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  • SNP Counting

    This may seem like a silly question, but I need to know how to count SNPs.

    I am comparing my results with those of my closest STR match, same surname, 103/111.

    He and I share 93 novel variants and have no differing known SNPs.

    There are 7 SNPs for which he has the ancestral value and I have the derived.

    There are 7 different SNPs for which I have the ancestral value and he has the derived.

    So for purposes of estimating the TMRCA do I use 7 or 14 SNP differences?

    Thanks for any insights.

    Jim

  • #2
    Originally posted by jbarry6899 View Post
    This may seem like a silly question, but I need to know how to count SNPs.

    I am comparing my results with those of my closest STR match, same surname, 103/111.

    He and I share 93 novel variants and have no differing known SNPs.

    There are 7 SNPs for which he has the ancestral value and I have the derived.

    There are 7 different SNPs for which I have the ancestral value and he has the derived.

    So for purposes of estimating the TMRCA do I use 7 or 14 SNP differences?

    Thanks for any insights.

    Jim
    I am not an expert but I think it may be 7. If we compare P312 to U106 we wouldn't add 36 to 36 for the average number of SNPs downstream of P311. That would be 72 in total. That is only my view on it.

    Comment


    • #3
      Originally posted by jbarry6899 View Post
      This may seem like a silly question, but I need to know how to count SNPs.

      Jim
      HI Jim:

      Out of curiosity; do you know the actual number of generations to a common ancestor? If you share the same surname is it safe to say the actual TMRCA is less than 500 years?

      Comment


      • #4
        We haven't identified the common ancestor but the surname history is well known and we are from the same general area in Ireland.

        If 7 is correct, then the STR TMRCA from the Tip Report is roughly the same as the SNP TMRCA from Doug McDonald's Calculator:

        STR: 13 generations (50% probability); S. D. 5
        SNP: 14.5 generations; S. D. 4.5

        Jim

        Comment


        • #5
          Originally posted by jbarry6899 View Post
          We haven't identified the common ancestor but the surname history is well known and we are from the same general area in Ireland.

          If 7 is correct, then the STR TMRCA from the Tip Report is roughly the same as the SNP TMRCA from Doug McDonald's Calculator:

          STR: 13 generations (50% probability); S. D. 5
          SNP: 14.5 generations; S. D. 4.5

          Jim
          If 7 Big-Y SNPs is correct, then it could be 7x135 per SNP which is further back than you think.

          Comment


          • #6
            Originally posted by jbarry6899 View Post
            There are 7 SNPs for which he has the ancestral value and I have the derived. There are 7 different SNPs for which I have the ancestral value and he has the derived. So for purposes of estimating the TMRCA do I use 7 or 14 SNP differences?
            I'm not familiar with Doug McDonald's SNP Calculator, but I think you would want to look at how he expects the the number of SNPs to be input (either the average or the total for the two paternal lines). 14.5 generations seems to recent for a difference of 14 SNPs, so I would guess Doug use the total difference between the two lines.

            Comment


            • #7
              Originally posted by GST View Post
              I'm not familiar with Doug McDonald's SNP Calculator, but I think you would want to look at how he expects the the number of SNPs to be input (either the average or the total for the two paternal lines). 14.5 generations seems to recent for a difference of 14 SNPs, so I would guess Doug use the total difference between the two lines.
              Average the number of SNPs found back to the shared ancestor. The number of counted SNPs would be essentially the same as the number of private no-star and one-Star snps identified by the FGC analysis of a BAM file. The U106 SNP analysis process provides almost identical number and list of SNPs as the FGC analysis.

              Comment


              • #8
                For my calculator, you add the two lists. Just like for
                STRs its the number of differences.

                Note that FTDNA is listing large numbers of unreliable
                SNPs. I would disregard any SNP which is in the region
                22,2xx,xxx area.

                Comment

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