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Thread: FTDNA vs Yfull "private" SNP confusion?

  1. #1
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    Question FTDNA vs Yfull "private" SNP confusion?

    Hi Forum!

    I have a BigY kit at FTDNA with a close BigY match.
    The match and I have 26 shared novel SNPs and then I have another 4 novel "private" SNPs at FTDNA.

    FTDNA has these 4 private SNPs for me - all "high confidence" according to FTDNA :

    16604xxx
    22271xxx
    22974xxx
    7511xxx

    I have joined Yfull 6 months ago, and my match joined some weeks ago, so he is not finalized yet.
    So all the shared and novel SNPs from FTDNA are currently shown as my novel SNPs on Yfull.
    Yet, on Yfull only 3 of my 4 "private" FTDNA SNPs are shown as novel SNPs:

    16604xxx - "Best quality" (0 probality of error)
    22974xxx - "Acceptable quality" (0.072 probality of error)
    7511xxx - "Acceptable quality" (0.013 probality of error)

    22271xxx is not showing up on Yfull at all - not even as "Ambiguous quality"
    I can see that Yfull has found a total of 28 SNPs with "best" or "acceptable" quality - compared to the 30 at FTDNA (22271xxx must be one of the 2 missing SNPs).

    Now - who do I have to believe - FTDNA or Yfull - and do I have 22271xxx as a private SNP or not?

    Thanks
    Anders

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     JMcB (02-06-2017)

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    That's in the DYZ19 zone, essentially a massive STR. Calls from this area should always be treated with caution plus it's a nightmare to develop primers.

    http://ybrowse.org/gb2/gbrowse/chrY?...6800..22512940

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    Hi Jdean!

    Thanks! Can you give me a few words on what that means?
    I guess it means that FTDNA announces a private SNP in an area where SNPs can not be trusted?

    Kind regards and thanks
    Anders

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    Quote Originally Posted by A.Morup View Post
    Hi Jdean!

    Thanks! Can you give me a few words on what that means?
    I guess it means that FTDNA announces a private SNP in an area where SNPs can not be trusted?

    Kind regards and thanks
    Anders
    FTDNA's process is automated so yes they do throw out SNPs that will get rejected once they are inspected properly, that's why it's always a good idea to get somebody who knows what they are doing to check the results over.

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    Quote Originally Posted by A.Morup View Post
    I guess it means that FTDNA announces a private SNP in an area where SNPs can not be trusted?
    Trust is in the eye of the beholder. YFull prefers to apply strict academically defensible criteria, because one of their goals is to provide a complete haplotree of the human race that academia can trust.

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    Thanks to Jdean and Igmayka!

    I also prefer "strict academically defensible criteria"

    Would testing 22271xxx at Yseq.net on myself confirm this SNP - or should I just ignore it and stick to my 3 "good" private SNPs?

    I know that my close match and I have a common ancestor around the year 1600 - we have not found him yet, but we are getting closer. I have contacted decendants from other male lines in my known male line and asked them to test (at my expense) at Yseq for these 3 or 4 private SNPs, so I can find out at what generation they occured and thereby making my private SNPs really private! Any thoughts?
    I have already got the first positive answer!

    Thanks
    Anders

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    Quote Originally Posted by A.Morup View Post
    Would testing 22271xxx at Yseq.net on myself confirm this SNP - or should I just ignore it and stick to my 3 "good" private SNPs?
    In order to develop primers (the chemistry used to cut out and amplify the relevant section) Thomas would have to identify unique section of DNA upstream and downstream of the relevant position, but DYZ19 is a very large 125 base pair STR (so 125 loci repeated over and over) making the task pretty impossible.

    BTW FTDNA aren't the only people who call SNPs in this area, apparently strict academics are drawn to it too ; )

    http://ybrowse.org/gb2/gbrowse/chrY?...3870..22365869
    Last edited by jdean; 02-06-2017 at 05:55 PM.

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    Thanks Jdean!

    I will stick to my 3 Yfull private SNPs and be pleased that I did join Yfull!

    / Anders

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    Quote Originally Posted by A.Morup View Post
    Thanks Jdean!

    I will stick to my 3 Yfull private SNPs and be pleased that I did join Yfull!

    / Anders
    Did you join a group there? There's a P312 (400+ members) and U152 (150+ members) group. When you join a group all members have their info available for others to look up through a SNP and position browser. They can only view 10 positions at a time so it's really only useful for reviewing specific locations that you're after. You can't really use it to poke around trying to find mutations since there are millions of locations and you can only look at 10 at a time.

    Anyway you can go to the Y-Browser in the group and enter your 4 positions and see the values at that location for all members of the group. I did that for my FTDNA variants and saw lots of good info. Some variants were above U152, some were very unstable, others were not read in many members but still seemed stable and then you had the good ones where only your little group had the mutation and everyone else had the original value.

    So that's one of the best things about YFULL that I love is that you can check positions against large groups and see if it's stable enough on your own.

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    Hi Osiris!

    Just ran my remaining 3 private SNPs through the Yfull U152 group and I do look pretty unique on those positions :-)

    Thanks!
    Anders

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