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Thread: Northern Eurasia K19 Calculator

  1. #1
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    Northern Eurasia K19 Calculator

    l was exploring the genetic structure of North-Eurasian (Northern Europe + Russia + Central Asia + East Asia) populations with ADMIXTURE.

    The following calculator was created:

    https://www.dropbox.com/s/wg5xtfap3l...19.tar.gz?dl=0

    It has the following components (some components peaked in more than one population for instance Karel and Komi so the component is named: Karel-Komi):

    Buryat
    Karel-Komi
    Udmurt
    Tajik-Bashkir
    Chuvash
    Ket-Selkup
    Ulchi
    Chukchi
    Balto-Slavic (peaks in Lithuanians and Belarusians)
    Eskimo
    Chechen2
    Megrel-Abkhaz
    Itelmen-Koryak
    Northwest-European (peaks in Orcadians, English and French)
    Khanty-Mansi
    Yakut
    Nganasan
    Japanese-Chinese
    Chechen-Kumyk

    Inevitably, some components will be acting as proxies for the components that are simply not there.

    My results:

    0.70% Buryat
    9.11% Karel-Komi
    2.45% Udmurt
    4.69% Tajik-Bashkir
    4.73% Chuvash
    0.03% Ket-Selkup
    0.00% Ulchi
    0.00% Chukchi
    34.72% Balto-Slavic
    0.70% Eskimo
    1.09% Chechen2
    7.82% Megrel-Abkhaz
    0.07% Itelmen-Koryak
    23.36% Northwest-European
    1.83% Khanty-Mansi
    0.00% Yakut
    0.00% Nganasan
    0.00% Japanese-Chinese
    8.71% Chechen-Kumyk

    firemonkey:

    0.28% Buryat
    12.03% Karel-Komi
    1.27% Udmurt
    5.88% Tajik-Bashkir
    3.30% Chuvash
    0.27% Ket-Selkup
    0.00% Ulchi
    0.00% Chukchi
    15.09% Balto-Slavic
    1.28% Eskimo
    1.62% Chechen2
    7.39% Megrel-Abkhaz
    0.00% Itelmen-Koryak
    43.89% Northwest-European
    1.15% Khanty-Mansi
    0.00% Yakut
    0.00% Nganasan
    0.02% Japanese-Chinese
    6.54% Chechen-Kumyk

    I think this is a pretty nice calc for some populations that may have some Siberian ancestry e.g. Russians, Finns etc.
    Of course this calc is also pretty exotic and not all people will benefit from it. I am especially thinking about the people from Southern Europe, Middle East, India, Africa.
    For K25 and other calculators by me you can send me you raw data to my email: Hidden Content

  2. The Following 23 Users Say Thank You to michal3141 For This Useful Post:

     Просигој (03-06-2018),  Alain (01-11-2019),  Askye (03-05-2018),  Calamus (03-06-2018),  Exosuits (03-06-2018),  firemonkey (03-06-2018),  Huck Finn (03-06-2018),  Jessie (03-05-2018),  JMcB (12-30-2018),  jortita (03-06-2018),  khanabadoshi (03-06-2018),  kush (03-07-2018),  Kylo_Ren (03-05-2018),  Mike_G (03-13-2018),  Modernancientdna (03-05-2018),  NiloSaharan (05-06-2018),  Radboud (03-09-2018),  Sea Warrior (03-06-2018),  SSlava (05-18-2018),  StarDS9 (03-06-2018),  Tomenable (03-10-2018),  Username (05-18-2018),  Volat (12-17-2018)

  3. #2
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    Thanks @michal3141 looks very interesting, if you have time run my data please

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     michal3141 (03-05-2018)

  5. #3
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    Modernancientdna:

    0.70% Buryat
    11.18% Karel-Komi
    2.08% Udmurt
    5.03% Tajik-Bashkir
    2.99% Chuvash
    0.18% Ket-Selkup
    0.40% Ulchi
    0.00% Chukchi
    35.70% Balto-Slavic
    0.08% Eskimo
    1.15% Chechen2
    8.02% Megrel-Abkhaz
    0.15% Itelmen-Koryak
    23.96% Northwest-European
    1.28% Khanty-Mansi
    0.04% Yakut
    0.00% Nganasan
    0.00% Japanese-Chinese
    7.07% Chechen-Kumyk

    Who can beat my Chuvash score? (4.73%)
    For K25 and other calculators by me you can send me you raw data to my email: Hidden Content

  6. The Following 4 Users Say Thank You to michal3141 For This Useful Post:

     Exosuits (03-06-2018),  JMcB (12-30-2018),  jortita (03-06-2018),  Modernancientdna (03-05-2018)

  7. #4
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    What/how many samples were used in the Chinese-Japanese component?

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     michal3141 (03-06-2018)

  9. #5
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    Quote Originally Posted by michal3141 View Post
    Who can beat my Chuvash score? (4.73%)
    We are very similar on this calc, highest Balto-Slavic for now

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  11. #6
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    FINAL ADMIXTURE PROPORTIONS:
    ----------------------------

    0.00% Buryat
    10.05% Karel-Komi
    0.07% Udmurt
    4.14% Tajik-Bashkir
    4.00% Chuvash
    1.59% Ket-Selkup
    0.00% Ulchi
    0.67% Chukchi
    16.60% Balto-Slavic
    0.00% Eskimo
    1.68% Chechen2
    5.87% Megrel-Abkhaz
    0.00% Itelmen-Koryak
    45.44% Northwest-European
    1.48% Khanty-Mansi
    0.02% Yakut
    0.00% Nganasan
    0.00% Japanese-Chinese
    8.39% Chechen-Kumyk

  12. The Following 5 Users Say Thank You to Askye For This Useful Post:

     JMcB (12-30-2018),  jortita (03-06-2018),  michal3141 (03-05-2018),  Modernancientdna (03-05-2018),  NiloSaharan (05-06-2018)

  13. #7
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    Does it give meaningful results for West Asians/Near Easterners?
    Turks/Kurds/Iranians/Caucasus have ANE admixture.

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  15. #8
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    I have given it a try.


    19 ancestral populations
    76261 total SNPs
    0 flipped SNPs
    22450 heterozygous SNPs
    0 no-calls
    9046 absent SNPs
    0.881381 genotype rate
    mode genomewide

    9046 SNPs missing (no-call or absent)


    3.85% Buryat
    3.31% Karel-Komi

    0.89% Udmurt
    10.68% Tajik-Bashkir
    0.83% Chuvash
    0.00% Ket-Selkup
    0.00% Ulchi
    0.00% Chukchi
    6.95% Balto-Slavic
    0.00% Eskimo
    1.34% Chechen2
    33.87% Megrel-Abkhaz
    1.29% Itelmen-Koryak
    19.35% Northwest-European

    0.00% Khanty-Mansi
    0.01% Yakut
    0.00% Nganasan
    1.19% Japanese-Chinese
    16.45% Chechen-Kumyk

  16. The Following 4 Users Say Thank You to Lupus82 For This Useful Post:

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  17. #9
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    Kurdistan Adygea
    19 ancestral populations
    76261 total SNPs
    5 flipped SNPs
    24572 heterozygous SNPs
    41 no-calls
    3468 absent SNPs
    0.953987 genotype rate
    mode genomewide

    3509 SNPs missing (no-call or absent)


    5312 total iterations
    9.999E-08 final dQ

    ----------------------------
    FINAL ADMIXTURE PROPORTIONS:
    ----------------------------

    3.52% Buryat
    2.44% Karel-Komi
    1.51% Udmurt
    11.95% Tajik-Bashkir
    2.39% Chuvash
    0.01% Ket-Selkup
    0.00% Ulchi
    0.01% Chukchi
    3.51% Balto-Slavic
    1.33% Eskimo
    0.94% Chechen2
    32.06% Megrel-Abkhaz
    0.00% Itelmen-Koryak
    18.70% Northwest-European
    0.00% Khanty-Mansi
    0.01% Yakut
    0.02% Nganasan
    2.21% Japanese-Chinese
    19.39% Chechen-Kumyk

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  19. #10
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    Quote Originally Posted by michal3141 View Post
    l was exploring the genetic structure of North-Eurasian (Northern Europe + Russia + Central Asia + East Asia) populations with ADMIXTURE.

    The following calculator was created:

    https://www.dropbox.com/s/wg5xtfap3l...19.tar.gz?dl=0

    It has the following components (some components peaked in more than one population for instance Karel and Komi so the component is named: Karel-Komi):

    Buryat
    Karel-Komi
    Udmurt
    Tajik-Bashkir
    Chuvash
    Ket-Selkup
    Ulchi
    Chukchi
    Balto-Slavic (peaks in Lithuanians and Belarusians)
    Eskimo
    Chechen2
    Megrel-Abkhaz
    Itelmen-Koryak
    Northwest-European (peaks in Orcadians, English and French)
    Khanty-Mansi
    Yakut
    Nganasan
    Japanese-Chinese
    Chechen-Kumyk

    Inevitably, some components will be acting as proxies for the components that are simply not there.

    My results:

    0.70% Buryat
    9.11% Karel-Komi
    2.45% Udmurt
    4.69% Tajik-Bashkir
    4.73% Chuvash
    0.03% Ket-Selkup
    0.00% Ulchi
    0.00% Chukchi
    34.72% Balto-Slavic
    0.70% Eskimo
    1.09% Chechen2
    7.82% Megrel-Abkhaz
    0.07% Itelmen-Koryak
    23.36% Northwest-European
    1.83% Khanty-Mansi
    0.00% Yakut
    0.00% Nganasan
    0.00% Japanese-Chinese
    8.71% Chechen-Kumyk

    firemonkey:

    0.28% Buryat
    12.03% Karel-Komi
    1.27% Udmurt
    5.88% Tajik-Bashkir
    3.30% Chuvash
    0.27% Ket-Selkup
    0.00% Ulchi
    0.00% Chukchi
    15.09% Balto-Slavic
    1.28% Eskimo
    1.62% Chechen2
    7.39% Megrel-Abkhaz
    0.00% Itelmen-Koryak
    43.89% Northwest-European
    1.15% Khanty-Mansi
    0.00% Yakut
    0.00% Nganasan
    0.02% Japanese-Chinese
    6.54% Chechen-Kumyk

    I think this is a pretty nice calc for some populations that may have some Siberian ancestry e.g. Russians, Finns etc.
    Of course this calc is also pretty exotic and not all people will benefit from it. I am especially thinking about the people from Southern Europe, Middle East, India, Africa.
    Hi Michal - Could you run my data for me? Thanks.

  20. The Following 2 Users Say Thank You to Jessie For This Useful Post:

     JMcB (12-30-2018),  michal3141 (03-06-2018)

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