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Novel variants per generation = 1?

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  • #16
    There are also about 50 "novel" SNPs where the reference sequence has the derived variant - almost everyone tested will find each of these SNPs on their novel list, apart from the small minority who match the reference sequence at that point (or maybe noone at all if the SNP is private or was a glitch in the process which establised the reference). Hopefully when these SNPs are removed from the novel category it is done consistently for everyone.

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    • #17
      I appreciate all of the discussion around my question, and I agree with most of it, but I what I am trying to ask is whether there was any extra effort during Big Y testing to obtain results for certain specified Known SNPs.

      Was there a list of important Known SNPs where extra efforts were made to make sure results for them were included in the Big Y results?

      Or was the Big Y test just run and if certain Known SNPs happened to be among the results, they were reported as such, and if not, so be it?

      Thanks for any further insights.

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      • #18
        Greetings, fellow Morrison,

        It might be worth considering that FTDNA could as a business need to speculate on global needs, where what might apply to one global region might not apply to another region, and so perhaps FTDNA could have then set its focus broadly, to worldwide. And that could then have lead to some local/regional/specific confusion and consternation, as where so many of us could be so focused on our local concerns.

        But it seems likely that FTDNA will work toward eventually getting those wrinkles ironed out, too.

        Yet the more who test, the better and the sooner the overall picture will become!

        Best,

        Doug

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        • #19
          Originally posted by morrisondna View Post
          I appreciate all of the discussion around my question, and I agree with most of it, but I what I am trying to ask is whether there was any extra effort during Big Y testing to obtain results for certain specified Known SNPs.

          Was there a list of important Known SNPs where extra efforts were made to make sure results for them were included in the Big Y results?

          Or was the Big Y test just run and if certain Known SNPs happened to be among the results, they were reported as such, and if not, so be it?

          Thanks for any further insights.
          The Big Y test used a different technology. Older tests, as I understand it, had a chip with tests for specific known SNPs. Every test using a specific chip looked at the same SNPs. Very standard for everyone. It was a matching rather than a sequencing.

          The Big Y uses next generation sequencing and really reads DNA strands. That opens the door to discover new SNPs, novel variants not in the list of known SNPs. It also means there may be uncertainty in how a strand was read, which can lead to differences between which SNPs are read in a given kit, and to differences in data quality for parts of the read.

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          • #20
            Originally posted by JohnG View Post
            It also means there may be uncertainty in how a strand was read, which can lead to differences between which SNPs are read in a given kit, and to differences in data quality for parts of the read.
            JohnG,

            That's my understanding as well. So, to some extent there will be an equal percentage of Known SNPs and Novel Variants that are present, but not read for any particular test.

            The "no calls" are reported for the "Known SNP" list, but for "Novel Variants", we don't know if a variant not reported is not present or a "no call" from the basic FTDNA reports. Then, until further investigation of detailed results is done, we need to keep in mind that either case could be true.

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