Created
August 28, 2014 21:48
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| ##fileformat=VCFv4.1 | |
| ##INFO=<ID=EFFECT,Number=1,Type=String,Description="variant effect (UTR5,UTR3,intronic,splicing,missense,stoploss,stopgain,startloss,duplication,frameshift-insertion,frameshift-deletion,non-frameshift-deletion,non-frameshift-insertion,synonymous)"> | |
| ##INFO=<ID=HGVS,Number=1,Type=String,Description="HGVS Nomenclature"> | |
| ##center=Complete Genomics | |
| #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT GS000036397 | |
| chr1 11854476 rs1801131 T . . PASS TYPE=SNP GT:DP:AD 0/0:79:79,79 | |
| chr1 11856378 rs1801133 G . . PASS TYPE=SNP GT:DP:AD 0/0:119:119,119 | |
| chr1 97547947 rs67376798 T . . PASS TYPE=SNP GT:DP:AD 0/0:47:47,47 | |
| chr1 97915614 rs3918290 C . . PASS TYPE=SNP GT:DP:AD 0/0:53:53,53 | |
| chr3 14187449 rs2228001 G T . PASS EFFECT=MISSENSE;HGVS=XPC:NM_001145769.1:exon16:c.2704C>A:p.Q902K;TYPE=SNP GT:DP:AD 0/1:38:22,16 | |
| chr4 89052323 rs2231142 G . . PASS TYPE=SNP GT:DP:AD 0/0:34:34,34 | |
| chr4 89061114 rs2231137 C . . PASS TYPE=SNP GT:DP:AD 0/0:48:48,48 | |
| chr6 18130918 rs1142345 T . . PASS TYPE=SNP GT:DP:AD 0/0:41:41,41 | |
| chr6 18131012 rs1800584 C . . PASS TYPE=SNP GT:DP:AD 0/0:55:55,55 | |
| chr6 18139228 rs1800460 C . . PASS TYPE=SNP GT:DP:AD 0/0:49:49,49 | |
| chr6 18143955 rs1800462 C . . PASS TYPE=SNP GT:DP:AD 0/0:57:57,57 | |
| chr6 29913298 rs1061235 A . . PASS TYPE=SNP GT:DP:AD 0/0:58:58,58 | |
| chr6 30699384 rs3909184 G . . PASS TYPE=SNP GT:DP:AD 0/0:70:70,70 | |
| chr6 30946148 rs2844682 G . . PASS TYPE=SNP GT:DP:AD 0/0:59:59,59 | |
| chr6 31431780 rs2395029 T . . PASS TYPE=SNP GT:DP:AD 0/0:63:63,63 | |
| chr7 87138645 rs1045642 A G . PASS EFFECT=SYNONYMOUS;HGVS=ABCB1:NM_000927.4:exon27:c.3435T>C:p.I1145I;TYPE=SNP GT:DP:AD 0/1:44:22,22 | |
| chr7 87160618 rs2032582 A C . PASS EFFECT=MISSENSE;HGVS=ABCB1:NM_000927.4:exon22:c.2677T>G:p.S893A;TYPE=SNP GT:DP:AD 0/1:37:20,17 | |
| chr7 87179601 rs1128503 A G . PASS EFFECT=SYNONYMOUS;HGVS=ABCB1:NM_000927.4:exon13:c.1236T>C:p.G412G;TYPE=SNP GT:DP:AD 0/1:34:16,18 | |
| chr7 99270539 rs776746 C . . PASS TYPE=SNP GT:DP:AD 0/0:64:64,64 | |
| chr10 96521657 rs12248560 C . . PASS TYPE=SNP GT:DP:AD 0/0:65:65,65 | |
| chr10 96522463 rs28399504 A . . PASS TYPE=SNP GT:DP:AD 0/0:70:70,70 | |
| chr10 96535173 rs41291556 T . . PASS TYPE=SNP GT:DP:AD 0/0:82:82,82 | |
| chr10 96535246 rs17884712 G . . PASS TYPE=SNP GT:DP:AD 0/0:47:47,47 | |
| chr10 96540410 rs4986893 G . . PASS TYPE=SNP GT:DP:AD 0/0:57:57,57 | |
| chr10 96541616 rs4244285 G A . PASS EFFECT=SYNONYMOUS;HGVS=CYP2C19:NM_000769.1:exon5:c.681G>A:p.P227P;TYPE=SNP GT:DP:AD 0/1:15:11,4 | |
| chr10 96702047 rs1799853 C . . PASS TYPE=SNP GT:DP:AD 0/0:61:61,61 | |
| chr10 96709039 rs9332131 AA . . PASS TYPE=INDEL GT:DP:AD 0/0:44:44,44 | |
| chr10 96741053 rs1057910 A . . PASS TYPE=SNP GT:DP:AD 0/0:52:52,52 | |
| chr10 96741058 rs28371686 C . . PASS TYPE=SNP GT:DP:AD 0/0:61:61,61 | |
| chr11 113270828 rs1800497 G . . PASS TYPE=SNP GT:DP:AD 0/0:32:32,32 | |
| chr11 120663363 rs1954787 T C . PASS EFFECT=INTRONIC;HGVS=GRIK4:XM_005271519.1:intron3:c.83-10039T>C;TYPE=SNP GT:DP:AD 1/1:61:61,61 | |
| chr12 21329738 rs2306283 A . . PASS TYPE=SNP GT:DP:AD 0/0:46:46,46 | |
| chr12 21331549 rs4149056 T . . PASS TYPE=SNP GT:DP:AD 0/0:27:27,27 | |
| chr16 31107689 rs9923231 C T . PASS EFFECT=UPSTREAM;HGVS=VKORC1:VKORC1(dist=990);TYPE=SNP GT:DP:AD 0/1:36:15,21 | |
| chr19 15990431 rs2108622 C . . PASS TYPE=SNP GT:DP:AD 0/0:74:74,74 | |
| chr19 39738787 rs12979860 C T . PASS EFFECT=ncRNA_INTRONIC;HGVS=IFNL4:NR_074079.1:intron1:n.429-152G>A;TYPE=SNP GT:DP:AD 0/1:40:25,15 | |
| chr21 46957794 rs1051266 T C . PASS EFFECT=MISSENSE;HGVS=SLC19A1:XM_005261163.1:exon2:c.80A>G:p.H27R;TYPE=SNP GT:DP:AD 0/1:25:11,14 | |
| chr22 19950235 rs4633 C T . PASS EFFECT=SYNONYMOUS;HGVS=COMT:NM_007310.2:exon1:c.36C>T:p.H12H;TYPE=SNP GT:DP:AD 0/1:30:20,10 | |
| chr22 19951207 rs4818 C G . PASS EFFECT=SYNONYMOUS;HGVS=COMT:NM_007310.2:exon2:c.258C>G:p.L86L;TYPE=SNP GT:DP:AD 0/1:27:15,12 | |
| chr22 19951271 rs4680 G A . PASS EFFECT=MISSENSE;HGVS=COMT:NM_007310.2:exon2:c.322G>A:p.V108M;TYPE=SNP GT:DP:AD 0/1:41:22,19 | |
| chr22 42522074 rs35028622 C A . PASS EFFECT=DOWNSTREAM;HGVS=CYP2D6:CYP2D6(dist=427);TYPE=SNP GT:DP:AD 0/1:47:23,24 | |
| chr22 42522613 rs1135840 G C . PASS EFFECT=SYNONYMOUS;HGVS=CYP2D6:NM_001025161.2:exon8:c.1304G>G [WARNING: mRNA/genome discrepancy: "C"/"G" strand=-]:p.S435S;TYPE=SNP GT:DP:AD 0/1:42:17,25 | |
| chr22 42522638 rs28371735 G . . PASS TYPE=SNP GT:DP:AD 0/0:36:36,36 | |
| chr22 42522660 G4125_4133T A . . PASS TYPE=INDEL GT:DP:AD 0/0:50:50,50 | |
| chr22 42522939 rs61737947 T . . PASS TYPE=SNP GT:DP:AD 0/0:56:56,56 | |
| chr22 42523003 rs28371731 A G . PASS EFFECT=INTRONIC;HGVS=CYP2D6:NM_001025161.2:intron6:c.1021-9T>C;TYPE=SNP GT:DP:AD 1/1:29:29,29 | |
| chr22 42523533 rs72549346 C . . PASS TYPE=INDEL GT:DP:AD 0/0:81:81,81 | |
| chr22 42523592 rs72549347 G . . PASS TYPE=SNP GT:DP:AD 0/0:22:22,22 | |
| chr22 42523805 rs28371725 C . . PASS TYPE=SNP GT:DP:AD 0/0:60:60,60 | |
| chr22 42523843 rs72549349 C . . PASS TYPE=SNP GT:DP:AD 0/0:61:61,61 | |
| chr22 42523858 rs5030867 T . . PASS TYPE=SNP GT:DP:AD 0/0:70:70,70 | |
| chr22 42523943 rs16947 A N . PASS EFFECT=MISSENSE;HGVS=CYP2D6:NM_001025161.2:exon5:c.733C>N [WARNING: mRNA/genome discrepancy: "T"/"G" strand=-]:p.R245;TYPE=SNP GT:DP:AD ./.:63:63,. | |
| chr22 42524176 rs5030656 CTT . . PASS TYPE=INDEL GT:DP:AD 0/0:49:49,49 | |
| chr22 42524203 rs72549351 AGTC . . PASS TYPE=INDEL GT:DP:AD 0/0:38:38,38 | |
| chr22 42524213 rs72549352 C . . PASS TYPE=INDEL GT:DP:AD 0/0:31:31,31 | |
| chr22 42524244 rs35742686 TG . . PASS TYPE=INDEL GT:DP:AD 0/0:44:44,44 | |
| chr22 42524251 rs72549353 AGTT . . PASS TYPE=INDEL GT:DP:AD 0/0:49:49,49 | |
| chr22 42524819 rs72549354 C . . PASS TYPE=INDEL GT:DP:AD 0/0:51:51,51 | |
| chr22 42524929 rs72549356 T . . PASS TYPE=INDEL GT:DP:AD 0/0:64:64,64 | |
| chr22 42524947 rs3892097 C T . PASS EFFECT=SPLICING;HGVS=CYP2D6:NM_001025161.2:exon3:c.353-1G>A;TYPE=SNP GT:DP:AD 0/1:41:17,24 | |
| chr22 42525035 rs5030865 C . . PASS TYPE=SNP GT:DP:AD 0/0:54:54,54 | |
| chr22 42525086 rs5030655 AC . . PASS TYPE=INDEL GT:DP:AD 0/0:60:60,60 | |
| chr22 42525132 rs1058164 G C . PASS EFFECT=SYNONYMOUS;HGVS=CYP2D6:NM_000106.5:exon3:c.408G>G [WARNING: mRNA/genome discrepancy: "C"/"T" strand=-]:p.V136V;TYPE=SNP GT:DP:AD 0/1:31:20,11 | |
| chr22 42525134 rs61736512 C . . PASS TYPE=SNP GT:DP:AD 0/0:56:56,56 | |
| chr22 42525772 rs28371706 G . . PASS TYPE=SNP GT:DP:AD 0/0:73:73,73 | |
| chr22 42525912 rs5030863 C . . PASS TYPE=SNP GT:DP:AD 0/0:22:22,22 | |
| chr22 42526580 rs1080995 G N . PASS EFFECT=INTRONIC;HGVS=CYP2D6:NM_001025161.2:intron1:c.180+34C>N;TYPE=SNP GT:DP:AD ./.:9:9,9 | |
| chr22 42526657 rs72549357 AG . . PASS TYPE=INDEL GT:DP:AD 0/0:29:29,29 | |
| chr22 42526670 rs5030862 C . . PASS TYPE=SNP GT:DP:AD 0/0:10:10,10 | |
| chr22 42526694 rs1065852 G A . PASS EFFECT=MISSENSE;HGVS=CYP2D6:NM_001025161.2:exon1:c.100C>T:p.P34S;TYPE=SNP GT:DP:AD 0/1:27:9,18 | |
| chr22 42526763 rs769258 C . . PASS TYPE=SNP GT:DP:AD 0/0:47:47,47 | |
| chr22 42528028 rs28735595 C T . PASS EFFECT=INTERGENIC;HGVS=CYP2D6(dist=1145),CYP2D7P1(dist=8186);TYPE=SNP GT:DP:AD 0/1:48:17,. | |
| chr22 42528224 rs28588594 G A . PASS EFFECT=INTERGENIC;HGVS=CYP2D6(dist=1341),CYP2D7P1(dist=7990);TYPE=SNP GT:DP:AD 0/1:43:20,23 | |
| chr22 42528382 rs1080985 C G . PASS EFFECT=INTERGENIC;HGVS=CYP2D6(dist=1499),CYP2D7P1(dist=7832);TYPE=SNP GT:DP:AD 1/1:41:40,40 |
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