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view test-data/input.vcf @ 1:7a54ac4976d0 draft
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| author | elixir-it |
|---|---|
| date | Mon, 01 Oct 2018 11:21:05 -0400 |
| parents | 786c9295d2be |
| children |
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##fileformat=VCFv4.1 ##fileDate=20180622 ##phasing=none ##reference=file:///export/galaxy/database/files/000/dataset_3.dat ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> ##FORMAT=<ID=IGT,Number=1,Type=String,Description="Genotype when called independently (only filled if called in joint prior mode)"> ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Total read depth"> ##FORMAT=<ID=DP4,Number=4,Type=Integer,Description="# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases"> ##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description="Occurrence count for each base at this site (A,C,G,T)"> ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype quality"> ##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description="Joint genotype quality (only filled if called in join prior mode)"> ##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description="Variant allele quality"> ##FORMAT=<ID=BQ,Number=.,Type=Integer,Description="Average base quality"> ##FORMAT=<ID=MQ,Number=1,Type=Integer,Description="Average mapping quality across all reads"> ##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description="Average mapping quality for each allele present in the genotype"> ##FORMAT=<ID=SS,Number=1,Type=Integer,Description="Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown"> ##FORMAT=<ID=SSC,Number=1,Type=Integer,Description="Somatic Score"> #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NORMAL TUMOR chr1 133129 . G A . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:376:187,124,29,36:65,0,311,0:161:.:0:32:5:4:0:. 0/1:0/1:907:361,249,237,60:296,1,610,0:214:.:214:29,32:24:22,25:2:218 chr1 133160 . G A . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:351:158,147,16,30:46,0,305,0:145:.:0:33:13:12:0:. 0/1:0/1:871:370,354,61,86:145,0,724,2:30:.:30:32,33:35:36,35:2:57 chr1 133483 . G T . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:388:203,111,46,28:2,0,314,72:1:.:0:29:1:0:0:. 0/1:0/1:1101:577,245,160,119:1,0,822,278:41:.:41:29,30:11:10,14:2:71 chr1 1250144 . T C . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:10:4,6,0,0:0,0,0,10:57:.:0:29:22:22:0:. 0/1:0/1:18:9,6,0,3:0,3,0,15:6:.:6:33,29:52:35,55:2:28 chr1 2280653 . A G . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:55:24,16,2,13:40,0,15,0:55:.:0:25:15:19:0:. 0/1:0/1:70:15,19,8,28:34,0,36,0:118:.:118:25,30:28:41,15:2:28 chr1 2280736 . A G . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:8:2,6,0,0:8,0,0,0:51:.:0:31:18:18:0:. 0/1:0/1:8:2,3,0,3:5,0,3,0:19:.:19:27,31:25:20,34:2:24 chr1 11522650 . G A . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:6:4,2,0,0:0,0,6,0:18:.:0:30:1:1:0:. 1/1:1/1:2:0,1,0,1:1,0,1,0:3:.:3:33:35:40:2:18 chr1 57636120 . C A . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:34:14,12,8,0:8,26,0,0:55:.:0:21:54:60:0:. 0/1:0/1:44:16,12,16,0:16,28,0,0:1:.:1:14,21:56:51,59:2:25 chr1 72135390 . C A . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:53:36,7,0,10:10,43,0,0:53:.:0:24:27:26:0:. 0/1:0/1:90:60,4,3,23:26,64,0,0:57:.:57:23,24:51:45,54:2:26 chr1 116600445 . G A . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:24:0,22,0,2:2,0,22,0:55:.:0:33:32:34:0:. 0/1:0/1:30:0,20,0,10:10,0,20,0:42:.:42:32,33:48:27,58:2:28 chr1 116600446 . A G . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:22:0,22,0,0:22,0,0,0:93:.:0:30:34:34:0:. 0/1:0/1:29:0,20,0,9:20,0,9,0:28:.:28:30,32:48:58,25:2:55 chr1 125167865 . T C . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:4:3,1,0,0:0,0,0,4:14:.:0:29:0:0:0:. 1/1:1/1:1:0,0,0,1:0,1,0,0:22:.:22:34:22:22:2:16 chr1 143192820 . G A . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:6:4,2,0,0:0,0,6,0:18:.:0:30:0:0:0:. 1/1:1/1:2:0,1,1,0:1,0,1,0:26:.:26:32:20:40:2:19 chr1 143192836 . C T . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:6:4,2,0,0:0,6,0,0:18:.:0:30:0:0:0:. 1/1:1/1:2:0,1,1,0:0,1,0,1:25:.:25:31:20:40:2:18 chr1 147517696 . C T . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:6:0,6,0,0:0,6,0,0:45:.:0:33:60:60:0:. 0/1:0/1:9:1,4,1,3:0,5,0,4:63:.:63:33,32:60:60,60:2:18 chr1 148359371 . C A . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:8:8,0,0,0:0,8,0,0:51:.:0:32:38:38:0:. 0/1:0/1:15:12,0,0,3:3,12,0,0:3:.:3:29,33:55:60,54:2:23 chr1 149390829 . C A . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:33:0,12,3,18:20,12,0,1:2:.:0:27:3:8:0:. 0/1:0/1:39:1,22,1,15:16,23,0,0:20:.:20:31,25:33:12,48:2:25 chr1 151171163 . A G . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:2:0,2,0,0:2,0,0,0:33:.:0:33:60:60:0:. 1/1:1/1:1:0,0,0,1:0,0,1,0:30:.:30:32:60:60:2:16 chr1 152303901 . C G . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:563:229,216,52,66:1,445,117,0:11:.:0:32:0:0:0:. 0/1:0/1:2572:939,1036,377,220:2,1975,595,0:93:.:93:32,32:15:16,12:2:120 chr1 152303983 . C T . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:614:273,243,43,55:0,516,0,98:73:.:0:33:3:3:0:. 0/1:0/1:2851:1013,1052,312,474:0,2065,0,786:228:.:228:33,31:28:29,27:2:247 chr1 152304107 . C G . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:394:195,173,13,13:0,368,26,0:255:.:0:33:18:20:0:. 0/1:0/1:1708:624,733,200,151:0,1357,351,0:155:.:155:33,32:41:47,18:2:182 chr1 152304122 . G A . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:389:186,184,5,14:19,0,370,0:255:.:0:29:23:25:0:. 0/1:0/1:1605:602,679,166,158:324,0,1281,0:114:.:114:30,29:47:16,55:2:141 chr1 152304150 . G C . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:433:164,184,41,44:0,85,348,0:218:.:0:30:24:29:0:. 0/1:0/1:1470:533,682,135,120:0,255,1215,0:116:.:116:33,30:53:22,59:2:143 chr1 152306079 . T C . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:578:205,203,83,87:0,170,0,408:2:.:0:31:0:0:0:. 0/1:0/1:3958:1466,1740,451,301:0,750,2,3206:203:.:203:33,31:14:19,12:2:63 chr1 152306338 . C T . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:411:137,165,68,41:0,302,0,109:135:.:0:30:22:27:0:. 0/1:0/1:4985:2106,2070,462,347:3,4176,2,804:228:.:228:30,32:50:54,31:2:108 chr1 152306380 . T G . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:487:206,225,32,24:0,0,56,431:203:.:0:31:10:9:0:. 0/1:0/1:5056:2043,2014,517,482:1,0,998,4057:228:.:228:29,32:36:39,35:2:228 chr1 152307694 . C G . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:537:220,192,50,75:0,412,125,0:57:.:0:33:1:1:0:. 0/1:0/1:2374:820,645,307,602:0,1465,909,0:228:.:228:32,31:22:19,27:2:145 chr1 152307789 . C G . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:574:227,204,65,78:1,431,142,0:7:.:0:32:0:0:0:. 0/1:0/1:2091:717,763,159,452:2,1480,609,0:228:.:228:32,31:14:13,17:2:111 chr1 152307871 . C T . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:445:209,207,16,13:2,416,0,27:80:.:0:33:6:6:0:. 0/1:0/1:1915:846,652,315,102:1,1498,1,415:228:.:228:33,30:28:29,23:2:250 chr1 152307896 . G A . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:367:184,183,0,0:0,0,367,0:114:.:0:29:9:9:0:. 0/1:0/1:1801:593,587,615,6:620,0,1180,1:228:.:228:31,29:34:26,39:2:250 chr1 152307995 . C G . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:429:173,167,41,48:0,340,89,0:135:.:0:33:15:17:0:. 0/1:0/1:3096:1236,990,353,517:1,2226,869,0:228:.:228:33,32:44:49,34:2:108 chr1 152308083 . T C . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:422:192,182,18,30:2,46,0,374:255:.:0:31:36:41:0:. 0/1:0/1:2559:1011,1235,84,229:2,311,0,2246:64:.:64:28,31:55:26,59:2:91 chr1 152308424 . T G . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:422:170,175,45,32:0,0,77,345:64:.:0:32:37:39:0:. 0/1:0/1:3124:1059,1130,507,428:0,2,933,2189:228:.:228:29,31:55:48,58:2:37 chr1 152308814 . A G . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:424:122,174,86,42:296,1,127,0:88:.:0:31:21:27:0:. 0/1:0/1:3521:1103,1235,588,595:2338,1,1182,0:228:.:228:30,29:52:58,40:2:61 chr1 152310807 . C T . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:394:172,150,22,50:2,322,0,70:51:.:0:30:40:40:0:. 0/1:0/1:2461:670,644,573,574:4,1314,3,1140:228:.:228:30,30:53:60,46:2:24 chr1 158607804 . C A . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:8:0,8,0,0:0,8,0,0:51:.:0:33:60:60:0:. 0/1:0/1:10:1,7,1,1:2,8,0,0:6:.:6:31,33:60:60,60:2:23 chr1 161363118 . C T . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:171:24,101,8,38:0,125,0,46:77:.:0:33:10:9:0:. 0/1:0/1:326:37,152,29,108:0,189,0,137:228:.:228:33,31:35:33,37:2:50 chr1 161444478 . T A . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:90:27,33,21,9:30,0,0,60:47:.:0:31:4:4:0:. 0/1:0/1:85:39,15,25,6:31,0,0,54:61:.:61:31,31:13:20,9:2:20 chr1 161444486 . A G . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:86:23,33,21,9:56,0,30,0:43:.:0:30:4:5:0:. 0/1:0/1:73:29,13,25,6:42,0,31,0:74:.:74:29,26:15:12,20:2:16 chr1 161444488 . A G . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:88:22,35,21,10:57,0,31,0:42:.:0:30:4:5:0:. 0/1:0/1:74:30,13,24,7:43,0,31,0:72:.:72:29,28:15:12,19:2:15 chr1 161444514 . T A . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:99:10,60,19,10:29,0,0,70:54:.:0:29:3:3:0:. 0/1:0/1:70:10,25,22,13:35,0,0,35:98:.:153:29,29:17:21,12:2:33 chr1 161444527 . C G . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:125:13,90,12,10:0,103,22,0:6:.:0:32:2:1:0:. 0/1:0/1:74:15,38,12,9:0,53,21,0:85:.:85:32,31:16:14,23:2:109 chr1 178725267 . G A . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:10:10,0,0,0:0,0,10,0:57:.:0:28:56:56:0:. 0/1:0/1:10:7,0,1,2:3,0,7,0:25:.:25:28,28:60:60,60:2:30 chr1 203166324 . C T . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:6:6,0,0,0:0,6,0,0:45:.:0:34:60:60:0:. 0/1:0/1:8:6,0,2,0:0,6,0,2:11:.:11:33,33:60:60,60:2:18 chr1 222468242 . T C . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:61:19,37,0,5:0,5,0,56:21:.:0:31:4:4:0:. 1/1:1/1:84:4,4,17,59:0,76,0,8:116:.:240:26:33:34:2:21 chr1 223947556 . G A . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:91:64,7,20,0:20,0,71,0:1:.:0:28:0:0:0:. 0/1:0/1:65:42,3,19,1:20,0,45,0:26:.:38:32,28:16:26,11:2:57 chr1 223947588 . G T . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:117:85,18,7,7:0,0,103,14:1:.:0:32:0:0:0:. 1/1:1/1:87:39,24,20,4:0,0,63,24:11:.:60:29:11:28:2:20 chr1 223947978 . G T . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:254:171,20,53,10:0,0,191,63:1:.:0:32:1:2:0:. 0/1:0/1:430:205,20,192,13:0,0,225,205:225:.:225:32,30:35:39,31:2:134 chr1 223948062 . G A . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:304:132,66,44,62:104,0,198,2:62:.:0:29:20:30:0:. 0/1:0/1:1124:380,206,360,178:537,0,586,1:228:.:228:31,29:47:36,58:2:35 chr1 223948558 . C T . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:40:8,27,1,4:0,35,0,5:1:.:0:28:1:1:0:. 0/1:0/1:154:10,64,21,59:0,74,0,80:176:.:220:28,31:22:23,22:2:49 chr1 223949699 . T C . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:189:94,95,0,0:0,0,0,189:28:.:0:30:1:1:0:. 0/1:0/1:370:104,102,99,65:0,164,0,206:206:.:206:30,31:25:18,30:2:233 chr1 223950486 . C T . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:79:14,4,49,12:0,18,0,61:58:.:0:30:10:31:0:. 0/1:0/1:115:19,6,52,38:0,25,0,90:73:.:177:30,30:31:56,25:2:31 chr1 227976709 . T C . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:10:8,2,0,0:0,0,0,10:22:.:0:25:1:1:0:. 1/1:1/1:91:3,1,82,5:0,86,1,4:25:.:25:32:3:2:2:20 chr1 227977309 . A G . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:170:101,30,27,12:131,0,38,1:116:.:0:31:9:11:0:. 0/1:0/1:461:185,51,194,31:236,0,225,0:228:.:228:31,28:38:48,27:2:113 chr1 234978406 . C G . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:2:2,0,0,0:0,2,0,0:33:.:0:32:60:60:0:. 1/1:1/1:1:0,0,1,0:0,0,1,0:12:.:12:12:60:60:2:15 chr1 234978426 . C G . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:2:2,0,0,0:0,2,0,0:33:.:0:31:60:60:0:. 1/1:1/1:1:0,0,1,0:0,0,1,0:30:.:30:35:60:60:2:16 chr1 234978429 . T C . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:2:2,0,0,0:0,0,0,2:33:.:0:34:60:60:0:. 1/1:1/1:1:0,0,1,0:0,1,0,0:25:.:25:25:60:60:2:16 chr1 240207797 . G A . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:161:61,72,12,16:26,2,133,0:59:.:0:28:20:18:0:. 0/1:0/1:245:67,113,13,52:64,1,180,0:34:.:34:30,28:38:47,35:2:32 chr1 240207800 . C A . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:152:57,69,12,14:22,126,4,0:95:.:0:30:18:17:0:. 0/1:0/1:225:60,107,14,44:53,167,5,0:8:.:8:30,29:37:45,34:2:35 chr1 240207806 . C T . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:144:57,65,10,12:1,122,0,21:114:.:0:32:15:14:0:. 0/1:0/1:216:59,105,12,40:1,164,0,51:13:.:13:31,29:34:31,45:2:40 chr1 240207812 . G A,T . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/2:0/2:124:22,15,33,54:12,8,37,67:37:.:69:21,26:10:5,12:1:. 1/2:1/2:185:12,4,50,119:31,10,16,128:95:.:165:27,26:28:38,27:2:69 chr1 240208175 . T G . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:125:51,50,10,14:0,7,17,101:155:.:0:28:31:36:0:. 0/1:0/1:146:64,47,12,23:0,5,30,111:2:.:2:29,27:47:24,53:2:29 chr1 240472659 . G T . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:6:0,6,0,0:0,0,6,0:45:.:0:25:60:60:0:. 0/1:0/1:7:0,5,0,2:0,0,5,2:8:.:8:28,30:60:60,60:2:18 chr1 242810191 . T G . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:71:26,30,3,12:0,0,15,56:88:.:0:30:18:22:0:. 0/1:0/1:171:59,40,54,18:0,0,72,99:219:.:219:31,30:39:35,42:2:61 chr1 242810198 . T G . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:79:24,34,3,18:0,0,21,58:76:.:0:30:16:21:0:. 0/1:0/1:177:57,38,54,28:0,0,82,95:228:.:228:30,30:39:35,42:2:49 chr1 243052907 . C T . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:7:0,7,0,0:0,7,0,0:15:.:0:25:0:0:0:. 0/1:0/1:17:0,11,0,6:0,11,0,6:23:.:23:28,31:25:26,24:2:21 chr1 244891249 . C T . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:6:0,6,0,0:0,6,0,0:45:.:0:30:60:60:0:. 0/1:0/1:7:0,5,0,2:0,5,0,2:4:.:4:22,28:54:60,40:2:18 chr2 3035112 . T C . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:263:82,120,30,31:0,59,2,202:64:.:0:29:49:57:0:. 0/1:0/1:559:136,265,60,98:0,157,1,401:167:.:167:27,30:53:35,60:2:37 chr2 3329166 . G C . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:66:24,30,6,6:0,12,54,0:73:.:0:31:28:32:0:. 0/1:0/1:64:19,28,10,7:0,13,47,4:19:.:19:28,31:39:23,47:2:43 chr2 3329223 . G C . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:34:11,16,5,2:0,7,27,0:51:.:0:32:34:43:0:. 0/1:0/1:36:9,13,6,8:0,7,22,7:0:.:76:30,31:42:29,51:2:27 chr2 3329230 . G A . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:30:9,12,7,2:7,0,21,2:44:.:0:32:35:46:0:. 0/1:0/1:31:8,10,5,8:12,0,18,1:116:.:116:30,31:44:31,52:2:17 chr2 3329243 . A G . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:29:13,14,0,2:27,0,2,0:68:.:0:30:34:36:0:. 0/1:0/1:31:9,11,2,9:20,0,11,0:59:.:59:30,31:39:48,22:2:41 chr2 3775131 . G C . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:172:79,50,25,18:0,43,129,0:117:.:0:30:33:42:0:. 0/1:0/1:366:184,70,41,71:0,112,254,0:48:.:48:32,30:39:21,47:2:75 chr2 10080680 . C T . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:6:6,0,0,0:0,6,0,0:45:.:0:34:60:60:0:. 0/1:0/1:5:3,0,2,0:0,3,0,2:18:.:18:34,32:60:60,60:2:18 chr2 19985338 . C T . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:41:18,5,0,18:2,23,0,16:45:.:0:32:17:24:0:. 0/1:0/1:32:15,5,0,12:1,20,0,11:14:.:14:32,28:23:27,15:2:18 chr2 39404606 . C T . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:6:0,6,0,0:0,6,0,0:45:.:0:24:40:40:0:. 0/1:0/1:10:0,6,0,4:0,6,0,4:30:.:30:28,26:50:57,39:2:18 chr2 39404609 . C T . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:6:0,6,0,0:0,6,0,0:45:.:0:31:40:40:0:. 0/1:0/1:9:0,5,0,4:0,5,0,4:7:.:7:32,17:49:56,39:2:18 chr2 68306124 . C A . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:8:8,0,0,0:0,8,0,0:51:.:0:32:60:60:0:. 0/1:0/1:8:6,0,0,2:2,6,0,0:3:.:3:29,32:57:50,59:2:23 chr2 86942193 . T G . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:279:133,92,27,27:0,0,54,225:31:.:0:32:2:2:0:. 0/1:0/1:771:252,262,121,136:0,1,256,514:228:.:228:31,31:17:21,16:2:213 chr2 86942348 . C G . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:141:12,100,4,25:0,112,29,0:12:.:0:26:2:2:0:. 0/1:0/1:265:11,176,5,73:0,187,78,0:11:.:11:26,32:26:25,27:2:38 chr2 86942392 . C G . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:21:0,16,0,5:0,16,5,0:1:.:0:23:0:0:0:. 0/1:0/1:41:0,32,0,9:0,32,9,0:12:.:12:27,29:19:15,31:2:21 chr2 89625699 . G A . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:201:108,46,32,15:47,0,154,0:1:.:0:32:0:0:0:. 0/1:0/1:393:143,74,110,66:176,0,217,0:141:.:146:30,32:8:11,7:2:125