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Thread: Upcoming S/C Asian Calculator

  1. #1
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    Lightbulb Upcoming S/C Asian Calculator

    The analysis and quality control phase is complete for the upcoming K12/K13 calculator based on Narasimhan et al ancient Central and South Asian genomes. Quality control includes pruning based on read depth coverage and outlier status. This has been done to increase accuracy in the calculator. Ancient genomes from prior studies by Olaide and Mathieson have been incorporated to create the most robust ancient calculator to date based primarily on Chalcollithic and Bronze Age genomes.

    Sample project member results will be posted by the end of the day.

    Here are the components


    Central & South Asia
    Turan-Central
    Indus Valley Civilization
    AASI
    Eurasian Steppe
    Steppe-MLBA-W
    Steppe-MLBA-E
    Siberian-HG
    Scythian-East
    W Asia
    Kura-Araxes
    Europe
    SE European Neolithic Farmers
    Bell Beakers
    WHG
    Latvian-HG
    Sub-Saharan


    Edit: There is also an E Asian modern component based on Simmons high coverage Dai and Han, since I realize that folks E of India will also be using the calculator, and didn’t want Scythian E or some other eastern shifted comp becoming an outlet for those individuals
    Last edited by Kurd; 04-16-2018 at 12:18 AM.
    EurasianDNA.com - A study of the population history of West & South Asia.

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  3. #2
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    Looking forward to it, will this be published as a GenePlaza or ADMIXTURE calculator?

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     kingjohn (04-16-2018)

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    Sounds great! Which samples are you using for IVC and Turan?
    Paternal - Y-DNA: J2b2* (J-M241) Z2432+ Z2433+ Y978+ (J-Y978*) (YFull: YF02959) (FTDNA Kit B6225), mtDNA: M18a (FTDNA Kit 329180)
    Maternal- Y-DNA: R1a1a1b2a1a* L657+ Y7+ (R-Y16494) (FTDNA Kit 311047), mtDNA: M30b (FTDNA Kit B6225) (Mother's Mother's Father: R1a1a1b2a1a* Y7+ (FTDNA Kit 329181))

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    Quote Originally Posted by ZephyrousMandaru View Post
    Looking forward to it, will this be published as a GenePlaza or ADMIXTURE calculator?
    My algorithms are not compatible with dodecad script which is what Gedmatch needs, and thus it will only be available at GenePlaza.

    To maintain the accuracy in my calculators I can’t use DIY Dodecad. This said, I’m quite pleased with the results for individuals from Europe to Bangladesh
    EurasianDNA.com - A study of the population history of West & South Asia.

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    Quote Originally Posted by Dr_McNinja View Post
    Sounds great! Which samples are you using for IVC and Turan?
    Only samples with the highest read depth coverages in an attempt to increase accuracy a little over the results in the paper and also to increase overall genotype rate

    From IVC:

    Barikot_IA
    Katelai_IA
    Loebanr_IA
    Udegram_IA


    From Turan
    Parkhai_EBA
    Parkhai_EN
    Parkhai_LBA
    Parkhai_MBA
    Tepe_Anau_EN
    Tepe_Hissar_C

    Would you like for me to post yours with the other project members?
    EurasianDNA.com - A study of the population history of West & South Asia.

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    Although the current version does not have a BMAC component, I tested one with the BMAC component. For those anxious to know the highest scorers were Kurds-Iranians-Pashtuns with scores >20%, however, the Turan-Central allele frequencies are quite close to BMAC in the current version.

    The recently published ancients have helped clear some of the fog / ambiguity seen in prior calculators. An example is parsing between Scythian and MLBA-E. Of course there are other examples
    EurasianDNA.com - A study of the population history of West & South Asia.

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  13. #7
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    Quote Originally Posted by Kurd View Post
    My algorithms are not compatible with dodecad script which is what Gedmatch needs, and thus it will only be available at GenePlaza.

    To maintain the accuracy in my calculators I can’t use DIY Dodecad. This said, I’m quite pleased with the results for individuals from Europe to Bangladesh
    Koom che zeria rawarri taso mana programing language, C?
    Last edited by surbakhunWeesste; 04-16-2018 at 12:35 AM.

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    Quote Originally Posted by surbakhunWeesste View Post
    Koom che zeria rawarri taso mana programing language, C?
    I use Unix shell for some scripts (d C d zaamano sara zma kaar yi )
    EurasianDNA.com - A study of the population history of West & South Asia.

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  16. #9
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    Would you like for me to post yours with the other project members?
    Yes, please!
    Paternal - Y-DNA: J2b2* (J-M241) Z2432+ Z2433+ Y978+ (J-Y978*) (YFull: YF02959) (FTDNA Kit B6225), mtDNA: M18a (FTDNA Kit 329180)
    Maternal- Y-DNA: R1a1a1b2a1a* L657+ Y7+ (R-Y16494) (FTDNA Kit 311047), mtDNA: M30b (FTDNA Kit B6225) (Mother's Mother's Father: R1a1a1b2a1a* Y7+ (FTDNA Kit 329181))

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    Here they are with comments and observations to follow in about an hour. Dr McNinja just saw your reply will post yours in about an hour.

    POPULATION .Kurd-Iraq .Kurd-Iraq (Halgurd) .Kurd-Feyli .Zephyrous .Hanna Anatolian Greek
    Central & South Asia 38.71% 34.13% 43.62% 32.28% 32.14% 29.25%
    Turan-Central 21.59% 22.72% 26.25% 21.64% 16.44% 20.06%
    Indus Valley Civilization 14.83% 11.41% 14.42% 9.53% 13.58% 7.78%
    AASI 2.29% 0.00% 2.94% 1.12% 2.13% 1.42%
    Eurasian Steppe 15.99% 18.43% 13.11% 11.58% 15.99% 7.43%
    Steppe-MLBA-W 7.84% 6.89% 0.41% 10.09% 9.50% 4.71%
    Steppe-MLBA-E 0.55% 5.37% 5.38% 0.00% 2.54% 0.61%
    Siberian-HG 0.00% 0.00% 0.00% 0.00% 0.00% 1.78%
    Scythian-East 7.60% 6.17% 7.32% 1.48% 3.95% 0.33%
    W Asia 9.71% 11.30% 10.52% 9.66% 10.75% 8.22%
    Kura-Araxes 9.71% 11.30% 10.52% 9.66% 10.75% 8.22%
    Europe 33.56% 32.86% 30.90% 43.16% 38.08% 52.58%
    SE European Neolithic Farmers 24.82% 24.90% 24.17% 32.92% 30.01% 36.36%
    Bell Beakers 8.74% 7.96% 6.73% 10.24% 8.07% 16.22%
    WHG 0.00% 0.00% 0.00% 0.00% 0.00% 0.00%
    Latvian-HG 0.00% 0.00% 0.00% 0.00% 0.00% 0.00%
    E Asian 0.58% 0.46% 0.00% 0.00% 2.17% 1.42%
    Sub-Saharan 1.44% 2.83% 1.85% 3.33% 0.87% 1.09%
    EurasianDNA.com - A study of the population history of West & South Asia.

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