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runRenaming.sh.save
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[Restored contents truncated]
03 77 1 2430617 . C T 2513.03 . AC=2;AF=1.00;AN=2;DP=78;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.97;QD=32.64;SOR=1.079 GT:AD:DP:GQ:PL 1/1:0,77:77:99:2527,231,0 Haplotypecaller . . .
1 2433900 2433900 C T exonic PLCH2 . nonsynonymous SNV PLCH2:NM_001303012:exon21:c.C2930T:p.P977L . . . 0.135 0.262 T 0.007 0.131 B 0.003 0.080 B . . . 1 0.090 P . . . 1.87 0.241 -0.44 0.146 N 0.067 0.068 -0.925 0.449 T 0.000 0.000 T . . . 0.334 0.126 6.020 0.757 0.108 0.129 0.173 N c -1.382 -1.418 0.800 0.241 0.581 0.326 0 1.31 0.207 0.458 0.214 -0.530 0.049 0.000 0.063 0.000 0.016 8.026 er_leg|Spleen 1 1564.03 45 1 2433900 . C T 1564.03 . .
1 2444414 2444414 G A exonic PANK4 . nonsynonymous SNV PANK4:NM_018216:exon13:c.C1664T:p.A555V . . . . 0.086 0.496 T 0.769 0.419 P 0.119 0.306 B 0.364 0.136 N 1 0.090 P 2.18 0.615 M 3.19 0.074 -2.49 0.561 N 0.034 0.420 -0.867 0.508 T 0.000 0.000 T . . . 3.130 0.436 22.6 0.996 0.735 0.655 0.325 D c -0.119 -0.125 1.000 0.747 0.672 0.522 0 5.59 0.846 3.998 0.565 1.045 0.669 0.610 0.276 0.006 0.095 18.568 . G A 4718.03 . AC=2;AF=1.00;AN=2;BaseQRankSum=-2.528e+00;DP=160;ExcessHet=3.0103;FS=3.017;MLEAC=2;MLEAF=1.00;MQ=60.00;MQRankSum=0.00;QD=29.67;ReadPosRankSum=-3.400e-01;SOR=0.130 GT:AD:DP:GQ:PL 1/1:2,157:159:99:4732,392,0 Haplotypecaller . . .
1 2452569 2452569 T C exonic PANK4 . synonymous SNV PANK4:NM_018216:exon3:c.A417G:p.K139K . . . . . 2399.03 65 1 2452569 . T C 2399.03 . AC=2;AF=1.00;AN=2;DP=65;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=29.89;SOR=3.293 GT:AD:DP:GQ:PL
1 2462818 2462818 T C intergenic HES5;TNFRSF14-AS1 dist=1134;dist=18541 . . . . . . . 68.28 2 1 2462818 . T C 68.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=34.14;SOR=0.693 GT:AD:DP:GQ:PL
1 2462835 2462835 A G intergenic HES5;TNFRSF14-AS1 dist=1151;dist=18524 . . . . . . . 72.28 2 1 2462835 . A G 72.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=37.07;SOR=0.693 GT:AD:DP:GQ:PL
1 2465095 2465095 C T intergenic HES5;TNFRSF14-AS1 dist=3411;dist=16264 . . . . . . . 37.28 2 1 2465095 . C T 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL
1 2465144 2465144 C T intergenic HES5;TNFRSF14-AS1 dist=3460;dist=16215 . . . . . . . 37.28 2 1 2465144 . C T 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL
1 2493730 2493730 G T intronic TNFRSF14 . . . . . . . . . . . 0.5 32.60 3 1 2493730 . G T 32.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-9.670e-01;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=10.87;ReadPosRankSum=0.00;SOR=0.223 GT:AD:DP:GQ:PL 0/1:1,2:3:34:40,0,34 Haplotypecaller . . .
1 2496582 2496582 G C UTR3 TNFRSF14 NM_003820:c.*1870G>C;NM_001297605:c.*2024G>C . . . . . . 448.02 13 1 2496582 . G C 448.02 . AC=2;AF=1.00;AN=2;DP=13;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=34.46;SOR=0.836 GT:AD:DP:GQ:PL
1 2518186 2518186 A G upstream FAM213B dist=3 . . . . . . . . . . . 100.10 4 1 2518186 . A G 100.10 . AC=2;AF=1.00;AN=2;DP=4;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=25.02;SOR=1.609 GT:AD:DP:GQ:PL
1 2522392 2522392 G A UTR3 FAM213B;MMEL1 NM_001195736:c.*1526G>A;NM_152371:c.*1526G>A;NM_001195740:c.*1526G>A;NM_001195741:c.*1526G>A;NM_001195738:c.*1539G>A;NM_001195737:c.*1526G>A;NM_033467:c.*37C>T . . . . . . . . . . . . 2506.03 75 1 2522392 . G A 2506.03 . AC=2;AF=1.00;AN=2;DP=75;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=33.41;SOR=1.022 GT:AD:DP:GQ:PL 1/1:0,75:75:99:2520,225,0 Haplotypecaller . . .
1 2527678 2527678 A G intronic MMEL1 . . . . . . . . . . . . 1384.03 36 1 2527678 . A G 1384.03 . AC=2;AF=1.00;AN=2;DP=36;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=28.89;SOR=3.797 GT:AD:DP:GQ:PL
1 2528133 2528133 T C intronic MMEL1 . . . . . . . . . . . . 5494.03 174 1 2528133 . T C 5494.03 . AC=2;AF=1.00;AN=2;BaseQRankSum=1.42;DP=174;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQRankSum=0.00;QD=31.57;ReadPosRankSum=-1.575e+00;SOR=1.039 GT:AD:DP:GQ:PL 1/1:2,172:174:99:5508,471,0 Haplotypecaller . . .
1 2529192 2529192 A G intronic MMEL1 . . . . . . . . . . . . 37.28 2 1 2529192 . A G 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL
1 2529360 2529360 G A intronic MMEL1 . . . . . . . . . . . . 95.80 3 1 2529360 . G A 95.80 . AC=2;AF=1.00;AN=2;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=31.93;SOR=2.833 GT:AD:DP:GQ:PL
1 2529437 2529437 C T intronic MMEL1 . . . . . . . . . . . . 194.93 6 1 2529437 . C T 194.93 . AC=2;AF=1.00;AN=2;DP=6;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=32.49;SOR=1.329 GT:AD:DP:GQ:PL
1 2530341 2530341 - G intronic MMEL1 . . . . . . . . . . . . 583.06 16 1 2530341 . A AG 583.06 . AC=2;AF=1.00;AN=2;DP=17;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=31.43;SOR=4.174 GT:AD:DP:GQ:PL
1 2560735 2560735 A G intronic MMEL1 . . . . . . . . . . . . 886.03 28 1 2560735 . A G 886.03 . AC=2;AF=1.00;AN=2;DP=28;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=31.64;SOR=1.863 GT:AD:DP:GQ:PL
1 2560882 2560882 G A exonic MMEL1 . synonymous SNV MMEL1:NM_033467:exon2:c.C42T:p.A14A . . . . . 2517.03 58 1 2560882 . G A 2517.03 . AC=2;AF=1.00;AN=2;DP=59;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=29.47;SOR=0.914 GT:AD:DP:GQ:PGT:PID:PL:PS 1|1:0,58:58:99:1|1:2560882_G_A:2531,184,0:2560882 Haplotypecaller . . .
1 2560903 2560903 T G exonic MMEL1 . synonymous SNV MMEL1:NM_033467:exon2:c.A21C:p.P7P . . . . . 2772.03 64 1 2560903 . T G 2772.03 . AC=2;AF=1.00;AN=2;DP=65;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=32.35;SOR=0.822 GT:AD:DP:GQ:PGT:PID:PL:PS 1|1:0,64:64:99:1|1:2560882_G_A:2786,202,0:2560882 Haplotypecaller . . .
1 2561260 2561262 CCC - intronic MMEL1 . . . . . . . . . . . . 78.28 2 1 2561259 . GCCC G 78.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=31.82;SOR=0.693 GT:AD:DP:GQ:PL
1 2561286 2561286 T G intronic MMEL1 . . . . . . . . . . . . 37.28 2 1 2561286 . T G 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL
1 2564183 2564183 T C intronic MMEL1 . . . . . . . . . . . . 224.98 7 1 2564183 . T C 224.98 . AC=2;AF=1.00;AN=2;DP=7;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=32.14;SOR=4.174 GT:AD:DP:GQ:PL
1 2564465 2564465 T C UTR5 MMEL1 NM_033467:c.-3542A>G . . . . . . . . . . 38.28 2 1 2564465 . T C 38.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=19.14;SOR=2.303 GT:AD:DP:GQ:PL
1 2573199 2573199 A G exonic TTC34 . synonymous SNV TTC34:NM_001242672:exon7:c.T1309C:p.L437L . . . . 2717.03 77 1 2573199 . A G 2717.03 . AC=2;AF=1.00;AN=2;DP=77;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=29.61;SOR=1.150 GT:AD:DP:GQ:PL
1 2573903 2573903 C T intronic TTC34 . . . . . . . . . . . . 107.10 4 1 2573903 . C T 107.10 . AC=2;AF=1.00;AN=2;DP=4;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=26.77;SOR=0.693 GT:AD:DP:GQ:PL
1 2616387 2616387 C T intronic TTC34 . . . . . . . . . . . . 52.28 2 1 2616387 . C T 52.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=27.00;QD=26.14;SOR=2.303 GT:AD:DP:GQ:PL
1 2616440 2616440 C A intronic TTC34 . . . . . . . . . . . . 52.28 2 1 2616440 . C A 52.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=27.00;QD=26.14;SOR=2.303 GT:AD:DP:GQ:PL
1 2628326 2628326 A G intronic TTC34 . . . . . . . . . . . . 37.28 2 1 2628326 . A G 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=25.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL
1 2628697 2628697 G C intronic TTC34 . . . . . . . . . . . . 93.92 5 1 2628697 . G C 93.92 . AC=2;AF=1.00;AN=2;DP=5;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=54.79;QD=18.78;SOR=1.022 GT:AD:DP:GQ:PL
1 2700117 2700117 C G intronic TTC34 . . . . . . . . . . . . 1254.03 38 1 2700117 . C G 1254.03 . AC=2;AF=1.00;AN=2;DP=38;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=33.00;SOR=3.912 GT:AD:DP:GQ:PL
1 2704471 2704471 C T intronic TTC34 . . . . . . . . . . . . 142.10 4 1 2704471 . C T 142.10 . AC=2;AF=1.00;AN=2;DP=4;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=30.00;SOR=3.258 GT:AD:DP:GQ:PL
1 2722743 2722743 T A intergenic TTC34;ACTRT2 dist=16513;dist=215303 . . . . . . . . 37.28 2 1 2722743 . T A 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL
1 2727866 2727866 T A intergenic TTC34;ACTRT2 dist=21636;dist=210180 . . . . . . . . 37.28 2 1 2727866 . T A 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL
1 2736097 2736097 C A intergenic TTC34;ACTRT2 dist=29867;dist=201949 . . . . . . . . 94.80 3 1 2736097 . C A 94.80 . AC=2;AF=1.00;AN=2;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=31.60;SOR=1.179 GT:AD:DP:GQ:PL
1 2761530 2761530 T C intergenic TTC34;ACTRT2 dist=55300;dist=176516 . . . . . . . . 78.28 2 1 2761530 . T C 78.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=50.99;QD=32.87;SOR=2.303 GT:AD:DP:GQ:PGT:PID:PL:PS 1|1:0,2:2:6:1|1:2761530_T_C:90,6,0:2761530 Haplotypecaller . . .
1 2761532 2761532 T C intergenic TTC34;ACTRT2 dist=55302;dist=176514 . . . . . . . . 78.28 2 1 2761532 . T C 78.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=50.99;QD=31.78;SOR=2.303 GT:AD:DP:GQ:PGT:PID:PL:PS 1|1:0,2:2:6:1|1:2761530_T_C:90,6,0:2761530 Haplotypecaller . . .
1 2761608 2761608 C T intergenic TTC34;ACTRT2 dist=55378;dist=176438 . . . . . . . . 58.80 3 1 2761608 . C T 58.80 . AC=2;AF=1.00;AN=2;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=54.16;QD=19.60;SOR=1.179 GT:AD:DP:GQ:PL
1 2765797 2765797 G T intergenic TTC34;ACTRT2 dist=59567;dist=172249 . . . . . . . . 37.28 2 1 2765797 . G T 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL
1 2765871 2765871 C - intergenic TTC34;ACTRT2 dist=59641;dist=172175 . . . . . . . . 59.28 2 1 2765870 . GC G 59.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=29.64;SOR=0.693 GT:AD:DP:GQ:PL
1 2775803 2775880 AAGGAGAGGAAGAAAGGAAGGGAGGCAAGAAGGAAGGAAGCAGGGAGGAAGGAAGGAGGAAGGAGGAAGGAAGGAAGA - intergenic TTC34;ACTRT2 dist=69573;dist=162166 . . . . . . . . . . . . . . . . . . . 216.97 6 1 2775802 . GAAGGAGAGGAAGAAAGGAAGGGAGGCAAGAAGGAAGGAAGCAGGGAGGAAGGAAGGAGGAAGGAGGAAGGAAGGAAGA G 216.97 . AC=2;AF=1.00;AN=2;DP=8;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=54.85;QD=28.53;SOR=1.329 GT:AD:DP:GQ:PL 1/1:0,6:6:19:231,19,0 Haplotypecaller . . .
1 2779159 2779159 C G intergenic TTC34;ACTRT2 dist=72929;dist=158887 . . . . . . . . 70.28 2 1 2779159 . C G 70.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=31.86;SOR=0.693 GT:AD:DP:GQ:PL
1 2789906 2789906 C G intergenic TTC34;ACTRT2 dist=83676;dist=148140 . . . . . . . . 39.28 2 1 2789906 . C G 39.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=19.64;SOR=2.303 GT:AD:DP:GQ:PL
1 2815609 2815612 AAAC - intergenic TTC34;ACTRT2 dist=109379;dist=122434 . . . . . . . . 78.28 2 1 2815608 . AAAAC A 78.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=30.18;SOR=0.693 GT:AD:DP:GQ:PL
1 2823785 2823785 G T intergenic TTC34;ACTRT2 dist=117555;dist=114261 . . . . . . . . 0.5 33.93 3 1 2823785 . G T 33.93 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.967;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=11.31;ReadPosRankSum=-9.670e-01;SOR=0.223 GT:AD:DP:GQ:PL 0/1:1,2:3:1:41,0,1 Haplotypecaller . . .
1 2837815 2837815 C - intergenic TTC34;ACTRT2 dist=131585;dist=100231 . . . . . . . . 53.28 2 1 2837814 . TC T 53.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=26.64;SOR=0.693 GT:AD:DP:GQ:PL
1 2876525 2876525 T C intergenic TTC34;ACTRT2 dist=170295;dist=61521 . . . . . . . . 53.28 2 1 2876525 . T C 53.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=26.64;SOR=0.693 GT:AD:DP:GQ:PL
1 2883617 2883617 T A intergenic TTC34;ACTRT2 dist=177387;dist=54429 . . . . . . . . 37.28 2 1 2883617 . T A 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL
1 2886954 2886954 - A intergenic TTC34;ACTRT2 dist=180724;dist=51092 . . . . . . . . 100.84 3 1 2886954 . G GA 100.84 . AC=2;AF=1.00;AN=2;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=33.61;SOR=1.179 GT:AD:DP:GQ:PL
1 2886988 2886988 G A intergenic TTC34;ACTRT2 dist=180758;dist=51058 . . . . . . . . 0.5 67.61 4 1 2886988 . G A 67.61 . AC=1;AF=0.500;AN=2;BaseQRankSum=-3.190e-01;DP=4;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=16.90;ReadPosRankSum=-3.190e-01;SOR=0.446 GT:AD:DP:GQ:PL 0/1:1,3:4:18:75,0,18 Haplotypecaller . . .
1 2888461 2888461 T C intergenic TTC34;ACTRT2 dist=182231;dist=49585 . . . . . . . . 59.28 2 1 2888461 . T C 59.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=29.64;SOR=2.303 GT:AD:DP:GQ:PL
1 2895553 2895553 C T intergenic TTC34;ACTRT2 dist=189323;dist=42493 . . . . . . . . 0.5 39.60 4 1 2895553 . C T 39.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.150e+00;DP=4;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=9.90;ReadPosRankSum=1.15;SOR=0.916 GT:AD:DP:GQ:PL 0/1:1,3:4:31:47,0,31 Haplotypecaller . . .
1 2897093 2897093 G A intergenic TTC34;ACTRT2 dist=190863;dist=40953 . . . . . . . . 63.28 2 1 2897093 . G A 63.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=31.64;SOR=2.303 GT:AD:DP:GQ:PL
1 2897183 2897183 G A intergenic TTC34;ACTRT2 dist=190953;dist=40863 . . . . . . . . 0.5 32.60 3 1 2897183 . G A 32.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-9.670e-01;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=10.87;ReadPosRankSum=-9.670e-01;SOR=0.223 GT:AD:DP:GQ:PL 0/1:1,2:3:34:40,0,34 Haplotypecaller . . .
1 2902128 2902128 C T intergenic TTC34;ACTRT2 dist=195898;dist=35918 . . . . . . . . 37.28 2 1 2902128 . C T 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL
1 2938989 2938989 G A exonic ACTRT2 . nonsynonymous SNV ACTRT2:NM_080431:exon1:c.G739A:p.G247R . . . . 0.007 0.599 D 1.0 0.899 D 0.996 0.832 D 0.000 0.559 D 0.000 0.588 P 4.01 0.969 H -4.24 0.970 -7.42 0.948 D 0.282 0.341 -1.629 0.000 T 0.004 0.013 T . . . 5.231 0.707 25.6 0.999 0.969 0.976 0.758 D c 0.773 0.642 0.789 0.240 0.428 0.059 0 4.85 0.622 6.676 0.741 0.953 0.551 1.000 0.715 0.234 0.225 11.170 ssHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQRankSum=0.00;QD=33.95;ReadPosRankSum=0.852;SOR=0.634 GT:AD:DP:GQ:PL 1/1:1,119:120:99:4088,327,0 Haplotypecaller . . .
1 2947893 2947893 C G intergenic ACTRT2;LINC00982 dist=8426;dist=28288 . . . . . . . 37.28 2 1 2947893 . C G 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL
1 2983963 2983963 G A ncRNA_exonic LINC00982 . . . . . . . . . . . 3210.03 97 1 2983963 . G A 3210.03 . AC=2;AF=1.00;AN=2;BaseQRankSum=1.74;DP=97;ExcessHet=3.0103;FS=3.635;MLEAC=2;MLEAF=1.00;MQ=60.00;MQRankSum=0.00;QD=33.09;ReadPosRankSum=-7.100e-02;SOR=0.707 GT:AD:DP:GQ:PL 1/1:1,96:97:99:3224,281,0 Haplotypecaller . . .
1 2993807 2993807 C G intronic PRDM16 . . . . . . . . . . . . 60.28 2 1 2993807 . C G 60.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=30.14;SOR=2.303 GT:AD:DP:GQ:PL
1 3013277 3013277 T C intronic PRDM16 . . . . . . . . . . . . 0.5 32.60 3 1 3013277 . T C 32.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-9.670e-01;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=10.87;ReadPosRankSum=-9.670e-01;SOR=0.223 GT:AD:DP:GQ:PL 0/1:1,2:3:30:40,0,30 Haplotypecaller . . .
1 3017718 3017718 G T intronic PRDM16 . . . . . . . . . . . . 0.5 32.60 3 1 3017718 . G T 32.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-9.670e-01;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=10.87;ReadPosRankSum=0.431;SOR=0.223 GT:AD:DP:GQ:PL 0/1:1,2:3:34:40,0,34 Haplotypecaller . . .
1 3017751 3017751 C T intronic PRDM16 . . . . . . . . . . . . 0.5 32.60 3 1 3017751 . C T 32.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-9.670e-01;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=10.87;ReadPosRankSum=-9.670e-01;SOR=0.223 GT:AD:DP:GQ:PL 0/1:1,2:3:35:40,0,35 Haplotypecaller . . .
1 3024367 3024367 T C intronic PRDM16 . . . . . . . . . . . . 37.28 2 1 3024367 . T C 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL
1 3087373 3087373 A T intronic PRDM16 . . . . . . . . . . . . 66.28 2 1 3087373 . A T 66.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=33.14;SOR=2.303 GT:AD:DP:GQ:PL
1 3092716 3092716 - ATCCATCCATCC intronic PRDM16 . . . . . . . . . . . 145.14 4 1 3092716 . T TATCCATCCATCC 145.14 . AC=2;AF=1.00;AN=2;DP=4;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=31.99;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,4:4:12:159,12,0 Haplotypecaller . . .
1 3104630 3104630 A G intronic PRDM16 . . . . . . . . . . . . 61.28 2 1 3104630 . A G 61.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=30.64;SOR=2.303 GT:AD:DP:GQ:PL
1 3122460 3122460 C G intronic PRDM16 . . . . . . . . . . . . 66.28 2 1 3122460 . C G 66.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=33.14;SOR=0.693 GT:AD:DP:GQ:PL
1 3144884 3144884 G T intronic PRDM16 . . . . . . . . . . . . 37.28 2 1 3144884 . G T 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL
1 3149145 3149145 G A intronic PRDM16 . . . . . . . . . . . . 62.28 2 1 3149145 . G A 62.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=31.14;SOR=2.303 GT:AD:DP:GQ:PL
1 3149771 3149771 G T intronic PRDM16 . . . . . . . . . . . . 37.28 2 1 3149771 . G T 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL
1 3189732 3189732 T A intronic PRDM16 . . . . . . . . . . . . 62.28 2 1 3189732 . T A 62.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=31.14;SOR=0.693 GT:AD:DP:GQ:PL
1 3212193 3212193 A G intronic PRDM16 . . . . . . . . . . . . 0.5 89.60 9 1 3212193 . A G 89.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.26;DP=9;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=9.96;ReadPosRankSum=1.51;SOR=1.022 GT:AD:DP:GQ:PL 0/1:6,3:9:97:97,0,207 Haplotypecaller . . .
1 3212922 3212922 C G intronic PRDM16 . . . . . . . . . . . . 67.80 3 1 3212922 . C G 67.80 . AC=2;AF=1.00;AN=2;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=22.60;SOR=1.179 GT:AD:DP:GQ:PL
1 3212946 3212946 A G intronic PRDM16 . . . . . . . . . . . . 68.80 3 1 3212946 . A G 68.80 . AC=2;AF=1.00;AN=2;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=22.93;SOR=1.179 GT:AD:DP:GQ:PL
1 3215320 3215320 A T intronic PRDM16 . . . . . . . . . . . . 0.5 30.60 7 1 3215320 . A T 30.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.368e+00;DP=7;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=4.37;ReadPosRankSum=0.328;SOR=0.446 GT:AD:DP:GQ:PL 0/1:4,3:7:38:38,0,103 Haplotypecaller . . .
1 3237209 3237209 G A intronic PRDM16 . . . . . . . . . . . . 64.28 2 1 3237209 . G A 64.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=32.14;SOR=2.303 GT:AD:DP:GQ:PL
1 3246093 3246093 G A intronic PRDM16 . . . . . . . . . . . . 37.28 2 1 3246093 . G A 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL
1 3252166 3252166 - AC intronic PRDM16 . . . . . . . . . . . . 43.32 2 1 3252166 . A AAC 43.32 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=21.66;SOR=0.693 GT:AD:DP:GQ:PL
1 3260470 3260470 G T intronic PRDM16 . . . . . . . . . . . . 0.5 61.60 3 1 3260470 . G T 61.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-9.670e-01;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=20.53;ReadPosRankSum=0.967;SOR=0.223 GT:AD:DP:GQ:PL 0/1:1,2:3:32:69,0,32 Haplotypecaller . . .
1 3264190 3264190 A C intronic PRDM16 . . . . . . . . . . . . 0.5 32.60 3 1 3264190 . A C 32.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-9.670e-01;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=10.87;ReadPosRankSum=0.00;SOR=0.223 GT:AD:DP:GQ:PL 0/1:1,2:3:29:40,0,29 Haplotypecaller . . .
1 3274706 3274706 T C intronic PRDM16 . . . . . . . . . . . . 71.80 3 1 3274706 . T C 71.80 . AC=2;AF=1.00;AN=2;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=23.93;SOR=1.179 GT:AD:DP:GQ:PL
1 3287769 3287772 CCAC - intronic PRDM16 . . . . . . . . . . . . 78.28 2 1 3287768 . TCCAC T 78.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=27.54;SOR=0.693 GT:AD:DP:GQ:PL
1 3297799 3297799 A C intronic PRDM16 . . . . . . . . . . . . 64.28 2 1 3297799 . A C 64.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=32.14;SOR=2.303 GT:AD:DP:GQ:PL
1 3300807 3300807 C T intronic PRDM16 . . . . . . . . . . . . 61.28 2 1 3300807 . C T 61.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=30.64;SOR=0.693 GT:AD:DP:GQ:PL
1 3301721 3301721 C T exonic PRDM16 . synonymous SNV PRDM16:NM_022114:exon4:c.C444T:p.S148S,PRDM16:NM_199454:exon4:c.C444T:p.S148S 228417 not_specified MedGen:CN169374 criteria_provided,_multiple_submitters,_no_conflicts Benign . . . . . . . 0.5 1121.60 59 1 3301721 . C T 1121.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-4.445e+00;DP=59;ExcessHet=3.0103;FS=7.460;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=19.01;ReadPosRankSum=0.839;SOR=0.124 GT:AD:DP:GQ:PL 0/1:22,37:59:99:1129,0,695 Haplotypecaller . . .
1 3304901 3304901 A G intronic PRDM16 . . . . . . . . . . . . 37.28 2 1 3304901 . A G 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL
1 3310928 3310928 - CG intronic PRDM16 . . . . . . . . . . . . 77.32 2 1 3310928 . C CCG 77.32 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=34.14;SOR=2.303 GT:AD:DP:GQ:PL
1 3311261 3311261 C T intronic PRDM16 . . . . . . . . . . . . 0.5 125.60 7 1 3311261 . C T 125.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.189e+00;DP=7;ExcessHet=3.0103;FS=3.680;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=17.94;ReadPosRankSum=2.19;SOR=2.494 GT:AD:DP:GQ:PL 0/1:3,4:7:99:133,0,107 Haplotypecaller . . .
1 3312914 3312914 T G intronic PRDM16 . . . . . . . . . . . . 0.5 308.60 20 1 3312914 . T G 308.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.86;DP=20;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=15.43;ReadPosRankSum=1.33;SOR=1.038 GT:AD:DP:GQ:PL 0/1:11,9:20:99:316,0,308 Haplotypecaller . . .
1 3319602 3319632 CCCTCCTCTGAGTCTTCCTCCCCTTCCCGTG - intronic PRDM16 . . . . . . . . . 0.5 69.60 8 1 3319601 . ACCCTCCTCTGAGTCTTCCTCCCCTTCCCGTG A 69.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.135;DP=9;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=8.70;ReadPosRankSum=-1.570e-01;SOR=1.270 GT:AD:DP:GQ:PL 0/1:5,3:8:77:77,0,239 Haplotypcaller . . .
1 3319674 3319674 C T intronic PRDM16 . . . . . . . . . . . . 0.5 56.60 3 1 3319674 . C T 56.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-9.670e-01;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=18.87;ReadPosRankSum=-9.670e-01;SOR=1.179 GT:AD:DP:GQ:PL 0/1:1,2:3:34:64,0,34 Haplotypecaller . . .
1 3328358 3328358 T C exonic PRDM16 . nonsynonymous SNV PRDM16:NM_022114:exon9:c.T1597C:p.S533P,PRDM16:NM_199454:exon9:c.T1597C:p.S533P 228438 not_specified MedGen:CN169374 criteria_provided,_multiple_submitters,_no_conflicts Benign 0.651 0.061 T 0.0 0.026 B 0.0 0.013 B 0.005 0.328 N 0.909 0.289 P -1.7 0.004 N 3.38 0.060 T 1.31 0.010 N 0.026 0.009 -0.955 0.401 T 0.000 0.000 T . .58 0.164 0.426 0.261 0.826 0.345 14.274 0.656 . . . 10987.03 323 1 3328358 . T C 10987.03 . AC=2;AF=1.00;AN=2;DP=323;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=34.02;SOR=0.831 GT:AD:DP:GQ:PL 1/1:0,323:323:99:11001,966,0 Haplotypecaller . . .
1 3340116 3340116 A G intronic PRDM16 . . . . . . . . . . . . 37.28 2 1 3340116 . A G 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL
1 3350134 3350134 T C intronic PRDM16 . . . . . . . . . . . . 0.5 319.73 11 1 3350134 . T C 319.73 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.478;DP=11;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=54.37;MQRankSum=1.28;QD=29.07;ReadPosRankSum=-7.980e-01;SOR=3.442 GT:AD:DP:GQ:PL 0/1:1,10:11:5:327,0,5 Haplotypecaller . . .
1 3353949 3353949 A G UTR3 PRDM16 NM_022114:c.*3574A>G;NM_199454:c.*3574A>G . . . . . . . 37.28 2 1 3353949 . A G 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL
1 3383593 3383593 G T intronic ARHGEF16 . . . . . . . . . . . 881.03 26 1 3383593 . G T 881.03 . AC=2;AF=1.00;AN=2;DP=26;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=33.89;SOR=6.593 GT:AD:DP:GQ:PL
1 3383665 3383665 G A intronic ARHGEF16 . . . . . . . . . . . 2823.03 82 1 3383665 . G A 2823.03 . AC=2;AF=1.00;AN=2;DP=82;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=34.43;SOR=2.805 GT:AD:DP:GQ:PL
1 3383898 3383898 A G exonic ARHGEF16 . synonymous SNV ARHGEF16:NM_014448:exon4:c.A801G:p.P267P . . . 3551.03 98 1 3383898 . A G 3551.03 . AC=2;AF=1.00;AN=2;DP=98;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=25.40;SOR=2.718 GT:AD:DP:GQ:PL
1 3385129 3385129 G A intronic ARHGEF16 . . . . . . . . . . . 35.44 1 1 3385129 . G A 35.44 . AC=2;AF=1.00;AN=2;DP=1;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=27.98;SOR=1.609 GT:AD:DP:GQ:PGT:PID:PL:PS 1|1:0,1:1:3:1|1:3385129_G_A:45,3,0:3385129 Haplotypecaller . . .
1 3385139 3385139 G T intronic ARHGEF16 . . . . . . . . . . . 70.28 2 1 3385139 . G T 70.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=24.64;SOR=2.303 GT:AD:DP:GQ:PGT:PID:PL:PS 1|1:0,2:2:6:1|1:3385129_G_A:82,6,0:3385129 Haplotypecaller . . .
1 3385250 3385250 C A intronic ARHGEF16 . . . . . . . . . . . 578.03 17 1 3385250 . C A 578.03 . AC=2;AF=1.00;AN=2;DP=17;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=34.00;SOR=5.784 GT:AD:DP:GQ:PL
1 3385330 3385330 T C intronic ARHGEF16 . . . . . . . . . . . 1709.03 55 1 3385330 . T C 1709.03 . AC=2;AF=1.00;AN=2;DP=55;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=31.07;SOR=1.371 GT:AD:DP:GQ:PL
1 3389727 3389727 C T exonic ARHGEF16 . nonsynonymous SNV ARHGEF16:NM_014448:exon7:c.C1108T:p.H370Y . . 0.476 0.228 T 0.004 0.147 B 0.012 0.220 B 0.000 0.629 D 0.000 0.588 P 1.935 0.520 L 0.07 0.617 -2.16 0.547 N 0.255 0.311 -0.940 0.427 T 0.000 0.000 T . . . 1.043 0.194 10.90 0.914 0.201 0.840 0.428 D c -0.426 -0.327 1.000 0.500 0.696 0.567 0 3.43 0.382 1.729 0.375 0.925 0.434 0.681 0.282 0.649 0.298 7.811 erebellum|Esophagus_Mucosa|Nerve_Tibial|Skin_Not_Sun_Exposed_Suprapubic|Skin_Sun_Exposed_Lower_leg|Testis 1 3751.03 121 1 3389727 . 3751.03 . AC=2;AF=1.00;AN=2;DP=121;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=31.00;SOR=1.142 GT:AD:DP:GQ:PL 1/1:0,121:121:99:3765,363,0 Haplotypecaller . . .
1 3390238 3390238 T A intronic ARHGEF16 . . . . . . . . . . . 3866.03 113 1 3390238 . T A 3866.03 . AC=2;AF=1.00;AN=2;DP=114;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=34.21;SOR=1.828 GT:AD:DP:GQ:PL 1/1:0,113:113:99:3880,340,0 Haplotypecaller . . .
1 3391022 3391022 G A intronic ARHGEF16 . . . . . . . . . . . 211.93 6 1 3391022 . G A 211.93 . AC=2;AF=1.00;AN=2;DP=6;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=33.00;SOR=3.912 GT:AD:DP:GQ:PL
1 3394224 3394224 - G intronic ARHGEF16 . . . . . . . . . . . 162.96 5 1 3394224 . C CG 162.96 . AC=2;AF=1.00;AN=2;DP=5;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=32.59;SOR=3.611 GT:AD:DP:GQ:PL
1 3394250 3394250 C T intronic ARHGEF16 . . . . . . . . . . . 218.93 6 1 3394250 . C T 218.93 . AC=2;AF=1.00;AN=2;DP=6;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=30.03;SOR=3.912 GT:AD:DP:GQ:PL
1 3394456 3394456 T C exonic ARHGEF16 . synonymous SNV ARHGEF16:NM_014448:exon11:c.T1491C:p.S497S . . . 3007.03 89 1 3394456 . T C 3007.03 . AC=2;AF=1.00;AN=2;DP=89;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=33.79;SOR=1.557 GT:AD:DP:GQ:PL
1 3394640 3394640 A G intronic ARHGEF16 . . . . . . . . . . . 1938.03 50 1 3394640 . A G 1938.03 . AC=2;AF=1.00;AN=2;DP=50;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=29.37;SOR=4.091 GT:AD:DP:GQ:PL
1 3394674 3394674 T C intronic ARHGEF16 . . . . . . . . . . . 1286.03 38 1 3394674 . T C 1286.03 . AC=2;AF=1.00;AN=2;DP=39;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=33.84;SOR=5.892 GT:AD:DP:GQ:PL
1 3395039 3395039 G A exonic ARHGEF16 . synonymous SNV ARHGEF16:NM_014448:exon12:c.G1677A:p.V559V . . . 7665.03 241 1 3395039 . G A 7665.03 . AC=2;AF=1.00;AN=2;DP=241;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=31.81;SOR=0.843 GT:AD:DP:GQ:PL 1/1:0,241:241:99:7679,721,0 Haplotypecaller . . .
1 3395229 3395229 T C intronic ARHGEF16 . . . . . . . . . . . 865.03 25 1 3395229 . T C 865.03 . AC=2;AF=1.00;AN=2;DP=25;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=34.60;SOR=6.518 GT:AD:DP:GQ:PL
1 3395974 3395975 CC - intronic ARHGEF16 . . . . . . . . . . . 3862.03 90 1 3395973 . ACC A 3862.03 . AC=2;AF=1.00;AN=2;DP=90;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=31.53;SOR=2.303 GT:AD:DP:GQ:PL
1 3396609 3396609 C T intronic ARHGEF16 . . . . . . . . . . . 749.03 20 1 3396609 . C T 749.03 . AC=2;AF=1.00;AN=2;DP=20;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=28.93;SOR=6.091 GT:AD:DP:GQ:PL
1 3397188 3397188 T C UTR3 ARHGEF16 NM_014448:c.*37T>C . . . . . . . . . 2611.03 83 1 3397188 . T C 2611.03 . AC=2;AF=1.00;AN=2;DP=83;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=31.46;SOR=0.717 GT:AD:DP:GQ:PL
1 3397415 3397415 - CT UTR3 ARHGEF16 NM_014448:c.*264_*265insCT . . . . . . . . 119.84 3 1 3397415 . C CCT 119.84 . AC=2;AF=1.00;AN=2;DP=4;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=28.80;SOR=2.833 GT:AD:DP:GQ:PL
1 3397564 3397564 C T UTR3 ARHGEF16 NM_014448:c.*413C>T . . . . . . . . . 37.28 2 1 3397564 . C T 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL
1 3405693 3405693 T C UTR3 MEGF6 NM_001409:c.*1399A>G . . . . . . . . . . 70.28 2 1 3405693 . T C 70.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=31.66;SOR=2.303 GT:AD:DP:GQ:PL
1 3405732 3405732 C T UTR3 MEGF6 NM_001409:c.*1360G>A . . . . . . . . . . 0.5 32.60 3 1 3405732 . C T 32.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-9.670e-01;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=10.87;ReadPosRankSum=0.00;SOR=0.223 GT:AD:DP:GQ:PL 0/1:1,2:3:34:40,0,34 Haplotypecaller . . .
1 3407212 3407212 C T intronic MEGF6 . . . . . . . . . . . . 0.5 280.61 9 1 3407212 . C T 280.61 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.593e+00;DP=9;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=31.18;ReadPosRankSum=-5.890e-01;SOR=0.859 GT:AD:DP:GQ:PL 0/1:1,8:9:17:288,0,17 Haplotypecaller . . .
1 3407693 3407693 G - intronic MEGF6 . . . . . . . . . . . . 0.5 77.64 42 1 3407692 . TG T 77.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.62;DP=55;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=1.94;ReadPosRankSum=-3.470e-01;SOR=0.083 GT:AD:DP:GQ:PL 0/1:33,7:42:85:85,0,777 Haplotypecaller . . .
1 3413426 3413426 A G intronic MEGF6 . . . . . . . . . . . . 0.5 1251.60 76 1 3413426 . A G 1251.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.95;DP=77;ExcessHet=3.0103;FS=6.130;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=16.47;ReadPosRankSum=-1.770e-01;SOR=1.619 GT:AD:DP:GQ:PL 0/1:37,39:76:99:1259,0,1153 Haplotypecaller . . .
1 3413868 3413868 C G exonic MEGF6 . nonsynonymous SNV MEGF6:NM_001409:exon27:c.G3410C:p.G1137A . . . 0.01 0.564 D 0.942 0.510 P 0.902 0.623 P 0.000 0.481 N 0.979 0.277 P 3.55 0.934 H -0.09 0.718 -3.94 0.750 D 0.161 0.193 -1.091 0.053 T 0.000 0.000 T . . . 3.174 0.441 22.7 0.984 0.406 0.308 0.240 N c -0.167 -0.463 0.998 0.360 0.646 0.450 0 0.090 0.137 0.800 0.265 0.935 0.490 0.104 0.227 0.007 0.100 6.295 . C G 419.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.73;DP=33;ExcessHet=3.0103;FS=9.678;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=12.72;ReadPosRankSum=0.184;SOR=2.694 GT:AD:DP:GQ:PL 0/1:20,13:33:99:427,0,616 Haplotypecaller . . .
1 3414105 3414105 C T intronic MEGF6 . . . . . . . . . . . . 0.5 263.60 17 1 3414105 . C T 263.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.239e+00;DP=17;ExcessHet=3.0103;FS=1.913;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=15.51;ReadPosRankSum=1.47;SOR=1.270 GT:AD:DP:GQ:PL 0/1:7,10:17:99:271,0,213 Haplotypecaller . . .
1 3416449 3416449 C A exonic MEGF6 . nonsynonymous SNV MEGF6:NM_001409:exon22:c.G2747T:p.R916L . . . . 0.335 0.134 T 0.045 0.204 B 0.098 0.289 B 0.683 0.102 N 1 0.090 P 1.805 0.477 L -0.28 0.676 -4.44 0.776 D 0.149 0.416 -0.976 0.358 T 0.000 0.000 T . . . 2.090 0.312 16.79 0.940 0.234 0.195 0.205 N c -1.101 -1.168 0.756 0.234 0.706 0.609 0 -4.22 0.035 -1.812 0.018 -1.291 0.014 0.000 0.063 0.007 0.100 10.162 . AC=2;AF=1.00;AN=2;DP=54;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=30.72;SOR=0.931 GT:AD:DP:GQ:PL 1/1:0,54:54:99:1673,162,Haplotypecaller . . .
1 3417131 3417131 A G intronic MEGF6 . . . . . . . . . . . . 815.03 26 1 3417131 . A G 815.03 . AC=2;AF=1.00;AN=2;DP=26;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=31.35;SOR=1.981 GT:AD:DP:GQ:PL
1 3417960 3417960 G A intronic MEGF6 . . . . . . . . . . . . 1087.03 34 1 3417960 . G A 1087.03 . AC=2;AF=1.00;AN=2;DP=34;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=31.97;SOR=1.418 GT:AD:DP:GQ:PL
1 3418171 3418171 A G intronic MEGF6 . . . . . . . . . . . . 418.02 11 1 3418171 . A G 418.02 . AC=2;AF=1.00;AN=2;DP=11;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=33.81;SOR=2.494 GT:AD:DP:GQ:PL
1 3418391 3418391 C T exonic MEGF6 . synonymous SNV MEGF6:NM_001409:exon18:c.G2283A:p.P761P . . . . . 0.5 1557.60 91 1 3418391 . C T 1557.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.873e+00;DP=91;ExcessHet=3.0103;FS=1.780;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=17.12;ReadPosRankSum=-1.563e+00;SOR=0.498 GT:AD:DP:GQ:PL 0/1:35,56:91:99:1565,0,924 Haplotypecaller . .
1 3418565 3418565 T C intronic MEGF6 . . . . . . . . . . . . 1542.03 48 1 3418565 . T C 1542.03 . AC=2;AF=1.00;AN=2;DP=48;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=32.13;SOR=4.003 GT:AD:DP:GQ:PL
1 3430812 3430812 A - intronic MEGF6 . . . . . . . . . . . . 39.28 2 1 3430811 . CA C 39.28 . AC=2;AF=1.00;AN=2;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=57.76;QD=19.64;SOR=2.303 GT:AD:DP:GQ:PL
1 3440647 3440647 T C intronic MEGF6 . . . . . . . . . . . . 264.98 7 1 3440647 . T C 264.98 . AC=2;AF=1.00;AN=2;DP=7;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=28.07;SOR=2.584 GT:AD:DP:GQ:PL
1 3440943 3440943 A C intronic MEGF6 . . . . . . . . . . . . 0.5 96.60 8 1 3440943 . A C 96.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.37;DP=8;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=12.08;ReadPosRankSum=-1.699e+00;SOR=0.368 GT:AD:DP:GQ:PL 0/1:5,3:8:99:104,0,155 Haplotypecaller . . .
1 3447914 3447914 G C intronic MEGF6 . . . . . . . . . . . . 60.28 2 1 3447914 . G C 60.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=30.14;SOR=2.303 GT:AD:DP:GQ:PL
1 3466095 3466095 T C intronic MEGF6 . . . . . . . . . . . . 0.5 58.60 4 1 3466095 . T C 58.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.38;DP=4;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=14.65;ReadPosRankSum=0.674;SOR=0.693 GT:AD:DP:GQ:PL 0/1:2,2:4:37:66,0,37 Haplotypecaller . . .
1 3470869 3470869 T G intronic MEGF6 . . . . . . . . . . . . 40.28 2 1 3470869 . T G 40.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=20.14;SOR=2.303 GT:AD:DP:GQ:PL
1 3470888 3470888 G C intronic MEGF6 . . . . . . . . . . . . 0.5 67.60 3 1 3470888 . G C 67.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=22.53;ReadPosRankSum=0.967;SOR=1.179 GT:AD:DP:GQ:PL 0/1:1,2:3:34:75,0,34 Haplotypecaller . . .
1 3476347 3476347 G A intronic MEGF6 . . . . . . . . . . . . 0.5 32.60 3 1 3476347 . G A 32.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-9.670e-01;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=10.87;ReadPosRankSum=0.967;SOR=0.223 GT:AD:DP:GQ:PL 0/1:1,2:3:33:40,0,33 Haplotypecaller . . .
1 3477415 3477418 GGCT - intronic MEGF6 . . . . . . . . . . . . 0.5 364.60 11 1 3477414 . GGGCT G 364.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-8.750e-01;DP=11;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=33.15;ReadPosRankSum=-1.335e+00;SOR=1.179 GT:AD:DP:GQ:PL 0/1:2,9:11:91:372,0,91 Haplotypecaller . . .
1 3478596 3478596 T C intronic MEGF6 . . . . . . . . . . . . 73.28 2 1 3478596 . T C 73.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=29.04;SOR=0.693 GT:AD:DP:GQ:PL
1 3489064 3489064 C T intronic MEGF6 . . . . . . . . . . . . 60.70 3 1 3489064 . C T 60.70 . AC=2;AF=1.00;AN=2;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=39.13;QD=20.23;SOR=1.179 GT:AD:DP:GQ:PL
1 3493264 3493264 A T intronic MEGF6 . . . . . . . . . . . . 37.28 2 1 3493264 . A T 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL
1 3494529 3494529 A G intronic MEGF6 . . . . . . . . . . . . 72.28 2 1 3494529 . A G 72.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=28.82;SOR=2.303 GT:AD:DP:GQ:PL
1 3495108 3495108 G A intronic MEGF6 . . . . . . . . . . . . 37.28 2 1 3495108 . G A 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL
1 3495225 3495225 G A intronic MEGF6 . . . . . . . . . . . . 37.28 2 1 3495225 . G A 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL
1 3496328 3496328 T C intronic MEGF6 . . . . . . . . . . . . 193.93 6 1 3496328 . T C 193.93 . AC=2;AF=1.00;AN=2;DP=6;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=32.32;SOR=3.912 GT:AD:DP:GQ:PL
1 3496479 3496479 T C exonic MEGF6 . nonsynonymous SNV MEGF6:NM_001409:exon4:c.A391G:p.S131G . . . . 1.0 0.010 T 0.0 0.026 B 0.0 0.013 B 0.014 0.287 N 1 0.090 P 0.655 0.162 N -2.92 0.918 1.7 0.006 N 0.023 0.006 -0.951 0.409 T 0.000 0.000 T . . . -0.908 0.036 0.025 0.153 0.004 0.001 0.007 N c -1.158 -1.117 0.021 0.134 0.696 0.567 0 4.35 0.513 0.204 0.170 -0.052 0.122 0.000 0.063 0.011 0.114 8.494 3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=27.21;SOR=1.179 GT:AD:DP:GQ:PL 1/1:0,18:18:54:648,54,0 Haplotypecaller . . .
1 3497208 3497208 - C intronic MEGF6 . . . . . . . . . . . . 0.5 45.64 3 1 3497208 . G GC 45.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;DP=3;ExcessHet=3.0103;FS=4.771;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=15.21;ReadPosRankSum=0.967;SOR=2.225 GT:AD:DP:GQ:PL 0/1:1,2:3:22:53,0,22 Haplotypecaller . . .
1 3498486 3498486 A C intronic MEGF6 . . . . . . . . . . . . 76.80 3 1 3498486 . A C 76.80 . AC=2;AF=1.00;AN=2;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=25.60;SOR=1.179 GT:AD:DP:GQ:PL
1 3498683 3498683 G A intronic MEGF6 . . . . . . . . . . . . 62.28 2 1 3498683 . G A 62.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=31.14;SOR=2.303 GT:AD:DP:GQ:PL
1 3498740 3498740 T C intronic MEGF6 . . . . . . . . . . . . 69.80 3 1 3498740 . T C 69.80 . AC=2;AF=1.00;AN=2;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=23.27;SOR=1.179 GT:AD:DP:GQ:PL
1 3504447 3504447 T G intronic MEGF6 . . . . . . . . . . . . 0.5 68.60 3 1 3504447 . T G 68.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=22.87;ReadPosRankSum=-9.670e-01;SOR=0.223 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:1,2:3:71:0|1:3504447_T_G:76,0,71:3504447 Haplotypecaller . . .
1 3504450 3504450 C A intronic MEGF6 . . . . . . . . . . . . 0.5 68.60 2 1 3504450 . C A 68.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-6.740e-01;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=34.30;ReadPosRankSum=-6.740e-01;SOR=1.447 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:1,1:2:71:0|1:3504447_T_G:76,0,71:3504447 Haplotypecaller . . .
1 3512341 3512341 C T intronic MEGF6 . . . . . . . . . . . . 0.5 128.60 7 1 3512341 . C T 128.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.981e+00;DP=7;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=18.37;ReadPosRankSum=0.366;SOR=0.527 GT:AD:DP:GQ:PL 0/1:2,5:7:57:136,0,57 Haplotypecaller . . .
1 3512516 3512516 T C intronic MEGF6 . . . . . . . . . . . . 37.28 2 1 3512516 . T C 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL
1 3512800 3512800 T C intronic MEGF6 . . . . . . . . . . . . 94.80 3 1 3512800 . T C 94.80 . AC=2;AF=1.00;AN=2;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=31.60;SOR=2.833 GT:AD:DP:GQ:PL
1 3518743 3518743 C T intronic MEGF6 . . . . . . . . . . . . 92.80 3 1 3518743 . C T 92.80 . AC=2;AF=1.00;AN=2;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=30.93;SOR=2.833 GT:AD:DP:GQ:PL
1 3518857 3518857 A C intronic MEGF6 . . . . . . . . . . . . 329.02 10 1 3518857 . A C 329.02 . AC=2;AF=1.00;AN=2;DP=10;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=32.90;SOR=4.804 GT:AD:DP:GQ:PL
1 3518944 3518944 T C intronic MEGF6 . . . . . . . . . . . . 0.5 583.60 40 1 3518944 . T C 583.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.16;DP=40;ExcessHet=3.0103;FS=1.582;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=14.59;ReadPosRankSum=-1.056e+00;SOR=0.301 GT:AD:DP:GQ:PL 0/1:20,20:40:99:591,0,628 Haplotypecaller . . .
1 3519179 3519179 C T intronic MEGF6 . . . . . . . . . . . . 0.5 954.60 68 1 3519179 . C T 954.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.56;DP=68;ExcessHet=3.0103;FS=3.819;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=14.04;ReadPosRankSum=0.221;SOR=0.323 GT:AD:DP:GQ:PL 0/1:33,35:68:99:962,0,885 Haplotypecaller . . .
1 3520672 3520672 A C intronic MEGF6 . . . . . . . . . . . . 37.28 2 1 3520672 . A C 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL
1 3523829 3523829 T C intronic MEGF6 . . . . . . . . . . . . 74.80 3 1 3523829 . T C 74.80 . AC=2;AF=1.00;AN=2;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=24.93;SOR=1.179 GT:AD:DP:GQ:PL
1 3526390 3526390 A G intronic MEGF6 . . . . . . . . . . . . 69.28 2 1 3526390 . A G 69.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=34.64;SOR=0.693 GT:AD:DP:GQ:PL
1 3527076 3527076 - CA intronic MEGF6 . . . . . . . . . . . . 166.14 4 1 3527076 . C CCA 166.14 . AC=2;AF=1.00;AN=2;DP=4;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=30.45;SOR=0.693 GT:AD:DP:GQ:PL
1 3527944 3527944 C G UTR5 MEGF6 NM_001409:c.-112G>C . . . . . . . . . . 2311.03 63 1 3527944 . C G 2311.03 . AC=2;AF=1.00;AN=2;DP=63;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=29.99;SOR=2.340 GT:AD:DP:GQ:PL
1 3528082 3528082 T C upstream MEGF6 dist=23 . . . . . . . . . . . 861.03 23 1 3528082 . T C 861.03 . AC=2;AF=1.00;AN=2;DP=25;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=27.15;SOR=1.708 GT:AD:DP:GQ:PL
1 3528260 3528260 C T upstream MEGF6 dist=201 . . . . . . . . . . 59.28 2 1 3528260 . C T 59.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=29.64;SOR=2.303 GT:AD:DP:GQ:PL
1 3528674 3528674 G A upstream MEGF6 dist=615 . . . . . . . . . . 61.28 2 1 3528674 . G A 61.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=30.64;SOR=2.303 GT:AD:DP:GQ:PL
1 3528841 3528841 T C upstream MEGF6 dist=782 . . . . . . . . . . 213.98 7 1 3528841 . T C 213.98 . AC=2;AF=1.00;AN=2;DP=7;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=30.57;SOR=1.609 GT:AD:DP:GQ:PL
1 3534792 3534792 G C intergenic MEGF6;TPRG1L dist=6733;dist=6764 . . . . . . . . 78.28 2 1 3534792 . G C 78.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=29.04;SOR=0.693 GT:AD:DP:GQ:PGT:PID:PL:PS 1|1:0,2:2:6:1|1:3534792_G_C:90,6,0:3534792 Haplotypecaller . . .
1 3534808 3534808 G A intergenic MEGF6;TPRG1L dist=6749;dist=6748 . . . . . . . . 78.28 2 1 3534808 . G A 78.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=34.43;SOR=0.693 GT:AD:DP:GQ:PGT:PID:PL:PS 1|1:0,2:2:6:1|1:3534792_G_C:90,6,0:3534792 Haplotypecaller . . .
1 3535550 3535550 G A intergenic MEGF6;TPRG1L dist=7491;dist=6006 . . . . . . . . 78.28 2 1 3535550 . G A 78.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=31.35;SOR=2.303 GT:AD:DP:GQ:PGT:PID:PL:PS 1|1:0,2:2:6:1|1:3535550_G_A:90,6,0:3535550 Haplotypecaller . . .
1 3535556 3535556 C T intergenic MEGF6;TPRG1L dist=7497;dist=6000 . . . . . . . . 78.28 2 1 3535556 . C T 78.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=28.30;SOR=2.303 GT:AD:DP:GQ:PGT:PID:PL:PS 1|1:0,2:2:6:1|1:3535550_G_A:90,6,0:3535550 Haplotypecaller . . .
1 3535557 3535557 A G intergenic MEGF6;TPRG1L dist=7498;dist=5999 . . . . . . . . 78.28 2 1 3535557 . A G 78.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=28.93;SOR=2.303 GT:AD:DP:GQ:PGT:PID:PL:PS 1|1:0,2:2:6:1|1:3535550_G_A:90,6,0:3535550 Haplotypecaller . . .
1 3535678 3535678 A G intergenic MEGF6;TPRG1L dist=7619;dist=5878 . . . . . . . . 78.28 2 1 3535678 . A G 78.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=30.52;SOR=2.303 GT:AD:DP:GQ:PGT:PID:PL:PS 1|1:0,2:2:6:1|1:3535678_A_G:90,6,0:3535678 Haplotypecaller . . .
1 3535680 3535680 G C intergenic MEGF6;TPRG1L dist=7621;dist=5876 . . . . . . . . 78.28 2 1 3535680 . G C 78.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=28.43;SOR=2.303 GT:AD:DP:GQ:PGT:PID:PL:PS 1|1:0,2:2:6:1|1:3535678_A_G:90,6,0:3535678 Haplotypecaller . . .
1 3542106 3542106 - G intronic TPRG1L . . . . . . . . . . . . 0.5 362.64 42 1 3542106 . T TG 362.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.13;DP=46;ExcessHet=3.0103;FS=4.675;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=8.63;ReadPosRankSum=-1.128e+00;SOR=1.109 GT:AD:DP:GQ:PL 0/1:26,16:42:99:370,0,684 Haplotypecaller . . .
1 3544236 3544236 A - intronic TPRG1L . . . . . . . . . . . . 0.5 1544.60 101 1 3544235 . TA T 1544.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.737;DP=113;ExcessHet=3.0103;FS=5.813;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=15.29;ReadPosRankSum=-1.870e-01;SOR=0.306 GT:AD:DP:GQ:PL 0/1:49,52:101:99:1552,0,1436 Haplotypecaller . . .
1 3544346 3544346 T C intronic TPRG1L . . . . . . . . . . . . 0.5 648.60 31 1 3544346 . T C 648.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=4.34;DP=31;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=20.92;ReadPosRankSum=0.100;SOR=1.044 GT:AD:DP:GQ:PL 0/1:13,18:31:99:656,0,364 Haplotypecaller . . .
1 3545176 3545194 TTCTGGGAGCTCCTCCCCC - UTR3 TPRG1L NM_182752:c.*9_*27delTTCTGGGAGCTCCTCCCCC . . . . . 4441.03 99 1 3545175 . GTTCTGGGAGCTCCTCCCCC G 4441.03 . AC=2;AF=1.00;AN=2;DP=139;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=30.83;SOR=1.732 GT:AD:DP:GQ:PL 1/1:0,99:99:99:4455,310,0 Haplotypecaller . . .
1 3548136 3548136 T C exonic WRAP73 . synonymous SNV WRAP73:NM_017818:exon11:c.A1134G:p.A378A . . . . 2599.03 86 1 3548136 . T C 2599.03 . AC=2;AF=1.00;AN=2;DP=86;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=30.22;SOR=0.788 GT:AD:DP:GQ:PL
1 3548342 3548342 G A intronic WRAP73 . . . . . . . . . . . . 0.5 269.60 11 1 3548342 . G A 269.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.099;DP=11;ExcessHet=3.0103;FS=5.643;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=24.51;ReadPosRankSum=0.481;SOR=3.611 GT:AD:DP:GQ:PL 0/1:3,8:11:83:277,0,83 Haplotypecaller . . .
1 3548542 3548542 T C intronic WRAP73 . . . . . . . . . . . . 0.5 105.60 5 1 3548542 . T C 105.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.65;DP=5;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=21.12;ReadPosRankSum=0.00;SOR=1.022 GT:AD:DP:GQ:PL 0/1:2,3:5:48:113,0,48 Haplotypecaller . . .
1 3549852 3549852 G A intronic WRAP73 . . . . . . . . . . . . 0.5 847.60 41 1 3549852 . G A 847.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-4.704e+00;DP=42;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=20.67;ReadPosRankSum=-5.400e-02;SOR=1.206 GT:AD:DP:GQ:PL 0/1:16,25:41:99:855,0,537 Haplotypecaller . .
1 3550162 3550162 G A intronic WRAP73 . . . . . . . . . . . . 0.5 314.60 21 1 3550162 . G A 314.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-3.417e+00;DP=22;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=14.98;ReadPosRankSum=-1.621e+00;SOR=0.610 GT:AD:DP:GQ:PL 0/1:11,10:21:99:322,0,391 Haplotypecaller . .
1 3552780 3552780 A G intronic WRAP73 . . . . . . . . . . . . 108.80 3 1 3552780 . A G 108.80 . AC=2;AF=1.00;AN=2;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=27.64;SOR=2.833 GT:AD:DP:GQ:PL
1 3553789 3553789 T C intronic WRAP73 . . . . . . . . . . . . 169.93 6 1 3553789 . T C 169.93 . AC=2;AF=1.00;AN=2;DP=6;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=28.32;SOR=2.303 GT:AD:DP:GQ:PL
1 3554988 3554988 C T intronic WRAP73 . . . . . . . . . . . . 0.5 67.60 4 1 3554988 . C T 67.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.150e+00;DP=4;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=16.90;ReadPosRankSum=0.319;SOR=1.609 GT:AD:DP:GQ:PL 0/1:1,3:4:31:75,0,31 Haplotypecaller . . .
1 3555428 3555428 G T intronic WRAP73 . . . . . . . . . . . . 0.5 1112.60 69 1 3555428 . G T 1112.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.214e+00;DP=69;ExcessHet=3.0103;FS=10.310;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=16.12;ReadPosRankSum=-7.270e-01;SOR=2.011 GT:AD:DP:GQ:PL 0/1:30,39:69:99:1120,0,854 Haplotypecaller . .
1 3563513 3563513 C - intronic WRAP73 . . . . . . . . . . . . 0.5 539.60 31 1 3563512 . GC G 539.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-3.007e+00;DP=31;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=17.41;ReadPosRankSum=-2.536e+00;SOR=0.756 GT:AD:DP:GQ:PL 0/1:15,16:31:99:547,0,513 Haplotypecaller . .
1 3566626 3566633 GCAGGCTG - UTR5 WRAP73 NM_017818:c.-63_-70delCAGCCTGC . . . . . . . . 0.5 625.60 44 1 3566625 . AGCAGGCTG A 625.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.407e+00;DP=46;ExcessHet=3.0103;FS=1.450;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=14.22;ReadPosRankSum=0.663;SOR=1.112 GT:AD:DP:GQ:PL 0/1:27,17:44:99:633,0,1072 Haplotypecaller . .
1 3566706 3566706 G A upstream WRAP73 dist=35 . . . . . . . . . . . 521.03 16 1 3566706 . G A 521.03 . AC=2;AF=1.00;AN=2;DP=16;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=32.56;SOR=5.670 GT:AD:DP:GQ:PL
1 3574419 3574419 T A intronic TP73 . . . . . . . . . . . . 0.5 73.60 3 1 3574419 . T A 73.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-9.670e-01;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=24.53;ReadPosRankSum=0.00;SOR=0.223 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:1,2:3:67:0|1:3574419_T_A:81,0,67:3574419 Haplotypecaller . . .
1 3574420 3574420 C A intronic TP73 . . . . . . . . . . . . 0.5 73.60 3 1 3574420 . C A 73.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-9.670e-01;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=24.53;ReadPosRankSum=0.00;SOR=0.223 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:1,2:3:67:0|1:3574419_T_A:81,0,67:3574419 Haplotypecaller . . .
1 3575101 3575101 T A intronic TP73 . . . . . . . . . . . . 37.28 2 1 3575101 . T A 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL
1 3575190 3575190 T C intronic TP73 . . . . . . . . . . . . 37.28 2 1 3575190 . T C 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL
1 3587505 3587505 T C intronic TP73 . . . . . . . . . . . . 37.28 2 1 3587505 . T C 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL
1 3590425 3590425 G A intronic TP73 . . . . . . . . . . . . 0.5 32.60 3 1 3590425 . G A 32.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-9.670e-01;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=10.87;ReadPosRankSum=0.00;SOR=0.223 GT:AD:DP:GQ:PL 0/1:1,2:3:33:40,0,33 Haplotypecaller . . .
1 3596143 3596144 CT - intronic TP73 . . . . . . . . . . . . 0.5 67.60 4 1 3596142 . ACT A 67.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.383e+00;DP=4;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=16.90;ReadPosRankSum=0.00;SOR=0.105 GT:AD:DP:GQ:PL 0/1:2,2:4:75:75,0,75 Haplotypecaller . . .
1 3599514 3599514 C T intronic TP73 . . . . . . . . . . . . 0.5 840.60 54 1 3599514 . C T 840.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.621e+00;DP=54;ExcessHet=3.0103;FS=4.657;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=15.57;ReadPosRankSum=0.286;SOR=1.863 GT:AD:DP:GQ:PL 0/1:26,28:54:99:848,0,776 Haplotypecaller . . .
1 3599751 3599751 G - intronic TP73 . . . . . . . . . . . . 0.5 1066.60 78 1 3599750 . TG T 1066.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-6.720e-01;DP=89;ExcessHet=3.0103;FS=1.004;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=13.67;ReadPosRankSum=0.020;SOR=0.522 GT:AD:DP:GQ:PL 0/1:36,42:78:99:1074,0,884 Haplotypecaller . . .
1 3608011 3608011 C T intronic TP73 . . . . . . . . . . . . 63.28 2 1 3608011 . C T 63.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=31.64;SOR=0.693 GT:AD:DP:GQ:PL
1 3618714 3618714 T G intronic TP73 . . . . . . . . . . . . 72.28 2 1 3618714 . T G 72.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=27.23;SOR=0.693 GT:AD:DP:GQ:PL
1 3619707 3619707 T A intronic TP73 . . . . . . . . . . . . 37.28 2 1 3619707 . T A 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL
1 3624256 3624256 G A exonic TP73 . synonymous SNV TP73:NM_001126240:exon2:c.G183A:p.S61S,TP73:NM_001126241:exon2:c.G183A:p.S61S,TP73:NM_001126242:exon2:c.G183A:p.S61S,TP73:NM_001204189:exon2:c.G183A:p.S61S,TP73:NM_001204190:exon2:c.G183A:p.S61S,TP73:NM_001204191:exon2:c.G183A:p.S61S,TP73:NM_001204192:exon2:c.G117A:p.S39S,TP73:NM_001204184:exon4:c.G330A:p.S110S,TP73:NM_001204185:exon4:c.G330A:p.S110S,TP73:NM_001204186:exon4:c.G330A:p.S110S,TP73:NM_001204187:exon4:c.G330A:p.S110S,TP73:NM_001204188:exon4:c.G330A:p.S110S,TP73:NM_005427:exon4:c.G330A:p.S110S . . . . . . 0.5 3564.60 295 1 3624256 . G A 3564.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.753e+00;DP=295;ExcessHet=3.0103;FS=3.194;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=12.08;ReadPosRankSum=0.870;SOR=0.532 GT:AD:DP:GQ:PL 0/1:154,141:295:99:3572,0,4200 Haplotypecaller . . .
1 3626728 3626728 C T intronic TP73 . . . . . . . . . . . . 62.28 2 1 3626728 . C T 62.28 . AC=2;AF=1.00;AN=2;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=31.14;SOR=0.693 GT:AD:DP:GQ:PL
1 3628341 3628341 C T intronic TP73 . . . . . . . . . . . . 0.5 32.60 3 1 3628341 . C T 32.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-9.670e-01;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=10.87;ReadPosRankSum=0.00;SOR=0.223 GT:AD:DP:GQ:PL 0/1:1,2:3:23:40,0,23 Haplotypecaller . . .
1 3637247 3637247 G C intronic TP73 . . . . . . . . . . . . 0.5 61.60 4 1 3637247 . G C 61.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.150e+00;DP=4;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=15.40;ReadPosRankSum=0.319;SOR=0.916 GT:AD:DP:GQ:PL 0/1:1,3:4:30:69,0,30 Haplotypecaller . . .
1 3638674 3638674 C T exonic TP73 . synonymous SNV TP73:NM_001126240:exon3:c.C372T:p.T124T,TP73:NM_001126241:exon3:c.C372T:p.T124T,TP73:NM_001126242:exon3:c.C372T:p.T124T,TP73:NM_001204189:exon3:c.C372T:p.T124T,TP73:NM_001204190:exon3:c.C372T:p.T124T,TP73:NM_001204191:exon3:c.C372T:p.T124T,TP73:NM_001204192:exon3:c.C306T:p.T102T,TP73:NM_001204184:exon5:c.C519T:p.T173T,TP73:NM_001204185:exon5:c.C519T:p.T173T,TP73:NM_001204186:exon5:c.C519T:p.T173T,TP73:NM_001204187:exon5:c.C519T:p.T173T,TP73:NM_001204188:exon5:c.C519T:p.T173T,TP73:NM_005427:exon5:c.C519T:p.T173T . . . . . 0.5 3184.60 235 1 3638674 . C T 3184.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-3.910e-01;DP=237;ExcessHet=3.0103;FS=1.628;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=13.55;ReadPosRankSum=-2.600e-02;SOR=0.810 GT:AD:DP:GQ:PL 0/1:112,123:235:99:3192,0,3041 Haplotypecaller . .
1 3638834 3638834 C T intronic TP73 . . . . . . . . . . . . 0.5 211.60 25 1 3638834 . C T 211.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.62;DP=25;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=8.46;ReadPosRankSum=-2.920e-01;SOR=0.223 GT:AD:DP:GQ:PL 0/1:17,8:25:99:219,0,523 Haplotypecaller . . .
1 3640085 3640085 C G intronic TP73 . . . . . . . . . . . . 0.5 457.60 26 1 3640085 . C G 457.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.03;DP=26;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=17.60;ReadPosRankSum=1.32;SOR=0.846 GT:AD:DP:GQ:PL 0/1:12,14:26:99:465,0,189 Haplotypecaller . . .
1 3640135 3640138 CTGC - intronic TP73 . . . . . . . . . . . . 0.5 251.60 17 1 3640134 . TCTGC T 251.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.570e-01;DP=19;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=14.80;ReadPosRankSum=0.490;SOR=0.425 GT:AD:DP:GQ:PL 0/1:10,7:17:99:259,0,399 Haplotypecaller . . .
1 3644349 3644349 A G intronic TP73 . . . . . . . . . . . . 0.5 955.60 71 1 3644349 . A G 955.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.39;DP=71;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=13.46;ReadPosRankSum=1.22;SOR=0.593 GT:AD:DP:GQ:PL 0/1:37,34:71:99:963,0,1113 Haplotypecaller . . .
1 3644374 3644374 A G intronic TP73 . . . . . . . . . . . . 0.5 895.60 52 1 3644374 . A G 895.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.98;DP=52;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=17.22;ReadPosRankSum=0.971;SOR=0.529 GT:AD:DP:GQ:PL 0/1:25,27:52:99:903,0,801 Haplotypecaller . . .
1 3644669 3644669 C T intronic TP73 . . . . . . . . . . . . 0.5 621.60 36 1 3644669 . C T 621.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.928e+00;DP=36;ExcessHet=3.0103;FS=1.511;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=17.27;ReadPosRankSum=0.487;SOR=0.368 GT:AD:DP:GQ:PL 0/1:14,22:36:99:629,0,395 Haplotypecaller . . .
1 3644805 3644805 A G intronic TP73 . . . . . . . . . . . . 0.5 1503.60 110 1 3644805 . A G 1503.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.670;DP=110;ExcessHet=3.0103;FS=0.713;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=13.67;ReadPosRankSum=0.506;SOR=0.836 GT:AD:DP:GQ:PL 0/1:52,58:110:99:1511,0,1261 Haplotypecaller . . .
1 3644858 3644858 G C intronic TP73 . . . . . . . . . . . . 0.5 814.60 67 1 3644858 . G C 814.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.774e+00;DP=67;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=12.16;ReadPosRankSum=0.593;SOR=0.762 GT:AD:DP:GQ:PL 0/1:37,30:67:99:822,0,1176 Haplotypecaller . . .
1 3645052 3645052 A G intronic TP73 . . . . . . . . . . . . 0.5 183.60 6 1 3645052 . A G 183.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.38;DP=6;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=30.60;ReadPosRankSum=1.38;SOR=2.303 GT:AD:DP:GQ:PL 0/1:1,5:6:23:191,0,23 Haplotypecaller . . .
1 3646192 3646192 G A intronic TP73 . . . . . . . . . . . . 0.5 1562.60 79 1 3646192 . G A 1562.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-5.236e+00;DP=79;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=19.78;ReadPosRankSum=-4.360e-01;SOR=0.750 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:34,45:79:99:0|1:3646192_G_A:1570,0,1239:3646192 Haplotypecaller . . .
1 3646214 3646214 T C intronic TP73 . . . . . . . . . . . . 0.5 1192.60 58 1 3646214 . T C 1192.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.521e+00;DP=58;ExcessHet=3.0103;FS=1.368;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=20.56;ReadPosRankSum=0.568;SOR=0.361 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:29,29:58:99:0|1:3646192_G_A:1200,0,1096:3646192 Haplotypecaller . . .
1 3646291 3646291 G A intronic TP73 . . . . . . . . . . . . 0.5 239.60 16 1 3646291 . G A 239.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-3.951e+00;DP=16;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=14.98;ReadPosRankSum=-8.750e-01;SOR=0.693 GT:AD:DP:GQ:PL 0/1:8,8:16:99:247,0,287 Haplotypecaller . . .
1 3651797 3651797 G T UTR3 TP73 NM_001204188:c.*2154G>T;NM_001204184:c.*2471G>T;NM_001204185:c.*2488G>T;NM_005427:c.*2154G>T;NM_001204187:c.*2154G>T;NM_001204186:c.*2471G>T;NM_001204189:c.*2471G>T;NM_001204191:c.*2154G>T;NM_001126242:c.*2488G>T;NM_001126241:c.*2471G>T;NM_001126240:c.*2154G>T;NM_001204190:c.*2154G>T;NM_001204192:c.*2154G>T . . . . . . . . . . . . . . 37.28 2 1 3651797 . G T 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693
1 3662845 3662845 A G ncRNA_exonic TP73-AS1 . . . . . . . . . . . 0.5 225.60 9 1 3662845 . A G 225.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.52;DP=9;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=25.07;ReadPosRankSum=0.241;SOR=1.402 GT:AD:DP:GQ:PL 0/1:3,6:9:68:233,0,68 Haplotypecaller . . .
1 3668781 3668781 G T upstream CCDC27 dist=184 . . . . . . . . . . 0.5 119.60 9 1 3668781 . G T 119.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.465e+00;DP=9;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=13.29;ReadPosRankSum=0.231;SOR=1.609 GT:AD:DP:GQ:PL 0/1:5,4:9:99:127,0,169 Haplotypecaller . . .
1 3669172 3669172 C T exonic CCDC27 . nonsynonymous SNV CCDC27:NM_152492:exon1:c.C127T:p.R43C . . . . 0.141 0.255 T 0.949 0.518 P 0.272 0.382 B 0.029 0.017 N 1 0.090 P 0 0.065 N 1.96 0.223 -0.5 0.158 N 0.037 0.048 -1.047 0.152 T 0.002 0.005 T . . . 3.953 0.532 23.6 0.527 0.047 0.010 0.038 N c -1.051 -1.230 0.981 0.302 0.497 0.185 0 -4.49 0.032 -0.084 0.111 -0.491 0.052 0.000 0.063 0.000 0.016 6.563 59;ExcessHet=3.0103;FS=1.512;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=10.86;ReadPosRankSum=-5.390e-01;SOR=0.812 GT:AD:DP:GQ:PL 0/1:149,110:259:99:2819,0,4199 Haplotypecaller . . .
1 3669201 3669201 A G exonic CCDC27 . synonymous SNV CCDC27:NM_152492:exon1:c.A156G:p.P52P . . . . . 0.5 4204.60 238 1 3669201 . A G 4204.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.318;DP=238;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=17.67;ReadPosRankSum=0.324;SOR=0.697 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:128,110:238:99:0|1:3669201_A_G:4212,0,4977:3669201 Haplotypecaller . . .
1 3669205 3669205 C G exonic CCDC27 . nonsynonymous SNV CCDC27:NM_152492:exon1:c.C160G:p.Q54E . . . . 1.0 0.010 T 0.0 0.026 B 0.0 0.013 B 0.650 0.059 N 1 0.090 P -0.69 0.019 N 2.26 0.176 0.36 0.037 N 0.007 0.003 -0.912 0.466 T 0.000 0.000 T . . . -3.140 0.001 0.001 0.296 0.016 0.002 0.012 N c -1.783 -1.846 0.998 0.366 0.497 0.185 0 -5.54 0.023 -1.373 0.027 -1.584 0.009 0.000 0.063 0.000 0.016 7.909 =-1.162e+00;DP=228;ExcessHet=3.0103;FS=2.278;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=18.15;ReadPosRankSum=0.636;SOR=0.535 GT:AD:DP:GQ:PGT:PID:PL:P0|1:122,106:228:99:0|1:3669201_A_G:4146,0,4899:3669201 Haplotypecaller . . .
1 3671027 3671027 T C intronic CCDC27 . . . . . . . . . . . . 0.5 128.60 6 1 3671027 . T C 128.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.842;DP=6;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=21.43;ReadPosRankSum=-4.310e-01;SOR=1.329 GT:AD:DP:GQ:PL 0/1:2,4:6:46:136,0,46 Haplotypecaller . . .
1 3671791 3671791 A G intronic CCDC27 . . . . . . . . . . . . 0.5 375.60 21 1 3671791 . A G 375.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.43;DP=21;ExcessHet=3.0103;FS=6.923;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=17.89;ReadPosRankSum=1.39;SOR=1.938 GT:AD:DP:GQ:PL 0/1:9,12:21:99:383,0,275 Haplotypecaller . . .
1 3677933 3677933 T C exonic CCDC27 . nonsynonymous SNV CCDC27:NM_152492:exon5:c.T800C:p.M267T . . . . 0.3 0.145 T 0.0 0.026 B 0.0 0.013 B 0.161 0.177 N 1 0.090 P -1.1 0.010 N 2.31 0.168 0.64 0.024 N 0.007 0.000 -1.015 0.254 T 0.000 0.000 T . . . -1.579 0.015 0.002 0.238 0.010 0.011 0.040 N c -1.934 -1.895 0.020 0.132 0.497 0.185 0 -1.31 0.087 -0.597 0.058 -0.580 0.045 0.531 0.270 0.546 0.279 0.040 essHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=15.71;ReadPosRankSum=-6.640e-01;SOR=0.817 GT:AD:DP:GQ:PL 0/1:24,36:60:99:950,0,59Haplotypecaller . . .
1 3678221 3678221 G C intronic CCDC27 . . . . . . . . . . . . 0.5 41.60 3 1 3678221 . G C 41.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-9.670e-01;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=13.87;ReadPosRankSum=-9.670e-01;SOR=1.179 GT:AD:DP:GQ:PL 0/1:1,2:3:33:49,0,33 Haplotypecaller . . .
1 3679139 3679139 T C intronic CCDC27 . . . . . . . . . . . . 0.5 164.60 10 1 3679139 . T C 164.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-3.850e-01;DP=10;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=16.46;ReadPosRankSum=-1.050e-01;SOR=0.527 GT:AD:DP:GQ:PL 0/1:3,7:10:57:172,0,57 Haplotypecaller . . .
1 3679307 3679307 T C intronic CCDC27 . . . . . . . . . . . . 0.5 59.60 6 1 3679307 . T C 59.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.645e+00;DP=6;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=9.93;ReadPosRankSum=0.189;SOR=0.132 GT:AD:DP:GQ:PL 0/1:3,3:6:67:67,0,93 Haplotypecaller . . .
1 3680056 3680056 G A intronic CCDC27 . . . . . . . . . . . . 0.5 1001.60 98 1 3680056 . G A 1001.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.890e+00;DP=98;ExcessHet=3.0103;FS=5.198;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=10.22;ReadPosRankSum=-1.850e-01;SOR=1.208 GT:AD:DP:GQ:PL 0/1:59,39:98:99:1009,0,1728 Haplotypecaller . .
1 3683690 3683690 A C intronic CCDC27 . . . . . . . . . . . . 1663.03 42 1 3683690 . A C 1663.03 . AC=2;AF=1.00;AN=2;DP=42;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=56.32;QD=31.92;SOR=5.235 GT:AD:DP:GQ:PL
1 3684107 3684107 T A intronic CCDC27 . . . . . . . . . . . . 214.93 6 1 3684107 . T A 214.93 . AC=2;AF=1.00;AN=2;DP=6;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=31.19;SOR=3.912 GT:AD:DP:GQ:PL
1 3687739 3687739 C A intronic CCDC27 . . . . . . . . . . . . 0.5 106.60 9 1 3687739 . C A 106.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-7.120e-01;DP=9;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=11.84;ReadPosRankSum=0.700;SOR=0.527 GT:AD:DP:GQ:PL 0/1:5,4:9:99:114,0,142 Haplotypecaller . . .
1 3688324 3688324 T A downstream CCDC27 dist=115 . . . . . . . . . . 0.5 93.60 5 1 3688324 . T A 93.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.04;DP=5;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=18.72;ReadPosRankSum=0.00;SOR=1.022 GT:AD:DP:GQ:PL 0/1:2,3:5:53:101,0,53 Haplotypecaller . . .
1 3691470 3691470 A C intronic SMIM1 . . . . . . . . . . . . 37.28 2 1 3691470 . A C 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL
1 3691727 3691727 A C intronic SMIM1 . . . . . . . . . . . . 0.5 206.60 11 1 3691727 . A C 206.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.07;DP=11;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=18.78;ReadPosRankSum=0.437;SOR=0.859 GT:AD:DP:GQ:PL 0/1:5,6:11:99:214,0,153 Haplotypecaller . . .
1 3692240 3692240 T C intronic SMIM1 . . . . . . . . . . . . 0.5 233.60 13 1 3692240 . T C 233.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.89;DP=13;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=17.97;ReadPosRankSum=-4.730e-01;SOR=0.859 GT:AD:DP:GQ:PL 0/1:6,7:13:99:241,0,162 Haplotypecaller . . .
1 3693032 3693032 A G downstream SMIM1 dist=486 . . . . . . . . . . 157.92 5 1 3693032 . A G 157.92 . AC=2;AF=1.00;AN=2;DP=5;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=31.58;SOR=1.981 GT:AD:DP:GQ:PL
1 3699568 3699568 G C intronic LRRC47 . . . . . . . . . . . . 169.92 5 1 3699568 . G C 169.92 . AC=2;AF=1.00;AN=2;DP=5;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=33.98;SOR=3.611 GT:AD:DP:GQ:PL
1 3701491 3701491 A G intronic LRRC47 . . . . . . . . . . . . 230.98 7 1 3701491 . A G 230.98 . AC=2;AF=1.00;AN=2;DP=7;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=33.00;SOR=4.174 GT:AD:DP:GQ:PL
1 3703337 3703337 G C intronic LRRC47 . . . . . . . . . . . . 0.5 243.60 12 1 3703337 . G C 243.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-7.290e-01;DP=12;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=20.30;ReadPosRankSum=-1.114e+00;SOR=1.022 GT:AD:DP:GQ:PL 0/1:5,7:12:99:251,0,157 Haplotypecaller . . .
1 3704041 3704041 C T intronic LRRC47 . . . . . . . . . . . . 0.5 547.60 31 1 3704041 . C T 547.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.040e+00;DP=31;ExcessHet=3.0103;FS=3.774;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=17.66;ReadPosRankSum=-9.420e-01;SOR=2.256 GT:AD:DP:GQ:PL 0/1:13,18:31:99:555,0,383 Haplotypecaller . .
1 3706246 3706246 G A intronic LRRC47 . . . . . . . . . . . . 0.5 53.60 6 1 3706246 . G A 53.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.524;DP=6;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=8.93;ReadPosRankSum=-8.420e-01;SOR=1.179 GT:AD:DP:GQ:PL 0/1:4,2:6:61:61,0,115 Haplotypecaller . . .
1 3707456 3707456 - C intronic LRRC47 . . . . . . . . . . . . 98.84 3 1 3707456 . G GC 98.84 . AC=2;AF=1.00;AN=2;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=32.95;SOR=1.179 GT:AD:DP:GQ:PL
1 3713077 3713077 G T upstream LRRC47 dist=9 . . . . . . . . . . . 0.5 668.60 50 1 3713077 . G T 668.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-3.083e+00;DP=50;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=13.37;ReadPosRankSum=-2.360e-01;SOR=0.763 GT:AD:DP:GQ:PL 0/1:21,29:50:99:676,0,607 Haplotypecaller . .
1 3722288 3722288 A T intergenic LRRC47;CEP104 dist=9220;dist=6357 . . . . . . . . 58.28 2 1 3722288 . A T 58.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=29.14;SOR=0.693 GT:AD:DP:GQ:PL
1 3722309 3722309 C T intergenic LRRC47;CEP104 dist=9241;dist=6336 . . . . . . . . 63.28 2 1 3722309 . C T 63.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=31.64;SOR=0.693 GT:AD:DP:GQ:PL
1 3722485 3722485 T C intergenic LRRC47;CEP104 dist=9417;dist=6160 . . . . . . . . 60.28 2 1 3722485 . T C 60.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=30.14;SOR=2.303 GT:AD:DP:GQ:PL
1 3726326 3726326 C T intergenic LRRC47;CEP104 dist=13258;dist=2319 . . . . . . . . 143.10 4 1 3726326 . C T 143.10 . AC=2;AF=1.00;AN=2;DP=4;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=33.56;SOR=3.258 GT:AD:DP:GQ:PL
1 3726851 3726851 T C intergenic LRRC47;CEP104 dist=13783;dist=1794 . . . . . . . . 37.28 2 1 3726851 . T C 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL
1 3731654 3731654 - T UTR3 CEP104 NM_014704:c.*311_*312insA . . . . . . . . . 0.5 326.68 10 1 3731654 . C CT 326.68 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.530e-01;DP=10;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=32.67;ReadPosRankSum=-3.850e-01;SOR=3.258 GT:AD:DP:GQ:PL 0/1:1,9:10:10:334,0,10 Haplotypecaller . . .
1 3732103 3732103 T C intronic CEP104 . . . . . . . . . . . . 1039.03 32 1 3732103 . T C 1039.03 . AC=2;AF=1.00;AN=2;BaseQRankSum=-1.685e+00;DP=32;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQRankSum=0.00;QD=32.47;ReadPosRankSum=0.325;SOR=5.549 GT:AD:DP:GQ:PL 1/1:1,31:32:59:1053,59,0 Haplotypecaller . . .
1 3732172 3732172 C T intronic CEP104 . . . . . . . . . . . . 646.03 18 1 3732172 . C T 646.03 . AC=2;AF=1.00;AN=2;DP=18;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=33.57;SOR=5.892 GT:AD:DP:GQ:PL
1 3732596 3732596 G T intronic CEP104 . . . . . . . . . . . . 487.02 13 1 3732596 . G T 487.02 . AC=2;AF=1.00;AN=2;DP=13;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=33.42;SOR=5.283 GT:AD:DP:GQ:PL
1 3732639 3732639 T A intronic CEP104 . . . . . . . . . . . . 518.03 15 1 3732639 . T A 518.03 . AC=2;AF=1.00;AN=2;DP=15;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=34.54;SOR=5.549 GT:AD:DP:GQ:PL
1 3732707 3732707 T C intronic CEP104 . . . . . . . . . . . . 1215.03 34 1 3732707 . T C 1215.03 . AC=2;AF=1.00;AN=2;DP=34;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=31.23;SOR=2.049 GT:AD:DP:GQ:PL
1 3732782 3732782 T C intronic CEP104 . . . . . . . . . . . . 1930.03 57 1 3732782 . T C 1930.03 . AC=2;AF=1.00;AN=2;DP=57;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=33.86;SOR=0.728 GT:AD:DP:GQ:PL
1 3742179 3742179 G A intronic CEP104 . . . . . . . . . . . . 416.02 12 1 3742179 . G A 416.02 . AC=2;AF=1.00;AN=2;DP=12;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=34.67;SOR=5.136 GT:AD:DP:GQ:PL
1 3743109 3743109 A G intronic CEP104 . . . . . . . . . . . . 5070.03 117 1 3743109 . A G 5070.03 . AC=2;AF=1.00;AN=2;DP=117;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=26.59;SOR=3.611 GT:AD:DP:GQ:PGT:PID:PL:PS 1|1:0,117:117:99:1|1:3743109_A_G:5084,358,0:3743109 Haplotypecaller . . .
1 3743132 3743132 T C intronic CEP104 . . . . . . . . . . . . 5176.03 117 1 3743132 . T C 5176.03 . AC=2;AF=1.00;AN=2;DP=117;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=27.54;SOR=3.611 GT:AD:DP:GQ:PGT:PID:PL:PS 1|1:0,117:117:99:1|1:3743109_A_G:5190,358,0:3743109 Haplotypecaller . . .
1 3743319 3743319 G A intronic CEP104 . . . . . . . . . . . . 0.5 2810.60 243 1 3743319 . G A 2810.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.322e+00;DP=243;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=11.57;ReadPosRankSum=0.882;SOR=0.708 GT:AD:DP:GQ:PL 0/1:142,101:243:99:2818,0,4135 Haplotypecaller . . .
1 3743391 3743391 C T intronic CEP104 . . . . . . . . . . . . 0.5 2039.60 120 1 3743391 . C T 2039.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=5.87;DP=120;ExcessHet=3.0103;FS=7.566;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=17.00;ReadPosRankSum=-4.600e-01;SOR=1.775 GT:AD:DP:GQ:PL 0/1:53,67:120:99:2047,0,1382 Haplotypecaller . . .
1 3743433 3743433 - G intronic CEP104 . . . . . . . . . . . . 1912.06 54 1 3743433 . T TG 1912.06 . AC=2;AF=1.00;AN=2;DP=55;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=36.09;SOR=5.136 GT:AD:DP:GQ:PL
1 3743553 3743553 - A intronic CEP104 . . . . . . . . . . . . 0.5 181.64 11 1 3743553 . C CA 181.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-3.290e-01;DP=12;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=16.51;ReadPosRankSum=1.51;SOR=1.270 GT:AD:DP:GQ:PL 0/1:4,7:11:94:189,0,94 Haplotypecaller . . .
1 3745557 3745557 G T intronic CEP104 . . . . . . . . . . . . 222.98 7 1 3745557 . G T 222.98 . AC=2;AF=1.00;AN=2;DP=7;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=31.85;SOR=4.174 GT:AD:DP:GQ:PL
1 3745721 3745721 C T intronic CEP104 . . . . . . . . . . . . 0.5 280.60 36 1 3745721 . C T 280.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.954e+00;DP=36;ExcessHet=3.0103;FS=8.300;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=7.79;ReadPosRankSum=-9.960e-01;SOR=2.925 GT:AD:DP:GQ:PL 0/1:25,11:36:99:288,0,788 Haplotypecaller . .
1 3745787 3745787 T C intronic CEP104 . . . . . . . . . . . . 3461.03 99 1 3745787 . T C 3461.03 . AC=2;AF=1.00;AN=2;DP=100;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=34.96;SOR=1.449 GT:AD:DP:GQ:PL 1/1:0,99:99:99:3475,297,0 Haplotypecaller . . .
1 3746116 3746116 A G intronic CEP104 . . . . . . . . . . . . 278.98 7 1 3746116 . A G 278.98 . AC=2;AF=1.00;AN=2;DP=7;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=27.76;SOR=2.584 GT:AD:DP:GQ:PL
1 3746254 3746254 T C intronic CEP104 . . . . . . . . . . . . 553.03 14 1 3746254 . T C 553.03 . AC=2;AF=1.00;AN=2;DP=14;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=30.63;SOR=3.912 GT:AD:DP:GQ:PL
1 3746585 3746585 T G intronic CEP104 . . . . . . . . . . . . 0.5 73.60 3 1 3746585 . T G 73.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.967;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=24.53;ReadPosRankSum=0.967;SOR=1.179 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:1,2:3:27:0|1:3746585_T_G:81,0,27:3746585 Haplotypcaller . . .
1 3746589 3746589 C G intronic CEP104 . . . . . . . . . . . . 0.5 73.60 2 1 3746589 . C G 73.60 . AC=1;AF=0.500;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=32.16;SOR=2.303 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:0,2:2:27:0|1:3746585_T_G:81,0,27:3746585 Haplotypecaller . . .
1 3747603 3747603 T C intronic CEP104 . . . . . . . . . . . . 707.03 18 1 3747603 . T C 707.03 . AC=2;AF=1.00;AN=2;DP=18;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=26.67;SOR=5.892 GT:AD:DP:GQ:PL
1 3748085 3748085 A G intronic CEP104 . . . . . . . . . . . . 0.5 67.60 3 1 3748085 . A G 67.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.967;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=22.53;ReadPosRankSum=0.967;SOR=1.179 GT:AD:DP:GQ:PL 0/1:1,2:3:29:75,0,29 Haplotypecaller . . .
1 3750167 3750167 G A intronic CEP104 . . . . . . . . . . . . 51.28 2 1 3750167 . G A 51.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=25.64;SOR=2.303 GT:AD:DP:GQ:PL
1 3750731 3750731 T G intronic CEP104 . . . . . . . . . . . . 939.03 24 1 3750731 . T G 939.03 . AC=2;AF=1.00;AN=2;DP=24;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=32.18;SOR=4.977 GT:AD:DP:GQ:PL
1 3751728 3751728 - T intronic CEP104 . . . . . . . . . . . . 0.5 249.64 61 1 3751728 . G GT 249.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.110e-01;DP=85;ExcessHet=3.0103;FS=4.550;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=4.30;ReadPosRankSum=-9.660e-01;SOR=1.429 GT:AD:DP:GQ:PL 0/1:42,16:61:99:257,0,1030 Haplotypecaller . .
1 3751966 3751966 C G intronic CEP104 . . . . . . . . . . . . 181.92 5 1 3751966 . C G 181.92 . AC=2;AF=1.00;AN=2;DP=5;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=28.65;SOR=3.611 GT:AD:DP:GQ:PL
1 3752121 3752121 G A intronic CEP104 . . . . . . . . . . . . 0.5 62.60 3 1 3752121 . G A 62.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-9.670e-01;DP=3;ExcessHet=3.0103;FS=4.771;MLEAC=1;MLEAF=0.500;MQ=47.61;MQRankSum=-9.670e-01;QD=20.87;ReadPosRankSum=-9.670e-01;SOR=2.225 GT:AD:DP:GQ:PL 0/1:1,2:3:34:70,0,34 Haplotypecaller . . .
1 3752739 3752739 G A intronic CEP104 . . . . . . . . . . . . 0.5 59.60 4 1 3752739 . G A 59.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-3.190e-01;DP=4;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=14.90;ReadPosRankSum=0.319;SOR=1.609 GT:AD:DP:GQ:PL 0/1:1,3:4:24:67,0,24 Haplotypecaller . . .
1 3752792 3752792 G A intronic CEP104 . . . . . . . . . . . . 0.5 84.60 6 1 3752792 . G A 84.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.890e-01;DP=6;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=14.10;ReadPosRankSum=0.189;SOR=0.693 GT:AD:DP:GQ:PL 0/1:3,3:6:92:92,0,93 Haplotypecaller . . .
1 3753013 3753013 G C intronic CEP104 . . . . . . . . . . . . 0.5 399.60 27 1 3753013 . G C 399.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-3.474e+00;DP=28;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.59;MQRankSum=-1.610e-01;QD=14.80;ReadPosRankSum=-8.060e-01;SOR=0.465 GT:AD:DP:GQ:PL 0/1:15,12:27:99:407,0,565 Haplotypecaller .
1 3753057 3753062 ACCAAG - exonic CEP104 . frameshift deletion CEP104:NM_014704:exon10:c.1314_1317del:p.V440Lfs*22 . . 0.5 208.60 62 1 3753056 . TACCAAG T 208.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.22;DP=68;ExcessHet=3.0103;FS=10.422;MLEAC=1;MLEAF=0.500;MQ=57.97;MQRankSum=-4.312e+00;QD=3.36;ReadPosRankSum=3.33;SOR=2.448 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:49,13:62:99:0|1:3753056_TACCAAG_T:216,0,2000:3753056 Haplotypecaller . . .
1 3753063 3753063 G T exonic CEP104 . nonsynonymous SNV CEP104:NM_014704:exon10:c.C1313A:p.T438N . . . 0.437 0.101 T 0.376 0.324 B 0.109 0.310 B 0.041 0.240 N 1 0.090 N 1.735 0.450 L 2.23 0.181 -0.12 0.164 N 0.048 0.181 -1.047 0.152 T 0.025 0.105 T . . . -0.070 0.087 1.962 0.894 0.182 0.377 0.256 N c -0.737 -0.709 0.186 0.179 0.706 0.609 0 3.73 0.418 3.069 0.495 0.095 0.197 0.124 0.230 0.440 0.261 15.137 -2.557e+00;DP=61;ExcessHet=3.0103;FS=8.142;MLEAC=1;MLEAF=0.500;MQ=58.52;MQRankSum=-4.891e+00;QD=3.45;ReadPosRankSum=1.26;SOR=2.338 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:48,13:61:99:0|1:3753056_TACCAAG_T:218,0,1978:3753056 Haplotypecaller . . .
1 3755675 3755675 T C exonic CEP104 . synonymous SNV CEP104:NM_014704:exon8:c.A744G:p.E248E . . . . . 7122.03 207 1 3755675 . T C 7122.03 . AC=2;AF=1.00;AN=2;DP=207;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=34.41;SOR=1.195 GT:AD:DP:GQ:PL 1/1:0,207:207:99:7136,620,0 Haplotypecaller . . .
1 3755869 3755869 T C intronic CEP104 . . . . . . . . . . . . 761.03 18 1 3755869 . T C 761.03 . AC=2;AF=1.00;AN=2;DP=18;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=28.33;SOR=5.892 GT:AD:DP:GQ:PGT:PID:PL:PS 1|1:0,18:18:54:1|1:3755869_T_C:775,54,0:3755869 Haplotypecaller . . .
1 3755875 3755875 T G intronic CEP104 . . . . . . . . . . . . 710.03 17 1 3755875 . T G 710.03 . AC=2;AF=1.00;AN=2;DP=17;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=28.36;SOR=4.294 GT:AD:DP:GQ:PGT:PID:PL:PS 1|1:0,17:17:51:1|1:3755869_T_C:724,51,0:3755869 Haplotypecaller . . .
1 3756493 3756493 T C intronic CEP104 . . . . . . . . . . . . 937.03 27 1 3756493 . T C 937.03 . AC=2;AF=1.00;AN=2;DP=27;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=34.70;SOR=6.666 GT:AD:DP:GQ:PL
1 3756530 3756530 C A intronic CEP104 . . . . . . . . . . . . 0.5 131.60 11 1 3756530 . C A 131.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-3.067e+00;DP=11;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=11.96;ReadPosRankSum=-1.750e-01;SOR=0.551 GT:AD:DP:GQ:PL 0/1:6,5:11:99:139,0,219 Haplotypecaller . . .
1 3759784 3759784 A G intronic CEP104 . . . . . . . . 0.0 0.912 D . 0.090 P . . . . . . 0.63 0.024 N 0.044 0.024 -1.025 0.222 T 0.000 0.000 T . -0.071 0.087 1.955 0.100 0.001 0.001 0.006 N c -1.132 -1.357 1.000 0.403 0.476 0.093 0 -0.249 0.123 -0.506 0.064 -0.745 0.035 0.001 0.137 0.009 0.108 . .=53;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=31.73;SOR=3.300 GT:AD:DP:GQ:PL 1/1:0,53:53:99:2035,159,0 Haplotypecaller
1 3761465 3761465 T A intronic CEP104 . . . . . . . . . . . . 0.5 753.60 59 1 3761465 . T A 753.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.701e+00;DP=63;ExcessHet=3.0103;FS=0.988;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=12.77;ReadPosRankSum=0.175;SOR=0.527 GT:AD:DP:GQ:PL 0/1:31,28:59:99:761,0,892 Haplotypecaller . . .
1 3761650 3761650 A G intronic CEP104 . . . . . . . . . . . . 1153.03 28 1 3761650 . A G 1153.03 . AC=2;AF=1.00;AN=2;DP=28;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=31.55;SOR=0.997 GT:AD:DP:GQ:PL
1 3761772 3761772 C T intronic CEP104 . . . . . . . . . . . . 0.5 1164.60 79 1 3761772 . C T 1164.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.967e+00;DP=79;ExcessHet=3.0103;FS=6.775;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=14.74;ReadPosRankSum=0.648;SOR=1.529 GT:AD:DP:GQ:PL 0/1:39,40:79:99:1172,0,1174 Haplotypecaller . . .
1 3762080 3762080 T C intronic CEP104 . . . . . . . . . . . . 367.01 9 1 3762080 . T C 367.01 . AC=2;AF=1.00;AN=2;DP=9;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=30.45;SOR=4.615 GT:AD:DP:GQ:PL
1 3764216 3764216 C T intronic CEP104 . . . . . . . . . . . . 0.5 359.60 36 1 3764216 . C T 359.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-3.244e+00;DP=36;ExcessHet=3.0103;FS=2.653;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=9.99;ReadPosRankSum=-4.200e-01;SOR=1.355 GT:AD:DP:GQ:PL 0/1:24,12:36:99:367,0,878 Haplotypecaller . .
1 3764878 3764878 C T intronic CEP104 . . . . . . . . . . . . 0.5 50.60 4 1 3764878 . C T 50.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;DP=4;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=50.25;MQRankSum=-1.383e+00;QD=12.65;ReadPosRankSum=0.674;SOR=0.105 GT:AD:DP:GQ:PL 0/1:2,2:4:40:58,0,40 Haplotypecaller . . .
1 3764979 3764979 C A intronic CEP104 . . . . . . . . . . . . 0.5 155.60 8 1 3764979 . C A 155.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-6.470e-01;DP=8;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=57.63;MQRankSum=-4.890e-01;QD=19.45;ReadPosRankSum=0.703;SOR=1.179 GT:AD:DP:GQ:PL 0/1:3,5:8:90:163,0,90 Haplotypecaller . . .
1 3765055 3765055 C T intronic CEP104 . . . . . . . . . . . . 0.5 210.60 13 1 3765055 . C T 210.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.124e+00;DP=13;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=53.20;MQRankSum=-1.294e+00;QD=16.20;ReadPosRankSum=0.422;SOR=0.836 GT:AD:DP:GQ:PL 0/1:6,7:13:99:218,0,191 Haplotypecaller . . .
1 3765549 3765549 G A intronic CEP104 . . . . . . . . . . . . 65.28 2 1 3765549 . G A 65.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=32.64;SOR=2.303 GT:AD:DP:GQ:PL
1 3769033 3769033 A T intronic CEP104 . . . . . . . . . . . . 0.5 2593.60 118 1 3769033 . A T 2593.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.03;DP=119;ExcessHet=3.0103;FS=10.337;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=21.98;ReadPosRankSum=-5.020e-01;SOR=0.350 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:52,66:118:99:0|1:3769033_A_T:2601,0,3042:3769033 Haplotypecaller . . .
1 3769034 3769034 A T intronic CEP104 . . . . . . . . . . . . 0.5 2593.60 118 1 3769034 . A T 2593.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.637;DP=119;ExcessHet=3.0103;FS=12.061;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=21.98;ReadPosRankSum=-2.490e-01;SOR=0.389 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:53,65:118:99:0|1:3769033_A_T:2601,0,3042:3769033 Haplotypecaller . . .
1 3769172 3769172 T C intronic CEP104 . . . . . . . . . . . . 0.5 613.60 25 1 3769172 . T C 613.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.60;DP=25;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=24.54;ReadPosRankSum=0.292;SOR=1.609 GT:AD:DP:GQ:PL 0/1:8,17:25:99:621,0,242 Haplotypecaller . . .
1 3769231 3769231 A G intronic CEP104 . . . . . . . . . . . . 0.5 157.60 13 1 3769231 . A G 157.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.97;DP=14;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=12.12;ReadPosRankSum=-6.380e-01;SOR=0.368 GT:AD:DP:GQ:PL 0/1:8,5:13:99:165,0,271 Haplotypecaller . . .
1 3769262 3769262 C T intronic CEP104 . . . . . . . . . . . . 0.5 84.60 7 1 3769262 . C T 84.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.19;DP=8;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=12.09;ReadPosRankSum=-2.189e+00;SOR=0.495 GT:AD:DP:GQ:PL 0/1:4,3:7:92:92,0,122 Haplotypecaller . . .
1 3769276 3769276 G C intronic CEP104 . . . . . . . . . . . . 0.5 152.60 6 1 3769276 . G C 152.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.83;DP=7;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=25.43;ReadPosRankSum=1.83;SOR=1.329 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:2,4:6:60:0|1:3769276_G_C:160,0,60:3769276 Haplotypcaller . . .
1 3769286 3769286 C T intronic CEP104 . . . . . . . . . . . . 164.10 3 1 3769286 . C T 164.10 . AC=2;AF=1.00;AN=2;DP=4;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=29.30;SOR=2.833 GT:AD:DP:GQ:PGT:PID:PL:PS 1|1:0,3:3:12:1|1:3769276_G_C:178,12,0:3769276 Haplotypecaller . . .
1 3770395 3770395 C A intronic CEP104 . . . . . . . . . . . . 37.28 2 1 3770395 . C A 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL
1 3774130 3774130 A G UTR5 DFFB NM_001320136:c.-8197A>G;NM_004402:c.-38A>G;NM_001320132:c.-8152A>G;NM_001282669:c.-38A>G . 0.5 1104.60 59 1 3774130 . A G 1104.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.114e+00;DP=59;ExcessHet=3.0103;FS=9.788;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=18.72;ReadPosRankSum=0.737;SOR=1.926 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:31,28:59:99:0|1:3774130_A_G:1112,0,1860:3774130 Haplotypecaller . . .
1 3774138 3774138 T C UTR5 DFFB NM_001320136:c.-8189T>C;NM_004402:c.-30T>C;NM_001320132:c.-8144T>C;NM_001282669:c.-30T>C . 0.5 1289.60 75 1 3774138 . T C 1289.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.49;DP=75;ExcessHet=3.0103;FS=9.987;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=17.19;ReadPosRankSum=-6.630e-01;SOR=1.723 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:39,36:75:99:0|1:3774130_A_G:1297,0,1970:3774130 Haplotypecaller . . .
1 3774296 3774296 A G intronic DFFB . . . . . . . . . . . . 0.5 355.60 17 1 3774296 . A G 355.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.27;DP=17;ExcessHet=3.0103;FS=3.854;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=20.92;ReadPosRankSum=1.52;SOR=2.387 GT:AD:DP:GQ:PL 0/1:7,10:17:99:363,0,218 Haplotypecaller . . .
1 3774312 3774312 T C intronic DFFB . . . . . . . . . . . . 0.5 251.60 11 1 3774312 . T C 251.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.74;DP=12;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=22.87;ReadPosRankSum=1.60;SOR=1.270 GT:AD:DP:GQ:PL 0/1:4,7:11:99:259,0,108 Haplotypecaller . . .
1 3775454 3775454 C G intronic DFFB . . . . . . . . . . . . 1614.03 43 1 3775454 . C G 1614.03 . AC=2;AF=1.00;AN=2;DP=44;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=30.48;SOR=5.283 GT:AD:DP:GQ:PL
1 3782115 3782115 G A intronic DFFB . . . . . . . . . . . . 0.5 259.60 32 1 3782115 . G A 259.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.68;DP=32;ExcessHet=3.0103;FS=2.268;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=8.11;ReadPosRankSum=0.854;SOR=0.223 GT:AD:DP:GQ:PL 0/1:21,11:32:99:267,0,606 Haplotypecaller . . .
1 3782608 3782608 C T intronic DFFB . . . . . . . . . . . . 0.5 464.60 35 1 3782608 . C T 464.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-4.558e+00;DP=35;ExcessHet=3.0103;FS=7.420;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=13.27;ReadPosRankSum=-2.279e+00;SOR=1.219 GT:AD:DP:GQ:PL 0/1:18,17:35:99:472,0,625 Haplotypecaller . .
1 3784454 3784454 T C intronic DFFB . . . . . . . . . . . . 0.5 715.60 28 1 3784454 . T C 715.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.03;DP=28;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=25.56;ReadPosRankSum=1.51;SOR=1.382 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:10,18:28:99:0|1:3784454_T_C:723,0,718:3784454 Haplotypecaller . . .
1 3784464 3784464 G A intronic DFFB . . . . . . . . . . . . 0.5 807.60 34 1 3784464 . G A 807.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-3.160e+00;DP=34;ExcessHet=3.0103;FS=4.175;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=23.75;ReadPosRankSum=1.60;SOR=2.522 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:13,21:34:99:0|1:3784454_T_C:815,0,783:378445Haplotypecaller . . .
1 3786189 3786189 G A exonic DFFB . synonymous SNV DFFB:NM_001282669:exon5:c.G603A:p.T201T,DFFB:NM_001320132:exon5:c.G384A:p.T128T,DFFB:NM_001320136:exon5:c.G339A:p.T113T,DFFB:NM_004402:exon5:c.G531A:p.T177T . . . . . . . . . . 0.5 512.60 29 1 3786189 . G A 512.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.04;DP=29;ExcessHet=3.0103;FS=5.552;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=17.68;ReadPosRankSum=0.864;SOR=2.531 GT:AD:DP:GQ:PL 0/1:12,17:29:99:520,0,301 Haplotypecaller . . .
1 3788978 3788978 - A intronic DFFB . . . . . . . . . . . . 0.5 235.64 66 1 3788978 . G GA 235.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.238;DP=82;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.88;MQRankSum=0.00;QD=3.57;ReadPosRankSum=-3.740e-01;SOR=0.836 GT:AD:DP:GQ:PL 0/1:49,17:66:99:243,0,1056 Haplotypecaller . . .
1 3789194 3789194 - CGGCCC intronic DFFB . . . . . . . . . . . . 4328.06 98 1 3789194 . G GCGGCCC 4328.06 . AC=2;AF=1.00;AN=2;DP=99;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.52;QD=29.74;SOR=3.657 GT:AD:DP:GQ:PGT:PID:PL:PS 1|1:0,98:98:99:1|1:3789194_G_GCGGCCC:4342,321,0:3789194 Haplotypecaller . . .
1 3789195 3789195 - GTCCCTGCCGC intronic DFFB . . . . . . . . . . . 4328.06 90 1 3789195 . T TGTCCCTGCCGC 4328.06 . AC=2;AF=1.00;AN=2;DP=91;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.48;QD=32.31;SOR=4.011 GT:AD:DP:GQ:PGT:PID:PL:PS 1|1:0,90:90:99:1|1:3789194_G_GCGGCCC:4342,321,0:3789194 Haplotypecaller . . .
1 3789319 3789319 A G intronic DFFB . . . . . . . . . . . . 0.5 204.60 25 1 3789319 . A G 204.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.03;DP=25;ExcessHet=3.0103;FS=4.409;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=8.18;ReadPosRankSum=-2.630e-01;SOR=1.863 GT:AD:DP:GQ:PL 0/1:17,8:25:99:212,0,550 Haplotypecaller . . .
1 3789362 3789362 C T intronic DFFB . . . . . . . . . . . . 0.5 205.60 14 1 3789362 . C T 205.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-3.588e+00;DP=14;ExcessHet=3.0103;FS=3.680;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=14.69;ReadPosRankSum=0.500;SOR=2.303 GT:AD:DP:GQ:PL 0/1:6,8:14:99:213,0,215 Haplotypecaller . . .
1 3789662 3789662 A G intronic DFFB . . . . . . . . . . . . 820.03 20 1 3789662 . A G 820.03 . AC=2;AF=1.00;AN=2;DP=20;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.30;QD=30.20;SOR=6.091 GT:AD:DP:GQ:PL
1 3794767 3794767 G T intronic DFFB . . . . . . . . . . . . 35.44 1 1 3794767 . G T 35.44 . AC=2;AF=1.00;AN=2;DP=1;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=29.87;SOR=1.609 GT:AD:DP:GQ:PGT:PID:PL:PS 1|1:0,1:1:3:1|1:3794767_G_T:45,3,0:3794767 Haplotypecaller . . .
1 3794787 3794787 C A intronic DFFB . . . . . . . . . . . . 58.28 2 1 3794787 . C A 58.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=29.14;SOR=0.693 GT:AD:DP:GQ:PGT:PID:PL:PS 1|1:0,2:2:6:1|1:3794767_G_T:70,6,0:3794767 Haplotypecaller . . .
1 3800242 3800242 A G exonic DFFB . synonymous SNV DFFB:NM_001282669:exon7:c.A1026G:p.P342P,DFFB:NM_001320132:exon7:c.A807G:p.P269P,DFFB:NM_001320136:exon7:c.A762G:p.P254P,DFFB:NM_004402:exon7:c.A954G:p.P318P . . . . . . . . . . 0.5 3850.60 284 1 3800242 . A G 3850.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.147;DP=284;ExcessHet=3.0103;FS=2.565;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=13.56;ReadPosRankSum=-9.720e-01;SOR=0.845 GT:AD:DP:GQ:PL 0/1:143,141:284:99:3858,0,3822 Haplotypecaller . . .
1 3800480 3800480 G T UTR3 DFFB NM_001320136:c.*175G>T;NM_004402:c.*175G>T;NM_001320132:c.*175G>T;NM_001282669:c.*175G>T . 0.5 534.60 34 1 3800480 . G T 534.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.799e+00;DP=35;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=15.72;ReadPosRankSum=-2.534e+00;SOR=0.693 GT:AD:DP:GQ:PL 0/1:17,17:34:99:542,0,582 Haplotypecaller . .
1 3806643 3806643 T A intronic C1orf174 . . . . . . . . . . . 0.5 1657.60 145 1 3806643 . T A 1657.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.83;DP=145;ExcessHet=3.0103;FS=1.312;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=11.43;ReadPosRankSum=0.024;SOR=0.821 GT:AD:DP:GQ:PL 0/1:82,63:145:99:1665,0,2263 Haplotypecaller . . .
1 3807122 3807122 G A intronic C1orf174 . . . . . . . . . . . 0.5 569.60 37 1 3807122 . G A 569.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=4.26;DP=37;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=15.39;ReadPosRankSum=-4.600e-02;SOR=0.223 GT:AD:DP:GQ:PL 0/1:18,19:37:99:577,0,497 Haplotypecaller . . .
1 3807388 3807388 G A exonic C1orf174 . synonymous SNV C1orf174:NM_207356:exon3:c.C363T:p.L121L . . . 0.5 2294.60 172 1 3807388 . G A 2294.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.496;DP=172;ExcessHet=3.0103;FS=2.673;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=13.34;ReadPosRankSum=-1.606e+00;SOR=0.934 GT:AD:DP:GQ:PL 0/1:83,89:172:99:2302,0,2108 Haplotypecaller . . .
1 3807593 3807593 G C exonic C1orf174 . nonsynonymous SNV C1orf174:NM_207356:exon3:c.C158G:p.T53R . . . 1.0 0.010 T 0.0 0.026 B 0.0 0.013 B 0.000 0.559 N 1 0.090 P -2.08 0.002 N 3.42 0.055 4.18 0.000 N 0.071 0.059 -1.001 0.297 T 0.000 0.000 T . . . -0.465 0.058 0.268 0.101 0.001 0.009 0.034 N c -1.378 -1.187 1.000 0.517 0.707 0.730 0 4.36 0.515 0.120 0.154 0.067 0.174 0.440 0.263 0.479 0.267 5.550 000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=31.30;SOR=1.232 GT:AD:DP:GQ:PL 1/1:0,108:108:99:3936,324,0 Haplotypecaller . . .
1 3809326 3809326 C T intronic C1orf174 . . . . . . . . . . . 0.5 1565.60 80 1 3809326 . C T 1565.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.127e+00;DP=80;ExcessHet=3.0103;FS=1.104;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=19.57;ReadPosRankSum=0.667;SOR=1.001 GT:AD:DP:GQ:PL 0/1:31,49:80:99:1573,0,806 Haplotypecaller . . .
1 3816588 3816588 C - intronic C1orf174 . . . . . . . . . . . 0.5 196.60 7 1 3816587 . GC G 196.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.981e+00;DP=8;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=28.09;ReadPosRankSum=-3.660e-01;SOR=1.609 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:2,5:7:69:0|1:3816587_GC_G:204,0,69:3816587 Haplotypecaller . . .
1 3816598 3816598 A C intronic C1orf174 . . . . . . . . . . . 0.5 193.60 7 1 3816598 . A C 193.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.98;DP=7;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=27.66;ReadPosRankSum=-3.660e-01;SOR=1.609 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:2,5:7:99:0|1:3816587_GC_G:201,0,100:3816587 Haplotypecaller . . .
1 3816604 3816604 G A intronic C1orf174 . . . . . . . . . . . 0.5 145.60 9 1 3816604 . G A 145.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.20;DP=9;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=16.18;ReadPosRankSum=1.44;SOR=0.527 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:5,4:9:99:0|1:3816587_GC_G:153,0,165:3816587 Haplotypcaller . . .
1 3816683 3816683 A G intronic C1orf174 . . . . . . . . . . . 0.5 191.60 19 1 3816683 . A G 191.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.89;DP=19;ExcessHet=3.0103;FS=5.798;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=10.08;ReadPosRankSum=0.169;SOR=2.419 GT:AD:DP:GQ:PL 0/1:12,7:19:99:199,0,366 Haplotypecaller . . .
1 3816893 3816893 C T upstream C1orf174;LINC01134 dist=75 . . . . . . . . . 0.5 346.60 26 1 3816893 . C T 346.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.980e+00;DP=26;ExcessHet=3.0103;FS=1.617;MLEAC=1;MLEAF=0.500;MQ=59.36;MQRankSum=1.25;QD=13.33;ReadPosRankSum=1.17;SOR=1.244 GT:AD:DP:GQ:PL 0/1:11,15:26:99:354,0,243 Haplotypecaller . . .
1 3816950 3816950 C T upstream C1orf174;LINC01134 dist=18 . . . . . . . . . 0.5 194.60 18 1 3816950 . C T 194.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-3.699e+00;DP=18;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=10.81;ReadPosRankSum=-1.453e+00;SOR=0.368 GT:AD:DP:GQ:PL 0/1:11,7:18:99:202,0,413 Haplotypecaller . .
1 3817605 3817605 C T ncRNA_intronic LINC01134 . . . . . . . . . . . 0.5 55.60 3 1 3817605 . C T 55.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-9.670e-01;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=18.53;ReadPosRankSum=0.967;SOR=0.223 GT:AD:DP:GQ:PL 0/1:1,2:3:33:63,0,33 Haplotypecaller . . .
1 3824992 3824992 C - ncRNA_intronic LINC01134 . . . . . . . . . . . 78.28 2 1 3824991 . TC T 78.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=29.27;SOR=0.693 GT:AD:DP:GQ:PGT:PID:PL:PS 1|1:0,2:2:6:1|1:3824991_TC_T:90,6,0:3824991 Haplotypecaller . . .
1 3824994 3825000 CTCTCTC - ncRNA_intronic LINC01134 . . . . . . . . . . . 78.28 2 1 3824993 . TCTCTCTC T 78.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=28.24;SOR=0.693 GT:AD:DP:GQ:PGT:PID:PL:PS 1|1:0,2:2:6:1|1:3824991_TC_T:90,6,0:3824991 Haplotypecaller . . .
1 3829614 3829614 A G ncRNA_intronic LINC01134 . . . . . . . . . . . 37.28 2 1 3829614 . A G 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL
1 3834408 3834408 T C intergenic LINC01134;LINC01346 dist=2397;dist=166264 . . . . . . . 0.5 30.60 4 1 3834408 . T C 30.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;DP=4;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=7.65;ReadPosRankSum=0.674;SOR=0.105 GT:AD:DP:GQ:PL 0/1:2,2:4:36:38,0,36 Haplotypecaller . . .
1 4002126 4002126 T C ncRNA_intronic LINC01346 . . . . . . . . . . . 37.28 2 1 4002126 . T C 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL
1 4015553 4015553 C A intergenic LINC01346;LINC01777 dist=2910;dist=456558 . . . . . . . 0.5 32.60 3 1 4015553 . C A 32.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-9.670e-01;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=10.87;ReadPosRankSum=0.967;SOR=0.223 GT:AD:DP:GQ:PL 0/1:1,2:3:34:40,0,34 Haplotypecaller . . .
1 4019237 4019237 T C intergenic LINC01346;LINC01777 dist=6594;dist=452874 . . . . . . . 37.28 2 1 4019237 . T C 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL
1 4034246 4034246 A G intergenic LINC01346;LINC01777 dist=21603;dist=437865 . . . . . . . 37.28 2 1 4034246 . A G 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL
1 4037665 4037665 T C intergenic LINC01346;LINC01777 dist=25022;dist=434446 . . . . . . . 70.10 4 1 4037665 . T C 70.10 . AC=2;AF=1.00;AN=2;DP=4;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=17.52;SOR=0.693 GT:AD:DP:GQ:PL
1 4041181 4041181 G C intergenic LINC01346;LINC01777 dist=28538;dist=430930 . . . . . . . 37.28 2 1 4041181 . G C 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL
1 4060963 4060963 G T intergenic LINC01346;LINC01777 dist=48320;dist=411148 . . . . . . . 0.5 32.60 3 1 4060963 . G T 32.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-9.670e-01;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=10.87;ReadPosRankSum=0.967;SOR=0.223 GT:AD:DP:GQ:PL 0/1:1,2:3:35:40,0,35 Haplotypecaller . . .
1 4070571 4070571 A T intergenic LINC01346;LINC01777 dist=57928;dist=401540 . . . . . . . 0.5 58.60 8 1 4070571 . A T 58.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.992;DP=8;ExcessHet=3.0103;FS=3.332;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=7.33;ReadPosRankSum=-6.190e-01;SOR=2.303 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:6,2:8:66:0|1:4070571_A_T:66,0,305:4070571 Haplotypecaller . . .
1 4070588 4070588 C T intergenic LINC01346;LINC01777 dist=57945;dist=401523 . . . . . . . 0.5 58.60 8 1 4070588 . C T 58.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.24;DP=8;ExcessHet=3.0103;FS=3.680;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=7.33;ReadPosRankSum=0.00;SOR=2.236 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:6,2:8:66:0|1:4070571_A_T:66,0,305:4070571 Haplotypcaller . . .
1 4072209 4072209 G T intergenic LINC01346;LINC01777 dist=59566;dist=399902 . . . . . . . 116.92 5 1 4072209 . G T 116.92 . AC=2;AF=1.00;AN=2;DP=5;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=23.38;SOR=1.022 GT:AD:DP:GQ:PL
1 4072276 4072276 T C intergenic LINC01346;LINC01777 dist=59633;dist=399835 . . . . . . . 0.5 151.60 7 1 4072276 . T C 151.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.07;DP=7;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=21.66;ReadPosRankSum=-1.465e+00;SOR=1.022 GT:AD:DP:GQ:PL 0/1:2,5:7:28:159,0,28 Haplotypecaller . . .
1 4084710 4084710 G A intergenic LINC01346;LINC01777 dist=72067;dist=387401 . . . . . . . 37.28 2 1 4084710 . G A 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL
1 4103930 4103930 T C intergenic LINC01346;LINC01777 dist=91287;dist=368181 . . . . . . . 0.5 91.60 6 1 4103930 . T C 91.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.935;DP=6;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=15.27;ReadPosRankSum=-5.980e-01;SOR=0.132 GT:AD:DP:GQ:PL 0/1:3,3:6:98:99,0,98 Haplotypecaller . . .
1 4105365 4105365 G A intergenic LINC01346;LINC01777 dist=92722;dist=366746 . . . . . . . 37.28 2 1 4105365 . G A 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL
1 4107345 4107345 G T intergenic LINC01346;LINC01777 dist=94702;dist=364766 . . . . . . . 66.28 2 1 4107345 . G T 66.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=33.14;SOR=2.303 GT:AD:DP:GQ:PL
1 4108092 4108092 T C intergenic LINC01346;LINC01777 dist=95449;dist=364019 . . . . . . . 37.28 2 1 4108092 . T C 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL
1 4115928 4115928 G C intergenic LINC01346;LINC01777 dist=103285;dist=356183 . . . . . . . 79.80 3 1 4115928 . G C 79.80 . AC=2;AF=1.00;AN=2;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=26.60;SOR=1.179 GT:AD:DP:GQ:PL
1 4121291 4121291 G A intergenic LINC01346;LINC01777 dist=108648;dist=350820 . . . . . . . 64.28 2 1 4121291 . G A 64.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=32.14;SOR=0.693 GT:AD:DP:GQ:PL
1 4122571 4122571 - CC intergenic LINC01346;LINC01777 dist=109928;dist=349540 . . . . . . . 35.48 1 1 4122571 . T TCC 35.48 . AC=2;AF=1.00;AN=2;DP=1;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=33.98;SOR=1.609 GT:AD:DP:GQ:PL
1 4148023 4148023 C T intergenic LINC01346;LINC01777 dist=135380;dist=324088 . . . . . . . 76.80 3 1 4148023 . C T 76.80 . AC=2;AF=1.00;AN=2;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=25.60;SOR=1.179 GT:AD:DP:GQ:PL
1 4151751 4151751 T C intergenic LINC01346;LINC01777 dist=139108;dist=320360 . . . . . . . 74.28 2 1 4151751 . T C 74.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=32.17;SOR=2.303 GT:AD:DP:GQ:PL
1 4189629 4189629 T C intergenic LINC01346;LINC01777 dist=176986;dist=282482 . . . . . . . 37.28 2 1 4189629 . T C 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL
1 4198600 4198600 C T intergenic LINC01346;LINC01777 dist=185957;dist=273511 . . . . . . . 78.28 2 1 4198600 . C T 78.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=33.74;SOR=0.693 GT:AD:DP:GQ:PGT:PID:PL:PS 1|1:0,2:2:6:1|1:4198600_C_T:90,6,0:4198600 Haplotypecaller . . .
1 4198602 4198602 C G intergenic LINC01346;LINC01777 dist=185959;dist=273509 . . . . . . . 78.28 2 1 4198602 . C G 78.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=29.25;SOR=0.693 GT:AD:DP:GQ:PGT:PID:PL:PS 1|1:0,2:2:6:1|1:4198600_C_T:90,6,0:4198600 Haplotypecaller . . .
1 4235768 4235768 G A intergenic LINC01346;LINC01777 dist=223125;dist=236343 . . . . . . . 0.5 298.60 20 1 4235768 . G A 298.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.439e+00;DP=20;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=14.93;ReadPosRankSum=0.609;SOR=0.721 GT:AD:DP:GQ:PL 0/1:9,11:20:99:306,0,285 Haplotypecaller . . .
1 4240178 4240178 T C intergenic LINC01346;LINC01777 dist=227535;dist=231933 . . . . . . . 37.28 2 1 4240178 . T C 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL
1 4273962 4273962 T C intergenic LINC01346;LINC01777 dist=261319;dist=198149 . . . . . . . 90.80 3 1 4273962 . T C 90.80 . AC=2;AF=1.00;AN=2;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=30.27;SOR=2.833 GT:AD:DP:GQ:PL
1 4276511 4276511 - GGGCT intergenic LINC01346;LINC01777 dist=263868;dist=195600 . . . . . . . 121.84 3 1 4276511 . G GGGGCT 121.84 . AC=2;AF=1.00;AN=2;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=29.92;SOR=1.179 GT:AD:DP:GQ:PL
1 4279562 4279562 C T intergenic LINC01346;LINC01777 dist=266919;dist=192549 . . . . . . . 37.28 2 1 4279562 . C T 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL
1 4361337 4361337 C A intergenic LINC01346;LINC01777 dist=348694;dist=110774 . . . . . . . 37.28 2 1 4361337 . C A 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL
1 4364407 4364407 G A intergenic LINC01346;LINC01777 dist=351764;dist=107704 . . . . . . . 78.28 2 1 4364407 . G A 78.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=34.73;SOR=0.693 GT:AD:DP:GQ:PGT:PID:PL:PS 1|1:0,2:2:6:1|1:4364407_G_A:90,6,0:4364407 Haplotypecaller . . .
1 4364415 4364415 C T intergenic LINC01346;LINC01777 dist=351772;dist=107696 . . . . . . . 78.28 2 1 4364415 . C T 78.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=28.22;SOR=0.693 GT:AD:DP:GQ:PGT:PID:PL:PS 1|1:0,2:2:6:1|1:4364407_G_A:90,6,0:4364407 Haplotypecaller . . .
1 4364416 4364416 A G intergenic LINC01346;LINC01777 dist=351773;dist=107695 . . . . . . . 78.28 2 1 4364416 . A G 78.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=30.25;SOR=0.693 GT:AD:DP:GQ:PGT:PID:PL:PS 1|1:0,2:2:6:1|1:4364407_G_A:90,6,0:4364407 Haplotypecaller . . .
1 4364422 4364422 C A intergenic LINC01346;LINC01777 dist=351779;dist=107689 . . . . . . . 78.28 2 1 4364422 . C A 78.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=28.90;SOR=0.693 GT:AD:DP:GQ:PGT:PID:PL:PS 1|1:0,2:2:6:1|1:4364407_G_A:90,6,0:4364407 Haplotypecaller . . .
1 4365471 4365471 G T intergenic LINC01346;LINC01777 dist=352828;dist=106640 . . . . . . . 37.28 2 1 4365471 . G T 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL
1 4381823 4381823 G T intergenic LINC01346;LINC01777 dist=369180;dist=90288 . . . . . . . 37.28 2 1 4381823 . G T 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL
1 4416102 4416102 G A intergenic LINC01346;LINC01777 dist=403459;dist=56009 . . . . . . . 37.28 2 1 4416102 . G A 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL
1 4460816 4460816 A - intergenic LINC01346;LINC01777 dist=448173;dist=11295 . . . . . . . 63.28 2 1 4460815 . GA G 63.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=31.64;SOR=0.693 GT:AD:DP:GQ:PL
1 4475766 4475766 T C ncRNA_intronic LINC01777 . . . . . . . . . . . 37.28 2 1 4475766 . T C 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL
1 4486095 4486095 A G intergenic LINC01777;LINC01646 dist=1351;dist=145452 . . . . . . . 126.10 4 1 4486095 . A G 126.10 . AC=2;AF=1.00;AN=2;DP=4;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=31.52;SOR=0.693 GT:AD:DP:GQ:PL
1 4489398 4489398 T C intergenic LINC01777;LINC01646 dist=4654;dist=142149 . . . . . . . 37.28 2 1 4489398 . T C 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL
1 4497313 4497313 A G intergenic LINC01777;LINC01646 dist=12569;dist=134234 . . . . . . . 93.80 3 1 4497313 . A G 93.80 . AC=2;AF=1.00;AN=2;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=31.27;SOR=2.833 GT:AD:DP:GQ:PL
1 4497875 4497875 G A intergenic LINC01777;LINC01646 dist=13131;dist=133672 . . . . . . . 37.28 2 1 4497875 . G A 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL
1 4506325 4506325 T G intergenic LINC01777;LINC01646 dist=21581;dist=125222 . . . . . . . 37.28 2 1 4506325 . T G 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL
1 4514082 4514082 A G intergenic LINC01777;LINC01646 dist=29338;dist=117465 . . . . . . . 111.10 4 1 4514082 . A G 111.10 . AC=2;AF=1.00;AN=2;DP=4;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=27.77;SOR=0.693 GT:AD:DP:GQ:PL
1 4560871 4560871 A G intergenic LINC01777;LINC01646 dist=76127;dist=70676 . . . . . . . 0.5 146.60 5 1 4560871 . A G 146.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.28;DP=5;ExcessHet=3.0103;FS=3.979;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=29.32;ReadPosRankSum=0.00;SOR=1.447 GT:AD:DP:GQ:PL 0/1:1,4:5:25:154,0,25 Haplotypecaller . . .
1 4573804 4573804 C T intergenic LINC01777;LINC01646 dist=89060;dist=57743 . . . . . . . 0.5 32.60 3 1 4573804 . C T 32.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-9.670e-01;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=10.87;ReadPosRankSum=-9.670e-01;SOR=0.223 GT:AD:DP:GQ:PL 0/1:1,2:3:33:40,0,33 Haplotypecaller . . .
1 4594772 4594772 C T intergenic LINC01777;LINC01646 dist=110028;dist=36775 . . . . . . . 37.28 2 1 4594772 . C T 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL
1 4599036 4599041 AAACTC - intergenic LINC01777;LINC01646 dist=114292;dist=32506 . . . . . . . 78.28 2 1 4599035 . TAAACTC T 78.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=34.67;SOR=0.693 GT:AD:DP:GQ:PL
1 4636263 4636263 G A ncRNA_intronic LINC01646 . . . . . . . . . . . 37.28 2 1 4636263 . G A 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL
1 4674026 4674026 A G intergenic LINC01646;AJAP1 dist=30262;dist=41079 . . . . . . . . 37.28 2 1 4674026 . A G 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL
1 4677729 4677729 T C intergenic LINC01646;AJAP1 dist=33965;dist=37376 . . . . . . . . 0.5 33.93 3 1 4677729 . T C 33.93 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.967;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=11.31;ReadPosRankSum=0.967;SOR=0.223 GT:AD:DP:GQ:PL 0/1:1,2:3:1:41,0,1 Haplotypecaller . . .
1 4711301 4711301 C T intergenic LINC01646;AJAP1 dist=67537;dist=3804 . . . . . . . . 238 8 1 4711301 . C T 238 . AC=2;AF=1.00;AN=2;DP=8;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=29.75;SOR=0.693 GT:AD:DP:GQ:PL
1 4713045 4713045 A G intergenic LINC01646;AJAP1 dist=69281;dist=2060 . . . . . . . . 78.80 3 1 4713045 . A G 78.80 . AC=2;AF=1.00;AN=2;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=26.27;SOR=1.179 GT:AD:DP:GQ:PL
1 4743023 4743023 C G intronic AJAP1 . . . . . . . . . . . . 37.28 2 1 4743023 . C G 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL
1 4750013 4750013 C G intronic AJAP1 . . . . . . . . . . . . 78.28 2 1 4750013 . C G 78.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=32.28;SOR=2.303 GT:AD:DP:GQ:PL
1 4753963 4753963 G T intronic AJAP1 . . . . . . . . . . . . 37.28 2 1 4753963 . G T 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL
1 4771665 4771665 G C intronic AJAP1 . . . . . . . . . . . . 106.80 3 1 4771665 . G C 106.80 . AC=2;AF=1.00;AN=2;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=36.29;SOR=2.833 GT:AD:DP:GQ:PL
1 4771695 4771695 G C intronic AJAP1 . . . . . . . . . . . . 72.28 2 1 4771695 . G C 72.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=30.30;SOR=2.303 GT:AD:DP:GQ:PL
1 4772053 4772053 T C exonic AJAP1 . synonymous SNV AJAP1:NM_001042478:exon2:c.T123C:p.C41C,AJAP1:NM_018836:exon2:c.T123C:p.C41C 0.5 1848.60 149 1 4772053 . T C 1848.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.647;DP=149;ExcessHet=3.0103;FS=11.423;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=12.41;ReadPosRankSum=-1.791e+00;SOR=0.431 GT:AD:DP:GQ:PL 0/1:78,71:149:99:1856,0,2010 Haplotypecaller . . .
1 4772717 4772717 G A exonic AJAP1 . nonsynonymous SNV AJAP1:NM_001042478:exon2:c.G787A:p.G263R,AJAP1:NM_018836:exon2:c.G787A:p.G263R . . . . . 0.261 0.165 T 0.999 0.764 D 0.892 0.615 P 0.004 0.346 N 0.829 0.288 1.67 0.430 L 0.9 0.453 T -3.86 0.724 D 0.13 0.149 -1.012 0.263 T 0.000 0.000 T . . . 2.786 0.396 21.3 0.987 0.444 0.832 0.420 DNP, C-terminal . . 1 5853.03 183 1 4772717 . G 5853.03 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.167;DP=184;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQRankSum=0.00;QD=31.98;ReadPosRankSum=-1.165e+00;SOR=0.232 GT:AD:DP:GQ:PL 1/1:1,182:183:99:5867,512,0 Haplotypecaller . . .
1 4789585 4789585 G A intronic AJAP1 . . . . . . . . . . . . 60.28 2 1 4789585 . G A 60.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=30.14;SOR=2.303 GT:AD:DP:GQ:PL
1 4789645 4789645 - CTGTCCTCTCTCCTAGCTCTGGTGCCCTGAGATG intronic AJAP1 . . . . . . . . 78.32 2 1 4789645 . T TCTGTCCTCTCTCCTAGCTCTGGTGCCCTGAGATG 78.32 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=37.71;SOR=2.303 GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 Haplotypecaller . . .
1 4794865 4794865 C T intronic AJAP1 . . . . . . . . . . . . 37.28 2 1 4794865 . C T 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL
1 4805434 4805434 A G intronic AJAP1 . . . . . . . . . . . . 37.28 2 1 4805434 . A G 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL
1 4808454 4808454 G A intronic AJAP1 . . . . . . . . . . . . 0.5 58.60 3 1 4808454 . G A 58.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-9.670e-01;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=19.53;ReadPosRankSum=0.967;SOR=0.223 GT:AD:DP:GQ:PL 0/1:1,2:3:35:66,0,35 Haplotypecaller . . .
1 4824063 4824063 C A intronic AJAP1 . . . . . . . . . . . . 76.80 3 1 4824063 . C A 76.80 . AC=2;AF=1.00;AN=2;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=25.60;SOR=1.179 GT:AD:DP:GQ:PL
1 4829835 4829835 A G intronic AJAP1 . . . . . . . . . . . . 0.5 738.60 45 1 4829835 . A G 738.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-4.788e+00;DP=45;ExcessHet=3.0103;FS=3.002;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=16.41;ReadPosRankSum=-3.910e-01;SOR=0.160 GT:AD:DP:GQ:PL 0/1:19,26:45:99:746,0,580 Haplotypecaller . .
1 4830406 4830406 T C intronic AJAP1 . . . . . . . . . . . . 78.28 2 1 4830406 . T C 78.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=25.52;SOR=0.693 GT:AD:DP:GQ:PGT:PID:PL:PS 1|1:0,2:2:6:1|1:4830406_T_C:90,6,0:4830406 Haplotypecaller . . .
1 4830409 4830409 T C intronic AJAP1 . . . . . . . . . . . . 78.28 2 1 4830409 . T C 78.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=31.32;SOR=0.693 GT:AD:DP:GQ:PGT:PID:PL:PS 1|1:0,2:2:6:1|1:4830406_T_C:90,6,0:4830406 Haplotypecaller . . .
1 4832144 4832148 TTTTT - intronic AJAP1 . . . . . . . . . . . . 391.01 9 1 4832143 . ATTTTT A 391.01 . AC=2;AF=1.00;AN=2;DP=9;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=35.16;SOR=4.615 GT:AD:DP:GQ:PGT:PID:PL:PS 1|1:0,9:9:27:1|1:4832143_ATTTTT_A:405,27,0:4832143 Haplotypecaller . . .
1 4832155 4832155 - AA intronic AJAP1 . . . . . . . . . . . . 391.05 9 1 4832155 . T TAA 391.05 . AC=2;AF=1.00;AN=2;DP=9;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=29.69;SOR=4.615 GT:AD:DP:GQ:PGT:PID:PL:PS 1|1:0,9:9:27:1|1:4832143_ATTTTT_A:405,27,0:4832143 Haplotypecaller . . .
1 4834202 4834202 G C intronic AJAP1 . . . . . . . . . . . . 111.80 3 1 4834202 . G C 111.80 . AC=2;AF=1.00;AN=2;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=29.03;SOR=2.833 GT:AD:DP:GQ:PL
1 4834229 4834229 T C intronic AJAP1 . . . . . . . . . . . . 72.28 2 1 4834229 . T C 72.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=29.23;SOR=2.303 GT:AD:DP:GQ:PL
1 4834420 4834420 C T intronic AJAP1 . . . . . . . . . . . . 0.5 785.60 42 1 4834420 . C T 785.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.810e+00;DP=42;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=18.70;ReadPosRankSum=1.12;SOR=1.022 GT:AD:DP:GQ:PL 0/1:18,24:42:99:793,0,573 Haplotypecaller . . .
1 4834851 4834851 T C intronic AJAP1 . . . . . . . . . . . . 145.92 6 1 4834851 . T C 145.92 . AC=2;AF=1.00;AN=2;DP=6;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=24.32;SOR=3.912 GT:AD:DP:GQ:PL
1 4836121 4836121 A G intronic AJAP1 . . . . . . . . . . . . 37.28 2 1 4836121 . A G 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL
1 4847845 4847845 G A intergenic AJAP1;MIR4417 dist=3994;dist=776286 . . . . . . . . 0.5 1557.60 104 1 4847845 . G A 1557.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.22;DP=104;ExcessHet=3.0103;FS=6.227;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=14.98;ReadPosRankSum=2.08;SOR=1.050 GT:AD:DP:GQ:PL 0/1:52,52:104:99:1565,0,1427 Haplotypecaller . . .
1 4874505 4874505 G A intergenic AJAP1;MIR4417 dist=30654;dist=749626 . . . . . . . . 65.28 2 1 4874505 . G A 65.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=32.64;SOR=0.693 GT:AD:DP:GQ:PL
1 4877043 4877043 C A intergenic AJAP1;MIR4417 dist=33192;dist=747088 . . . . . . . . 37.28 2 1 4877043 . C A 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL
1 4883095 4883095 T C intergenic AJAP1;MIR4417 dist=39244;dist=741036 . . . . . . . . 37.28 2 1 4883095 . T C 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=26.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL
1 4887689 4887690 AC - intergenic AJAP1;MIR4417 dist=43838;dist=736441 . . . . . . . . 59.28 2 1 4887688 . AAC A 59.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=29.64;SOR=0.693 GT:AD:DP:GQ:PL
1 4913559 4913559 T G intergenic AJAP1;MIR4417 dist=69708;dist=710572 . . . . . . . . 72.28 2 1 4913559 . T G 72.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=28.85;SOR=2.303 GT:AD:DP:GQ:PL
1 4928358 4928358 T C intergenic AJAP1;MIR4417 dist=84507;dist=695773 . . . . . . . . 68.28 2 1 4928358 . T C 68.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=34.14;SOR=2.303 GT:AD:DP:GQ:PL
1 4955387 4955387 - ACAC intergenic AJAP1;MIR4417 dist=111536;dist=668744 . . . . . . . . 78.32 2 1 4955387 . G GACAC 78.32 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=30.59;SOR=0.693 GT:AD:DP:GQ:PL
1 4959786 4959786 A G intergenic AJAP1;MIR4417 dist=115935;dist=664345 . . . . . . . . 78.80 3 1 4959786 . A G 78.80 . AC=2;AF=1.00;AN=2;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=26.27;SOR=1.179 GT:AD:DP:GQ:PL
1 4959811 4959811 T C intergenic AJAP1;MIR4417 dist=115960;dist=664320 . . . . . . . . 74.28 2 1 4959811 . T C 74.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=27.90;SOR=2.303 GT:AD:DP:GQ:PL
1 4969942 4969942 T C intergenic AJAP1;MIR4417 dist=126091;dist=654189 . . . . . . . . 78.80 3 1 4969942 . T C 78.80 . AC=2;AF=1.00;AN=2;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=26.27;SOR=1.179 GT:AD:DP:GQ:PL
1 4974563 4974563 T C intergenic AJAP1;MIR4417 dist=130712;dist=649568 . . . . . . . . 37.28 2 1 4974563 . T C 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL
1 5004328 5004328 G A intergenic AJAP1;MIR4417 dist=160477;dist=619803 . . . . . . . . 61.28 2 1 5004328 . G A 61.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=30.64;SOR=0.693 GT:AD:DP:GQ:PL
1 5010142 5010142 T C intergenic AJAP1;MIR4417 dist=166291;dist=613989 . . . . . . . . 37.28 2 1 5010142 . T C 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL
1 5021170 5021170 A G intergenic AJAP1;MIR4417 dist=177319;dist=602961 . . . . . . . . 72.28 2 1 5021170 . A G 72.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=32.67;SOR=2.303 GT:AD:DP:GQ:PL
1 5021200 5021200 T G intergenic AJAP1;MIR4417 dist=177349;dist=602931 . . . . . . . . 121.10 4 1 5021200 . T G 121.10 . AC=2;AF=1.00;AN=2;DP=4;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=30.27;SOR=1.609 GT:AD:DP:GQ:PL
1 5023430 5023430 A G intergenic AJAP1;MIR4417 dist=179579;dist=600701 . . . . . . . . 37.28 2 1 5023430 . A G 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL
1 5043734 5043734 C A intergenic AJAP1;MIR4417 dist=199883;dist=580397 . . . . . . . . 37.28 2 1 5043734 . C A 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL
1 5044082 5044082 T A intergenic AJAP1;MIR4417 dist=200231;dist=580049 . . . . . . . . 78.28 2 1 5044082 . T A 78.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=27.99;SOR=2.303 GT:AD:DP:GQ:PGT:PID:PL:PS 1|1:0,2:2:6:1|1:5044082_T_A:90,6,0:5044082 Haplotypecaller . . .
1 5044089 5044089 C G intergenic AJAP1;MIR4417 dist=200238;dist=580042 . . . . . . . . 116.80 3 1 5044089 . C G 116.80 . AC=2;AF=1.00;AN=2;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=27.62;SOR=1.179 GT:AD:DP:GQ:PGT:PID:PL:PS 1|1:0,3:3:9:1|1:5044082_T_A:130,9,0:5044082 Haplotypecaller . . .
1 5044116 5044116 T C intergenic AJAP1;MIR4417 dist=200265;dist=580015 . . . . . . . . 121.80 3 1 5044116 . T C 121.80 . AC=2;AF=1.00;AN=2;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=28.59;SOR=1.179 GT:AD:DP:GQ:PL
1 5044137 5044137 G T intergenic AJAP1;MIR4417 dist=200286;dist=579994 . . . . . . . . 35.44 1 1 5044137 . G T 35.44 . AC=2;AF=1.00;AN=2;DP=1;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=25.72;SOR=1.609 GT:AD:DP:GQ:PGT:PID:PL:PS 1|1:0,1:1:3:1|1:5044137_G_T:45,3,0:5044137 Haplotypecaller . . .
1 5044138 5044138 G A intergenic AJAP1;MIR4417 dist=200287;dist=579993 . . . . . . . . 35.44 1 1 5044138 . G A 35.44 . AC=2;AF=1.00;AN=2;DP=1;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=31.95;SOR=1.609 GT:AD:DP:GQ:PGT:PID:PL:PS 1|1:0,1:1:3:1|1:5044137_G_T:45,3,0:5044137 Haplotypecaller . . .
1 5050112 5050113 TC - intergenic AJAP1;MIR4417 dist=206261;dist=574018 . . . . . . . . 0.5 55.60 10 1 5050111 . GTC G 55.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-8.120e-01;DP=12;ExcessHet=3.0103;FS=3.010;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=5.56;ReadPosRankSum=-6.480e-01;SOR=0.916 GT:AD:DP:GQ:PL 0/1:7,3:10:63:63,0,220 Haplotypecaller . . .
1 5076798 5076798 - GTTT intergenic AJAP1;MIR4417 dist=232947;dist=547333 . . . . . . . . 78.32 2 1 5076798 . C CGTTT 78.32 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=32.48;SOR=0.693 GT:AD:DP:GQ:PL
1 5215736 5215736 T C intergenic AJAP1;MIR4417 dist=371885;dist=408395 . . . . . . . . 99.80 3 1 5215736 . T C 99.80 . AC=2;AF=1.00;AN=2;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=33.27;SOR=1.179 GT:AD:DP:GQ:PL
1 5216780 5216780 G C intergenic AJAP1;MIR4417 dist=372929;dist=407351 . . . . . . . . 77.80 3 1 5216780 . G C 77.80 . AC=2;AF=1.00;AN=2;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=25.93;SOR=1.179 GT:AD:DP:GQ:PL
1 5275156 5275156 T - intergenic AJAP1;MIR4417 dist=431305;dist=348975 . . . . . . . . 45.28 2 1 5275155 . AT A 45.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=22.64;SOR=0.693 GT:AD:DP:GQ:PL
1 5277746 5277746 G T intergenic AJAP1;MIR4417 dist=433895;dist=346385 . . . . . . . . 37.28 2 1 5277746 . G T 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL
1 5306601 5306601 C T intergenic AJAP1;MIR4417 dist=462750;dist=317530 . . . . . . . . 0.5 32.60 3 1 5306601 . C T 32.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-9.670e-01;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=55.15;MQRankSum=-9.670e-01;QD=10.87;ReadPosRankSum=0.967;SOR=0.223 GT:AD:DP:GQ:PL 0/1:1,2:3:23:40,0,23 Haplotypecaller . . .
1 5306682 5306751 CTTCCTTCTTTCCTTCCTTCCTTCCTTTCCTCCTTCCTTTTTCTTCCTTCCCTCCCTCCCTCCTTCCTGT - intergenic AJAP1;MIR4417 dist=462831;dist=317380 165.10 4 1 5306681 . CCTTCCTTCTTTCCTTCCTTCCTTCCTTTCCTCCTTCCTTTTTCTTCCTTCCCTCCCTCCCTCCTTCCTGT C 165.10 . AC=2;AF=1.00;AN=2;DP=4;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=23.34;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,4:4:12:179,12,0 Haplotypecaller . . .
1 5327732 5327732 C G intergenic AJAP1;MIR4417 dist=483881;dist=296399 . . . . . . . . 72.80 3 1 5327732 . C G 72.80 . AC=2;AF=1.00;AN=2;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=24.27;SOR=1.179 GT:AD:DP:GQ:PL
1 5327760 5327760 C T intergenic AJAP1;MIR4417 dist=483909;dist=296371 . . . . . . . . 76.80 3 1 5327760 . C T 76.80 . AC=2;AF=1.00;AN=2;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=25.60;SOR=1.179 GT:AD:DP:GQ:PL
1 5342617 5342617 C T intergenic AJAP1;MIR4417 dist=498766;dist=281514 . . . . . . . . 37.28 2 1 5342617 . C T 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL
1 5343032 5343032 T C intergenic AJAP1;MIR4417 dist=499181;dist=281099 . . . . . . . . 60.28 2 1 5343032 . T C 60.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=30.14;SOR=2.303 GT:AD:DP:GQ:PL
1 5348914 5348914 C T intergenic AJAP1;MIR4417 dist=505063;dist=275217 . . . . . . . . 37.28 2 1 5348914 . C T 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL
1 5358384 5358384 A G intergenic AJAP1;MIR4417 dist=514533;dist=265747 . . . . . . . . 76.28 2 1 5358384 . A G 76.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=28.37;SOR=2.303 GT:AD:DP:GQ:PL
1 5368769 5368769 A G intergenic AJAP1;MIR4417 dist=524918;dist=255362 . . . . . . . . 66.28 2 1 5368769 . A G 66.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=33.14;SOR=0.693 GT:AD:DP:GQ:PL
1 5369936 5369936 T G intergenic AJAP1;MIR4417 dist=526085;dist=254195 . . . . . . . . 37.28 2 1 5369936 . T G 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL
1 5370012 5370012 T A intergenic AJAP1;MIR4417 dist=526161;dist=254119 . . . . . . . . 37.28 2 1 5370012 . T A 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL
1 5374400 5374400 - CCCCCCCC intergenic AJAP1;MIR4417 dist=530549;dist=249731 . . . . . . . 121.84 3 1 5374400 . A ACCCCCCCC 121.84 . AC=2;AF=1.00;AN=2;DP=4;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=55.68;QD=29.82;SOR=2.833 GT:AD:DP:GQ:PGT:PID:PL:PS 1|1:0,3:3:9:1|1:5374400_A_ACCCCCCCC:135,9,0:5374400 Haplotypecaller . . .
1 5374410 5374410 G C intergenic AJAP1;MIR4417 dist=530559;dist=249721 . . . . . . . . 0.5 127.60 4 1 5374410 . G C 127.60 . AC=1;AF=0.500;AN=2;DP=4;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=55.68;QD=31.90;SOR=1.609 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:0,4:4:23:0|1:5374400_A_ACCCCCCCC:135,0,23:5374400 Haplotypecaller . . .
1 5374414 5374414 G C intergenic AJAP1;MIR4417 dist=530563;dist=249717 . . . . . . . . 0.5 85.60 4 1 5374414 . G C 85.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.150e+00;DP=4;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=21.40;ReadPosRankSum=1.15;SOR=0.916 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:1,3:4:26:0|1:5374400_A_ACCCCCCCC:93,0,26:5374400 Haplotypecaller . . .
1 5374437 5374437 - TCTGCC intergenic AJAP1;MIR4417 dist=530586;dist=249694 . . . . . . . . 255.97 5 1 5374437 . T TTCTGCC 255.97 . AC=2;AF=1.00;AN=2;DP=5;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=29.80;SOR=1.022 GT:AD:DP:GQ:PL
1 5396750 5396750 A G intergenic AJAP1;MIR4417 dist=552899;dist=227381 . . . . . . . . 73.28 2 1 5396750 . A G 73.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=28.34;SOR=0.693 GT:AD:DP:GQ:PL
1 5454794 5454794 - AAGG intergenic AJAP1;MIR4417 dist=610943;dist=169337 . . . . . . . . 0.5 73.64 2 1 5454794 . A AAAGG 73.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.674;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=35.40;ReadPosRankSum=0.674;SOR=1.447 GT:AD:DP:GQ:PL 0/1:1,1:2:48:81,0,48 Haplotypecaller . . .
1 5468540 5468540 G A intergenic AJAP1;MIR4417 dist=624689;dist=155591 . . . . . . . . 37.28 2 1 5468540 . G A 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL
1 5525791 5525791 G A intergenic AJAP1;MIR4417 dist=681940;dist=98340 . . . . . . . . 37.28 2 1 5525791 . G A 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL
1 5542347 5542347 - C intergenic AJAP1;MIR4417 dist=698496;dist=81784 . . . . . . . . 63.32 2 1 5542347 . A AC 63.32 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=31.66;SOR=2.303 GT:AD:DP:GQ:PL
1 5546166 5546166 T C intergenic AJAP1;MIR4417 dist=702315;dist=77965 . . . . . . . . 37.28 2 1 5546166 . T C 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL
1 5589167 5589167 G A intergenic AJAP1;MIR4417 dist=745316;dist=34964 . . . . . . . . 37.28 2 1 5589167 . G A 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL
1 5621921 5621921 - TGG intergenic AJAP1;MIR4417 dist=778070;dist=2210 . . . . . . . . 0.5 122.64 16 1 5621921 . A ATGG 122.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.63;DP=23;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=7.66;ReadPosRankSum=1.82;SOR=0.804 GT:AD:DP:GQ:PL 0/1:12,4:16:99:130,0,456 Haplotypecaller . . .
1 5643758 5643758 C T intergenic MIR4417;MIR4689 dist=19555;dist=278974 . . . . . . . . 108.10 4 1 5643758 . C T 108.10 . AC=2;AF=1.00;AN=2;DP=4;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=27.02;SOR=1.609 GT:AD:DP:GQ:PL
1 5655723 5655723 G C intergenic MIR4417;MIR4689 dist=31520;dist=267009 . . . . . . . . 65.28 2 1 5655723 . G C 65.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=32.64;SOR=0.693 GT:AD:DP:GQ:PL
1 5659908 5659908 G C intergenic MIR4417;MIR4689 dist=35705;dist=262824 . . . . . . . . 37.28 2 1 5659908 . G C 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL
1 5679733 5679733 T G intergenic MIR4417;MIR4689 dist=55530;dist=242999 . . . . . . . . 37.28 2 1 5679733 . T G 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL
1 5684831 5684831 C A intergenic MIR4417;MIR4689 dist=60628;dist=237901 . . . . . . . . 37.28 2 1 5684831 . C A 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL
1 5710673 5710673 G A intergenic MIR4417;MIR4689 dist=86470;dist=212059 . . . . . . . . 37.28 2 1 5710673 . G A 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL
1 5715175 5715175 C T intergenic MIR4417;MIR4689 dist=90972;dist=207557 . . . . . . . . 37.28 2 1 5715175 . C T 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL
1 5716288 5716288 A - intergenic MIR4417;MIR4689 dist=92085;dist=206444 . . . . . . . . 104.80 3 1 5716287 . GA G 104.80 . AC=2;AF=1.00;AN=2;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=34.93;SOR=2.833 GT:AD:DP:GQ:PL
1 5717925 5717925 A T intergenic MIR4417;MIR4689 dist=93722;dist=204807 . . . . . . . . 67.28 2 1 5717925 . A T 67.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=33.64;SOR=2.303 GT:AD:DP:GQ:PL
1 5717948 5717948 C T intergenic MIR4417;MIR4689 dist=93745;dist=204784 . . . . . . . . 45.80 3 1 5717948 . C T 45.80 . AC=2;AF=1.00;AN=2;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=15.27;SOR=1.179 GT:AD:DP:GQ:PL
1 5718016 5718016 A C intergenic MIR4417;MIR4689 dist=93813;dist=204716 . . . . . . . . 64.28 2 1 5718016 . A C 64.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=32.14;SOR=0.693 GT:AD:DP:GQ:PL
1 5733806 5733806 A G intergenic MIR4417;MIR4689 dist=109603;dist=188926 . . . . . . . . 121.80 3 1 5733806 . A G 121.80 . AC=2;AF=1.00;AN=2;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=52.31;QD=29.26;SOR=1.179 GT:AD:DP:GQ:PGT:PID:PL:PS 1|1:0,3:3:9:1|1:5733806_A_G:135,9,0:5733806 Haplotypecaller . . .
1 5733814 5733814 C A intergenic MIR4417;MIR4689 dist=109611;dist=188918 . . . . . . . . 121.80 3 1 5733814 . C A 121.80 . AC=2;AF=1.00;AN=2;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=52.31;QD=30.83;SOR=1.179 GT:AD:DP:GQ:PGT:PID:PL:PS 1|1:0,3:3:9:1|1:5733806_A_G:135,9,0:5733806 Haplotypecaller . . .
1 5733818 5733818 T C intergenic MIR4417;MIR4689 dist=109615;dist=188914 . . . . . . . . 121.80 3 1 5733818 . T C 121.80 . AC=2;AF=1.00;AN=2;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=52.31;QD=27.55;SOR=1.179 GT:AD:DP:GQ:PGT:PID:PL:PS 1|1:0,3:3:9:1|1:5733806_A_G:135,9,0:5733806 Haplotypecaller . . .
1 5733820 5733820 T C intergenic MIR4417;MIR4689 dist=109617;dist=188912 . . . . . . . . 121.80 3 1 5733820 . T C 121.80 . AC=2;AF=1.00;AN=2;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=52.31;QD=27.56;SOR=1.179 GT:AD:DP:GQ:PGT:PID:PL:PS 1|1:0,3:3:9:1|1:5733806_A_G:135,9,0:5733806 Haplotypecaller . . .
1 5733821 5733821 G A intergenic MIR4417;MIR4689 dist=109618;dist=188911 . . . . . . . . 121.80 3 1 5733821 . G A 121.80 . AC=2;AF=1.00;AN=2;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=52.31;QD=32.87;SOR=1.179 GT:AD:DP:GQ:PGT:PID:PL:PS 1|1:0,3:3:9:1|1:5733806_A_G:135,9,0:5733806 Haplotypecaller . . .
1 5733825 5733825 G A intergenic MIR4417;MIR4689 dist=109622;dist=188907 . . . . . . . . 121.80 3 1 5733825 . G A 121.80 . AC=2;AF=1.00;AN=2;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=52.31;QD=33.62;SOR=1.179 GT:AD:DP:GQ:PGT:PID:PL:PS 1|1:0,3:3:9:1|1:5733806_A_G:135,9,0:5733806 Haplotypecaller . . .
1 5733828 5733828 C A intergenic MIR4417;MIR4689 dist=109625;dist=188904 . . . . . . . . 121.80 3 1 5733828 . C A 121.80 . AC=2;AF=1.00;AN=2;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=52.31;QD=33.52;SOR=1.179 GT:AD:DP:GQ:PGT:PID:PL:PS 1|1:0,3:3:9:1|1:5733806_A_G:135,9,0:5733806 Haplotypecaller . . .
1 5733850 5733850 A T intergenic MIR4417;MIR4689 dist=109647;dist=188882 . . . . . . . . 85.10 4 1 5733850 . A T 85.10 . AC=2;AF=1.00;AN=2;DP=4;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=51.74;QD=21.27;SOR=0.693 GT:AD:DP:GQ:PL
1 5733863 5733863 A G intergenic MIR4417;MIR4689 dist=109660;dist=188869 . . . . . . . . 63.80 3 1 5733863 . A G 63.80 . AC=2;AF=1.00;AN=2;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=53.23;QD=21.27;SOR=1.179 GT:AD:DP:GQ:PL
1 5733887 5733887 T C intergenic MIR4417;MIR4689 dist=109684;dist=188845 . . . . . . . . 37.28 2 1 5733887 . T C 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=54.78;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL
1 5749750 5749750 C G intergenic MIR4417;MIR4689 dist=125547;dist=172982 . . . . . . . . 30.44 1 1 5749750 . C G 30.44 . AC=2;AF=1.00;AN=2;DP=1;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=30.44;SOR=1.609 GT:AD:DP:GQ:PL
1 5754119 5754119 G A intergenic MIR4417;MIR4689 dist=129916;dist=168613 . . . . . . . . 60.28 2 1 5754119 . G A 60.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=30.14;SOR=0.693 GT:AD:DP:GQ:PL
1 5770265 5770265 C A intergenic MIR4417;MIR4689 dist=146062;dist=152467 . . . . . . . . 63.28 2 1 5770265 . C A 63.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=31.64;SOR=0.693 GT:AD:DP:GQ:PL
1 5770508 5770508 A C intergenic MIR4417;MIR4689 dist=146305;dist=152224 . . . . . . . . 157.10 4 1 5770508 . A C 157.10 . AC=2;AF=1.00;AN=2;DP=4;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=27.36;SOR=3.258 GT:AD:DP:GQ:PL
1 5770702 5770702 A G intergenic MIR4417;MIR4689 dist=146499;dist=152030 . . . . . . . . 1317.03 46 1 5770702 . A G 1317.03 . AC=2;AF=1.00;AN=2;BaseQRankSum=-1.570e-01;DP=47;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQRankSum=0.00;QD=28.63;ReadPosRankSum=1.66;SOR=0.324 GT:AD:DP:GQ:PL 1/1:1,45:46:99:1331,100,0 Haplotypecaller . . .
1 5770815 5770823 GGGAAGGAG - intergenic MIR4417;MIR4689 dist=146612;dist=151909 . . . . . . . 298 8 1 5770814 . AGGGAAGGAG A 298 . AC=2;AF=1.00;AN=2;DP=8;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=30.63;SOR=4.407 GT:AD:DP:GQ:PL 1/1:0,8:8:24:312,24,0 Haplotypecaller . . .
1 5770860 5770860 G A intergenic MIR4417;MIR4689 dist=146657;dist=151872 . . . . . . . . 261.98 7 1 5770860 . G A 261.98 . AC=2;AF=1.00;AN=2;DP=7;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=31.62;SOR=2.584 GT:AD:DP:GQ:PL
1 5774876 5774876 A G intergenic MIR4417;MIR4689 dist=150673;dist=147856 . . . . . . . . 37.28 2 1 5774876 . A G 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL
1 5794578 5794578 T C intergenic MIR4417;MIR4689 dist=170375;dist=128154 . . . . . . . . 66.28 2 1 5794578 . T C 66.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=33.14;SOR=2.303 GT:AD:DP:GQ:PL
1 5799895 5799895 C A intergenic MIR4417;MIR4689 dist=175692;dist=122837 . . . . . . . . 37.28 2 1 5799895 . C A 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL
1 5803975 5803975 C A intergenic MIR4417;MIR4689 dist=179772;dist=118757 . . . . . . . . 72.80 3 1 5803975 . C A 72.80 . AC=2;AF=1.00;AN=2;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=24.27;SOR=1.179 GT:AD:DP:GQ:PL
1 5804365 5804365 T C intergenic MIR4417;MIR4689 dist=180162;dist=118367 . . . . . . . . 37.28 2 1 5804365 . T C 37.28 . AC=2;AF=1.00;AN=2;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=53.92;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL
1 5810612 5810615 TGTC - intergenic MIR4417;MIR4689 dist=186409;dist=112117 . . . . . . . . 144.10 4 1 5810611 . TTGTC T 144.10 . AC=2;AF=1.00;AN=2;DP=4;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=28.71;SOR=0.693 GT:AD:DP:GQ:PL
1 5846064 5846064 G A intergenic MIR4417;MIR4689 dist=221861;dist=76668 . . . . . . . . 37.28 2 1 5846064 . G A 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL
1 5853260 5853260 A G intergenic MIR4417;MIR4689 dist=229057;dist=69472 . . . . . . . . 54.28 2 1 5853260 . A G 54.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=27.14;SOR=2.303 GT:AD:DP:GQ:PL
1 5868463 5868463 G T intergenic MIR4417;MIR4689 dist=244260;dist=54269 . . . . . . . . 37.28 2 1 5868463 . G T 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL
1 5869497 5869497 - CAA intergenic MIR4417;MIR4689 dist=245294;dist=53235 . . . . . . . . 0.5 115.64 4 1 5869497 . T TCAA 115.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.319;DP=5;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=28.91;ReadPosRankSum=1.15;SOR=0.916 GT:AD:DP:GQ:PL 0/1:1,3:4:43:123,0,43 Haplotypecaller . . .
1 5873771 5873771 A G intergenic MIR4417;MIR4689 dist=249568;dist=48961 . . . . . . . . 0.5 255.60 12 1 5873771 . A G 255.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.85;DP=12;ExcessHet=3.0103;FS=6.532;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=21.30;ReadPosRankSum=-4.900e-01;SOR=1.739 GT:AD:DP:GQ:PL 0/1:4,8:12:31:263,0,31 Haplotypecaller . . .
1 5884017 5884017 G A intergenic MIR4417;MIR4689 dist=259814;dist=38715 . . . . . . . . 37.28 2 1 5884017 . G A 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL
1 5889908 5889908 A G intergenic MIR4417;MIR4689 dist=265705;dist=32824 . . . . . . . . 35.44 1 1 5889908 . A G 35.44 . AC=2;AF=1.00;AN=2;DP=1;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=32.79;SOR=1.609 GT:AD:DP:GQ:PGT:PID:PL:PS 1|1:0,1:1:3:1|1:5889908_A_G:45,3,0:5889908 Haplotypecaller . . .
1 5889911 5889911 G A intergenic MIR4417;MIR4689 dist=265708;dist=32821 . . . . . . . . 35.44 1 1 5889911 . G A 35.44 . AC=2;AF=1.00;AN=2;DP=1;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=32.28;SOR=1.609 GT:AD:DP:GQ:PGT:PID:PL:PS 1|1:0,1:1:3:1|1:5889908_A_G:45,3,0:5889908 Haplotypecaller . . .
1 5889918 5889918 C T intergenic MIR4417;MIR4689 dist=265715;dist=32814 . . . . . . . . 35.44 1 1 5889918 . C T 35.44 . AC=2;AF=1.00;AN=2;DP=1;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=34.51;SOR=1.609 GT:AD:DP:GQ:PGT:PID:PL:PS 1|1:0,1:1:3:1|1:5889908_A_G:45,3,0:5889908 Haplotypecaller . . .
1 5892326 5892326 G A intergenic MIR4417;MIR4689 dist=268123;dist=30406 . . . . . . . . 52.28 2 1 5892326 . G A 52.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=26.14;SOR=0.693 GT:AD:DP:GQ:PGT:PID:PL:PS 1|1:0,2:2:6:1|1:5892326_G_A:64,6,0:5892326 Haplotypecaller . . .
1 5892327 5892327 G T intergenic MIR4417;MIR4689 dist=268124;dist=30405 . . . . . . . . 52.28 2 1 5892327 . G T 52.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=26.14;SOR=0.693 GT:AD:DP:GQ:PGT:PID:PL:PS 1|1:0,2:2:6:1|1:5892326_G_A:64,6,0:5892326 Haplotypecaller . . .
1 5923788 5923788 T G intronic NPHP4 . . . . . . . . . . . . 1800.03 46 1 5923788 . T G 1800.03 . AC=2;AF=1.00;AN=2;DP=46;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=29.49;SOR=3.258 GT:AD:DP:GQ:PL
1 5934490 5934490 A G intronic NPHP4 . . . 249999 not_specified MedGen:CN169374 criteria_provided,_single_submitter Benign . . . . . . . . . . . . . . . . . . 4284.03 131 1 5934490 . A G 4284.03 . AC=2;AF=1.00;AN=2;DP=137;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=32.70;SOR=1.232 GT:AD:DP:GQ:PL 1/1:0,131:131:99:4298,393,0 Haplotypecaller . . .
1 5934837 5934837 C T intronic NPHP4 . . . . . . . . . . . . 1672.03 44 1 5934837 . C T 1672.03 . AC=2;AF=1.00;AN=2;DP=44;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=28.72;SOR=3.816 GT:AD:DP:GQ:PL
1 5935162 5935162 A T splicing NPHP4 NM_001291593:exon18:c.1279-2T>A;NM_001291594:exon17:c.1282-2T>A;NM_015102:exon21:c.2818-2T>A 177885 not_specified MedGen:CN169374 criteria_provided,_single_submitter Benign . . . . . . . . . 1250.03 37 1 5935162 . A T 1250.03 . AC=2;AF=1.00;AN=2;DP=37;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=33.78;SOR=3.442 GT:AD:DP:GQ:PL 1/1:0,37:37:99:1264,111,0 Haplotypecaller . . .
1 5935222 5935222 T C intronic NPHP4 . . . . . . . . . . . . 491.02 12 1 5935222 . T C 491.02 . AC=2;AF=1.00;AN=2;DP=12;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=21.26;SOR=5.136 GT:AD:DP:GQ:PL
1 5937091 5937091 T C intronic NPHP4 . . . . . . . . . . . . 416.02 11 1 5937091 . T C 416.02 . AC=2;AF=1.00;AN=2;DP=11;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=25.19;SOR=4.977 GT:AD:DP:GQ:PL
1 5937391 5937391 C T intronic NPHP4 . . . 250004 not_specified MedGen:CN169374 criteria_provided,_single_submitter Benign . . . . . . . . . . . . . . . . . . 5219.03 163 1 5937391 . C T 5219.03 . AC=2;AF=1.00;AN=2;DP=163;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=32.02;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,163:163:99:5233,489,0 Haplotypecaller . . .
1 5939544 5939544 T G intronic NPHP4 . . . . . . . . . . . . 5236.03 151 1 5939544 . T G 5236.03 . AC=2;AF=1.00;AN=2;DP=152;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=34.68;SOR=0.909 GT:AD:DP:GQ:PL 1/1:0,151:151:99:5250,452,0 Haplotypecaller . . .
1 5939837 5939837 G A intronic NPHP4 . . . . . . . . . . . . 163.92 5 1 5939837 . G A 163.92 . AC=2;AF=1.00;AN=2;DP=5;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=32.78;SOR=3.611 GT:AD:DP:GQ:PL
1 5948677 5948677 G A intronic NPHP4 . . . . . . . . . . . . 3498.03 111 1 5948677 . G A 3498.03 . AC=2;AF=1.00;AN=2;BaseQRankSum=1.46;DP=111;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQRankSum=0.00;QD=31.51;ReadPosRankSum=-7.760e-01;SOR=0.711 GT:AD:DP:GQ:PL 1/1:2,109:111:99:3512,283,0 Haplotypecaller . . .
1 5948864 5948864 C T intronic NPHP4 . . . . . . . . . . . . 661.03 19 1 5948864 . C T 661.03 . AC=2;AF=1.00;AN=2;DP=20;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=34.79;SOR=5.994 GT:AD:DP:GQ:PL
1 5958184 5958184 T C intronic NPHP4 . . . . . . . . . . . . 127.92 5 1 5958184 . T C 127.92 . AC=2;AF=1.00;AN=2;DP=5;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=25.58;SOR=1.022 GT:AD:DP:GQ:PL
1 5961870 5961870 G A intronic NPHP4 . . . . . . . . . . . . 37.28 2 1 5961870 . G A 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL
1 5964991 5964991 T C intronic NPHP4 . . . . . . . . . . . . 178.92 5 1 5964991 . T C 178.92 . AC=2;AF=1.00;AN=2;DP=5;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=32.55;SOR=1.022 GT:AD:DP:GQ:PL
1 5967064 5967064 G T intronic NPHP4 . . . . . . . . . . . . 182.92 5 1 5967064 . G T 182.92 . AC=2;AF=1.00;AN=2;DP=5;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=30.16;SOR=3.611 GT:AD:DP:GQ:PL
1 5977982 5977982 A G intronic NPHP4 . . . . . . . . . . . . 116.80 3 1 5977982 . A G 116.80 . AC=2;AF=1.00;AN=2;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=30.01;SOR=1.179 GT:AD:DP:GQ:PL
1 6007446 6007446 C T intronic NPHP4 . . . . . . . . . . . . 94.80 3 1 6007446 . C T 94.80 . AC=2;AF=1.00;AN=2;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=31.60;SOR=2.833 GT:AD:DP:GQ:PL
1 6027167 6027167 C A intronic NPHP4 . . . . . . . . . . . . 0.5 287.66 10 1 6027167 . C A 287.66 . AC=1;AF=0.500;AN=2;BaseQRankSum=-3.850e-01;DP=10;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=28.77;ReadPosRankSum=1.65;SOR=3.258 GT:AD:DP:GQ:PL 0/1:1,9:10:9:295,0,9 Haplotypecaller . . .
1 6027252 6027252 A G intronic NPHP4 . . . . . . . . . . . . 913.03 28 1 6027252 . A G 913.03 . AC=2;AF=1.00;AN=2;DP=28;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=32.61;SOR=2.147 GT:AD:DP:GQ:PL
1 6029087 6029087 A - intronic NPHP4 . . . . . . . . . . . . 0.5 220.93 19 1 6029086 . CA C 220.93 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.354;DP=31;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.24;MQRankSum=0.00;QD=16.99;ReadPosRankSum=-1.105e+00;SOR=1.179 GT:AD:DP:GQ:PL 0/1:4,9:19:47:226,0,47 Haplotypecaller . . .
1 6037967 6037967 G A intronic NPHP4 . . . . . . . . . . . . 109.80 3 1 6037967 . G A 109.80 . AC=2;AF=1.00;AN=2;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=33.45;SOR=1.179 GT:AD:DP:GQ:PGT:PID:PL:PS 1|1:0,3:3:9:1|1:6037967_G_A:123,9,0:6037967 Haplotypecaller . . .
1 6037969 6037969 G A intronic NPHP4 . . . . . . . . . . . . 109.80 2 1 6037969 . G A 109.80 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=28.50;SOR=0.693 GT:AD:DP:GQ:PGT:PID:PL:PS 1|1:0,2:2:9:1|1:6037967_G_A:123,9,0:6037967 Haplotypecaller . . .
1 6038583 6038583 G C intronic NPHP4 . . . . . . . . . . . . 1464.03 38 1 6038583 . G C 1464.03 . AC=2;AF=1.00;AN=2;BaseQRankSum=-1.805e+00;DP=38;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQRankSum=0.00;QD=34.17;ReadPosRankSum=-1.141e+00;SOR=5.892 GT:AD:DP:GQ:PL 1/1:1,37:38:71:1478,71,0 Haplotypecaller . . .
1 6039905 6039905 T C intronic NPHP4 . . . . . . . . . . . . 37.28 2 1 6039905 . T C 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL
1 6059322 6059322 G A intronic KCNAB2 . . . . . . . . . . . . 37.28 2 1 6059322 . G A 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL
1 6062612 6062612 C T intronic KCNAB2 . . . . . . . . . . . . 37.28 2 1 6062612 . C T 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL
1 6094135 6094135 A G intronic KCNAB2 . . . . . . . . . . . . 37.28 2 1 6094135 . A G 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL
1 6099172 6099172 C A intronic KCNAB2 . . . . . . . . . . . . 37.28 2 1 6099172 . C A 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL
1 6099339 6099339 A G intronic KCNAB2 . . . . . . . . . . . . 72.28 2 1 6099339 . A G 72.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=30.69;SOR=0.693 GT:AD:DP:GQ:PL
1 6100313 6100313 A G intronic KCNAB2 . . . . . . . . . . . . 404.02 10 1 6100313 . A G 404.02 . AC=2;AF=1.00;AN=2;DP=10;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=29.35;SOR=3.258 GT:AD:DP:GQ:PL
1 6105911 6105911 C A intronic KCNAB2 . . . . . . . . . . . . 37.28 2 1 6105911 . C A 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL
1 6108165 6108165 A G intronic KCNAB2 . . . . . . . . . . . . 103.10 4 1 6108165 . A G 103.10 . AC=2;AF=1.00;AN=2;DP=4;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=25.77;SOR=0.693 GT:AD:DP:GQ:PL
1 6112653 6112653 G T intronic KCNAB2 . . . . . . . . . . . . 37.28 2 1 6112653 . G T 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL
1 6115839 6115839 T C intronic KCNAB2 . . . . . . . . . . . . 76.28 2 1 6115839 . T C 76.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=31.58;SOR=2.303 GT:AD:DP:GQ:PL
1 6133046 6133046 G C intronic KCNAB2 . . . . . . . . . . . . 225.98 7 1 6133046 . G C 225.98 . AC=2;AF=1.00;AN=2;DP=7;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=32.28;SOR=4.174 GT:AD:DP:GQ:PL
1 6145023 6145023 C T intronic KCNAB2 . . . . . . . . . . . . 0.5 296.60 11 1 6145023 . C T 296.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.362e+00;DP=11;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=26.96;ReadPosRankSum=-1.097e+00;SOR=2.494 GT:AD:DP:GQ:PL 0/1:2,9:11:50:304,0,50 Haplotypecaller . . .
1 6145273 6145273 G A exonic KCNAB2 . synonymous SNV KCNAB2:NM_001199863:exon5:c.G90A:p.V30V,KCNAB2:NM_001199862:exon6:c.G390A:p.V130V,KCNAB2:NM_172130:exon6:c.G249A:p.V83V,KCNAB2:NM_001199860:exon7:c.G291A:p.V97V,KCNAB2:NM_001199861:exon7:c.G291A:p.V97V,KCNAB2:NM_003636:exon7:c.G291A:p.V97V 0.5 777.60 63 1 6145273 . G A 777.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-4.537e+00;DP=63;ExcessHet=3.0103;FS=2.302;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=12.34;ReadPosRankSum=0.571;SOR=0.368 GT:AD:DP:GQ:PL 0/1:33,30:63:99:785,0,1078 Haplotypecaller . . .
1 6145365 6145365 A G intronic KCNAB2 . . . . . . . . . . . . 0.5 136.60 14 1 6145365 . A G 136.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.383;DP=14;ExcessHet=3.0103;FS=3.680;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=9.76;ReadPosRankSum=0.879;SOR=0.105 GT:AD:DP:GQ:PL 0/1:8,6:14:99:144,0,241 Haplotypecaller . . .
1 6145379 6145379 C T intronic KCNAB2 . . . . . . . . . . . . 0.5 113.60 9 1 6145379 . C T 113.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.06;DP=9;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=12.62;ReadPosRankSum=1.71;SOR=0.527 GT:AD:DP:GQ:PL 0/1:5,4:9:99:121,0,150 Haplotypecaller . . .
1 6145465 6145465 T G intronic KCNAB2 . . . . . . . . . . . . 0.5 218.60 10 1 6145465 . T G 218.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.82;DP=10;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=21.86;ReadPosRankSum=1.94;SOR=0.307 GT:AD:DP:GQ:PL 0/1:4,6:10:99:226,0,99 Haplotypecaller . . .
1 6147298 6147298 C T intronic KCNAB2 . . . . . . . . . . . . 0.5 439.60 23 1 6147298 . C T 439.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-4.133e+00;DP=23;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=19.11;ReadPosRankSum=-1.260e-01;SOR=1.179 GT:AD:DP:GQ:PL 0/1:9,14:23:99:447,0,303 Haplotypecaller . .
1 6147341 6147341 A C intronic KCNAB2 . . . . . . . . . . . . 0.5 726.60 41 1 6147341 . A C 726.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=4.35;DP=42;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=17.72;ReadPosRankSum=0.588;SOR=0.741 GT:AD:DP:GQ:PL 0/1:20,21:41:99:734,0,626 Haplotypecaller . . .
1 6148766 6148766 T A intronic KCNAB2 . . . . . . . . . . . . 144.01 5 1 6148766 . T A 144.01 . AC=2;AF=1.00;AN=2;DP=6;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=28.74;SOR=3.611 GT:AD:DP:GQ:PL
1 6149053 6149053 C T intronic KCNAB2 . . . . . . . . . . . . 0.5 544.60 37 1 6149053 . C T 544.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.35;DP=37;ExcessHet=3.0103;FS=7.808;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=14.72;ReadPosRankSum=-1.212e+00;SOR=0.129 GT:AD:DP:GQ:PL 0/1:16,21:37:99:552,0,382 Haplotypecaller . . .
1 6149122 6149122 G A intronic KCNAB2 . . . . . . . . . . . . 0.5 538.60 30 1 6149122 . G A 538.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-3.988e+00;DP=30;ExcessHet=3.0103;FS=2.980;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=17.95;ReadPosRankSum=-1.101e+00;SOR=0.174 GT:AD:DP:GQ:PL 0/1:12,18:30:99:546,0,418 Haplotypecaller . .
1 6154417 6154417 C T intronic KCNAB2 . . . . . . . . . . . . 0.5 484.60 28 1 6154417 . C T 484.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.353e+00;DP=28;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=17.31;ReadPosRankSum=0.443;SOR=0.610 GT:AD:DP:GQ:PL 0/1:9,19:28:99:492,0,204 Haplotypecaller . . .
1 6155332 6155332 T C intronic KCNAB2 . . . . . . . . . . . . 0.5 476.60 23 1 6155332 . T C 476.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.91;DP=23;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=20.72;ReadPosRankSum=1.03;SOR=0.859 GT:AD:DP:GQ:PL 0/1:8,15:23:99:484,0,216 Haplotypecaller . . .
1 6155925 6155925 C - intronic KCNAB2 . . . . . . . . . . . . 0.5 40.60 4 1 6155924 . TC T 40.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;DP=7;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=10.15;ReadPosRankSum=1.38;SOR=0.105 GT:AD:DP:GQ:PL 0/1:2,2:4:27:48,0,27 Haplotypecaller . . .
1 6157297 6157297 T C intronic KCNAB2 . . . . . . . . . . . . 0.5 567.60 25 1 6157297 . T C 567.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.16;DP=25;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=22.70;ReadPosRankSum=1.79;SOR=0.495 GT:AD:DP:GQ:PL 0/1:9,16:25:99:575,0,244 Haplotypecaller . . .
1 6158562 6158562 A G exonic KCNAB2 . synonymous SNV KCNAB2:NM_001199863:exon14:c.A831G:p.S277S,KCNAB2:NM_172130:exon15:c.A990G:p.S330S,KCNAB2:NM_001199860:exon16:c.A1032G:p.S344S,KCNAB2:NM_001199861:exon16:c.A1032G:p.S344S,KCNAB2:NM_001199862:exon16:c.A1176G:p.S392S,KCNAB2:NM_003636:exon16:c.A1032G:p.S344S . . . . . . . . . . . . . . . . . . 0.5 2146.60 153 1 6158562 . A G8e+00;SOR=1.391 GT:AD:DP:GQ:PL 0/1:74,79:153:99:2154,0,1937 Haplotypecaller . .
1 6159032 6159032 A G UTR3 KCNAB2 NM_001199861:c.*398A>G;NM_003636:c.*398A>G;NM_172130:c.*398A>G;NM_001199860:c.*398A>G;NM_001199862:c.*398A>G;NM_001199863:c.*398A>G . . . . . . . . . . . . . . . . 0.5 67.60 3 1 6159032 . A G 67.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.967;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=22.53;ReadPosRankSum=-9.670e-01;SOR=1.179 GT:AD:DP:GQ:PL 0/1:1,2:3:31:75,0,31 Haplotypecaller . . .
1 6162054 6162054 T C UTR3 CHD5 NM_015557:c.*3480A>G . . . . . . . . . . 0.5 890.60 76 1 6162054 . T C 890.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.90;DP=76;ExcessHet=3.0103;FS=1.029;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=11.72;ReadPosRankSum=-1.616e+00;SOR=0.970 GT:AD:DP:GQ:PL 0/1:44,32:76:99:898,0,1348 Haplotypecaller . . .
1 6162583 6162583 G A UTR3 CHD5 NM_015557:c.*2951C>T . . . . . . . . . . 70.80 3 1 6162583 . G A 70.80 . AC=2;AF=1.00;AN=2;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=23.60;SOR=1.179 GT:AD:DP:GQ:PL
1 6170301 6170303 ACT - intronic CHD5 . . . . . . . . . . . . 0.5 580.60 29 1 6170300 . CACT C 580.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.343e+00;DP=29;ExcessHet=3.0103;FS=1.550;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=20.02;ReadPosRankSum=1.87;SOR=0.352 GT:AD:DP:GQ:PL 0/1:14,15:29:99:588,0,691 Haplotypecaller . . .
1 6170425 6170425 G - intronic CHD5 . . . . . . . . . . . . 3296.03 82 1 6170424 . CG C 3296.03 . AC=2;AF=1.00;AN=2;DP=85;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=26.46;SOR=0.902 GT:AD:DP:GQ:PL
1 6171992 6171992 C A intronic CHD5 . . . . . . . . . . . . 0.5 838.60 48 1 6171992 . C A 838.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-5.210e-01;DP=48;ExcessHet=3.0103;FS=8.408;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=17.47;ReadPosRankSum=-4.200e-02;SOR=1.546 GT:AD:DP:GQ:PL 0/1:20,28:48:99:846,0,570 Haplotypecaller . .
1 6172840 6172840 C T intronic CHD5 . . . . . . . . . . . . 0.5 337.60 18 1 6172840 . C T 337.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.220e+00;DP=18;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=18.76;ReadPosRankSum=-4.000e-01;SOR=0.914 GT:AD:DP:GQ:PL 0/1:8,10:18:99:345,0,246 Haplotypecaller . .
1 6172875 6172875 G A intronic CHD5 . . . . . . . . . . . . 820.03 23 1 6172875 . G A 820.03 . AC=2;AF=1.00;AN=2;DP=23;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=31.40;SOR=6.358 GT:AD:DP:GQ:PL
1 6173408 6173408 G A intronic CHD5 . . . . . . . . . . . . 0.5 58.60 3 1 6173408 . G A 58.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-9.670e-01;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=19.53;ReadPosRankSum=0.00;SOR=1.179 GT:AD:DP:GQ:PL 0/1:1,2:3:34:66,0,34 Haplotypecaller . . .
1 6183748 6183748 A G intronic CHD5 . . . . . . . . . . . . 0.5 69.61 3 1 6183748 . A G 69.61 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.967;DP=3;ExcessHet=3.0103;FS=4.771;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=23.20;ReadPosRankSum=-4.310e-01;SOR=2.225 GT:AD:DP:GQ:PL 0/1:1,2:3:16:77,0,16 Haplotypecaller . . .
1 6183762 6183762 A - intronic CHD5 . . . . . . . . . . . . 98.80 3 1 6183761 . TA T 98.80 . AC=2;AF=1.00;AN=2;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=32.93;SOR=1.179 GT:AD:DP:GQ:PL
1 6183847 6183847 T C intronic CHD5 . . . . . . . . . . . . 0.5 99.60 4 1 6183847 . T C 99.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.15;DP=4;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=24.90;ReadPosRankSum=0.319;SOR=0.446 GT:AD:DP:GQ:PL 0/1:1,3:4:23:107,0,23 Haplotypecaller . . .
1 6184092 6184092 A G exonic CHD5 . nonsynonymous SNV CHD5:NM_015557:exon31:c.T4615C:p.S1539P . . . . 0.365 0.117 T 0.0 0.026 B 0.0 0.013 B 0.024 0.262 N 1.000 0.090 P 0.345 0.112 N -2.8 0.911 -0.06 0.079 N 0.013 0.005 -0.976 0.359 T 0.000 0.000 T . . . 2.368 0.346 18.61 0.973 0.329 0.005 0.025 N c -0.930 -0.794 0.053 0.150 0.646 0.450 0 3.35 0.373 0.362 0.199 0.062 0.168 0.161 0.236 0.946 0.421 6.147 000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=34.90;SOR=1.958 GT:AD:DP:GQ:PL 1/1:0,102:102:99:3574,306,0 Haplotypecaller . . .
1 6184192 6184192 A G intronic CHD5 . . . . . . . . . . . . 0.5 1582.60 124 1 6184192 . A G 1582.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.68;DP=124;ExcessHet=3.0103;FS=4.846;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=12.76;ReadPosRankSum=0.402;SOR=1.175 GT:AD:DP:GQ:PL 0/1:68,56:124:99:1590,0,1806 Haplotypecaller . . .
1 6184286 6184286 A G intronic CHD5 . . . . . . . . . . . . 0.5 646.60 39 1 6184286 . A G 646.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.86;DP=39;ExcessHet=3.0103;FS=1.448;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=16.58;ReadPosRankSum=0.337;SOR=0.432 GT:AD:DP:GQ:PL 0/1:20,19:39:99:654,0,576 Haplotypecaller . . .
1 6184728 6184728 T G intronic CHD5 . . . . . . . . . . . . 0.5 182.60 13 1 6184728 . T G 182.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.141;DP=13;ExcessHet=3.0103;FS=4.150;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=14.05;ReadPosRankSum=3.16;SOR=2.636 GT:AD:DP:GQ:PL 0/1:5,8:13:99:190,0,104 Haplotypecaller . . .
1 6185064 6185064 G A intronic CHD5 . . . . . . . . . . . . 0.5 176.60 13 1 6185064 . G A 176.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.39;DP=13;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=13.58;ReadPosRankSum=-5.520e-01;SOR=0.569 GT:AD:DP:GQ:PL 0/1:7,6:13:99:184,0,211 Haplotypecaller . . .
1 6185532 6185532 G A intronic CHD5 . . . . . . . . . . . . 0.5 348.60 27 1 6185532 . G A 348.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.354e+00;DP=27;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=12.91;ReadPosRankSum=0.693;SOR=0.646 GT:AD:DP:GQ:PL 0/1:16,11:27:99:356,0,551 Haplotypecaller . . .
1 6186961 6186961 A G intronic CHD5 . . . . . . . . . . . . 69.28 2 1 6186961 . A G 69.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=34.64;SOR=2.303 GT:AD:DP:GQ:PL
1 6188045 6188045 G - intronic CHD5 . . . . . . . . . . . . 0.5 98.60 7 1 6188044 . TG T 98.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.800e-01;DP=8;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=14.09;ReadPosRankSum=0.00;SOR=0.941 GT:AD:DP:GQ:PL 0/1:3,4:7:74:106,0,74 Haplotypecaller . . .
1 6188377 6188377 G A intronic CHD5 . . . . . . . . . . . . 0.5 107.60 11 1 6188377 . G A 107.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.609e+00;DP=11;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=9.78;ReadPosRankSum=0.542;SOR=1.270 GT:AD:DP:GQ:PL 0/1:7,4:11:99:115,0,264 Haplotypecaller . . .
1 6188546 6188546 G A intronic CHD5 . . . . . . . . . . . . 0.5 469.60 41 1 6188546 . G A 469.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.673e+00;DP=41;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=11.45;ReadPosRankSum=1.22;SOR=0.586 GT:AD:DP:GQ:PL 0/1:24,17:41:99:477,0,778 Haplotypecaller . . .
1 6188779 6188779 G C intronic CHD5 . . . . . . . . . . . . 0.5 658.60 41 1 6188779 . G C 658.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.831e+00;DP=41;ExcessHet=3.0103;FS=1.323;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=16.06;ReadPosRankSum=-2.670e+00;SOR=1.174 GT:AD:DP:GQ:PL 0/1:19,22:41:99:666,0,625 Haplotypecaller . .
1 6190611 6190611 A G intronic CHD5 . . . . . . . . . . . . 0.5 88.60 6 1 6190611 . A G 88.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.598;DP=6;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=14.77;ReadPosRankSum=1.65;SOR=0.693 GT:AD:DP:GQ:PL 0/1:3,3:6:96:96,0,100 Haplotypecaller . . .
1 6195024 6195024 C T intronic CHD5 . . . . . . . . . . . . 0.5 407.60 28 1 6195024 . C T 407.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-4.616e+00;DP=28;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=14.56;ReadPosRankSum=-1.380e-01;SOR=0.693 GT:AD:DP:GQ:PL 0/1:14,14:28:99:415,0,525 Haplotypecaller . .
1 6195493 6195493 G A intronic CHD5 . . . . . . . . . . . . 0.5 489.60 37 1 6195493 . G A 489.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-5.566e+00;DP=37;ExcessHet=3.0103;FS=3.050;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=13.23;ReadPosRankSum=-3.220e-01;SOR=2.015 GT:AD:DP:GQ:PL 0/1:21,16:37:99:497,0,782 Haplotypecaller . .
1 6195548 6195548 C T intronic CHD5 . . . . . . . . . . . . 0.5 105.60 12 1 6195548 . C T 105.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.45;DP=12;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=8.80;ReadPosRankSum=0.988;SOR=0.269 GT:AD:DP:GQ:PL 0/1:8,4:12:99:113,0,247 Haplotypecaller . . .
1 6196493 6196493 A G intronic CHD5 . . . . . . . . . . . . 0.5 62.60 12 1 6196493 . A G 62.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.838e+00;DP=13;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=5.22;ReadPosRankSum=0.891;SOR=0.148 GT:AD:DP:GQ:PL 0/1:9,3:12:70:70,0,300 Haplotypecaller . . .
1 6196517 6196517 G A intronic CHD5 . . . . . . . . . . . . 0.5 189.60 17 1 6196517 . G A 189.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.48;DP=18;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=11.15;ReadPosRankSum=-1.954e+00;SOR=0.425 GT:AD:DP:GQ:PL 0/1:10,7:17:99:197,0,303 Haplotypecaller . . .
1 6196869 6196869 A G exonic CHD5 . synonymous SNV CHD5:NM_015557:exon16:c.T2493C:p.I831I . . . . . 0.5 1185.60 91 1 6196869 . A G 1185.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.75;DP=91;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=13.03;ReadPosRankSum=-2.350e-01;SOR=0.729 GT:AD:DP:GQ:PL 0/1:50,41:91:99:1193,0,1339 Haplotypecaller . . .
1 6196943 6196943 A G intronic CHD5 . . . . . . . . . . . . 0.5 1039.60 68 1 6196943 . A G 1039.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.86;DP=69;ExcessHet=3.0103;FS=8.927;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=15.29;ReadPosRankSum=0.661;SOR=0.190 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:40,28:68:99:0|1:6196943_A_G:1047,0,1912:6196943 Haplotypecaller . . .
1 6196951 6196951 T A intronic CHD5 . . . . . . . . . . . . 0.5 1060.60 69 1 6196951 . T A 1060.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=4.17;DP=70;ExcessHet=3.0103;FS=9.174;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=15.37;ReadPosRankSum=0.456;SOR=0.170 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:40,29:69:99:0|1:6196943_A_G:1068,0,1874:6196943 Haplotypecaller . . .
1 6197092 6197092 A G intronic CHD5 . . . . . . . . . . . . 0.5 319.60 11 1 6197092 . A G 319.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.03;DP=11;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=29.05;ReadPosRankSum=1.18;SOR=1.802 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:3,8:11:99:0|1:6197092_A_G:327,0,172:6197092 Haplotypcaller . . .
1 6197107 6197107 G A intronic CHD5 . . . . . . . . . . . . 0.5 319.60 11 1 6197107 . G A 319.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.029e+00;DP=11;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=29.05;ReadPosRankSum=-8.000e-03;SOR=1.802 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:3,8:11:99:0|1:6197092_A_G:327,0,171:6197092 Haplotypecaller . . .
1 6197142 6197144 GGA - intronic CHD5 . . . . . . . . . . . . 0.5 190.60 9 1 6197141 . TGGA T 190.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.38;DP=9;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=21.18;ReadPosRankSum=-1.180e+00;SOR=0.892 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:4,5:9:99:0|1:6197141_TGGA_T:198,0,244:619714Haplotypecaller . . .
1 6197161 6197161 C T intronic CHD5 . . . . . . . . . . . . 0.5 193.60 7 1 6197161 . C T 193.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.189e+00;DP=7;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=27.66;ReadPosRankSum=-1.368e+00;SOR=0.941 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:3,4:7:99:0|1:6197141_TGGA_T:201,0,195:6197141 Haplotypecaller . . .
1 6197165 6197165 G C intronic CHD5 . . . . . . . . . . . . 0.5 151.60 5 1 6197165 . G C 151.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.645e+00;DP=5;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=30.32;ReadPosRankSum=-5.240e-01;SOR=1.022 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:2,3:5:99:0|1:6197141_TGGA_T:159,0,198:6197141 Haplotypecaller . . .
1 6204161 6204161 G A exonic CHD5 . synonymous SNV CHD5:NM_015557:exon12:c.C1857T:p.Y619Y . . . . . 0.5 2096.60 170 1 6204161 . G A 2096.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-7.150e-01;DP=170;ExcessHet=3.0103;FS=0.565;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=12.33;ReadPosRankSum=-1.154e+00;SOR=0.701 GT:AD:DP:GQ:PL 0/1:88,82:170:99:2104,0,2399 Haplotypecaller . .
1 6204266 6204266 A G intronic CHD5 . . . . . . . . . . . . 0.5 1075.60 77 1 6204266 . A G 1075.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.40;DP=78;ExcessHet=3.0103;FS=2.529;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=13.97;ReadPosRankSum=-1.990e-01;SOR=0.368 GT:AD:DP:GQ:PL 0/1:40,37:77:99:1083,0,1241 Haplotypecaller . . .
1 6204411 6204411 G A intronic CHD5 . . . . . . . . . . . . 0.5 127.60 11 1 6204411 . G A 127.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-9.380e-01;DP=11;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=11.60;ReadPosRankSum=-5.220e-01;SOR=1.609 GT:AD:DP:GQ:PL 0/1:6,5:11:99:135,0,182 Haplotypecaller . . .
1 6206648 6206648 C A intronic CHD5 . . . . . . . . . . . . 0.5 346.60 26 1 6206648 . C A 346.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-3.381e+00;DP=26;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=13.33;ReadPosRankSum=1.29;SOR=0.693 GT:AD:DP:GQ:PL 0/1:13,13:26:99:354,0,440 Haplotypecaller . . .
1 6209550 6209550 G T intronic CHD5 . . . . . . . . . . . . 0.5 1290.60 85 1 6209550 . G T 1290.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-5.377e+00;DP=85;ExcessHet=3.0103;FS=2.080;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=15.18;ReadPosRankSum=-1.268e+00;SOR=0.467 GT:AD:DP:GQ:PL 0/1:37,48:85:99:1298,0,1182 Haplotypecaller . .
1 6211340 6211340 T C intronic CHD5 . . . . . . . . . . . . 0.5 147.60 8 1 6211340 . T C 147.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.53;DP=8;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=18.45;ReadPosRankSum=0.00;SOR=1.179 GT:AD:DP:GQ:PL 0/1:3,5:8:93:155,0,93 Haplotypecaller . . .
1 6219288 6219291 CACA - intronic CHD5 . . . . . . . . . . . . 0.5 727.06 26 1 6219287 . TCACA T,TCA 727.06 . AC=1,1;AF=0.500,0.500;AN=2;BaseQRankSum=1.61;DP=31;ExcessHet=3.0103;FS=0.000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=60.00;MQRankSum=0.00;QD=27.96;ReadPosRankSum=-1.340e-01;SOR=5.136 GT:AD:DP:GQ:PL 1/2:1,4,21:26:42:744,585,622,88,0,42 Haplotypcaller . . .
1 6219290 6219291 CA - intronic CHD5 . . . . . . . . . . . . 0.5 727.06 26 1 6219287 . TCACA T,TCA 727.06 . AC=1,1;AF=0.500,0.500;AN=2;BaseQRankSum=1.61;DP=31;ExcessHet=3.0103;FS=0.000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=60.00;MQRankSum=0.00;QD=27.96;ReadPosRankSum=-1.340e-01;SOR=5.136 GT:AD:DP:GQ:PL 1/2:1,4,21:26:42:744,585,622,88,0,42 Haplotypcaller . . .
1 6222501 6222501 C A intronic CHD5 . . . . . . . . . . . . 73.80 3 1 6222501 . C A 73.80 . AC=2;AF=1.00;AN=2;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=24.60;SOR=1.179 GT:AD:DP:GQ:PL
1 6239937 6239937 - G intronic CHD5 . . . . . . . . . . . . 1363.06 33 1 6239937 . C CG 1363.06 . AC=2;AF=1.00;AN=2;DP=33;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=35.35;SOR=4.743 GT:AD:DP:GQ:PL
1 6269120 6269120 T G intronic RNF207 . . . . . . . . . . . . 0.5 74.60 66 1 6269120 . T G 74.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-3.313e+00;DP=66;ExcessHet=3.0103;FS=100.594;MLEAC=1;MLEAF=0.500;MQ=59.75;MQRankSum=-1.732e+00;QD=1.13;ReadPosRankSum=-7.560e-01;SOR=5.667 GT:AD:DP:GQ:PL 0/1:50,16:66:82:82,0,1454 Haplotypecaller .
1 6283506 6283506 C G UTR3 ICMT NM_012405:c.*1634G>C . . . . . . . . . . 37.28 2 1 6283506 . C G 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL
1 6291919 6291919 A - intronic ICMT . . . . . . . . . . . . 0.5 105.64 58 1 6291918 . TA T 105.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.030e-01;DP=91;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.45;MQRankSum=-1.490e-01;QD=2.52;ReadPosRankSum=-4.480e-01;SOR=0.439 GT:AD:DP:GQ:PL 0/1:33,9:58:99:113,0,889 Haplotypecaller . .
1 6299671 6299671 G A downstream LINC00337 dist=169 . . . . . . . . . 0.5 32.60 3 1 6299671 . G A 32.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-9.670e-01;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=10.87;ReadPosRankSum=-9.670e-01;SOR=0.223 GT:AD:DP:GQ:PL 0/1:1,2:3:34:40,0,34 Haplotypecaller . . .
1 6301282 6301282 A G intergenic LINC00337;HES3 dist=1780;dist=2970 . . . . . . . . 60.28 2 1 6301282 . A G 60.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=30.14;SOR=2.303 GT:AD:DP:GQ:PL
1 6305053 6305053 C T intronic HES3 . . . . . . . . . . . . 0.5 98.60 5 1 6305053 . C T 98.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.674;DP=5;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=56.57;MQRankSum=0.842;QD=19.72;ReadPosRankSum=0.524;SOR=0.223 GT:AD:DP:GQ:PL 0/1:2,3:5:36:106,0,36 Haplotypecaller . . .
1 6305292 6305292 C A exonic HES3 . nonsynonymous SNV HES3:NM_001024598:exon4:c.C286A:p.P96T . . . . 0.792 0.032 T 0.063 0.219 B 0.017 0.170 B . . . 1 0.090 P 1.355 0.339 L 1.57 0.293 -0.11 0.087 N 0.056 0.039 -0.997 0.308 T 0.000 0.000 T . . . -0.242 0.073 0.892 0.735 0.100 0.065 0.124 N c -0.884 -0.842 1.0 0.983 0.789 0.998 0 2.4 0.284 1.810 0.383 -1.230 0.015 0.891 0.310 0.003 0.074 6.431 =-3.096e+00;DP=59;ExcessHet=3.0103;FS=8.392;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=10.25;ReadPosRankSum=0.040;SOR=1.966 GT:AD:DP:GQ:PL 0/1:36,22:58:99:602,0,1142 Haplotypecaller . . .
1 6305303 6305303 C A exonic HES3 . synonymous SNV HES3:NM_001024598:exon4:c.C297A:p.A99A . . . . . 0.5 696.60 66 1 6305303 . C A 696.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.174;DP=66;ExcessHet=3.0103;FS=12.370;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=10.55;ReadPosRankSum=0.423;SOR=2.228 GT:AD:DP:GQ:PL 0/1:41,25:66:99:704,0,1248 Haplotypecaller . . .
1 6309319 6309319 C G UTR3 GPR153 NM_207370:c.*79G>C . . . . . . . . . . 0.5 194.60 13 1 6309319 . C G 194.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.694;DP=13;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=14.97;ReadPosRankSum=-2.750e-01;SOR=0.551 GT:AD:DP:GQ:PL 0/1:7,6:13:99:202,0,218 Haplotypecaller . . .
1 6312431 6312431 C T intronic GPR153 . . . . . . . . . . . . 0.5 52.60 4 1 6312431 . C T 52.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.150e+00;DP=4;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=13.15;ReadPosRankSum=-3.190e-01;SOR=0.446 GT:AD:DP:GQ:PL 0/1:1,3:4:29:60,0,29 Haplotypecaller . . .
1 6312478 6312478 T G intronic GPR153 . . . . . . . . . . . . 0.5 93.60 4 1 6312478 . T G 93.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-3.190e-01;DP=4;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=23.40;ReadPosRankSum=-3.190e-01;SOR=0.446 GT:AD:DP:GQ:PL 0/1:1,3:4:28:101,0,28 Haplotypecaller . . .
1 6313938 6313938 C T exonic GPR153 . nonsynonymous SNV GPR153:NM_207370:exon3:c.G626A:p.R209H . . . . 0.394 0.107 T 0.012 0.151 B 0.011 0.145 B 0.002 0.369 N 0.411 0.324 P 0.695 0.181 N 0.97 0.425 -0.35 0.129 N 0.146 0.172 -1.009 0.273 T 0.000 0.000 T . . . 1.052 0.195 10.95 0.937 0.230 0.512 0.286 D c -0.983 -0.894 0.889 0.258 0.660 0.495 0 2.03 0.256 -0.046 0.118 -0.902 0.026 0.653 0.280 0.000 0.016 7.468 . C T 424.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.300e-01;DP=36;ExcessHet=3.0103;FS=7.544;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=11.79;ReadPosRankSum=0.366;SOR=2.049 GT:AD:DP:GQ:PL 0/1:20,16:36:99:432,0,614 Haplotypecaller . . .
1 6314349 6314349 A G intronic GPR153 . . . . . . . . . . . . 963.03 26 1 6314349 . A G 963.03 . AC=2;AF=1.00;AN=2;DP=26;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=27.61;SOR=1.022 GT:AD:DP:GQ:PL
1 6314479 6314479 C T intronic GPR153 . . . . . . . . . . . . 0.5 620.60 42 1 6314479 . C T 620.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-5.042e+00;DP=42;ExcessHet=3.0103;FS=3.222;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=14.78;ReadPosRankSum=-1.084e+00;SOR=0.173 GT:AD:DP:GQ:PL 0/1:22,20:42:99:628,0,785 Haplotypecaller . .
1 6314822 6314822 T C exonic GPR153 . synonymous SNV GPR153:NM_207370:exon2:c.A144G:p.T48T . . . . . 0.5 2368.60 145 1 6314822 . T C 2368.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-3.490e-01;DP=145;ExcessHet=3.0103;FS=1.351;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=16.34;ReadPosRankSum=2.15;SOR=0.873 GT:AD:DP:GQ:PL 0/1:65,80:145:99:2376,0,1804 Haplotypecaller . . .
1 6318591 6318591 G C intronic GPR153 . . . . . . . . . . . . 109.80 3 1 6318591 . G C 109.80 . AC=2;AF=1.00;AN=2;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=25.41;SOR=1.179 GT:AD:DP:GQ:PL
1 6356760 6356760 G T intronic ACOT7 . . . . . . . . . . . . 37.28 2 1 6356760 . G T 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL
1 6453520 6453520 - G UTR5 ACOT7 NM_007274:c.-62_-61insC . . . . . . . . . . 147.14 4 1 6453520 . C CG 147.14 . AC=2;AF=1.00;AN=2;DP=4;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=33.40;SOR=1.609 GT:AD:DP:GQ:PL
1 6500604 6500604 - G intronic ESPN . . . . . . . . . . . . 301.02 6 1 6500604 . C CG 301.02 . AC=2;AF=1.00;AN=2;DP=9;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.36;QD=30.20;SOR=2.303 GT:AD:DP:GQ:PGT:PID:PL:PS 1|1:0,6:6:21:1|1:6500604_C_CG:315,21,0:6500604 Haplotypecaller . . .
1 6500611 6500611 C - intronic ESPN . . . . . . . . . . . . 368.01 7 1 6500610 . AC A 368.01 . AC=2;AF=1.00;AN=2;DP=10;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.43;QD=31.98;SOR=2.584 GT:AD:DP:GQ:PGT:PID:PL:PS 1|1:0,7:7:27:1|1:6500604_C_CG:382,27,0:6500604 Haplotypecaller . . .
1 6500626 6500626 - G intronic ESPN . . . . . . . . . . . . .^Z . . . . . . . . . . . . . . . . . . . 601.06 14 1 6500626 . C CG 601.06 . AC=2;AF=1.00;AN=2;DP=17;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.66;QD=28.65;SOR=1.329 GT:AD:DP:GQ:PGT:PID:PL:PS
[7]+ Stopped grep --color=auto "Haplotype" DS-bkm-085-T_Combined_RECAL.germline_combined.csv
(muse) [vym1@compute-e-16-237 out]$ grep "germline" DS-bkm-085-T_Combined_RECAL.germline_combined.csv
(muse) [vym1@compute-e-16-237 out]$ ls
DS-bkm-085-T_Combined_RECAL DS-bkm-085-T_Combined_RECAL.germline_combined.csv
DS-bkm-085-T_Combined_RECAL.bad_somatic_reads.vcf DS-bkm-085-T_Combined_RECAL.somatic.csv
(muse) [vym1@compute-e-16-237 out]$ cd DS-bkm-085-T_Combined_RECAL
(muse) [vym1@compute-e-16-237 DS-bkm-085-T_Combined_RECAL]$ ls
annotation_files cut_filtering intersection_files
(muse) [vym1@compute-e-16-237 DS-bkm-085-T_Combined_RECAL]$ cd annotation_files/
(muse) [vym1@compute-e-16-237 annotation_files]$ ls
DS-bkm-085-T_Combined_RECAL.germline_variants_filtered.avinput
DS-bkm-085-T_Combined_RECAL.germline_variants_filtered.hg19_multianno.txt
DS-bkm-085-T_Combined_RECAL.germline_variants_filtered.hg19_multianno.txt.LABELED
DS-bkm-085-T_Combined_RECAL.germline_variants_filtered.hg19_multianno.txt.LABELED.levels
DS-bkm-085-T_Combined_RECAL.germline_variants_filtered.hg19_multianno.vcf
DS-bkm-085-T_Combined_RECAL.germline_variants_filtered.vcf
DS-bkm-085-T_Combined_RECAL.M2_Risk_variants_filtered.avinput
DS-bkm-085-T_Combined_RECAL.M2_Risk_variants_filtered.hg19_multianno.txt
DS-bkm-085-T_Combined_RECAL.M2_Risk_variants_filtered.hg19_multianno.txt.LABELED
DS-bkm-085-T_Combined_RECAL.M2_Risk_variants_filtered.hg19_multianno.txt.LABELED.levels
DS-bkm-085-T_Combined_RECAL.M2_Risk_variants_filtered.hg19_multianno.vcf
DS-bkm-085-T_Combined_RECAL.M2_Risk_variants_filtered.vcf
DS-bkm-085-T_Combined_RECAL.somatic_variants_filtered_1.vcf
DS-bkm-085-T_Combined_RECAL.somatic_variants_filtered_2.avinput
DS-bkm-085-T_Combined_RECAL.somatic_variants_filtered_2.hg19_multianno.txt
DS-bkm-085-T_Combined_RECAL.somatic_variants_filtered_2.hg19_multianno.txt.levels
DS-bkm-085-T_Combined_RECAL.somatic_variants_filtered_2.hg19_multianno.vcf
DS-bkm-085-T_Combined_RECAL.somatic_variants_filtered_2.vcf
(muse) [vym1@compute-e-16-237 annotation_files]$ less DS-bkm-085-T_Combined_RECAL.M2_Risk_variants_filtered.vcf
(muse) [vym1@compute-e-16-237 annotation_files]$ less DS-bkm-085-T_Combined_RECAL.M2_Risk_variants_filtered.hg19_multianno.txt.LABELED.levels
(muse) [vym1@compute-e-16-237 annotation_files]$ less DS-bkm-085-T_Combined_RECAL.M2_Risk_variants_filtered.hg19_multianno.txt.LABELED
(muse) [vym1@compute-e-16-237 annotation_files]$ cd ..
(muse) [vym1@compute-e-16-237 DS-bkm-085-T_Combined_RECAL]$ ls
annotation_files cut_filtering intersection_files
(muse) [vym1@compute-e-16-237 DS-bkm-085-T_Combined_RECAL]$ cd ..
(muse) [vym1@compute-e-16-237 out]$ ls
DS-bkm-085-T_Combined_RECAL DS-bkm-085-T_Combined_RECAL.germline_combined.csv
DS-bkm-085-T_Combined_RECAL.bad_somatic_reads.vcf DS-bkm-085-T_Combined_RECAL.somatic.csv
(muse) [vym1@compute-e-16-237 out]$ ls
DS-bkm-085-T_Combined_RECAL DS-bkm-085-T_Combined_RECAL.germline_combined.csv
DS-bkm-085-T_Combined_RECAL.bad_somatic_reads.vcf DS-bkm-085-T_Combined_RECAL.somatic.csv
(muse) [vym1@compute-e-16-237 out]$ sh /n/data1/hms/dbmi/park/victor/scripts/SNVCurate/Annotate.sh ${PWD}/out ${PWD}/.Mutect2 hg19 ${PWD}/bam_files/Mutect.csv ${PWD}/.GenotypeGVCFs
/n/data1/hms/dbmi/park/victor/scripts/SNVCurate/Annotate.sh: line 23: cd: /n/data1/hms/dbmi/park/victor/other/pipeline_test/out/out: No such file or directory
(muse) [vym1@compute-e-16-237 out]$ cd ..
(muse) [vym1@compute-e-16-237 pipeline_test]$ sh /n/data1/hms/dbmi/park/victor/scripts/SNVCurate/Annotate.sh ${PWD}/out ${PWD}/.Mutect2 hg19 ${PWD}/bam_files/Mutect.csv ${PWD}/.GenotypeGVCFs
rm: cannot remove ‘*csv’: No such file or directory
rm: cannot remove ‘*vcf’: No such file or directory
NOTICE: Running with system command <convert2annovar.pl -includeinfo -allsample -withfreq -format vcf4 DS-bkm-085-T_Combined_RECAL.somatic_variants_filtered_2.vcf > DS-bkm-085-T_Combined_RECAL.somatic_variants_filtered_2.avinput>
NOTICE: Finished reading 192 lines from VCF file
NOTICE: A total of 58 locus in VCF file passed QC threshold, representing 58 SNPs (31 transitions and 27 transversions) and 0 indels/substitutions
NOTICE: Finished writing allele frequencies based on 58 SNP genotypes (31 transitions and 27 transversions) and 0 indels/substitutions for 1 samples
NOTICE: Running with system command </home/mk446/bin/annovar/table_annovar.pl DS-bkm-085-T_Combined_RECAL.somatic_variants_filtered_2.avinput /home/mk446/bin/annovar/humandb/ -outfile DS-bkm-085-T_Combined_RECAL.somatic_variants_filtered_2 -buildver hg19 -remove -protocol refGene,clinvar_20190305,dbnsfp33a -operation g,f,f -nastring . -polish -otherinfo>
-----------------------------------------------------------------
NOTICE: Processing operation=g protocol=refGene
NOTICE: Running with system command <annotate_variation.pl -geneanno -buildver hg19 -dbtype refGene -outfile DS-bkm-085-T_Combined_RECAL.somatic_variants_filtered_2.refGene -exonsort DS-bkm-085-T_Combined_RECAL.somatic_variants_filtered_2.avinput /home/mk446/bin/annovar/humandb/>
NOTICE: Output files were written to DS-bkm-085-T_Combined_RECAL.somatic_variants_filtered_2.refGene.variant_function, DS-bkm-085-T_Combined_RECAL.somatic_variants_filtered_2.refGene.exonic_variant_function
NOTICE: Reading gene annotation from /home/mk446/bin/annovar/humandb/hg19_refGene.txt ... Done with 63481 transcripts (including 15216 without coding sequence annotation) for 27720 unique genes
NOTICE: Processing next batch with 58 unique variants in 58 input lines
NOTICE: Reading FASTA sequences from /home/mk446/bin/annovar/humandb/hg19_refGeneMrna.fa ... Done with 121 sequences
WARNING: A total of 405 sequences will be ignored due to lack of correct ORF annotation
NOTICE: Running with system command <coding_change.pl DS-bkm-085-T_Combined_RECAL.somatic_variants_filtered_2.refGene.exonic_variant_function.orig /home/mk446/bin/annovar/humandb//hg19_refGene.txt /home/mk446/bin/annovar/humandb//hg19_refGeneMrna.fa -alltranscript -out DS-bkm-085-T_Combined_RECAL.somatic_variants_filtered_2.refGene.fa -newevf DS-bkm-085-T_Combined_RECAL.somatic_variants_filtered_2.refGene.exonic_variant_function>
-----------------------------------------------------------------
NOTICE: Processing operation=f protocol=clinvar_20190305
NOTICE: Finished reading 5 column headers for '-dbtype clinvar_20190305'
NOTICE: Running system command <annotate_variation.pl -filter -dbtype clinvar_20190305 -buildver hg19 -outfile DS-bkm-085-T_Combined_RECAL.somatic_variants_filtered_2 DS-bkm-085-T_Combined_RECAL.somatic_variants_filtered_2.avinput /home/mk446/bin/annovar/humandb/ -otherinfo>
NOTICE: the --dbtype clinvar_20190305 is assumed to be in generic ANNOVAR database format
NOTICE: Variants matching filtering criteria are written to DS-bkm-085-T_Combined_RECAL.somatic_variants_filtered_2.hg19_clinvar_20190305_dropped, other variants are written to DS-bkm-085-T_Combined_RECAL.somatic_variants_filtered_2.hg19_clinvar_20190305_filtered
NOTICE: Processing next batch with 58 unique variants in 58 input lines
NOTICE: Database index loaded. Total number of bins is 45822 and the number of bins to be scanned is 17
NOTICE: Scanning filter database /home/mk446/bin/annovar/humandb/hg19_clinvar_20190305.txt...Done
-----------------------------------------------------------------
NOTICE: Processing operation=f protocol=dbnsfp33a
NOTICE: Finished reading 66 column headers for '-dbtype dbnsfp33a'
NOTICE: Running system command <annotate_variation.pl -filter -dbtype dbnsfp33a -buildver hg19 -outfile DS-bkm-085-T_Combined_RECAL.somatic_variants_filtered_2 DS-bkm-085-T_Combined_RECAL.somatic_variants_filtered_2.avinput /home/mk446/bin/annovar/humandb/ -otherinfo>
NOTICE: the --dbtype dbnsfp33a is assumed to be in generic ANNOVAR database format
NOTICE: Variants matching filtering criteria are written to DS-bkm-085-T_Combined_RECAL.somatic_variants_filtered_2.hg19_dbnsfp33a_dropped, other variants are written to DS-bkm-085-T_Combined_RECAL.somatic_variants_filtered_2.hg19_dbnsfp33a_filtered
NOTICE: Processing next batch with 58 unique variants in 58 input lines
NOTICE: Database index loaded. Total number of bins is 550512 and the number of bins to be scanned is 51
NOTICE: Scanning filter database /home/mk446/bin/annovar/humandb/hg19_dbnsfp33a.txt...Done
-----------------------------------------------------------------
NOTICE: Multianno output file is written to DS-bkm-085-T_Combined_RECAL.somatic_variants_filtered_2.hg19_multianno.txt
NOTICE: Reading from DS-bkm-085-T_Combined_RECAL.somatic_variants_filtered_2.hg19_multianno.txt
-----------------------------------------------------------------
NOTICE: VCF output is written to DS-bkm-085-T_Combined_RECAL.somatic_variants_filtered_2.hg19_multianno.vcf
NOTICE: Running with system command <convert2annovar.pl -includeinfo -allsample -withfreq -format vcf4 DS-bkm-085-T_Combined_RECAL.germline_variants_filtered.vcf > DS-bkm-085-T_Combined_RECAL.germline_variants_filtered.avinput>
NOTICE: Finished reading 134 lines from VCF file
NOTICE: A total of 0 locus in VCF file passed QC threshold, representing 0 SNPs (0 transitions and 0 transversions) and 0 indels/substitutions
NOTICE: Finished writing allele frequencies based on 0 SNP genotypes (0 transitions and 0 transversions) and 0 indels/substitutions for 1 samples
NOTICE: Running with system command </home/mk446/bin/annovar/table_annovar.pl DS-bkm-085-T_Combined_RECAL.germline_variants_filtered.avinput /home/mk446/bin/annovar/humandb/ -outfile DS-bkm-085-T_Combined_RECAL.germline_variants_filtered -buildver hg19 -remove -protocol refGene,clinvar_20190305,dbnsfp33a -operation g,f,f -nastring . -polish -otherinfo>
-----------------------------------------------------------------
NOTICE: Processing operation=g protocol=refGene
NOTICE: Running with system command <annotate_variation.pl -geneanno -buildver hg19 -dbtype refGene -outfile DS-bkm-085-T_Combined_RECAL.germline_variants_filtered.refGene -exonsort DS-bkm-085-T_Combined_RECAL.germline_variants_filtered.avinput /home/mk446/bin/annovar/humandb/>
NOTICE: Output files were written to DS-bkm-085-T_Combined_RECAL.germline_variants_filtered.refGene.variant_function, DS-bkm-085-T_Combined_RECAL.germline_variants_filtered.refGene.exonic_variant_function
NOTICE: Reading gene annotation from /home/mk446/bin/annovar/humandb/hg19_refGene.txt ... Done with 63481 transcripts (including 15216 without coding sequence annotation) for 27720 unique genes
NOTICE: Running with system command <coding_change.pl DS-bkm-085-T_Combined_RECAL.germline_variants_filtered.refGene.exonic_variant_function.orig /home/mk446/bin/annovar/humandb//hg19_refGene.txt /home/mk446/bin/annovar/humandb//hg19_refGeneMrna.fa -alltranscript -out DS-bkm-085-T_Combined_RECAL.germline_variants_filtered.refGene.fa -newevf DS-bkm-085-T_Combined_RECAL.germline_variants_filtered.refGene.exonic_variant_function>
-----------------------------------------------------------------
NOTICE: Processing operation=f protocol=clinvar_20190305
NOTICE: Finished reading 5 column headers for '-dbtype clinvar_20190305'
NOTICE: Running system command <annotate_variation.pl -filter -dbtype clinvar_20190305 -buildver hg19 -outfile DS-bkm-085-T_Combined_RECAL.germline_variants_filtered DS-bkm-085-T_Combined_RECAL.germline_variants_filtered.avinput /home/mk446/bin/annovar/humandb/ -otherinfo>
NOTICE: the --dbtype clinvar_20190305 is assumed to be in generic ANNOVAR database format
NOTICE: Variants matching filtering criteria are written to DS-bkm-085-T_Combined_RECAL.germline_variants_filtered.hg19_clinvar_20190305_dropped, other variants are written to DS-bkm-085-T_Combined_RECAL.germline_variants_filtered.hg19_clinvar_20190305_filtered
-----------------------------------------------------------------
NOTICE: Processing operation=f protocol=dbnsfp33a
NOTICE: Finished reading 66 column headers for '-dbtype dbnsfp33a'
NOTICE: Running system command <annotate_variation.pl -filter -dbtype dbnsfp33a -buildver hg19 -outfile DS-bkm-085-T_Combined_RECAL.germline_variants_filtered DS-bkm-085-T_Combined_RECAL.germline_variants_filtered.avinput /home/mk446/bin/annovar/humandb/ -otherinfo>
NOTICE: the --dbtype dbnsfp33a is assumed to be in generic ANNOVAR database format
NOTICE: Variants matching filtering criteria are written to DS-bkm-085-T_Combined_RECAL.germline_variants_filtered.hg19_dbnsfp33a_dropped, other variants are written to DS-bkm-085-T_Combined_RECAL.germline_variants_filtered.hg19_dbnsfp33a_filtered
-----------------------------------------------------------------
NOTICE: Multianno output file is written to DS-bkm-085-T_Combined_RECAL.germline_variants_filtered.hg19_multianno.txt
NOTICE: Reading from DS-bkm-085-T_Combined_RECAL.germline_variants_filtered.hg19_multianno.txt
-----------------------------------------------------------------
NOTICE: VCF output is written to DS-bkm-085-T_Combined_RECAL.germline_variants_filtered.hg19_multianno.vcf
Use of uninitialized value $pre_anno_string in concatenation (.) or string at /home/mk446/bin/annovar/table_annovar.pl line 191, <MANNO> line 1.
Use of uninitialized value in join or string at /home/mk446/bin/annovar/table_annovar.pl line 192, <MANNO> line 1.
Use of uninitialized value in join or string at /home/mk446/bin/annovar/table_annovar.pl line 192, <MANNO> line 1.
Use of uninitialized value in join or string at /home/mk446/bin/annovar/table_annovar.pl line 192, <MANNO> line 1.
Use of uninitialized value in join or string at /home/mk446/bin/annovar/table_annovar.pl line 192, <MANNO> line 1.
Use of uninitialized value in join or string at /home/mk446/bin/annovar/table_annovar.pl line 192, <MANNO> line 1.
Use of uninitialized value in join or string at /home/mk446/bin/annovar/table_annovar.pl line 192, <MANNO> line 1.
Use of uninitialized value in join or string at /home/mk446/bin/annovar/table_annovar.pl line 192, <MANNO> line 1.
NOTICE: Running with system command <convert2annovar.pl -includeinfo -allsample -withfreq -format vcf4 DS-bkm-085-T_Combined_RECAL.M2_Risk_variants_filtered.vcf > DS-bkm-085-T_Combined_RECAL.M2_Risk_variants_filtered.avinput>
NOTICE: Finished reading 885 lines from VCF file
NOTICE: A total of 758 locus in VCF file passed QC threshold, representing 632 SNPs (469 transitions and 163 transversions) and 126 indels/substitutions
NOTICE: Finished writing allele frequencies based on 7584 SNP genotypes (5628 transitions and 1956 transversions) and 1512 indels/substitutions for 12 samples
NOTICE: Running with system command </home/mk446/bin/annovar/table_annovar.pl DS-bkm-085-T_Combined_RECAL.M2_Risk_variants_filtered.avinput /home/mk446/bin/annovar/humandb/ -outfile DS-bkm-085-T_Combined_RECAL.M2_Risk_variants_filtered -buildver hg19 -remove -protocol refGene,clinvar_20190305,dbnsfp33a -operation g,f,f -nastring . -polish -otherinfo>
-----------------------------------------------------------------
NOTICE: Processing operation=g protocol=refGene
NOTICE: Running with system command <annotate_variation.pl -geneanno -buildver hg19 -dbtype refGene -outfile DS-bkm-085-T_Combined_RECAL.M2_Risk_variants_filtered.refGene -exonsort DS-bkm-085-T_Combined_RECAL.M2_Risk_variants_filtered.avinput /home/mk446/bin/annovar/humandb/>
NOTICE: Output files were written to DS-bkm-085-T_Combined_RECAL.M2_Risk_variants_filtered.refGene.variant_function, DS-bkm-085-T_Combined_RECAL.M2_Risk_variants_filtered.refGene.exonic_variant_function
NOTICE: Reading gene annotation from /home/mk446/bin/annovar/humandb/hg19_refGene.txt ... Done with 63481 transcripts (including 15216 without coding sequence annotation) for 27720 unique genes
NOTICE: Processing next batch with 758 unique variants in 758 input lines
NOTICE: Reading FASTA sequences from /home/mk446/bin/annovar/humandb/hg19_refGeneMrna.fa ... Done with 452 sequences
WARNING: A total of 405 sequences will be ignored due to lack of correct ORF annotation
NOTICE: Running with system command <coding_change.pl DS-bkm-085-T_Combined_RECAL.M2_Risk_variants_filtered.refGene.exonic_variant_function.orig /home/mk446/bin/annovar/humandb//hg19_refGene.txt /home/mk446/bin/annovar/humandb//hg19_refGeneMrna.fa -alltranscript -out DS-bkm-085-T_Combined_RECAL.M2_Risk_variants_filtered.refGene.fa -newevf DS-bkm-085-T_Combined_RECAL.M2_Risk_variants_filtered.refGene.exonic_variant_function>
-----------------------------------------------------------------
NOTICE: Processing operation=f protocol=clinvar_20190305
NOTICE: Finished reading 5 column headers for '-dbtype clinvar_20190305'
NOTICE: Running system command <annotate_variation.pl -filter -dbtype clinvar_20190305 -buildver hg19 -outfile DS-bkm-085-T_Combined_RECAL.M2_Risk_variants_filtered DS-bkm-085-T_Combined_RECAL.M2_Risk_variants_filtered.avinput /home/mk446/bin/annovar/humandb/ -otherinfo>
NOTICE: the --dbtype clinvar_20190305 is assumed to be in generic ANNOVAR database format
NOTICE: Variants matching filtering criteria are written to DS-bkm-085-T_Combined_RECAL.M2_Risk_variants_filtered.hg19_clinvar_20190305_dropped, other variants are written to DS-bkm-085-T_Combined_RECAL.M2_Risk_variants_filtered.hg19_clinvar_20190305_filtered
NOTICE: Processing next batch with 758 unique variants in 758 input lines
NOTICE: Database index loaded. Total number of bins is 45822 and the number of bins to be scanned is 116
NOTICE: Scanning filter database /home/mk446/bin/annovar/humandb/hg19_clinvar_20190305.txt...Done
-----------------------------------------------------------------
NOTICE: Processing operation=f protocol=dbnsfp33a
NOTICE: Finished reading 66 column headers for '-dbtype dbnsfp33a'
NOTICE: Running system command <annotate_variation.pl -filter -dbtype dbnsfp33a -buildver hg19 -outfile DS-bkm-085-T_Combined_RECAL.M2_Risk_variants_filtered DS-bkm-085-T_Combined_RECAL.M2_Risk_variants_filtered.avinput /home/mk446/bin/annovar/humandb/ -otherinfo>
NOTICE: the --dbtype dbnsfp33a is assumed to be in generic ANNOVAR database format
NOTICE: Variants matching filtering criteria are written to DS-bkm-085-T_Combined_RECAL.M2_Risk_variants_filtered.hg19_dbnsfp33a_dropped, other variants are written to DS-bkm-085-T_Combined_RECAL.M2_Risk_variants_filtered.hg19_dbnsfp33a_filtered
NOTICE: Processing next batch with 758 unique variants in 758 input lines
NOTICE: Database index loaded. Total number of bins is 550512 and the number of bins to be scanned is 355
NOTICE: Scanning filter database /home/mk446/bin/annovar/humandb/hg19_dbnsfp33a.txt...Done
-----------------------------------------------------------------
NOTICE: Multianno output file is written to DS-bkm-085-T_Combined_RECAL.M2_Risk_variants_filtered.hg19_multianno.txt
NOTICE: Reading from DS-bkm-085-T_Combined_RECAL.M2_Risk_variants_filtered.hg19_multianno.txt
-----------------------------------------------------------------
NOTICE: VCF output is written to DS-bkm-085-T_Combined_RECAL.M2_Risk_variants_filtered.hg19_multianno.vcf
12
0
0
NOTICE: Running with system command <convert2annovar.pl -includeinfo -allsample -withfreq -format vcf4 /n/data1/hms/dbmi/park/victor/other/pipeline_test/.GenotypeGVCFs/DS-bkm-085-N_Combined_RECAL.vcf > DS-bkm-085-N_Combined_RECAL.avinput>
NOTICE: Finished reading 287249 lines from VCF file
NOTICE: A total of 287123 locus in VCF file passed QC threshold, representing 247440 SNPs (165166 transitions and 82274 transversions) and 40774 indels/substitutions
NOTICE: Finished writing allele frequencies based on 247440 SNP genotypes (165166 transitions and 82274 transversions) and 40774 indels/substitutions for 1 samples
WARNING: 258 invalid alternative alleles found in input file
NOTICE: Running with system command </home/mk446/bin/annovar/table_annovar.pl DS-bkm-085-N_Combined_RECAL.avinput /home/mk446/bin/annovar/humandb/ -outfile DS-bkm-085-N_Combined_RECAL -buildver hg19 -remove -protocol refGene,clinvar_20190305,dbnsfp33a -operation g,f,f -nastring . -polish -otherinfo>
-----------------------------------------------------------------
NOTICE: Processing operation=g protocol=refGene
NOTICE: Running with system command <annotate_variation.pl -geneanno -buildver hg19 -dbtype refGene -outfile DS-bkm-085-N_Combined_RECAL.refGene -exonsort DS-bkm-085-N_Combined_RECAL.avinput /home/mk446/bin/annovar/humandb/>
NOTICE: Output files were written to DS-bkm-085-N_Combined_RECAL.refGene.variant_function, DS-bkm-085-N_Combined_RECAL.refGene.exonic_variant_function
NOTICE: Reading gene annotation from /home/mk446/bin/annovar/humandb/hg19_refGene.txt ... Done with 63481 transcripts (including 15216 without coding sequence annotation) for 27720 unique genes
NOTICE: Processing next batch with 288472 unique variants in 288472 input lines
NOTICE: Reading FASTA sequences from /home/mk446/bin/annovar/humandb/hg19_refGeneMrna.fa ... Done with 21696 sequences
WARNING: A total of 405 sequences will be ignored due to lack of correct ORF annotation
NOTICE: Running with system command <coding_change.pl DS-bkm-085-N_Combined_RECAL.refGene.exonic_variant_function.orig /home/mk446/bin/annovar/humandb//hg19_refGene.txt /home/mk446/bin/annovar/humandb//hg19_refGeneMrna.fa -alltranscript -out DS-bkm-085-N_Combined_RECAL.refGene.fa -newevf DS-bkm-085-N_Combined_RECAL.refGene.exonic_variant_function>
Warning: 1 transcripts are flagged as having potential ORF issues (premature stopcodon or lack of stop codon)
-----------------------------------------------------------------
NOTICE: Processing operation=f protocol=clinvar_20190305
NOTICE: Finished reading 5 column headers for '-dbtype clinvar_20190305'
NOTICE: Running system command <annotate_variation.pl -filter -dbtype clinvar_20190305 -buildver hg19 -outfile DS-bkm-085-N_Combined_RECAL DS-bkm-085-N_Combined_RECAL.avinput /home/mk446/bin/annovar/humandb/ -otherinfo>
NOTICE: the --dbtype clinvar_20190305 is assumed to be in generic ANNOVAR database format
NOTICE: Variants matching filtering criteria are written to DS-bkm-085-N_Combined_RECAL.hg19_clinvar_20190305_dropped, other variants are written to DS-bkm-085-N_Combined_RECAL.hg19_clinvar_20190305_filtered
NOTICE: Processing next batch with 288472 unique variants in 288472 input lines
NOTICE: Database index loaded. Total number of bins is 45822 and the number of bins to be scanned is 18233
NOTICE: Scanning filter database /home/mk446/bin/annovar/humandb/hg19_clinvar_20190305.txt...Done
-----------------------------------------------------------------
NOTICE: Processing operation=f protocol=dbnsfp33a
NOTICE: Finished reading 66 column headers for '-dbtype dbnsfp33a'
NOTICE: Running system command <annotate_variation.pl -filter -dbtype dbnsfp33a -buildver hg19 -outfile DS-bkm-085-N_Combined_RECAL DS-bkm-085-N_Combined_RECAL.avinput /home/mk446/bin/annovar/humandb/ -otherinfo>
NOTICE: the --dbtype dbnsfp33a is assumed to be in generic ANNOVAR database format
NOTICE: Variants matching filtering criteria are written to DS-bkm-085-N_Combined_RECAL.hg19_dbnsfp33a_dropped, other variants are written to DS-bkm-085-N_Combined_RECAL.hg19_dbnsfp33a_filtered
NOTICE: Processing next batch with 288472 unique variants in 288472 input lines
NOTICE: Database index loaded. Total number of bins is 550512 and the number of bins to be scanned is 43709
NOTICE: Scanning filter database /home/mk446/bin/annovar/humandb/hg19_dbnsfp33a.txt...Done
-----------------------------------------------------------------
NOTICE: Multianno output file is written to DS-bkm-085-N_Combined_RECAL.hg19_multianno.txt
NOTICE: Reading from DS-bkm-085-N_Combined_RECAL.hg19_multianno.txt
-----------------------------------------------------------------
NOTICE: VCF output is written to DS-bkm-085-N_Combined_RECAL.hg19_multianno.vcf
(muse) [vym1@compute-e-16-237 pipeline_test]$ ls
bam_files databases out
(muse) [vym1@compute-e-16-237 pipeline_test]$ cd out
(muse) [vym1@compute-e-16-237 out]$ ls
DS-bkm-085-T_Combined_RECAL DS-bkm-085-T_Combined_RECAL.germline_combined.csv
DS-bkm-085-T_Combined_RECAL.bad_somatic_reads.vcf DS-bkm-085-T_Combined_RECAL.somatic.csv
(muse) [vym1@compute-e-16-237 out]$ packet_write_wait: Connection to 134.174.159.24 port 22: Broken pipe
(base) Victors-MacBook-Pro:~ Victor$ ssh [email protected]
Password:
Duo two-factor login for vym1
Enter a passcode or select one of the following options:
1. Duo Push to XXX-XXX-8777
2. Phone call to XXX-XXX-8777
3. SMS passcodes to XXX-XXX-8777
Passcode or option (1-3): 1
Pushed a login request to your device...
Success. Logging you in...
Welcome to O2 (Orchestra 2)!
___ ____
/ _ \ |___ \
| | | | __) |
| |_| | / __/
\___/ |_____|
You've landed on login05 which is a
8 core system with 15.51 GiB memory
running kernel 3.10.0 born on 2018-12-04
==== O2 ===================================================================
News (Mar 16 2020)
+-------------------------------------------------------------------------------+
| * As part of Harvard Medical School's response to COVID-19, |
| HMS Research Computing is now working remotely. More details at: |
| https://it.hms.harvard.edu/rc |
| |
| * RC is moving all training and consulting sessions online, using Zoom. |
| |
| To get started with Zoom, please see: |
| https://it.hms.harvard.edu/zoom-available-hms-users |
| |
| Training updates, such as online meeting links, will be posted at: |
| https://wiki.rc.hms.harvard.edu/display/O2/User+Training |
| |
| * HMS VPN is not required for using O2. Only use VPN when absolutely needed. |
| |
| ** Copying large data over VPN can greatly impact its performance! |
| |
| * Status updates and upcoming service outages are posted at: |
| https://wiki.rc.hms.harvard.edu/display/O2/O2+Cluster+Status |
+-------------------------------------------------------------------------------+
------------------------------
Contact HMS Research Computing:
E-mail [email protected]
Web https://rc.hms.harvard.edu
Twitter @hms_rc
===========================================================================
(base) [vym1@login05 ~]$ cd /n/data1/hms/dbmi/park/victor
(base) [vym1@login05 victor]$ ls
Craig Craig.2 data Doga other Peter references scripts software UserIDs.csv Vinay Walsh_Park_UserIDs.csv WP_IDs WP_lab_names
(base) [vym1@login05 victor]$ cd scripts
(base) [vym1@login05 scripts]$ ls
FoundationOne.ipynb SamtoolsMpileup vcf.hg19_multianno.csv
GATK_Germline_SNPs_Indels sequenza-utils-3.0.0 vcf.hg38_multianno.csv
GATK_Somatic_SNPs_Indels sequenza-utils-3.0.0.tar.gz vcf.invalid_input
Gerburg_WES_Filtration_Pipeline.ipynb SNVCurate vcf.refGene.invalid_input
LnCAP.bedpe Somatic_Variant_Filtration_Workflow-Normal-Data_BMSN_CE_Data.ipynb vcfTools
other Somatic_Variant_Filtration_Workflow-Normal-Data_BMSN_CE_Data_ORIGINAL.ipynb
random_tests Somatic_Variant_Filtration_Workflow_TEST.ipynb
(base) [vym1@login05 scripts]$ cd SNVCurate/
(base) [vym1@login05 SNVCurate]$ ls
Add_Read_Info.py Filter_Mutect_Germlines_txt.py GenotypeGVCFS_read.py HaplotypeCaller_read.py MuSE_read.py README.md SetupDatabases.sh
Annotate.sh Filter.sh HaplotypeCaller_4.1.2.0.py Intersect.sh Mutect2.py RenameSampleVCF.sh
Clean.sh GenomicsDBImport_read.py HaplotypeCaller_original.py Label_Source.py Mutect2_read.py runAll.sh
config.json GenotypeGVCFs.py HaplotypeCaller.py MuSE.py PoN_filter.py RunFilter.sh
(base) [vym1@login05 SNVCurate]$ git status
# On branch master
nothing to commit, working directory clean
(base) [vym1@login05 SNVCurate]$ ls
Add_Read_Info.py Filter_Mutect_Germlines_txt.py GenotypeGVCFS_read.py HaplotypeCaller_read.py MuSE_read.py README.md SetupDatabases.sh
Annotate.sh Filter.sh HaplotypeCaller_4.1.2.0.py Intersect.sh Mutect2.py RenameSampleVCF.sh
Clean.sh GenomicsDBImport_read.py HaplotypeCaller_original.py Label_Source.py Mutect2_read.py runAll.sh
config.json GenotypeGVCFs.py HaplotypeCaller.py MuSE.py PoN_filter.py RunFilter.sh
(base) [vym1@login05 SNVCurate]$ git pull
remote: Enumerating objects: 3, done.
remote: Counting objects: 100% (3/3), done.
remote: Compressing objects: 100% (3/3), done.
remote: Total 3 (delta 0), reused 0 (delta 0), pack-reused 0
Unpacking objects: 100% (3/3), done.
From https://github.com/vymao/SNVCurate
dbea305..1bf8526 master -> origin/master
Updating dbea305..1bf8526
Fast-forward
README.md | 92 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++----------------------------------
1 file changed, 58 insertions(+), 34 deletions(-)
(base) [vym1@login05 SNVCurate]$ conda activate muse
(muse) [vym1@login05 SNVCurate]$ conda env export > environment.yml
(muse) [vym1@login05 SNVCurate]$ ls
Add_Read_Info.py environment.yml GenotypeGVCFs.py HaplotypeCaller.py MuSE.py PoN_filter.py RunFilter.sh
Annotate.sh Filter_Mutect_Germlines_txt.py GenotypeGVCFS_read.py HaplotypeCaller_read.py MuSE_read.py README.md SetupDatabases.sh
Clean.sh Filter.sh HaplotypeCaller_4.1.2.0.py Intersect.sh Mutect2.py RenameSampleVCF.sh
config.json GenomicsDBImport_read.py HaplotypeCaller_original.py Label_Source.py Mutect2_read.py runAll.sh
(muse) [vym1@login05 SNVCurate]$ git add -A
(muse) [vym1@login05 SNVCurate]$ git push origin master
Username for 'https://github.com': ^C
(muse) [vym1@login05 SNVCurate]$ git commit -m "Added environment"
[master 3ca9164] Added environment
Committer: Mao <[email protected]>
Your name and email address were configured automatically based
on your username and hostname. Please check that they are accurate.
You can suppress this message by setting them explicitly:
git config --global user.name "Your Name"
git config --global user.email [email protected]
After doing this, you may fix the identity used for this commit with:
git commit --amend --reset-author
1 file changed, 51 insertions(+)
create mode 100644 environment.yml
(muse) [vym1@login05 SNVCurate]$ git push origin master
Username for 'https://github.com': vymao