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Big Y SNP - "no results"

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  • Big Y SNP - "no results"

    My (brother's) Big Y (B156609) results received 10/31/17. Predicted Haplogroup R-A4658. I have several questions:

    1) I should therefore be DF27+ but DF27 shows "no results" - why? I do have + downstream Z195+, Z274+, DF17+. But I would still think Big Y would give a DF27 result.

    2) My terminal SNP A4658 is (?) - indeterminate - yet I am assigned to this Group - why? As far as I can tell all other SNP's downstream from DF17 are negative and all SNP's downstream from A4658 are negative. Is A4658 therefore "presumed positive"?

    3) Why doesn't my Haplotree show all results from my Big Y? It
    only shows "positive" SNP's, 1 "presumed positive" and no "tested negative"? It also continues to advertise that I should order the DF27 Pack even though I have done Big Y.

  • #2
    Because of the way the Big Y looks at Y-DNA there are regions that won't get a lot of coverage. The DF27 SNP is a tricky one. As long as you are positive for SNPs downstream of it it does not matter. However, you can look it up in your raw data.

    Go to your Big Y Results/Matches pages. Click on Download Raw Data. You must be logged into this kit to see it, admins won't have access to this data. At the bottom find the green Download VCF button and click it. Extract the files from the zip file. You can use a program like Notepad++ (google it) or similar work processing program to open the variants.vcf file to look inside. Now search for a position by pressing Ctrl-F.

    For DF27 you will want to look for 19218314 which is the hg38 position. When in doubt you can always check for a SNP's position over at by searching for the SNP name. Not all SNPs may be there, specially if they are recently named.

    In a kit I manage, I can see the it has the DF27 SNP as it has 19218314 G A but does not have "PASS". In this case the position did not get much coverage so it did not pass FTDNA's minimum standard to show it as positive.

    It is possible in your case it missed that region completely. That would explain the no-call. If you are unable to find that position through the search function then it does not have data for it. The Big Y does not test for the whole Y chromosome. It just looks for a chunk of it that makes up the good parts.

    The haplotree does not come with all SNPs found in the Big Y. Some of them can be recurrent which means they happen in multiple haplogroups and are not trustworthy to be on the tree. They may still be of some limited use, but it varies. Some people have chosen to take the DF27 SNP pack to better confirm their downstream SNPs that did not get enough coverage but this is not required. You can just ignore it. It is automatic and does not take Big Y into consideration when being displayed.

    As for A4658, you may wish to contact your haplogroup admin to see what they think of those results. By the sounds of it you are DF17 > A4658. The known downstream SNPs are simply not your branch. You just split at A4658 from the others. Which means you have new SNPs they don't have. Take a look at the Big Tree branch of DF17 shown here.


    • #3
      I will contact the group administrator about my "indeterminate" A4658 to confirm that they think this is correct.

      My problem with the YDNA Haplotree not showing my negative tests sounds like a technical glitch of some sort so I will contact technical support.