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Pseudoautosomal regions

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  • #16
    Originally posted by Ann Turner View Post

    However, people with mother/child data at FTDNA see these numbers in the Chromosome Browser table

    Segment boundaries: 1,370,495 to 154,570,039 (?build 36 numbers)
    Number of SNPs 18,092
    cM: 195.93
    So that seems to include part of the PAR1 region at the end of the short arm tips of the X and Y, but not the PAR2 region which is at the end of the long arm tips and would be in the 155,000,000 plus range. I think it would include the PAR3 region if one has it.

    So in the 1.37-2.4+ range one might see SNPs from a Y chromosome, I think.

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    • #17
      Originally posted by JohnG View Post
      We usually talk about the Y chromosome as something very different from the X. But, if I have it right, there are 2 (or now 3) small pseudo-autosomal regions on the Y that are homologous to the X, and can bind together and crossover. I wonder how this is handled in the new X matching. There are probably more questions than these but I have these.

      1) Do the pseudo-autosomal regions of the Y get used in the X match? That might mean a male had 2 values of a SNP and would match people his mother did not because of that.
      2) I believe this means there are cases where a female will get an allele from their father's Y chromosome and a male can get an allele from their father's X chromosome. How does this affect matching, and our logic in using the matches?
      edit.. nevermind you got it... FTDNA removes the almost all of the PAR loci from the data.

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      • #18
        Originally posted by Ann Turner View Post
        I may need to backtrack on my statements here. I was basing my numbers on my son's transfer from 23andMe.

        However, people with mother/child data at FTDNA see these numbers in the Chromosome Browser table

        Segment boundaries: 1,370,495 to 154,570,039 (?build 36 numbers)
        Number of SNPs 18,092
        cM: 195.93

        Could someone review a raw data download for the position of the 1st and last SNPs (build 36 and 37)?

        The cM total appears to be based on female transmissions when I look at the Rutgers website. Rutgers reports sex-averaged rates for the autosomes, but not the X. Female rates are about 1.7 times higher for the autosomes and would be even more lopsided for the X, which stays intact every time it passes from a father to his daughter.

        http://compgen.rutgers.edu/RutgersMap/MapBrowser.aspx
        Yes Ann, X interpolation should match Rutgers

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        • #19
          Originally posted by Ann Turner View Post
          23andMe reports XY SNPs on the X chromosome, with SNPs covering the territory at the tips of the chromosome, from positions 1 to 2,697,868 and 154,939,018 to 155,236,747.

          It appears that FTDNA is not including XY SNPs in the X file, which starts at 2,700,157 and ends at 154,916,845. (The SNPs are in alphabetical order by rs number, so you need to sort by position.)

          AncestryDNA reports XY SNPs on chromosome "25", which may be the way the Illumina base calling software works. IF so, it's possible that FTDNA could report those, but they're small potatoes compared to the total size of the X.

          In any event, it doesn't sound like the pseudo-autosomal region is impacting the X matches here.
          Illumina does report all three types of SNPs, X, XY and Y tested on their OmniExpress chip - then and labels them as such. I have the entire SNP list somewhere for the 12 sample Omni Chip. It's a large list.

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          • #20
            Originally posted by Ann Turner View Post
            The cM total appears to be based on female transmissions when I look at the Rutgers website. Rutgers reports sex-averaged rates for the autosomes, but not the X. Female rates are about 1.7 times higher for the autosomes and would be even more lopsided for the X, which stays intact every time it passes from a father to his daughter.

            http://compgen.rutgers.edu/RutgersMap/MapBrowser.aspx
            Hi,

            We are open to other ideas. Please feel free to send me a message, Ann, at my [email protected] address. Your knowledge is most appreciated.

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