Admixture Runs (SGDP Plus)

[ Raw: I ] [ With Maf / LD Pruning: II ] [ With Maf / LD Pruning / Geno: III: K 2 ] [ III: K 11 ] [ III: K 20 ] [ III: K 40 ] [ III: K 50 ] [ III: K 64 ] [ III: K Overclustering ] [ With SGDP Plus: IV: K 10, 20, 40, 50, 64 ] [ Interpretion Methods Results ]

III. Auswertungsexperimente

(1) ./make_nnls.R Tarrega Germany_Erfurt_ME Ireland_Kilteasheen_AngloSaxon_EMedieval_Norman Germany_Anderten_Saxon_Medieval (mittelalterliche Proben als Anker)

2 Populationen: Tarrega 44.72, Norman 55,28. Mitfit: 0.568461.

2 Populationen: Tarrega 36.94, Erfurt_ME 63,06. Misfit: 0.568468.

2 Populationen: Erfurt_ME 79.3, Saxon 20.7. Misfit: 0.568498.

2 Populationen: Tarrega 75.98, Saxon 24,02. Misfit: 0.568629.

4 Populationen: Saxon 6.18, Norman 39.53, Erfurt_E 35.12, Tarrega 19.18. Misfit: 0.568284.

5 Populationen (+ French): Tarrega 0.51, Erfurt_ME 0.41, Norman 1.11, Saxon 0.0, French 97.97. Misfit: 0.003069.

5 Populationen (+ English): Tarrega 0.0, Erfurt_ME 0.43, Norman 0.81, Saxon 0.0, English 98.76. Misfit: 0.003305.

5 Populationen (+ Basque): Tarrega 0.0, Erfurt_ME 0.0, Norman 0.69, Saxon 0.83, Basque 98.49. Misfit: 0.004129.

5 Populationen (+ Hungarian): Tarrega 0.0, Erfurt_ME 0.0, Norman 0.0, Saxon 0.0, Hungarian 100.0. Misfit: 0.006451.

5 Populationen (+ Bergamo): Tarrega 0.14, Erfurt_ME 0.0, Norman 0.48, Saxon 0.0, Bergamo 99.38. Misfit: 0.062901.

5 Populationen (+ Sardinian): Tarrega 0.0, Erfurt_ME 0.0, Norman 2.4, Saxon 0.63, Sardinian 96.96. Misfit: 0.296521.

5 Populationen (+ Turkish): Tarrega 4.51, Erfurt_ME 8.41, Norman 10.06, Saxon 0.84, Turkish 76.18. Misfit: 0.549354.

5 Populationen (+ Yemenite_Jew): Tarrega 8.0, Erfurt_ME 14.66 Norman 16.5, Saxon 2.58, Yemenite_Jew 58.26. Misfit: 0.554035.

5 Populationen (+ Mixe): Tarrega 16.77, Erfurt_ME 30.7, Norman 34.56, Saxon 5.4, Mixe 12.57. Misfit: 0.568133.

5 Populationen (+ Han): Tarrega 19.17, Erfurt_ME 35.1, Norman 39.51, Saxon 6.18, Han 0.04. Misfit: 0.568284.

(2) ./make_nnls.R French English Yemenite_Jew X Y (moderne Populationen als Anker)

Basque 49.7 ( ~ "Ibero-Phoenician"), Norwegian 26.39, Finnish 9.39, Saxon 0.08 ( = 36.01 "German"), English 8.47, Norman 0.89 ( = 9.36 "White North American"), Samaritan 1.43, Palestinian 0.76, Yemenite_Jew 1.08 ( = 3.27 "Levantine"), Polish 0.22 ( ~ "East European"), Mixe 0.91, Surui 0.22 ( = 1,13 "Mi'kmaq"), Onge 0.44. Misfit: 0.000316.

Basque 48.18, Norwegian 26.54, Mixe 0.92, Finnish 9.74, English 9.74, Samaritan 1.47, Palestinian 0.77, Yemenite_Jew 1.25, Saxon 0.06, Norman 0.9, Surui 0.22. Misfit: 0.000337.

Basque 48.18, Norwegian 26.14, Mixe 0.92, Finnish 10.45, English 9.73, Samaritan 1.48, Palestinian 0.78, Yemenite_Jew 1.32, Saxon 0.06, Norman 0.91, Piapoco 0.01. Misfit: 0.000342.

Basque 57.51, Norwegian 26.49, Mixe 0.92, Finnish 5.71, English 6.36, Samaritan 1.32, Palestinian 0.71, Saxon 0.84, Norman 0.84. Misfit: 0.000351.

Basque 57.6, Norwegian 27.66, Mixe 0.92, Finnish 4.76, English 6.99, Samaritan 1.35, Palestinian 0.72. Misfit: 0.000362.

Jordanian 0.29, Basque 57.32, Norwegian 26.81, Mixe 0.94, Finnish 4.86, English 8.50, Samaritan 1.28. Misfit: 0.000374.

Samaritan 1.28, Hungarian 2.71, Basque 59.44, Norwegian 35.72, Mixe 0.85. Misfit: 0.000391.

Jordanian 2.64, Basque 51.98, Norwegian 26.38, Mixe 0.94, Finnish 5.79, English 4.55, Polish 7.72. Misfit: 0.000401.

Jordanian 3.45, Basque 49.98, Norwegian 26.47, Mixe 0.93, Finnish 11.05, English 8.11. Misfit: 0.000414.

Jordanian 2.98, Hungarian 0.0, Basque 52.23, Norwegian 44.03, Mixe 0.76. Misfit: 0.000461.

Samaritan 1.32, Hungarian 1.46, Basque 60.06, Norwegian 37.16. Misfit: 0.000463.

Samaritan 2.03, Palestinian 0.87, Yemenite_Jew 6.92, Erfurt_ME 0.7, Tarrega 0.0, Norwegian 27.35, Finnish 20.66, Norman 1.1, Saxon 0.0, Polish 5.66, English 33.34, Mixe 0.87, Surui 0.17, Onge 0.32. Misfit: 0.000505.

English 16.95, Hungarian 4.24, Basque 53.67, Polish 23.94, Mixe 1.2. Misfit: 0.000609.

English 17.16, Hungarian 4.29, Basque 54.32, Polish 24.23, Tarrega 0.0. Misfit: 0.000760.

French 0.0, English 38.76, Hungarian 15.3, Basque 45.95, Bergamo 0.0. Misfit: 0.001025.

French 21.9, English 74.62, Yemenite_Jew 2.32, Sardinian 0.0, Mixe 1.16. Misfit: 0.001738.

.make_nnls_SGDP_only.R (NNLS für Set nur mit SGDP)

Norwegian 37.87, Basque 15.36, Sardinian 8.76, Jordanian 0.16, Tuscan 4.89, French 16.67, Estonian 16.28. Misfit: 0.000162.

(3) Rscript qpadm_ureurope.R

Set mit mittelalterlichen Samples und ausgewählten Kontrollgruppen: 1272 variants and 65 people pass filters and QC. Total genotyping rate is 0.479519. 34556692 variants removed due to missing genotype data (--geno). Qpadm nicht möglich.

Set mit modernen Samples (nur SGDP): qpadm_modern_power.bed has 346 samples and 138004 SNPs. Kontrollgruppen: "Mbuti", "Papuan", "Australian", "Han", "Yoruba", "Yadava", "Bougainville", "Khomani_San", "Eskimo_Sireniki".

target	left	weight	se	z
[SampleName]	Sardinian	0.588	0.275	2.13
[SampleName]	Russian	0.412	0.325	1.27
[SampleName]	Karitiana	0.00000879	0.0521	0.000169

target	left	weight	se	z
[SampleName]	Sardinian	0.502	0.253	1.98
[SampleName]	Norwegian	0.478	0.278	1.72
[SampleName]	Karitiana	0.0202	0.0291	0.695

target	left	weight	se	z
[SampleName]	Sardinian	0.482	0.255	1.98
[SampleName]	Norwegian	0.490	0.279	1.72
[SampleName]	Karitiana	0.0166	0.0314	0.695
[SampleName]	Onge	0.0112	0.0345	0.324

target	left	weight	se	z
[SampleName]	Spanish	0.965	0.0160	60.4
[SampleName]	Karitiana	0.0349	0.0160	2.19

target	left	weight	se	z
[SampleName]	Basque	0.969	0.0160	60.7
[SampleName]	Karitiana	0.0313	0.0160	1.96

target	left	weight	se	z
[SampleName]	French	0.982	0.0249	39.5
[SampleName]	Mozabite	0.0177	0.0249	0.711

target	left	weight	se	z
[SampleName]	French	0.976	0.0402	24.3
[SampleName]	Mozabite	0.0205	0.0284	0.724
[SampleName]	Mixe	0.00316	0.0179	0.117

target	left	weight	se	z
[SampleName]	Hungarian	0.997	0.0446	22.4
[SampleName]	Mozabite	0.0278	0.0318	0.0874
[SampleName]	Mixe	0.000423	0.0193	0.0219

P-Wert: Null. No genetic linkage map found. Defining blocks by base pair distance of 2e+06.

(4) PCA 25 header tabs

(a) plink1.9 --bfile panel_plus_me --pca 25 header tabs --out my_real_pca_results --allow-no-sex (Set: Medieval Samples plus MySample)

Total genotyping rate is 0.322968. 1141987 variants and 34 people pass filters and QC. Excluding 26919 variants on non-autosomes from relationship matrix calc.

Rscript make_averages.R

SampleName_MA, 0.012252,-0.022156,0.006345,-0.004774,0.001434,-0.002313,-0.000648,0.010925,-0.004162,-0.010324,0.005016,-0.001093,-0.007692,0.002848,0.001599,0.008114,-0.009925,-0.005543,0.008777,0.069642,0.017809,-0.099580,-0.124251,-0.062746,0.073447 Germany_Anderten_Saxon_Medieval,-0.142740,-0.082505,-0.099105,0.090542,0.132369,-0.026463,-0.090423,0.061225,0.048356,-0.097548,0.045496,-0.001004,-0.030863,-0.012113,-0.007756,0.040455,-0.008269,-0.009459,0.012084,0.101406,-0.008390,-0.011636,0.074725,-0.000689,-0.023937 Germany_Erfurt_ME,0.068268,0.340139,0.084590,0.038703,0.003066,0.016601,-0.005861,0.017579,0.049601,0.098238,0.007752,0.085287,-0.013794,0.021761,0.006160,0.046365,-0.012892,0.007079,0.013755,0.134144,-0.044288,-0.010828,0.056863,-0.007005,0.029035 Ireland_Kilteasheen_AngloSaxon_EMedieval_Norman,0.072419,-0.137567,0.055262,-0.111032,-0.110281,0.018587,0.079725,-0.039610,-0.070872,0.030232,-0.046628,-0.036209,0.030694,0.006690,0.007323,-0.043460,0.007949,0.002797,0.003430,0.120384,-0.021406,-0.005639,0.064318,-0.008693,0.006592 Tarrega,0.013411,0.022579,-0.012338,0.011691,-0.008082,-0.002825,0.002175,-0.016558,-0.000205,0.002172,0.003334,-0.004771,0.002096,-0.006470,-0.000654,-0.014175,0.005745,0.002118,-0.021479,-0.174663,0.033728,0.022678,-0.112451,0.018601,-0.013007

(b) plink1.9 --bfile final_dataset --pca 25 header tabs --out my_real_pca_results2 --allow-no-sex (Set: Modern SGDP-Samples plus MySample)

Total genotyping rate is 0.998312. 139193 variants and 346 people pass filters and QC.

SampleName_SGDP, -0.015913,0.088097,-0.005700,-0.007694,0.011497,0.048446,0.031258,-0.055418,-0.020579,0.088388,-0.021551,-0.023231,-0.009127,0.033999,0.009645,0.003942,-0.006740,-0.029179,-0.000699,0.025985,0.018730,0.008409,-0.038073,-0.016876,-0.015259

Complete file: my_g25_population_averages2.txt

plink1.9 --bfile final_dataset_geno --pca 25 header tabs --out my_real_pca_results4 --allow-no-sex (SGDP-Set with Maf and Geno Filters and LD Pruning)

Total genotyping rate is 0.999319. 137857 variants and 346 people pass filters and QC.

SampleName_SGDP_Geno,-0.015659,0.088360,-0.005438,-0.007221,0.011930,0.049412,0.030919,-0.055656,-0.022932,0.087214,-0.019714,0.024844,0.008221,-0.033015,-0.009715,-0.001735,-0.007833,-0.027229,0.002162,0.024636,-0.018539,0.000132,-0.028678,0.012446,-0.027017

Complete file: my_g25_population_averages4.txt

(c) plink1.9 --bfile final_admixture_denser --pca 25 header tabs --out my_real_pca_results3 --allow-no-sex (Set: Modern SGDP-Samples plus medival samples plus MySample)

Total genotyping rate is 0.958439. 79604 variants and 379 people pass filters and QC.

SampleName_SGDP_MA, -0.016276,0.075704,0.005189,-0.007520,0.005177,0.005603,-0.046274,0.015661,0.057733,-0.001577,0.007036,0.011055,-0.017389,0.041176,-0.018521,-0.007981,-0.004719,-0.005910,-0.003695,-0.003569,0.011679,-0.011557,0.012994,0.003994,0.000098 Albanian,-0.015199,0.076580,0.001178,0.004560,-0.006252,-0.023197,-0.031257,-0.007370,0.003151,-0.003587,-0.010866,-0.031989,-0.004415,-0.016445,0.011929,-0.007536,0.012262,0.012174,0.001873,0.001149,-0.009269,0.004767,0.001694,0.013114,0.004060 Basque,-0.014950,0.078500,0.000016,-0.000535,0.007710,0.008912,-0.008551,0.002066,0.029657,-0.012857,-0.008562,-0.025930,-0.009925,-0.006924,-0.011514,-0.012875,0.007442,0.006262,-0.009021,0.004265,0.001077,-0.003578,0.009308,0.016698,-0.000762 BedouinB,-0.002935,0.067821,-0.002099,0.008964,-0.018623,-0.009370,-0.030390,0.026320,-0.007104,0.014497,-0.003580,-0.012812,-0.038892,-0.052886,0.094367,-0.010641,0.015136,0.034250,-0.010402,-0.007951,-0.005175,0.023031,0.012793,0.012879,-0.003349 Bergamo,-0.014936,0.077780,0.000582,0.000391,0.020080,-0.007029,-0.014642,0.002268,0.015741,-0.007935,-0.021645,-0.028783,-0.011357,-0.019521,0.001543,-0.008270,0.009665,0.003602,-0.006316,0.008514,-0.003903,0.004627,-0.003109,0.007064,0.014141 Brahmin,-0.019797,0.026604,-0.011188,0.014283,0.019007,0.027972,0.004369,-0.043481,-0.105769,0.012098,0.024059,0.065105,0.010738,0.023772,-0.016252,0.011104,-0.001923,-0.000899,0.004221,0.003526,0.004327,-0.005361,0.009284,-0.010660,-0.003941 Brahui,-0.014591,0.047348,-0.005638,0.003476,0.007852,0.006663,0.009967,-0.030499,-0.061624,0.016648,0.019042,0.036536,-0.006545,0.007562,0.002184,0.013590,0.001518,-0.002772,0.001495,-0.003567,-0.000243,0.002104,0.005388,-0.002699,-0.003848 Bulgarian,-0.014916,0.073797,0.000721,0.001196,0.020973,0.005531,-0.029760,-0.004836,0.011779,0.006200,-0.014381,-0.014584,0.006332,-0.027993,0.001931,0.002187,0.003843,-0.005234,0.004341,-0.002078,-0.005609,-0.006317,0.004174,0.001596,-0.001624 Crete,-0.012771,0.069972,-0.000626,0.002816,0.027296,0.032665,-0.053743,0.014927,0.018426,0.008132,-0.008805,0.016087,-0.018852,-0.019145,0.038131,-0.000776,0.014632,0.012656,-0.008692,-0.007784,-0.004814,-0.000191,0.002277,0.013046,-0.000325 Czech,-0.018636,0.073876,0.002905,-0.004687,0.005645,-0.007034,-0.010693,-0.025691,0.026876,0.042337,-0.018459,-0.021440,0.016958,-0.007353,-0.026406,0.001172,0.014132,-0.002008,0.005165,0.009346,0.006160,-0.000030,0.004479,0.009632,0.008663 Druze,-0.009102,0.069507,-0.004036,0.004206,-0.000318,0.001514,-0.022218,0.002682,-0.003807,0.008739,0.008143,0.021964,-0.012775,-0.050468,0.045896,0.007290,0.021025,0.018354,-0.005112,-0.011807,-0.000276,0.001301,0.004393,0.004139,0.009898 English,-0.016339,0.075756,0.001080,-0.003505,0.027429,0.044720,-0.026887,-0.010870,0.018062,0.000424,-0.031917,-0.046836,0.005086,-0.003293,-0.019405,-0.010212,-0.002674,-0.009846,-0.005883,0.006576,-0.003033,0.000843,-0.004857,0.006463,-0.000940 Estonian,-0.019234,0.067353,0.005132,-0.005990,0.054609,0.042970,-0.034459,-0.006426,0.045774,-0.007933,0.002631,0.003867,0.005914,0.016486,-0.034649,0.005371,0.008432,0.000237,-0.011882,-0.012502,0.000765,-0.020105,0.012018,0.010227,0.006570 Finnish,-0.020102,0.065560,0.006825,-0.003795,0.024197,-0.001893,-0.017961,-0.027719,0.024304,0.000990,-0.000359,-0.047484,0.012166,0.010434,-0.037891,0.003519,0.002350,0.003610,0.002973,0.000745,0.001211,-0.004506,0.001109,0.004588,0.007341 French,-0.016758,0.075459,0.001658,0.000162,-0.006904,0.036256,-0.018422,-0.019552,0.013209,-0.007871,-0.004350,-0.055096,0.009417,-0.013861,-0.015122,-0.012803,-0.001441,-0.007155,0.004421,0.003489,0.002139,-0.006095,-0.002753,0.007222,-0.002318 Georgian,-0.013059,0.071584,-0.001256,0.003295,-0.016067,-0.020584,-0.024466,0.001829,-0.007092,0.027871,-0.003433,0.034673,-0.017813,-0.011206,0.028607,0.019925,0.016049,0.016265,-0.005113,0.009622,-0.010807,0.009020,0.013153,0.005299,0.016197 Germany_Anderten_Saxon_Medieval,-0.016525,0.079363,0.003261,-0.007812,0.031211,0.014800,0.017035,-0.002174,0.110448,-0.037401,0.014738,0.016936,0.153361,0.129773,-0.015670,-0.008379,0.124392,-0.040079,0.082432,0.051790,-0.019848,0.030932,-0.038212,0.004573,0.007919 Germany_Erfurt_ME,-0.010612,0.079011,0.001467,0.005380,0.033474,-0.073412,0.000936,0.029474,0.044283,0.002755,-0.029635,0.075384,-0.052822,-0.118780,0.110948,0.003865,-0.134513,-0.183685,0.064757,0.008099,0.048085,-0.021455,-0.029521,-0.045174,-0.089514 Greek,-0.013109,0.074848,-0.001783,0.004177,-0.018035,0.022481,-0.002121,0.013217,0.004663,0.004996,-0.017576,-0.007484,-0.030701,-0.002879,0.022301,0.001774,0.012908,0.000515,0.002133,0.003424,0.003215,0.004872,0.007235,0.016202,-0.001366 Hungarian,-0.016692,0.074560,0.005084,-0.002793,0.016086,-0.010337,-0.012155,-0.003463,0.031239,-0.025318,0.007096,-0.021871,-0.007336,0.002572,-0.024589,0.000763,0.010921,0.000044,-0.003403,-0.001599,0.002365,-0.003504,0.005950,0.006984,0.002475 Icelandic,-0.017099,0.072349,0.003652,-0.005432,0.006611,0.026700,-0.020489,-0.038385,0.039899,0.064834,-0.001037,-0.024859,0.009490,0.009405,-0.015863,-0.003014,-0.000864,-0.008291,-0.005890,0.005475,-0.005972,-0.009985,-0.000234,0.009774,0.003097 Iranian,-0.012666,0.058861,-0.002409,0.002993,0.041130,0.022569,-0.015924,-0.000184,-0.023040,0.017960,-0.019311,0.032362,-0.028332,-0.002674,0.037386,0.002559,0.014528,0.012255,-0.012358,-0.007292,0.008541,0.000235,-0.000758,0.008454,-0.010313 Iraqi_Jew,-0.010044,0.070338,-0.003135,0.006434,-0.001601,0.019448,-0.000459,0.015947,-0.016898,0.008504,-0.032102,0.015525,-0.021836,-0.036796,0.051666,0.001784,0.019443,0.018943,-0.010711,-0.004466,-0.002952,0.010693,0.009835,0.020846,0.002882 Iraqw,0.058782,0.008420,0.004352,0.002786,-0.009514,-0.016254,-0.027658,0.020733,-0.007533,0.022154,0.028234,0.004877,0.000680,-0.059115,0.058848,-0.000233,0.029526,0.053269,-0.022132,-0.010213,-0.034115,0.028200,0.000821,0.012449,0.033952 Ireland_Kilteasheen_AngloSaxon_EMedieval_Norman,-0.017621,0.078482,0.004740,-0.007337,0.027128,0.007564,-0.035776,-0.038222,0.071716,0.033016,0.009513,-0.060353,0.031073,0.018152,-0.156442,-0.109105,-0.136905,0.041023,-0.074592,-0.033360,0.003035,-0.026838,0.010066,-0.026583,0.022013 Jordanian,-0.004198,0.065282,-0.001260,0.006461,0.001433,0.004599,-0.002901,0.013169,-0.003568,0.017222,0.000753,0.010986,-0.023144,-0.049220,0.047195,0.002431,0.016405,0.018119,-0.001788,-0.005233,-0.004672,0.007809,0.008641,-0.002703,0.002465 Kashmiri_Pandit,-0.020622,0.035245,-0.006235,0.012111,0.002701,0.021355,-0.005425,-0.018113,-0.080489,-0.028265,0.007989,0.046728,-0.001982,0.023456,-0.023396,0.026374,0.002155,-0.002743,-0.000688,-0.002313,-0.003228,-0.002204,0.010821,-0.009733,0.003062 Mixe,-0.052949,-0.053420,0.089835,-0.141254,0.006343,0.013008,0.011951,-0.002227,-0.007223,0.003016,0.003855,0.017816,0.000546,-0.018167,0.015565,-0.038715,-0.002037,0.008394,-0.010351,-0.002560,0.001048,-0.005641,-0.001683,-0.002390,0.003035 Mozabite,0.018801,0.050486,0.001276,0.005660,0.009344,0.040170,0.002527,0.048419,0.006319,-0.014937,-0.005668,-0.039687,-0.027879,-0.027417,0.052339,-0.009227,0.018413,0.017290,-0.007497,-0.008507,-0.005865,0.015046,0.008536,0.016576,-0.005290 North_Ossetian,-0.017208,0.059504,0.001114,0.007391,0.022391,0.036234,-0.038280,-0.006025,-0.003329,-0.002455,0.006273,0.029860,-0.002006,-0.033784,0.012385,0.021147,0.013936,0.008723,-0.001059,-0.000666,0.006345,-0.005511,-0.002033,0.005379,0.013588 Norwegian,-0.018781,0.071701,0.002930,-0.007282,0.048006,0.042518,-0.000260,0.003912,0.053432,-0.019310,-0.011043,0.012444,0.013368,0.005015,-0.040718,0.003364,0.006579,-0.000737,-0.009475,-0.012594,-0.008923,0.000635,0.003256,-0.005402,0.002491 Onge,-0.025649,-0.027405,-0.035685,0.029254,-0.022253,0.038971,-0.007051,-0.015902,-0.110772,-0.013045,0.004640,0.040781,0.028264,0.015092,-0.035546,-0.041037,-0.034965,-0.017242,0.012316,0.014529,-0.010932,0.002418,-0.034866,0.018451,0.022187 Orcadian,-0.016495,0.073034,0.005551,-0.004218,0.016260,-0.006059,-0.015983,-0.033439,0.034618,0.049139,-0.001236,-0.030428,0.004240,0.003402,-0.019301,-0.007436,-0.001390,-0.004967,-0.005736,0.006615,-0.002592,-0.008721,0.000825,0.007677,-0.002812 Palestinian,-0.003501,0.065766,-0.001895,0.005781,0.007694,0.018487,-0.014041,0.017460,-0.011414,-0.019282,0.008227,-0.008780,-0.030814,-0.043612,0.050576,-0.003538,0.018385,0.019474,-0.003530,-0.003865,-0.000228,0.003551,0.002087,0.011458,0.004477 Pathan,-0.019504,0.040274,-0.004406,0.006704,0.045122,0.005149,-0.003775,-0.026413,-0.083074,0.003653,-0.002982,0.053382,-0.002420,0.021018,-0.010320,0.013722,0.007945,0.012815,-0.002329,0.003567,0.008603,-0.006551,0.001165,-0.005672,0.000977 Polish,-0.016105,0.071829,0.000014,-0.005458,0.029991,0.051914,0.018508,-0.026145,0.047706,0.005014,0.012777,-0.015375,-0.003168,-0.013001,-0.019062,-0.008004,0.001246,0.000229,0.000764,-0.014798,0.014451,-0.013887,0.008099,-0.001573,-0.004309 Russian,-0.020278,0.059209,0.007310,-0.002512,0.023197,0.033091,-0.028053,-0.015699,0.051481,0.030464,0.016180,-0.004507,-0.004040,0.027216,-0.020450,0.014848,0.010223,0.003092,-0.005026,-0.004324,0.000046,-0.012210,0.008294,0.005947,-0.002468 Saami,-0.027024,0.038785,0.013657,0.000778,0.043738,0.007185,-0.014325,-0.023453,0.036325,0.020237,-0.025063,-0.041840,0.011590,0.013409,-0.045560,0.049861,0.007648,0.005859,-0.000320,0.000892,-0.002296,-0.000019,0.001711,0.001172,0.012394 Saharawi,0.016362,0.052977,0.001210,0.005764,0.000972,-0.003217,-0.000395,0.029994,-0.004657,0.011449,-0.001637,-0.031152,-0.009247,-0.062385,0.044765,-0.011841,0.014710,0.025994,-0.004300,-0.009047,-0.006459,0.007781,-0.000256,0.008164,0.003377 Samaritan,-0.008066,0.073436,-0.004027,0.004744,-0.014452,-0.003974,-0.021538,0.026418,-0.005319,-0.014375,0.005614,0.038257,-0.007229,-0.071503,0.043863,-0.000508,0.029063,0.032990,0.003952,-0.017030,0.000599,0.011876,0.004604,0.006659,0.020840 Sardinian,-0.012364,0.081178,0.000089,0.003422,-0.007555,-0.000659,-0.020029,0.009477,0.042136,0.008737,0.007851,-0.019841,-0.022455,-0.021079,0.023876,-0.017774,0.010339,0.001546,-0.001077,-0.002351,-0.001800,-0.005359,0.005867,0.009948,-0.005271 Spanish,-0.013705,0.075840,-0.000329,-0.001198,0.000818,0.022540,-0.008172,-0.000409,0.037316,0.021840,-0.011421,-0.011546,-0.004664,-0.021449,0.003877,-0.009414,-0.005574,0.003188,-0.001741,0.001193,-0.001416,0.001372,0.008017,0.015119,0.004631 Surui,-0.055441,-0.055131,0.094453,-0.153913,-0.002917,-0.006777,-0.007763,0.004793,-0.026065,0.010484,-0.009418,0.002814,0.002086,-0.003450,0.027904,-0.071553,0.002835,0.002796,-0.006068,-0.002379,-0.007259,0.009072,0.002655,-0.001896,-0.006353 Tarrega,-0.007387,0.074163,-0.003905,-0.001988,-0.145148,-0.066807,0.108173,0.067858,-0.007200,-0.077658,-0.034061,-0.009151,-0.020414,0.022753,-0.019734,0.005523,0.002538,0.000933,0.002346,0.002651,0.005808,0.002125,0.003406,-0.001337,-0.002610 Turkish,-0.014515,0.063658,0.000385,0.007900,0.004199,0.023491,-0.009870,0.009815,-0.007158,0.012009,-0.022670,-0.016082,-0.033005,0.000517,0.044518,0.006404,0.014294,0.018691,-0.006856,0.003140,-0.000340,0.012079,0.004154,0.004331,-0.008419 Tuscan,-0.014359,0.076923,0.001994,0.001108,-0.001972,-0.018374,-0.003314,0.008621,0.016937,-0.016418,-0.002526,-0.027650,-0.027509,-0.003381,0.021751,-0.006591,0.014085,0.005920,0.001082,-0.006753,-0.000514,-0.008412,0.002969,-0.000020,-0.007469 Yemenite_Jew,-0.002423,0.068395,-0.003672,0.007996,0.005769,-0.024530,-0.015435,0.014900,-0.005950,0.027691,-0.000407,0.014787,-0.039317,-0.054859,0.078941,-0.006526,0.035655,0.037343,-0.009281,0.000444,-0.006948,0.021334,0.005787,0.015622,0.002842

Complete file: my_g25_population_averages3.txt

Abgleich mit simulierten G25 Koordinaten, skaliert nach Eurogenes-Standard (keine Vergleichsgrundlage):

sample_simulated_g25_scaled,0.127118,0.138078,0.061664,0.036808,0.042363,0.015958,0.004988,0.003535,0.011501,0.008269,-0.005335,0.004502,-0.008623,0.002375,0.011562,0.008136,-0.001418,-0.001284,0.002660,0.003101,0.009321,-0.002190,0.002085,0.007818,0.005323

(d) vahaduo.github.io/vahaduo (Distances Selected Samples SGDP + MA)

Distance to:	SampleName
0.07401210	Russian
0.08050403	Hungarian
0.08381535	Estonian
0.08612183	Basque
0.09404699	Sardinian
0.09547174	Spanish
0.10023862	Norwegian
0.10322525	Tuscan
0.10355739	Finnish
0.10370240	Bulgarian
0.10439516	Orcadian
0.10681300	Bergamo
0.10781833	Greek
0.10789566	Crete
0.11127521	Czech
0.11196990	Icelandic
0.11356206	English
0.11424907	Albanian
0.11432787	Polish
0.11830513	French
0.12274385	North_Ossetian
0.12553693	Georgian
0.12671697	Turkish
0.13056338	Saami
0.13344145	Iranian
0.14043744	Druze
0.14463085	Jordanian
0.14525401	Palestinian
0.15256101	Iraqi_Jew
0.15615037	Brahui
0.15637419	Mozabite
0.16496939	Samaritan
0.16505226	Saharawi
0.16929639	Kashmiri_Pandit
0.17458328	Pathan
0.17827562	Yemenite_Jew
0.18046981	BedouinB
0.19854582	sample_simulated_g25_scaled
0.20493563	Brahmin
0.20779100	Iraqw
0.23880109	Onge
0.24031188	Mixe
0.25894328	Surui
0.26033090	Tarrega
0.26354348	Ireland_Kilteasheen_AngloSaxon_EMedieval_Norman
0.28297988	Germany_Anderten_Saxon_Medieval
0.35505566	Germany_Erfurt_ME

(e) vahaduo.github.io/vahaduo (Distances Complete SGDP+MA Samples)

Distance to:	SampleName
0.07401210	Russian
0.08050403	Hungarian
0.08381535	Estonian
0.08612183	Basque
0.09404699	Sardinian
0.09547174	Spanish
0.09931708	Maori
0.10023862	Norwegian
0.10322525	Tuscan
0.10355739	Finnish
0.10370240	Bulgarian
0.10439516	Orcadian
0.10681300	Bergamo
0.10731372	Lezgin
0.10781833	Greek
0.10789566	Crete
0.11127521	Czech
0.11196990	Icelandic
0.11356206	English
0.11397229	Adygei
0.11424907	Albanian
0.11432787	Polish
0.11830513	French
0.12274385	North_Ossetian
0.12553693	Georgian
0.12671697	Turkish
0.12835549	Tajik
0.13056338	Saami
0.13131029	Abkhasian
0.13344145	Iranian
0.13701146	Chechen
0.13848339	Uygur
0.14043744	Druze
0.14045034	Burusho
0.14308799	Armenian
0.14463085	Jordanian
0.14525401	Palestinian
0.14597358	Hazara
0.15256101	Iraqi_Jew
0.15259802	Tubalar
0.15520251	Tlingit
0.15615037	Brahui
0.15637419	Mozabite
0.16387500	Mansi
0.16496939	Samaritan
0.16505226	Saharawi
0.16566232	Kyrgyz
0.16869217	Cree
0.16905383	Chukchi
0.16929639	Kashmiri_Pandit

(f) vahaduo.github.io/vahaduo (Single Mode Selected SGDP+MA Samples)

Target: SampleName Distance: 5.5720% / 0.05572012
40.8	Russian
18.4	Crete
13.6	Estonian
9.8	Tarrega
8.4	Ireland_Kilteasheen_AngloSaxon_EMedieval_Norman
5.0	Germany_Anderten_Saxon_Medieval
4.0	Germany_Erfurt_ME

(g) vahaduo.github.io/vahaduo (Multi Mode Complete SGDP+MA Samples, without Maori/Miao)

Target	Distance	Crete	Estonian	Saxon_Medieval	Erfurt_ME	Ireland_Kilteasheen_Norman	Lezgin	Mixtec	Russian	Tarrega
SampleName	0.05571388	18.0	13.4	5.0	4.0	8.6	1.0	0.2	40.2	9.6

(h) vahaduo.github.io/vahaduo (Distances Set of Complete SGDP Samples without MA Samples, final_dataset)

Distance to:	SampleName
0.05861064	Icelandic
0.06179774	English
0.06321238	Hungarian
0.07021550	Norwegian
0.07043423	Orcadian
0.07621494	French
0.08323196	Polish
0.08602913	Czech
0.09331285	Finnish
0.09804208	Estonian
0.10152774	Russian
0.12973190	Bulgarian
0.13274871	Bergamo
0.13865895	Tuscan
0.13951420	Spanish
0.14088675	Basque
0.15796106	Albanian
0.17836277	Maori
0.19260491	Crete
0.19528783	Uygur
0.19996488	Greek
0.20520075	Hazara
0.20981267	Kyrgyz
0.21668757	Chukchi
0.21815570	Tubalar
[...]
0.24338697	Turkish
0.24381916	Sindhi
0.24427359	Saami
0.24491521	Palestinian
0.24858766	Lezgin
[...]
0.25732897	Iranian
0.25746132	Armenian
0.26026554	North_Ossetian
0.26052663	Mixtec
0.26086147	Iraqi_Jew
[...]
0.26600958	Sardinian
0.29903512	Yemenite_Jew
0.31932877	Jordanian
0.37179271	Samaritan
0.43864190	Saharawi

Set SGDP without MA Samples (final_dataset_geno with Maf and Geno Filters and LD Pruning)

Distance to:	SampleName
0.05634010	Icelandic
0.06060490	English
0.06303751	Hungarian
0.06800178	Orcadian
0.07342989	Norwegian
0.07497899	Polish
0.07603280	French
0.08548837	Czech
0.09662956	Finnish
0.09993134	Estonian
0.10287890	Russian
0.12916700	Bulgarian
0.12990495	Bergamo
0.13653458	Tuscan
0.13819052	Spanish

(i) vahaduo.github.io/vahaduo (Single/Multi Mode Runs Set of Complete SGDP Samples without Australian and without MA Samples, final_dataset)

Run #1 (Single Mode)

Target: SampleName Distance: 2.2918% / 0.02291798
22.0	Orcadian
19.8	Finnish
19.4	Estonian
14.8	Norwegian
11.2	Sardinian
6.0	Basque
4.4	BedouinB
2.2	Surui
0.2	French

Run #2 (Multi Mode, Add Dist. Col. = No)

Target	Distance	Basque	BedouinB	Estonian	Finnish	French	Norwegian	Orcadian	Sardinian	Surui
SampleName	0.02291345	4.8	4.4	19.4	19.0	0.8	15.4	22.6	11.6	2.0

Run #3 (Multi Mode, Add Dist. Col. = 0.25x, Recalculate = No)

Target	Distance	BedouinB	Estonian	Finnish	French	Hungarian	Norwegian	Orcadian	Sardinian
SampleName	0.02779523	3.4	12.2	0.8	24.0	12.2	23.8	22.4	1.2

Die verschiedenen Monte-Carlo-Simulationen variieren leicht. Run #4 mit final_dataset_geno ohne Australian / Bantu, Multi Mode, Add Dist. Col. = 0.25x, Recalculate = No, Run #5 with Add Dist. Col. = No.

(5) Vergleich NNLS - PCA (Urgroßeltern)

Method	4x "German"			1x "English-American"	1x "Acadian-American"			2x "Ashkenazic-Sephardic"						Quality
NNLS SGDP+MA K 64	Norwegian	Finnish	Saxon	English	Norman	Mixe	Surui	Basque	Samaritan	Palestinian	Yemenite_Jew	Polish	Onge	Misfit
	26.39	9.39	0.08	8.47	0.89	0.91	0.22	49.7	1.43	0.76	1.08	0.22	0.44	0.000316
NNLS SGDP K 64 (final_dataset_geno)	Norwegian				French			Basque	Sardinian	Tuscan	Jordanian	Estonian		Misfit
	37.87				16.67			15.36	8.76	4.89	0.16	16.28		0.000162
PCA 25 SGDP+MA	Russian		Saxon	Norman		Mixtec		Crete	Tarrega		Erfurt_ME	Estonian	Lezgin	Distance
	40.2		5.0	8.6		0.2		18.0	9.6		4.0	13.4	1.0	0.05571388
PCA 25 SGDP Run #2 (final_dataset)	Norwegian	Finnish	Orcadian		French	Surui		Sardinian	Basque	BedouinB		Estonian		Distance
	15.4	19.0	22.6		0.8	2.0		11.6	4.8	4.4		19.4		0.02291345
PCA 25 SGDP Run #3 (ADR 0.25, final_dataset)	Norwegian	Finnish	Orcadian		French			Sardinian	Hungarian	BedouinB		Estonian		Distance
	23.8	0.8	22.4		24.0			1.2	12.2	3.4		12.2		0.02779523
PCA 25 SGDP Run #4 (ADR 0.25, final_dataset_geno)	Norwegian	Icelandish	Orcadian		French	Surui		Sardinian	Hungarian	BedouinB	Czech	Estonian		Distance
	23.4	17.4	17.4		14.0	0.2		3.6	16.6	2.4	0.4	4.6		0.02865856
PCA 25 SGDP Run #5 (final_dataset_geno)	Norwegian	Finnish	Icelandish	Orcadian		Surui		Sardinian	Hungarian	BedouinB		Estonian		Distance
	20.4	12.0	5.2	20.4		2.4		13.6	4.6	3.2		18.2		0.02431329

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