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misnomer001

steppe_en SiS pass

misnomer001
Feb 19th, 2020
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  1. allsnps: YES
  2. ## qpAdm version: 1000
  3. seed: 1758149174
  4. read 1073741824 bytes
  5. read 1350149235 bytes
  6. packed geno read OK
  7. end of inpack
  8.  
  9. left pops:
  10. Steppe_Eneolithic
  11. Georgia_Kotias.SG
  12. Caucasus_Eneolithic
  13. Russia_Khvalynsk_EN
  14. Shahr_I_Sokhta_BA1
  15.  
  16. right pops:
  17. Mbuti.DG
  18. Russia_AfontovaGora3
  19. EEHG
  20. WEHG
  21. Anatolia_N
  22. Russia_Shamanka_EN.SG
  23. Onge.DG
  24. PPN
  25. China_Tianyuan
  26. Russia_MA1_HG
  27. Ust_Ishim.DG
  28. Georgia_Satsurblia.SG
  29. Ganj_Dareh_N
  30. WSHG
  31.  
  32. 0 Steppe_Eneolithic 3
  33. 1 Georgia_Kotias.SG 1
  34. 2 Caucasus_Eneolithic 3
  35. 3 Russia_Khvalynsk_EN 3
  36. 4 Shahr_I_Sokhta_BA1 8
  37. 5 Mbuti.DG 5
  38. 6 Russia_AfontovaGora3 1
  39. 7 EEHG 5
  40. 8 WEHG 36
  41. 9 Anatolia_N 23
  42. 10 Russia_Shamanka_EN.SG 10
  43. 11 Onge.DG 2
  44. 12 PPN 11
  45. 13 China_Tianyuan 1
  46. 14 Russia_MA1_HG 1
  47. 15 Ust_Ishim.DG 1
  48. 16 Georgia_Satsurblia.SG 1
  49. 17 Ganj_Dareh_N 8
  50. 18 WSHG 3
  51. jackknife block size: 0.050
  52. snps: 1150535 indivs: 126
  53. number of blocks for block jackknife: 552
  54. ## ncols: 1150535
  55. coverage: Steppe_Eneolithic 1017729
  56. coverage: Georgia_Kotias.SG 1149097
  57. coverage: Caucasus_Eneolithic 784983
  58. coverage: Russia_Khvalynsk_EN 758497
  59. coverage: Shahr_I_Sokhta_BA1 940504
  60. coverage: Mbuti.DG 1150376
  61. coverage: Russia_AfontovaGora3 265583
  62. coverage: EEHG 1052093
  63. coverage: WEHG 1141246
  64. coverage: Anatolia_N 1136560
  65. coverage: Russia_Shamanka_EN.SG 1149998
  66. coverage: Onge.DG 1120748
  67. coverage: PPN 847771
  68. coverage: China_Tianyuan 885079
  69. coverage: Russia_MA1_HG 805960
  70. coverage: Ust_Ishim.DG 1062044
  71. coverage: Georgia_Satsurblia.SG 801311
  72. coverage: Ganj_Dareh_N 1057358
  73. coverage: WSHG 858019
  74. dof (jackknife): 465.457
  75. numsnps used: 1150535
  76. codimension 1
  77. f4info:
  78. f4rank: 3 dof: 10 chisq: 14.964 tail: 0.133374643 dofdiff: 12 chisqdiff: -14.964 taildiff: 1
  79. B:
  80. scale 1.000 1.000 1.000
  81. Russia_AfontovaGora3 0.907 0.309 -0.247
  82. EEHG 2.093 0.479 0.660
  83. WEHG 1.345 0.475 1.470
  84. Anatolia_N -0.005 -0.037 1.935
  85. Russia_Shamanka_EN.SG 0.568 0.258 -0.773
  86. Onge.DG 0.299 -0.198 -0.541
  87. PPN -0.093 -0.532 1.383
  88. China_Tianyuan 0.490 -0.219 -0.476
  89. Russia_MA1_HG 1.243 0.095 -0.372
  90. Ust_Ishim.DG 0.252 0.093 -0.116
  91. Georgia_Satsurblia.SG -0.423 3.397 0.740
  92. Ganj_Dareh_N -0.395 -0.637 -1.435
  93. WSHG 1.839 0.229 -0.899
  94. A:
  95. scale 318.094 1307.768 1817.143
  96. Georgia_Kotias.SG -1.168 1.757 -0.311
  97. Caucasus_Eneolithic -0.988 -0.477 1.821
  98. Russia_Khvalynsk_EN 0.769 -0.122 0.127
  99. Shahr_I_Sokhta_BA1 -1.033 -0.818 -0.755
  100.  
  101.  
  102. full rank
  103. f4info:
  104. f4rank: 4 dof: 0 chisq: 0.000 tail: 1 dofdiff: 10 chisqdiff: 14.964 taildiff: 0.133374643
  105. B:
  106. scale 253.881 288.868 453.868 277.104
  107. Russia_AfontovaGora3 -0.803 -1.011 0.776 -0.915
  108. EEHG -1.850 -1.803 2.233 -2.088
  109. WEHG -1.194 -0.871 1.453 -1.507
  110. Anatolia_N -0.163 0.501 -0.093 -0.277
  111. Russia_Shamanka_EN.SG -0.429 -0.764 0.532 -0.489
  112. Onge.DG -0.349 -0.437 0.262 -0.200
  113. PPN -0.190 0.520 -0.108 -0.026
  114. China_Tianyuan -0.564 -0.588 0.426 -0.394
  115. Russia_MA1_HG -1.259 -1.382 0.966 -1.236
  116. Ust_Ishim.DG -0.292 -0.361 0.105 -0.313
  117. Georgia_Satsurblia.SG 1.492 0.204 -0.716 -0.354
  118. Ganj_Dareh_N 0.149 -0.009 -0.582 0.576
  119. WSHG -1.704 -2.060 1.718 -1.714
  120. A:
  121. scale 2.000 2.000 2.000 2.000
  122. Georgia_Kotias.SG 2.000 0.000 0.000 0.000
  123. Caucasus_Eneolithic 0.000 2.000 0.000 0.000
  124. Russia_Khvalynsk_EN 0.000 0.000 2.000 0.000
  125. Shahr_I_Sokhta_BA1 0.000 0.000 0.000 2.000
  126.  
  127.  
  128. best coefficients: 0.151 0.067 0.583 0.198
  129. Jackknife mean: 0.151024760 0.067654819 0.583117905 0.198202517
  130. std. errors: 0.037 0.043 0.016 0.037
  131.  
  132. error covariance (* 1,000,000)
  133. 1337 -865 2 -475
  134. -865 1882 -178 -839
  135. 2 -178 249 -72
  136. -475 -839 -72 1386
  137.  
  138.  
  139. summ: Steppe_Eneolithic 4 0.133375 0.151 0.068 0.583 0.198 1337 -865 2 -475 1882 ...
  140. -178 -839 249 -72 1386
  141.  
  142. fixed pat wt dof chisq tail prob
  143. 0000 0 10 14.964 0.133375 0.151 0.067 0.583 0.198
  144. 0001 1 11 41.484 1.98924e-05 0.232 0.171 0.596 0.000
  145. 0010 1 11 262.249 0 -72.183 58.742 0.000 14.441 infeasible
  146. 0100 1 11 17.275 0.100014 0.182 0.000 0.589 0.229
  147. 1000 1 11 34.171 0.000339176 0.000 0.156 0.586 0.259
  148. 0011 2 12 267.097 0 -31.496 32.496 0.000 0.000 infeasible
  149. 0101 2 12 56.969 8.00759e-08 0.383 0.000 0.617 0.000
  150. 0110 2 12 353.465 0 8.876 0.000 0.000 -7.876 infeasible
  151. 1001 2 12 77.520 1.22366e-11 0.000 0.404 0.596 0.000
  152. 1010 2 12 395.018 0 0.000 6.251 0.000 -5.251 infeasible
  153. 1100 2 12 51.091 8.97745e-07 0.000 0.000 0.609 0.391
  154. 0111 3 13 746.938 0 1.000 0.000 0.000 0.000
  155. 1011 3 13 795.838 0 0.000 1.000 0.000 0.000
  156. 1101 3 13 504.382 0 0.000 0.000 1.000 0.000
  157. 1110 3 13 1173.164 0 0.000 0.000 0.000 1.000
  158. best pat: 0000 0.133375 - -
  159. best pat: 0100 0.100014 chi(nested): 2.310 p-value for nested model: 0.128513
  160. best pat: 1100 8.97745e-07 chi(nested): 33.816 p-value for nested model: 6.05691e-09
  161. best pat: 1101 1.71688e-99 chi(nested): 453.291 p-value for nested model: 1.38961e-100
  162.  
  163. coeffs: 0.151 0.067 0.583 0.198
  164.  
  165. ## dscore:: f_4(Base, Fit, Rbase, right2)
  166. ## genstat:: f_4(Base, Fit, right1, right2)
  167.  
  168. details: Georgia_Kotias.SG Russia_AfontovaGora3 -0.003163 -12.764669
  169. details: Caucasus_Eneolithic Russia_AfontovaGora3 -0.003499 -13.088926
  170. details: Russia_Khvalynsk_EN Russia_AfontovaGora3 0.001709 7.243282
  171. details: Shahr_I_Sokhta_BA1 Russia_AfontovaGora3 -0.003300 -15.793994
  172. dscore: Russia_AfontovaGora3 f4: -0.000373 Z: -2.049881
  173.  
  174. details: Georgia_Kotias.SG EEHG -0.007285 -15.986097
  175. details: Caucasus_Eneolithic EEHG -0.006243 -15.906861
  176. details: Russia_Khvalynsk_EN EEHG 0.004921 14.543104
  177. details: Shahr_I_Sokhta_BA1 EEHG -0.007534 -24.867435
  178. dscore: EEHG f4: -0.000149 Z: -0.539160
  179.  
  180. details: Georgia_Kotias.SG WEHG -0.004702 -12.636536
  181. details: Caucasus_Eneolithic WEHG -0.003016 -8.738217
  182. details: Russia_Khvalynsk_EN WEHG 0.003201 10.704693
  183. details: Shahr_I_Sokhta_BA1 WEHG -0.005437 -20.661500
  184. dscore: WEHG f4: -0.000127 Z: -0.535849
  185.  
  186. details: Georgia_Kotias.SG Anatolia_N -0.000641 -1.952120
  187. details: Caucasus_Eneolithic Anatolia_N 0.001735 5.669741
  188. details: Russia_Khvalynsk_EN Anatolia_N -0.000206 -0.841744
  189. details: Shahr_I_Sokhta_BA1 Anatolia_N -0.001000 -4.470336
  190. dscore: Anatolia_N f4: -0.000299 Z: -1.501936
  191.  
  192. details: Georgia_Kotias.SG Russia_Shamanka_EN.SG -0.001689 -4.752182
  193. details: Caucasus_Eneolithic Russia_Shamanka_EN.SG -0.002645 -7.999353
  194. details: Russia_Khvalynsk_EN Russia_Shamanka_EN.SG 0.001171 4.313257
  195. details: Shahr_I_Sokhta_BA1 Russia_Shamanka_EN.SG -0.001765 -6.849818
  196. dscore: Russia_Shamanka_EN.SG f4: -0.000101 Z: -0.467187
  197.  
  198. details: Georgia_Kotias.SG Onge.DG -0.001374 -3.308420
  199. details: Caucasus_Eneolithic Onge.DG -0.001513 -4.230557
  200. details: Russia_Khvalynsk_EN Onge.DG 0.000577 1.952804
  201. details: Shahr_I_Sokhta_BA1 Onge.DG -0.000723 -2.632449
  202. dscore: Onge.DG f4: -0.000117 Z: -0.472430
  203.  
  204. details: Georgia_Kotias.SG PPN -0.000747 -2.209746
  205. details: Caucasus_Eneolithic PPN 0.001801 5.428586
  206. details: Russia_Khvalynsk_EN PPN -0.000238 -0.851181
  207. details: Shahr_I_Sokhta_BA1 PPN -0.000094 -0.380407
  208. dscore: PPN f4: -0.000149 Z: -0.688634
  209.  
  210. details: Georgia_Kotias.SG China_Tianyuan -0.002223 -4.682022
  211. details: Caucasus_Eneolithic China_Tianyuan -0.002035 -4.660959
  212. details: Russia_Khvalynsk_EN China_Tianyuan 0.000939 2.601409
  213. details: Shahr_I_Sokhta_BA1 China_Tianyuan -0.001422 -4.523007
  214. dscore: China_Tianyuan f4: -0.000208 Z: -0.725333
  215.  
  216. details: Georgia_Kotias.SG Russia_MA1_HG -0.004959 -10.399572
  217. details: Caucasus_Eneolithic Russia_MA1_HG -0.004784 -11.685864
  218. details: Russia_Khvalynsk_EN Russia_MA1_HG 0.002128 5.933038
  219. details: Shahr_I_Sokhta_BA1 Russia_MA1_HG -0.004462 -13.705671
  220. dscore: Russia_MA1_HG f4: -0.000717 Z: -2.499934
  221.  
  222. details: Georgia_Kotias.SG Ust_Ishim.DG -0.001150 -2.590370
  223. details: Caucasus_Eneolithic Ust_Ishim.DG -0.001249 -3.226798
  224. details: Russia_Khvalynsk_EN Ust_Ishim.DG 0.000232 0.776781
  225. details: Shahr_I_Sokhta_BA1 Ust_Ishim.DG -0.001129 -3.626101
  226. dscore: Ust_Ishim.DG f4: -0.000347 Z: -1.406666
  227.  
  228. details: Georgia_Kotias.SG Georgia_Satsurblia.SG 0.005878 11.719397
  229. details: Caucasus_Eneolithic Georgia_Satsurblia.SG 0.000706 1.803152
  230. details: Russia_Khvalynsk_EN Georgia_Satsurblia.SG -0.001577 -4.822651
  231. details: Shahr_I_Sokhta_BA1 Georgia_Satsurblia.SG -0.001276 -4.334466
  232. dscore: Georgia_Satsurblia.SG f4: -0.000236 Z: -0.915712
  233.  
  234. details: Georgia_Kotias.SG Ganj_Dareh_N 0.000586 1.584105
  235. details: Caucasus_Eneolithic Ganj_Dareh_N -0.000031 -0.095385
  236. details: Russia_Khvalynsk_EN Ganj_Dareh_N -0.001282 -4.977498
  237. details: Shahr_I_Sokhta_BA1 Ganj_Dareh_N 0.002078 8.413868
  238. dscore: Ganj_Dareh_N f4: -0.000248 Z: -1.178751
  239.  
  240. details: Georgia_Kotias.SG WSHG -0.006711 -16.209018
  241. details: Caucasus_Eneolithic WSHG -0.007132 -16.708995
  242. details: Russia_Khvalynsk_EN WSHG 0.003785 10.538602
  243. details: Shahr_I_Sokhta_BA1 WSHG -0.006187 -19.482569
  244. dscore: WSHG f4: -0.000517 Z: -1.770692
  245.  
  246. gendstat: Mbuti.DG Russia_AfontovaGora3 -2.050
  247. gendstat: Mbuti.DG EEHG -0.539
  248. gendstat: Mbuti.DG WEHG -0.536
  249. gendstat: Mbuti.DG Anatolia_N -1.502
  250. gendstat: Mbuti.DG Russia_Shamanka_EN.SG -0.467
  251. gendstat: Mbuti.DG Onge.DG -0.472
  252. gendstat: Mbuti.DG PPN -0.689
  253. gendstat: Mbuti.DG China_Tianyuan -0.725
  254. gendstat: Mbuti.DG Russia_MA1_HG -2.500
  255. gendstat: Mbuti.DG Ust_Ishim.DG -1.407
  256. gendstat: Mbuti.DG Georgia_Satsurblia.SG -0.916
  257. gendstat: Mbuti.DG Ganj_Dareh_N -1.179
  258. gendstat: Mbuti.DG WSHG -1.771
  259. gendstat: Russia_AfontovaGora3 EEHG 0.825
  260. gendstat: Russia_AfontovaGora3 WEHG 0.971
  261. gendstat: Russia_AfontovaGora3 Anatolia_N 0.305
  262. gendstat: Russia_AfontovaGora3 Russia_Shamanka_EN.SG 1.148
  263. gendstat: Russia_AfontovaGora3 Onge.DG 0.926
  264. gendstat: Russia_AfontovaGora3 PPN 0.867
  265. gendstat: Russia_AfontovaGora3 China_Tianyuan 0.537
  266. gendstat: Russia_AfontovaGora3 Russia_MA1_HG -1.228
  267. gendstat: Russia_AfontovaGora3 Ust_Ishim.DG 0.091
  268. gendstat: Russia_AfontovaGora3 Georgia_Satsurblia.SG 0.459
  269. gendstat: Russia_AfontovaGora3 Ganj_Dareh_N 0.497
  270. gendstat: Russia_AfontovaGora3 WSHG -0.527
  271. gendstat: EEHG WEHG 0.097
  272. gendstat: EEHG Anatolia_N -0.597
  273. gendstat: EEHG Russia_Shamanka_EN.SG 0.187
  274. gendstat: EEHG Onge.DG 0.102
  275. gendstat: EEHG PPN 0.000
  276. gendstat: EEHG China_Tianyuan -0.181
  277. gendstat: EEHG Russia_MA1_HG -2.062
  278. gendstat: EEHG Ust_Ishim.DG -0.620
  279. gendstat: EEHG Georgia_Satsurblia.SG -0.257
  280. gendstat: EEHG Ganj_Dareh_N -0.358
  281. gendstat: EEHG WSHG -1.453
  282. gendstat: WEHG Anatolia_N -0.990
  283. gendstat: WEHG Russia_Shamanka_EN.SG 0.116
  284. gendstat: WEHG Onge.DG 0.038
  285. gendstat: WEHG PPN -0.100
  286. gendstat: WEHG China_Tianyuan -0.272
  287. gendstat: WEHG Russia_MA1_HG -2.122
  288. gendstat: WEHG Ust_Ishim.DG -0.810
  289. gendstat: WEHG Georgia_Satsurblia.SG -0.361
  290. gendstat: WEHG Ganj_Dareh_N -0.510
  291. gendstat: WEHG WSHG -1.480
  292. gendstat: Anatolia_N Russia_Shamanka_EN.SG 0.959
  293. gendstat: Anatolia_N Onge.DG 0.750
  294. gendstat: Anatolia_N PPN 0.928
  295. gendstat: Anatolia_N China_Tianyuan 0.315
  296. gendstat: Anatolia_N Russia_MA1_HG -1.503
  297. gendstat: Anatolia_N Ust_Ishim.DG -0.191
  298. gendstat: Anatolia_N Georgia_Satsurblia.SG 0.234
  299. gendstat: Anatolia_N Ganj_Dareh_N 0.262
  300. gendstat: Anatolia_N WSHG -0.784
  301. gendstat: Russia_Shamanka_EN.SG Onge.DG -0.072
  302. gendstat: Russia_Shamanka_EN.SG PPN -0.206
  303. gendstat: Russia_Shamanka_EN.SG China_Tianyuan -0.402
  304. gendstat: Russia_Shamanka_EN.SG Russia_MA1_HG -2.228
  305. gendstat: Russia_Shamanka_EN.SG Ust_Ishim.DG -0.993
  306. gendstat: Russia_Shamanka_EN.SG Georgia_Satsurblia.SG -0.461
  307. gendstat: Russia_Shamanka_EN.SG Ganj_Dareh_N -0.677
  308. gendstat: Russia_Shamanka_EN.SG WSHG -1.575
  309. gendstat: Onge.DG PPN -0.125
  310. gendstat: Onge.DG China_Tianyuan -0.304
  311. gendstat: Onge.DG Russia_MA1_HG -1.859
  312. gendstat: Onge.DG Ust_Ishim.DG -0.831
  313. gendstat: Onge.DG Georgia_Satsurblia.SG -0.372
  314. gendstat: Onge.DG Ganj_Dareh_N -0.530
  315. gendstat: Onge.DG WSHG -1.261
  316. gendstat: PPN China_Tianyuan -0.193
  317. gendstat: PPN Russia_MA1_HG -1.940
  318. gendstat: PPN Ust_Ishim.DG -0.729
  319. gendstat: PPN Georgia_Satsurblia.SG -0.303
  320. gendstat: PPN Ganj_Dareh_N -0.459
  321. gendstat: PPN WSHG -1.232
  322. gendstat: China_Tianyuan Russia_MA1_HG -1.471
  323. gendstat: China_Tianyuan Ust_Ishim.DG -0.437
  324. gendstat: China_Tianyuan Georgia_Satsurblia.SG -0.079
  325. gendstat: China_Tianyuan Ganj_Dareh_N -0.136
  326. gendstat: China_Tianyuan WSHG -0.961
  327. gendstat: Russia_MA1_HG Ust_Ishim.DG 1.115
  328. gendstat: Russia_MA1_HG Georgia_Satsurblia.SG 1.410
  329. gendstat: Russia_MA1_HG Ganj_Dareh_N 1.636
  330. gendstat: Russia_MA1_HG WSHG 0.717
  331. gendstat: Ust_Ishim.DG Georgia_Satsurblia.SG 0.346
  332. gendstat: Ust_Ishim.DG Ganj_Dareh_N 0.368
  333. gendstat: Ust_Ishim.DG WSHG -0.528
  334. gendstat: Georgia_Satsurblia.SG Ganj_Dareh_N -0.046
  335. gendstat: Georgia_Satsurblia.SG WSHG -0.829
  336. gendstat: Ganj_Dareh_N WSHG -0.919
  337.  
  338. ##end of qpAdm: 251.997 seconds cpu 1478.193 Mbytes in use
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