Added 43 sequences from San Diego

andersen-lab · Jun 10, 2024 · 42481c0 · 42481c0
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commit 42481c0
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Showing 46 changed files with 101,115 additions and 60 deletions.
diff --git a/consensus_sequences/CA-SEARCH-140112.fasta b/consensus_sequences/CA-SEARCH-140112.fasta
diff --git a/consensus_sequences/CA-SEARCH-140114.fasta b/consensus_sequences/CA-SEARCH-140114.fasta
diff --git a/consensus_sequences/CA-SEARCH-140116.fasta b/consensus_sequences/CA-SEARCH-140116.fasta
diff --git a/consensus_sequences/CA-SEARCH-140117.fasta b/consensus_sequences/CA-SEARCH-140117.fasta
diff --git a/consensus_sequences/CA-SEARCH-140118.fasta b/consensus_sequences/CA-SEARCH-140118.fasta
diff --git a/consensus_sequences/CA-SEARCH-140119.fasta b/consensus_sequences/CA-SEARCH-140119.fasta
diff --git a/consensus_sequences/CA-SEARCH-140120.fasta b/consensus_sequences/CA-SEARCH-140120.fasta
diff --git a/consensus_sequences/CA-SEARCH-140122.fasta b/consensus_sequences/CA-SEARCH-140122.fasta
diff --git a/consensus_sequences/CA-SEARCH-140124.fasta b/consensus_sequences/CA-SEARCH-140124.fasta
diff --git a/consensus_sequences/CA-SEARCH-140125.fasta b/consensus_sequences/CA-SEARCH-140125.fasta
diff --git a/consensus_sequences/CA-SEARCH-140126.fasta b/consensus_sequences/CA-SEARCH-140126.fasta
diff --git a/consensus_sequences/CA-SEARCH-140127.fasta b/consensus_sequences/CA-SEARCH-140127.fasta
diff --git a/consensus_sequences/CA-SEARCH-140128.fasta b/consensus_sequences/CA-SEARCH-140128.fasta
diff --git a/consensus_sequences/CA-SEARCH-140130.fasta b/consensus_sequences/CA-SEARCH-140130.fasta
diff --git a/consensus_sequences/CA-SEARCH-140131.fasta b/consensus_sequences/CA-SEARCH-140131.fasta
diff --git a/consensus_sequences/CA-SEARCH-140132.fasta b/consensus_sequences/CA-SEARCH-140132.fasta
diff --git a/consensus_sequences/CA-SEARCH-140133.fasta b/consensus_sequences/CA-SEARCH-140133.fasta
diff --git a/consensus_sequences/CA-SEARCH-140134.fasta b/consensus_sequences/CA-SEARCH-140134.fasta
diff --git a/consensus_sequences/CA-SEARCH-140137.fasta b/consensus_sequences/CA-SEARCH-140137.fasta
diff --git a/consensus_sequences/CA-SEARCH-140142.fasta b/consensus_sequences/CA-SEARCH-140142.fasta
diff --git a/consensus_sequences/CA-SEARCH-140144.fasta b/consensus_sequences/CA-SEARCH-140144.fasta
diff --git a/consensus_sequences/CA-SEARCH-140146.fasta b/consensus_sequences/CA-SEARCH-140146.fasta
diff --git a/consensus_sequences/CA-SEARCH-140149.fasta b/consensus_sequences/CA-SEARCH-140149.fasta
diff --git a/consensus_sequences/CA-SEARCH-140150.fasta b/consensus_sequences/CA-SEARCH-140150.fasta
diff --git a/consensus_sequences/CA-SEARCH-140151.fasta b/consensus_sequences/CA-SEARCH-140151.fasta
diff --git a/consensus_sequences/CA-SEARCH-140154.fasta b/consensus_sequences/CA-SEARCH-140154.fasta
diff --git a/consensus_sequences/CA-SEARCH-140157.fasta b/consensus_sequences/CA-SEARCH-140157.fasta
diff --git a/consensus_sequences/CA-SEARCH-140159.fasta b/consensus_sequences/CA-SEARCH-140159.fasta
diff --git a/consensus_sequences/CA-SEARCH-140160.fasta b/consensus_sequences/CA-SEARCH-140160.fasta
diff --git a/consensus_sequences/CA-SEARCH-140161.fasta b/consensus_sequences/CA-SEARCH-140161.fasta
diff --git a/consensus_sequences/CA-SEARCH-140162.fasta b/consensus_sequences/CA-SEARCH-140162.fasta
diff --git a/consensus_sequences/CA-SEARCH-140164.fasta b/consensus_sequences/CA-SEARCH-140164.fasta
diff --git a/consensus_sequences/CA-SEARCH-140166.fasta b/consensus_sequences/CA-SEARCH-140166.fasta
diff --git a/consensus_sequences/CA-SEARCH-140167.fasta b/consensus_sequences/CA-SEARCH-140167.fasta
diff --git a/consensus_sequences/CA-SEARCH-140168.fasta b/consensus_sequences/CA-SEARCH-140168.fasta
diff --git a/consensus_sequences/CA-SEARCH-140169.fasta b/consensus_sequences/CA-SEARCH-140169.fasta
diff --git a/consensus_sequences/CA-SEARCH-140170.fasta b/consensus_sequences/CA-SEARCH-140170.fasta
diff --git a/consensus_sequences/CA-SEARCH-140172.fasta b/consensus_sequences/CA-SEARCH-140172.fasta
diff --git a/consensus_sequences/CA-SEARCH-140173.fasta b/consensus_sequences/CA-SEARCH-140173.fasta
diff --git a/consensus_sequences/CA-SEARCH-140174.fasta b/consensus_sequences/CA-SEARCH-140174.fasta
diff --git a/consensus_sequences/CA-SEARCH-140176.fasta b/consensus_sequences/CA-SEARCH-140176.fasta
diff --git a/consensus_sequences/CA-SEARCH-140178.fasta b/consensus_sequences/CA-SEARCH-140178.fasta
diff --git a/consensus_sequences/CA-SEARCH-140179.fasta b/consensus_sequences/CA-SEARCH-140179.fasta
diff --git a/lineage_report.csv b/lineage_report.csv
@@ -25491,23 +25491,66 @@ CA-SEARCH-140107,JN.1.4.7,0.0,,Omicron (BA.2-like),0.92,0.03,scorpio call: Alt a
 CA-SEARCH-140108,XDP,0.0,,Omicron (BA.2-like),0.92,0.03,scorpio call: Alt alleles 57; Ref alleles 2; Amb alleles 0; Oth alleles 3,PUSHER-v1.27,4.3.1,0.3.19,v0.1.12,False,pass,Ambiguous_content:0.02,Usher placements: XDP(1/1); scorpio lineage BA.2 conflicts with inference lineage XDP
 CA-SEARCH-140109,JN.1,0.5,,Omicron (BA.2-like),0.92,0.03,scorpio call: Alt alleles 57; Ref alleles 2; Amb alleles 0; Oth alleles 3,PUSHER-v1.27,4.3.1,0.3.19,v0.1.12,False,pass,Ambiguous_content:0.02,Usher placements: JN.1(2/4) JN.1.15(1/4) JN.1.28(1/4)
 CA-SEARCH-140110,JN.1,0.0,,Omicron (BA.2-like),0.92,0.03,scorpio call: Alt alleles 57; Ref alleles 2; Amb alleles 0; Oth alleles 3,PUSHER-v1.27,4.3.1,0.3.19,v0.1.12,False,pass,Ambiguous_content:0.02,Usher placements: JN.1(1/1)
+CA-SEARCH-140112,JN.1,0.5,,Omicron (BA.2-like),0.92,0.03,scorpio call: Alt alleles 57; Ref alleles 2; Amb alleles 0; Oth alleles 3,PUSHER-v1.27,4.3.1,0.3.19,v0.1.12,False,pass,Ambiguous_content:0.02,Usher placements: JN.1(1/2) JN.1.3(1/2)
+CA-SEARCH-140114,JN.1.13.1,0.0,,Omicron (BA.2-like),0.89,0.03,scorpio call: Alt alleles 55; Ref alleles 2; Amb alleles 2; Oth alleles 3,PUSHER-v1.27,4.3.1,0.3.19,v0.1.12,False,pass,Ambiguous_content:0.02,Usher placements: JN.1.13.1(1/1)
 CA-SEARCH-140115,JN.1.26,0.0,,Omicron (BA.2-like),0.92,0.03,scorpio call: Alt alleles 57; Ref alleles 2; Amb alleles 0; Oth alleles 3,PUSHER-v1.27,4.3.1,0.3.19,v0.1.12,False,pass,Ambiguous_content:0.02,Usher placements: JN.1.26(1/1)
+CA-SEARCH-140116,JN.1.4.7,0.0,,Omicron (BA.2-like),0.92,0.03,scorpio call: Alt alleles 57; Ref alleles 2; Amb alleles 0; Oth alleles 3,PANGO-v1.27,4.3.1,0.3.19,v0.1.12,True,pass,Ambiguous_content:0.02,Assigned from designation hash.
+CA-SEARCH-140117,JN.1,0.0,,Omicron (BA.2-like),0.92,0.03,scorpio call: Alt alleles 57; Ref alleles 2; Amb alleles 0; Oth alleles 3,PUSHER-v1.27,4.3.1,0.3.19,v0.1.12,False,pass,Ambiguous_content:0.02,Usher placements: JN.1(1/1)
+CA-SEARCH-140118,JN.1.18,0.5,,Omicron (BA.2-like),0.92,0.03,scorpio call: Alt alleles 57; Ref alleles 2; Amb alleles 0; Oth alleles 3,PUSHER-v1.27,4.3.1,0.3.19,v0.1.12,False,pass,Ambiguous_content:0.02,Usher placements: JN.1.16.1(1/2) JN.1.18(1/2)
+CA-SEARCH-140119,JN.1.4,0.0,,Omicron (BA.2-like),0.92,0.03,scorpio call: Alt alleles 57; Ref alleles 2; Amb alleles 0; Oth alleles 3,PUSHER-v1.27,4.3.1,0.3.19,v0.1.12,False,pass,Ambiguous_content:0.02,Usher placements: JN.1.4(1/1)
+CA-SEARCH-140120,JN.1.4,0.0,,Omicron (BA.2-like),0.92,0.03,scorpio call: Alt alleles 57; Ref alleles 2; Amb alleles 0; Oth alleles 3,PUSHER-v1.27,4.3.1,0.3.19,v0.1.12,False,pass,Ambiguous_content:0.02,Usher placements: JN.1.4(1/1)
 CA-SEARCH-140121,XDK.1,0.0,,Omicron (BA.2-like),0.89,0.05,scorpio call: Alt alleles 55; Ref alleles 3; Amb alleles 0; Oth alleles 4,PUSHER-v1.27,4.3.1,0.3.19,v0.1.12,False,pass,Ambiguous_content:0.02,Usher placements: XDK.1(1/1); scorpio lineage BA.2 conflicts with inference lineage XDK.1
+CA-SEARCH-140122,XDP,0.0,,Omicron (BA.2-like),0.92,0.03,scorpio call: Alt alleles 57; Ref alleles 2; Amb alleles 0; Oth alleles 3,PUSHER-v1.27,4.3.1,0.3.19,v0.1.12,False,pass,Ambiguous_content:0.02,Usher placements: XDP(1/1); scorpio lineage BA.2 conflicts with inference lineage XDP
 CA-SEARCH-140123,JN.1.8.1,0.0,,Omicron (BA.2-like),0.9,0.03,scorpio call: Alt alleles 56; Ref alleles 2; Amb alleles 1; Oth alleles 3,PUSHER-v1.27,4.3.1,0.3.19,v0.1.12,False,pass,Ambiguous_content:0.02,Usher placements: JN.1.8.1(1/1)
+CA-SEARCH-140124,JN.1.4,0.0,,Omicron (BA.2-like),0.92,0.03,scorpio call: Alt alleles 57; Ref alleles 2; Amb alleles 2; Oth alleles 1,PUSHER-v1.27,4.3.1,0.3.19,v0.1.12,False,pass,Ambiguous_content:0.03,Usher placements: JN.1.4(1/1)
+CA-SEARCH-140125,JN.1.4.7,0.0,,Omicron (BA.2-like),0.92,0.03,scorpio call: Alt alleles 57; Ref alleles 2; Amb alleles 0; Oth alleles 3,PUSHER-v1.27,4.3.1,0.3.19,v0.1.12,False,pass,Ambiguous_content:0.02,Usher placements: JN.1.4.7(1/1)
+CA-SEARCH-140126,JN.1.32,0.0,,Omicron (BA.2-like),0.92,0.03,scorpio call: Alt alleles 57; Ref alleles 2; Amb alleles 0; Oth alleles 3,PUSHER-v1.27,4.3.1,0.3.19,v0.1.12,False,pass,Ambiguous_content:0.02,Usher placements: JN.1.32(1/1)
+CA-SEARCH-140127,JN.1.4.5,0.0,,Omicron (BA.2-like),0.92,0.03,scorpio call: Alt alleles 57; Ref alleles 2; Amb alleles 0; Oth alleles 3,PUSHER-v1.27,4.3.1,0.3.19,v0.1.12,False,pass,Ambiguous_content:0.02,Usher placements: JN.1.4.5(1/1)
+CA-SEARCH-140128,JN.1.4,0.0,,Omicron (BA.2-like),0.92,0.03,scorpio call: Alt alleles 57; Ref alleles 2; Amb alleles 2; Oth alleles 1,PUSHER-v1.27,4.3.1,0.3.19,v0.1.12,False,pass,Ambiguous_content:0.03,Usher placements: JN.1.4(1/1)
+CA-SEARCH-140130,JN.1.4.5,0.0,,Omicron (BA.2-like),0.92,0.03,scorpio call: Alt alleles 57; Ref alleles 2; Amb alleles 0; Oth alleles 3,PUSHER-v1.27,4.3.1,0.3.19,v0.1.12,False,pass,Ambiguous_content:0.02,Usher placements: JN.1.4.5(1/1)
+CA-SEARCH-140131,JN.1.4,0.0,,Omicron (BA.2-like),0.92,0.03,scorpio call: Alt alleles 57; Ref alleles 2; Amb alleles 0; Oth alleles 3,PUSHER-v1.27,4.3.1,0.3.19,v0.1.12,False,pass,Ambiguous_content:0.02,Usher placements: JN.1.4(1/1)
+CA-SEARCH-140132,JN.1,0.0,,Omicron (BA.2-like),0.92,0.03,scorpio call: Alt alleles 57; Ref alleles 2; Amb alleles 0; Oth alleles 3,PUSHER-v1.27,4.3.1,0.3.19,v0.1.12,False,pass,Ambiguous_content:0.02,Usher placements: JN.1(1/1)
+CA-SEARCH-140133,JN.1,0.0,,Omicron (BA.2-like),0.92,0.03,scorpio call: Alt alleles 57; Ref alleles 2; Amb alleles 0; Oth alleles 3,PUSHER-v1.27,4.3.1,0.3.19,v0.1.12,False,pass,Ambiguous_content:0.02,Usher placements: JN.1(1/1)
+CA-SEARCH-140134,JN.1.39,0.0,,Omicron (BA.2-like),0.92,0.03,scorpio call: Alt alleles 57; Ref alleles 2; Amb alleles 0; Oth alleles 3,PUSHER-v1.27,4.3.1,0.3.19,v0.1.12,False,pass,Ambiguous_content:0.02,Usher placements: JN.1.39(1/1)
 CA-SEARCH-140136,JN.1,0.0,,Omicron (BA.2-like),0.92,0.03,scorpio call: Alt alleles 57; Ref alleles 2; Amb alleles 0; Oth alleles 3,PUSHER-v1.27,4.3.1,0.3.19,v0.1.12,False,pass,Ambiguous_content:0.02,Usher placements: JN.1(1/1)
+CA-SEARCH-140137,JN.1.39,0.0,,Omicron (BA.2-like),0.92,0.03,scorpio call: Alt alleles 57; Ref alleles 2; Amb alleles 0; Oth alleles 3,PUSHER-v1.27,4.3.1,0.3.19,v0.1.12,False,pass,Ambiguous_content:0.02,Usher placements: JN.1.39(1/1)
 CA-SEARCH-140138,XDK.1,0.0,,Omicron (BA.2-like),0.89,0.05,scorpio call: Alt alleles 55; Ref alleles 3; Amb alleles 0; Oth alleles 4,PUSHER-v1.27,4.3.1,0.3.19,v0.1.12,False,pass,Ambiguous_content:0.02,Usher placements: XDK.1(1/1); scorpio lineage BA.2 conflicts with inference lineage XDK.1
 CA-SEARCH-140139,JN.1.4,0.5,,Omicron (BA.2-like),0.9,0.03,scorpio call: Alt alleles 56; Ref alleles 2; Amb alleles 1; Oth alleles 3,PUSHER-v1.27,4.3.1,0.3.19,v0.1.12,False,pass,Ambiguous_content:0.02,Usher placements: JN.1.4(1/2) JN.1.4.6(1/2)
 CA-SEARCH-140140,JN.1,0.0,,Omicron (BA.2-like),0.92,0.03,scorpio call: Alt alleles 57; Ref alleles 2; Amb alleles 0; Oth alleles 3,PUSHER-v1.27,4.3.1,0.3.19,v0.1.12,False,pass,Ambiguous_content:0.02,Usher placements: JN.1(1/1)
+CA-SEARCH-140142,JN.1.16,0.0,,Omicron (BA.2-like),0.92,0.03,scorpio call: Alt alleles 57; Ref alleles 2; Amb alleles 0; Oth alleles 3,PUSHER-v1.27,4.3.1,0.3.19,v0.1.12,False,pass,Ambiguous_content:0.02,Usher placements: JN.1.16(1/1)
 CA-SEARCH-140143,KP.2.2,0.0,,Omicron (BA.2-like),0.92,0.03,scorpio call: Alt alleles 57; Ref alleles 2; Amb alleles 0; Oth alleles 3,PUSHER-v1.27,4.3.1,0.3.19,v0.1.12,False,pass,Ambiguous_content:0.02,Usher placements: KP.2.2(1/1)
+CA-SEARCH-140144,KV.2,0.0,,Omicron (BA.2-like),0.92,0.03,scorpio call: Alt alleles 57; Ref alleles 2; Amb alleles 0; Oth alleles 3,PUSHER-v1.27,4.3.1,0.3.19,v0.1.12,False,pass,Ambiguous_content:0.02,Usher placements: KV.2(2/2)
 CA-SEARCH-140145,JN.1.4,0.0,,Omicron (BA.2-like),0.9,0.03,scorpio call: Alt alleles 56; Ref alleles 2; Amb alleles 0; Oth alleles 4,PUSHER-v1.27,4.3.1,0.3.19,v0.1.12,False,pass,Ambiguous_content:0.02,Usher placements: JN.1.4(1/1)
+CA-SEARCH-140146,JN.1.16,0.0,,Omicron (BA.2-like),0.92,0.03,scorpio call: Alt alleles 57; Ref alleles 2; Amb alleles 0; Oth alleles 3,PUSHER-v1.27,4.3.1,0.3.19,v0.1.12,False,pass,Ambiguous_content:0.02,Usher placements: JN.1.16(1/1)
 CA-SEARCH-140147,JN.1.7,0.0,,Omicron (BA.2-like),0.92,0.03,scorpio call: Alt alleles 57; Ref alleles 2; Amb alleles 0; Oth alleles 3,PUSHER-v1.27,4.3.1,0.3.19,v0.1.12,False,pass,Ambiguous_content:0.02,Usher placements: JN.1.7(1/1)
 CA-SEARCH-140148,JN.1.4,0.0,,Omicron (BA.2-like),0.9,0.03,scorpio call: Alt alleles 56; Ref alleles 2; Amb alleles 1; Oth alleles 3,PUSHER-v1.27,4.3.1,0.3.19,v0.1.12,False,pass,Ambiguous_content:0.02,Usher placements: JN.1.4(1/1)
+CA-SEARCH-140149,JN.1.4,0.5,,Omicron (BA.2-like),0.9,0.03,scorpio call: Alt alleles 56; Ref alleles 2; Amb alleles 1; Oth alleles 3,PUSHER-v1.27,4.3.1,0.3.19,v0.1.12,False,pass,Ambiguous_content:0.02,Usher placements: JN.1.4(1/2) JN.1.4.6(1/2)
+CA-SEARCH-140150,JN.1.1,0.0,,Omicron (BA.2-like),0.92,0.03,scorpio call: Alt alleles 57; Ref alleles 2; Amb alleles 0; Oth alleles 3,PUSHER-v1.27,4.3.1,0.3.19,v0.1.12,False,pass,Ambiguous_content:0.02,Usher placements: JN.1.1(1/1)
+CA-SEARCH-140151,JN.1.4.5,0.0,,Omicron (BA.2-like),0.92,0.03,scorpio call: Alt alleles 57; Ref alleles 2; Amb alleles 0; Oth alleles 3,PUSHER-v1.27,4.3.1,0.3.19,v0.1.12,False,pass,Ambiguous_content:0.02,Usher placements: JN.1.4.5(1/1)
 CA-SEARCH-140152,JN.1.4,0.0,,Omicron (BA.2-like),0.92,0.03,scorpio call: Alt alleles 57; Ref alleles 2; Amb alleles 0; Oth alleles 3,PUSHER-v1.27,4.3.1,0.3.19,v0.1.12,False,pass,Ambiguous_content:0.02,Usher placements: JN.1.4(1/1)
 CA-SEARCH-140153,JN.1,0.0,,Omicron (BA.2-like),0.92,0.03,scorpio call: Alt alleles 57; Ref alleles 2; Amb alleles 0; Oth alleles 3,PUSHER-v1.27,4.3.1,0.3.19,v0.1.12,False,pass,Ambiguous_content:0.02,Usher placements: JN.1(1/1)
+CA-SEARCH-140154,JN.1.4,0.0,,Omicron (BA.2-like),0.92,0.03,scorpio call: Alt alleles 57; Ref alleles 2; Amb alleles 0; Oth alleles 3,PUSHER-v1.27,4.3.1,0.3.19,v0.1.12,False,pass,Ambiguous_content:0.02,Usher placements: JN.1.4(1/1)
 CA-SEARCH-140155,JN.1.4,0.5,,Omicron (BA.2-like),0.92,0.03,scorpio call: Alt alleles 57; Ref alleles 2; Amb alleles 0; Oth alleles 3,PUSHER-v1.27,4.3.1,0.3.19,v0.1.12,False,pass,Ambiguous_content:0.02,Usher placements: JN.1.4(1/2) JN.1.4.5(1/2)
+CA-SEARCH-140157,JN.1.46,0.0,,Omicron (BA.2-like),0.92,0.03,scorpio call: Alt alleles 57; Ref alleles 2; Amb alleles 0; Oth alleles 3,PUSHER-v1.27,4.3.1,0.3.19,v0.1.12,False,pass,Ambiguous_content:0.02,Usher placements: JN.1.46(1/1)
+CA-SEARCH-140159,JN.1.4,0.0,,Omicron (BA.2-like),0.92,0.03,scorpio call: Alt alleles 57; Ref alleles 2; Amb alleles 0; Oth alleles 3,PUSHER-v1.27,4.3.1,0.3.19,v0.1.12,False,pass,Ambiguous_content:0.02,Usher placements: JN.1.4(1/1)
+CA-SEARCH-140160,JN.1.4,0.0,,Omicron (BA.2-like),0.92,0.03,scorpio call: Alt alleles 57; Ref alleles 2; Amb alleles 0; Oth alleles 3,PUSHER-v1.27,4.3.1,0.3.19,v0.1.12,False,pass,Ambiguous_content:0.02,Usher placements: JN.1.4(1/1)
+CA-SEARCH-140161,KP.2,0.0,,Omicron (BA.2-like),0.9,0.03,scorpio call: Alt alleles 56; Ref alleles 2; Amb alleles 0; Oth alleles 4,PUSHER-v1.27,4.3.1,0.3.19,v0.1.12,False,pass,Ambiguous_content:0.02,Usher placements: KP.2(1/1)
+CA-SEARCH-140162,XDK.1,0.0,,Omicron (BA.2-like),0.9,0.03,scorpio call: Alt alleles 56; Ref alleles 2; Amb alleles 0; Oth alleles 4,PUSHER-v1.27,4.3.1,0.3.19,v0.1.12,False,pass,Ambiguous_content:0.02,Usher placements: XDK.1(1/1); scorpio lineage BA.2 conflicts with inference lineage XDK.1
 CA-SEARCH-140163,JN.1,0.5,,Omicron (BA.2-like),0.92,0.03,scorpio call: Alt alleles 57; Ref alleles 2; Amb alleles 0; Oth alleles 3,PUSHER-v1.27,4.3.1,0.3.19,v0.1.12,False,pass,Ambiguous_content:0.02,Usher placements: JN.1(1/2) JN.1.3(1/2)
+CA-SEARCH-140164,JN.1,0.0,,Omicron (BA.2-like),0.92,0.03,scorpio call: Alt alleles 57; Ref alleles 2; Amb alleles 1; Oth alleles 2,PUSHER-v1.27,4.3.1,0.3.19,v0.1.12,False,pass,Ambiguous_content:0.02,Usher placements: JN.1(1/1)
+CA-SEARCH-140166,JN.1,0.0,,Omicron (BA.2-like),0.92,0.03,scorpio call: Alt alleles 57; Ref alleles 2; Amb alleles 0; Oth alleles 3,PUSHER-v1.27,4.3.1,0.3.19,v0.1.12,False,pass,Ambiguous_content:0.02,Usher placements: JN.1(1/1)
+CA-SEARCH-140167,JN.1.4.5,0.0,,Omicron (BA.2-like),0.92,0.03,scorpio call: Alt alleles 57; Ref alleles 2; Amb alleles 0; Oth alleles 3,PUSHER-v1.27,4.3.1,0.3.19,v0.1.12,False,pass,Ambiguous_content:0.02,Usher placements: JN.1.4.5(1/1)
+CA-SEARCH-140168,XDV,0.0,,Omicron (BA.2-like),0.94,0.02,scorpio call: Alt alleles 58; Ref alleles 1; Amb alleles 0; Oth alleles 3,PUSHER-v1.27,4.3.1,0.3.19,v0.1.12,False,pass,Ambiguous_content:0.02,Usher placements: XDV(1/1); scorpio lineage BA.2 conflicts with inference lineage XDV
+CA-SEARCH-140169,JN.1,0.5,,Omicron (BA.2-like),0.9,0.03,scorpio call: Alt alleles 56; Ref alleles 2; Amb alleles 1; Oth alleles 3,PUSHER-v1.27,4.3.1,0.3.19,v0.1.12,False,pass,Ambiguous_content:0.03,Usher placements: JN.1(1/2) JN.1.3(1/2)
+CA-SEARCH-140170,JN.1,0.5,,Omicron (BA.2-like),0.92,0.03,scorpio call: Alt alleles 57; Ref alleles 2; Amb alleles 0; Oth alleles 3,PUSHER-v1.27,4.3.1,0.3.19,v0.1.12,False,pass,Ambiguous_content:0.02,Usher placements: JN.1(1/2) JN.1.3(1/2)
 CA-SEARCH-140171,JN.1.18,0.5,,Omicron (BA.2-like),0.92,0.03,scorpio call: Alt alleles 57; Ref alleles 2; Amb alleles 0; Oth alleles 3,PUSHER-v1.27,4.3.1,0.3.19,v0.1.12,False,pass,Ambiguous_content:0.02,Usher placements: JN.1.16.1(1/2) JN.1.18(1/2)
+CA-SEARCH-140172,XDP.1,0.0,,Omicron (BA.2-like),0.92,0.03,scorpio call: Alt alleles 57; Ref alleles 2; Amb alleles 0; Oth alleles 3,PUSHER-v1.27,4.3.1,0.3.19,v0.1.12,False,pass,Ambiguous_content:0.02,Usher placements: XDP.1(1/1); scorpio lineage BA.2 conflicts with inference lineage XDP.1
+CA-SEARCH-140173,JN.1.7,0.0,,Omicron (BA.2-like),0.92,0.03,scorpio call: Alt alleles 57; Ref alleles 2; Amb alleles 0; Oth alleles 3,PUSHER-v1.27,4.3.1,0.3.19,v0.1.12,False,pass,Ambiguous_content:0.02,Usher placements: JN.1.7(1/1)
+CA-SEARCH-140174,KP.1.1,0.0,,Omicron (BA.2-like),0.9,0.03,scorpio call: Alt alleles 56; Ref alleles 2; Amb alleles 1; Oth alleles 3,PUSHER-v1.27,4.3.1,0.3.19,v0.1.12,False,pass,Ambiguous_content:0.02,Usher placements: KP.1.1(1/1)
 CA-SEARCH-140175,JN.1.18,0.5,,Omicron (BA.2-like),0.92,0.03,scorpio call: Alt alleles 57; Ref alleles 2; Amb alleles 0; Oth alleles 3,PUSHER-v1.27,4.3.1,0.3.19,v0.1.12,False,pass,Ambiguous_content:0.02,Usher placements: JN.1.16.1(1/2) JN.1.18(1/2)
+CA-SEARCH-140176,JN.1.4.3,0.0,,Omicron (BA.2-like),0.92,0.03,scorpio call: Alt alleles 57; Ref alleles 2; Amb alleles 0; Oth alleles 3,PUSHER-v1.27,4.3.1,0.3.19,v0.1.12,False,pass,Ambiguous_content:0.02,Usher placements: JN.1.4.3(1/1)
+CA-SEARCH-140178,JN.1.32,0.0,,Omicron (BA.2-like),0.92,0.03,scorpio call: Alt alleles 57; Ref alleles 2; Amb alleles 0; Oth alleles 3,PUSHER-v1.27,4.3.1,0.3.19,v0.1.12,False,pass,Ambiguous_content:0.02,Usher placements: JN.1.32(1/1)
+CA-SEARCH-140179,JN.1.7.1,0.0,,Omicron (BA.2-like),0.92,0.03,scorpio call: Alt alleles 57; Ref alleles 2; Amb alleles 0; Oth alleles 3,PANGO-v1.27,4.3.1,0.3.19,v0.1.12,True,pass,Ambiguous_content:0.02,Assigned from designation hash.
 CA-SEARCH-18104,B.1.429,0.0,,Epsilon (B.1.429-like),1.0,0.0,scorpio call: Alt alleles 14; Ref alleles 0; Amb alleles 0; Oth alleles 0,PUSHER-v1.27,4.3.1,0.3.19,v0.1.12,False,pass,Ambiguous_content:0.02,Usher placements: B.1.429(1/1)
 CA-SEARCH-18105,B.1.1.7,0.0,,Alpha (B.1.1.7-like),0.96,0.04,scorpio call: Alt alleles 22; Ref alleles 1; Amb alleles 0; Oth alleles 0,PUSHER-v1.27,4.3.1,0.3.19,v0.1.12,False,pass,Ambiguous_content:0.02,Usher placements: B.1.1.7(1/1)
 CA-SEARCH-18106,B.1.427,0.0,,Epsilon (B.1.427-like),0.92,0.0,scorpio call: Alt alleles 12; Ref alleles 0; Amb alleles 1; Oth alleles 0,PUSHER-v1.27,4.3.1,0.3.19,v0.1.12,False,pass,Ambiguous_content:0.02,Usher placements: B.1.427(1/1)