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Understanding Mitochondrial DNA Raw Data

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  • Understanding Mitochondrial DNA Raw Data

    First, I have no experience with this, so I'm going to guess at what I think this means. Please correct my misinterpretations.

    The following five lines from my Geno 2.0 raw data file all seem to refer to the same location being tested, 15047.

    GRC12124251_ChipNGv1_37946_F09,1SNP15047FG_A,0,C,C
    GRC12124251_ChipNGv1_37946_F09,1SNP15047RG_A,0,C,C
    GRC12124251_ChipNGv1_37946_F09,2SNP15047FG_A,0,C,C
    GRC12124251_ChipNGv1_37946_F09,3SNP15047FG_A,0,T,C
    GRC12124251_ChipNGv1_37946_F09,4SNP15047FG_A,0,T,C

    Are these five separate probes testing the same location?
    Why do four of the five contain FG_A after the location, and one contains RG_A?
    What do the FG_A and RG_A mean?
    Shouldn't all the results (the last two values) be the same and equal to each other (i.e., all C,C or G,G, etc)?
    Do differing values in those two columns, or from one probe to another indicate heteroplasmy?

    Inquiring minds want to know!

  • #2
    Yes, those are five different probes for the same position.

    James Lick has a beta version of his utility.

    http://dna.jameslick.com/mthap-new/mthap.cgi

    He is studying the issue of heteroplasmy vs miscalls. He would undoubtedly like to see your mtDNA data. You can send him your CSV file [email protected].

    The F and R probably stand for forward and reverse directions.

    Nominally, the G_A notation refers to ancestral and derived alleles. In your example, the allele is posted as C, the value that would be obtained on the reverse strand when the forward strand is a G.

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    • #3
      Thanks Ann. I've already sent the data to James. His comments on an apparent heteroplasmy at a different location is what piqued my curiosity.

      I'm waiting for FMS results to see if the heteroplasmy is real.

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