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Legend_9813

Admixtools 1 vs Admixtools 2

Legend_9813
Feb 22nd, 2023
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  1. Admixtools 1 output
  2.  
  3. qpAdm: parameter file: parqpadm
  4. ### THE INPUT PARAMETERS
  5. ##PARAMETER NAME: VALUE
  6. indivname: custom.ind
  7. snpname: custom.snp
  8. genotypename: custom.geno
  9. popleft: left
  10. popright: right
  11. inbreed: NO
  12. allsnps: YES
  13. ## qpAdm version: 1520
  14. seed: 8726517
  15. inbreed set NO
  16. inbreed set NO
  17. tmp: /tmp/fsx.266
  18.  
  19. left pops:
  20. Russia_Khvalynsk_Eneolithic_CHG
  21. EHG
  22. Russia_Caucasus_Eneolithic
  23. TTK
  24.  
  25. right pops:
  26. Mbuti.DG
  27. WHG
  28. CHG
  29. WSHG
  30. Onge.DG
  31. Turkey_N
  32. Levant_PPN
  33. EHG_Mesolithic
  34. Iraq_Nemrik9_PPN
  35. Iran_GanjDareh_N
  36. Mongolia_North_N
  37. Turkey_Boncuklu_N
  38. Russia_AfontovaGora3
  39. Serbia_IronGates_Mesolithic
  40.  
  41. codimension 1
  42. f4info:
  43. f4rank: 2 dof: 11 chisq: 35.804 tail: 0.000182417623 dofdiff: 13 chisqdiff: -35.804 taildiff: 1
  44. B:
  45. scale 1.000 1.000
  46. WHG 0.668 1.831
  47. CHG -0.765 -0.396
  48. WSHG 1.850 -0.413
  49. Onge.DG 0.335 -0.394
  50. Turkey_N -0.391 0.405
  51. Levant_PPN -0.355 0.484
  52. EHG_Mesolithic 1.745 1.657
  53. Iraq_Nemrik9_PPN -0.454 -0.183
  54. Iran_GanjDareh_N -0.260 -0.779
  55. Mongolia_North_N 0.592 -0.219
  56. Turkey_Boncuklu_N -0.274 0.495
  57. Russia_AfontovaGora3 1.954 -1.006
  58. Serbia_IronGates_Mesolithic 0.770 2.019
  59. A:
  60. scale 70.071 179.083
  61. EHG 0.678 1.044
  62. Russia_Caucasus_Eneolithic -1.432 0.203
  63. TTK 0.699 -1.367
  64.  
  65.  
  66. full rank
  67. f4info:
  68. f4rank: 3 dof: 0 chisq: 0.000 tail: 1 dofdiff: 11 chisqdiff: 35.804 taildiff: 0.000182417623
  69. B:
  70. scale 79.275 49.484 80.746
  71. WHG 1.264 -0.648 -0.752
  72. CHG -0.984 0.507 -0.709
  73. WSHG 1.158 -2.000 1.622
  74. Onge.DG 0.073 -0.396 0.454
  75. Turkey_N -0.115 0.414 -0.597
  76. Levant_PPN 0.008 0.423 -0.489
  77. EHG_Mesolithic 2.127 -1.684 0.370
  78. Iraq_Nemrik9_PPN -0.412 0.475 -0.251
  79. Iran_GanjDareh_N -0.797 -0.007 -0.082
  80. Mongolia_North_N 0.244 -0.712 0.421
  81. Turkey_Boncuklu_N 0.037 0.307 -0.552
  82. Russia_AfontovaGora3 1.316 -1.888 2.670
  83. Serbia_IronGates_Mesolithic 1.396 -0.767 -0.824
  84. A:
  85. scale 1.732 1.732 1.732
  86. EHG 1.732 0.000 0.000
  87. Russia_Caucasus_Eneolithic 0.000 1.732 0.000
  88. TTK 0.000 0.000 1.732
  89.  
  90.  
  91. best coefficients: 0.356 0.325 0.320
  92. totmean: 0.356 0.325 0.320
  93. boot mean: 0.355 0.325 0.320
  94. std. errors: 0.033 0.019 0.038
  95.  
  96. error covariance (* 1,000,000)
  97. 1111 -23 -1087
  98. -23 364 -341
  99. -1087 -341 1428
  100.  
  101.  
  102. summ: Russia_Khvalynsk_Eneolithic_CHG 3 0.000182 0.355 0.325 0.320 1111 -23 -1087 364 -341 ...
  103. 1428
  104.  
  105. fixed pat wt dof chisq tail prob
  106. 000 0 11 35.804 0.000182418 0.356 0.325 0.320
  107. 001 1 12 120.455 5.01532e-20 0.598 0.402 0.000
  108. 010 1 12 294.118 0 0.222 0.000 0.778
  109. 100 1 12 137.215 2.18332e-23 0.000 0.345 0.655
  110. 011 2 13 716.488 0 1.000 0.000 0.000
  111. 101 2 13 850.214 0 0.000 1.000 0.000
  112. 110 2 13 319.166 0 0.000 0.000 1.000
  113. best pat: 000 0.000182418 - -
  114. best pat: 001 5.01532e-20 chi(nested): 84.651 p-value for nested model: 3.55974e-20
  115. best pat: 110 2.32411e-60 not nested
  116.  
  117. coeffs: 0.356 0.325 0.320
  118.  
  119. ## dscore:: f_4(Base, Fit, Rbase, right2)
  120. ## genstat:: f_4(Base, Fit, right1, right2)
  121.  
  122. details: EHG WHG 0.015947 10.411016
  123. details: Russia_Caucasus_Eneolithic WHG -0.013091 -6.395293
  124. details: TTK WHG -0.009319 -4.352662
  125. dscore: WHG f4: -0.001555 Z: -1.012363
  126.  
  127. details: EHG CHG -0.012416 -8.617436
  128. details: Russia_Caucasus_Eneolithic CHG 0.010247 4.597711
  129. details: TTK CHG -0.008782 -3.877489
  130. dscore: CHG f4: -0.003899 Z: -2.431878
  131.  
  132. details: EHG WSHG 0.014613 8.929201
  133. details: Russia_Caucasus_Eneolithic WSHG -0.040416 -18.567506
  134. details: TTK WSHG 0.020086 8.599005
  135. dscore: WSHG f4: -0.001497 Z: -0.895881
  136.  
  137. details: EHG Onge.DG 0.000925 0.670602
  138. details: Russia_Caucasus_Eneolithic Onge.DG -0.008004 -4.118992
  139. details: TTK Onge.DG 0.005626 2.639351
  140. dscore: Onge.DG f4: -0.000470 Z: -0.313938
  141.  
  142. details: EHG Turkey_N -0.001448 -1.283486
  143. details: Russia_Caucasus_Eneolithic Turkey_N 0.008373 5.269423
  144. details: TTK Turkey_N -0.007400 -4.423763
  145. dscore: Turkey_N f4: -0.000163 Z: -0.135618
  146.  
  147. details: EHG Levant_PPN 0.000107 0.082356
  148. details: Russia_Caucasus_Eneolithic Levant_PPN 0.008552 4.626352
  149. details: TTK Levant_PPN -0.006054 -2.924416
  150. dscore: Levant_PPN f4: 0.000878 Z: 0.616052
  151.  
  152. details: EHG EHG_Mesolithic 0.026836 16.294206
  153. details: Russia_Caucasus_Eneolithic EHG_Mesolithic -0.034029 -15.353557
  154. details: TTK EHG_Mesolithic 0.004581 1.937133
  155. dscore: EHG_Mesolithic f4: -0.000033 Z: -0.019301
  156.  
  157. details: EHG Iraq_Nemrik9_PPN -0.005192 -3.050358
  158. details: Russia_Caucasus_Eneolithic Iraq_Nemrik9_PPN 0.009594 4.018798
  159. details: TTK Iraq_Nemrik9_PPN -0.003113 -1.069276
  160. dscore: Iraq_Nemrik9_PPN f4: 0.000272 Z: 0.147166
  161.  
  162. details: EHG Iran_GanjDareh_N -0.010057 -8.441441
  163. details: Russia_Caucasus_Eneolithic Iran_GanjDareh_N -0.000141 -0.083910
  164. details: TTK Iran_GanjDareh_N -0.001015 -0.569691
  165. dscore: Iran_GanjDareh_N f4: -0.003948 Z: -3.171606
  166.  
  167. details: EHG Mongolia_North_N 0.003075 2.330217
  168. details: Russia_Caucasus_Eneolithic Mongolia_North_N -0.014384 -7.955547
  169. details: TTK Mongolia_North_N 0.005213 2.675140
  170. dscore: Mongolia_North_N f4: -0.001908 Z: -1.381080
  171.  
  172. details: EHG Turkey_Boncuklu_N 0.000468 0.349722
  173. details: Russia_Caucasus_Eneolithic Turkey_Boncuklu_N 0.006208 3.490563
  174. details: TTK Turkey_Boncuklu_N -0.006841 -3.255149
  175. dscore: Turkey_Boncuklu_N f4: -0.000006 Z: -0.004001
  176.  
  177. details: EHG Russia_AfontovaGora3 0.016598 6.938025
  178. details: Russia_Caucasus_Eneolithic Russia_AfontovaGora3 -0.038156 -12.564909
  179. details: TTK Russia_AfontovaGora3 0.033069 9.196726
  180. dscore: Russia_AfontovaGora3 f4: 0.004093 Z: 1.681216
  181.  
  182. details: EHG Serbia_IronGates_Mesolithic 0.017611 13.581625
  183. details: Russia_Caucasus_Eneolithic Serbia_IronGates_Mesolithic -0.015507 -8.662928
  184. details: TTK Serbia_IronGates_Mesolithic -0.010206 -5.734789
  185. dscore: Serbia_IronGates_Mesolithic f4: -0.002031 Z: -1.523672
  186.  
  187. gendstat: Mbuti.DG WHG -1.012
  188. gendstat: Mbuti.DG CHG -2.432
  189. gendstat: Mbuti.DG WSHG -0.896
  190. gendstat: Mbuti.DG Onge.DG -0.314
  191. gendstat: Mbuti.DG Turkey_N -0.136
  192. gendstat: Mbuti.DG Levant_PPN 0.616
  193. gendstat: Mbuti.DG EHG_Mesolithic -0.019
  194. gendstat: Mbuti.DG Iraq_Nemrik9_PPN 0.147
  195. gendstat: Mbuti.DG Iran_GanjDareh_N -3.172
  196. gendstat: Mbuti.DG Mongolia_North_N -1.381
  197. gendstat: Mbuti.DG Turkey_Boncuklu_N -0.004
  198. gendstat: Mbuti.DG Russia_AfontovaGora3 1.681
  199. gendstat: Mbuti.DG Serbia_IronGates_Mesolithic -1.524
  200. gendstat: WHG CHG -1.262
  201. gendstat: WHG WSHG 0.031
  202. gendstat: WHG Onge.DG 0.628
  203. gendstat: WHG Turkey_N 1.050
  204. gendstat: WHG Levant_PPN 1.488
  205. gendstat: WHG EHG_Mesolithic 0.921
  206. gendstat: WHG Iraq_Nemrik9_PPN 0.907
  207. gendstat: WHG Iran_GanjDareh_N -1.403
  208. gendstat: WHG Mongolia_North_N -0.219
  209. gendstat: WHG Turkey_Boncuklu_N 1.015
  210. gendstat: WHG Russia_AfontovaGora3 2.166
  211. gendstat: WHG Serbia_IronGates_Mesolithic -0.474
  212. gendstat: CHG WSHG 1.226
  213. gendstat: CHG Onge.DG 1.944
  214. gendstat: CHG Turkey_N 2.674
  215. gendstat: CHG Levant_PPN 2.880
  216. gendstat: CHG EHG_Mesolithic 1.982
  217. gendstat: CHG Iraq_Nemrik9_PPN 2.120
  218. gendstat: CHG Iran_GanjDareh_N -0.032
  219. gendstat: CHG Mongolia_North_N 1.154
  220. gendstat: CHG Turkey_Boncuklu_N 2.501
  221. gendstat: CHG Russia_AfontovaGora3 2.986
  222. gendstat: CHG Serbia_IronGates_Mesolithic 1.138
  223. gendstat: WSHG Onge.DG 0.569
  224. gendstat: WSHG Turkey_N 0.824
  225. gendstat: WSHG Levant_PPN 1.303
  226. gendstat: WSHG EHG_Mesolithic 0.880
  227. gendstat: WSHG Iraq_Nemrik9_PPN 0.810
  228. gendstat: WSHG Iran_GanjDareh_N -1.430
  229. gendstat: WSHG Mongolia_North_N -0.241
  230. gendstat: WSHG Turkey_Boncuklu_N 0.860
  231. gendstat: WSHG Russia_AfontovaGora3 2.498
  232. gendstat: WSHG Serbia_IronGates_Mesolithic -0.341
  233. gendstat: Onge.DG Turkey_N 0.224
  234. gendstat: Onge.DG Levant_PPN 0.858
  235. gendstat: Onge.DG EHG_Mesolithic 0.246
  236. gendstat: Onge.DG Iraq_Nemrik9_PPN 0.362
  237. gendstat: Onge.DG Iran_GanjDareh_N -2.273
  238. gendstat: Onge.DG Mongolia_North_N -1.016
  239. gendstat: Onge.DG Turkey_Boncuklu_N 0.298
  240. gendstat: Onge.DG Russia_AfontovaGora3 1.827
  241. gendstat: Onge.DG Serbia_IronGates_Mesolithic -1.049
  242. gendstat: Turkey_N Levant_PPN 1.045
  243. gendstat: Turkey_N EHG_Mesolithic 0.085
  244. gendstat: Turkey_N Iraq_Nemrik9_PPN 0.260
  245. gendstat: Turkey_N Iran_GanjDareh_N -3.382
  246. gendstat: Turkey_N Mongolia_North_N -1.402
  247. gendstat: Turkey_N Turkey_Boncuklu_N 0.176
  248. gendstat: Turkey_N Russia_AfontovaGora3 1.800
  249. gendstat: Turkey_N Serbia_IronGates_Mesolithic -1.828
  250. gendstat: Levant_PPN EHG_Mesolithic -0.533
  251. gendstat: Levant_PPN Iraq_Nemrik9_PPN -0.319
  252. gendstat: Levant_PPN Iran_GanjDareh_N -3.411
  253. gendstat: Levant_PPN Mongolia_North_N -1.876
  254. gendstat: Levant_PPN Turkey_Boncuklu_N -0.707
  255. gendstat: Levant_PPN Russia_AfontovaGora3 1.258
  256. gendstat: Levant_PPN Serbia_IronGates_Mesolithic -2.130
  257. gendstat: EHG_Mesolithic Iraq_Nemrik9_PPN 0.144
  258. gendstat: EHG_Mesolithic Iran_GanjDareh_N -2.213
  259. gendstat: EHG_Mesolithic Mongolia_North_N -1.137
  260. gendstat: EHG_Mesolithic Turkey_Boncuklu_N 0.016
  261. gendstat: EHG_Mesolithic Russia_AfontovaGora3 1.719
  262. gendstat: EHG_Mesolithic Serbia_IronGates_Mesolithic -1.469
  263. gendstat: Iraq_Nemrik9_PPN Iran_GanjDareh_N -2.368
  264. gendstat: Iraq_Nemrik9_PPN Mongolia_North_N -1.111
  265. gendstat: Iraq_Nemrik9_PPN Turkey_Boncuklu_N -0.147
  266. gendstat: Iraq_Nemrik9_PPN Russia_AfontovaGora3 1.398
  267. gendstat: Iraq_Nemrik9_PPN Serbia_IronGates_Mesolithic -1.239
  268. gendstat: Iran_GanjDareh_N Mongolia_North_N 1.442
  269. gendstat: Iran_GanjDareh_N Turkey_Boncuklu_N 2.956
  270. gendstat: Iran_GanjDareh_N Russia_AfontovaGora3 3.251
  271. gendstat: Iran_GanjDareh_N Serbia_IronGates_Mesolithic 1.315
  272. gendstat: Mongolia_North_N Turkey_Boncuklu_N 1.373
  273. gendstat: Mongolia_North_N Russia_AfontovaGora3 2.425
  274. gendstat: Mongolia_North_N Serbia_IronGates_Mesolithic -0.089
  275. gendstat: Turkey_Boncuklu_N Russia_AfontovaGora3 1.674
  276. gendstat: Turkey_Boncuklu_N Serbia_IronGates_Mesolithic -1.614
  277. gendstat: Russia_AfontovaGora3 Serbia_IronGates_Mesolithic -2.607
  278.  
  279. removing /tmp/fsx.266
  280. ##end of qpAdm: 6.401 seconds cpu 1.106 Mbytes in use
  281.  
  282. Admixtools 2 output
  283.  
  284. $weights
  285. # A tibble: 3 × 5
  286. target left weight se z
  287. <chr> <chr> <dbl> <dbl> <dbl>
  288. 1 Russia_Khvalynsk_Eneolithic_CHG EHG 0.419 0.0787 5.32
  289. 2 Russia_Khvalynsk_Eneolithic_CHG Russia_Caucasus_Eneolithic 0.293 0.0450 6.52
  290. 3 Russia_Khvalynsk_Eneolithic_CHG TTK 0.288 0.0839 3.43
  291.  
  292. $rankdrop
  293. # A tibble: 3 × 7
  294. f4rank dof chisq p dofdiff chisqdiff p_nested
  295. <int> <int> <dbl> <dbl> <int> <dbl> <dbl>
  296. 1 2 11 5.75 8.90e- 1 13 151. 1.07e- 25
  297. 2 1 24 157. 1.54e- 21 15 573. 2.21e-112
  298. 3 0 39 730. 3.10e-128 NA NA NA
  299.  
  300. $popdrop
  301. # A tibble: 7 × 14
  302. pat wt dof chisq p f4rank EHG Russia_Caucasus_Eneolithic TTK feasible best dofdiff chisqdiff p_nested
  303. <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <lgl> <lgl> <dbl> <dbl> <dbl>
  304. 1 000 0 11 5.75 8.90e- 1 2 0.419 0.293 0.288 TRUE NA NA NA NA
  305. 2 001 1 12 29.1 3.78e- 3 1 0.633 0.367 NA TRUE TRUE 0 -42.4 1
  306. 3 010 1 12 71.5 1.69e-10 1 0.305 NA 0.695 TRUE TRUE 0 11.9 0
  307. 4 100 1 12 59.6 2.64e- 8 1 NA 0.320 0.680 TRUE TRUE NA NA NA
  308. 5 011 2 13 203. 2.90e-36 0 1 NA NA TRUE NA NA NA NA
  309. 6 101 2 13 263. 1.25e-48 0 NA 1 NA TRUE NA NA NA NA
  310. 7 110 2 13 108. 5.49e-17 0 NA NA 1 TRUE NA NA NA NA
  311.  
  312. > right = c('Mbuti.DG', 'WHG', 'CHG', 'WSHG', 'Onge.DG', 'Turkey_N', 'Levant_PPN', 'EHG_Mesolithic', 'Iraq_Nemrik9_PPN', 'Iran_GanjDareh_N', 'Mongolia_North_N', 'Turkey_Boncuklu_N', 'Russia_AfontovaGora3', 'Serbia_IronGates_Mesolithic')
  313. > left = c('EHG', 'Russia_Caucasus_Eneolithic', 'TTK')
  314. > target = 'Russia_Khvalynsk_Eneolithic_CHG'
  315. > qpadm(prefix, left, right, target, maxmiss = 1, adjust_pseudohaploid = TRUE)
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