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4310Re: [I-M223] Re: Cont2a/Cont1 CTS6433+ sector tree

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  • Wayne Roberts
    Aug 9 4:44 PM
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      Hello Joao,
      YFull can only work with what is currently listed in the ISOGG Y-Tree and what is found in the bam files of participants.
      With the ISOGG tree, it currently lists Z78, then L1198, then Z190 then Z79. New participants are placed on the YFull tree under a known terminal SNP and as YFull reads bam files, it works out the order of SNPs found derived. So if we have say six participants with known terminal SNPs L1198 and Z79, they are first placed at L1198 or Z190 or Z79. Because all will be Z78+, Z171+, Z185+, Z180+, L1198+, Z166+ and Z187+, YFull is unable to work out the mutation order of these SNPs and this is why many are groups together. What is needed is a participant that is Z78+ Z185- or L1198+ Z166- and so on, so YFull can work out the order. Fortunately with Hogarth being Z78+ Z171+ and Z185-, this will help to break up the grouping when his analysis is completed. With future Big Y tests, it is hoped that further seperation of SNPs will become evident.
      Ideally, we need Big Y participants that are known to be Z185+ Z180- and Z180+ L1198- and L1198+ Z166- and Z166+ Z187-. Perhaps in the new round of discount Big Y testing we can recuit such participants. We also have another SNP, S20905 that fits somewhere in between L1198 and Z190. It looks as if it is between Z166, Z187 and Z190 because IDs YF01719, YF01950 and YF01785 (you) are ancestral for S20905 and we know you are Z166+ and Z187+.
      I hope that is clear enough of an explanation.
      ----- Original Message -----
      Sent: Sunday, August 10, 2014 3:47 AM
      Subject: Re: [I-M223] Re: Cont2a/Cont1 CTS6433+ sector tree


      Thanks Wayne for including the family names in the respective branches of our sector in the M-223 tree. It's much easier to see who are our closest cousins this way (than having just ID numbers).
      I was wondering why Yfull was not going further than the L1198 SNP given that we know that Z166 is further downstream. But I realized that Z166 was not read by BigY. On the other hand, Z187 was included in the BigY and I'm clearly positive and if I'm not mistaken is at the same level of Z166. So why haven't they opened a new branch down L1198?  Thanks! JOAO

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