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Thread: Big Y results for N-L1025

  1. #1
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    Big Y results for N-L1025

    I did my best to compare the Novel Variants of the 8 N-L1025 Big Y results in my project: kits 174607, B2967, N11423, N58382, 175141, N101084, 133144, and 119958. I have the devastating disadvantage of no access to a YFull interpretation for any of these.

    Nevertheless, one pattern was obvious: shared SNPs among N11423, N58382, and N101084--the kits that have 24 (instead of 22) at DYS413b.

    14920763
    16861269
    22977344
    23830333
    25047772 (noisy, according to my own I2a YFull)
    25999090
    26237856

    A second, somewhat less reliable pattern is that of shared SNPs between 174607 and B2967. Note that Thomas Krahn considers any SNP in the 222-226 range to be "problematic."

    8514346 (M2014)
    16692095 (noisy, but can use primers for V45)
    22477884 (noisy)
    22477925

    I simply cannot go further without at least indirect access to the YFull interpretation of an N-L1025. YFull can verify that an individual is truly ancestral at a given location--indicating that those who are derived have a genuinely useful SNP. So for example, to verify that M2014 is genuinely useful, I would need an N-L1025 (other than 174607 or B2967) to check that he is truly ancestral (i.e., very low probability of derived) at 8514346.
    Last edited by lgmayka; 04-25-2014 at 11:59 PM.

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  3. #2
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    Update on my Big Y investigation

    A kind soul gave me access to a YFull analysis of one of these N-L1025 BAM files. I now see only two reliable relationships, as shown below. Reqd indicates that I have requested an individual SNP test from FTDNA.

    Kits N11423, N58382, and N101084 (the kits with DYS413b=24) tested positive for these 6 SNPs. Others tested negative.
    14920763 C > T Z16974
    16861269 T > G Z16975 Reqd
    22977344 G > A Z16976
    23830333 C > G Z16977
    25999090 G > A Z16978
    26237856 G > T Z16979

    Kits B2967 and 175141 tested positive for these two SNPs. Others tested negative.
    23386291 T > C Z16980
    23815649 C > G Z16981 Reqd

    It would be useful to have one more YFull analysis of an L1025 kit.

  4. #3
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    Quote Originally Posted by lgmayka View Post
    Kits N11423, N58382, and N101084 (the kits with DYS413b=24) tested positive for these 6 SNPs. Others tested negative.
    14920763 C > T Z16974
    16861269 T > G Z16975 Reqd
    22977344 G > A Z16976
    23830333 C > G Z16977
    25999090 G > A Z16978
    26237856 G > T Z16979
    16861269 (T>G) is now available as an individual SNP test from FTDNA. Due to my mistake, though, the Advanced menu calls it LGM2.
    Quote Originally Posted by lgmayka View Post
    Kits B2967 and 175141 tested positive for these two SNPs. Others tested negative.
    23386291 T > C Z16980
    23815649 C > G Z16981 Reqd
    Kit N6569 also has these two SNPs.

    Moreover, N6569 and B2967 share these novel variants. Others do not list them.

    7411987 - Z17078
    17299529 - Z17079, requested from FTDNA, should be able to use primers for L1189
    17882269- Z17080
    21312826 - Z17081
    22459893 - Z17082 (region is allegedly noisy)

    According to a post in another forum, kit 149750 (to which I do not have access) also has these five.

  5. #4
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    YFull's new haplotree for N-L1025 shows some new structure.

    - CTS8173 is shared by entries YF01792 and YF01751. We need to know the STR haplotypes (e.g., kit numbers) of these two.

    - Z4869 is shared by N-L551 and YF01488. We need to know the STR haplotype of YF01488.

    I have asked FTDNA to provide individual SNP tests for CTS8173 and Z4869.
    Last edited by lgmayka; 06-29-2014 at 03:05 PM.

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    Quote Originally Posted by lgmayka View Post
    YFull's new haplotree for N-L1025 shows some new structure.

    - CTS8173 is shared by entries YF01792 and YF01751. We need to know the STR haplotypes (e.g., kit numbers) of these two.

    - Z4869 is shared by N-L551 and YF01488. We need to know the STR haplotype of YF01488.
    The pair of CTS8173+ entries are kits 175141 and N6569. These two were already known to share Z16981.

    The Z4869+ L551- entry is kit N58382.

  7. #6
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    Quote Originally Posted by lgmayka View Post
    The pair of CTS8173+ entries are kits 175141 and N6569. These two were already known to share Z16981.
    Z16981 is now available for order from FTDNA.

  8. #7
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    I should have posted my YF01738, f174607 as an update to your Big Y N-L1025 thread.

  9. #8
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    YFull's latest haplotree for N-L1025 exhibits some interesting new structure.

    Y4755 = Z16980 (23386291 T > C)
    Y4756 = Z16981 (23815649 C > G)
    Y4706 = (15610361 T > C)
    Y4702 = (9460967 G > something)
    Y4704 = (17598779 C > something)
    Y4707 = (16175412 C > something)
    Y4708 = (19494388 C > something)
    Y4711 = (14828233 C > something)
    Y4712 = (15055448 G > something)
    Y4713 = (17757862 C > something)
    Y4703 = (14247678 T > something)
    Y4705 = (18386356 C > something)
    Y4709 = (14407264 C > something)
    Y4710 = (21649141 C > something)

    Z16981 is already individually testable at FTDNA. I have requested FTDNA to offer a test for Y4706.

  10. #9
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    Quote Originally Posted by lgmayka View Post
    The pair of CTS8173+ entries are kits 175141 and N6569. These two were already known to share Z16981.
    CTS8173 is now available for individual SNP test order from FTDNA. YFull's haplotree, based on a very small number of samples, shows CTS8173 to be at the same level as Z16981 (Y4756).

  11. #10
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    Quote Originally Posted by lgmayka View Post
    - Z4869 is shared by N-L551 and YF01488.
    YFull has now decided that Z4869 is too unstable for practical use:
    ---
    SNP Z4869 I removed from the tree, as unstable.
    Z4869 is contrary to the existing structure and positive in several other haplogroups.

    ---

    Similarly, Yseq declined to offer a test for Z4869:
    ---
    Z4869: 100.0% identical to ChrY:6264802..6265802
    ---

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