 +Allele 256 0.028699355502354 + + +Cluster 06 +Locus 001 +Allele 092 0.104478408668088 +Allele 094 0.102227355949059 +Allele 096 0.093391925002950 +Allele 098 0.096873956946038 +Allele 100 0.108435855247472 +Allele 102 0.093553921210386 +Allele 104 0.121900170462269 +Allele 106 0.097952517581104 +Allele 108 0.089427437792582 +Allele 110 0.091758451140049 + +Locus 002 +Allele 094 0.070917667754166 +Allele 096 0.066816057735000 +Allele 098 0.072963118273727 +Allele 100 0.077205751662168 +Allele 102 0.071069881107264 +Allele 104 0.093504279203555 +Allele 106 0.083757315821727 +Allele 108 0.065710311223748 +Allele 110 0.067860785290445 +Allele 112 0.069089874421125 +Allele 114 0.064774396623321 +Allele 124 0.066806030147337 +Allele 126 0.064888101841532 +Allele 149 0.064636428894889 + +Locus 003 +Allele 118 0.046530264888428 +Allele 122 0.046741173154840 +Allele 124 0.053346778701140 +Allele 126 0.069886196482630 +Allele 128 0.046875483607888 +Allele 130 0.048376864072004 +Allele 132 0.047537045918671 +Allele 137 0.047647067199163 +Allele 202 0.047560335123976 +Allele 204 0.046577628724512 +Allele 206 0.046417763889938 +Allele 208 0.059655921333038 +Allele 210 0.047009769359040 +Allele 212 0.048513782262425 +Allele 214 0.053542831663439 +Allele 216 0.046841227890171 +Allele 218 0.047328212775926 +Allele 220 0.046635472567841 +Allele 224 0.048017227372977 +Allele 226 0.054958953011955 + +Locus 004 +Allele 124 0.041056066975526 +Allele 126 0.042693640371455 +Allele 127 0.045830944816335 +Allele 128 0.042238254343536 +Allele 130 0.041092839342879 +Allele 132 0.043162939501464 +Allele 134 0.040776933068853 +Allele 135 0.053246348074153 +Allele 137 0.044857987897634 +Allele 151 0.043930265982080 +Allele 208 0.044038185746533 +Allele 210 0.041897609240611 +Allele 212 0.041269798880088 +Allele 214 0.040935519124718 +Allele 216 0.043752374123496 +Allele 218 0.043566703999570 +Allele 220 0.041619293472204 +Allele 222 0.050185815164349 +Allele 224 0.041246978224916 +Allele 226 0.042118136251099 +Allele 228 0.041120077525710 +Allele 233 0.048239177996261 +Allele 238 0.041124109876531 + +Locus 005 +Allele 121 0.054039524791038 +Allele 123 0.062608207001566 +Allele 125 0.052713117228424 +Allele 127 0.051647317585117 +Allele 129 0.057756024116695 +Allele 130 0.051620204541619 +Allele 131 0.053064183869706 +Allele 133 0.053506383087584 +Allele 135 0.056127969710788 +Allele 136 0.052891394925272 +Allele 137 0.055479050858785 +Allele 138 0.061383241041693 +Allele 139 0.058773369656328 +Allele 141 0.052050583355630 +Allele 145 0.060835129643638 +Allele 146 0.054296203828187 +Allele 148 0.059638413050598 +Allele 150 0.051569681707330 + +Locus 006 +Allele 121 0.043879774234464 +Allele 123 0.045658195400268 +Allele 125 0.043591872147883 +Allele 129 0.042818011485283 +Allele 131 0.043438257012145 +Allele 133 0.051079672587214 +Allele 135 0.045042055129217 +Allele 136 0.042701582871030 +Allele 137 0.054029567508160 +Allele 138 0.043961465120190 +Allele 139 0.045996322663792 +Allele 141 0.043207572811680 +Allele 143 0.042702317340387 +Allele 145 0.045144282664838 +Allele 146 0.042837708822918 +Allele 147 0.047853820329579 +Allele 148 0.045867925857467 +Allele 150 0.044541255269875 +Allele 151 0.042819154640234 +Allele 152 0.057351303624301 +Allele 156 0.042729554996924 +Allele 161 0.042748327482152 + +Locus 007 +Allele 093 0.046482183563310 +Allele 095 0.045484808596378 +Allele 096 0.043008095445859 +Allele 097 0.043824493055628 +Allele 099 0.045354537914590 +Allele 100 0.043436551216043 +Allele 101 0.052042543271341 +Allele 103 0.053319750549465 +Allele 105 0.043480737087204 +Allele 107 0.043335514208670 +Allele 109 0.046028126387779 +Allele 110 0.043174940013411 +Allele 125 0.042852696486139 +Allele 161 0.042902664774872 +Allele 165 0.042806817312662 +Allele 167 0.046064034889766 +Allele 169 0.046141984674539 +Allele 171 0.051594290067753 +Allele 173 0.048916125018356 +Allele 175 0.043373826799663 +Allele 177 0.043144068945540 +Allele 181 0.043231209721033 + +Locus 008 +Allele 095 0.039241066466081 +Allele 097 0.041456841096925 +Allele 099 0.039411886964282 +Allele 100 0.040163217328221 +Allele 101 0.048716087439614 +Allele 103 0.051179456192137 +Allele 105 0.039525875011537 +Allele 107 0.040101789647265 +Allele 109 0.042410041486846 +Allele 110 0.039766475496446 +Allele 113 0.042227062671642 +Allele 121 0.040619836844700 +Allele 123 0.039646967889622 +Allele 131 0.039497655446199 +Allele 167 0.039661530150202 +Allele 169 0.040545631551448 +Allele 171 0.046933327766125 +Allele 173 0.045270654537441 +Allele 175 0.043336421836638 +Allele 177 0.039917117551961 +Allele 179 0.039486894143117 +Allele 181 0.041015797074588 +Allele 183 0.040046395840858 +Allele 185 0.039821969566108 + +Locus 009 +Allele 108 0.035530763095078 +Allele 115 0.032697798214430 +Allele 121 0.033735355234960 +Allele 123 0.034395193190643 +Allele 125 0.035443300168319 +Allele 127 0.033104092717554 +Allele 129 0.033719129322159 +Allele 131 0.033097021522957 +Allele 133 0.034704970382846 +Allele 135 0.036756881388164 +Allele 137 0.032964251321117 +Allele 139 0.033752787875635 +Allele 145 0.032884992856525 +Allele 147 0.038863139688863 +Allele 149 0.032821330839620 +Allele 152 0.034856008619589 +Allele 218 0.032574679445340 +Allele 220 0.033675049458018 +Allele 222 0.035596323112076 +Allele 224 0.035289972828451 +Allele 226 0.036401404126318 +Allele 228 0.032958703213560 +Allele 230 0.032732619185093 +Allele 232 0.041164696381071 +Allele 234 0.035135043192020 +Allele 236 0.032544181656827 +Allele 238 0.036990144421677 +Allele 240 0.032778790177716 +Allele 250 0.032831376363374 + +Locus 010 +Allele 123 0.027444102363643 +Allele 125 0.026925383241481 +Allele 127 0.027118192612124 +Allele 129 0.028934884232224 +Allele 131 0.028499071331242 +Allele 133 0.028426496763120 +Allele 135 0.026751944297544 +Allele 137 0.027717671656611 +Allele 139 0.027301540813512 +Allele 141 0.027262020545466 +Allele 143 0.026695534954260 +Allele 145 0.026712566516347 +Allele 147 0.031712088455594 +Allele 149 0.029981336184756 +Allele 152 0.026629044182952 +Allele 155 0.026963710913602 +Allele 157 0.028477607988200 +Allele 220 0.026588110403027 +Allele 222 0.030051492578473 +Allele 224 0.026668474253284 +Allele 226 0.028826793422808 +Allele 228 0.026750096751352 +Allele 230 0.027831824147554 +Allele 232 0.026646871797304 +Allele 234 0.028237380605850 +Allele 236 0.032487349323106 +Allele 238 0.029149028773198 +Allele 240 0.027207155936779 +Allele 242 0.026928146030329 +Allele 244 0.026947006493192 +Allele 246 0.026965042421706 +Allele 248 0.026613622961163 +Allele 250 0.026706149471839 +Allele 252 0.026721628370586 +Allele 254 0.026611288434073 +Allele 256 0.028509340771699 + + +Cluster 07 +Locus 001 +Allele 092 0.038362374935015 +Allele 094 0.395932844825370 +Allele 096 0.164956892594843 +Allele 098 0.088190554665585 +Allele 100 0.024340541280246 +Allele 102 0.083470655227535 +Allele 104 0.105327650698444 +Allele 106 0.048439529075629 +Allele 108 0.026388991787389 +Allele 110 0.024589964909944 + +Locus 002 +Allele 094 0.107526529233783 +Allele 096 0.076895974568203 +Allele 098 0.150859448940921 +Allele 100 0.065363529655556 +Allele 102 0.107043571727945 +Allele 104 0.192396236548684 +Allele 106 0.124685890421381 +Allele 108 0.064805741945903 +Allele 110 0.036955136659123 +Allele 112 0.022555418759597 +Allele 114 0.013127490275269 +Allele 124 0.011620520882812 +Allele 126 0.012962813913972 +Allele 149 0.013201696466853 + +Locus 003 +Allele 118 0.018960912352973 +Allele 122 0.031463081394781 +Allele 124 0.182868481877745 +Allele 126 0.087931307250169 +Allele 128 0.062583178606417 +Allele 130 0.036238690462335 +Allele 132 0.061916320701812 +Allele 137 0.011541936939574 +Allele 202 0.011527477047132 +Allele 204 0.025264577523249 +Allele 206 0.012683632119897 +Allele 208 0.114031858393418 +Allele 210 0.037353308087920 +Allele 212 0.098871878141629 +Allele 214 0.069437575509260 +Allele 216 0.044142396684434 +Allele 218 0.050096673934955 +Allele 220 0.012428874897662 +Allele 224 0.023789214180615 +Allele 226 0.006868623894022 + +Locus 004 +Allele 124 0.024550031622866 +Allele 126 0.028752696650699 +Allele 127 0.008107116213547 +Allele 128 0.041687557689717 +Allele 130 0.043019454745133 +Allele 132 0.171574738194389 +Allele 134 0.012420847636721 +Allele 135 0.093135398229073 +Allele 137 0.063933695226191 +Allele 151 0.009547214174301 +Allele 208 0.014751564200268 +Allele 210 0.011385117787588 +Allele 212 0.085961352112135 +Allele 214 0.037108828233582 +Allele 216 0.070704004376379 +Allele 218 0.015747958395660 +Allele 220 0.048548467104106 +Allele 222 0.053724622120840 +Allele 224 0.092230912451260 +Allele 226 0.035899521875787 +Allele 228 0.018527885333757 +Allele 233 0.006693858385694 +Allele 238 0.011987157240304 + +Locus 005 +Allele 121 0.057806559215628 +Allele 123 0.053152461265037 +Allele 125 0.039051280105824 +Allele 127 0.013183281018694 +Allele 129 0.028877452463389 +Allele 130 0.026978523349528 +Allele 131 0.127018928536120 +Allele 133 0.072690824944818 +Allele 135 0.056186561904832 +Allele 136 0.120572967423713 +Allele 137 0.023848302046549 +Allele 138 0.092992662698672 +Allele 139 0.095917140383276 +Allele 141 0.026574334303560 +Allele 145 0.034115008736689 +Allele 146 0.071158877644128 +Allele 148 0.046503750871543 +Allele 150 0.013371083087998 + +Locus 006 +Allele 121 0.025030423181706 +Allele 123 0.023292031614585 +Allele 125 0.018600245944388 +Allele 129 0.026290262271319 +Allele 131 0.117160641669099 +Allele 133 0.072125208818001 +Allele 135 0.109808571018163 +Allele 136 0.026267217685685 +Allele 137 0.041123414187508 +Allele 138 0.018146603119607 +Allele 139 0.049542481538764 +Allele 141 0.019275328299108 +Allele 143 0.013182580772930 +Allele 145 0.056929172468401 +Allele 146 0.052237825435256 +Allele 147 0.008628464192796 +Allele 148 0.108384075439982 +Allele 150 0.077007556235937 +Allele 151 0.013127780081515 +Allele 152 0.090908427815073 +Allele 156 0.019760061281577 +Allele 161 0.013171626928603 + +Locus 007 +Allele 093 0.049286779530473 +Allele 095 0.071467166222169 +Allele 096 0.013416054302145 +Allele 097 0.153860380833115 +Allele 099 0.037352578343114 +Allele 100 0.059389809657870 +Allele 101 0.038835026218699 +Allele 103 0.051678869360978 +Allele 105 0.019750050608227 +Allele 107 0.026762398612296 +Allele 109 0.010395826045705 +Allele 110 0.013157241175974 +Allele 125 0.013475628137730 +Allele 161 0.013455034344308 +Allele 165 0.026842944505707 +Allele 167 0.043378477276000 +Allele 169 0.063883741037183 +Allele 171 0.138353667919841 +Allele 173 0.075166912998206 +Allele 175 0.046886366982574 +Allele 177 0.020146674741958 +Allele 181 0.013058371145725 + +Locus 008 +Allele 095 0.013277002974245 +Allele 097 0.051362916601282 +Allele 099 0.026554376471309 +Allele 100 0.038662761677821 +Allele 101 0.116872673294072 +Allele 103 0.088265104821921 +Allele 105 0.039928890520986 +Allele 107 0.079244458649887 +Allele 109 0.016737585769382 +Allele 110 0.019600480788416 +Allele 113 0.016296697622370 +Allele 121 0.018368932342915 +Allele 123 0.019626154994498 +Allele 131 0.013268933866600 +Allele 167 0.013377286752573 +Allele 169 0.025084237322286 +Allele 171 0.091728727874306 +Allele 173 0.087635953581320 +Allele 175 0.047418770991919 +Allele 177 0.079359046515740 +Allele 179 0.013304854277933 +Allele 181 0.031820662868514 +Allele 183 0.025938957034255 +Allele 185 0.026264532385449 + +Locus 009 +Allele 108 0.026917292079485 +Allele 115 0.011884840129439 +Allele 121 0.010907547648549 +Allele 123 0.039631852188113 +Allele 125 0.086035101522823 +Allele 127 0.041188883279014 +Allele 129 0.045901631675449 +Allele 131 0.047111296826713 +Allele 133 0.092189794298467 +Allele 135 0.025547600075398 +Allele 137 0.017680811817266 +Allele 139 0.016565489373714 +Allele 145 0.017581029822873 +Allele 147 0.006464948855845 +Allele 149 0.011899093036081 +Allele 152 0.008647553328127 +Allele 218 0.011666317886648 +Allele 220 0.087875257802505 +Allele 222 0.109215386190421 +Allele 224 0.085833131525038 +Allele 226 0.037764746810112 +Allele 228 0.023380693601098 +Allele 230 0.017750025801562 +Allele 232 0.021313200076957 +Allele 234 0.032223852181291 +Allele 236 0.017780055319975 +Allele 238 0.019510207526723 +Allele 240 0.017691491873228 +Allele 250 0.011840867447085 + +Locus 010 +Allele 123 0.010409067628955 +Allele 125 0.011067686664224 +Allele 127 0.033633073532635 +Allele 129 0.037036070121749 +Allele 131 0.042976103974335 +Allele 133 0.065609407247155 +Allele 135 0.073357734634453 +Allele 137 0.067217023333721 +Allele 139 0.015969993439770 +Allele 141 0.038976943957338 +Allele 143 0.011185225168038 +Allele 145 0.017145570901847 +Allele 147 0.011666648261134 +Allele 149 0.018707468175032 +Allele 152 0.011381056863210 +Allele 155 0.011126929523561 +Allele 157 0.014008636814232 +Allele 220 0.011244113938887 +Allele 222 0.018743307082845 +Allele 224 0.045739608832303 +Allele 226 0.053269842005160 +Allele 228 0.028103089220319 +Allele 230 0.032659024297401 +Allele 232 0.039889462284701 +Allele 234 0.037623057111212 +Allele 236 0.038949025168030 +Allele 238 0.054021688104290 +Allele 240 0.027325001053523 +Allele 242 0.033705182329453 +Allele 244 0.010809533557335 +Allele 246 0.016811139548563 +Allele 248 0.011370472502788 +Allele 250 0.011311254803879 +Allele 252 0.016841761947255 +Allele 254 0.011271003380395 +Allele 256 0.008837792590273 + + + +Estimated Mixing Proportions +0.010947333333333 +0.011007466666667 +0.009209466666667 +0.011228800000000 +0.013110133333333 +0.011629600000000 +0.932867200000000 + + + diff --git a/inst/files/tess/tess_21.txt b/inst/files/tess/tess_21.txt new file mode 100644 index 0000000..7a69193 --- /dev/null +++ b/inst/files/tess/tess_21.txt @@ -0,0 +1,2014 @@ +Estimated Clustering Probabilities for Samples +Sample ***Cluster 01*** ***Cluster 02*** ***Cluster 03*** ***Cluster 04*** ***Cluster 05*** ***Cluster 06*** ***Cluster 07*** ***Cluster 08*** +000001: 0.000220000000000 0.998230000000000 0.000570000000000 0.000360000000000 0.000110000000000 0.000340000000000 0.000160000000000 0.000010000000000 1 +000002: 0.000000000000000 0.999850000000000 0.000000000000000 0.000040000000000 0.000110000000000 0.000000000000000 0.000000000000000 0.000000000000000 1 +000003: 0.000000000000000 1.000000000000000 0.000000000000000 0.000000000000000 0.000000000000000 0.000000000000000 0.000000000000000 0.000000000000000 1 +000004: 0.000160000000000 0.998510000000000 0.000210000000000 0.000100000000000 0.000220000000000 0.000060000000000 0.000390000000000 0.000350000000000 1 +000005: 0.002620000000000 0.992800000000000 0.000210000000000 0.001530000000000 0.000850000000000 0.001050000000000 0.000300000000000 0.000640000000000 1 +000006: 0.000040000000000 0.999850000000000 0.000000000000000 0.000000000000000 0.000000000000000 0.000110000000000 0.000000000000000 0.000000000000000 1 +000007: 0.021950000000000 0.829460000000000 0.025730000000000 0.022750000000000 0.023320000000000 0.023930000000000 0.028880000000000 0.023980000000000 1 +000008: 0.000000000000000 1.000000000000000 0.000000000000000 0.000000000000000 0.000000000000000 0.000000000000000 0.000000000000000 0.000000000000000 1 +000009: 0.000640000000000 0.992540000000000 0.001230000000000 0.001000000000000 0.000760000000000 0.000520000000000 0.001710000000000 0.001600000000000 1 +000010: 0.006390000000000 0.959840000000000 0.003090000000000 0.011670000000000 0.003170000000000 0.003990000000000 0.007440000000000 0.004410000000000 1 +000011: 0.000210000000000 0.998910000000000 0.000000000000000 0.000280000000000 0.000470000000000 0.000000000000000 0.000090000000000 0.000040000000000 1 +000012: 0.000000000000000 1.000000000000000 0.000000000000000 0.000000000000000 0.000000000000000 0.000000000000000 0.000000000000000 0.000000000000000 1 +000013: 0.000070000000000 0.999930000000000 0.000000000000000 0.000000000000000 0.000000000000000 0.000000000000000 0.000000000000000 0.000000000000000 1 +000014: 0.000000000000000 0.999580000000000 0.000000000000000 0.000120000000000 0.000000000000000 0.000000000000000 0.000000000000000 0.000300000000000 1 +000015: 0.007380000000000 0.952880000000000 0.007530000000000 0.007630000000000 0.005260000000000 0.007150000000000 0.005770000000000 0.006400000000000 1 +000016: 0.000000000000000 1.000000000000000 0.000000000000000 0.000000000000000 0.000000000000000 0.000000000000000 0.000000000000000 0.000000000000000 1 +000017: 0.000110000000000 0.992060000000000 0.001410000000000 0.001190000000000 0.001330000000000 0.002790000000000 0.000480000000000 0.000630000000000 1 +000018: 0.000620000000000 0.997110000000000 0.000510000000000 0.000610000000000 0.000240000000000 0.000180000000000 0.000210000000000 0.000520000000000 1 +000019: 0.027910000000000 0.832450000000000 0.023550000000000 0.025230000000000 0.026720000000000 0.018660000000000 0.021460000000000 0.024020000000000 1 +000020: 0.015870000000000 0.901100000000000 0.002710000000000 0.006700000000000 0.016330000000000 0.012740000000000 0.026130000000000 0.018420000000000 1 +000021: 0.001710000000000 0.968600000000000 0.004290000000000 0.003900000000000 0.003420000000000 0.004950000000000 0.007010000000000 0.006120000000000 1 +000022: 0.159380000000000 0.067760000000000 0.114240000000000 0.128650000000000 0.116070000000000 0.128730000000000 0.146420000000000 0.138750000000000 1 +000023: 0.000000000000000 0.999400000000000 0.000110000000000 0.000120000000000 0.000000000000000 0.000000000000000 0.000000000000000 0.000370000000000 1 +000024: 0.000000000000000 0.999910000000000 0.000000000000000 0.000080000000000 0.000000000000000 0.000000000000000 0.000010000000000 0.000000000000000 1 +000025: 0.000000000000000 0.999670000000000 0.000110000000000 0.000000000000000 0.000220000000000 0.000000000000000 0.000000000000000 0.000000000000000 1 +000026: 0.000220000000000 0.997880000000000 0.000640000000000 0.000690000000000 0.000380000000000 0.000000000000000 0.000020000000000 0.000170000000000 1 +000027: 0.000060000000000 0.999870000000000 0.000050000000000 0.000000000000000 0.000000000000000 0.000000000000000 0.000020000000000 0.000000000000000 1 +000028: 0.000000000000000 0.999360000000000 0.000000000000000 0.000070000000000 0.000270000000000 0.000000000000000 0.000020000000000 0.000280000000000 1 +000029: 0.008790000000000 0.957750000000000 0.006210000000000 0.008460000000000 0.006640000000000 0.004530000000000 0.004350000000000 0.003270000000000 1 +000030: 0.066410000000000 0.502150000000000 0.102240000000000 0.067420000000000 0.047120000000000 0.069030000000000 0.082330000000000 0.063300000000000 1 +000031: 0.005730000000000 0.964420000000000 0.004400000000000 0.005130000000000 0.003720000000000 0.004830000000000 0.007920000000000 0.003850000000000 1 +000032: 0.000000000000000 0.999760000000000 0.000000000000000 0.000000000000000 0.000240000000000 0.000000000000000 0.000000000000000 0.000000000000000 1 +000033: 0.001850000000000 0.982170000000000 0.002800000000000 0.000580000000000 0.002660000000000 0.001820000000000 0.004520000000000 0.003600000000000 1 +000034: 0.000340000000000 0.997310000000000 0.000000000000000 0.000000000000000 0.000000000000000 0.000000000000000 0.002310000000000 0.000040000000000 1 +000035: 0.006650000000000 0.975150000000000 0.002250000000000 0.004810000000000 0.002000000000000 0.003870000000000 0.003020000000000 0.002250000000000 1 +000036: 0.001230000000000 0.986910000000000 0.002440000000000 0.002010000000000 0.001840000000000 0.001350000000000 0.001570000000000 0.002650000000000 1 +000037: 0.000000000000000 0.999970000000000 0.000000000000000 0.000030000000000 0.000000000000000 0.000000000000000 0.000000000000000 0.000000000000000 1 +000038: 0.001400000000000 0.987960000000000 0.000860000000000 0.001630000000000 0.001380000000000 0.002290000000000 0.001670000000000 0.002810000000000 1 +000039: 0.001970000000000 0.985250000000000 0.001170000000000 0.002540000000000 0.002210000000000 0.002040000000000 0.001700000000000 0.003120000000000 1 +000040: 0.000000000000000 0.999670000000000 0.000000000000000 0.000190000000000 0.000000000000000 0.000100000000000 0.000040000000000 0.000000000000000 1 +000041: 0.000260000000000 0.996050000000000 0.000200000000000 0.001960000000000 0.000080000000000 0.000720000000000 0.000190000000000 0.000540000000000 1 +000042: 0.000000000000000 1.000000000000000 0.000000000000000 0.000000000000000 0.000000000000000 0.000000000000000 0.000000000000000 0.000000000000000 1 +000043: 0.000460000000000 0.999530000000000 0.000000000000000 0.000000000000000 0.000000000000000 0.000000000000000 0.000000000000000 0.000010000000000 1 +000044: 0.002270000000000 0.985810000000000 0.001450000000000 0.001330000000000 0.002600000000000 0.002430000000000 0.000960000000000 0.003150000000000 1 +000045: 0.028420000000000 0.770290000000000 0.037980000000000 0.035040000000000 0.036590000000000 0.031980000000000 0.030540000000000 0.029160000000000 1 +000046: 0.000000000000000 0.999950000000000 0.000050000000000 0.000000000000000 0.000000000000000 0.000000000000000 0.000000000000000 0.000000000000000 1 +000047: 0.000570000000000 0.995760000000000 0.000410000000000 0.000270000000000 0.000780000000000 0.000430000000000 0.000000000000000 0.001780000000000 1 +000048: 0.007690000000000 0.936480000000000 0.007060000000000 0.009300000000000 0.008570000000000 0.010070000000000 0.008160000000000 0.012670000000000 1 +000049: 0.039800000000000 0.736360000000000 0.023770000000000 0.026670000000000 0.043850000000000 0.037880000000000 0.057570000000000 0.034100000000000 1 +000050: 0.000660000000000 0.989700000000000 0.001470000000000 0.002000000000000 0.000890000000000 0.001160000000000 0.002140000000000 0.001980000000000 1 +000051: 0.106650000000000 0.432730000000000 0.061920000000000 0.084490000000000 0.078400000000000 0.066660000000000 0.065580000000000 0.103570000000000 1 +000052: 0.010810000000000 0.932050000000000 0.003280000000000 0.002860000000000 0.013800000000000 0.013070000000000 0.009120000000000 0.015010000000000 1 +000053: 0.000000000000000 0.999910000000000 0.000000000000000 0.000000000000000 0.000000000000000 0.000000000000000 0.000000000000000 0.000090000000000 1 +000054: 0.001350000000000 0.984370000000000 0.000790000000000 0.003430000000000 0.002480000000000 0.003560000000000 0.000780000000000 0.003240000000000 1 +000055: 0.000430000000000 0.998380000000000 0.000030000000000 0.000000000000000 0.000750000000000 0.000000000000000 0.000310000000000 0.000100000000000 1 +000056: 0.000460000000000 0.998520000000000 0.000020000000000 0.000380000000000 0.000000000000000 0.000180000000000 0.000240000000000 0.000200000000000 1 +000057: 0.004490000000000 0.978390000000000 0.001770000000000 0.001870000000000 0.001120000000000 0.004830000000000 0.001310000000000 0.006220000000000 1 +000058: 0.000000000000000 0.998740000000000 0.000050000000000 0.000000000000000 0.000000000000000 0.000200000000000 0.000080000000000 0.000930000000000 1 +000059: 0.079190000000000 0.554840000000000 0.052270000000000 0.065400000000000 0.038010000000000 0.063470000000000 0.075050000000000 0.071770000000000 1 +000060: 0.033160000000000 0.828590000000000 0.017120000000000 0.014640000000000 0.024070000000000 0.024280000000000 0.030910000000000 0.027230000000000 1 +000061: 0.000000000000000 0.998700000000000 0.000120000000000 0.000210000000000 0.000020000000000 0.000830000000000 0.000120000000000 0.000000000000000 1 +000062: 0.001810000000000 0.986550000000000 0.001400000000000 0.001540000000000 0.002190000000000 0.001940000000000 0.003260000000000 0.001310000000000 1 +000063: 0.001210000000000 0.991140000000000 0.002860000000000 0.000590000000000 0.000410000000000 0.000780000000000 0.001490000000000 0.001520000000000 1 +000064: 0.107290000000000 0.295000000000000 0.091650000000000 0.102360000000000 0.074940000000000 0.102740000000000 0.106870000000000 0.119150000000000 1 +000065: 0.004930000000000 0.962650000000000 0.002740000000000 0.004050000000000 0.002920000000000 0.007180000000000 0.003020000000000 0.012510000000000 1 +000066: 0.002000000000000 0.981310000000000 0.001510000000000 0.001130000000000 0.001350000000000 0.002440000000000 0.001250000000000 0.009010000000000 1 +000067: 0.001090000000000 0.996810000000000 0.000090000000000 0.000290000000000 0.000160000000000 0.000590000000000 0.000380000000000 0.000590000000000 1 +000068: 0.000000000000000 0.998160000000000 0.000180000000000 0.000110000000000 0.000140000000000 0.000930000000000 0.000000000000000 0.000480000000000 1 +000069: 0.011710000000000 0.930340000000000 0.007340000000000 0.013870000000000 0.009280000000000 0.009330000000000 0.007800000000000 0.010330000000000 1 +000070: 0.002240000000000 0.984940000000000 0.005970000000000 0.001170000000000 0.001930000000000 0.000290000000000 0.002630000000000 0.000830000000000 1 +000071: 0.000020000000000 0.999680000000000 0.000000000000000 0.000000000000000 0.000000000000000 0.000140000000000 0.000010000000000 0.000150000000000 1 +000072: 0.001250000000000 0.977050000000000 0.002900000000000 0.002690000000000 0.004640000000000 0.003170000000000 0.003350000000000 0.004950000000000 1 +000073: 0.000370000000000 0.995420000000000 0.001100000000000 0.000650000000000 0.000750000000000 0.000120000000000 0.001550000000000 0.000040000000000 1 +000074: 0.003540000000000 0.981360000000000 0.001100000000000 0.002420000000000 0.000750000000000 0.003290000000000 0.002030000000000 0.005510000000000 1 +000075: 0.005750000000000 0.972660000000000 0.003030000000000 0.003480000000000 0.002480000000000 0.005610000000000 0.001080000000000 0.005910000000000 1 + + + +Estimated Allele Frequencies +Cluster 01 +Locus 001 +Allele 092 0.102254538615875 +Allele 094 0.103166382210456 +Allele 096 0.094833606266653 +Allele 098 0.100798842929665 +Allele 100 0.106200415865899 +Allele 102 0.096132997154171 +Allele 104 0.117450719180492 +Allele 106 0.096845629629132 +Allele 108 0.089552861234718 +Allele 110 0.092764006912937 + +Locus 002 +Allele 094 0.070553698638980 +Allele 096 0.067992247486006 +Allele 098 0.075626491969450 +Allele 100 0.075042735498218 +Allele 102 0.070710897815935 +Allele 104 0.089134030893488 +Allele 106 0.081148526218942 +Allele 108 0.066705696752474 +Allele 110 0.068573535995313 +Allele 112 0.070845911280531 +Allele 114 0.065548129870315 +Allele 124 0.067365030078466 +Allele 126 0.065812127162096 +Allele 149 0.064940940339785 + +Locus 003 +Allele 118 0.046867182214804 +Allele 122 0.046946969441255 +Allele 124 0.053376292230112 +Allele 126 0.068326514700827 +Allele 128 0.047415280783521 +Allele 130 0.048375122999058 +Allele 132 0.048030106444006 +Allele 137 0.047970628978598 +Allele 202 0.048054099771939 +Allele 204 0.046656194839449 +Allele 206 0.046601185466552 +Allele 208 0.060574536244484 +Allele 210 0.047585112243033 +Allele 212 0.048172871061095 +Allele 214 0.052753893799234 +Allele 216 0.046870391434417 +Allele 218 0.047224850926448 +Allele 220 0.047082609772711 +Allele 224 0.047692201824079 +Allele 226 0.053423954824378 + +Locus 004 +Allele 124 0.041339944150405 +Allele 126 0.042943230123645 +Allele 127 0.045029150994315 +Allele 128 0.042527954120424 +Allele 130 0.041535860887155 +Allele 132 0.042948786176783 +Allele 134 0.040937097423767 +Allele 135 0.053407576454287 +Allele 137 0.044612723886077 +Allele 151 0.043711954142181 +Allele 208 0.045053425661612 +Allele 210 0.041971042593336 +Allele 212 0.041826450585693 +Allele 214 0.041290709888394 +Allele 216 0.044025857335082 +Allele 218 0.043463559342184 +Allele 220 0.041938484046996 +Allele 222 0.048233133436474 +Allele 224 0.041441512997749 +Allele 226 0.042336408754059 +Allele 228 0.041157042344980 +Allele 233 0.047051033080625 +Allele 238 0.041217061573775 + +Locus 005 +Allele 121 0.055221139651867 +Allele 123 0.060733386076600 +Allele 125 0.053060169129247 +Allele 127 0.051989287041156 +Allele 129 0.057061653326051 +Allele 130 0.051682452702310 +Allele 131 0.053156946405873 +Allele 133 0.053525609771171 +Allele 135 0.057656791347068 +Allele 136 0.053053507831959 +Allele 137 0.055327799380956 +Allele 138 0.060525846204612 +Allele 139 0.058030297205034 +Allele 141 0.051882881570583 +Allele 145 0.059297640400295 +Allele 146 0.054939390586781 +Allele 148 0.060834474304893 +Allele 150 0.052020727063543 + +Locus 006 +Allele 121 0.044157933011627 +Allele 123 0.045313949523824 +Allele 125 0.043843500242808 +Allele 129 0.042825015146907 +Allele 131 0.043518654612214 +Allele 133 0.050069439199543 +Allele 135 0.044804597855062 +Allele 136 0.042989970779098 +Allele 137 0.054277983032924 +Allele 138 0.044346470344530 +Allele 139 0.045664646169537 +Allele 141 0.043058722527962 +Allele 143 0.043010218138532 +Allele 145 0.044938542572940 +Allele 146 0.043283801696428 +Allele 147 0.046735101777155 +Allele 148 0.046555807409001 +Allele 150 0.044510725540561 +Allele 151 0.042891538294255 +Allele 152 0.057200136368994 +Allele 156 0.043067491268135 +Allele 161 0.042935754487962 + +Locus 007 +Allele 093 0.048117441936962 +Allele 095 0.045450223715449 +Allele 096 0.043234366247240 +Allele 097 0.043880830429209 +Allele 099 0.045729226218933 +Allele 100 0.043532540541031 +Allele 101 0.050371630015230 +Allele 103 0.051943053508060 +Allele 105 0.043518998433648 +Allele 107 0.043267679893754 +Allele 109 0.045874152615979 +Allele 110 0.043132062214482 +Allele 125 0.042824652617124 +Allele 161 0.043113344276854 +Allele 165 0.043110704629555 +Allele 167 0.046396396458103 +Allele 169 0.046072402653504 +Allele 171 0.052563936693629 +Allele 173 0.047539884211926 +Allele 175 0.043433456433103 +Allele 177 0.043473077390744 +Allele 181 0.043419938865479 + +Locus 008 +Allele 095 0.039923329857261 +Allele 097 0.041428064247830 +Allele 099 0.039613973600332 +Allele 100 0.040209682221327 +Allele 101 0.046979876449879 +Allele 103 0.049679513832988 +Allele 105 0.039387619420145 +Allele 107 0.040197943411535 +Allele 109 0.042207898550293 +Allele 110 0.039814753230656 +Allele 113 0.043745443413870 +Allele 121 0.041211351775287 +Allele 123 0.040323988823159 +Allele 131 0.039539576517060 +Allele 167 0.039612710485546 +Allele 169 0.040853572970793 +Allele 171 0.046374121533577 +Allele 173 0.043887353639724 +Allele 175 0.044812962553699 +Allele 177 0.040010238323223 +Allele 179 0.039679417478214 +Allele 181 0.040700438132606 +Allele 183 0.039826754942889 +Allele 185 0.039979414588108 + +Locus 009 +Allele 108 0.035279682951772 +Allele 115 0.032914810834247 +Allele 121 0.033826693921171 +Allele 123 0.034533344254718 +Allele 125 0.035290063026732 +Allele 127 0.033288851918866 +Allele 129 0.033723854991732 +Allele 131 0.033253796378991 +Allele 133 0.034632047304771 +Allele 135 0.036267070920055 +Allele 137 0.033045542739366 +Allele 139 0.033884704976294 +Allele 145 0.032888485705408 +Allele 147 0.037727565169363 +Allele 149 0.032657533440846 +Allele 152 0.036093634649024 +Allele 218 0.032905438206247 +Allele 220 0.033526414594355 +Allele 222 0.036903446665491 +Allele 224 0.035014569101492 +Allele 226 0.035833215301905 +Allele 228 0.032973901113469 +Allele 230 0.032830645547410 +Allele 232 0.039999769263320 +Allele 234 0.035455890304644 +Allele 236 0.033020645623171 +Allele 238 0.036079303649189 +Allele 240 0.033018921652907 +Allele 250 0.033130155793044 + +Locus 010 +Allele 123 0.027332492790990 +Allele 125 0.026963311541407 +Allele 127 0.026967389939322 +Allele 129 0.028830319974151 +Allele 131 0.028357483291893 +Allele 133 0.028862402759544 +Allele 135 0.027106521985341 +Allele 137 0.027327013474405 +Allele 139 0.027430796393355 +Allele 141 0.027316767415762 +Allele 143 0.026861001884927 +Allele 145 0.026718684693125 +Allele 147 0.030856992897189 +Allele 149 0.029445456807254 +Allele 152 0.026799294977379 +Allele 155 0.026869449287576 +Allele 157 0.029198607679740 +Allele 220 0.026736866096266 +Allele 222 0.029413571298927 +Allele 224 0.026542367436750 +Allele 226 0.029933017177586 +Allele 228 0.026897598436372 +Allele 230 0.027607645610155 +Allele 232 0.026799829705244 +Allele 234 0.028232667898467 +Allele 236 0.031870937646469 +Allele 238 0.028913216737086 +Allele 240 0.027479919224828 +Allele 242 0.026887291704180 +Allele 244 0.027016168415592 +Allele 246 0.026923799220093 +Allele 248 0.026791681884836 +Allele 250 0.026871138071163 +Allele 252 0.026916884010802 +Allele 254 0.026640571372409 +Allele 256 0.028280840259414 + + +Cluster 02 +Locus 001 +Allele 092 0.038705522682578 +Allele 094 0.396223826650215 +Allele 096 0.165249146331358 +Allele 098 0.087871132595749 +Allele 100 0.023873486718563 +Allele 102 0.083698257367678 +Allele 104 0.104606874189043 +Allele 106 0.048715916965192 +Allele 108 0.026387943219140 +Allele 110 0.024667893280480 + +Locus 002 +Allele 094 0.107805250532745 +Allele 096 0.077190414305902 +Allele 098 0.150544754699951 +Allele 100 0.065458245547571 +Allele 102 0.107112964723833 +Allele 104 0.192315875298431 +Allele 106 0.124578299941765 +Allele 108 0.064809563368980 +Allele 110 0.037134934668783 +Allele 112 0.022445104682178 +Allele 114 0.013166935903111 +Allele 124 0.011413338921954 +Allele 126 0.012871356804480 +Allele 149 0.013152960600317 + +Locus 003 +Allele 118 0.018932901002911 +Allele 122 0.031451698954451 +Allele 124 0.182824537303463 +Allele 126 0.088161249763833 +Allele 128 0.062657765630385 +Allele 130 0.035904016931074 +Allele 132 0.062119941869818 +Allele 137 0.011545655582314 +Allele 202 0.011543409311670 +Allele 204 0.025283976306486 +Allele 206 0.012577495753774 +Allele 208 0.113459845769433 +Allele 210 0.037290295781828 +Allele 212 0.099325598202931 +Allele 214 0.069634326439338 +Allele 216 0.044068962061728 +Allele 218 0.049923354435607 +Allele 220 0.012553550196848 +Allele 224 0.023985711266856 +Allele 226 0.006755707435248 + +Locus 004 +Allele 124 0.024459768749280 +Allele 126 0.028603710810439 +Allele 127 0.008015493052641 +Allele 128 0.041923845729013 +Allele 130 0.042930331354883 +Allele 132 0.171736717826267 +Allele 134 0.012403348763386 +Allele 135 0.093053544500074 +Allele 137 0.063828589858532 +Allele 151 0.009656196850232 +Allele 208 0.014637228149951 +Allele 210 0.011019343312868 +Allele 212 0.085976379010173 +Allele 214 0.037043336671033 +Allele 216 0.071144211782102 +Allele 218 0.015554911473613 +Allele 220 0.048592971877292 +Allele 222 0.053909331252801 +Allele 224 0.092338453762184 +Allele 226 0.036110238490095 +Allele 228 0.018369923969380 +Allele 233 0.006648391205909 +Allele 238 0.012043731547846 + +Locus 005 +Allele 121 0.057797969049725 +Allele 123 0.053204471819715 +Allele 125 0.039594148659210 +Allele 127 0.013321520598754 +Allele 129 0.028676427017806 +Allele 130 0.026943003041813 +Allele 131 0.127486025608285 +Allele 133 0.072370344127234 +Allele 135 0.055833952509895 +Allele 136 0.120437951816036 +Allele 137 0.023882035474456 +Allele 138 0.092210655451837 +Allele 139 0.095695489151639 +Allele 141 0.026846716846405 +Allele 145 0.034253820990322 +Allele 146 0.071672796865383 +Allele 148 0.046321687295843 +Allele 150 0.013450983675640 + +Locus 006 +Allele 121 0.025202209157057 +Allele 123 0.023263171104173 +Allele 125 0.018623339060391 +Allele 129 0.026375117967440 +Allele 131 0.117619998989025 +Allele 133 0.071916787061191 +Allele 135 0.109762486448609 +Allele 136 0.026124354569692 +Allele 137 0.040890397212465 +Allele 138 0.018007316818324 +Allele 139 0.049343920825294 +Allele 141 0.019240823912800 +Allele 143 0.013172688470065 +Allele 145 0.056322010378255 +Allele 146 0.052453761310316 +Allele 147 0.008512370726621 +Allele 148 0.108578320882186 +Allele 150 0.076947791853931 +Allele 151 0.013143615706383 +Allele 152 0.091517565596629 +Allele 156 0.019866474554558 +Allele 161 0.013115477394596 + +Locus 007 +Allele 093 0.049256927819888 +Allele 095 0.071010936405965 +Allele 096 0.013425935872805 +Allele 097 0.154039134356250 +Allele 099 0.037342899437118 +Allele 100 0.059975493583973 +Allele 101 0.038857492949719 +Allele 103 0.051739322983936 +Allele 105 0.019763260662913 +Allele 107 0.026711586475447 +Allele 109 0.010050319029888 +Allele 110 0.013158417743972 +Allele 125 0.013486435134775 +Allele 161 0.013406415859834 +Allele 165 0.026923514127310 +Allele 167 0.043475415830697 +Allele 169 0.063548666047281 +Allele 171 0.138347368867085 +Allele 173 0.075430189561215 +Allele 175 0.046865786236772 +Allele 177 0.020182860749201 +Allele 181 0.013001620263950 + +Locus 008 +Allele 095 0.013233931071105 +Allele 097 0.050927120987851 +Allele 099 0.026576527937834 +Allele 100 0.038847490617410 +Allele 101 0.117333606486762 +Allele 103 0.088512934758531 +Allele 105 0.039951608581766 +Allele 107 0.079103553169677 +Allele 109 0.016536301157892 +Allele 110 0.019613845586095 +Allele 113 0.016084897388904 +Allele 121 0.018548400350965 +Allele 123 0.019570139057166 +Allele 131 0.013235268174299 +Allele 167 0.013320475489033 +Allele 169 0.025362962382807 +Allele 171 0.091755054882070 +Allele 173 0.087588134891577 +Allele 175 0.047349585880456 +Allele 177 0.079204949485435 +Allele 179 0.013277842545706 +Allele 181 0.031650202238564 +Allele 183 0.026148157864425 +Allele 185 0.026267009013666 + +Locus 009 +Allele 108 0.027006483281352 +Allele 115 0.011827473666303 +Allele 121 0.010488466412124 +Allele 123 0.039409284962560 +Allele 125 0.085796874433366 +Allele 127 0.041141196300321 +Allele 129 0.046231642607656 +Allele 131 0.047071004894044 +Allele 133 0.092780479335749 +Allele 135 0.025446637782731 +Allele 137 0.017719625753977 +Allele 139 0.016596231345788 +Allele 145 0.017733846778563 +Allele 147 0.006365299450389 +Allele 149 0.011835097061085 +Allele 152 0.008501479545287 +Allele 218 0.011784372954682 +Allele 220 0.088112934715205 +Allele 222 0.108954873132954 +Allele 224 0.085841889423244 +Allele 226 0.037950398949448 +Allele 228 0.023539632811019 +Allele 230 0.017739634281412 +Allele 232 0.021145097499330 +Allele 234 0.032369567299451 +Allele 236 0.017730371828620 +Allele 238 0.019439665592463 +Allele 240 0.017625399546498 +Allele 250 0.011815038354377 + +Locus 010 +Allele 123 0.010102863140592 +Allele 125 0.011065812545348 +Allele 127 0.033649102211513 +Allele 129 0.037079799742137 +Allele 131 0.042772209143702 +Allele 133 0.065660822698646 +Allele 135 0.073783619187989 +Allele 137 0.067189689932126 +Allele 139 0.015965468154172 +Allele 141 0.039004992766493 +Allele 143 0.011234814346598 +Allele 145 0.017156649113312 +Allele 147 0.011687437450403 +Allele 149 0.018651483911651 +Allele 152 0.011333622853543 +Allele 155 0.011245275341669 +Allele 157 0.013874471837618 +Allele 220 0.011330194221276 +Allele 222 0.018647557257945 +Allele 224 0.045740293202108 +Allele 226 0.053086317858318 +Allele 228 0.028213544802080 +Allele 230 0.032834409426100 +Allele 232 0.039870033536890 +Allele 234 0.037342871217804 +Allele 236 0.038898605046695 +Allele 238 0.054222759866560 +Allele 240 0.027547338508412 +Allele 242 0.033736182445848 +Allele 244 0.010854780458971 +Allele 246 0.016789297061444 +Allele 248 0.011307349611456 +Allele 250 0.011342614202868 +Allele 252 0.016852135978634 +Allele 254 0.011406306807358 +Allele 256 0.008519274111721 + + +Cluster 03 +Locus 001 +Allele 092 0.101861180593191 +Allele 094 0.101900598532000 +Allele 096 0.094151357020844 +Allele 098 0.098790048985872 +Allele 100 0.107548277592979 +Allele 102 0.095630974990193 +Allele 104 0.113996632495096 +Allele 106 0.101454801913405 +Allele 108 0.091253527991743 +Allele 110 0.093412599884673 + +Locus 002 +Allele 094 0.070527511590167 +Allele 096 0.067947883207221 +Allele 098 0.072631796100699 +Allele 100 0.073467489855168 +Allele 102 0.073010364447859 +Allele 104 0.086186619345154 +Allele 106 0.084038485001149 +Allele 108 0.066698196659701 +Allele 110 0.068725647701047 +Allele 112 0.070131341765111 +Allele 114 0.066175805327796 +Allele 124 0.067401950895350 +Allele 126 0.066825022693761 +Allele 149 0.066231885409816 + +Locus 003 +Allele 118 0.047075782220186 +Allele 122 0.047738895948651 +Allele 124 0.053809664692316 +Allele 126 0.063182009471337 +Allele 128 0.047604567152547 +Allele 130 0.049289648068058 +Allele 132 0.048271488008755 +Allele 137 0.048069025435291 +Allele 202 0.048475492693257 +Allele 204 0.047381438771363 +Allele 206 0.047207385664052 +Allele 208 0.057910477098925 +Allele 210 0.047813270162312 +Allele 212 0.048562376958863 +Allele 214 0.054439327634153 +Allele 216 0.047538328308567 +Allele 218 0.047818019591373 +Allele 220 0.047410429954098 +Allele 224 0.048419254528503 +Allele 226 0.051983117637398 + +Locus 004 +Allele 124 0.041580355531585 +Allele 126 0.042038028349589 +Allele 127 0.044731153716554 +Allele 128 0.042408709559466 +Allele 130 0.041804691437739 +Allele 132 0.043321379481349 +Allele 134 0.041532783857862 +Allele 135 0.050545097095629 +Allele 137 0.046723674979440 +Allele 151 0.043507411998067 +Allele 208 0.043934029559482 +Allele 210 0.042931794226619 +Allele 212 0.042109037784958 +Allele 214 0.041650501365534 +Allele 216 0.043201028579461 +Allele 218 0.045312568944002 +Allele 220 0.042349045479347 +Allele 222 0.047174432293339 +Allele 224 0.041986110297092 +Allele 226 0.042367930710634 +Allele 228 0.041431776834117 +Allele 233 0.045822616487321 +Allele 238 0.041535841430812 + +Locus 005 +Allele 121 0.054540095876909 +Allele 123 0.059385067656261 +Allele 125 0.053015034562301 +Allele 127 0.052743516944451 +Allele 129 0.056903175701250 +Allele 130 0.053169467944159 +Allele 131 0.053896372149618 +Allele 133 0.054697584905304 +Allele 135 0.056055232786887 +Allele 136 0.053384150555920 +Allele 137 0.054984727021144 +Allele 138 0.062564568233448 +Allele 139 0.057708986172668 +Allele 141 0.053212719500136 +Allele 145 0.057809131347204 +Allele 146 0.054926096008543 +Allele 148 0.058360255468978 +Allele 150 0.052643817164824 + +Locus 006 +Allele 121 0.044080475922833 +Allele 123 0.045662668554776 +Allele 125 0.043409859088814 +Allele 129 0.043246927182429 +Allele 131 0.044170292340147 +Allele 133 0.048506328589646 +Allele 135 0.045366144095524 +Allele 136 0.043640789323122 +Allele 137 0.051518291507765 +Allele 138 0.044381005241684 +Allele 139 0.047896728254110 +Allele 141 0.043657626346209 +Allele 143 0.043596066036860 +Allele 145 0.046345938475540 +Allele 146 0.043807359001524 +Allele 147 0.047049021952068 +Allele 148 0.045870970170104 +Allele 150 0.044485560669378 +Allele 151 0.043650400881266 +Allele 152 0.052727996029106 +Allele 156 0.043128482284695 +Allele 161 0.043801068052398 + +Locus 007 +Allele 093 0.046339458343485 +Allele 095 0.045770576687851 +Allele 096 0.043525805538326 +Allele 097 0.044225819966528 +Allele 099 0.045095202187584 +Allele 100 0.044112276767063 +Allele 101 0.049333020016687 +Allele 103 0.050361161636189 +Allele 105 0.043772066867758 +Allele 107 0.043601686795576 +Allele 109 0.047575659060853 +Allele 110 0.044034591479628 +Allele 125 0.043583861479494 +Allele 161 0.043674886685493 +Allele 165 0.043584804000085 +Allele 167 0.045439405737383 +Allele 169 0.047623838112950 +Allele 171 0.050333727533094 +Allele 173 0.047323342190161 +Allele 175 0.043379203712129 +Allele 177 0.043600688804935 +Allele 181 0.043708916396747 + +Locus 008 +Allele 095 0.040100538120784 +Allele 097 0.041919297813321 +Allele 099 0.040013297733725 +Allele 100 0.040658105030212 +Allele 101 0.045797543725054 +Allele 103 0.047565634481420 +Allele 105 0.039936513913057 +Allele 107 0.040401778372245 +Allele 109 0.043992672360947 +Allele 110 0.040291274793140 +Allele 113 0.042130135912103 +Allele 121 0.040742013882827 +Allele 123 0.040243043804800 +Allele 131 0.040112633019821 +Allele 167 0.040104385007841 +Allele 169 0.040743543291399 +Allele 171 0.046353200621574 +Allele 173 0.043562053468614 +Allele 175 0.043089552903149 +Allele 177 0.040256722210375 +Allele 179 0.040022176838161 +Allele 181 0.041539241159949 +Allele 183 0.040292148360631 +Allele 185 0.040132493174851 + +Locus 009 +Allele 108 0.034765556526520 +Allele 115 0.033128395788634 +Allele 121 0.034238565725006 +Allele 123 0.033974322875345 +Allele 125 0.036662187735797 +Allele 127 0.033346729411623 +Allele 129 0.034268428130620 +Allele 131 0.033617180670162 +Allele 133 0.034319508762196 +Allele 135 0.035899393858220 +Allele 137 0.033124682652775 +Allele 139 0.034076864256933 +Allele 145 0.033309592204389 +Allele 147 0.036683998681095 +Allele 149 0.033261397527014 +Allele 152 0.034974974054113 +Allele 218 0.033193773709898 +Allele 220 0.034091388678740 +Allele 222 0.035348602731685 +Allele 224 0.035667678360336 +Allele 226 0.035280430049282 +Allele 228 0.033415680259747 +Allele 230 0.033239014731151 +Allele 232 0.039872062536835 +Allele 234 0.034554700165578 +Allele 236 0.033302506601113 +Allele 238 0.035892434468042 +Allele 240 0.033373168766493 +Allele 250 0.033116780080663 + +Locus 010 +Allele 123 0.027762558842639 +Allele 125 0.026978197059305 +Allele 127 0.027272227329084 +Allele 129 0.028364118648652 +Allele 131 0.029553280331299 +Allele 133 0.028150575004929 +Allele 135 0.027075580300309 +Allele 137 0.027698942561200 +Allele 139 0.027553476351642 +Allele 141 0.027258075628590 +Allele 143 0.026938429883935 +Allele 145 0.026826112456172 +Allele 147 0.029779804923758 +Allele 149 0.029265827075446 +Allele 152 0.026901641754707 +Allele 155 0.027081994231098 +Allele 157 0.028496518445840 +Allele 220 0.026971199479957 +Allele 222 0.029209633698167 +Allele 224 0.026972711281575 +Allele 226 0.028627477742978 +Allele 228 0.027018783942766 +Allele 230 0.027924048613359 +Allele 232 0.026925798199984 +Allele 234 0.028667398810900 +Allele 236 0.030468716379581 +Allele 238 0.028573413314923 +Allele 240 0.027223243333686 +Allele 242 0.027163070938138 +Allele 244 0.026880182298394 +Allele 246 0.027042965433296 +Allele 248 0.026849482260683 +Allele 250 0.027000134759511 +Allele 252 0.027137230644223 +Allele 254 0.026944884187629 +Allele 256 0.029442263851646 + + +Cluster 04 +Locus 001 +Allele 092 0.102522477460090 +Allele 094 0.102564523403521 +Allele 096 0.095012852997789 +Allele 098 0.099678924878655 +Allele 100 0.105291263609453 +Allele 102 0.096653610622594 +Allele 104 0.115797230959172 +Allele 106 0.098575421457026 +Allele 108 0.090749014654246 +Allele 110 0.093154679957455 + +Locus 002 +Allele 094 0.070222965821283 +Allele 096 0.067649362953752 +Allele 098 0.074094553264387 +Allele 100 0.075389121173006 +Allele 102 0.071643209555299 +Allele 104 0.087847832290054 +Allele 106 0.081933355366608 +Allele 108 0.067084655261358 +Allele 110 0.068204061997784 +Allele 112 0.070817595598213 +Allele 114 0.065899200838122 +Allele 124 0.067327557731194 +Allele 126 0.066192528035657 +Allele 149 0.065694000113285 + +Locus 003 +Allele 118 0.047240240348216 +Allele 122 0.047289608125581 +Allele 124 0.052981154268258 +Allele 126 0.065262843993269 +Allele 128 0.047429700468085 +Allele 130 0.049331653287753 +Allele 132 0.048468116537991 +Allele 137 0.048295734040054 +Allele 202 0.048358689404923 +Allele 204 0.047185555000838 +Allele 206 0.046927363467394 +Allele 208 0.058832465032456 +Allele 210 0.047723027308206 +Allele 212 0.048770075688131 +Allele 214 0.053216601088779 +Allele 216 0.047230007707669 +Allele 218 0.047221377925282 +Allele 220 0.047156816077884 +Allele 224 0.048449765850582 +Allele 226 0.052629204378652 + +Locus 004 +Allele 124 0.041734598592131 +Allele 126 0.042654718692041 +Allele 127 0.045066955348704 +Allele 128 0.041799045507418 +Allele 130 0.041687288478745 +Allele 132 0.043250141283708 +Allele 134 0.041117618328686 +Allele 135 0.052014446440423 +Allele 137 0.045236502803176 +Allele 151 0.043671975376411 +Allele 208 0.045005874556401 +Allele 210 0.042706139150304 +Allele 212 0.042413947538286 +Allele 214 0.041397628099754 +Allele 216 0.043061766012318 +Allele 218 0.043694998004266 +Allele 220 0.042228538729608 +Allele 222 0.047897176387999 +Allele 224 0.041663770173500 +Allele 226 0.042156454184030 +Allele 228 0.041507862852396 +Allele 233 0.046320928056466 +Allele 238 0.041711625403228 + +Locus 005 +Allele 121 0.054086047450816 +Allele 123 0.059890636371689 +Allele 125 0.053000967967492 +Allele 127 0.052276183021080 +Allele 129 0.057421571222594 +Allele 130 0.052372334333130 +Allele 131 0.053944605508120 +Allele 133 0.054191874935064 +Allele 135 0.056970921287053 +Allele 136 0.053497247026930 +Allele 137 0.055558552241564 +Allele 138 0.060498030909274 +Allele 139 0.058691253298372 +Allele 141 0.052303428129114 +Allele 145 0.058676788398664 +Allele 146 0.054646954956644 +Allele 148 0.059559073027523 +Allele 150 0.052413529914876 + +Locus 006 +Allele 121 0.043548731255726 +Allele 123 0.045315548199084 +Allele 125 0.043688002872186 +Allele 129 0.043528253833440 +Allele 131 0.043969941020767 +Allele 133 0.049229407487463 +Allele 135 0.045409586414852 +Allele 136 0.043354274783569 +Allele 137 0.053098917862346 +Allele 138 0.044114914797239 +Allele 139 0.046119973172815 +Allele 141 0.043625069979859 +Allele 143 0.043169913438197 +Allele 145 0.045986203065234 +Allele 146 0.043584160834347 +Allele 147 0.046947160313248 +Allele 148 0.045374470942529 +Allele 150 0.044996459456853 +Allele 151 0.043375940301520 +Allele 152 0.054883612211084 +Allele 156 0.043297405185138 +Allele 161 0.043382052572506 + +Locus 007 +Allele 093 0.047467985597956 +Allele 095 0.045264802389765 +Allele 096 0.043402873803923 +Allele 097 0.044215095916421 +Allele 099 0.045192562856853 +Allele 100 0.043917373757600 +Allele 101 0.049898561228350 +Allele 103 0.051334382458034 +Allele 105 0.043636264401519 +Allele 107 0.043718220411026 +Allele 109 0.045819660224295 +Allele 110 0.043673869382323 +Allele 125 0.043438787597059 +Allele 161 0.043468469336678 +Allele 165 0.043536289672840 +Allele 167 0.045220937069879 +Allele 169 0.046482647918111 +Allele 171 0.051296402217222 +Allele 173 0.048136145406387 +Allele 175 0.043638214871012 +Allele 177 0.043471561762282 +Allele 181 0.043768891720460 + +Locus 008 +Allele 095 0.039907219409041 +Allele 097 0.041794041943297 +Allele 099 0.039862479211002 +Allele 100 0.040797162216636 +Allele 101 0.046265233493595 +Allele 103 0.048413140845008 +Allele 105 0.039968677455209 +Allele 107 0.040367795149168 +Allele 109 0.042559110058751 +Allele 110 0.040248916261786 +Allele 113 0.042872706707345 +Allele 121 0.040962460096806 +Allele 123 0.040302531888275 +Allele 131 0.039900447794359 +Allele 167 0.039738825224681 +Allele 169 0.040619037211530 +Allele 171 0.045261470298042 +Allele 173 0.044084610818917 +Allele 175 0.044085655247939 +Allele 177 0.040610433005274 +Allele 179 0.039840791946715 +Allele 181 0.041172801932202 +Allele 183 0.040161637836165 +Allele 185 0.040202813948260 + +Locus 009 +Allele 108 0.034986736638477 +Allele 115 0.033111523364641 +Allele 121 0.034134430027240 +Allele 123 0.034100136445744 +Allele 125 0.035570008057203 +Allele 127 0.033359264091015 +Allele 129 0.034112614142633 +Allele 131 0.033686645016532 +Allele 133 0.034096412985872 +Allele 135 0.036128531793491 +Allele 137 0.032997334909834 +Allele 139 0.034153519992865 +Allele 145 0.033193488998405 +Allele 147 0.037204799162892 +Allele 149 0.033188568407185 +Allele 152 0.035588318827613 +Allele 218 0.033028016521055 +Allele 220 0.033939787347972 +Allele 222 0.036077307570173 +Allele 224 0.035515880185865 +Allele 226 0.035626560638111 +Allele 228 0.033509670198700 +Allele 230 0.033154211049606 +Allele 232 0.039223911817216 +Allele 234 0.034572855649982 +Allele 236 0.033088848976916 +Allele 238 0.036306189944180 +Allele 240 0.033257991427016 +Allele 250 0.033086435811566 + +Locus 010 +Allele 123 0.027730333309457 +Allele 125 0.026961667945091 +Allele 127 0.027315758319754 +Allele 129 0.028509094694494 +Allele 131 0.028636269214621 +Allele 133 0.028137466341491 +Allele 135 0.027163723663412 +Allele 137 0.027540298222531 +Allele 139 0.027487270431355 +Allele 141 0.027343617860926 +Allele 143 0.027106230019570 +Allele 145 0.026818612398690 +Allele 147 0.030152425633135 +Allele 149 0.029473604273166 +Allele 152 0.026764298261468 +Allele 155 0.026831807218974 +Allele 157 0.028878892139263 +Allele 220 0.026916115159053 +Allele 222 0.029317711131024 +Allele 224 0.026706848521426 +Allele 226 0.029326794717268 +Allele 228 0.027140724160243 +Allele 230 0.027728765490784 +Allele 232 0.027040615397584 +Allele 234 0.028689753672493 +Allele 236 0.031015757419535 +Allele 238 0.028588620665992 +Allele 240 0.027290197830803 +Allele 242 0.027245230259884 +Allele 244 0.026994210575507 +Allele 246 0.027079011552951 +Allele 248 0.026924442811044 +Allele 250 0.026759958964701 +Allele 252 0.026976287397706 +Allele 254 0.026909228406631 +Allele 256 0.028498355917974 + + +Cluster 05 +Locus 001 +Allele 092 0.100318462883736 +Allele 094 0.104182550677381 +Allele 096 0.096481358349831 +Allele 098 0.101463033158676 +Allele 100 0.103957964561154 +Allele 102 0.097669189900817 +Allele 104 0.112084643927706 +Allele 106 0.097759498956266 +Allele 108 0.092054173109346 +Allele 110 0.094029124475085 + +Locus 002 +Allele 094 0.069420470107329 +Allele 096 0.068090113245403 +Allele 098 0.075613859776593 +Allele 100 0.074020794666163 +Allele 102 0.070616384780273 +Allele 104 0.084693323919296 +Allele 106 0.080452972187231 +Allele 108 0.067598823774954 +Allele 110 0.069108184610292 +Allele 112 0.070851741754119 +Allele 114 0.066972703995748 +Allele 124 0.069278740731566 +Allele 126 0.066757827814759 +Allele 149 0.066524058636272 + +Locus 003 +Allele 118 0.047506105361798 +Allele 122 0.047611160513430 +Allele 124 0.053690423222724 +Allele 126 0.063054045673158 +Allele 128 0.047657413416995 +Allele 130 0.049132984782993 +Allele 132 0.048368865278641 +Allele 137 0.048568461014435 +Allele 202 0.048392129502229 +Allele 204 0.047354862776289 +Allele 206 0.047493606556682 +Allele 208 0.058901173951724 +Allele 210 0.047718823767745 +Allele 212 0.048802542271073 +Allele 214 0.051390875633024 +Allele 216 0.047636709363931 +Allele 218 0.048215646195842 +Allele 220 0.047494830982563 +Allele 224 0.048463130955256 +Allele 226 0.052546208779465 + +Locus 004 +Allele 124 0.041679264678725 +Allele 126 0.043616743638925 +Allele 127 0.044462822322516 +Allele 128 0.042765761844266 +Allele 130 0.041875312627377 +Allele 132 0.043242187539893 +Allele 134 0.041537407107027 +Allele 135 0.051388637103329 +Allele 137 0.044587132366509 +Allele 151 0.043098565177910 +Allele 208 0.044552915873796 +Allele 210 0.042706833925867 +Allele 212 0.042252973442954 +Allele 214 0.041854832616898 +Allele 216 0.044514697213296 +Allele 218 0.043170507009060 +Allele 220 0.042566420049080 +Allele 222 0.046430536133790 +Allele 224 0.041973599856062 +Allele 226 0.042527777079949 +Allele 228 0.041719208335517 +Allele 233 0.045682036214113 +Allele 238 0.041793827843141 + +Locus 005 +Allele 121 0.055873746207153 +Allele 123 0.059306641338420 +Allele 125 0.053212555921866 +Allele 127 0.052896862667993 +Allele 129 0.056509897302396 +Allele 130 0.052515013669065 +Allele 131 0.053351236025406 +Allele 133 0.054788250189509 +Allele 135 0.057313649365273 +Allele 136 0.053889690558079 +Allele 137 0.054584863993396 +Allele 138 0.061528335603196 +Allele 139 0.056702473320971 +Allele 141 0.052947417156062 +Allele 145 0.058213864678529 +Allele 146 0.055202915771573 +Allele 148 0.058777416315869 +Allele 150 0.052385169915242 + +Locus 006 +Allele 121 0.044372528972877 +Allele 123 0.046390855200616 +Allele 125 0.044118026244670 +Allele 129 0.043414158089853 +Allele 131 0.044137202817584 +Allele 133 0.049155824056170 +Allele 135 0.045352226060837 +Allele 136 0.043292991210176 +Allele 137 0.051281685398309 +Allele 138 0.045136510067736 +Allele 139 0.045299555816214 +Allele 141 0.043895644745041 +Allele 143 0.043508736448831 +Allele 145 0.045789863015145 +Allele 146 0.043837915187406 +Allele 147 0.046164797342452 +Allele 148 0.046161769343384 +Allele 150 0.045041784140264 +Allele 151 0.043324771539150 +Allele 152 0.053314867885341 +Allele 156 0.043442303361340 +Allele 161 0.043565983056606 + +Locus 007 +Allele 093 0.046995714362430 +Allele 095 0.046450128278569 +Allele 096 0.043845566636261 +Allele 097 0.044357229706368 +Allele 099 0.046027500868822 +Allele 100 0.044096316458308 +Allele 101 0.048141453987404 +Allele 103 0.050674385437153 +Allele 105 0.043759014697001 +Allele 107 0.043977045447856 +Allele 109 0.045532253300776 +Allele 110 0.043527091909251 +Allele 125 0.043678555712633 +Allele 161 0.043720225730175 +Allele 165 0.043622252029664 +Allele 167 0.046772483289430 +Allele 169 0.045649311130037 +Allele 171 0.050833586633852 +Allele 173 0.046890152917789 +Allele 175 0.043874988260379 +Allele 177 0.043550075778029 +Allele 181 0.044024667427816 + +Locus 008 +Allele 095 0.040041661560053 +Allele 097 0.042082031183963 +Allele 099 0.040014200128167 +Allele 100 0.040890465431305 +Allele 101 0.045057813034204 +Allele 103 0.048603355953558 +Allele 105 0.040281792350746 +Allele 107 0.040492455649099 +Allele 109 0.041871284804067 +Allele 110 0.040326646893283 +Allele 113 0.043036005880831 +Allele 121 0.040929941101401 +Allele 123 0.040417381547346 +Allele 131 0.040135947811470 +Allele 167 0.040216331907379 +Allele 169 0.040854221782531 +Allele 171 0.044438039844388 +Allele 173 0.042863869658348 +Allele 175 0.044552440282088 +Allele 177 0.040541608277130 +Allele 179 0.040078781044395 +Allele 181 0.041723325538882 +Allele 183 0.040412275621583 +Allele 185 0.040138122713784 + +Locus 009 +Allele 108 0.034402047378477 +Allele 115 0.033154806380614 +Allele 121 0.034384782397412 +Allele 123 0.034969389172978 +Allele 125 0.035093587615493 +Allele 127 0.033412906014951 +Allele 129 0.033996886431781 +Allele 131 0.033480547125628 +Allele 133 0.034704324765132 +Allele 135 0.035549011587823 +Allele 137 0.033169807002540 +Allele 139 0.034155659416888 +Allele 145 0.033270510205175 +Allele 147 0.036690216629224 +Allele 149 0.033356846336113 +Allele 152 0.035665428454607 +Allele 218 0.033208942860473 +Allele 220 0.034084090039605 +Allele 222 0.036179880514474 +Allele 224 0.035662395460282 +Allele 226 0.035218698169529 +Allele 228 0.033317763037557 +Allele 230 0.033359407616546 +Allele 232 0.038372791517256 +Allele 234 0.035622693607169 +Allele 236 0.033195692397530 +Allele 238 0.035443027667736 +Allele 240 0.033570343389868 +Allele 250 0.033307516807140 + +Locus 010 +Allele 123 0.027861124251335 +Allele 125 0.027197255997019 +Allele 127 0.027155665622135 +Allele 129 0.028080793611370 +Allele 131 0.028202970792577 +Allele 133 0.028894010589029 +Allele 135 0.027194053828682 +Allele 137 0.027680348665328 +Allele 139 0.027575146638974 +Allele 141 0.027687264627399 +Allele 143 0.026957323542652 +Allele 145 0.026871156161979 +Allele 147 0.030036499764689 +Allele 149 0.028953422423766 +Allele 152 0.026901354823819 +Allele 155 0.026867996172250 +Allele 157 0.029106430060781 +Allele 220 0.027067603355472 +Allele 222 0.028883896994737 +Allele 224 0.026868706356957 +Allele 226 0.029553640935941 +Allele 228 0.027111947805832 +Allele 230 0.027655219077225 +Allele 232 0.026930824719080 +Allele 234 0.028507290501562 +Allele 236 0.031040214836344 +Allele 238 0.027927052339688 +Allele 240 0.027569517122648 +Allele 242 0.027259994260959 +Allele 244 0.027423262264011 +Allele 246 0.027081648745583 +Allele 248 0.026836000150150 +Allele 250 0.026935062863390 +Allele 252 0.026998057214346 +Allele 254 0.026917473576397 +Allele 256 0.028209769305895 + + +Cluster 06 +Locus 001 +Allele 092 0.102657235221974 +Allele 094 0.103856335060983 +Allele 096 0.095129820286188 +Allele 098 0.098581474275640 +Allele 100 0.105329316736377 +Allele 102 0.095602469874996 +Allele 104 0.115740822181935 +Allele 106 0.097751930449708 +Allele 108 0.091801479976627 +Allele 110 0.093549115935573 + +Locus 002 +Allele 094 0.070889197858808 +Allele 096 0.067969361385055 +Allele 098 0.074252522587229 +Allele 100 0.074664310300872 +Allele 102 0.071640034570541 +Allele 104 0.087374794905348 +Allele 106 0.082185058059900 +Allele 108 0.066998796014713 +Allele 110 0.068165334840462 +Allele 112 0.070055596281735 +Allele 114 0.065937499861897 +Allele 124 0.068025673321105 +Allele 126 0.066249350420921 +Allele 149 0.065592469591420 + +Locus 003 +Allele 118 0.047206768336300 +Allele 122 0.047259978547891 +Allele 124 0.053737499500473 +Allele 126 0.064895943747377 +Allele 128 0.047624047258535 +Allele 130 0.049138354397240 +Allele 132 0.048398962963205 +Allele 137 0.047762086581001 +Allele 202 0.048064061503825 +Allele 204 0.047073179412447 +Allele 206 0.047261380804525 +Allele 208 0.058588968492350 +Allele 210 0.047631051648416 +Allele 212 0.048482088248313 +Allele 214 0.053261924513987 +Allele 216 0.047369417570400 +Allele 218 0.047851344078127 +Allele 220 0.047320087218650 +Allele 224 0.048496319662288 +Allele 226 0.052576535514649 + +Locus 004 +Allele 124 0.041813811588669 +Allele 126 0.043219302404950 +Allele 127 0.044914383681974 +Allele 128 0.042541264397888 +Allele 130 0.041515918334806 +Allele 132 0.043226781926626 +Allele 134 0.040983545226988 +Allele 135 0.051167291014462 +Allele 137 0.044794862221499 +Allele 151 0.043758345037860 +Allele 208 0.044041789712192 +Allele 210 0.042426221809771 +Allele 212 0.042097144926132 +Allele 214 0.041411865947401 +Allele 216 0.044040830471864 +Allele 218 0.044238682926428 +Allele 220 0.042157214553767 +Allele 222 0.048082715583683 +Allele 224 0.041893620040521 +Allele 226 0.042138426177598 +Allele 228 0.041566141344485 +Allele 233 0.046347095676587 +Allele 238 0.041622744993850 + +Locus 005 +Allele 121 0.055101398731154 +Allele 123 0.059776862040176 +Allele 125 0.053585708739835 +Allele 127 0.052504671234753 +Allele 129 0.057440479887593 +Allele 130 0.052260921874984 +Allele 131 0.053564213821742 +Allele 133 0.054483679686872 +Allele 135 0.056483834968207 +Allele 136 0.053547151602467 +Allele 137 0.055201432369948 +Allele 138 0.061285189114873 +Allele 139 0.058089450117095 +Allele 141 0.052305100600769 +Allele 145 0.058281618153321 +Allele 146 0.054670581875381 +Allele 148 0.059233836515424 +Allele 150 0.052183868665410 + +Locus 006 +Allele 121 0.043994881400912 +Allele 123 0.045860183702219 +Allele 125 0.043934051272857 +Allele 129 0.043289981847806 +Allele 131 0.043836324002622 +Allele 133 0.048939859209975 +Allele 135 0.045449063735631 +Allele 136 0.043318176978466 +Allele 137 0.052377248672382 +Allele 138 0.044808683653025 +Allele 139 0.046136310609188 +Allele 141 0.043866386759391 +Allele 143 0.043302128073424 +Allele 145 0.045406239923303 +Allele 146 0.043321539416490 +Allele 147 0.047353402639767 +Allele 148 0.045934042651682 +Allele 150 0.044870012001919 +Allele 151 0.043638393761988 +Allele 152 0.054276292871716 +Allele 156 0.042930341420608 +Allele 161 0.043156455394625 + +Locus 007 +Allele 093 0.046592657271484 +Allele 095 0.045670747473623 +Allele 096 0.043508749842325 +Allele 097 0.044158079909626 +Allele 099 0.045697100712565 +Allele 100 0.043987410345744 +Allele 101 0.050091033464038 +Allele 103 0.050594815580258 +Allele 105 0.043789734473491 +Allele 107 0.043608876953690 +Allele 109 0.046302579538691 +Allele 110 0.043661584144448 +Allele 125 0.043408824905916 +Allele 161 0.043444713575946 +Allele 165 0.043324937435184 +Allele 167 0.046287602293657 +Allele 169 0.046501836199231 +Allele 171 0.051092389314757 +Allele 173 0.047506811779172 +Allele 175 0.043534692086034 +Allele 177 0.043475241826682 +Allele 181 0.043759580873437 + +Locus 008 +Allele 095 0.039988844869480 +Allele 097 0.041635921276092 +Allele 099 0.039903782637175 +Allele 100 0.040788373531947 +Allele 101 0.046903314230084 +Allele 103 0.048285027055110 +Allele 105 0.039904390525495 +Allele 107 0.040478152842746 +Allele 109 0.042317537675676 +Allele 110 0.040084495655470 +Allele 113 0.042392380824298 +Allele 121 0.040811690923581 +Allele 123 0.040365396676324 +Allele 131 0.040045854119271 +Allele 167 0.039998897258573 +Allele 169 0.040759685128782 +Allele 171 0.045821136085592 +Allele 173 0.044155229603028 +Allele 175 0.043735476988283 +Allele 177 0.040373921360086 +Allele 179 0.040039746408306 +Allele 181 0.040932940732469 +Allele 183 0.040282479718117 +Allele 185 0.039995323874016 + +Locus 009 +Allele 108 0.035139684135796 +Allele 115 0.033240195686136 +Allele 121 0.033986631046848 +Allele 123 0.034896583077516 +Allele 125 0.035663429133703 +Allele 127 0.033318012747482 +Allele 129 0.033924281896208 +Allele 131 0.033390021520182 +Allele 133 0.034659600304502 +Allele 135 0.036083531580878 +Allele 137 0.033199311295546 +Allele 139 0.033716365855893 +Allele 145 0.033299121839553 +Allele 147 0.036912924645681 +Allele 149 0.033069689904089 +Allele 152 0.035098595058439 +Allele 218 0.032973579697353 +Allele 220 0.033802440914176 +Allele 222 0.035776798969730 +Allele 224 0.035271335046226 +Allele 226 0.035697395387246 +Allele 228 0.033270645058878 +Allele 230 0.033063343516249 +Allele 232 0.039295377937703 +Allele 234 0.035343685542360 +Allele 236 0.033115397093278 +Allele 238 0.036361052604505 +Allele 240 0.033427427846936 +Allele 250 0.033003540656911 + +Locus 010 +Allele 123 0.027491914353685 +Allele 125 0.027119081283949 +Allele 127 0.027233488100643 +Allele 129 0.028854313200207 +Allele 131 0.028552742356373 +Allele 133 0.028562798445307 +Allele 135 0.027040951560251 +Allele 137 0.027720182423353 +Allele 139 0.027488272080552 +Allele 141 0.027369983224153 +Allele 143 0.026980270117197 +Allele 145 0.026777758433673 +Allele 147 0.030211719888710 +Allele 149 0.029631291975888 +Allele 152 0.026995093604143 +Allele 155 0.026804070341613 +Allele 157 0.028438194516042 +Allele 220 0.026698371364158 +Allele 222 0.029550530515434 +Allele 224 0.026871234084766 +Allele 226 0.029176585432094 +Allele 228 0.026962739327571 +Allele 230 0.027875934476183 +Allele 232 0.026844151858627 +Allele 234 0.028201066050375 +Allele 236 0.031056645064336 +Allele 238 0.028670024888627 +Allele 240 0.027400558079687 +Allele 242 0.027146215709323 +Allele 244 0.027073540976241 +Allele 246 0.027091480059133 +Allele 248 0.026959232479966 +Allele 250 0.026845958529034 +Allele 252 0.027005916305403 +Allele 254 0.026746206305424 +Allele 256 0.028551482587879 + + +Cluster 07 +Locus 001 +Allele 092 0.102572413167378 +Allele 094 0.103028784692769 +Allele 096 0.096339865237205 +Allele 098 0.098645441818873 +Allele 100 0.107066589970478 +Allele 102 0.094147631641201 +Allele 104 0.116140052113886 +Allele 106 0.098973968969781 +Allele 108 0.089645831276954 +Allele 110 0.093439421111470 + +Locus 002 +Allele 094 0.070104454401886 +Allele 096 0.067798873533512 +Allele 098 0.072796980672431 +Allele 100 0.074744085257217 +Allele 102 0.072713829272076 +Allele 104 0.088536140803687 +Allele 106 0.084540830205246 +Allele 108 0.066128172911862 +Allele 110 0.068432314482121 +Allele 112 0.069057122742337 +Allele 114 0.065601305985580 +Allele 124 0.068423441695121 +Allele 126 0.065550046992610 +Allele 149 0.065572401044313 + +Locus 003 +Allele 118 0.046989736107962 +Allele 122 0.047044462485475 +Allele 124 0.055258406067528 +Allele 126 0.066261733323218 +Allele 128 0.047047456364900 +Allele 130 0.048368476278373 +Allele 132 0.048066732482983 +Allele 137 0.047356988661767 +Allele 202 0.047721535378692 +Allele 204 0.046926859100164 +Allele 206 0.046616588354739 +Allele 208 0.059492440469847 +Allele 210 0.047061583247666 +Allele 212 0.049203125503481 +Allele 214 0.053860018307344 +Allele 216 0.046984772149202 +Allele 218 0.047282534875951 +Allele 220 0.047106645180360 +Allele 224 0.048230486647827 +Allele 226 0.053119419012522 + +Locus 004 +Allele 124 0.041128448970442 +Allele 126 0.043972163671535 +Allele 127 0.045010768321455 +Allele 128 0.042506461160616 +Allele 130 0.041498771272304 +Allele 132 0.043068032801942 +Allele 134 0.041030243562457 +Allele 135 0.051477288730074 +Allele 137 0.045294887705872 +Allele 151 0.043588487762417 +Allele 208 0.043625444888025 +Allele 210 0.042200768855318 +Allele 212 0.041751199252250 +Allele 214 0.041230849530593 +Allele 216 0.045273403544740 +Allele 218 0.044404585412316 +Allele 220 0.041897071347665 +Allele 222 0.048358219409475 +Allele 224 0.041777535736243 +Allele 226 0.042004489116665 +Allele 228 0.041004610033168 +Allele 233 0.046411240877612 +Allele 238 0.041485028036814 + +Locus 005 +Allele 121 0.055679633497898 +Allele 123 0.060663195090784 +Allele 125 0.053840191837247 +Allele 127 0.052024360616047 +Allele 129 0.057108608394751 +Allele 130 0.052102865754387 +Allele 131 0.053038018705596 +Allele 133 0.053817943013959 +Allele 135 0.055767734878853 +Allele 136 0.052834891604404 +Allele 137 0.055254078850144 +Allele 138 0.062854680699143 +Allele 139 0.057651153769091 +Allele 141 0.052493934930799 +Allele 145 0.059229667247057 +Allele 146 0.054728859031284 +Allele 148 0.058890818039718 +Allele 150 0.052019364038839 + +Locus 006 +Allele 121 0.044074684358414 +Allele 123 0.046483340749988 +Allele 125 0.044306621797790 +Allele 129 0.042950255591822 +Allele 131 0.043812013185031 +Allele 133 0.049588771814883 +Allele 135 0.044662478415232 +Allele 136 0.042939000838758 +Allele 137 0.052504790445937 +Allele 138 0.045321038638922 +Allele 139 0.046537102513416 +Allele 141 0.043155502328418 +Allele 143 0.042977708128978 +Allele 145 0.045753283065302 +Allele 146 0.043245374723941 +Allele 147 0.046934948479817 +Allele 148 0.045804596133138 +Allele 150 0.045017810168512 +Allele 151 0.042868492150749 +Allele 152 0.054887431542160 +Allele 156 0.043143396301993 +Allele 161 0.043031358626802 + +Locus 007 +Allele 093 0.046009887237109 +Allele 095 0.046027110947066 +Allele 096 0.043087901556491 +Allele 097 0.044024913439056 +Allele 099 0.046548879624450 +Allele 100 0.043523295297171 +Allele 101 0.050178178023479 +Allele 103 0.051722646429266 +Allele 105 0.043338772209116 +Allele 107 0.043537962233440 +Allele 109 0.046423359120043 +Allele 110 0.043476565630778 +Allele 125 0.043276617128841 +Allele 161 0.043132103350432 +Allele 165 0.043212589507270 +Allele 167 0.047552434138481 +Allele 169 0.046509841763503 +Allele 171 0.050852077121956 +Allele 173 0.048006123727650 +Allele 175 0.043296398169290 +Allele 177 0.042897188401126 +Allele 181 0.043365154943986 + +Locus 008 +Allele 095 0.039730797380678 +Allele 097 0.041201274048744 +Allele 099 0.039873338214458 +Allele 100 0.040352041831476 +Allele 101 0.046801084590980 +Allele 103 0.050232520862377 +Allele 105 0.039741146919988 +Allele 107 0.039879813235970 +Allele 109 0.042800497510887 +Allele 110 0.040107809865665 +Allele 113 0.042341103508912 +Allele 121 0.040753170870161 +Allele 123 0.040086008662528 +Allele 131 0.039704658445965 +Allele 167 0.039680813494235 +Allele 169 0.040878327663894 +Allele 171 0.046874546606111 +Allele 173 0.043869514944574 +Allele 175 0.044280710537716 +Allele 177 0.040036006570491 +Allele 179 0.039677945547124 +Allele 181 0.041135937012202 +Allele 183 0.040145480185190 +Allele 185 0.039815451489672 + +Locus 009 +Allele 108 0.035213994800529 +Allele 115 0.032977702186149 +Allele 121 0.033814656377359 +Allele 123 0.034712097599658 +Allele 125 0.035782793984969 +Allele 127 0.033215806424834 +Allele 129 0.034132582216259 +Allele 131 0.032879791594367 +Allele 133 0.035131152613910 +Allele 135 0.036250401284706 +Allele 137 0.032984671922432 +Allele 139 0.033731550971304 +Allele 145 0.032948511540543 +Allele 147 0.037345619839043 +Allele 149 0.033106313074750 +Allele 152 0.034821724728920 +Allele 218 0.033073161537293 +Allele 220 0.034016276146481 +Allele 222 0.035350122507834 +Allele 224 0.035378896024158 +Allele 226 0.035747483997419 +Allele 228 0.033105267118109 +Allele 230 0.033214451230635 +Allele 232 0.040066056329551 +Allele 234 0.036123280325825 +Allele 236 0.032957793564526 +Allele 238 0.035996275430475 +Allele 240 0.032915321333050 +Allele 250 0.033006243294915 + +Locus 010 +Allele 123 0.027338621661824 +Allele 125 0.027053523212125 +Allele 127 0.026914520541538 +Allele 129 0.028603787624457 +Allele 131 0.028865650830249 +Allele 133 0.029091641246400 +Allele 135 0.027240653896115 +Allele 137 0.027565080893164 +Allele 139 0.027353967133803 +Allele 141 0.027564145411096 +Allele 143 0.026812173333391 +Allele 145 0.026833998657604 +Allele 147 0.030477087488320 +Allele 149 0.029330367980145 +Allele 152 0.026611698627811 +Allele 155 0.026835513782597 +Allele 157 0.028452864867363 +Allele 220 0.026815503426066 +Allele 222 0.029594825779700 +Allele 224 0.026751871253362 +Allele 226 0.028792081717139 +Allele 228 0.026703694167371 +Allele 230 0.027997544842013 +Allele 232 0.026817393513901 +Allele 234 0.028163394866610 +Allele 236 0.031915705389788 +Allele 238 0.028842993344394 +Allele 240 0.027490951235065 +Allele 242 0.027146273154511 +Allele 244 0.027262974532433 +Allele 246 0.027015106882046 +Allele 248 0.026570725643275 +Allele 250 0.026805888539323 +Allele 252 0.026942126386732 +Allele 254 0.026686590688882 +Allele 256 0.028739057449385 + + +Cluster 08 +Locus 001 +Allele 092 0.103353539905431 +Allele 094 0.103685029638718 +Allele 096 0.093921899691735 +Allele 098 0.100477732877988 +Allele 100 0.104500232300427 +Allele 102 0.097108773678204 +Allele 104 0.116498935923024 +Allele 106 0.096945935158664 +Allele 108 0.090683388945058 +Allele 110 0.092824531880757 + +Locus 002 +Allele 094 0.070566738220270 +Allele 096 0.068136802065467 +Allele 098 0.076312086500578 +Allele 100 0.074258730223880 +Allele 102 0.070908436272861 +Allele 104 0.088197817495109 +Allele 106 0.081674335422701 +Allele 108 0.066737942517097 +Allele 110 0.068027523824784 +Allele 112 0.071221600032794 +Allele 114 0.065159318445660 +Allele 124 0.067372037148096 +Allele 126 0.065967162554435 +Allele 149 0.065459469276271 + +Locus 003 +Allele 118 0.046819577064001 +Allele 122 0.046955843100427 +Allele 124 0.053167854634544 +Allele 126 0.067204573639409 +Allele 128 0.047954752840320 +Allele 130 0.048492760532135 +Allele 132 0.047848333343480 +Allele 137 0.047798244326745 +Allele 202 0.047918942338442 +Allele 204 0.046974909670932 +Allele 206 0.046931028023896 +Allele 208 0.060325039368823 +Allele 210 0.048223963056408 +Allele 212 0.048684550479371 +Allele 214 0.052776034246715 +Allele 216 0.047032637149921 +Allele 218 0.047518707238342 +Allele 220 0.046569745528901 +Allele 224 0.047914331741236 +Allele 226 0.052888171675953 + +Locus 004 +Allele 124 0.041490709231914 +Allele 126 0.043000948897048 +Allele 127 0.045257888540422 +Allele 128 0.042349007255793 +Allele 130 0.041251883581550 +Allele 132 0.043145198903756 +Allele 134 0.041065820079427 +Allele 135 0.052859099076350 +Allele 137 0.044575925604419 +Allele 151 0.043667465431360 +Allele 208 0.045350064636395 +Allele 210 0.041933385181374 +Allele 212 0.042228752595022 +Allele 214 0.041038759897129 +Allele 216 0.043783628494387 +Allele 218 0.043465918481443 +Allele 220 0.042135872723556 +Allele 222 0.049095922470914 +Allele 224 0.041614307580881 +Allele 226 0.041796856795413 +Allele 228 0.041221318069576 +Allele 233 0.046255982701849 +Allele 238 0.041415283770022 + +Locus 005 +Allele 121 0.054663192037278 +Allele 123 0.059680746140762 +Allele 125 0.053359822168479 +Allele 127 0.052056641818381 +Allele 129 0.057320512301554 +Allele 130 0.051838579342207 +Allele 131 0.053266048920589 +Allele 133 0.054182915424237 +Allele 135 0.057856070183141 +Allele 136 0.053806137312660 +Allele 137 0.054779769239096 +Allele 138 0.060606202688945 +Allele 139 0.058392079655416 +Allele 141 0.052298510923457 +Allele 145 0.058454140862565 +Allele 146 0.054717025578911 +Allele 148 0.060733912885294 +Allele 150 0.051987692517025 + +Locus 006 +Allele 121 0.043905619085766 +Allele 123 0.045426029471320 +Allele 125 0.044085236733562 +Allele 129 0.043081198986452 +Allele 131 0.043689178578947 +Allele 133 0.049582015072391 +Allele 135 0.044946253836727 +Allele 136 0.043283419784627 +Allele 137 0.054293904931068 +Allele 138 0.044231112411297 +Allele 139 0.045587957503082 +Allele 141 0.043383604779710 +Allele 143 0.042712761577218 +Allele 145 0.045175456178939 +Allele 146 0.043259411875210 +Allele 147 0.047383541700747 +Allele 148 0.046407733557100 +Allele 150 0.044674365069707 +Allele 151 0.042991185567021 +Allele 152 0.056160891889148 +Allele 156 0.042899406840159 +Allele 161 0.042839714569803 + +Locus 007 +Allele 093 0.047694743317142 +Allele 095 0.045891736532508 +Allele 096 0.042791722993436 +Allele 097 0.043823015942825 +Allele 099 0.045485844190225 +Allele 100 0.043946275273308 +Allele 101 0.050804436812796 +Allele 103 0.051017468941951 +Allele 105 0.043517037525086 +Allele 107 0.043274208515431 +Allele 109 0.045632970642466 +Allele 110 0.043317431209676 +Allele 125 0.043017435225557 +Allele 161 0.042890112194106 +Allele 165 0.043217793130509 +Allele 167 0.046071264712693 +Allele 169 0.046819588962867 +Allele 171 0.052297248397592 +Allele 173 0.047943438253833 +Allele 175 0.043265751536016 +Allele 177 0.043397694111920 +Allele 181 0.043882781578056 + +Locus 008 +Allele 095 0.039727061022762 +Allele 097 0.041044228282661 +Allele 099 0.039772465056870 +Allele 100 0.040684168164851 +Allele 101 0.048052201794278 +Allele 103 0.048733104549043 +Allele 105 0.039706900937241 +Allele 107 0.040396408780104 +Allele 109 0.041733789304942 +Allele 110 0.039847066750903 +Allele 113 0.043421881944190 +Allele 121 0.040641380467140 +Allele 123 0.040002557289421 +Allele 131 0.039894170843468 +Allele 167 0.039542697123090 +Allele 169 0.040950569321039 +Allele 171 0.045944842682030 +Allele 173 0.044732777291428 +Allele 175 0.044758420059522 +Allele 177 0.040070845202202 +Allele 179 0.039518287629369 +Allele 181 0.040819921269250 +Allele 183 0.040083289013724 +Allele 185 0.039920965220471 + +Locus 009 +Allele 108 0.034932612591813 +Allele 115 0.032911240651581 +Allele 121 0.033810509453392 +Allele 123 0.034468049028306 +Allele 125 0.035705010656537 +Allele 127 0.033213616728159 +Allele 129 0.033628730949706 +Allele 131 0.033522913161866 +Allele 133 0.034860972148029 +Allele 135 0.036476657568454 +Allele 137 0.032934674559604 +Allele 139 0.033770292148058 +Allele 145 0.032935649845860 +Allele 147 0.037060317364067 +Allele 149 0.032942941241077 +Allele 152 0.035994970182264 +Allele 218 0.032910693467272 +Allele 220 0.033929316772661 +Allele 222 0.036865686918052 +Allele 224 0.035329390833146 +Allele 226 0.035826553017448 +Allele 228 0.033383560472140 +Allele 230 0.032828539399755 +Allele 232 0.039030861227694 +Allele 234 0.035286390428199 +Allele 236 0.032850710613658 +Allele 238 0.036638067326979 +Allele 240 0.033005623511881 +Allele 250 0.032945447732339 + +Locus 010 +Allele 123 0.027340706534345 +Allele 125 0.027065761552689 +Allele 127 0.026986068846105 +Allele 129 0.028686912300808 +Allele 131 0.028384125474351 +Allele 133 0.028390022973798 +Allele 135 0.026922802635729 +Allele 137 0.027656720024064 +Allele 139 0.027612121007440 +Allele 141 0.027485903041365 +Allele 143 0.026840412822004 +Allele 145 0.026636053722156 +Allele 147 0.030190277392756 +Allele 149 0.029885865887045 +Allele 152 0.026711492533005 +Allele 155 0.026817028364671 +Allele 157 0.029248729866094 +Allele 220 0.026856623045399 +Allele 222 0.029801247256486 +Allele 224 0.026632238044006 +Allele 226 0.029956982088145 +Allele 228 0.027236667671122 +Allele 230 0.027648126926318 +Allele 232 0.026849659788996 +Allele 234 0.028264292021820 +Allele 236 0.031136274799989 +Allele 238 0.028710755580864 +Allele 240 0.027435877332664 +Allele 242 0.027077752571898 +Allele 244 0.027206262138289 +Allele 246 0.026970321772839 +Allele 248 0.026807611345116 +Allele 250 0.026715039306995 +Allele 252 0.026869560256886 +Allele 254 0.026787205230973 +Allele 256 0.028176497842769 + + + +Estimated Mixing Proportions +0.010664133333333 +0.933123200000000 +0.008535866666667 +0.009196266666667 +0.008280133333333 +0.009271466666667 +0.010316400000000 +0.010612533333333 + + + diff --git a/inst/files/tess3.rds b/inst/files/tess3.rds new file mode 100644 index 0000000..119971d Binary files /dev/null and b/inst/files/tess3.rds differ diff --git a/inst/files/tessgrplabels.txt b/inst/files/tessgrplabels.txt new file mode 100644 index 0000000..6da0c17 --- /dev/null +++ b/inst/files/tessgrplabels.txt @@ -0,0 +1,75 @@ +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop A +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B +Pop B diff --git a/man/analyseQ.Rd b/man/analyseQ.Rd new file mode 100644 index 0000000..f05fd43 --- /dev/null +++ b/man/analyseQ.Rd @@ -0,0 +1,56 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/pophelper.R +\name{analyseQ} +\alias{analyseQ} +\title{Analyse STRUCTURE, TESS, BAPS or BASIC text runs. Wrapper around several smaller functions.} +\usage{ +analyseQ(files = NULL, evannomethod = TRUE, clumppexport = TRUE, + plotruns = TRUE, imgoutput = "sep", grplab = NA, clustercol = NA, + writetable = TRUE, sorttable = TRUE) +} +\arguments{ +\item{files}{A character or character vector of one or more STRUCTURE, TESS, BAPS or BASIC run files. Use \code{choose.files(multi=TRUE)} to choose interactively.} + +\item{evannomethod}{A logical indicating if evanno method should be performed. Applies only to STRUCTURE runs.} + +\item{clumppexport}{A logical indicating if files must be exported for clumpp.} + +\item{plotruns}{A logical indicating if selected files should be exported as barplots.} + +\item{imgoutput}{A character indicating if files are plotted as separate image files ("sep") or joined into a single image ("join").} + +\item{grplab}{A dataframe with one or more columns (group label sets), and rows equal to the number of individuals.} + +\item{clustercol}{A character vector of colours for colouring clusters. If NA, colours are automatically generated. K 1 to 12 are custom unique colours while K>12 are coloured by function \code{rich.color()}.} + +\item{writetable}{A logical T or F. Setting to TRUE writes the output table to the working directory.} + +\item{sorttable}{A logical indicating if the output table must be sorted. Sorts table by loci, ind and K when available.} +} +\value{ +If a single file is selected, a single dataframe is returned. If +multiple files are selected, a list with multiple dataframes is returned. +} +\description{ +A single function to analyse STRUCTURE, TESS, BAPS or BASIC text runs. Converts runs to a qlist, then tabulate, summarise, perform evanno method, export clumpp and plots runs. +} +\details{ +The function \code{analyseQ} is a wrapper around several other \code{pophelper} functions. All arguments for all these other functions are not available. If more arguments/options are required, consider running the functions separately. + +See the \href{http://royfrancis.github.io/pophelper/}{vignette} for more details. +} +\examples{ +\dontrun{ +# structure files +sfiles <- list.files(path=system.file("files/structure",package="pophelper"),full.names=TRUE) +analyseQ(sfiles) + +# tess files +tfiles <- list.files(path=system.file("files/tess",package="pophelper"),full.names=TRUE) +analyseQ(tfiles) + +# admixture files +afiles <- list.files(path=system.file("files/admixture",package="pophelper"),full.names=TRUE) +analyseQ(afiles) +} +} diff --git a/man/checkQ.Rd b/man/checkQ.Rd new file mode 100644 index 0000000..b37539c --- /dev/null +++ b/man/checkQ.Rd @@ -0,0 +1,19 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/pophelper.R +\name{checkQ} +\alias{checkQ} +\title{Internal: Check input filetype.} +\usage{ +checkQ(files = NULL, warn = FALSE) +} +\arguments{ +\item{files}{A character or character vector of one or more input text files or a list of dataframes.} + +\item{warn}{A logical indicating if a warning must be displayed for file those are not STRUCTURE, TESS or BASIC file.} +} +\value{ +A character or character vector indicating input type 'STRUCTURE', 'TESS', 'BASIC', 'CLUMPP', 'list', 'data.frame', 'UNIDENTIFIED' for all selected files. +} +\description{ +Internal: Check input filetype. +} diff --git a/man/clumppExport.Rd b/man/clumppExport.Rd new file mode 100644 index 0000000..f441e9b --- /dev/null +++ b/man/clumppExport.Rd @@ -0,0 +1,86 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/pophelper.R +\name{clumppExport} +\alias{clumppExport} +\title{Generate CLUMPP output from a qlist} +\usage{ +clumppExport(qlist = NULL, prefix = NA, parammode = NA, paramrep = NA, + useexe = FALSE) +} +\arguments{ +\item{qlist}{A qlist (list of dataframes). An output from \code{\link{readQ}}.} + +\item{prefix}{A character prefix for folder names. By default, set to 'pop'.} + +\item{parammode}{A numeric 1, 2 or 3 indicating the algorithm option for CLUMPP paramfile. Calculated +automatically by default. Set this value to 3 if CLUMPP runs too long. See details.} + +\item{paramrep}{A numeric indicating the number of repeats for CLUMPP paramfile. Calculated +automatically by default. See details.} + +\item{useexe}{A logical indicating if CLUMPP executable must be run automatically based on system OS (experimental). May not work on all OS and versions.} +} +\value{ +The combined file and paramfile are written into respective folders +named by K. +} +\description{ +Takes a qlist and combines several repeats for each K into a +single file along with a parameter file suitable for input to CLUMPP. The two +output files are organised into folders by K. CLUMPP is executed automatically +when \code{useexe=T}, else the CLUMPP executable file can be copied to the +output directories and run to reorder the clusters for each K. +} +\details{ +When multiple repeats are run for each K in runs, the order of +clusters may be jumbled for each run. Therefore, when plotting multiple runs +within each K, the colours cannot be assigned correctly. The software CLUMPP +helps to overcome this issue by reordering the clusters correctly. This +function \code{clumppExport()} takes multiple runs for each K and combines +them into a single file and generates a parameter file for easy use with +CLUMPP. Further details for CLUMPP can be found here: Jakobsson, M., and +Rosenberg, N. A. (2007). CLUMPP: a cluster matching and permutation program +for dealing with label switching and multimodality in analysis of population +structure. Bioinformatics, 23(14), 1801-1806.\cr +\cr +\strong{parammode}\cr +The parammode (M) is the type of algorithm used. Option 1 is 'FullSearch' +(takes the longest time), option 2 is 'Greedy' and option 3 is 'LargeKGreedy' +(fastest). If clumpp takes more than a few minutes, consider changing parammode +to a higher number (ex. from 2 to 3), or open the exported paramfile and manually +change GREEDY_OPTION to 3.\cr +\cr +The parammode and paramrep for CLUMPP paramfile is set based on this calculation. +T <- factorial(k)*((runs*(runs-1))/2)*k*ind, where k is number of +populations, runs is number of runs for k and ind is number of individuals. +If T <= 100000000, then parammode is 2 and paramrep is 20, otherwise +parammode is 3 and paramrep is set to 500.\cr +\cr +To find out more about parammode (algorithm type) and paramrep (repeats), +refer to CLUMPP documentation.\cr + +\strong{useexe}\cr +This option automatically runs the CLUMPP executable that is provided with this package. +The CLUMPP executable was obtained from \url{https://web.stanford.edu/group/rosenberglab/clumpp.html}. +Remember to cite CLUMPP if this option is used.\cr + +See the \href{http://royfrancis.github.io/pophelper/}{vignette} for more details. +} +\examples{ + +\dontrun{ + +# generate input files for CLUMPP from STRUCTURE files +sfiles <- list.files(path=system.file("files/structure",package="pophelper"),full.names=TRUE) +clumppExport(readQ(sfiles)) + +# auto execute CLUMPP +clumppExport(readQ(sfiles),useexe=TRUE) + +# generate input files for CLUMPP from ADMIXTURE files +afiles <- list.files(path=system.file("files/admixture",package="pophelper"),full.names=TRUE) +clumppExport(readQ(afiles)) + +} + +} diff --git a/man/collectClumppOutput.Rd b/man/collectClumppOutput.Rd new file mode 100644 index 0000000..7e24bae --- /dev/null +++ b/man/collectClumppOutput.Rd @@ -0,0 +1,37 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/pophelper.R +\name{collectClumppOutput} +\alias{collectClumppOutput} +\title{Collect CLUMPP output files from multiple folders} +\usage{ +collectClumppOutput(prefix = "pop", filetype = "aligned", runsdir = NA, + newdir = NA, quiet = FALSE) +} +\arguments{ +\item{prefix}{A character indicating the prefix of the CLUMPP directories before the underscore. For ex. if the directories are pop_K2, then prefix is pop.} + +\item{filetype}{A character indicating the type of file to be copied. Options are 'aligned' to copy aligned files only, 'merged' to copy merged files only and 'both' to copy both files.} + +\item{runsdir}{A character denoting the directory containing CLUMPP output files in multiple directories. Use \code{choose.dir()} for interactively selecting the directory. If NA, the current working directory is used.} + +\item{newdir}{A character indicating the name of the new directory to be created with the collected runs. IF NA, the a directory name joining prefix and filetype is created.} + +\item{quiet}{A logical indicating if a message is to be displayed showing the number of folders processed and number of files processed.} +} +\value{ +Two integers are ruturned. The first denotes the number of directories processed. The second number denotes the number files copied. +} +\description{ +Collect CLUMPP output files from multiple folders to one folder +} +\details{ +Within each CLUMPP output folder, the function searches for filenames containing combination of prefix and filetype. This file is copied to the new folder. Therefore, do not manually rename CLUMPP output files or output directories. + +See the \href{http://royfrancis.github.io/pophelper/}{vignette} for more details. +} +\examples{ +\dontrun{ +collectClumppOutput(runsdir="path") +collectClumppOutput(prefix="pop",runsdir="path") +} +} diff --git a/man/collectRunsTess.Rd b/man/collectRunsTess.Rd new file mode 100644 index 0000000..28f3e68 --- /dev/null +++ b/man/collectRunsTess.Rd @@ -0,0 +1,31 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/pophelper.R +\name{collectRunsTess} +\alias{collectRunsTess} +\title{Collect TESS cluster run files from multiple folders} +\usage{ +collectRunsTess(runsdir = NA, newdir = NA, quiet = FALSE) +} +\arguments{ +\item{runsdir}{A character path indicating the directory containing TESS runs in multiple directories. Use \code{choose.dir()} for interactively selecting the directory. If NA, or no directory is selected, the current working directory is used.} + +\item{newdir}{A character indicating the name of the new directory to be created with the collected runs. IF NA, the default name 'AllTESSRuns' is used.} + +\item{quiet}{A logical indicating if a message is to be displayed for directories without TESS runs and number of runs copied and renamed.} +} +\value{ +Two integers are ruturned. The first denotes the number of TESS run files copied and renamed. The second number denotes number of directories without TESS run files. +} +\description{ +Collect TESS cluster run files from multiple folders to one folder and rename each run by folder name +} +\details{ +Within each TESS run folder, the function searches for filename ending with 'TR.txt' as the cluster file. This file is copied to the new folder and renamed as the name of the respective run directory. Therefore, DO NOT manually rename original run files or directories. + +See the \href{http://royfrancis.github.io/pophelper/}{vignette} for more details. +} +\examples{ +\dontrun{ +collectRunsTess("path") +} +} diff --git a/man/distructColours.Rd b/man/distructColours.Rd new file mode 100644 index 0000000..fd4b460 --- /dev/null +++ b/man/distructColours.Rd @@ -0,0 +1,20 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/pophelper.R +\name{distructColours} +\alias{distructColours} +\alias{distructColors} +\title{Internal: Vector of 90 Distruct colours} +\usage{ +distructColours() +} +\value{ +Returns a character vector of 90 colours recognised by Distruct. +} +\description{ +Internal: Vector of 90 Distruct colours. +} +\examples{ +distructColours(); +distructColours()[1:5]; +distructColours()[10:15]; +} diff --git a/man/distructExport.Rd b/man/distructExport.Rd new file mode 100644 index 0000000..7a20523 --- /dev/null +++ b/man/distructExport.Rd @@ -0,0 +1,136 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/pophelper.R +\name{distructExport} +\alias{distructExport} +\title{Generate files for DISTRUCT.} +\usage{ +distructExport(qlist = NULL, grplabbottom = NA, grplabtop = NA, + grpmean = FALSE, overwritedirs = FALSE, printtitle = FALSE, + clustercol = NA, grayscale = FALSE, printcolorbrewer = FALSE, + sepline = T, seplinewidth = 0.2, borderlinewidth = 1.2, + indlinewidth = 0.2, fontsize = 6, topdist = 5, bottomdist = -7, + figheight = 36, indwidth = 1, orientation = 0, xorigin = NA, + yorigin = NA, xscale = 1, yscale = 1, toplabangle = 60, + bottomlabangle = 60, echodata = TRUE, printdata = FALSE, + quiet = FALSE, useexe = FALSE) +} +\arguments{ +\item{qlist}{A qlist (list of dataframes). An output from \code{\link{readQ}}.} + +\item{grplabbottom}{A character vector of group labels to be plotted below the plot. The vector must be the same length as number of individuals. See details.} + +\item{grplabtop}{An optional character vector of group labels to be plotted above the plot. The vector must be the same length as number of individuals. See details.} + +\item{grpmean}{A logical indicating if individual values are to be plotted (F) or group means are to be plotted (T).} + +\item{overwritedirs}{A logical indicating if existing directories must be overwritten (T) automatically or not (F).} + +\item{printtitle}{A logical indicating if the filename must be printed as the title on the plot.} + +\item{clustercol}{A character vector of colours equal to the number of clusters. Note these are not R colours. Use \code{distructColours()} or refer to DISTRUCT manual for colours. +With multiple files, number of colours must equal input file with highest number of clusters.} + +\item{grayscale}{A logical indicating if clusters must be shown in grayscale.} + +\item{printcolorbrewer}{A logical indicating if the colours provided in \code{clustercol} are ColorBrewer colours. See details.} + +\item{sepline}{A logical indicating if divider lines must be drawn between groups (T).} + +\item{seplinewidth}{A numeric indicating width of sepline.} + +\item{borderlinewidth}{A numeric indicating width of border around the plot.} + +\item{indlinewidth}{A numeric indicating width of border around individual bars and ticks.} + +\item{fontsize}{A numeric indicating font size of group labels.} + +\item{topdist}{A numeric indicating distance of top labels from the top edge of the plot.} + +\item{bottomdist}{A numeric indicating distance of bottom labels from the bottom edge of the plot. Usually a negative number.} + +\item{figheight}{A numeric indicating height of the plot.} + +\item{indwidth}{A numeric indicating width of each individual bar. The width of the plot depends on this value.} + +\item{orientation}{An integer (0,1,2,3) indicating orientation of the plot. See details.} + +\item{xorigin}{A numeric indicating lower left x-coordinate of the plot. See details.} + +\item{yorigin}{A numeric indicating lower left y-coordinate of the plot. See details.} + +\item{xscale}{A numeric indicating scaling for the x direction.} + +\item{yscale}{A numeric indicating scaling for the y direction.} + +\item{toplabangle}{A numeric between 0 and 180 indicating angle of top labels.} + +\item{bottomlabangle}{A numeric between 0 and 180 indicating angle of bottom labels.} + +\item{echodata}{A logical. Not really sure what this does.} + +\item{printdata}{A logical indicating if head and tail of data must be shown in display on running DISTRUCT.} + +\item{quiet}{A logical TRUE or FALSE. Set to TRUE by default to print verbose statements to screen.} + +\item{useexe}{A logical indicating if DISTRUCT executable is automatically run based on system OS (experimental). Does not work on UNIX systems.} +} +\value{ +The function does not return anything. The function creates directories for each input file and +populates it with files necessary to run DISTRUCT. The files are individual q-matrix file (xx-indq.txt), +population q-matrix file (xx-popq.txt), a cluster colour file (xx-colours.txt) and drawparams file. If +group labels were defined, then (xx-poplab-bottom.txt) or (xx-poplab-top.txt) are also exported. The +DISTRUCT executable is run in this directory to generate an xx.ps file. +} +\description{ +Create DISTRUCT input files from a qlist. +} +\details{ +\strong{Orientation} \cr +0 for horizontal orientation (default) \cr +1 for vertical orientation \cr +2 for reverse horizontal orientation \cr +3 for reverse vertical orientation \cr +\cr +\strong{Origin} \cr +Default values of origin for a given orientation: \cr +orientation, xorigin, yorigin \cr +0,72,288 \cr +1,360,72 \cr +2,540,504 \cr +3,288,720 \cr +If plot exceeds canvas size, consider shifting \code{xorigin} to the left and/or decreasing \code{indwidth}.\cr +\cr +\strong{Colorbrewer colours} \cr +Colorbrewer colours are not automatically generated for now. Refer to DISTRUCT manual for colour names. \cr +Replace the colour names in xx-colours.txt output file with selected colorbrewer colours (ex: Accent_3_qual_1). \cr +\cr +\strong{useexe}\cr +This option automatically runs the DISTRUCT executable that is provided with this package. +Note that the executable is 64bit LSB requiring a 64bit system. The DISTRUCT executable was obtained from +here \url{https://web.stanford.edu/group/rosenberglab/distruct.html}. Remember to cite DISTRUCT if this option is used.\cr + +See the \href{http://royfrancis.github.io/pophelper/}{vignette} for more details. +} +\examples{ +\dontrun{ +# read some data +slist <- readQ(list.files(path=system.file("files/structure",package="pophelper"),full.names=TRUE)) +grps1 <- read.delim(system.file("files/structuregrplabels.txt",package="pophelper"),header=FALSE, stringsAsFactor=F) +grps2 <- read.delim(system.file("files/structuregrplabels2.txt",package="pophelper"),header=FALSE, stringsAsFactor=F) + +# plot without labels +distructExport(slist[1]) + +# plot with bottom group label +distructExport(slist[1],grplabbottom=grps1$V1) + +# plot with top group label +distructExport(slist[1],grplabtop=grps2$V1) + +# plot group mean values +distructExport(slist[1],grplabbottom=grps1$V1,grpmean=T) + +# automatically run DESTRUCT +distructExport(slist[1],useexe=T) +} +} diff --git a/man/evannoMethodStructure.Rd b/man/evannoMethodStructure.Rd new file mode 100644 index 0000000..f609f79 --- /dev/null +++ b/man/evannoMethodStructure.Rd @@ -0,0 +1,109 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/pophelper.R +\name{evannoMethodStructure} +\alias{evannoMethodStructure} +\title{Perform the Evanno method for STRUCTURE runs.} +\usage{ +evannoMethodStructure(data = NULL, writetable = FALSE, exportplot = FALSE, + returnplot = FALSE, returndata = TRUE, pointsize = NA, pointtype = 20, + pointcol = "steelblue", linesize = NA, linecol = "steelblue", + ebwidth = 0.2, ebcol = "grey30", textcol = "grey30", basesize = 6, + gridsize = NA, imgtype = "png", height = NA, width = NA, dpi = 300, + units = "cm", theme = "theme_bw", font = "", na.rm = TRUE, + quiet = TRUE, outputfilename = "evannoMethodStructure") +} +\arguments{ +\item{data}{A dataframe with summarised runs. An output from \code{summariseQ()} derived from STRUCTURE runs. Must have minimum 7 columns named elpdmean, elpdsd, k, runs, loci, elpdmax and elpdmin.} + +\item{writetable}{A logical indicating if the output table is to be exported as a file in the working directory.} + +\item{exportplot}{A logical indicating if the Evanno plots are to be exported as an image in the working directory. If Evanno method cannot be computed, a kPlot (elpd over k) is exported instead.} + +\item{returnplot}{A logical indicating if the plot must be returned. A gtable object is returned alone when \code{returndata=F}. When \code{returndata=T}, the gtable object is returned in a list. See 'Value'.} + +\item{returndata}{A logical indicating if the data must be returned. A data.frame object is returned alone when \code{returnplot=F}. When \code{returnplot=T}, the data.frame object is returned in a list. See 'Value'.} + +\item{pointsize}{A numeric indicating size of points. Default for \code{basesize=6} is 1.8.} + +\item{pointcol}{A colour character for the colour of points. Defaults to "steelblue".} + +\item{linesize}{A numeric indicating the thickness of the line. Default for \code{basesize=6} is 0.24.} + +\item{linecol}{A colour character for the colour of line. Defaults to "steelblue".} + +\item{ebwidth}{A numeric indicating size od width of error abrs. Defaults to 0.2.} + +\item{ebcol}{A colour character for colour for errorbar. Defaults to "grey30".} + +\item{textcol}{A colour character for all text elements on the plot. Defaults to "grey30".} + +\item{basesize}{A numeric indicating the base size of various plot elements such as pointsize, linesize etc. Increase basesize with larger figure dimensions. Defaults to 6. Manually specified arguments (eg: pointsize) override basesize.} + +\item{gridsize}{A numeric indicating thickness of background grid. Default for \code{basesize=6} is 0.18.} + +\item{imgtype}{A character indicating the type of exported image. Default set to 'png'. Other possible +options are 'jpeg', 'tiff' or 'pdf'.} + +\item{height}{A numeric denoting the height of exported image. Default units in 'cm'.} + +\item{width}{A numeric denoting the width of exported image. Default units in 'cm'.} + +\item{dpi}{A numeric denoting the resolution of exported image. Default set to 300. If \code{imgtype="pdf"}, dpi is fixed at 300.} + +\item{units}{A character denoting the unit of measure of the export image. Default is 'cm'. Other options are 'px', 'in' or 'mm'.} + +\item{theme}{A character indicating ggplot theme to be used. Use like "theme_grey", "theme_bw" etc.} + +\item{font}{A character indicating font family to be used in the plots. Uses default system fonts by default for jpeg, png and tiff. Uses 'Helvetica' as default for pdf. Use package \code{extrafonts} to import custom fonts. See vignette for examples.} + +\item{na.rm}{Default set to FALSE. Does not remove NAs for plot and this +generates warnings from \code{ggplot}. If set to TRUE, NAs are removed before +plotting and warning messages from \code{ggplot} are avoided.} + +\item{quiet}{A logical indicating if messages must be printed to console.} + +\item{outputfilename}{A character indicating output file name. Defaults to 'evannoMethodStructure'.} + +\item{pointype}{A character or number for the type of points. Defaults to 20. Same as pch in standard R.} +} +\value{ +When \code{returndata=T} and \code{returnplot=F}, a data.frame is returned. +When \code{returndata=F} and \code{returnplot=T}, a gtable plot object is returned. +When \code{returndata=T} and \code{returnplot=T}, a list with data.frame and gtable object is returned. + +The data.frame contains Evanno results sorted by K. The table has 16 +columns namely Mean estimated ln probability of data, Standard deviation, +Value of K, Number of runs for each K, Number of runs for each K, Number of +individuals for each K, Number of loci for each K, Estimated ln probability +of data plus standard deviation, Estimated ln probability of data minus +standard deviation, First derivative, Max error of first derivative, Min +error of first derivative, Second derivative, Max error of second derivative, +Min error of second derivative and the Third derivative. + +The gtable object is a result of \code{gridExtra::arrangeGrob()}. This is +suitable for plotting in a report. +} +\description{ +The Evanno method for detecting the appropriate number of population clusters from STRUCTURE results. Creates table and figure with +Evanno method derivatives. Refer to return for detailed list of columns. See details for Evanno method reference. +} +\details{ +The Evanno method is based on the paper: Evanno, G., Regnaut, S., +and Goudet, J. (2005). Detecting the number of clusters of individuals using +the software STRUCTURE: a simulation study. Molecular ecology, 14(8), +2611-2620. The Evanno plot generated from this function can be recreated +from the returned dataframe if furthur customisation is required. + +See the \href{http://royfrancis.github.io/pophelper/}{vignette} for more details. +} +\examples{ + +\dontrun{ +sfiles <- list.files(path=system.file("files/structure",package="pophelper"),full.names=TRUE) +tr1 <- tabulateQ(readQ(sfiles)) +sr1 <- summariseQ(tr1) +evannoMethodStructure(sr1) +evannoMethodStructure(data=sr1,exportplot=T) +} + +} diff --git a/man/getColors.Rd b/man/getColors.Rd new file mode 100644 index 0000000..0b7138d --- /dev/null +++ b/man/getColors.Rd @@ -0,0 +1,20 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/pophelper.R +\name{getColors} +\alias{getColors} +\title{Internal: Generate colours based on number of K} +\usage{ +getColors(k) +} +\arguments{ +\item{k}{A numeric indicating the number of colours required} +} +\value{ +Returns a character vector of k colours in hexadecimal format +} +\description{ +Internal: Generate colours based on number of K. +} +\details{ +Colours 1 to 12 are custom unique colours. Colours beyond 15 are generated from colour ramp \code{rich.colors()} from package \code{gplots}. +} diff --git a/man/getDim.Rd b/man/getDim.Rd new file mode 100644 index 0000000..75638f3 --- /dev/null +++ b/man/getDim.Rd @@ -0,0 +1,39 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/pophelper.R +\name{getDim} +\alias{getDim} +\title{Internal: Get dimensions for figures.} +\usage{ +getDim(ind = NA, units = NA, height = NA, width = NA, dpi = NA, + imgtype = NA, grplabheight = NA, labs = NA, plotnum = NA, + showindlab = FALSE, sharedindlab = TRUE) +} +\arguments{ +\item{ind}{A numeric indicating the number of individuals.} + +\item{units}{A character indicating the unit of dimension: "cm","mm","in".} + +\item{height}{A numeric indicating the height of each plot.} + +\item{width}{A numeric indicating the width of each plot.} + +\item{dpi}{A numeric indicating the resolution of the figure.} + +\item{imgtype}{A character denoting image format. "png", "jpeg" or "pdf".} + +\item{grplabheight}{A numeric denoting the height of the label panel.} + +\item{labs}{An integer denoting number of label groups.} + +\item{plotnum}{A numeric indicating the number of plots in the figure.} + +\item{showindlab}{A logical indicating of indlab is displayed.} + +\item{sharedindlab}{A logical indicating if shared indlab is in use.} +} +\value{ +a vector with height and width. +} +\description{ +Internal: Generate height and width of figure based on number of individuals. +} diff --git a/man/getOS.Rd b/man/getOS.Rd new file mode 100644 index 0000000..c28cc6d --- /dev/null +++ b/man/getOS.Rd @@ -0,0 +1,14 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/pophelper.R +\name{getOS} +\alias{getOS} +\title{Internal: Find current OS} +\usage{ +getOS() +} +\value{ +Returns a character in lowercase with OS name 'windows', 'mac' or 'linux'. +} +\description{ +Find current OS +} diff --git a/man/getPlotParams.Rd b/man/getPlotParams.Rd new file mode 100644 index 0000000..906295f --- /dev/null +++ b/man/getPlotParams.Rd @@ -0,0 +1,31 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/pophelper.R +\name{getPlotParams} +\alias{getPlotParams} +\title{Internal: Generate parameters for plots with labels} +\usage{ +getPlotParams(grplab = NA, plotnum = 1, grplabsize = NA, + grplabangle = NA, grplabjust = NA, pointsize = NA, linesize = NA) +} +\arguments{ +\item{grplab}{A character vector of labels same length as number of individuals.} + +\item{plotnum}{A numeric indicating the number of plots on the figure.} + +\item{grplabsize}{A numeric indicating the size of the labels.} + +\item{grplabangle}{A numeric indicating the angle/rotation of labels. 0 is horizontal while 90 is vertical.} + +\item{grplabjust}{A numeric indicating the justification of labels. Defaults to 0.5 if grplabangle=0 or 1 if grplabangle between 20 and 135.} + +\item{pointsize}{A numeric indicating the size of points on label marker line.} + +\item{linesize}{A numeric indicating the thickness of the label marker line.} +} +\value{ +A list with following plot parameters: grplab, plotnum, grplabsize, +grplabangle, grplabjust, pointsize, linesize. +} +\description{ +Internal: Generates various parameters required for plotting with labels. +} diff --git a/man/grpLabels.Rd b/man/grpLabels.Rd new file mode 100644 index 0000000..1086334 --- /dev/null +++ b/man/grpLabels.Rd @@ -0,0 +1,35 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/pophelper.R +\name{grpLabels} +\alias{grpLabels} +\title{Internal: Handles grp subset/order} +\usage{ +grpLabels(dframe = NULL, grplab = NA, selgrp = NA, subsetgrp = NA, + ordergrp = FALSE, grpmean = FALSE, grplabpos = NA, linepos = NA, + indlabwithgrplab = TRUE, indlabsep = "_") +} +\arguments{ +\item{grplab}{A dataframe with group labels} + +\item{selgrp}{A character denoting selected group label set} + +\item{subsetgrp}{A character or character vector of grp name(s) to subset/reorder} + +\item{ordergrp}{A logical indicating if individuals must be ordered by group labels} + +\item{grpmean}{A logical indicating if q-matrix must be converted from individual to group mean.} + +\item{grplabpos}{A numeric indicating y-axis position of labels} + +\item{linepos}{A numeric indicating y-axis position of label line} + +\item{df}{A q-matrix dataframe} +} +\value{ +Returns a list with subsetted/reordered q-matrix, a character vector +of original/subsetted/reordered grplab dataframe, grplabpos and linepos. +} +\description{ +Internal: Takes a q-matrix dataframe along with grp labels. Pop labels +can be reordered or subsetted. The function also creates labelpos and markerpos dfs. +} diff --git a/man/is.qlist.Rd b/man/is.qlist.Rd new file mode 100644 index 0000000..6819aaa --- /dev/null +++ b/man/is.qlist.Rd @@ -0,0 +1,17 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/pophelper.R +\name{is.qlist} +\alias{is.qlist} +\title{Verify if a qlist is formatted correctly.} +\usage{ +is.qlist(qlist = NULL) +} +\arguments{ +\item{qlist}{A qlist object.} +} +\value{ +Nothing. +} +\description{ +Verify if a qlist is formatted correctly. +} diff --git a/man/plotQ.Rd b/man/plotQ.Rd new file mode 100644 index 0000000..7ea6e72 --- /dev/null +++ b/man/plotQ.Rd @@ -0,0 +1,385 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/pophelper.R +\name{plotQ} +\alias{plotQ} +\title{Generate barplots from qlists.} +\usage{ +plotQ(qlist = NULL, imgoutput = "sep", clustercol = NA, sortind = NA, + grplab = NA, selgrp = NA, ordergrp = FALSE, subsetgrp = NA, + grpmean = FALSE, panelspacer = 0.1, showsp = TRUE, sppos = "right", + splab = NA, splabsize = NULL, splabangle = NULL, splabcol = "grey30", + splabface = "plain", spbgcol = NA, showtitle = FALSE, titlelab = NA, + titlehjust = 0, titlevjust = 0.5, titlesize = NULL, + titlecol = "grey30", titleface = "plain", titlespacer = 1.4, + titleangle = 0, showsubtitle = FALSE, subtitlelab = NA, + subtitlehjust = 0, subtitlevjust = 0.5, subtitlesize = NULL, + subtitlecol = "grey30", subtitleface = "plain", subtitlespacer = 1.5, + subtitleangle = 0, grplabspacer = 0, grplabheight = NA, + grplabpos = 0.25, grplabsize = NA, grplabangle = NA, grplabjust = NA, + grplabcol = "grey30", grplabalpha = 1, showindlab = FALSE, + sharedindlab = TRUE, useindlab = FALSE, indlabwithgrplab = FALSE, + indlabspacer = 1.5, indlabheight = 0.2, indlabsep = " ", + indlabsize = NULL, indlabangle = 90, indlabvjust = 0.5, + indlabhjust = 1, indlabcol = "grey30", pointsize = NA, + pointcol = "grey30", pointbgcol = "grey30", pointtype = "|", + pointalpha = 1, linepos = 0.75, linesize = NA, linecol = "grey30", + linetype = 1, linealpha = 1, showdiv = TRUE, divgrp = NA, + divcol = "white", divtype = "21", divsize = 0.25, divalpha = 1, + showlegend = FALSE, legendlab = NA, legendpos = "right", + legendkeysize = 4, legendtextsize = 3, legendmargin = c(0.5, 0.5, 0.5, + 0), barsize = 1, barbordersize = 0, barbordercolour = NA, + showyaxis = FALSE, showticks = FALSE, ticksize = 0.1, + ticklength = 0.03, outputfilename = NA, imgtype = "png", height = NA, + width = NA, dpi = 300, units = "cm", theme = "theme_grey", + basesize = 5, font = "", na.rm = TRUE, quiet = FALSE, + panelratio = c(3, 1), exportplot = TRUE, returnplot = FALSE, + returndata = FALSE) +} +\arguments{ +\item{qlist}{A qlist (list of dataframes). An output from \code{\link{readQ}}.} + +\item{imgoutput}{A character with options: 'sep' or 'join'.If set to "sep", each run is plotted as separate image file. If set to "join", multiple runs are joined into a single image.} + +\item{clustercol}{A vector of colours for clusters. If NA, colours are automatically generated. K=1 to K=12 are custom unique colours while K>12 are coloured by function \code{gplots::rich.colors()}.} + +\item{sortind}{A character indicating how individuals are sorted. Default is NA (Same order of individuals as in input file). Other options are 'all' (sorting by values of all clusters), by any one cluster (eg. 'Cluster1') or 'labels' (sorting by individual labels). See details.} + +\item{grplab}{A dataframe with one or more columns (group label sets), and rows equal to the number of individuals. See details.} + +\item{selgrp}{A single character denoting a selected group label set. The selected label must be a group label title used in \code{grplab}. See details.} + +\item{ordergrp}{A logical indicating if individuals must be grouped into contiguous blocks based on \code{grplab} starting with \code{selgrp}.} + +\item{subsetgrp}{A character or character vector with group names to subset or reorder groups. Only applicable when \code{grplab} is in use. Default is NA. See details.} + +\item{grpmean}{A logical indicating if q-matrix must be converted from individual values to group mean values. Applicable only when \code{grplab} is in use and mean is calculated over \code{selgrp}.} + +\item{panelspacer}{A numeric indicating the spacing between barplot panels in cm. Defaults to 0.06cm.} + +\item{showsp}{A logical indicating if strip panels on right side must be shown. Strip panel by default displays file name and K value. Defaults to TRUE.} + +\item{sppos}{A character indicating position of strip panel. One of 'right' or 'left'. Defaults to 'right'.} + +\item{splab}{A character or character vector denoting items displayed in the strip panels. Length must be equal to number of runs.} + +\item{splabsize}{A numeric indicating the size of the strip panel label. Computed automatically when set to NULL. Note that overall text size can be controlled using \code{basesize}.} + +\item{splabangle}{A numeric indicating angle/rotation of the strip panel label. Defaults to NULL. Automatically set to -90.} + +\item{splabcol}{A character indicating the colour of the strip panel label. Defaults to "grey30".} + +\item{splabface}{A character indicating the font face of strip panel label. One of 'plain', 'italic', 'bold' or 'bold.italic'. Defaults to 'plain'. Applicable only when \code{showsp=T}.} + +\item{spbgcol}{A character denoting the background colour of the strip panel. Defaults to white.} + +\item{showtitle}{A logical indicating if plot title must be shown on the top. Defaults to FALSE. If TRUE and \code{titlelab=NA}, file name is displayed by default.} + +\item{titlelab}{A character or character vector for title text. Defaults to NA, and when \code{showtitle=TRUE} displays file name.} + +\item{titlehjust}{A numeric denoting the horizontal justification of the title. Defaults to 0 (left).} + +\item{titlevjust}{A numeric denoting the vertical justification of the title. Defaults to 0.5 (center).} + +\item{titlesize}{A numeric indicating the size of the title text. Computed automatically when set to NULL. Note that overall text size can be controlled using \code{basesize}.} + +\item{titlecol}{A colour character for title. Defaults to "grey30".} + +\item{titleface}{A character indicating the font face of title label. One of 'plain', 'italic', 'bold' or 'bold.italic'. Defaults to 'plain'. Applicable only when \code{showtitle=T}.} + +\item{titlespacer}{A numeric indicating the space below the title. Defaults to 1.2.} + +\item{titleangle}{A numeric indicating the angle/rotation of the title. Defaults to 0.} + +\item{showsubtitle}{A logical indicating if plot subtitle must be shown on the top. Defaults to FALSE. If TRUE and \code{subtitlelab=NA}, file name is displayed by default.} + +\item{subtitlelab}{A character or character vector for subtitle text. Defaults to NA, and when \code{showsubtitle=TRUE} displays file name.} + +\item{subtitlehjust}{A numeric denoting the horizontal justification of the subtitle. Defaults to 0 (left).} + +\item{subtitlevjust}{A numeric denoting the vertical justification of the subtitle. Defaults to 0.5 (center).} + +\item{subtitlesize}{A numeric indicating the size of the subtitle text. Computed automatically when set to NULL. Note that overall text size can be controlled using \code{basesize}.} + +\item{subtitlecol}{A colour character for subtitle. Defaults to "grey30".} + +\item{subtitleface}{A character indicating the font face of subtitle label. One of 'plain', 'italic', 'bold' or 'bold.italic'. Defaults to 'plain'. Applicable only when \code{showsubtitle=T}.} + +\item{subtitlespacer}{A numeric indicating the space below the subtitle. Defaults to 1.2.} + +\item{subtitleangle}{A numeric indicating the angle/rotation of the subtitle. Defaults to 0.} + +\item{grplabspacer}{A numeric indicating the space between the plot panels and the group label area in cm. Defaults to 0cm. Applicable only when \code{grplab} are in use.} + +\item{grplabheight}{A numeric indicating the height of the group label area in cm. Defaults to 0.4cm. Multiple group sets are multiplied by 0.4. Applicable only with \code{grplab}. See details.} + +\item{grplabpos}{A numeric indicating the y position of the group labels. Applicable only with group labels. Defaults to 0.} + +\item{grplabsize}{A numeric indicating the size of the group labels. Default range between 1.5 - 2.5 depending on number of individuals. This text size is not affected by \code{basesize}.} + +\item{grplabangle}{A numeric indicating the angle/rotation of group labels. 0 is horizontal while 90 is vertical. Default is 0.} + +\item{grplabjust}{A numeric indicating the justification of group labels. Defaults to 0.5 if grplabangle=0 or 1 if grplabangle between 20 and 135.} + +\item{grplabcol}{A colour character for the colour of group labels. Defaults to "grey30".} + +\item{grplabalpha}{A numeric between 0 and 1 denoting transparency of group labels. Defaults to 1.} + +\item{showindlab}{A logical indicating if individual labels must be shown. See details.} + +\item{sharedindlab}{A logical indicating if only one set of shared individual labels must be shown below all plots. Applicable only when \code{imgoutput="join"}. Individual labels are visible only when \code{showindlab=TRUE}.} + +\item{useindlab}{A logical indicating if individual labels must be read from the rownames of qlist dataframes and used as individual labels. See details.} + +\item{indlabwithgrplab}{A logical indicating if individual labels must be concatenated with grplab. Applies only when grplab is in use. Relevant for sorting by label.} + +\item{indlabspacer}{A numeric denoting space between the individual label and the plot area. Default set to 0.} + +\item{indlabheight}{A numeric indicating space below the individual label panel. Increase to 0.1, 0.2 etc if labels are clipped off.} + +\item{indlabsep}{A character used as separator when concatenating individual labels and group labels. Defaults to space \code{indlabsep=" "}.} + +\item{indlabsize}{A numeric indicating the size of the individual labels. Computed automatically when set to NULL. Note that overall text size can be controlled using \code{basesize}.} + +\item{indlabangle}{A numeric indicating the angle/rotation of individual labels. 0 is horizontal while 90 is vertical. Defaults to 90.} + +\item{indlabvjust}{A numeric denoting vertical justification of the individual labels. Defaults to 0.5.} + +\item{indlabhjust}{A numeric denoting the horizontal justification of the individual labels. Defaults to 1.} + +\item{indlabcol}{A colour character for the colour of individual labels. Defaults to "grey30".} + +\item{pointsize}{A numeric indicating the size of points on label marker line. Default range between 1.2 - 3.2 depending on number of individuals.} + +\item{pointcol}{A colour character for the colour of points on the label marker line. Defaults to "grey30".} + +\item{pointbgcol}{A colour character for the background of marker point for certain point types.} + +\item{pointtype}{A character or number for the type of points on the label marker line. Defaults to |. Same as pch in standard R.} + +\item{pointalpha}{A numeric between 0 and 1 denoting transparency of the points. Defaults to 1.} + +\item{linepos}{A numeric indicating the y position of the label marker line and the points. Applicable only with group labels. Defaults to 1.} + +\item{linesize}{A numeric indicating the thickness of the label marker line. Default range between 0.3 and 0.6 depending on number of individuals.} + +\item{linecol}{A colour character for the label marker line. Defaults to "grey30".} + +\item{linetype}{A numeric indicating the type of line for marker line. Same as lty in standard R. Default value is 1.} + +\item{linealpha}{A numeric between 0 and 1 denoting transparency of the marker line. Defaults to 1.} + +\item{showdiv}{A logical indicating if divider lines between groups must be drawn. Applicable only when group labels are in use.} + +\item{divgrp}{A character or character vector with one or more group label titles denoting which groups are used to draw divider lines. This must be a group label title used in \code{grplab}. If not provided, the value in \code{selgrp} is used by default.} + +\item{divcol}{A character or hexadecimal colour denoting the colour of the divider line. Default is white.} + +\item{divtype}{A numeric indicating the type of line for the divider line. Same as lty in standard R. Default value is '21'.} + +\item{divsize}{A numeric indicating the thickness of the divider line. Default is 0.25.} + +\item{divalpha}{A numeric between 0 and 1 denoting transparency of the divider line. Defaults to 1.} + +\item{showlegend}{A logical indicating if legend denoting cluster colours must be plotted. Defaults to FALSE.} + +\item{legendlab}{A character or character vector to for legend cluster labels. Must be equal to max number of clusters.} + +\item{legendpos}{A character 'right' or 'left' denoting position of the legend. Defaults to 'left'.} + +\item{legendkeysize}{A numeric indicating size of the legend key. Defaults to 4.} + +\item{legendtextsize}{A numeric indicating size of the legend text. Defaults to 3.} + +\item{legendmargin}{A numeric vector of length 4 indicating top, right, bottom and left margins of the legend.} + +\item{barsize}{A numeric indicating the width of the bars. Defaults to 1.} + +\item{barbordersize}{A numeric indicating border size of bars. Defaults to 0. Visible only when \code{barbordercolour} is not NA.} + +\item{barbordercolour}{A single colour for bar border. Defaults to NA. Visible only when \code{barbordersize} is larger than zero and set to a colour other than NA.} + +\item{showyaxis}{A logical indicating if y-axis labels should be displayed or not. Defaults to FALSE. Y-axis size is same as \code{indlabsize}.} + +\item{showticks}{A logical indicating if ticks on axis should be displayed or not. Defaults to FALSE. Applies to x and y axis. Y-axis ticks are visible only when \code{showyaxis=TRUE}. Tick colour is same as \code{indlabcol}.} + +\item{ticksize}{A numeric indicating size of ticks. Defaults to 0.2. Applies to both x and y axis.} + +\item{ticklength}{A numeric indicating length of tick marks in cm. Defaults to 0.03. Applies to both x and y axis.} + +\item{outputfilename}{A character or character vector denoting output file name without file extension. See details.} + +\item{imgtype}{A character indicating output image file type. Possible options are "png","jpeg","tiff" or "pdf".} + +\item{height}{A numeric indicating the height of a single run panel. By default, automatically generated based on number of runs. Separate plots use 1.8cm and joined plots use 1.2cm for single panel. See details.} + +\item{width}{A numeric indicating the width of the whole plot. By default, automatically generated based on number of individuals. Ranges between 5cm and 30cm.} + +\item{dpi}{A numeric indicating the image resolution in pixels per inch (PPI). Defaults to 300. If \code{imgtype="pdf"}, dpi is fixed at 300.} + +\item{units}{A numeric indicating the units of height and width. Default set to "cm". Other options are 'px', 'in' or 'mm'.} + +\item{theme}{A character indicating ggplot theme to be used. Use like "theme_grey", "theme_bw" etc.} + +\item{basesize}{A numeric indicating overall text size. Defaults to 5 suitable for export. Set to 11 for returned plot.} + +\item{font}{A character indicating font family to be used in the plots. Uses default system fonts by default for jpeg, png and tiff. Uses 'Helvetica' as default for pdf. Use package \code{extrafonts} to import custom fonts. See vignette for examples.} + +\item{na.rm}{A logical indicating if NAs are removed from data, else \code{ggplot} prints warning messages for NAs. If set to TRUE, NAs are removed before plotting and \code{ggplot} NA warning is suppressed.} + +\item{quiet}{A logical indicating if any messages are printed to console.} + +\item{panelratio}{A two value integer vector denoting ratio of plot panel to grplab panel. Defaults to \code{c(3,1)}. Applicable only when \code{grplab} is in use.} + +\item{exportplot}{A logical indicating if a plot image must be exported into the working directory.} + +\item{returnplot}{A logical indicating if ggplot plot objects must be returned. See 'Value'.} + +\item{returndata}{A logical indicating if processed data must be returned. See 'Value'.} +} +\value{ +When \code{returnplot=TRUE}, plot object(s) are returned. When \code{grplab=NA}, +a ggplot2 object is returned. When \code{grplab} is in use, a gtable (output from gridExtra::arrangeGrob()) +list is returned. When \code{returndata=TRUE}, the input qlist is modified (sorted, subsetted etc) +and returned. If \code{grplab} is in use, a list of modified qlist and grplab is returned. +If \code{returnplot=TRUE} and \code{returndata=TRUE} are both set, then a named list +(plot,data) is returned. The plot item contains the ggplot2 object or gtable and +the data contains qlist (and grplab). +} +\description{ +Generate separate or joined barplots (group-level) from qlists. +} +\details{ +\strong{sortind}\cr +This argument takes one character as input. Default NA means individuals are +plotted in the same order as input. Individuals can be ordered by any one cluster. +For ex. \code{sortind="Cluster1"} or \code{sortind="Cluster2"}. +To order by all clusters as the 'Sort by Q' option in STRUCTURE software, +use \code{sortind="all"}. When using \code{sortind="label"}, individuals are +sorted by individual labels (along with grplab if present). Individual +labels can be displayed using \code{showindlab=T}. When using \code{sortind} +with \code{grplab}, individuals are sorted within the groups.\cr + +\strong{grplab}\cr +\code{grplab} must be a data.frame. One or more label sets can be provided. Each +label set must be a character vector equal to the number of individuals +present in the qlist. +For example, we can provide one group label set as such:\cr +\code{grplab=data.frame(labs=c("Grp A","Grp A","Grp B","Grp B"),stringsAsFactors=F)}\cr + +Two group label sets can be provided as such:\cr +\code{grplab=data.frame(labs=c("Grp A","Grp A","Grp B","Grp B"),loc=c("Loc 1","Loc 2","Loc 2","Loc 2"),stringsAsFactors=F)}\cr + +\strong{selgrp}\cr +When multiple group label sets are in use, \code{selgrp} defines which +group label set is used for group ordering (\code{ordergrp}), subsetting (\code{subsetgrp}) +and group mean (\code{grpmean}). \code{selgrp} is also used for plotting divider +lines and and sorting (\code{sortind}). If \code{selgrp} is not specified, +the first group label set is used by default.\cr + +\strong{ordergrp}\cr +When using \code{grplab}, labels may not be in contiguous blocks. Using \code{ordergrp=TRUE}, +regroups individuals into contiguous blocks for all group label sets starting with \code{selgrp}.\cr + +\strong{subsetgrp}\cr +This argument takes one or more characters as input. Use only group labels used +in one of the group label sets in \code{grplab}. For ex. In case of a group label +set 'labs' with two grps in order 'Grp A' and 'Grp B', use \code{subsetgrp=c("Grp B","Grp A")} +to change order of groups. Use \code{subsetgrp="Grp B"} to subset only Grp B. +When using multiple group label sets, use \code{selgrp} to declare which group label set to subset.\cr + +\strong{outputfilename}\cr +Default is \code{outputfilename=NA} which means that output file names are automatically generated. +When \code{imgoutput="sep"}, the names of the qlist are used to create output labels. When \code{imgoutput="join"}, +one output label is created for all input files in this format: JoinedNFiles-YYYYMMDDHHMMSS, +where N stands for number of runs joined, and the ending stands for current system date and time. +If \code{outputfilename} is provided, when \code{imgoutput="sep"}, \code{outputfilename} must be +a character vector equal to length of input runs. When \code{imgoutput="join"}, \code{outputfilename} +must be a character of length one. File extensions like .png etc must not be provided.\cr + +\strong{height}\cr +Argument \code{height} denotes the height of one run panel. With joined plots, the \code{height} is multiplied by number of runs. The height does not include label panel. The \code{grplabheight} is used to define the full height of the lab panel. If \code{grplabheight} is not provided, it is calculated based on the number of group label sets. +final_image_height = (height*num_of_runs)+grplabheight +It is possible to set either height or width and leave other as default.\cr + +\strong{indlab}\cr +When \code{showindlab=T}, individual labels are shown/displayed. When \code{showindlab=F}, +individual labels are not shown/displayed on the graph, although they are present in the underlying data. +Therefore, \code{showindlab} only control display of labels on the plot and nothing to +do with label control in the data.\cr +The default \code{useindlab=F}, creates labels numerically in the +original order of data but with zero padding. For example, if there are 10 individuals, +labels are 01, 02 up to 10. if there are 100 individuals, then labels are 001, 002 up +to 100. Zero padding to ensure optimal sorting. When \code{useindlab=T}, labels +are used from rownames of qlist dataframes. They are usually labelled 1,2,3.. if +read in using \code{readQ()}. This can be an issue with sorting by labels \code{sortind="label"}. +For STRUCTURE files with individual labels, they can be read +in automatically using \code{readQ(indlabfromfile=T)}.\cr +When group labels are in use, \code{grplab}, they are added to the individual +labels in both cases \code{useindlab=T} and \code{useindlab=F} separated by \code{indlabsep}. +Default \code{indlabsep=" "} adds a space between individual label and grplab. For example, +group labels 'popA', 'popA'... will be '01 popA', '02 popA'... when \code{useindlab=F} +and usually '1 popA', '2 popA'... when \code{useindlab=T}. When multiple group labels +are in use, the are similarly concatenated one after the other to individual names +in the order in which the group labels were provided. + +See the \href{http://royfrancis.github.io/pophelper/}{vignette} for more details. +} +\examples{ +slist <- readQ(list.files(path=system.file("files/structure",package="pophelper"),full.names=TRUE)) + +# plot one separate figure +plotQ(qlist=slist[1]) + +# plot two separate figures +plotQ(qlist=slist[1:2]) + +# plot a joined figure with multiple plots +plotQ(qlist=slist[1:2],imgoutput="join") + +# sort individuals +plotQ(qlist=slist[c(1,3)],sortind="all") +plotQ(qlist=slist[c(1,3)],sortind="Cluster1") +plotQ(qlist=slist[c(1,3)],sortind="label") +plotQ(qlist=slist[c(1,3)],sortind="all",imgoutput="join") + +# read group labels +md <- read.delim(system.file("files/metadata.txt", package="pophelper"), header=T,stringsAsFactors=F) + +# plot with one group label set +plotQ(qlist=slist[1],grplab=md[,2,drop=F]) +plotQ(qlist=slist[1:2],grplab=md[,2,drop=F],imgoutput="join") + +# sort within groups +plotQ(qlist=slist[1:2],grplab=md[,2,drop=F],imgoutput="join",sortind="all") +plotQ(qlist=slist[1:2],grplab=md[,2,drop=F],imgoutput="join",sortind="Cluster1") +plotQ(qlist=slist[1:2],grplab=md[,2,drop=F],imgoutput="join",sortind="label") + +# reorder groups +plotQ(qlist=slist[1],grplab=md[,2,drop=F],subsetgrp=c("CatB","CatA")) + +# multiple group label sets and ordergrp +plotQ(qlist=slist[1],grplab=md,ordergrp=TRUE) +plotQ(qlist=slist[1:2],grplab=md,ordergrp=TRUE,imgoutput="join") + +# sort in second label group set cat +plotQ(qlist=slist[1],grplab=md,selgrp="cat",sortind="all") + +# use default individual labels +plotQ(slist[1],showindlab=T,width=15) + +# use custom individual labels +inds <- read.delim(system.file("files/structureindlabels.txt",package="pophelper"),header=FALSE,stringsAsFactors=FALSE) +rownames(slist[[1]]) <- inds$V1 +plotQ(slist[1],showindlab=T,useindlab=T,width=15) + +# change cluster colours +plotQ(slist[1],clustercol=c("steelblue","coral")) + +# plot a custom dataframe +temp <- list("custom"=data.frame(Cluster1=c(0.2,0.3,0.6,0.8),Cluster2=c(0.8,0.7,0.4,0.2))) +plotQ(temp) + +} +\seealso{ +\code{\link{plotQMultiline}} +} diff --git a/man/plotQMultiline.Rd b/man/plotQMultiline.Rd new file mode 100644 index 0000000..f265768 --- /dev/null +++ b/man/plotQMultiline.Rd @@ -0,0 +1,261 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/pophelper.R +\name{plotQMultiline} +\alias{plotQMultiline} +\title{Plot a qlist as individual-level multiline barplot} +\usage{ +plotQMultiline(qlist = NULL, spl = NA, lpp = NA, clustercol = NA, + sortind = NA, grplab = NA, selgrp = NA, ordergrp = FALSE, + subsetgrp = NA, grpmean = FALSE, showindlab = TRUE, useindlab = FALSE, + indlabwithgrplab = FALSE, indlabsep = " ", indlabsize = 5, + indlabangle = 90, indlabvjust = 0.5, indlabhjust = 1, + indlabcol = "grey30", indlabspacer = 1.5, showgrplab = TRUE, + grplabsize = 7, grplabcol = "grey30", grplabbgcol = "#DCDCDC", + showtitle = FALSE, titlelab = NA, titlehjust = 0, titlevjust = 0.5, + titlesize = 9, titlecol = "grey30", titleface = "plain", + titlespacer = 3, titleangle = 0, showsubtitle = FALSE, + subtitlelab = NA, subtitlehjust = 0, subtitlevjust = 0.5, + subtitlesize = 7, subtitlecol = "grey30", subtitleface = "plain", + subtitlespacer = 4, subtitleangle = 0, showlegend = FALSE, + legendlab = NA, legendpos = "right", legendkeysize = 6, + legendtextsize = 8, legendmargin = c(1, 1, 1, 0), barsize = 0.9, + barbordersize = 0, barbordercolour = NA, showticks = FALSE, + showyaxis = FALSE, ticksize = 0.1, ticklength = 0.03, + outputfilename = NA, imgtype = "png", height = NA, width = NA, + dpi = 300, units = "cm", mar = c(0.1, 0.5, 0.1, 0.5), + theme = "theme_grey", basesize = 5, font = "", na.rm = FALSE, + quiet = FALSE, exportplot = TRUE, returnplot = FALSE, + returndata = FALSE) +} +\arguments{ +\item{qlist}{A qlist (list of dataframes). An output from \code{\link{readQ}}.} + +\item{spl}{An integer indicating samples per line. Defaults to 60.} + +\item{lpp}{An integer indicating lines per page. Defaults to 11.} + +\item{clustercol}{A character vector of colours for clusters.} + +\item{sortind}{A character indicating how individuals are sorted. Default is NA (Same order of individuals as in input file). Other options are 'all' (sorting by values of all clusters), by any one cluster (eg. 'Cluster1') or 'labels' (sorting by individual labels). See details.} + +\item{grplab}{A dataframe with one or more columns (group label sets), and rows equal to the number of individuals. See details.} + +\item{selgrp}{A single character denoting a selected group label set. The selected label must be a group label title used in \code{grplab}. See details.} + +\item{ordergrp}{A logical indicating if individuals must be grouped into contiguous blocks based on \code{grplab} starting with \code{selgrp}.} + +\item{subsetgrp}{A character or character vector with group names to subset or reorder groups. Only applicable when \code{grplab} is in use. Default is NA. See details.} + +\item{grpmean}{A logical indicating if q-matrix must be converted from individual values to group mean values. Applicable only when \code{grplab} is in use and mean is calculated over \code{selgrp}.} + +\item{showindlab}{A logical indicating if individual labels must be shown below the bars. To hide labels, set \code{showindlab=FALSE}. See details.} + +\item{useindlab}{A logical indicating if individual labels must be read from the rownames of qlist dataframes and used as labels. See details.} + +\item{indlabsep}{A character used as separator when concatenating individual labels and group labels. Defaults to space \code{indlabsep=" "}.} + +\item{indlabsize}{A numeric denoting size of the individual labels. Defaults to 5.} + +\item{indlabangle}{A numeric denoting the angle of the individual labels. Defaults to 90.} + +\item{indlabvjust}{A numeric denoting vertical justification of the individual labels. Defaults to 0.5.} + +\item{indlabhjust}{A numeric denoting the horizontal justification of the individual labels. Defaults to 1.} + +\item{indlabcol}{A colour for individual labels. Defaults to 'grey30'.} + +\item{indlabspacer}{A numeric denoting space between the individual label and the plot area. Default set to 0.} + +\item{showgrplab}{A logical indicating if group labels \code{grplab} must be displayed on the plot.} + +\item{grplabsize}{A numeric denoting size of the group labels. Defaults to 7.} + +\item{grplabcol}{A colour for group labels. Defaults to 'grey30'.} + +\item{grplabbgcol}{A colour for group label background. Defaults to 'white'.} + +\item{titlelab}{A character or character vector for title text. Defaults to NA, and when \code{showtitle=TRUE} displays file name.} + +\item{titlehjust}{A numeric denoting the horizontal justification of the title. Defaults to 0 (left).} + +\item{titlevjust}{A numeric denoting the vertical justification of the title. Defaults to 0.5 (center).} + +\item{titlesize}{A numeric indicating the size of the title text. Defaults to 5 points.} + +\item{titlecol}{A colour character for title. Defaults to "grey30".} + +\item{titleface}{A character indicating the font face of title label. One of 'plain', 'italic', 'bold' or 'bold.italic'. Defaults to 'plain'. Applicable only when \code{showtitle=T}.} + +\item{titlespacer}{A numeric indicating the space below the title. Defaults to 1.2.} + +\item{titleangle}{A numeric indicating the angle/rotation of the title. Defaults to 0.} + +\item{showsubtitle}{A logical indicating if plot subtitle must be shown on the top. Defaults to FALSE. If TRUE and \code{subtitlelab=NA}, file name is displayed by default.} + +\item{subtitlelab}{A character or character vector for subtitle text. Defaults to NA, and when \code{showsubtitle=TRUE} displays K value like K=2.} + +\item{subtitlehjust}{A numeric denoting the horizontal justification of the subtitle. Defaults to 0 (left).} + +\item{subtitlevjust}{A numeric denoting the vertical justification of the subtitle. Defaults to 0.5 (center).} + +\item{subtitlesize}{A numeric indicating the size of the subtitle text. Defaults to 5 points.} + +\item{subtitlecol}{A colour character for subtitle. Defaults to "grey30".} + +\item{subtitleface}{A character indicating the font face of subtitle label. One of 'plain', 'italic', 'bold' or 'bold.italic'. Defaults to 'plain'. Applicable only when \code{showsubtitle=T}.} + +\item{subtitlespacer}{A numeric indicating the space below the subtitle. Defaults to 1.2.} + +\item{subtitleangle}{A numeric indicating the angle/rotation of the subtitle. Defaults to 0.} + +\item{barsize}{A numeric indicating the width of the bars. Defaults to 0.9.} + +\item{barbordersize}{A numeric indicating border size of bars. Defaults to 0. Visible only when \code{barbordercolour} is not NA.} + +\item{barbordercolour}{A single colour for bar border. Defaults to NA. Visible only when \code{barbordersize} is larger than zero and set to a colour other than NA.} + +\item{showticks}{A logical indicating if ticks on axis should be displayed or not. Defaults to FALSE.} + +\item{showyaxis}{A logical indicating if y-axis labels should be displayed or not. Defaults to FALSE.} + +\item{outputfilename}{A character or character vector denoting output file name without file extension. See details.} + +\item{imgtype}{A character denoting figure output format. Options are 'png', 'jpeg', 'tiff' or 'pdf'.} + +\item{height}{A numeric denoting height of the full figure. If NA, height is set to 29.7cm (A4 height).} + +\item{width}{A numeric denoting width of the full figure. If NA, width is set to 21cm (A4 width).} + +\item{dpi}{A numeric denoting resolution of the figure. Default is 300. If \code{imgtype="pdf"}, dpi is fixed at 300 and does not have any effect..} + +\item{units}{A character denoting the units of dimension of the figure. Default is "cm". Other options are 'px', 'in' or 'mm'.} + +\item{mar}{A four number vector denoting distance of top, right, bottom and left margins in \code{units}.} + +\item{theme}{A character indicating ggplot theme to be used. Use like "theme_grey", "theme_bw" etc.} + +\item{font}{A character indicating font family to be used in the plots. Uses default system fonts by default for jpeg, png and tiff. Uses 'Helvetica' as default for pdf. Use package \code{extrafonts} to import custom fonts. See vignette for examples.} + +\item{na.rm}{Default set to FALSE. NAs are not removed from data, therefore \code{ggplot} prints warning messages for NAs. If set to TRUE, NAs are removed before plotting and \code{ggplot} NA warning is suppressed.} +} +\description{ +Plot a qlist as individual-level barplot with multiple lines. +} +\details{ +Figures are always created to A4 size. Any plotted row will span the width of the figure. +Note that this function is slow and may take several minutes when plotting mutiple runs. + +\strong{indlab}\cr +\code{plotQMultiline()} labels each individual separately. When \code{showindlab=T}, +individual labels are shown/displayed. When \code{showindlab=F}, individual labels are +not shown/displayed on the graph, although they are present in the underlying data. +Therefore, \code{showindlab} only control display of labels on the plot and nothing to +do with label control in the data.\cr +The default \code{useindlab=F}, creates labels numerically in the +original order of data but with zero padding. For example, if there are 10 individuals, +labels are 01, 02 up to 10. if there are 100 individuals, then labels are 001, 002 up +to 100. Zero padding to ensure optimal sorting. When \code{useindlab=T}, labels +are used from rownames of qlist dataframes. They are usually labelled 1,2,3.. if +read in using \code{readQ()}. This can be an issue with sorting by labels \code{sortind="label"}. +For STRUCTURE files with individual labels, they can be read +in automatically using \code{readQ(indlabfromfile=T)}.\cr +When group labels are in use, \code{grplab}, they are added to the individual +labels in both cases \code{useindlab=T} and \code{useindlab=F} separated by \code{indlabsep}. +Default \code{indlabsep=" "} adds a space between individual label and grplab. For example, +group labels 'popA', 'popA'... will be '01 popA', '02 popA'... when \code{useindlab=F} +and usually '1 popA', '2 popA'... when \code{useindlab=T}. When multiple group labels +are in use, the are similarly concatenated one after the other to individual names +in the order in which the group labels were provided. + +\strong{sortind}\cr +This argument takes one character as input. Default NA means individuals are +plotted in the same order as input. Individuals can be ordered by any one cluster. +For ex. \code{sortind="Cluster1"} or \code{sortind="Cluster2"}. +To order by all clusters as the 'Sort by Q' option in STRUCTURE software, +use \code{sortind="all"}. To order by individual labels, use \code{sortind="label"}. +When using \code{sortind} with \code{grplab}, individuals +are sorted within the groups.\cr + +\strong{grplab}\cr +\code{grplab} must be a list. One or more label sets can be provided. Each +label set must be a character vector equal to the number of individuals +present in the qlist. +For example, we can provide one set of grp labels as such:\cr +\code{labs1 <- c("Grp A","Grp A","Grp B","Grp B")}\cr +\code{grplab=list("grp"=labs1)}\cr + +A second set of grp labels can be provided as such: +\code{labs2 <- c("Loc 1","Loc 1","Loc 2","Loc 3")}\cr +\code{grplab=list("population"=labs1,"location"=labs2)}\cr + +\strong{subsetgrp}\cr +This argument takes one or more characters as input. Use only group labels +exactly as used in the \code{grplab} vector. For ex. In case of two grps in +order 'Pop A' and 'Pop B', use \code{subsetgrp=c("Pop B","Pop A")} to change +order of groups. Use \code{subsetgrp="Pop B"} to subset only Pop B.\cr + +\strong{outputfilename}\cr +Output file names are created automatically by default using the input qlist names. +When number of individuals exceed one page and extra pages are created, incremental +numbers are added to the run name like so: -1, -2 etc. Custom file name can be provided +to \code{outputfilename}. The number of labels must be equal to the number of input +runs. Incremental numbers are still added if extra pages are created. + +See the \href{http://royfrancis.github.io/pophelper/}{vignette} for more details. +} +\examples{ +\dontrun{ +sfiles <- list.files(path=system.file("files/structure",package="pophelper"),full.names=TRUE) +slist <- readQ(sfiles) + +# basic +plotQMultiline(slist[1]) + +# multiple files +plotQMultiline(slist[1:3]) + +# adjust samples per line (spl) and lines per page (lpp) +plotQMultiline(slist[1],spl=30) +plotQMultiline(slist[1],lpp=8) +plotQMultiline(slist[1],spl=75,lpp=10) + +# sort individuals +plotQMultiline(slist[1],sortind="all") +plotQMultiline(slist[1],sortind="Cluster1") +plotQMultiline(slist[1],sortind="label") + +# use custom individual labels +inds <- read.delim(system.file("files/structureindlabels.txt",package="pophelper"),header=FALSE,stringsAsFactors=FALSE) +rownames(slist[[1]]) <- inds$V1 +plotQMultiline(slist[1],useindlab=T) + +# change cluster colours +plotQMultiline(slist[1],clustercol=c("steelblue","coral")) + +# change bar width and height +plotQMultiline(slist[1],barsize=1,spl=149,indlabsize=3,height=5) + +# read group labels +md <- read.delim(system.file("files/metadata.txt", package="pophelper"), header=T,stringsAsFactors=F) + +# plot with one group label set +plotQMultiline(qlist=slist[1],grplab=md[,2,drop=F]) +plotQMultiline(qlist=slist[1],grplab=md[,2,drop=F],useindlab=T) + +# sort ind within groups +plotQMultiline(qlist=slist[1],grplab=md[,2,drop=F],sortind="Cluster1") +plotQMultiline(qlist=slist[1],grplab=md[,2,drop=F],sortind="all") +plotQMultiline(qlist=slist[1],grplab=md[,2,drop=F],sortind="label") + +# subset or reorder groups +plotQMultiline(qlist=slist[1],grplab=md[,2,drop=F],subsetgrp=c("CatB")) +plotQMultiline(qlist=slist[1],grplab=md[,2,drop=F],subsetgrp=c("Cat B","CatA")) + +# using multiple group label sets +plotQMultiline(qlist=slist[1],grplab=md,ordergrp=TRUE) + +# subset on a group from second group label set +plotQMultiline(qlist=slist[1],grplab=md,selgrp="cat",subsetgrp="CatB") + +} +} diff --git a/man/readQ.Rd b/man/readQ.Rd new file mode 100644 index 0000000..dfce72c --- /dev/null +++ b/man/readQ.Rd @@ -0,0 +1,95 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/pophelper.R +\name{readQ} +\alias{readQ} +\title{Convert run files (q-matrices) to qlist.} +\usage{ +readQ(files = NULL, filetype = "auto", indlabfromfile = FALSE) +} +\arguments{ +\item{files}{A character or character vector of one or more files.} + +\item{filetype}{A character indicating input filetype. Options are 'auto','structure','tess','baps', +'basic' or 'clumpp'. See details.} + +\item{indlabfromfile}{A logical indicating if individual labels must be read +from input file and used as row names for resulting dataframe. Spaces in +labels may be replaced with _. Currently only applicable to STRUCTURE runs files.} +} +\value{ +A list of lists with dataframes is returned. List items are named by input filenames. +File extensions such as '.txt','.csv','.tsv' and '.meanQ' are removed from filename. +In case filenames are missing or not available, lists are named sample1, sample2 etc. +For STRUCTURE runs, if individual labels are present in the run file and \code{indlabfromfile=T}, +they are added to the dataframe as row names. Structure metadata including loci, +burnin, reps, elpd, mvll, and vll is added as attributes to each dataframe. +For CLUMPP files, multiple runs within one file are suffixed by -1, -2 etc. +} +\description{ +Takes one or more STRUCTURE, TESS, BAPS, numeric delimited run files or +CLUMPP format files and converts them to a qlist (list of dataframes). +} +\details{ +STRUCTURE, TESS and BAPS run files have unique layout and format (See vignette). BASIC files can be Admixture run files, +fastStructure meanQ files or any tab-delimited, space-delimited or comma-delimited tabular data +without a header. CLUMPP files can be COMBINED, ALIGNED or +MERGED files. COMBINED files are generated from \code{clumppExport}. ALIGNED and +MERGED files are generated by CLUMPP. + +To convert TESS3 R objects to pophelper qlist, see \code{\link{readQTess3}}. + +See the \href{http://royfrancis.github.io/pophelper/}{vignette} for more details. +} +\examples{ + +# STRUCTURE files +sfiles <- list.files(path=system.file("files/structure",package="pophelper"),full.names=TRUE) +# create a qlist of all runs +slist <- readQ(sfiles) +slist <- readQ(sfiles,filetype="structure") + +# use ind names from file +readQ(sfiles[1],indlabfromfile=T) + +# access the first run +readQ(sfiles)[[1]] + +# access names of runs +names(slist) + +# TESS files +tfiles <- list.files(path=system.file("files/tess",package="pophelper"),full.names=TRUE) +# create a qlist +readQ(tfiles) + +# BASIC files +afiles <- list.files(path=system.file("files/admixture",package="pophelper"),full.names=TRUE) +# create a qlist +readQ(afiles) + +# CLUMPP files +tabs1 <- system.file("files/STRUCTUREpop_K4-combined.txt",package="pophelper") +tabs2 <- system.file("files/STRUCTUREpop_K4-combined-aligned.txt",package="pophelper") +tabs3 <- system.file("files/STRUCTUREpop_K4-combined-merged.txt",package="pophelper") + +# create a qlist +readQ(tabs1) +readQ(tabs2) +readQ(tabs3) + +# manually create qlist +df1 <- data.frame(Cluster1=c(0.2,0.4,0.6,0.2),Cluster2=c(0.8,0.6,0.4,0.8)) +df2 <- data.frame(Cluster1=c(0.3,0.1,0.5,0.6),Cluster2=c(0.7,0.9,0.5,0.4)) + +# one-element qlist +q1 <- list("sample1"=df1) +str(q1) + +# two-element qlist +q2 <- list("sample1"=df1,"sample2"=df2) +str(q2) + +} +\seealso{ +\code{\link{readQTess3}} +} diff --git a/man/readQBaps.Rd b/man/readQBaps.Rd new file mode 100644 index 0000000..712e9f4 --- /dev/null +++ b/man/readQBaps.Rd @@ -0,0 +1,27 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/pophelper.R +\name{readQBaps} +\alias{readQBaps} +\title{Convert BAPS cluster files to qlist.} +\usage{ +readQBaps(files = NULL) +} +\arguments{ +\item{files}{A character or character vector of one or more BAPS cluster run files. Use \code{choose.files(multi=TRUE)} +to select interactively.} +} +\value{ +A list of lists with dataframes is returned. List items are named by input filename. +} +\description{ +Takes one or more BAPS cluster run files and converts them to a +list of dataframes. +} +\details{ +See the \href{http://royfrancis.github.io/pophelper/}{vignette} for more details. +} +\examples{ +bfiles <- list.files(path=system.file("files/baps",package="pophelper"),full.names=TRUE) +# create a qlist +readQBaps(bfiles) +} diff --git a/man/readQBasic.Rd b/man/readQBasic.Rd new file mode 100644 index 0000000..894bbd2 --- /dev/null +++ b/man/readQBasic.Rd @@ -0,0 +1,28 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/pophelper.R +\name{readQBasic} +\alias{readQBasic} +\title{Convert delimited text files to qlist.} +\usage{ +readQBasic(files = NULL) +} +\arguments{ +\item{files}{A character or character vector of one or more delimited text files. Use \code{choose.files(multi=TRUE)} +to select interactively.} +} +\value{ +A list of lists with dataframes is returned. List items are named by input filename. +} +\description{ +Takes one or more delimited numeric text files and converts each of +them to separate dataframes. +} +\details{ +Input files can be Admixture run files, fastStructure meanQ files. +or any tab-delimited, space-delimited or comma-delimited tabular data without header. +} +\examples{ +afiles <- list.files(path=system.file("files/admixture",package="pophelper"),full.names=TRUE) +# create a qlist +readQBasic(afiles) +} diff --git a/man/readQClumpp.Rd b/man/readQClumpp.Rd new file mode 100644 index 0000000..38ab20c --- /dev/null +++ b/man/readQClumpp.Rd @@ -0,0 +1,33 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/pophelper.R +\name{readQClumpp} +\alias{readQClumpp} +\title{Convert CLUMPP format numeric text files to qlist.} +\usage{ +readQClumpp(files = NULL) +} +\arguments{ +\item{files}{A character or character vector of one or more COMBINED, ALIGNED or +MERGED files. COMBINED files are generated from \code{clumppExport}. ALIGNED and +MERGED files are generated by CLUMPP. Use \code{choose.files(multi=TRUE)} to +select interactively.} +} +\value{ +A list of lists with dataframes is returned. Each list item is named by +input filename. Multiple runs within one file are suffixed by -1, -2 etc. +} +\description{ +Takes one or more CLUMPP format numeric text files and converts +them to a list of dataframes. +} +\examples{ +tabs1 <- system.file("files/STRUCTUREpop_K4-combined.txt",package="pophelper") +tabs2 <- system.file("files/STRUCTUREpop_K4-combined-aligned.txt",package="pophelper") +tabs3 <- system.file("files/STRUCTUREpop_K4-combined-merged.txt",package="pophelper") + +# create a qlist +readQClumpp(tabs1) +readQClumpp(tabs2) +readQClumpp(tabs3) + +} diff --git a/man/readQStructure.Rd b/man/readQStructure.Rd new file mode 100644 index 0000000..78d9a20 --- /dev/null +++ b/man/readQStructure.Rd @@ -0,0 +1,37 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/pophelper.R +\name{readQStructure} +\alias{readQStructure} +\title{Convert STRUCTURE run files to qlist.} +\usage{ +readQStructure(files = NULL, indlabfromfile = FALSE) +} +\arguments{ +\item{files}{A character or character vector of one or more STRUCTURE run files. Use \code{choose.files(multi=TRUE)} +to select interactively.} + +\item{indlabfromfile}{A logical indicating if individual labels must be read from input file and used as row names for resulting dataframe. Spaces in labels may be replaced with _.} +} +\value{ +A list of lists with dataframes is returned. If individual labels are +present in the STRUCTURE file, they are added to the dataframe as row names. Structure +metadata including loci, burnin, reps, elpd, mvll, and vll is added as attributes +to each dataframe. List items are named by input filenames. +} +\description{ +Takes one or more STRUCTURE run files and converts them to a list of dataframes. +} +\examples{ +sfiles <- list.files(path=system.file("files/structure",package="pophelper"),full.names=TRUE) +# create a qlist of all runs +slist <- readQStructure(sfiles) + +# use ind names from file +readQStructure(sfiles[1],indlabfromfile=T) + +# access the first run +readQStructure(sfiles)[[1]] + +# access names of runs +names(slist) +} diff --git a/man/readQTess.Rd b/man/readQTess.Rd new file mode 100644 index 0000000..fecc392 --- /dev/null +++ b/man/readQTess.Rd @@ -0,0 +1,27 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/pophelper.R +\name{readQTess} +\alias{readQTess} +\title{Convert TESS cluster files to qlist.} +\usage{ +readQTess(files = NULL) +} +\arguments{ +\item{files}{A character or character vector of one or more TESS cluster run files. Use \code{choose.files(multi=TRUE)} +to select interactively.} +} +\value{ +A list of lists with dataframes is returned. List items are named by input filename. +} +\description{ +Takes one or more TESS cluster run files and converts them to a +list of dataframes. +} +\details{ +Use collectRunsTess() to collect TESS runs into one directory. +} +\examples{ +tfiles <- list.files(path=system.file("files/tess",package="pophelper"),full.names=TRUE) +# create a qlist +readQTess(tfiles) +} diff --git a/man/readQTess3.Rd b/man/readQTess3.Rd new file mode 100644 index 0000000..2928d85 --- /dev/null +++ b/man/readQTess3.Rd @@ -0,0 +1,28 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/pophelper.R +\name{readQTess3} +\alias{readQTess3} +\title{Convert TESS3 R object to pophelper qlist.} +\usage{ +readQTess3(t3list = NULL, progressbar = FALSE) +} +\arguments{ +\item{t3list}{A TESS3 object. An output from function \code{tess3()} from package \code{tess3r}.} + +\item{progressbar}{A logical indicating if execution progress must be shown.} +} +\value{ +A list of lists with dataframes (qlist) is returned. Each list item is named by +as sample1, sample2 etc. Within TESS3, 'tess3Main' attributes L, n, ploidy, K, rmse +and crossentropy are preserved as attributes in the qlist dataframe. +} +\description{ +Takes a TESS3 R object and convert to pophelper qlist for use with pophelper. +} +\details{ +See the \href{http://royfrancis.github.io/pophelper/}{vignette} for more details. +} +\examples{ +t3obj <- readRDS(system.file("files/tess3.rds",package="pophelper")) +t3list <- readQTess3(t3obj) +} diff --git a/man/sortInd.Rd b/man/sortInd.Rd new file mode 100644 index 0000000..c374126 --- /dev/null +++ b/man/sortInd.Rd @@ -0,0 +1,35 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/pophelper.R +\name{sortInd} +\alias{sortInd} +\title{Internal: Handles individual sorting} +\usage{ +sortInd(dframe = NULL, grplab = NA, selgrp = NA, sortind = NA, + grplabpos = NA, linepos = NA) +} +\arguments{ +\item{dframe}{A q-matrix dataframe} + +\item{grplab}{A dataframe with group labels} + +\item{selgrp}{A single character denoting selected group label set. See details.} + +\item{sortind}{A character indicating how individuals are sorted. Default is NA (Same order of individuals as in input file). Other options are 'all' (sorting by values of all clusters), by any one cluster (eg. 'Cluster1') or 'labels' (sorting by individual labels).} + +\item{grplabpos}{A numeric indicating y-axis position of labels} + +\item{linepos}{A numeric indicating y-axis position of label line} +} +\value{ +Returns a list with ordered q-matrix dataframe and ordered grplab. +} +\description{ +Internal: Handles individual sorting +} +\details{ +When multiple group label sets are in use, \code{selgrp} defines which +group label set is used for group ordering (\code{ordergrp}), subsetting (\code{subsetgrp}) +and group mean (\code{grpmean}). \code{selgrp} is also used for plotting divider +lines and and sorting (\code{sortind}). If \code{selgrp} is not specified, the +first group label set is used by default. +} diff --git a/man/summariseQ.Rd b/man/summariseQ.Rd new file mode 100644 index 0000000..5ff3cdd --- /dev/null +++ b/man/summariseQ.Rd @@ -0,0 +1,46 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/pophelper.R +\name{summariseQ} +\alias{summariseQ} +\alias{summarizeQ} +\title{Summarise a tabulated dataframe} +\usage{ +summariseQ(data = NULL, writetable = FALSE) +} +\arguments{ +\item{data}{A dataframe with tabulated runs. An output from \code{tabulateQ()}. +Must have minimum 2 columns named k and ind.} + +\item{writetable}{A logical indicating if the output table is to be exported as +a tab-delimited text file in the working directory.} +} +\value{ +Returns a dataframe with all values of K sorted by K. The table has +3 columns namely value of K, number of runs for each K and number of individuals. +If the input file is derived from STRUCTURE runs, the table is sorted by loci as well. +Other columns include elpdmean, elpdsd, elpdmin and elpdmax. +} +\description{ +Creates a summary table from a tabulated dataframe of two or more +runs with k, number of runs and individuals. +} +\details{ +See the \href{http://royfrancis.github.io/pophelper/}{vignette} for more details. +} +\examples{ + +# STRUCTURE files +sfiles <- list.files(path=system.file("files/structure",package="pophelper"),full.names=TRUE) +slist <- readQ(sfiles) +tr1 <- tabulateQ(slist) +summariseQ(tr1) + +# ADMIXTURE files +afiles <- list.files(path=system.file("files/admixture",package="pophelper"),full.names=TRUE) +tr1 <- tabulateQ(readQ(afiles)) +summariseQ(tr1) + +} +\seealso{ +\code{\link{tabulateQ}} +} diff --git a/man/tabulateQ.Rd b/man/tabulateQ.Rd new file mode 100644 index 0000000..05e1c11 --- /dev/null +++ b/man/tabulateQ.Rd @@ -0,0 +1,57 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/pophelper.R +\name{tabulateQ} +\alias{tabulateQ} +\title{Tabulate runs from a qlist} +\usage{ +tabulateQ(qlist = NULL, writetable = FALSE, sorttable = TRUE) +} +\arguments{ +\item{qlist}{A qlist (list of dataframes). An output from \code{\link{readQ}}.} + +\item{writetable}{A logical indicating if the output table must be exported as +a tab-delimited text file in the working directory.} + +\item{sorttable}{A logical indicating if output table is to be sorted. Sorts table by ind and K.} +} +\value{ +Returns a dataframe with filenames (if list is not named, then sample1, sample2 etc. is used), +K and number of individuals of all runs sorted by ind and K (if \code{sorttable=T}). +The row numbers of the output table denotes the file number selected. This is helpful +if a particular file from the table needs to +be identified in the selection vector. If input files come from STRUCTURE runs, +columns loci, burnin, reps, elpd, mvll and vll are also returned. In input files come +from TESS3, columns loci, gif, rmse, crossentropy and ploidy are included as well. +} +\description{ +Takes a qlist of one of more numeric dataframes and creates a +table with filenames, K and number of individuals. +} +\details{ +The input must be a list of dataframes. If one dataframe is used, then it +must be inside a list. If the list items are named, then the item name is used as +filename, else sample1, sample2 etc. is used. + +See the \href{http://royfrancis.github.io/pophelper/}{vignette} for more details. +} +\examples{ + +# STRUCTURE files +sfiles <- list.files(path=system.file("files/structure",package="pophelper"),full.names=TRUE) +slist <- readQ(sfiles) +tabulateQ(qlist=slist) + +# TESS files +tfiles <- list.files(path=system.file("files/tess",package="pophelper"),full.names=TRUE) +tlist <- readQ(tfiles) +tabulateQ(qlist=tlist) + +# ADMIXTURE files +afiles <- list.files(path=system.file("files/admixture",package="pophelper"),full.names=TRUE) +alist <- readQ(afiles) +tabulateQ(qlist=alist) + +} +\seealso{ +\code{\link{summariseQ}} +} diff --git a/man/unitConverter.Rd b/man/unitConverter.Rd new file mode 100644 index 0000000..f03dee2 --- /dev/null +++ b/man/unitConverter.Rd @@ -0,0 +1,23 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/pophelper.R +\name{unitConverter} +\alias{unitConverter} +\title{Internal: Convert value between dimension units} +\usage{ +unitConverter(value = NA, fromunit = NA, tounit = NA, dpi = NA) +} +\arguments{ +\item{value}{A numeric value or numeric vector to convert} + +\item{fromunit}{A character indicating the current unit of the value. Options are "cm", "mm", "in" or "px".} + +\item{tounit}{A character indicating the unit to change to. Options are "cm", "mm", "in" or "px".} + +\item{dpi}{A numeric indicating the resolution for pixel conversion. This should be in PPI (pixels per inch).} +} +\value{ +Returns a numeric value or numeric vector in changed units. +} +\description{ +Internal: Convert value between dimension units +} diff --git a/man/verifyGrplab.Rd b/man/verifyGrplab.Rd new file mode 100644 index 0000000..1f6ae39 --- /dev/null +++ b/man/verifyGrplab.Rd @@ -0,0 +1,17 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/pophelper.R +\name{verifyGrplab} +\alias{verifyGrplab} +\title{Verify if a grplab dataframe is formatted correctly.} +\usage{ +verifyGrplab(grplab = NULL) +} +\arguments{ +\item{grplab}{A dataframe with character fields.} +} +\value{ +Nothing. +} +\description{ +Verify if a grplab dataframe is formatted correctly. +} diff --git a/tests/testmanual/test-all.R b/tests/testmanual/test-all.R new file mode 100644 index 0000000..094d00b --- /dev/null +++ b/tests/testmanual/test-all.R @@ -0,0 +1,1347 @@ +# Test Script +# v2.2.5 +# 11-Jan-2018 + +library(testthat) +library(pophelper) +#devtools::test() + +# Start ------------------------------------------------------------------------ + +#Preparation +deleteoutput <- TRUE +testfont <- FALSE +testtiff <- FALSE + +if(testfont) +{ + library(extrafont) + font_import(pattern="^Verdana",prompt=F) + loadfonts() +} + +#create a new folder and set as wd +currwd <- getwd() +if(basename(currwd) != "pophelper-demo") +{ + dir.create(paste(currwd,"/pophelper-demo",sep="")) + setwd(paste(currwd,"/pophelper-demo",sep="")) +}else{ + file.remove(list.files()) +} + +#read sample STRUCTURE files from R package +sfiles <- list.files(path=system.file("files/structure",package="pophelper"),full.names=TRUE) +sfiles1 <- list.files(path=system.file("files/structure-ci",package="pophelper"),full.names=TRUE) +#read sample TESS files from R package +tfiles <- list.files(path=system.file("files/tess",package="pophelper"),full.names=TRUE) +#read sample ADMIXTURE files from R package +afiles <- list.files(path=system.file("files/admixture",package="pophelper"),full.names=TRUE) +#read sample fastSTRUCTURE files from R package +ffiles <- list.files(path=system.file("files/faststructure",package="pophelper"),full.names=TRUE) +#read sample BAPS files from R package +bfiles <- list.files(path=system.file("files/baps",package="pophelper"),full.names=TRUE) +#read sample MATRIX files from R package +mcfiles <- list.files(path=system.file("files/basic/comma",package="pophelper"),full.names=TRUE) +mtfiles <- list.files(path=system.file("files/basic/tab",package="pophelper"),full.names=TRUE) +msfiles <- list.files(path=system.file("files/basic/space",package="pophelper"),full.names=TRUE) +tabs1 <- c(system.file("files/STRUCTUREpop_K4-combined.txt",package="pophelper"), + system.file("files/STRUCTUREpop_K4-combined-aligned.txt",package="pophelper"), + system.file("files/STRUCTUREpop_K4-combined-merged.txt",package="pophelper")) +grps1 <- read.delim(system.file("files/structuregrplabels.txt",package="pophelper"),header=FALSE,stringsAsFactors=F) +grps2 <- read.delim(system.file("files/structuregrplabels2.txt",package="pophelper"),header=FALSE,stringsAsFactors=F) + +ftype <- c("sfiles","sfiles1","tfiles","afiles","ffiles", + "mcfiles","mtfiles","msfiles","tabs1","bfiles") + +# checkQ -------------------------------------------------------------------- + +#checkQ +context("Check runs") +cat("checkQ ---------------------------------------------------------------\n") + +len <- length(ftype) +for(i in 1:len) +{ + cat(paste0("Running ",i," of ",len,". ")) + files <- get(ftype[i]) + + # check file type ------------------------------------------------------------ + cat(paste0("filetype; ")) + cr <- pophelper:::checkQ(files) + + # check length + expect_equal(length(cr$type),length(files)) + + # check type + if(i==1|i==2) { + expect_equal(unique(cr$type),"STRUCTURE") + expect_equal(unique(cr$subtype),NA) + } + + if(i==3) { + expect_equal(unique(cr$type),"TESS") + expect_equal(unique(cr$subtype),NA) + } + if(i>3 && i<9) { + expect_equal(unique(cr$type),"BASIC") + if(i!=6) expect_equal(unique(cr$subtype),"SPACE") + if(i==6) expect_equal(unique(cr$subtype),"COMMA") + } + + if(i==9) { + expect_equal(unique(cr$type),"CLUMPP") + expect_equal(unique(cr$subtype),NA) + } + + if(i==10) { + expect_equal(unique(cr$type),"BAPS") + expect_equal(unique(cr$subtype),NA) + } + + # readq -------------------------------------------------------------------- + cat(paste0("readq; ")) + expect_equal(class(pophelper::readQ(files)),"list") + + if(unique(cr$type) == "STRUCTURE") + { + expect_equal(class(pophelper::readQStructure(files)),"list") + expect_error(pophelper::readQ(files,filetype="tess")) + expect_error(pophelper::readQ(files,filetype="basic")) + expect_error(pophelper::readQ(files,filetype="baps")) + expect_error(pophelper::readQ(files,filetype="clumpp")) + } + + if(unique(cr$type) == "TESS") + { + expect_equal(class(pophelper::readQTess(files)),"list") + expect_error(pophelper::readQ(files,filetype="structure")) + expect_error(pophelper::readQ(files,filetype="basic")) + expect_error(pophelper::readQ(files,filetype="baps")) + expect_error(pophelper::readQ(files,filetype="clumpp")) + } + + if(unique(cr$type) == "BASIC") + { + expect_equal(class(pophelper::readQBasic(files)),"list") + expect_error(pophelper::readQ(files,filetype="structure")) + expect_error(pophelper::readQ(files,filetype="tess")) + expect_error(pophelper::readQ(files,filetype="baps")) + expect_error(pophelper::readQ(files,filetype="clumpp")) + } + + if(unique(cr$type) == "BAPS") + { + expect_equal(class(pophelper::readQBaps(files)),"list") + expect_error(pophelper::readQ(files,filetype="structure")) + expect_error(pophelper::readQ(files,filetype="tess")) + expect_error(pophelper::readQ(files,filetype="basic")) + expect_error(pophelper::readQ(files,filetype="clumpp")) + } + + if(unique(cr$type) == "CLUMPP") + { + expect_equal(class(pophelper::readQClumpp(files)),"list") + expect_error(pophelper::readQ(files,filetype="structure")) + expect_error(pophelper::readQ(files,filetype="basic")) + expect_error(pophelper::readQ(files,filetype="baps")) + expect_error(pophelper::readQ(files,filetype="tess")) + } + + # error for empty input + expect_error(pophelper::readQStructure()) + expect_error(pophelper::readQTess()) + expect_error(pophelper::readQBasic()) + expect_error(pophelper::readQClumpp()) + expect_error(pophelper::readQTess3()) + expect_error(pophelper::readQBaps()) + expect_error(readQ()) + + ql <- pophelper::readQ(files) + + # qlist structure ---------------------------------------------------------- + cat(paste0("qlist; ")) + + expect_equal(class(ql),"list") + expect_equal(class(ql[1]),"list") + expect_equal(class(ql[[1]]),"data.frame") + + # tabulate ----------------------------------------------------------------- + cat(paste0("tabulateq; ")) + + tr <- pophelper::tabulateQ(qlist=ql,writetable=TRUE) + # check if file has been exported + expect_equal("tabulateQ.txt" %in% list.files(),TRUE) + if(deleteoutput) file.remove("tabulateQ.txt") + + expect_equal(class(tr),"data.frame") + # except clumpp, num of samples must match tabulated rows + if(tolower(unique(cr$type)) != "clumpp") expect_equal(nrow(tr),length(files)) + # error for empty input + expect_error(tabulateQ()) + + # checks on tabulate obj + + + # summarise ---------------------------------------------------------------- + cat(paste0("summarise; ")) + + sr <- pophelper::summariseQ(tr,writetable=TRUE) + # check if file has been exported + expect_equal("summariseQ.txt" %in% list.files(),TRUE) + if(deleteoutput) file.remove("summariseQ.txt") + + # check if data.frame + expect_equal(class(sr),"data.frame") + # error for empty output + expect_error(summariseQ()) +} + +# readQTess3 ------------------------------------------------------------------- + +context("readQTess3") +cat("readQTess3 ---------------------------------------------------------------\n") + +t3obj <- readRDS(system.file("files/tess3.rds",package="pophelper")) +t3list <- readQTess3(t3obj) + +# is.qlist --------------------------------------------------------------------- + +context("is.qlist") +cat("is.qlist ---------------------------------------------------------------\n") +q1 <- readQ(sfiles) + +expect_silent(is.qlist(q1)) +names(q1)[2] <- NA +expect_error(is.qlist(q1)) +names(q1)[2] <- "" +expect_error(is.qlist(q1)) +names(q1)[2] <- "trial" +names(q1)[3] <- "trial" +expect_error(is.qlist(q1)) +q1[3] <- "new" +expect_error(is.qlist(q1)) + +# evannoMethodStucture --------------------------------------------------------- + +context("Evanno method") +cat("evannoMethodStructure ----------------------------------------------------\n") + +#returns dataframe +sr <- summariseQ(tabulateQ(readQ(sfiles)),writetable=FALSE) +expect_equal(class(evannoMethodStructure(sr)),"data.frame") + +#export text output +evannoMethodStructure(sr,writetable=TRUE) +expect_equal("evannoMethodStructure.txt" %in% list.files(),TRUE) +if(deleteoutput) file.remove("evannoMethodStructure.txt") + +#return text +ev <- evannoMethodStructure(sr,writetable=F,returndata=T) +expect_equal(class(ev),"data.frame") + +#return plot +ev <- evannoMethodStructure(sr,writetable=F,returnplot=T,returndata=F) +expect_equal(class(ev)[1],"gtable") + +#return plot and text +ev <- evannoMethodStructure(sr,writetable=F,returnplot=T,returndata=T) +expect_equal(class(ev),"list") +expect_equal(class(ev[[1]]),"data.frame") +expect_equal(class(ev[[2]])[1],"gtable") + +#outputfilename +evannoMethodStructure(sr,writetable=TRUE,exportplot=T,outputfilename="candy") +expect_equal("candy.txt" %in% list.files(),TRUE) +expect_equal("candy.png" %in% list.files(),TRUE) +if(deleteoutput) file.remove("candy.txt") +if(deleteoutput) file.remove("candy.png") + +#PLOTS +#export plot png +evannoMethodStructure(sr,exportplot=TRUE) +if(deleteoutput) file.remove("evannoMethodStructure.png") + +#export plot jpeg +evannoMethodStructure(sr,exportplot=TRUE,imgtype="jpeg") +if(deleteoutput) file.remove("evannoMethodStructure.jpg") + +if(testtiff) +{ + #export plot tiff + evannoMethodStructure(sr,exportplot=TRUE,imgtype="tiff") + if(deleteoutput) file.remove("evannoMethodStructure.tiff") +} + +#export plot pdf +evannoMethodStructure(sr,exportplot=TRUE,imgtype="pdf") +if(deleteoutput) file.remove("evannoMethodStructure.pdf") + +#change errorbar features, pointcol, linecol +evannoMethodStructure(sr,exportplot=TRUE,ebwidth=0.1, + ebcol="coral",pointcol="firebrick", + linecol="green",textcol="blue",gridsize=0.6) +if(deleteoutput) file.remove("evannoMethodStructure.png") + +#change plot linesize, pointsize +evannoMethodStructure(sr,exportplot=TRUE,linesize=0.9,pointsize=8) +if(deleteoutput) file.remove("evannoMethodStructure.png") + +#plot change dim, dpi, units, basesize for web plot +evannoMethodStructure(sr,exportplot=TRUE,height=800,width=800,dpi=72,units="px",basesize=20) +if(deleteoutput) file.remove("evannoMethodStructure.png") + +#change font +if(testfont) +{ + evannoMethodStructure(sr,exportplot=TRUE,font="Verdana") + if(deleteoutput) file.remove("evannoMethodStructure.png") + + #change theme + evannoMethodStructure(sr1,exportplot=TRUE,font="Verdana",theme="theme_grey") + if(deleteoutput) file.remove("evannoMethodStructure.png") +} + +#ERRORS +#error only 2 values of k +expect_error(evannoMethodStructure(sr[1:2,],exportplot=TRUE)) +expect_equal("evannoMethodStructure.png" %in% list.files(),TRUE) +if(deleteoutput) file.remove("evannoMethodStructure.png") + +#error test kplot features +expect_error(evannoMethodStructure(sr[1:2,],exportplot=TRUE,linesize=1,pointsize=8)) +expect_equal("evannoMethodStructure.png" %in% list.files(),TRUE) +if(deleteoutput) file.remove("evannoMethodStructure.png") + +#error test kplot features +expect_error(evannoMethodStructure(sr[1:2,],exportplot=TRUE,ebwidth=0.05, + ebcol="coral",pointcol="firebrick", + linecol="green",textcol="blue", + gridsize=0.6,theme="theme_grey",font="Verdana")) +expect_equal("evannoMethodStructure.png" %in% list.files(),TRUE) +if(deleteoutput) file.remove("evannoMethodStructure.png") + +if(testfont) +{ + expect_error(evannoMethodStructure(sr[1:2,],exportplot=TRUE,font="Verdana")) + expect_equal("evannoMethodStructure.png" %in% list.files(),TRUE) + if(deleteoutput) file.remove("evannoMethodStructure.png") +} + +#error non sequential values of k +expect_error(evannoMethodStructure(sr[c(1,2,4),],exportplot=TRUE)) +expect_equal("evannoMethodStructure.png" %in% list.files(),TRUE) +if(deleteoutput) file.remove("evannoMethodStructure.png") + +#warning less than 2 runs +expect_error(evannoMethodStructure(sr[4:5,])) + +test_that("Errors",{ + expect_error(evannoMethodStructure()) + expect_error(evannoMethodStructure(sfiles)) + expect_error(evannoMethodStructure(readQ(tfiles))) + expect_error(evannoMethodStructure(readQ(sfiles))) +}) + +# clumppExport ----------------------------------------------------------------- + +#clumppExport +context("Clumpp Output") +cat("clumppExport -------------------------------------------------------------\n") + +clumppExport(readQ(sfiles)) +expect_equal(all(grepl("pop",list.dirs()[-1])),TRUE) +if(deleteoutput) unlink("pop*", recursive = TRUE, force = TRUE) + +if(FALSE) { + +#structure clumpp export check prefix +clumppExport(readQ(sfiles),prefix="Boom") +expect_equal(all(grepl("Boom",list.dirs()[-1])),TRUE) +if(deleteoutput) unlink("Boom*", recursive = TRUE, force = TRUE) + +#structure clumpp export useexe +clumppExport(readQ(sfiles),useexe=T) +expect_equal(all(grepl("pop",list.dirs()[-1])),TRUE) +if(deleteoutput) unlink("pop*", recursive = TRUE, force = TRUE) + +#tess clumpp export check +clumppExport(readQ(tfiles)) +expect_equal(all(grepl("pop",list.dirs()[-1])),TRUE) +if(deleteoutput) unlink("pop*", recursive = TRUE, force = TRUE) + +#tess clumpp export check prefix +clumppExport(readQ(tfiles),prefix="Hahaha") +expect_equal(all(grepl("Hahaha",list.dirs()[-1])),TRUE) +if(deleteoutput) unlink("Hahaha*", recursive = TRUE, force = TRUE) + +#tess clumpp export check +clumppExport(readQ(tfiles),useexe=TRUE) +expect_equal(all(grepl("pop",list.dirs()[-1])),TRUE) +if(deleteoutput) unlink("pop*", recursive = TRUE, force = TRUE) + +#matrix clumpp export check +clumppExport(readQ(afiles),useexe=TRUE) +expect_equal(all(grepl("pop",list.dirs()[-1])),TRUE) +if(deleteoutput) unlink("pop*", recursive = TRUE, force = TRUE) + +#tructure clumpp export check prefix +clumppExport(readQ(sfiles),prefix="Nanana") +expect_equal(all(grepl("Nanana",list.dirs()[-1])),TRUE) +if(deleteoutput) unlink("Nanana*", recursive = TRUE, force = TRUE) + +#matrix clumpp export check +clumppExport(readQ(afiles)) +expect_equal(all(grepl("pop",list.dirs()[-1])),TRUE) +if(deleteoutput) unlink("pop*", recursive = TRUE, force = TRUE) + +#matrix clumpp export check +clumppExport(readQ(ffiles)) +expect_equal(all(grepl("pop",list.dirs()[-1])),TRUE) +if(deleteoutput) unlink("pop*", recursive = TRUE, force = TRUE) + +#structure clumpp list export check +clumppExport(readQ(sfiles)) +expect_equal(all(grepl("pop",list.dirs()[-1])),TRUE) +if(deleteoutput) unlink("pop*", recursive = TRUE, force = TRUE) + +context("Clumpp Output useexe") + +#structure clumpp export useexe +clumppExport(readQ(sfiles),useexe=T) +expect_equal(sum(grepl("aligned",list.files(recursive=T))),6) +expect_equal(sum(grepl("merged",list.files(recursive=T))),6) +if(deleteoutput) unlink("pop*", recursive = TRUE, force = TRUE) + +#tess clumpp export useexe +clumppExport(readQ(tfiles),useexe=T) +expect_equal(sum(grepl("aligned",list.files(recursive=T))),7) +expect_equal(sum(grepl("merged",list.files(recursive=T))),7) +if(deleteoutput) unlink("pop*", recursive = TRUE, force = TRUE) + +#matrix admixture clumpp export useexe +clumppExport(readQ(afiles),useexe=T) +expect_equal(sum(grepl("aligned",list.files(recursive=T))),1) +expect_equal(sum(grepl("merged",list.files(recursive=T))),1) +if(deleteoutput) unlink("pop*", recursive = TRUE, force = TRUE) + +} + +# collectClumppOutput ---------------------------------------------------------- + +context("Collect clumpp output") +cat("collectClumppOutput ------------------------------------------------------\n") + +clumppExport(readQ(sfiles),useexe=T) + +collectClumppOutput(filetype = "aligned") +expect_equal(sum(grepl("aligned",list.dirs())),1) + +collectClumppOutput(filetype = "merged") +expect_equal(sum(grepl("merged",list.dirs())),1) + +collectClumppOutput(filetype = "both") +expect_equal(sum(grepl("both",list.dirs())),1) + +if(deleteoutput) unlink("pop*", recursive=TRUE, force=TRUE) + +# getPlotParams ---------------------------------------------------------------- + +context("getPlotParams") +cat("getPlotParams ------------------------------------------------------------\n") + +pophelper:::getPlotParams(grplab=grps1$V1, plotnum=1) +pophelper:::getPlotParams(grplab=grps1$V1, plotnum=2) +pophelper:::getPlotParams(grplab=grps1$V1, plotnum=1,grplabsize=5,grplabangle=90,grplabjust=0.5,pointsize=2,linesize=1) + +# grpLabels -------------------------------------------------------------------- + +context("grpLabels") +cat("grpLabels ---------------------------------------------------------------\n") + +grps1 <- read.delim(system.file("files/structuregrplabels.txt",package="pophelper"),header=FALSE,stringsAsFactors=F) +test_that("check if grps df",{expect_equal(class(grps1),"data.frame")}) + +grps2 <- read.delim(system.file("files/structuregrplabels2.txt",package="pophelper"),header=FALSE,stringsAsFactors=F) +test_that("check if grps df",{expect_equal(class(grps2),"data.frame")}) + +slist <- readQ(sfiles[1]) + +test_that("grplab data.frame error",{ +expect_error(pophelper:::grpLabels(df=slist[[1]],grplab=grps1$V1)) +}) + +test_that("return list",{ +expect_equal(class(pophelper:::grpLabels(df=slist[[1]],grplab=grps1)),"list") +}) + +test_that("subsetgrp not present in grplabel",{ +expect_error(pophelper:::grpLabels(df=slist[[1]],grplab=grps1,subsetgrp="popk")) +}) + +test_that("subsetgrp Pop B",{ + expect_equal(unique(pophelper:::grpLabels(df=slist[[1]],grplab=grps1,subsetgrp="Pop B")$grplab)$V1,"Pop B") +}) + +test_that("subsetgrp change order",{ + expect_equal(unique(pophelper:::grpLabels(df=slist[[1]],grplab=grps1,subsetgrp=c("Pop B","Pop A"))$grplab)$V1,c("Pop B","Pop A")) +}) + +test_that("ordergrp",{ + expect_equal(unique(pophelper:::grpLabels(df=slist[[1]],grplab=grps1)$grplab)$V1,c("Pop A","Pop B")) +}) + +# sortInd ---------------------------------------------------------------------- + +test_that("return NA",{ +expect_equal(pophelper:::sortInd(slist[[1]])$grplab,NA) +}) + +grplabs <- read.delim(system.file("files/grplab.txt",package="pophelper"),stringsAsFactors=F) + +test_that("original order",{ +expect_equal(rownames(pophelper:::sortInd(slist[[1]],grplab=grplabs)$dframe),as.character(1:149)) +}) + +test_that("error sortind",{ +expect_error(pophelper:::sortInd(slist[[1]],grplab=grplabs,sortind="blue")) +}) + +pophelper:::sortInd(slist[[1]],grplab=grplabs,sortind="all") +pophelper:::sortInd(slist[[1]],grplab=grplabs,sortind="label") +pophelper:::sortInd(slist[[1]],grplab=grplabs,sortind="Cluster2") +pophelper:::sortInd(slist[[1]],grplab=grplabs,selgrp="mixed",sortind="all") + +# plotQ -------------------------------------------------------------- + +context("plotQ") +cat("plotQ ----------------------------------------------------------\n") + +slist <- readQ(sfiles) +grpsrep <- read.delim(system.file("files/structuregrplabels-rep.txt",package="pophelper"),header=FALSE,stringsAsFactors=F) +grplabs <- read.delim(system.file("files/grplab.txt",package="pophelper"),stringsAsFactors=F) + +imgout <- c("sep","join") + +for(i in 1:length(imgout)) +{ + + imgo <- imgout[i] + + #plot one sep + plotQ(slist[1]) + + #plot many + plotQ(slist[1:2],imgoutput=imgo) + + #plot many outputfilename + plotQ(slist[1:2],imgoutput="sep",outputfilename=c("this","that")) + + #showsp + plotQ(slist[1:2],imgoutput=imgo,showsp=F) + + #showsp + plotQ(slist[1:2],imgoutput=imgo,splab=c("this","that"),splabsize=8,splabcol="blue",splabface="bold",spbgcol="green") + + #change barsize + plotQ(slist[1:2],imgoutput=imgo,barsize=0.8) + + #one ind plot + t1 <- slist[1:2] + t1[[1]] <- t1[[1]][1,] + t1[[2]] <- t1[[2]][1,] + plotQ(t1[1:2],imgoutput=imgo) + + #1 ind with lab + plotQ(t1[1:2],imgoutput=imgo,grplab=data.frame("lab"="A",stringsAsFactors=F)) + + #check orderind cluster + plotQ(slist[1:2],imgoutput=imgo,sortind="Cluster1",sharedindlab=F) + + #check orderind all + plotQ(slist[1:2],imgoutput=imgo,sortind="all",sharedindlab=F) + + #check orderind label + plotQ(slist[1:2],imgoutput=imgo,sortind="label") + + #clustercol + plotQ(slist[1:2],imgoutput=imgo,clustercol=c("red","green")) + + #single labels + plotQ(slist[1:2],imgoutput=imgo,grplab=grplabs[,1,drop=FALSE]) + + #single labels showsp + plotQ(slist[1:2],imgoutput=imgo,grplab=grplabs[,1,drop=FALSE],splab=c("this","that"),splabsize=8,splabcol="blue",splabface="bold",spbgcol="green") + + #showsp pos + plotQ(slist[1:2],imgoutput=imgo,grplab=grplabs[,1,drop=FALSE],splab=c("this","that"),sppos="left") + + #single labels ordergrp + plotQ(slist[1:2],imgoutput=imgo,grplab=grplabs[,1,drop=FALSE],ordergrp=TRUE) + + #single labels ordergrp sortind all + plotQ(slist[1:2],imgoutput=imgo,grplab=grplabs[,1,drop=FALSE],ordergrp=TRUE,sortind="all",sharedindlab=F) + + #single labels ordergrp sortind Cluster1 + plotQ(slist[1:2],imgoutput=imgo,grplab=grplabs[,1,drop=FALSE],ordergrp=TRUE,sortind="Cluster1",sharedindlab=F) + + #single labels ordergrp sortind label + plotQ(slist[1:2],imgoutput=imgo,grplab=grplabs[,1,drop=FALSE],ordergrp=TRUE,sortind="label") + + #single labels ordergrp sortind label show indlab + plotQ(slist[1:2],imgoutput=imgo,grplab=grplabs[,1,drop=FALSE],ordergrp=TRUE,sortind="label",showindlab=TRUE) + + #multiple labels + plotQ(slist[1:2],imgoutput=imgo,grplab=grplabs) + + #multiple labels grpmean + plotQ(slist[1:2],imgoutput=imgo,grplab=grplabs,grpmean=T) + + #multiple labels grpmean ordergrp + plotQ(slist[1:2],imgoutput=imgo,grplab=grplabs,grpmean=T,ordergrp=T) + + #multiple labels ordergrp + plotQ(slist[1:2],imgoutput=imgo,grplab=grplabs,ordergrp=TRUE) + + #multiple labels selgrp ordergrp + plotQ(slist[1:2],imgoutput=imgo,grplab=grplabs,selgrp="mixed",ordergrp=TRUE) + + #multiple labels selgrp ordergrp divgrp + plotQ(slist[1:2],imgoutput=imgo,grplab=grplabs,selgrp="mixed",ordergrp=TRUE,divgrp="lab2") + + #multiple labels selgrp ordergrp divgrp double + plotQ(slist[1:2],imgoutput=imgo,grplab=grplabs,selgrp="mixed",ordergrp=TRUE,divgrp=c("lab2","lab1")) + + #multiple labels selgrp ordergrp + plotQ(slist[1:2],imgoutput=imgo,grplab=grplabs,selgrp="lab2",ordergrp=TRUE) + + #multiple labels ordergrp sortind all + plotQ(slist[1:2],imgoutput=imgo,grplab=grplabs,ordergrp=TRUE,sortind="all",sharedindlab=F) + + #multiple labels selgrp ordergrp sortind all + plotQ(slist[1:2],imgoutput=imgo,grplab=grplabs,selgrp="lab2",ordergrp=TRUE,sortind="all",sharedindlab=F) + + #multiple labels sortind Cluster1 + plotQ(slist[1:2],imgoutput=imgo,grplab=grplabs,sortind="Cluster1",sharedindlab=F) + + #multiple labels ordergrp sortind label + plotQ(slist[1:2],imgoutput=imgo,grplab=grplabs,ordergrp=TRUE,sortind="label") + + #multiple labels ordergrp sortind label show indlab + plotQ(slist[1:2],imgoutput=imgo,grplab=grplabs,ordergrp=TRUE,sortind="label",showindlab=TRUE) + + #multiple labels grpmean + plotQ(slist[1:2],imgoutput=imgo,grplab=grplabs,grpmean=T) + + #multiple labels grpmean showindlab + plotQ(slist[1:2],imgoutput=imgo,grplab=grplabs,grpmean=T,showindlab=TRUE,width=15) + + #multiple labels ordergrp subsetgrp + plotQ(slist[1:2],imgoutput=imgo,grplab=grplabs,ordergrp=T,subsetgrp="b") + + #multiple labels ordergrp reorder + plotQ(slist[1:2],imgoutput=imgo,grplab=grplabs,ordergrp=T,subsetgrp=c("c","b")) + + #multiple labels selgrp ordergrp reorder + plotQ(slist[1:2],imgoutput=imgo,grplab=grplabs,selgrp="mixed",ordergrp=T,subsetgrp=c("fds","erd")) + + #multiple labels selgrp ordergrp reorder showindlab + plotQ(slist[1:2],imgoutput=imgo,grplab=grplabs,selgrp="mixed",ordergrp=T,subsetgrp=c("fds","erd"),showindlab=TRUE,width=15) + + #single label line size + plotQ(slist[1:2],imgoutput=imgo,grplab=grplabs,linesize=2,linecol="green",linetype="22",linealpha=0.6,pointsize=0.6,pointtype=16,pointalpha=0.6,pointcol="red") + + #imgtype jpeg + plotQ(slist[1:2],imgoutput=imgo,grplab=grplabs,imgtype="jpeg") + + #imgtype pdf + plotQ(slist[1:2],imgoutput=imgo,grplab=grplabs,imgtype="pdf") + + if(testtiff) + { + #imgtype tiff + plotQ(slist[1:2],imgoutput=imgo,grplab=grplabs,imgtype="tiff") + } + + #check output sep with rep labels + plotQ(slist[1:2],imgoutput=imgo,grplab=grpsrep) + + #check grpmean with rep labels + plotQ(slist[1:2],imgoutput=imgo,grplab=grpsrep,grpmean=T) + + #check grpmean with rep labels sortind + plotQ(slist[1:2],imgoutput=imgo,grplab=grpsrep,sortind="all",sharedindlab=F) + + #check grpmean with rep labels sortind + plotQ(slist[1:2],imgoutput=imgo,grplab=grpsrep,sortind="label") + + #check grpmean with rep labels sortind showindlab + plotQ(slist[1:2],imgoutput=imgo,grplab=grpsrep,sortind="label",showindlab=T,width=15) + + expect_error(plotQ(slist[1:2],imgoutput=imgo,grplab=grpsrep,subsetgrp="Pop A")) + + #use ordergrp + plotQ(slist[1:2],imgoutput=imgo,grplab=grpsrep,subsetgrp="Pop A",ordergrp=T) + + #indlabwithgrplab F + plotQ(slist[1:2],imgoutput=imgo,showindlab=T,useindlab=F,indlabwithgrplab=F,grplab=grplabs) + + #indlabwithgrplab T + plotQ(slist[1:2],imgoutput=imgo,showindlab=T,useindlab=F,indlabwithgrplab=T,grplab=grplabs) + + #sharedindlab + if(imgo=="join") + { + #sharedindlab off + plotQ(slist[1:2],imgoutput=imgo,showindlab=T,sharedindlab=F) + #sharedindlab on + plotQ(slist[1:2],imgoutput=imgo,showindlab=T,sharedindlab=T) + #sharedindlab on with sort label + plotQ(slist[1:2],imgoutput=imgo,showindlab=T,sharedindlab=T,sort="label") + #sharedindlab with sort all + expect_error(plotQ(slist[1:2],imgoutput=imgo,showindlab=T,sortind="all")) + #sharedindlab with sort cluster + expect_error(plotQ(slist[1:2],imgoutput=imgo,showindlab=T,sortind="Cluster1")) + #sharedindlab off with grplab + plotQ(slist[1:2],imgoutput=imgo,showindlab=T,sharedindlab=F,grplab=grplabs) + #sharedindlab on with grplab + plotQ(slist[1:2],imgoutput=imgo,showindlab=T,sharedindlab=T,grplab=grplabs,width=16) + #shared indlab with repeated grplab + plotQ(slist[1:2],imgoutput=imgo,showindlab=T,sharedindlab=T,grplab=grpsrep) + #sharedindlab with grplab subset + plotQ(slist[1:2],imgoutput=imgo,showindlab=T,sharedindlab=T,grplab=grplabs,subsetgrp="a",width=16) + #sharedindlab with reorder + plotQ(slist[1:2],imgoutput=imgo,showindlab=T,sharedindlab=T,grplab=grplabs,subsetgrp=c("b","a"),width=16) + } + + #showyaxis + plotQ(slist[1:2],imgoutput=imgo,showyaxis=T) + + #showyaxis grplab + plotQ(slist[1:2],imgoutput=imgo,showyaxis=T,grplab=grplabs) + + #showyaxis ticks + plotQ(slist[1:2],imgoutput=imgo,showyaxis=T,showticks=T,showindlab=T) + + #showyaxis ticks ticksize ticklength + plotQ(slist[1:2],imgoutput=imgo,showyaxis=T,showticks=T,showindlab=T,ticksize=0.5,ticklength=0.5) + + #basesize + plotQ(slist[1:2],imgoutput=imgo,showyaxis=T,showindlab=T,basesize=12) + + #panelratio + plotQ(slist[1:2],imgoutput=imgo,grplab=grplabs,panelratio=c(2,4)) + + #legend + plotQ(slist[1:2],imgoutput=imgo,showlegend=T) + + #legendmargin + plotQ(slist[1:2],imgoutput=imgo,showlegend=T,legendmargin=c(4,4,4,4)) + + #exportplot + plotQ(slist[1:2],imgoutput=imgo,exportplot=F) + + #returnplot + p <- plotQ(slist[1:2],imgoutput=imgo,exportplot=F,returnplot=T) + expect_equal(class(p),"list") + expect_equal(names(p),c("plot","data")) + expect_equal(class(p[[1]][[1]])[1],"gg") + + #returnplot returndata + p <- plotQ(slist[1:2],imgoutput=imgo,exportplot=F,returnplot=T,returndata=T,grplab=grplabs) + expect_equal(class(p),"list") + expect_equal(names(p),c("plot","data")) + expect_equal(class(p[[1]][[1]])[1],"gtable") +} + +#ERRORS + +#input not list +expect_error(plotQ(slist[[1]])) + +#check less colours +expect_error(plotQ(slist[1],clustercol="red")) + +#showsp +expect_error(plotQ(slist[1],showsp="a")) + +#splab +expect_error(plotQ(slist[1],splab=NULL)) + +if(testfont) +{ + #change font + plotQ(qlist=slist[1:2],grplab=grplabs,font="Verdana") + + #join change font + plotQ(qlist=slist[1:2],imgoutput="join",grplab=grplabs,font="Verdana") + + if(testtiff) + { + #tiff output single + plotQ(qlist=slist[1],grplab=grplabs,font="Verdana",imgtype="tiff") + } +} + +if(deleteoutput) file.remove(list.files()) + +#barbordersize +#barbordercolour +plotQ(slist[1],barbordersize=0.1,barbordercolour="black") + +#splabangle +plotQ(slist[1]) +plotQ(slist[1],splabangle=-90) +plotQ(slist[1],sppos="left") +plotQ(slist[1],sppos="left",splabangle=90) +plotQ(slist[1],showsp=F) +plotQ(slist[1:2],imgoutput = "join",outputfilename = "structure_01") +plotQ(slist[1:2],imgoutput="join",splabangle=90,outputfilename = "structure_01") +plotQ(slist[1:2],imgoutput="join",grplab=grplabs,splabangle=90,outputfilename = "structure_01") + +#title and subtitle +plotQ(slist[1]) +plotQ(slist[1],showtitle=T) +plotQ(slist[1],showsubtitle=T) +plotQ(slist[1],showtitle=T,showsubtitle=T) +plotQ(slist[1],showtitle=T,showsubtitle=T,titlelab="Galapagos",subtitlelab="Sample from the region of Galapagos") +plotQ(slist[1],showtitle=T,showsubtitle=T,titlecol="green",subtitlecol="blue",titlehjust=1,subtitlehjust=1) +plotQ(slist[1],showtitle=T,showsubtitle=T,titlevjust=0,subtitlevjust=0) +plotQ(slist[1],showtitle=T,showsubtitle=T,titleangle=45,subtitleangle=45) +plotQ(slist[1],showtitle=T,showsubtitle=T,grplab=grplabs) +plotQ(slist[1],showtitle=T,showsubtitle=T,titlelab="Galapagos", + subtitlelab="Sample from the region of Galapagos",grplab=grplabs) +plotQ(slist[1:2],imgoutput="join") +plotQ(slist[1:2],imgoutput="join",showtitle=T,showsubtitle=T) +plotQ(slist[1:2],imgoutput="join",outputfilename="structure_01") +plotQ(slist[1:2],imgoutput="join",outputfilename="structure_01",showtitle=T,showsubtitle=T, + titlelab="Galapagos",subtitlelab="Sample from the region of Galapagos") +plotQ(slist[1:2],imgoutput="join",outputfilename="structure_01",showtitle=T,showsubtitle=T, + titlelab="Galapagos",subtitlelab="Sample from the region of Galapagos",grplab=grplabs,sppos="left") +plotQ(slist[1:2],imgoutput="join",outputfilename="structure_01",showtitle=T,showsubtitle=T, + titlelab="Galapagos",subtitlelab="Sample from the region of Galapagos", + showlegend=F,legendpos="right") +plotQ(slist[1:2],imgoutput="join",outputfilename="structure_01",showtitle=T, + titlelab="Galapagos",showlegend=T,legendpos="right") + +#indlabspacer +plotQ(slist[1],showindlab=T) +plotQ(slist[1],showindlab=T,indlabspacer=5) +plotQ(slist[1],showindlab=T,indlabspacer=-1) +plotQ(slist[1:2],showindlab=T,indlabspacer=5) +plotQ(slist[1:2],imgoutput="join",showindlab=T,indlabspace=-1,outputfilename="structure_01") + +if(deleteoutput) file.remove(list.files()) + +# plotQ Clumpp -------------------------------------------------------------- + +context("plotQ Clumpp") +cat("plotQ Clumpp --------------------------------------------------------------\n") + +tabs1 <- c(system.file("files/STRUCTUREpop_K4-combined.txt",package="pophelper"), + system.file("files/STRUCTUREpop_K4-combined-aligned.txt",package="pophelper"), + system.file("files/STRUCTUREpop_K4-combined-merged.txt",package="pophelper")) + +#check output table +plotQ(qlist=readQ(tabs1)) + +#check output table +plotQ(qlist=readQ(tabs1),grpmean=T) + +#check output table sort cluster +plotQ(qlist=readQ(tabs1),sortind="Cluster1") + +#check output table sort cluster +plotQ(qlist=readQ(tabs1),imgoutput="join",sortind="Cluster1",sharedindlab=F) + +#check output table pop lab +plotQ(qlist=readQ(tabs1),grplab=grps1) + +#check output table pop lab sort all +plotQ(qlist=readQ(tabs1),imgoutput="sep",grplab=grplabs,sortind="all") + +#check output table pop lab sort cluster +plotQ(qlist=readQ(tabs1),imgoutput="sep",grplab=grplabs,sortind="Cluster1") + +#check output table pop lab pop mean +plotQ(qlist=readQ(tabs1),imgoutput="sep",grplab=grplabs,grpmean=T) + +#check output table pop lab rep +plotQ(qlist=readQ(tabs1),imgoutput="sep",grplab=grpsrep) + +#check output table pop lab rep sort +plotQ(qlist=readQ(tabs1),imgoutput="sep",grplab=grpsrep,sortind="all") + +#check output table pop lab rep sort pop mean +plotQ(qlist=readQ(tabs1),imgoutput="sep",grplab=grpsrep,sortind="all",grpmean=T) + +if(deleteoutput) file.remove(list.files()) + +expect_error(plotQ(qlist=readQ(tabs1),imgoutput="sep",grplab=grpsrep,subsetgrp="Pop B")) + +# plotQMultiline --------------------------------------------------------------- +cat("plotQMultiline -----------------------------------------------------------\n") + +slist <- readQ(list.files(path=system.file("files/structure",package="pophelper"),full.names=TRUE)) +grpsrep <- read.delim(system.file("files/structuregrplabels-rep.txt",package="pophelper"),header=FALSE,stringsAsFactors=F) +grplabs <- read.delim(system.file("files/grplab.txt",package="pophelper"),stringsAsFactors=F) + +#plotQMultiline +context("plotQMultiline") + +#sfiles 1 check output +plotQMultiline(slist[1]) + +#sfiles 1 check output sort cluster +plotQMultiline(slist[1],sortind="Cluster1") + +#sfiles 1 check output sort all +plotQMultiline(slist[1],sortind="all") + +#sfiles >1 check output +plotQMultiline(slist[1:2]) + +#sfiles >1 sort cluster +plotQMultiline(slist[1:2],sortind="Cluster1") + +#sfiles >1 sort all +plotQMultiline(slist[1:2],sortind="all") + +#sfiles 1 sort NA indlabfromfile +plotQMultiline(slist[1:2],sortind=NA,useindlab=T) + +#sfiles 1 sort all indlabfromfile=T +plotQMultiline(slist[1:2],sortind="all",useindlab=T) + +#jpeg output +plotQMultiline(slist[1],imgtype="jpeg") + +if(testtiff) +{ + #tiff output + plotQMultiline(slist[1],imgtype="tiff") +} + +#pdf output +plotQMultiline(slist[1],imgtype="pdf") + +inds <- read.delim(system.file("files/structureindlabels.txt",package="pophelper"),header=FALSE,stringsAsFactors=F) + +#files 1 indlab +rownames(slist[[1]]) <- inds$V1 +plotQMultiline(slist[1],useindlab=T) + +#sfiles 1 check output sort cluster1 indlab +plotQMultiline(slist[1],sortind="Cluster1",useindlab=T) + +#grplab with useind one lab +plotQMultiline(slist[1],barsize=1,lpp=7,grplab=grplabs[,1,drop=F],useindlab=T) + +#grplab with useind two lab +plotQMultiline(slist[1],barsize=1,lpp=7,grplab=grplabs[,1:2],useindlab=T) + +#grplab with useind +plotQMultiline(slist[1],barsize=1,lpp=7,grplab=grplabs,useindlab=T) + +#grplab with useind and selgrp +plotQMultiline(slist[1],barsize=1,lpp=7,grplab=grplabs,useindlab=T,selgrp="lab2") + +#grplab with useind and selgrp, ordergrp +plotQMultiline(slist[1],barsize=1,lpp=6,grplab=grplabs,useindlab=T,selgrp="mixed",ordergrp=T) + +#grplab with useind, sortind cluster1 +plotQMultiline(slist[1],barsize=1,lpp=7,grplab=grplabs,useindlab=T, sortind="Cluster1") + +#grplab with useind, sortind all +plotQMultiline(slist[1],barsize=1,lpp=7,grplab=grplabs,useindlab=T, sortind="all") + +#grplab with useind, sortind label +plotQMultiline(slist[1],barsize=1,lpp=7,grplab=grplabs,useindlab=T, sortind="label") + +#grplab without useind, sortind label +plotQMultiline(slist[1],barsize=1,lpp=7,grplab=grplabs,useindlab=F, sortind="label") + +#grplab without useind, subset +plotQMultiline(slist[1],barsize=1,lpp=7,grplab=grplabs,useindlab=F, subsetgrp="b") + +#grplab without useind, reorder +plotQMultiline(slist[1],barsize=1,lpp=7,grplab=grplabs,useindlab=F, subsetgrp=c("b","a")) + +#grplab without useind, reorder, selgrp, orgergrp +plotQMultiline(slist[1],barsize=1,lpp=7,grplab=grplabs,useindlab=F, selgrp="mixed",ordergrp=TRUE,subsetgrp=c("fds","rga")) + +#grplab without useind, sort cluster, subset +plotQMultiline(slist[1],barsize=1,lpp=7,grplab=grplabs,useindlab=F, sortind="Cluster1", subsetgrp=c("c")) + +#grplab with useind, sort cluster, reorder +plotQMultiline(slist[1],barsize=1,lpp=7,grplab=grplabs,useindlab=T, sortind="Cluster1", subsetgrp=c("b","c")) + +#grplab without useind, sort label, reorder +plotQMultiline(slist[1],barsize=1,lpp=7,grplab=grplabs, grpmean=T) + +#modify options +plotQMultiline(slist[1],lpp=7,grplab=grplabs,indlabsize=5,indlabangle=45,indlabvjust=1,indlabhjust=1,indlabcol="darkgreen", + grplabsize=4,grplabbgcol="skyblue",grplabcol="red",clustercol=c("coral","steelblue"),showticks=T,showyaxis=T, + mar=c(0.1,0.5,0.1,0.5),theme="theme_bw") + +#output file type +plotQMultiline(slist[1],grplab=grplabs,imgtype="jpeg") + +#output file type +plotQMultiline(slist[1],grplab=grplabs,imgtype="pdf") + +#output file type +if(testtiff) plotQMultiline(slist[1],grplab=grplabs,imgtype="tiff") + +#grplab theme font +if(testfont) plotQMultiline(slist[1],theme="theme_bw",font="Verdana") + +#barbordersize +#barbordercolour +plotQMultiline(slist[1],barbordercolour="red",barbordersize=0.2) +plotQMultiline(slist[1],barbordercolour="black",barbordersize=0.2,barsize=1) + +#indlabspacer +plotQMultiline(slist[1]) +plotQMultiline(slist[1],indlabspacer=3) +plotQMultiline(slist[1],indlabspacer=-1) + +#title and subtitle +plotQMultiline(slist[1]) +plotQMultiline(slist[1],showtitle=T,showsubtitle=T) +plotQMultiline(slist[1],showtitle=T,showsubtitle=T,lpp=6, + titlelab="Galapagos",subtitlelab="Sample from the region of Galapagos") +plotQMultiline(slist[1],showtitle=T,showsubtitle=T,lpp=6,titlehjust=1,titlecol="blue") + +#indlabwithgrplab +plotQMultiline(slist[1],grplab=grplabs,indlabwithgrplab=T) + +#show legend +plotQMultiline(slist[1],showlegend=T) + +#show legend grplab +plotQMultiline(slist[1],showlegend=T,grplab=grplabs) + +#show legend legend size +plotQMultiline(slist[1],showlegend=T,legendkeysize=15,legendtextsize=10) + +#show legend legend margin +plotQMultiline(slist[1],showlegend=T,legendmargin=c(15,15,15,15)) + +#ticks +plotQMultiline(slist[1],showyaxis=T,showticks=T,ticklength=2) + +#quiet +plotQMultiline(slist[1],quiet=T) + +#exportplot +plotQMultiline(slist[1],exportplot=F) + +#returnplot +p <- plotQMultiline(slist[1],exportplot=F,returnplot=T) +expect_equal(class(p),"list") +expect_equal(names(p),c("plot","data")) +expect_equal(class(p[[1]][[1]][[1]])[1],"gtable") + +#returnplot returndata +p <- plotQMultiline(slist[1],exportplot=F,returnplot=T,returndata=T,grplab=grplabs) +expect_equal(class(p),"list") +expect_equal(names(p),c("plot","data")) +expect_equal(class(p[[1]][[1]][[1]])[1],"gtable") + +#many runs +plotQMultiline(slist[1:3],spl=20,lpp=4) + +if(deleteoutput) file.remove(list.files()) + +# collectTessRuns -------------------------------------------------------------- + +context("Collect Tess runs ----------------------------------------------------\n") + +# analyseQ ------------------------------------------------------------------ + +context("analyseQ Structure") +cat("analyseQ Structure ------------------------------------------------------\n") + +analyseQ(sfiles) +test_that("check output",{ + expect_equal(any(grepl("evannoMethodStructure.png",list.files())),TRUE) + expect_equal(any(grepl("evannoMethodStructure.txt",list.files())),TRUE) + expect_equal(any(grepl("tabulateQ.txt",list.files())),TRUE) + expect_equal(any(grepl("summariseQ.txt",list.files())),TRUE) + expect_equal(any(grepl("structure_01.png",list.files())),TRUE) + expect_equal(any(grepl("structure_17.png",list.files())),TRUE) + expect_equal(any(grepl("./pop_K2",list.dirs())),TRUE) + expect_equal(any(grepl("./pop_K7",list.dirs())),TRUE) +}) +if(deleteoutput) unlink(list.dirs()[-1],recursive = T,force = T) +if(deleteoutput) file.remove(list.files()) + +context("analyseQ Tess") +cat("analyseQ Tess\n") + +analyseQ(tfiles) +test_that("check output",{ + expect_equal(any(grepl("tabulateQ.txt",list.files())),TRUE) + expect_equal(any(grepl("summariseQ.txt",list.files())),TRUE) + expect_equal(any(grepl("tess_01.png",list.files())),TRUE) + expect_equal(any(grepl("tess_21.png",list.files())),TRUE) + expect_equal(any(grepl("./pop_K2",list.dirs())),TRUE) + expect_equal(any(grepl("./pop_K8",list.dirs())),TRUE) +}) +if(deleteoutput) unlink(list.dirs()[-1],recursive = T,force = T) +if(deleteoutput) file.remove(list.files()) + +context("analyseQ Admixture") +cat("analyseQ Admixture\n") + +analyseQ(afiles) +test_that("check output",{ + expect_equal(any(grepl("tabulateQ.txt",list.files())),TRUE) + expect_equal(any(grepl("summariseQ.txt",list.files())),TRUE) + expect_equal(any(grepl("admixture_01.png",list.files())),TRUE) + expect_equal(any(grepl("admixture_10.png",list.files())),TRUE) + expect_equal(any(grepl("./pop_K2",list.dirs())),TRUE) +}) +if(deleteoutput) unlink(list.dirs()[-1],recursive = T,force = T) +if(deleteoutput) file.remove(list.files()) + +context("analyseQ BAPS") +cat("analyseQ BAPS\n") + +analyseQ(bfiles) +test_that("check output",{ + expect_equal(any(grepl("tabulateQ.txt",list.files())),TRUE) + expect_equal(any(grepl("summariseQ.txt",list.files())),TRUE) + expect_equal(any(grepl("baps_k2.png",list.files())),TRUE) + expect_equal(any(grepl("./pop_K2",list.dirs())),TRUE) +}) +if(deleteoutput) unlink(list.dirs()[-1],recursive = T,force = T) +if(deleteoutput) file.remove(list.files()) + +# distructExport Structure ----------------------------------------------------- + +context("distructExport Structure") +cat("distructExport Structure ------------------------------------------------\n") + +grps1 <- read.delim(system.file("files/structuregrplabels.txt",package="pophelper"),header=FALSE) + +#ind one file +distructExport(qlist = readQ(sfiles)[1]) +test_that("destructExport structure one file",{ + expect_equal(any(grepl("drawparams",list.files("./structure_01-distruct"))),TRUE) +}) +if(deleteoutput) unlink(list.files(),recursive=T,force=T) + +#both top and bottom labels +distructExport(readQ(sfiles)[1],grplabbottom=as.character(grps1$V1),grplabtop=as.character(grps1$V1),grpmean=T) +test_that("destructExport structure top and bottom labels",{ + expect_equal(any(grepl("drawparams",list.files("./structure_01-distruct"))),TRUE) +}) +if(deleteoutput) unlink(list.files(),recursive=T,force=T) + +#both top and bottom labels quiet +distructExport(readQ(sfiles)[1],grplabbottom=as.character(grps1$V1),grplabtop=as.character(grps1$V1),quiet=T) +test_that("destructExport structure top and botoom labels quiet",{ + expect_equal(any(grepl("drawparams",list.files("./structure_01-distruct"))),TRUE) +}) +if(deleteoutput) unlink(list.files(),recursive=T,force=T) + +#no bottom labels +distructExport(readQ(sfiles)[1],grplabbottom=NA,grplabtop=as.character(grps1$V1)) +test_that("destructExport structure no bottom labels",{ + expect_equal(any(grepl("drawparams",list.files("./structure_01-distruct"))),TRUE) +}) +if(deleteoutput) unlink(list.files(),recursive=T,force=T) + +#no top labels +distructExport(readQ(sfiles)[1],grplabbottom=as.character(grps1$V1),grplabtop=NA) +test_that("destructExport structure no top labels",{ + expect_equal(any(grepl("drawparams",list.files("./structure_01-distruct"))),TRUE) +}) +if(deleteoutput) unlink(list.files(),recursive=T,force=T) + +#no both labels +distructExport(readQ(sfiles)[1],grplabbottom=NA,grplabtop=NA) +test_that("destructExport structure both labels",{ + expect_equal(any(grepl("drawparams",list.files("./structure_01-distruct"))),TRUE) +}) +if(deleteoutput) unlink(list.files(),recursive=T,force=T) + +#multiple files +distructExport(readQ(sfiles)[2:5],grplabbottom=as.character(grps1$V1)) +test_that("destructExport structure multiple files",{ + expect_equal(length(list.files()),4) +}) +if(deleteoutput) unlink(list.files(),recursive=T,force=T) + +#pop mean true +distructExport(readQ(sfiles)[1],grplabbottom=as.character(grps1$V1),grpmean=T) +test_that("destructExport structure grpmean true",{ + expect_equal(any(grepl("drawparams",list.files("./structure_01-distruct"))),TRUE) +}) +if(deleteoutput) unlink(list.files(),recursive=T,force=T) + +#multiple files with grpmean +distructExport(readQ(sfiles)[2:5],grplabbottom=as.character(grps1$V1),grpmean=T) +test_that("destructExport structure multiple files",{ + expect_equal(length(list.files()),4) +}) +if(deleteoutput) unlink(list.files(),recursive=T,force=T) + +#other colours +distructExport(readQ(sfiles)[1],grplabbottom=as.character(grps1$V1),clustercol=pophelper:::distructColours()[43:44]) +test_that("destructExport structure other colours",{ + expect_equal(any(grepl("drawparams",list.files("./structure_01-distruct"))),TRUE) +}) +if(deleteoutput) unlink(list.files(),recursive=T,force=T) + +#multiple files use exe +if(pophelper:::getOS()!="unix64") +{ + distructExport(readQ(sfiles)[2:5],grplabbottom=as.character(grps1$V1),useexe=T) + test_that("destructExport structure use exe",{ + expect_equal(length(list.files()),4) + }) + if(deleteoutput) unlink(list.files(),recursive=T,force=T) +} + +#multiple files grpmean use exe +if(pophelper:::getOS()!="unix64") +{ + distructExport(readQ(sfiles)[2:5],grplabbottom=as.character(grps1$V1),grpmean=T,useexe=T) + test_that("destructExport structure grpmean use exe",{ + expect_equal(length(list.files()),4) + }) + if(deleteoutput) unlink(list.files(),recursive=T,force=T) +} + +#other colours use exe +if(pophelper:::getOS()!="unix64") +{ + distructExport(readQ(sfiles)[1],grplabbottom=as.character(grps1$V1),clustercol=pophelper:::distructColours()[43:44],useexe=T) + test_that("destructExport structure other colours use exe",{ + expect_equal(any(grepl("drawparams",list.files("./structure_01-distruct"))),TRUE) + }) + if(deleteoutput) unlink(list.files(),recursive=T,force=T) +} + +# distructExport Tess ---------------------------------------------------------- + +context("exportDistruct Tess") +cat("distructExport Tess ------------------------------------------------------\n") + +grps1 <- read.delim(system.file("files/tessgrplabels.txt",package="pophelper"),header=FALSE) + +#both top and bottom labels +distructExport(readQ(tfiles)[3],grplabbottom=as.character(grps1$V1),grplabtop=as.character(grps1$V1)) +test_that("exportDistruct Tess top and bottom labels",{ + expect_equal(any(grepl("drawparams",list.files("./tess_03-distruct"))),TRUE) +}) +if(deleteoutput) unlink(list.files(),recursive=T,force=T) + +#both top and bottom labels quiet +distructExport(readQ(tfiles)[3],grplabbottom=as.character(grps1$V1),grplabtop=as.character(grps1$V1),quiet=T) +test_that("exportDistruct Tess top and bottom labels quiet",{ + expect_equal(any(grepl("drawparams",list.files("./tess_03-distruct"))),TRUE) +}) +if(deleteoutput) unlink(list.files(),recursive=T,force=T) + +#no bottom labels +distructExport(readQ(tfiles)[3],grplabbottom=NA,grplabtop=as.character(grps1$V1)) +test_that("exportDistruct Tess no bottom labels",{ + expect_equal(any(grepl("drawparams",list.files("./tess_03-distruct"))),TRUE) +}) +if(deleteoutput) unlink(list.files(),recursive=T,force=T) + +#multiple files +distructExport(readQ(tfiles)[2:5],grplabbottom=as.character(grps1$V1)) +test_that("exportDistruct Tess multiple files",{ + expect_equal(length(list.files()),4) +}) +if(deleteoutput) unlink(list.files(),recursive=T,force=T) + +#multiple files with grpmean +distructExport(readQ(tfiles)[2:5],grplabbottom=as.character(grps1$V1),grpmean=T) +test_that("exportDistruct Tess pop mean",{ + expect_equal(length(list.files()),4) +}) +if(deleteoutput) unlink(list.files(),recursive=T,force=T) + +# distructExport basic -------------------------------------------------------- + +if(deleteoutput) unlink(list.files(),recursive=T,force=T) +context("distructExport Other formats") +cat("distructExport Basic -----------------------------------------------------\n") + +#admixture multiple +distructExport(qlist = readQ(afiles)[1:4],grpmean=F) +test_that("exportDistruct Admixture",{ + expect_equal(length(list.files()),4) +}) +if(deleteoutput) unlink(list.files(),recursive=T,force=T) + +#admixture multiple grpmean +distructExport(qlist = readQ(afiles)[1:4],grpmean=T) +test_that("exportDistruct Admixture pop mean",{ + expect_equal(length(list.files()),4) +}) +if(deleteoutput) unlink(list.files(),recursive=T,force=T) + +#faststructure +distructExport(qlist = readQ(ffiles)[2:3],grpmean=F) +test_that("exportDistruct faststructure",{ + expect_equal(length(list.files()),2) +}) +if(deleteoutput) unlink(list.files(),recursive=T,force=T) + +#basic files comma +distructExport(qlist = readQ(mcfiles)[2:3],grpmean=F) +test_that("exportDistruct basic Comma",{ + expect_equal(length(list.files()),2) +}) +if(deleteoutput) unlink(list.files(),recursive=T,force=T) + +#basic files tab +distructExport(qlist = readQ(mtfiles)[2:3],grpmean=F) +test_that("exportDistruct basic tab",{ + expect_equal(length(list.files()),2) +}) +if(deleteoutput) unlink(list.files(),recursive=T,force=T) + +#basic files space +distructExport(qlist = readQ(msfiles)[2:3],grpmean=F) +test_that("exportDistruct basic space",{ + expect_equal(length(list.files()),2) +}) +if(deleteoutput) unlink(list.files(),recursive=T,force=T) + +#tab no grpmean +distructExport(qlist = readQ(tabs1),grpmean=F) +test_that("exportDistruct Admixture",{ + expect_equal(length(list.files()),7) +}) +if(deleteoutput) unlink(list.files(),recursive=T,force=T) + +#tab grpmean +distructExport(qlist = readQ(tabs1),grpmean=T) +test_that("exportDistruct Admixture",{ + expect_equal(length(list.files()),7) +}) +if(deleteoutput) unlink(list.files(),recursive=T,force=T) + +#tab no grpmean use exe +if(pophelper:::getOS()!="unix64") +{ + distructExport(qlist = readQ(tabs1),useexe=T) + test_that("exportDistruct Admixture",{ + expect_equal(length(list.files()),7) + }) + if(deleteoutput) unlink(list.files(),recursive=T,force=T) +} + +# End -------------------------------------------------------------------------- + +setwd(currwd) +if(deleteoutput) unlink("pophelper-demo",recursive = T,force = T) + diff --git a/tests/testmanual/testthat.R b/tests/testmanual/testthat.R new file mode 100644 index 0000000..7b66323 --- /dev/null +++ b/tests/testmanual/testthat.R @@ -0,0 +1,3 @@ +library(testthat) +library(pophelper) +test_check("pophelper") \ No newline at end of file diff --git a/vignettes/clumpp-aligned.png b/vignettes/clumpp-aligned.png new file mode 100644 index 0000000..f0c4db1 Binary files /dev/null and b/vignettes/clumpp-aligned.png differ diff --git a/vignettes/clumpp-folder.png b/vignettes/clumpp-folder.png new file mode 100644 index 0000000..f0de5c0 Binary files /dev/null and b/vignettes/clumpp-folder.png differ diff --git a/vignettes/clumpp-format.png b/vignettes/clumpp-format.png new file mode 100644 index 0000000..edb243b Binary files /dev/null and b/vignettes/clumpp-format.png differ diff --git a/vignettes/clumpp-output.png b/vignettes/clumpp-output.png new file mode 100644 index 0000000..cb75ba1 Binary files /dev/null and b/vignettes/clumpp-output.png differ diff --git a/vignettes/clumpp-unaligned.png b/vignettes/clumpp-unaligned.png new file mode 100644 index 0000000..08f498a Binary files /dev/null and b/vignettes/clumpp-unaligned.png differ diff --git a/vignettes/destruct-structure.png b/vignettes/destruct-structure.png new file mode 100644 index 0000000..a50bfaf Binary files /dev/null and b/vignettes/destruct-structure.png differ diff --git a/vignettes/evanno-plot.png b/vignettes/evanno-plot.png new file mode 100644 index 0000000..5230048 Binary files /dev/null and b/vignettes/evanno-plot.png differ diff --git a/vignettes/input-preview.png b/vignettes/input-preview.png new file mode 100644 index 0000000..fb659dd Binary files /dev/null and b/vignettes/input-preview.png differ diff --git a/vignettes/plotq-overview.png b/vignettes/plotq-overview.png new file mode 100644 index 0000000..f966c85 Binary files /dev/null and b/vignettes/plotq-overview.png differ diff --git a/vignettes/plotq.png b/vignettes/plotq.png new file mode 100644 index 0000000..8c549c2 Binary files /dev/null and b/vignettes/plotq.png differ diff --git a/vignettes/plotqmultiline-colours.png b/vignettes/plotqmultiline-colours.png new file mode 100644 index 0000000..09105f1 Binary files /dev/null and b/vignettes/plotqmultiline-colours.png differ diff --git a/vignettes/plotqmultiline-overview.png b/vignettes/plotqmultiline-overview.png new file mode 100644 index 0000000..c2379f2 Binary files /dev/null and b/vignettes/plotqmultiline-overview.png differ diff --git a/vignettes/plotqmultiline.png b/vignettes/plotqmultiline.png new file mode 100644 index 0000000..b1eef2a Binary files /dev/null and b/vignettes/plotqmultiline.png differ diff --git a/vignettes/structure-files.png b/vignettes/structure-files.png new file mode 100644 index 0000000..c4f70c9 Binary files /dev/null and b/vignettes/structure-files.png differ diff --git a/vignettes/vignette.Rmd b/vignettes/vignette.Rmd new file mode 100644 index 0000000..edb09d7 --- /dev/null +++ b/vignettes/vignette.Rmd @@ -0,0 +1,2331 @@ +--- +title: "Pophelper 2.2.5" +output: + bookdown::html_document2: + code_folding: "none" + toc: true + toc_depth: 3 + toc_float: + collapsed: true + smooth_scroll: true + number_sections: true + self_contained: true + highlight: tango + theme: flatly +vignette: > + %\VignetteIndexEntry{pophelper tutorial} + %\VignetteEngine{knitr::rmarkdown} + \usepackage[utf8]{inputenc} +--- + +__Roy M Francis__ | `r format(Sys.time(),"%d-%b-%Y")` + +```{r,echo=FALSE,message=FALSE,results='hide',warning=FALSE,eval=TRUE} +options(rpubs.upload.method="internal") +knitr::opts_chunk$set(collapse=TRUE) +#source("D:/Data/Dropbox/Rwork/pophelperRpackage/pophelper/R/pophelper.R") +library(pophelper) +library(captioner) +library(gridExtra) +library(extrafont) + +tc <- captioner::captioner(prefix="Tab. ") +fc <- captioner::captioner(prefix="Fig. ") +``` + +# Introduction + +This vignette/tutorial aims to demonstrate the use of R package `pophelper`. This package contains functions that are useful for processing output results from programs used in the analysis of population structure such as ADMIXTURE^1^, FASTSTRUCTURE^6^, STRUCTURE^5^, TESS^3^, BAPS^8^ and any q-matrix output as a numeric tabular delimited file. + +These softwares are popular programs used to discriminate populations, to determine population structure and to reveal the genetic composition of individuals using molecular markers. These programs generally use allelic frequency information to assign individuals to a pre-defined number of populations (*K*). The assignment is usually run for a range of *K* such as from *K*=2 to *K*=10. Multiple repeats are also usually carried out for each *K*. Each output file for each repeat of *K* showing the assignment probabilities of all individuals is referred to as the run file, cluster file or q-matrix file. `pophelper` has a set of functions that include reading into R, tabulating, summarising and plotting these run files. + +This vignette covers the use of all important functions in the `pophelper` package. The demonstration is ordered in the manner of a typical workflow. Input and output codes are printed in a font different from body text like `this`. + +---- + +# Installation + +The first step is to install the `pophelper` library. The source code is available from [GitHub](https://github.com/royfrancis/pophelper). You need to have R (>= 3.3.0) installed on your system. + +It is best to first install the dependency packages. + +```{r,echo=TRUE,eval=FALSE,results='hide'} +install.packages(c("Cairo","devtools","ggplot2","gridExtra","gtable","tidyr"),dependencies=T) +``` + +Then, install `pophelper` package from `github` using the function `install_github()` from `devtools` package. + +```{r,echo=TRUE,eval=FALSE,results='hide'} +# Install the current version of pophelper +devtools::install_github('royfrancis/pophelper') +``` + +Note that `ggplot2` version must be 2.2.0 or higher. Once the package is installed, the package is loaded as shown below. + +```{r,echo=TRUE,eval=FALSE,results='hide'} +# load library +library(pophelper) + +# check version +packageDescription("pophelper", fields="Version") +``` + +The next step is to set the working directory. The working directory is a folder that usually contains the run files of interest so as to allow R to access it. The working directory must have read-write-execute permissions. Functions may produce outputs such as text files or images which will be exported to the working directory. The working directory can be set by running the command below using a path or by selecting the folder interactively in the popup window. + +```{r,echo=TRUE,eval=FALSE,results='hide'} +setwd("path") +setwd(choose.dir()) +``` + +Standard help and documentation for all functions are obtained using `?`. + +```{r,echo=TRUE,eval=FALSE,results='hide'} +?tabulateQ +?summariseQ +?collectRunsTess +# if using RStudio, press tab inside function to see arguments. +# readQ() +``` + +For functions where one or more files need to be selected, the selection can be performed interactively. Windows users can use `choose.files(multi=T)` for multi-selection or `file.choose()` for single selection. Mac users can use `file.choose()` for single selection and `tk_choose.files()` from `tcltk` package for multiple selection. + +---- + +# Functions & Overview +All user functions in the `pophelper` package are listed below. + +```{r, eval=FALSE,echo=TRUE} +# convert q-matrix run files (structure, tess 2.3 etc) to R qlist object +readQ() +# convert TESS 3 R object to qlist object +readQTess3() +# collate/tabulate a qlist +tabulateQ() +# summarise an output from tabulateQ() +summariseQ() +# generate CLUMPP input/output files +clumppExport() +# collect CLUMPP output into a common directory +collectClumppOutput() +# create single-line barplots from qlist +plotQ() +# create multi-line barplots from qlist +PlotQMultiline() +# export files for DISTRUCT from qlist +distructExport() +# Run and plot the Evanno method for STRUCTURE data +evannoMethodStructure() +# collect TESS output from multiple directories into one +collectRunsTess() + +# wrapper function to tabulate, summarise, perform evanno method, clumpp output and generate barplots from filenames/paths. +analyseQ() +``` + +---- + +# Input files +Generally speaking, there are five input file formats that can be defined. All are text formats. These are STRUCTURE run files, TESS run files (-TR files in folders), BAPS, BASIC (simple delimited files) or a CLUMPP associated file. + +STRUCTURE, TESS 2.3 and BAPS run files have specific format as shown below in __Fig. 1__. BASIC files are numeric delimited tabular file like ADMIXTURE run files and FASTSTRUCTURE meanQ files. They can also be a generic numeric tabular tab, space or comma-delimited files without headers. CLUMPP associated files are COMBINED, ALIGNED or MERGED files for use with CLUMPP. The COMBINED file is generated using the function `clumppExport()`. The ALIGNED and MERGED files are generated by CLUMPP. A sample CLUMPP format is shown in __Fig. 2__. + +![input-preview](input-preview.png) +`r fc(name="fc_inputfilepreview",caption="_A preview of the input files. STRUCTURE (Left), TESS 2.3 (middle left), BAPS (middle right) and BASIC file (right)._")` + +![clumpp-format](clumpp-format.png) +`r fc(name="fc_clumppfilepreview",caption="_A preview of the CLUMPP format file._")` + +Sample files for inspection can be downloaded here. [STRUCTURE 2.3.4](https://github.com/royfrancis/pophelper/tree/master/inst/files/structure), [TESS 2.3](https://github.com/royfrancis/pophelper/tree/master/inst/files/tess), [BAPS ](https://github.com/royfrancis/pophelper/tree/master/inst/files/baps), [ADMIXTURE](https://github.com/royfrancis/pophelper/tree/master/inst/files/admixture), [fastSTRUCTURE](https://github.com/royfrancis/pophelper/tree/master/inst/files/faststructure), [TAB delimited](https://github.com/royfrancis/pophelper/tree/master/inst/files/basic/tab), [COMMA delimited](https://github.com/royfrancis/pophelper/tree/master/inst/files/basic/comma), [SPACE delimited](https://github.com/royfrancis/pophelper/tree/master/inst/files/basic/space), [COMBINED CLUMPP file](https://github.com/royfrancis/pophelper/blob/master/inst/files/STRUCTUREpop_K4-combined.txt), [ALIGNED CLUMPP file](https://github.com/royfrancis/pophelper/blob/master/inst/files/STRUCTUREpop_K4-combined-aligned.txt) and [MERGED CLUMPP file](https://github.com/royfrancis/pophelper/blob/master/inst/files/STRUCTUREpop_K4-combined-merged.txt). + +The plotting functions `plotQ()` and `plotQMultiline()` require group labels as 'data.frame' datatype which can be read into R from a tab-delimited or csv file. 'data.frame' is used rather than a character data type because multiple label sets can be used. The labels for `distructExport()` must be character datatype. For a sample tab-delimited group labels file, [click here](https://github.com/royfrancis/pophelper/blob/master/inst/files/metadata.txt). + +Once the run files are read into R, it is stored internally as a 'qlist' object. For more information on 'qlist' objects and advanced operations on 'qlist', see section: 'Working with qlists'. Internal details of 'qlist' is not critical to working with this package. + +---- + +# Workflow + +In this section, we will look at how these functions are used, their syntax and typical order of workflow. The workflow is similar for all input filetypes. A few specific functions are specific to certain filetypes. + +![Workflow](workflow.png) +`r fc(name="fc_wokflow",caption="_Workflow for all filetypes. Files/objects are indicated in black text and functions are indicated in blue. External executables are indicated in green. For CLUMPP and DISTRUCT results, the executables must be run manually or set argument \x60useexe=T\x60 for automatic execution. The \x60analyseQ()\x60 function is a wrapper function which can be used to run several functions together. This is indicated by the orange path. Functions indicated with superscripts 1 and 2 are only applicable to specific filetypes. \x60collectRunsTess()\x60 is used to consolidate and rename TESS runs. \x60evannoMethodStructure()\x60 is used to perform the Evanno method for STRUCTURE runs._")` + +The `pophelper` library must be loaded and a working directory must be set. + +```{r, eval=FALSE,echo=TRUE} +library(pophelper) +setwd("path-to-wd") +``` + +## collectRunsTess + +This function is applicable only to TESS 2.3 runs. Unlike STRUCTURE runs which are exported into a single directory, TESS output files are exported into separate directories by run. This means that one needs to go into individual folders to obtain the run file. The function `collectRunsTess()` collects TESS cluster files from individual run folders into one new folder and rename each runfile by the folder name. Set working directory first and run basic usage. + +```{r,echo=FALSE, eval=FALSE, results='hide'} +# basic usage +collectRunsTess(runsdir="D://Data/Dropbox/Rwork/pophelperRpackage/tessoriginal") +``` + +```{r,echo=TRUE, eval=FALSE} +# basic usage +collectRunsTess(runsdir="path-to-tess-runs-root-dir") + +# another usage +path <- "path-to-tess-runs-root-dir" +collectRunsTess(runsdir=path) + +# another usage +collectRunsTess(runsdir=choose.dir()) +``` + +Within each TESS run folder, the function searches for filename ending with 'TR.txt' as the cluster file. This file is copied to the new folder and renamed with the name of the respective run directory. Therefore, DO NOT manually rename original TESS run files or directories. + +## readQ + +All input filetypes (STRUCTURE, TESS 2.3, BASIC, CLUMPP) can be read into R and converted to a 'qlist' object using the function `readQ()`. The argument `filetype` is used to specify the input filetype. By default, `filetype` is set to 'auto' which automatically detects input filetype. If this does not work, `filetype` can also be manually set. + +```{r, eval=FALSE,echo=TRUE} +readQ() # automatically detects input filetype +readQ(filetype="auto") # automatically detects input filetype +readQ(filetype="structure") # Convert STRUCTURE run files to qlist +readQ(filetype="tess") # Convert TESS run files to qlist +readQ(filetype="basic") # Convert delimited numeric text files to qlist +readQ(filetype="clumpp") # Convert CLUMPP format files to qlist +``` + +When specifying location to a file locally, use one of below: + +```{r, eval=FALSE,echo=TRUE} +# file is located in the current working directory. use full filename. +sfiles <- "file.structure" +sfiles <- "file.txt" +# file is located in a directory relative to the current working directory. +sfiles <- "./path/path/file.txt" +# absolute path. +sfiles <- "C:/path/path/path/file.txt" + +readQ(files=sfiles) +``` + +For this tutorial, we will use the sample files accompanied with this package. Therefore we read file from within the R package. + +```{r, echo=TRUE, eval=TRUE, results='hide'} +# STRUCTURE files (do not use this command to read local files) +sfiles <- list.files(path=system.file("files/structure",package="pophelper"), full.names=T) +# basic usage +slist <- readQ(files=sfiles) +readQ(files=sfiles,filetype="structure") +# select files interactively +# readQ(files=choose.files(multi=TRUE)) +# check class of ouput +class(slist) +# view head of first converted file +head(slist[[1]]) + +# TESS files (do not use this command to read local files) +tfiles <- list.files(path=system.file("files/tess",package="pophelper"), full.names=T) +tlist <- readQ(files=tfiles) +# select files interactively +# readQ(files=choose.files(multi=TRUE)) + +# use BAPS files (do not use this command to read local files) +bfiles<- list.files(path=system.file("files/baps",package="pophelper"), full.names=T) +blist <- readQ(files=bfiles) + +# use ADMIXTURE files (do not use this command to read local files) +afiles<- list.files(path=system.file("files/admixture",package="pophelper"), full.names=T) +alist <- readQ(files=afiles) + +# use FASTSTRUCTURE files (do not use this command to read local files) +ffiles <- list.files(path=system.file("files/faststructure",package="pophelper"), full.names=T) +flist <- readQ(files=ffiles) + +# use space-delimited text files (do not use this command to read local files) +msfiles <- list.files(path=system.file("files/basic/space",package="pophelper"), full.names=T) +mslist <- readQ(files=msfiles) + +# use tab-delimited text files (do not use this command to read local files) +mtfiles <- list.files(path=system.file("files/basic/tab",package="pophelper"), full.names=T) +mtlist <- readQ(files=mtfiles) + +# use comma-separated text files (do not use this command to read local files) +mcfiles <- list.files(path=system.file("files/basic/comma",package="pophelper"), full.names=T) +mclist <- readQ(files=mcfiles) +``` + +TESS 3 when run within R produces a `tess3` object. This object can be converted to a pophelper qlist using the function `readQTess3()`. Runs are labelled sample1, sample2 etc. + +```{r,echo=TRUE, eval=FALSE, results='hide'} +t3obj <- readRDS(system.file("files/tess3.rds",package="pophelper")) +t3list <- readQTess3(t3obj) +``` + +Each run is converted to dataframes of assignment probabilities of all individuals in *K* clusters denoted as Cluster1, Cluster 2 etc. The dataframes are placed in named lists. The names are obtained from filenames. Filename suffixes such as .txt, .csv, .tsv and .meanQ are dropped. In case filenames are missing or not available, lists are named sample1, sample2 etc. + +Each 'data.frame' has some associated metadata, which is especially important for STRUCTURE runs. When reading in STRUCTURE runs using `readQ()`, metadata such as number of loci, number of burnins, reps, estimated log probability etc., which are required for the Evanno method are stored with each 'data.frame' as attributes. + +TESS 3 attributes ind, k, loci, gif, rmse, crossentropy and ploidy are retained. + +The attributes of the run can be accessed as below. + +```{r,echo=TRUE, eval=FALSE, results='hide'} +# qlist attributes +attributes(slist) +# dataframe attributes +attributes(slist[[1]]) +``` + +If individual labels are present in the STRUCTURE file, they can be imported as rownames by setting `indlabfromfile=T`. Space in labels may be replaced by underscore. Incorrect parsing with internal population flags may introduce underscores. If duplicate labels are found, the labels are not imported. This is applicable only for STRUCTURE files. + +```{r,echo=TRUE, eval=FALSE, results='hide'} +# include individual names from STRUCTURE file as row names +slist <- readQ(files=sfiles, indlabfromfile=T) + +# read only one file +readQ(files=sfiles[1], indlabfromfile=T) +``` + +CLUMPP files (COMBINED, ALIGNED and MERGED) files can also be converted to a 'qlist' using `readQ()`. We use some sample files from the package. To create CLUMPP files, see section on clumppExport. + +```{r,echo=TRUE, eval=FALSE, results='hide'} +co <- system.file("files/STRUCTUREpop_K4-combined.txt", package="pophelper") +al <- system.file("files/STRUCTUREpop_K4-combined-aligned.txt", package="pophelper") +me <- system.file("files/STRUCTUREpop_K4-combined-merged.txt", package="pophelper") + +readQ(co) +readQ(al) +readQ(me) + +readQ(co,filetype="clumpp") +``` + +For CLUMPP files containing multiple runs, each run name is suffixed by a -1, -2 etc. `names(readQ(co))`. + +For information on the 'qlist' object and advanced operations on 'qlist', see section 'Working with qlists'. + +## tabulateQ +The function `tabulateQ()` takes a 'qlist' and produces a table of runs with various parameters. The results can be pointed to a variable for further use. + +```{r,echo=TRUE, eval=FALSE, results='hide'} +# basic usage +tr1 <- tabulateQ(qlist=slist) +tabulateQ(tlist) +tabulateQ(alist, writetable=TRUE) + +# choose files +# files=choose.files(multi=TRUE) +tabulateQ(qlist=readQ(files)) + +?tabulateQ +tabulateQ(qlist=NULL, writetable=FALSE, sorttable=TRUE) +# To write results to working directory, set writetable=TRUE +# Result table is sorted by loci, ind and k. To see original order, set sorttable=FALSE +``` + +For all filetypes, the `tabulateQ()` function returns a table with three columns namely filename, *K* and number of individuals. Note that by default the table is sorted by ind and *K*. + +`r tc(name="tc_tabulatedtess",caption="_A tabulated table of TESS runs._")` + +```{r, echo=TRUE, eval=TRUE} +head(tabulateQ(tlist)) +``` + +To keep runs in the original order, use `sorttable=FALSE`. + +`r tc(name="tc_tabulatedtess_notsorted",caption="_A tabulated table of TESS runs unsorted._")` +```{r, echo=TRUE, eval=TRUE} +head(tabulateQ(tlist,sorttable=FALSE)) +``` + +For STRUCTURE runs, the `tabulateQ()` function produces additional columns namely number of loci, number of burn-ins, number of replicates (reps), estimated ln probability of data (elpd), mean value of ln likelihood (mvll) and variance of ln likelihood (vll). The table is sorted by loci, ind and *K*. + +`r tc(name="tc_tabulatedstructure",caption="_A tabulated table of STRUCTURE runs._")` +```{r, echo=TRUE, eval=TRUE} +head(tabulateQ(slist)) +``` + +Missing values are given NA. The tabulated output can be written to the working directory as a text file by setting the argument `writetable=T`. + +## summariseQ + +The table produced using `tabulateQ()` can be further collapsed by *K* based on the number of runs. The output table from `tabulateQ()` can be passed as input to `summariseQ()`. + +```{r, echo=TRUE, eval=FALSE} +# basic usage +sr1 <- summariseQ(tr1) +summariseQ(tr1, writetable=TRUE) + +# another usage +# sr1 <- summariseQ(tabulateQ(qlist=choose.files())) +``` + +`r tc(name="tc_summarisedtess",caption="_A summarised table of TESS runs._")` +```{r, echo=FALSE, eval=TRUE} +head(summariseQ(tabulateQ(tlist))) +``` + +For all filetypes the `summariseQ()` function returns 3 columns namely individuals, *K* and the number of runs. + +For STRUCTURE runs, the `summariseQ()` function returns additional 5 columns namely loci, Mean estimated ln probability of data, standard deviation of estimated ln probability of data, estimated ln probability of data minus standard deviation and estimated ln probability of data plus standard deviation. + +`r tc(name="tc_summarisedstructure",caption="_A summarised table of STRUCTURE runs._")` +```{r, echo=TRUE, eval=TRUE} +head(summariseQ(tabulateQ(slist))) +``` + +The summarised runs can be written to the working directory as a text file by setting the argument `writetable=T`. + +## evannoMethodStructure + +This function is only applicable to STRUCTURE runs. + +The Evanno method^2^ is used to estimate the optimal number of *K*. The summarised runs table output from`summariseQ()` function can be input to `evannoMethodStructure()`. The `evannoMethodStructure()` function creates an Evanno derivative plot if suitable conditions are met. A resulting table is also returned. The plot can be written to file using argument `exportplot=T`. The table can be written to file using `writetable=T`. + +```{r,echo=TRUE, eval=FALSE} +# basic usage +evannoMethodStructure(data=sr1) + +# another usage +em <- evannoMethodStructure(summariseQ(tabulateQ(slist))) + +# to export a plot +evannoMethodStructure(data=sr1,exportplot=T) + +# do not compute plot, only return results as table +em <- evannoMethodStructure(data=sr1,exportplot=F,returnplot=F) + +# to export plot and table +evannoMethodStructure(data=sr1,exportplot=T,writetable=T,na.rm=T) + +# returns both data and plot +p <- evannoMethodStructure(data=sr1,exportplot=F,returnplot=T) + +# to return only plot and save it +p <- evannoMethodStructure(data=sr1,exportplot=F,returnplot=T,returndata=F) +``` + +```{r,echo=TRUE, eval=TRUE,fig.height=5,fig.width=5} +sr1 <- summariseQ(tabulateQ(slist)) +p <- evannoMethodStructure(data=sr1,exportplot=F,returnplot=T,returndata=F,basesize=12,linesize=0.7) +grid.arrange(p) +``` + +`r fc(name="fc_evannoplot",caption="_Plots produced from the Evanno method._")` + +The Evanno method results table has 15 columns namely number of loci (loci), number of individuals (ind), *K* value (k), number of runs (runs), Mean estimated ln probability of data (elpdmean), Standard deviation (elpdsd), Estimated ln probability of data minus standard deviation (elpdmin), Estimated ln probability of data plus standard deviation (elpdmax), First derivative (lnk1), Max error of first derivative (lnk1max), Min error of first derivative (lnk1min), Second derivative (lnk2), Max error of second derivative (lnk2max), Min error of second derivative (lnk2min) and deltaK. + +`r tc(name="tc_evannoresults",caption="_Results of the Evanno method._")` + +```{r, echo=FALSE, eval=TRUE} +evannoMethodStructure(summariseQ(tabulateQ(slist))) +``` + +The peak of deltaK is usually used to estimate the best value of *K*. + +The Evanno method can be computed only if these criteria are met: At least 3 values of *K* must be available, values of *K* must be sequential (ie; there must not be missing values of *K*), number of individuals and loci must be same in all runs. If number of repeats for any *K* is less than 2, then results may not be reliable. In case the Evanno method cannot be computed, a plot of ELPD over *K* is produced referred to as the kPlot. + +```{r,echo=TRUE, eval=TRUE,fig.height=3,fig.width=3} +p <- evannoMethodStructure(data=sr1[-3,],exportplot=F,returnplot=T,returndata=F,basesize=12,linesize=0.7) +grid.arrange(p) +``` + +`r fc(name="fc_evannoplot_kplot",caption="_K plot._")` + +## clumppExport + +When multiple repeats are run for each *K*, the order of clusters may be jumbled for each run. Therefore, when plotting multiple runs within each *K*, the colours cannot be assigned correctly as shown in figure below. + +```{r,echo=TRUE, eval=FALSE} +sfiles <- list.files(path=system.file("files/structure",package="pophelper"), full.names=T) +slist <- readQ(sfiles) + +plotQ(slist[c(3,4,10)],imgoutput="join") +``` + +![clumpp-unaligned](clumpp-unaligned.png) +`r fc(name="fc_clumppunaligned",caption="_Three runs of K=3 with jumbled clusters._")` + +The software CLUMPP helps to overcome this issue by reordering the clusters correctly. To read more about CLUMPP^4^, see references. + +![clumpp-folder-preview](clumpp-folder.png) +`r fc(name="fc_clumppfolder",caption="_Directories created from clumpp export (left) and the contents of each folder (right)._")` + +The function `clumppExport()` takes a 'qlist', combines runs by *K* and generates a combined data file and a paramfile in separate directories. The combined file contains the tabular cluster data from all the repeats and runs. The paramfile contains information for the CLUMPP executable. The name for the folder can be changed optionally using the argument `prefix="something"`. When the argument `useexe=T` is used, the CLUMPP executable (included with `pophelper`) will be run automatically. This may not work on all OS and versions. Remember to cite CLUMPP^4^ if this option is used. + +```{r,echo=TRUE, eval=FALSE} +# basic usage +clumppExport(qlist=slist, useexe=T) + +# select files interactively +# clumppExport(qlist=choose.files(multi=TRUE), useexe=T) + +?clumppExport +clumppExport(qlist=NULL, prefix=NA, parammode=NA, paramrep=NA, useexe=T) +# export folders are prefixed as pop by default, to change, use prefix="foo" +# To change clumpp algorithm, set parammode=1, parammode=2 or parammode=3. +# If clumpp is slow, increase parammode +# To change number of clumpp repeats, set paramrep=200, paramrep=500 etc. + +# optionally change folder name +clumppExport(qlist=slist, prefix="Set1", useexe=T) +``` + +If CLUMPP does not run automatically using `useexe=T`, the CLUMPP executable can be copied and pasted into each of these directories and executed by running it. + +The CLUMPP executable uses the combined file and the param file to generate three output files: aligned file, merged file and misc file. + +![clumpp-folder-results](clumpp-output.png) +`r fc(name="fc_clumppoutput",caption="_Directory showing CLUMPP results: aligned file, merged file and misc file._")` + +The aligned file contains all the runs as in the combined file after realignment of clusters. In contrast, the merged file contains only one table which merges all the aligned runs to create a consensus run. The merged file makes sense only if all the aligned runs have similar assignments. The merged file is not recommended for downstream use unless you know what you are doing. The miscfile contains run parameters and other details. + +We run our example samples. + +```{r, echo=TRUE, eval=FALSE} +# generate clumpp files, run clumpp and produce aligned files +clumppExport(slist[c(3,4,10)],useexe=T) +``` + +``` +Folder created: pop_K3 +pop_K3-combined.txt exported. +paramfile exported. + + +----------------------------------------------------------------- +----------------------------------------------------------------- +CLUMPP by M. Jakobsson and N. A. Rosenberg (2007) + Code by M. Jakobsson + Version 1.1.2 (May 2009) +----------------------------------------------------------------- +----------------------------------------------------------------- + + +Parameter settings +----------------------- Main parameters ------------------------- +DATATYPE = 1 +INDFILE = +POPFILE = pop_K3-combined.txt +OUTFILE = pop_K3-combined-merged.txt +MISCFILE = pop_K3-combined-miscfile.txt +K = 3 +C = 149 +R = 3 +M = 2 +W = 0 +S = 2 +- Additional options for the Greedy and LargeKGreedy algorithms - +GREEDY_OPTION = 2 +REPEATS = 20 +PERMUTATIONFILE = +----------------------- Optional outputs ------------------------ +PRINT_PERMUTED_DATA = 1 +PERMUTED_DATAFILE = pop_K3-combined-aligned.txt +PRINT_EVERY_PERM = 0 +EVERY_PERMFILE = +PRINT_RANDOM_INPUTORDERFILE = 0 +RANDOM_INPUTORDERFILE = +----------------------- Advanced options ------------------------ +OVERRIDE_WARNINGS = 0 +ORDER_BY_RUN = 0 + + +In total, 20 configurations of runs and clusters will be tested. + +Running... +---------------------------------- +Best estimate of H' Repeat number (of 20) +0.995447938961547 1 + + +Results +---------------------------------- +The highest value of H' is: 0.995447938961547 + +The list of permutation of the clusters that produces that +H' value is (each run is on a separate row) +3 2 1 +1 2 3 +3 2 1 + +The program finished in (days:hours:minutes:seconds) +0:0:0:0 + +Press Return to exit... +----------------------- +Run completed. +``` + +The aligned file can be read in and plotted. + +```{r, echo=TRUE,eval=FALSE} +# read aligned file +aligned <- readQ("./pop_K3/pop_K3-combined-aligned.txt") + +#plot +plotQ(aligned,imgoutput="join") +``` + +![clumpp-unaligned](clumpp-aligned.png) +`r fc(name="fc_clumpp_aligned",caption="_Three runs of K=3 with clusters aligned using CLUMPP._")` + +Note that CLUMPP can only be used to align clusters with a given *K*. Clusters cannot be aligned across multiple *K*. To align clusters across multiple *K*, see [CLUMPAK](http://clumpak.tau.ac.il/). + +## collectClumppOutput + +The CLUMPP output files are now distributed in multiple folders. The aligned, merged or both files can be copied from multiple folders into a single folder for further analyses using the function `collectClumppOutput()`. The working directory is set suitably before running this function. This function need a `prefix` argument which denotes the prefix used in the previous function or the text before the underscore. For ex. a directory named `pop_K2` has the prefix `pop`. + +```{r,echo=TRUE, eval=FALSE} +# set working directory +setwd(choose.dir()) +# collect aligned files. Default prefix is pop +collectClumppOutput() + +# working directory can also be set using runsdir argument +collectClumppOutput(runsdir=choose.dir()) + +# collect both aligned and merged files +collectClumppOutput(filetype="both") + +?collectClumppOutput +collectClumppOutput(prefix="pop", filetype="aligned", runsdir=NA, ++ newdir=NA, quiet=FALSE) + +# to change which files are copied, set filetype="aligned", filetype="both" or +# filetype="merged" +# to change name of new directory, set newdir="somename" + +?collectClumppOutput() +``` + +Collecting the aligned and merged files into a single folder can be helpful in plotting these files. From the command above, both aligned and merged files are copied into a new directory `pop-aligned` within the working directory. + +## analyseQ + +This is a wrapper function for easily performing several `pophelper` functions in one function. Input files can be STRUCTURE, TESS or BASIC run files. The `analyseQ()` function performs a tabulation of runs, summarising of runs, perform Evanno method (for STRUCTURE runs only), exports clumpp output and generates barplots. + +```{r,echo=TRUE, eval=FALSE} +# basic usage +analyseQ(choose.files()) + +sfiles <- list.files(path=system.file("files/structure",package="pophelper"),full.names=T) +analyseQ(files=sfiles) +tfiles <- list.files(path=system.file("files/tess",package="pophelper"),full.names=T) +analyseQ(files=tlist) +sfiles <- list.files(path=system.file("files/structure",package="pophelper"),full.names=T) +analyseQ(files=alist) +``` + +# Plotting +## plotQ + +The function `plotQ()` is used to create stacked assignment barplots from a 'qlist'. All individuals are shown on a single row. A schematic of the plot parts is shown below. + +![plotq-overview](plotq-overview.png) +`r fc(name="fc_plotqoverview",caption="_An overview of the components of a \x60plotQ()\x60 figure and most of the arguments used to modify them._")` + +The full code used to create the above figure is shown below. Details are explained further on. + +```{r,echo=TRUE, eval=FALSE} +sfiles <- list.files(path=system.file("files/structure",package="pophelper"), full.names=T) +slist <- readQ(files=sfiles,indlabfromfile=T) + +threelabset <- read.delim(system.file("files/metadata.txt", package="pophelper"), header=T,stringsAsFactors=F) +twolabset <- threelabset[,2:3] + +plotQ(slist[2:3],imgoutput="join",showindlab=T,grplab=twolabset, + subsetgrp=c("Brazil","Greece"),selgrp="loc",ordergrp=T,showlegend=T, + showtitle=T,showsubtitle=T,titlelab="The Great Structure", + subtitlelab="The amazing population structure of your favourite organism.", + height=1.6,indlabsize=2.3,indlabheight=0.08,indlabspacer=-1, + barbordercolour="white",barbordersize=0,outputfilename="plotq",imgtype="png") +``` + +### Separate and Joined plots + +The `imgoutput` argument is used to indicate if multiple runs must be plotted as separate plots or as a joined plot. When `imgoutput="sep"`, each run file is plotted and exported as separate figures. When `imgoutput="join"`, all selected run files are plotted as a single figure and exported. Default is set as `imgoutput="sep"`. + +```{r,echo=TRUE, eval=FALSE} +# plot first run separately +plotQ(qlist=slist[1]) + +# plot multiple runs separately +plotQ(qlist=slist[1:3]) +# same as above +plotQ(qlist=slist[1:3], imgoutput="sep") + +# join files into one figure +plotQ(qlist=readQ(sfiles)[c(1,3)], imgoutput="join") +``` + +For the purpose of this document, we will use a short dataset with 29 individuals. The plot is designed for export, therefore, a few arguments need to be modified. + +```{r,echo=TRUE,eval=TRUE,fig.height=2,fig.width=6} +# creating a short dataset +slist1 <- sapply(slist,function(x) x[c(1:5,20:25,50:55,100:105,130:135),]) + +# normal usage +# p <- plotQ(slist1[1]) +# modified for this document +p <- plotQ(slist1[1],returnplot=T,exportplot=F,quiet=T,basesize=11) +print(p$plot[[1]]) +``` + +`r fc(name="fc_plotqnolab_sep",caption="_Single run plotted separately._")` + +```{r,echo=TRUE,eval=TRUE,fig.height=3,fig.width=6} +p <- plotQ(slist1[c(1,3)],imgoutput="join",returnplot=T,exportplot=F,quiet=T,basesize=11) +print(p$plot[[1]]) +``` + +`r fc(name="fc_plotqnolab_join",caption="_Two runs joined together in one image._")` + +The spacing between panels in a 'join' plot can be adjusted using `panelspacer`. + +### Strip panel + +The panel on the right side of the plot is the strip panel. The strip panel is displayed by default (`showsp=T`). The strip panel shows labels referred to as the strip labels or strip panel labels. The strip panel by default shows the filename and the *K* value. Strip panel label can be changed to show custom labels or the panel can be turned off altogether. If custom labels are provided, they must be equal to the number of runs. + +```{r,echo=TRUE, eval=FALSE} +# turn off strip panel +plotQ(qlist=slist1[1], showsp=F) +# move strip panel to the left +plotQ(qlist=slist1[1], sppos="left") +plotQ(qlist=slist1[1:3], imgoutput="join", sppos="left") +# custom strip panel label showing filename only +plotQ(qlist=slist1[1], splab=names(slist1)[1]) + +# custom strip panel label showing k only +fn1 <- function(x) attr(x,"k") +spnames <- paste0("K=",sapply(slist1,fn1)) +plotQ(qlist=slist1[1], splab=spnames[1]) + +# two-line strip panel label +plotQ(qlist=slist1[1:3], splab=paste0(names(slist1)[1:3],"\n",c("run1","run2","run3"))) +plotQ(qlist=slist1[1:3], imgoutput="join", + splab=paste0(names(slist1)[1:3],"\n",c("run1","run2","run3"))) + +# change colour of strip label on plot +plotQ(qlist=slist1[1], splabcol="blue") +# change size of strip label on plot +plotQ(qlist=slist1[1], splabsize=7) +# change font face of strip label on plot +plotQ(qlist=slist1[1], splabface="bold") +# hide strip label on plot +plotQ(qlist=slist1[1], splabcol="white") +# change strip panel background colour +plotQ(qlist=slist1[1], spbgcol="coral") +``` + +```{r,echo=TRUE,eval=TRUE,fig.height=2,fig.width=8} + +# modified for this document +p1 <- plotQ(slist1[1],returnplot=T,exportplot=F,quiet=T,basesize=11, + sppos="left",splabcol="red",spbgcol="grey") +p2 <- plotQ(slist1[1:2],imgoutput="join",returnplot=T,exportplot=F,quiet=T,basesize=11, + sppos="left",splabcol="red",spbgcol="grey",splab=c("This one","That one")) + +grid.arrange(p1$plot[[1]],p2$plot[[1]],ncol=2) +``` + +`r fc(name="fc_plotqstrippanel",caption="_Modifications to the strip panel shown on 'sep' plot (left) and 'join' plot (right)._")` + +### Cluster colours + +Each cluster gets a distinct colour. Up to 12 clusters get colours assigned from a pre-defined palette which was creted for this package. I arbitrary call this the 'standard' colours. Clusters >12 get colours derived from the function `rich.colors()` from package `gplots`. The colours can also be manually supplied to `clustercol` as a character of R colours or hexadecimal values. The length of colours must be equal to the maximum *K* value in the runs provided. + +Examples of how to provide custom colours. + +```{r,echo=TRUE,eval=FALSE} +# change colour of clusters +plotQ(qlist=slist1[3:4], imgoutput="join", + clustercol=c("coral","steelblue","lightblue","purple","orange")) + +plotQ(qlist=slist1[16:17], imgoutput="join", + clustercol=c("#A6CEE3", "#3F8EAA", "#79C360", "#E52829", "#FDB762","#ED8F47","#9471B4")) +``` + +Here are the default colours used. + +```{r,echo=TRUE,eval=TRUE,fig.height=1,fig.width=8} +clist <- list( +"standard_12"=c("#2121D9","#9999FF","#DF0101","#04B404","#FFFB23","#FF9326","#A945FF","#0089B2","#B26314","#610B5E","#FE2E9A","#BFF217"), +"rich.colors"=pophelper:::getColours(13)) + +# add length of palettes +lengths <- sapply(clist,length) + +par(mar=c(0.2,4.5,0.2,0)) +par(mfrow=c(length(clist),1)) + +for(i in 1:length(clist)) +{ + {barplot(rep(1,max(lengths)),col=c(clist[[i]],rep("white",max(lengths)-length(clist[[i]]))),axes=F,border=F) + text(x=-0.1,y=0.5,adj=1,label=names(clist)[i],xpd=T)} +} +``` + +`r fc(name="fc_cols",caption="_(A) Top: Colour palette used when K<=12. (B) Bottom: Colour function used when K>12._")` + +Here are some more colours to play with. + +```{r,echo=TRUE,eval=TRUE,fig.height=5.5,fig.width=8} +clist <- list( +"shiny"=c("#1D72F5","#DF0101","#77CE61", "#FF9326","#A945FF","#0089B2","#FDF060","#FFA6B2","#BFF217","#60D5FD","#CC1577","#F2B950","#7FB21D","#EC496F","#326397","#B26314","#027368","#A4A4A4","#610B5E"), +"strong"=c("#11A4C8","#63C2C5","#1D4F9F","#0C516D","#2A2771","#396D35","#80C342","#725DA8","#B62025","#ED2224","#ED1943","#ED3995","#7E277C","#F7EC16","#F8941E","#8C2A1C","#808080"), +"oceanfive"=c("#00A0B0", "#6A4A3C", "#CC333F", "#EB6841", "#EDC951"), +"keeled"=c("#48B098", "#91CB62", "#FFEE3B", "#FB9013", "#FF3C28"), +"vintage"=c("#400F13", "#027368", "#A3BF3F", "#F2B950", "#D93A2B"), +"muted"=c("#46BDDD","#82DDCE","#F5F06A","#F5CC6A","#F57E6A"), +"teal"=c("#CFF09E","#A8DBA8","#79BD9A","#3B8686","#0B486B"), +"merry"=c("#5BC0EB","#FDE74C","#9BC53D","#E55934","#FA7921"), +"funky"=c("#A6CEE3", "#3F8EAA", "#79C360", "#E52829", "#FDB762","#ED8F47","#9471B4"), +"retro"=c("#01948E","#A9C4E2","#E23560","#01A7B3","#FDA963","#323665","#EC687D"), +"cb_paired"=c("#A6CEE3","#1F78B4","#B2DF8A","#33A02C","#FB9A99","#E31A1C","#FDBF6F","#FF7F00","#CAB2D6","#6A3D9A","#FFFF99","#B15928"), +"cb_set3"=c("#8DD3C7","#FFFFB3","#BEBADA","#FB8072","#80B1D3","#FDB462","#B3DE69","#FCCDE5","#D9D9D9","#BC80BD","#CCEBC5","#FFED6F"), +"morris"=c("#4D94CC","#34648A","#8B658A","#9ACD32","#CC95CC","#9ACD32","#8B3A39","#CD6601","#CC5C5B","#8A4500"), +"wong"=c("#000000","#E69F00","#56B4E9","#009E73","#F0E442","#006699","#D55E00","#CC79A7"), +"krzywinski"=c("#006E82","#8214A0","#005AC8","#00A0FA","#FA78FA","#14D2DC","#AA0A3C","#FA7850","#0AB45A","#F0F032","#A0FA82","#FAE6BE")) + +# add length of palettes +lengths <- sapply(clist,length) +names(clist) <- paste0(names(clist),"_",lengths) + +par(mar=c(0.2,6,0.2,0)) +par(mfrow=c(length(clist),1)) + +for(i in 1:length(clist)) +{ + {barplot(rep(1,max(lengths)),col=c(clist[[i]],rep("white",max(lengths)-length(clist[[i]]))),axes=F,border=F) + text(x=-0.1,y=0.5,adj=1,label=names(clist)[i],xpd=T,cex=1.2)} +} +``` + +```{r,echo=TRUE,eval=TRUE,fig.height=1.2,fig.width=8} +kelly <- c("#F2F3F4","#222222","#F3C300","#875692","#F38400","#A1CAF1","#BE0032","#C2B280","#848482","#008856","#E68FAC","#0067A5","#F99379","#604E97","#F6A600","#B3446C","#DCD300","#882D17","#8DB600", "#654522","#E25822","#2B3D26") + +par(mar=c(0.2,4.5,0.2,0)) +par(mfrow=c(2,1)) + +{barplot(rep(1,11),col=kelly[1:11],axes=F,border=F) +text(x=-0.1,y=0.5,adj=1,label="kelly_22",xpd=T) +barplot(rep(1,11),col=kelly[12:22],axes=F,border=F)} +``` + +`r fc(name="fc_more_cols",caption="_Examples of a few custom colour palettes. Shows name and the number of colours in the palette._")` + +```{r,echo=TRUE,eval=TRUE,fig.height=4,fig.width=6} +# modified for this document +p1 <- plotQ(slist[c(1,4:8)],imgoutput="join",returnplot=T,exportplot=F,quiet=T,basesize=11, + clustercol=clist$shiny,splab=paste0("K=",sapply(slist[c(1,4:8)],ncol))) + +p1$plot[[1]] +``` + +`r fc(name="fc_customcol_shiny",caption="_Using 'shiny' custom colours._")` + +```{r,echo=TRUE,eval=TRUE,fig.height=4,fig.width=6} +# modified for this document +p1 <- plotQ(slist[c(1,4:8)],imgoutput="join",returnplot=T,exportplot=F,quiet=T,basesize=11, + clustercol=clist$wong,splab=paste0("K=",sapply(slist[c(1,4:8)],ncol))) + +p1$plot[[1]] +``` + +`r fc(name="fc_customcol_wong",caption="_Using 'wong' custom colours._")` + +```{r,echo=TRUE,eval=TRUE,fig.height=4,fig.width=6} +# modified for this document +p1 <- plotQ(slist[c(1,4:8)],imgoutput="join",returnplot=T,exportplot=F,quiet=T,basesize=11, + clustercol=kelly,splab=paste0("K=",sapply(slist[c(1,4:8)],ncol))) + +rm(clist,lengths,kelly) +p1$plot[[1]] +``` + +`r fc(name="fc_customcol_kelly",caption="_Using 'kelly' custom colours._")` + +Except for the 'standard' and 'shiny' colours, none of the palettes are created by myself. Please cite the relevant source if you use them. + +`r tc(name="tc_colours",caption="_Colour palettes and sources._")` + +|Palette|Num of colours|Source| +|---|---|---| +|standard|12|This package| +|rich.colors|Any|[gplots](https://cran.r-project.org/web/packages/gplots/index.html)| +|shiny|19|This package| +|strong|17|Missing source| +|oceanfive|5|[colourlovers](http://www.colourlovers.com/palette/1473/Ocean_Five)| +|keeled|5|[colourlovers](http://www.colourlovers.com/palette/1162333/Keeled)| +|vintage|5|Missing source| +|muted|5|Missing source| +|teal|5|[colourlovers](http://www.colourlovers.com/palette/580974/Adrift_in_Dreams)| +|merry|5|Missing source| +|funky|7|Missing source| +|retro|7|Missing source| +|cb_paired|12|[Colorbrewer](http://colorbrewer2.org/#type=qualitative&scheme=Paired&n=12)| +|cb_set3|12|[Colorbrewer](http://colorbrewer2.org/#type=qualitative&scheme=Set3&n=12)| +|morris|10|[Morris et. al., 2012](http://www.pnas.org/content/110/2/453.full)| +|wong|8|[Wong, 2011](https://www.nature.com/articles/nmeth.1618?WT.ec_id=NMETH-201106)| +|krzywinski|12|[Martin Krywinski](http://mkweb.bcgsc.ca/colorblind/)| +|tatarize|64|[Tatarize](https://stackoverflow.com/questions/33295120/how-to-generate-gif-256-colors-palette)| + +Check out [colourlovers](http://www.colourlovers.com/palettes), [coolors](https://coolors.co/), [Adobe colors](https://color.adobe.com/explore/), [Colorbrewer](http://colorbrewer2.org) etc for more colour palettes. + +### Legend + +A legend denoting colours and labels for clusters can be shown on the top of plots by setting `showlegend=T`. + +```{r,echo=TRUE,eval=FALSE} +# show legend +plotQ(qlist=slist1[3], showlegend=T) +# move to right side +plotQ(qlist=slist1[3], showlegend=T, legendpos="right") +# change legend key size +plotQ(qlist=slist1[3], showlegend=T, legendkeysize=5) +# change legend text size +plotQ(qlist=slist1[3], showlegend=T, legendtextsize=5) +``` + +The clusters in 'qlist' are by default named Cluster1, Cluster2 etc. The cluster names can be renamed by providing custom labels to argument `legendlab`. The length of `legendlab` must be equal to the max number of clusters in the selected runs. + +```{r,echo=TRUE, eval=TRUE} +# number of columns or K value in selected runs +sapply(slist1[c(1,3)],ncol) +# joined plot with custom legend labels +# plotQ(qlist=slist[c(1,3)], imgoutput="join", showlegend=T, legendlab=c("group1","group2","group3")) +``` + +```{r,echo=TRUE,eval=TRUE,fig.height=2.5,fig.width=8} +# modified for this document +p1 <- plotQ(slist1[1],returnplot=T,exportplot=F,quiet=T,basesize=11, + showlegend=T, legendlab=c("group1","group2"), + legendkeysize=10,legendtextsize=10,legendmargin=c(2,2,2,0)) + +p2 <- plotQ(slist1[c(1,3)],imgoutput="join",returnplot=T,exportplot=F,quiet=T,basesize=11, + showlegend=T, legendlab=c("group1","group2","group3"), + legendkeysize=10,legendtextsize=10,legendmargin=c(2,2,2,0)) + +grid.arrange(p1$plot[[1]],p2$plot[[1]],ncol=2) +``` + +`r fc(name="fc_plotqlegend",caption="_(A) Left: Default legend when \x60showlegend=T\x60. (B) Right: Joined plot with custom legend labels using \x60legendlab=c('group1','group2','group3')\x60._")` + +### Y-axis + +The y-axis is turned off by default. This can be displayed using `showyaxis`. The tick marks can be displayed using `showticks`. This turns on ticks for both x and y axes. + +```{r,echo=TRUE,eval=FALSE} +# show y axis +plotQ(qlist=slist1[3], showyaxis=T) +# adjust size of y axis text +plotQ(qlist=slist1[3], showyaxis=T, indlabsize=6) +# show y axis and ticks on both axes +plotQ(qlist=slist1[3], showyaxis=T, showticks=T) +# adjust tick size and tick length +plotQ(qlist=slist1[3], showyaxis=T, showticks=T, ticksize=0.3, ticklength=0.2) +``` + +If y axis text overlap with a panel below, increase `panelspacer`. + +```{r,echo=TRUE,eval=TRUE,fig.height=2,fig.width=8} +# modified for this document +p1 <- plotQ(slist1[1],returnplot=T,exportplot=F,quiet=T,basesize=11, + showyaxis=T,showticks=T) + +p2 <- plotQ(slist1[c(1,3)],imgoutput="join",returnplot=T,exportplot=F,quiet=T,basesize=11, + showyaxis=T,showticks=T,panelspacer=0.4) + +grid.arrange(p1$plot[[1]],p2$plot[[1]],ncol=2) +``` + +`r fc(name="fc_plotq_legend_yaxis",caption="_Displaying y-axis labels and ticks._")` + +### Individual labels + +Individual labels are row names of the 'qlist' dataframes. Individual labels although not displayed by default on the plots, are present in the underlying data. The final individual labels in the plotted data depends on the row labels of the input data, and argument `useindlab`. + +The default `useindlab=F`, creates labels numerically in the original order of data but with zero padding. For example, if there are 10 individuals, labels are 01, 02 up to 10. if there are 100 individuals, then labels are 001, 002 up to 100. Zero padding to ensure optimal sorting. When `useindlab=T`, labels are used from the rownames of 'qlist' dataframes. They are usually labelled 1,2,3.. if read in using `readQ()`. + +```{r,echo=TRUE, eval=TRUE} +sfiles <- list.files(path=system.file("files/structure",package="pophelper"),full.names=T) +# without indlabfromfile +slist <- readQ(files=sfiles) +head(slist[[1]]) +``` + +This is not optimal for sorting by labels `sortind="label"`. For STRUCTURE files with individual labels, they can be read in automatically using `readQ(indlabfromfile=T)`. `indlabfromfile` only works for STRUCTURE files and not for other run files. + +```{r,echo=TRUE, eval=TRUE} +# with useindlabfromfile +slist <- readQ(files=sfiles, indlabfromfile=TRUE) +head(slist[[1]]) +``` + +The rownames of 'qlist' can also be modified by the user by adding custom individual labels. + +```{r,echo=TRUE, eval=FALSE} +inds <- read.delim(system.file("files/structureindlabels.txt",package="pophelper"),header=FALSE,stringsAsFactors=F) +# add indlab to one run +rownames(slist[[1]]) <- inds$V1 +# if all runs are equal length, add indlab to all runs +if(length(unique(sapply(slist,nrow)))==1) slist <- lapply(slist,"rownames<-",inds$V1) +# show row names of all runs and all samples +lapply(slist, rownames) +``` + +Individual labels can be shown on the plot using `showindlab=TRUE`. + +```{r,echo=TRUE,eval=TRUE,fig.height=2,fig.width=8} +# modified for this document +p1 <- plotQ(slist1[1],returnplot=T,exportplot=F,quiet=T,basesize=11, + showindlab=T) + +p2 <- plotQ(slist1[c(1,3)],imgoutput="join",returnplot=T,exportplot=F,quiet=T,basesize=11, + showindlab=T) + +grid.arrange(p1$plot[[1]],p2$plot[[1]],ncol=2) +``` + +`r fc(name="fc_plotqindlab_default",caption="_Default individual labels displayed on 'sep' plot (left) and 'join' plot (right)._")` + +In the example below, individual labels from the qlist is used. + +```{r,echo=TRUE,eval=TRUE,fig.height=2.5,fig.width=8} +# modified for this document +p1 <- plotQ(slist1[1],returnplot=T,exportplot=F,quiet=T,basesize=11, + showindlab=T,useindlab=T,showyaxis=T) + +p2 <- plotQ(slist1[c(1,3)],imgoutput="join",returnplot=T,exportplot=F,quiet=T,basesize=11, + showindlab=T,useindlab=T,showyaxis=T,panelspacer=0.3) + +grid.arrange(p1$plot[[1]],p2$plot[[1]],ncol=2) +``` + +`r fc(name="fc_plotqindlab_useindlab",caption="_Individual labels displayed on 'sep' plot (left) and 'join' plot (right). Labels from the qlist are used._")` + +When using `imgoutput='join'`, a common individual label is displayed below all runs. This is because by default `sharedindlab=T`. Set `sharedindlab=F` for displaying labels under each panel. `sharedindlab` must be set to FALSE when sorting individuals. More details about this is explained below in 'Sort individuals'. + +```{r,echo=TRUE,eval=TRUE,fig.height=3,fig.width=6} +# modified for this document +p2 <- plotQ(slist1[c(1,3)],imgoutput="join",returnplot=T,exportplot=F,quiet=T,basesize=11, + showindlab=T,useindlab=T,sharedindlab=F,showyaxis=T,showticks=T,indlabcol="coral", + indlabangle=45,indlabvjust=1) +p2$plot[[1]] +``` + +`r fc(name="fc_plotqindlab_ticks",caption="_Individual labels displayed under each panel of a 'join' plot. Y axis and ticks are also displayed. Some adjustments to the labels are also shown._")` + +The spacing between the panel and individual labels can be controlled using `indlabspacer`. The height of the individual label area is controlled by `indlabheight`. When group labels (`grplab`) are in use, they can be concatenated to the individual labels. More details are explained below in 'Sort individuals' and 'Group labels'. + +### Sort individuals + +Individuals in a plot are by default plotted in the order as in the input data. The individuals can be sorted based on the value of any one of the clusters ('Cluster1'), 'all' or 'label'. The 'all' option produces a sort similar to that in the software STRUCTURE. All clusters are taken into account to sort individuals. When using the name of a cluster, like 'Cluster1', 'Cluster2' etc, all individuals are sorted by value of the specified cluster. + +```{r,echo=TRUE, eval=FALSE} +# sorted by cluster 1 +plotQ(slist1[c(1,3)], sortind="Cluster1") +# sorted by cluster 2 +plotQ(slist1[1], sortind="Cluster2") +# sorted by all +plotQ(slist1[c(1,3)], sortind="all") + +# sorted by cluster 3 +plotQ(slist1[1], sortind="Cluster3") # gives error because this file contains only 2 clusters + +# sorted by cluster 1, three files joined plot +plotQ(slist1[c(1,3)], sortind="Cluster1", imgoutput="join") +plotQ(slist1[c(1,3)], sortind="all", imgoutput="join") +``` + +```{r,echo=TRUE,eval=TRUE,fig.height=2,fig.width=8} +# modified for this document +p1 <- plotQ(slist1[1],returnplot=T,exportplot=F,quiet=T,basesize=11, + sort="Cluster1") + +p2 <- plotQ(slist1[c(1,3)],imgoutput="join",returnplot=T,exportplot=F,quiet=T,basesize=11, + sort="Cluster1",sharedindlab=F) + +grid.arrange(p1$plot[[1]],p2$plot[[1]],ncol=2) +``` + +`r fc(name="fc_plotq_sort_nolab",caption="_(A) Left: 'sep' plot sorted by 'Cluster1'. (B) Right: 'join' plot sorted by 'Cluster1'._")` + +```{r,echo=TRUE,eval=TRUE,fig.height=2.5,fig.width=8} +# modified for this document +p1 <- plotQ(slist1[1],returnplot=T,exportplot=F,quiet=T,basesize=11, + sort="all",showindlab=T,showyaxis=T,showticks=T) + +p2 <- plotQ(slist1[c(1,3)],imgoutput="join",returnplot=T,exportplot=F,quiet=T,basesize=11, + sort="all",sharedindlab=F,showindlab=T,showyaxis=T,showticks=T) + +grid.arrange(p1$plot[[1]],p2$plot[[1]],ncol=2) +``` + +`r fc(name="fc_plotq_sort_indlab",caption="_(A) Left: 'sep' plot sorted by 'all'. (B) Right: 'join' plot sorted by 'all'. Individual labels and y-axis is displayed._")` + +When using `sortind="label"`, individuals are sorted by individual labels. Individuals are labelled numerically padded with zeros when `useindlab=F`. Labels are taken from the qlist when `useindlab=T`. + +### Group labels + +One or more sets of group labels can be added to the bottom of barplots by providing a 'data.frame' object. The number of rows of the 'data.frame' must be equal to the number of individuals. The header of the 'data.frame' is the group label set title. + +```{r, echo=TRUE, eval=FALSE} +# group labels with one group label set +data.frame(lab1=c("A","A","A","B","B")) +# group labels with two group label sets +data.frame(type=c("A","A","A","B","B"),loc=c("Brazil","Brazil","Chile","Chile","Chile")) +``` + +In this demonstration, we will use group labels in the `pophelper` library. This is a 'data.frame' with three columns, ie; three group label sets. + +```{r, echo=TRUE,eval=TRUE} +slist1 <- sapply(slist,function(x) x[c(1:5,20:25,50:55,100:105,130:135),]) + +# read labels for STRUCTURE runs +threelabset <- read.delim(system.file("files/metadata.txt", package="pophelper"), header=T,stringsAsFactors=F) +head(threelabset) +# length of labels equal to number of individuals? +nrow(threelabset) +# check if labels are a character data type +sapply(threelabset, is.character) + +# create short set to match slist1 +threelabset1 <- threelabset[c(1:5,20:25,50:55,100:105,130:135),] +twolabset1 <- threelabset1[,2:3] +``` + +Make sure that the labels are character datatype. When reading from a text file, use `stringsAsFactors=F` to ensure that each column in the dataframe is a character and not a factor. From the above label dataframe, we can choose to use one label set or multiple. + +For now we use a single label set. Note the use of `drop=FALSE` to preserve the single label set as a 'data.frame'. + +```{r, echo=TRUE,eval=TRUE} +onelabset1 <- threelabset1[,2,drop=FALSE] +head(onelabset1) +#plotQ(qlist=slist[1], grplab=threelabset, outputfilename="structure-single-grplab") +``` + +The group labels panel has the text labels, horizontal lines called marker lines and marker line divisions called marker points. Many aspects of these can be adjusted. For marker lines, the line position, line thickness, line type and line colour can be adjusted. For marker points, the point position, point type, point size and point colour can be adjusted. + +```{r,echo=TRUE,eval=TRUE,fig.height=4,fig.width=6} +# modified for this document +p1 <- plotQ(slist1[1],returnplot=T,exportplot=F,quiet=T,basesize=11, + grplab=onelabset1,grplabsize=4,linesize=0.8,pointsize=4) + +p2 <- plotQ(slist1[c(1,3)],imgoutput="join",returnplot=T,exportplot=F,quiet=T,basesize=11, + grplab=onelabset1,grplabsize=4,linesize=0.8,pointsize=4) + +grid.arrange(p1$plot[[1]],p2$plot[[1]],nrow=2) +``` + +`r fc(name="fc_plotq_grplab_default",caption="_Barplot with one group label set. 'sep' plot (top) and 'join' plot (bottom)._")` + +The group label set title or the header of the group label 'data.frame' is shown on the right strip panel. Individual labels can be displayed along with group labels. + +```{r,echo=TRUE,eval=TRUE,fig.height=2,fig.width=8} +# modified for this document +p1 <- plotQ(slist1[1],returnplot=T,exportplot=F,quiet=T,basesize=11, + grplab=onelabset1,grplabsize=3.5,linesize=0.8,pointsize=3,showindlab=T) + +p2 <- plotQ(slist1[c(1,3)],imgoutput="join",returnplot=T,exportplot=F,quiet=T,basesize=11, + grplab=onelabset1,grplabsize=3.5,linesize=0.8,pointsize=3,showindlab=T) + +grid.arrange(p1$plot[[1]],p2$plot[[1]],ncol=2) +``` + +`r fc(name="fc_plotq_grplab_indlab",caption="_Barplot with one group label set. 'sep' plot (left) and 'join' plot (right). Individual labels are also displayed_")` + +When group labels are in use (`grplab`), they can be concatenated to the individual labels in both cases `useindlab=T` and `useindlab=F`, separated by `indlabsep`. Default `indlabsep=" "` adds a space between individual label and grplab. For example, group labels 'popA', 'popA'... will be '01 popA', '02 popA'... when `useindlab=F` and usually '1 popA', '2 popA'... when `useindlab=T`. When multiple group labels are in use, the are similarly concatenated one after the other to individual names in the order in which the group labels were provided. + +Group labels can be concatenated to the individual labels using the argument `indlabwithgrplab=T`. The absolute height of the group label panel is controlled with `grplabheight`. The ratio of the plot panels and group label panel is controlled with `panelratio`. The default `panelratio` is 3:1. + +```{r,echo=TRUE,eval=TRUE,fig.height=3,fig.width=8} +# modified for this document +p1 <- plotQ(slist1[1],returnplot=T,exportplot=F,quiet=T,basesize=11, + grplab=onelabset1,grplabsize=3.5,linesize=0.8,pointsize=3, + showindlab=T,indlabwithgrplab=T) + +p2 <- plotQ(slist1[c(1,3)],imgoutput="join",returnplot=T,exportplot=F,quiet=T,basesize=11, + grplab=onelabset1,grplabsize=3.5,linesize=0.8,pointsize=3, + showindlab=T,indlabwithgrplab=T) + +grid.arrange(p1$plot[[1]],p2$plot[[1]],ncol=2) +``` + +`r fc(name="fc_plotq_grplab_indlab_badpanel",caption="_Barplot with one group label set. Group labels are concatenated to the individual labels. 'sep' plot (left) and 'join' plot (right). _")` + +The individual labels take up most of the plot area. The group labels take up a lot of space on the top plot. The total plot height can be increased and the panel ratio needs to be adjusted. + +```{r,echo=TRUE,eval=TRUE,fig.height=3,fig.width=8} +# modified for this document +p1 <- plotQ(slist1[1],returnplot=T,exportplot=F,quiet=T,basesize=11, + grplab=onelabset1,grplabsize=3.5,linesize=0.8,pointsize=3, + showindlab=T,indlabwithgrplab=T,panelratio=c(7,1)) + +p2 <- plotQ(slist1[c(1,3)],imgoutput="join",returnplot=T,exportplot=F,quiet=T,basesize=11, + grplab=onelabset1,grplabsize=3.5,linesize=0.8,pointsize=3, + showindlab=T,indlabwithgrplab=T,panelratio=c(5,1)) + +grid.arrange(p1$plot[[1]],p2$plot[[1]],ncol=2) +``` + +`r fc(name="fc_plotq_grplab_indlab_goodpanel",caption="_Barplot with one group label set and concatenated individual labels as well as corrected panel ratio. 'sep' plot (left) and 'join' plot (right)._")` + +### Sorting with group labels + +When individuals can be sorted while using group labels, they are sorted within their groups. + +```{r,echo=TRUE,eval=TRUE,fig.height=2,fig.width=8} +# modified for this document +p1 <- plotQ(slist1[1],returnplot=T,exportplot=F,quiet=T,basesize=11, + grplab=onelabset1,grplabsize=3.5,linesize=0.8,pointsize=3, + sortind="Cluster1",panelratio=c(5,1)) + +p2 <- plotQ(slist1[c(1,3)],imgoutput="join",returnplot=T,exportplot=F,quiet=T,basesize=11, + grplab=onelabset1,grplabsize=3.5,linesize=0.8,pointsize=3, + sharedindlab=F,sortind="all") + +grid.arrange(p1$plot[[1]],p2$plot[[1]],ncol=2) +``` + +`r fc(name="fc_plotq_grplab_sort",caption="_Sorting of individuals with group labels. Note that sorting happens within the selected group label set. 'sep' plot (left) showing sorting by 'Cluster1' and 'join' plot (right) showing sorting by 'all'._")` + +Turning on individual labels help to identify individuals. Shown for 'join' plot below. + +```{r,echo=TRUE,eval=TRUE,fig.height=3,fig.width=6} +# modified for this document +p2 <- plotQ(slist1[c(1,3)],imgoutput="join",returnplot=T,exportplot=F,quiet=T,basesize=11, + grplab=onelabset1,grplabsize=4,linesize=0.8,pointsize=3, + sharedindlab=F,sortind="all",showindlab=T) + +grid.arrange(p2$plot[[1]]) +``` + +`r fc(name="fc_plotq_grplab_sort_indlab",caption="_Sorting of individuals with group labels in a 'join' plot. Unshared individual labels are displayed._")` + +Sorting by `label` sorts all individuals by the individual label. Since this is same across all runs and K, a shared individual label is possible when `imgoutput="join"`. If group labels are concatenated to the individual labels, the full concatenated string will determine the final sort order of the individuals. See previous section 'Individual labels' and 'Sort individuals' for more information. + +```{r,echo=TRUE,eval=TRUE,fig.height=2.5,fig.width=8} +# modified for this document +p1 <- plotQ(slist1[c(1,3)],imgoutput="join",returnplot=T,exportplot=F,quiet=T,basesize=11, + grplab=onelabset1,grplabsize=3.5,linesize=0.8,pointsize=3, + sharedindlab=T,sortind="label",showindlab=T,useindlab=F) + +p2 <- plotQ(slist1[c(1,3)],imgoutput="join",returnplot=T,exportplot=F,quiet=T,basesize=11, + grplab=onelabset1,grplabsize=3.5,linesize=0.8,pointsize=3, + sharedindlab=T,sortind="label",showindlab=T,useindlab=T) + +grid.arrange(p1$plot[[1]],p2$plot[[1]],ncol=2) +``` + +`r fc(name="fc_plotq_grplab_sort_indlab_useindlab",caption="_Sorting of individuals with group labels in a 'join' plot. Both plots are sorted by 'label' Left plot uses default individual labels (\x60useindlab=F\x60) while the right plot uses individual labels from the qlist (\x60useindlab=T\x60). Note the difference in sorting order._")` + +### Subset/reorder groups + +When using group labels, the plot can be subsetted or reordered based on group labels. Below are examples using group labels with single group label set. + +```{r, echo=TRUE, eval=FALSE} +# subsetting groups +plotQ(slist[1], grplab=onelabset, subsetgrp="CatB") +# change order of groups +plotQ(slist[1], grplab=onelabset, subsetgrp=c("CatB","CatA")) + +# subsetting group and sorting individuals +plotQ(slist[1], grplab=onelabset, subsetgrp="CatB",sortind="Cluster1") +plotQ(slist[1], grplab=onelabset, subsetgrp="CatA",sortind="all") + +# change order of groups and sorting individuals +plotQ(slist[1], grplab=onelabset, subsetgrp=c("CatB","CatA"), sortind="Cluster1") +plotQ(slist[c(1,3)], grplab=onelabset, subsetgrp=c("CatB","CatA"), sortind="all", imgoutput="join") +``` + +```{r,echo=TRUE,eval=TRUE,fig.height=2,fig.width=10} +# modified for this document +p1 <- plotQ(slist1[c(1,3)],imgoutput="join",returnplot=T,exportplot=F,quiet=T,basesize=11, + grplab=onelabset1,grplabsize=3.5,linesize=0.8,pointsize=3,showindlab=T) + +p2 <- plotQ(slist1[c(1,3)],imgoutput="join",returnplot=T,exportplot=F,quiet=T,basesize=11, + grplab=onelabset1,grplabsize=3.5,linesize=0.8,pointsize=3,showindlab=T, + subsetgrp="CatB") + +p3 <- plotQ(slist1[c(1,3)],imgoutput="join",returnplot=T,exportplot=F,quiet=T,basesize=11, + grplab=onelabset1,grplabsize=3.5,linesize=0.8,pointsize=3,showindlab=T, + subsetgrp=c("CatB","CatA")) + +grid.arrange(p1$plot[[1]],p2$plot[[1]],p3$plot[[1]],ncol=3) +``` +`r fc(name="fc_plotq_grplab_subsetreorder",caption="_'join' plots showing subsetting and reordering using group labels. Left shows a 'join' plot with one group label set. Middle shows subset on 'CatB'. Right shows reordering 'CatB' and 'CatA'. Individual labels are displayed to show change in positions._")` + +We can also sort along with subset and reordering. + +```{r,echo=TRUE,eval=TRUE,fig.height=3,fig.width=10} +# modified for this document +p1 <- plotQ(slist1[c(1,3)],imgoutput="join",returnplot=T,exportplot=F,quiet=T,basesize=11, + grplab=onelabset1,grplabsize=3.5,linesize=0.8,pointsize=3,showindlab=T) + +p2 <- plotQ(slist1[c(1,3)],imgoutput="join",returnplot=T,exportplot=F,quiet=T,basesize=11, + grplab=onelabset1,grplabsize=3.5,linesize=0.8,pointsize=3,showindlab=T, + subsetgrp="CatA",sort="Cluster1",sharedindlab=F) + +p3 <- plotQ(slist1[c(1,3)],imgoutput="join",returnplot=T,exportplot=F,quiet=T,basesize=11, + grplab=onelabset1,grplabsize=3.5,linesize=0.8,pointsize=3,showindlab=T, + subsetgrp=c("CatB","CatA"),sort="Cluster1",sharedindlab=F) + +p4 <- plotQ(slist1[c(1,3)],imgoutput="join",returnplot=T,exportplot=F,quiet=T,basesize=11, + grplab=onelabset1,grplabsize=3.5,linesize=0.8,pointsize=3,showindlab=T, + subsetgrp="CatA",sort="all",sharedindlab=F) + +p5 <- plotQ(slist1[c(1,3)],imgoutput="join",returnplot=T,exportplot=F,quiet=T,basesize=11, + grplab=onelabset1,grplabsize=3.5,linesize=0.8,pointsize=3,showindlab=T, + subsetgrp=c("CatB","CatA"),sort="all",sharedindlab=F) + +grid.arrange(p1$plot[[1]],p2$plot[[1]],p3$plot[[1]],p4$plot[[1]],p5$plot[[1]], + layout_matrix=matrix(c(1,2,3,1,4,5),ncol=3,byrow=T)) +``` +`r fc(name="fc_plotq_grplab_subsetreorder_sort",caption="_'join' plots showing subsetting and reordering using group labels and sorting. Left shows a 'join' plot with one group label set. Middle top shows subset on 'CatA' and sorted by 'Cluster1'. Middle bottom shows subset on 'CatA' and sorted by 'all'. Right top shows reorder to 'CatB,CatA' and sorted by 'Cluster1'. Right bottom shows reorder to 'CatB,CatA' and sorted by 'all'. Individual labels are displayed to show change in positions._")` + +All of the above can be extended to group labels with more than one set. For more details for group labels with more than one label set, see 'Multiple label sets'. + +### Group mean + +An additional feature is the ability to plot mean values (`grpmean=T`) by group when group labels are in use. + +```{r,echo=TRUE, eval=FALSE} +# group mean +plotQ(slist[4], grplab=onelabset, grpmean=T) +plotQ(readQ(al), imgoutput="join", grplab=onelabset, grpmean=T) +``` + +```{r,echo=TRUE,eval=TRUE,fig.height=3,fig.width=10} +# modified for this document +p1 <- plotQ(slist1[1],returnplot=T,exportplot=F,quiet=T,basesize=11, + grplab=onelabset1,grplabsize=3.5,linesize=0.8,pointsize=3,showindlab=T, + grpmean=T) + +p2 <- plotQ(slist1[c(1,3,5)],imgoutput="join",returnplot=T,exportplot=F,quiet=T,basesize=11, + grplab=onelabset1,grplabsize=3.5,linesize=0.8,pointsize=3,showindlab=T, + grpmean=T) + +grid.arrange(p1$plot[[1]],p2$plot[[1]],ncol=2) +``` + +`r fc(name="fc_plotq_grplab_grpmean",caption="_'sep' and 'join' plots showing mean values by group (grpmean)._")` + +### Order groups + +In the example group label so far, the labels were already in contiguous blocks. But, if labels are not in contiguous blocks, ie; there are duplicated non-contiguous blocks of labels, many of the options such as sorting, subsetting etc cannot be used. Below illustrates this concept. + +```{r, echo=TRUE, eval=FALSE} +Contiguous block: A,A,A,A,B,B,C,C,C +Non-contiguous block: A,A,A,B,B,A,A,C,C +``` + +Here we use a single group label set which is in non-contiguous blocks. And we plot the data. + +```{r, echo=TRUE,eval=TRUE,fig.height=2,fig.width=6} +onelabsetrep <- threelabset1[,1,drop=FALSE] + +# multiple blocks of duplicate labels +rle(onelabsetrep$type)$values + +# modified for this document +p1 <- plotQ(slist1[1],returnplot=T,exportplot=F,quiet=T,basesize=11, + grplab=onelabsetrep,grplabsize=3.5,linesize=0.8,pointsize=3,showindlab=T) + +grid.arrange(p1$plot[[1]]) +``` + +`r fc(name="fc_plotq_grplab_ordergrp_bad",caption="_Non-contiguous labels._")` + +As seen above, Temperate appears twice and Tropical appears three times. Options such as `subsetgrp` do not work with non-contiguous blocks of labels. + +``` +plotQ(qlist=slist1[1], grplab=onelabsetrep, subsetgrp="Tropical") #gives error + +Error in pophelper:::grpLabels(dframe = df1, grplab = grplabloop, selgrp = selgrp, : grpLabels: Duplicated contiguous block of labels in 'selgrp'. Change grplab, selgrp or use 'ordergrp=TRUE'. +``` + +Non-contiguous labels can be grouped into contiguous blocks using `ordergrp=TRUE`. When using this, the labels are sorted alphabetically along with the data. The individuals are no longer in the original order as input. + +```{r, echo=TRUE,eval=TRUE,fig.height=2,fig.width=6} +# modified for this document +p1 <- plotQ(slist1[1],returnplot=T,exportplot=F,quiet=T,basesize=11, + grplab=onelabsetrep,grplabsize=3.5,linesize=0.8,pointsize=3,showindlab=T, + ordergrp=T) + +grid.arrange(p1$plot[[1]]) +``` + +`r fc(name="fc_plotq_grplab_ordergrp",caption="_Non-contiguous labels ordered to contiguous blocks._")` + +Ordered group labels can now be sorted, subsetted or reordered. + +```{r, echo=TRUE,eval=TRUE,fig.height=2,fig.width=10} +# modified for this document +p1 <- plotQ(slist1[1],returnplot=T,exportplot=F,quiet=T,basesize=11, + grplab=onelabsetrep,grplabsize=3.5,linesize=0.8,pointsize=3,showindlab=T, + ordergrp=T,sort="all") + +p2 <- plotQ(slist1[1],returnplot=T,exportplot=F,quiet=T,basesize=11, + grplab=onelabsetrep,grplabsize=3.5,linesize=0.8,pointsize=3,showindlab=T, + ordergrp=T,subset="Tropical") + +p3 <- plotQ(slist1[1],returnplot=T,exportplot=F,quiet=T,basesize=11, + grplab=onelabsetrep,grplabsize=3.5,linesize=0.8,pointsize=3,showindlab=T, + ordergrp=T,subset=c("Tropical","Temperate")) + + +grid.arrange(p1$plot[[1]],p2$plot[[1]],p3$plot[[1]],ncol=3) +``` + +`r fc(name="fc_plotq_grplab_ordergrp_final",caption="_Ordered grplabs used for sorting, subsetting and reordering._")` + +### Multiple label sets + +More than one set of group label sets can be be added to the plot simply by providing more columns in the `grplab` 'data.frame'. + +```{r, echo=TRUE, eval=TRUE} +head(threelabset1) +``` + +```{r,echo=TRUE,eval=TRUE,fig.height=2.5,fig.width=8} +# modified for this document +p1 <- plotQ(slist1[1],returnplot=T,exportplot=F,quiet=T,basesize=11, + grplab=threelabset1,grplabsize=3.5,linesize=0.8,pointsize=3) +p2 <- plotQ(slist1[c(1,3)],imgoutput="join",returnplot=T,exportplot=F,quiet=T,basesize=11, + grplab=threelabset1,grplabsize=3.5,linesize=0.8,pointsize=3) +grid.arrange(p1$plot[[1]],p2$plot[[1]],ncol=2) +``` + +`r fc(name="fc_plotq_grplab_three",caption="_Barplot with three group label sets. 'sep' plot (top) and 'join' plot (bottom)._")` + +When plotting with mutiple group label sets, one group label set is defined as the selected group. This is declared using the argument `selgrp`. The value in `selgrp` must be one the group label set titles (headers in the grplab 'data.frame'). If `selgrp` is not explicitly specified, the first group label set is taken as `selgrp`. If only one group label set is used, then `selgrp` is automatically the title of that set. `selgrp` denotes which label set is used for `subsetgrp`, `ordergrp` and `grpmean`. `sortind` will sort within `selgrp`. + +```{r,echo=TRUE,eval=TRUE,fig.height=2.5,fig.width=8} +# modified for this document +p1 <- plotQ(slist1[1],returnplot=T,exportplot=F,quiet=T,basesize=11, + grplab=threelabset1,grplabsize=3.5,linesize=0.8,pointsize=3,panelratio=c(5,1), + selgrp="cat",sort="Cluster1") + +p2 <- plotQ(slist1[c(1,3)],imgoutput="join",returnplot=T,exportplot=F,quiet=T,basesize=11, + grplab=threelabset1,grplabsize=3.5,linesize=0.8,pointsize=3,sharedindlab=F, + selgrp="cat",sort="all") + +grid.arrange(p1$plot[[1]],p2$plot[[1]],ncol=2) +``` + +`r fc(name="fc_plotq_grplab_mlsort",caption="_Sorting when using multiple group label sets._")` + +Subsetting and reordering works similarly when using multiple label sets. + +```{r,echo=TRUE,eval=TRUE,fig.height=3,fig.width=10} +# modified for this document +p1 <- plotQ(slist1[c(1,3)],imgoutput="join",returnplot=T,exportplot=F,quiet=T,basesize=11, + grplab=threelabset1,grplabsize=3.5,linesize=0.8,pointsize=3,showindlab=T) + +p2 <- plotQ(slist1[c(1,3)],imgoutput="join",returnplot=T,exportplot=F,quiet=T,basesize=11, + grplab=threelabset1,grplabsize=3.5,linesize=0.8,pointsize=3,showindlab=T, + subsetgrp="CatB",selgrp="cat") + +p3 <- plotQ(slist1[c(1,3)],imgoutput="join",returnplot=T,exportplot=F,quiet=T,basesize=11, + grplab=threelabset1,grplabsize=3.5,linesize=0.8,pointsize=3,showindlab=T, + subsetgrp=c("CatB","CatA"),selgrp="cat") + +grid.arrange(p1$plot[[1]],p2$plot[[1]],p3$plot[[1]],ncol=3) +``` + +`r fc(name="fc_plotq_grplab_subsetreorder_multipleset",caption="_Joined plots showing subsetting and reordering using group labels with three label sets. Left shows a joined plot with one group label set. Middle shows subset on 'CatB'. Right shows reordering 'CatB' and 'CatA'. Individual labels are displayed to show change in positions._")` + +When using multiple label sets containing non-contiguous labels, `ordergrp` orders all group label sets into contiguous blocks starting with `selgrp`. This is shown in previous figures. + +```{r,echo=TRUE,eval=TRUE,fig.height=3,fig.width=10} +# modified for this document +p1 <- plotQ(slist1[c(1,3)],imgoutput="join",returnplot=T,exportplot=F,quiet=T,basesize=11, + grplab=threelabset1,grplabsize=3.5,linesize=0.8,pointsize=3,showindlab=T) + +p2 <- plotQ(slist1[c(1,3)],imgoutput="join",returnplot=T,exportplot=F,quiet=T,basesize=11, + grplab=threelabset1,grplabsize=3.5,linesize=0.8,pointsize=3,showindlab=T, + selgrp="type",ordergrp=T) + +p3 <- plotQ(slist1[c(1,3)],imgoutput="join",returnplot=T,exportplot=F,quiet=T,basesize=11, + grplab=threelabset1,grplabsize=3.5,linesize=0.8,pointsize=3,showindlab=T, + selgrp="type",ordergrp=T,subsetgrp="Temperate") + +grid.arrange(p1$plot[[1]],p2$plot[[1]],p3$plot[[1]],ncol=3) +``` + +`r fc(name="fc_plotq_grplab_subsetreorder_multipleset_ordergrp",caption="_Joined plots showing ordergrp using group labels with three label sets. Left shows a joined plot with three group label sets. Group label set 'type' has non-contiguous labels. Middle shows the data ordered using \x60selgrp='type'\x60. Right shows subsetting 'Temperate' from group label set 'type'._")` + +### Divider line + +The white dotted line dividing the groups on the plot panels when using group labels is called the divider line. By default, the divider line is drawn between groups in the first group label set (See figures above). This can be changed by providing titles of group labels to the argument `divgrp`. `divgrp` can also take more than one label set, which means divider lines can be drawn for multiple group label sets simultaneously. Divider lines can be turned off using `showdiv=FALSE`. + +```{r,echo=TRUE,eval=TRUE,fig.height=3,fig.width=8} +# modified for this document +p1 <- plotQ(slist1[c(1,3)],imgoutput="join",returnplot=T,exportplot=F,quiet=T,basesize=11, + grplab=threelabset1,grplabsize=3.5,linesize=0.8,pointsize=3,showindlab=T,ordergrp=T) + +p2 <- plotQ(slist1[c(1,3)],imgoutput="join",returnplot=T,exportplot=F,quiet=T,basesize=11, + grplab=threelabset1,grplabsize=3.5,linesize=0.8,pointsize=3,showindlab=T,ordergrp=T, + divgrp=c("type","cat")) + +grid.arrange(p1$plot[[1]],p2$plot[[1]],ncol=2) +``` + +`r fc(name="fc_plotq_divgrp",caption="_(A) Left: Default divider lines for 'type'. (B) Right: Divider lines for both group label sets 'type' and 'cat'._")` + +The divider liness can also be modified and adjusted. + +```{r, echo=TRUE, eval=FALSE} +# change div colour, type and thickness +plotQ(slist[1], grplab=threelabset, divcol="coral", divtype=1, divsize=0.8, divalpha=0.5) +``` + +```{r,echo=TRUE,eval=TRUE,fig.height=3,fig.width=6} +# modified for this document +p1 <- plotQ(slist1[c(1,3)],imgoutput="join",returnplot=T,exportplot=F,quiet=T,basesize=11, + grplab=threelabset1,grplabsize=3.5,linesize=0.8,pointsize=3,showindlab=T,ordergrp=T, + divgrp="loc",divcol="green",divtype=4,divsize=1) + +grid.arrange(p1$plot[[1]]) +``` + +`r fc(name="fc_plotq_divgrp_mod",caption="_Adjustments to the divider line._")` + +### Title and subtitle + +Title and/or subtitle can be added to separate or joined plots. Title and subtitle are displayed using `showtitle=T` and `showsubtitle=T` respectively. The file name is displayed by default. Custom label can be provided using `titlelab` or `subtitlelab`. If multiple plots are exported, then a character vector of labels equal to number of plots must be provided. + +```{r,echo=TRUE,eval=TRUE,fig.height=3,fig.width=10} +# modified for this document +p1 <- plotQ(slist1[1],returnplot=T,exportplot=F,quiet=T,basesize=11, + showtitle=T,showsubtitle=T) + +p2 <- plotQ(slist1[c(1,3)],imgoutput="join",returnplot=T,exportplot=F,quiet=T,basesize=11, + showtitle=T,showsubtitle=T) + +p3 <- plotQ(slist1[c(1,3)],imgoutput="join",returnplot=T,exportplot=F,quiet=T,basesize=11, + showtitle=T,showsubtitle=T,titlelab="Structure plot", + subtitlelab="Population structure of some organism.") + +grid.arrange(p1$plot[[1]],p2$plot[[1]],p3$plot[[1]],layout_matrix=matrix(c(1,2,3,NA,2,3),ncol=3,byrow=T)) +``` + +`r fc(name="fc_plotq_title",caption="_(A) Left: Default title and subtitle for a 'sep' plot. (B) Middle: Default title and subtitle for a 'join' plot. (C) Right: Custom title and subtitle in a 'join' plot._")` + +### Other options + +__Plot visual adjustments__ + +Examples of some of plot options that can be modified. + +```{r,echo=TRUE, eval=FALSE} +# adjust label angle and justification +plotQ(slist1[1], grplab=threelabset1, grplabangle=-90, grplabjust=0.5) + +# adjust grplabheight to fit labels +plotQ(slist1[1], grplab=threelabset1, grplabangle=-90, grplabjust=0.4, grplabheight=3) + +# when grplabheight is high enough, use grplabpos to move labels vertically +plotQ(slist1[1], grplab=threelabset1, grplabheight=3, grplabpos=0.5) +plotQ(slist1[1], grplab=threelabset1, grplabheight=3, grplabpos=0.3) + +# adjust grplabel colour +plotQ(slist1[1] ,grplab=threelabset1, grplabcol="green") + +# adjust marker points +plotQ(slist1[1], grplab=threelabset1, pointtype=21, pointsize=0.4, pointcol="steelblue", pointbgcol="red") +plotQ(slist1[1], grplab=threelabset1, pointtype="$", pointcol="green", pointsize=2) + +# adjust marker line +plotQ(slist1[1], grplab=threelabset1, linesize=0.5, linecol="steelblue") +plotQ(slist1[1], grplab=threelabset1, linecol="steelblue", linetype=3, linesize=0.2) +``` + +Multiple plot argument adjustments to obtain a new label style. + +```{r,echo=TRUE,eval=TRUE,fig.height=2,fig.width=6} +# modified for this document +p1 <- plotQ(slist1[1],returnplot=T,exportplot=F,quiet=T,basesize=11, + grplab=onelabset1,grplabsize=3.5,pointsize=6,linesize=7,linealpha=0.2, + pointcol="white",grplabpos=0.5,linepos=0.5,grplabheight=0.75) + +grid.arrange(p1$plot[[1]]) +``` + +`r fc(name="fc_plotqnewlook",caption="_Group labels in a different style._")` + +The argument `basesize` can be used to change text size of most text objects. This can be helpful to increase or decrease the size of all text. The default basesize is 5. Some of the elements not affected by `basesize` adjustment are `grplabsize` and `legendtextsize`. + +__Exporting and returning__ + +By default, when plotting, an image is exported into the working directory. This is the intended behaviour and the plot element sizes is tuned for export. Exporting can be turned off by `exportplot=FALSE`. By setting `returnplot=TRUE`, the plot object can be returned and saved as a variable for plotting later or further customisation. By setting `returndata=TRUE`, the internally processed data (qlist and grplab) can be returned to be saved to a variable. The returned object is a list and has the following structure: + +``` +$list ++--$plot ++--$data + +--$qlist + +--$grplab +``` + +The plot slot consists of a list of one or more plots. If the plot was plotted without group labels, a ggplot2 object is returned. If the plot was plotted with group labels, a gtable (result of gridExtra::arrangeGrob()) is returned. The plot slot is NA if `returnplot=FALSE`. The data slot has a list of qlist and grplab. The data slot is populated only if `returndata=TRUE`. And the grplab slot is populated only if group labels were used. + +```{r,echo=TRUE,eval=TRUE,fig.height=2,fig.width=6} +# return plot only +p1 <- plotQ(slist1[1],returnplot=T,exportplot=F) +print(p1) +``` + +Note that p1 has a ggplot2 plot object and the other slots are empty. + +```{r,echo=TRUE,eval=TRUE} +# return plot and data (withgrplab) +p1 <- plotQ(slist1[1],returnplot=T,exportplot=F,returndata=T,grplab=onelabset1) +print(p1) +``` + +Note that p1 has a gtable plot object and data slot with qlist and grplab. The qlist accessed using `p1$data$qlist` and grplab data.frame accessed using `p1$data$grplab[[1]]` can used as input to `plotQ()` or `plotQMultiline()`. + +__Using RMarkdown__ + +As explained in the prvious section, plots can be returned and saved. This can be handy when creating a report using RMarkdown. The returned plot(s) can be drawn using `gridExtra::grid.arrange()`. + +```{r,echo=TRUE,eval=TRUE,fig.height=2,fig.width=6} +# return plot and data (withgrplab) +p1 <- plotQ(slist1[1],returnplot=T,exportplot=F,grplab=onelabset1, + grplabsize=3.5,linesize=0.8,pointsize=3) +grid.arrange(p1$plot[[1]]) +``` + +__Export dimensions and resolution__ + +The height, width, resolution and figure format can be changed as shown below. The `height` specifies the height of one panel if the plot is joined. The function multiplies the height values by the number of panels. Similarly, the `grplabheight` specifies the height of the group label panel with one group label set. Multiple label sets are multipled. The width of the plot is automatically calculated based on the number of individuals. This ranges from 5cm to 30cm. + +```{r,echo=TRUE, eval=FALSE} +slist <- readQ(sfiles) + +# change height and width of figure +plotQ(qlist=slist1[1], imgoutput="sep", height=1.5, width=8) +plotQ(qlist=slist1[1:3], imgoutput="join", height=1.5, width=8) + +# change resolution +plotQ(qlist=slist1[1], dpi=600) +# change export figure format +plotQ(qlist=slist1[1], imgtype="tiff") +plotQ(qlist=slist1[1], imgtype="pdf") +``` + +__Export filename__ + +The output file name is automatically generated. When `imgoutput="sep"`, the names of the 'qlist' are used to create output labels. When `imgoutput="join"`, one output label is created for all input files in this format: `JoinedNFiles-YYYYMMDDHHMMSS`, where N stands for number of runs joined, and the ending stands for current system date and time. + +A custom output file name can be provided using `outputfilename`. When using `imgoutput="sep"`, `outputfilename` must be a character vector equal to length of input runs. When `imgoutput="join"`, `outputfilename` must be a character of length one. File extensions like .png etc must not be provided. + +__Custom font__ + +Custom fonts can be used for the text in the plot using package `extrafont`. Fonts are rendered well only by pdf imagetype. I have only tried this on Windows OS. Refer to the `extrafont` package for more information. + +```{r,echo=TRUE,eval=TRUE,fig.height=2,fig.width=6} +library(extrafont) +font_import(pattern="Gidole",prompt=F) +loadfonts() +fonts() + +p <- plotQ(slist1[1],returnplot=T,exportplot=F,basesize=11, + grplabsize=3.5,linesize=0.8,pointsize=3, + grplab=onelabset1,font="Gidole") +grid.arrange(p$plot[[1]]) +``` + +`r fc(name="fc_plotq_font",caption="_Plot with custom font._")` + +`plotQ()` function has numerous arguments to tweak the plot as required. See `?plotQ` for more arguments and descriptions. + +__Plotting CLUMPP output__ + +In similar manner, the `plotQ` function can be used to plot from COMBINED, ALIGNED or MERGED files. + +```{r,echo=TRUE,eval=TRUE,fig.height=3,fig.width=10} +# select files from package +co <- system.file("files/STRUCTUREpop_K4-combined.txt",package="pophelper") +al <- system.file("files/STRUCTUREpop_K4-combined-aligned.txt",package="pophelper") +me <- system.file("files/STRUCTUREpop_K4-combined-merged.txt",package="pophelper") + +# all runs within the file are plotted +# combined +p1 <- plotQ(readQ(co),imgoutput="join",returnplot=T,exportplot=F,basesize=11) +# aligned +p2 <- plotQ(readQ(al),imgoutput="join",returnplot=T,exportplot=F,basesize=11) +# merged only one run +p3 <- plotQ(readQ(me),returnplot=T,exportplot=F,basesize=11) + +grid.arrange(p1$plot[[1]],p2$plot[[1]],p3$plot[[1]], + layout_matrix=matrix(c(1,2,NA,1,2,3,1,2,NA),ncol=3,byrow=T)) +``` + +`r fc(name="fc_plotqclumppnolab",caption="_(A) Left: Combined file (Three STRUCTURE runs for K=4). (B) Middle: Aligned file (Three STRUCTURE runs for K=4 aligned using CLUMPP). (C) Right: Merged file (Three runs for K=4 merged into one table/figure using CLUMPP)._")` + +## plotQMultiline + +The `plotQMultiline` function is also used to plot barplots from a 'qlist'. The barplots can be plotted in multiple rows with individual labels to enable easier identification of individuals. The figure is produced as A4 size by default. The number of samples per line `spl` and the number of lines per page `lpp` is automatically calculated but it can also be specified manually. A schematic of the plot parts is shown below. + +![plotqmultiline-overview](plotqmultiline-overview.png) +`r fc(name="fc_plotqmultilineoverview",caption="_An overview of the components of a \x60plotQMultiline()\x60 figure and some of the arguments used to modify them._")` + +It is recommended to read through the `plotQ` section first because many of the arguments are same and better explanied there. + +`plotQMultiline()` plots one run per page. And multiple pages are exported for multiple runs. The output filename is the 'qlist' name followed by a number. Eg: filename-1.png. In case the number of individuals do not fit on a page, extra pages are exported per run. Then extra pages are named filename-2, filename-3 etc. But, the number of samples on a page can be manually controlled using `spl` and `lpp`. + +### Basic usage + +```{r,echo=TRUE, eval=TRUE} +#do not use this command to read local files +sfiles <- list.files(path=system.file("files/structure",package="pophelper"), full.names=T) +slist <- readQ(files=sfiles,indlabfromfile=T) +``` + +```{r,echo=TRUE, eval=TRUE,fig.height=4,fig.width=8} +#normal usage +#plotQMultiline(slist[1]) + +#modified for this document +p <- plotQMultiline(slist[1],exportplot=F,returnplot=T) +grid.arrange(p$plot[[1]][[1]]) +``` + +`r fc(name="fc_pqm_basic",caption="_Basic \x60plotQMultiline()\x60 plot. One run is spread across the whole page._")` + +The number of individuals per line (samples per line `spl`) and the number of lines per page `lpp` can be controlled separately or together. + +```{r,echo=TRUE, eval=TRUE,fig.height=4,fig.width=8} +#normal usage +#plotQMultiline(slist[1],spl=60) + +#modified for this document +p <- plotQMultiline(slist[1],exportplot=F,returnplot=T,spl=60) +grid.arrange(p$plot[[1]][[1]]) +``` + +`r fc(name="fc_pqm_spl",caption="_Basic \x60plotQMultiline()\x60 plot. One run is spread across the whole page._")` + +When `spl` is fixed to 60, a new line created to accomodate the rest of the samples. + +```{r,echo=TRUE, eval=TRUE,fig.height=4,fig.width=8} +#normal usage +#plotQMultiline(slist[1],lpp=4) + +#modified for this document +p <- plotQMultiline(slist[1],exportplot=F,returnplot=T,lpp=4) +grid.arrange(p$plot[[1]][[1]]) +``` + +`r fc(name="fc_pqm_lpp",caption="_Adjustment of lines per page._")` + +`lpp` can be increased to control aspect ratio of the plot. Decreasing `lpp` such that all samples cannot fit on one page or sometimes fixing `lpp` without adjusting `spl` forces creation of a new page. + +More examples of adjustments. + +```{r,echo=TRUE, eval=FALSE} +# basic usage +plotQMultiline(slist[1]) +plotQMultiline(slist[1:3]) + +# manually modifying samples per line and lines per page +plotQMultiline(slist[1], lpp=10) +plotQMultiline(slist[1], spl=75, lpp=9) +plotQMultiline(slist[1], spl=149, lpp=9) + +# works with combined, aligned or merged files +co <- system.file("files/STRUCTUREpop_K4-combined.txt", package="pophelper") +plotQMultiline(readQ(co),spl=75, lpp=10) + +# change bar width and turn off labels +al <- system.file("files/STRUCTUREpop_K4-combined-aligned.txt", package="pophelper") +plotQMultiline(readQ(al), barsize=1, indlab=F) +# yaxis labels and ticks and modified height and width +plotQMultiline(readQ(al), spl=75, lpp=2, indlab=T, showyaxis=T, showticks=T, height=5, width=20) +# modified spl +me <- system.file("files/STRUCTUREpop_K4-combined-merged.txt", package="pophelper") +plotQMultiline(readQ(me), spl=38, height=8, width=14) +``` + +### Individual labels + +`plotMultiline()` labels individuals numerically with padded zeros (01,02,03..). The number of padded zeros depend on the total number of individuals. Less than 100 individuals start with 01, 02... while hundreds of individuals start with 001, 002.. etc. Labels with padded zeros are better suited for sorting. This is default behaviour `useindlab=F`. Instead of automatically creating the labels, predefined labels can be used from the rownames of input data by specifying `useindlab=T`. Custom labels can be manually added as rownames anytime. + +```{r,echo=TRUE, eval=FALSE} +# get a qlist +list1 <- slist[1] +# show rownames +rownames(list1[[1]]) + +# default labels +plotQMultiline(list1, useindlab=F) + +# read some individual labels +inds <- read.delim(system.file("files/structureindlabels.txt",package="pophelper"), + header=FALSE, stringsAsFactors=FALSE) + +# add labels as rownames to qlist +rownames(list1[[1]]) <- inds$V1 + +# show custom labels. +plotQMultiline(list1,useindlab=T) + +# long ind name +longlabs <- paste0("this_is_a_real_long_label_",inds$V1) +rownames(list1[[1]]) <- longlabs +plotQMultiline(list1, useindlab=T) +plotQMultiline(list1, useindlab=T, spl=75, lpp=4) +plotQMultiline(list1, useindlab=T, spl=75, lpp=4) + +# if all runs are equal length, add indlab to all runs +if(length(unique(sapply(slist,nrow)))==1) slist <- lapply(slist,"rownames<-",inds$V1) +# show row names of all runs and all samples +lapply(slist,rownames) +``` + +Note that runs read in using `readQ()` have rownames 1,2,3.. etc which may not be optimal for sorting by individual labels. For STRUCTURE files with individual labels in them, using `readQ(indlabfromfile=T)` will read them in as rownames. See section `readQ()`. + +Individual labels are displayed on the plot by default when `showindlab=T`. They can be turned off by `showindlab=F`. Note that this only controls the display of individual labels on the plot. The labels are still present in the underlying data and are still in use for sorting etc. + +```{r,echo=TRUE, eval=TRUE,fig.height=4,fig.width=8} +#modified for this document +p1 <- plotQMultiline(slist[1],exportplot=F,returnplot=T,barsize=1) +p2 <- plotQMultiline(slist[1],exportplot=F,returnplot=T,barsize=1,useindlab=T) +grid.arrange(p1$plot[[1]][[1]],p2$plot[[1]][[1]],nrow=2) +``` + +`r fc(name="fc_pqm_useindlab",caption="_Top shows default ind labs and bottom shows ind labs from file._")` + +### Sort individuals + +Similar to `plotQ()`, the individuals can be sorted based on the value of any one of the clusters ('Cluster1'), 'all' or 'label'. The 'all' option produces a sort similar to that in the software STRUCTURE. All clusters are taken into account to sort individuals. When using the name of a cluster, like 'Cluster1', 'Cluster2' etc, all individuals are sorted by value of the specified cluster. + +Using `sortind="label"` sorts individuals by individual labels. The default `useindlab=F`, creates labels numerically in the original order of data but with zero padding. For example, if there are 10 individuals, labels are 01, 02 up to 10. if there are 100 individuals, then labels are 001, 002 up to 100. Zero padding to ensure optimal sorting. When `useindlab=T`, labels are used from rownames of 'qlist' dataframes. They are usually labelled 1,2,3.. if read in using `readQ()`. This can be an issue with sorting by labels `sortind="label"`. For STRUCTURE files with individual labels, they can be read in automatically using `readQ(indlabfromfile=T)`. The rownames of 'qlist' dataframes can also be modified by the user. + +```{r,echo=TRUE, eval=TRUE,fig.height=4,fig.width=8} +#modified for this document +p1 <- plotQMultiline(slist[1],exportplot=F,returnplot=T,lpp=1,barsize=1,useindlab=T) +p2 <- plotQMultiline(slist[1],exportplot=F,returnplot=T,lpp=1,barsize=1,useindlab=T,sortind="Cluster1") +p3 <- plotQMultiline(slist[1],exportplot=F,returnplot=T,lpp=1,barsize=1,useindlab=T,sortind="all") +p4 <- plotQMultiline(slist[1],exportplot=F,returnplot=T,lpp=1,barsize=1,useindlab=T,sortind="label") +grid.arrange(p1$plot[[1]][[1]],p2$plot[[1]][[1]],p3$plot[[1]][[1]],p4$plot[[1]][[1]],nrow=4) +``` + +`r fc(name="fc_pqm_sort",caption="_Various sorting options. Original order, ordered by Cluster1, ordered by all clusters and ordered by individual labels._")` + +### Group labels + +One or more sets of group labels can be added to the bottom of barplots by providing a 'data.frame' object. The number of rows of the 'data.frame' must be equal to the number of individuals. The header of the 'data.frame' is the group label set title. See section 'Group labels' under 'plotQ' for more information about group labels. + +```{r,echo=TRUE, eval=TRUE} +#do not use this command to read local files +threelabset <- read.delim(system.file("files/metadata.txt", package="pophelper"), header=T,stringsAsFactors=F) +twolabset <- threelabset[,2:3] +onelabset <- threelabset[,2,drop=F] +``` + +```{r,echo=TRUE, eval=TRUE,fig.height=3,fig.width=8} +#modified for this document +p1 <- plotQMultiline(slist[1],exportplot=F,returnplot=T,barsize=1,grplab=onelabset) +grid.arrange(p1$plot[[1]][[1]]) +``` + +`r fc(name="fc_pqm_grplab_one",caption="_Using group labels with one label set._")` + +Group labels are displayed on the top of the plot as strip panels by default. A gap is added between individuals of different label groups. By setting `indlabwithgrplab=T`, group labels can be concatenated to the individual labels using separator `indlabsep`. The default label separator is space. For example, individuals 1 and 2 with group labels popA and popB produces labels '1 popA' and '2 popB'. Top strip panels can be turned off using `showgrplab=FALSE`. + +```{r,echo=TRUE, eval=TRUE,fig.height=3,fig.width=8} +#modified for this document +p1 <- plotQMultiline(slist[1],exportplot=F,returnplot=T,barsize=1,grplab=onelabset,indlabwithgrplab=T) +grid.arrange(p1$plot[[1]][[1]]) +``` + +`r fc(name="fc_pqm_grplab_one_con",caption="_Using group labels with group labels concatenated to individual labels._")` + +Multiple group label sets can be added. When using multiple group label sets, argument `selgrp` is used to declare which is the selected/active group. `selgrp` is used for `subsetgrp`, `grpmean` and `ordergrp`. `sortind` will sort within `selgrp`. If labels are in non-contiguous blocks, set `ordergrp=T` to order all labels into contiguous blocks starting with `selgrp`. + +```{r,echo=TRUE, eval=TRUE,fig.height=3,fig.width=8} +#modified for this document +p1 <- plotQMultiline(slist[1],exportplot=F,returnplot=T,barsize=1,grplab=threelabset,ordergrp=T) +grid.arrange(p1$plot[[1]][[1]]) +``` + +`r fc(name="fc_pqm_grplab_multiple",caption="_Using group labels with three label set._")` + +### Subset/reorder groups + +When using group labels, the plot can be subsetted or reordered based on group labels. When sorting individuals, all individuals are sorted by full individual names when using `sortind="labels"`. But when using `sortind="Cluster1"` or `sortind="all"`, individuals are sorted within groups. + +```{r,echo=TRUE, eval=TRUE,fig.height=3,fig.width=8} +#modified for this document +p1 <- plotQMultiline(slist[1],exportplot=F,returnplot=T,barsize=1,grplab=threelabset,ordergrp=T,subsetgrp="Tropical") +grid.arrange(p1$plot[[1]][[1]]) +``` + +`r fc(name="fc_pqm_grplab_subset",caption="_Using group labels with subsetting._")` + +```{r,echo=TRUE, eval=TRUE,fig.height=3,fig.width=8} +#modified for this document +p1 <- plotQMultiline(slist[1],exportplot=F,returnplot=T,barsize=1,grplab=threelabset,ordergrp=T,selgrp="loc",subsetgrp=c("Greece","Brazil")) +grid.arrange(p1$plot[[1]][[1]]) +``` + +`r fc(name="fc_pqm_grplab_reorder",caption="_Using group labels where selected group lab set 'loc' was reordered 'Greece,Brazil'._")` + +More examples of sorting, subsetting and reordering. + +```{r, echo=TRUE, eval=FALSE} +# subsetting groups +plotQMultiline(list1, grplab=threelabset, ordergrp=T, subsetgrp="Tropical") +# change order of groups +plotQMultiline(list1, grplab=threelabset, ordergrp=T, subsetgrp=c("Tropical","Temperate")) + +# subsetting group and sorting individuals +plotQMultiline(list1, grplab=threelabset, ordergrp=T, subsetgrp="Tropical", sortind="Cluster1") +plotQMultiline(list1, grplab=threelabset, ordergrp=T, subsetgrp="Tropical", sortind="all") + +# change order of groups and sorting individuals +plotQMultiline(list1, grplab=threelabset, ordergrp=T, subsetgrp=c("Tropical","Temperate"), sortind="Cluster1") + +# use second group label set for subsetting and sorting +plotQMultiline(list1, grplab=threelabset, selgrp="cat", subsetgrp=c("CatA","CatB"), sortind="all") +``` + +### Title and subtitle + +Title and/or subtitle can be displayed using `showtitle=T` and `showsubtitle=T` respectively. The file name is displayed by default. Custom label can be provided using `titlelab` or `subtitlelab`. If multiple plots are exported, then a character vector of labels equal to number of plots must be provided. Title/subtitle is only displayed in the topmost panel on the first page (in case of multiple pages). + +```{r,echo=TRUE, eval=TRUE,fig.height=3,fig.width=8} +#modified for this document +p1 <- plotQMultiline(slist[1],exportplot=F,returnplot=T,barsize=1,grplab=threelabset,ordergrp=T, + showtitle=T,showsubtitle=T,titlelab="Structure plot", + subtitlelab="Population structure of my organism.") +grid.arrange(p1$plot[[1]][[1]]) +``` + +`r fc(name="fc_pqm_title",caption="_Displaying titles and subtitles._")` + +### Legend + +Legend can be displayed using `showlegend=T`. The file name is displayed by default. The clusters in 'qlist' are by default named Cluster1, Cluster2 etc. The cluster names can be renamed by providing custom labels to argument `legendlab`. The length of `legendlab` must be equal to the max number of clusters in the selected runs. Legend is only displayed in the topmost panel on the first page (in case of multiple pages). + +```{r,echo=TRUE, eval=TRUE,fig.height=3,fig.width=8} +#modified for this document +p1 <- plotQMultiline(slist[1],exportplot=F,returnplot=T,barsize=1,grplab=threelabset,ordergrp=T, + showlegend=T,legendkeysize=8,legendtextsize=10,legendlab=c("group1","group2")) +grid.arrange(p1$plot[[1]][[1]]) +``` + +`r fc(name="fc_pqm_legend",caption="_Displaying Legend._")` + +### Other options + +The cluster colours can be changed by passing a vector of colours to the argument `clustercol`. For examples of colour palettes, see section under `plotQ()`, 'Cluster colours'. + +```{r,echo=TRUE, eval=FALSE} +# change cluster colours +plotQMultiline(list1, useindlab=T, clustercol=c("steelblue","coral","darkorchid3")) + +# customise grplabels and indlabels +plotQMultiline(list1, grplab=onelabset, grplabcol="steelblue", grplabbgcol="slategray1", + indlabcol="darkgreen", indlabangle=45, indlabvjust=1, indlabhjust=1, + height=12, mar=c(0,0,0,0.5)) + +# create plot similar to plotQ +plotQMultiline(list1, useindlab=T, barsize=1, spl=149, lpp=1, height=5) +``` + +![plotqmultiline-colours](plotqmultiline-colours.png) +`r fc(name="fc_plotqmultilinecolours",caption="_Multiline plots with (left) standard colours, (middle) \x60rich.colors()\x60 from \x60gplots\x60 package and (right) \x60brewer.pal(8,'Spectral')\x60 from \x60RColorBrewer\x60 package._")` + +Output file names are created automatically by default using the input 'qlist' names. When number of individuals exceed one page and extra pages are created, incremental numbers are added to the run name like so: -1, -2 etc. Custom file name can be provided to \code{outputfilename}. The number of labels must be equal to the number of input runs. Incremental numbers are still added if extra pages are created. + +The plot can be returned and saved as done in this document. + +```{r,echo=TRUE, eval=TRUE,fig.height=3,fig.width=8} +#modified for this document +p <- plotQMultiline(slist[1],exportplot=F,returnplot=T) +print(p) +``` + +The returned object is a list with slots: plot and data. The plot slot contains a gtable plot object (result from gridExtra::arrangeGrob()) and the data slot contains two slots: qlist and grplab. The qlist contains the processed qlist and the grplab contains processed group labels. In the above example, only the plot slot is filled because only `returnplot=T` was used. The data is also returned if `returndata=T` is used. + +Note that this function can be slow and takes several minutes to run depending on number of individuals and number of files selected. + +## distructExport + +DISTRUCT^7^ is one of the original programs written to generate assignment barplots from a q-matrix. This function generates all output files necessary to run DISTRUCT from a 'qlist'. A directory labelled 'filename-distruct' is created for each input file. Each directory contains the 'filename-indq.txt', 'filename-grpq.txt', 'filename-colours.txt' and 'drawparams'. If grplab is in use, then 'filename-grplabbottom.txt' and/or 'filename-grplabtop.txt' are also created. The DISTRUCT executable can be run in this directory to create a 'filename.ps' postcript vector file. Using `useexe=T` will run the DISTRUCT executable automatically. Remember to cite DISTRUCT^7^ if this option is used. The 'filename.ps' file can be imported into a vector image editing software or seen using a viewer. + +```{r,echo=TRUE, eval=FALSE} +# basic usage +distructExport(slist[1]) +distructExport(slist[1], quiet=T) +# with bottom labels +distructExport(qlist=slist[1], grplabbottom=grp1$V1) +# with group mean +distructExport(slist[1], grpmean=T) +# grayscale colours +distructExport(slist[1], grayscale=T) +# automatically run distruct executable +distructExport(slist[1], useexe=T) + +# TESS files +distructExport(tlist[2]) +# ADMIXTURE files, adjust if plot does not fit on canvas +distructExport(alist[3], indwidth=0.36, xorigin=15) +# CLUMPP files +distructExport(readQ(co)) +distructExport(readQ(al)) +distructExport(readQ(me)) +``` + +![distructexport](destruct-structure.png) +`r fc(name="fc_destruct",caption="_Left: DISTRUCT plot with \x60grpmean=F\x60. Middle: DISTRUCT plot with \x60grpmean=T\x60. Right: DISTRUCT plot with \x60grayscale=T\x60_")` + +The `useexe=T` argument may not work on all OS and systems. + +---- + +# Working with qlists + +The `readQ()` function in `pophelper` is used to read in these different input file types and convert them into an R list object. This list is referred to as a 'qlist'. For those familiar with R, a 'qlist' is just a regular list datatype in R. Each table/file is converted to a 'data.frame' object which is stored in a list. Multiple runs would be a list of lists. + +A schematic data structure of a two run 'qlist' would look like below: + +```{r, eval=FALSE} +$list ++--$list ++ +--$data.frame ++--$list + +--$data.frame +``` + +An example is shown below + +```{r, eval=FALSE,echo=TRUE} +sfiles <- list.files(path=system.file("files/structure",package="pophelper"),full.names=T) +sf <- readQ(files=sfiles[1:2]) +str(sf) +``` + +The function `is.qlist()` can be used to verify if a 'qlist' meets the basic structure to work with `pophelper` functions. `is.qlist()` returns `TRUE` if yes else `FALSE` with warnings. + +```{r, eval=FALSE,echo=TRUE} +is.qlist(sf) +``` + +A 'qlist' can also be create manually or generated in R just like any other list without using the `readQ()` function in `pophelper`. But, note that `evannoMethodStructure()` needs the attributes associated with the 'data.frame'. Other functions currently do not use the attributes. + +Here is a toy 'qlist' object + +```{r, eval=FALSE,echo=TRUE} +# create two data frames +df1 <- data.frame(Cluster1=c(0.2,0.4,0.6,0.2), Cluster2=c(0.8,0.6,0.4,0.8)) +df2 <- data.frame(Cluster1=c(0.3,0.1,0.5,0.6), Cluster2=c(0.7,0.9,0.5,0.4)) + +# one-element qlist +q1 <- list("sample1"=df1) +str(q1) + +# two-element qlist +q2 <- list("sample1"=df1, "sample2"=df2) +str(q2) + +is.qlist(q1) +is.qlist(q2) +``` + +Below are some useful R routines that can be used to subset and filter a 'qlist'. Since 'qlist' is a regular R list, all the below scripts are regular R scripts and nothing specific to this package or this object. + +```{r,echo=TRUE,eval=FALSE} +# Read some STRUCTURE files (do not use this command to read local files) +sfiles <- list.files(path=system.file("files/structure",package="pophelper"), full.names=T) +slist <- readQ(files=sfiles) + +#Subsetting and filtering on an qlist (R list of dataframes). + +# get number of runs +length(slist) +# get names of runs +names(slist) +# get number of clusters in each run +sapply(slist,ncol) +# get number of individuals in each run +sapply(slist,nrow) + +# Filtering runs +# get runs by position +slist[1:2] +slist[c(3,6,7)] +# get a specific run by name +slist[grep("structure_15",names(slist))] +# get a run based on run name starting with a certain string +slist[grep("^structure",names(slist))] +# get a run based on run name ending with a certain string +slist[grep("12$",names(slist))] +# get runs with more than 2 clusters +slist[sapply(slist,function(x) ncol(x)>2)] +# get runs where any individual has probabilities greater than 0.5 in the first cluster +slist[sapply(slist,function(x) any(x[,1]>0.5))] + +# Filtering clusters +# get the first cluster from all runs +lapply(slist,"[",1) +# get clusters by position from all runs. +# Can't use 1:3 because first run contain only 2 clusters. +lapply(slist,"[",1:2) + +# Filtering individuals +# get individuals by row position from all runs +sapply(slist,function(x) x[2:30,]) +# get an individual by name from all runs +sapply(slist,function(x) x[match("I13379",rownames(x)),]) +# get multiple individuals by name from all runs +sapply(slist,function(x) x[match(c("I13379","I12616"),rownames(x)),]) +# or +labs <- c("I13379","I12616") +sapply(slist,function(x) x[match(labs,rownames(x)),]) +# get individuals that start with a certain string from all runs +sapply(slist,function(x) x[grep("^I133",rownames(x)),]) +# get individuals that end with a certain string from all runs +sapply(slist,function(x) x[grep("3$",rownames(x)),]) +# get individuals that contain a certain string from all runs +sapply(slist,function(x) x[grep("388",rownames(x)),]) +# get individuals with probabilities greater than 0.2 +# in the first cluster from all runs +sapply(slist,function(x) x[x[,1]>0.2,]) +``` + +---- + +# Working code + +Here is a list of all functions in a order typical of workflow. The steps are applicable to all run types unless indicated. + +```{r,echo=TRUE, eval=FALSE} + +# collect runs (only for TESS 2.3 output) +collectRunsTess(runsdir=choose.dir()) + +# choose runs +files <- choose.files(multi=TRUE) +qlist <- readQ(files) + +# convert TESS 3 object to qlist (only for TESS 3) +tlist <- readQTess3(tess3object) + +# tabulate runs +df1 <- tabulateQ(qlist) +# summarise runs +df2 <- summariseQ(df1) + +# Evanno method (only for STRUCTURE runs) +evannoMethodStructure(df2, exportplot=T) + +# clumpp export +clumppExport(qlist) +# collect clumpp output +collectClumppOutput(prefix="pop", filetype="aligned") +# plot runs +plotQ(qlist) +plotQ(qlist,imgoutput="join") +# plot multiline +plotQMultiline(qlist[1]) +plotQMultiline(qlist[1], spl=70, lpp=10) + +# or all together +analyseQ(qfiles) +``` + +Many of the functionalities in this package have been implented in the online tool [Pophelper web app](https://www.pophelper.com). For those who prefer a graphical web interface, this may be useful. + +---- + +# References + +1. [Alexander D.H., Novembre, J. and Lange K. (2009). Fast model-based estimation of ancestry in unrelated individuals. Genome Research, 19:1655-1664](http://genome.cshlp.org/content/19/9/1655.long) + +2. [Evanno G., Regnaut S., and Goudet J. (2005). Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Molecular ecology, 14(8), 2611-2620](http://onlinelibrary.wiley.com/doi/10.1111/j.1365-294X.2005.02553.x/abstract) + +3. [Francois O., and Durand E. (2010). Spatially explicit Bayesian clustering models in population genetics. Molecular Ecology Resources, 10(5), 773-784](http://onlinelibrary.wiley.com/doi/10.1111/j.1755-0998.2010.02868.x/abstract) + +4. [Jakobsson M., and Rosenberg N. A. (2007). CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics, 23(14), 1801-1806](http://bioinformatics.oxfordjournals.org/content/23/14/1801.short) + +5. [Pritchard J. K., Stephens M., & Donnelly P. (2000). Inference of population structure using multilocus genotype data. Genetics, 155(2), 945-959](http://www.genetics.org/content/155/2/945.short) + +6. [Raj A., Stephens M., Pritchard J.K. (2014). fastSTRUCTURE: variational inference of population structure in large SNP data sets. Genetics 197, 573-589](http://www.genetics.org/content/early/2014/04/14/genetics.114.164350) + +7. [Rosenberg, Noah A. "DISTRUCT: a program for the graphical display of population structure." Molecular Ecology Notes 4.1 (2004): 137-138.](http://onlinelibrary.wiley.com/doi/10.1046/j.1471-8286.2003.00566.x/abstract) + +8. [Corander, J., Waldmann, P., Marttinen, P., & Sillanpaa, M. J. (2004). BAPS 2: enhanced possibilities for the analysis of genetic population structure. Bioinformatics, 20(15), 2363-2369.](https://academic.oup.com/bioinformatics/article/20/15/2363/233009/BAPS-2-enhanced-possibilities-for-the-analysis-of) + +---- + +# Useful Links + +* [STRUCTURE program](http://web.stanford.edu/group/pritchardlab/structure.html) +* [TESS program](http://membres-timc.imag.fr/Olivier.Francois/tess.html) +* [BAPS program](http://www.helsinki.fi/bsg/software/BAPS/) +* [ADMIXTURE program](https://www.genetics.ucla.edu/software/admixture/) +* [fastSTRUCTURE program](https://rajanil.github.io/fastStructure/) +* [CLUMPP program](http://www.stanford.edu/group/rosenberglab/clumpp.html) +* [Structure Harvester](http://taylor0.biology.ucla.edu/structureHarvester) +* [Adegenet R package](http://adegenet.r-forge.r-project.org/) +* [Distruct program](https://web.stanford.edu/group/rosenberglab/distruct.html) +* [CLUMPAK](http://clumpak.tau.ac.il/) + +---- + +# Compatibility + +The current version of `pophelper` has been tested on the following systems: + ++ Windows 10 64bit, R 3.4.3 + +```{coffee,echo=TRUE, eval=FALSE} +R version 3.4.3 (2017-11-30) +Platform: x86_64-w64-mingw32/x64 (64-bit) +Running under: Windows >= 8 x64 (build 9200) + +Matrix products: default + +locale: +[1] LC_COLLATE=English_United Kingdom.1252 +[2] LC_CTYPE=English_United Kingdom.1252 +[3] LC_MONETARY=English_United Kingdom.1252 +[4] LC_NUMERIC=C +[5] LC_TIME=English_United Kingdom.1252 + +attached base packages: +[1] stats graphics grDevices utils datasets methods base + +other attached packages: +[1] pophelper_2.2.5 ggplot2_2.2.1 Cairo_1.5-9 + +loaded via a namespace (and not attached): + [1] Rcpp_0.12.14 tidyr_0.7.2 grid_3.4.3 plyr_1.8.4 + [5] gtable_0.2.0 magrittr_1.5 scales_0.5.0 pillar_1.0.1 + [9] rlang_0.1.6 lazyeval_0.2.1 tools_3.4.3 glue_1.2.0 +[13] purrr_0.2.4 munsell_0.4.3 compiler_3.4.3 colorspace_1.3-2 +[17] gridExtra_2.3 tibble_1.4.1 +``` + ++ Windows 10 64bit, R 3.3.3 + +```{coffee,echo=TRUE, eval=FALSE} +R version 3.3.3 (2017-03-06) +Platform: x86_64-w64-mingw32/x64 (64-bit) +Running under: Windows >= 8 x64 (build 9200) + +locale: +[1] LC_COLLATE=English_United Kingdom.1252 +[2] LC_CTYPE=English_United Kingdom.1252 +[3] LC_MONETARY=English_United Kingdom.1252 +[4] LC_NUMERIC=C +[5] LC_TIME=English_United Kingdom.1252 + +attached base packages: +[1] stats graphics grDevices utils datasets methods base + +other attached packages: +[1] pophelper_2.2.4 ggplot2_2.2.1 Cairo_1.5-9 testthat_1.0.2 + +loaded via a namespace (and not attached): + [1] Rcpp_0.12.14 tidyr_0.7.2 digest_0.6.12 crayon_1.3.4 + [5] grid_3.3.3 R6_2.2.2 plyr_1.8.4 gtable_0.2.0 + [9] magrittr_1.5 scales_0.5.0 rlang_0.1.4 lazyeval_0.2.1 +[13] rstudioapi_0.7 labeling_0.3 tools_3.3.3 glue_1.2.0 +[17] purrr_0.2.4 munsell_0.4.3 colorspace_1.3-2 tidyselect_0.2.3 +[21] gridExtra_2.3 tibble_1.3.4 +``` + ++ Windows 7 64bit, R 3.4.0 + +DISTRUCT executable worked but unstable. + +```{coffee,echo=TRUE, eval=FALSE} +R version 3.4.0 (2017-04-21) +Platform: x86_64-w64-mingw32/x64 (64-bit) +Running under: Windows 7 x64 (build 7601) Service Pack 1 + +Matrix products: default + +locale: +[1] LC_COLLATE=English_United Kingdom.1252 +[2] LC_CTYPE=English_United Kingdom.1252 +[3] LC_MONETARY=English_United Kingdom.1252 +[4] LC_NUMERIC=C +[5] LC_TIME=English_United Kingdom.1252 + +attached base packages: +[1] stats graphics grDevices utils datasets methods base + +other attached packages: +[1] pophelper_2.2.4 ggplot2_2.2.1 Cairo_1.5-9 testthat_1.0.2 + +loaded via a namespace (and not attached): + [1] Rcpp_0.12.14 compiler_3.4.0 git2r_0.19.0 plyr_1.8.4 + [5] bindr_0.1 tools_3.4.0 digest_0.6.12 memoise_1.1.0 + [9] tibble_1.3.4 gtable_0.2.0 pkgconfig_2.0.1 rlang_0.1.2 +[13] curl_2.8.1 bindrcpp_0.2 gridExtra_2.3 withr_2.0.0 +[17] httr_1.3.0 dplyr_0.7.2 stringr_1.2.0 knitr_1.16 +[21] devtools_1.13.3 grid_3.4.0 tidyselect_0.2.0 glue_1.1.1 +[25] R6_2.2.2 tidyr_0.7.2 purrr_0.2.3 reshape2_1.4.2 +[29] magrittr_1.5 scales_0.5.0 assertthat_0.2.0 colorspace_1.3-2 +[33] labeling_0.3 stringi_1.1.5 lazyeval_0.2.0 munsell_0.4.3 +[37] crayon_1.3.2 +``` + ++ Scientific Linux 6.8 (Carbon) 64bit, R 3.4.0 + +```{coffee,echo=TRUE, eval=FALSE} +R version 3.4.0 (2017-04-21) +Platform: x86_64-pc-linux-gnu (64-bit) +Running under: Scientific Linux release 6.9 (Carbon) + +Matrix products: default +BLAS: /pica/sw/apps/R/x86_64/3.4.0/milou/lib64/R/lib/libRblas.so +LAPACK: /pica/sw/apps/R/x86_64/3.4.0/milou/lib64/R/lib/libRlapack.so + +locale: + [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C + [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 + [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 + [7] LC_PAPER=en_US.UTF-8 LC_NAME=C + [9] LC_ADDRESS=C LC_TELEPHONE=C +[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C + +attached base packages: +[1] stats graphics grDevices utils datasets methods base + +other attached packages: +[1] pophelper_2.2.1 ggplot2_2.2.1 Cairo_1.5-9 testthat_1.0.2 + +loaded via a namespace (and not attached): + [1] Rcpp_0.12.12 bindr_0.1 knitr_1.16 magrittr_1.5 + [5] devtools_1.13.3 munsell_0.4.3 colorspace_1.3-2 R6_2.2.2 + [9] rlang_0.1.1 stringr_1.2.0 dplyr_0.7.2 httr_1.2.1 +[13] plyr_1.8.4 tools_3.4.0 grid_3.4.0 gtable_0.2.0 +[17] git2r_0.19.0 withr_2.0.0 assertthat_0.2.0 lazyeval_0.2.0 +[21] digest_0.6.12 tibble_1.3.3 crayon_1.3.2 bindrcpp_0.2 +[25] gridExtra_2.2.1 reshape2_1.4.2 tidyr_0.6.3 curl_2.8.1 +[29] glue_1.1.1 memoise_1.1.0 labeling_0.3 stringi_1.1.5 +[33] compiler_3.4.0 scales_0.4.1 pkgconfig_2.0.1 +``` + +--- + +# Disclaimer + +The `pophelper` R package is offered free and without warranty of any kind, either expressed or implied. I will not be held liable to you for any damage arising out of the use, modification or inability to use this program. `pophelper` R package can be used, redistributed and/or modified freely for non-commercial purposes subject to the original source being properly cited. Licensed under GPL-3. Please make sure you verify all your results. + +---- + +# Contact + +If you have any comments, suggestions or issues, report on the [Github issues page](https://github.com/royfrancis/pophelper/issues). + +__End of Document.__ diff --git a/vignettes/workflow.png b/vignettes/workflow.png new file mode 100644 index 0000000..82c60aa Binary files /dev/null and b/vignettes/workflow.png differ