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cMs or SNPs?

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  • cMs or SNPs?

    I've started analyzing my FF matches both by cM (total and segments) but by SNPs contained therein. I've noticed several cases where large segments contain significantly smaller numbers of SNPs, whereas some smaller segments are far more SNP dense. So this leads me to be slightly confused, and ask if the chance of a DNA segment fragmenting is more of a function of length or of SNP density?

  • #2
    SNP coverage is not so smooth

    I believe (but you should verify with others) this is because the SNPs being tested are not evenly spaced throughout the genome. So, a small segment could be in a region with lots of SNPs and a large segment could be in a region where only a few SNPs are tested. At least this is the way I understand the situation.

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    • #3
      Hi Canyon: I agree and understand that various portions of the DNA are more SNP-dense than others.

      My question is around the chance of segmentation. So, if I have a 20cm segment with 5000 SNPs and another 20cm segment with 7000 SNPs, is one more likely than the other to split during recombination? If the more-dense SNP segment is more likely to split, that makes such a segment more "meaningful" when I see it as having originated more recently. Likewise, a particularly long but SNP-sparse segment is less meaningful.

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      • #4
        I understand that recombination is accounted for in centiMorgans, so that is why just counting SNPs is not a valid measure.

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        • #5
          Originally posted by dna View Post
          I understand that recombination is accounted for in centiMorgans, so that is why just counting SNPs is not a valid measure.
          Interesting; I hadn't heard that before. I have heard somewhere that the chance of a segment surviving intact during recombination is approximately (100 - length in cM)%

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          • #6
            Originally posted by sjadelson View Post
            Interesting; I hadn't heard that before. I have heard somewhere that the chance of a segment surviving intact during recombination is approximately (100 - length in cM)%
            Are large segments of dna passed on without recombining?

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            • #7
              http://www.genome.gov/glossary/index.cfm?id=28
              A centimorgan is a unit used to measure genetic linkage. One centimorgan equals a one percent chance that a marker on a chromosome will become separated from a second marker on the same chromosome due to crossing over in a single generation. It translates to approximately one million base pairs of DNA sequence in the human genome. The centimorgan is named after the American geneticist Thomas Hunt Morgan.
              I am not a geneticist...

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              • #8
                Nice, thanks dna. I guess that's where my (100 - cm)% figure originated.

                I believe this answers my original question neatly.

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