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007_crop.vcf
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007_crop.vcf
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#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT /scratch/ccmb_flux/keerthis/PASJIS_analysis/007_report_illumina_PE_Algn.sorted.bam
chr1 14907 . A G 94 . DP=76;VDB=0.0348;AF1=0.5;AC1=1;DP4=10,23,13,21;MQ=18;FQ=67;PV4=0.61,1.3e-17,1,1 GT:PL:GQ 0/1:124,0,94:97
chr1 14930 . A G 132 . DP=59;VDB=0.0448;AF1=0.5;AC1=1;DP4=4,11,9,23;MQ=23;FQ=52;PV4=1,2.4e-12,1,0.41 GT:PL:GQ 0/1:162,0,79:82
chr1 17538 . C A 6.98 . DP=64;VDB=0.0091;AF1=0.4999;AC1=1;DP4=17,28,3,9;MQ=22;FQ=9.53;PV4=0.51,2.2e-11,1,1 GT:PL:GQ 0/1:36,0,140:37
chr1 63697 . T C 3.41 . DP=2;VDB=0.0137;AF1=1;AC1=2;DP4=0,0,0,2;MQ=20;FQ=-33 GT:PL:GQ 1/1:32,6,0:4
chr1 91515 . A C 53 . DP=35;VDB=0.0001;AF1=0.5;AC1=1;DP4=2,23,2,8;MQ=27;FQ=56;PV4=0.56,1.9e-05,1,1 GT:PL:GQ 0/1:83,0,120:86
chr1 91536 . G T 70 . DP=34;VDB=0.0157;AF1=0.5;AC1=1;DP4=2,16,2,13;MQ=35;FQ=73;PV4=1,1.6e-12,1,1 GT:PL:GQ 0/1:100,0,201:99
chr1 91581 . G A 42 . DP=18;VDB=0.0033;AF1=0.5;AC1=1;DP4=0,7,0,11;MQ=36;FQ=45;PV4=1,6e-14,0.22,1 GT:PL:GQ 0/1:72,0,119:75
chr1 136048 . C T 6.98 . DP=119;VDB=0.0245;AF1=0.4999;AC1=1;DP4=23,39,10,23;MQ=14;FQ=9.53;PV4=0.65,5.2e-16,1,1 GT:PL:GQ 0/1:36,0,71:37
chr1 234466 . C T 23 . DP=60;VDB=0.0448;AF1=0.5;AC1=1;DP4=1,27,2,15;MQ=16;FQ=26;PV4=0.55,0.00081,1,1 GT:PL:GQ 0/1:53,0,74:56
chr1 235936 . G T 3.56 . DP=5;VDB=0.0000;AF1=0.503;AC1=1;DP4=2,0,3,0;MQ=18;FQ=-8.86;PV4=1,0.0033,1,1 GT:PL:GQ 0/1:31,0,19:25
chr1 235940 . G T 3.56 . DP=5;VDB=0.0000;AF1=0.503;AC1=1;DP4=2,0,3,0;MQ=18;FQ=-8.86;PV4=1,0.0034,1,1 GT:PL:GQ 0/1:31,0,19:25
chr1 523825 . C T 6.98 . DP=47;VDB=0.0033;AF1=0.4999;AC1=1;DP4=2,27,1,16;MQ=15;FQ=8.83;PV4=1,1,1,1 GT:PL:GQ 0/1:36,0,43:37
chr1 564621 . C T 50.3 . DP=5;VDB=0.0157;AF1=1;AC1=2;DP4=0,0,2,3;MQ=21;FQ=-42 GT:PL:GQ 1/1:83,15,0:27
chr1 571874 . A G 26.8 . DP=2;VDB=0.0137;AF1=1;AC1=2;DP4=0,0,0,2;MQ=37;FQ=-33 GT:PL:GQ 1/1:58,6,0:10
chr1 663097 . G C 76 . DP=63;VDB=0.0400;AF1=1;AC1=2;DP4=12,9,10,19;MQ=14;FQ=-36;PV4=0.15,5.2e-11,1,1 GT:PL:GQ 1/1:108,9,0:16
chr1 672209 . G A 17.3 . DP=5;VDB=0.0226;AF1=1;AC1=2;DP4=0,1,1,3;MQ=15;FQ=-35;PV4=1,1,1,1 GT:PL:GQ 1/1:49,8,0:13
chr1 726039 . A T 3.41 . DP=2;VDB=0.0137;AF1=1;AC1=2;DP4=0,0,2,0;MQ=23;FQ=-33 GT:PL:GQ 1/1:32,6,0:4
chr1 726082 . G C 15.1 . DP=6;VDB=0.0000;AF1=0.5;AC1=1;DP4=2,1,3,0;MQ=27;FQ=16.9;PV4=1,0.089,0.3,1 GT:PL:GQ 0/1:45,0,50:47
chr1 754964 . C T 10.2 . DP=2;VDB=0.0137;AF1=1;AC1=2;DP4=0,0,2,0;MQ=23;FQ=-33 GT:PL:GQ 1/1:41,6,0:8
chr1 761732 . C T 158 . DP=20;VDB=0.0091;AF1=1;AC1=2;DP4=0,0,9,9;MQ=31;FQ=-81 GT:PL:GQ 1/1:191,54,0:99
chr1 762589 . G C 46 . DP=13;VDB=0.0199;AF1=1;AC1=2;DP4=1,1,6,0;MQ=20;FQ=-36;PV4=0.25,0.0022,1,1 GT:PL:GQ 1/1:78,9,0:16
chr1 762592 . C G 32.5 . DP=13;VDB=0.0199;AF1=1;AC1=2;DP4=1,1,5,0;MQ=20;FQ=-34;PV4=0.29,0.00097,1,1 GT:PL:GQ 1/1:64,7,0:12
chr1 762601 . T C 27.2 . DP=16;VDB=0.0199;AF1=0.5163;AC1=1;DP4=1,3,3,1;MQ=19;FQ=-15.1;PV4=0.49,0.2,1,1 GT:PL:GQ 0/1:57,0,12:15
chr1 787399 . G T,C 171 . DP=36;VDB=0.0545;AF1=1;AC1=2;DP4=0,3,10,16;MQ=27;FQ=-76;PV4=0.53,0.0018,1,1 GT:PL:GQ 1/1:204,49,0,197,52,191:95
chr1 788713 . T C 34.3 . DP=14;VDB=0.0462;AF1=1;AC1=2;DP4=3,0,10,0;MQ=16;FQ=-41;PV4=1,1.8e-06,1,0.0081 GT:PL:GQ 1/1:67,14,0:25
chr1 789256 . T C 222 . DP=92;VDB=0.0245;AF1=1;AC1=2;DP4=4,3,34,33;MQ=33;FQ=-155;PV4=1,0.069,1,0.14 GT:PL:GQ 1/1:255,128,0:99
chr1 790696 . ca cATa 52.4 . INDEL;DP=3;VDB=0.0000;AF1=1;AC1=2;DP4=0,0,3,0;MQ=37;FQ=-43.5 GT:PL:GQ 1/1:92,9,0:16
chr1 802381 . T C 3.98 . DP=2;VDB=0.0137;AF1=1;AC1=2;DP4=0,0,2,0;MQ=18;FQ=-33 GT:PL:GQ 1/1:33,6,0:5
chr1 808631 . G A 129 . DP=37;VDB=0.0400;AF1=0.5;AC1=1;DP4=9,4,22,0;MQ=35;FQ=132;PV4=0.014,1,0.13,1 GT:PL:GQ 0/1:159,0,183:99
chr1 808922 . G A 103 . DP=62;VDB=0.0494;AF1=1;AC1=2;DP4=3,3,12,23;MQ=19;FQ=-84;PV4=0.65,1.7e-06,1,0.084 GT:PL:GQ 1/1:136,57,0:99
chr1 808928 . C T 3.54 . DP=62;VDB=0.0448;AF1=0.4998;AC1=1;DP4=13,19,6,9;MQ=24;FQ=5.47;PV4=1,6.7e-06,0.2,1 GT:PL:GQ 0/1:31,0,203:30
chr1 809876 . A G 175 . DP=65;VDB=0.0551;AF1=0.5;AC1=1;DP4=6,9,19,23;MQ=37;FQ=161;PV4=0.77,1.4e-12,1,0.21 GT:PL:GQ 0/1:205,0,188:99
chr1 812072 . C A 4.13 . DP=6;VDB=0.0137;AF1=0.4998;AC1=1;DP4=3,1,2,0;MQ=37;FQ=6.2;PV4=1,0.032,1,0.29 GT:PL:GQ 0/1:32,0,106:31
chr1 812267 . A G 76 . DP=9;VDB=0.0425;AF1=1;AC1=2;DP4=0,2,0,6;MQ=27;FQ=-36;PV4=1,0.095,1,0.052 GT:PL:GQ 1/1:108,9,0:16
chr1 812284 . C G 65.2 . DP=12;VDB=0.0157;AF1=1;AC1=2;DP4=0,2,0,9;MQ=31;FQ=-43;PV4=1,4.3e-05,1,1 GT:PL:GQ 1/1:98,16,0:29
chr1 817901 . G T 17.1 . DP=3;VDB=0.0309;AF1=1;AC1=2;DP4=0,0,0,3;MQ=20;FQ=-36 GT:PL:GQ 1/1:49,9,0:15
chr1 821038 . C T 6.98 . DP=3;VDB=0.0244;AF1=0.5003;AC1=1;DP4=1,0,2,0;MQ=33;FQ=3.2;PV4=1,0.1,0.33,1 GT:PL:GQ 0/1:36,0,28:31
chr1 821043 . T C 5.46 . DP=3;VDB=0.0244;AF1=0.5003;AC1=1;DP4=1,0,2,0;MQ=33;FQ=3.03;PV4=1,0.017,0.33,1 GT:PL:GQ 0/1:34,0,28:31
chr1 826086 . T C 11.1 . DP=2;VDB=0.0137;AF1=1;AC1=2;DP4=0,0,0,2;MQ=37;FQ=-33 GT:PL:GQ 1/1:42,6,0:9
chr1 826123 . A G 6.02 . DP=2;VDB=0.0137;AF1=1;AC1=2;DP4=0,0,0,2;MQ=37;FQ=-33 GT:PL:GQ 1/1:36,6,0:6
chr1 852875 . C T 59 . DP=9;VDB=0.0157;AF1=0.5;AC1=1;DP4=4,0,4,0;MQ=37;FQ=56.6;PV4=1,1,1,1 GT:PL:GQ 0/1:89,0,85:87
chr1 853378 . G T 5.46 . DP=14;VDB=0.0137;AF1=0.4999;AC1=1;DP4=9,0,2,0;MQ=37;FQ=7.8;PV4=1,1,1,0.48 GT:PL:GQ 0/1:34,0,134:34
chr1 854777 . A G 15.2 . DP=4;VDB=0.0137;AF1=0.504;AC1=1;DP4=1,0,1,1;MQ=33;FQ=-9.51;PV4=1,1,0.33,1 GT:PL:GQ 0/1:45,0,18:21
chr1 864726 . T A 15.9 . DP=2;VDB=0.0137;AF1=1;AC1=2;DP4=0,0,2,0;MQ=37;FQ=-33 GT:PL:GQ 1/1:47,6,0:10
chr1 877715 . C G 18.6 . DP=4;VDB=0.0460;AF1=1;AC1=2;DP4=0,0,0,4;MQ=34;FQ=-39 GT:PL:GQ 1/1:51,12,0:20
chr1 878999 . A G 25 . DP=7;VDB=0.0359;AF1=0.5;AC1=1;DP4=3,0,4,0;MQ=37;FQ=27.9;PV4=1,0.0012,1,0.027 GT:PL:GQ 0/1:55,0,72:58
chr1 881627 . G A 19.1 . DP=14;VDB=0.0400;AF1=0.5;AC1=1;DP4=3,2,1,3;MQ=35;FQ=22;PV4=0.52,0.011,0.44,1 GT:PL:GQ 0/1:49,0,102:52
chr1 883625 . A G 21.5 . DP=5;VDB=0.0033;AF1=1;AC1=2;DP4=0,0,0,4;MQ=37;FQ=-39 GT:PL:GQ 1/1:54,12,0:21
chr1 887801 . A G 56 . DP=15;VDB=0.0048;AF1=0.5;AC1=1;DP4=4,0,9,0;MQ=36;FQ=45.8;PV4=1,0.0012,0.26,1 GT:PL:GQ 0/1:86,0,73:76
chr1 888659 . T C 16.1 . DP=8;VDB=0.0212;AF1=0.5;AC1=1;DP4=0,2,0,3;MQ=35;FQ=17.3;PV4=1,0.0014,0.25,1 GT:PL:GQ 0/1:46,0,49:47
chr1 889638 . G C 29 . DP=10;VDB=0.0494;AF1=0.5;AC1=1;DP4=0,5,2,2;MQ=37;FQ=32;PV4=0.17,7e-08,1,1 GT:PL:GQ 0/1:59,0,109:62
chr1 892745 . G A 32 . DP=13;VDB=0.0540;AF1=0.5;AC1=1;DP4=0,7,0,5;MQ=37;FQ=35;PV4=1,0.0053,1,0.42 GT:PL:GQ 0/1:62,0,121:65
chr1 894573 . G A 6.98 . DP=8;VDB=0.0334;AF1=0.4999;AC1=1;DP4=0,4,0,3;MQ=36;FQ=9.53;PV4=1,0.0026,0.14,0.35 GT:PL:GQ 0/1:36,0,91:37
chr1 897325 . G C 19.1 . DP=13;VDB=0.0015;AF1=0.5;AC1=1;DP4=0,4,0,3;MQ=36;FQ=22;PV4=1,0.086,0.14,1 GT:PL:GQ 0/1:49,0,82:52
chr1 900972 . T G 32.5 . DP=4;VDB=0.0424;AF1=1;AC1=2;DP4=0,0,3,1;MQ=37;FQ=-39 GT:PL:GQ 1/1:65,12,0:21
chr1 901187 . C A 3.54 . DP=4;VDB=0.0137;AF1=0.4998;AC1=1;DP4=1,1,0,2;MQ=37;FQ=5.46;PV4=1,0.018,1,1 GT:PL:GQ 0/1:31,0,62:30
chr1 908524 . G T 5.46 . DP=5;VDB=0.0000;AF1=0.4999;AC1=1;DP4=1,1,3,0;MQ=37;FQ=7.69;PV4=0.4,0.0076,1,0.28 GT:PL:GQ 0/1:34,0,49:34
chr1 909309 . T C 3.01 . DP=5;VDB=0.0000;AF1=0.4998;AC1=1;DP4=0,2,3,0;MQ=37;FQ=4.7;PV4=0.1,0.0031,1,0.21 GT:PL:GQ 0/1:30,0,46:28
chr1 909419 . C T 26 . DP=4;VDB=0.0137;AF1=0.5004;AC1=1;DP4=0,1,0,2;MQ=37;FQ=3.54;PV4=1,0.33,1,1 GT:PL:GQ 0/1:56,0,28:31
chr1 909555 . A G 41.1 . DP=7;VDB=0.0245;AF1=1;AC1=2;DP4=0,0,6,1;MQ=37;FQ=-48 GT:PL:GQ 1/1:74,21,0:39
chr1 909768 . A G 164 . DP=24;VDB=0.0245;AF1=1;AC1=2;DP4=0,0,13,7;MQ=36;FQ=-87 GT:PL:GQ 1/1:197,60,0:99
chr1 910394 . C T 41 . DP=12;VDB=0.0002;AF1=0.5;AC1=1;DP4=2,1,4,2;MQ=37;FQ=42.3;PV4=1,0.00061,1,0.013 GT:PL:GQ 0/1:71,0,74:72
chr1 910438 . A G 179 . DP=13;VDB=0.0400;AF1=1;AC1=2;DP4=0,0,7,3;MQ=35;FQ=-57 GT:PL:GQ 1/1:212,30,0:57
chr1 912049 . T C 42 . DP=4;VDB=0.0114;AF1=0.502;AC1=1;DP4=0,1,0,3;MQ=37;FQ=-6.96;PV4=1,1,1,0.21 GT:PL:GQ 0/1:72,0,21:24
chr1 915141 . T A 6.98 . DP=14;VDB=0.0245;AF1=0.4999;AC1=1;DP4=6,2,3,0;MQ=37;FQ=9.53;PV4=1,0.023,1,1 GT:PL:GQ 0/1:36,0,164:37
chr1 915227 . A G 38 . DP=5;VDB=0.0157;AF1=1;AC1=2;DP4=0,0,0,3;MQ=37;FQ=-36 GT:PL:GQ 1/1:70,9,0:16
chr1 916389 . G T 3.54 . DP=3;VDB=0.0137;AF1=0.5002;AC1=1;DP4=1,0,2,0;MQ=33;FQ=-3.4;PV4=1,0.19,0.33,1 GT:PL:GQ 0/1:31,0,28:29
chr1 943468 . T C 76 . DP=9;VDB=0.0490;AF1=1;AC1=2;DP4=0,0,8,0;MQ=34;FQ=-51 GT:PL:GQ 1/1:109,24,0:45
chr1 943687 . G C 76 . DP=48;VDB=0.0400;AF1=0.5;AC1=1;DP4=0,19,0,25;MQ=37;FQ=79;PV4=1,7.5e-13,1,0.095 GT:PL:GQ 0/1:106,0,151:99
chr1 943771 . C A 12.3 . DP=9;VDB=0.0137;AF1=0.5;AC1=1;DP4=0,7,0,2;MQ=37;FQ=15.1;PV4=1,1,1,1 GT:PL:GQ 0/1:42,0,123:44
chr1 943907 . C G 24.8 . DP=2;VDB=0.0137;AF1=1;AC1=2;DP4=0,0,0,2;MQ=37;FQ=-33 GT:PL:GQ 1/1:56,6,0:10
chr1 948921 . T C 20.8 . DP=3;VDB=0.0182;AF1=1;AC1=2;DP4=0,0,1,1;MQ=32;FQ=-33 GT:PL:GQ 1/1:52,6,0:10
chr1 949235 . G A 15.9 . DP=2;VDB=0.0137;AF1=1;AC1=2;DP4=0,0,2,0;MQ=37;FQ=-33 GT:PL:GQ 1/1:47,6,0:10
chr1 949654 . A G 80.5 . DP=5;VDB=0.0015;AF1=1;AC1=2;DP4=0,0,2,2;MQ=34;FQ=-39 GT:PL:GQ 1/1:113,12,0:21
chr1 949925 . C T 76.1 . DP=10;VDB=0.0001;AF1=1;AC1=2;DP4=0,0,0,7;MQ=37;FQ=-48 GT:PL:GQ 1/1:109,21,0:39
chr1 981087 . A G 21.8 . DP=3;VDB=0.0231;AF1=1;AC1=2;DP4=0,0,2,0;MQ=37;FQ=-33 GT:PL:GQ 1/1:53,6,0:10
chr1 981931 . A G 39.8 . DP=2;VDB=0.0146;AF1=1;AC1=2;DP4=0,0,1,1;MQ=37;FQ=-33 GT:PL:GQ 1/1:71,6,0:10
chr1 982444 . A G 27.5 . DP=5;VDB=0.0540;AF1=1;AC1=2;DP4=0,0,0,4;MQ=37;FQ=-39 GT:PL:GQ 1/1:60,12,0:21
chr1 982462 . T C 33.8 . DP=3;VDB=0.0307;AF1=1;AC1=2;DP4=0,0,0,2;MQ=37;FQ=-33 GT:PL:GQ 1/1:65,6,0:10
chr1 982941 . T C 85 . DP=15;VDB=0.0540;AF1=1;AC1=2;DP4=0,0,6,2;MQ=37;FQ=-51 GT:PL:GQ 1/1:118,24,0:45