github.com/vertgenlab/gonomics@v1.0.0/cmd/vcfFormat/testdata/test_table.vcf (about) 1 ##fileformat=VCFv4.2 2 ##fileDate=20220209 3 ##source=github.com/vertgenlab/gonomics 4 ##phasing=none 5 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> 6 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Total Depth"> 7 ##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Depth of Each Allele"> 8 ##FORMAT=<ID=PV,Number=A,Type=Float,Description="p value for Each Alternate Allele"> 9 ##INFO=<ID=MaxPopAF,Number=1,Type=Float,Description="Maximum allele frequency of any population in CellBase",Source="bioinfo.hpc.cam.ac.uk/cellbase/webservices",Version="v4"> 10 ##INFO=<ID=Consequence,Number=1,Type=String,Description="Variant consequence",Source="bioinfo.hpc.cam.ac.uk/cellbase/webservices",Version="v4"> 11 ##INFO=<ID=Gene,Number=1,Type=String,Description="Nearest gene",Source="bioinfo.hpc.cam.ac.uk/cellbase/webservices",Version="v4"> 12 ##INFO=<ID=Transcript,Number=1,Type=String,Description="Ensembl transcript id",Source="bioinfo.hpc.cam.ac.uk/cellbase/webservices",Version="v4"> 13 ##INFO=<ID=ProteinEffect,Number=1,Type=String,Description="Effect of variant on protein",Source="bioinfo.hpc.cam.ac.uk/cellbase/webservices",Version="v4"> 14 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT S2007.recal S2032.recal S4322.recal S4388.recal S4390.recal 15 chr1 14997 . A C,T 0 NO_NORMAL Consequence=splice_region_variant;Gene=DDX11L1;Transcript=ENST00000456328 GT:DP:AD:PV 0/1:797:795,1,1:1,1 0/0:111:111,0,0:1,1 0/1:981:975,3,0:1,1 0/1:653:625,28,0:3e-17,1 0/0:982:981,0,0:1,1 16 chr1 17606 . A G 0 NO_NORMAL MaxPopAF=0.0043;Consequence=splice_region_variant;Gene=DDX11L1;Transcript=ENST00000456328 GT:DP:AD:PV 0/0:1477:1472,0:1 0/1:111:97,12:2e-19 0/0:1560:1549,0:1 0/0:862:854,0:1 0/1:1581:1574,2:1 17 chr1 69231 . C G 0 NO_NORMAL Consequence=missense_variant;Gene=OR4F5;Transcript=ENST00000641515;ProteinEffect=HIS47GLN GT:DP:AD:PV 0/1:1095:1082,11:0.0005 0/0:146:146,0:1 0/0:1362:1360,0:1 0/0:767:767,0:1 0/1:1846:1837,8:1 18 chr1 69356 . G T 0 NO_NORMAL Consequence=missense_variant;Gene=OR4F5;Transcript=ENST00000641515;ProteinEffect=GLY89VAL GT:DP:AD:PV 0/0:494:494,0:1 0/0:137:137,0:1 0/1:607:600,7:6e-06 0/0:566:566,0:1 0/0:1566:1566,0:1 19 chr1 69369 . G A 0 NO_NORMAL MaxPopAF=0.0005;Consequence=synonymous_variant;Gene=OR4F5;Transcript=ENST00000641515;ProteinEffect=GLN93GLN GT:DP:AD:PV 0/0:399:399,0:1 0/0:135:134,0:1 0/1:477:412,64:1e-55 0/0:582:582,0:1 0/0:1645:1645,0:1 20 chr1 69437 . A G 0 NO_NORMAL Consequence=missense_variant;Gene=OR4F5;Transcript=ENST00000641515;ProteinEffect=TYR116CYS GT:DP:AD:PV 0/0:62:61,0:1 0/0:188:188,0:1 0/1:63:61,2:0.0003 0/0:803:803,0:1 0/0:2508:2505,0:1 21 chr1 137334 . C T 0 NO_NORMAL MaxPopAF=0.0036;Consequence=2KB_upstream_variant;Gene=CICP27;Transcript=ENST00000442987 GT:DP:AD:PV 0/0:56:56,0:1 .:0:0,0:1 0/0:62:62,0:1 .:0:0,0:1 0/1:77:64,13:3e-06 22 chr1 137377 . G T 0 NO_NORMAL MaxPopAF=0.0091;Consequence=2KB_upstream_variant;Gene=CICP27;Transcript=ENST00000442987 GT:DP:AD:PV 0/0:91:91,0:1 .:0:0,0:1 0/0:107:107,0:1 0/0:73:73,0:1 0/1:123:116,7:0.0003 23 chr1 137411 . G A 0 NO_NORMAL Consequence=2KB_upstream_variant;Gene=CICP27;Transcript=ENST00000442987 GT:DP:AD:PV 0/0:117:117,0:1 .:0:0,0:1 0/1:137:125,12:5e-08 0/0:105:105,0:1 0/0:179:179,0:1 24 chr1 137486 . A G 0 NO_NORMAL MaxPopAF=0.0015;Consequence=2KB_upstream_variant;Gene=CICP27;Transcript=ENST00000442987 GT:DP:AD:PV 0/0:168:168,0:1 .:0:0,0:1 0/0:206:204,0:1 0/1:128:115,11:2e-09 0/0:282:281,0:1 25 chr1 137487 . A C 0 NO_NORMAL MaxPopAF=0.0015;Consequence=2KB_upstream_variant;Gene=CICP27;Transcript=ENST00000442987 GT:DP:AD:PV 0/0:169:169,0:1 .:0:0,0:1 0/1:206:203,3:1 0/1:129:116,13:5e-08 0/1:284:283,1:1 26 chr1 137552 . T C 0 NO_NORMAL MaxPopAF=0.0014;Consequence=2KB_upstream_variant;Gene=CICP27;Transcript=ENST00000442987 GT:DP:AD:PV 0/0:177:176,0:1 .:0:0,0:1 0/0:185:184,0:1 0/0:119:119,0:1 0/1:302:270,30:2e-13 27 chr1 137560 . GC G 0 NO_NORMAL Consequence=2KB_upstream_variant;Gene=CICP27;Transcript=ENST00000442987 GT:DP:AD:PV 0/0:183:183,0:1 .:0:0,0:1 0/0:178:178,0:1 0/0:115:115,0:1 0/1:295:268,27:3e-12 28 chr1 137987 . G A 0 NO_NORMAL MaxPopAF=0.00014;Consequence=2KB_upstream_variant;Gene=CICP27;Transcript=ENST00000442987 GT:DP:AD:PV 0/0:77:76,0:1 .:0:0,0:1 0/0:79:79,0:1 0/1:69:64,5:0.0003 0/0:126:126,0:1 29 chr1 138864 . G A 0 NO_NORMAL Consequence=2KB_upstream_variant;Gene=CICP27;Transcript=ENST00000442987 GT:DP:AD:PV 0/0:622:621,0:1 0/1:63:61,2:0.0004 0/0:589:586,0:1 0/0:542:542,0:1 0/0:1229:1227,0:1 30 chr1 138875 . G A 0 NO_NORMAL MaxPopAF=0.00017;Consequence=2KB_upstream_variant;Gene=CICP27;Transcript=ENST00000442987 GT:DP:AD:PV 0/0:646:646,0:1 0/0:65:64,0:1 0/0:598:596,0:1 0/1:572:563,9:2e-06 0/1:1267:1263,1:1 31 chr1 138909 . C T 0 NO_NORMAL MaxPopAF=0.0089;Consequence=2KB_upstream_variant;Gene=CICP27;Transcript=ENST00000442987 GT:DP:AD:PV 0/0:711:711,0:1 0/0:58:58,0:1 0/1:649:622,27:1e-20 0/0:651:650,0:1 0/0:1415:1413,0:1 32 chr1 138955 . G T 0 NO_NORMAL Consequence=2KB_upstream_variant;Gene=CICP27;Transcript=ENST00000442987 GT:DP:AD:PV 0/0:814:814,0:1 0/0:90:90,0:1 0/0:740:740,0:1 0/1:811:800,11:1e-08 0/0:1792:1792,0:1 33 chr1 138980 . G T 0 NO_NORMAL MaxPopAF=0.00091;Consequence=2KB_upstream_variant;Gene=CICP27;Transcript=ENST00000442987 GT:DP:AD:PV 0/1:832:801,31:1e-05 0/0:102:102,0:1 0/1:764:734,29:2e-05 0/1:912:899,13:1 0/1:1989:1981,8:1 34 chr1 139054 . T C 0 NO_NORMAL Consequence=2KB_upstream_variant;Gene=CICP27;Transcript=ENST00000442987 GT:DP:AD:PV 0/0:855:853,0:1 0/1:135:133,2:0.0007 0/0:686:686,0:1 0/0:1034:1033,0:1 0/0:2296:2293,0:1 35 chr1 139115 . G T 0 NO_NORMAL Consequence=2KB_upstream_variant;Gene=CICP27;Transcript=ENST00000442987 GT:DP:AD:PV 0/1:977:976,1:1 0/1:110:107,3:0.0002 0/0:810:810,0:1 0/1:1098:1097,1:1 0/1:2321:2320,1:1 36 chr1 139132 . G T 0 NO_NORMAL Consequence=2KB_upstream_variant;Gene=CICP27;Transcript=ENST00000442987 GT:DP:AD:PV 0/0:989:989,0:1 0/1:105:102,3:0.0006 0/1:874:873,1:1 0/1:1079:1074,3:1 0/1:2327:2323,2:1 37 chr1 139191 . C A 0 NO_NORMAL Consequence=2KB_upstream_variant;Gene=CICP27;Transcript=ENST00000442987 GT:DP:AD:PV 0/1:1056:1055,1:1 0/1:101:98,3:0.0003 0/0:1163:1161,0:1 0/1:1190:1189,1:1 0/1:2295:2292,3:1 38 chr1 139200 . G A 0 NO_NORMAL Consequence=2KB_upstream_variant;Gene=CICP27;Transcript=ENST00000442987 GT:DP:AD:PV 0/0:1076:1076,0:1 0/0:94:93,0:1 0/1:1209:1189,19:3e-05 0/1:1184:1172,11:1 0/1:2321:2313,7:1 39 chr1 139208 . G A 0 NO_NORMAL MaxPopAF=0.00023;Consequence=2KB_upstream_variant;Gene=CICP27;Transcript=ENST00000442987 GT:DP:AD:PV 0/0:1074:1074,0:1 0/0:91:91,0:1 0/1:1225:1208,17:2e-12 0/0:1171:1170,0:1 0/0:2323:2322,0:1 40 chr1 139356 . T C 0 NO_NORMAL MaxPopAF=0.0039;Consequence=2KB_upstream_variant;Gene=CICP27;Transcript=ENST00000442987 GT:DP:AD:PV 0/1:792:789,1:1 0/0:72:72,0:1 0/1:754:733,18:5e-12 0/0:749:749,0:1 0/1:1780:1776,1:1 41 chr1 139363 . T C 0 NO_NORMAL MaxPopAF=0.0019;Consequence=2KB_upstream_variant;Gene=CICP27;Transcript=ENST00000442987 GT:DP:AD:PV 0/1:767:760,1:1 0/0:64:64,0:1 0/1:730:719,10:2e-06 0/0:717:716,0:1 0/1:1720:1717,1:1 42 chr1 139415 . G T 0 NO_NORMAL Consequence=2KB_upstream_variant;Gene=CICP27;Transcript=ENST00000442987 GT:DP:AD:PV 0/0:632:632,0:1 0/0:67:67,0:1 0/0:577:577,0:1 0/1:594:588,6:3e-05 0/0:1463:1461,0:1 43 chr1 139491 . G A 0 NO_NORMAL Consequence=2KB_upstream_variant;Gene=CICP27;Transcript=ENST00000442987 GT:DP:AD:PV 0/1:593:589,2:1 0/1:68:64,4:3e-06 0/0:586:586,0:1 0/0:553:552,0:1 0/0:1401:1397,0:1 44 chr1 139666 . T G 0 NO_NORMAL Consequence=2KB_upstream_variant;Gene=CICP27;Transcript=ENST00000442987 GT:DP:AD:PV 0/1:280:271,9:1 .:0:0,0:1 0/1:328:315,13:0.4 0/1:272:250,22:0.0001 0/1:747:730,16:1 45 chr1 139685 . G A 0 NO_NORMAL MaxPopAF=0.0011;Consequence=2KB_upstream_variant;Gene=CICP27;Transcript=ENST00000442987 GT:DP:AD:PV 0/0:220:219,0:1 .:0:0,0:1 0/0:278:277,0:1 0/0:214:214,0:1 0/1:645:625,15:1e-05 46 chr1 177463 . A G 0 NO_NORMAL Consequence=upstream_gene_variant;Gene=AL627309.5;Transcript=ENST00000466557 GT:DP:AD:PV 0/0:391:391,0:1 .:0:0,0:1 0/0:371:370,0:1 0/0:224:224,0:1 0/1:446:409,37:6e-20 47 chr1 182441 . T A 0 NO_NORMAL Consequence=2KB_upstream_variant;Gene=FO538757.2;Transcript=ENST00000624431 GT:DP:AD:PV 0/1:76:68,8:0.3 .:0:0,0:1 0/1:60:48,12:0.0009 .:0:0,0:1 0/0:93:93,0:1 48 chr1 182529 . G A 0 NO_NORMAL Consequence=2KB_upstream_variant;Gene=FO538757.2;Transcript=ENST00000624431 GT:DP:AD:PV 0/0:303:303,0:1 .:0:0,0:1 0/0:222:222,0:1 0/0:153:153,0:1 0/1:271:263,8:4e-05 49 chr1 182631 . A G 0 NO_NORMAL Consequence=2KB_upstream_variant;Gene=FO538757.2;Transcript=ENST00000624431 GT:DP:AD:PV 0/1:1023:1021,1:1 0/0:60:60,0:1 0/0:869:867,0:1 0/0:640:639,0:1 0/1:923:790,133:3e-79 50 chr1 182640 . C A 0 NO_NORMAL Consequence=2KB_upstream_variant;Gene=FO538757.2;Transcript=ENST00000624431 GT:DP:AD:PV 0/1:1087:1082,5:1 0/1:62:58,4:0.0002 0/1:943:940,2:1 0/0:700:700,0:1 0/1:971:964,7:1 51 chr1 182668 . T C 0 NO_NORMAL Consequence=2KB_upstream_variant;Gene=FO538757.2;Transcript=ENST00000624431 GT:DP:AD:PV 0/1:1135:1133,2:1 0/1:62:58,4:4e-05 0/1:995:991,3:1 0/0:737:737,0:1 0/1:977:973,4:1 52 chr1 182678 . A G 0 NO_NORMAL Consequence=2KB_upstream_variant;Gene=FO538757.2;Transcript=ENST00000624431 GT:DP:AD:PV 0/1:1167:1164,2:1 0/1:55:52,3:0.0004 0/1:1009:1006,2:1 0/0:753:753,0:1 0/1:971:967,4:1 53 chr1 182686 . A G 0 NO_NORMAL Consequence=2KB_upstream_variant;Gene=FO538757.2;Transcript=ENST00000624431 GT:DP:AD:PV 0/1:1183:975,207:1e-08 0/0:51:51,0:1 0/1:1004:844,154:0.004 0/1:747:600,144:1e-08 0/0:955:952,0:1 54 chr1 182688 . A G 0 NO_NORMAL Consequence=2KB_upstream_variant;Gene=FO538757.2;Transcript=ENST00000624431 GT:DP:AD:PV 0/1:1184:1180,2:1 0/1:50:47,3:0.0003 0/1:1009:1005,2:1 0/0:747:747,0:1 0/1:963:957,4:1 55 chr1 184246 . T C 0 NO_NORMAL Consequence=2KB_downstream_variant;Gene=FO538757.2;Transcript=ENST00000624431 GT:DP:AD:PV 0/0:392:391,0:1 .:0:0,0:1 0/0:332:332,0:1 0/1:197:178,19:3e-16 0/0:315:315,0:1 56 chr1 185194 . G C 0 NO_NORMAL Consequence=2KB_downstream_variant;Gene=FO538757.2;Transcript=ENST00000624431 GT:DP:AD:PV 0/1:448:209,238:3e-17 .:0:0,0:1 0/1:338:219,119:1 0/1:243:154,89:1 0/1:314:259,55:1 57 chr1 188130 . A G 0 NO_NORMAL Consequence=splice_region_variant;Gene=FO538757.2;Transcript=ENST00000624431 GT:DP:AD:PV 0/1:751:744,2:1 0/1:61:52,9:1e-14 0/0:942:941,0:1 0/0:538:534,0:1 0/0:882:880,0:1 58 chr1 195425 . C G 0 NO_NORMAL Consequence=2KB_upstream_variant;Gene=FO538757.1;Transcript=ENST00000623083 GT:DP:AD:PV 0/1:82:47,35:0.0005 .:0:0,0:1 0/1:58:37,21:0.1 .:0:0,0:1 0/1:97:85,12:1 59 chr1 195438 . T A 0 NO_NORMAL Consequence=2KB_upstream_variant;Gene=FO538757.1;Transcript=ENST00000623083 GT:DP:AD:PV 0/0:74:74,0:1 .:0:0,0:1 0/0:53:53,0:1 .:0:0,0:1 0/1:82:74,8:0.0005 60 chr1 199681 . C T 0 NO_NORMAL Consequence=upstream_gene_variant;Gene=FO538757.1;Transcript=ENST00000623083 GT:DP:AD:PV 0/1:65:62,3:1 .:0:0,0:1 0/1:76:60,16:3e-05 .:0:0,0:1 0/1:106:100,3:1 61 chr1 199869 . C T 0 NO_NORMAL Consequence=upstream_gene_variant;Gene=FO538757.1;Transcript=ENST00000623083 GT:DP:AD:PV 0/1:69:59,10:3e-06 .:0:0,0:1 0/0:56:56,0:1 .:0:0,0:1 0/0:107:107,0:1 62 chr1 199878 . T C 0 NO_NORMAL Consequence=upstream_gene_variant;Gene=FO538757.1;Transcript=ENST00000623083 GT:DP:AD:PV 0/1:67:62,2:1 .:0:0,0:1 0/1:56:45,11:2e-05 .:0:0,0:1 0/1:105:103,1:1 63 chr1 200960 . T C 0 NO_NORMAL Consequence=intergenic_variant GT:DP:AD:PV 0/0:179:179,0:1 .:0:0,0:1 0/0:247:246,0:1 0/0:184:184,0:1 0/1:351:278,72:2e-34 64 chr1 205549 . G C 0 NO_NORMAL Consequence=TF_binding_site_variant GT:DP:AD:PV 0/0:118:118,0:1 .:0:0,0:1 0/1:148:135,13:2e-07 0/0:77:77,0:1 0/0:130:130,0:1 65 chr1 205611 . C T 0 NO_NORMAL Consequence=intergenic_variant GT:DP:AD:PV 0/1:269:226,43:0.0007 .:0:0,0:1 0/1:367:337,30:1 0/1:201:184,17:1 0/1:298:270,28:1 66 chr1 205688 . G A 0 NO_NORMAL Consequence=intergenic_variant GT:DP:AD:PV 0/1:631:523,107:3e-09 0/1:61:60,1:1 0/1:644:642,1:1 0/1:477:443,34:1 0/1:664:547,117:2e-11 67 chr1 205748 . G C 0 NO_NORMAL Consequence=intergenic_variant GT:DP:AD:PV 0/1:817:650,164:2e-08 0/1:77:73,4:1 0/0:685:683,0:1 0/1:616:553,61:1 0/1:874:669,204:4e-19 68 chr1 205757 . C T 0 NO_NORMAL Consequence=intergenic_variant GT:DP:AD:PV 0/1:833:586,245:1 0/1:75:51,24:0.5 0/1:705:449,256:0.0005 0/1:641:463,173:1 0/1:878:598,277:0.4 69 chr1 205818 . C T 0 NO_NORMAL Consequence=intergenic_variant GT:DP:AD:PV 0/1:799:553,245:1 0/1:89:60,29:1 0/1:701:406,293:1e-06 0/1:607:424,183:1 0/1:862:562,298:0.4 70 chr1 205855 . T C 0 NO_NORMAL Consequence=intergenic_variant GT:DP:AD:PV 0/1:650:445,202:1 0/1:62:42,20:1 0/1:610:357,252:4e-05 0/1:454:308,146:1 0/1:714:473,240:1 71 chr1 205873 . G A 0 NO_NORMAL Consequence=intergenic_variant GT:DP:AD:PV 0/0:561:560,0:1 0/1:56:54,2:0.0007 0/0:539:537,0:1 0/0:388:387,0:1 0/0:627:627,0:1 72 chr1 205882 . T C 0 NO_NORMAL Consequence=intergenic_variant GT:DP:AD:PV 0/1:538:296,241:1 0/1:52:28,24:1 0/1:516:307,208:1 0/1:366:174,191:0.04 0/1:589:265,322:5e-05 73 chr1 205918 . A T 0 NO_NORMAL Consequence=intergenic_variant GT:DP:AD:PV 0/1:446:444,1:1 .:0:0,0:1 0/1:435:431,1:1 0/1:282:266,16:4e-11 0/0:496:496,0:1 74 chr1 205931 . A G 0 NO_NORMAL Consequence=intergenic_variant GT:DP:AD:PV 0/1:386:350,32:0.1 .:0:0,0:1 0/1:389:387,1:1 0/1:236:223,12:1 0/1:439:384,54:2e-07 75 chr1 205932 . A G 0 NO_NORMAL Consequence=intergenic_variant GT:DP:AD:PV 0/1:386:355,29:0.2 .:0:0,0:1 0/0:386:383,0:1 0/1:235:223,12:1 0/1:434:378,54:2e-08 76 chr1 205980 . C T 0 NO_NORMAL Consequence=intergenic_variant GT:DP:AD:PV 0/0:282:282,0:1 .:0:0,0:1 0/1:269:223,45:5e-28 0/0:163:163,0:1 0/0:307:307,0:1 77 chr1 206076 . TC T 0 NO_NORMAL Consequence=intergenic_variant GT:DP:AD:PV 0/0:422:420,0:1 .:0:0,0:1 0/0:377:377,0:1 0/1:259:252,6:2e-05 0/0:445:445,0:1 78 chr1 206154 . C T 0 NO_NORMAL Consequence=intergenic_variant GT:DP:AD:PV 0/0:549:548,0:1 .:0:0,0:1 0/0:539:539,0:1 0/1:354:349,4:0.0009 0/0:621:619,0:1 79 chr1 206436 . C G 0 NO_NORMAL Consequence=intergenic_variant GT:DP:AD:PV 0/1:56:39,17:0.0001 .:0:0,0:1 .:0:0,0:1 .:0:0,0:1 0/1:57:55,2:1 80 chr1 206443 . G A 0 NO_NORMAL Consequence=intergenic_variant GT:DP:AD:PV 0/1:50:35,15:0.0003 .:0:0,0:1 .:0:0,0:1 .:0:0,0:1 0/1:54:52,2:1 81 chr1 450790 . C A 0 NO_NORMAL Consequence=missense_variant;Gene=AL732372.2;Transcript=ENST00000455207 GT:DP:AD:PV 0/1:693:692,1:1 .:0:0,0:1 0/0:958:958,0:1 0/1:586:579,7:6e-05 0/0:805:805,0:1 82 chr1 450942 . A G 0 NO_NORMAL Consequence=missense_variant;Gene=AL732372.2;Transcript=ENST00000455207 GT:DP:AD:PV 0/1:894:893,1:1 0/1:59:50,9:5e-16 0/1:1384:1381,1:1 0/0:766:766,0:1 0/0:1156:1154,0:1 83 chr1 451360 . C T 0 NO_NORMAL Consequence=missense_variant;Gene=AL732372.2;Transcript=ENST00000455207 GT:DP:AD:PV 0/0:950:948,0:1 .:0:0,0:1 0/1:1137:1111,23:1 0/1:335:307,27:2e-10 0/1:837:816,20:0.3 84 chr1 451466 . T G 0 NO_NORMAL Consequence=missense_variant;Gene=AL732372.2;Transcript=ENST00000455207 GT:DP:AD:PV 0/0:1067:1066,0:1 0/1:55:53,2:0.0005 0/1:1230:1229,1:1 0/0:568:567,0:1 0/0:1088:1085,0:1 85 chr1 451475 . G A 0 NO_NORMAL Consequence=synonymous_variant;Gene=AL732372.2;Transcript=ENST00000455207 GT:DP:AD:PV 0/0:1059:1056,0:1 0/0:56:56,0:1 0/1:1225:1132,92:6e-45 0/1:607:604,3:1 0/0:1114:1113,0:1 86 chr1 451532 . C T 0 NO_NORMAL Consequence=synonymous_variant;Gene=AL732372.2;Transcript=ENST00000455207 GT:DP:AD:PV 0/0:958:956,0:1 0/1:60:52,8:2e-15 0/0:1166:1164,0:1 0/0:634:634,0:1 0/0:1097:1096,0:1 87 chr1 451584 . G A 0 NO_NORMAL Consequence=missense_variant;Gene=AL732372.2;Transcript=ENST00000455207 GT:DP:AD:PV 0/0:737:734,0:1 0/0:51:51,0:1 0/1:922:853,68:8e-34 0/0:505:504,0:1 0/1:843:841,2:1 88 chr1 492762 . GC G 0 NO_NORMAL Consequence=splice_region_variant;Gene=AL732372.2;Transcript=ENST00000455464 GT:DP:AD:PV 0/0:95:95,0:1 .:0:0,0:1 0/0:140:139,0:1 0/0:88:88,0:1 0/1:122:114,8:3e-05 89 chr1 492769 . G A 0 NO_NORMAL Consequence=splice_region_variant;Gene=AL732372.2;Transcript=ENST00000455464 GT:DP:AD:PV 0/0:94:94,0:1 .:0:0,0:1 0/0:141:141,0:1 0/1:87:82,5:0.0003 0/0:126:126,0:1 90 chr1 498046 . C T 0 NO_NORMAL Consequence=splice_donor_variant;Gene=AL732372.2;Transcript=ENST00000455464 GT:DP:AD:PV 0/1:105:36,68:1e-07 .:0:0,0:1 0/1:140:66,73:0.003 0/1:86:56,30:1 0/1:176:134,42:1 91 chr1 685802 . C A 0 NO_NORMAL Consequence=missense_variant;Gene=AL669831.3;Transcript=ENST00000419394 GT:DP:AD:PV 0/0:852:852,0:1 0/1:59:57,2:0.0007 0/0:1232:1232,0:1 0/0:703:702,0:1 0/1:1032:1031,1:1 92 chr1 685883 . A T 0 NO_NORMAL Consequence=missense_variant;Gene=AL669831.3;Transcript=ENST00000419394 GT:DP:AD:PV 0/0:960:960,0:1 0/1:70:68,2:0.0007 0/0:1462:1462,0:1 0/1:785:784,1:1 0/0:1285:1285,0:1 93 chr1 685918 . A G 0 NO_NORMAL Consequence=missense_variant;Gene=AL669831.3;Transcript=ENST00000419394 GT:DP:AD:PV 0/0:889:886,0:1 0/1:53:42,10:6e-19 0/0:1284:1280,0:1 0/1:713:711,1:1 0/0:1183:1182,0:1 94 chr1 686174 . GC G 0 NO_NORMAL Consequence=frameshift_variant;Gene=AL669831.3;Transcript=ENST00000419394 GT:DP:AD:PV 0/0:707:704,0:1 .:0:0,0:1 0/0:1048:1042,0:1 0/1:539:533,6:2e-05 0/0:971:969,0:1 95 chr1 686266 . A C 0 NO_NORMAL Consequence=missense_variant;Gene=AL669831.3;Transcript=ENST00000419394 GT:DP:AD:PV 0/0:920:917,0:1 0/1:59:40,19:2e-34 0/1:1114:1109,1:1 0/0:434:432,0:1 0/0:975:975,0:1 96 chr1 686281 . G C 0 NO_NORMAL Consequence=missense_variant;Gene=AL669831.3;Transcript=ENST00000419394 GT:DP:AD:PV 0/0:951:950,0:1 0/1:63:60,2:0.0009 0/1:1122:1119,1:1 0/0:408:407,0:1 0/0:972:966,0:1 97 chr1 686390 . G A 0 NO_NORMAL Consequence=missense_variant;Gene=AL669831.3;Transcript=ENST00000419394 GT:DP:AD:PV 0/0:1032:1032,0:1 0/1:56:48,8:2e-15 0/0:1160:1158,0:1 0/0:409:408,0:1 0/0:1045:1044,0:1 98 chr1 686415 . C G 0 NO_NORMAL Consequence=missense_variant;Gene=AL669831.3;Transcript=ENST00000419394 GT:DP:AD:PV 0/0:1061:1061,0:1 0/1:59:57,2:0.0002 0/0:1187:1186,0:1 0/0:455:454,0:1 0/0:1129:1129,0:1 99 chr1 686451 . G A 0 NO_NORMAL Consequence=synonymous_variant;Gene=AL669831.3;Transcript=ENST00000419394 GT:DP:AD:PV 0/0:1127:1127,0:1 0/0:70:70,0:1 0/1:1269:1196,69:2e-37 0/0:539:538,0:1 0/0:1228:1226,0:1 100 chr1 686508 . C T 0 NO_NORMAL Consequence=synonymous_variant;Gene=AL669831.3;Transcript=ENST00000419394 GT:DP:AD:PV 0/1:1024:1021,3:1 0/1:76:60,16:4e-26 0/0:1214:1214,0:1 0/0:585:585,0:1 0/0:1180:1180,0:1