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misnomer001

Loebanr pass

misnomer001
Aug 12th, 2022
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  1. qpAdm: parameter file: parqpadm
  2. ### THE INPUT PARAMETERS
  3. ##PARAMETER NAME: VALUE
  4. popleft: left
  5. popright: right
  6. details: YES
  7. allsnps: YES
  8. inbreed: NO
  9. oldallsnps: NO
  10. S1: newpush
  11. S1X: newpush
  12. indivname: newpush.ind
  13. snpname: newpush.snp
  14. genotypename: newpush.geno
  15. ## qpAdm version: 1520
  16. seed: 1089612823
  17. inbreed set NO
  18. inbreed set NO
  19. tmp: /tmp/fsx.19446
  20.  
  21. left pops:
  22. Pakistan_Loebanr_IA
  23. Swat_nosteppe
  24. Kazakhstan_MLBA_Dali
  25. Uzbekistan_Dzharkutan_BA_1
  26.  
  27. right pops:
  28. Mbuti.DG
  29. CHG
  30. EHG
  31. China_YR_MN
  32. Turkey_Boncuklu_N
  33. Russia_Shamanka_Eneolithic.SG
  34. WSHG
  35. Turkey_N
  36. PPN
  37. Serbia_IronGates_Mesolithic
  38. Russia_MLBA_Sintashta
  39. Iran_GanjDareh_N
  40. ONG.SG
  41.  
  42. codimension 1
  43. f4info:
  44. f4rank: 2 dof: 10 chisq: 10.081 tail: 0.43337702 dofdiff: 12 chisqdiff: -10.081 taildiff: 1
  45. B:
  46. scale 1.000 1.000
  47. CHG 0.536 -1.210
  48. EHG 1.604 0.664
  49. China_YR_MN -0.077 1.303
  50. Turkey_Boncuklu_N 1.086 -0.375
  51. Russia_Shamanka_Eneolithic.SG 0.163 1.238
  52. WSHG 1.112 0.610
  53. Turkey_N 0.997 -0.710
  54. PPN 0.778 -0.930
  55. Serbia_IronGates_Mesolithic 1.682 0.543
  56. Russia_MLBA_Sintashta 1.488 0.070
  57. Iran_GanjDareh_N -0.079 -1.857
  58. ONG.SG -0.202 1.112
  59. A:
  60. scale 117.529 297.658
  61. Swat_nosteppe -0.442 0.491
  62. Kazakhstan_MLBA_Dali 1.651 0.362
  63. Uzbekistan_Dzharkutan_BA_1 0.282 -1.621
  64.  
  65.  
  66. full rank
  67. f4info:
  68. f4rank: 3 dof: 0 chisq: 0.000 tail: 1 dofdiff: 10 chisqdiff: 10.081 taildiff: 0.43337702
  69. B:
  70. scale 233.119 70.441 170.256
  71. CHG -1.126 0.401 1.256
  72. EHG -1.278 1.636 -0.022
  73. China_YR_MN 0.465 0.029 -1.282
  74. Turkey_Boncuklu_N -1.173 1.050 0.778
  75. Russia_Shamanka_Eneolithic.SG 0.296 0.273 -1.105
  76. WSHG -0.759 1.171 -0.106
  77. Turkey_N -1.172 0.940 1.070
  78. PPN -1.121 0.684 1.173
  79. Serbia_IronGates_Mesolithic -1.228 1.743 0.204
  80. Russia_MLBA_Sintashta -1.398 1.470 0.500
  81. Iran_GanjDareh_N -0.698 -0.229 1.666
  82. ONG.SG 0.511 -0.109 -1.164
  83. A:
  84. scale 1.732 1.732 1.732
  85. Swat_nosteppe 1.732 0.000 0.000
  86. Kazakhstan_MLBA_Dali 0.000 1.732 0.000
  87. Uzbekistan_Dzharkutan_BA_1 0.000 0.000 1.732
  88.  
  89.  
  90. best coefficients: 0.642 0.134 0.224
  91. totmean: 0.642 0.134 0.224
  92. boot mean: 0.642 0.134 0.224
  93. std. errors: 0.017 0.010 0.018
  94.  
  95. error covariance (* 1,000,000)
  96. 298 -41 -257
  97. -41 93 -52
  98. -257 -52 309
  99.  
  100.  
  101. summ: Pakistan_Loebanr_IA 3 0.433377 0.642 0.134 0.224 298 -41 -257 93 -52 ...
  102. 309
  103.  
  104. fixed pat wt dof chisq tail prob
  105. 000 0 10 10.081 0.433377 0.642 0.134 0.224
  106. 001 1 11 141.391 8.49045e-25 0.829 0.171 0.000
  107. 010 1 11 171.395 0 0.722 0.000 0.278
  108. 100 1 11 919.747 0 0.000 0.202 0.798
  109. 011 2 12 342.517 0 1.000 0.000 0.000
  110. 101 2 12 1521.733 0 0.000 1.000 0.000
  111. 110 2 12 1033.638 0 0.000 0.000 1.000
  112. best pat: 000 0.433377 - -
  113. best pat: 001 8.49045e-25 chi(nested): 131.309 p-value for nested model: 2.11885e-30
  114. best pat: 011 5.31314e-66 chi(nested): 201.126 p-value for nested model: 1.18621e-45
  115.  
  116. coeffs: 0.642 0.134 0.224
  117.  
  118. ## dscore:: f_4(Base, Fit, Rbase, right2)
  119. ## genstat:: f_4(Base, Fit, right1, right2)
  120.  
  121. details: Swat_nosteppe CHG -0.004831 -7.417504
  122. details: Kazakhstan_MLBA_Dali CHG 0.005686 5.122072
  123. details: Uzbekistan_Dzharkutan_BA_1 CHG 0.007376 10.266308
  124. dscore: CHG f4: -0.000689 Z: -1.342966
  125.  
  126. details: Swat_nosteppe EHG -0.005482 -8.707108
  127. details: Kazakhstan_MLBA_Dali EHG 0.023218 20.661154
  128. details: Uzbekistan_Dzharkutan_BA_1 EHG -0.000128 -0.186444
  129. dscore: EHG f4: -0.000447 Z: -0.895248
  130.  
  131. details: Swat_nosteppe China_YR_MN 0.001996 3.397163
  132. details: Kazakhstan_MLBA_Dali China_YR_MN 0.000414 0.397428
  133. details: Uzbekistan_Dzharkutan_BA_1 China_YR_MN -0.007532 -11.793481
  134. dscore: China_YR_MN f4: -0.000352 Z: -0.757528
  135.  
  136. details: Swat_nosteppe Turkey_Boncuklu_N -0.005033 -9.066938
  137. details: Kazakhstan_MLBA_Dali Turkey_Boncuklu_N 0.014903 14.310173
  138. details: Uzbekistan_Dzharkutan_BA_1 Turkey_Boncuklu_N 0.004569 7.182628
  139. dscore: Turkey_Boncuklu_N f4: -0.000216 Z: -0.490635
  140.  
  141. details: Swat_nosteppe Russia_Shamanka_Eneolithic.SG 0.001270 2.290116
  142. details: Kazakhstan_MLBA_Dali Russia_Shamanka_Eneolithic.SG 0.003881 3.964429
  143. details: Uzbekistan_Dzharkutan_BA_1 Russia_Shamanka_Eneolithic.SG -0.006492 -10.823285
  144. dscore: Russia_Shamanka_Eneolithic.SG f4: -0.000122 Z: -0.284855
  145.  
  146. details: Swat_nosteppe WSHG -0.003257 -4.897870
  147. details: Kazakhstan_MLBA_Dali WSHG 0.016623 13.266927
  148. details: Uzbekistan_Dzharkutan_BA_1 WSHG -0.000624 -0.867638
  149. dscore: WSHG f4: -0.000010 Z: -0.019688
  150.  
  151. details: Swat_nosteppe Turkey_N -0.005029 -10.449160
  152. details: Kazakhstan_MLBA_Dali Turkey_N 0.013345 15.792722
  153. details: Uzbekistan_Dzharkutan_BA_1 Turkey_N 0.006284 11.450955
  154. dscore: Turkey_N f4: -0.000037 Z: -0.097672
  155.  
  156. details: Swat_nosteppe PPN -0.004809 -7.744438
  157. details: Kazakhstan_MLBA_Dali PPN 0.009716 9.184872
  158. details: Uzbekistan_Dzharkutan_BA_1 PPN 0.006887 10.263236
  159. dscore: PPN f4: -0.000246 Z: -0.508203
  160.  
  161. details: Swat_nosteppe Serbia_IronGates_Mesolithic -0.005266 -9.646369
  162. details: Kazakhstan_MLBA_Dali Serbia_IronGates_Mesolithic 0.024742 24.992853
  163. details: Uzbekistan_Dzharkutan_BA_1 Serbia_IronGates_Mesolithic 0.001196 2.014868
  164. dscore: Serbia_IronGates_Mesolithic f4: 0.000193 Z: 0.448723
  165.  
  166. details: Swat_nosteppe Russia_MLBA_Sintashta -0.005997 -12.308846
  167. details: Kazakhstan_MLBA_Dali Russia_MLBA_Sintashta 0.020874 24.751563
  168. details: Uzbekistan_Dzharkutan_BA_1 Russia_MLBA_Sintashta 0.002935 5.637706
  169. dscore: Russia_MLBA_Sintashta f4: -0.000404 Z: -1.039282
  170.  
  171. details: Swat_nosteppe Iran_GanjDareh_N -0.002994 -5.481238
  172. details: Kazakhstan_MLBA_Dali Iran_GanjDareh_N -0.003252 -3.485621
  173. details: Uzbekistan_Dzharkutan_BA_1 Iran_GanjDareh_N 0.009784 16.409627
  174. dscore: Iran_GanjDareh_N f4: -0.000163 Z: -0.389943
  175.  
  176. details: Swat_nosteppe ONG.SG 0.002192 3.700741
  177. details: Kazakhstan_MLBA_Dali ONG.SG -0.001546 -1.546867
  178. details: Uzbekistan_Dzharkutan_BA_1 ONG.SG -0.006835 -11.209014
  179. dscore: ONG.SG f4: -0.000332 Z: -0.705062
  180.  
  181. gendstat: Mbuti.DG CHG -1.343
  182. gendstat: Mbuti.DG EHG -0.895
  183. gendstat: Mbuti.DG China_YR_MN -0.758
  184. gendstat: Mbuti.DG Turkey_Boncuklu_N -0.491
  185. gendstat: Mbuti.DG Russia_Shamanka_Eneolithic.SG -0.285
  186. gendstat: Mbuti.DG WSHG -0.020
  187. gendstat: Mbuti.DG Turkey_N -0.098
  188. gendstat: Mbuti.DG PPN -0.508
  189. gendstat: Mbuti.DG Serbia_IronGates_Mesolithic 0.449
  190. gendstat: Mbuti.DG Russia_MLBA_Sintashta -1.039
  191. gendstat: Mbuti.DG Iran_GanjDareh_N -0.390
  192. gendstat: Mbuti.DG ONG.SG -0.705
  193. gendstat: CHG EHG 0.460
  194. gendstat: CHG China_YR_MN 0.603
  195. gendstat: CHG Turkey_Boncuklu_N 0.965
  196. gendstat: CHG Russia_Shamanka_Eneolithic.SG 1.088
  197. gendstat: CHG WSHG 1.195
  198. gendstat: CHG Turkey_N 1.521
  199. gendstat: CHG PPN 0.810
  200. gendstat: CHG Serbia_IronGates_Mesolithic 1.916
  201. gendstat: CHG Russia_MLBA_Sintashta 0.697
  202. gendstat: CHG Iran_GanjDareh_N 1.150
  203. gendstat: CHG ONG.SG 0.655
  204. gendstat: EHG China_YR_MN 0.180
  205. gendstat: EHG Turkey_Boncuklu_N 0.494
  206. gendstat: EHG Russia_Shamanka_Eneolithic.SG 0.676
  207. gendstat: EHG WSHG 0.897
  208. gendstat: EHG Turkey_N 0.952
  209. gendstat: EHG PPN 0.388
  210. gendstat: EHG Serbia_IronGates_Mesolithic 1.633
  211. gendstat: EHG Russia_MLBA_Sintashta 0.112
  212. gendstat: EHG Iran_GanjDareh_N 0.582
  213. gendstat: EHG ONG.SG 0.214
  214. gendstat: China_YR_MN Turkey_Boncuklu_N 0.269
  215. gendstat: China_YR_MN Russia_Shamanka_Eneolithic.SG 0.713
  216. gendstat: China_YR_MN WSHG 0.628
  217. gendstat: China_YR_MN Turkey_N 0.694
  218. gendstat: China_YR_MN PPN 0.197
  219. gendstat: China_YR_MN Serbia_IronGates_Mesolithic 1.158
  220. gendstat: China_YR_MN Russia_MLBA_Sintashta -0.118
  221. gendstat: China_YR_MN Iran_GanjDareh_N 0.378
  222. gendstat: China_YR_MN ONG.SG 0.047
  223. gendstat: Turkey_Boncuklu_N Russia_Shamanka_Eneolithic.SG 0.207
  224. gendstat: Turkey_Boncuklu_N WSHG 0.384
  225. gendstat: Turkey_Boncuklu_N Turkey_N 0.594
  226. gendstat: Turkey_Boncuklu_N PPN -0.066
  227. gendstat: Turkey_Boncuklu_N Serbia_IronGates_Mesolithic 1.123
  228. gendstat: Turkey_Boncuklu_N Russia_MLBA_Sintashta -0.561
  229. gendstat: Turkey_Boncuklu_N Iran_GanjDareh_N 0.118
  230. gendstat: Turkey_Boncuklu_N ONG.SG -0.229
  231. gendstat: Russia_Shamanka_Eneolithic.SG WSHG 0.222
  232. gendstat: Russia_Shamanka_Eneolithic.SG Turkey_N 0.204
  233. gendstat: Russia_Shamanka_Eneolithic.SG PPN -0.241
  234. gendstat: Russia_Shamanka_Eneolithic.SG Serbia_IronGates_Mesolithic 0.737
  235. gendstat: Russia_Shamanka_Eneolithic.SG Russia_MLBA_Sintashta -0.707
  236. gendstat: Russia_Shamanka_Eneolithic.SG Iran_GanjDareh_N -0.094
  237. gendstat: Russia_Shamanka_Eneolithic.SG ONG.SG -0.536
  238. gendstat: WSHG Turkey_N -0.055
  239. gendstat: WSHG PPN -0.394
  240. gendstat: WSHG Serbia_IronGates_Mesolithic 0.433
  241. gendstat: WSHG Russia_MLBA_Sintashta -0.885
  242. gendstat: WSHG Iran_GanjDareh_N -0.292
  243. gendstat: WSHG ONG.SG -0.592
  244. gendstat: Turkey_N PPN -0.532
  245. gendstat: Turkey_N Serbia_IronGates_Mesolithic 0.753
  246. gendstat: Turkey_N Russia_MLBA_Sintashta -1.481
  247. gendstat: Turkey_N Iran_GanjDareh_N -0.330
  248. gendstat: Turkey_N ONG.SG -0.637
  249. gendstat: PPN Serbia_IronGates_Mesolithic 0.969
  250. gendstat: PPN Russia_MLBA_Sintashta -0.386
  251. gendstat: PPN Iran_GanjDareh_N 0.167
  252. gendstat: PPN ONG.SG -0.153
  253. gendstat: Serbia_IronGates_Mesolithic Russia_MLBA_Sintashta -2.291
  254. gendstat: Serbia_IronGates_Mesolithic Iran_GanjDareh_N -0.843
  255. gendstat: Serbia_IronGates_Mesolithic ONG.SG -1.119
  256. gendstat: Russia_MLBA_Sintashta Iran_GanjDareh_N 0.679
  257. gendstat: Russia_MLBA_Sintashta ONG.SG 0.163
  258. gendstat: Iran_GanjDareh_N ONG.SG -0.349
  259.  
  260. removing /tmp/fsx.19446
  261. ##end of qpAdm: 11.086 seconds cpu 1.040 Mbytes in use
  262.  
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