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Thread: What is ZZ11 and what do we do with it?

  1. #21
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    Quote Originally Posted by Williamson View Post
    I trust these numbers. BigY tests have great coverage in the region around 22286799, and that position is also the best place for ZZ11+ reads to align. The reads with the ZZ11 mutation are generally about 1/3 to 1/2 of them. If they were there, they'd show up.
    So these really are back-mutations, then, right? since the sequencing is not likely out of whack.

    Then the question is all about the mutation rate for these locations and the duration for which we need a low probability of mutation.

  2. #22
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    Quote Originally Posted by lgmayka View Post
    The "mystery" is that it is very prone to back-mutation. Both members of R-Y18894 are entirely ancestral (396C and 392C) at 22286799.

    The practical danger is that naive customers might actually take the ZZ11 level seriously: A customer might test ZZ11- and assume that he is also DF27- U152- , which is not a safe conclusion.
    Could you explain what you mean by "take the ZZ11 level seriously"? Either there is a mutation that happened between P312 and DF27 and U152 or there isn't. It sounds like you're suggesting there isn't. Or are you suggesting we just don't have enough data yet?

    As for testing ZZ11- and assuming he is also DF27- and U152-, I agree with you that's a problem. I think it should become better known that one shouldn't put all their faith in any single mutation. There are R-DF13 men right now who are in fact DF13- after having lost that mutation. Had there not be additional downstream SNPs, he too may have come to the wrong conclusion.

  3. #23
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    Quote Originally Posted by Williamson View Post
    I trust these numbers. BigY tests have great coverage in the region around 22286799, and that position is also the best place for ZZ11+ reads to align. The reads with the ZZ11 mutation are generally about 1/3 to 1/2 of them. If they were there, they'd show up.
    Does checking the opposite strand help in any manner?

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    Quote Originally Posted by Williamson View Post
    ... There are R-DF13 men right now who are in fact DF13- after having lost that mutation. Had there not be additional downstream SNPs, he too may have come to the wrong conclusion.
    I thought there was something funky with DF13 going on but thought it must have just been lab error or Geno 2 integration screw-ups. Does Z2542 seem to work better? I remember FTDNA didn't want to do DF13 back in the M343 Backbone Pack a year ago and chose Z2542 instead.

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    No. I believe any knowledge of what strand a read came from is only determined by mapping that read somewhere. In this case, it would amount to the same thing as looking at different positions within DYZ19. Some reads with the ZZ11 mutation do in fact get mapped to alternate positions, but that number is typically small compared to what is mapped to 22286799. Shorter reads have more ambiguity than the longer 165bp Big Y reads.

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    Quote Originally Posted by Mikewww View Post
    I thought there was something funky with DF13 going on but thought it must have just been lab error or Geno 2 integration screw-ups. Does Z2542 seem to work better? I remember FTDNA didn't want to do DF13 back in the M343 Backbone Pack a year ago and chose Z2542 instead.
    It's an interesting question. I don' know the answer. DF13 shows up more consistently in BigY results than Z2542 does. If there were problems with Z2542, I wouldn't be able to identify them as easily as I can with DF13.

  7. #27
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    Quote Originally Posted by Mikewww View Post
    So these really are back-mutations, then, right? since the sequencing is not likely out of whack.

    Then the question is all about the mutation rate for these locations and the duration for which we need a low probability of mutation.
    Yes, that's the case. "Back mutation" here needs to be understood to refer to a few different mechanisms for losing the mutation, but they all have the same net effect.

    We can try to estimate a rate until a more detailed analysis can be done. For arguments sake, let's say we currently identify one ZZ11 back mutation for every 100 R-ZZ11 men we look at. ZZ11 is about 4500 years old, so that would be 180 generations at 25yrs/generation. I want to estimate the number of transmission events (father to son) since ZZ11 within that group of 100 men. I going to say 120 per man on average. So that would give one back mutation for every 12,000 transmission events. I'm open to hearing different suggestions for these numbers.

    If we consider a lone P312* guy, we can now estimate the chance he might belong to R-ZZ11 even if he tested ZZ11-. It would be just 180/12000 = 1.5%. It's not a small number and certainly larger than anyone would want it to be. Fortunately, we don't have many P312* men.

    To help the situation, we do actually have the INDEL, Z38841. I have asked for this INDEL to be included in YBrowse a couple times, but it doesn't seem to have made it yet. I think the problem with its inclusion is the way it is defined. The mutation is already in the reference sequence. Z38841 refers to a change from 10 repeats of GAATG to 9. The reference sequence already has 9 repeats.

    Unlike ZZ11, Z38841 can be Sanger sequenced and can be ordered from YSEQ. I have had Thomas Krahn test me for it, and sure enough I have 10 repeats. (I belong to R-L21) Thomas is reluctant to offer it as anything that will be useful for phylogeny, so it's not in the catalog. If you order a test for FGC20785, it will come up. Keep in mind, like ZZ11, we do expect some men to not have the expected value.

    I'm sure we could estimate the mutation rate for Z38841 as well. Even if we assume it mutates 10 times as quickly as ZZ11, which I don't think it does, the two combined would greatly improve our confidence in predicting the true R-ZZ11 status for P312* men.

    As an FYI, I have checked the BAM files of both P312* men I know of Keyes (104079) and Harbottle (278973) and both are negative for ZZ11 and Z38841.
    Last edited by Williamson; 04-22-2016 at 09:05 PM. Reason: Added Z38841 data on two existing P312* men

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