##fileformat=VCFv4.1 ##fileDate=201600825 ##reference=hs37d5/GRCh37 ##resource_version=v1.0.8 ##phasing=partial ##source=JenniferYen ##source=A_variant_by_any_name:quantifying_annotation_discordance_across_tools_and_clinical_databases ##source=Modified_by_AngieHinrichs_for_UCSC_testing ##updates=https://github.com/personalis/hgvslib #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 1 5935162 PTV001:NM_015102.3:c.2818-2T>A A T 88 PASS . GT:GATK:AD:DP:GQ 0/1:0/1:3,2:5:56 1 12065948 PTV002:NM_014874.3:c.1676C>T C T . PASS . GT:GATK:AD:DP:GQ 1/.:1/1:0,20:20 1 46655125 PTV003:NM_017739.3:c.1895+5_1895+8delGTGA CTCAC C . PASS . GT:GATK:AD:DP:GQ 0/1:0/1:3,2:5:42 1 68912523 PTV004:NM_000329.2:c.106_114delCTCTGGCTC TGAGCCAGAG T 109 PASS . GT:GATK:AD:DP:GQ 0/1:0/1:3,2:5:109 1 68912526 PTV005:NM_000329.2:c.109_114delTGGCTC GCCAGAG G 80 PASS . GT:GATK:AD:DP:GQ 0/1:0/1:3,2:5:101 1 109817590 PTV006:NM_001408.2:c.*919G>T G T 77 PASS . GT:GATK:AD:DP:GQ 0/1:0/1:3,2:5:20 1 145597475 PTV007:NM_006468.6:c.1070+35_1070+38delACTT GAAGT G . PASS . GT:GATK:AD:DP:GQ 0/1:0/1:10,15:20 1 153791300 PTV008:NM_020699.2:c.562_563delCA CTG C 81 PASS . GT:GATK:AD:DP:GQ 0/1:0/1:3,2:5:21 1 156104666 PTV009:NM_005572.3:c.711_734delinsCCCC TTGAGAGCCGGCTGGCGGATGCGCT TCCCC 30 PASS . GT:GATK:AD:DP:GQ 0/1:0/1:3,2:5:22 1 156108541 PTV010:NM_170707.3:c.1961dupG G GG 31 PASS . GT:GATK:AD:DP:GQ 0/1:0/1:3,2:5:23 1 161279695 PTV011:NM_000530.6:c.1A>T T A 32 PASS . GT:GATK:AD:DP:GQ 0/1:0/1:3,2:5:24 # ASH changed NM_000139 to NM_000130 to be consistent with genomic coords and NP_ in Table S1 1 169519049 PTV012:NM_000130.4:c.1601G>A T . 99 PASS . GT:GATK:AD:DP:GQ 0/1:0/1:3,2:5:109 1 226125468 PTV013:NM_003240.3:c.774C>T G A 83 PASS . GT:GATK:AD:DP:GQ 0/1:0/1:3,2:5:105 10 89623035 PTV014:NM_001126049.1:c.-794_-792delTGC CGCA C . PASS . GT:GATK:AD:DP:GQ 0/1:0/1:10,10:20 11 62457852 PTV015:NM_032667.6:c.1184G>T C A 79 PASS . GT:GATK:AD:DP:GQ 0/1:0/1:3,2:5:89 11 108178710 PTV016:NM_000051.3:c.5761_5762insT A AT 76 PASS . GT:GATK:AD:DP:GQ 0/1:0/1:3,2:5:90 11 111735981 PTV017:NM_024740.2:c.406-7C>T G A 90 PASS . GT:GATK:AD:DP:GQ 0/1:0/1:2,2:5:100 12 110230580 PTV018:NM_021625.4:c.1701C>G G C 102 PASS . GT:GATK:AD:DP:GQ 0/1:0/1:3,2:5:92 12 22018712 PTV019:NM_005691.2:c.2199-1302delG TC T 76 PASS . GT:GATK:AD:DP:GQ 0/1:0/1:3,2:5:91 12 52912946 PTV020:NM_000424.3:c.556-2A>G T C 58 PASS . GT:GATK:AD:DP:GQ 0/1:0/1:3,2:5:58 12 103234292 PTV022 TC T 80 PASS . GT:GATK:AD:DP:GQ 1/1:1/1:5,10:5:20 12 103311124 PTV023:NM_000277.1:c.-215A>G T C 53 PASS . GT:GATK:AD:DP:GQ 0/1:0/1:3,2:5:51 12 111064166 PTV024:NM_001082538.2:c.342-1G>A G A . PASS . GT:GATK:AD:DP:GQ 1/1:1/1:1,22:20 12 123738430 PTV025:NM_152269.4:c.210delA CA C 100 PASS . GT:GATK:AD:DP:GQ 0/1:0/1:3,2:5:93 13 31789169 PTV026:NM_194318.3:c.71-5delT CT C 59 PASS . GT:GATK:AD:DP:GQ 0/1:0/1:3,2:5:94 14 62187287 PTV027:NM_001530.3:c.223G>A G A 96 PASS . GT:GATK:AD:DP:GQ 0/1:0/1:3,2:5:86 14 62188231 PTV028:NM_001530.3:c.231_232delinsGA TT GA 96 PASS . GT:GATK:AD:DP:GQ 0/1:0/1:3,2:5:86 # ASH Changed NM_001530 to NM_139318 to match genomic coords, NP_, gene in Table S1 14 63174827 PTV029:NM_139318.4:c.2366G>T C A 77 PASS . GT:GATK:AD:DP:GQ 0/1:0/1:3,2:5:95 15 42680000 PTV030:NM_000070.2:c.550delA CA C 78 PASS . GT:GATK:AD:DP:GQ 0/1:0/1:3,2:5:96 15 42680000 PTV031:NM_000070.2:c.550dupA CA CAA 100 PASS . GT:GATK:AD:DP:GQ 0/1:0/1:3,2:5:97 15 42703179 PTV032:NM_000070.2:c.2361_2362insTCA T TTCA 90 PASS . GT:GATK:AD:DP:GQ 0/1:0/1:3,2:5:98 15 42703179 PTV033:NM_000070.2:c.2362_2363delinsTCATCT TAG TTCATCT 79 PASS . GT:GATK:AD:DP:GQ 0/1:0/1:3,2:5:99 15 48782203 PTV034:NM_000138.4:c.2927G>A C T 101 PASS . GT:GATK:AD:DP:GQ 0/1:0/1:3,2:5:109 15 89873415 PTV036:NM_002693.2:c.752C>T G A 33 PASS . GT:GATK:AD:DP:GQ 0/1:0/1:3,2:5:25 16 2103394 PTV037:NM_000548.3:c.277C>T C T 34 PASS . GT:GATK:AD:DP:GQ 0/1:0/1:3,2:5:26 16 3779300 PTV038:NM_004380.2:c.5748G>C C G 35 PASS . GT:GATK:AD:DP:GQ 0/1:0/1:3,2:5:27 16 5128843 PTV039:NM_019109.4:c.826C>G C G 36 PASS . GT:GATK:AD:DP:GQ 0/1:0/1:3,2:5:28 16 74808559 PTV040:NM_024306.4:c.95G>A C T 37 PASS . GT:GATK:AD:DP:GQ 0/1:0/1:3,2:5:29 16 89574804 PTV041:NM_003119.2:c.-22C>A C A 79 PASS . GT:GATK:AD:DP:GQ 0/1:0/1:3,2:5:30 16 89574826 PTV042:NM_003119.2:c.1A>C A C 38 PASS . GT:GATK:AD:DP:GQ 0/1:0/1:3,2:5:31 16 89574914 PTV043:NM_003119.2:c.90dupT G GT 39 PASS . GT:GATK:AD:DP:GQ 0/1:0/1:3,2:5:32 16 89574916 PTV044:NM_003119.2:c.89_91dupGTC C CGTC 40 PASS . GT:GATK:AD:DP:GQ 0/1:0/1:3,2:5:33 16 89575009 PTV045:NM_003119.2:c.183+1G>A G A 41 PASS . GT:GATK:AD:DP:GQ 0/1:0/1:3,2:5:34 16 89575040 PTV046CA:NM_003119.2:c.183+32_183+33insA C CA 82 PASS . GT:GATK:AD:DP:GQ 0/1:0/1:3,2:5:100 16 89575040 PTV046A:NM_003119.2:c.183+32C>A C A 82 PASS . GT:GATK:AD:DP:GQ 0/1:0/1:3,2:5:100 16 89576896 PTV047:NM_003119.2:c.184-2A>C A C 42 PASS . GT:GATK:AD:DP:GQ 0/1:0/1:3,2:5:35 16 89576930 PTV048TT:NM_003119.2:c.216dupT T TT 43 PASS . GT:GATK:AD:DP:GQ 0/1:0/1:3,2:5:36 16 89576930 PTV048TA:NM_003119.2:c.216_217insA T TA 43 PASS . GT:GATK:AD:DP:GQ 0/1:0/1:3,2:5:36 16 89576931 PTV049:NM_003119.2:c.216_217dupTG G GTG 77 PASS . GT:GATK:AD:DP:GQ 0/1:0/1:3,2:5:38 16 89598368 PTV050:NM_003119.2:c.1046_1071delGCCCCCCCGGCTGTGGGAAGACGCTG CGGCCCCCCCGGCTGTGGGAAGACGCT C 77 PASS . GT:GATK:AD:DP:GQ 0/1:0/1:3,2:5:39 16 89613145 PTV052:NM_003119.2:c.1529C>T C T 77 PASS . GT:GATK:AD:DP:GQ 0/1:0/1:3,2:5:41 17 7578194 PTV053:NM_000546.5:c.652_654delGTG GCAC G 77 PASS . GT:GATK:AD:DP:GQ 0/1:0/1:3,2:5:55 17 7578523 PTV054:NM_000546.5:c.406dupC T TG . PASS . GT:GATK:AD:DP:GQ 0/1:0/1:10,11:5:20 17 17119692 PTV055:NM_144997.5:c.1300+2T>G A C 78 PASS . GT:GATK:AD:DP:GQ 0/1:0/1:3,2:5:42 17 41197588 PTV056:NM_007294.3:c.*103_*106delTGTC GGACA G . PASS . GT:GATK:AD:DP:GQ 1/.:1/1:0,20:20 17 41256884 PTV057:NM_007294.3:c.301+1G>C C G 44 PASS . GT:GATK:AD:DP:GQ 0/1:0/1:3,2:5:43 17 42991428 PTV058:NM_002055.4:c.490G>T C A 45 PASS . GT:GATK:AD:DP:GQ 0/1:0/1:3,2:5:44 17 48252809 PTV059:NM_000023.2:c.*11A>T A T . PASS . GT:GATK:AD:DP:GQ 0/1:0/1:20,20:20 17 62022709 PTV060:NM_000334.4:c.3720+9_3720+10dupGA G GTC 46 PASS . GT:GATK:AD:DP:GQ 0/1:0/1:3,2:5:45 17 62022711 PTV061:NM_000334.4:c.3720+8_3720+9insA C CT 46 PASS . GT:GATK:AD:DP:GQ 0/1:0/1:3,2:5:45 17 62023005 PTV062:NM_000334.4:c.3442-8_3442-7insGC G GGC 43 PASS . GT:GATK:AD:DP:GQ 0/1:0/1:3,2:5:46 17 62023006 PTV063:NM_000334.4:c.3442-8G>T C A 49 PASS . GT:GATK:AD:DP:GQ 0/1:0/1:3,2:5:47 17 62034787 PTV064:NM_000334.4:c.2111C>T G A 50 PASS . GT:GATK:AD:DP:GQ 0/1:0/1:3,2:5:48 18 24128261 PTV065:NM_001142730.2:c.234_239delGGAGGA GTCCTCC G 110 PASS . GT:GATK:AD:DP:GQ 0/1:0/1:3,2:5:109 19 15291774 PTV066:NM_000435.2:c.2992C>T G A 51 PASS . GT:GATK:AD:DP:GQ 0/1:0/1:3,2:5:49 19 15311794 PTV067:NM_000435.2:c.-78T>C A G 52 PASS . GT:GATK:AD:DP:GQ 0/1:0/1:3,2:5:50 19 39076592 PTV068:NM_000540.2:c.14818G>A G A 53 PASS . GT:GATK:AD:DP:GQ 0/1:0/1:3,2:5:51 2 50149352 PTV070:NM_001135659.1:c.4374A>G T C 101 PASS . GT:GATK:AD:DP:GQ 0/1:0/1:3,2:5:59 2 50847195 PTV071:NM_001135659.1:c.1405C>T G A 60 PASS . GT:GATK:AD:DP:GQ 0/1:0/1:3,2:5:60 2 71825797 PTV072:NM_003494.3:c.3624C>G C G 60 PASS . GT:GATK:AD:DP:GQ 0/1:0/1:3,2:5:61 2 166179712 PTV073:NM_021007.2:c.1718G>C G C 102 PASS . GT:GATK:AD:DP:GQ 0/1:0/1:3,2:5:109 2 166183371 PTV074:NM_021007.2:c.2026A>G A G 107 PASS . GT:GATK:AD:DP:GQ 0/1:0/1:3,2:5:62 2 166929889 PTV075:NM_001165963.1:c.233_242delinsGT GTCCAGGTCCT GAC 61 PASS . GT:GATK:AD:DP:GQ 0/1:0/1:3,2:5:63 2 166929891 PTV076:NM_001165963.1:c.233_240delAGGACCTG CCAGGTCCT C 62 PASS . GT:GATK:AD:DP:GQ 0/1:0/1:3,2:5:64 2 179393504 PTV077:NM_133378.4:c.99270C>A G T 77 PASS . GT:GATK:AD:DP:GQ 0/1:0/1:3,2:5:65 2 185803444 PTV078:NM_194250.1:c.3324_3347delAGCTGCTGCAGCTGCAGCTGCAGC TGCAGCTGCTGCAGCTGCAGCTGCA T . PASS . GT:GATK:AD:DP:GQ 1/1:1/1:10,8:5:20 2 201950249 PTV079:NM_002491.2:c.208G>T G T 63 PASS . GT:GATK:AD:DP:GQ 0/1:0/1:3,2:5:66 2 238268730 PTV080:NM_004369.3:c.6282+1G>T C A 64 PASS . GT:GATK:AD:DP:GQ 0/1:0/1:3,2:5:67 21 43897396 PTV081:NM_080860.2:c.727+5G>A C T 54 PASS . GT:GATK:AD:DP:GQ 0/1:0/1:3,2:5:52 22 30064360 PTV082:NM_000268.3:c.924_925insCGACGC G GCGACGC 55 PASS . GT:GATK:AD:DP:GQ 0/1:0/1:3,2:5:53 3 10188187 PTV084 TGTCCCGATAG T 80 PASS . GT:GATK:AD:DP:GQ 0/1:0/1:3,2,2:7:102 3 50402127 PTV085:NM_006030.2:c.3402A>C T G 65 PASS . GT:GATK:AD:DP:GQ 0/1:0/1:3,2:5:68 3 50402890 PTV086:NM_006030.2:c.2995C>T G A 80 PASS . GT:GATK:AD:DP:GQ 0/1:0/1:3,2:5:69 3 57851007 PTV087:NM_007159.2:c.1135+565delG AG A 66 PASS . GT:GATK:AD:DP:GQ 0/1:0/1:3,2:5:70 3 122003832 PTV088:NM_000388.3:c.3031C= G C 97 PASS . GT:GATK:AD:DP:GQ 0/1:0/1:3,2:5:109 4 153332910 PTV089:NM_033632.3:c.45_46insCCT C CAGG 75 PASS . GT:GATK:AD:DP:GQ 0/1:0/1:3,2:5:88 5 1295183 PTV090:NM_198253.2:c.-79C>T G A 100 PASS . GT:GATK:AD:DP:GQ 0/1:0/1:3,2:5:109 5 77396835 PTV091:NM_003664.4:c.2409_2411delGAA TTTC T 92 PASS . GT:GATK:AD:DP:GQ 0/1:0/1:3,2:5:108 5 118811422 PTV092:NM_000414.3:c.302+1_302+5delGTGAG GGTGAG G 67 PASS . GT:GATK:AD:DP:GQ 0/1:0/1:3,2:5:71 5 131705587 PTV093:NM_003060.3:c.-75delG CG C 106 PASS . GT:GATK:AD:DP:GQ 0/1:0/1:3,2:5:106 5 148406482 PTV094:NM_024577.3:c.2813A>G T C 68 PASS . GT:GATK:AD:DP:GQ 0/1:0/1:3,2:5:72 6 110036337 PTV095:NM_014845.5:c.123_124insCAG T TCAG 71 PASS . GT:GATK:AD:DP:GQ 0/1:0/1:3,2:5:75 6 110036337 PTV096:NM_014845.5:c.124_126delGAT TGAT T 81 PASS . GT:GATK:AD:DP:GQ 0/1:0/1:3,2:5:76 6 152651802 PTV097:NM_033071.3:c.13805G>T C A 72 PASS . GT:GATK:AD:DP:GQ 0/1:0/1:3,2:5:77 6 152737643 PTV098:NM_033071.3:c.5950G>C C G 0.2 LowQual . GT:GATK:AD:DP:GQ 0/1:0/1:3,2:5:78 7 55242465 PTV100:NM_005228.3:c.2236_2250delGAATTAAGAGAAGCA GGAATTAAGAGAAGCA G 56 PASS . GT:GATK:AD:DP:GQ 0/1:0/1:3,2:5:54 7 75932111 PTV102:NM_001540.3:c.82C>A C A 84 PASS . GT:GATK:AD:DP:GQ 0/1:0/1:3,2:5:79 7 91652178 PTV103:NM_005751.4:c.4004_4006dupAAC A AAAC 92 PASS . GT:GATK:AD:DP:GQ 0/1:0/1:3,2:5:108 7 117199644 PTV104:NM_000492.3:c.1521_1523delCTT ATCT A 85 PASS . GT:GATK:AD:DP:GQ 0/1:0/1:3,2:5:80 7 140453136 PTV105:NM_004333.4:c.1798_1799delinsAG AC CT 85 PASS . GT:GATK:AD:DP:GQ 0/1:0/1:3,2:5:80 7 143013488 PTV108:NM_000083.2:c.180+3A>T A T 73 PASS . GT:GATK:AD:DP:GQ 0/1:0/1:3,2:5:81 7 143018934 PTV109:NM_000083.2:c.689G>A G A 74 PASS . GT:GATK:AD:DP:GQ 0/1:0/1:3,2:5:82 7 143048771 PTV110:NM_000083.2:c.2680C>T C T 86 PASS . GT:GATK:AD:DP:GQ 0/1:0/1:3,2:5:83 8 1871951 PTV111:NM_014629.2:c.2399C>T C T 104 PASS . GT:GATK:AD:DP:GQ 0/1:0/1:3,2:5:84 9 13112056 PTV112:NM_003829.4:c.5603dupC T TG 94 PASS . GT:GATK:AD:DP:GQ 0/1:0/1:3,2:5:85 9 21971208 PTV113:NM_000077.4:c.151-1G>T C A 55 PASS . GT:GATK:AD:DP:GQ 0/1:0/1:3,2:5:53 9 35683240 PTV114:NM_003289.3:c.773-3dupC T TG . PASS . GT:GATK:AD:DP:GQ 1/1:1/1:10,8:5:20 9 135796754 PTV115:NM_000368.4:c.733C>T G A 97 PASS . GT:GATK:AD:DP:GQ 0/1:0/1:3,2:5:87 # ASH Replaced HSCHR6_MHC_MANN_CTG1 with hg19's chr6_mann_hap4: chr6_mann_hap4 3848158 PTV121:NM_021983.4:c.490G>C T G 88 PASS . GT:GATK:AD:DP:GQ 0/1:0/1:3,2:5:56 chr6_mann_hap4 3851043 PTV122:NM_021983.4:c.346G>T C A 57 PASS . GT:GATK:AD:DP:GQ 0/1:0/1:3,2:5:57 X 70443101 PTV123:NM_000166.5:c.-101C>T C T 90 PASS . GT:GATK:AD:DP:GQ 0/1:0/1:2,2:5:100 X 107845202 PTV124G:NM_000495.4:c.2130_2135delACCACC GACCACC G 80 PASS . GT:GATK:AD:DP:GQ 0/1:0/1:3,2,2:7:102 X 107845202 PTV124GACC:NM_000495.4:c.2133_2135delACC GACCACC GACC 80 PASS . GT:GATK:AD:DP:GQ 0/1:0/1:3,2,2:7:102 X 153296777 PTV125:NM_004992.3:c.502C>T G A 83 PASS . GT:GATK:AD:DP:GQ 0/1:0/1:3,2:5:104