1 897460 . A C . artifact_in_normal;panel_of_normals CONTQ=93;DP=929;ECNT=1;GERMQ=563;MBQ=30,24;MFRL=206,174;MMQ=60,60;MPOS=5;NALOD=-8.066e-01;NLOD=14.32;PON;POPAF=5.60;SAAF=0.010,0.253,0.250;SAPP=1.00,0.00,0.00;TLOD=275.96 GT:AD:AF:DP:F1R2:F2R1 0/0:69,4:0.046:73:22,4:47,0 0/1:102,42:0.278:144:44,26:58,16 0/1:86,5:0.029:91:43,3:43,2 0/1:62,21:0.238:83:27,9:35,12 0/1:57,23:0.285:80:29,16:28,7 0/1:82,39:0.322:121:38,20:44,19 0/1:86,20:0.173:106:43,9:43,11 0/1:89,38:0.291:127:44,19:45,19 1 981860 . GC G,GCC . multiallelic;str_contraction CONTQ=93;DP=863;ECNT=1;GERMQ=1805,1773;MBQ=32,32,33;MFRL=186,187,197;MMQ=60,60,60;MPOS=14,14;NALOD=-2.822e+00,1.45;NLOD=14.57,22.16;POPAF=4.00,3.78;RPA=8,7,9;RU=C;SAAF=0.030,0.020,0.031;SAPP=1.449e-03,6.900e-03,0.992;STR;TLOD=9.40,16.95 GT:AD:AF:DP:F1R2:F2R1 0/0:71,3,0:0.047,0.012:74:21,2,0:50,1,0 0/1/2:132,2,5:0.020,0.041:139:72,1,4:60,1,1 0/1/2:77,4,1:0.058,0.022:82:39,1,0:38,3,1 0/1/2:59,2,0:0.044,0.014:61:29,1,0:30,1,0 0/1/2:55,1,5:0.030,0.093:61:31,0,2:24,1,3 0/1/2:108,3,1:0.033,0.016:112:53,0,1:55,3,0 0/1/2:88,0,2:9.809e-03,0.031:90:43,0,1:45,0,1 0/1/2:114,0,6:7.432e-03,0.053:120:51,0,1:63,0,5 1 985443 . AGG A,AG . artifact_in_normal;germline_risk;multiallelic;panel_of_normals CONTQ=93;DP=509;ECNT=2;GERMQ=257,0;MBQ=32,33,32;MFRL=310,547,335;MMQ=60,60,60;MPOS=20,26;NALOD=1.28,-3.818e+01;NLOD=4.84,-3.875e+01;PON;POPAF=5.60,5.60;RPA=15,13,14;RU=G;SAAF=0.667,0.667,0.675;SAPP=0.026,0.013,0.961;STR;TLOD=5.98,544.36 GT:AD:AF:DP:F1R2:F2R1 0/0:15,0,16:0.026,0.502:31:5,0,4:10,0,12 0/1/2:38,0,45:9.254e-03,0.538:83:13,0,16:25,0,29 0/1/2:13,4,51:0.067,0.739:68:2,2,22:11,2,29 0/1/2:7,1,37:0.039,0.812:45:3,0,19:4,1,18 0/1/2:10,0,13:0.033,0.542:23:5,0,7:5,0,6 0/1/2:25,1,23:0.034,0.464:49:12,0,13:13,1,10 0/1/2:2,1,41:0.039,0.902:44:1,1,19:1,0,22 0/1/2:12,0,12:0.026,0.481:24:4,0,5:8,0,7 1 985451 . G A . t_lod CONTQ=93;DP=457;ECNT=2;GERMQ=1066;MBQ=31,33;MFRL=323,547;MMQ=60,60;MPOS=21;NALOD=1.57;NLOD=9.92;POPAF=5.60;SAAF=0.020,0.020,0.019;SAPP=5.033e-03,1.812e-03,0.993;TLOD=4.65 GT:AD:AF:DP:F1R2:F2R1 0/0:33,0:0.026:33:9,0:24,0 0/1:97,0:9.739e-03:97:35,0:62,0 0/1:66,4:0.068:70:25,2:41,2 0/1:49,1:0.037:50:24,0:25,1 0/1:25,0:0.035:25:12,0:13,0 0/1:53,1:0.035:54:27,0:26,1 0/1:45,1:0.040:46:22,1:23,0 0/1:32,0:0.028:32:14,0:18,0 1 1007252 . CG C . t_lod CONTQ=93;DP=453;ECNT=1;GERMQ=971;MBQ=31,31;MFRL=177,207;MMQ=60,60;MPOS=23;NALOD=1.93;NLOD=24.65;POPAF=5.60;RPA=7,6;RU=G;SAAF=0.010,0.020,0.021;SAPP=3.377e-03,4.608e-03,0.992;STR;TLOD=4.43 GT:AD:AF:DP:F1R2:F2R1 0/0:82,0:0.012:82:27,0:55,0 0/1:53,1:0.034:54:24,1:29,0 0/1:36,0:0.024:36:17,0:19,0 0/1:29,1:0.060:30:13,0:16,1 0/1:29,1:0.058:30:9,0:20,1 0/1:43,1:0.041:44:18,1:25,0 0/1:50,2:0.054:52:21,1:29,1 0/1:39,0:0.021:39:20,0:19,0 1 1078309 . TC T . str_contraction CONTQ=93;DP=867;ECNT=1;GERMQ=1999;MBQ=32,32;MFRL=178,173;MMQ=60,60;MPOS=26;NALOD=0.406;NLOD=19.43;POPAF=4.63;RPA=8,7;RU=C;SAAF=0.010,0.010,0.013;SAPP=1.640e-03,1.987e-03,0.996;STR;TLOD=5.35 GT:AD:AF:DP:F1R2:F2R1 0/0:74,1:0.025:75:23,0:51,1 0/1:101,0:8.978e-03:101:54,0:47,0 0/1:57,0:0.016:57:21,0:36,0 0/1:92,1:0.020:93:32,0:60,1 0/1:87,1:0.021:88:30,1:57,0 0/1:113,4:0.041:117:46,1:67,3 0/1:89,3:0.041:92:43,1:46,2 0/1:126,0:7.296e-03:126:56,0:70,0 1 1111343 . A G . artifact_in_normal;base_quality;mapping_quality;panel_of_normals CONTQ=93;DP=2192;ECNT=1;GERMQ=3101;MBQ=30,13;MFRL=188,198;MMQ=60,29;MPOS=13;NALOD=-6.011e+00;NLOD=36.41;PON;POPAF=5.60;SAAF=0.020,0.030,0.030;SAPP=0.045,6.131e-04,0.954;TLOD=7.50 GT:AD:AF:DP:F1R2:F2R1 0/0:191,11:0.039:202:77,5:114,6 0/1:193,10:0.019:203:107,4:86,6 0/1:75,1:0.011:76:47,0:28,1 0/1:143,2:6.178e-03:145:72,1:71,1 0/1:120,3:7.670e-03:123:59,1:61,2 0/1:152,3:0.024:155:92,2:60,1 0/1:189,6:0.015:195:80,0:109,6 0/1:226,9:0.027:235:122,2:104,7 1 1115835 . A C . artifact_in_normal;bad_haplotype;base_quality;clustered_events;panel_of_normals CONTQ=93;DP=316;ECNT=3;GERMQ=435;MBQ=31,9;MFRL=229,195;MMQ=60,60;MPOS=15;NALOD=-1.913e+00;NLOD=6.18;PON;POPAF=2.43;SAAF=0.00,0.101,0.105;SAPP=0.973,5.037e-05,0.026;TLOD=26.58 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS 0|0:40,2:0.064:42:19,0:21,2:0|1:1115835_A_C:1115835 0|1:58,11:0.151:69:35,6:23,5:0|1:1115835_A_C:1115835 0|1:44,4:0.084:48:23,3:21,1:0|1:1115835_A_C:1115835 0|1:18,2:0.132:20:9,1:9,1:0|1:1115835_A_C:1115835 0|1:17,4:0.202:21:7,1:10,3:0|1:1115835_A_C:1115835 0|1:38,1:0.028:39:14,1:24,0:0|1:1115835_A_C:1115835 0|1:36,1:0.029:37:16,0:20,1:0|1:1115835_A_C:1115835 0|1:27,5:0.138:32:19,4:8,1:0|1:1115835_A_C:1115835 1 1115852 . A C . artifact_in_normal;bad_haplotype;clustered_events CONTQ=93;DP=498;ECNT=3;GERMQ=1159;MBQ=30,26;MFRL=188,197;MMQ=60,60;MPOS=7;NALOD=-1.462e+00;NLOD=11.94;POPAF=5.60;SAAF=0.00,0.030,0.030;SAPP=0.312,6.742e-04,0.687;TLOD=13.58 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS 0|0:59,2:0.043:61:24,0:35,2:0|1:1115835_A_C:1115835 0|1:93,6:0.061:99:55,3:38,3:0|1:1115835_A_C:1115835 0|1:67,3:0.049:70:34,2:33,1:0|1:1115835_A_C:1115835 0|1:41,1:0.039:42:18,1:23,0:0|1:1115835_A_C:1115835 0|1:30,1:0.054:31:14,0:16,1:0|1:1115835_A_C:1115835 0|1:54,0:0.018:54:19,0:35,0:0|1:1115835_A_C:1115835 0|1:65,0:0.015:65:32,0:33,0:0|1:1115835_A_C:1115835 0|1:69,2:0.041:71:41,1:28,1:0|1:1115835_A_C:1115835 1 1115857 . T C . artifact_in_normal;base_quality;clustered_events CONTQ=93;DP=530;ECNT=3;GERMQ=1028;MBQ=31,11;MFRL=189,178;MMQ=60,60;MPOS=5;NALOD=-1.565e+00;NLOD=11.26;POPAF=5.60;SAAF=0.00,0.051,0.054;SAPP=0.986,1.284e-05,0.014;TLOD=19.60 GT:AD:AF:DP:F1R2:F2R1 0/0:60,3:0.047:63:23,1:37,2 0/1:88,9:0.083:97:53,5:35,4 0/1:69,2:0.037:71:35,1:34,1 0/1:44,2:0.046:46:20,2:24,0 0/1:31,1:0.059:32:15,0:16,1 0/1:53,2:0.021:55:18,1:35,1 0/1:63,3:0.019:66:30,0:33,3 0/1:69,5:0.051:74:39,4:30,1 1 1116222 . CG C . str_contraction CONTQ=93;DP=602;ECNT=1;GERMQ=1127;MBQ=28,29;MFRL=176,169;MMQ=60,60;MPOS=18;NALOD=1.50;NLOD=16.78;POPAF=3.24;RPA=8,7;RU=G;SAAF=0.020,0.020,0.021;SAPP=0.028,1.224e-03,0.971;STR;TLOD=6.08 GT:AD:AF:DP:F1R2:F2R1 0/0:56,0:0.016:56:16,0:40,0 0/1:70,0:0.012:70:35,0:35,0 0/1:31,1:0.055:32:18,1:13,0 0/1:32,2:0.079:34:22,2:10,0 0/1:47,1:0.038:48:24,1:23,0 0/1:70,3:0.052:73:43,1:27,2 0/1:73,1:0.024:74:32,0:41,1 0/1:54,0:0.015:54:27,0:27,0 1 1139883 . GGGGA G . str_contraction CONTQ=93;DP=688;ECNT=1;GERMQ=881;MBQ=31,30;MFRL=180,176;MMQ=60,60;MPOS=18;NALOD=1.51;NLOD=7.42;POPAF=4.43;RPA=4,3;RU=GGGA;SAAF=0.030,0.010,0.027;SAPP=2.393e-03,8.095e-03,0.990;STR;TLOD=15.18 GT:AD:AF:DP:F1R2:F2R1 0/0:25,0:0.031:25:11,0:14,0 0/1:72,1:0.024:73:39,1:33,0 0/1:48,3:0.046:51:28,3:20,0 0/1:36,0:0.020:36:17,0:19,0 0/1:28,0:0.026:28:13,0:15,0 0/1:48,2:0.055:50:22,1:26,1 0/1:43,1:0.040:44:15,1:28,0 0/1:50,2:0.053:52:23,2:27,0 1 1147976 . AC A,CC,ACC . artifact_in_normal CONTQ=93;DP=285;ECNT=1;GERMQ=454,431,525;MBQ=29,31,14,28;MFRL=184,179,190,162;MMQ=60,60,29,29;MPOS=28,14,22;NALOD=-6.613e-01,0.964,0.966;NLOD=4.21,7.07,7.13;POPAF=5.60,5.60,5.60;SAAF=0.040,0.051,0.055;SAPP=0.012,3.690e-03,0.984;TLOD=12.31,4.11,4.47 GT:AD:AF:DP:F1R2:F2R1 0/0:23,1,0,0:0.070,0.035,0.035:24:9,1,0,0:14,0,0,0 0/1/2/3:48,4,4,3:0.076,0.035,0.062:59:23,3,3,0:25,1,1,3 0/1/2/3:30,3,2,0:0.100,0.036,0.025:35:14,3,2,0:16,0,0,0 0/1/2/3:22,1,3,0:0.061,0.114,0.031:26:13,0,3,0:9,1,0,0 0/1/2/3:10,1,0,2:0.110,0.061,0.172:13:4,0,0,0:6,1,0,2 0/1/2/3:35,0,1,1:0.024,0.028,0.047:37:18,0,1,0:17,0,0,1 0/1/2/3:18,0,2,0:0.038,0.103,0.041:20:7,0,2,0:11,0,0,0 0/1/2/3:27,2,5,1:0.075,0.120,0.050:35:15,1,5,0:12,1,0,1 1 1229340 . TCGGGG T . artifact_in_normal;str_contraction CONTQ=93;DP=294;ECNT=1;GERMQ=459;MBQ=31,31;MFRL=280,167;MMQ=60,29;MPOS=27;NALOD=-1.534e+00;NLOD=3.49;POPAF=4.69;RPA=4,3;RU=CGGGG;SAAF=0.020,0.00,0.018;SAPP=2.838e-03,8.458e-03,0.989;STR;TLOD=5.33 GT:AD:AF:DP:F1R2:F2R1 0/0:26,1:0.064:27:12,0:14,1 0/1:40,1:0.044:41:17,0:23,1 0/1:38,0:0.022:38:22,0:16,0 0/1:13,0:0.058:13:8,0:5,0 0/1:13,0:0.058:13:7,0:6,0 0/1:12,1:0.126:13:6,0:6,1 0/1:23,0:0.036:23:6,0:17,0 0/1:26,1:0.066:27:10,1:16,0 1 1254549 . C G . PASS CONTQ=93;DP=781;ECNT=1;GERMQ=1190;MBQ=33,31;MFRL=204,305;MMQ=60,60;MPOS=17;NALOD=1.84;NLOD=20.16;POPAF=5.60;SAAF=0.091,0.101,0.103;SAPP=7.574e-03,3.870e-03,0.989;TLOD=136.70 GT:AD:AF:DP:F1R2:F2R1 0/0:67,0:0.014:67:27,0:40,0 0/1:112,0:8.252e-03:112:56,0:56,0 0/1:71,11:0.142:82:34,4:37,7 0/1:69,21:0.236:90:37,12:32,9 0/1:64,0:0.014:64:24,0:40,0 0/1:97,0:9.452e-03:97:52,0:45,0 0/1:56,33:0.374:89:24,13:32,20 0/1:99,0:9.519e-03:99:53,0:46,0 1 1267342 . A C . artifact_in_normal;base_quality CONTQ=93;DP=736;ECNT=1;GERMQ=1187;MBQ=27,9;MFRL=308,245;MMQ=60,60;MPOS=20;NALOD=-9.880e-01;NLOD=14.86;POPAF=5.60;SAAF=0.020,0.081,0.083;SAPP=1.000,1.215e-10,1.984e-07;TLOD=12.68 GT:AD:AF:DP:F1R2:F2R1 0/0:72,4:0.034:76:29,3:43,1 0/1:129,14:0.078:143:50,6:79,8 0/1:116,3:9.383e-03:119:63,0:53,3 0/1:70,10:0.085:80:29,5:41,5 0/1:43,4:0.076:47:15,0:28,4 0/1:57,5:0.051:62:27,5:30,0 0/1:75,8:0.077:83:24,2:51,6 0/1:52,5:0.033:57:23,2:29,3 1 1268990 . GTGC G . str_contraction CONTQ=93;DP=1348;ECNT=1;GERMQ=3233;MBQ=33,33;MFRL=175,172;MMQ=60,60;MPOS=25;NALOD=2.10;NLOD=36.07;POPAF=4.61;RPA=4,3;RU=TGC;SAAF=0.010,0.010,6.823e-03;SAPP=4.707e-04,5.248e-03,0.994;STR;TLOD=11.11 GT:AD:AF:DP:F1R2:F2R1 0/0:120,0:7.909e-03:120:37,0:83,0 0/1:186,2:0.015:188:81,2:105,0 0/1:80,0:0.011:80:30,0:50,0 0/1:128,0:7.274e-03:128:70,0:58,0 0/1:124,1:0.015:125:60,0:64,1 0/1:118,1:0.016:119:52,1:66,0 0/1:179,1:0.011:180:69,0:110,1 0/1:204,2:0.014:206:98,1:106,1 1 1271479 . G A . PASS CONTQ=93;DP=392;ECNT=1;GERMQ=524;MBQ=28,33;MFRL=177,282;MMQ=60,60;MPOS=20;NALOD=1.71;NLOD=15.00;POPAF=5.60;SAAF=0.131,0.141,0.147;SAPP=8.118e-03,0.025,0.967;TLOD=116.92 GT:AD:AF:DP:F1R2:F2R1 0/0:50,0:0.019:50:21,0:29,0 0/1:65,0:0.014:65:28,0:37,0 0/1:44,11:0.210:55:19,5:25,6 0/1:22,16:0.425:38:13,10:9,6 0/1:40,0:0.023:40:18,0:22,0 0/1:37,0:0.025:37:26,0:11,0 0/1:25,18:0.422:43:15,11:10,7 0/1:39,2:0.069:41:16,1:23,1 1 1290606 . C G . read_position;strand_artifact CONTQ=93;DP=176;ECNT=1;GERMQ=269;MBQ=33,23;MFRL=190,172;MMQ=60,60;MPOS=3;NALOD=1.83;NLOD=19.07;POPAF=5.60;SAAF=0.172,0.00,0.169;SAPP=7.460e-11,1.000,3.355e-08;TLOD=15.56 GT:AD:AF:DP:F1R2:F2R1 0/0:64,0:0.015:64:33,0:31,0 0/1:11,3:0.229:14:5,1:6,2 0/1:3,3:0.486:6:0,1:3,2 0/1:12,2:0.159:14:5,2:7,0 0/1:5,0:0.137:5:2,0:3,0 0/1:5,1:0.238:6:3,0:2,1 0/1:13,0:0.065:13:2,0:11,0 0/1:20,5:0.207:25:12,3:8,2 1 1309985 . AGT A . str_contraction CONTQ=93;DP=265;ECNT=1;GERMQ=504;MBQ=32,32;MFRL=188,191;MMQ=60,60;MPOS=19;NALOD=1.05;NLOD=8.71;POPAF=5.60;RPA=5,4;RU=GT;SAAF=0.00,0.040,0.038;SAPP=0.018,3.593e-03,0.978;STR;TLOD=13.44 GT:AD:AF:DP:F1R2:F2R1 0/0:29,0:0.030:29:6,0:23,0 0/1:25,0:0.033:25:6,0:19,0 0/1:15,0:0.050:15:2,0:13,0 0/1:24,2:0.104:26:6,0:18,2 0/1:23,2:0.110:25:5,0:18,2 0/1:30,2:0.087:32:12,1:18,1 0/1:31,1:0.057:32:11,0:20,1 0/1:29,0:0.029:29:9,0:20,0 1 1323945 . GTCTC G,GTC . artifact_in_normal;germline_risk;multiallelic CONTQ=93;DP=393;ECNT=2;GERMQ=2,0;MBQ=32,32,32;MFRL=180,268,193;MMQ=60,60,60;MPOS=30,25;NALOD=0.800,-3.957e+01;NLOD=2.62,-3.870e+01;POPAF=5.60,5.60;RPA=9,7,8;RU=TC;SAAF=0.788,0.778,0.795;SAPP=0.026,0.020,0.954;STR;TLOD=23.94,393.15 GT:AD:AF:DP:F1R2:F2R1 0/0:3,0,12:0.042,0.738:15:0,0,5:3,0,7 0/1/2:4,0,36:0.016,0.870:40:3,0,16:1,0,20 0/1/2:1,1,3:0.174,0.564:5:0,0,1:1,1,2 0/1/2:1,2,11:0.135,0.752:14:1,1,5:0,1,6 0/1/2:4,0,12:0.033,0.716:16:1,0,3:3,0,9 0/1/2:12,5,40:0.074,0.712:57:4,4,20:8,1,20 0/1/2:5,2,10:0.103,0.594:17:3,1,4:2,1,6 0/1/2:5,3,12:0.121,0.605:20:3,1,4:2,2,8 1 1323963 . C A . panel_of_normals CONTQ=93;DP=347;ECNT=2;GERMQ=565;MBQ=33,32;MFRL=185,177;MMQ=60,60;MPOS=19;NALOD=0.564;NLOD=5.02;PON;POPAF=5.60;SAAF=0.040,0.051,0.053;SAPP=0.023,2.439e-03,0.974;TLOD=23.63 GT:AD:AF:DP:F1R2:F2R1 0/0:17,0:0.048:17:7,0:10,0 0/1:58,1:0.031:59:27,1:31,0 0/1:11,0:0.075:11:3,0:8,0 0/1:17,0:0.047:17:9,0:8,0 0/1:22,2:0.112:24:8,1:14,1 0/1:73,7:0.097:80:37,4:36,3 0/1:23,0:0.035:23:13,0:10,0 0/1:30,3:0.110:33:16,2:14,1 1 1326099 . G GA . str_contraction CONTQ=93;DP=585;ECNT=1;GERMQ=1282;MBQ=33,34;MFRL=183,183;MMQ=60,60;MPOS=23;NALOD=1.58;NLOD=10.52;POPAF=5.60;RPA=9,10;RU=A;SAAF=0.020,0.020,0.025;SAPP=2.545e-03,5.640e-03,0.992;STR;TLOD=8.42 GT:AD:AF:DP:F1R2:F2R1 0/0:35,0:0.026:35:14,0:21,0 0/1:88,2:0.031:90:30,0:58,2 0/1:29,1:0.060:30:14,1:15,0 0/1:67,2:0.041:69:31,1:36,1 0/1:48,1:0.037:49:30,1:18,0 0/1:100,1:0.018:101:49,0:51,1 0/1:52,2:0.051:54:25,1:27,1 0/1:78,3:0.046:81:32,2:46,1 1 1334663 . AGCC A . artifact_in_normal;str_contraction CONTQ=93;DP=426;ECNT=1;GERMQ=767;MBQ=33,33;MFRL=260,243;MMQ=60,60;MPOS=27;NALOD=-1.480e+00;NLOD=3.83;POPAF=3.66;RPA=7,6;RU=GCC;SAAF=0.020,0.00,0.023;SAPP=5.782e-03,5.451e-03,0.989;STR;TLOD=13.92 GT:AD:AF:DP:F1R2:F2R1 0/0:27,1:0.061:28:13,1:14,0 0/1:34,1:0.051:35:17,1:17,0 0/1:46,2:0.059:48:25,1:21,1 0/1:55,0:0.017:55:23,0:32,0 0/1:21,0:0.038:21:8,0:13,0 0/1:21,1:0.079:22:13,1:8,0 0/1:77,3:0.048:80:33,2:44,1 0/1:38,0:0.022:38:14,0:24,0 1 1418507 . TA T . str_contraction;t_lod CONTQ=93;DP=616;ECNT=1;GERMQ=1537;MBQ=32,26;MFRL=179,164;MMQ=60,60;MPOS=13;NALOD=1.41;NLOD=12.29;POPAF=5.60;RPA=8,7;RU=A;SAAF=0.010,0.00,0.013;SAPP=4.478e-03,2.975e-03,0.993;STR;TLOD=3.53 GT:AD:AF:DP:F1R2:F2R1 0/0:41,0:0.020:41:7,0:34,0 0/1:93,3:0.040:96:32,1:61,2 0/1:48,1:0.039:49:16,0:32,1 0/1:47,0:0.020:47:14,0:33,0 0/1:74,0:0.013:74:35,0:39,0 0/1:101,1:0.019:102:39,0:62,1 0/1:70,1:0.026:71:33,1:37,0 0/1:86,1:0.022:87:43,1:43,0 1 1560851 . A C . bad_haplotype;base_quality;clustered_events;mapping_quality;t_lod CONTQ=93;DP=381;ECNT=3;GERMQ=971;MBQ=32,10;MFRL=205,168;MMQ=60,29;MPOS=31;NALOD=0.386;NLOD=9.79;POPAF=5.60;SAAF=0.00,0.020,0.015;SAPP=0.048,8.889e-04,0.951;TLOD=5.22 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS 0|0:41,1:0.045:42:7,1:34,0:0|1:1560851_A_C:1560851 0|1:55,1:0.033:56:27,1:28,0:0|1:1560851_A_C:1560851 0|1:65,0:0.015:65:37,0:28,0:0|1:1560851_A_C:1560851 0|1:38,1:0.049:39:20,0:18,1:0|1:1560851_A_C:1560851 0|1:24,0:0.038:24:16,0:8,0:0|1:1560851_A_C:1560851 0|1:61,0:0.016:61:30,0:31,0:0|1:1560851_A_C:1560851 0|1:47,3:0.064:50:25,2:22,1:0|1:1560851_A_C:1560851 0|1:35,0:0.027:35:20,0:15,0:0|1:1560851_A_C:1560851 1 1560856 . T C . bad_haplotype;base_quality;clustered_events;mapping_quality;t_lod CONTQ=93;DP=391;ECNT=3;GERMQ=1027;MBQ=32,11;MFRL=208,168;MMQ=60,29;MPOS=33;NALOD=0.462;NLOD=10.99;POPAF=5.60;SAAF=0.00,0.010,0.014;SAPP=0.047,8.497e-04,0.952;TLOD=5.13 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS 0|0:45,1:0.041:46:9,1:36,0:0|1:1560851_A_C:1560851 0|1:59,1:0.032:60:26,1:33,0:0|1:1560851_A_C:1560851 0|1:67,0:0.014:67:37,0:30,0:0|1:1560851_A_C:1560851 0|1:40,1:0.046:41:21,0:19,1:0|1:1560851_A_C:1560851 0|1:25,0:0.037:25:15,0:10,0:0|1:1560851_A_C:1560851 0|1:64,0:0.015:64:30,0:34,0:0|1:1560851_A_C:1560851 0|1:48,3:0.063:51:26,2:22,1:0|1:1560851_A_C:1560851 0|1:37,0:0.026:37:21,0:16,0:0|1:1560851_A_C:1560851 1 1560865 . T C . bad_haplotype;base_quality;clustered_events;mapping_quality;t_lod CONTQ=93;DP=408;ECNT=3;GERMQ=1045;MBQ=32,10;MFRL=219,168;MMQ=60,29;MPOS=29;NALOD=0.395;NLOD=9.79;POPAF=5.60;SAAF=0.00,0.010,0.014;SAPP=0.026,9.598e-04,0.973;TLOD=5.06 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS 0|0:41,1:0.044:42:10,1:31,0:0|1:1560851_A_C:1560851 0|1:65,1:0.029:66:29,1:36,0:0|1:1560851_A_C:1560851 0|1:69,0:0.014:69:37,0:32,0:0|1:1560851_A_C:1560851 0|1:45,1:0.041:46:23,0:22,1:0|1:1560851_A_C:1560851 0|1:26,0:0.036:26:15,0:11,0:0|1:1560851_A_C:1560851 0|1:60,0:0.016:60:28,0:32,0:0|1:1560851_A_C:1560851 0|1:45,3:0.067:48:27,2:18,1:0|1:1560851_A_C:1560851 0|1:40,0:0.023:40:21,0:19,0:0|1:1560851_A_C:1560851 1 1562384 . G A . artifact_in_normal CONTQ=93;DP=899;ECNT=1;GERMQ=2204;MBQ=29,34;MFRL=190,174;MMQ=60,60;MPOS=23;NALOD=-2.002e+00;NLOD=22.34;POPAF=5.60;SAAF=0.010,0.010,0.015;SAPP=8.259e-04,6.714e-03,0.992;TLOD=14.84 GT:AD:AF:DP:F1R2:F2R1 0/0:100,3:0.030:103:36,3:64,0 0/1:159,2:0.018:161:77,0:82,2 0/1:89,0:0.011:89:41,0:48,0 0/1:81,0:0.012:81:36,0:45,0 0/1:72,5:0.076:77:38,4:34,1 0/1:112,2:0.025:114:58,2:54,0 0/1:108,0:8.840e-03:108:53,0:55,0 0/1:111,2:0.026:113:58,1:53,1 1 1566067 . GA G . PASS CONTQ=93;DP=85;ECNT=1;GERMQ=123;MBQ=31,30;MFRL=335,330;MMQ=60,60;MPOS=30;NALOD=1.02;NLOD=2.70;POPAF=5.60;SAAF=0.081,0.040,0.085;SAPP=0.022,0.013,0.966;TLOD=5.84 GT:AD:AF:DP:F1R2:F2R1 0/0:9,0:0.088:9:1,0:8,0 0/1:10,2:0.210:12:3,1:7,1 0/1:14,3:0.208:17:4,0:10,3 0/1:3,0:0.182:3:2,0:1,0 0/1:3,0:0.190:3:0,0:3,0 0/1:3,0:0.200:3:0,0:3,0 0/1:7,0:0.096:7:1,0:6,0 0/1:14,0:0.059:14:7,0:7,0 1 1576325 . T C . mapping_quality CONTQ=93;DP=480;ECNT=1;GERMQ=1236;MBQ=33,30;MFRL=192,485;MMQ=23,29;MPOS=22;NALOD=1.76;NLOD=17.08;POPAF=5.60;SAAF=0.00,0.020,0.021;SAPP=5.137e-03,4.737e-03,0.990;TLOD=9.43 GT:AD:AF:DP:F1R2:F2R1 0/0:57,0:0.017:57:23,0:34,0 0/1:80,0:0.012:80:42,0:38,0 0/1:34,4:0.124:38:13,2:21,2 0/1:48,1:0.039:49:20,0:28,1 0/1:49,1:0.038:50:22,0:27,1 0/1:67,0:0.015:67:30,0:37,0 0/1:56,3:0.065:59:24,2:32,1 0/1:76,0:0.013:76:43,0:33,0 1 1580724 . G GT . mapping_quality;str_contraction CONTQ=93;DP=1049;ECNT=1;GERMQ=1863;MBQ=33,33;MFRL=176,172;MMQ=23,23;MPOS=22;NALOD=1.93;NLOD=44.12;POPAF=5.60;RPA=9,10;RU=T;SAAF=0.051,0.030,0.047;SAPP=2.564e-03,7.790e-03,0.990;STR;TLOD=31.41 GT:AD:AF:DP:F1R2:F2R1 0/0:147,0:5.974e-03:147:40,0:107,0 0/1:96,3:0.037:99:51,2:45,1 0/1:27,0:0.031:27:5,0:22,0 0/1:87,4:0.051:91:30,2:57,2 0/1:72,5:0.074:77:38,1:34,4 0/1:93,4:0.048:97:37,0:56,4 0/1:110,9:0.080:119:47,4:63,5 0/1:139,6:0.046:145:66,1:73,5 1 1586816 . C T . bad_haplotype;clustered_events;panel_of_normals CONTQ=93;DP=674;ECNT=3;GERMQ=1707;MBQ=31,33;MFRL=173,173;MMQ=60,33;MPOS=26;NALOD=1.79;NLOD=18.06;PON;POPAF=2.44;SAAF=0.00,0.020,0.020;SAPP=5.602e-03,3.130e-03,0.991;TLOD=26.57 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS 0|0:60,0:0.016:60:18,0:42,0:0|1:1586816_C_T:1586816 0|1:138,2:0.021:140:67,1:71,1:0|1:1586816_C_T:1586816 0|1:21,0:0.043:21:7,0:14,0:0|1:1586816_C_T:1586816 0|1:33,1:0.056:34:10,0:23,1:0|1:1586816_C_T:1586816 0|1:87,1:0.022:88:43,0:44,1:0|1:1586816_C_T:1586816 0|1:118,3:0.032:121:55,2:63,1:0|1:1586816_C_T:1586816 0|1:51,3:0.071:54:24,1:27,2:0|1:1586816_C_T:1586816 0|1:145,2:0.020:147:75,2:70,0:0|1:1586816_C_T:1586816 1 1586834 . A T . bad_haplotype;clustered_events CONTQ=93;DP=771;ECNT=3;GERMQ=1949;MBQ=32,30;MFRL=170,173;MMQ=60,33;MPOS=31;NALOD=1.81;NLOD=18.96;POPAF=5.60;SAAF=0.00,0.020,0.018;SAPP=0.011,1.404e-03,0.987;TLOD=25.95 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS 0|0:63,0:0.015:63:20,0:43,0:0|1:1586816_C_T:1586816 0|1:141,2:0.020:143:74,1:67,1:0|1:1586816_C_T:1586816 0|1:23,0:0.039:23:9,0:14,0:0|1:1586816_C_T:1586816 0|1:36,1:0.050:37:11,0:25,1:0|1:1586816_C_T:1586816 0|1:100,1:0.019:101:53,0:47,1:0|1:1586816_C_T:1586816 0|1:145,3:0.027:148:71,2:74,1:0|1:1586816_C_T:1586816 0|1:57,3:0.064:60:29,1:28,2:0|1:1586816_C_T:1586816 0|1:160,2:0.018:162:78,2:82,0:0|1:1586816_C_T:1586816 1 1586881 . G A . artifact_in_normal;clustered_events;mapping_quality;t_lod CONTQ=93;DP=994;ECNT=3;GERMQ=2475;MBQ=29,33;MFRL=174,272;MMQ=60,29;MPOS=16;NALOD=-1.106e+00;NLOD=22.08;POPAF=5.60;SAAF=0.010,0.010,0.011;SAPP=1.607e-03,1.308e-03,0.997;TLOD=5.19 GT:AD:AF:DP:F1R2:F2R1 0/0:94,2:0.030:96:34,1:60,1 0/1:168,2:0.017:170:95,2:73,0 0/1:34,1:0.031:35:15,0:19,1 0/1:56,1:0.033:57:21,1:35,0 0/1:116,1:0.016:117:59,1:57,0 0/1:183,2:0.016:185:91,1:92,1 0/1:73,0:0.013:73:38,0:35,0 0/1:184,2:0.015:186:87,2:97,0 1 1586977 . G GT . str_contraction CONTQ=93;DP=321;ECNT=1;GERMQ=545;MBQ=32,33;MFRL=183,223;MMQ=29,36;MPOS=25;NALOD=1.22;NLOD=3.92;POPAF=5.60;RPA=9,10;RU=T;SAAF=0.040,0.00,0.036;SAPP=0.013,6.573e-03,0.981;STR;TLOD=6.40 GT:AD:AF:DP:F1R2:F2R1 0/0:13,0:0.058:13:3,0:10,0 0/1:46,1:0.037:47:30,1:16,0 0/1:7,1:0.190:8:3,0:4,1 0/1:10,1:0.142:11:4,1:6,0 0/1:37,0:0.024:37:21,0:16,0 0/1:47,3:0.074:50:25,2:22,1 0/1:29,0:0.030:29:13,0:16,0 0/1:36,2:0.070:38:17,1:19,1 1 1588744 . AGCG A . artifact_in_normal;mapping_quality CONTQ=93;DP=1164;ECNT=1;GERMQ=1569;MBQ=32,33;MFRL=173,166;MMQ=37,29;MPOS=26;NALOD=-1.202e+01;NLOD=5.99;POPAF=5.60;SAAF=0.121,0.020,0.117;SAPP=1.623e-10,1.000,2.424e-07;TLOD=376.54 GT:AD:AF:DP:F1R2:F2R1 0/0:87,5:0.064:92:42,1:45,4 0/1:185,17:0.088:202:89,7:96,10 0/1:4,0:0.167:4:1,0:3,0 0/1:97,5:0.058:102:46,4:51,1 0/1:121,18:0.135:139:68,6:53,12 0/1:192,34:0.153:226:108,16:84,18 0/1:109,6:0.060:115:49,2:60,4 0/1:220,43:0.166:263:104,20:116,23 1 1589057 . TAAG T . PASS CONTQ=93;DP=149;ECNT=1;GERMQ=166;MBQ=32,32;MFRL=341,473;MMQ=29,36;MPOS=17;NALOD=1.02;NLOD=2.70;POPAF=5.60;RPA=2,1;RU=AAG;SAAF=0.152,0.111,0.155;SAPP=0.025,0.017,0.957;STR;TLOD=61.38 GT:AD:AF:DP:F1R2:F2R1 0/0:9,0:0.088:9:7,0:2,0 0/1:28,5:0.171:33:14,2:14,3 0/1:3,3:0.500:6:3,1:0,2 0/1:32,2:0.082:34:14,0:18,2 0/1:12,4:0.278:16:3,1:9,3 0/1:3,0:0.200:3:1,0:2,0 0/1:25,6:0.211:31:8,3:17,3 0/1:6,0:0.125:6:3,0:3,0 1 1599654 . C G . mapping_quality CONTQ=93;DP=207;ECNT=1;GERMQ=454;MBQ=32,33;MFRL=348,531;MMQ=46,29;MPOS=12;NALOD=1.28;NLOD=5.41;POPAF=5.60;SAAF=0.00,0.040,0.039;SAPP=7.238e-03,0.013,0.980;TLOD=8.81 GT:AD:AF:DP:F1R2:F2R1 0/0:18,0:0.050:18:6,0:12,0 0/1:34,0:0.027:34:22,0:12,0 0/1:12,0:0.068:12:7,0:5,0 0/1:36,4:0.118:40:16,1:20,3 0/1:21,1:0.082:22:11,1:10,0 0/1:12,0:0.071:12:4,0:8,0 0/1:30,2:0.087:32:17,2:13,0 0/1:26,0:0.036:26:15,0:11,0 1 1600051 . C G . artifact_in_normal;bad_haplotype;clustered_events CONTQ=93;DP=474;ECNT=4;GERMQ=425;MBQ=28,30;MFRL=316,341;MMQ=37,37;MPOS=10;NALOD=-1.918e-01;NLOD=15.10;POPAF=5.60;SAAF=0.222,0.00,0.217;SAPP=0.011,0.048,0.941;TLOD=260.73 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS 0|0:66,2:0.041:68:22,0:44,2:0|1:1600051_C_G:1600051 0|1:54,4:0.082:58:20,1:34,3:0|1:1600051_C_G:1600051 0|1:25,2:0.102:27:10,2:15,0:0|1:1600051_C_G:1600051 0|1:55,24:0.309:79:29,10:26,14:0|1:1600051_C_G:1600051 0|1:25,7:0.236:32:14,4:11,3:0|1:1600051_C_G:1600051 0|1:44,16:0.274:60:21,10:23,6:0|1:1600051_C_G:1600051 0|1:54,16:0.236:70:24,7:30,9:0|1:1600051_C_G:1600051 0|1:42,14:0.258:56:20,6:22,8:0|1:1600051_C_G:1600051 1 1600061 . G A . bad_haplotype;clustered_events CONTQ=93;DP=445;ECNT=4;GERMQ=393;MBQ=33,30;MFRL=320,350;MMQ=37,37;MPOS=19;NALOD=1.80;NLOD=18.35;POPAF=5.60;SAAF=0.242,0.030,0.245;SAPP=0.012,0.049,0.939;TLOD=285.42 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS 0|0:61,0:0.016:61:22,0:39,0:0|1:1600051_C_G:1600051 0|1:44,2:0.047:46:18,1:26,1:0|1:1600051_C_G:1600051 0|1:23,0:0.039:23:8,0:15,0:0|1:1600051_C_G:1600051 0|1:54,31:0.367:85:29,14:25,17:0|1:1600051_C_G:1600051 0|1:22,6:0.233:28:12,4:10,2:0|1:1600051_C_G:1600051 0|1:42,18:0.306:60:19,13:23,5:0|1:1600051_C_G:1600051 0|1:55,18:0.254:73:23,9:32,9:0|1:1600051_C_G:1600051 0|1:37,15:0.296:52:19,6:18,9:0|1:1600051_C_G:1600051 1 1600091 . TTG T . artifact_in_normal;clustered_events CONTQ=93;DP=482;ECNT=4;GERMQ=131;MBQ=31,31;MFRL=357,365;MMQ=37,37;MPOS=21;NALOD=-1.461e+00;NLOD=3.96;POPAF=5.60;SAAF=0.333,0.293,0.337;SAPP=0.017,0.042,0.942;TLOD=282.71 GT:AD:AF:DP:F1R2:F2R1 0/0:30,2:0.087:32:11,2:19,0 0/1:41,3:0.085:44:20,3:21,0 0/1:19,2:0.128:21:8,1:11,1 0/1:65,43:0.397:108:34,19:31,24 0/1:21,13:0.388:34:10,7:11,6 0/1:37,22:0.376:59:16,20:21,2 0/1:67,38:0.365:105:31,21:36,17 0/1:29,21:0.422:50:16,11:13,10 1 1600092 . TG T . artifact_in_normal;clustered_events CONTQ=93;DP=482;ECNT=4;GERMQ=102;MBQ=33,31;MFRL=354,366;MMQ=37,37;MPOS=20;NALOD=-5.795e-02;NLOD=4.75;POPAF=5.60;SAAF=0.374,0.333,0.371;SAPP=0.016,0.045,0.939;TLOD=12.76 GT:AD:AF:DP:F1R2:F2R1 0/0:29,3:0.083:32:11,2:18,1 0/1:40,4:0.067:44:20,3:20,1 0/1:20,2:0.073:22:8,1:12,1 0/1:60,48:0.386:108:34,19:26,29 0/1:21,13:0.326:34:10,7:11,6 0/1:30,29:0.453:59:13,23:17,6 0/1:66,38:0.300:104:31,20:35,18 0/1:28,22:0.386:50:16,11:12,11 1 1633002 . G GC . artifact_in_normal CONTQ=93;DP=1012;ECNT=2;GERMQ=1645;MBQ=32,32;MFRL=225,214;MMQ=37,37;MPOS=24;NALOD=-6.592e+00;NLOD=13.58;POPAF=5.60;RPA=1,2;RU=C;SAAF=0.081,0.071,0.083;SAPP=1.775e-03,0.015,0.983;STR;TLOD=61.83 GT:AD:AF:DP:F1R2:F2R1 0/0:101,8:0.069:109:47,3:54,5 0/1:145,14:0.092:159:70,5:75,9 0/1:98,9:0.091:107:39,4:59,5 0/1:110,10:0.068:120:56,5:54,5 0/1:76,6:0.059:82:31,2:45,4 0/1:111,11:0.052:122:59,5:52,6 0/1:145,12:0.069:157:62,6:83,6 0/1:101,9:0.077:110:45,7:56,2 1 1633003 . C CG,CCG,CCGG . artifact_in_normal;germline_risk;multiallelic;panel_of_normals CONTQ=93;DP=1012;ECNT=2;GERMQ=1237,0,1065;MBQ=28,29,32,31;MFRL=214,191,266,186;MMQ=37,37,37,37;MPOS=28,26,19;NALOD=-2.191e-03,-1.166e+02,-9.552e-01;NLOD=22.49,-1.320e+02,6.33;PON;POPAF=5.60,5.60,5.60;SAAF=0.414,0.434,0.445;SAPP=0.239,2.413e-03,0.759;TLOD=12.92,633.49,11.86 GT:AD:AF:DP:F1R2:F2R1 0/0:45,1,57,2:0.018,0.514,0.026:105:19,1,27,0:26,0,30,2 0/1/2/3:73,4,77,3:0.024,0.489,0.024:157:32,3,38,1:41,1,39,2 0/1/2/3:56,1,47,3:0.017,0.441,0.036:107:23,0,19,2:33,1,28,1 0/1/2/3:71,2,40,3:0.023,0.348,0.033:116:32,2,23,2:39,0,17,1 0/1/2/3:31,2,43,4:0.017,0.531,0.049:80:10,0,19,4:21,2,24,0 0/1/2/3:67,4,45,6:0.034,0.368,0.050:122:37,4,20,3:30,0,25,3 0/1/2/3:91,7,55,3:0.039,0.352,0.024:156:38,2,26,1:53,5,29,2 0/1/2/3:57,1,50,0:0.017,0.450,8.691e-03:108:27,0,25,0:30,1,25,0 1 1653189 . G GT . str_contraction CONTQ=93;DP=286;ECNT=1;GERMQ=460;MBQ=33,33;MFRL=182,186;MMQ=29,34;MPOS=29;NALOD=1.32;NLOD=5.42;POPAF=5.60;RPA=9,10;RU=T;SAAF=0.040,0.020,0.043;SAPP=0.019,7.014e-03,0.974;STR;TLOD=6.01 GT:AD:AF:DP:F1R2:F2R1 0/0:18,0:0.046:18:7,0:11,0 0/1:28,1:0.059:29:13,1:15,0 0/1:3,0:0.189:3:1,0:2,0 0/1:21,0:0.038:21:7,0:14,0 0/1:21,3:0.148:24:11,1:10,2 0/1:37,1:0.046:38:23,1:14,0 0/1:27,2:0.086:29:14,0:13,2 0/1:40,1:0.043:41:17,1:23,0 1 1684347 . CCCT C,CCCTCCT . artifact_in_normal;germline_risk;multiallelic;str_contraction CONTQ=93;DP=464;ECNT=1;GERMQ=191,0;MBQ=33,33,33;MFRL=174,176,175;MMQ=60,60,60;MPOS=12,19;NALOD=1.29,-6.040e+01;NLOD=5.13,-6.096e+01;POPAF=5.60,5.60;RPA=9,8,10;RU=CCT;SAAF=0.576,0.586,0.596;SAPP=0.017,0.025,0.958;STR;TLOD=26.07,526.95 GT:AD:AF:DP:F1R2:F2R1 0/0:14,0,16:0.026,0.515:30:6,0,6:8,0,10 0/1/2:26,3,19:0.071,0.391:48:15,1,9:11,2,10 0/1/2:3,0,13:0.042,0.749:16:2,0,8:1,0,5 0/1/2:2,1,17:0.075,0.798:20:0,1,7:2,0,10 0/1/2:12,1,13:0.058,0.485:26:5,0,6:7,1,7 0/1/2:24,4,26:0.082,0.474:54:6,3,9:18,1,17 0/1/2:4,0,32:0.020,0.853:36:3,0,13:1,0,19 0/1/2:22,2,17:0.061,0.408:41:9,1,8:13,1,9 1 1848802 . G A . PASS CONTQ=93;DP=175;ECNT=1;GERMQ=255;MBQ=31,32;MFRL=342,424;MMQ=60,60;MPOS=16;NALOD=1.13;NLOD=3.61;POPAF=5.60;SAAF=0.111,0.101,0.119;SAPP=0.024,8.155e-03,0.968;TLOD=41.39 GT:AD:AF:DP:F1R2:F2R1 0/0:12,0:0.070:12:7,0:5,0 0/1:28,0:0.033:28:14,0:14,0 0/1:18,7:0.296:25:8,7:10,0 0/1:21,6:0.233:27:8,3:13,3 0/1:14,0:0.061:14:4,0:10,0 0/1:22,0:0.041:22:13,0:9,0 0/1:22,6:0.235:28:8,3:14,3 0/1:15,0:0.059:15:6,0:9,0 1 1896228 . CA C . artifact_in_normal;str_contraction;t_lod CONTQ=93;DP=465;ECNT=1;GERMQ=1126;MBQ=33,32;MFRL=188,219;MMQ=60,60;MPOS=17;NALOD=-2.959e-01;NLOD=6.49;POPAF=5.60;RPA=8,7;RU=A;SAAF=0.010,0.010,0.015;SAPP=1.339e-03,0.057,0.941;STR;TLOD=3.34 GT:AD:AF:DP:F1R2:F2R1 0/0:31,1:0.056:32:14,1:17,0 0/1:68,0:0.014:68:35,0:33,0 0/1:38,2:0.070:40:27,1:11,1 0/1:37,1:0.048:38:13,1:24,0 0/1:43,0:0.022:43:18,0:25,0 0/1:72,0:0.013:72:45,0:27,0 0/1:72,0:0.013:72:38,0:34,0 0/1:64,3:0.057:67:28,1:36,2 1 1920434 . TAA T,TA,TAAA . artifact_in_normal;multiallelic CONTQ=93;DP=424;ECNT=1;GERMQ=495,103,279;MBQ=32,31,32,31;MFRL=173,175,173,169;MMQ=60,60,60,60;MPOS=26,18,18;NALOD=0.933,-5.647e+00,-4.908e-01;NLOD=6.19,-3.214e+00,3.84;POPAF=5.60,5.60,5.60;RPA=14,12,13,15;RU=A;SAAF=0.253,0.222,0.256;SAPP=0.020,0.018,0.963;STR;TLOD=12.14,112.29,45.24 GT:AD:AF:DP:F1R2:F2R1 0/0:19,0,4,2:0.030,0.170,0.081:25:2,0,0,0:17,0,4,2 0/1/2/3:21,1,14,10:0.039,0.300,0.217:46:3,0,0,2:18,1,14,8 0/1/2/3:15,0,4,3:0.038,0.191,0.152:22:0,0,0,0:15,0,4,3 0/1/2/3:22,1,10,3:0.048,0.269,0.098:36:6,0,3,0:16,1,7,3 0/1/2/3:28,2,6,4:0.067,0.158,0.101:40:8,0,3,1:20,2,3,3 0/1/2/3:54,6,21,9:0.061,0.242,0.100:90:10,2,5,3:44,4,16,6 0/1/2/3:24,2,8,4:0.070,0.214,0.097:38:7,1,4,0:17,1,4,4 0/1/2/3:42,1,8,9:0.030,0.139,0.141:60:4,1,0,5:38,0,8,4 1 2118724 . CT C,CTT,CTTTT . artifact_in_normal;germline_risk;multiallelic;str_contraction CONTQ=93;DP=225;ECNT=2;GERMQ=205,0,226;MBQ=33,33,33,33;MFRL=188,186,171,172;MMQ=60,60,60,60;MPOS=21,21,12;NALOD=0.530,-6.069e+00,0.488;NLOD=2.40,-7.912e+00,0.058;POPAF=5.60,5.60,5.60;RPA=11,10,12,14;RU=T;SAAF=0.293,0.263,0.297;SAPP=0.025,0.014,0.961;STR;TLOD=11.49,77.13,4.55 GT:AD:AF:DP:F1R2:F2R1 0/0:5,0,3,0:0.065,0.382,0.074:8:0,0,1,0:5,0,2,0 0/1/2/3:4,2,6,0:0.182,0.445,0.055:12:2,1,4,0:2,1,2,0 0/1/2/3:0,0,1,0:0.188,0.443,0.183:1:0,0,0,0:0,0,1,0 0/1/2/3:14,0,1,0:0.044,0.100,0.047:15:8,0,0,0:6,0,1,0 0/1/2/3:13,2,7,1:0.108,0.297,0.070:23:8,2,2,1:5,0,5,0 0/1/2/3:24,3,12,4:0.077,0.292,0.112:43:12,2,4,1:12,1,8,3 0/1/2/3:21,1,2,0:0.067,0.130,0.039:24:7,0,0,0:14,1,2,0 0/1/2/3:26,2,14,0:0.064,0.326,0.021:42:14,2,6,0:12,0,8,0 1 2118742 . CT C,CTT . multiallelic;str_contraction CONTQ=93;DP=173;ECNT=2;GERMQ=270,229;MBQ=33,34,33;MFRL=202,292,185;MMQ=60,60,60;MPOS=22,20;NALOD=0.715,0.715;NLOD=2.40,2.40;POPAF=5.60,5.60;RPA=10,9,11;RU=T;SAAF=0.091,0.071,0.094;SAPP=0.020,8.940e-03,0.971;STR;TLOD=7.32,13.81 GT:AD:AF:DP:F1R2:F2R1 0/0:8,0,0:0.088,0.088:8:1,0,0:7,0,0 0/1/2:11,0,0:0.071,0.071:11:7,0,0:4,0,0 0/1/2:2,0,0:0.200,0.200:2:0,0,0:2,0,0 0/1/2:15,1,1:0.098,0.098:17:7,1,1:8,0,0 0/1/2:17,0,0:0.047,0.047:17:9,0,0:8,0,0 0/1/2:28,2,6:0.075,0.178:36:14,0,3:14,2,3 0/1/2:16,2,0:0.138,0.042:18:5,0,0:11,2,0 0/1/2:27,2,5:0.077,0.139:34:14,2,3:13,0,2 1 2124345 . TTTG T . artifact_in_normal;str_contraction CONTQ=93;DP=1480;ECNT=1;GERMQ=3190;MBQ=31,31;MFRL=173,174;MMQ=60,60;MPOS=26;NALOD=-4.977e-01;NLOD=36.98;POPAF=5.16;RPA=6,5;RU=TTG;SAAF=0.020,0.020,0.021;SAPP=9.745e-04,3.786e-03,0.995;STR;TLOD=53.30 GT:AD:AF:DP:F1R2:F2R1 0/0:137,1:0.014:138:44,0:93,1 0/1:160,4:0.030:164:70,2:90,2 0/1:93,2:0.030:95:49,0:44,2 0/1:152,3:0.025:155:72,1:80,2 0/1:136,3:0.028:139:70,0:66,3 0/1:168,4:0.028:172:69,3:99,1 0/1:162,3:0.024:165:73,2:89,1 0/1:208,4:0.023:212:90,2:118,2 1 2333494 . CCTG C . str_contraction CONTQ=93;DP=526;ECNT=1;GERMQ=1204;MBQ=33,32;MFRL=296,209;MMQ=60,60;MPOS=25;NALOD=1.68;NLOD=13.21;POPAF=4.48;RPA=4,3;RU=CTG;SAAF=0.00,0.010,0.012;SAPP=2.356e-03,0.013,0.985;STR;TLOD=8.95 GT:AD:AF:DP:F1R2:F2R1 0/0:44,0:0.021:44:14,0:30,0 0/1:71,0:0.013:71:36,0:35,0 0/1:39,1:0.046:40:24,0:15,1 0/1:51,0:0.017:51:23,0:28,0 0/1:54,0:0.017:54:30,0:24,0 0/1:58,2:0.048:60:29,1:29,1 0/1:61,2:0.045:63:28,2:33,0 0/1:62,0:0.015:62:30,0:32,0 1 2338009 . A G . PASS CONTQ=93;DP=1255;ECNT=1;GERMQ=1436;MBQ=32,29;MFRL=191,321;MMQ=60,60;MPOS=15;NALOD=2.14;NLOD=40.28;POPAF=5.60;SAAF=0.152,0.172,0.171;SAPP=0.034,1.936e-03,0.964;TLOD=372.28 GT:AD:AF:DP:F1R2:F2R1 0/0:134,0:7.179e-03:134:49,0:85,0 0/1:198,0:4.787e-03:198:91,0:107,0 0/1:63,35:0.361:98:29,17:34,18 0/1:79,53:0.403:132:50,32:29,21 0/1:112,0:8.278e-03:112:53,0:59,0 0/1:121,1:0.015:122:54,1:67,0 0/1:89,82:0.478:171:48,41:41,41 0/1:179,2:0.016:181:81,1:98,1 1 2442720 . AC A . t_lod CONTQ=93;DP=789;ECNT=1;GERMQ=2008;MBQ=33,33;MFRL=173,175;MMQ=60,60;MPOS=13;NALOD=1.70;NLOD=14.12;POPAF=5.60;RPA=7,6;RU=C;SAAF=0.00,0.010,0.010;SAPP=1.951e-03,8.226e-03,0.990;STR;TLOD=3.01 GT:AD:AF:DP:F1R2:F2R1 0/0:47,0:0.020:47:17,0:30,0 0/1:149,1:0.012:150:80,1:69,0 0/1:83,0:0.011:83:35,0:48,0 0/1:57,1:0.032:58:23,1:34,0 0/1:86,2:0.033:88:39,2:47,0 0/1:103,2:0.027:105:52,0:51,2 0/1:74,0:0.013:74:39,0:35,0 0/1:120,1:0.016:121:51,0:69,1 1 2526191 . G GC . str_contraction CONTQ=93;DP=445;ECNT=1;GERMQ=945;MBQ=32,32;MFRL=186,175;MMQ=60,60;MPOS=14;NALOD=0.420;NLOD=9.23;POPAF=5.60;RPA=8,9;RU=C;SAAF=0.020,0.020,0.026;SAPP=1.522e-03,0.028,0.971;STR;TLOD=6.42 GT:AD:AF:DP:F1R2:F2R1 0/0:39,1:0.046:40:24,0:15,1 0/1:62,1:0.029:63:30,0:32,1 0/1:46,3:0.076:49:23,2:23,1 0/1:52,1:0.035:53:26,0:26,1 0/1:42,0:0.021:42:19,0:23,0 0/1:37,0:0.024:37:24,0:13,0 0/1:52,1:0.034:53:15,1:37,0 0/1:46,3:0.076:49:23,2:23,1 1 2530259 . GGA G . str_contraction CONTQ=93;DP=390;ECNT=1;GERMQ=640;MBQ=31,31;MFRL=199,182;MMQ=60,60;MPOS=18;NALOD=1.47;NLOD=7.81;POPAF=2.70;RPA=6,5;RU=GA;SAAF=0.040,0.00,0.038;SAPP=0.013,6.810e-03,0.980;STR;TLOD=15.71 GT:AD:AF:DP:F1R2:F2R1 0/0:26,0:0.033:26:10,0:16,0 0/1:59,6:0.103:65:29,4:30,2 0/1:11,0:0.071:11:6,0:5,0 0/1:24,1:0.071:25:14,1:10,0 0/1:31,0:0.026:31:9,0:22,0 0/1:39,3:0.088:42:22,0:17,3 0/1:41,0:0.021:41:20,0:21,0 0/1:45,0:0.018:45:24,0:21,0 1 2560818 . CCAG C . artifact_in_normal;str_contraction CONTQ=93;DP=559;ECNT=2;GERMQ=761;MBQ=32,32;MFRL=174,174;MMQ=60,60;MPOS=26;NALOD=-3.776e+00;NLOD=11.08;POPAF=4.66;RPA=7,6;RU=CAG;SAAF=0.040,0.040,0.049;SAPP=2.803e-03,9.087e-03,0.988;STR;TLOD=37.41 GT:AD:AF:DP:F1R2:F2R1 0/0:65,2:0.042:67:31,1:34,1 0/1:40,0:0.020:40:21,0:19,0 0/1:44,4:0.098:48:23,3:21,1 0/1:37,0:0.022:37:17,0:20,0 0/1:38,1:0.045:39:22,0:16,1 0/1:27,3:0.121:30:15,0:12,3 0/1:44,2:0.060:46:19,1:25,1 0/1:63,5:0.085:68:36,2:27,3 1 2560821 . G C . panel_of_normals;t_lod CONTQ=93;DP=541;ECNT=2;GERMQ=1337;MBQ=33,32;MFRL=172,188;MMQ=60,60;MPOS=19;NALOD=1.60;NLOD=21.97;PON;POPAF=5.60;SAAF=0.010,0.010,0.014;SAPP=6.863e-04,0.056,0.944;TLOD=5.05 GT:AD:AF:DP:F1R2:F2R1 0/0:73,0:0.013:73:37,0:36,0 0/1:59,1:0.032:60:29,0:30,1 0/1:56,2:0.037:58:29,1:27,1 0/1:47,1:0.039:48:22,1:25,0 0/1:57,1:0.033:58:32,0:25,1 0/1:47,0:0.019:47:23,0:24,0 0/1:61,1:0.031:62:30,0:31,1 0/1:86,0:0.011:86:50,0:36,0 1 2985620 . AGGC A . artifact_in_normal;str_contraction CONTQ=93;DP=255;ECNT=1;GERMQ=567;MBQ=33,32;MFRL=197,204;MMQ=60,60;MPOS=16;NALOD=-1.574e+00;NLOD=3.59;POPAF=5.60;RPA=8,7;RU=GGC;SAAF=0.020,0.020,0.023;SAPP=2.899e-03,6.259e-03,0.991;STR;TLOD=9.15 GT:AD:AF:DP:F1R2:F2R1 0/0:26,1:0.066:27:12,0:14,1 0/1:44,1:0.042:45:22,0:22,1 0/1:20,1:0.086:21:10,1:10,0 0/1:19,0:0.047:19:10,0:9,0 0/1:20,0:0.045:20:8,0:12,0 0/1:43,1:0.043:44:18,0:25,1 0/1:17,0:0.052:17:9,0:8,0 0/1:45,2:0.061:47:16,0:29,2 1 3394388 . TC T . artifact_in_normal;t_lod CONTQ=93;DP=473;ECNT=1;GERMQ=1061;MBQ=31,32;MFRL=190,241;MMQ=60,60;MPOS=23;NALOD=-1.641e+00;NLOD=6.70;POPAF=5.60;RPA=7,6;RU=C;SAAF=0.00,0.020,0.016;SAPP=2.863e-03,0.015,0.982;STR;TLOD=3.63 GT:AD:AF:DP:F1R2:F2R1 0/0:41,2:0.066:43:13,1:28,1 0/1:59,2:0.046:61:30,1:29,1 0/1:59,0:0.016:59:26,0:33,0 0/1:42,1:0.043:43:19,1:23,0 0/1:40,0:0.023:40:18,0:22,0 0/1:46,0:0.020:46:25,0:21,0 0/1:55,2:0.049:57:28,0:27,2 0/1:70,1:0.026:71:38,0:32,1 1 3549862 . GT G,GTT,GTTT . artifact_in_normal;multiallelic;str_contraction CONTQ=93;DP=505;ECNT=1;GERMQ=671,599,1004;MBQ=34,33,33,34;MFRL=179,175,176,171;MMQ=60,60,60,60;MPOS=18,14,11;NALOD=-2.307e+00,-1.820e+00,0.973;NLOD=1.49,1.94,6.41;POPAF=5.60,5.60,5.60;RPA=11,10,12,13;RU=T;SAAF=0.081,0.111,0.113;SAPP=0.019,0.014,0.967;STR;TLOD=44.56,58.83,3.83 GT:AD:AF:DP:F1R2:F2R1 0/0:20,2,2,0:0.105,0.105,0.034:24:10,1,1,0:10,1,1,0 0/1/2/3:60,7,5,0:0.103,0.077,0.013:72:38,4,4,0:22,3,1,0 0/1/2/3:32,4,2,0:0.118,0.069,0.023:38:25,3,1,0:7,1,1,0 0/1/2/3:34,1,7,1:0.041,0.169,0.042:43:15,0,3,0:19,1,4,1 0/1/2/3:42,1,7,0:0.036,0.146,0.018:50:15,0,2,0:27,1,5,0 0/1/2/3:53,7,12,3:0.096,0.175,0.047:75:30,1,7,3:23,6,5,0 0/1/2/3:55,6,4,0:0.100,0.071,0.014:65:22,3,4,0:33,3,0,0 0/1/2/3:77,8,8,2:0.085,0.090,0.030:95:37,1,2,1:40,7,6,1 1 3645985 . GGCA G . artifact_in_normal;str_contraction;t_lod CONTQ=93;DP=1139;ECNT=1;GERMQ=2149;MBQ=31,31;MFRL=187,157;MMQ=60,60;MPOS=22;NALOD=-7.072e-01;NLOD=17.02;POPAF=5.39;RPA=4,3;RU=GCA;SAAF=0.010,0.010,5.747e-03;SAPP=1.832e-03,9.970e-04,0.997;STR;TLOD=5.11 GT:AD:AF:DP:F1R2:F2R1 0/0:71,1:0.025:72:27,0:44,1 0/1:125,2:0.022:127:53,1:72,1 0/1:63,1:0.029:64:35,1:28,0 0/1:90,0:9.428e-03:90:39,0:51,0 0/1:93,1:0.019:94:47,1:46,0 0/1:100,0:8.338e-03:100:38,0:62,0 0/1:97,0:8.599e-03:97:41,0:56,0 0/1:124,0:6.767e-03:124:50,0:74,0 1 3753032 . GTTTT G,GT,GTT,GTTT,GTTTTT,GTTTTTT,GTTTTTTT,GTTTTTTTTT . artifact_in_normal;germline_risk;multiallelic;read_position CONTQ=93;DP=298;ECNT=1;GERMQ=0,1,0,0,0,0,1,0;MBQ=28,25,28,27,27,28,28,29,29;MFRL=172,162,177,174,178,172,220,173,167;MMQ=60,29,60,60,60,60,60,45,60;MPOS=4,28,19,15,25,25,27,25;NALOD=0.319,0.299,0.277,0.276,-1.467e+00,0.113,0.242,-5.401e-01;NLOD=2.28,1.98,1.68,1.60,-4.047e+00,-4.273e+00,-1.057e+00,-2.974e+00;POPAF=5.60,5.60,5.60,5.60,5.60,5.60,5.60,5.60;RPA=24,20,21,22,23,25,26,27,29;RU=T;SAAF=0.505,0.566,0.567;SAPP=0.045,0.018,0.937;STR;TLOD=14.77,10.82,16.34,34.94,46.07,6.87,5.40,3.16 GT:AD:AF:DP:F1R2:F2R1 0/0:2,0,0,0,0,1,0,0,1:0.055,0.058,0.062,0.062,0.227,0.100,0.069,0.150:4:2,0,0,0,0,1,0,0,0:0,0,0,0,0,0,0,0,1 0/1/2/3/4/5/6/7/8:2,3,1,3,2,4,0,0,3:0.126,0.061,0.127,0.090,0.203,0.039,0.042,0.196:18:2,3,1,3,2,4,0,0,2:0,0,0,0,0,0,0,0,1 0/1/2/3/4/5/6/7/8:1,0,2,0,0,0,0,0,0:0.070,0.219,0.070,0.070,0.083,0.115,0.115,0.114:3:1,0,2,0,0,0,0,0,0:0,0,0,0,0,0,0,0,0 0/1/2/3/4/5/6/7/8:0,0,1,1,2,1,2,0,0:0.050,0.112,0.112,0.191,0.107,0.213,0.082,0.079:7:0,0,1,1,2,1,1,0,0:0,0,0,0,0,0,1,0,0 0/1/2/3/4/5/6/7/8:1,2,1,1,2,6,2,2,2:0.090,0.060,0.060,0.079,0.256,0.107,0.159,0.126:19:1,1,0,1,0,2,1,1,1:0,1,1,0,2,4,1,1,1 0/1/2/3/4/5/6/7/8:12,8,5,6,15,10,4,3,0:0.092,0.071,0.083,0.198,0.170,0.063,0.123,0.023:63:8,4,4,4,10,6,2,2,0:4,4,1,2,5,4,2,1,0 0/1/2/3/4/5/6/7/8:4,0,1,1,4,6,0,0,0:0.033,0.072,0.074,0.201,0.279,0.035,0.054,0.054:16:2,0,1,0,3,3,0,0,0:2,0,0,1,1,3,0,0,0 0/1/2/3/4/5/6/7/8:9,2,0,4,4,11,3,1,5:0.050,0.017,0.092,0.095,0.296,0.085,0.042,0.140:39:5,0,0,3,3,10,2,1,1:4,2,0,1,1,1,1,0,4 1 3807629 . GA G . artifact_in_normal;str_contraction;t_lod CONTQ=93;DP=506;ECNT=1;GERMQ=1116;MBQ=33,33;MFRL=254,302;MMQ=60,60;MPOS=25;NALOD=-1.485e+00;NLOD=6.02;POPAF=5.60;RPA=8,7;RU=A;SAAF=0.020,0.00,0.015;SAPP=0.017,2.681e-03,0.980;STR;TLOD=3.48 GT:AD:AF:DP:F1R2:F2R1 0/0:37,2:0.070:39:9,1:28,1 0/1:71,2:0.039:73:28,1:43,1 0/1:21,0:0.039:21:9,0:12,0 0/1:46,1:0.039:47:20,0:26,1 0/1:46,0:0.020:46:18,0:28,0 0/1:61,1:0.030:62:28,1:33,0 0/1:69,1:0.026:70:38,0:31,1 0/1:78,1:0.023:79:35,1:43,0 1 4772545 . G A . PASS CONTQ=93;DP=751;ECNT=1;GERMQ=1635;MBQ=29,33;MFRL=177,196;MMQ=60,60;MPOS=23;NALOD=1.74;NLOD=15.90;POPAF=5.60;SAAF=0.040,0.040,0.049;SAPP=2.425e-03,5.023e-03,0.993;TLOD=58.71 GT:AD:AF:DP:F1R2:F2R1 0/0:53,0:0.018:53:16,0:37,0 0/1:165,0:5.994e-03:165:95,0:70,0 0/1:44,8:0.152:52:15,7:29,1 0/1:47,13:0.227:60:20,7:27,6 0/1:93,0:0.011:93:46,0:47,0 0/1:143,0:6.861e-03:143:67,0:76,0 0/1:55,13:0.200:68:25,8:30,5 0/1:107,0:9.204e-03:107:47,0:60,0 1 5939837 . GCA ACA,G . artifact_in_normal;germline_risk;multiallelic CONTQ=93;DP=147;ECNT=2;GERMQ=0,119;MBQ=29,32,29;MFRL=355,356,344;MMQ=60,60,60;MPOS=25,30;NALOD=-4.741e+00,0.847;NLOD=-4.250e+00,3.16;POPAF=5.60,5.60;SAAF=0.273,0.283,0.302;SAPP=0.025,0.011,0.964;TLOD=73.96,20.16 GT:AD:AF:DP:F1R2:F2R1 0/0:6,2,0:0.231,0.068:8:4,1,0:2,1,0 0/1/2:9,7,3:0.356,0.163:19:7,4,1:2,3,2 0/1/2:8,2,1:0.178,0.134:11:2,1,1:6,1,0 0/1/2:9,1,1:0.115,0.140:11:4,1,1:5,0,0 0/1/2:7,4,0:0.338,0.067:11:3,4,0:4,0,0 0/1/2:8,9,1:0.445,0.093:18:4,5,0:4,4,1 0/1/2:21,1,5:0.061,0.193:27:11,0,3:10,1,2 0/1/2:5,5,0:0.464,0.071:10:3,2,0:2,3,0 1 5939876 . AAC A . str_contraction CONTQ=93;DP=136;ECNT=2;GERMQ=226;MBQ=29,26;MFRL=371,441;MMQ=60,60;MPOS=20;NALOD=0.954;NLOD=2.41;POPAF=5.60;RPA=7,6;RU=AC;SAAF=0.071,0.051,0.078;SAPP=4.600e-03,0.025,0.971;STR;TLOD=18.91 GT:AD:AF:DP:F1R2:F2R1 0/0:8,0:0.100:8:4,0:4,0 0/1:13,1:0.121:14:9,1:4,0 0/1:15,2:0.156:17:7,1:8,1 0/1:15,0:0.059:15:9,0:6,0 0/1:9,0:0.086:9:5,0:4,0 0/1:15,2:0.156:17:8,2:7,0 0/1:29,3:0.117:32:14,1:15,2 0/1:10,1:0.150:11:6,1:4,0 1 5940063 . GCA G . str_contraction CONTQ=93;DP=313;ECNT=2;GERMQ=592;MBQ=33,34;MFRL=311,211;MMQ=60,60;MPOS=11;NALOD=1.50;NLOD=9.03;POPAF=5.60;RPA=7,6;RU=CA;SAAF=0.020,0.020,0.025;SAPP=2.838e-03,0.014,0.983;STR;TLOD=7.07 GT:AD:AF:DP:F1R2:F2R1 0/0:30,0:0.031:30:15,0:15,0 0/1:40,0:0.022:40:22,0:18,0 0/1:24,0:0.033:24:12,0:12,0 0/1:33,0:0.026:33:18,0:15,0 0/1:10,0:0.071:10:4,0:6,0 0/1:26,1:0.066:27:7,1:19,0 0/1:40,2:0.066:42:23,1:17,1 0/1:25,2:0.100:27:13,2:12,0 1 5940091 . GCA G,GCACA . artifact_in_normal;multiallelic;str_contraction CONTQ=93;DP=367;ECNT=2;GERMQ=549,544;MBQ=33,33,33;MFRL=225,190,197;MMQ=60,60,60;MPOS=30,19;NALOD=-9.850e-01,-3.477e+00;NLOD=6.85,2.40;POPAF=5.60,5.60;RPA=7,6,8;RU=CA;SAAF=0.00,0.061,0.059;SAPP=0.021,5.126e-03,0.974;STR;TLOD=28.88,18.21 GT:AD:AF:DP:F1R2:F2R1 0/0:30,1,2:0.050,0.081:33:14,0,1:16,1,1 0/1/2:36,5,3:0.119,0.083:44:20,2,1:16,3,2 0/1/2:22,1,0:0.072,0.036:23:10,0,0:12,1,0 0/1/2:29,0,2:0.024,0.085:31:18,0,0:11,0,2 0/1/2:23,2,1:0.101,0.066:26:13,2,0:10,0,1 0/1/2:39,2,3:0.059,0.083:44:15,2,2:24,0,1 0/1/2:34,3,1:0.090,0.046:38:17,2,0:17,1,1 0/1/2:42,1,0:0.041,0.021:43:21,0,0:21,1,0 1 6157480 . C A . PASS CONTQ=93;DP=965;ECNT=1;GERMQ=1355;MBQ=32,31;MFRL=174,174;MMQ=60,60;MPOS=17;NALOD=1.92;NLOD=24.07;POPAF=5.60;SAAF=0.121,0.121,0.130;SAPP=0.049,1.869e-03,0.949;TLOD=230.03 GT:AD:AF:DP:F1R2:F2R1 0/0:80,0:0.012:80:27,0:53,0 0/1:169,0:5.748e-03:169:102,0:67,0 0/1:34,28:0.453:62:20,12:14,16 0/1:33,30:0.475:63:18,13:15,17 0/1:118,2:0.024:120:59,2:59,0 0/1:161,3:0.024:164:85,1:76,2 0/1:53,44:0.452:97:29,19:24,25 0/1:166,3:0.018:169:81,1:85,2 1 6184728 . TGG T,TG,GGG . multiallelic;panel_of_normals CONTQ=93;DP=214;ECNT=1;GERMQ=10,0,86;MBQ=29,30,23,26;MFRL=226,225,306,201;MMQ=60,60,60,60;MPOS=18,13,2;NALOD=0.608,-6.724e+00,0.859;NLOD=0.627,-6.963e+00,5.39;PON;POPAF=5.60,5.60,5.60;SAAF=0.758,0.00,0.759;SAPP=5.077e-03,0.577,0.418;TLOD=6.47,13.98,101.71 GT:AD:AF:DP:F1R2:F2R1 0/0:1,0,3,0:0.093,0.528,0.044:4:0,0,1,0:1,0,2,0 0/1/2/3:5,0,3,18:0.040,0.220,0.415:26:3,0,1,10:2,0,2,8 0/1/2/3:4,2,3,8:0.171,0.236,0.294:17:2,1,1,2:2,1,2,6 0/1/2/3:2,1,0,7:0.211,0.087,0.358:10:2,0,0,3:0,1,0,4 0/1/2/3:1,0,0,5:0.147,0.143,0.381:6:0,0,0,2:1,0,0,3 0/1/2/3:4,1,2,11:0.107,0.163,0.451:18:1,0,0,2:3,1,2,9 0/1/2/3:2,0,1,5:0.091,0.225,0.310:8:0,0,1,1:2,0,0,4 0/1/2/3:1,0,0,6:0.098,0.098,0.509:7:0,0,0,1:1,0,0,5 1 6219287 . TCACA T,TCA,TCACACA . artifact_in_normal;germline_risk;multiallelic CONTQ=93;DP=214;ECNT=1;GERMQ=0,0,40;MBQ=32,32,32,32;MFRL=322,318,331,251;MMQ=60,60,60,37;MPOS=16,18,32;NALOD=-7.171e+00,-1.512e+01,0.709;NLOD=-1.073e+01,-1.872e+01,3.11;POPAF=5.60,5.60,5.60;RPA=16,14,15,17;RU=CA;SAAF=0.717,0.737,0.742;SAPP=0.027,0.026,0.947;STR;TLOD=46.94,195.02,8.26 GT:AD:AF:DP:F1R2:F2R1 0/0:5,3,6,0:0.210,0.400,0.050:14:2,0,2,0:3,3,4,0 0/1/2/3:6,2,11,2:0.117,0.489,0.114:21:3,1,3,2:3,1,8,0 0/1/2/3:3,1,4,0:0.163,0.429,0.072:8:0,1,2,0:3,0,2,0 0/1/2/3:1,2,22,0:0.101,0.802,0.031:25:0,0,12,0:1,2,10,0 0/1/2/3:3,2,4,0:0.214,0.361,0.075:9:3,2,2,0:0,0,2,0 0/1/2/3:8,4,6,3:0.200,0.282,0.156:21:3,2,4,1:5,2,2,2 0/1/2/3:2,9,18,0:0.304,0.581,0.027:29:1,4,8,0:1,5,10,0 0/1/2/3:2,3,7,0:0.233,0.528,0.053:12:0,1,2,0:2,2,5,0 1 6252965 . CCA C . artifact_in_normal;str_contraction CONTQ=93;DP=682;ECNT=1;GERMQ=1412;MBQ=33,32;MFRL=175,197;MMQ=60,60;MPOS=12;NALOD=-3.134e+00;NLOD=7.29;POPAF=0.757;RPA=5,4;RU=CA;SAAF=0.00,0.010,9.921e-03;SAPP=2.035e-03,6.804e-03,0.991;STR;TLOD=5.75 GT:AD:AF:DP:F1R2:F2R1 0/0:49,2:0.056:51:16,0:33,2 0/1:102,0:8.864e-03:102:54,0:48,0 0/1:21,0:0.038:21:10,0:11,0 0/1:49,1:0.037:50:24,0:25,1 0/1:55,0:0.016:55:22,0:33,0 0/1:102,1:0.018:103:45,0:57,1 0/1:70,3:0.052:73:43,3:27,0 0/1:100,0:9.082e-03:100:45,0:55,0 1 6257784 . C CT . str_contraction;t_lod CONTQ=93;DP=996;ECNT=1;GERMQ=2133;MBQ=33,34;MFRL=172,197;MMQ=60,60;MPOS=14;NALOD=1.73;NLOD=29.71;POPAF=5.60;RPA=8,9;RU=T;SAAF=0.010,0.010,0.012;SAPP=6.981e-04,0.011,0.988;STR;TLOD=3.01 GT:AD:AF:DP:F1R2:F2R1 0/0:99,0:9.250e-03:99:35,0:64,0 0/1:150,0:6.014e-03:150:83,0:67,0 0/1:11,1:0.141:12:4,0:7,1 0/1:44,1:0.039:45:23,0:21,1 0/1:94,1:0.019:95:45,1:49,0 0/1:129,3:0.028:132:60,0:69,3 0/1:51,0:0.016:51:29,0:22,0 0/1:188,2:0.014:190:86,1:102,1 1 6272136 . GA G . PASS CONTQ=93;DP=546;ECNT=1;GERMQ=1166;MBQ=32,31;MFRL=190,205;MMQ=60,60;MPOS=30;NALOD=1.52;NLOD=9.02;POPAF=1.20;SAAF=0.020,0.010,0.024;SAPP=2.923e-03,4.941e-03,0.992;TLOD=7.67 GT:AD:AF:DP:F1R2:F2R1 0/0:30,0:0.029:30:13,0:17,0 0/1:85,1:0.021:86:39,0:46,1 0/1:60,0:0.016:60:34,0:26,0 0/1:61,0:0.015:61:26,0:35,0 0/1:43,0:0.021:43:27,0:16,0 0/1:69,5:0.077:74:36,3:33,2 0/1:71,1:0.013:72:37,1:34,0 0/1:49,4:0.089:53:21,3:28,1 1 6295798 . GAGC G . str_contraction;t_lod CONTQ=93;DP=159;ECNT=1;GERMQ=395;MBQ=34,32;MFRL=163,142;MMQ=60,60;MPOS=30;NALOD=1.66;NLOD=12.93;POPAF=5.60;RPA=5,4;RU=AGC;SAAF=0.00,0.020,0.019;SAPP=7.659e-03,4.457e-03,0.988;STR;TLOD=3.23 GT:AD:AF:DP:F1R2:F2R1 0/0:43,0:0.022:43:18,0:25,0 0/1:7,0:0.107:7:4,0:3,0 0/1:7,1:0.200:8:3,0:4,1 0/1:13,0:0.064:13:5,0:8,0 0/1:15,0:0.059:15:5,0:10,0 0/1:10,1:0.154:11:7,1:3,0 0/1:13,0:0.061:13:7,0:6,0 0/1:38,0:0.025:38:18,0:20,0 1 6324568 . GT G . t_lod CONTQ=93;DP=307;ECNT=1;GERMQ=780;MBQ=31,31;MFRL=205,168;MMQ=60,60;MPOS=17;NALOD=1.27;NLOD=5.11;POPAF=5.60;RPA=5,4;RU=T;SAAF=0.00,0.020,0.018;SAPP=3.285e-03,0.015,0.981;STR;TLOD=3.43 GT:AD:AF:DP:F1R2:F2R1 0/0:17,0:0.052:17:5,0:12,0 0/1:40,0:0.024:40:21,0:19,0 0/1:26,1:0.069:27:11,0:15,1 0/1:36,0:0.026:36:17,0:19,0 0/1:24,1:0.073:25:14,1:10,0 0/1:76,3:0.049:79:26,2:50,1 0/1:43,0:0.022:43:24,0:19,0 0/1:31,0:0.030:31:15,0:16,0 1 6473522 . AT A,ATT . str_contraction CONTQ=93;DP=241;ECNT=1;GERMQ=535,492;MBQ=33,33,33;MFRL=338,368,349;MMQ=60,60,60;MPOS=26,16;NALOD=0.694,0.707;NLOD=4.54,4.81;POPAF=5.60,5.60;RPA=9,8,10;RU=T;SAAF=0.040,0.00,0.044;SAPP=0.013,7.969e-03,0.979;STR;TLOD=3.92,5.58 GT:AD:AF:DP:F1R2:F2R1 0/0:15,0,0:0.053,0.052:15:4,0,0:11,0,0 0/1/2:17,0,1:0.045,0.092:18:10,0,0:7,0,1 0/1/2:17,0,0:0.050,0.050:17:7,0,0:10,0,0 0/1/2:56,1,3:0.031,0.048:60:15,0,1:41,1,2 0/1/2:19,0,0:0.045,0.045:19:7,0,0:12,0,0 0/1/2:19,1,2:0.080,0.091:22:6,0,2:13,1,0 0/1/2:56,2,3:0.046,0.060:61:33,0,2:23,2,1 0/1/2:10,1,0:0.139,0.067:11:5,0,0:5,1,0 1 6488131 . CA C . str_contraction CONTQ=93;DP=354;ECNT=1;GERMQ=806;MBQ=31,32;MFRL=309,287;MMQ=60,60;MPOS=26;NALOD=1.61;NLOD=11.37;POPAF=5.60;RPA=8,7;RU=A;SAAF=0.00,0.030,0.028;SAPP=5.134e-03,0.012,0.983;STR;TLOD=7.10 GT:AD:AF:DP:F1R2:F2R1 0/0:38,0:0.024:38:11,0:27,0 0/1:45,4:0.096:49:23,4:22,0 0/1:35,0:0.026:35:22,0:13,0 0/1:42,0:0.023:42:22,0:20,0 0/1:34,0:0.027:34:17,0:17,0 0/1:40,2:0.067:42:21,0:19,2 0/1:53,1:0.034:54:20,0:33,1 0/1:28,1:0.063:29:17,1:11,0 1 6500675 . G C . artifact_in_normal;mapping_quality;panel_of_normals CONTQ=93;DP=277;ECNT=2;GERMQ=574;MBQ=28,29;MFRL=184,141;MMQ=60,29;MPOS=5;NALOD=-7.281e-02;NLOD=9.97;PON;POPAF=5.60;SAAF=0.00,0.040,0.038;SAPP=0.114,1.605e-03,0.884;TLOD=10.84 GT:AD:AF:DP:F1R2:F2R1 0/0:44,1:0.043:45:11,0:33,1 0/1:47,2:0.057:49:23,1:24,1 0/1:32,2:0.083:34:21,1:11,1 0/1:23,1:0.077:24:8,1:15,0 0/1:12,2:0.188:14:5,1:7,1 0/1:20,0:0.045:20:10,0:10,0 0/1:24,0:0.038:24:11,0:13,0 0/1:43,1:0.042:44:22,1:21,0 1 6500712 . C G . artifact_in_normal;mapping_quality;panel_of_normals CONTQ=93;DP=466;ECNT=2;GERMQ=749;MBQ=30,29;MFRL=174,136;MMQ=60,29;MPOS=30;NALOD=-1.032e+00;NLOD=13.31;PON;POPAF=5.60;SAAF=0.061,0.101,0.100;SAPP=0.029,3.014e-03,0.968;TLOD=60.01 GT:AD:AF:DP:F1R2:F2R1 0/0:63,2:0.044:65:19,1:44,1 0/1:80,7:0.089:87:45,4:35,3 0/1:40,4:0.096:44:20,1:20,3 0/1:32,5:0.152:37:10,5:22,0 0/1:30,5:0.162:35:14,2:16,3 0/1:34,4:0.124:38:18,3:16,1 0/1:43,2:0.063:45:21,1:22,1 0/1:92,12:0.121:104:51,4:41,8 1 6500867 . A G . mapping_quality CONTQ=93;DP=300;ECNT=1;GERMQ=656;MBQ=33,31;MFRL=192,176;MMQ=60,29;MPOS=26;NALOD=1.66;NLOD=13.31;POPAF=5.60;SAAF=0.040,0.00,0.042;SAPP=1.906e-03,0.081,0.917;TLOD=11.57 GT:AD:AF:DP:F1R2:F2R1 0/0:45,0:0.021:45:22,0:23,0 0/1:42,2:0.065:44:23,1:19,1 0/1:30,2:0.087:32:21,1:9,1 0/1:13,2:0.177:15:7,1:6,1 0/1:30,1:0.034:31:13,1:17,0 0/1:24,0:0.036:24:14,0:10,0 0/1:36,1:0.050:37:20,1:16,0 0/1:51,2:0.054:53:36,0:15,2 1 6505827 . A C . artifact_in_normal;base_quality;panel_of_normals CONTQ=93;DP=739;ECNT=1;GERMQ=1120;MBQ=27,16;MFRL=179,243;MMQ=60,60;MPOS=6;NALOD=1.31;NLOD=20.94;PON;POPAF=5.60;SAAF=0.020,0.101,0.103;SAPP=1.00,0.00,0.00;TLOD=22.65 GT:AD:AF:DP:F1R2:F2R1 0/0:97,7:0.038:104:40,2:57,5 0/1:113,9:0.057:122:55,6:58,3 0/1:51,4:0.040:55:20,1:31,3 0/1:56,4:0.047:60:29,3:27,1 0/1:58,14:0.173:72:25,7:33,7 0/1:71,11:0.118:82:30,4:41,7 0/1:77,9:0.061:86:39,8:38,1 0/1:98,9:0.051:107:46,6:52,3 1 6509036 . ACCG A . str_contraction CONTQ=93;DP=565;ECNT=1;GERMQ=1327;MBQ=32,32;MFRL=172,172;MMQ=60,65;MPOS=7;NALOD=1.92;NLOD=22.49;POPAF=3.21;RPA=4,3;RU=CCG;SAAF=0.010,0.010,0.014;SAPP=4.018e-03,1.706e-03,0.994;STR;TLOD=8.67 GT:AD:AF:DP:F1R2:F2R1 0/0:75,0:0.012:75:36,0:39,0 0/1:70,0:0.014:70:35,0:35,0 0/1:32,1:0.056:33:12,1:20,0 0/1:47,0:0.020:47:30,0:17,0 0/1:50,1:0.037:51:25,0:25,1 0/1:42,1:0.043:43:17,0:25,1 0/1:57,1:0.033:58:22,1:35,0 0/1:118,2:0.024:120:53,0:65,2 1 6529182 . TTCC T . artifact_in_normal;clustered_events;str_contraction CONTQ=93;DP=966;ECNT=3;GERMQ=1767;MBQ=31,31;MFRL=183,175;MMQ=60,60;MPOS=24;NALOD=-5.083e-01;NLOD=16.98;POPAF=5.60;RPA=8,7;RU=TCC;SAAF=0.040,0.020,0.036;SAPP=1.712e-03,8.698e-03,0.990;STR;TLOD=40.09 GT:AD:AF:DP:F1R2:F2R1 0/0:69,1:0.026:70:15,0:54,1 0/1:130,6:0.050:136:73,4:57,2 0/1:32,0:0.028:32:17,0:15,0 0/1:79,0:0.012:79:46,0:33,0 0/1:85,6:0.074:91:32,2:53,4 0/1:121,8:0.068:129:70,3:51,5 0/1:104,0:8.927e-03:104:51,0:53,0 0/1:112,5:0.043:117:60,1:52,4 1 6529186 . TC T . bad_haplotype;clustered_events CONTQ=93;DP=901;ECNT=3;GERMQ=1876;MBQ=33,31;MFRL=183,180;MMQ=60,60;MPOS=6;NALOD=1.91;NLOD=21.30;POPAF=5.60;RPA=2,1;RU=C;SAAF=0.020,0.020,0.019;SAPP=6.239e-03,1.240e-03,0.993;STR;TLOD=13.11 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS 0|0:71,0:0.012:71:19,0:52,0:0|1:6529186_TC_T:6529186 0|1:146,1:0.013:147:83,1:63,0:0|1:6529186_TC_T:6529186 0|1:24,0:0.034:24:13,0:11,0:0|1:6529186_TC_T:6529186 0|1:48,2:0.054:50:29,1:19,1:0|1:6529186_TC_T:6529186 0|1:85,3:0.043:88:32,0:53,3:0|1:6529186_TC_T:6529186 0|1:139,3:0.027:142:70,3:69,0:0|1:6529186_TC_T:6529186 0|1:71,2:0.038:73:34,2:37,0:0|1:6529186_TC_T:6529186 0|1:116,1:0.016:117:58,0:58,1:0|1:6529186_TC_T:6529186 1 6529189 . TCC T . bad_haplotype;clustered_events CONTQ=93;DP=930;ECNT=3;GERMQ=1917;MBQ=32,31;MFRL=183,180;MMQ=60,60;MPOS=-2147483648;NALOD=1.92;NLOD=22.20;POPAF=5.60;SAAF=0.020,0.020,0.018;SAPP=6.090e-03,1.223e-03,0.993;TLOD=13.01 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS 0|0:74,0:0.012:74:20,0:54,0:0|1:6529186_TC_T:6529186 0|1:150,1:0.013:151:84,1:66,0:0|1:6529186_TC_T:6529186 0|1:24,0:0.034:24:13,0:11,0:0|1:6529186_TC_T:6529186 0|1:51,2:0.051:53:30,1:21,1:0|1:6529186_TC_T:6529186 0|1:86,3:0.043:89:33,0:53,3:0|1:6529186_TC_T:6529186 0|1:141,3:0.027:144:72,3:69,0:0|1:6529186_TC_T:6529186 0|1:72,2:0.037:74:35,2:37,0:0|1:6529186_TC_T:6529186 0|1:116,1:0.015:117:58,0:58,1:0|1:6529186_TC_T:6529186 1 6536010 . TCTC T . artifact_in_normal;str_contraction CONTQ=93;DP=2042;ECNT=1;GERMQ=3233;MBQ=33,33;MFRL=177,181;MMQ=60,60;MPOS=26;NALOD=-5.455e+00;NLOD=33.17;POPAF=4.24;RPA=6,5;RU=CTC;SAAF=0.020,0.020,0.026;SAPP=8.553e-04,0.022,0.977;STR;TLOD=99.90 GT:AD:AF:DP:F1R2:F2R1 0/0:153,3:0.025:156:59,1:94,2 0/1:293,9:0.033:302:141,5:152,4 0/1:115,6:0.057:121:51,2:64,4 0/1:197,6:0.034:203:106,5:91,1 0/1:205,4:0.024:209:91,3:114,1 0/1:158,2:0.018:160:76,0:82,2 0/1:248,6:0.027:254:109,2:139,4 0/1:328,8:0.027:336:168,4:160,4 1 6638842 . CGCT C . str_contraction CONTQ=93;DP=621;ECNT=1;GERMQ=1050;MBQ=29,32;MFRL=181,256;MMQ=60,60;MPOS=30;NALOD=1.64;NLOD=9.81;POPAF=3.55;RPA=7,6;RU=GCT;SAAF=0.030,0.040,0.045;SAPP=0.021,1.540e-03,0.977;STR;TLOD=50.70 GT:AD:AF:DP:F1R2:F2R1 0/0:33,0:0.023:33:15,0:18,0 0/1:85,2:0.033:87:32,1:53,1 0/1:30,4:0.137:34:18,2:12,2 0/1:52,3:0.069:55:28,1:24,2 0/1:41,3:0.086:44:18,0:23,3 0/1:85,4:0.054:89:50,3:35,1 0/1:69,1:0.026:70:41,0:28,1 0/1:61,3:0.059:64:29,2:32,1 1 6680068 . TGAA T . artifact_in_normal;str_contraction CONTQ=93;DP=1012;ECNT=1;GERMQ=1939;MBQ=33,33;MFRL=192,208;MMQ=60,60;MPOS=20;NALOD=-6.232e-01;NLOD=20.35;POPAF=4.91;RPA=5,4;RU=GAA;SAAF=0.020,0.020,0.019;SAPP=1.599e-03,3.504e-03,0.995;STR;TLOD=24.96 GT:AD:AF:DP:F1R2:F2R1 0/0:82,1:0.023:83:28,0:54,1 0/1:133,3:0.028:136:57,3:76,0 0/1:43,0:0.020:43:22,0:21,0 0/1:63,3:0.057:66:31,1:32,2 0/1:92,0:9.714e-03:92:45,0:47,0 0/1:122,4:0.032:126:49,1:73,3 0/1:82,2:0.034:84:38,2:44,0 0/1:126,1:0.015:127:69,1:57,0 1 6685231 . CCCG C . artifact_in_normal;str_contraction CONTQ=93;DP=537;ECNT=1;GERMQ=1367;MBQ=31,31;MFRL=194,195;MMQ=60,49;MPOS=22;NALOD=-6.712e-01;NLOD=19.54;POPAF=5.60;RPA=4,3;RU=CCG;SAAF=0.010,0.010,0.012;SAPP=8.006e-04,0.018,0.981;STR;TLOD=7.45 GT:AD:AF:DP:F1R2:F2R1 0/0:79,1:0.024:80:28,0:51,1 0/1:30,1:0.059:31:16,0:14,1 0/1:92,2:0.031:94:52,2:40,0 0/1:92,1:0.021:93:47,0:45,1 0/1:21,0:0.043:21:12,0:9,0 0/1:17,0:0.053:17:6,0:11,0 0/1:136,1:0.014:137:64,1:72,0 0/1:38,0:0.025:38:21,0:17,0 1 6693976 . GA G,GAA . artifact_in_normal;multiallelic;str_contraction CONTQ=93;DP=242;ECNT=1;GERMQ=411,220;MBQ=33,34,33;MFRL=212,185,305;MMQ=60,60,60;MPOS=26,24;NALOD=0.715,-8.843e-01;NLOD=4.77,1.99;POPAF=5.60,5.60;RPA=10,9,11;RU=A;SAAF=0.121,0.162,0.160;SAPP=0.017,0.015,0.968;STR;TLOD=6.21,39.82 GT:AD:AF:DP:F1R2:F2R1 0/0:15,0,1:0.051,0.103:16:7,0,1:8,0,0 0/1/2:23,0,2:0.033,0.105:25:11,0,1:12,0,1 0/1/2:13,0,1:0.058,0.116:14:6,0,0:7,0,1 0/1/2:20,2,8:0.088,0.272:30:14,1,3:6,1,5 0/1/2:18,1,0:0.084,0.043:19:9,1,0:9,0,0 0/1/2:37,1,8:0.039,0.174:46:20,1,5:17,0,3 0/1/2:22,0,4:0.033,0.170:26:10,0,1:12,0,3 0/1/2:25,3,7:0.099,0.189:35:13,1,4:12,2,3 1 6700129 . T TA . base_quality;panel_of_normals CONTQ=93;DP=330;ECNT=1;GERMQ=317;MBQ=11,10;MFRL=174,182;MMQ=60,60;MPOS=15;NALOD=0.802;NLOD=3.15;PON;POPAF=5.60;RPA=1,2;RU=A;SAAF=0.152,0.00,0.155;SAPP=0.010,0.038,0.952;STR;TLOD=5.81 GT:AD:AF:DP:F1R2:F2R1 0/0:13,1:0.079:14:4,0:9,1 0/1:33,5:0.120:38:4,0:29,5 0/1:2,1:0.373:3:0,0:2,1 0/1:15,5:0.210:20:5,4:10,1 0/1:31,2:0.060:33:11,1:20,1 0/1:75,11:0.098:86:33,1:42,10 0/1:20,11:0.326:31:8,4:12,7 0/1:42,5:0.067:47:20,2:22,3 1 6727802 . TTC T,TTCTC . artifact_in_normal;multiallelic;str_contraction CONTQ=93;DP=1344;ECNT=1;GERMQ=2149,3048;MBQ=33,34,33;MFRL=172,175,174;MMQ=60,60,60;MPOS=24,29;NALOD=-3.302e+00,1.50;NLOD=17.67,25.93;POPAF=5.60,5.60;RPA=6,5,7;RU=TC;SAAF=0.040,0.071,0.076;SAPP=0.861,1.054e-04,0.139;STR;TLOD=186.69,8.47 GT:AD:AF:DP:F1R2:F2R1 0/0:84,3,0:0.040,0.010:87:35,0,0:49,3,0 0/1/2:214,10,3:0.047,0.013:227:106,5,1:108,5,2 0/1/2:29,2,0:0.085,0.028:31:9,1,0:20,1,0 0/1/2:73,4,0:0.059,0.011:77:37,2,0:36,2,0 0/1/2:124,15,1:0.108,0.013:140:53,5,1:71,10,0 0/1/2:197,15,1:0.069,8.825e-03:213:109,6,0:88,9,1 0/1/2:108,10,2:0.086,0.024:120:50,5,1:58,5,1 0/1/2:249,26,2:0.093,0.010:277:122,15,0:127,11,2 1 6946388 . ATTTTATGT A . PASS CONTQ=93;DP=614;ECNT=2;GERMQ=1549;MBQ=33,23;MFRL=177,341;MMQ=60,29;MPOS=14;NALOD=1.32;NLOD=11.10;POPAF=5.60;SAAF=0.010,0.00,0.013;SAPP=0.012,2.383e-03,0.986;TLOD=12.04 GT:AD:AF:DP:F1R2:F2R1 0/0:37,0:0.024:37:16,0:21,0 0/1:79,5:0.069:84:37,5:42,0 0/1:15,2:0.157:17:6,2:9,0 0/1:69,0:0.014:69:33,0:36,0 0/1:63,0:0.015:63:23,0:40,0 0/1:106,0:9.045e-03:106:59,0:47,0 0/1:67,0:0.014:67:32,0:35,0 0/1:128,0:7.450e-03:128:67,0:61,0 1 6946397 . T TAAAAAAAA . base_quality CONTQ=93;DP=556;ECNT=2;GERMQ=1213;MBQ=32,16;MFRL=178,324;MMQ=60,29;MPOS=8;NALOD=0.947;NLOD=8.74;POPAF=5.60;RPA=8,16;RU=A;SAAF=0.020,0.010,0.018;SAPP=0.019,3.114e-03,0.978;STR;TLOD=17.41 GT:AD:AF:DP:F1R2:F2R1 0/0:29,0:0.030:29:14,0:15,0 0/1:62,6:0.098:68:27,6:35,0 0/1:14,2:0.167:16:5,2:9,0 0/1:55,0:0.016:55:26,0:29,0 0/1:53,0:0.017:53:19,0:34,0 0/1:94,0:0.010:94:53,0:41,0 0/1:54,0:0.017:54:26,0:28,0 0/1:94,0:9.204e-03:94:50,0:44,0 1 7527829 . TCTTC T . artifact_in_normal;str_contraction CONTQ=93;DP=1416;ECNT=1;GERMQ=2743;MBQ=31,32;MFRL=178,169;MMQ=60,60;MPOS=19;NALOD=-2.879e+00;NLOD=31.47;POPAF=5.60;RPA=5,4;RU=CTTC;SAAF=0.020,0.020,0.021;SAPP=1.993e-03,1.671e-03,0.996;STR;TLOD=41.11 GT:AD:AF:DP:F1R2:F2R1 0/0:133,2:0.021:135:44,1:89,1 0/1:182,5:0.031:187:82,2:100,3 0/1:58,0:0.014:58:33,0:25,0 0/1:112,2:0.025:114:49,1:63,1 0/1:118,1:0.016:119:51,0:67,1 0/1:132,8:0.063:140:56,3:76,5 0/1:131,3:0.029:134:60,2:71,1 0/1:196,1:9.372e-03:197:83,0:113,1 1 7809728 . CT C,CTT,CTTT . artifact_in_normal;clustered_events;germline_risk;multiallelic;str_contraction CONTQ=93;DP=413;ECNT=3;GERMQ=112,0,0;MBQ=31,28,31,30;MFRL=180,166,179,181;MMQ=60,60,60,60;MPOS=11,17,19;NALOD=0.603,-1.690e+01,0.604;NLOD=3.02,-1.671e+01,1.01;POPAF=5.60,5.60,5.60;RPA=12,11,13,14;RU=T;SAAF=0.687,0.707,0.710;SAPP=0.030,0.025,0.945;STR;TLOD=18.38,444.87,83.60 GT:AD:AF:DP:F1R2:F2R1 0/0:3,0,8,0:0.063,0.607,0.063:11:2,0,8,0:1,0,0,0 0/1/2/3:19,1,22,3:0.040,0.468,0.068:45:9,1,19,3:10,0,3,0 0/1/2/3:2,0,2,2:0.089,0.273,0.318:6:0,0,2,2:2,0,0,0 0/1/2/3:9,1,19,3:0.041,0.571,0.111:32:5,1,11,2:4,0,8,1 0/1/2/3:8,1,27,9:0.042,0.551,0.204:45:5,1,13,3:3,0,14,6 0/1/2/3:29,7,71,25:0.057,0.529,0.191:132:22,4,39,13:7,3,32,12 0/1/2/3:10,1,33,9:0.037,0.598,0.161:53:6,0,20,6:4,1,13,3 0/1/2/3:10,3,39,10:0.060,0.608,0.166:62:8,1,20,7:2,2,19,3 1 7809741 . C T . artifact_in_normal;clustered_events CONTQ=93;DP=432;ECNT=3;GERMQ=968;MBQ=31,29;MFRL=179,276;MMQ=60,60;MPOS=13;NALOD=-7.947e-01;NLOD=2.35;POPAF=5.60;SAAF=0.020,0.030,0.035;SAPP=5.349e-03,0.022,0.973;TLOD=18.15 GT:AD:AF:DP:F1R2:F2R1 0/0:17,1:0.099:18:13,0:4,1 0/1:41,11:0.217:52:34,2:7,9 0/1:4,2:0.373:6:4,0:0,2 0/1:33,1:0.032:34:20,0:13,1 0/1:50,0:0.019:50:23,0:27,0 0/1:140,0:6.981e-03:140:80,0:60,0 0/1:55,0:0.017:55:34,0:21,0 0/1:67,0:0.014:67:38,0:29,0 1 7809743 . TGG T . artifact_in_normal;clustered_events CONTQ=93;DP=454;ECNT=3;GERMQ=1065;MBQ=30,28;MFRL=179,292;MMQ=60,60;MPOS=6;NALOD=-3.011e-01;NLOD=3.87;POPAF=5.60;SAAF=0.010,0.030,0.028;SAPP=4.486e-03,0.022,0.974;TLOD=12.30 GT:AD:AF:DP:F1R2:F2R1 0/0:22,1:0.078:23:14,0:8,1 0/1:49,9:0.156:58:36,1:13,8 0/1:4,2:0.365:6:4,0:0,2 0/1:35,1:0.030:36:22,0:13,1 0/1:50,0:0.019:50:23,0:27,0 0/1:142,0:6.883e-03:142:81,0:61,0 0/1:57,0:0.017:57:36,0:21,0 0/1:73,0:0.013:73:39,0:34,0 1 7826653 . GCA G,ACA,GCACA . artifact_in_normal;multiallelic CONTQ=93;DP=479;ECNT=1;GERMQ=807,925,864;MBQ=33,33,32,33;MFRL=183,181,180,189;MMQ=60,60,60,60;MPOS=27,14,24;NALOD=-1.532e+00,-8.670e-01,-1.467e+00;NLOD=3.31,4.89,2.96;POPAF=5.60,5.60,5.60;SAAF=0.040,0.00,0.038;SAPP=0.013,6.648e-03,0.980;TLOD=24.11,3.68,13.64 GT:AD:AF:DP:F1R2:F2R1 0/0:21,1,1,1:0.068,0.062,0.069:24:7,0,1,0:14,1,0,1 0/1/2/3:80,6,2,0:0.076,0.028,0.010:88:41,5,0,0:39,1,2,0 0/1/2/3:19,0,0,0:0.043,0.042,0.043:19:8,0,0,0:11,0,0,0 0/1/2/3:33,2,1,0:0.073,0.060,0.031:36:16,1,0,0:17,1,1,0 0/1/2/3:34,1,0,3:0.046,0.020,0.094:38:12,1,0,1:22,0,0,2 0/1/2/3:54,3,0,5:0.059,0.012,0.090:62:29,2,0,3:25,1,0,2 0/1/2/3:34,0,0,0:0.022,0.027,0.038:34:15,0,0,0:19,0,0,0 0/1/2/3:72,1,2,0:0.023,0.022,0.011:75:34,1,0,0:38,0,2,0 1 7838211 . TTCA T . str_contraction CONTQ=93;DP=931;ECNT=1;GERMQ=1991;MBQ=32,31;MFRL=170,184;MMQ=60,60;MPOS=20;NALOD=1.91;NLOD=21.56;POPAF=5.39;RPA=5,4;RU=TCA;SAAF=0.010,0.020,0.019;SAPP=3.726e-03,1.302e-03,0.995;STR;TLOD=28.63 GT:AD:AF:DP:F1R2:F2R1 0/0:72,0:0.012:72:31,0:41,0 0/1:124,3:0.030:127:63,1:61,2 0/1:3,0:0.182:3:1,0:2,0 0/1:56,1:0.033:57:26,0:30,1 0/1:87,0:0.010:87:45,0:42,0 0/1:145,5:0.039:150:76,3:69,2 0/1:91,3:0.041:94:43,2:48,1 0/1:167,1:0.011:168:77,1:90,0 1 7845482 . AT A,ATT . str_contraction CONTQ=93;DP=412;ECNT=1;GERMQ=814,884;MBQ=31,31,30;MFRL=187,210,211;MMQ=60,60,60;MPOS=20,10;NALOD=1.11,1.10;NLOD=6.91,6.61;POPAF=5.60,5.60;RPA=9,8,10;RU=T;SAAF=0.00,0.040,0.040;SAPP=8.804e-03,7.063e-03,0.984;STR;TLOD=13.67,4.04 GT:AD:AF:DP:F1R2:F2R1 0/0:22,0,0:0.037,0.038:22:12,0,0:10,0,0 0/1/2:54,2,1:0.048,0.032:57:29,1,0:25,1,1 0/1/2:11,2,0:0.174,0.061:13:6,1,0:5,1,0 0/1/2:44,3,0:0.078,0.018:47:25,0,0:19,3,0 0/1/2:39,0,0:0.022,0.022:39:18,0,0:21,0,0 0/1/2:69,3,4:0.049,0.062:76:33,1,4:36,2,0 0/1/2:53,1,1:0.032,0.033:55:25,0,1:28,1,0 0/1/2:46,2,1:0.056,0.037:49:26,2,0:20,0,1 1 7861156 . T TTG . PASS CONTQ=93;DP=1317;ECNT=1;GERMQ=3117;MBQ=31,31;MFRL=171,174;MMQ=60,60;MPOS=18;NALOD=0.894;NLOD=19.99;POPAF=5.60;SAAF=0.010,0.010,0.012;SAPP=8.292e-04,2.486e-03,0.997;TLOD=5.69 GT:AD:AF:DP:F1R2:F2R1 0/0:75,1:0.024:76:27,1:48,0 0/1:184,2:0.015:186:90,0:94,2 0/1:10,0:0.079:10:4,0:6,0 0/1:105,1:0.017:106:53,1:52,0 0/1:128,2:0.021:130:56,0:72,2 0/1:245,2:0.011:247:111,2:134,0 0/1:126,3:0.029:129:48,1:78,2 0/1:262,3:0.014:265:107,3:155,0 1 7904093 . A AT . str_contraction CONTQ=93;DP=344;ECNT=1;GERMQ=652;MBQ=33,32;MFRL=180,177;MMQ=60,65;MPOS=14;NALOD=0.825;NLOD=7.48;POPAF=5.60;RPA=9,10;RU=T;SAAF=0.030,0.030,0.036;SAPP=0.051,3.006e-03,0.946;STR;TLOD=6.21 GT:AD:AF:DP:F1R2:F2R1 0/0:30,1:0.051:31:10,0:20,1 0/1:41,1:0.044:42:21,1:20,0 0/1:2,1:0.396:3:2,1:0,0 0/1:18,1:0.091:19:9,1:9,0 0/1:29,0:0.029:29:17,0:12,0 0/1:70,5:0.069:75:28,0:42,5 0/1:28,0:0.032:28:14,0:14,0 0/1:53,1:0.033:54:20,1:33,0 1 7907971 . CA C,CAA . artifact_in_normal;multiallelic;panel_of_normals;str_contraction CONTQ=93;DP=534;ECNT=1;GERMQ=1111,845;MBQ=33,34,32;MFRL=178,169,178;MMQ=60,60,60;MPOS=10,12;NALOD=-3.504e-01,-1.845e+00;NLOD=7.99,5.30;PON;POPAF=5.24,5.60;RPA=9,8,10;RU=A;SAAF=0.071,0.00,0.073;SAPP=0.013,0.012,0.975;STR;TLOD=5.49,35.50 GT:AD:AF:DP:F1R2:F2R1 0/0:34,1,2:0.048,0.073:37:6,0,1:28,1,1 0/1/2:42,1,5:0.038,0.102:48:12,1,3:30,0,2 0/1/2:2,0,0:0.200,0.200:2:1,0,0:1,0,0 0/1/2:44,0,2:0.020,0.060:46:23,0,2:21,0,0 0/1/2:59,3,5:0.056,0.084:67:26,3,1:33,0,4 0/1/2:90,1,15:0.017,0.142:106:39,0,6:51,1,9 0/1/2:55,0,1:0.016,0.032:56:24,0,0:31,0,1 0/1/2:103,3,3:0.034,0.034:109:43,1,3:60,2,0 1 7912944 . GA G,GAA . artifact_in_normal;multiallelic;str_contraction CONTQ=93;DP=637;ECNT=1;GERMQ=1106,1184;MBQ=31,31,31;MFRL=183,201,181;MMQ=60,60,60;MPOS=13,12;NALOD=-2.162e+00,-2.109e-01;NLOD=1.73,4.44;POPAF=5.60,5.60;RPA=10,9,11;RU=A;SAAF=0.040,0.051,0.052;SAPP=5.440e-03,0.013,0.982;STR;TLOD=29.31,19.83 GT:AD:AF:DP:F1R2:F2R1 0/0:21,2,1:0.105,0.071:24:10,1,1:11,1,0 0/1/2:83,5,4:0.061,0.051:92:44,1,3:39,4,1 0/1/2:1,0,1:0.167,0.416:2:1,0,0:0,0,1 0/1/2:50,4,1:0.085,0.033:55:26,3,0:24,1,1 0/1/2:81,2,4:0.031,0.054:87:45,2,3:36,0,1 0/1/2:115,9,6:0.073,0.051:130:63,6,5:52,3,1 0/1/2:59,5,3:0.082,0.046:67:29,3,1:30,2,2 0/1/2:101,2,3:0.026,0.035:106:47,1,1:54,1,2 1 7913184 . CAAA C,CA,CAA,CAAAA,CAAAAA . artifact_in_normal;germline_risk;multiallelic;read_position CONTQ=93;DP=347;ECNT=1;GERMQ=210,101,0,0,163;MBQ=30,30,30,30,30,28;MFRL=326,321,324,330,331,287;MMQ=60,60,60,60,60,60;MPOS=1,8,17,4,21;NALOD=0.395,0.394,-1.456e+00,-6.426e+00,0.366;NLOD=2.35,2.05,-1.689e+00,-7.125e+00,-9.806e-02;POPAF=5.60,5.60,5.60,5.60,5.60;RPA=16,13,14,15,17,18;RU=A;SAAF=0.323,0.313,0.337;SAPP=8.591e-03,0.029,0.962;STR;TLOD=12.41,47.90,86.08,62.53,10.93 GT:AD:AF:DP:F1R2:F2R1 0/0:2,0,0,1,4,0:0.068,0.068,0.157,0.398,0.073:7:1,0,0,1,3,0:1,0,0,0,1,0 0/1/2/3/4/5:9,0,3,8,8,2:0.023,0.097,0.249,0.268,0.073:30:4,0,2,4,7,1:5,0,1,4,1,1 0/1/2/3/4/5:3,0,0,3,1,0:0.077,0.077,0.308,0.153,0.077:7:2,0,0,2,1,0:1,0,0,1,0,0 0/1/2/3/4/5:27,2,5,11,9,4:0.044,0.091,0.186,0.160,0.071:58:12,2,3,5,6,2:15,0,2,6,3,2 0/1/2/3/4/5:12,2,1,4,2,1:0.094,0.067,0.174,0.124,0.080:22:4,1,0,2,1,0:8,1,1,2,1,1 0/1/2/3/4/5:21,4,9,14,11,5:0.059,0.136,0.209,0.183,0.077:64:14,3,7,7,6,2:7,1,2,7,5,3 0/1/2/3/4/5:29,2,8,10,8,2:0.036,0.139,0.163,0.140,0.045:59:12,2,3,6,3,1:17,0,5,4,5,1 0/1/2/3/4/5:13,2,4,8,7,1:0.069,0.122,0.221,0.195,0.047:35:5,0,2,4,5,0:8,2,2,4,2,1 1 7980911 . CCTT C . read_position;str_contraction CONTQ=93;DP=1094;ECNT=2;GERMQ=2842;MBQ=33,31;MFRL=173,165;MMQ=60,60;MPOS=4;NALOD=0.654;NLOD=24.63;POPAF=5.60;RPA=4,3;RU=CTT;SAAF=0.010,0.010,7.576e-03;SAPP=5.893e-04,4.338e-03,0.995;STR;TLOD=6.25 GT:AD:AF:DP:F1R2:F2R1 0/0:92,1:0.020:93:31,1:61,0 0/1:161,0:5.969e-03:161:73,0:88,0 0/1:26,0:0.035:26:14,0:12,0 0/1:101,0:9.411e-03:101:56,0:45,0 0/1:115,0:8.343e-03:115:47,0:68,0 0/1:196,4:0.024:200:102,1:94,3 0/1:120,2:0.024:122:61,0:59,2 0/1:198,1:9.740e-03:199:98,1:100,0 1 7980985 . TA T,TAA . multiallelic;str_contraction CONTQ=93;DP=916;ECNT=2;GERMQ=1415,1546;MBQ=32,32,32;MFRL=173,168,167;MMQ=60,60,60;MPOS=19,16;NALOD=0.339,0.387;NLOD=12.70,12.79;POPAF=5.60,5.60;RPA=10,9,11;RU=A;SAAF=0.051,0.040,0.051;SAPP=0.029,2.338e-03,0.969;STR;TLOD=31.83,15.63 GT:AD:AF:DP:F1R2:F2R1 0/0:50,1,1:0.033,0.033:52:13,0,0:37,1,1 0/1/2:99,7,4:0.066,0.042:110:38,2,0:61,5,4 0/1/2:12,1,1:0.108,0.107:14:1,1,0:11,0,1 0/1/2:65,0,1:0.013,0.027:66:30,0,0:35,0,1 0/1/2:74,3,2:0.043,0.034:79:31,1,1:43,2,1 0/1/2:114,9,2:0.069,0.021:125:49,4,1:65,5,1 0/1/2:81,7,6:0.075,0.071:94:31,3,5:50,4,1 0/1/2:131,4,3:0.032,0.026:138:59,2,1:72,2,2 1 8022800 . CTTTT C,CT,CTT,CTTT,CTTTTT,CTTTTTT,CTTTTTTT . artifact_in_normal;germline_risk;multiallelic;panel_of_normals CONTQ=93;DP=804;ECNT=1;GERMQ=579,420,174,0,78,429,527;MBQ=33,33,33,33,33,33,32,33;MFRL=177,176,158,176,174,176,183,169;MMQ=60,60,60,60,60,60,60,29;MPOS=20,15,20,21,20,20,21;NALOD=0.619,-1.172e+00,-2.198e+00,-1.020e+01,-6.774e+00,0.536,-1.159e+00;NLOD=5.97,1.83,-2.075e+00,-1.066e+01,-5.055e+00,2.73,1.99;PON;POPAF=5.60,5.60,5.60,5.60,5.60,5.60,5.60;RPA=19,15,16,17,18,20,21,22;RU=T;SAAF=0.343,0.364,0.367;SAPP=0.012,0.012,0.975;STR;TLOD=9.70,30.99,67.91,165.29,65.42,19.12,6.18 GT:AD:AF:DP:F1R2:F2R1 0/0:8,0,1,2,7,5,0,1:0.025,0.053,0.080,0.234,0.197,0.034,0.075:24:8,0,0,2,5,4,0,1:0,0,1,0,2,1,0,0 0/1/2/3/4/5/6/7:29,2,3,15,14,11,2,1:0.030,0.043,0.175,0.166,0.141,0.037,0.023:77:23,2,3,13,12,9,2,1:6,0,0,2,2,2,0,0 0/1/2/3/4/5/6/7:3,0,0,0,3,0,0,0:0.070,0.070,0.071,0.289,0.071,0.070,0.070:6:3,0,0,0,3,0,0,0:0,0,0,0,0,0,0,0 0/1/2/3/4/5/6/7:29,0,2,8,14,9,2,3:0.011,0.035,0.110,0.190,0.131,0.035,0.053:67:16,0,1,4,12,6,0,3:13,0,1,4,2,3,2,0 0/1/2/3/4/5/6/7:39,1,2,5,20,7,6,1:0.020,0.031,0.055,0.221,0.083,0.080,0.022:81:26,1,1,1,9,5,4,0:13,0,1,4,11,2,2,1 0/1/2/3/4/5/6/7:43,4,9,14,34,15,7,2:0.028,0.070,0.096,0.252,0.121,0.060,0.019:128:31,2,4,7,21,9,4,0:12,2,5,7,13,6,3,2 0/1/2/3/4/5/6/7:29,3,3,4,18,17,1,3:0.041,0.042,0.053,0.204,0.218,0.021,0.047:78:20,3,1,4,13,7,0,0:9,0,2,0,5,10,1,3 0/1/2/3/4/5/6/7:61,1,4,10,32,13,5,2:0.013,0.033,0.074,0.232,0.101,0.043,0.021:128:29,1,2,4,16,8,5,1:32,0,2,6,16,5,0,1 1 8025310 . CT C,CTT . artifact_in_normal;multiallelic;str_contraction CONTQ=93;DP=842;ECNT=2;GERMQ=1843,1884;MBQ=33,33,33;MFRL=194,191,175;MMQ=60,60,60;MPOS=20,21;NALOD=-1.616e+00,0.065;NLOD=11.39,14.21;POPAF=5.60,5.60;RPA=9,8,10;RU=T;SAAF=0.00,0.020,0.025;SAPP=5.025e-03,6.245e-03,0.989;STR;TLOD=15.01,11.80 GT:AD:AF:DP:F1R2:F2R1 0/0:54,2,1:0.048,0.032:57:31,2,1:23,0,0 0/1/2:113,3,0:0.032,7.971e-03:116:74,3,0:39,0,0 0/1/2:25,2,1:0.096,0.063:28:20,1,1:5,1,0 0/1/2:86,0,2:0.011,0.032:88:43,0,1:43,0,1 0/1/2:92,1,3:0.019,0.039:96:51,1,1:41,0,2 0/1/2:98,5,5:0.052,0.053:108:60,5,2:38,0,3 0/1/2:96,1,0:0.019,9.643e-03:97:49,1,0:47,0,0 0/1/2:165,5,5:0.032,0.032:175:85,1,3:80,4,2 1 8025320 . A T . artifact_in_normal CONTQ=93;DP=886;ECNT=2;GERMQ=2072;MBQ=32,29;MFRL=191,184;MMQ=60,60;MPOS=22;NALOD=-7.238e-01;NLOD=11.57;POPAF=5.60;SAAF=0.010,0.020,0.019;SAPP=1.963e-03,8.938e-03,0.989;TLOD=10.25 GT:AD:AF:DP:F1R2:F2R1 0/0:59,5:0.046:64:36,1:23,4 0/1:122,3:0.016:125:82,0:40,3 0/1:26,2:0.070:28:21,1:5,1 0/1:91,2:0.031:93:45,1:46,1 0/1:104,0:9.297e-03:104:57,0:47,0 0/1:115,3:0.033:118:68,3:47,0 0/1:100,1:9.597e-03:101:52,1:48,0 0/1:181,3:0.021:184:92,1:89,2 1 8029500 . TG T,TGG . artifact_in_normal;multiallelic;str_contraction;strand_artifact CONTQ=93;DP=765;ECNT=1;GERMQ=481,853;MBQ=29,32,30;MFRL=170,174,176;MMQ=60,60,60;MPOS=20,23;NALOD=-3.018e+00,1.22;NLOD=4.00,11.31;POPAF=4.22,1.16;RPA=10,9,11;RU=G;SAAF=0.152,0.00,0.147;SAPP=9.501e-06,0.995,4.513e-03;STR;TLOD=87.11,7.24 GT:AD:AF:DP:F1R2:F2R1 0/0:37,3,1:0.088,0.022:41:20,1,1:17,2,0 0/1/2:64,11,3:0.133,0.037:78:35,4,3:29,7,0 0/1/2:2,0,0:0.171,0.169:2:2,0,0:0,0,0 0/1/2:21,3,1:0.134,0.064:25:12,3,0:9,0,1 0/1/2:38,8,1:0.159,0.019:47:19,4,1:19,4,0 0/1/2:94,24,3:0.183,0.024:121:50,10,3:44,14,0 0/1/2:35,4,3:0.099,0.085:42:17,1,1:18,3,2 0/1/2:76,7,2:0.079,0.031:85:39,2,2:37,5,0 1 8384575 . G C . artifact_in_normal;base_quality;read_position CONTQ=93;DP=1458;ECNT=1;GERMQ=2832;MBQ=33,14;MFRL=177,181;MMQ=60,60;MPOS=4;NALOD=1.67;NLOD=30.50;POPAF=5.60;SAAF=0.010,0.061,0.059;SAPP=1.00,0.00,0.00;TLOD=25.96 GT:AD:AF:DP:F1R2:F2R1 0/0:116,6:0.011:122:41,3:75,3 0/1:252,13:0.021:265:130,8:122,5 0/1:132,3:8.092e-03:135:64,1:68,2 0/1:140,13:0.065:153:57,6:83,7 0/1:137,7:0.026:144:66,4:71,3 0/1:154,8:0.023:162:77,6:77,2 0/1:180,14:0.058:194:89,3:91,11 0/1:178,16:0.068:194:91,7:87,9 1 8385485 . GA G,GAA . multiallelic;str_contraction CONTQ=93;DP=479;ECNT=1;GERMQ=737,863;MBQ=32,32,33;MFRL=179,180,198;MMQ=60,60,60;MPOS=18,30;NALOD=1.06,1.07;NLOD=8.58,8.91;POPAF=5.60,5.60;RPA=10,9,11;RU=A;SAAF=0.071,0.061,0.076;SAPP=0.034,3.448e-03,0.963;STR;TLOD=27.58,10.41 GT:AD:AF:DP:F1R2:F2R1 0/0:29,0,0:0.029,0.028:29:7,0,0:22,0,0 0/1/2:30,4,0:0.108,0.025:34:9,2,0:21,2,0 0/1/2:6,1,0:0.190,0.092:7:2,1,0:4,0,0 0/1/2:53,5,2:0.085,0.034:60:26,2,1:27,3,1 0/1/2:39,2,2:0.063,0.049:43:17,1,0:22,1,2 0/1/2:75,9,4:0.109,0.053:88:34,3,2:41,6,2 0/1/2:40,2,2:0.061,0.061:44:20,1,1:20,1,1 0/1/2:87,4,4:0.042,0.049:95:42,1,1:45,3,3 1 8601191 . TAC T . str_contraction CONTQ=93;DP=241;ECNT=1;GERMQ=371;MBQ=33,33;MFRL=191,183;MMQ=60,60;MPOS=10;NALOD=1.08;NLOD=6.31;POPAF=5.60;RPA=7,6;RU=AC;SAAF=0.061,0.071,0.076;SAPP=4.226e-03,0.068,0.927;STR;TLOD=26.71 GT:AD:AF:DP:F1R2:F2R1 0/0:21,0:0.041:21:9,0:12,0 0/1:24,2:0.104:26:12,0:12,2 0/1:1,0:0.333:1:1,0:0,0 0/1:18,0:0.044:18:4,0:14,0 0/1:18,4:0.204:22:7,2:11,2 0/1:39,3:0.090:42:18,2:21,1 0/1:29,2:0.089:31:14,1:15,1 0/1:29,2:0.089:31:13,1:16,1 1 8716283 . TTC T,TTCTC . artifact_in_normal;multiallelic;str_contraction CONTQ=93;DP=1232;ECNT=1;GERMQ=2501,2684;MBQ=31,31,30;MFRL=176,198,170;MMQ=60,60,37;MPOS=20,11;NALOD=-2.525e+00,1.60;NLOD=24.21,29.99;POPAF=5.60,5.60;RPA=6,5,7;RU=TC;SAAF=0.020,0.010,0.018;SAPP=3.091e-03,2.793e-03,0.994;STR;TLOD=25.90,10.25 GT:AD:AF:DP:F1R2:F2R1 0/0:98,2,0:0.026,8.531e-03:100:39,1,0:59,1,0 0/1/2:195,6,2:0.032,0.014:203:82,4,1:113,2,1 0/1/2:28,1,0:0.056,0.029:29:10,0,0:18,1,0 0/1/2:88,1,0:0.020,9.901e-03:89:41,1,0:47,0,0 0/1/2:117,3,0:0.031,7.307e-03:120:43,2,0:74,1,0 0/1/2:127,2,3:0.021,0.029:132:52,1,0:75,1,3 0/1/2:92,0,0:8.747e-03,9.137e-03:92:40,0,0:52,0,0 0/1/2:205,3,3:0.018,0.018:211:93,2,2:112,1,1 1 8934790 . A AT . str_contraction CONTQ=93;DP=261;ECNT=1;GERMQ=456;MBQ=32,33;MFRL=271,280;MMQ=60,60;MPOS=19;NALOD=0.880;NLOD=3.61;POPAF=5.60;RPA=10,11;RU=T;SAAF=0.051,0.071,0.068;SAPP=6.301e-03,0.021,0.973;STR;TLOD=17.36 GT:AD:AF:DP:F1R2:F2R1 0/0:12,0:0.066:12:8,0:4,0 0/1:29,2:0.089:31:20,1:9,1 0/1:2,1:0.392:3:2,1:0,0 0/1:20,1:0.084:21:13,1:7,0 0/1:21,2:0.119:23:12,1:9,1 0/1:61,3:0.059:64:29,1:32,2 0/1:31,3:0.109:34:13,3:18,0 0/1:42,3:0.083:45:24,0:18,3 1 9006103 . T TTC . PASS CONTQ=93;DP=420;ECNT=2;GERMQ=795;MBQ=31,32;MFRL=195,185;MMQ=60,60;MPOS=17;NALOD=0.644;NLOD=2.44;POPAF=5.60;SAAF=0.040,0.00,0.041;SAPP=8.624e-03,8.208e-03,0.983;TLOD=10.67 GT:AD:AF:DP:F1R2:F2R1 0/0:8,0:0.083:8:1,0:7,0 0/1:23,1:0.071:24:6,0:17,1 0/1:10,0:0.075:10:5,0:5,0 0/1:47,2:0.055:49:21,0:26,2 0/1:50,1:0.036:51:23,1:27,0 0/1:74,4:0.060:78:33,1:41,3 0/1:56,2:0.047:58:16,0:40,2 0/1:69,4:0.065:73:22,1:47,3 1 9006105 . T C . PASS CONTQ=93;DP=413;ECNT=2;GERMQ=722;MBQ=31,33;MFRL=192,215;MMQ=60,60;MPOS=19;NALOD=1.08;NLOD=2.71;POPAF=5.60;SAAF=0.061,0.051,0.063;SAPP=0.041,3.773e-03,0.955;TLOD=21.65 GT:AD:AF:DP:F1R2:F2R1 0/0:9,0:0.079:9:1,0:8,0 0/1:23,0:0.036:23:5,0:18,0 0/1:11,1:0.139:12:5,0:6,1 0/1:45,6:0.130:51:18,4:27,2 0/1:50,1:0.036:51:24,0:26,1 0/1:81,2:0.034:83:34,2:47,0 0/1:49,9:0.152:58:15,1:34,8 0/1:71,3:0.051:74:22,1:49,2 1 9307011 . TC T,TCC . artifact_in_normal;multiallelic;str_contraction CONTQ=93;DP=1895;ECNT=1;GERMQ=3233,3233;MBQ=30,30,30;MFRL=171,172,166;MMQ=60,60,60;MPOS=20,19;NALOD=-4.452e-03,0.278;NLOD=46.98,46.47;POPAF=3.12,3.22;RPA=8,7,9;RU=C;SAAF=0.010,0.020,0.017;SAPP=9.517e-04,2.270e-03,0.997;STR;TLOD=18.77,5.82 GT:AD:AF:DP:F1R2:F2R1 0/0:170,2,2:0.016,0.016:174:75,2,0:95,0,2 0/1/2:242,6,5:0.025,0.022:253:133,5,3:109,1,2 0/1/2:92,3,0:0.037,9.458e-03:95:51,1,0:41,2,0 0/1/2:187,3,1:0.019,9.260e-03:191:95,1,0:92,2,1 0/1/2:169,2,0:0.016,5.442e-03:171:83,0,0:86,2,0 0/1/2:182,2,5:0.014,0.030:189:87,1,1:95,1,4 0/1/2:263,3,1:0.014,6.494e-03:267:125,1,0:138,2,1 0/1/2:277,5,3:0.020,0.013:285:147,2,0:130,3,3 1 9633387 . GTT G,GT,GTTT,GTTTT . artifact_in_normal;multiallelic;panel_of_normals CONTQ=93;DP=397;ECNT=1;GERMQ=607,246,224,554;MBQ=33,32,33,34,33;MFRL=175,143,176,166,164;MMQ=60,60,60,60,60;MPOS=5,17,16,17;NALOD=0.664,-4.862e+00,-6.341e+00,-1.112e+00;NLOD=5.39,-2.254e+00,-5.439e+00,1.43;PON;POPAF=5.60,5.60,5.60,5.60;RPA=12,10,11,13,14;RU=T;SAAF=0.111,0.162,0.163;SAPP=0.032,5.731e-03,0.962;STR;TLOD=5.04,64.76,54.96,3.63 GT:AD:AF:DP:F1R2:F2R1 0/0:13,0,3,4,1:0.037,0.153,0.191,0.076:21:10,0,3,4,1:3,0,0,0,0 0/1/2/3/4:12,1,4,8,2:0.057,0.156,0.283,0.093:27:10,1,3,8,2:2,0,1,0,0 0/1/2/3/4:4,0,0,0,0:0.100,0.109,0.109,0.109:4:4,0,0,0,0:0,0,0,0,0 0/1/2/3/4:22,0,3,0,0:0.029,0.127,0.031,0.031:25:16,0,2,0,0:6,0,1,0,0 0/1/2/3/4:39,0,5,3,1:0.018,0.112,0.074,0.037:48:21,0,1,1,0:18,0,4,2,1 0/1/2/3/4:65,4,14,14,3:0.045,0.139,0.145,0.033:100:36,2,8,8,1:29,2,6,6,2 0/1/2/3/4:29,0,6,7,0:0.020,0.145,0.162,0.020:42:14,0,4,4,0:15,0,2,3,0 0/1/2/3/4:45,0,10,8,0:0.014,0.156,0.131,0.014:63:25,0,8,3,0:20,0,2,5,0 1 9633514 . A AT . str_contraction CONTQ=93;DP=422;ECNT=1;GERMQ=814;MBQ=32,31;MFRL=170,193;MMQ=60,60;MPOS=20;NALOD=1.45;NLOD=7.52;POPAF=5.60;RPA=9,10;RU=T;SAAF=0.040,0.020,0.037;SAPP=0.019,5.914e-03,0.975;STR;TLOD=9.26 GT:AD:AF:DP:F1R2:F2R1 0/0:25,0:0.034:25:17,0:8,0 0/1:43,2:0.061:45:29,1:14,1 0/1:2,0:0.236:2:1,0:1,0 0/1:16,2:0.147:18:7,0:9,2 0/1:52,0:0.017:52:23,0:29,0 0/1:94,7:0.076:101:54,4:40,3 0/1:30,1:0.034:31:18,1:12,0 0/1:73,0:0.012:73:45,0:28,0 1 9770690 . CAGAGAG C,CAG,CAGAG,CAGAGAGAG,CAGAGAGAGAG . artifact_in_normal;germline_risk;multiallelic;panel_of_normals CONTQ=93;DP=1958;ECNT=2;GERMQ=1595,1228,482,0,1034;MBQ=34,33,33,33,34,33;MFRL=185,242,195,179,175,184;MMQ=60,60,60,60,60,60;MPOS=23,24,26,27,27;NALOD=-1.081e+00,-9.493e-01,-1.219e+01,-8.793e+01,-7.113e+00;NLOD=26.28,23.15,5.58,-9.983e+01,-1.217e+01;PON;POPAF=5.60,5.60,5.60,5.60,5.60;RPA=11,8,9,10,12,13;RU=AG;SAAF=0.313,0.283,0.314;SAPP=5.918e-03,0.023,0.971;STR;TLOD=21.77,96.04,349.87,601.40,53.00 GT:AD:AF:DP:F1R2:F2R1 0/0:49,1,1,6,33,4:0.015,0.016,0.064,0.364,0.051:94:21,1,0,1,11,1:28,0,1,5,22,3 0/1/2/3/4/5:97,2,8,31,74,6:0.011,0.035,0.139,0.347,0.031:218:46,1,1,12,33,4:51,1,7,19,41,2 0/1/2/3/4/5:33,0,1,12,10,0:0.013,0.029,0.212,0.177,0.014:56:13,0,0,2,5,0:20,0,1,10,5,0 0/1/2/3/4/5:74,0,5,19,2,1:6.805e-03,0.050,0.186,0.032,0.020:101:27,0,3,9,2,0:47,0,2,10,0,1 0/1/2/3/4/5:62,2,7,17,40,5:0.016,0.048,0.122,0.327,0.045:133:25,2,4,8,24,4:37,0,3,9,16,1 0/1/2/3/4/5:90,8,13,36,52,15:0.034,0.054,0.165,0.253,0.075:214:44,3,4,16,31,9:46,5,9,20,21,6 0/1/2/3/4/5:85,1,7,20,3,0:0.012,0.058,0.161,0.032,6.662e-03:116:40,0,5,9,1,0:45,1,2,11,2,0 0/1/2/3/4/5:87,1,5,14,61,2:8.061e-03,0.028,0.078,0.379,0.016:170:37,0,1,5,29,2:50,1,4,9,32,0 1 9770720 . TAGAC T . str_contraction CONTQ=93;DP=1573;ECNT=2;GERMQ=2548;MBQ=32,32;MFRL=187,264;MMQ=60,60;MPOS=22;NALOD=2.04;NLOD=26.23;POPAF=5.60;RPA=5,4;RU=AGAC;SAAF=0.020,0.010,0.016;SAPP=6.110e-03,1.834e-03,0.992;STR;TLOD=27.27 GT:AD:AF:DP:F1R2:F2R1 0/0:88,0:9.360e-03:88:42,0:46,0 0/1:154,4:0.030:158:60,3:94,1 0/1:45,0:0.018:45:24,0:21,0 0/1:108,1:0.017:109:47,1:61,0 0/1:104,5:0.047:109:40,2:64,3 0/1:132,2:0.021:134:69,2:63,0 0/1:145,1:0.013:146:61,1:84,0 0/1:163,1:0.011:164:75,1:88,0 1 9770835 . GGTTT G . artifact_in_normal;str_contraction CONTQ=93;DP=542;ECNT=1;GERMQ=902;MBQ=31,32;MFRL=329,371;MMQ=60,60;MPOS=22;NALOD=-1.400e+00;NLOD=5.03;POPAF=5.60;RPA=6,5;RU=GTTT;SAAF=0.020,0.020,0.028;SAPP=0.015,1.681e-03,0.983;STR;TLOD=22.47 GT:AD:AF:DP:F1R2:F2R1 0/0:31,1:0.055:32:9,1:22,0 0/1:66,3:0.055:69:37,2:29,1 0/1:22,1:0.077:23:12,1:10,0 0/1:37,2:0.070:39:18,1:19,1 0/1:39,1:0.046:40:16,1:23,0 0/1:51,0:0.017:51:33,0:18,0 0/1:76,3:0.048:79:36,0:40,3 0/1:50,0:0.017:50:31,0:19,0 1 9790639 . CCCT C . artifact_in_normal;str_contraction CONTQ=93;DP=1464;ECNT=2;GERMQ=3233;MBQ=31,31;MFRL=174,179;MMQ=60,60;MPOS=25;NALOD=-4.433e+00;NLOD=29.20;POPAF=5.39;RPA=4,3;RU=CCT;SAAF=0.010,0.010,0.012;SAPP=6.854e-04,3.954e-03,0.995;STR;TLOD=24.64 GT:AD:AF:DP:F1R2:F2R1 0/0:135,3:0.028:138:42,1:93,2 0/1:191,2:0.015:193:93,2:98,0 0/1:104,0:9.220e-03:104:39,0:65,0 0/1:152,3:0.025:155:78,1:74,2 0/1:123,1:0.015:124:60,1:63,0 0/1:155,3:0.024:158:63,1:92,2 0/1:151,2:0.019:153:59,2:92,0 0/1:200,2:0.014:202:92,1:108,1 1 9790725 . TTCC T . artifact_in_normal;str_contraction CONTQ=93;DP=1239;ECNT=2;GERMQ=2560;MBQ=31,32;MFRL=181,208;MMQ=60,60;MPOS=25;NALOD=-8.464e-01;NLOD=26.98;POPAF=4.29;RPA=4,3;RU=TCC;SAAF=0.020,0.010,0.016;SAPP=2.906e-03,1.805e-03,0.995;STR;TLOD=25.38 GT:AD:AF:DP:F1R2:F2R1 0/0:104,1:0.017:105:25,1:79,0 0/1:144,2:0.020:146:66,0:78,2 0/1:75,1:0.025:76:29,1:46,0 0/1:127,3:0.030:130:54,2:73,1 0/1:114,0:8.003e-03:114:56,0:58,0 0/1:99,3:0.037:102:44,1:55,2 0/1:134,2:0.014:136:51,1:83,1 0/1:164,3:0.023:167:69,1:95,2 1 9833181 . G GA . read_position;str_contraction CONTQ=93;DP=502;ECNT=1;GERMQ=1003;MBQ=31,30;MFRL=257,298;MMQ=60,60;MPOS=4;NALOD=1.40;NLOD=6.91;POPAF=5.60;RPA=9,10;RU=A;SAAF=0.00,0.051,0.048;SAPP=8.233e-03,0.013,0.979;STR;TLOD=21.97 GT:AD:AF:DP:F1R2:F2R1 0/0:23,0:0.039:23:10,0:13,0 0/1:66,1:0.028:67:37,0:29,1 0/1:12,0:0.068:12:7,0:5,0 0/1:56,1:0.032:57:25,0:31,1 0/1:63,0:0.015:63:27,0:36,0 0/1:84,10:0.114:94:42,6:42,4 0/1:72,7:0.097:79:35,4:37,3 0/1:60,2:0.045:62:27,2:33,0 1 10032031 . GA G . str_contraction CONTQ=93;DP=204;ECNT=1;GERMQ=448;MBQ=31,31;MFRL=301,300;MMQ=60,60;MPOS=19;NALOD=1.08;NLOD=5.96;POPAF=5.60;RPA=9,8;RU=A;SAAF=0.00,0.040,0.036;SAPP=7.555e-03,9.133e-03,0.983;STR;TLOD=5.42 GT:AD:AF:DP:F1R2:F2R1 0/0:20,0:0.042:20:8,0:12,0 0/1:28,1:0.063:29:11,1:17,0 0/1:8,0:0.100:8:1,0:7,0 0/1:17,0:0.053:17:9,0:8,0 0/1:13,1:0.125:14:5,1:8,0 0/1:35,3:0.099:38:16,2:19,1 0/1:30,1:0.059:31:16,0:14,1 0/1:32,0:0.029:32:15,0:17,0 1 10057233 . A C . artifact_in_normal;base_quality CONTQ=93;DP=293;ECNT=1;GERMQ=352;MBQ=26,10;MFRL=205,202;MMQ=60,60;MPOS=6;NALOD=-9.676e-01;NLOD=6.22;POPAF=5.60;SAAF=0.020,0.131,0.135;SAPP=0.921,1.843e-04,0.078;TLOD=8.41 GT:AD:AF:DP:F1R2:F2R1 0/0:42,4:0.079:46:16,1:26,3 0/1:37,7:0.131:44:23,2:14,5 0/1:58,2:0.020:60:34,2:24,0 0/1:21,4:0.156:25:11,3:10,1 0/1:10,2:0.190:12:3,0:7,2 0/1:23,3:0.104:26:2,2:21,1 0/1:28,8:0.182:36:13,4:15,4 0/1:22,5:0.147:27:10,2:12,3 1 10067013 . CT C,CTT . multiallelic;str_contraction CONTQ=93;DP=691;ECNT=1;GERMQ=1330,1311;MBQ=33,33,33;MFRL=171,181,162;MMQ=60,60,60;MPOS=23,20;NALOD=1.15,1.13;NLOD=6.90,6.32;POPAF=5.60,5.60;RPA=9,8,10;RU=T;SAAF=0.030,0.020,0.029;SAPP=1.695e-03,6.234e-03,0.992;STR;TLOD=11.19,11.31 GT:AD:AF:DP:F1R2:F2R1 0/0:21,0,0:0.035,0.037:21:10,0,0:11,0,0 0/1/2:100,2,2:0.026,0.026:104:61,2,2:39,0,0 0/1/2:24,1,0:0.070,0.034:25:13,0,0:11,1,0 0/1/2:32,2,0:0.072,0.023:34:13,1,0:19,1,0 0/1/2:64,2,1:0.029,0.026:67:34,1,0:30,1,1 0/1/2:152,2,6:0.017,0.040:160:64,1,3:88,1,3 0/1/2:40,2,1:0.061,0.040:43:17,1,0:23,1,1 0/1/2:88,3,5:0.039,0.059:96:46,2,3:42,1,2 1 10132437 . CT C,CTT . artifact_in_normal;multiallelic;str_contraction CONTQ=93;DP=329;ECNT=2;GERMQ=468,587;MBQ=33,33,33;MFRL=309,287,311;MMQ=60,60,60;MPOS=22,27;NALOD=-1.033e+00,0.830;NLOD=0.138,2.97;POPAF=5.60,5.60;RPA=10,9,11;RU=T;SAAF=0.071,0.061,0.080;SAPP=3.034e-03,0.020,0.977;STR;TLOD=24.16,10.18 GT:AD:AF:DP:F1R2:F2R1 0/0:9,1,0:0.148,0.070:10:4,0,0:5,1,0 0/1/2:24,2,0:0.101,0.033:26:15,1,0:9,1,0 0/1/2:1,1,0:0.410,0.181:2:1,0,0:0,1,0 0/1/2:39,4,4:0.098,0.098:47:21,2,4:18,2,0 0/1/2:25,2,2:0.092,0.092:29:14,1,0:11,1,2 0/1/2:59,6,2:0.084,0.041:67:33,3,1:26,3,1 0/1/2:51,4,2:0.080,0.048:57:29,1,1:22,3,1 0/1/2:43,2,1:0.059,0.039:46:22,1,1:21,1,0 1 10132493 . CTT C,CT,CTTT . multiallelic;panel_of_normals CONTQ=93;DP=442;ECNT=2;GERMQ=809,502,504;MBQ=33,33,33,33;MFRL=180,150,185,170;MMQ=60,60,60,60;MPOS=14,20,17;NALOD=0.827,0.827,-6.978e-01;NLOD=4.80,4.76,1.83;PON;POPAF=5.60,5.60,5.60;RPA=11,9,10,12;RU=T;SAAF=0.111,0.111,0.123;SAPP=3.074e-03,0.045,0.952;STR;TLOD=6.31,58.57,43.74 GT:AD:AF:DP:F1R2:F2R1 0/0:14,0,0,1:0.048,0.048,0.102:15:11,0,0,1:3,0,0,0 0/1/2/3:37,1,5,7:0.037,0.112,0.139:50:29,0,5,4:8,1,0,3 0/1/2/3:2,0,0,0:0.143,0.143,0.169:2:0,0,0,0:2,0,0,0 0/1/2/3:31,0,4,2:0.023,0.120,0.071:37:13,0,3,2:18,0,1,0 0/1/2/3:35,0,9,2:0.019,0.198,0.058:46:17,0,1,0:18,0,8,2 0/1/2/3:81,2,11,15:0.024,0.101,0.141:109:46,1,3,7:35,1,8,8 0/1/2/3:50,2,5,3:0.044,0.089,0.061:60:35,1,2,2:15,1,3,1 0/1/2/3:56,1,7,7:0.025,0.101,0.105:71:23,0,2,4:33,1,5,3 1 10167385 . AGGT A . str_contraction CONTQ=93;DP=747;ECNT=1;GERMQ=1565;MBQ=33,34;MFRL=177,190;MMQ=60,60;MPOS=17;NALOD=1.80;NLOD=17.41;POPAF=5.60;RPA=5,4;RU=GGT;SAAF=0.010,0.00,9.901e-03;SAPP=9.185e-03,1.941e-03,0.989;STR;TLOD=8.33 GT:AD:AF:DP:F1R2:F2R1 0/0:58,0:0.016:58:19,0:39,0 0/1:103,1:0.018:104:47,1:56,0 0/1:5,0:0.128:5:3,0:2,0 0/1:53,1:0.034:54:26,0:27,1 0/1:51,1:0.035:52:26,0:25,1 0/1:101,0:8.698e-03:101:51,0:50,0 0/1:78,0:0.011:78:32,0:46,0 0/1:109,2:0.026:111:56,2:53,0 1 10177680 . TAA T,TA,TAAA . artifact_in_normal;multiallelic CONTQ=93;DP=315;ECNT=1;GERMQ=501,171,254;MBQ=32,32,32,31;MFRL=196,338,198,189;MMQ=60,60,60,60;MPOS=18,24,18;NALOD=0.932,-2.522e+00,-4.205e+00;NLOD=5.11,1.582e-03,-2.558e+00;POPAF=5.60,5.60,5.60;RPA=12,10,11,13;RU=A;SAAF=0.202,0.162,0.204;SAPP=0.022,0.023,0.956;STR;TLOD=3.45,71.16,27.39 GT:AD:AF:DP:F1R2:F2R1 0/0:13,0,2,3:0.038,0.127,0.179:18:2,0,1,1:11,0,1,2 0/1/2/3:26,0,7,6:0.021,0.176,0.164:39:8,0,2,3:18,0,5,3 0/1/2/3:2,0,0,0:0.139,0.161,0.161:2:0,0,0,0:2,0,0,0 0/1/2/3:22,0,5,3:0.026,0.170,0.116:30:12,0,1,1:10,0,4,2 0/1/2/3:18,1,7,0:0.064,0.267,0.032:26:10,1,4,0:8,0,3,0 0/1/2/3:44,1,17,3:0.028,0.253,0.057:65:27,1,7,2:17,0,10,1 0/1/2/3:30,1,4,2:0.044,0.112,0.071:37:11,0,1,1:19,1,3,1 0/1/2/3:34,1,5,9:0.037,0.112,0.182:49:17,1,3,6:17,0,2,3 1 10186836 . G GT . str_contraction;t_lod CONTQ=93;DP=875;ECNT=1;GERMQ=2149;MBQ=34,34;MFRL=171,174;MMQ=60,60;MPOS=20;NALOD=1.64;NLOD=12.33;POPAF=5.60;RPA=8,9;RU=T;SAAF=0.00,0.010,0.013;SAPP=4.793e-03,1.743e-03,0.993;STR;TLOD=4.36 GT:AD:AF:DP:F1R2:F2R1 0/0:41,0:0.023:41:19,0:22,0 0/1:128,4:0.036:132:74,3:54,1 0/1:12,0:0.071:12:7,0:5,0 0/1:88,1:0.021:89:44,0:44,1 0/1:77,1:0.024:78:37,1:40,0 0/1:158,3:0.023:161:96,1:62,2 0/1:125,1:0.015:126:75,0:50,1 0/1:154,0:6.061e-03:154:81,0:73,0 1 10292359 . CAT C,CATAT . artifact_in_normal;multiallelic;str_contraction CONTQ=93;DP=1112;ECNT=1;GERMQ=1825,2213;MBQ=33,33,33;MFRL=175,176,177;MMQ=60,60,60;MPOS=20,20;NALOD=-5.109e+00,-3.112e-01;NLOD=13.15,18.82;POPAF=2.98,2.44;RPA=6,5,7;RU=AT;SAAF=0.040,0.051,0.050;SAPP=4.142e-03,2.513e-03,0.993;STR;TLOD=84.87,16.57 GT:AD:AF:DP:F1R2:F2R1 0/0:72,3,1:0.046,0.024:76:37,1,0:35,2,1 0/1/2:130,3,4:0.027,0.035:137:62,2,2:68,1,2 0/1/2:20,0,0:0.039,0.040:20:7,0,0:13,0,0 0/1/2:88,5,1:0.059,0.019:94:46,4,1:42,1,0 0/1/2:81,4,1:0.055,0.021:86:41,3,0:40,1,1 0/1/2:151,8,4:0.052,0.029:163:68,4,3:83,4,1 0/1/2:122,9,0:0.073,6.838e-03:131:49,3,0:73,6,0 0/1/2:171,11,2:0.064,0.015:184:90,6,0:81,5,2 1 10318734 . AAAAAC A . str_contraction CONTQ=93;DP=1625;ECNT=1;GERMQ=3233;MBQ=30,31;MFRL=176,182;MMQ=60,29;MPOS=33;NALOD=2.08;NLOD=31.96;POPAF=5.09;RPA=3,2;RU=AAAAC;SAAF=0.010,0.010,5.766e-03;SAPP=4.252e-03,4.247e-04,0.995;STR;TLOD=10.53 GT:AD:AF:DP:F1R2:F2R1 0/0:107,0:8.281e-03:107:40,0:67,0 0/1:202,1:9.373e-03:203:106,0:96,1 0/1:10,0:0.075:10:6,0:4,0 0/1:167,0:5.565e-03:167:81,0:86,0 0/1:123,1:0.015:124:62,0:61,1 0/1:211,4:0.023:215:106,2:105,2 0/1:233,0:3.984e-03:233:105,0:128,0 0/1:261,1:7.240e-03:262:131,1:130,0 1 10336241 . CA C,CAA . artifact_in_normal;multiallelic;str_contraction CONTQ=93;DP=425;ECNT=1;GERMQ=650,735;MBQ=33,33,33;MFRL=322,324,253;MMQ=60,60,60;MPOS=19,11;NALOD=-8.857e-01,0.901;NLOD=0.733,3.57;POPAF=5.60,5.60;RPA=10,9,11;RU=A;SAAF=0.051,0.061,0.066;SAPP=4.131e-03,0.034,0.962;STR;TLOD=25.45,14.80 GT:AD:AF:DP:F1R2:F2R1 0/0:11,1,0:0.128,0.060:12:6,1,0:5,0,0 0/1/2:50,7,2:0.121,0.046:59:21,4,1:29,3,1 0/1/2:7,1,0:0.180,0.088:8:6,1,0:1,0,0 0/1/2:54,3,2:0.058,0.047:59:26,2,2:28,1,0 0/1/2:44,1,1:0.039,0.039:46:29,0,0:15,1,1 0/1/2:43,4,7:0.082,0.133:54:26,4,2:17,0,5 0/1/2:57,2,2:0.043,0.045:61:23,1,1:34,1,1 0/1/2:56,4,2:0.073,0.044:62:26,1,0:30,3,2 1 10357206 . ATTTT A,AT,ATT,ATTT,ATTTTT,ATTTTTT . artifact_in_normal;germline_risk;mapping_quality;multiallelic;panel_of_normals CONTQ=93;DP=1605;ECNT=1;GERMQ=1590,1204,582,0,575,1312;MBQ=32,31,31,31,31,32,32;MFRL=176,157,166,175,172,176,181;MMQ=60,29,60,60,60,60,60;MPOS=16,22,18,21,20,21;NALOD=1.04,1.03,-7.996e+00,-1.247e+01,-5.708e+00,0.989;NLOD=19.94,14.21,-2.543e+00,-1.102e+01,3.75,15.99;PON;POPAF=5.60,5.60,5.60,5.60,5.60,5.60;RPA=17,13,14,15,16,18,19;RU=T;SAAF=0.313,0.333,0.337;SAPP=0.043,3.241e-03,0.954;STR;TLOD=20.91,80.87,175.14,439.22,140.27,30.85 GT:AD:AF:DP:F1R2:F2R1 0/0:39,0,0,6,10,7,0:0.010,0.011,0.092,0.152,0.109,0.012:62:17,0,0,2,5,5,0:22,0,0,4,5,2,0 0/1/2/3/4/5/6:81,1,8,16,46,20,10:9.903e-03,0.047,0.085,0.245,0.114,0.058:182:55,0,6,6,28,9,1:26,1,2,10,18,11,9 0/1/2/3/4/5/6:7,1,0,2,5,0,1:0.089,0.043,0.135,0.271,0.043,0.052:16:4,0,0,2,5,0,1:3,1,0,0,0,0,0 0/1/2/3/4/5/6:65,1,3,9,27,4,2:0.016,0.032,0.081,0.233,0.044,0.027:111:36,0,1,5,13,2,1:29,1,2,4,14,2,1 0/1/2/3/4/5/6:78,4,8,16,33,24,7:0.026,0.050,0.097,0.191,0.138,0.044:170:37,1,4,10,17,12,1:41,3,4,6,16,12,6 0/1/2/3/4/5/6:90,9,20,32,58,21,7:0.031,0.082,0.129,0.238,0.100,0.029:237:46,4,8,18,33,13,1:44,5,12,14,25,8,6 0/1/2/3/4/5/6:93,2,6,13,42,21,3:0.015,0.036,0.072,0.227,0.115,0.020:180:50,2,4,8,22,10,2:43,0,2,5,20,11,1 0/1/2/3/4/5/6:163,2,7,34,82,47,12:7.120e-03,0.023,0.098,0.234,0.130,0.034:347:83,0,4,15,47,21,9:80,2,3,19,35,26,3 1 10384711 . CTT C,CT,CTTT,CTTTT . artifact_in_normal;multiallelic CONTQ=93;DP=698;ECNT=1;GERMQ=418,196,184,706;MBQ=31,30,30,30,31;MFRL=205,193,210,221,207;MMQ=60,60,60,60,60;MPOS=5,13,17,21;NALOD=0.793,-6.209e-01,-2.288e+00,0.780;NLOD=5.41,2.97,0.097,4.75;POPAF=5.60,5.60,5.60,5.60;RPA=13,11,12,14,15;RU=T;SAAF=0.222,0.263,0.265;SAPP=0.040,0.015,0.945;STR;TLOD=92.74,169.00,160.72,13.32 GT:AD:AF:DP:F1R2:F2R1 0/0:15,0,1,2,0:0.039,0.080,0.129,0.040:18:12,0,1,2,0:3,0,0,0,0 0/1/2/3/4:44,5,8,12,2:0.077,0.112,0.167,0.034:71:39,4,5,9,2:5,1,3,3,0 0/1/2/3/4:7,3,2,3,1:0.191,0.142,0.192,0.095:16:7,3,2,3,1:0,0,0,0,0 0/1/2/3/4:58,7,19,10,6:0.065,0.185,0.108,0.064:100:32,6,5,3,3:26,1,14,7,3 0/1/2/3/4:38,5,13,11,2:0.081,0.189,0.157,0.040:69:19,2,8,3,1:19,3,5,8,1 0/1/2/3/4:64,25,30,30,3:0.160,0.200,0.200,0.023:152:29,11,15,14,0:35,14,15,16,3 0/1/2/3/4:51,10,17,20,1:0.096,0.173,0.201,0.018:99:26,7,9,10,0:25,3,8,10,1 0/1/2/3/4:46,4,22,19,3:0.046,0.235,0.205,0.035:94:25,2,8,9,1:21,2,14,10,2 1 10385044 . GA G,GAA . multiallelic;str_contraction CONTQ=93;DP=710;ECNT=1;GERMQ=1397,1524;MBQ=33,33,32;MFRL=225,334,330;MMQ=60,60,60;MPOS=12,14;NALOD=7.450e-03,1.35;NLOD=8.19,10.73;POPAF=5.60,5.60;RPA=9,8,10;RU=A;SAAF=0.030,0.020,0.034;SAPP=0.015,5.511e-03,0.979;STR;TLOD=17.51,6.60 GT:AD:AF:DP:F1R2:F2R1 0/0:35,1,0:0.047,0.022:36:15,0,0:20,1,0 0/1/2:77,3,2:0.044,0.034:82:35,1,0:42,2,2 0/1/2:16,0,0:0.049,0.051:16:7,0,0:9,0,0 0/1/2:104,3,6:0.025,0.059:113:42,1,3:62,2,3 0/1/2:64,1,0:0.027,0.014:65:20,0,0:44,1,0 0/1/2:96,5,3:0.055,0.036:104:54,3,1:42,2,2 0/1/2:95,4,0:0.047,9.085e-03:99:41,2,0:54,2,0 0/1/2:88,3,0:0.041,0.010:91:45,3,0:43,0,0 1 10396696 . A AT . str_contraction CONTQ=93;DP=1165;ECNT=1;GERMQ=2345;MBQ=31,31;MFRL=172,166;MMQ=60,60;MPOS=14;NALOD=1.74;NLOD=29.78;POPAF=4.78;RPA=9,10;RU=T;SAAF=0.020,0.030,0.030;SAPP=4.770e-03,1.699e-03,0.994;STR;TLOD=20.15 GT:AD:AF:DP:F1R2:F2R1 0/0:99,0:9.210e-03:99:36,0:63,0 0/1:147,3:0.024:150:78,2:69,1 0/1:14,1:0.113:15:10,1:4,0 0/1:100,2:0.027:102:35,1:65,1 0/1:119,3:0.028:122:55,2:64,1 0/1:143,6:0.040:149:69,4:74,2 0/1:127,4:0.036:131:59,3:68,1 0/1:177,7:0.041:184:81,2:96,5 1 10399812 . A AT . clustered_events;panel_of_normals;str_contraction;t_lod CONTQ=93;DP=1568;ECNT=3;GERMQ=3233;MBQ=32,30;MFRL=174,166;MMQ=60,70;MPOS=12;NALOD=1.69;NLOD=27.07;PON;POPAF=5.60;RPA=8,9;RU=T;SAAF=0.010,0.010,8.634e-03;SAPP=4.738e-03,5.635e-04,0.995;STR;TLOD=3.88 GT:AD:AF:DP:F1R2:F2R1 0/0:90,0:0.010:90:33,0:57,0 0/1:237,1:7.389e-03:238:129,1:108,0 0/1:32,0:0.029:32:13,0:19,0 0/1:148,0:6.065e-03:148:75,0:73,0 0/1:161,1:0.011:162:88,1:73,0 0/1:211,4:0.022:215:109,1:102,3 0/1:173,3:0.021:176:87,2:86,1 0/1:301,2:8.998e-03:303:138,1:163,1 1 10399821 . A T . artifact_in_normal;bad_haplotype;base_quality;clustered_events;mapping_quality;t_lod CONTQ=93;DP=1644;ECNT=3;GERMQ=3233;MBQ=32,11;MFRL=173,184;MMQ=60,29;MPOS=18;NALOD=-3.096e+00;NLOD=26.21;POPAF=5.60;SAAF=0.00,0.010,4.038e-03;SAPP=4.979e-03,3.135e-04,0.995;TLOD=3.73 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS 0|0:115,2:0.025:117:49,0:66,2:0|1:10399821_A_T:10399821 0|1:272,4:0.016:276:148,0:124,4:0|1:10399821_A_T:10399821 0|1:34,2:0.075:36:15,0:19,2:0|1:10399821_A_T:10399821 0|1:181,0:5.389e-03:181:85,0:96,0:0|1:10399821_A_T:10399821 0|1:186,0:5.259e-03:186:99,0:87,0:0|1:10399821_A_T:10399821 0|1:250,0:3.915e-03:250:125,0:125,0:0|1:10399821_A_T:10399821 0|1:209,0:4.673e-03:209:104,0:105,0:0|1:10399821_A_T:10399821 0|1:348,0:2.833e-03:348:163,0:185,0:0|1:10399821_A_T:10399821 1 10399822 . TGAAGC T . artifact_in_normal;bad_haplotype;clustered_events;t_lod CONTQ=93;DP=1721;ECNT=3;GERMQ=3233;MBQ=33,29;MFRL=173,184;MMQ=60,29;MPOS=18;NALOD=-2.970e+00;NLOD=29.25;POPAF=5.60;SAAF=0.00,0.010,3.922e-03;SAPP=5.031e-03,3.003e-04,0.995;TLOD=3.66 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS 0|0:125,2:0.023:127:55,0:70,2:0|1:10399821_A_T:10399821 0|1:280,4:0.016:284:155,0:125,4:0|1:10399821_A_T:10399821 0|1:34,2:0.074:36:15,0:19,2:0|1:10399821_A_T:10399821 0|1:186,0:5.259e-03:186:87,0:99,0:0|1:10399821_A_T:10399821 0|1:193,0:5.083e-03:193:102,0:91,0:0|1:10399821_A_T:10399821 0|1:253,0:3.882e-03:253:127,0:126,0:0|1:10399821_A_T:10399821 0|1:222,0:4.364e-03:222:109,0:113,0:0|1:10399821_A_T:10399821 0|1:356,0:2.747e-03:356:163,0:193,0:0|1:10399821_A_T:10399821 1 10402009 . CAAAA C,CA,CAA,CAAA,CAAAAA,CAAAAAA . artifact_in_normal;germline_risk;multiallelic CONTQ=93;DP=532;ECNT=1;GERMQ=145,25,0,0,0,66;MBQ=33,34,32,33,33,33,31;MFRL=183,173,168,177,189,309,169;MMQ=60,60,60,60,60,60,60;MPOS=18,18,25,19,18,3;NALOD=0.370,0.354,-1.332e+00,-1.046e+01,0.304,0.185;NLOD=2.49,1.43,-2.756e+00,-1.074e+01,-1.291e-01,-8.779e-01;POPAF=5.60,5.60,5.60,5.60,5.60,5.60;RPA=17,13,14,15,16,18,19;RU=A;SAAF=0.657,0.687,0.691;SAPP=0.037,0.021,0.942;STR;TLOD=8.00,34.28,71.74,365.42,43.14,8.86 GT:AD:AF:DP:F1R2:F2R1 0/0:0,0,0,1,5,0,1:0.057,0.059,0.145,0.464,0.069,0.140:7:0,0,0,0,3,0,0:0,0,0,1,2,0,1 0/1/2/3/4/5/6:7,0,2,2,18,4,1:0.021,0.069,0.067,0.487,0.118,0.045:34:5,0,2,0,12,4,1:2,0,0,2,6,0,0 0/1/2/3/4/5/6:0,0,0,1,0,0,0:0.122,0.122,0.274,0.121,0.120,0.120:1:0,0,0,0,0,0,0:0,0,0,1,0,0,0 0/1/2/3/4/5/6:11,0,1,11,24,5,2:0.015,0.031,0.197,0.415,0.097,0.048:54:5,0,1,7,9,2,1:6,0,0,4,15,3,1 0/1/2/3/4/5/6:17,3,2,8,21,7,3:0.055,0.044,0.134,0.333,0.114,0.053:61:12,2,0,6,6,4,1:5,1,2,2,15,3,2 0/1/2/3/4/5/6:27,3,11,16,37,8,6:0.027,0.106,0.149,0.337,0.079,0.055:108:18,1,4,7,19,5,6:9,2,7,9,18,3,0 0/1/2/3/4/5/6:7,1,2,6,36,5,2:0.028,0.043,0.105,0.571,0.090,0.044:59:4,0,2,3,12,3,2:3,1,0,3,24,2,0 0/1/2/3/4/5/6:17,2,5,10,56,8,0:0.025,0.056,0.103,0.544,0.087,9.148e-03:98:9,1,3,6,31,4,0:8,1,2,4,25,4,0 1 10408837 . ATTT A,AT,ATT,ATTTT,ATTTTT,ATTTTTT . artifact_in_normal;germline_risk;mapping_quality;multiallelic;panel_of_normals CONTQ=93;DP=1389;ECNT=1;GERMQ=1287,921,343,0,399,1018;MBQ=33,32,33,33,33,32,32;MFRL=175,165,165,173,170,170,176;MMQ=60,29,60,60,60,60,29;MPOS=24,21,25,21,19,15;NALOD=-1.270e+00,1.14,-5.506e+00,-5.434e+01,-1.428e+00,-6.831e-01;NLOD=12.93,13.95,4.21,-6.477e+01,-1.479e+01,-4.148e+00;PON;POPAF=5.60,5.60,5.60,5.60,5.60,5.60;RPA=14,11,12,13,15,16,17;RU=T;SAAF=0.414,0.394,0.413;SAPP=0.018,0.012,0.970;STR;TLOD=9.61,58.37,188.87,529.95,98.13,13.48 GT:AD:AF:DP:F1R2:F2R1 0/0:13,1,0,4,28,2,2:0.028,0.013,0.077,0.527,0.059,0.045:50:3,0,0,1,9,0,0:10,1,0,3,19,2,2 0/1/2/3/4/5/6:45,0,1,10,56,17,2:5.882e-03,0.012,0.072,0.426,0.139,0.014:131:15,0,0,4,18,6,0:30,0,1,6,38,11,2 0/1/2/3/4/5/6:4,0,1,3,2,0,0:0.047,0.109,0.227,0.185,0.054,0.054:10:2,0,0,2,1,0,0:2,0,1,1,1,0,0 0/1/2/3/4/5/6:75,1,4,16,20,1,1:0.014,0.037,0.131,0.167,0.015,0.015:118:39,0,2,8,8,1,0:36,1,2,8,12,0,1 0/1/2/3/4/5/6:61,0,7,17,64,11,2:5.309e-03,0.044,0.101,0.390,0.075,0.018:162:30,0,3,5,22,6,0:31,0,4,12,42,5,2 0/1/2/3/4/5/6:72,3,13,29,67,18,4:0.017,0.062,0.137,0.321,0.092,0.023:206:33,1,8,15,22,6,3:39,2,5,14,45,12,1 0/1/2/3/4/5/6:82,1,9,23,17,5,2:0.013,0.065,0.157,0.126,0.041,0.020:139:34,1,1,13,7,1,2:48,0,8,10,10,4,0 0/1/2/3/4/5/6:101,3,7,28,84,23,4:0.014,0.029,0.109,0.334,0.093,0.019:250:39,3,2,14,37,9,1:62,0,5,14,47,14,3 1 10412666 . G GT . str_contraction;t_lod CONTQ=93;DP=1451;ECNT=1;GERMQ=3233;MBQ=33,33;MFRL=175,169;MMQ=60,60;MPOS=26;NALOD=0.621;NLOD=27.63;POPAF=5.60;RPA=8,9;RU=T;SAAF=0.010,0.010,8.793e-03;SAPP=5.459e-04,3.419e-03,0.996;STR;TLOD=3.20 GT:AD:AF:DP:F1R2:F2R1 0/0:101,1:0.018:102:36,1:65,0 0/1:213,0:4.504e-03:213:112,0:101,0 0/1:14,0:0.060:14:8,0:6,0 0/1:156,1:0.012:157:76,0:80,1 0/1:141,1:0.013:142:64,0:77,1 0/1:234,0:4.080e-03:234:120,0:114,0 0/1:182,3:0.020:185:91,1:91,2 0/1:300,6:0.021:306:151,3:149,3 1 10425063 . CAAA C,CA,CAA,CAAAA,CAAAAA,CAAAAAA,CAAAAAAA . artifact_in_normal;germline_risk;multiallelic CONTQ=93;DP=307;ECNT=1;GERMQ=96,68,58,0,0,0,25;MBQ=32,30,31,31,33,33,34,33;MFRL=245,320,300,197,186,217,313,274;MMQ=60,60,60,60,60,60,60,33;MPOS=30,8,0,28,28,25,18;NALOD=0.439,0.439,0.439,-4.592e+00,-3.165e+00,0.339,0.341;NLOD=3.23,3.23,3.05,-7.394e+00,-7.776e+00,-2.679e+00,-1.118e+00;POPAF=5.60,5.60,5.60,5.60,5.60,5.60,5.60;RPA=16,13,14,15,17,18,19,20;RU=A;SAAF=0.576,0.606,0.607;SAPP=0.020,0.033,0.947;STR;TLOD=6.30,11.28,9.12,91.48,113.20,27.10,6.24 GT:AD:AF:DP:F1R2:F2R1 0/0:3,0,0,0,3,2,0,0:0.050,0.050,0.050,0.247,0.227,0.064,0.064:8:2,0,0,0,1,0,0,0:1,0,0,0,2,2,0,0 0/1/2/3/4/5/6/7:6,1,0,3,4,6,3,0:0.055,0.029,0.115,0.172,0.245,0.136,0.031:23:4,1,0,3,1,2,3,0:2,0,0,0,3,4,0,0 0/1/2/3/4/5/6/7:4,1,0,0,2,3,2,0:0.094,0.045,0.045,0.152,0.205,0.151,0.047:12:2,1,0,0,0,1,1,0:2,0,0,0,2,2,1,0 0/1/2/3/4/5/6/7:6,0,0,2,8,16,5,0:0.020,0.020,0.066,0.203,0.389,0.133,0.021:37:3,0,0,2,7,10,4,0:3,0,0,0,1,6,1,0 0/1/2/3/4/5/6/7:6,0,1,0,6,8,3,1:0.028,0.056,0.028,0.215,0.278,0.120,0.059:25:3,0,0,0,2,6,2,1:3,0,1,0,4,2,1,0 0/1/2/3/4/5/6/7:19,1,5,3,23,15,1,2:0.025,0.076,0.050,0.310,0.217,0.024,0.040:69:11,1,2,3,14,10,1,1:8,0,3,0,9,5,0,1 0/1/2/3/4/5/6/7:4,0,1,0,6,12,9,4:0.021,0.043,0.021,0.163,0.311,0.228,0.101:36:2,0,1,0,6,7,4,2:2,0,0,0,0,5,5,2 0/1/2/3/4/5/6/7:3,2,1,1,13,14,3,1:0.059,0.039,0.040,0.305,0.343,0.087,0.043:38:1,1,0,0,4,8,2,1:2,1,1,1,9,6,1,0 1 10435441 . TTTG T . str_contraction CONTQ=93;DP=2050;ECNT=1;GERMQ=3233;MBQ=31,31;MFRL=175,174;MMQ=60,60;MPOS=23;NALOD=1.91;NLOD=40.66;POPAF=4.91;RPA=6,5;RU=TTG;SAAF=0.010,0.010,0.014;SAPP=6.409e-04,7.838e-03,0.992;STR;TLOD=35.03 GT:AD:AF:DP:F1R2:F2R1 0/0:136,0:6.298e-03:136:50,0:86,0 0/1:217,1:8.448e-03:218:90,0:127,1 0/1:32,1:0.054:33:18,0:14,1 0/1:186,3:0.020:189:102,1:84,2 0/1:167,2:0.017:169:75,1:92,1 0/1:163,5:0.035:168:67,3:96,2 0/1:230,2:0.012:232:95,1:135,1 0/1:292,4:0.016:296:128,0:164,4 1 10479055 . GTT G,GT,GTTT,GTTTT . artifact_in_normal;multiallelic CONTQ=93;DP=468;ECNT=1;GERMQ=635,407,156,500;MBQ=33,31,33,32,32;MFRL=186,168,191,187,186;MMQ=60,60,60,60,60;MPOS=22,23,18,19;NALOD=0.538,-2.846e+00,-3.134e+00,0.542;NLOD=2.39,-1.593e+00,-2.558e+00,2.11;POPAF=5.60,5.60,5.60,5.60;RPA=12,10,11,13,14;RU=T;SAAF=0.242,0.202,0.239;SAPP=0.013,0.025,0.963;STR;TLOD=4.20,31.42,119.66,17.19 GT:AD:AF:DP:F1R2:F2R1 0/0:7,0,1,2,0:0.059,0.130,0.198,0.058:10:4,0,1,2,0:3,0,0,0,0 0/1/2/3/4:13,1,2,5,2:0.061,0.104,0.215,0.103:23:8,0,2,2,0:5,1,0,3,2 0/1/2/3/4:4,0,2,3,0:0.065,0.200,0.295,0.070:9:3,0,2,1,0:1,0,0,2,0 0/1/2/3/4:27,0,6,10,2:0.019,0.139,0.227,0.051:45:11,0,3,3,1:16,0,3,7,1 0/1/2/3/4:36,0,3,7,2:0.020,0.089,0.147,0.054:48:16,0,3,5,0:20,0,0,2,2 0/1/2/3/4:74,4,5,24,5:0.039,0.050,0.222,0.044:112:33,3,2,10,3:41,1,3,14,2 0/1/2/3/4:36,0,3,10,2:0.016,0.070,0.196,0.052:51:19,0,2,4,1:17,0,1,6,1 0/1/2/3/4:46,0,3,15,4:0.012,0.053,0.222,0.063:68:24,0,1,6,2:22,0,2,9,2 1 10716609 . AC A . artifact_in_normal;str_contraction;t_lod CONTQ=93;DP=376;ECNT=1;GERMQ=844;MBQ=31,30;MFRL=192,182;MMQ=60,60;MPOS=13;NALOD=-7.496e-01;NLOD=2.61;POPAF=5.60;RPA=8,7;RU=C;SAAF=0.00,0.020,0.022;SAPP=3.990e-03,0.012,0.984;STR;TLOD=5.09 GT:AD:AF:DP:F1R2:F2R1 0/0:18,1:0.092:19:4,0:14,1 0/1:77,4:0.060:81:40,2:37,2 0/1:33,1:0.054:34:19,1:14,0 0/1:22,0:0.040:22:15,0:7,0 0/1:28,1:0.063:29:18,1:10,0 0/1:70,1:0.026:71:38,1:32,0 0/1:39,0:0.023:39:13,0:26,0 0/1:47,0:0.020:47:25,0:22,0 1 11030214 . AAAGG A . str_contraction CONTQ=93;DP=239;ECNT=1;GERMQ=342;MBQ=30,30;MFRL=245,188;MMQ=60,70;MPOS=20;NALOD=0.992;NLOD=6.57;POPAF=5.60;RPA=5,4;RU=AAGG;SAAF=0.040,0.040,0.052;SAPP=0.096,2.986e-03,0.901;STR;TLOD=8.06 GT:AD:AF:DP:F1R2:F2R1 0/0:22,0:0.036:22:9,0:13,0 0/1:25,2:0.101:27:16,1:9,1 0/1:9,2:0.226:11:9,0:0,2 0/1:13,0:0.057:13:7,0:6,0 0/1:11,1:0.133:12:4,0:7,1 0/1:35,2:0.074:37:16,1:19,1 0/1:16,0:0.047:16:2,0:14,0 0/1:18,0:0.041:18:10,0:8,0 1 11132250 . CA C . str_contraction;t_lod CONTQ=93;DP=796;ECNT=1;GERMQ=1841;MBQ=34,34;MFRL=180,164;MMQ=60,60;MPOS=23;NALOD=0.979;NLOD=14.00;POPAF=5.60;RPA=8,7;RU=A;SAAF=0.010,0.00,0.011;SAPP=7.816e-03,2.154e-03,0.990;STR;TLOD=3.74 GT:AD:AF:DP:F1R2:F2R1 0/0:47,0:0.019:47:15,0:32,0 0/1:101,3:0.037:104:49,2:52,1 0/1:36,0:0.025:36:14,0:22,0 0/1:88,0:0.011:88:38,0:50,0 0/1:73,1:0.025:74:35,0:38,1 0/1:126,1:0.014:127:54,0:72,1 0/1:88,0:0.010:88:52,0:36,0 0/1:104,2:0.026:106:47,1:57,1 1 11134470 . AT A,ATT,ATTT,ATTTT . artifact_in_normal;multiallelic;str_contraction CONTQ=93;DP=296;ECNT=1;GERMQ=135,128,308,374;MBQ=32,33,33,32,28;MFRL=199,287,220,173,175;MMQ=60,60,60,60,29;MPOS=17,18,18,17;NALOD=-7.492e-01,-6.888e-01,0.721,0.723;NLOD=1.01,1.03,3.25,3.53;POPAF=5.60,5.60,5.60,5.60;RPA=14,13,15,16,17;RU=T;SAAF=0.212,0.172,0.216;SAPP=0.015,0.024,0.962;STR;TLOD=44.74,52.24,11.58,4.00 GT:AD:AF:DP:F1R2:F2R1 0/0:10,1,1,0,0:0.111,0.109,0.048,0.048:12:2,0,0,0,0:8,1,1,0,0 0/1/2/3/4:25,5,2,0,0:0.161,0.078,0.026,0.026:32:15,3,1,0,0:10,2,1,0,0 0/1/2/3/4:3,0,2,0,0:0.096,0.299,0.098,0.098:5:3,0,1,0,0:0,0,1,0,0 0/1/2/3/4:17,4,6,2,0:0.142,0.206,0.086,0.027:29:5,3,3,1,0:12,1,3,1,0 0/1/2/3/4:15,3,3,2,0:0.141,0.141,0.105,0.034:23:11,3,1,0,0:4,0,2,2,0 0/1/2/3/4:33,7,11,4,3:0.095,0.200,0.082,0.066:58:16,5,4,1,2:17,2,7,3,1 0/1/2/3/4:22,7,7,2,1:0.168,0.183,0.068,0.045:39:12,2,2,0,1:10,5,5,2,0 0/1/2/3/4:23,10,7,0,0:0.235,0.177,0.021,0.021:40:13,7,4,0,0:10,3,3,0,0 1 11140623 . ACACACAC A,AAC,AACAC . artifact_in_normal;germline_risk;multiallelic CONTQ=93;DP=1051;ECNT=1;GERMQ=264,61,0;MBQ=30,31,31,31;MFRL=173,171,172,180;MMQ=70,29,29,38;MPOS=35,35,34;NALOD=0.602,-1.683e+00,0.086;NLOD=2.41,-7.467e+00,-7.095e+00;POPAF=5.60,5.60,5.60;SAAF=0.444,0.404,0.444;SAPP=9.491e-03,0.031,0.960;TLOD=5.84,31.14,102.23 GT:AD:AF:DP:F1R2:F2R1 0/0:2,0,1,2:0.043,0.149,0.558:5:0,0,0,0:2,0,1,2 0/1/2/3:9,3,4,6:0.098,0.183,0.237:22:0,0,0,1:9,3,4,5 0/1/2/3:0,0,0,1:0.064,0.143,0.691:1:0,0,0,1:0,0,0,0 0/1/2/3:20,5,12,27:0.050,0.159,0.483:64:6,2,7,14:14,3,5,13 0/1/2/3:17,4,6,18:0.056,0.129,0.502:45:8,2,3,8:9,2,3,10 0/1/2/3:73,8,14,32:0.043,0.122,0.279:127:32,3,9,15:41,5,5,17 0/1/2/3:16,3,7,31:0.023,0.075,0.649:57:7,2,4,16:9,1,3,15 0/1/2/3:40,3,3,25:0.016,0.037,0.380:71:21,2,2,12:19,1,1,13 1 11175116 . TA T,TAA . multiallelic;str_contraction CONTQ=93;DP=180;ECNT=1;GERMQ=161,177;MBQ=31,31,30;MFRL=335,359,375;MMQ=60,60,60;MPOS=18,19;NALOD=0.589,0.590;NLOD=2.40,2.41;POPAF=5.60,5.60;RPA=11,10,12;RU=A;SAAF=0.131,0.131,0.152;SAPP=0.029,6.575e-03,0.965;STR;TLOD=26.53,18.56 GT:AD:AF:DP:F1R2:F2R1 0/0:8,0,0:0.086,0.086:8:1,0,0:7,0,0 0/1/2:11,2,1:0.135,0.115:14:1,0,0:10,2,1 0/1/2:0,0,1:0.250,0.500:1:0,0,0:0,0,1 0/1/2:21,4,4:0.155,0.154:29:8,1,2:13,3,2 0/1/2:17,2,6:0.106,0.240:25:6,1,2:11,1,4 0/1/2:19,3,2:0.146,0.090:24:8,1,0:11,2,2 0/1/2:20,7,2:0.232,0.092:29:6,0,1:14,7,1 0/1/2:18,1,0:0.085,0.043:19:6,0,0:12,1,0 1 11177067 . C T . PASS CONTQ=93;DP=860;ECNT=1;GERMQ=1218;MBQ=33,30;MFRL=169,179;MMQ=60,60;MPOS=24;NALOD=1.80;NLOD=18.61;POPAF=5.60;SAAF=0.101,0.121,0.119;SAPP=0.013,2.852e-03,0.984;TLOD=174.66 GT:AD:AF:DP:F1R2:F2R1 0/0:62,0:0.016:62:33,0:29,0 0/1:148,0:6.488e-03:148:80,0:68,0 0/1:13,10:0.441:23:6,6:7,4 0/1:38,37:0.491:75:15,23:23,14 0/1:106,1:0.018:107:44,1:62,0 0/1:144,0:6.570e-03:144:67,0:77,0 0/1:52,38:0.426:90:16,15:36,23 0/1:142,1:0.011:143:71,1:71,0 1 11187618 . AT A,ATT . artifact_in_normal;str_contraction CONTQ=93;DP=269;ECNT=1;GERMQ=550,404;MBQ=33,32,31;MFRL=250,251,301;MMQ=60,60,60;MPOS=9,14;NALOD=0.826,-9.926e-01;NLOD=3.27,0.447;POPAF=5.60,5.60;RPA=9,8,10;RU=T;SAAF=0.071,0.071,0.080;SAPP=4.476e-03,0.028,0.968;STR;TLOD=4.88,21.63 GT:AD:AF:DP:F1R2:F2R1 0/0:10,0,1:0.070,0.141:11:8,0,1:2,0,0 0/1/2:30,1,2:0.054,0.082:33:24,1,2:6,0,0 0/1/2:15,0,0:0.053,0.053:15:14,0,0:1,0,0 0/1/2:49,2,3:0.052,0.069:54:33,0,1:16,2,2 0/1/2:26,1,2:0.059,0.092:29:11,1,1:15,0,1 0/1/2:32,1,5:0.048,0.136:38:19,0,1:13,1,4 0/1/2:42,1,5:0.037,0.116:48:20,0,1:22,1,4 0/1/2:14,0,1:0.056,0.110:15:8,0,1:6,0,0 1 11293367 . TA T,TAA . artifact_in_normal;multiallelic;str_contraction CONTQ=93;DP=346;ECNT=1;GERMQ=345,486;MBQ=30,30,30;MFRL=274,329,209;MMQ=60,60,60;MPOS=13,14;NALOD=-2.917e+00,0.708;NLOD=-1.147e+00,4.43;POPAF=5.60,5.60;RPA=11,10,12;RU=A;SAAF=0.111,0.101,0.118;SAPP=2.462e-03,0.136,0.862;STR;TLOD=40.96,12.93 GT:AD:AF:DP:F1R2:F2R1 0/0:13,2,0:0.163,0.052:15:11,1,0:2,1,0 0/1/2:33,5,3:0.119,0.089:41:19,3,2:14,2,1 0/1/2:5,1,0:0.220,0.107:6:4,1,0:1,0,0 0/1/2:39,4,4:0.090,0.089:47:21,0,2:18,4,2 0/1/2:25,2,2:0.084,0.092:29:9,0,2:16,2,0 0/1/2:50,8,5:0.127,0.082:63:28,4,3:22,4,2 0/1/2:40,4,1:0.096,0.039:45:20,2,0:20,2,1 0/1/2:32,6,3:0.145,0.070:41:14,6,1:18,0,2 1 11319228 . CA C,CAA . multiallelic;str_contraction CONTQ=93;DP=577;ECNT=1;GERMQ=1219,1125;MBQ=32,32,32;MFRL=184,170,164;MMQ=60,60,60;MPOS=27,25;NALOD=1.28,1.28;NLOD=10.82,10.81;POPAF=5.60,5.60;RPA=9,8,10;RU=A;SAAF=0.00,0.040,0.042;SAPP=7.292e-03,0.012,0.981;STR;TLOD=9.23,17.64 GT:AD:AF:DP:F1R2:F2R1 0/0:36,0,0:0.026,0.026:36:14,0,0:22,0,0 0/1/2:97,1,3:0.018,0.037:101:47,1,0:50,0,3 0/1/2:22,1,1:0.072,0.043:24:14,1,0:8,0,1 0/1/2:49,0,2:0.017,0.053:51:26,0,1:23,0,1 0/1/2:44,1,5:0.035,0.111:50:19,1,2:25,0,3 0/1/2:88,4,4:0.049,0.049:96:46,1,2:42,3,2 0/1/2:48,2,0:0.055,0.018:50:23,1,0:25,1,0 0/1/2:87,2,4:0.030,0.051:93:43,0,1:44,2,3 1 11731927 . AG A,AGG . multiallelic;str_contraction CONTQ=93;DP=760;ECNT=1;GERMQ=1624,1525;MBQ=33,33,33;MFRL=174,178,166;MMQ=60,60,60;MPOS=24,19;NALOD=1.50,0.481;NLOD=17.08,14.10;POPAF=5.60,5.60;RPA=9,8,10;RU=G;SAAF=0.030,0.040,0.039;SAPP=5.231e-03,2.749e-03,0.992;STR;TLOD=17.60,23.30 GT:AD:AF:DP:F1R2:F2R1 0/0:55,0,1:0.016,0.032:56:22,0,0:33,0,1 0/1/2:111,6,7:0.054,0.062:124:57,1,4:54,5,3 0/1/2:49,1,0:0.036,0.018:50:26,1,0:23,0,0 0/1/2:56,1,1:0.031,0.031:58:26,1,0:30,0,1 0/1/2:82,1,6:0.021,0.074:89:37,0,2:45,1,4 0/1/2:100,4,4:0.044,0.044:108:52,3,3:48,1,1 0/1/2:72,2,3:0.035,0.048:77:45,1,2:27,1,1 0/1/2:114,3,3:0.031,0.031:120:63,1,0:51,2,3 1 11832332 . CT C . str_contraction CONTQ=93;DP=435;ECNT=1;GERMQ=1055;MBQ=33,34;MFRL=185,160;MMQ=60,60;MPOS=10;NALOD=1.07;NLOD=9.30;POPAF=5.09;RPA=8,7;RU=T;SAAF=0.020,0.00,0.019;SAPP=9.169e-03,3.615e-03,0.987;STR;TLOD=6.15 GT:AD:AF:DP:F1R2:F2R1 0/0:31,0:0.029:31:11,0:20,0 0/1:64,1:0.029:65:35,0:29,1 0/1:19,0:0.048:19:9,0:10,0 0/1:41,0:0.023:41:17,0:24,0 0/1:51,0:0.018:51:17,0:34,0 0/1:70,2:0.040:72:35,1:35,1 0/1:55,2:0.050:57:30,2:25,0 0/1:67,2:0.041:69:30,2:37,0 1 11838901 . T G . artifact_in_normal;base_quality;t_lod CONTQ=93;DP=431;ECNT=1;GERMQ=720;MBQ=32,9;MFRL=187,180;MMQ=60,60;MPOS=18;NALOD=0.597;NLOD=8.44;POPAF=5.60;SAAF=0.081,0.00,0.084;SAPP=2.935e-05,0.980,0.020;TLOD=3.64 GT:AD:AF:DP:F1R2:F2R1 0/0:42,4:0.060:46:12,3:30,1 0/1:80,8:0.025:88:32,7:48,1 0/1:37,0:0.026:37:13,0:24,0 0/1:33,4:0.102:37:12,3:21,1 0/1:26,5:0.103:31:17,3:9,2 0/1:64,4:0.021:68:32,3:32,1 0/1:46,8:0.120:54:16,4:30,4 0/1:50,2:0.040:52:19,2:31,0 1 11850990 . GCA G,ACA,GCACA . artifact_in_normal;multiallelic;panel_of_normals CONTQ=93;DP=1503;ECNT=1;GERMQ=2943,2950,2656;MBQ=33,33,32,33;MFRL=180,304,176,188;MMQ=60,60,60,60;MPOS=28,20,22;NALOD=1.50,1.52,-3.513e-01;NLOD=34.76,37.18,27.21;PON;POPAF=5.60,5.60,5.60;SAAF=0.020,0.010,0.023;SAPP=1.164e-03,0.014,0.985;TLOD=9.27,8.13,32.81 GT:AD:AF:DP:F1R2:F2R1 0/0:100,0,0,1:7.851e-03,7.552e-03,0.018:101:40,0,0,1:60,0,0,0 0/1/2/3:131,2,3,4:0.019,0.021,0.033:140:69,2,3,1:62,0,0,3 0/1/2/3:47,2,0,5:0.047,0.013,0.089:54:25,1,0,0:22,1,0,5 0/1/2/3:147,0,2,3:5.467e-03,0.015,0.025:152:85,0,0,2:62,0,2,1 0/1/2/3:92,0,1,3:8.464e-03,0.015,0.038:96:41,0,0,1:51,0,1,2 0/1/2/3:130,2,1,3:0.019,0.011,0.027:136:65,0,1,1:65,2,0,2 0/1/2/3:191,2,1,3:0.013,7.891e-03,0.015:197:98,1,1,3:93,1,0,0 0/1/2/3:185,0,1,1:4.475e-03,8.338e-03,9.640e-03:187:90,0,1,0:95,0,0,1 1 11918911 . GGCT G . artifact_in_normal;str_contraction CONTQ=93;DP=887;ECNT=2;GERMQ=2092;MBQ=31,31;MFRL=183,176;MMQ=60,60;MPOS=17;NALOD=-7.211e-01;NLOD=17.52;POPAF=5.60;RPA=5,4;RU=GCT;SAAF=0.010,0.00,7.331e-03;SAPP=1.238e-03,2.805e-03,0.996;STR;TLOD=7.55 GT:AD:AF:DP:F1R2:F2R1 0/0:72,1:0.025:73:29,0:43,1 0/1:126,0:7.452e-03:126:57,0:69,0 0/1:51,1:0.035:52:23,1:28,0 0/1:61,0:0.014:61:29,0:32,0 0/1:85,2:0.033:87:40,2:45,0 0/1:108,1:0.018:109:52,0:56,1 0/1:83,0:0.011:83:36,0:47,0 0/1:163,1:0.012:164:66,0:97,1 1 11918927 . TCTG T . panel_of_normals;str_contraction CONTQ=93;DP=913;ECNT=2;GERMQ=1669;MBQ=33,32;MFRL=184,187;MMQ=60,60;MPOS=29;NALOD=0.533;NLOD=14.02;PON;POPAF=5.60;RPA=7,6;RU=CTG;SAAF=0.051,0.040,0.048;SAPP=4.938e-03,4.759e-03,0.990;STR;TLOD=74.11 GT:AD:AF:DP:F1R2:F2R1 0/0:55,1:0.031:56:18,1:37,0 0/1:129,4:0.037:133:62,3:67,1 0/1:53,2:0.051:55:24,1:29,1 0/1:64,1:0.029:65:30,0:34,1 0/1:77,7:0.093:84:38,4:39,3 0/1:103,10:0.095:113:50,5:53,5 0/1:79,7:0.090:86:37,3:42,4 0/1:168,3:0.023:171:73,1:95,2 1 12014543 . CA C . str_contraction;t_lod CONTQ=93;DP=701;ECNT=1;GERMQ=1740;MBQ=33,33;MFRL=174,174;MMQ=60,60;MPOS=28;NALOD=0.050;NLOD=7.46;POPAF=5.60;RPA=8,7;RU=A;SAAF=0.00,0.010,0.011;SAPP=2.164e-03,8.677e-03,0.989;STR;TLOD=3.03 GT:AD:AF:DP:F1R2:F2R1 0/0:34,1:0.053:35:15,0:19,1 0/1:130,0:7.440e-03:130:69,0:61,0 0/1:27,0:0.034:27:14,0:13,0 0/1:42,0:0.022:42:18,0:24,0 0/1:81,2:0.034:83:42,1:39,1 0/1:124,4:0.038:128:56,2:68,2 0/1:77,0:0.012:77:37,0:40,0 0/1:123,1:0.015:124:56,0:67,1 1 12023750 . G A . t_lod CONTQ=93;DP=792;ECNT=2;GERMQ=2176;MBQ=33,31;MFRL=184,172;MMQ=60,60;MPOS=9;NALOD=1.99;NLOD=27.68;POPAF=5.60;SAAF=0.010,0.00,7.396e-03;SAPP=1.430e-03,2.529e-03,0.996;TLOD=4.06 GT:AD:AF:DP:F1R2:F2R1 0/0:92,0:0.010:92:30,0:62,0 0/1:124,1:0.016:125:58,0:66,1 0/1:45,0:0.021:45:17,0:28,0 0/1:56,0:0.017:56:24,0:32,0 0/1:93,1:0.021:94:43,0:50,1 0/1:144,1:0.013:145:57,0:87,1 0/1:102,2:0.028:104:31,0:71,2 0/1:107,0:9.001e-03:107:44,0:63,0 1 12023765 . TTCC T . str_contraction CONTQ=93;DP=731;ECNT=2;GERMQ=1230;MBQ=31,31;MFRL=189,212;MMQ=60,60;MPOS=22;NALOD=1.84;NLOD=17.03;POPAF=5.60;RPA=5,4;RU=TCC;SAAF=0.051,0.00,0.049;SAPP=2.934e-03,0.031,0.966;STR;TLOD=60.91 GT:AD:AF:DP:F1R2:F2R1 0/0:57,0:0.015:57:16,0:41,0 0/1:99,4:0.047:103:47,2:52,2 0/1:26,3:0.127:29:8,1:18,2 0/1:28,2:0.090:30:12,1:16,1 0/1:69,2:0.040:71:31,1:38,1 0/1:98,9:0.091:107:43,2:55,7 0/1:70,2:0.039:72:25,1:45,1 0/1:79,2:0.035:81:37,2:42,0 1 12030946 . T G . artifact_in_normal;base_quality CONTQ=93;DP=733;ECNT=1;GERMQ=1147;MBQ=30,10;MFRL=245,294;MMQ=60,60;MPOS=16;NALOD=0.024;NLOD=12.94;POPAF=5.60;SAAF=0.091,0.020,0.094;SAPP=0.013,0.016,0.971;TLOD=9.89 GT:AD:AF:DP:F1R2:F2R1 0/0:66,6:0.054:72:19,3:47,3 0/1:131,20:0.093:151:62,8:69,12 0/1:57,1:0.018:58:25,1:32,0 0/1:86,10:0.059:96:35,6:51,4 0/1:65,7:0.032:72:24,5:41,2 0/1:50,4:0.037:54:22,1:28,3 0/1:92,11:0.065:103:41,4:51,7 0/1:79,5:0.032:84:33,1:46,4 1 12073251 . GA G,GAA . str_contraction CONTQ=93;DP=154;ECNT=1;GERMQ=268,278;MBQ=33,33,32;MFRL=331,318,356;MMQ=60,60,37;MPOS=10,11;NALOD=0.838,0.838;NLOD=3.30,3.31;POPAF=5.60,5.60;RPA=11,10,12;RU=A;SAAF=0.030,0.061,0.059;SAPP=9.413e-03,0.019,0.971;STR;TLOD=5.65,4.73 GT:AD:AF:DP:F1R2:F2R1 0/0:11,0,0:0.068,0.068:11:8,0,0:3,0,0 0/1/2:12,1,0:0.122,0.060:13:3,0,0:9,1,0 0/1/2:3,0,1:0.143,0.285:4:0,0,1:3,0,0 0/1/2:32,2,1:0.077,0.051:35:18,1,0:14,1,1 0/1/2:11,1,0:0.131,0.065:12:6,1,0:5,0,0 0/1/2:19,2,3:0.090,0.146:24:9,1,2:10,1,1 0/1/2:29,1,0:0.057,0.029:30:14,0,0:15,1,0 0/1/2:6,0,1:0.094,0.195:7:2,0,0:4,0,1 1 12252333 . CTGTGTG C,CTG,CTGTG,CTGTGTGTG . artifact_in_normal;multiallelic CONTQ=93;DP=1664;ECNT=1;GERMQ=1219,779,118,783;MBQ=33,33,33,33,33;MFRL=174,188,179,176,172;MMQ=60,29,60,60,60;MPOS=29,29,27,19;NALOD=-6.001e+00,-1.079e+01,-2.005e+01,-9.939e+00;NLOD=6.34,-3.612e+00,-1.612e+01,1.40;POPAF=5.60,5.60,5.60,5.60;RPA=15,12,13,14,16;RU=TG;SAAF=0.232,0.263,0.264;SAPP=0.018,0.015,0.968;STR;TLOD=8.84,80.99,351.74,64.82 GT:AD:AF:DP:F1R2:F2R1 0/0:53,4,5,10,6:0.048,0.067,0.129,0.084:78:18,2,0,4,1:35,2,5,6,5 0/1/2/3/4:78,1,7,17,9:0.012,0.060,0.149,0.084:112:48,1,4,7,6:30,0,3,10,3 0/1/2/3/4:22,1,3,7,1:0.043,0.097,0.203,0.045:34:8,0,2,3,1:14,1,1,4,0 0/1/2/3/4:72,1,7,26,4:0.013,0.062,0.231,0.041:110:36,1,7,21,1:36,0,0,5,3 0/1/2/3/4:47,1,3,15,7:0.019,0.044,0.199,0.099:73:23,0,2,5,1:24,1,1,10,6 0/1/2/3/4:59,0,6,14,4:7.661e-03,0.073,0.174,0.045:83:29,0,4,7,3:30,0,2,7,1 0/1/2/3/4:83,1,6,37,10:0.011,0.044,0.252,0.076:137:44,0,4,18,5:39,1,2,19,5 0/1/2/3/4:71,2,7,39,10:0.017,0.055,0.299,0.077:129:32,0,1,18,5:39,2,6,21,5 1 12294475 . AT A . str_contraction CONTQ=93;DP=553;ECNT=1;GERMQ=1096;MBQ=33,32;MFRL=178,179;MMQ=60,60;MPOS=16;NALOD=1.01;NLOD=4.80;POPAF=5.60;RPA=8,7;RU=T;SAAF=0.040,0.030,0.043;SAPP=0.025,6.200e-03,0.968;STR;TLOD=23.77 GT:AD:AF:DP:F1R2:F2R1 0/0:16,0:0.049:16:5,0:11,0 0/1:70,4:0.064:74:38,2:32,2 0/1:8,0:0.097:8:2,0:6,0 0/1:48,0:0.019:48:22,0:26,0 0/1:57,2:0.048:59:22,0:35,2 0/1:97,6:0.066:103:50,3:47,3 0/1:77,3:0.048:80:43,2:34,1 0/1:93,5:0.059:98:44,3:49,2 1 12368705 . GTTT G,GT,GTT,GTTTT,GTTTTT,GTTTTTT . multiallelic;panel_of_normals CONTQ=93;DP=672;ECNT=1;GERMQ=648,485,165,192,466,674;MBQ=32,32,32,32,32,31,33;MFRL=184,183,186,184,186,186,184;MMQ=60,37,60,60,60,60,29;MPOS=16,18,21,19,16,17;NALOD=-2.470e-01,0.611,-2.862e+00,0.633,-3.138e+00,0.639;NLOD=1.41,1.58,-2.077e+00,2.48,-1.852e+00,2.81;PON;POPAF=5.60,5.60,5.60,5.60,5.60,5.60;RPA=15,12,13,14,16,17,18;RU=T;SAAF=0.253,0.212,0.252;SAPP=0.014,0.029,0.957;STR;TLOD=11.63,42.81,131.75,132.00,32.47,6.56 GT:AD:AF:DP:F1R2:F2R1 0/0:9,1,0,2,0,2,0:0.085,0.040,0.145,0.037,0.140,0.036:14:5,0,0,1,0,1,0:4,1,0,1,0,1,0 0/1/2/3/4/5/6:28,1,4,9,16,6,1:0.026,0.066,0.135,0.234,0.098,0.027:65:12,0,1,4,7,2,1:16,1,3,5,9,4,0 0/1/2/3/4/5/6:5,0,0,2,1,0,0:0.063,0.063,0.203,0.132,0.062,0.062:8:3,0,0,1,0,0,0:2,0,0,1,1,0,0 0/1/2/3/4/5/6:41,0,4,13,14,1,0:0.012,0.061,0.173,0.191,0.022,0.012:73:18,0,0,4,4,0,0:23,0,4,9,10,1,0 0/1/2/3/4/5/6:32,3,4,9,10,3,3:0.050,0.072,0.140,0.153,0.063,0.058:64:16,2,2,2,6,1,1:16,1,2,7,4,2,2 0/1/2/3/4/5/6:55,6,10,28,26,12,1:0.042,0.075,0.202,0.188,0.090,0.013:138:22,1,5,13,8,2,0:33,5,5,15,18,10,1 0/1/2/3/4/5/6:37,0,5,8,9,2,3:0.012,0.080,0.125,0.141,0.041,0.053:64:17,0,1,4,5,0,2:20,0,4,4,4,2,1 0/1/2/3/4/5/6:78,2,3,18,17,4,3:0.022,0.029,0.142,0.136,0.038,0.025:125:44,2,0,7,8,1,0:34,0,3,11,9,3,3 1 12398426 . AT A,ATT,ATTT . artifact_in_normal;multiallelic;str_contraction CONTQ=93;DP=525;ECNT=1;GERMQ=917,687,983;MBQ=33,33,33,33;MFRL=183,173,175,176;MMQ=60,60,60,60;MPOS=30,20,27;NALOD=0.868,-4.915e-01,0.862;NLOD=8.97,5.90,8.43;POPAF=5.60,5.60,5.60;RPA=10,9,11,12;RU=T;SAAF=0.101,0.071,0.097;SAPP=0.022,0.013,0.965;STR;TLOD=12.10,52.22,5.55 GT:AD:AF:DP:F1R2:F2R1 0/0:28,0,1,0:0.028,0.058,0.028:29:19,0,0,0:9,0,1,0 0/1/2/3:69,4,7,2:0.048,0.094,0.028:82:33,3,3,0:36,1,4,2 0/1/2/3:4,0,2,0:0.097,0.300,0.097:6:1,0,2,0:3,0,0,0 0/1/2/3:49,1,2,0:0.034,0.052,0.017:52:18,0,0,0:31,1,2,0 0/1/2/3:52,0,3,1:0.015,0.065,0.032:56:21,0,1,0:31,0,2,1 0/1/2/3:71,3,9,3:0.034,0.119,0.036:86:35,0,3,1:36,3,6,2 0/1/2/3:48,3,5,1:0.063,0.097,0.032:57:20,1,3,1:28,2,2,0 0/1/2/3:60,4,10,2:0.060,0.140,0.030:76:30,2,3,0:30,2,7,2 1 12409468 . CT C,CTT . artifact_in_normal;multiallelic;str_contraction CONTQ=93;DP=620;ECNT=1;GERMQ=849,789;MBQ=33,33,33;MFRL=265,190,180;MMQ=60,60,60;MPOS=16,24;NALOD=-6.866e-01,-5.637e-01;NLOD=2.47,2.37;POPAF=5.60,5.60;RPA=10,9,11;RU=T;SAAF=0.081,0.061,0.079;SAPP=0.043,5.941e-03,0.951;STR;TLOD=32.18,38.68 GT:AD:AF:DP:F1R2:F2R1 0/0:15,1,1:0.087,0.091:17:7,1,1:8,0,0 0/1/2:26,4,2:0.140,0.075:32:12,2,1:14,2,1 0/1/2:8,0,1:0.076,0.160:9:3,0,0:5,0,1 0/1/2:61,4,2:0.070,0.030:67:26,2,1:35,2,1 0/1/2:56,2,4:0.043,0.074:62:24,1,3:32,1,1 0/1/2:108,10,10:0.082,0.079:128:52,4,4:56,6,6 0/1/2:60,5,7:0.076,0.105:72:28,3,3:32,2,4 0/1/2:75,2,8:0.031,0.100:85:39,0,2:36,2,6 1 12632789 . GGGA G . str_contraction CONTQ=93;DP=1398;ECNT=1;GERMQ=2601;MBQ=32,31;MFRL=174,186;MMQ=60,60;MPOS=23;NALOD=2.03;NLOD=27.80;POPAF=5.60;RPA=4,3;RU=GGA;SAAF=0.010,0.010,0.013;SAPP=1.968e-03,1.439e-03,0.997;STR;TLOD=20.66 GT:AD:AF:DP:F1R2:F2R1 0/0:93,0:9.396e-03:93:38,0:55,0 0/1:192,1:9.541e-03:193:85,0:107,1 0/1:46,1:0.038:47:21,0:25,1 0/1:72,1:0.025:73:37,0:35,1 0/1:128,1:0.014:129:55,0:73,1 0/1:125,5:0.045:130:64,2:61,3 0/1:100,1:0.018:101:52,1:48,0 0/1:185,1:9.912e-03:186:88,1:97,0 1 12785492 . C CT . PASS CONTQ=93;DP=1258;ECNT=2;GERMQ=2835;MBQ=33,33;MFRL=185,178;MMQ=60,60;MPOS=18;NALOD=1.05;NLOD=24.51;POPAF=4.21;RPA=1,2;RU=T;SAAF=0.010,0.020,0.023;SAPP=8.966e-03,8.749e-04,0.990;STR;TLOD=15.99 GT:AD:AF:DP:F1R2:F2R1 0/0:90,1:0.020:91:46,0:44,1 0/1:151,3:0.024:154:95,3:56,0 0/1:44,1:0.041:45:24,1:20,0 0/1:151,2:0.018:153:79,1:72,1 0/1:109,6:0.058:115:55,2:54,4 0/1:194,4:0.020:198:96,2:98,2 0/1:186,5:0.030:191:86,3:100,2 0/1:173,3:0.021:176:80,2:93,1 1 12785493 . TG T . PASS CONTQ=93;DP=1256;ECNT=2;GERMQ=3078;MBQ=32,33;MFRL=184,182;MMQ=60,60;MPOS=18;NALOD=0.942;NLOD=25.22;POPAF=4.91;SAAF=0.010,0.010,0.012;SAPP=5.260e-03,6.743e-04,0.994;TLOD=5.90 GT:AD:AF:DP:F1R2:F2R1 0/0:93,1:0.020:94:45,1:48,0 0/1:154,0:6.028e-03:154:98,0:56,0 0/1:45,0:0.021:45:25,0:20,0 0/1:153,2:0.018:155:81,1:72,1 0/1:114,1:0.016:115:56,1:58,0 0/1:195,4:0.024:199:97,2:98,2 0/1:191,2:0.014:193:88,1:103,1 0/1:174,3:0.021:177:82,0:92,3 1 12853308 . C G . bad_haplotype;mapping_quality;strand_artifact CONTQ=93;DP=475;ECNT=2;GERMQ=1241;MBQ=33,32;MFRL=319,171;MMQ=55,29;MPOS=7;NALOD=1.70;NLOD=14.75;POPAF=5.60;SAAF=0.020,0.00,0.015;SAPP=8.861e-10,1.000,2.239e-06;TLOD=8.18 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS 0|0:49,0:0.019:49:35,0:14,0:0|1:12853308_C_G:12853308 0|1:60,4:0.075:64:35,2:25,2:0|1:12853308_C_G:12853308 0|1:21,0:0.044:21:14,0:7,0:0|1:12853308_C_G:12853308 0|1:72,0:0.013:72:36,0:36,0:0|1:12853308_C_G:12853308 0|1:39,0:0.024:39:19,0:20,0:0|1:12853308_C_G:12853308 0|1:92,0:0.011:92:55,0:37,0:0|1:12853308_C_G:12853308 0|1:78,2:0.036:80:38,2:40,0:0|1:12853308_C_G:12853308 0|1:43,0:0.022:43:24,0:19,0:0|1:12853308_C_G:12853308 1 12853315 . C A . bad_haplotype;mapping_quality;strand_artifact;t_lod CONTQ=93;DP=554;ECNT=2;GERMQ=1525;MBQ=31,34;MFRL=315,176;MMQ=55,29;MPOS=20;NALOD=0.104;NLOD=13.13;POPAF=5.60;SAAF=0.010,0.00,8.016e-03;SAPP=7.791e-08,1.000,2.418e-04;TLOD=4.80 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS 0|0:54,1:0.035:55:38,1:16,0:0|1:12853308_C_G:12853308 0|1:71,4:0.065:75:44,2:27,2:0|1:12853308_C_G:12853308 0|1:34,0:0.028:34:21,0:13,0:0|1:12853308_C_G:12853308 0|1:87,0:0.011:87:41,0:46,0:0|1:12853308_C_G:12853308 0|1:46,0:0.021:46:23,0:23,0:0|1:12853308_C_G:12853308 0|1:96,0:0.010:96:57,0:39,0:0|1:12853308_C_G:12853308 0|1:97,0:0.010:97:50,0:47,0:0|1:12853308_C_G:12853308 0|1:64,0:0.015:64:43,0:21,0:0|1:12853308_C_G:12853308 1 12853872 . A T . mapping_quality CONTQ=93;DP=263;ECNT=1;GERMQ=587;MBQ=31,31;MFRL=418,499;MMQ=38,29;MPOS=20;NALOD=1.26;NLOD=5.06;POPAF=5.60;SAAF=0.030,0.020,0.035;SAPP=3.017e-03,8.369e-03,0.989;TLOD=9.62 GT:AD:AF:DP:F1R2:F2R1 0/0:17,0:0.052:17:8,0:9,0 0/1:26,2:0.098:28:16,1:10,1 0/1:23,0:0.039:23:11,0:12,0 0/1:70,4:0.066:74:32,1:38,3 0/1:30,0:0.031:30:13,0:17,0 0/1:3,0:0.175:3:2,0:1,0 0/1:63,2:0.033:65:30,2:33,0 0/1:8,0:0.089:8:4,0:4,0 1 12907201 . G C . artifact_in_normal;clustered_events;mapping_quality CONTQ=93;DP=492;ECNT=3;GERMQ=952;MBQ=33,32;MFRL=190,188;MMQ=29,22;MPOS=13;NALOD=-2.679e+00;NLOD=4.86;POPAF=5.60;SAAF=0.00,0.061,0.057;SAPP=9.646e-03,0.013,0.977;TLOD=51.67 GT:AD:AF:DP:F1R2:F2R1 0/0:38,2:0.070:40:15,1:23,1 0/1:64,7:0.109:71:25,3:39,4 0/1:11,1:0.143:12:3,0:8,1 0/1:58,6:0.105:64:31,4:27,2 0/1:44,0:0.022:44:19,0:25,0 0/1:94,3:0.040:97:41,1:53,2 0/1:82,6:0.077:88:32,2:50,4 0/1:63,2:0.044:65:35,1:28,1 1 12907227 . C T . artifact_in_normal;clustered_events;mapping_quality;panel_of_normals CONTQ=93;DP=819;ECNT=3;GERMQ=1091;MBQ=32,33;MFRL=178,169;MMQ=29,25;MPOS=17;NALOD=-2.313e+00;NLOD=10.52;PON;POPAF=5.60;SAAF=0.091,0.121,0.126;SAPP=0.021,0.014,0.965;TLOD=156.79 GT:AD:AF:DP:F1R2:F2R1 0/0:61,3:0.059:64:23,2:38,1 0/1:102,18:0.155:120:40,7:62,11 0/1:15,2:0.158:17:8,1:7,1 0/1:70,10:0.133:80:33,6:37,4 0/1:68,7:0.103:75:27,3:41,4 0/1:140,19:0.123:159:65,9:75,10 0/1:107,16:0.132:123:42,7:65,9 0/1:132,19:0.130:151:73,8:59,11 1 12907245 . C A . artifact_in_normal;clustered_events;mapping_quality;panel_of_normals CONTQ=93;DP=854;ECNT=3;GERMQ=1148;MBQ=33,32;MFRL=176,168;MMQ=36,25;MPOS=29;NALOD=-6.012e-01;NLOD=19.21;PON;POPAF=5.60;SAAF=0.00,0.131,0.130;SAPP=0.095,4.902e-03,0.900;TLOD=169.90 GT:AD:AF:DP:F1R2:F2R1 0/0:82,2:0.034:84:36,1:46,1 0/1:116,18:0.139:134:47,7:69,11 0/1:11,2:0.197:13:8,1:3,1 0/1:69,7:0.101:76:30,3:39,4 0/1:74,8:0.107:82:30,4:44,4 0/1:124,20:0.143:144:62,9:62,11 0/1:98,17:0.153:115:40,7:58,10 0/1:137,22:0.142:159:72,10:65,12 1 12907358 . T C . artifact_in_normal;clustered_events;mapping_quality;panel_of_normals CONTQ=93;DP=1886;ECNT=20;GERMQ=3032;MBQ=33,29;MFRL=182,165;MMQ=60,29;MPOS=17;NALOD=-3.751e+01;NLOD=4.30;PON;POPAF=5.60;SAAF=0.081,0.051,0.077;SAPP=2.771e-09,1.000,7.441e-06;TLOD=322.81 GT:AD:AF:DP:F1R2:F2R1 0/0:211,16:0.074:227:80,5:131,11 0/1:305,23:0.071:328:126,10:179,13 0/1:28,5:0.171:33:13,2:15,3 0/1:197,5:0.029:202:96,4:101,1 0/1:165,12:0.072:177:82,4:83,8 0/1:274,35:0.114:309:135,14:139,21 0/1:211,16:0.074:227:97,9:114,7 0/1:330,30:0.084:360:152,14:178,16 1 12907370 . A T . artifact_in_normal;bad_haplotype;clustered_events;mapping_quality;panel_of_normals CONTQ=93;DP=2026;ECNT=20;GERMQ=3233;MBQ=31,32;MFRL=180,164;MMQ=60,29;MPOS=8;NALOD=-3.465e+01;NLOD=13.11;PON;POPAF=5.60;SAAF=0.071,0.040,0.069;SAPP=1.918e-10,1.000,6.067e-07;TLOD=357.85 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS 0|0:223,13:0.059:236:83,5:140,8:0|1:12907370_A_T:12907370 0|1:342,20:0.058:362:137,10:205,10:0|1:12907370_A_T:12907370 0|1:28,5:0.171:33:12,2:16,3:0|1:12907370_A_T:12907370 0|1:202,14:0.069:216:95,9:107,5:0|1:12907370_A_T:12907370 0|1:204,10:0.051:214:99,3:105,7:0|1:12907370_A_T:12907370 0|1:274,34:0.113:308:140,12:134,22:0|1:12907370_A_T:12907370 0|1:237,20:0.081:257:110,12:127,8:0|1:12907370_A_T:12907370 0|1:379,21:0.055:400:175,8:204,13:0|1:12907370_A_T:12907370 1 12907379 . TC CA . artifact_in_normal;bad_haplotype;clustered_events;mapping_quality;panel_of_normals CONTQ=93;DP=2062;ECNT=20;GERMQ=3233;MBQ=33,32;MFRL=179,536;MMQ=46,29;MPOS=13;NALOD=-2.079e+00;NLOD=68.06;PON;POPAF=5.60;SAAF=0.010,0.010,0.013;SAPP=1.887e-03,7.510e-04,0.997;TLOD=50.47 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS 0|0:254,2:0.012:256:93,1:161,1:0|1:12907379_TC_CA:12907379 0|1:342,1:5.777e-03:343:135,0:207,1:0|1:12907379_TC_CA:12907379 0|1:27,0:0.034:27:12,0:15,0:0|1:12907379_TC_CA:12907379 0|1:213,9:0.045:222:101,6:112,3:0|1:12907379_TC_CA:12907379 0|1:225,2:0.013:227:105,1:120,1:0|1:12907379_TC_CA:12907379 0|1:303,2:9.747e-03:305:155,2:148,0:0|1:12907379_TC_CA:12907379 0|1:258,7:0.030:265:118,5:140,2:0|1:12907379_TC_CA:12907379 0|1:414,3:9.520e-03:417:178,2:236,1:0|1:12907379_TC_CA:12907379 1 12907385 . G A . artifact_in_normal;bad_haplotype;clustered_events;mapping_quality;panel_of_normals CONTQ=93;DP=2025;ECNT=20;GERMQ=3233;MBQ=33,32;MFRL=179,164;MMQ=60,29;MPOS=11;NALOD=-2.199e+01;NLOD=37.46;PON;POPAF=5.60;SAAF=0.040,0.020,0.037;SAPP=4.826e-05,0.866,0.134;TLOD=170.34 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS 0|0:250,9:0.038:259:96,3:154,6:0|1:12907370_A_T:12907370 0|1:323,5:0.018:328:130,1:193,4:0|1:12907370_A_T:12907370 0|1:24,1:0.074:25:10,1:14,0:0|1:12907370_A_T:12907370 0|1:209,9:0.045:218:101,6:108,3:0|1:12907370_A_T:12907370 0|1:223,5:0.026:228:110,3:113,2:0|1:12907370_A_T:12907370 0|1:275,17:0.061:292:140,10:135,7:0|1:12907370_A_T:12907370 0|1:246,13:0.054:259:109,6:137,7:0|1:12907370_A_T:12907370 0|1:400,16:0.041:416:171,9:229,7:0|1:12907370_A_T:12907370 1 12907400 . G A . artifact_in_normal;bad_haplotype;clustered_events;mapping_quality CONTQ=93;DP=1958;ECNT=20;GERMQ=3233;MBQ=33,31;MFRL=180,188;MMQ=46,29;MPOS=21;NALOD=-2.043e+00;NLOD=70.16;POPAF=5.60;SAAF=0.020,0.020,0.021;SAPP=4.920e-04,0.016,0.983;TLOD=65.72 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS 0|0:261,2:0.011:263:103,1:158,1:0|1:12907379_TC_CA:12907379 0|1:303,5:0.019:308:128,2:175,3:0|1:12907379_TC_CA:12907379 0|1:28,0:0.033:28:11,0:17,0:0|1:12907379_TC_CA:12907379 0|1:199,7:0.038:206:92,5:107,2:0|1:12907379_TC_CA:12907379 0|1:216,2:0.013:218:103,2:113,0:0|1:12907379_TC_CA:12907379 0|1:254,4:0.019:258:130,3:124,1:0|1:12907379_TC_CA:12907379 0|1:262,10:0.040:272:114,5:148,5:0|1:12907379_TC_CA:12907379 0|1:391,8:0.022:399:166,6:225,2:0|1:12907379_TC_CA:12907379 1 12907408 . T A . artifact_in_normal;bad_haplotype;clustered_events;mapping_quality;panel_of_normals CONTQ=93;DP=1907;ECNT=20;GERMQ=3233;MBQ=33,33;MFRL=179,171;MMQ=46,29;MPOS=21;NALOD=-1.081e+01;NLOD=51.68;PON;POPAF=5.60;SAAF=0.051,0.020,0.052;SAPP=2.253e-12,1.000,8.595e-09;TLOD=195.88 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS 0|0:248,6:0.027:254:96,3:152,3:0|1:12907370_A_T:12907370 0|1:284,12:0.043:296:122,4:162,8:0|1:12907370_A_T:12907370 0|1:29,1:0.062:30:13,0:16,1:0|1:12907370_A_T:12907370 0|1:180,8:0.047:188:86,5:94,3:0|1:12907370_A_T:12907370 0|1:196,9:0.048:205:92,7:104,2:0|1:12907370_A_T:12907370 0|1:225,17:0.073:242:117,8:108,9:0|1:12907370_A_T:12907370 0|1:237,18:0.074:255:106,8:131,10:0|1:12907370_A_T:12907370 0|1:364,18:0.049:382:154,7:210,11:0|1:12907370_A_T:12907370 1 12907438 . A G . artifact_in_normal;bad_haplotype;clustered_events;mapping_quality CONTQ=93;DP=1919;ECNT=20;GERMQ=3233;MBQ=33,30;MFRL=176,209;MMQ=46,29;MPOS=21;NALOD=-2.080e+00;NLOD=67.45;POPAF=5.60;SAAF=0.020,0.020,0.025;SAPP=2.235e-03,1.128e-03,0.997;TLOD=87.30 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS 0|0:252,2:0.012:254:97,1:155,1:0|1:12907438_A_G:12907438 0|1:283,8:0.031:291:116,5:167,3:0|1:12907438_A_G:12907438 0|1:22,0:0.042:22:11,0:11,0:0|1:12907438_A_G:12907438 0|1:161,6:0.037:167:69,4:92,2:0|1:12907438_A_G:12907438 0|1:201,2:0.015:203:96,2:105,0:0|1:12907438_A_G:12907438 0|1:249,5:0.023:254:128,3:121,2:0|1:12907438_A_G:12907438 0|1:252,12:0.049:264:111,6:141,6:0|1:12907438_A_G:12907438 0|1:396,7:0.020:403:167,5:229,2:0|1:12907438_A_G:12907438 1 12907440 . G T . artifact_in_normal;bad_haplotype;clustered_events;mapping_quality;panel_of_normals;strand_artifact CONTQ=93;DP=1898;ECNT=20;GERMQ=3233;MBQ=33,32;MFRL=177,170;MMQ=46,29;MPOS=28;NALOD=-3.279e+00;NLOD=63.46;PON;POPAF=5.60;SAAF=0.030,0.00,0.029;SAPP=3.473e-12,1.000,1.511e-08;TLOD=100.83 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS 0|0:248,3:0.016:251:96,2:152,1:0|1:12907440_G_T:12907440 0|1:278,8:0.031:286:115,3:163,5:0|1:12907440_G_T:12907440 0|1:19,1:0.089:20:10,0:9,1:0|1:12907440_G_T:12907440 0|1:167,1:0.012:168:75,0:92,1:0|1:12907440_G_T:12907440 0|1:187,8:0.046:195:91,6:96,2:0|1:12907440_G_T:12907440 0|1:238,10:0.044:248:124,3:114,7:0|1:12907440_G_T:12907440 0|1:256,6:0.026:262:118,2:138,4:0|1:12907440_G_T:12907440 0|1:381,11:0.030:392:163,2:218,9:0|1:12907440_G_T:12907440 1 12907446 . C T . artifact_in_normal;bad_haplotype;clustered_events;mapping_quality CONTQ=93;DP=1837;ECNT=20;GERMQ=3233;MBQ=33,31;MFRL=176,209;MMQ=46,29;MPOS=16;NALOD=-2.079e+00;NLOD=68.06;POPAF=5.60;SAAF=0.020,0.020,0.022;SAPP=2.259e-03,1.037e-03,0.997;TLOD=81.23 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS 0|0:254,2:0.012:256:97,1:157,1:0|1:12907438_A_G:12907438 0|1:283,8:0.031:291:114,5:169,3:0|1:12907438_A_G:12907438 0|1:19,0:0.048:19:9,0:10,0:0|1:12907438_A_G:12907438 0|1:158,3:0.025:161:73,3:85,0:0|1:12907438_A_G:12907438 0|1:201,2:0.015:203:102,2:99,0:0|1:12907438_A_G:12907438 0|1:244,3:0.016:247:125,1:119,2:0|1:12907438_A_G:12907438 0|1:246,12:0.050:258:114,6:132,6:0|1:12907438_A_G:12907438 0|1:395,7:0.020:402:168,5:227,2:0|1:12907438_A_G:12907438