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Thread: Non Shared Variants

  1. #1
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    Non Shared Variants

    I tested Big Y-500 and my first cousin tested Big Y-700.
    One aspect of my first cousinís results that Iím trying to still figure out is why we have more non-shared variants (10) between ourselves with a common patrilineal ancestor born in 1908 than he does with another man (7 non-shared variants) with a different surname where the estimated TMRCA is 350 ybp. This other man tested Big Y-700 as well and Iím pretty sure that the discrepancy lies with the testing coverage but Iím not sure why my first cousin has less non-shared variants with him. If someone on this forum could explain why to me Iíd appreciate it. There are several SNPs where I only have a few reads but either Iím positive or negative for them and my first cousin is the opposite.
    I1> DF29> Z58> Z59> Z2041> Z2040> Z382> S26361> S16414> FGC24354> FGC24357> FGC24356> S10350> FGC75802> Y125947> S21197> BY149414> BY188003> BY188570

    YFull id: YF15884

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     JMcB (04-09-2019)

  3. #2
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    For one of these non-shared variant SNPs I have 5 reads. 4 are for the ancestral (reference) allele and 1 is for the derived (genotyped) allele. Ftdna says Iím negative for this SNP while my first cousin is positive but shouldnít I be a ďno callĒ or ambiguous with only 5 reads that donít have the same results?
    Last edited by mwauthy; 04-09-2019 at 01:16 PM. Reason: Addition

  4. #3
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    It does sound like differences in coverage to me.

    If you can get your cousin and his other match to send you their CSV files (button to download from the Named Variants tab on the FTDNA Big Y results page) you can put your 3 CSV files through this tool: http://www.jdvtools.com/CSVAnalysis/. If you like watching videos there is a training video for the tool at https://www.youtube.com/watch?v=RlXxDxVaEDI.

    It won't show you differences in coverage regions between the tests exactly but you'll get a better comparison of which SNPs were called positive or negative or no-called in each test (you'll get no-calls if you uncheck the option to only include SNPs found in all tests). You'll also get an assessment of whether each SNP falls into 4 different definitions of "quality regions". That matters partly if you're using any specific method of TMRCA calculations - like YFull's which uses the combBed or Iain McDonald's which uses the McDonald regions, etc, but generally if a SNP isn't in ANY of those regions it may be problematic.

    But the tool will only report what's in the CSV files which should match what's reported in the FTDNA tools, and yes I've seen those be wrong also at times even against FTDNA's own criteria for calling SNPs. If you report those cases to the FTDNA support email they will generally check them out and correct them if necessary.

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     JMcB (04-09-2019)

  6. #4
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    Quote Originally Posted by Dave-V View Post
    It does sound like differences in coverage to me.

    If you can get your cousin and his other match to send you their CSV files (button to download from the Named Variants tab on the FTDNA Big Y results page) you can put your 3 CSV files through this tool: http://www.jdvtools.com/CSVAnalysis/. If you like watching videos there is a training video for the tool at https://www.youtube.com/watch?v=RlXxDxVaEDI.

    It won't show you differences in coverage regions between the tests exactly but you'll get a better comparison of which SNPs were called positive or negative or no-called in each test (you'll get no-calls if you uncheck the option to only include SNPs found in all tests). You'll also get an assessment of whether each SNP falls into 4 different definitions of "quality regions". That matters partly if you're using any specific method of TMRCA calculations - like YFull's which uses the combBed or Iain McDonald's which uses the McDonald regions, etc, but generally if a SNP isn't in ANY of those regions it may be problematic.

    But the tool will only report what's in the CSV files which should match what's reported in the FTDNA tools, and yes I've seen those be wrong also at times even against FTDNA's own criteria for calling SNPs. If you report those cases to the FTDNA support email they will generally check them out and correct them if necessary.
    I think many of these SNPs are in problematic areas based on Yfull not using them for analysis and they probably arenít going to affect the Haplotree.

    My question is why are they being reported as positive or negative SNPs by Ftdna and as non-shared Variants if there are less than 10 reads with different allele results? I thought Ftdna used a minimum of 10 reads?

  7. #5
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    Quote Originally Posted by mwauthy View Post
    My question is why are they being reported as positive or negative SNPs by Ftdna and as non-shared Variants if there are less than 10 reads with different allele results? I thought Ftdna used a minimum of 10 reads?
    Perhaps they report them as non-matching if one kit is reported as positive while the other isn't even if the SNP hasn't been read enough times? One of my dad has two non-matching variants with a match. My dad is negative for both but has only 4 reads for one and 6 reads for the other. I would accept that my dad is actually negative for these SNPs though since all reads were negative even if there are less than 10 reads.
    Ancestry: Ireland (Paper trail ≅ 81.25% Roscommon, 12.5% Galway, 6.25% Mayo)
    Paternal ancestor (Y): Kelly b. c1830 in Co. Roscommon (UŪ Maine)
    Father's mtDNA: Fleming b. c1831 in Co. Roscommon (H27e/H-c1d*)
    Maternal ancestor: McDermott b. c1814 in Co. Roscommon (H6a1b2/H6-a5a2a2)
    Paternal great grandfather (mt): Connella b. c1798 in Co. Roscommon (T2a1a8)

  8. #6
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    Quote Originally Posted by FionnSneachta View Post
    Perhaps they report them as non-matching if one kit is reported as positive while the other isn't even if the SNP hasn't been read enough times? One of my dad has two non-matching variants with a match. My dad is negative for both but has only 4 reads for one and 6 reads for the other. I would accept that my dad is actually negative for these SNPs though since all reads were negative even if there are less than 10 reads.
    I agree with you if all of the reads are showing the same results. If I have different results then there should be a minimum amount of reads and a minimum percentage of the same result. I forget the exact threshold Yfull uses but I think itís greater than 90%. For example, one of my SNPs in Yfull is 89A and 3G for a percentage of 96.6% so itís used for analysis. Why is Ftdna giving me non-shared Variants with people when the results are 1A and 3G for only 75%? Considering Ftdna is already pretty strict with their 30 non-shared Variants threshold for matching should they be including these questionable SNPs?

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