Here's the HarappaWorld Oracle to go with the HarappaWorld admixture results and DIYHarappaWorld.
It works similar to the old Ref3 Harappa Oracle, with a couple of differences. One, there is no panasian switch since the Pan-Asian dataset is not included in this calculator.
I have added an optional mincount argument. It picks only those groups where the number of individuals is equal to or more than mincount for the Oracle calculation. By default mincount is 2, so only those groups which have 2 or more samples are used to compute your Oracle results.
Let's look at my top 20 Oracle results in mixed mode excluding population groups with less than 4 individuals.
HarappaOracle(c(26.46,36.82,14.22,4.78,0.00,1.32,0.86,0.04,0.19,0.06,3.63,8.07,0.00,2.44,0.43,0.67),k=20,mincount=4,mixedmode=T)
[,1] [,2]
[1,] "18.1% egyptian_behar_12 + 81.9% punjabi-arain_xing_25" "2.3361"
[2,] "18.1% egypt_henn2012_19 + 81.9% punjabi-arain_xing_25" "2.5615"
[3,] "80.7% punjabi-arain_xing_25 + 19.3% yemenese_behar_8" "2.8388"
[4,] "18.4% palestinian_hgdp_46 + 81.6% punjabi-arain_xing_25" "2.9944"
[5,] "84.7% punjabi-arain_xing_25 + 15.3% yemen-jew_behar_15" "3.0923"
[6,] "19.1% jordanian_behar_20 + 80.9% punjabi-arain_xing_25" "3.1877"
[7,] "18% egypt_henn2012_19 + 82% sindhi_hgdp_24" "3.4814"
[8,] "17.9% egyptian_behar_12 + 82.1% sindhi_hgdp_24" "3.5554"
[9,] "20.3% jordanian_behar_20 + 79.7% punjabi_harappa_7" "3.6161"
[10,] "18.9% egyptian_behar_12 + 81.1% punjabi_harappa_7" "3.6587"
[11,] "19.5% palestinian_hgdp_46 + 80.5% punjabi_harappa_7" "3.7079"
[12,] "19% egypt_henn2012_19 + 81% punjabi_harappa_7" "3.8303"
[13,] "18.3% palestinian_hgdp_46 + 81.7% sindhi_hgdp_24" "3.8762"
[14,] "80.4% punjabi-arain_xing_25 + 19.6% syrian_behar_16" "3.8908"
[15,] "19% lebanese_behar_7 + 81% punjabi-arain_xing_25" "4.0494"
[16,] "18.9% jordanian_behar_20 + 81.1% sindhi_hgdp_24" "4.078"
[17,] "79.9% punjabi_harappa_7 + 20.1% yemenese_behar_8" "4.1222"
[18,] "15.1% bedouin_hgdp_46 + 84.9% punjabi-arain_xing_25" "4.1522"
[19,] "85.3% punjabi-arain_xing_25 + 14.7% saudi_behar_20" "4.2014"
[20,] "79.1% punjabi_harappa_7 + 20.9% syrian_behar_16" "4.2191"
These results are closer to my actual reported ancestry than the ones from reference 3 oracle.
my results in mixedmode
[1,] "27.7% bene-israel-jew_behar_4 + 72.3% romanian_behar_16"
[2,] "73.9% bulgarian_yunusbayev_13 + 26.1% cochin-jew_behar_4"
[3,] "23.4% cochin-jew_behar_4 + 76.6% romanian_behar_16"
[4,] "25.9% bengali-brahmin_harappa_3 + 74.1% tuscan_1000genomes_11"
[5,] "26.4% brahmin-uttar-pradesh_metspalu_8 + 73.6% tuscan_1000genomes_11"
[6,] "28.1% nepalese-1_xing_12 + 71.9% tuscan_1000genomes_11"
[7,] "25.9% bengali-brahmin_harappa_3 + 74.1% tuscan_hgdp_8"
[8,] "73.1% tuscan_1000genomes_11 + 26.9% up-brahmin_harappa_3"
[9,] "26.5% brahmin-uttar-pradesh_metspalu_8 + 73.5% tuscan_hgdp_8"
[10,] "28.1% nepalese-1_xing_12 + 71.9% tuscan_hgdp_8"
[,2]
[1,] "4.0734"
[2,] "4.3665"
[3,] "4.3956"
[4,] "4.6612"
[5,] "4.6841"
[6,] "4.7251"
[7,] "4.7737"
[8,] "4.7794"
[9,] "4.8067"
[10,] "4.8637"
Try it with mincount=1. I want to see what you get with the one Serbian in my data.
thanks for reminding me zack, i didnt knew that i need to put in mincount=1 to see the serbian.
here are the results but at k=20 the serbian doesnt pop up
> HarappaOracle(c(10.90, 12.19, 23.27, 23.73, 0.47, 0.24, 0.88, 1.06, 0.89, 0.00, 21.16, 4.98, 0.24, 0.00, 0.00, 0.00),k=20,mincount=1,mixedmode=T)
[,1]
[1,] "27.9% bene-israel-jew_behar_4 + 72.1% romanian_behar_16"
[2,] "29.4% rajasthani-brahmin_harappa_1 + 70.6% tuscan_1000genomes_11"
[3,] "25.7% bengali-brahmin_harappa_3 + 74.3% tuscan_1000genomes_11"
[4,] "26.3% brahmin-uttar-pradesh_metspalu_8 + 73.7% tuscan_1000genomes_11"
[5,] "27.9% nepalese-1_xing_12 + 72.1% tuscan_1000genomes_11"
[6,] "73.2% tuscan_1000genomes_11 + 26.8% up-brahmin_harappa_3"
[7,] "29.4% rajasthani-brahmin_harappa_1 + 70.6% tuscan_hgdp_8"
[8,] "25.8% bengali-brahmin_harappa_3 + 74.2% tuscan_hgdp_8"
[9,] "73.8% bulgarian_yunusbayev_13 + 26.2% cochin-jew_behar_4"
[10,] "26.3% brahmin-uttar-pradesh_metspalu_8 + 73.7% tuscan_hgdp_8"
[11,] "28% nepalese-1_xing_12 + 72% tuscan_hgdp_8"
[12,] "73.2% tuscan_hgdp_8 + 26.8% up-brahmin_harappa_3"
[13,] "23.5% cochin-jew_behar_4 + 76.5% romanian_behar_16"
[14,] "29.7% rajasthani-brahmin_harappa_1 + 70.3% tuscan_hapmap_102"
[15,] "26.6% bihari-brahmin_harappa_1 + 73.4% tuscan_1000genomes_11"
[16,] "74.5% tuscan_1000genomes_11 + 25.5% vaish_reich_4"
[17,] "28.2% nepalese-1_xing_12 + 71.8% tuscan_hapmap_102"
[18,] "26.3% bihari-muslim_harappa_4 + 73.7% tuscan_1000genomes_11"
[19,] "24.7% rajasthani_harappa_1 + 75.3% tuscan_1000genomes_11"
[20,] "26% bengali-brahmin_harappa_3 + 74% tuscan_hapmap_102"
[,2]
[1,] "4.1715"
[2,] "4.3678"
[3,] "4.3679"
[4,] "4.3979"
[5,] "4.4113"
[6,] "4.4611"
[7,] "4.5007"
[8,] "4.5067"
[9,] "4.5392"
[10,] "4.5468"
[11,] "4.5774"
[12,] "4.5862"
[13,] "4.622"
[14,] "4.6853"
[15,] "4.7337"
[16,] "4.7577"
[17,] "4.8099"
[18,] "4.8272"
[19,] "4.8367"
[20,] "4.8464"
> HarappaOracle(c(11, 12, 23, 24, 0, 0, 1, 1, 1, 0, 21, 5, 0, 0, 0, 0),k=20,mincount=1,mixedmode=T)
[,1]
[1,] "27.7% bene-israel-jew_behar_4 + 72.3% romanian_behar_16"
[2,] "73.9% bulgarian_yunusbayev_13 + 26.1% cochin-jew_behar_4"
[3,] "23.4% cochin-jew_behar_4 + 76.6% romanian_behar_16"
[4,] "25.9% bengali-brahmin_harappa_3 + 74.1% tuscan_1000genomes_11"
[5,] "29.5% rajasthani-brahmin_harappa_1 + 70.5% tuscan_1000genomes_11"
[6,] "26.4% brahmin-uttar-pradesh_metspalu_8 + 73.6% tuscan_1000genomes_11"
[7,] "28.1% nepalese-1_xing_12 + 71.9% tuscan_1000genomes_11"
[8,] "25.9% bengali-brahmin_harappa_3 + 74.1% tuscan_hgdp_8"
[9,] "73.1% tuscan_1000genomes_11 + 26.9% up-brahmin_harappa_3"
[10,] "29.6% rajasthani-brahmin_harappa_1 + 70.4% tuscan_hgdp_8"
[11,] "26.5% brahmin-uttar-pradesh_metspalu_8 + 73.5% tuscan_hgdp_8"
[12,] "28.1% nepalese-1_xing_12 + 71.9% tuscan_hgdp_8"
[13,] "78.2% bulgarian_yunusbayev_13 + 21.8% karnataka_harappa_3"
[14,] "73% tuscan_hgdp_8 + 27% up-brahmin_harappa_3"
[15,] "79% bulgarian_yunusbayev_13 + 21% gujarati-patel_harappa_2"
[16,] "77.7% bulgarian_yunusbayev_13 + 22.3% kerala-muslim_harappa_1"
[17,] "76.8% bulgarian_yunusbayev_13 + 23.2% kerala-christian_harappa_5"
[18,] "29.8% rajasthani-brahmin_harappa_1 + 70.2% tuscan_hapmap_102"
[19,] "30.4% bene-israel-jew_behar_4 + 69.6% bulgarian_yunusbayev_13"
[20,] "26.8% bihari-brahmin_harappa_1 + 73.2% tuscan_1000genomes_11"
[,2]
[1,] "4.0734"
[2,] "4.3665"
[3,] "4.3956"
[4,] "4.6612"
[5,] "4.6763"
[6,] "4.6841"
[7,] "4.7251"
[8,] "4.7737"
[9,] "4.7794"
[10,] "4.7839"
[11,] "4.8067"
[12,] "4.8637"
[13,] "4.8648"
[14,] "4.8793"
[15,] "4.8805"
[16,] "4.8926"
[17,] "4.9237"
[18,] "4.9652"
[19,] "5.0094"
[20,] "5.0134"
not even at k=50 the serbian pops up
in single mode i do get out serbian in the top ten
[1,] "romanian_behar_16" "14.4756"
[2,] "tuscan_1000genomes_11" "16.4935"
[3,] "bulgarian_yunusbayev_13" "16.5094"
[4,] "tuscan_hgdp_8" "16.5727"
[5,] "tuscan_hapmap_102" "16.7916"
[6,] "ashkenazi_harappa_4" "17.2808"
[7,] "ashkenazy-jew_behar_21" "18.9325"
[8,] "italian_hgdp_13" "19.6899"
[9,] "serbian_harappa_1" "19.9766"
[10,] "turk-aydin_hodoglugil_20" "20.8152"
here is mine with mincount=4:
[1,] "97.7% ap-brahmin_xing_25 + 2.3% druze_hgdp_42" "1.3992"
[2,] "93% ap-brahmin_xing_25 + 7% bene-israel-jew_behar_4" "1.4733"
[3,] "58% piramalai-kallar_metspalu_8 + 42% punjabi-jatt_harappa_5" "1.4739"
[4,] "97.6% ap-brahmin_xing_25 + 2.4% georgia-jew_behar_4" "1.4854"
[5,] "97.5% ap-brahmin_xing_25 + 2.5% iraq-jew_behar_10" "1.5054"
[6,] "97.6% ap-brahmin_xing_25 + 2.4% azerbaijan-jew_behar_8" "1.508"
[7,] "97.5% ap-brahmin_xing_25 + 2.5% iranian-jew_behar_4" "1.5132"
[8,] "97.6% ap-brahmin_xing_25 + 2.4% armenian_yunusbayev_16" "1.5167"
[9,] "97.6% ap-brahmin_xing_25 + 2.4% armenian_behar_19" "1.5189"
[10,] "97.5% ap-brahmin_xing_25 + 2.5% syrian_behar_16" "1.5192"
[11,] "97.9% ap-brahmin_xing_25 + 2.1% yemen-jew_behar_15" "1.5252"
[12,] "97.6% ap-brahmin_xing_25 + 2.4% assyrian_harappa_6" "1.5259"
[13,] "49.6% punjabi-jatt_harappa_5 + 50.4% sakilli_chaubey_4" "1.5263"
[14,] "97.6% ap-brahmin_xing_25 + 2.4% palestinian_hgdp_46" "1.533"
[15,] "97.9% ap-brahmin_xing_25 + 2.1% georgian_behar_20" "1.534"
[16,] "97.7% ap-brahmin_xing_25 + 2.3% cypriot_behar_12" "1.5444"
[17,] "97.6% ap-brahmin_xing_25 + 2.4% lebanese_behar_7" "1.5479"
[18,] "2.1% abhkasian_yunusbayev_20 + 97.9% ap-brahmin_xing_25" "1.5488"
[19,] "97.6% ap-brahmin_xing_25 + 2.4% jordanian_behar_20" "1.5543"
[20,] "85.1% ap-brahmin_xing_25 + 14.9% cochin-jew_behar_4" "1.5613"
Thanks for the new tools, Zack.
Excluding Mizrahim, these are the top Assyrian population matches:
HarappaOracle("assyrian_harappa_6")
"iraqi-mandaean_harappa_2" "5.6235"
"armenian_yunusbayev_16" "6.7647"
"armenian_behar_19" "9.5842"
"kurd_yunusbayev_6" "10.9039"
> HarappaOracle(c(0.00,11.10,5.81,50.58,0.08,0.03,0.00,0.00,0.61,0.00,31.64,0.02,0.11,0.02,0.00,0.00),k=40,mincount=4,mixedmode=T)
[,1] [,2]
[1,] "1.9% urkarah_xing_18 + 98.1% utahn-white_1000genomes_100" "0.9847"
[2,] "1.7% lezgin_behar_18 + 98.3% utahn-white_1000genomes_100" "1.0251"
[3,] "15% bulgarian_yunusbayev_13 + 85% orcadian_hgdp_15" "1.0645"
[4,] "1.8% stalskoe_xing_5 + 98.2% utahn-white_1000genomes_100" "1.0712"
[5,] "1.6% chechen_yunusbayev_20 + 98.4% utahn-white_1000genomes_100" "1.0765"
[6,] "81.4% british_1000genomes_99 + 18.6% hungarian_behar_19" "1.1112"
[7,] "1.8% tajik_yunusbayev_15 + 98.2% utahn-white_1000genomes_100" "1.1168"
[8,] "1.4% kalash_hgdp_23 + 98.6% utahn-white_1000genomes_100" "1.1278"
[9,] "1.5% kumyk_yunusbayev_14 + 98.5% utahn-white_1000genomes_100" "1.135"
[10,] "1.4% adygei_hgdp_17 + 98.6% utahn-white_1000genomes_100" "1.1378"
[11,] "1.3% north-ossetian_yunusbayev_15 + 98.7% utahn-white_1000genomes_100" "1.1444"
[12,] "1.3% balkar_yunusbayev_19 + 98.7% utahn-white_1000genomes_100" "1.1501"
[13,] "1.4% pathan_hgdp_23 + 98.6% utahn-white_1000genomes_100" "1.164"
[14,] "1.1% abhkasian_yunusbayev_20 + 98.9% utahn-white_1000genomes_100" "1.1743"
[15,] "1.2% balochi_hgdp_24 + 98.8% utahn-white_1000genomes_100" "1.1824"
[16,] "1.1% brahui_hgdp_25 + 98.9% utahn-white_1000genomes_100" "1.1839"
[17,] "1.1% makrani_hgdp_25 + 98.9% utahn-white_1000genomes_100" "1.1863"
[18,] "1.3% burusho_hgdp_25 + 98.7% utahn-white_1000genomes_100" "1.1865"
[19,] "1% georgian_behar_20 + 99% utahn-white_1000genomes_100" "1.1879"
[20,] "1.5% nogai_yunusbayev_16 + 98.5% utahn-white_1000genomes_100" "1.2011"
with my own run
HarappaWorld Calculator with v3 Genome Data
10.90% S-Indian
12.19% Baloch
23.27% Caucasian
23.73% NE-Euro
0.47% SE-Asian
0.24% Siberian
0.88% NE-Asian
1.06% Papuan
0.89% American
0.00% Beringian
21.16% Mediterranean
4.98% SW-Asian
0.24% San
0.00% E-African
0.00% Pygmy
0.00% W-African
Oracle with the same Results
[1,] "27.9% bene-israel-jew_behar_4 + 72.1% romanian_behar_16"
[2,] "25.7% bengali-brahmin_harappa_3 + 74.3% tuscan_1000genomes_11"
[3,] "26.3% brahmin-uttar-pradesh_metspalu_8 + 73.7% tuscan_1000genomes_11"
[4,] "27.9% nepalese-1_xing_12 + 72.1% tuscan_1000genomes_11"
[5,] "73.2% tuscan_1000genomes_11 + 26.8% up-brahmin_harappa_3"
[6,] "25.8% bengali-brahmin_harappa_3 + 74.2% tuscan_hgdp_8"
[7,] "73.8% bulgarian_yunusbayev_13 + 26.2% cochin-jew_behar_4"
[8,] "26.3% brahmin-uttar-pradesh_metspalu_8 + 73.7% tuscan_hgdp_8"
[9,] "28% nepalese-1_xing_12 + 72% tuscan_hgdp_8"
[10,] "73.2% tuscan_hgdp_8 + 26.8% up-brahmin_harappa_3"
[11,] "23.5% cochin-jew_behar_4 + 76.5% romanian_behar_16"
[12,] "74.5% tuscan_1000genomes_11 + 25.5% vaish_reich_4"
[13,] "28.2% nepalese-1_xing_12 + 71.8% tuscan_hapmap_102"
[14,] "26.3% bihari-muslim_harappa_4 + 73.7% tuscan_1000genomes_11"
[15,] "26% bengali-brahmin_harappa_3 + 74% tuscan_hapmap_102"
[16,] "73% tuscan_hapmap_102 + 27% up-brahmin_harappa_3"
[17,] "26.5% brahmin-uttar-pradesh_metspalu_8 + 73.5% tuscan_hapmap_102"
[18,] "26.4% bihari-muslim_harappa_4 + 73.6% tuscan_hgdp_8"
[19,] "74.4% tuscan_hgdp_8 + 25.6% vaish_reich_4"
[20,] "29.7% haryana-jatt_harappa_3 + 70.3% tuscan_1000genomes_11"
[,2]
[1,] "4.1715"
[2,] "4.3679"
[3,] "4.3979"
[4,] "4.4113"
[5,] "4.4611"
[6,] "4.5067"
[7,] "4.5392"
[8,] "4.5468"
[9,] "4.5774"
[10,] "4.5862"
[11,] "4.622"
[12,] "4.7577"
[13,] "4.8099"
[14,] "4.8272"
[15,] "4.8464"
[16,] "4.8766"
[17,] "4.8806"
[18,] "4.8849"
[19,] "4.8862"
[20,] "4.9369"
Awesome tool Zack!
This is my run with mincount = 4
HarappaOracle(c(58.30,32.29,2.87,0,2.03,0.66,0.00,0.71,0,1.46,0,1.67,0,0,0,0),k=20,mincount=4,mixedmode=T)
[,1] [,2]
[1,] "20.2% gond_metspalu_4 + 79.8% velama_metspalu_10" "1.6673"
[2,] "11.9% santhal_reich_7 + 88.1% velama_metspalu_10" "1.777"
[3,] "8.2% brahui_hgdp_25 + 91.8% piramalai-kallar_metspalu_8" "1.8474"
[4,] "8.6% balochi_hgdp_24 + 91.4% piramalai-kallar_metspalu_8" "1.8812"
[5,] "4.7% brahui_hgdp_25 + 95.3% kurumba_metspalu_4" "1.911"
[6,] "24.6% satnami_reich_4 + 75.4% velama_metspalu_10" "1.913"
[7,] "95.3% kurumba_metspalu_4 + 4.7% makrani_hgdp_25" "1.9212"
[8,] "5% balochi_hgdp_24 + 95% kurumba_metspalu_4" "1.9275"
[9,] "8.1% makrani_hgdp_25 + 91.9% piramalai-kallar_metspalu_8" "1.9483"
[10,] "18.4% chenchu_reich_5 + 81.6% velama_metspalu_10" "1.9877"
[11,] "87.6% piramalai-kallar_metspalu_8 + 12.4% sindhi_hgdp_24" "2.0516"
[12,] "21.1% kerala-christian_harappa_5 + 78.9% kurumba_metspalu_4" "2.0544"
[13,] "20.7% kurumba_reich_9 + 79.3% velama_metspalu_10" "2.0588"
[14,] "10.1% ho_chaubey_5 + 89.9% velama_metspalu_10" "2.0817"
[15,] "93% kurumba_metspalu_4 + 7% sindhi_hgdp_24" "2.0829"
[16,] "43.8% hallaki_reich_7 + 56.2% velama_metspalu_10" "2.0857"
[17,] "14.5% sahariya_reich_4 + 85.5% velama_metspalu_10" "2.0989"
[18,] "33% kerala-christian_harappa_5 + 67% piramalai-kallar_metspalu_8" "2.1142"
[19,] "21.7% hakkipikki_metspalu_4 + 78.3% velama_metspalu_10" "2.1228"
[20,] "9.8% kharia_reich_4 + 90.2% velama_metspalu_10" "2.1428"
Admixture results for sinhalese_harappa_2
> HarappaOracle("sinhalese_harappa_2",k=20,mixedmode=T)
[,1] [,2]
[1,] "sinhalese_harappa_2" "0"
[2,] "67.9% tamil-nadar_harappa_2 + 32.1% tharu_metspalu_2" "0.9424"
[3,] "32.3% singapore-indian_sgvp_83 + 67.7% tamil-nadar_harappa_2" "1.0127"
[4,] "16.2% brahmin-tamil-nadu_metspalu_2 + 83.8% tamil-nadar_harappa_2" "1.1174"
[5,] "78.4% andhra-pradesh_harappa_3 + 21.6% karnataka_harappa_3" "1.1367"
[6,] "48.9% singapore-indian_sgvp_83 + 51.1% vysya_reich_5" "1.1548"
[7,] "23.4% dharkar_metspalu_11 + 76.6% kurumba_metspalu_4" "1.1752"
[8,] "71.6% kurumba_metspalu_4 + 28.4% singapore-indian_sgvp_83" "1.1767"
[9,] "17.3% iyengar-brahmin_harappa_7 + 82.7% tamil-nadar_harappa_2" "1.1853"
[10,] "13.4% gujarati-b_hapmap_34 + 86.6% tamil-nadar_harappa_2" "1.1858"
[11,] "72% kurumba_metspalu_4 + 28% tharu_metspalu_2" "1.1896"
[12,] "79.7% ap-reddy_harappa_3 + 20.3% gond_metspalu_4" "1.1946"
[13,] "15.4% karnataka-brahmin_harappa_3 + 84.6% kurumba_metspalu_4" "1.1998"
[14,] "69.9% dusadh_metspalu_6 + 30.1% velama_reich_3" "1.2069"
[15,] "85.7% tamil-nadar_harappa_2 + 14.3% up-kshatriya_metspalu_7" "1.2118"
[16,] "17.6% karnataka-brahmin_harappa_3 + 82.4% tamil-nadar_harappa_2" "1.2126"
[17,] "10.5% gujarati_harappa_3 + 89.5% tamil-nadar_harappa_2" "1.2141"
[18,] "15% meghawal_reich_5 + 85% tamil-nadar_harappa_2" "1.2236"
[19,] "17.1% iyer-brahmin_harappa_10 + 82.9% tamil-nadar_harappa_2" "1.226"
[20,] "56.6% piramalai-kallar_metspalu_8 + 43.4% singapore-indian_sgvp_83" "1.2409"