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  • mtDNA calls

    There appears to be reasonable coverage for the mtDNA present in the BAM file. Looks like the haplogroup is H2a2a1 for this one sample. Now the number of extra bases does make me wonder about the assembly.....

    Any comments on what others are seeing for mtDNA?

  • #2
    The two bams I looked at had almost complete mtDNA coverage,
    with only regions in the 6000s and very small regions near 1200 and in the 16000s near the wraparound to zero showing
    no coverage in one. One would be absolutely adequate
    for haplogroup use, the other one, possibly not due
    to the gap near 16400. However, if you have
    HVR1 and HVR2 it would be quite nice to cover most
    of the coding region.

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    • #3
      The CRS is the reference sequence for Build 37, and it is H2a2a1. Are you saying you found no differences from the CRS?

      I'm not sure what you mean by "number of extra bases." Are you surprised to see mtDNA at all? FGC and people with exome sequence data from the 23andMe pilot project have mtDNA coverage, even though it wasn't targeted. My theory was that mtDNA sneaks through because there are thousands of times more copies.

      I don't have the wherewithal to look at BAM files directly, but I have looked at a few cases where mtDNA values have been extracted. The results seem worthwhile, even if not perfect compared to Sanger sequencing.

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      • #4
        As to comparing to Sanger sequencing, in the two BigY bams
        I looked at the vast majority of the mtDNA was quite
        good coverage and clearly perfectly adequate for reliable
        data. I didn't download an mtDNA fasta file so as
        to be able to assign things, however.

        I also looked at the bam in the autosomal areas and
        it really is essentially the Sahara Desert. There's
        likely zero medical stuff there, and if it appears there is,
        its likely unreliable. The Y enrichment is clearly working
        as its supposed to, i.e. targeted.

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