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Thread: Y Chromosome Haplogroup assignments for ~2500 ancient samples

  1. #31
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    Quote Originally Posted by kolgeh View Post
    Check the reports. I've used automated pipeline for these assignments.
    Where is the Terminal SNP for each assignment, without it the longhand haplogroup is meaningless?

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  3. #32
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    Quote Originally Posted by Jatt1 View Post
    Where is the Terminal SNP for each assignment, without it the longhand haplogroup is meaningless?
    Terminal snp and all other called snps for each sample are in this zip file.

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  5. #33
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    Quote Originally Posted by Coldmountains View Post
    I am not really an expert about this but i found him to be psoitive for Y26+ and M780+ what would mean he is Y3+ but on the otherside he is is negative for Z2479,M746,S4582 so he is Z93-. But someone else who understand more of it should check it. Would be quite a big finding.
    AM00483/M780/Y26 i.e. 21610995 is a C to T snp. So most probably this positive call is due to dna damage.

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  7. #34
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    @Kolgeh

    Is the list that you have presented from this link ?

    https://umap.openstreetmap.fr/en/map...6/51.000/2.000


    My Path = ( K-M9+, TL-P326+, T-M184+, L490+, M70+, PF5664+, L131+, L446+, CTS933+, CTS3767+, CTS8862+, Z19945+ )


    Grandfather via paternal grandmother = I1-L22 ydna
    Great grandmother paternal side = T1a1e mtdna

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  9. #35
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    Thanks. At least it confirms I haven't missed an errant DF19 somewhere, recently -- the only one in the list is RMPR31 (R31).
    R1b>M269>L23>L51>L11>P312>DF19>DF88>FGC11833 >S4281>S4268>Z17112>BY44243

    Ancestors: Francis Cooke (M223/I2a2a) b1583; Hester Mahieu (Cooke) (J1c2 mtDNA) b.1584; Richard Warren (E-M35) b1578; Elizabeth Walker (Warren) (H1j mtDNA) b1583;
    John Mead (I2a1/P37.2) b1634; Rev. Joseph Hull (I1, L1301+ L1302-) b1595; Benjamin Harrington (M223/I2a2a-Y5729) b1618; Joshua Griffith (L21>DF13) b1593;
    John Wing (U106) b1584; Thomas Gunn (DF19) b1605; Hermann Wilhelm (DF19) b1635

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  11. #36
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    Quote Originally Posted by vettor View Post
    @Kolgeh

    Is the list that you have presented from this link ?

    https://umap.openstreetmap.fr/en/map...6/51.000/2.000
    No, I've used latest version of Reich-lab curated dataset of published ancient DNA and recently published datasets from Max Planck Jena-lab and Reich-lab.

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  13. #37
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    So the Yumin sample is N-TAT? Rad. Since 2014 they've found a few of their sites. Apparently the original (Yumin) they later determined to be the spare winter residence vs Simagou. The Baikal region is just so blah compared to the contemporary warmer weather neolithic proper, TAT needed its own more relatable culture and the LN Xueshan around Beijing has been cast as derivative. Inner Mongolia works and for a para-Chinese context also.

    I've read about three sites so far, Yumin, Wulanchabu and Simagou, all in central Inner Mongolia not too distant from Beijing but spanning the 7th millennium BC. The Baikal EN group, or at least Shamanka and Lokomotiv feature no TAT yet but abundant L666, later more prevalent in China of course. DA345 Ust Ida LN is TAT.

    Just discovered that German Bell Beaker sample I6481 you claim to be L392/L1026? Seriously doubt it unless there's a relation to Bolshoy. No offense. Anybody know the autosomal profile?
    Last edited by Nibelung; 06-02-2020 at 08:16 PM.
    Scandinavian-love structure

    recent and recently discovered Swedish, Danish and Norwegian (many 4th/5th cousins)
    recent East/North German
    Anglo-Saxon from recent rural English (Derbyshire/Staffordshire) with possible trace Danish
    1/16 Bronze Age Swedish from Finland/Karelia
    medieval Norwegian and Danish via Ireland (possibly surviving structure)
    other English and German (regions unknown)
    other NW to NE European

    closest modern Sweden2
    closest ancient Sigtuna vik84001

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  15. #38
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    Thank you.
    But this is still difficult to deal with this is sort of haplogroups.
    1. Because there is a problem to understand the long a1b1a2b1a1b2b1b haplogroup names, that change with each new ISOGG version.
    2. It takes time to go, unzip, search for a description and understand where does the sample come from.

    Quote Originally Posted by kolgeh View Post
    AM00483/M780/Y26 i.e. 21610995 is a C to T snp. So most probably this positive call is due to dna damage.
    WHat was your algorythm of automatica haplogroup assignment? I'd say in about 90% of cases we can trust the C->T calls.
    It is important to see other positive SNPs how "far" are they from a final haplogroup, and of course to check negative SNP calls.
    I guess in is very important to distinguish pre-haplogroup calss, haplogroup* calls, cases with low coverage, e.t.c.
    BT for a low-coverage sample is one story, an actual new unknown BT haplogroup - quite a different one.

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  17. #39
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    Quote Originally Posted by artemv View Post
    Thank you.
    But this is still difficult to deal with this is sort of haplogroups.
    1. Because there is a problem to understand the long a1b1a2b1a1b2b1b haplogroup names, that change with each new ISOGG version.
    2. It takes time to go, unzip, search for a description and understand where does the sample come from.


    WHat was your algorythm of automatica haplogroup assignment? I'd say in about 90% of cases we can trust the C->T calls.
    It is important to see other positive SNPs how "far" are they from a final haplogroup, and of course to check negative SNP calls.
    I guess in is very important to distinguish pre-haplogroup calss, haplogroup* calls, cases with low coverage, e.t.c.
    BT for a low-coverage sample is one story, an actual new unknown BT haplogroup - quite a different one.
    I've used a stochastic search algorithm (something like penalized optimization) to reduce probability of error and of course some of these assignments are erroneous but haplogroup assignment for ancient samples is prone to error because of nature of data.
    Distinguishing different samples based on coverage, * calls and ... is a great idea but it needs a devoted person who doesn't have any job and other works to do.

    And about C->T calls you're right, but in this case we have upstream ancestral calls and a strange location (Czech_EBA), so it's probably due to dna damage.
    Last edited by kolgeh; 06-02-2020 at 08:50 PM.

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  19. #40
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    Are you sure about SZ20 Hungary_Langobard_lc I1 (post #8)? I haven't checked the BAM file myself but SZ20 is R1a1a1b2a2a in the Supplementary Data of the Amorim et al paper and I believe it's been checked by other folks on this forum to verify SNPs downstream of R-U106 (U106/S21>Z2265>Z381/S263).

    For I1282 Iberia_C I or I1a1a4a1a1b2 (post #9) this is unlikely to be I1. I'd previously been through the BAM file manually and there are 9 SNPs with ancestral alleles on the I1 level and no derived SNPs. Probably a false positive for the downstream SNP that defines I1a1a4a1a1b2.

    For OBKR_117_d Germany_EBA_Lech I or I2a1a1a1a1a1a2a or I1a1b1a4a1a1, we're fairly sure that this is not I1 due to negative for five I1 level SNPs and no positive SNPs on the I1 level - the L258 result likely a false positive (one read).

    Some of these samples (I10899/Car1, SF11, BAL051) have a have a mixture of positive and negative calls for SNPs on the I1 level, so I've been calling these ones as pre-I1 (after the split from I2, before the TMRCA of modern I1 individuals) rather than I1.
    Haplogroup I1 Ancient DNA Samples Map: Hidden Content

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