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flag_translations.txt
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flag_translations.txt
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Read Filter
A 1 indicates the following statement is true
A 0 indicates the following statement is false
Group 1: Neither Mapped(141, 77) (n)
77
1 Paired in sequencing
0 Proper Pair
1 Self unmapped
1 mate unmapped
0 self strand
0 mate strand
1 self read 1
0 self read 2
141
1 Paired in sequencing
0 Proper Pair
1 Self unmapped
1 mate unmapped
0 self strand
0 mate strand
0 self read 1
1 self read 2
Group 2: One mapped (181, 117, 137, 133, 73, 89, 69, 153) (m)
181
1 Paired in sequencing
0 Proper Pair
1 Self unmapped
0 mate unmapped
1 self strand
1 mate strand
0 self read 1
1 self read 2
117
1 Paired in sequencing
0 Proper Pair
1 Self unmapped
0 mate unmapped
1 self strand
1 mate strand
1 self read 1
0 self read 2
137
1 Paired in sequencing
0 Proper Pair
0 Self unmapped
1 mate unmapped
0 self strand
0 mate strand
0 self read 1
1 self read 2
133
1 Paired in sequencing
0 Proper Pair
1 Self unmapped
0 mate unmapped
0 self strand
0 mate strand
0 self read 1
1 self read 2
73
1 Paired in sequencing
0 Proper Pair
0 Self unmapped
1 mate unmapped
0 self strand
0 mate strand
1 self read 1
0 self read 2
89
1 Paired in sequencing
0 Proper Pair
0 Self unmapped
1 mate unmapped
1 self strand
0 mate strand
1 self read 1
0 self read 2
69
1 Paired in sequencing
0 Proper Pair
1 Self unmapped
0 mate unmapped
0 self strand
0 mate strand
1 self read 1
0 self read 2
153
1 Paired in sequencing
0 Proper Pair
0 Self unmapped
1 mate unmapped
1 self strand
0 mate strand
0 self read 1
1 self read 2
Group 3: Both mapped, non-propper pair (97, 81, 161, 145, 129, 65, 177, 113) (p)
97
1 Paired in sequencing
0 Proper Pair
0 Self unmapped
0 mate unmapped
0 self strand
1 mate strand
1 self read 1
0 self read 2
81
1 Paired in sequencing
0 Proper Pair
0 Self unmapped
0 mate unmapped
1 self strand
0 mate strand
1 self read 1
0 self read 2
161
1 Paired in sequencing
0 Proper Pair
0 Self unmapped
0 mate unmapped
0 self strand
1 mate strand
0 self read 1
1 self read 2
145
1 Paired in sequencing
0 Proper Pair
0 Self unmapped
0 mate unmapped
1 self strand
0 mate strand
0 self read 1
1 self read 2
129
1 Paired in sequencing
0 Proper Pair
0 Self unmapped
0 mate unmapped
0 self strand
0 mate strand
0 self read 1
1 self read 2
65
1 Paired in sequencing
0 Proper Pair
0 Self unmapped
0 mate unmapped
0 self strand
0 mate strand
1 self read 1
0 self read 2
177
1 Paired in sequencing
0 Proper Pair
0 Self unmapped
0 mate unmapped
1 self strand
1 mate strand
0 self read 1
1 self read 2
113
1 Paired in sequencing
0 Proper Pair
0 Self unmapped
0 mate unmapped
1 self strand
1 mate strand
1 self read 1
0 self read 2
Group 4: Both mapped, propper pair (99, 83, 163, 147) (d)
99
1 Paired in sequencing
1 Proper Pair
0 Self unmapped
0 mate unmapped
0 self strand
1 mate strand
1 self read 1
0 self read 2
83
1 Paired in sequencing
1 Proper Pair
0 Self unmapped
0 mate unmapped
1 self strand
0 mate strand
1 self read 1
0 self read 2
163
1 Paired in sequencing
1 Proper Pair
0 Self unmapped
0 mate unmapped
0 self strand
1 mate strand
0 self read 1
1 self read 2
147
1 Paired in sequencing
1 Proper Pair
0 Self unmapped
0 mate unmapped
1 self strand
0 mate strand
0 self read 1
1 self read 2
Group 5: Mapped Single Ended Reads (0, 16) (S)
0
0 Paired in sequencing
0 Proper Pair
0 Self unmapped
0 mate unmapped
0 self strand
0 mate strand
0 self read 1
0 self read 2
16
0 Paired in sequencing
0 Proper Pair
0 Self unmapped
0 mate unmapped
1 self strand
0 mate strand
0 self read 1
0 self read 2
Group 6: Unmapped Single Ended Reads (4) (s)
4
0 Paired in sequencing
0 Proper Pair
1 Self unmapped
0 mate unmapped
0 self strand
0 mate strand
0 self read 1
0 self read 2
--read_type 'dpm' # default for paired end
--read_type 'S' # default for non-paired end
--read_type 'd' # only case for which consensus pairing makes sense
filters
overlap (o)
Ns (n)
Chromosome (C)# Future?
Softclip (s)
cigar (c)
--filter 'os' #default?