From 1da6cd516f1c2c96bfb55f4a42c78dbac8182230 Mon Sep 17 00:00:00 2001 From: Sebastian Schoenherr Date: Wed, 20 Dec 2023 12:50:05 +0100 Subject: [PATCH] Add new variants file --- tests/data/report/variants_ann.txt | 184 ----------------------------- 1 file changed, 184 deletions(-) diff --git a/tests/data/report/variants_ann.txt b/tests/data/report/variants_ann.txt index 0176c31..e723f17 100644 --- a/tests/data/report/variants_ann.txt +++ b/tests/data/report/variants_ann.txt @@ -50,83 +50,6 @@ NA19435.mapped.ILLUMINA.bwa.LWK.exome.20130415.bam.mt.bam PASS 16355 C T 1.00 T NA19435.mapped.ILLUMINA.bwa.LWK.exome.20130415.bam.mt.bam PASS 16362 T C 0.969 C - 32 15 17 1 16362C transition MT-DLOOP1 CR 955 81 2.5 0 1 23527 246 0.120046124 0.001255211 H:6272,A:5761,U:3796,D:2234,M:633,L3:621,W:541,R:537,L2:374,K:368,E:330,G:292,T:270,J:238,F:221,I:219,C:199,HV:160,V:131,B:100,L4:75,L0:39,N:36,L1:34,X:26,Y:12,L5:5,Q:2,Z:1 TCTCG[T/C]CCCCA 1 NA19435.mapped.ILLUMINA.bwa.LWK.exome.20130415.bam.mt.bam PASS 16399 A G 1.00 G - 26 11 15 1 16399G transition MT-DLOOP1 CR 113 21 4.8 0 0 0 6773 104 0.03455912 0.0005306583 U:5693,H:229,T:182,L3:159,L2:111,M:53,L4:50,F:46,V:35,B:33,K:32,J:26,R:22,C:20,L1:18,A:15,D:14,N:11,Y:10,HV:5,I:3,X:3,G:2,Z:1 CCTTG[A/G]CCACC 0 NA19435.mapped.ILLUMINA.bwa.LWK.exome.20130415.bam.mt.bam PASS 16519 T C 1.00 C - 6 3 3 1 16519C transition MT-DLOOP1 CR 0 11 125992 310 0.6428721 0.0015817699 H:49765,T:16791,K:14657,U:9371,B:4661,I:4320,J:4189,W:3234,X:2748,M:2333,L3:2099,A:1680,L1:1580,N:1408,C:1303,V:1071,L2:1066,D:882,R:733,F:698,HV:684,E:233,L0:167,G:154,L4:58,Z:48,P:33,Y:25,Q:1 CAGGG[T/C]CATAA 0 -HG00245.mapped.ILLUMINA.bwa.GBR.exome.20121211.bam.mt.bam PASS 152 T C 1.00 C - 37 13 24 1 152C transition MT-DLOOP2 CR 1223 197 1 1 0 1 43990 1503 0.22445825 0.0076690326 H:10316,U:6126,K:5566,T:5328,J:3365,L2:2381,I:1959,L1:1580,N:1210,A:1072,L3:955,HV:764,B:657,D:522,M:490,C:312,F:272,R:266,W:199,L0:178,G:101,Z:100,V:96,X:90,L4:37,E:35,L5:4,Y:4,P:3,L6:1,S:1 CATCC[T/C]ATTAT 0 -HG00245.mapped.ILLUMINA.bwa.GBR.exome.20121211.bam.mt.bam PASS 263 A G 1.00 G - 30 17 13 1 263G transition MT-DLOOP2 CR 5297 2 8.8 1 0 193861 11 0.9891725 5.6127315E-05 H:69957,U:24424,T:16915,J:15981,K:14811,A:6179,V:5226,B:4906,I:4397,HV:4175,M:3293,W:3235,L3:3083,C:2810,X:2768,L2:2528,D:2249,N:1688,L1:1661,R:1245,F:929,L0:394,E:334,G:299,Y:132,Z:101,L4:80,P:41,Q:11,L5:7,L6:1,S:1 CAGCC[A/G]CTTTC 0 -HG00245.mapped.ILLUMINA.bwa.GBR.exome.20121211.bam.mt.bam PASS 750 A G 1.00 G - 47 22 25 1 750G transition MT-RNR1 rRNA 5388 1 10 1 0 0 192986 13 0.98470783 6.6332286E-05 H:68880,U:24516,T:16961,J:15995,K:14812,A:6232,V:5227,B:4913,I:4415,HV:4172,M:3313,W:3242,C:3083,X:2782,L3:2713,L2:2529,D:2274,N:1670,L1:1660,R:1248,F:926,L0:416,E:334,G:299,Y:132,Z:101,L4:80,P:41,Q:11,L5:7,L6:1,S:1 AAAGG[A/G]ACAAG 0 -HG00245.mapped.ILLUMINA.bwa.GBR.exome.20121211.bam.mt.bam PASS 1438 A G 1.00 G - 35 18 17 1 1438G transition MT-RNR1 rRNA 5216 1 10 1 1 8 189889 18 0.96890545 9.1844704E-05 H:66674,U:24479,T:16955,J:15974,K:14805,A:6216,V:5227,B:4906,I:4351,HV:4180,M:3292,W:3245,L3:3087,C:2951,X:2788,L2:2525,D:2176,N:1689,R:1241,F:929,L1:801,L0:393,E:334,G:299,Y:132,Z:100,L4:79,P:41,Q:11,L5:7,L6:1,S:1 AAACT[A/G]AGAGT 0 -HG00245.mapped.ILLUMINA.bwa.GBR.exome.20121211.bam.mt.bam BLACKLISTED 3107 N T 0.093 T - 43 17 26 1 3107T -HG00245.mapped.ILLUMINA.bwa.GBR.exome.20121211.bam.mt.bam PASS 3992 C T 1.00 T - 26 12 14 1 3992T transition MT-ND1 Coding 39 3 8.1 0 1 T229M 2 T M 229 0.664 0.892809495 0.442307692 I 7 2905 10 0.014822714 5.1024836E-05 H:2845,T:29,J:16,U:7,K:4,D:3,R:1 ATACA[C/T]AAACA 0 -HG00245.mapped.ILLUMINA.bwa.GBR.exome.20121211.bam.mt.bam PASS 4418 T C 1.00 C - 23 9 14 1 4418C transition MT-TM tRNA 4 2 8.8 0 1 1 538 10 0.0027451362 5.1024836E-05 H:386,A:99,I:22,M:8,T:7,U:7,B:4,D:2,G:1,K:1,L2:1 CTAAA[T/C]AAGCT 0 -HG00245.mapped.ILLUMINA.bwa.GBR.exome.20121211.bam.mt.bam PASS 4769 A G 1.00 G - 7 5 2 1 4769G transition MT-ND2 Coding 5361 2 8.8 1 1 6 191445 4 0.9768449 2.0409934E-05 H:67068,U:24450,T:16997,J:15994,K:14794,A:6228,V:5228,B:4863,I:4415,HV:4180,M:3311,W:3244,L3:3096,C:3074,X:2789,L2:2530,D:2275,N:1691,L1:1663,R:1204,F:929,L0:416,E:333,G:299,Y:132,Z:101,L4:80,P:41,Q:11,L5:7,L6:1,S:1 ATAAT[A/G]GCTAT 0 -HG00245.mapped.ILLUMINA.bwa.GBR.exome.20121211.bam.mt.bam PASS 6776 T C 1.00 C - 9 2 7 1 6776C transition MT-CO1 Coding 108 3 8.1 0 1 8 7606 66 0.03880949 0.00033676391 H:7593,M:5,D:2,U:2,A:1,HV:1,L2:1,W:1 CACCA[T/C]ATATT 0 -HG00245.mapped.ILLUMINA.bwa.GBR.exome.20121211.bam.mt.bam PASS 8860 A G 1.00 G - 6 0 6 1 8860G transition MT-ATP6 Coding 5417 1 10 1 0 T112A 1 T A 112 0.369 0.287079116 0.75 V 5 193581 40 0.98774385 0.00020409934 H:69519,U:24441,T:16949,J:15952,K:14755,A:6209,V:5209,B:4891,I:4363,HV:4168,M:3291,W:3239,L3:3079,C:3061,X:2781,L2:2497,D:2265,N:1685,L1:1648,R:1239,F:927,L0:410,E:333,G:298,Y:132,Z:101,L4:78,P:41,Q:11,L5:7,L6:1,S:1 CGGGC[A/G]CAGTG 0 -HG00245.mapped.ILLUMINA.bwa.GBR.exome.20121211.bam.mt.bam PASS 8950 G A 1.00 A - 36 19 17 1 8950A transition MT-ATP6 Coding 6 3 8.1 0 1 V142I 1 V I 142 0.439 0.375774268 0.711538462 V 2 234 13 0.0011939812 6.6332286E-05 H:150,U:60,T:9,M:8,HV:2,K:2,C:1,F:1,W:1 TACTA[G/A]TTATT 0 -HG00245.mapped.ILLUMINA.bwa.GBR.exome.20121211.bam.mt.bam PASS 10754 A C 1.00 C - 40 14 26 1 10754C transversion MT-ND4L Coding 7 1 10 0 0 625 1 0.0031890522 5.1024836E-06 H:624,L1:1 AACCT[A/C]CTCCA 0 -HG00245.mapped.ILLUMINA.bwa.GBR.exome.20121211.bam.mt.bam PASS 15326 A G 1.00 G - 57 34 23 1 15326G transition MT-CYB Coding 5397 1 10 1 1 T194A 1 T A 194 0.452 0.395040626 0.711538462 III 6 193970 20 0.9897287 0.00010204967 H:69739,U:24412,T:16959,J:15994,K:14814,A:6212,V:5218,B:4902,I:4415,HV:4157,M:3306,W:3226,L3:3095,C:3063,X:2788,L2:2494,D:2261,N:1687,L1:1663,R:1216,F:929,L0:416,E:334,G:299,Y:132,Z:98,L4:80,P:41,Q:11,L5:7,L6:1,S:1 TAGCA[A/G]CACTC 0 -HG00245.mapped.ILLUMINA.bwa.GBR.exome.20121211.bam.mt.bam PASS 16519 T C 1.00 C - 30 14 16 1 16519C transition MT-DLOOP1 CR 0 11 125992 310 0.6428721 0.0015817699 H:49765,T:16791,K:14657,U:9371,B:4661,I:4320,J:4189,W:3234,X:2748,M:2333,L3:2099,A:1680,L1:1580,N:1408,C:1303,V:1071,L2:1066,D:882,R:733,F:698,HV:684,E:233,L0:167,G:154,L4:58,Z:48,P:33,Y:25,Q:1 CAGGG[T/C]CATAA 0 -HG01060.mapped.ILLUMINA.bwa.PUR.exome.20120522.bam.mt.bam PASS 64 C T 1.00 T - 33 23 10 1 64T transition MT-DLOOP2 CR 151 17 5.2 0 0 5500 334 0.028063659 0.0017042294 A:4254,R:402,L0:221,H:169,HV:143,B:71,U:58,J:44,T:22,X:21,K:19,F:15,D:14,C:13,L2:10,V:7,M:5,L3:4,W:3,L1:2,G:1,I:1,N:1 TTCGT[C/T]TGGGG 0 -HG01060.mapped.ILLUMINA.bwa.PUR.exome.20120522.bam.mt.bam PASS 73 A G 1.00 G - 34 27 7 1 73G transition MT-DLOOP2 CR 4247 13 5.6 1 0 1 119934 60 0.61196125 0.000306149 U:24492,T:16962,J:15973,K:14791,A:6089,H:5724,B:4872,I:4409,M:3305,W:3229,C:3050,L3:3046,X:2786,L2:2527,D:2267,N:1686,L1:1657,F:929,R:825,E:334,G:298,HV:183,Y:132,Z:101,V:95,L4:80,P:40,L0:32,Q:11,L5:7,L6:1,S:1 GGGGT[A/G]TGCAC 0 -HG01060.mapped.ILLUMINA.bwa.PUR.exome.20120522.bam.mt.bam PASS 146 T C 1.00 C - 38 19 19 1 146C transition MT-DLOOP2 CR 787 122 1.8 1 0 1 25525 622 0.13024089 0.0031737448 K:6303,A:5755,H:3994,L2:2255,U:1427,T:1297,B:1084,J:1056,M:613,X:253,D:222,C:217,HV:178,R:169,L3:129,N:108,I:102,L1:77,F:67,L4:51,Y:37,L0:30,W:28,V:23,E:21,G:14,Q:10,P:2,Z:2,L6:1 CTGCC[T/C]CATCC 1 -HG01060.mapped.ILLUMINA.bwa.PUR.exome.20120522.bam.mt.bam PASS 153 A G 1.00 G - 45 22 23 1 153G transition MT-DLOOP2 CR 217 19 5 0 1 8488 125 0.04330988 0.00063781044 A:5194,X:2276,H:568,U:80,M:75,K:72,B:44,J:36,T:29,L2:19,C:18,V:18,I:13,D:12,L3:11,R:6,F:5,W:4,N:3,HV:2,Y:2,L0:1 ATCCT[A/G]TTATT 0 -HG01060.mapped.ILLUMINA.bwa.PUR.exome.20120522.bam.mt.bam PASS 235 A G 1.00 G - 47 20 27 1 235G transition MT-DLOOP2 CR 173 10 6.1 0 1 6435 63 0.03283448 0.00032145646 A:6002,H:103,U:65,J:52,T:51,X:34,L3:28,F:20,HV:20,K:11,N:11,V:10,B:7,D:6,M:6,C:5,R:3,L2:1 ACATA[A/G]TAATA 0 -HG01060.mapped.ILLUMINA.bwa.PUR.exome.20120522.bam.mt.bam PASS 263 A G 1.00 G - 44 16 28 1 263G transition MT-DLOOP2 CR 5297 2 8.8 1 0 193861 11 0.9891725 5.6127315E-05 H:69957,U:24424,T:16915,J:15981,K:14811,A:6179,V:5226,B:4906,I:4397,HV:4175,M:3293,W:3235,L3:3083,C:2810,X:2768,L2:2528,D:2249,N:1688,L1:1661,R:1245,F:929,L0:394,E:334,G:299,Y:132,Z:101,L4:80,P:41,Q:11,L5:7,L6:1,S:1 CAGCC[A/G]CTTTC 0 -HG01060.mapped.ILLUMINA.bwa.PUR.exome.20120522.bam.mt.bam PASS 514 C D 0.84 D 0.84 C 0.16 81 48 33 2 514D -HG01060.mapped.ILLUMINA.bwa.PUR.exome.20120522.bam.mt.bam PASS 515 A D 0.819 D 0.819 A 0.157 83 51 32 2 515D -HG01060.mapped.ILLUMINA.bwa.PUR.exome.20120522.bam.mt.bam PASS 663 A G 1.00 G - 79 35 44 1 663G transition MT-RNR1 rRNA 159 2 8.8 0 1 24 6214 16 0.031706832 8.163974E-05 A:6199,T:9,U:3,H:1,K:1,L3:1 GTCCT[A/G]GCCTT 0 -HG01060.mapped.ILLUMINA.bwa.PUR.exome.20120522.bam.mt.bam PASS 750 A G 1.00 G - 60 27 33 1 750G transition MT-RNR1 rRNA 5388 1 10 1 0 0 192986 13 0.98470783 6.6332286E-05 H:68880,U:24516,T:16961,J:15995,K:14812,A:6232,V:5227,B:4913,I:4415,HV:4172,M:3313,W:3242,C:3083,X:2782,L3:2713,L2:2529,D:2274,N:1670,L1:1660,R:1248,F:926,L0:416,E:334,G:299,Y:132,Z:101,L4:80,P:41,Q:11,L5:7,L6:1,S:1 AAAGG[A/G]ACAAG 0 -HG01060.mapped.ILLUMINA.bwa.PUR.exome.20120522.bam.mt.bam PASS 1438 A G 1.00 G - 46 24 22 1 1438G transition MT-RNR1 rRNA 5216 1 10 1 1 8 189889 18 0.96890545 9.1844704E-05 H:66674,U:24479,T:16955,J:15974,K:14805,A:6216,V:5227,B:4906,I:4351,HV:4180,M:3292,W:3245,L3:3087,C:2951,X:2788,L2:2525,D:2176,N:1689,R:1241,F:929,L1:801,L0:393,E:334,G:299,Y:132,Z:100,L4:79,P:41,Q:11,L5:7,L6:1,S:1 AAACT[A/G]AGAGT 0 -HG01060.mapped.ILLUMINA.bwa.PUR.exome.20120522.bam.mt.bam PASS 1736 A G 1.00 G - 43 22 21 1 1736G transition MT-RNR2 rRNA 158 1 10 0 1 6196 18 0.031614985 9.1844704E-05 A:6179,U:9,B:5,H:1,K:1,T:1 ACCCA[A/G]ATAAA 0 -HG01060.mapped.ILLUMINA.bwa.PUR.exome.20120522.bam.mt.bam PASS 2706 A G 1.00 G - 16 4 12 1 2706G transition MT-RNR2 rRNA 4392 1 10 1 0 2 124135 14 0.63339674 7.143477E-05 U:24425,T:16996,J:15734,K:14818,A:6229,V:5227,B:4906,I:4409,HV:4180,M:3287,W:3245,L3:3094,C:3082,X:2789,L2:2525,D:2242,N:1691,L1:1662,R:1249,F:927,L0:400,E:334,G:299,Y:132,Z:101,L4:75,P:41,H:16,Q:11,L5:7,L6:1,S:1 GGCAT[A/G]ACACA 0 -HG01060.mapped.ILLUMINA.bwa.PUR.exome.20120522.bam.mt.bam BLACKLISTED 3107 N T 0.192 T - 26 14 12 1 3107T -HG01060.mapped.ILLUMINA.bwa.PUR.exome.20120522.bam.mt.bam PASS 3202 T C 0.98 C - 49 25 24 1 3202C transition MT-RNR2 rRNA 4 2 8.8 0 1 0 255 11 0.0013011333 5.6127315E-05 A:157,H:48,J:21,T:5,U:5,I:3,L2:3,W:3,HV:2,M:2,X:2,K:1,L1:1,L3:1,V:1 TATTA[T/C]ACCCA 0 -HG01060.mapped.ILLUMINA.bwa.PUR.exome.20120522.bam.mt.bam PASS 4248 T C 1.00 C - 26 14 12 1 4248C transition MT-ND1 Coding 181 3 8.1 0 1 12 6494 35 0.033135526 0.00017858692 A:6162,E:219,H:40,J:26,T:13,U:12,HV:9,D:4,L3:3,B:2,C:2,K:1,R:1 AGCAT[T/C]CCCCC 1 -HG01060.mapped.ILLUMINA.bwa.PUR.exome.20120522.bam.mt.bam PASS 4769 A G 1.00 G - 16 16 0 1 4769G transition MT-ND2 Coding 5361 2 8.8 1 1 6 191445 4 0.9768449 2.0409934E-05 H:67068,U:24450,T:16997,J:15994,K:14794,A:6228,V:5228,B:4863,I:4415,HV:4180,M:3311,W:3244,L3:3096,C:3074,X:2789,L2:2530,D:2275,N:1691,L1:1663,R:1204,F:929,L0:416,E:333,G:299,Y:132,Z:101,L4:80,P:41,Q:11,L5:7,L6:1,S:1 ATAAT[A/G]GCTAT 0 -HG01060.mapped.ILLUMINA.bwa.PUR.exome.20120522.bam.mt.bam PASS 4824 A G 1.00 G - 34 26 8 1 4824G transition MT-ND2 Coding 161 3 8.1 0 1 T119A 1 T A 119 0.368 0.285977086 0.980769231 I 6242 13 0.0318497 6.6332286E-05 A:6175,B:24,F:12,J:11,L1:11,K:3,L3:2,M:2,D:1,H:1 AGGTT[A/G]CCCAA 0 -HG01060.mapped.ILLUMINA.bwa.PUR.exome.20120522.bam.mt.bam PASS 7028 C T 1.00 T - 32 9 23 1 7028T transition MT-CO1 Coding 4457 1 10 1 1 4 123485 202 0.63008016 0.0010307017 U:24306,T:16822,J:15855,K:14698,A:6167,V:5177,B:4871,I:4374,HV:4140,M:3283,W:3217,L3:3086,C:3059,X:2760,L2:2508,D:2261,N:1676,L1:1640,R:1237,F:921,L0:412,E:332,G:297,Y:131,Z:101,L4:80,P:40,H:14,Q:11,L5:7,L6:1,S:1 GTAGC[C/T]CACTT 0 -HG01060.mapped.ILLUMINA.bwa.PUR.exome.20120522.bam.mt.bam PASS 8027 G A 1.00 A - 37 19 18 1 8027A transition MT-CO2 Coding 161 7 6.7 0 1 A148T 1 A T 148 0.241 0.175466852 0.711538462 IV 6969 39 0.035559207 0.00019899686 A:5797,L1:804,H:120,U:96,C:23,J:17,R:17,K:15,L0:15,T:15,M:10,B:8,D:7,I:7,N:6,HV:4,X:4,L2:2,G:1,V:1 TTGAA[G/A]CCCCC 0 -HG01060.mapped.ILLUMINA.bwa.PUR.exome.20120522.bam.mt.bam PASS 8460 A G 1.00 G - 45 25 20 1 8460G transition MT-ATP8 Coding 20 3 8.1 0 1 N32S 2 N S 32 0.309 0.227918614 0.673076923 V 313 4 0.0015970774 2.0409934E-05 A:119,L0:90,J:48,H:38,T:7,L3:6,B:2,I:1,U:1,W:1 CACAA[A/G]CTACC 0 -HG01060.mapped.ILLUMINA.bwa.PUR.exome.20120522.bam.mt.bam PASS 8794 C T 1.00 T - 22 10 12 1 8794T transition MT-ATP6 Coding 158 1 10 0 1 H90Y 1 H Y 90 0.608 0.719810952 0.788461538 V 0 6115 33 0.031201687 0.00016838196 A:6105,HV:6,U:2,N:1,T:1 TGCCT[C/T]ACTCA 0 -HG01060.mapped.ILLUMINA.bwa.PUR.exome.20120522.bam.mt.bam PASS 8860 A G 1.00 G - 13 2 11 1 8860G transition MT-ATP6 Coding 5417 1 10 1 0 T112A 1 T A 112 0.369 0.287079116 0.75 V 5 193581 40 0.98774385 0.00020409934 H:69519,U:24441,T:16949,J:15952,K:14755,A:6209,V:5209,B:4891,I:4363,HV:4168,M:3291,W:3239,L3:3079,C:3061,X:2781,L2:2497,D:2265,N:1685,L1:1648,R:1239,F:927,L0:410,E:333,G:298,Y:132,Z:101,L4:78,P:41,Q:11,L5:7,L6:1,S:1 CGGGC[A/G]CAGTG 0 -HG01060.mapped.ILLUMINA.bwa.PUR.exome.20120522.bam.mt.bam PASS 11719 G A 1.00 A - 49 24 25 1 11719A transition MT-ND4 Coding 4272 3 8.1 1 1 14 115534 48 0.5895103 0.0002449192 U:24445,T:16959,J:15959,K:14799,A:6215,B:4902,I:4408,M:3306,W:3236,L3:3093,C:3076,X:2782,L2:2528,D:2273,N:1686,L1:1662,H:993,F:929,R:816,L0:416,E:334,G:297,Y:132,Z:98,L4:79,P:41,V:36,HV:14,Q:11,L5:7,L6:1,S:1 CACGG[G/A]CTTAC 0 -HG01060.mapped.ILLUMINA.bwa.PUR.exome.20120522.bam.mt.bam PASS 12007 G A 1.00 A - 52 32 20 1 12007A transition MT-ND4 Coding 337 14 5.5 0 1 2 9041 26 0.04613155 0.00013266457 A:5812,J:1845,M:467,L0:415,T:178,N:125,H:89,K:21,R:20,L2:16,D:10,L1:8,HV:7,U:7,B:6,C:3,I:3,X:3,L3:2,W:2,F:1,V:1 CAATG[G/A]GGCTC 0 -HG01060.mapped.ILLUMINA.bwa.PUR.exome.20120522.bam.mt.bam PASS 12705 C T 0.978 T - 45 21 24 1 12705T transition MT-ND5 Coding 2481 1 10 1 1 12 35323 91 0.18023501 0.00046432597 A:6125,I:4351,M:3286,W:3217,L3:3070,C:3053,X:2758,L2:2512,D:2245,N:1677,L1:1651,L0:413,E:330,G:297,Y:132,Z:101,L4:79,Q:11,L5:7,H:4,V:2,L6:1,S:1 CTCAT[C/T]TTCCT 1 -HG01060.mapped.ILLUMINA.bwa.PUR.exome.20120522.bam.mt.bam PASS 14766 C T 1.00 T - 36 16 20 1 14766T transition MT-CYB Coding 4286 1 10 1 0 T7I 2 T I 7 0.165 0.130992813 0.692307692 III 3 114700 34 0.58525485 0.00017348444 U:24456,T:16974,J:15968,K:14796,A:6223,B:4819,I:4412,M:3282,W:3243,L3:3090,C:3075,X:2786,L2:2530,D:2268,N:1690,L1:1654,R:1248,F:929,L0:415,G:299,E:167,Y:131,Z:100,L4:79,P:41,Q:11,L5:7,H:5,L6:1,S:1 CAAAA[C/T]TAACC 0 -HG01060.mapped.ILLUMINA.bwa.PUR.exome.20120522.bam.mt.bam PASS 15326 A G 1.00 G - 42 29 13 1 15326G transition MT-CYB Coding 5397 1 10 1 1 T194A 1 T A 194 0.452 0.395040626 0.711538462 III 6 193970 20 0.9897287 0.00010204967 H:69739,U:24412,T:16959,J:15994,K:14814,A:6212,V:5218,B:4902,I:4415,HV:4157,M:3306,W:3226,L3:3095,C:3063,X:2788,L2:2494,D:2261,N:1687,L1:1663,R:1216,F:929,L0:416,E:334,G:299,Y:132,Z:98,L4:80,P:41,Q:11,L5:7,L6:1,S:1 TAGCA[A/G]CACTC 0 -HG01060.mapped.ILLUMINA.bwa.PUR.exome.20120522.bam.mt.bam PASS 15924 A G 1.00 G - 70 33 37 1 15924G transition MT-TT tRNA 138 31 4.2 0 1 1 9925 112 0.050642148 0.00057147816 I:4341,U:2119,K:1988,H:518,A:223,M:97,L2:87,J:70,L1:65,T:65,V:63,W:60,B:50,D:50,L3:35,R:26,N:24,X:12,C:10,F:7,HV:5,G:4,P:3,L0:1,L5:1,Q:1 TGTAA[A/G]CCGGA 0 -HG01060.mapped.ILLUMINA.bwa.PUR.exome.20120522.bam.mt.bam PASS 16111 C T 0.968 T - 63 40 23 1 16111T transition MT-DLOOP1 CR 144 24 4.6 0 0 7040 94 0.035921484 0.00047963343 A:5007,H:616,B:479,U:323,M:104,L3:80,N:75,HV:72,T:39,K:34,F:30,I:30,L1:29,V:22,X:19,J:18,D:17,L0:14,L2:13,W:7,R:4,G:3,C:2,L5:2,Z:1 GCCAG[C/T]CACCA 0 -HG01060.mapped.ILLUMINA.bwa.PUR.exome.20120522.bam.mt.bam PASS 16223 C T 1.00 T - 48 25 23 1 16223T transition MT-DLOOP1 CR 2397 7 6.7 1 0 35639 196 0.18184741 0.0010000868 A:6047,I:4359,W:3177,L3:3042,M:3026,C:2985,X:2629,L2:2415,D:2167,N:1658,L1:1609,K:699,L0:406,E:328,G:295,H:231,U:227,Z:99,L4:77,B:57,V:29,HV:24,T:23,Q:11,L5:6,J:5,R:5,F:1,L6:1,S:1 CAACC[C/T]TCAAC 0 -HG01060.mapped.ILLUMINA.bwa.PUR.exome.20120522.bam.mt.bam PASS 16290 C T 1.00 T - 39 22 17 1 16290T transition MT-DLOOP1 CR 201 16 5.3 0 0 6842 67 0.034911193 0.0003418664 A:6150,H:182,U:115,J:104,M:65,L2:57,X:42,V:22,D:20,K:20,L1:13,T:13,W:8,B:6,I:5,L3:5,R:5,N:3,HV:2,L0:2,E:1,F:1,G:1 ACCTA[C/T]CCACC 0 -HG01060.mapped.ILLUMINA.bwa.PUR.exome.20120522.bam.mt.bam PASS 16319 G A 1.00 A - 51 20 31 1 16319A transition MT-DLOOP1 CR 308 39 3.8 0 0 9103 71 0.046447907 0.00036227633 A:6168,J:635,H:541,K:404,M:281,U:229,I:215,B:120,L3:102,D:94,N:67,C:60,T:42,V:37,R:26,W:20,X:14,HV:10,L2:10,Y:10,G:8,F:4,E:2,L1:2,P:1,S:1 ATAAA[G/A]CCATT 1 -HG01060.mapped.ILLUMINA.bwa.PUR.exome.20120522.bam.mt.bam PASS 16362 T C 0.982 C - 55 22 33 1 16362C transition MT-DLOOP1 CR 955 81 2.5 0 1 23527 246 0.120046124 0.001255211 H:6272,A:5761,U:3796,D:2234,M:633,L3:621,W:541,R:537,L2:374,K:368,E:330,G:292,T:270,J:238,F:221,I:219,C:199,HV:160,V:131,B:100,L4:75,L0:39,N:36,L1:34,X:26,Y:12,L5:5,Q:2,Z:1 TCTCG[T/C]CCCCA 1 -HG00285.mapped.ILLUMINA.bwa.FIN.exome.20120522.bam.mt.bam PASS 73 A G 1.00 G - 26 17 9 1 73G transition MT-DLOOP2 CR 4247 13 5.6 1 0 1 119934 60 0.61196125 0.000306149 U:24492,T:16962,J:15973,K:14791,A:6089,H:5724,B:4872,I:4409,M:3305,W:3229,C:3050,L3:3046,X:2786,L2:2527,D:2267,N:1686,L1:1657,F:929,R:825,E:334,G:298,HV:183,Y:132,Z:101,V:95,L4:80,P:40,L0:32,Q:11,L5:7,L6:1,S:1 GGGGT[A/G]TGCAC 0 -HG00285.mapped.ILLUMINA.bwa.FIN.exome.20120522.bam.mt.bam PASS 150 C T 1.00 T - 42 24 18 1 150T transition MT-DLOOP2 CR 604 74 2.7 0 0 19751 168 0.100779146 0.0008572172 U:8512,J:3334,L3:1817,H:1122,T:1066,L2:841,K:639,M:505,D:334,B:313,N:258,HV:152,W:135,R:132,V:116,F:99,I:98,C:74,G:63,A:42,L4:42,L1:22,X:19,L0:12,P:2,E:1,S:1 CTCAT[C/T]CTATT 0 -HG00285.mapped.ILLUMINA.bwa.FIN.exome.20120522.bam.mt.bam PASS 217 T C 1.00 C - 47 25 22 1 217C transition MT-DLOOP2 CR 37 7 6.7 0 1 2448 100 0.01249088 0.00051024836 U:2254,H:68,M:31,D:24,K:24,T:9,A:8,L3:6,B:5,R:4,V:4,F:3,C:2,HV:2,L2:2,I:1,W:1 TTAAT[T/C]AATGC 0 -HG00285.mapped.ILLUMINA.bwa.FIN.exome.20120522.bam.mt.bam PASS 263 A G 1.00 G - 41 18 23 1 263G transition MT-DLOOP2 CR 5297 2 8.8 1 0 193861 11 0.9891725 5.6127315E-05 H:69957,U:24424,T:16915,J:15981,K:14811,A:6179,V:5226,B:4906,I:4397,HV:4175,M:3293,W:3235,L3:3083,C:2810,X:2768,L2:2528,D:2249,N:1688,L1:1661,R:1245,F:929,L0:394,E:334,G:299,Y:132,Z:101,L4:80,P:41,Q:11,L5:7,L6:1,S:1 CAGCC[A/G]CTTTC 0 -HG00285.mapped.ILLUMINA.bwa.FIN.exome.20120522.bam.mt.bam PASS 302 A C 0.286 A 0.714 C 0.286 28 11 17 2 302C transversion MT-DLOOP2 CR 1 ACCAA[A/C]CCCCC 1 -HG00285.mapped.ILLUMINA.bwa.FIN.exome.20120522.bam.mt.bam PASS 750 A G 1.00 G - 42 30 12 1 750G transition MT-RNR1 rRNA 5388 1 10 1 0 0 192986 13 0.98470783 6.6332286E-05 H:68880,U:24516,T:16961,J:15995,K:14812,A:6232,V:5227,B:4913,I:4415,HV:4172,M:3313,W:3242,C:3083,X:2782,L3:2713,L2:2529,D:2274,N:1670,L1:1660,R:1248,F:926,L0:416,E:334,G:299,Y:132,Z:101,L4:80,P:41,Q:11,L5:7,L6:1,S:1 AAAGG[A/G]ACAAG 0 -HG00285.mapped.ILLUMINA.bwa.FIN.exome.20120522.bam.mt.bam PASS 1438 A G 1.00 G - 39 21 18 1 1438G transition MT-RNR1 rRNA 5216 1 10 1 1 8 189889 18 0.96890545 9.1844704E-05 H:66674,U:24479,T:16955,J:15974,K:14805,A:6216,V:5227,B:4906,I:4351,HV:4180,M:3292,W:3245,L3:3087,C:2951,X:2788,L2:2525,D:2176,N:1689,R:1241,F:929,L1:801,L0:393,E:334,G:299,Y:132,Z:100,L4:79,P:41,Q:11,L5:7,L6:1,S:1 AAACT[A/G]AGAGT 0 -HG00285.mapped.ILLUMINA.bwa.FIN.exome.20120522.bam.mt.bam PASS 2706 A G 1.00 G - 26 5 21 1 2706G transition MT-RNR2 rRNA 4392 1 10 1 0 2 124135 14 0.63339674 7.143477E-05 U:24425,T:16996,J:15734,K:14818,A:6229,V:5227,B:4906,I:4409,HV:4180,M:3287,W:3245,L3:3094,C:3082,X:2789,L2:2525,D:2242,N:1691,L1:1662,R:1249,F:927,L0:400,E:334,G:299,Y:132,Z:101,L4:75,P:41,H:16,Q:11,L5:7,L6:1,S:1 GGCAT[A/G]ACACA 0 -HG00285.mapped.ILLUMINA.bwa.FIN.exome.20120522.bam.mt.bam BLACKLISTED 3107 N T 0.086 T - 35 16 19 1 3107T -HG00285.mapped.ILLUMINA.bwa.FIN.exome.20120522.bam.mt.bam PASS 3197 T C 1.00 C - 47 28 19 1 3197C transition MT-RNR2 rRNA 227 4 7.6 0 0 1 14578 19 0.074384004 9.694719E-05 U:14334,H:166,B:43,J:10,C:9,W:9,L3:3,A:1,F:1,HV:1,X:1 CTTAG[T/C]ATTAT 0 -HG00285.mapped.ILLUMINA.bwa.FIN.exome.20120522.bam.mt.bam PASS 4769 A G 1.00 G - 11 9 2 1 4769G transition MT-ND2 Coding 5361 2 8.8 1 1 6 191445 4 0.9768449 2.0409934E-05 H:67068,U:24450,T:16997,J:15994,K:14794,A:6228,V:5228,B:4863,I:4415,HV:4180,M:3311,W:3244,L3:3096,C:3074,X:2789,L2:2530,D:2275,N:1691,L1:1663,R:1204,F:929,L0:416,E:333,G:299,Y:132,Z:101,L4:80,P:41,Q:11,L5:7,L6:1,S:1 ATAAT[A/G]GCTAT 0 -HG00285.mapped.ILLUMINA.bwa.FIN.exome.20120522.bam.mt.bam PASS 5656 A G 0.964 G - 28 8 20 1 5656G transition - 58 6 7 0 1 14 2682 16 0.01368486 8.163974E-05 U:2622,I:16,H:12,T:8,L5:5,A:4,V:3,F:2,J:2,K:2,M:2,N:2,B:1,L2:1 CCCTT[A/G]CTAGA 0 -HG00285.mapped.ILLUMINA.bwa.FIN.exome.20120522.bam.mt.bam PASS 6068 C T 1.00 T - 29 15 14 1 6068T transition MT-CO1 Coding 1 5 6 3 3.06149E-05 1.530745E-05 V:3,HV:2,L2:1 TACAA[C/T]GTTAT 0 -HG00285.mapped.ILLUMINA.bwa.FIN.exome.20120522.bam.mt.bam PASS 7028 C T 1.00 T - 28 10 18 1 7028T transition MT-CO1 Coding 4457 1 10 1 1 4 123485 202 0.63008016 0.0010307017 U:24306,T:16822,J:15855,K:14698,A:6167,V:5177,B:4871,I:4374,HV:4140,M:3283,W:3217,L3:3086,C:3059,X:2760,L2:2508,D:2261,N:1676,L1:1640,R:1237,F:921,L0:412,E:332,G:297,Y:131,Z:101,L4:80,P:40,H:14,Q:11,L5:7,L6:1,S:1 GTAGC[C/T]CACTT 0 -HG00285.mapped.ILLUMINA.bwa.FIN.exome.20120522.bam.mt.bam PASS 7768 A G 1.00 G - 29 18 11 1 7768G transition MT-CO2 Coding 109 1 10 0 1 1 6390 31 0.03260487 0.00015817699 U:6368,B:20,K:1,L2:1 GAAAT[A/G]GAAAC 0 -HG00285.mapped.ILLUMINA.bwa.FIN.exome.20120522.bam.mt.bam PASS 8860 A G 1.00 G - 12 4 8 1 8860G transition MT-ATP6 Coding 5417 1 10 1 0 T112A 1 T A 112 0.369 0.287079116 0.75 V 5 193581 40 0.98774385 0.00020409934 H:69519,U:24441,T:16949,J:15952,K:14755,A:6209,V:5209,B:4891,I:4363,HV:4168,M:3291,W:3239,L3:3079,C:3061,X:2781,L2:2497,D:2265,N:1685,L1:1648,R:1239,F:927,L0:410,E:333,G:298,Y:132,Z:101,L4:78,P:41,Q:11,L5:7,L6:1,S:1 CGGGC[A/G]CAGTG 0 -HG00285.mapped.ILLUMINA.bwa.FIN.exome.20120522.bam.mt.bam PASS 9477 G A 1.00 A - 43 23 20 1 9477A transition MT-CO3 Coding 222 4 7.6 0 1 V91I 1 V I 91 0.249 0.180949752 0.673076923 IV 12 14429 34 0.07362373 0.00017348444 U:14308,H:47,L3:28,K:17,T:7,D:5,B:4,A:3,HV:2,L1:2,M:2,I:1,J:1,R:1,V:1 CAGAA[G/A]TTTTT 0 -HG00285.mapped.ILLUMINA.bwa.FIN.exome.20120522.bam.mt.bam PASS 11467 A G 1.00 G - 48 25 23 1 11467G transition MT-ND4 Coding 732 2 8.8 0 1 39231 61 0.20017552 0.0003112515 U:24443,K:14738,H:49,T:1 CTCTT[A/G]AAACT 0 -HG00285.mapped.ILLUMINA.bwa.FIN.exome.20120522.bam.mt.bam PASS 11719 G A 1.00 A - 47 27 20 1 11719A transition MT-ND4 Coding 4272 3 8.1 1 1 14 115534 48 0.5895103 0.0002449192 U:24445,T:16959,J:15959,K:14799,A:6215,B:4902,I:4408,M:3306,W:3236,L3:3093,C:3076,X:2782,L2:2528,D:2273,N:1686,L1:1662,H:993,F:929,R:816,L0:416,E:334,G:297,Y:132,Z:98,L4:79,P:41,V:36,HV:14,Q:11,L5:7,L6:1,S:1 CACGG[G/A]CTTAC 0 -HG00285.mapped.ILLUMINA.bwa.FIN.exome.20120522.bam.mt.bam PASS 12308 A G 1.00 G - 56 27 29 1 12308G transition MT-TL2 tRNA 729 2 8.8 0 1 39183 28 0.19993061 0.00014286954 U:24391,K:14771,T:18,R:2,H:1 CCCAA[A/G]AATTT 0 -HG00285.mapped.ILLUMINA.bwa.FIN.exome.20120522.bam.mt.bam PASS 12372 G A 1.00 A - 42 22 20 1 12372A transition MT-ND5 Coding 790 8 6.5 0 0 3 39604 70 0.20207874 0.00035717385 U:24408,K:14749,N:226,M:66,H:55,B:17,J:14,T:13,A:11,HV:9,G:8,V:6,C:5,D:4,L3:4,I:3,X:2,F:1,L1:1,L2:1,W:1 ACCCT[G/A]ACTTC 0 -HG00285.mapped.ILLUMINA.bwa.FIN.exome.20120522.bam.mt.bam PASS 12618 G A 1.00 A - 54 20 34 1 12618A transition MT-ND5 Coding 34 9 6.3 0 1 19 1569 26 0.008005796 0.00013266457 U:1425,H:40,A:26,R:22,L2:12,M:12,C:5,B:3,F:3,K:3,L3:3,W:3,J:2,L1:2,T:2,D:1,G:1,I:1,L4:1,N:1,X:1 GCATT[G/A]TTCGT 0 -HG00285.mapped.ILLUMINA.bwa.FIN.exome.20120522.bam.mt.bam PASS 13617 T C 1.00 C - 49 17 32 1 13617C transition MT-ND5 Coding 220 2 8.8 0 1 14349 33 0.07321554 0.00016838196 U:14304,H:28,V:4,C:3,L2:3,M:3,D:2,A:1,L3:1 ATAAT[T/C]CTTCT 0 -HG00285.mapped.ILLUMINA.bwa.FIN.exome.20120522.bam.mt.bam PASS 14182 T C 1.00 C - 58 29 29 1 14182C transition MT-ND6 Coding 138 9 6.3 0 1 2 7171 16 0.03658991 8.163974E-05 U:6456,I:466,H:83,L0:45,L3:43,B:18,M:17,K:14,L2:7,J:6,L1:4,T:4,A:2,X:2,C:1,HV:1,N:1,R:1 ATATA[T/C]ACACC 0 -HG00285.mapped.ILLUMINA.bwa.FIN.exome.20120522.bam.mt.bam PASS 14766 C T 1.00 T - 61 28 33 1 14766T transition MT-CYB Coding 4286 1 10 1 0 T7I 2 T I 7 0.165 0.130992813 0.692307692 III 3 114700 34 0.58525485 0.00017348444 U:24456,T:16974,J:15968,K:14796,A:6223,B:4819,I:4412,M:3282,W:3243,L3:3090,C:3075,X:2786,L2:2530,D:2268,N:1690,L1:1654,R:1248,F:929,L0:415,G:299,E:167,Y:131,Z:100,L4:79,P:41,Q:11,L5:7,H:5,L6:1,S:1 CAAAA[C/T]TAACC 0 -HG00285.mapped.ILLUMINA.bwa.FIN.exome.20120522.bam.mt.bam PASS 15326 A G 1.00 G - 47 23 24 1 15326G transition MT-CYB Coding 5397 1 10 1 1 T194A 1 T A 194 0.452 0.395040626 0.711538462 III 6 193970 20 0.9897287 0.00010204967 H:69739,U:24412,T:16959,J:15994,K:14814,A:6212,V:5218,B:4902,I:4415,HV:4157,M:3306,W:3226,L3:3095,C:3063,X:2788,L2:2494,D:2261,N:1687,L1:1663,R:1216,F:929,L0:416,E:334,G:299,Y:132,Z:98,L4:80,P:41,Q:11,L5:7,L6:1,S:1 TAGCA[A/G]CACTC 0 -HG00285.mapped.ILLUMINA.bwa.FIN.exome.20120522.bam.mt.bam PASS 16189 T C 0.986 C - 69 34 35 1 16189C transition MT-DLOOP1 CR 1310 110 2 1 1 CCCCC[T/C]CCCCA 1 2 961 3572 -HG00285.mapped.ILLUMINA.bwa.FIN.exome.20120522.bam.mt.bam PASS 16192 C T 0.969 T - 64 33 31 1 16192T transition MT-DLOOP1 CR 242 25 4.5 0 0 CCTCC[C/T]CATGC 0 -HG00285.mapped.ILLUMINA.bwa.FIN.exome.20120522.bam.mt.bam PASS 16270 C T 1.00 T - 63 25 38 1 16270T transition MT-DLOOP1 CR 284 16 5.3 0 0 14952 109 0.07629233 0.0005561707 U:12934,L1:833,H:460,K:381,I:97,M:45,V:42,T:32,A:19,B:18,J:18,C:15,L2:13,D:10,W:9,L3:6,P:6,R:5,L0:3,X:2,F:1,G:1,HV:1,N:1 ACCCA[C/T]TAGGA 0 HG02236.mapped.ILLUMINA.bwa.IBS.exome.20130415.bam.mt.bam PASS 214 A G 0.926 G - 27 14 13 1 214G transition MT-DLOOP2 CR 9 8 6.5 0 1 568 791 0.0028982107 0.0040360643 A:243,C:65,H:61,K:39,B:33,T:24,U:19,D:18,J:16,M:14,R:9,W:8,Z:8,L3:6,N:3,F:2 TAATT[A/G]ATTAA 0 HG02236.mapped.ILLUMINA.bwa.IBS.exome.20130415.bam.mt.bam PASS 263 A G 1.00 G - 19 8 11 1 263G transition MT-DLOOP2 CR 5297 2 8.8 1 0 193861 11 0.9891725 5.6127315E-05 H:69957,U:24424,T:16915,J:15981,K:14811,A:6179,V:5226,B:4906,I:4397,HV:4175,M:3293,W:3235,L3:3083,C:2810,X:2768,L2:2528,D:2249,N:1688,L1:1661,R:1245,F:929,L0:394,E:334,G:299,Y:132,Z:101,L4:80,P:41,Q:11,L5:7,L6:1,S:1 CAGCC[A/G]CTTTC 0 HG02236.mapped.ILLUMINA.bwa.IBS.exome.20130415.bam.mt.bam STRAND_BIAS 571 C T 0.006 C 0.994 T 0.006 706 477 229 2 571T transition MT-DLOOP2 CR 4 1 10 0 1 1 73 3 0.0003724813 1.530745E-05 U:40,N:20,H:4,HV:3,D:2,L0:2,F:1,T:1 CACCC[C/T]CCACA 0 @@ -144,42 +67,6 @@ HG02236.mapped.ILLUMINA.bwa.IBS.exome.20130415.bam.mt.bam PASS 10007 T C 1.00 C HG02236.mapped.ILLUMINA.bwa.IBS.exome.20130415.bam.mt.bam PASS 15326 A G 1.00 G - 33 14 19 1 15326G transition MT-CYB Coding 5397 1 10 1 1 T194A 1 T A 194 0.452 0.395040626 0.711538462 III 6 193970 20 0.9897287 0.00010204967 H:69739,U:24412,T:16959,J:15994,K:14814,A:6212,V:5218,B:4902,I:4415,HV:4157,M:3306,W:3226,L3:3095,C:3063,X:2788,L2:2494,D:2261,N:1687,L1:1663,R:1216,F:929,L0:416,E:334,G:299,Y:132,Z:98,L4:80,P:41,Q:11,L5:7,L6:1,S:1 TAGCA[A/G]CACTC 0 HG02236.mapped.ILLUMINA.bwa.IBS.exome.20130415.bam.mt.bam PASS 16172 T C 0.946 C - 37 20 17 1 16172C transition MT-DLOOP1 CR 331 55 3.2 0 0 8705 210 0.044417117 0.0010715215 J:1957,H:1130,I:1105,U:945,F:506,T:499,L3:443,N:407,L0:389,HV:361,C:204,A:143,K:119,M:107,D:102,L1:68,B:54,R:54,L2:30,X:25,V:22,W:20,G:6,P:4,L4:3,E:1,Y:1 CCCAA[T/C]CCACA 0 HG02236.mapped.ILLUMINA.bwa.IBS.exome.20130415.bam.mt.bam PASS 16519 T C 0.909 C - 11 5 6 1 16519C transition MT-DLOOP1 CR 0 11 125992 310 0.6428721 0.0015817699 H:49765,T:16791,K:14657,U:9371,B:4661,I:4320,J:4189,W:3234,X:2748,M:2333,L3:2099,A:1680,L1:1580,N:1408,C:1303,V:1071,L2:1066,D:882,R:733,F:698,HV:684,E:233,L0:167,G:154,L4:58,Z:48,P:33,Y:25,Q:1 CAGGG[T/C]CATAA 0 -HG01354.mapped.ILLUMINA.bwa.CLM.exome.20120522.bam.mt.bam PASS 64 C T 1.00 T - 43 33 10 1 64T transition MT-DLOOP2 CR 151 17 5.2 0 0 5500 334 0.028063659 0.0017042294 A:4254,R:402,L0:221,H:169,HV:143,B:71,U:58,J:44,T:22,X:21,K:19,F:15,D:14,C:13,L2:10,V:7,M:5,L3:4,W:3,L1:2,G:1,I:1,N:1 TTCGT[C/T]TGGGG 0 -HG01354.mapped.ILLUMINA.bwa.CLM.exome.20120522.bam.mt.bam PASS 73 A G 1.00 G - 40 34 6 1 73G transition MT-DLOOP2 CR 4247 13 5.6 1 0 1 119934 60 0.61196125 0.000306149 U:24492,T:16962,J:15973,K:14791,A:6089,H:5724,B:4872,I:4409,M:3305,W:3229,C:3050,L3:3046,X:2786,L2:2527,D:2267,N:1686,L1:1657,F:929,R:825,E:334,G:298,HV:183,Y:132,Z:101,V:95,L4:80,P:40,L0:32,Q:11,L5:7,L6:1,S:1 GGGGT[A/G]TGCAC 0 -HG01354.mapped.ILLUMINA.bwa.CLM.exome.20120522.bam.mt.bam PASS 139 T C 0.342 T 0.658 C 0.342 38 19 19 2 139C transition MT-DLOOP2 CR 1 1 10 0 1 51 16 0.00026022666 8.163974E-05 W:26,B:18,M:4,A:1,C:1,H:1 TTGAT[T/C]CCTGC 0 -HG01354.mapped.ILLUMINA.bwa.CLM.exome.20120522.bam.mt.bam PASS 146 T C 1.00 C - 46 18 28 1 146C transition MT-DLOOP2 CR 787 122 1.8 1 0 1 25525 622 0.13024089 0.0031737448 K:6303,A:5755,H:3994,L2:2255,U:1427,T:1297,B:1084,J:1056,M:613,X:253,D:222,C:217,HV:178,R:169,L3:129,N:108,I:102,L1:77,F:67,L4:51,Y:37,L0:30,W:28,V:23,E:21,G:14,Q:10,P:2,Z:2,L6:1 CTGCC[T/C]CATCC 1 -HG01354.mapped.ILLUMINA.bwa.CLM.exome.20120522.bam.mt.bam PASS 153 A G 1.00 G - 45 18 27 1 153G transition MT-DLOOP2 CR 217 19 5 0 1 8488 125 0.04330988 0.00063781044 A:5194,X:2276,H:568,U:80,M:75,K:72,B:44,J:36,T:29,L2:19,C:18,V:18,I:13,D:12,L3:11,R:6,F:5,W:4,N:3,HV:2,Y:2,L0:1 ATCCT[A/G]TTATT 0 -HG01354.mapped.ILLUMINA.bwa.CLM.exome.20120522.bam.mt.bam PASS 235 A G 1.00 G - 51 23 28 1 235G transition MT-DLOOP2 CR 173 10 6.1 0 1 6435 63 0.03283448 0.00032145646 A:6002,H:103,U:65,J:52,T:51,X:34,L3:28,F:20,HV:20,K:11,N:11,V:10,B:7,D:6,M:6,C:5,R:3,L2:1 ACATA[A/G]TAATA 0 -HG01354.mapped.ILLUMINA.bwa.CLM.exome.20120522.bam.mt.bam PASS 263 A G 1.00 G - 47 23 24 1 263G transition MT-DLOOP2 CR 5297 2 8.8 1 0 193861 11 0.9891725 5.6127315E-05 H:69957,U:24424,T:16915,J:15981,K:14811,A:6179,V:5226,B:4906,I:4397,HV:4175,M:3293,W:3235,L3:3083,C:2810,X:2768,L2:2528,D:2249,N:1688,L1:1661,R:1245,F:929,L0:394,E:334,G:299,Y:132,Z:101,L4:80,P:41,Q:11,L5:7,L6:1,S:1 CAGCC[A/G]CTTTC 0 -HG01354.mapped.ILLUMINA.bwa.CLM.exome.20120522.bam.mt.bam PASS 514 C D 0.854 D 0.854 C 0.146 48 26 22 2 514D -HG01354.mapped.ILLUMINA.bwa.CLM.exome.20120522.bam.mt.bam PASS 515 A D 0.911 D 0.911 A 0.089 45 25 20 2 515D -HG01354.mapped.ILLUMINA.bwa.CLM.exome.20120522.bam.mt.bam PASS 663 A G 1.00 G - 52 29 23 1 663G transition MT-RNR1 rRNA 159 2 8.8 0 1 24 6214 16 0.031706832 8.163974E-05 A:6199,T:9,U:3,H:1,K:1,L3:1 GTCCT[A/G]GCCTT 0 -HG01354.mapped.ILLUMINA.bwa.CLM.exome.20120522.bam.mt.bam PASS 750 A G 1.00 G - 32 13 19 1 750G transition MT-RNR1 rRNA 5388 1 10 1 0 0 192986 13 0.98470783 6.6332286E-05 H:68880,U:24516,T:16961,J:15995,K:14812,A:6232,V:5227,B:4913,I:4415,HV:4172,M:3313,W:3242,C:3083,X:2782,L3:2713,L2:2529,D:2274,N:1670,L1:1660,R:1248,F:926,L0:416,E:334,G:299,Y:132,Z:101,L4:80,P:41,Q:11,L5:7,L6:1,S:1 AAAGG[A/G]ACAAG 0 -HG01354.mapped.ILLUMINA.bwa.CLM.exome.20120522.bam.mt.bam PASS 1438 A G 1.00 G - 41 25 16 1 1438G transition MT-RNR1 rRNA 5216 1 10 1 1 8 189889 18 0.96890545 9.1844704E-05 H:66674,U:24479,T:16955,J:15974,K:14805,A:6216,V:5227,B:4906,I:4351,HV:4180,M:3292,W:3245,L3:3087,C:2951,X:2788,L2:2525,D:2176,N:1689,R:1241,F:929,L1:801,L0:393,E:334,G:299,Y:132,Z:100,L4:79,P:41,Q:11,L5:7,L6:1,S:1 AAACT[A/G]AGAGT 0 -HG01354.mapped.ILLUMINA.bwa.CLM.exome.20120522.bam.mt.bam PASS 1736 A G 1.00 G - 60 29 31 1 1736G transition MT-RNR2 rRNA 158 1 10 0 1 6196 18 0.031614985 9.1844704E-05 A:6179,U:9,B:5,H:1,K:1,T:1 ACCCA[A/G]ATAAA 0 -HG01354.mapped.ILLUMINA.bwa.CLM.exome.20120522.bam.mt.bam PASS 2706 A G 1.00 G - 27 10 17 1 2706G transition MT-RNR2 rRNA 4392 1 10 1 0 2 124135 14 0.63339674 7.143477E-05 U:24425,T:16996,J:15734,K:14818,A:6229,V:5227,B:4906,I:4409,HV:4180,M:3287,W:3245,L3:3094,C:3082,X:2789,L2:2525,D:2242,N:1691,L1:1662,R:1249,F:927,L0:400,E:334,G:299,Y:132,Z:101,L4:75,P:41,H:16,Q:11,L5:7,L6:1,S:1 GGCAT[A/G]ACACA 0 -HG01354.mapped.ILLUMINA.bwa.CLM.exome.20120522.bam.mt.bam PASS 3107 N D 0.809 D 0.809 T 0.128 47 25 22 2 3107D -HG01354.mapped.ILLUMINA.bwa.CLM.exome.20120522.bam.mt.bam PASS 4248 T C 1.00 C - 25 12 13 1 4248C transition MT-ND1 Coding 181 3 8.1 0 1 12 6494 35 0.033135526 0.00017858692 A:6162,E:219,H:40,J:26,T:13,U:12,HV:9,D:4,L3:3,B:2,C:2,K:1,R:1 AGCAT[T/C]CCCCC 1 -HG01354.mapped.ILLUMINA.bwa.CLM.exome.20120522.bam.mt.bam PASS 4769 A G 1.00 G - 15 11 4 1 4769G transition MT-ND2 Coding 5361 2 8.8 1 1 6 191445 4 0.9768449 2.0409934E-05 H:67068,U:24450,T:16997,J:15994,K:14794,A:6228,V:5228,B:4863,I:4415,HV:4180,M:3311,W:3244,L3:3096,C:3074,X:2789,L2:2530,D:2275,N:1691,L1:1663,R:1204,F:929,L0:416,E:333,G:299,Y:132,Z:101,L4:80,P:41,Q:11,L5:7,L6:1,S:1 ATAAT[A/G]GCTAT 0 -HG01354.mapped.ILLUMINA.bwa.CLM.exome.20120522.bam.mt.bam PASS 4824 A G 1.00 G - 34 19 15 1 4824G transition MT-ND2 Coding 161 3 8.1 0 1 T119A 1 T A 119 0.368 0.285977086 0.980769231 I 6242 13 0.0318497 6.6332286E-05 A:6175,B:24,F:12,J:11,L1:11,K:3,L3:2,M:2,D:1,H:1 AGGTT[A/G]CCCAA 0 -HG01354.mapped.ILLUMINA.bwa.CLM.exome.20120522.bam.mt.bam PASS 6286 T C 1.00 C - 25 11 14 1 6286C transition MT-CO1 Coding 1 V128A 2 V A 128 0.717 1.094682209 1 IV 49 11 0.0002500217 5.6127315E-05 A:18,H:18,L3:4,D:3,U:3,T:1,V:1,W:1 AACAG[T/C]CTACC 0 -HG01354.mapped.ILLUMINA.bwa.CLM.exome.20120522.bam.mt.bam PASS 7028 C T 1.00 T - 22 7 15 1 7028T transition MT-CO1 Coding 4457 1 10 1 1 4 123485 202 0.63008016 0.0010307017 U:24306,T:16822,J:15855,K:14698,A:6167,V:5177,B:4871,I:4374,HV:4140,M:3283,W:3217,L3:3086,C:3059,X:2760,L2:2508,D:2261,N:1676,L1:1640,R:1237,F:921,L0:412,E:332,G:297,Y:131,Z:101,L4:80,P:40,H:14,Q:11,L5:7,L6:1,S:1 GTAGC[C/T]CACTT 0 -HG01354.mapped.ILLUMINA.bwa.CLM.exome.20120522.bam.mt.bam PASS 7124 A G 1.00 G - 42 18 24 1 7124G transition MT-CO1 Coding 2 1 10 0 1 6 523 3 0.002668599 1.530745E-05 A:512,H:5,C:2,K:2,D:1,R:1 GACCA[A/G]ACCTA 0 -HG01354.mapped.ILLUMINA.bwa.CLM.exome.20120522.bam.mt.bam PASS 8027 G A 1.00 A - 43 17 26 1 8027A transition MT-CO2 Coding 161 7 6.7 0 1 A148T 1 A T 148 0.241 0.175466852 0.711538462 IV 6969 39 0.035559207 0.00019899686 A:5797,L1:804,H:120,U:96,C:23,J:17,R:17,K:15,L0:15,T:15,M:10,B:8,D:7,I:7,N:6,HV:4,X:4,L2:2,G:1,V:1 TTGAA[G/A]CCCCC 0 -HG01354.mapped.ILLUMINA.bwa.CLM.exome.20120522.bam.mt.bam PASS 8794 C T 1.00 T - 22 6 16 1 8794T transition MT-ATP6 Coding 158 1 10 0 1 H90Y 1 H Y 90 0.608 0.719810952 0.788461538 V 0 6115 33 0.031201687 0.00016838196 A:6105,HV:6,U:2,N:1,T:1 TGCCT[C/T]ACTCA 0 -HG01354.mapped.ILLUMINA.bwa.CLM.exome.20120522.bam.mt.bam PASS 8860 A G 1.00 G - 10 2 8 1 8860G transition MT-ATP6 Coding 5417 1 10 1 0 T112A 1 T A 112 0.369 0.287079116 0.75 V 5 193581 40 0.98774385 0.00020409934 H:69519,U:24441,T:16949,J:15952,K:14755,A:6209,V:5209,B:4891,I:4363,HV:4168,M:3291,W:3239,L3:3079,C:3061,X:2781,L2:2497,D:2265,N:1685,L1:1648,R:1239,F:927,L0:410,E:333,G:298,Y:132,Z:101,L4:78,P:41,Q:11,L5:7,L6:1,S:1 CGGGC[A/G]CAGTG 0 -HG01354.mapped.ILLUMINA.bwa.CLM.exome.20120522.bam.mt.bam PASS 9098 T C 1.00 C - 63 43 20 1 9098C transition MT-ATP6 Coding 8 4 7.6 0 1 I191T 2 I T 191 0.685 0.967913242 0.942307692 V 313 22 0.0015970774 0.00011225463 B:157,L3:52,U:43,A:16,H:12,W:8,C:5,N:5,M:4,T:4,J:2,F:1,K:1,L2:1,L4:1,V:1 ACTTA[T/C]CATCT 0 -HG01354.mapped.ILLUMINA.bwa.CLM.exome.20120522.bam.mt.bam PASS 11016 G A 1.00 A - 39 21 18 1 11016A transition MT-ND4 Coding 32 17 5.2 0 1 S86N 2 S N 86 0.306 0.225303898 0.076923077 I 3 1280 31 0.006531179 0.00015817699 A:520,H:344,K:164,J:55,M:28,N:26,U:23,B:17,T:16,W:16,I:9,L2:9,HV:8,V:8,C:6,R:6,D:5,X:5,E:4,L3:4,F:2,Y:2,G:1,L0:1,L1:1 ATCCA[G/A]TGAAC 0 -HG01354.mapped.ILLUMINA.bwa.CLM.exome.20120522.bam.mt.bam PASS 11719 G A 1.00 A - 45 21 24 1 11719A transition MT-ND4 Coding 4272 3 8.1 1 1 14 115534 48 0.5895103 0.0002449192 U:24445,T:16959,J:15959,K:14799,A:6215,B:4902,I:4408,M:3306,W:3236,L3:3093,C:3076,X:2782,L2:2528,D:2273,N:1686,L1:1662,H:993,F:929,R:816,L0:416,E:334,G:297,Y:132,Z:98,L4:79,P:41,V:36,HV:14,Q:11,L5:7,L6:1,S:1 CACGG[G/A]CTTAC 0 -HG01354.mapped.ILLUMINA.bwa.CLM.exome.20120522.bam.mt.bam PASS 12007 G A 1.00 A - 51 25 26 1 12007A transition MT-ND4 Coding 337 14 5.5 0 1 2 9041 26 0.04613155 0.00013266457 A:5812,J:1845,M:467,L0:415,T:178,N:125,H:89,K:21,R:20,L2:16,D:10,L1:8,HV:7,U:7,B:6,C:3,I:3,X:3,L3:2,W:2,F:1,V:1 CAATG[G/A]GGCTC 0 -HG01354.mapped.ILLUMINA.bwa.CLM.exome.20120522.bam.mt.bam PASS 12705 C T 1.00 T - 66 34 32 1 12705T transition MT-ND5 Coding 2481 1 10 1 1 12 35323 91 0.18023501 0.00046432597 A:6125,I:4351,M:3286,W:3217,L3:3070,C:3053,X:2758,L2:2512,D:2245,N:1677,L1:1651,L0:413,E:330,G:297,Y:132,Z:101,L4:79,Q:11,L5:7,H:4,V:2,L6:1,S:1 CTCAT[C/T]TTCCT 1 -HG01354.mapped.ILLUMINA.bwa.CLM.exome.20120522.bam.mt.bam PASS 14766 C T 1.00 T - 50 18 32 1 14766T transition MT-CYB Coding 4286 1 10 1 0 T7I 2 T I 7 0.165 0.130992813 0.692307692 III 3 114700 34 0.58525485 0.00017348444 U:24456,T:16974,J:15968,K:14796,A:6223,B:4819,I:4412,M:3282,W:3243,L3:3090,C:3075,X:2786,L2:2530,D:2268,N:1690,L1:1654,R:1248,F:929,L0:415,G:299,E:167,Y:131,Z:100,L4:79,P:41,Q:11,L5:7,H:5,L6:1,S:1 CAAAA[C/T]TAACC 0 -HG01354.mapped.ILLUMINA.bwa.CLM.exome.20120522.bam.mt.bam PASS 15326 A G 0.976 G - 41 18 23 1 15326G transition MT-CYB Coding 5397 1 10 1 1 T194A 1 T A 194 0.452 0.395040626 0.711538462 III 6 193970 20 0.9897287 0.00010204967 H:69739,U:24412,T:16959,J:15994,K:14814,A:6212,V:5218,B:4902,I:4415,HV:4157,M:3306,W:3226,L3:3095,C:3063,X:2788,L2:2494,D:2261,N:1687,L1:1663,R:1216,F:929,L0:416,E:334,G:299,Y:132,Z:98,L4:80,P:41,Q:11,L5:7,L6:1,S:1 TAGCA[A/G]CACTC 0 -HG01354.mapped.ILLUMINA.bwa.CLM.exome.20120522.bam.mt.bam PASS 16111 C T 1.00 T - 65 27 38 1 16111T transition MT-DLOOP1 CR 144 24 4.6 0 0 7040 94 0.035921484 0.00047963343 A:5007,H:616,B:479,U:323,M:104,L3:80,N:75,HV:72,T:39,K:34,F:30,I:30,L1:29,V:22,X:19,J:18,D:17,L0:14,L2:13,W:7,R:4,G:3,C:2,L5:2,Z:1 GCCAG[C/T]CACCA 0 -HG01354.mapped.ILLUMINA.bwa.CLM.exome.20120522.bam.mt.bam PASS 16223 C T 1.00 T - 80 39 41 1 16223T transition MT-DLOOP1 CR 2397 7 6.7 1 0 35639 196 0.18184741 0.0010000868 A:6047,I:4359,W:3177,L3:3042,M:3026,C:2985,X:2629,L2:2415,D:2167,N:1658,L1:1609,K:699,L0:406,E:328,G:295,H:231,U:227,Z:99,L4:77,B:57,V:29,HV:24,T:23,Q:11,L5:6,J:5,R:5,F:1,L6:1,S:1 CAACC[C/T]TCAAC 0 -HG01354.mapped.ILLUMINA.bwa.CLM.exome.20120522.bam.mt.bam PASS 16290 C T 1.00 T - 72 34 38 1 16290T transition MT-DLOOP1 CR 201 16 5.3 0 0 6842 67 0.034911193 0.0003418664 A:6150,H:182,U:115,J:104,M:65,L2:57,X:42,V:22,D:20,K:20,L1:13,T:13,W:8,B:6,I:5,L3:5,R:5,N:3,HV:2,L0:2,E:1,F:1,G:1 ACCTA[C/T]CCACC 0 -HG01354.mapped.ILLUMINA.bwa.CLM.exome.20120522.bam.mt.bam PASS 16319 G A 1.00 A - 79 28 51 1 16319A transition MT-DLOOP1 CR 308 39 3.8 0 0 9103 71 0.046447907 0.00036227633 A:6168,J:635,H:541,K:404,M:281,U:229,I:215,B:120,L3:102,D:94,N:67,C:60,T:42,V:37,R:26,W:20,X:14,HV:10,L2:10,Y:10,G:8,F:4,E:2,L1:2,P:1,S:1 ATAAA[G/A]CCATT 1 -HG01354.mapped.ILLUMINA.bwa.CLM.exome.20120522.bam.mt.bam PASS 16362 T C 1.00 C - 57 27 30 1 16362C transition MT-DLOOP1 CR 955 81 2.5 0 1 23527 246 0.120046124 0.001255211 H:6272,A:5761,U:3796,D:2234,M:633,L3:621,W:541,R:537,L2:374,K:368,E:330,G:292,T:270,J:238,F:221,I:219,C:199,HV:160,V:131,B:100,L4:75,L0:39,N:36,L1:34,X:26,Y:12,L5:5,Q:2,Z:1 TCTCG[T/C]CCCCA 1 HG00180.mapped.ILLUMINA.bwa.FIN.exome.20130415.bam.mt.bam PASS 73 A G 1.00 G - 20 12 8 1 73G transition MT-DLOOP2 CR 4247 13 5.6 1 0 1 119934 60 0.61196125 0.000306149 U:24492,T:16962,J:15973,K:14791,A:6089,H:5724,B:4872,I:4409,M:3305,W:3229,C:3050,L3:3046,X:2786,L2:2527,D:2267,N:1686,L1:1657,F:929,R:825,E:334,G:298,HV:183,Y:132,Z:101,V:95,L4:80,P:40,L0:32,Q:11,L5:7,L6:1,S:1 GGGGT[A/G]TGCAC 0 HG00180.mapped.ILLUMINA.bwa.FIN.exome.20130415.bam.mt.bam PASS 263 A G 1.00 G - 24 11 13 1 263G transition MT-DLOOP2 CR 5297 2 8.8 1 0 193861 11 0.9891725 5.6127315E-05 H:69957,U:24424,T:16915,J:15981,K:14811,A:6179,V:5226,B:4906,I:4397,HV:4175,M:3293,W:3235,L3:3083,C:2810,X:2768,L2:2528,D:2249,N:1688,L1:1661,R:1245,F:929,L0:394,E:334,G:299,Y:132,Z:101,L4:80,P:41,Q:11,L5:7,L6:1,S:1 CAGCC[A/G]CTTTC 0 HG00180.mapped.ILLUMINA.bwa.FIN.exome.20130415.bam.mt.bam PASS 499 G A 0.03 G 0.97 A 0.03 198 171 27 2 499A transition MT-DLOOP2 CR 173 8 6.5 0 1 8032 44 0.040983148 0.00022450926 U:4073,B:3486,L3:124,T:120,H:69,I:47,K:27,L2:27,M:17,A:14,D:9,HV:4,C:3,J:3,L1:3,N:1,R:1,W:1,X:1,Y:1,Z:1 CCCCC[G/A]CCCAT 0 @@ -194,77 +81,6 @@ HG00180.mapped.ILLUMINA.bwa.FIN.exome.20130415.bam.mt.bam PASS 8860 A G 1.00 G HG00180.mapped.ILLUMINA.bwa.FIN.exome.20130415.bam.mt.bam PASS 15326 A G 1.00 G - 46 25 21 1 15326G transition MT-CYB Coding 5397 1 10 1 1 T194A 1 T A 194 0.452 0.395040626 0.711538462 III 6 193970 20 0.9897287 0.00010204967 H:69739,U:24412,T:16959,J:15994,K:14814,A:6212,V:5218,B:4902,I:4415,HV:4157,M:3306,W:3226,L3:3095,C:3063,X:2788,L2:2494,D:2261,N:1687,L1:1663,R:1216,F:929,L0:416,E:334,G:299,Y:132,Z:98,L4:80,P:41,Q:11,L5:7,L6:1,S:1 TAGCA[A/G]CACTC 0 HG00180.mapped.ILLUMINA.bwa.FIN.exome.20130415.bam.mt.bam PASS 16162 A G 1.00 G - 47 27 20 1 16162G transition MT-DLOOP1 CR 36 3 8.1 0 1 3860 56 0.019695586 0.00028573908 H:3499,F:212,U:41,V:40,T:31,A:5,J:5,K:5,D:4,I:4,C:3,M:3,N:3,L2:2,B:1,L1:1,R:1 TACAT[A/G]AAAAC 0 HG00180.mapped.ILLUMINA.bwa.FIN.exome.20130415.bam.mt.bam PASS 16519 T C 1.00 C - 19 8 11 1 16519C transition MT-DLOOP1 CR 0 11 125992 310 0.6428721 0.0015817699 H:49765,T:16791,K:14657,U:9371,B:4661,I:4320,J:4189,W:3234,X:2748,M:2333,L3:2099,A:1680,L1:1580,N:1408,C:1303,V:1071,L2:1066,D:882,R:733,F:698,HV:684,E:233,L0:167,G:154,L4:58,Z:48,P:33,Y:25,Q:1 CAGGG[T/C]CATAA 0 -HG03046.mapped.ILLUMINA.bwa.GWD.exome.20121211.bam.mt.bam PASS 73 A G 1.00 G - 65 29 36 1 73G transition MT-DLOOP2 CR 4247 13 5.6 1 0 1 119934 60 0.61196125 0.000306149 U:24492,T:16962,J:15973,K:14791,A:6089,H:5724,B:4872,I:4409,M:3305,W:3229,C:3050,L3:3046,X:2786,L2:2527,D:2267,N:1686,L1:1657,F:929,R:825,E:334,G:298,HV:183,Y:132,Z:101,V:95,L4:80,P:40,L0:32,Q:11,L5:7,L6:1,S:1 GGGGT[A/G]TGCAC 0 -HG03046.mapped.ILLUMINA.bwa.GWD.exome.20121211.bam.mt.bam PASS 150 C T 1.00 T - 33 16 17 1 150T transition MT-DLOOP2 CR 604 74 2.7 0 0 19751 168 0.100779146 0.0008572172 U:8512,J:3334,L3:1817,H:1122,T:1066,L2:841,K:639,M:505,D:334,B:313,N:258,HV:152,W:135,R:132,V:116,F:99,I:98,C:74,G:63,A:42,L4:42,L1:22,X:19,L0:12,P:2,E:1,S:1 CTCAT[C/T]CTATT 0 -HG03046.mapped.ILLUMINA.bwa.GWD.exome.20121211.bam.mt.bam PASS 152 T C 1.00 C - 33 16 17 1 152C transition MT-DLOOP2 CR 1223 197 1 1 0 1 43990 1503 0.22445825 0.0076690326 H:10316,U:6126,K:5566,T:5328,J:3365,L2:2381,I:1959,L1:1580,N:1210,A:1072,L3:955,HV:764,B:657,D:522,M:490,C:312,F:272,R:266,W:199,L0:178,G:101,Z:100,V:96,X:90,L4:37,E:35,L5:4,Y:4,P:3,L6:1,S:1 CATCC[T/C]ATTAT 0 -HG03046.mapped.ILLUMINA.bwa.GWD.exome.20121211.bam.mt.bam PASS 182 C T 1.00 T - 31 11 20 1 182T transition MT-DLOOP2 CR 177 10 6.1 0 0 2901 73 0.014802304 0.0003724813 L1:1573,L2:810,H:173,J:76,A:38,M:37,N:33,U:28,B:26,I:24,T:20,D:15,HV:13,F:8,L5:6,K:5,C:4,L4:4,R:3,L3:2,L6:1,V:1,X:1 TATTA[C/T]AGGCG 0 -HG03046.mapped.ILLUMINA.bwa.GWD.exome.20121211.bam.mt.bam PASS 195 T C 1.00 C - 33 13 20 1 195C transition MT-DLOOP2 CR 1031 113 2 1 0 1 34496 1050 0.17601527 0.0053576077 H:5473,U:5156,T:4235,K:3141,W:2774,X:2680,J:2428,L2:2412,HV:1441,L1:1324,L3:1142,M:520,V:347,B:317,C:226,N:183,A:152,D:134,R:122,E:116,F:74,L4:46,L0:25,G:12,L5:6,P:4,Y:2,Z:2,I:1,Q:1 CATAC[T/C]TACTA 0 -HG03046.mapped.ILLUMINA.bwa.GWD.exome.20121211.bam.mt.bam PASS 198 C T 1.00 T - 32 13 19 1 198T transition MT-DLOOP2 CR 118 24 4.6 0 0 1 2491 59 0.012710286 0.00030104653 L2:798,L1:384,U:225,L3:198,H:175,HV:153,T:106,X:90,A:86,J:54,W:51,C:44,M:41,K:26,B:13,F:12,N:8,L0:6,L4:5,R:5,G:4,I:3,V:3,D:1 ACTTA[C/T]TAAAG 0 -HG03046.mapped.ILLUMINA.bwa.GWD.exome.20121211.bam.mt.bam PASS 263 A G 1.00 G - 37 19 18 1 263G transition MT-DLOOP2 CR 5297 2 8.8 1 0 193861 11 0.9891725 5.6127315E-05 H:69957,U:24424,T:16915,J:15981,K:14811,A:6179,V:5226,B:4906,I:4397,HV:4175,M:3293,W:3235,L3:3083,C:2810,X:2768,L2:2528,D:2249,N:1688,L1:1661,R:1245,F:929,L0:394,E:334,G:299,Y:132,Z:101,L4:80,P:41,Q:11,L5:7,L6:1,S:1 CAGCC[A/G]CTTTC 0 -HG03046.mapped.ILLUMINA.bwa.GWD.exome.20121211.bam.mt.bam PASS 418 C T 1.00 T - 60 32 28 1 418T transition MT-DLOOP2 CR 6 1 10 0 1 245 0 0.0012501085 0 L2:241,H:2,T:1,U:1 GTATG[C/T]ACTTT 0 -HG03046.mapped.ILLUMINA.bwa.GWD.exome.20121211.bam.mt.bam PASS 514 C D 0.742 D 0.742 C 0.242 62 36 26 2 514D -HG03046.mapped.ILLUMINA.bwa.GWD.exome.20121211.bam.mt.bam PASS 515 A D 0.708 D 0.708 A 0.246 65 39 26 2 515D -HG03046.mapped.ILLUMINA.bwa.GWD.exome.20121211.bam.mt.bam PASS 523 A C 0.121 A 0.879 C 0.121 66 42 24 2 523C transversion MT-DLOOP2 CR 0 CACAC[A/C]CCGCT 1 -HG03046.mapped.ILLUMINA.bwa.GWD.exome.20121211.bam.mt.bam PASS 750 A G 1.00 G - 44 17 27 1 750G transition MT-RNR1 rRNA 5388 1 10 1 0 0 192986 13 0.98470783 6.6332286E-05 H:68880,U:24516,T:16961,J:15995,K:14812,A:6232,V:5227,B:4913,I:4415,HV:4172,M:3313,W:3242,C:3083,X:2782,L3:2713,L2:2529,D:2274,N:1670,L1:1660,R:1248,F:926,L0:416,E:334,G:299,Y:132,Z:101,L4:80,P:41,Q:11,L5:7,L6:1,S:1 AAAGG[A/G]ACAAG 0 -HG03046.mapped.ILLUMINA.bwa.GWD.exome.20121211.bam.mt.bam PASS 769 G A 1.00 A - 50 26 24 1 769A transition MT-RNR1 rRNA 433 5 7.3 1 1 1 4840 13 0.02469602 6.6332286E-05 L2:2526,L1:1659,L0:415,L4:80,H:51,L3:26,U:17,J:14,D:11,L5:7,X:7,A:6,B:6,N:4,T:4,C:1,HV:1,K:1,L6:1,M:1,R:1,W:1 ACGCA[G/A]CAATG 0 -HG03046.mapped.ILLUMINA.bwa.GWD.exome.20121211.bam.mt.bam PASS 1018 G A 1.00 A - 26 7 19 1 1018A transition MT-RNR1 rRNA 428 2 8.8 1 1 14 4812 10 0.02455315 5.1024836E-05 L2:2518,L1:1658,L0:416,L4:80,H:71,U:26,V:9,L5:7,K:6,T:5,A:4,M:3,C:2,L3:2,B:1,F:1,HV:1,L6:1,R:1 AAATA[G/A]ACTAC 0 -HG03046.mapped.ILLUMINA.bwa.GWD.exome.20121211.bam.mt.bam PASS 1438 A G 1.00 G - 34 16 18 1 1438G transition MT-RNR1 rRNA 5216 1 10 1 1 8 189889 18 0.96890545 9.1844704E-05 H:66674,U:24479,T:16955,J:15974,K:14805,A:6216,V:5227,B:4906,I:4351,HV:4180,M:3292,W:3245,L3:3087,C:2951,X:2788,L2:2525,D:2176,N:1689,R:1241,F:929,L1:801,L0:393,E:334,G:299,Y:132,Z:100,L4:79,P:41,Q:11,L5:7,L6:1,S:1 AAACT[A/G]AGAGT 0 -HG03046.mapped.ILLUMINA.bwa.GWD.exome.20121211.bam.mt.bam PASS 1442 G A 1.00 A - 30 14 16 1 1442A transition MT-RNR1 rRNA 50 8 6.5 0 1 1 987 5 0.005036151 2.5512418E-05 L2:751,K:83,A:71,U:20,H:12,B:11,R:10,J:9,L3:8,T:6,M:4,D:1,L1:1 TAAGA[G/A]TAGAG 0 -HG03046.mapped.ILLUMINA.bwa.GWD.exome.20121211.bam.mt.bam PASS 1706 C T 1.00 T - 40 19 21 1 1706T transition MT-RNR2 rRNA 13 1 10 0 1 1 395 1 0.002015481 5.1024836E-06 L2:391,W:2,H:1,N:1 TACTA[C/T]CAGAC 0 -HG03046.mapped.ILLUMINA.bwa.GWD.exome.20121211.bam.mt.bam PASS 2332 C T 1.00 T - 49 24 25 1 2332T transition MT-RNR2 rRNA 35 2 8.8 0 1 2 831 1 0.0042401636 5.1024836E-06 L2:808,L3:20,V:3 TCCTC[C/T]GCATA 0 -HG03046.mapped.ILLUMINA.bwa.GWD.exome.20121211.bam.mt.bam PASS 2358 A G 1.00 G - 47 24 23 1 2358G transition MT-RNR2 rRNA 13 1 10 0 1 392 1 0.0020001736 5.1024836E-06 L2:392 AAAAC[A/G]CTGAA 0 -HG03046.mapped.ILLUMINA.bwa.GWD.exome.20121211.bam.mt.bam PASS 2416 T C 1.00 C - 39 19 20 1 2416C transition MT-RNR2 rRNA 143 6 7 0 1 3 2696 9 0.013756295 4.5922352E-05 L2:2530,B:53,H:23,D:17,U:15,L3:14,T:11,L1:6,A:5,K:5,J:4,R:3,M:2,V:2,X:2,C:1,F:1,I:1,W:1 TACCC[T/C]CACTG 1 -HG03046.mapped.ILLUMINA.bwa.GWD.exome.20121211.bam.mt.bam PASS 2706 A G 0.975 G - 40 10 30 1 2706G transition MT-RNR2 rRNA 4392 1 10 1 0 2 124135 14 0.63339674 7.143477E-05 U:24425,T:16996,J:15734,K:14818,A:6229,V:5227,B:4906,I:4409,HV:4180,M:3287,W:3245,L3:3094,C:3082,X:2789,L2:2525,D:2242,N:1691,L1:1662,R:1249,F:927,L0:400,E:334,G:299,Y:132,Z:101,L4:75,P:41,H:16,Q:11,L5:7,L6:1,S:1 GGCAT[A/G]ACACA 0 -HG03046.mapped.ILLUMINA.bwa.GWD.exome.20121211.bam.mt.bam BLACKLISTED 3107 N T 0.071 T - 42 21 21 1 3107T -HG03046.mapped.ILLUMINA.bwa.GWD.exome.20121211.bam.mt.bam PASS 3594 C T 1.00 T - 43 20 23 1 3594T transition MT-ND1 Coding 409 1 10 1 1 1 4633 1 0.023639806 5.1024836E-06 L2:2526,L1:1660,L0:416,D:7,L5:7,A:6,T:5,H:3,J:1,L6:1,V:1 CTGGT[C/T]AACCT 0 -HG03046.mapped.ILLUMINA.bwa.GWD.exome.20121211.bam.mt.bam PASS 4104 A G 1.00 G - 3 0 3 1 4104G transition MT-ND1 Coding 405 1 10 1 1 1 3485 335 0.017782155 0.0017093319 L2:1878,L1:1254,L0:270,T:63,H:14,L5:3,N:2,B:1 CTTCT[A/G]ACCTC 0 -HG03046.mapped.ILLUMINA.bwa.GWD.exome.20121211.bam.mt.bam PASS 4370 T C 1.00 C - 18 9 9 1 4370C transition MT-TQ tRNA 13 1 10 0 1 1 411 3 0.0020971207 1.530745E-05 L2:390,W:6,K:3,B:2,H:2,L3:2,U:2,A:1,D:1,M:1,R:1 CAAAA[T/C]TCTCC 0 -HG03046.mapped.ILLUMINA.bwa.GWD.exome.20121211.bam.mt.bam PASS 4767 A G 1.00 G - 3 2 1 1 4767G transition MT-ND2 Coding 16 4 7.6 0 1 M100V 1 M V 100 0.379 0.298335705 0.692307692 I 2 611 13 0.0031176175 6.6332286E-05 L2:389,H:95,R:66,K:27,HV:8,A:7,J:5,T:5,L1:3,N:2,B:1,C:1,L3:1,M:1 TCATA[A/G]TAGCT 0 -HG03046.mapped.ILLUMINA.bwa.GWD.exome.20121211.bam.mt.bam PASS 4769 A G 1.00 G - 4 3 1 1 4769G transition MT-ND2 Coding 5361 2 8.8 1 1 6 191445 4 0.9768449 2.0409934E-05 H:67068,U:24450,T:16997,J:15994,K:14794,A:6228,V:5228,B:4863,I:4415,HV:4180,M:3311,W:3244,L3:3096,C:3074,X:2789,L2:2530,D:2275,N:1691,L1:1663,R:1204,F:929,L0:416,E:333,G:299,Y:132,Z:101,L4:80,P:41,Q:11,L5:7,L6:1,S:1 ATAAT[A/G]GCTAT 0 -HG03046.mapped.ILLUMINA.bwa.GWD.exome.20121211.bam.mt.bam PASS 4959 G A 1.00 A - 56 28 28 1 4959A transition MT-ND2 Coding 5 5 7.3 0 1 A164T 1 A T 164 0.421 0.350639224 0.788461538 I 105 32 0.0005357608 0.00016327947 T:31,H:21,K:21,D:11,U:5,L2:3,B:2,L1:2,L3:2,M:2,R:2,A:1,C:1,J:1 TCATA[G/A]CAGGC 0 -HG03046.mapped.ILLUMINA.bwa.GWD.exome.20121211.bam.mt.bam PASS 5027 C T 1.00 T - 46 21 25 1 5027T transition MT-ND2 Coding 17 2 8.8 0 1 6 436 3 0.0022246828 1.530745E-05 L2:394,HV:10,M:8,U:8,C:3,K:3,L3:3,J:2,T:2,B:1,D:1,V:1 ACCCA[C/T]ATAGG 0 -HG03046.mapped.ILLUMINA.bwa.GWD.exome.20121211.bam.mt.bam PASS 5331 C A 1.00 A - 56 27 29 1 5331A transversion MT-ND2 Coding 13 1 10 0 1 L288I 1 L I 288 0.671 0.917173174 0.692307692 I 0 400 1 0.0020409934 5.1024836E-06 L2:391,K:7,HV:1,T:1 CCCTC[C/A]TTAAC 0 -HG03046.mapped.ILLUMINA.bwa.GWD.exome.20121211.bam.mt.bam PASS 5814 T C 1.00 C - 40 19 21 1 5814C transition MT-TC tRNA 14 2 8.8 0 1 0 500 19 0.0025512418 9.694719E-05 L2:393,H:42,U:15,B:13,V:7,M:6,K:5,I:4,J:3,A:2,F:2,L1:2,R:2,C:1,HV:1,L3:1,Z:1 GAAAA[T/C]CACCT 0 -HG03046.mapped.ILLUMINA.bwa.GWD.exome.20121211.bam.mt.bam PASS 6026 G A 1.00 A - 50 22 28 1 6026A transition MT-CO1 Coding 84 6 7 0 1 4 852 7 0.004347316 3.5717385E-05 U:315,L2:244,C:212,T:33,H:32,K:12,B:2,D:1,N:1 GAGCT[G/A]GGCCA 0 -HG03046.mapped.ILLUMINA.bwa.GWD.exome.20121211.bam.mt.bam PASS 6713 C T 1.00 T - 13 4 9 1 6713T transition MT-CO1 Coding 15 3 8.1 0 1 16 464 11 0.0023675524 5.6127315E-05 L2:387,H:25,U:14,X:7,K:6,M:5,B:3,C:3,D:3,L1:3,L3:2,R:2,T:2,F:1,L0:1 GGATA[C/T]ATAGG 0 -HG03046.mapped.ILLUMINA.bwa.GWD.exome.20121211.bam.mt.bam PASS 7028 C T 1.00 T - 7 2 5 1 7028T transition MT-CO1 Coding 4457 1 10 1 1 4 123485 202 0.63008016 0.0010307017 U:24306,T:16822,J:15855,K:14698,A:6167,V:5177,B:4871,I:4374,HV:4140,M:3283,W:3217,L3:3086,C:3059,X:2760,L2:2508,D:2261,N:1676,L1:1640,R:1237,F:921,L0:412,E:332,G:297,Y:131,Z:101,L4:80,P:40,H:14,Q:11,L5:7,L6:1,S:1 GTAGC[C/T]CACTT 0 -HG03046.mapped.ILLUMINA.bwa.GWD.exome.20121211.bam.mt.bam PASS 7256 C T 1.00 T - 7 1 6 1 7256T transition MT-CO1 Coding 411 3 8.1 1 0 18 4195 151 0.021404918 0.000770475 L2:2363,L1:1421,L0:366,U:14,H:8,X:8,L5:7,L3:3,HV:2,D:1,L6:1,M:1 TGAAA[C/T]ATCCT 0 -HG03046.mapped.ILLUMINA.bwa.GWD.exome.20121211.bam.mt.bam PASS 7569 A G 1.00 G - 7 7 0 1 7569G transition MT-TD tRNA 5 3 8.1 0 1 0 159 4 0.0008112949 2.0409934E-05 U:118,L2:31,HV:4,C:2,H:2,J:2 AGGCT[A/G]AATCC 0 -HG03046.mapped.ILLUMINA.bwa.GWD.exome.20121211.bam.mt.bam PASS 7624 T A 1.00 A - 35 21 14 1 7624A transversion MT-CO2 Coding 29 1 10 0 0 15 748 1 0.0038166575 5.1024836E-06 L2:748 GCTAC[T/A]TCCCC 0 -HG03046.mapped.ILLUMINA.bwa.GWD.exome.20121211.bam.mt.bam PASS 8080 C T 1.00 T - 78 36 42 1 8080T transition MT-CO2 Coding 13 1 10 0 1 3 399 1 0.002035891 5.1024836E-06 L2:392,K:2,D:1,H:1,J:1,T:1,W:1 GCTGT[C/T]CCCAC 0 -HG03046.mapped.ILLUMINA.bwa.GWD.exome.20121211.bam.mt.bam PASS 8206 G A 1.00 A - 39 17 22 1 8206A transition MT-CO2 Coding 141 4 7.6 0 1 2 2658 8 0.013562401 4.081987E-05 L2:2525,H:59,B:44,L3:11,U:7,M:4,A:3,J:3,L1:1,T:1 TTCAT[G/A]CCCAT 0 -HG03046.mapped.ILLUMINA.bwa.GWD.exome.20121211.bam.mt.bam PASS 8387 G A 1.00 A - 44 24 20 1 8387A transition MT-ATP8 Coding 17 5 7.3 0 1 V8M 1 V M 8 0.528 0.529162889 0.230769231 V 1 539 17 0.0027502386 8.674222E-05 L2:394,H:56,L1:52,J:8,T:6,A:4,HV:4,C:3,D:3,L3:2,M:2,R:2,B:1,U:1,V:1 CTACC[G/A]TATGG 0 -HG03046.mapped.ILLUMINA.bwa.GWD.exome.20121211.bam.mt.bam PASS 8701 A G 0.967 G - 30 13 17 1 8701G transition MT-ATP6 Coding 1965 5 7.3 1 0 T59A 1 T A 59 0.14 0.11898395 0.673076923 V 3 17154 47 0.087528 0.00023981671 M:3285,L3:3074,C:3060,L2:2517,D:2178,L1:1603,L0:398,E:332,G:298,Z:101,H:91,L4:80,U:40,J:25,T:23,Q:11,B:8,L5:6,K:5,N:5,V:4,F:2,HV:2,I:2,R:2,A:1,L6:1 TGATA[A/G]CCATA 0 -HG03046.mapped.ILLUMINA.bwa.GWD.exome.20121211.bam.mt.bam PASS 9221 A G 1.00 G - 53 26 27 1 9221G transition MT-CO3 Coding 132 1 10 0 0 0 2562 7 0.013072562 3.5717385E-05 L2:2523,J:33,H:3,HV:2,L3:1 CAATC[A/G]CATGC 0 -HG03046.mapped.ILLUMINA.bwa.GWD.exome.20121211.bam.mt.bam PASS 9540 T C 0.988 C - 82 44 38 1 9540C transition MT-CO3 Coding 1966 1 10 1 1 8 17229 47 0.08791069 0.00023981671 M:3312,L3:3099,C:3027,L2:2529,D:2275,L1:1661,L0:415,E:334,G:299,Z:101,L4:80,I:44,H:26,Q:11,L5:7,B:2,U:2,A:1,F:1,HV:1,L6:1,T:1 CCCAA[T/C]TAGGA 0 -HG03046.mapped.ILLUMINA.bwa.GWD.exome.20121211.bam.mt.bam PASS 10115 T C 1.00 C - 44 28 16 1 10115C transition MT-ND3 Coding 133 2 8.8 0 1 1 2537 4 0.012945 2.0409934E-05 L2:2509,H:25,I:1,M:1,X:1 ATAAT[T/C]ATTAC 0 -HG03046.mapped.ILLUMINA.bwa.GWD.exome.20121211.bam.mt.bam PASS 10398 A G 1.00 G - 38 18 20 1 10398G transition MT-ND3 Coding 2516 20 4.9 1 1 T114A 1 T A 114 0.17 0.133536283 0.365384615 I 5 49322 289 0.2516647 0.0014746177 J:15207,K:11632,I:4351,M:3194,L3:3033,C:2970,L2:2504,D:2165,L1:1618,B:464,N:412,L0:409,E:321,G:287,W:137,Y:132,T:122,Z:98,L4:77,H:47,R:45,U:38,A:31,Q:11,L5:7,V:4,HV:3,L6:1,P:1,X:1 ACTGA[A/G]CCGAA 0 -HG03046.mapped.ILLUMINA.bwa.GWD.exome.20121211.bam.mt.bam PASS 10828 T C 0.98 C - 49 26 23 1 10828C transition MT-ND4 Coding 6 1 10 0 1 1 343 9 0.0017501517 4.5922352E-05 L2:249,H:38,K:14,L1:11,T:11,C:9,I:4,A:3,U:2,J:1,R:1 ATAAT[T/C]TGAAT 0 -HG03046.mapped.ILLUMINA.bwa.GWD.exome.20121211.bam.mt.bam PASS 10873 T C 1.00 C - 54 27 27 1 10873C transition MT-ND4 Coding 1966 1 10 1 0 3 17312 22 0.088334195 0.00011225463 M:3298,L3:3085,C:3064,L2:2527,D:2263,L1:1659,L0:414,E:330,G:297,Z:101,T:82,L4:80,H:53,K:16,Q:11,L5:7,U:7,A:5,F:4,B:2,J:2,W:2,L6:1,R:1,X:1 ATCCC[T/C]CTACT 1 -HG03046.mapped.ILLUMINA.bwa.GWD.exome.20121211.bam.mt.bam PASS 11002 A G 1.00 G - 51 21 30 1 11002G transition MT-ND4 Coding 48 8 6.5 0 1 1 1024 19 0.005224943 9.694719E-05 L3:417,J:290,R:92,H:53,U:50,X:30,L1:24,F:20,D:15,B:9,M:6,HV:4,K:3,L2:3,C:2,I:2,T:2,A:1,Z:1 AGCCA[A/G]CGCCA 0 -HG03046.mapped.ILLUMINA.bwa.GWD.exome.20121211.bam.mt.bam PASS 11719 G A 1.00 A - 46 25 21 1 11719A transition MT-ND4 Coding 4272 3 8.1 1 1 14 115534 48 0.5895103 0.0002449192 U:24445,T:16959,J:15959,K:14799,A:6215,B:4902,I:4408,M:3306,W:3236,L3:3093,C:3076,X:2782,L2:2528,D:2273,N:1686,L1:1662,H:993,F:929,R:816,L0:416,E:334,G:297,Y:132,Z:98,L4:79,P:41,V:36,HV:14,Q:11,L5:7,L6:1,S:1 CACGG[G/A]CTTAC 0 -HG03046.mapped.ILLUMINA.bwa.GWD.exome.20121211.bam.mt.bam PASS 11734 A G 1.00 G - 46 20 26 1 11734G transition MT-ND4 Coding 2 2 8.8 0 1 13 1 6.6332286E-05 5.1024836E-06 A:4,U:4,V:2,J:1,K:1,L2:1 TCATT[A/G]CTATT 0 -HG03046.mapped.ILLUMINA.bwa.GWD.exome.20121211.bam.mt.bam PASS 11944 T C 0.985 C - 67 29 38 1 11944C transition MT-ND4 Coding 158 8 6.5 0 1 1 2855 18 0.01456759 9.1844704E-05 L2:2477,D:128,T:98,H:81,L3:12,U:12,HV:11,A:9,K:9,C:3,M:3,N:3,I:2,J:2,X:2,L1:1,R:1,V:1 CTACT[T/C]ACAGG 0 -HG03046.mapped.ILLUMINA.bwa.GWD.exome.20121211.bam.mt.bam PASS 12236 G A 1.00 A - 51 25 26 1 12236A transition MT-TS2 tRNA 43 6 7 0 1 2 874 13 0.0044595706 6.6332286E-05 L2:759,H:51,U:18,J:10,L5:5,M:5,T:5,I:4,A:3,R:3,L1:2,L3:2,V:2,B:1,D:1,HV:1,K:1,X:1 CTCAT[G/A]CCCCC 0 -HG03046.mapped.ILLUMINA.bwa.GWD.exome.20121211.bam.mt.bam PASS 12705 C T 1.00 T - 54 28 26 1 12705T transition MT-ND5 Coding 2481 1 10 1 1 12 35323 91 0.18023501 0.00046432597 A:6125,I:4351,M:3286,W:3217,L3:3070,C:3053,X:2758,L2:2512,D:2245,N:1677,L1:1651,L0:413,E:330,G:297,Y:132,Z:101,L4:79,Q:11,L5:7,H:4,V:2,L6:1,S:1 CTCAT[C/T]TTCCT 1 -HG03046.mapped.ILLUMINA.bwa.GWD.exome.20121211.bam.mt.bam PASS 12948 A G 1.00 G - 67 36 31 1 12948G transition MT-ND5 Coding 13 1 10 0 1 394 3 0.0020103785 1.530745E-05 L2:389,H:5 CTTCT[A/G]AACGC 0 -HG03046.mapped.ILLUMINA.bwa.GWD.exome.20121211.bam.mt.bam PASS 13590 G A 1.00 A - 49 25 24 1 13590A transition MT-ND5 Coding 257 11 5.9 0 1 5 6384 19 0.032574255 9.694719E-05 B:3489,L2:2516,H:140,K:104,M:38,U:37,C:25,J:9,L3:9,T:5,A:3,R:3,I:2,D:1,HV:1,L1:1,W:1 TCCCT[G/A]ACAAG 0 -HG03046.mapped.ILLUMINA.bwa.GWD.exome.20121211.bam.mt.bam PASS 13650 C T 1.00 T - 43 23 20 1 13650T transition MT-ND5 Coding 412 4 7.6 1 0 0 4643 11 0.02369083 5.6127315E-05 L2:2518,L1:1658,L0:411,D:17,A:8,H:8,T:8,L5:7,J:2,M:2,U:2,K:1,L6:1 TTCCC[C/T]ACCCT 0 -HG03046.mapped.ILLUMINA.bwa.GWD.exome.20121211.bam.mt.bam PASS 13924 C T 1.00 T - 56 33 23 1 13924T transition MT-ND5 Coding 6 1 10 0 1 P530S 1 P S 530 0.773 1.357776882 0.923076923 I 245 1 0.0012501085 5.1024836E-06 L2:245 TCTAC[C/T]CTAGC 0 -HG03046.mapped.ILLUMINA.bwa.GWD.exome.20121211.bam.mt.bam PASS 14059 A G 1.00 G - 70 35 35 1 14059G transition MT-ND5 Coding 13 1 10 0 1 I575V 1 I V 575 0.41 0.33611392 0.961538462 I 413 2 0.0021073257 1.0204967E-05 L2:391,U:9,T:5,K:4,HV:3,B:1 CCTCC[A/G]TCATC 0 -HG03046.mapped.ILLUMINA.bwa.GWD.exome.20121211.bam.mt.bam PASS 14766 C T 1.00 T - 39 22 17 1 14766T transition MT-CYB Coding 4286 1 10 1 0 T7I 2 T I 7 0.165 0.130992813 0.692307692 III 3 114700 34 0.58525485 0.00017348444 U:24456,T:16974,J:15968,K:14796,A:6223,B:4819,I:4412,M:3282,W:3243,L3:3090,C:3075,X:2786,L2:2530,D:2268,N:1690,L1:1654,R:1248,F:929,L0:415,G:299,E:167,Y:131,Z:100,L4:79,P:41,Q:11,L5:7,H:5,L6:1,S:1 CAAAA[C/T]TAACC 0 -HG03046.mapped.ILLUMINA.bwa.GWD.exome.20121211.bam.mt.bam PASS 15110 G A 1.00 A - 73 44 29 1 15110A transition MT-CYB Coding 46 10 6.1 0 1 A122T 1 A T 122 0.441 0.378675985 0.211538462 III 29 1481 20 0.007556778 0.00010204967 L2:757,HV:163,U:147,H:95,L3:85,T:76,J:46,M:29,C:18,A:16,K:12,G:11,B:6,F:4,N:4,D:3,R:3,W:3,I:1,L0:1,L1:1 TGCTT[G/A]CAACT 0 -HG03046.mapped.ILLUMINA.bwa.GWD.exome.20121211.bam.mt.bam PASS 15217 G A 0.986 A - 74 37 37 1 15217A transition MT-CYB Coding 52 10 6.1 0 1 28 1160 20 0.005918881 0.00010204967 L2:754,U:103,H:102,J:45,D:40,M:34,L4:14,K:13,W:11,B:9,A:8,T:7,L5:5,X:5,C:3,HV:3,L1:3,L3:1 ATTGG[G/A]ACAGA 0 -HG03046.mapped.ILLUMINA.bwa.GWD.exome.20121211.bam.mt.bam PASS 15301 G A 1.00 A - 99 54 45 1 15301A transition MT-CYB Coding 1704 6 7 0 1 20 15883 23 0.081042744 0.000117357115 M:3309,L3:3092,C:3078,L2:2525,D:2274,E:333,G:297,U:209,K:200,B:149,H:122,Z:101,L4:80,L1:53,Q:11,J:10,T:10,HV:8,I:8,R:5,W:3,F:2,N:2,L6:1,X:1 ATCTT[G/A]CCCTT 0 -HG03046.mapped.ILLUMINA.bwa.GWD.exome.20121211.bam.mt.bam PASS 15326 A G 0.99 G - 104 52 52 1 15326G transition MT-CYB Coding 5397 1 10 1 1 T194A 1 T A 194 0.452 0.395040626 0.711538462 III 6 193970 20 0.9897287 0.00010204967 H:69739,U:24412,T:16959,J:15994,K:14814,A:6212,V:5218,B:4902,I:4415,HV:4157,M:3306,W:3226,L3:3095,C:3063,X:2788,L2:2494,D:2261,N:1687,L1:1663,R:1216,F:929,L0:416,E:334,G:299,Y:132,Z:98,L4:80,P:41,Q:11,L5:7,L6:1,S:1 TAGCA[A/G]CACTC 0 -HG03046.mapped.ILLUMINA.bwa.GWD.exome.20121211.bam.mt.bam PASS 16114 C A 1.00 A - 66 32 34 1 16114A transversion MT-DLOOP1 CR 31 6 7 0 0 1061 13 0.005413735 6.6332286E-05 U:588,L2:382,T:42,L1:19,H:8,V:4,F:3,D:2,G:2,J:2,K:2,M:2,R:2,B:1,L3:1,X:1 AGCCA[C/A]CATGA 0 -HG03046.mapped.ILLUMINA.bwa.GWD.exome.20121211.bam.mt.bam PASS 16129 G A 1.00 A - 72 37 35 1 16129A transition MT-DLOOP1 CR 673 76 2.6 1 0 14272 327 0.072822645 0.0016685121 I:4305,H:3590,M:1021,L1:718,U:583,K:571,F:560,L2:506,A:337,L0:317,D:308,B:214,C:212,L3:167,HV:166,N:163,W:126,T:101,R:78,V:60,X:60,Z:41,J:39,Q:11,G:7,L5:7,E:3,P:1 TGTAC[G/A]GTACC 0 -HG03046.mapped.ILLUMINA.bwa.GWD.exome.20121211.bam.mt.bam PASS 16213 G A 1.00 A - 61 33 28 1 16213A transition MT-DLOOP1 CR 45 14 5.5 0 1 1572 64 0.008021104 0.00032655895 L2:444,H:396,A:159,J:125,L1:71,X:68,U:65,K:56,T:50,B:33,W:31,R:23,M:15,V:10,C:8,HV:5,L3:4,G:3,I:2,N:2,D:1,F:1 GTACA[G/A]CAATC 0 -HG03046.mapped.ILLUMINA.bwa.GWD.exome.20121211.bam.mt.bam PASS 16223 C T 1.00 T - 62 31 31 1 16223T transition MT-DLOOP1 CR 2397 7 6.7 1 0 35639 196 0.18184741 0.0010000868 A:6047,I:4359,W:3177,L3:3042,M:3026,C:2985,X:2629,L2:2415,D:2167,N:1658,L1:1609,K:699,L0:406,E:328,G:295,H:231,U:227,Z:99,L4:77,B:57,V:29,HV:24,T:23,Q:11,L5:6,J:5,R:5,F:1,L6:1,S:1 CAACC[C/T]TCAAC 0 -HG03046.mapped.ILLUMINA.bwa.GWD.exome.20121211.bam.mt.bam PASS 16278 C T 1.00 T - 77 40 37 1 16278T transition MT-DLOOP1 CR 587 49 3.4 1 1 11334 120 0.05783155 0.000612298 X:2686,L2:2506,L1:1625,J:954,H:820,U:690,L3:619,B:201,T:159,G:157,C:121,L0:116,M:116,K:93,I:88,W:82,D:78,A:62,R:52,HV:48,P:23,N:12,V:10,L5:7,F:6,Z:2,L6:1 GGATA[C/T]CAACA 0 -HG03046.mapped.ILLUMINA.bwa.GWD.exome.20121211.bam.mt.bam PASS 16355 C T 1.00 T - 87 38 49 1 16355T transition MT-DLOOP1 CR 70 26 4.5 0 0 1 2018 101 0.010296811 0.00051535084 H:455,N:405,L2:281,J:194,HV:90,U:82,R:81,L1:56,F:46,L3:46,L4:46,T:46,K:38,A:29,B:23,M:18,X:17,C:16,I:13,W:13,D:9,L5:5,L0:4,V:4,G:1 AATCC[C/T]TTCTC 0 -HG03046.mapped.ILLUMINA.bwa.GWD.exome.20121211.bam.mt.bam PASS 16362 T C 1.00 C - 79 34 45 1 16362C transition MT-DLOOP1 CR 955 81 2.5 0 1 23527 246 0.120046124 0.001255211 H:6272,A:5761,U:3796,D:2234,M:633,L3:621,W:541,R:537,L2:374,K:368,E:330,G:292,T:270,J:238,F:221,I:219,C:199,HV:160,V:131,B:100,L4:75,L0:39,N:36,L1:34,X:26,Y:12,L5:5,Q:2,Z:1 TCTCG[T/C]CCCCA 1 -HG03046.mapped.ILLUMINA.bwa.GWD.exome.20121211.bam.mt.bam PASS 16390 G A 1.00 A - 68 27 41 1 16390A transition MT-DLOOP1 CR 270 33 4 0 0 6126 273 0.031257812 0.001392978 L2:2515,U:1035,N:837,J:351,E:334,H:276,R:108,A:106,T:86,V:73,B:64,I:64,D:62,M:49,X:40,K:29,L1:24,C:18,HV:14,F:13,L3:11,G:7,L0:6,W:4 ATAGG[G/A]GTCCC 0 HG01817.mapped.ILLUMINA.bwa.CDX.exome.20120522.bam.mt.bam PASS 73 A G 1.00 G - 47 29 18 1 73G transition MT-DLOOP2 CR 4247 13 5.6 1 0 1 119934 60 0.61196125 0.000306149 U:24492,T:16962,J:15973,K:14791,A:6089,H:5724,B:4872,I:4409,M:3305,W:3229,C:3050,L3:3046,X:2786,L2:2527,D:2267,N:1686,L1:1657,F:929,R:825,E:334,G:298,HV:183,Y:132,Z:101,V:95,L4:80,P:40,L0:32,Q:11,L5:7,L6:1,S:1 GGGGT[A/G]TGCAC 0 HG01817.mapped.ILLUMINA.bwa.CDX.exome.20120522.bam.mt.bam PASS 150 C T 0.982 T - 55 33 22 1 150T transition MT-DLOOP2 CR 604 74 2.7 0 0 19751 168 0.100779146 0.0008572172 U:8512,J:3334,L3:1817,H:1122,T:1066,L2:841,K:639,M:505,D:334,B:313,N:258,HV:152,W:135,R:132,V:116,F:99,I:98,C:74,G:63,A:42,L4:42,L1:22,X:19,L0:12,P:2,E:1,S:1 CTCAT[C/T]CTATT 0 HG01817.mapped.ILLUMINA.bwa.CDX.exome.20120522.bam.mt.bam PASS 199 T C 1.00 C - 48 22 26 1 199C transition MT-DLOOP2 CR 237 41 3.7 0 1 1 7841 210 0.04000857 0.0010715215 I:4331,M:881,K:558,N:446,U:335,H:327,W:293,T:184,B:107,L3:94,C:50,D:49,J:37,A:32,L4:27,V:27,L2:22,HV:12,F:6,R:6,L0:4,E:3,L1:3,L5:2,X:2,G:1,Y:1,Z:1 CTTAC[T/C]AAAGT 0