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Autosomal Segment Analyzer

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  • Autosomal Segment Analyzer

    http://www.y-str.org/2013/08/autosom...-analyzer.html

    I found this very useful for looking at specific or rare autosomal alleles in my dna.

  • #2
    Originally posted by 1798 View Post
    http://www.y-str.org/2013/08/autosom...-analyzer.html

    I found this very useful for looking at specific or rare autosomal alleles in my dna.
    To Felix
    Does it matter whether a genotype is TG instead of GT or TC instead of CT? The autosomal-segment-analyzer doesn't display some of these types in the pie chart.

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    • #3
      Me, Son, LBK
      GC 179, 181, 542
      TA 107, 121, 326
      AT 103, 101, 326
      TC 82,981, 81990, 54,498
      CT 0, 0, 56,795
      AG 82,867, 82,211, 54,245
      GA 0, 0, 56,516
      TG 18,914 18,756 12,477
      GT 0, 0, 12,787
      AC 19,103, 18,743, 12,339
      CA 0, 0, 12,890
      GG 130,797,130,548,176,624
      AA 112,329,112,612,157,793
      TT 112,066,112,473,156,793
      CC 131,411,131,312,177,411

      My Son and I don't have any SNPs with CT,GA,GT or CA genotypes. Does anyone know what the reason is?
      Last edited by 1798; 6 January 2015, 06:20 AM.

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      • #4
        Originally posted by 1798 View Post
        To Felix
        Does it matter whether a genotype is TG instead of GT or TC instead of CT? The autosomal-segment-analyzer doesn't display some of these types in the pie chart.
        The comparing algorithm treats TG same as GT and it doesn't matter. The pie chart is just for reference frequency based on OpenSNP frequency data represented as such.

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        • #5
          Originally posted by 1798 View Post
          Me, Son, LBK
          GC 179, 181, 542
          TA 107, 121, 326
          AT 103, 101, 326
          TC 82,981, 81990, 54,498
          CT 0, 0, 56,795
          AG 82,867, 82,211, 54,245
          GA 0, 0, 56,516
          TG 18,914 18,756 12,477
          GT 0, 0, 12,787
          AC 19,103, 18,743, 12,339
          CA 0, 0, 12,890
          GG 130,797,130,548,176,624
          AA 112,329,112,612,157,793
          TT 112,066,112,473,156,793
          CC 131,411,131,312,177,411

          My Son and I don't have any SNPs with CT,GA,GT or CA genotypes. Does anyone know what the reason is?
          The SNPs with the alleles GC,TA and AT have the least number in all our results. Does anyone know anything about these autosomal SNPs?

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          • #6
            no luck

            I downloaded the program and eveytime I run it on my ancestory.com raw data.. it never completes just kinda hangs up. do I need something else to use it?? thanks, gary

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            • #7
              Originally posted by gman35 View Post
              I downloaded the program and eveytime I run it on my ancestory.com raw data.. it never completes just kinda hangs up. do I need something else to use it?? thanks, gary
              It didn't work for me the first time but I deleted it and downloaded it again. I uploaded my son's and my dna files and it worked fine. It took around two hours.The only downside is that when you close it you have to start the whole process again. I am interested in the minor alleles that my son and I share.

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              • #8
                This SNP rs8187858 TT shows 0.01% in the pie chart of human population variants so it must be rare enough. It must be a European variant, maybe Irish as well.

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                • #9
                  Originally posted by 1798 View Post
                  This SNP rs8187858 TT shows 0.01% in the pie chart of human population variants so it must be rare enough. It must be a European variant, maybe Irish as well.
                  Please be cautious that the pie chart is based on OpenSNP dataset and not the entire human population. So, it may never be accurate but good enough to do basic calculations.

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                  • #10
                    Originally posted by felix View Post
                    Please be cautious that the pie chart is based on OpenSNP dataset and not the entire human population. So, it may never be accurate but good enough to do basic calculations.
                    I can check any of the SNPs out on the 1000g site but I am happy enough to be able to use the Autosomal Segment Analyzer.

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