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Please help me to interpret this line. How come I have this disease?

chr1 53676448 . G A 1495.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.48;ClippingRankSum=-5.270e-01;DP=79;ExcessHet=3.0103;FS=4.485;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.775;QD=19.18;ReadPosRankSum=0.403;SOR=0.581;set=variant2 GT:AD:DP:GQ:PL:CGIANN_VARNAME:CGIANN_1000GAF:CGIANN_ESP6500AF 0/1:29,49:78:99:1524,0,780:-,NM_000098.2(CPT2) c.1102G>A (p.V368I):-,0.5:-,0.456405
chr1 53676986 . C . . . END=53678942;NT GT ./.
chr1 53679264 . T . . . END=53680317;NT GT ./.
chr1 53680529 . a . . . END=53681541;NT GT ./.
chr1 53681771 . G . . . END=53682332;NT GT ./.
chr1 53682540 . G . . . END=53683699;NT GT ./.

I only saw one mutation with quite some information, and several other lines without information. How come I have a cpt-2 deficiency?

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Answers

  • andrewchenandrewchen Member
    edited July 2017

    More data (with several new lines)

    chr1 53580646 . C . . NT END=53600015;NT GT ./.
    chr1 53600201 . T . . NT END=53607949;NT GT ./.
    chr1 53608129 . C . . NT END=53662647;NT GT ./.
    chr1 53662853 . T . . NT END=53666319;NT GT ./.
    chr1 53666517 . A . . NT END=53667997;NT GT ./.
    chr1 53668182 . T . . NT END=53675682;NT GT ./.
    chr1 53675849 . C . . NT END=53675853;NT GT ./.
    chr1 53676448 . G A 1495.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.48;ClippingRankSum=-5.270e-01;DP=79;ExcessHet=3.0103;FS=4.485;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.775;QD=19.18;ReadPosRankSum=0.403;SOR=0.581;set=variant2 GT:AD:DP:GQ:PL:CGIANN_VARNAME:CGIANN_1000GAF:CGIANN_ESP6500AF 0/1:29,49:78:99:1524,0,780:-,NM_000098.2(CPT2) c.1102G>A (p.V368I):-,0.5:-,0.456405
    chr1 53676986 . C . . NT END=53678942;NT GT ./.
    chr1 53679264 . T . . NT END=53680317;NT GT ./.
    chr1 53680529 . a . . NT END=53681541;NT GT ./.
    chr1 53681771 . G . . NT END=53682332;NT GT ./.
    chr1 53682540 . G . . NT END=53683699;NT GT ./.

  • SheilaSheila Broad InstituteMember, Broadie, Moderator

    @andrewchen
    Hi,

    Sorry for the delay. Can you tell us how you produced the VCF? Did you follow Best Practices?

    Thanks,
    Sheila

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