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Huge number of mismatches between full mtDNA sequence and 23andme mtSNPs

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  • Huge number of mismatches between full mtDNA sequence and 23andme mtSNPs

    Dear all,

    I compared all 3923 mtDNA SNPs from a V3 23andme dataset to the full mtDNA genome that was received from FTDNA.
    I wrote a quick script that compares every mtDNA basepair to the one reported by 23andme. Of the 3923 23andme mt SNPs only 1087 are in common wheras 2836 are different.

    That probably means one cannot directly compare those two results. I am still interested in obtaining the rsXXXX values for my full mtDNA genome, any ideas how to tackle this?

    Regards

    EJ Blom

  • #2
    I realized that as soon as my mtDNA has an insertion or deletion as compared to the reference sequence (which is the basis of the positions I guess) the numbering is off. So I need to compare it with the reference sequence and do some basic SNP calling in order to find the right SNPs.

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    • #3
      Originally posted by ejblom View Post
      I realized that as soon as my mtDNA has an insertion or deletion as compared to the reference sequence (which is the basis of the positions I guess) the numbering is off. So I need to compare it with the reference sequence and do some basic SNP calling in order to find the right SNPs.
      You can upload your 23andMe mtDNA results to James Lick's mthap web tool. This will give you a list of the SNPs relative to the rCRS or RSRS reference sequences which you can then compare your FTDNA full sequences results.

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      • #4
        Originally posted by GST View Post
        You can upload your 23andMe mtDNA results to James Lick's mthap web tool. This will give you a list of the SNPs relative to the rCRS or RSRS reference sequences which you can then compare your FTDNA full sequences results.
        Thanks, that;s a nice tool. I ran the tool and it didn't produced the variants that I already thought were wrongly predicted. I also created an alignment of the rCRS and my own sequence and detected a shift of 2 basepairs. That ofcourse messed up the numbering. I could correct for this by checking the numbering of the rCRS and check my own sequence in the same column.

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        • #5
          Once you get the alignment worked out, you probably know that if there's a direct contradiction of results at the same position between here and 23andme, for mtdna, these results (ftdna) are far more accurate.

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