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yamnaya samara geoksyur pass 2

misnomer001
Feb 7th, 2020
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  1. allsnps: YES
  2. ## qpAdm version: 1000
  3. seed: 1874476475
  4. read 1073741824 bytes
  5. read 1324255962 bytes
  6. packed geno read OK
  7. end of inpack
  8.  
  9. left pops:
  10. Russia_Yamnaya_Samara
  11. EEHG
  12. Georgia_Kotias.SG
  13. Ukraine_Globular_Amphora
  14. Geoksyur_EN
  15.  
  16. right pops:
  17. Russia_MA1_HG
  18. Italy_Villabruna
  19. Russia_Kostenki14
  20. Luxembourg_Loschbour
  21. Anatolia_N
  22. Czech_Vestonice16
  23. Morocco_Iberomaurusian
  24. Russia_Shamanka_EN.SG
  25. Georgia_Satsurblia.SG
  26. Ganj_Dareh_N
  27. Onge.DG
  28. SE_Iberia_MLN
  29. PPN
  30.  
  31. 0 Russia_Yamnaya_Samara 8
  32. 1 EEHG 5
  33. 2 Georgia_Kotias.SG 1
  34. 3 Ukraine_Globular_Amphora 3
  35. 4 Geoksyur_EN 21
  36. 5 Russia_MA1_HG 1
  37. 6 Italy_Villabruna 1
  38. 7 Russia_Kostenki14 1
  39. 8 Luxembourg_Loschbour 1
  40. 9 Anatolia_N 23
  41. 10 Czech_Vestonice16 1
  42. 11 Morocco_Iberomaurusian 6
  43. 12 Russia_Shamanka_EN.SG 10
  44. 13 Georgia_Satsurblia.SG 1
  45. 14 Ganj_Dareh_N 8
  46. 15 Onge.DG 2
  47. 16 SE_Iberia_MLN 14
  48. 17 PPN 8
  49. jackknife block size: 0.050
  50. snps: 1150468 indivs: 115
  51. number of blocks for block jackknife: 713
  52. ## ncols: 1150468
  53. coverage: Russia_Yamnaya_Samara 1092113
  54. coverage: EEHG 1052093
  55. coverage: Georgia_Kotias.SG 1149097
  56. coverage: Ukraine_Globular_Amphora 1036892
  57. coverage: Geoksyur_EN 1018577
  58. coverage: Russia_MA1_HG 805960
  59. coverage: Italy_Villabruna 883779
  60. coverage: Russia_Kostenki14 1068326
  61. coverage: Luxembourg_Loschbour 460892
  62. coverage: Anatolia_N 1136560
  63. coverage: Czech_Vestonice16 732091
  64. coverage: Morocco_Iberomaurusian 1101342
  65. coverage: Russia_Shamanka_EN.SG 1149998
  66. coverage: Georgia_Satsurblia.SG 801311
  67. coverage: Ganj_Dareh_N 1057358
  68. coverage: Onge.DG 1120748
  69. coverage: SE_Iberia_MLN 985553
  70. coverage: PPN 835499
  71. dof (jackknife): 613.831
  72. numsnps used: 1150468
  73. codimension 1
  74. f4info:
  75. f4rank: 3 dof: 9 chisq: 13.552 tail: 0.139172097 dofdiff: 11 chisqdiff: -13.552 taildiff: 1
  76. B:
  77. scale 1.000 1.000 1.000
  78. Italy_Villabruna 0.660 1.609 1.188
  79. Russia_Kostenki14 0.774 0.298 0.082
  80. Luxembourg_Loschbour 0.341 0.931 0.818
  81. Anatolia_N 1.490 0.730 0.116
  82. Czech_Vestonice16 0.689 0.521 -0.005
  83. Morocco_Iberomaurusian 1.147 0.097 -0.115
  84. Russia_Shamanka_EN.SG 0.610 -0.371 0.017
  85. Georgia_Satsurblia.SG 0.954 -1.640 1.663
  86. Ganj_Dareh_N 1.207 -1.850 -2.545
  87. Onge.DG 0.815 -0.468 -0.311
  88. SE_Iberia_MLN 1.308 1.006 0.510
  89. PPN 1.314 0.403 -0.534
  90. A:
  91. scale 268.387 597.018 1451.975
  92. EEHG -1.017 0.507 -0.226
  93. Georgia_Kotias.SG 0.887 -1.331 1.581
  94. Ukraine_Globular_Amphora 1.348 1.268 -0.253
  95. Geoksyur_EN 0.601 -0.602 -1.177
  96.  
  97.  
  98. full rank
  99. f4info:
  100. f4rank: 4 dof: 0 chisq: 0.000 tail: 1 dofdiff: 9 chisqdiff: 13.552 taildiff: 0.139172097
  101. B:
  102. scale 266.743 253.965 173.799 353.352
  103. Italy_Villabruna -0.284 0.082 1.197 -0.310
  104. Russia_Kostenki14 -0.730 0.542 0.818 0.515
  105. Luxembourg_Loschbour -0.169 0.007 0.641 -0.299
  106. Anatolia_N -1.340 0.925 1.598 0.935
  107. Czech_Vestonice16 -0.507 0.378 0.851 0.438
  108. Morocco_Iberomaurusian -1.115 0.956 1.074 0.965
  109. Russia_Shamanka_EN.SG -0.661 0.790 0.445 0.685
  110. Georgia_Satsurblia.SG -1.387 2.267 0.219 0.902
  111. Ganj_Dareh_N -1.525 1.420 0.487 2.390
  112. Onge.DG -0.957 0.869 0.571 0.915
  113. SE_Iberia_MLN -1.102 0.719 1.529 0.580
  114. PPN -1.115 0.857 1.382 1.175
  115. A:
  116. scale 2.000 2.000 2.000 2.000
  117. EEHG 2.000 0.000 0.000 0.000
  118. Georgia_Kotias.SG 0.000 2.000 0.000 0.000
  119. Ukraine_Globular_Amphora 0.000 0.000 2.000 0.000
  120. Geoksyur_EN 0.000 0.000 0.000 2.000
  121.  
  122.  
  123. best coefficients: 0.470 0.221 0.129 0.179
  124. Jackknife mean: 0.470662205 0.220861140 0.129044513 0.179432141
  125. std. errors: 0.016 0.026 0.013 0.026
  126.  
  127. error covariance (* 1,000,000)
  128. 260 -100 -102 -59
  129. -100 681 -22 -559
  130. -102 -22 174 -50
  131. -59 -559 -50 667
  132.  
  133.  
  134. summ: Russia_Yamnaya_Samara 4 0.139172 0.471 0.221 0.129 0.179 260 -100 -102 -59 681 ...
  135. -22 -559 174 -50 667
  136.  
  137. fixed pat wt dof chisq tail prob
  138. 0000 0 9 13.552 0.139172 0.470 0.221 0.129 0.179
  139. 0001 1 10 53.903 5.05848e-08 0.481 0.384 0.135 0.000
  140. 0010 1 10 105.506 4.28474e-18 0.544 0.294 0.000 0.161
  141. 0100 1 10 88.141 1.25032e-14 0.504 0.000 0.132 0.364
  142. 1000 1 10 345.753 0 0.000 2.967 0.000 -1.967 infeasible
  143. 0011 2 11 126.312 9.68935e-22 0.542 0.458 0.000 0.000
  144. 0101 2 11 502.294 0 0.784 0.000 0.216 0.000
  145. 0110 2 11 172.414 0 0.592 0.000 0.000 0.408
  146. 1001 2 11 471.446 0 0.000 0.807 0.193 0.000
  147. 1010 2 11 339.838 0 0.000 2.346 0.000 -1.346 infeasible
  148. 1100 2 11 891.407 0 0.000 0.000 0.359 0.641
  149. 0111 3 12 642.022 0 1.000 0.000 0.000 0.000
  150. 1011 3 12 503.913 0 0.000 1.000 0.000 0.000
  151. 1101 3 12 1713.604 0 0.000 0.000 1.000 0.000
  152. 1110 3 12 1328.466 0 0.000 0.000 0.000 1.000
  153. best pat: 0000 0.139172 - -
  154. best pat: 0001 5.05848e-08 chi(nested): 40.351 p-value for nested model: 2.12219e-10
  155. best pat: 0011 9.68935e-22 chi(nested): 72.409 p-value for nested model: 1.74923e-17
  156. best pat: 1011 3.25721e-100 chi(nested): 377.601 p-value for nested model: 4.14263e-84
  157.  
  158. coeffs: 0.470 0.221 0.129 0.179
  159.  
  160. ## dscore:: f_4(Base, Fit, Rbase, right2)
  161. ## genstat:: f_4(Base, Fit, right1, right2)
  162.  
  163. details: EEHG Italy_Villabruna -0.001063 -2.989297
  164. details: Georgia_Kotias.SG Italy_Villabruna 0.000324 0.740463
  165. details: Ukraine_Globular_Amphora Italy_Villabruna 0.006887 19.342365
  166. details: Geoksyur_EN Italy_Villabruna -0.000877 -2.970233
  167. dscore: Italy_Villabruna f4: 0.000305 Z: 1.232003
  168.  
  169. details: EEHG Russia_Kostenki14 -0.002736 -7.376114
  170. details: Georgia_Kotias.SG Russia_Kostenki14 0.002135 4.705892
  171. details: Ukraine_Globular_Amphora Russia_Kostenki14 0.004709 12.622622
  172. details: Geoksyur_EN Russia_Kostenki14 0.001457 4.948276
  173. dscore: Russia_Kostenki14 f4: 0.000055 Z: 0.223355
  174.  
  175. details: EEHG Luxembourg_Loschbour -0.000635 -2.500348
  176. details: Georgia_Kotias.SG Luxembourg_Loschbour 0.000026 0.087374
  177. details: Ukraine_Globular_Amphora Luxembourg_Loschbour 0.003689 14.744960
  178. details: Geoksyur_EN Luxembourg_Loschbour -0.000846 -4.006823
  179. dscore: Luxembourg_Loschbour f4: 0.000033 Z: 0.188426
  180.  
  181. details: EEHG Anatolia_N -0.005024 -16.194811
  182. details: Georgia_Kotias.SG Anatolia_N 0.003642 8.955113
  183. details: Ukraine_Globular_Amphora Anatolia_N 0.009194 28.990136
  184. details: Geoksyur_EN Anatolia_N 0.002647 10.263086
  185. dscore: Anatolia_N f4: 0.000106 Z: 0.474922
  186.  
  187. details: EEHG Czech_Vestonice16 -0.001902 -6.005398
  188. details: Georgia_Kotias.SG Czech_Vestonice16 0.001487 3.804260
  189. details: Ukraine_Globular_Amphora Czech_Vestonice16 0.004896 15.401817
  190. details: Geoksyur_EN Czech_Vestonice16 0.001240 4.773433
  191. dscore: Czech_Vestonice16 f4: 0.000290 Z: 1.280363
  192.  
  193. details: EEHG Morocco_Iberomaurusian -0.004180 -12.799974
  194. details: Georgia_Kotias.SG Morocco_Iberomaurusian 0.003766 8.484087
  195. details: Ukraine_Globular_Amphora Morocco_Iberomaurusian 0.006181 18.713979
  196. details: Geoksyur_EN Morocco_Iberomaurusian 0.002732 9.851729
  197. dscore: Morocco_Iberomaurusian f4: 0.000156 Z: 0.661334
  198.  
  199. details: EEHG Russia_Shamanka_EN.SG -0.002478 -8.185294
  200. details: Georgia_Kotias.SG Russia_Shamanka_EN.SG 0.003110 7.783405
  201. details: Ukraine_Globular_Amphora Russia_Shamanka_EN.SG 0.002560 8.766327
  202. details: Geoksyur_EN Russia_Shamanka_EN.SG 0.001939 7.722025
  203. dscore: Russia_Shamanka_EN.SG f4: 0.000201 Z: 0.959528
  204.  
  205. details: EEHG Georgia_Satsurblia.SG -0.005200 -16.448450
  206. details: Georgia_Kotias.SG Georgia_Satsurblia.SG 0.008925 18.904755
  207. details: Ukraine_Globular_Amphora Georgia_Satsurblia.SG 0.001257 3.888644
  208. details: Geoksyur_EN Georgia_Satsurblia.SG 0.002554 9.285185
  209. dscore: Georgia_Satsurblia.SG f4: 0.000149 Z: 0.631363
  210.  
  211. details: EEHG Ganj_Dareh_N -0.005719 -17.755344
  212. details: Georgia_Kotias.SG Ganj_Dareh_N 0.005591 13.246473
  213. details: Ukraine_Globular_Amphora Ganj_Dareh_N 0.002800 8.761824
  214. details: Geoksyur_EN Ganj_Dareh_N 0.006764 24.916178
  215. dscore: Ganj_Dareh_N f4: 0.000121 Z: 0.534778
  216.  
  217. details: EEHG Onge.DG -0.003589 -10.916325
  218. details: Georgia_Kotias.SG Onge.DG 0.003422 7.694559
  219. details: Ukraine_Globular_Amphora Onge.DG 0.003283 10.046223
  220. details: Geoksyur_EN Onge.DG 0.002590 9.135883
  221. dscore: Onge.DG f4: -0.000043 Z: -0.185751
  222.  
  223. details: EEHG SE_Iberia_MLN -0.004132 -13.597593
  224. details: Georgia_Kotias.SG SE_Iberia_MLN 0.002833 7.248781
  225. details: Ukraine_Globular_Amphora SE_Iberia_MLN 0.008797 27.731273
  226. details: Geoksyur_EN SE_Iberia_MLN 0.001640 6.405369
  227. dscore: SE_Iberia_MLN f4: 0.000115 Z: 0.525649
  228.  
  229. details: EEHG PPN -0.004180 -14.335003
  230. details: Georgia_Kotias.SG PPN 0.003376 8.842375
  231. details: Ukraine_Globular_Amphora PPN 0.007951 25.059194
  232. details: Geoksyur_EN PPN 0.003326 12.468051
  233. dscore: PPN f4: 0.000405 Z: 1.883772
  234.  
  235. gendstat: Russia_MA1_HG Italy_Villabruna 1.232
  236. gendstat: Russia_MA1_HG Russia_Kostenki14 0.223
  237. gendstat: Russia_MA1_HG Luxembourg_Loschbour 0.188
  238. gendstat: Russia_MA1_HG Anatolia_N 0.475
  239. gendstat: Russia_MA1_HG Czech_Vestonice16 1.280
  240. gendstat: Russia_MA1_HG Morocco_Iberomaurusian 0.661
  241. gendstat: Russia_MA1_HG Russia_Shamanka_EN.SG 0.960
  242. gendstat: Russia_MA1_HG Georgia_Satsurblia.SG 0.631
  243. gendstat: Russia_MA1_HG Ganj_Dareh_N 0.535
  244. gendstat: Russia_MA1_HG Onge.DG -0.186
  245. gendstat: Russia_MA1_HG SE_Iberia_MLN 0.526
  246. gendstat: Russia_MA1_HG PPN 1.884
  247. gendstat: Italy_Villabruna Russia_Kostenki14 -1.056
  248. gendstat: Italy_Villabruna Luxembourg_Loschbour -1.269
  249. gendstat: Italy_Villabruna Anatolia_N -1.036
  250. gendstat: Italy_Villabruna Czech_Vestonice16 -0.066
  251. gendstat: Italy_Villabruna Morocco_Iberomaurusian -0.681
  252. gendstat: Italy_Villabruna Russia_Shamanka_EN.SG -0.506
  253. gendstat: Italy_Villabruna Georgia_Satsurblia.SG -0.619
  254. gendstat: Italy_Villabruna Ganj_Dareh_N -0.870
  255. gendstat: Italy_Villabruna Onge.DG -1.534
  256. gendstat: Italy_Villabruna SE_Iberia_MLN -0.985
  257. gendstat: Italy_Villabruna PPN 0.461
  258. gendstat: Russia_Kostenki14 Luxembourg_Loschbour -0.096
  259. gendstat: Russia_Kostenki14 Anatolia_N 0.259
  260. gendstat: Russia_Kostenki14 Czech_Vestonice16 0.991
  261. gendstat: Russia_Kostenki14 Morocco_Iberomaurusian 0.464
  262. gendstat: Russia_Kostenki14 Russia_Shamanka_EN.SG 0.751
  263. gendstat: Russia_Kostenki14 Georgia_Satsurblia.SG 0.377
  264. gendstat: Russia_Kostenki14 Ganj_Dareh_N 0.312
  265. gendstat: Russia_Kostenki14 Onge.DG -0.462
  266. gendstat: Russia_Kostenki14 SE_Iberia_MLN 0.286
  267. gendstat: Russia_Kostenki14 PPN 1.612
  268. gendstat: Luxembourg_Loschbour Anatolia_N 0.369
  269. gendstat: Luxembourg_Loschbour Czech_Vestonice16 1.163
  270. gendstat: Luxembourg_Loschbour Morocco_Iberomaurusian 0.558
  271. gendstat: Luxembourg_Loschbour Russia_Shamanka_EN.SG 0.834
  272. gendstat: Luxembourg_Loschbour Georgia_Satsurblia.SG 0.490
  273. gendstat: Luxembourg_Loschbour Ganj_Dareh_N 0.414
  274. gendstat: Luxembourg_Loschbour Onge.DG -0.347
  275. gendstat: Luxembourg_Loschbour SE_Iberia_MLN 0.403
  276. gendstat: Luxembourg_Loschbour PPN 1.826
  277. gendstat: Anatolia_N Czech_Vestonice16 0.913
  278. gendstat: Anatolia_N Morocco_Iberomaurusian 0.324
  279. gendstat: Anatolia_N Russia_Shamanka_EN.SG 0.662
  280. gendstat: Anatolia_N Georgia_Satsurblia.SG 0.226
  281. gendstat: Anatolia_N Ganj_Dareh_N 0.108
  282. gendstat: Anatolia_N Onge.DG -0.904
  283. gendstat: Anatolia_N SE_Iberia_MLN 0.082
  284. gendstat: Anatolia_N PPN 2.238
  285. gendstat: Czech_Vestonice16 Morocco_Iberomaurusian -0.606
  286. gendstat: Czech_Vestonice16 Russia_Shamanka_EN.SG -0.431
  287. gendstat: Czech_Vestonice16 Georgia_Satsurblia.SG -0.543
  288. gendstat: Czech_Vestonice16 Ganj_Dareh_N -0.782
  289. gendstat: Czech_Vestonice16 Onge.DG -1.457
  290. gendstat: Czech_Vestonice16 SE_Iberia_MLN -0.866
  291. gendstat: Czech_Vestonice16 PPN 0.534
  292. gendstat: Morocco_Iberomaurusian Russia_Shamanka_EN.SG 0.271
  293. gendstat: Morocco_Iberomaurusian Georgia_Satsurblia.SG -0.031
  294. gendstat: Morocco_Iberomaurusian Ganj_Dareh_N -0.202
  295. gendstat: Morocco_Iberomaurusian Onge.DG -1.068
  296. gendstat: Morocco_Iberomaurusian SE_Iberia_MLN -0.239
  297. gendstat: Morocco_Iberomaurusian PPN 1.396
  298. gendstat: Russia_Shamanka_EN.SG Georgia_Satsurblia.SG -0.252
  299. gendstat: Russia_Shamanka_EN.SG Ganj_Dareh_N -0.512
  300. gendstat: Russia_Shamanka_EN.SG Onge.DG -1.635
  301. gendstat: Russia_Shamanka_EN.SG SE_Iberia_MLN -0.548
  302. gendstat: Russia_Shamanka_EN.SG PPN 1.185
  303. gendstat: Georgia_Satsurblia.SG Ganj_Dareh_N -0.145
  304. gendstat: Georgia_Satsurblia.SG Onge.DG -0.891
  305. gendstat: Georgia_Satsurblia.SG SE_Iberia_MLN -0.166
  306. gendstat: Georgia_Satsurblia.SG PPN 1.206
  307. gendstat: Ganj_Dareh_N Onge.DG -0.941
  308. gendstat: Ganj_Dareh_N SE_Iberia_MLN -0.039
  309. gendstat: Ganj_Dareh_N PPN 1.661
  310. gendstat: Onge.DG SE_Iberia_MLN 0.862
  311. gendstat: Onge.DG PPN 2.291
  312. gendstat: SE_Iberia_MLN PPN 1.952
  313.  
  314. ##end of qpAdm: 288.052 seconds cpu 1441.575 Mbytes in use
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