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Thread: Harappa Ancestry Project

  1. #1
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    Default Harappa Ancestry Project

    Not sure if anyone follows the project. It is very well run. And there are a few European individuals participating.

    The site: Harappa Ancestry Project -Genetics and South Asia

    I am HRP0010 (Assyrian Iranian_Nestorian A005), by the way.

    I calculated the average values for groups with more than one participant, through HRP0150. Below, are the group average values, and all single participants not otherwise included among one of the listed groups:

    Code:
    AXXX	C1	C2	C3	C4	C5	C6	C7	C8	C9	C10	C11
    A001	0.77%	0.02%	0.41%	0.65%	11.79%	0.00%	70.98%	0.00%	8.62%	5.93%	0.82%
    A002	61.41%	31.62%	1.09%	4.04%	0.40%	0.97%	0.00%	0.14%	0.31%	0.02%	0.00%
    A003	55.80%	24.54%	0.72%	7.60%	7.22%	1.39%	0.00%	1.47%	1.26%	0.00%	0.00%
    A004	61.96%	29.84%	0.71%	5.96%	0.70%	0.45%	0.00%	0.29%	0.09%	0.00%	0.00%
    A005	24.94%	0.00%	0.00%	59.20%	15.26%	0.00%	0.00%	0.00%	0.18%	0.42%	0.00%
    A006	25.00%	0.00%	0.00%	58.12%	15.95%	0.34%	0.00%	0.00%	0.34%	0.24%	0.00%
    A007	26.73%	0.00%	0.00%	57.48%	15.61%	0.00%	0.00%	0.18%	0.00%	0.00%	0.00%
    A008	24.39%	0.69%	2.38%	44.17%	22.86%	4.00%	0.00%	0.00%	1.22%	0.30%	0.00%
    A009	50.93%	28.34%	10.42%	3.08%	5.34%	0.84%	0.00%	0.67%	0.39%	0.00%	0.00%
    A010	53.14%	23.14%	2.56%	4.46%	14.73%	1.13%	0.00%	0.30%	0.55%	0.00%	0.00%
    A011	54.62%	26.71%	4.43%	1.35%	10.82%	0.00%	0.00%	1.51%	0.54%	0.00%	0.00%
    A012	53.13%	28.76%	5.44%	4.47%	7.39%	0.52%	0.00%	0.00%	0.30%	0.00%	0.00%
    A013	50.93%	22.98%	0.58%	9.94%	12.71%	2.40%	0.00%	0.45%	0.00%	0.00%	0.00%
    A014	52.33%	18.29%	2.31%	7.02%	17.14%	0.00%	0.00%	1.32%	1.60%	0.00%	0.00%
    A015	57.12%	29.68%	1.75%	1.80%	9.36%	0.00%	0.00%	0.00%	0.30%	0.00%	0.00%
    A016	52.91%	21.58%	2.45%	8.14%	12.78%	0.97%	0.00%	0.00%	1.16%	0.00%	0.00%
    A017	52.70%	24.41%	1.91%	5.91%	12.20%	0.99%	0.00%	1.66%	0.21%	0.00%	0.00%
    A018	1.52%	1.73%	1.18%	17.98%	38.30%	0.00%	14.35%	0.00%	18.44%	1.13%	5.36%
    A019	3.86%	0.00%	2.45%	16.01%	77.24%	0.00%	0.00%	0.06%	0.38%	0.00%	0.00%
    A020	52.58%	29.59%	1.63%	5.00%	7.15%	0.08%	1.92%	0.92%	1.12%	0.00%	0.02%
    A021	13.59%	0.62%	0.00%	56.04%	12.92%	0.80%	4.61%	0.89%	0.00%	0.00%	10.52%
    A022	8.44%	1.12%	3.31%	17.11%	44.60%	0.41%	18.14%	0.80%	1.38%	2.54%	2.14%
    A023	16.61%	0.00%	0.00%	28.25%	52.61%	1.91%	0.00%	0.61%	0.00%	0.00%	0.00%
    A024	20.49%	0.00%	0.37%	44.64%	33.60%	0.79%	0.00%	0.00%	0.06%	0.04%	0.00%
    A025	59.37%	23.72%	0.48%	7.04%	7.22%	0.45%	0.00%	1.06%	0.66%	0.00%	0.00%
    A026	63.40%	26.22%	1.16%	3.37%	4.54%	0.12%	0.00%	0.66%	0.53%	0.00%	0.01%
    A027	56.00%	15.88%	1.84%	8.13%	15.23%	0.72%	0.00%	1.48%	0.72%	0.00%	0.00%
    A028	51.45%	12.67%	0.79%	15.02%	18.47%	0.78%	0.00%	0.00%	0.83%	0.00%	0.00%
    A029	56.11%	31.01%	2.68%	3.31%	5.39%	1.49%	0.00%	0.00%	0.00%	0.00%	0.00%
    A030	7.93%	0.76%	0.00%	30.99%	46.00%	0.91%	10.72%	0.69%	0.42%	1.14%	0.44%
    A031	51.07%	10.14%	0.43%	19.98%	16.13%	1.18%	0.14%	0.33%	0.60%	0.00%	0.00%
    A032	30.06%	11.70%	2.12%	13.03%	41.35%	0.71%	0.00%	1.02%	0.00%	0.00%	0.00%
    A033	12.97%	3.85%	0.04%	19.04%	63.50%	0.00%	0.00%	0.23%	0.00%	0.36%	0.00%
    A034	29.77%	0.54%	1.56%	44.84%	19.44%	2.17%	0.12%	0.09%	0.71%	0.28%	0.48%
    A035	34.16%	2.92%	0.28%	40.19%	17.23%	4.08%	0.00%	0.00%	0.44%	0.00%	0.68%
    A036	22.03%	0.99%	0.83%	57.65%	10.68%	0.30%	2.20%	0.94%	0.59%	0.74%	3.07%
    A037	22.79%	0.52%	0.00%	57.89%	15.83%	0.00%	0.00%	0.45%	0.64%	0.00%	1.88%
    A038	20.70%	0.00%	0.66%	61.40%	14.82%	0.00%	0.00%	0.78%	0.00%	0.00%	1.64%
    A039	5.82%	0.21%	0.00%	19.07%	73.69%	0.00%	0.00%	0.00%	1.20%	0.00%	0.00%
    A040	58.94%	29.33%	0.14%	6.92%	4.32%	0.00%	0.00%	0.34%	0.00%	0.00%	0.00%
    A041	56.17%	23.20%	0.24%	6.14%	11.50%	1.07%	0.00%	0.40%	1.29%	0.00%	0.00%
    A042	56.64%	25.73%	0.00%	7.84%	9.25%	0.26%	0.00%	0.00%	0.28%	0.00%	0.00%
    A043	56.51%	25.23%	0.00%	5.77%	12.48%	0.00%	0.00%	0.00%	0.00%	0.00%	0.00%
    A044	58.84%	25.92%	0.00%	4.58%	7.61%	2.88%	0.00%	0.00%	0.16%	0.00%	0.00%
    A045	55.23%	24.79%	1.79%	7.46%	10.68%	0.05%	0.00%	0.00%	0.00%	0.00%	0.00%
    A046	59.82%	27.21%	2.30%	5.37%	1.44%	0.00%	0.00%	2.41%	1.44%	0.00%	0.00%
    A047	50.58%	15.81%	0.36%	12.81%	18.13%	0.84%	0.00%	0.43%	1.02%	0.00%	0.00%
    A048	10.55%	0.00%	27.57%	10.08%	21.77%	28.79%	0.00%	0.00%	1.24%	0.00%	0.00%
    A049	57.88%	22.51%	0.88%	8.90%	7.41%	1.31%	0.00%	0.00%	0.90%	0.00%	0.22%
    A050	58.34%	26.90%	0.83%	9.76%	3.65%	0.00%	0.00%	0.48%	0.00%	0.00%	0.04%
    A051	57.67%	28.82%	3.02%	5.90%	3.51%	0.00%	0.00%	1.08%	0.00%	0.00%	0.00%
    A052	55.93%	24.47%	0.00%	9.15%	7.46%	1.82%	0.00%	0.85%	0.33%	0.00%	0.00%
    A053	58.15%	24.97%	2.10%	9.38%	4.02%	0.12%	0.00%	0.46%	0.64%	0.14%	0.00%
    A054	28.10%	0.17%	0.48%	46.05%	21.46%	1.85%	0.00%	0.00%	1.24%	0.00%	0.64%
    A055	29.79%	0.82%	0.83%	47.33%	18.54%	1.57%	0.12%	0.07%	0.37%	0.20%	0.34%
    A056	29.88%	0.00%	0.00%	44.80%	20.71%	2.19%	0.00%	0.00%	1.58%	0.35%	0.49%
    A057	57.84%	26.16%	0.00%	4.07%	9.63%	1.03%	0.00%	0.78%	0.49%	0.00%	0.00%
    A058	58.54%	23.19%	0.63%	8.15%	8.57%	0.00%	0.00%	0.00%	0.92%	0.00%	0.00%
    A059	2.20%	0.00%	1.75%	14.48%	22.57%	2.83%	7.14%	0.75%	46.43%	1.57%	0.28%
    A060	1.72%	0.32%	4.51%	18.18%	23.78%	0.35%	0.61%	0.31%	48.96%	1.26%	0.00%
    A061	54.05%	25.46%	1.23%	3.28%	13.08%	1.58%	0.00%	0.00%	1.32%	0.00%	0.00%
    A062	18.67%	0.10%	0.35%	58.48%	14.89%	0.83%	2.49%	0.00%	0.35%	0.00%	3.84%
    A063	6.87%	0.61%	0.20%	18.05%	73.72%	0.00%	0.00%	0.52%	0.00%	0.03%	0.00%
    A064	52.62%	17.65%	1.20%	10.55%	14.48%	1.63%	0.00%	0.33%	1.51%	0.02%	0.03%
    A065	52.95%	14.02%	0.00%	15.18%	15.02%	1.57%	0.00%	0.00%	1.25%	0.00%	0.00%
    A066	41.97%	12.12%	0.29%	24.10%	15.35%	0.62%	1.75%	0.28%	0.63%	0.59%	2.30%
    A067	53.42%	17.39%	0.13%	9.95%	16.55%	1.13%	0.00%	0.00%	1.42%	0.00%	0.00%
    A068	50.23%	14.24%	0.53%	12.93%	20.03%	0.30%	0.00%	0.28%	1.46%	0.00%	0.00%
    A069	54.65%	16.95%	0.68%	12.82%	11.82%	2.23%	0.00%	0.00%	0.84%	0.00%	0.00%
    A070	53.31%	17.63%	1.03%	8.10%	18.24%	1.44%	0.00%	0.00%	0.25%	0.00%	0.00%
    A071	51.05%	15.00%	2.31%	8.98%	20.97%	0.03%	0.00%	0.00%	1.31%	0.34%	0.00%
    A072	19.57%	6.36%	1.18%	30.74%	40.45%	0.19%	0.00%	0.55%	0.95%	0.00%	0.00%
    A073	6.44%	0.00%	0.00%	20.64%	70.44%	0.00%	0.39%	0.00%	0.87%	0.00%	1.23%
    A074	12.69%	2.66%	0.06%	20.45%	63.97%	0.00%	0.00%	0.00%	0.17%	0.00%	0.00%
    A075	11.34%	0.00%	0.11%	28.17%	55.58%	3.87%	0.39%	0.00%	0.54%	0.00%	0.00%
    A076	51.98%	11.24%	0.00%	14.96%	18.26%	1.90%	0.00%	0.48%	1.17%	0.00%	0.00%
    A077	52.35%	12.10%	0.00%	18.20%	12.76%	0.63%	1.95%	0.00%	1.44%	0.10%	0.47%
    A078	55.78%	28.21%	0.49%	4.74%	7.42%	2.56%	0.00%	0.44%	0.34%	0.00%	0.00%
    A079	50.74%	25.50%	5.09%	8.39%	9.90%	0.23%	0.00%	0.00%	0.09%	0.00%	0.04%
    A080	35.32%	18.40%	0.00%	10.21%	35.49%	0.24%	0.00%	0.13%	0.20%	0.00%	0.00%
    A081	59.37%	35.29%	2.03%	1.69%	0.51%	0.00%	0.00%	1.11%	0.00%	0.00%	0.00%
    A082	57.06%	24.82%	0.18%	7.42%	8.95%	0.14%	0.00%	0.37%	1.06%	0.00%	0.00%
    A083	57.02%	25.57%	1.35%	8.54%	6.42%	0.06%	0.00%	0.37%	0.68%	0.00%	0.00%
    A084	56.96%	24.78%	0.27%	6.56%	9.63%	0.21%	0.00%	0.91%	0.68%	0.00%	0.00%
    A085	55.89%	30.30%	3.56%	5.14%	3.15%	1.02%	0.00%	0.32%	0.21%	0.00%	0.41%
    A086	59.15%	32.61%	1.89%	4.27%	0.27%	0.21%	0.00%	1.53%	0.04%	0.00%	0.03%
    A087	58.63%	36.44%	1.38%	1.19%	0.13%	0.48%	0.00%	1.64%	0.00%	0.00%	0.12%
    A088	50.89%	9.33%	0.03%	15.34%	18.83%	1.87%	0.00%	0.54%	3.17%	0.00%	0.00%
    A089	20.78%	0.00%	1.92%	50.05%	23.88%	3.04%	0.00%	0.33%	0.00%	0.00%	0.00%
    A090	52.30%	20.94%	0.24%	6.47%	17.48%	1.27%	0.00%	0.50%	0.81%	0.00%	0.00%
    A091	56.71%	24.69%	1.44%	7.40%	9.19%	0.25%	0.00%	0.00%	0.32%	0.00%	0.00%
    A092	48.09%	20.90%	4.50%	13.15%	10.34%	2.40%	0.34%	0.00%	0.00%	0.00%	0.29%
    A093	55.76%	24.89%	2.23%	7.21%	9.78%	0.00%	0.00%	0.12%	0.00%	0.00%	0.00%
    A094	48.60%	18.71%	2.92%	12.64%	14.68%	0.00%	0.00%	0.46%	1.81%	0.00%	0.18%
    A095	49.52%	13.16%	0.00%	7.68%	26.53%	1.32%	0.00%	0.38%	1.40%	0.00%	0.00%
    A096	56.06%	19.05%	0.54%	7.52%	13.46%	1.66%	0.00%	0.18%	1.40%	0.00%	0.13%
    Components are not identical to Dodecad components. In fact, they may be significantly distinct.

    S Asian C1
    Onge C2
    E Asian C3
    SW Asian C4
    European C5
    Siberian C6
    W African C7
    Papuan C8
    American C9
    San/Pygmy C10
    E African C11

  2. #2
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    Afro-Belizean A001
    Andhra Pradesh A002
    Andhra Pradesh (Hyderabadi) A003
    Andhra Pradesh Reddy A004
    Assyrian Iranian_Nestorian A005
    Assyrian_AncientChurchofEast A006
    Assyrian_ChaldeanCatholic A007
    Azeri Turk A008
    Bengali A009
    Bengali Brahmin A010
    Bengali/Marathi/Goan A011
    Bengali/Oriya A012
    Bihar/Jharkhand Muslim A013
    Bihari Brahmin A014
    Bihari Kayastha A015
    Bihari Muslim A016
    Bihari Syed A017
    Brazilian A018
    British (1/2), Danish (1/2) A019
    Caribbean Indian A020
    Egyptian A021
    French/Martinique/Madagascar/Indian A022
    Gagauz Turk (1/2), Ukrainian (1/4), South Ossetian (1/4) A023
    Georgian A024
    Goan Catholic Brahmin A025
    Gujarati A026
    Gujarati Ganchi A027
    Halai Bhatia A028
    HRP0045 A029
    HRP0127 A030
    HRP0132 A031
    Indian (1/2), German (1/2) A032
    Indian (1/5-1/4), rest English/Irish/French A033
    Iranian A034
    Iranian Khorasani A035
    Iraqi Arab A036
    Iraqi Mandaean A037
    Iraqi/Egyptian Jewish A038
    Irish A039
    Karnataka A040
    Karnataka Brahmin A041
    Karnataka Iyengar A042
    Karnataka Iyengar Brahmin A043
    Karnataka Kannada Brahmin A044
    Karnataka Konkani Brahmin A045
    Karnataka Lingayat A046
    Kashmiri A047
    Kazakh A048
    Kerala Brahmin A049
    Kerala Christian A050
    Kerala Muslim Rawther A051
    Kerala Nair A052
    Kerala Syrian Christian A053
    Kurd (Iranian) A054
    Kurd (Iraqi) A055
    Kurd (Turkish) A056
    Maharashtra/Madhya Pradesh Saraswat Brahmin A057
    Mahrashtrian Desastha Brahmin A058
    Mexican with possible Indian ancenstry A059
    Mexican/Jewish A060
    Oriya Brahmin A061
    Palestinian A062
    Prussian/Swiss/Scot/English/possible South Asian A063
    Punjabi A064
    Punjabi (1/2), Sindhi (1/2) A065
    Punjabi (3/4), Egyptian (1/4) A066
    Punjabi Brahmin A067
    Punjabi Jatt A068
    Punjabi Pahari Rajput A069
    Punjabi Ramgarhia A070
    Rajasthani Brahmin A071
    Romani (1/2), Serb (1/2) A072
    Romany (1/2), Libyan Jew, Gujarati,Greek, African American A073
    Romany Gypsy A074
    Russian (1/2), Ashkenazi (1/2) A075
    Sindhi A076
    Sindhi (1/2), Balochi (1/2) A077
    Sourastrian A078
    Sri Lankan A079
    Sri Lankan (1/2), German/Polish (1/2) A080
    Sri Lankan (1/2), Telegu (1/2) A081
    Tamil Brahmin A082
    Tamil Brahmin Iyengar A083
    Tamil Brahmin Iyer A084
    Tamil Muslim A085
    Tamil Nadar A086
    Tamil Vishwakarma A087
    Thathai Bhatia A088
    Turkish A089
    UP Brahmin A090
    UP Kayasth A091
    UP Mixed Indian/Pakistani A092
    UP Mughal/Pathan A093
    UP Syed A094
    UP/Haryana Jatt A095
    UP/MP/Marathi A096

  3. #3
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    Do you have admixture scores for the Pathan, Burusho and Kalash?

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    Most of the West Asian population averages (and samples where N=1):

    Code:
    POP	C1	C2	C3	C4	C5	C6	C7	C8	C9	C10	C11
    ASY	26%	0%	0%	58%	16%	0%	0%	0%	0%	0%	0%
    AZR	24%	1%	2%	44%	23%	4%	0%	0%	1%	0%	0%
    IRN	30%	1%	2%	45%	19%	2%	0%	0%	1%	0%	0%
    KHO	34%	3%	0%	40%	17%	4%	0%	0%	0%	0%	1%
    KRD	29%	0%	0%	46%	20%	2%	0%	0%	1%	0%	0%
    MAN	23%	1%	0%	58%	16%	0%	0%	0%	1%	0%	2%
    TUR	21%	0%	2%	50%	24%	3%	0%	0%	0%	0%	0%
    Assyrians and Kurds are no longer separated along denominational and geographical lines respectively.

    ASY Assyrian N=4
    AZR Azeri Turk N=1
    IRN Iranian N=6
    KHO Iranian Khorasani N=1
    KRD Kurds N=6
    MAN Iraqi Mandaean N=1
    TUR Turk N=1
    Attached Thumbnails Attached Thumbnails Click image for larger version. 

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    Quote Originally Posted by Pallantides View Post
    Do you have admixture scores for the Pathan, Burusho and Kalash?
    Yes.

    Code:
    POP	C1	C2	C3	C4	C5	C6	C7	C8	C9	C10	C11
    BUR	47%	10%	6%	12%	18%	5%	0%	1%	2%	0%	0%
    KAL	60%	0%	3%	11%	22%	1%	0%	1%	2%	0%	0%
    PAT	48%	11%	1%	17%	19%	2%	0%	0%	1%	0%	0%

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    Quote Originally Posted by Transhumanist View Post
    Yes.

    Code:
    POP	C1	C2	C3	C4	C5	C6	C7	C8	C9	C10	C11
    BUR	47%	10%	6%	12%	18%	5%	0%	1%	2%	0%	0%
    KAL	60%	0%	3%	11%	22%	1%	0%	1%	2%	0%	0%
    PAT	48%	11%	1%	17%	19%	2%	0%	0%	1%	0%	0%


    Thanks, I wanted to see their East Asian, Siberian and American values

    East Asian

    Burusho:6%
    Kalash: 3%
    Pathan: 1%

    Siberian

    Burusho: 5%
    Kalash: 1%
    Pathan: 2%

    American

    Burusho: 2%
    Kalash: 2%
    Pathan: 1&

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    so the kalash are not that european after all

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    HarappaWorld Admixture (Posted by Zack on May 4, 2012)

    Here is a new admixture calculator. This uses populations all over the world and I got the best results (i.e., lowest crossvalidation error) at K=16.
    Fst distances for the run.

    I should have HarappaWorldOracle and DIYHarappaWorld calculators out in the next few days.

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    My K=16 values, rounded to nearest whole percent:

    0% S Indian
    21% Baloch
    50% Caucasian

    1% NE Euro
    0% SE Asian
    0% Siberian

    1% NE Asian
    0% Papuan
    0% American
    0% Beringian

    8% Mediterranean
    19% SW Asian

    0% San
    0% E African
    0% Pygmy
    0% W African

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    The Harappa World Admixture Calculator is now available for no-participants

    http://www.harappadna.org/2012/05/di...orld/#comments

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