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  • SNP Poor Regions

    Hi - I have several "SNP Poor Region, not tested for family finder" light gray sections on my Chromosome Browser results.

    What exactly does that mean (and I already am guessing there are not a lot of SNP's in those sections). Is this common to everyone (it happens to others, same locations, different locations, lesser or greater extent)? Would I have those same results if I took this test with other companies, or retested with FTDNA (meaning it is a permanent situation)? Or was there something specific to this test, and if so, what could it be?

    Thanks for helping me understand this detail.
    Chico -

  • #2
    I think the gray / SNP Poor regions are a general, across-the board thing - do not think they went, "oh, this is where you personally happen to have a SNP Poor area" - they know that will be a SNP Poor area, so do not look there.

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    • #3
      Whether the "SNP-poor" regions matter with respect to detecting matching segments depends on the recombinational length of the region itself, as expressed in centiMorgans. If the length of the region measured in this way is very short (say, much less than 1 cM), the probability that a recombinational event (a crossover) within the region could have happened and not be detected by the matching algorithm is small. On the other hand, if the distance between SNP's is on the order of 5 cM or more, the probability of an unnoticed crossover is (by definition of the centiMorgan unit) much higher.

      One sort of "SNP-poor" region is the neighborhood of the centromeres. For the human autosomes, most of these uncharted centromere regions are extremely short in terms of recombination (much less than 1 cM), so it should be safe to ignore any warnings about "SNP-poverty" for genealogical purposes, even though the length of the same regions in millions of base pairs may seem high. Whether a segment is passed on to the next generation depends on the probability of recombination, and not on the length of the segment in millions of base pairs.

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