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Big Y: Which Markers Tested Negative

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  • Big Y: Which Markers Tested Negative

    I am conducting a small family project and have run in to a question: I have a Big Y result A ordered on 19NOV2017 which returned a terminal hg of J-BY40162. I have another persons Big Y result B ordered 24APR2018 which returned the result of J-Y113483. J-Y113483 is upstream of J-BY40162 on the FTDNA Haplotree. So I am trying to determine if the Big Y B result means that this person was negative for J-BY40162. I have tried to look for the actual SNP results from the Big Y tests but all I can see are the positive results, not the negative ones. Furthermore the haplotree for result B does not highlight in red the two downstream sub-clades from J-Y113483 (of which J-BY40162 is one). I need to know whether A and B are in fact fully tested to the end of the sub-branch so that I can be sure whether I am comparing their actual terminal hg.

    Likewise the same question applies to a Big Y C result ordered 22APR2016 and showing J-Y113483 as the terminal hg. Does this mean that Big Y C has been tested for the two sub-haplogroups to J-Y113183? Or do I now need to do additional SNP testing on Big Y C to verify that he is not in one of these two sub-groups?

    Please note that in the first instance, Big Y B (J-Y113483) was tested after the downstream Big Y A (J-BY40162), while in the second instance, Big Y C (J-Y113483) was tested before the downstream Big Y A.(J-YBY40162).

    This is an extremely important point for this family so I appreciate a knowledgeable answer.
    Last edited by Adam; 8th January 2019, 12:53 PM.

  • #2
    The Haplotree(under the STR testing section) won't update negative SNP results from BigY into its database. There are probably back-end reasons for that(mostly because there is no reason to import in the thousands of negative results for the other haplogroup markers when "presumed negative" would do instead), and the other factor in play is that BigY, unlike a discrete SNP test, can "No Call" on a particular SNP Marker. While a discrete SNP Test is supposed to hammer away at it until it gets a result.

    Basically you're going to need to note down every marker that "defines" a particular SNP (usually under "more" on the haplotree) and search your SNP results to see if they were Negative, or "No Call" if you are certain it wasn't a positive result.

    "No Call" results can be searched by going to your BigY Results on the dashboard, and goto the column labeled "Derived?" and Select the dropdown option for "?" and see if the relevant marker shows up in the result list. Alternatively, you can search Derived "Yes" for positive results, or Derived "No" for negative results. The Default is to search for positive results.

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    • #3
      Interesting! I was wondering whether FTDNA looks at Big Y results (BAM file?) in sufficient detail to evaluate results into positive, negative, and "no-call" categories in the same way that "experts" such as Y-Full and the Big Tree do it. Would anyone like to weigh in on this? Are FTDNA, Y-Full, and Big Tree now largely in agreement on how they evaluate BAM files and assign terminal SNP's?

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      • #4
        bartarl260 Thanks for the reply. I can see now how to look for the markers which tested negative. One last question: the marker Y113483 shows up when I select the '?' option in the derived window. The result that comes up is: Derived: ?, On Y Tree: YES, Reference: G, Genotype: ?. Is this what you are referring to as a 'No Call'? If so, then why is this 'no called' marker (the only one for this position on the tree) being used to 'call' the terminal haplogroup for this person? Wouldn't it be more accurate to 'call' the terminal hg for this person as being the parent clade of the 'no-called' hg (i.e., ZS2374: which is the last positively tested marker)? Along these same lines, I would like to test this same SNP (Y113483) to get a second opinion for the 'no call-ed' person as well as for deeper testing on others who are not able to take the Big Y test, but YSEQ is resisting my request to formulate a primer for this marker saying it is unreliable. One more fact, I have checked five other results and all of them were able to produce a 'call' at Y113483. So it seems that it is only one person who was no called here. How can I re-test him for a result here?
        Last edited by Adam; 9th January 2019, 08:32 PM. Reason: moe information

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        • #5
          There are time lags in their system as they update things. I have only had my own BigY results for not quite 2 weeks yet, and I have two different haplogroup designations depending on where I look. Only in my case I was Negative for the SNP that defines my terminal SNP and many of its other markers as well. Which meant they had to redesignate the grouping to a SNP I actually do have. My dashboard shows my (newly minted) terminal SNP for one I do match on. The BigY results still show the old designation for a SNP I don't have. From comments others have made, those updates can take up to a month to move through their system.

          Edit to add: Group projects are showing the new designation as well, and did so from the start.

          and yes those "?" Entrys are the no calls I was talking about.
          Last edited by bartarl260; 9th January 2019, 09:47 PM.

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          • #6
            Originally posted by John McCoy View Post
            Interesting! I was wondering whether FTDNA looks at Big Y results (BAM file?) in sufficient detail to evaluate results into positive, negative, and "no-call" categories in the same way that "experts" such as Y-Full and the Big Tree do it. Would anyone like to weigh in on this? Are FTDNA, Y-Full, and Big Tree now largely in agreement on how they evaluate BAM files and assign terminal SNP's?
            Mostly, but not entirely. Yfull scores the results differently from Yseq and FTDNA, and they likewise have differing databases available to them for comparison purposes and creating new branches. As there isn't a 1 to 1 ratio of DNA Profiles available to them. Not everyone on FTDNA copies results to Yfull, but Yfull also has Yseq results. So a FTDNA test can match a Yseq test and split a clade on Yfull while FTDNA and Yseq remain largely clueless.

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            • #7
              "The result that comes up is: Derived: ?" This result at FTDNA means that the number of reads is 10 or less. (The number of reads in BAM files is the amount of times the NGS tests a location on the Y-Chromosome) YFull reports all locations down to zero reads (No Call). This limit at FTDNA has caused many problems in assigning the correct sub-clade, we have 2 persons in my project with the wrong assignment. R-BY3717 always has a low number of reads. FTDNA recently ordered single SNP tests on one of the members and corrected the sub-clade assignment at no cost to the member.

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