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misnomer001

steppe_en seh gabi ln fail

misnomer001
Feb 19th, 2020
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  1. allsnps: YES
  2. ## qpAdm version: 1000
  3. seed: 1746713666
  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. Iran_Seh_Gabi_LN
  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 Iran_Seh_Gabi_LN 1
  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: 119
  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: Iran_Seh_Gabi_LN 511723
  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): 465.014
  75. numsnps used: 1150535
  76. codimension 1
  77. f4info:
  78. f4rank: 3 dof: 10 chisq: 20.539 tail: 0.0245516192 dofdiff: 12 chisqdiff: -20.539 taildiff: 1
  79. B:
  80. scale 1.000 1.000 1.000
  81. Russia_AfontovaGora3 0.946 0.447 -0.187
  82. EEHG 2.012 0.064 0.051
  83. WEHG 1.298 0.432 1.151
  84. Anatolia_N -0.014 0.329 2.074
  85. Russia_Shamanka_EN.SG 0.620 0.446 -0.563
  86. Onge.DG 0.352 0.120 -0.159
  87. PPN -0.074 -0.119 1.708
  88. China_Tianyuan 0.557 0.077 -0.093
  89. Russia_MA1_HG 1.255 0.072 -0.377
  90. Ust_Ishim.DG 0.239 0.014 -0.195
  91. Georgia_Satsurblia.SG -0.433 3.246 -0.026
  92. Ganj_Dareh_N -0.477 -1.298 -1.724
  93. WSHG 1.870 0.194 -0.957
  94. A:
  95. scale 307.662 1232.536 1768.902
  96. Georgia_Kotias.SG -1.135 1.604 -0.752
  97. Caucasus_Eneolithic -0.934 -0.186 1.681
  98. Russia_Khvalynsk_EN 0.740 -0.136 0.083
  99. Iran_Seh_Gabi_LN -1.137 -1.172 -0.776
  100.  
  101.  
  102. full rank
  103. f4info:
  104. f4rank: 4 dof: 0 chisq: 0.000 tail: 1 dofdiff: 10 chisqdiff: 20.539 taildiff: 0.0245516192
  105. B:
  106. scale 253.881 288.868 453.868 236.816
  107. Russia_AfontovaGora3 -0.803 -1.011 0.776 -1.021
  108. EEHG -1.850 -1.803 2.233 -1.837
  109. WEHG -1.194 -0.871 1.453 -1.401
  110. Anatolia_N -0.163 0.501 -0.093 -0.348
  111. Russia_Shamanka_EN.SG -0.429 -0.764 0.532 -0.663
  112. Onge.DG -0.349 -0.437 0.262 -0.418
  113. PPN -0.190 0.520 -0.108 -0.157
  114. China_Tianyuan -0.564 -0.588 0.426 -0.592
  115. Russia_MA1_HG -1.259 -1.382 0.966 -1.252
  116. Ust_Ishim.DG -0.292 -0.361 0.105 -0.308
  117. Georgia_Satsurblia.SG 1.492 0.204 -0.716 -0.397
  118. Ganj_Dareh_N 0.149 -0.009 -0.582 0.825
  119. WSHG -1.704 -2.060 1.718 -1.735
  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. Iran_Seh_Gabi_LN 0.000 0.000 0.000 2.000
  126.  
  127.  
  128. best coefficients: 0.163 0.107 0.594 0.137
  129. Jackknife mean: 0.162058608 0.106789823 0.594295319 0.136856251
  130. std. errors: 0.038 0.042 0.016 0.029
  131.  
  132. error covariance (* 1,000,000)
  133. 1430 -1041 -5 -383
  134. -1041 1737 -243 -453
  135. -5 -243 244 4
  136. -383 -453 4 833
  137.  
  138.  
  139. summ: Steppe_Eneolithic 4 0.024552 0.162 0.107 0.594 0.137 1430 -1041 -5 -383 1737 ...
  140. -243 -453 244 4 833
  141.  
  142. fixed pat wt dof chisq tail prob
  143. 0000 0 10 20.539 0.0245516 0.163 0.107 0.594 0.137
  144. 0001 1 11 41.369 2.08158e-05 0.229 0.173 0.598 0.000
  145. 0010 1 11 259.210 0 36.286 -27.996 0.000 -7.289 infeasible
  146. 0100 1 11 26.755 0.00500257 0.225 0.000 0.609 0.166
  147. 1000 1 11 42.332 1.41905e-05 0.000 0.218 0.598 0.184
  148. 0011 2 12 266.209 0 -31.961 32.961 0.000 0.000 infeasible
  149. 0101 2 12 57.206 7.25675e-08 0.382 0.000 0.618 0.000
  150. 0110 2 12 348.935 0 4.478 0.000 0.000 -3.478 infeasible
  151. 1001 2 12 76.894 1.60893e-11 0.000 0.403 0.597 0.000
  152. 1010 2 12 372.446 0 0.000 4.867 0.000 -3.867 infeasible
  153. 1100 2 12 84.555 5.54116e-13 0.000 0.000 0.655 0.345
  154. 0111 3 13 746.577 0 1.000 0.000 0.000 0.000
  155. 1011 3 13 794.117 0 0.000 1.000 0.000 0.000
  156. 1101 3 13 502.344 0 0.000 0.000 1.000 0.000
  157. 1110 3 13 1204.606 0 0.000 0.000 0.000 1.000
  158. best pat: 0000 0.0245516 - -
  159. best pat: 0100 0.00500257 chi(nested): 6.217 p-value for nested model: 0.0126539
  160. best pat: 1001 1.60893e-11 not nested
  161. best pat: 1101 4.65072e-99 chi(nested): 425.451 p-value for nested model: 1.59262e-94
  162.  
  163. coeffs: 0.163 0.107 0.594 0.137
  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 -12.753509
  169. details: Caucasus_Eneolithic Russia_AfontovaGora3 -0.003499 -13.081301
  170. details: Russia_Khvalynsk_EN Russia_AfontovaGora3 0.001709 7.236672
  171. details: Iran_Seh_Gabi_LN Russia_AfontovaGora3 -0.004310 -13.948835
  172. dscore: Russia_AfontovaGora3 f4: -0.000461 Z: -2.508686
  173.  
  174. details: Georgia_Kotias.SG EEHG -0.007285 -15.985940
  175. details: Caucasus_Eneolithic EEHG -0.006243 -15.902404
  176. details: Russia_Khvalynsk_EN EEHG 0.004921 14.540556
  177. details: Iran_Seh_Gabi_LN EEHG -0.007758 -21.187535
  178. dscore: EEHG f4: 0.000014 Z: 0.050258
  179.  
  180. details: Georgia_Kotias.SG WEHG -0.004702 -12.630668
  181. details: Caucasus_Eneolithic WEHG -0.003016 -8.733290
  182. details: Russia_Khvalynsk_EN WEHG 0.003201 10.697032
  183. details: Iran_Seh_Gabi_LN WEHG -0.005915 -17.146836
  184. dscore: WEHG f4: 0.000007 Z: 0.031100
  185.  
  186. details: Georgia_Kotias.SG Anatolia_N -0.000641 -1.951021
  187. details: Caucasus_Eneolithic Anatolia_N 0.001735 5.665522
  188. details: Russia_Khvalynsk_EN Anatolia_N -0.000206 -0.840938
  189. details: Iran_Seh_Gabi_LN Anatolia_N -0.001470 -4.936823
  190. dscore: Anatolia_N f4: -0.000243 Z: -1.224110
  191.  
  192. details: Georgia_Kotias.SG Russia_Shamanka_EN.SG -0.001689 -4.749894
  193. details: Caucasus_Eneolithic Russia_Shamanka_EN.SG -0.002645 -7.993061
  194. details: Russia_Khvalynsk_EN Russia_Shamanka_EN.SG 0.001171 4.308513
  195. details: Iran_Seh_Gabi_LN Russia_Shamanka_EN.SG -0.002802 -8.545383
  196. dscore: Russia_Shamanka_EN.SG f4: -0.000244 Z: -1.134409
  197.  
  198. details: Georgia_Kotias.SG Onge.DG -0.001374 -3.307449
  199. details: Caucasus_Eneolithic Onge.DG -0.001513 -4.227590
  200. details: Russia_Khvalynsk_EN Onge.DG 0.000577 1.951673
  201. details: Iran_Seh_Gabi_LN Onge.DG -0.001765 -5.054459
  202. dscore: Onge.DG f4: -0.000283 Z: -1.133634
  203.  
  204. details: Georgia_Kotias.SG PPN -0.000747 -2.208740
  205. details: Caucasus_Eneolithic PPN 0.001801 5.424696
  206. details: Russia_Khvalynsk_EN PPN -0.000238 -0.850609
  207. details: Iran_Seh_Gabi_LN PPN -0.000664 -1.910860
  208. dscore: PPN f4: -0.000161 Z: -0.738300
  209.  
  210. details: Georgia_Kotias.SG China_Tianyuan -0.002223 -4.680345
  211. details: Caucasus_Eneolithic China_Tianyuan -0.002035 -4.659651
  212. details: Russia_Khvalynsk_EN China_Tianyuan 0.000939 2.599791
  213. details: Iran_Seh_Gabi_LN China_Tianyuan -0.002499 -5.778609
  214. dscore: China_Tianyuan f4: -0.000362 Z: -1.232354
  215.  
  216. details: Georgia_Kotias.SG Russia_MA1_HG -0.004959 -10.399497
  217. details: Caucasus_Eneolithic Russia_MA1_HG -0.004784 -11.683556
  218. details: Russia_Khvalynsk_EN Russia_MA1_HG 0.002128 5.931630
  219. details: Iran_Seh_Gabi_LN Russia_MA1_HG -0.005289 -13.240513
  220. dscore: Russia_MA1_HG f4: -0.000775 Z: -2.689206
  221.  
  222. details: Georgia_Kotias.SG Ust_Ishim.DG -0.001150 -2.589162
  223. details: Caucasus_Eneolithic Ust_Ishim.DG -0.001249 -3.225333
  224. details: Russia_Khvalynsk_EN Ust_Ishim.DG 0.000232 0.776197
  225. details: Iran_Seh_Gabi_LN Ust_Ishim.DG -0.001302 -3.292244
  226. dscore: Ust_Ishim.DG f4: -0.000360 Z: -1.439262
  227.  
  228. details: Georgia_Kotias.SG Georgia_Satsurblia.SG 0.005878 11.719613
  229. details: Caucasus_Eneolithic Georgia_Satsurblia.SG 0.000706 1.802495
  230. details: Russia_Khvalynsk_EN Georgia_Satsurblia.SG -0.001577 -4.820124
  231. details: Iran_Seh_Gabi_LN Georgia_Satsurblia.SG -0.001676 -4.375941
  232. dscore: Georgia_Satsurblia.SG f4: -0.000135 Z: -0.518916
  233.  
  234. details: Georgia_Kotias.SG Ganj_Dareh_N 0.000586 1.583469
  235. details: Caucasus_Eneolithic Ganj_Dareh_N -0.000031 -0.095328
  236. details: Russia_Khvalynsk_EN Ganj_Dareh_N -0.001282 -4.973672
  237. details: Iran_Seh_Gabi_LN Ganj_Dareh_N 0.003482 10.989740
  238. dscore: Ganj_Dareh_N f4: -0.000194 Z: -0.928868
  239.  
  240. details: Georgia_Kotias.SG WSHG -0.006711 -16.205165
  241. details: Caucasus_Eneolithic WSHG -0.007132 -16.704355
  242. details: Russia_Khvalynsk_EN WSHG 0.003785 10.535195
  243. details: Iran_Seh_Gabi_LN WSHG -0.007324 -18.377478
  244. dscore: WSHG f4: -0.000603 Z: -2.071449
  245.  
  246. gendstat: Mbuti.DG Russia_AfontovaGora3 -2.509
  247. gendstat: Mbuti.DG EEHG 0.050
  248. gendstat: Mbuti.DG WEHG 0.031
  249. gendstat: Mbuti.DG Anatolia_N -1.224
  250. gendstat: Mbuti.DG Russia_Shamanka_EN.SG -1.134
  251. gendstat: Mbuti.DG Onge.DG -1.134
  252. gendstat: Mbuti.DG PPN -0.738
  253. gendstat: Mbuti.DG China_Tianyuan -1.232
  254. gendstat: Mbuti.DG Russia_MA1_HG -2.689
  255. gendstat: Mbuti.DG Ust_Ishim.DG -1.439
  256. gendstat: Mbuti.DG Georgia_Satsurblia.SG -0.519
  257. gendstat: Mbuti.DG Ganj_Dareh_N -0.929
  258. gendstat: Mbuti.DG WSHG -2.071
  259. gendstat: Russia_AfontovaGora3 EEHG 1.768
  260. gendstat: Russia_AfontovaGora3 WEHG 1.845
  261. gendstat: Russia_AfontovaGora3 Anatolia_N 0.896
  262. gendstat: Russia_AfontovaGora3 Russia_Shamanka_EN.SG 0.921
  263. gendstat: Russia_AfontovaGora3 Onge.DG 0.639
  264. gendstat: Russia_AfontovaGora3 PPN 1.153
  265. gendstat: Russia_AfontovaGora3 China_Tianyuan 0.314
  266. gendstat: Russia_AfontovaGora3 Russia_MA1_HG -1.121
  267. gendstat: Russia_AfontovaGora3 Ust_Ishim.DG 0.352
  268. gendstat: Russia_AfontovaGora3 Georgia_Satsurblia.SG 1.089
  269. gendstat: Russia_AfontovaGora3 Ganj_Dareh_N 1.076
  270. gendstat: Russia_AfontovaGora3 WSHG -0.522
  271. gendstat: EEHG WEHG -0.028
  272. gendstat: EEHG Anatolia_N -1.026
  273. gendstat: EEHG Russia_Shamanka_EN.SG -1.027
  274. gendstat: EEHG Onge.DG -0.961
  275. gendstat: EEHG PPN -0.657
  276. gendstat: EEHG China_Tianyuan -1.147
  277. gendstat: EEHG Russia_MA1_HG -2.821
  278. gendstat: EEHG Ust_Ishim.DG -1.188
  279. gendstat: EEHG Georgia_Satsurblia.SG -0.444
  280. gendstat: EEHG Ganj_Dareh_N -0.761
  281. gendstat: EEHG WSHG -2.458
  282. gendstat: WEHG Anatolia_N -1.438
  283. gendstat: WEHG Russia_Shamanka_EN.SG -1.129
  284. gendstat: WEHG Onge.DG -1.061
  285. gendstat: WEHG PPN -0.783
  286. gendstat: WEHG China_Tianyuan -1.237
  287. gendstat: WEHG Russia_MA1_HG -2.755
  288. gendstat: WEHG Ust_Ishim.DG -1.379
  289. gendstat: WEHG Georgia_Satsurblia.SG -0.475
  290. gendstat: WEHG Ganj_Dareh_N -0.854
  291. gendstat: WEHG WSHG -2.300
  292. gendstat: Anatolia_N Russia_Shamanka_EN.SG -0.005
  293. gendstat: Anatolia_N Onge.DG -0.167
  294. gendstat: Anatolia_N PPN 0.490
  295. gendstat: Anatolia_N China_Tianyuan -0.410
  296. gendstat: Anatolia_N Russia_MA1_HG -1.861
  297. gendstat: Anatolia_N Ust_Ishim.DG -0.465
  298. gendstat: Anatolia_N Georgia_Satsurblia.SG 0.402
  299. gendstat: Anatolia_N Ganj_Dareh_N 0.253
  300. gendstat: Anatolia_N WSHG -1.289
  301. gendstat: Russia_Shamanka_EN.SG Onge.DG -0.181
  302. gendstat: Russia_Shamanka_EN.SG PPN 0.356
  303. gendstat: Russia_Shamanka_EN.SG China_Tianyuan -0.437
  304. gendstat: Russia_Shamanka_EN.SG Russia_MA1_HG -1.904
  305. gendstat: Russia_Shamanka_EN.SG Ust_Ishim.DG -0.475
  306. gendstat: Russia_Shamanka_EN.SG Georgia_Satsurblia.SG 0.378
  307. gendstat: Russia_Shamanka_EN.SG Ganj_Dareh_N 0.233
  308. gendstat: Russia_Shamanka_EN.SG WSHG -1.380
  309. gendstat: Onge.DG PPN 0.470
  310. gendstat: Onge.DG China_Tianyuan -0.258
  311. gendstat: Onge.DG Russia_MA1_HG -1.521
  312. gendstat: Onge.DG Ust_Ishim.DG -0.283
  313. gendstat: Onge.DG Georgia_Satsurblia.SG 0.459
  314. gendstat: Onge.DG Ganj_Dareh_N 0.357
  315. gendstat: Onge.DG WSHG -1.016
  316. gendstat: PPN China_Tianyuan -0.643
  317. gendstat: PPN Russia_MA1_HG -2.034
  318. gendstat: PPN Ust_Ishim.DG -0.725
  319. gendstat: PPN Georgia_Satsurblia.SG 0.091
  320. gendstat: PPN Ganj_Dareh_N -0.148
  321. gendstat: PPN WSHG -1.467
  322. gendstat: China_Tianyuan Russia_MA1_HG -1.184
  323. gendstat: China_Tianyuan Ust_Ishim.DG 0.005
  324. gendstat: China_Tianyuan Georgia_Satsurblia.SG 0.639
  325. gendstat: China_Tianyuan Ganj_Dareh_N 0.560
  326. gendstat: China_Tianyuan WSHG -0.737
  327. gendstat: Russia_MA1_HG Ust_Ishim.DG 1.248
  328. gendstat: Russia_MA1_HG Georgia_Satsurblia.SG 1.860
  329. gendstat: Russia_MA1_HG Ganj_Dareh_N 2.015
  330. gendstat: Russia_MA1_HG WSHG 0.608
  331. gendstat: Ust_Ishim.DG Georgia_Satsurblia.SG 0.705
  332. gendstat: Ust_Ishim.DG Ganj_Dareh_N 0.619
  333. gendstat: Ust_Ishim.DG WSHG -0.762
  334. gendstat: Georgia_Satsurblia.SG Ganj_Dareh_N -0.217
  335. gendstat: Georgia_Satsurblia.SG WSHG -1.392
  336. gendstat: Ganj_Dareh_N WSHG -1.411
  337.  
  338. ##end of qpAdm: 244.799 seconds cpu 1478.193 Mbytes in use
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