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Thread: 47 High Coverage Punjabi Sikh Indian Global 25 coordinates

  1. #1
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    AchaemenidEmpire1 Iran Sassanid Empire Iran Safavid Empire Iran Kurdistan Tajikistan

    47 High Coverage Punjabi Sikh Indian Global 25 coordinates

    A couple of months ago I stumbled across 47 low whole genome sequenced Punjabi Sikh samples from India. I spent 2 weeks extracting all of them yielding roughly 1.9 million high quality SNPs per sample. Davidski was kind enough to convert them into G25 coordinates and I thought I'd share them here. I've attached txt files with scaled and unscaled coords. Enjoy!

    Punjabi_Sikh_India scaled.txt

    Punjabi_Sikh_India unscaled.txt

    Unscaled:
    Punjabi_Sikh_India,0.0063915,0.0000745,-0.0275191,0.0249915,-0.0227851,0.0171064,0.0006957,0.0019064,-0.0004128,-0.0029723,-0.0035489,-0.0001149,-0.000234,-0.0051447,0.0076426,0.0064021,-0.0030255,0.0008553,0.0006149,-0.0083064,-0.0018404,-0.0044234,0.0006957,-0.0005957,0.0003574

    Scaled:
    Punjabi_Sikh_India,0.0727499,0.0007563,-0.1037804,0.0807225,-0.070121,0.0477081,0.001635,0.0043991,-0.0008443,-0.0054167,-0.005763,-0.0001722,-0.0003479,-0.0070804,0.0103725,0.0084886,-0.0039448,0.0010835,0.0007729,-0.0103881,-0.0022965,-0.0054696,0.0008575,-0.0007179,0.000428
    Last edited by Simorgh; 09-27-2020 at 08:19 PM.

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    Very nice. Looks like more than half of the samples have more than 25% AASI ancestry (25-30% range) based on my Vahaduo run.
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    Quote Originally Posted by Michalis Moriopoulos View Post
    Very nice. Looks like more than half of the samples have more than 25% AASI ancestry (25-30% range) based on my Vahaduo run.
    That's interesting I'm getting between 15-23% AASI for them. I think Matt's AASI sim and the purely South sim inflates the value a bit. Can you run them with DMXX's North West AASI sim? I believe it provides a better indication for purely NW folks.

    Code:
    AncestralIndianNorthWest_scaled,0.058062278,-0.24745847,-0.325699695,0.273535685,-0.119223593,0.177284363,0.005596483,0.058361388,0. 170617118,0.13535108,-0.00361402,0.035724435,-0.030872625,0.03748403,-0.013375715,-0.129868563,0.005831905,-0.02091509,-0.021039598,0.054171475,0.001207383,0.0099081,0.01 941486,0.05655002,-0.064804895
    AncestralIndianSouth_scaled,-0.007017607,-0.247268894,-0.229976338,0.16563825,-0.035368871,0.064331863,-0.015188881,0.027727614,0.147380455,0.101064071,-0.004664075,-0.004333522,0.003228897,0.026031903,-0.047720864,-0.045200255,0.010093749,0.000906224,0.000245098,0. 039040136,0.009429353,0.024010206,-0.003068505,0.015983546,-0.010868946
    edit: although adding his SouthSouth Sim does bump it up abit, combined of 20-25% but I'm not sure what the validity of these type of results truly is.
    Last edited by ThaYamamoto; 09-27-2020 at 11:47 PM.

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    I actually was using DMXX's simulations, but maybe the AASI NW sims I'm using are out of date because neither matches the coords you provided there. These are the sims I ran below. I aggregated them together for a total AASI score:

    Code:
    AASI_NW_Simulation_DMXX's:NW_SiSBA3,0.00626452,-0.26734243,-0.2643032,0.24953728,-0.07059554,0.1259178,-0.00227516,0.03540285,0.19403857,0.14887817,-0.0086271,0.01680744,-0.02608023,0.04392062,-0.03238295,-0.06722619,0.03334912,-0.00690446,-0.01318708,0.0388334,-0.00267339,0.01145176,0.01038688,0.04030307,-0.04887722
    AASI_NW_Simulation_DMXX's:NW_SGPT,0.01615338,-0.22505484,-0.37905649,0.18477363,-0.16668914,0.16382842,0.02481901,0.06452209,0.05034096,0.03784746,-0.05375015,0.01405764,-0.00918092,0.05309405,0.01625326,-0.04481805,0.00194808,-0.01253792,-0.0288336,0.0286508,0.03216633,-0.00013407,0.01228559,0.04037898,-0.00001027
    AASI_S_Simulation_DMXX's_Average,-0.007017607,-0.247268894,-0.229976338,0.16563825,-0.035368871,0.064331863,-0.015188881,0.027727614,0.147380455,0.101064071,-0.004664075,-0.004333522,0.003228897,0.026031903,-0.047720864,-0.045200255,0.010093749,0.000906224,0.000245098,0.039040136,0.009429353,0.024010206,-0.003068505,0.015983546,-0.010868946
    But I just ran the new samples using only the NW AASI sim coords you provided, and yeah, you get under 25% AASI for all of them using that. Not sure what to make of it. Do you have updated coords for all these sims that maybe I don't have?
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  9. #5
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    Quote Originally Posted by Michalis Moriopoulos View Post
    I actually was using DMXX's simulations, but maybe the AASI NW sims I'm using are out of date because neither matches the coords you provided there. These are the sims I ran below. I aggregated them together for a total AASI score:

    Code:
    AASI_NW_Simulation_DMXX's:NW_SiSBA3,0.00626452,-0.26734243,-0.2643032,0.24953728,-0.07059554,0.1259178,-0.00227516,0.03540285,0.19403857,0.14887817,-0.0086271,0.01680744,-0.02608023,0.04392062,-0.03238295,-0.06722619,0.03334912,-0.00690446,-0.01318708,0.0388334,-0.00267339,0.01145176,0.01038688,0.04030307,-0.04887722
    AASI_NW_Simulation_DMXX's:NW_SGPT,0.01615338,-0.22505484,-0.37905649,0.18477363,-0.16668914,0.16382842,0.02481901,0.06452209,0.05034096,0.03784746,-0.05375015,0.01405764,-0.00918092,0.05309405,0.01625326,-0.04481805,0.00194808,-0.01253792,-0.0288336,0.0286508,0.03216633,-0.00013407,0.01228559,0.04037898,-0.00001027
    AASI_S_Simulation_DMXX's_Average,-0.007017607,-0.247268894,-0.229976338,0.16563825,-0.035368871,0.064331863,-0.015188881,0.027727614,0.147380455,0.101064071,-0.004664075,-0.004333522,0.003228897,0.026031903,-0.047720864,-0.045200255,0.010093749,0.000906224,0.000245098,0.039040136,0.009429353,0.024010206,-0.003068505,0.015983546,-0.010868946
    But I just ran the new samples using only the NW AASI sim coords you provided, and yeah, you get under 25% AASI for all of them using that. Not sure what to make of it. Do you have updated coords for all these sims that maybe I don't have?
    Man you know what...I'm not sure where I got these from. I was sure they are DMXX's but if they not my bad...they are either from around here or the Eurogenes comments. I'll take a look around see if I can find where I sourced em from, I just remember that they were the newest sims I'd come across.

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    Ah okay found em, they are actually user agentlime's simulations. They seem to work quite well for me when I've been checking out Balochis/Brahuis/Makranis. Maybe he can provide more insight into them but I think their p good.

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    Quote Originally Posted by ThaYamamoto View Post
    That's interesting I'm getting between 15-23% AASI for them. I think Matt's AASI sim and the purely South sim inflates the value a bit. Can you run them with DMXX's North West AASI sim? I believe it provides a better indication for purely NW folks.

    Code:
    AncestralIndianNorthWest_scaled,0.058062278,-0.24745847,-0.325699695,0.273535685,-0.119223593,0.177284363,0.005596483,0.058361388,0. 170617118,0.13535108,-0.00361402,0.035724435,-0.030872625,0.03748403,-0.013375715,-0.129868563,0.005831905,-0.02091509,-0.021039598,0.054171475,0.001207383,0.0099081,0.01 941486,0.05655002,-0.064804895
    AncestralIndianSouth_scaled,-0.007017607,-0.247268894,-0.229976338,0.16563825,-0.035368871,0.064331863,-0.015188881,0.027727614,0.147380455,0.101064071,-0.004664075,-0.004333522,0.003228897,0.026031903,-0.047720864,-0.045200255,0.010093749,0.000906224,0.000245098,0. 039040136,0.009429353,0.024010206,-0.003068505,0.015983546,-0.010868946
    edit: although adding his SouthSouth Sim does bump it up abit, combined of 20-25% but I'm not sure what the validity of these type of results truly is.
    Thats what I get as well. With a huge sample size you get a better picture of things


    "sample": "Punjabi Sikh",
    "distance": 1.2031,
    "Shahr_I_Sokhta_BA2": 54.5,
    "TKM_IA": 44.5,
    "Chokhopani_2700BP": 1



    "sample": "Punjabi Sikh",
    "distance": 1.0465,
    "Shahr_I_Sokhta_BA2": 56,
    "KAZ_Kangju": 22.5,
    "TKM_IA": 21.5

    SIS2 = 8728/1459

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    Quote Originally Posted by pegasus View Post
    Thats what I get as well. With a huge sample size you get a better picture of things


    "sample": "Punjabi Sikh",
    "distance": 1.2031,
    "Shahr_I_Sokhta_BA2": 54.5,
    "TKM_IA": 44.5,
    "Chokhopani_2700BP": 1



    "sample": "Punjabi Sikh",
    "distance": 1.0465,
    "Shahr_I_Sokhta_BA2": 56,
    "KAZ_Kangju": 22.5,
    "TKM_IA": 21.5

    SIS2 = 8728/1459
    Right! I wish we had the relevant NW and South-South Aboriginals but for now I think these particular sims work fine when cross-compared with SiS like you've kindly done.

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    Quote Originally Posted by pegasus View Post
    Thats what I get as well. With a huge sample size you get a better picture of things


    "sample": "Punjabi Sikh",
    "distance": 1.2031,
    "Shahr_I_Sokhta_BA2": 54.5,
    "TKM_IA": 44.5,
    "Chokhopani_2700BP": 1



    "sample": "Punjabi Sikh",
    "distance": 1.0465,
    "Shahr_I_Sokhta_BA2": 56,
    "KAZ_Kangju": 22.5,
    "TKM_IA": 21.5

    SIS2 = 8728/1459
    How much AASI does SIS 2 (8728/1459) have?


    Quote Originally Posted by Michalis Moriopoulos View Post
    Very nice. Looks like more than half of the samples have more than 25% AASI ancestry (25-30% range) based on my Vahaduo run.
    Can you post your models with each simulated AASI variation you used?

    @Simorgh

    Thanks for the individual coordinates! The UK Sikh Diaspora is mostly Jatt + Ramgarhia/Tarkhan followed by Ravidassia (Chamar) AFAIK. There could be a few other groups represented though.
    Last edited by Sapporo; 09-29-2020 at 02:39 AM.
    pegasus modeling:
    sample": "Punjabi_Jat:Sapporo_AGUser",
    "fit": 1.1506,
    "IRN_Shahr_I_Sokhta_BA3": 43.33,
    "TKM_Gonur1_BA": 31.67,
    "RUS_Sintashta_MLBA": 25,
    "closestDistances": [

    avatar credit goes out to aaronbee2010

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    Is it possible to get the individual coordinates? Because Punjabi Sikh samples might contain like 10+ different kind of tribes. Else we end up PJL situation again.

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