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Thread: BAM Files is Available (A dynamic 6,000-year genetic history of Eurasia's Eastern )

  1. #81
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    Quote Originally Posted by Pribislav View Post
    UUS001; 1350-900 BC*; Uushigiin Uver, Khuvsgul Aimag; Mongolia; DSKC_MLBA; J1a2b-Z2331>Y15152


    Z2331 level: CTS463+ G>A (2A); PF4849/Z1855+ G>C (2C); PF4838+ G>A (1A); PF4857/CTS6161/Z1867+ G>A (1A); PF4863/Z1888/CTS11719+ G>A (2A)

    Y15152 level: Y15152/Z18297/FGC20898+ T>A (2A)

    Y15152>Z18293 level: *no calls*

    Y15152>Z18293>ZS2622 level: Y27285- G>A (1G); ZS2622- A>G (1A); ZS2601- G>T (1G)

    Y15152>Z18293>FGC20891 level: FGC20891/BY3836/ZS2589- G>A (2G)

    Y15152>ZS4336 level: *no calls*

    Y15152>ZS4336>Y125237 level: *no calls*

    Y15152>ZS4336>Y154827 level: FT47540- G>C (1G)

    Y15152>ZS4336>ZS4312 level: Y17403- C>T (1C)


    Someone more versed in autosomal should check where this sample plots in the PCA. He seems to cluster close to modern Kazakhs and related populations and not with the majority of DSKC samples, so he might be from the secondary burial, and incorrectly assigned to the earlier period. It should be noted that this sample wasn't RC dated. Even looking just the Y-haplogroup, it seems unlikely that this clearly NW Semitic/Amorite subclade somehow made its way to Mongolia during Bronze Age.

    Attachment 40718
    It isn't entirely impossible for Z18297 (Y15152) to be tied to East Semitic-speaking groups either, if you remember the tree I made (attempting to schematise how and where J1's phylogeny correlates with the Semitic language tree) I listed this branch as a potential correlate for the East Semitic branch:

     


    There are three reasons behind this assignment, first the TMRCA estimates of the lineages immediately downstream fit with the appearance of Old Akkadian in Mesopotamian epigraphy, second based on the overall distribution of this branch Mesopotamia is a good candidate and finally as one of the most basal branches it is likelier to be a fit for an equally "basal" branch of the Semitic language tree.

    So we could be dealing with someone of Mesopotamian descent along the paternal line. The sample in question is identified with the Deer Stone-Khirigsuur Complex (DSKC) which is conventionally dated to the Late Bronze Age, late enough for that kind of ancestry to make its way there. An Amorite origin might also fit the bill though.
    Last edited by Agamemnon; 10-28-2020 at 04:42 PM.
    מכורותיך ומולדותיך מארץ הכנעני אביך האמורי ואמך חתית
    יחזקאל פרק טז ג-


    ᾽Άλλο δέ τοι ἐρέω, σὺ δ᾽ ἐνὶ φρεσὶ βάλλεο σῇσιν:
    κρύβδην, μηδ᾽ ἀναφανδά, φίλην ἐς πατρίδα γαῖαν
    νῆα κατισχέμεναι: ἐπεὶ οὐκέτι πιστὰ γυναιξίν.


    -Αγαμέμνων; H Οδύσσεια, Ραψωδία λ

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  3. #82
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    Has J1a2b-Z2331 or closely related clades been found in any bronze age Central Asian Indo-Iranian related samples, or the preceding BMAC related samples?

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  5. #83
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    Quote Originally Posted by CopperAxe View Post
    Has J1a2b-Z2331 or closely related clades been found in any bronze age Central Asian Indo-Iranian related samples, or the preceding BMAC related samples?
    We have a P58 Scythian from Kazakhstan dated 2748-2496 calBP, unsure whether this is Z2331 however. There is a batch of J1-ZS6592 individuals from BMAC sites (Geoksiur and Gonur Tepe), but this is a non-P58 branch to begin with. See here.
    Last edited by Agamemnon; 10-28-2020 at 05:17 PM.
    מכורותיך ומולדותיך מארץ הכנעני אביך האמורי ואמך חתית
    יחזקאל פרק טז ג-


    ᾽Άλλο δέ τοι ἐρέω, σὺ δ᾽ ἐνὶ φρεσὶ βάλλεο σῇσιν:
    κρύβδην, μηδ᾽ ἀναφανδά, φίλην ἐς πατρίδα γαῖαν
    νῆα κατισχέμεναι: ἐπεὶ οὐκέτι πιστὰ γυναιξίν.


    -Αγαμέμνων; H Οδύσσεια, Ραψωδία λ

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  7. #84
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    Quote Originally Posted by Pribislav View Post
    I have those. I guess you're inspecting the VCF file directly?

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    Quote Originally Posted by Norfern-Ostrobothnian View Post
    I have those. I guess you're inspecting the VCF file directly?
    Well yes, but I prefer inspecting calls in TSV format. So BAM (mapped reads)>variant calling>VCF>TSV (tab-separated values).

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  10. #86
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    OLN010; 750-950 AD; Olon Dov, Arkhangai Aimag; Mongolia; Early Medieval Uyghur; R1b1a2a2-Z2103>Z2106>CTS8966>Y18961 (xPH4902)


    Z2103 level: Z2105+ C>A (4A); Z8130/S20902+ C>T (1T); Y4371/Z8128/M12149+ G>A (1A)

    Z2106 level: *no calls*

    CTS8966 level: *no calls*

    Y18961 level: Y18961+ T>C (1C)

    Y18961>BY3295 level: *no calls*

    Y18961>BY3295>PH4902 level: FGC48387- G>C (1G)

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  12. #87
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    Quote Originally Posted by Pribislav View Post
    Well yes, but I prefer inspecting calls in TSV format. So BAM (mapped reads)>variant calling>VCF>TSV (tab-separated values).
    What do you use to call variants?

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  14. #88
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    Quote Originally Posted by Agamemnon View Post
    We have a P58 Scythian from Kazakhstan dated 2748-2496 calBP, unsure whether this is Z2331 however.
    This is MJ-52? In the calls provided by Kolgeh, he is positive for 2 SNPs at the L620 level (Z2357 and Z2372), but negative for 1 SNP at L136 level (CTS3101) and 1 SNP at P58 level (CTS4823). The original paper says he was assigned to J1-P58 based on 3/10 positions (so pre-P58?). Has anyone had a closer look at this one?

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  16. #89
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    I would be interested to see an analysis of KHI001: unclassified LBA Khoit Tsenkher (Tarvagatain Am) Khovd 1056-905 BCE N1c2b2 (N-L665). Thank you in advance, if anybody is willing to analyse it.

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    Quote Originally Posted by teepean47 View Post
    What do you use to call variants?
    BCFtools. Extensive manual written by the authors can be found here: http://samtools.github.io/bcftools/bcftools.html

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