API tools faq
paste
misnomer001

yamnaya sarazm pass

misnomer001
Aug 1st, 2022
382
0
Never
Add comment
Not a member of Pastebin yet? Sign Up, it unlocks many cool features!
text 17.26 KB | None | 0 0
raw download clone embed print report
  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: 2067012370
  17. inbreed set NO
  18. inbreed set NO
  19. tmp: /tmp/fsx.13438
  20.  
  21. left pops:
  22. Russia_Samara_EBA_Yamnaya
  23. Russia_HG_Samara
  24. Georgia_Kotias.SG
  25. Tajikistan_C_Sarazm
  26. Germany_EN_LBK
  27. Ukraine_N
  28.  
  29. right pops:
  30. Mbuti.DG
  31. Serbia_IronGates_Mesolithic
  32. Iran_GanjDareh_N
  33. Sunghir
  34. China_YR_MN
  35. Turkey_N
  36. Georgia_Satsurblia.SG
  37. Russia_Yana_UP.SG
  38. Russia_Shamanka_Eneolithic.SG
  39. ONG.SG
  40. WSHG
  41. Tarim_EMBA1
  42.  
  43. codimension 1
  44. f4info:
  45. f4rank: 4 dof: 7 chisq: 10.742 tail: 0.150255735 dofdiff: 9 chisqdiff: -10.742 taildiff: 1
  46. B:
  47. scale 1.000 1.000 1.000 1.000
  48. Serbia_IronGates_Mesolithic 1.793 -1.610 2.342 1.299
  49. Iran_GanjDareh_N -0.289 0.855 -0.076 1.789
  50. Sunghir 0.501 -0.406 0.467 -0.130
  51. China_YR_MN 0.401 0.177 0.093 0.503
  52. Turkey_N -0.377 -1.835 -0.664 -2.325
  53. Georgia_Satsurblia.SG -0.624 1.396 2.012 -0.131
  54. Russia_Yana_UP.SG 0.578 -0.088 0.267 -0.314
  55. Russia_Shamanka_Eneolithic.SG 0.539 0.319 0.038 0.058
  56. ONG.SG 0.328 0.242 -0.082 0.149
  57. WSHG 1.798 0.698 -0.227 -0.347
  58. Tarim_EMBA1 1.672 1.228 -0.813 -0.419
  59. A:
  60. scale 87.320 156.234 265.907 502.334
  61. Russia_HG_Samara 1.040 0.122 -0.207 -0.684
  62. Georgia_Kotias.SG -1.358 0.739 1.746 -0.646
  63. Tajikistan_C_Sarazm -0.682 0.356 -1.132 1.810
  64. Germany_EN_LBK -1.037 -1.729 -0.262 -0.140
  65. Ukraine_N 0.729 -1.150 0.748 0.906
  66.  
  67.  
  68. full rank
  69. f4info:
  70. f4rank: 5 dof: 0 chisq: 0.000 tail: 1 dofdiff: 7 chisqdiff: 10.742 taildiff: 0.150255735
  71. B:
  72. scale 88.881 59.521 95.303 59.215 83.013
  73. Serbia_IronGates_Mesolithic 1.312 -1.360 -2.303 -0.407 2.936
  74. Iran_GanjDareh_N -0.628 0.308 0.939 -0.413 -0.503
  75. Sunghir 0.369 -0.443 -0.801 -0.144 0.670
  76. China_YR_MN 0.259 -0.358 -0.223 -0.455 0.253
  77. Turkey_N -0.369 -0.291 -0.741 1.507 0.331
  78. Georgia_Satsurblia.SG -0.901 1.780 -0.212 -0.640 -0.876
  79. Russia_Yana_UP.SG 0.453 -0.489 -0.816 -0.407 0.422
  80. Russia_Shamanka_Eneolithic.SG 0.448 -0.440 -0.434 -0.637 0.169
  81. ONG.SG 0.170 -0.336 -0.239 -0.440 0.042
  82. WSHG 2.056 -1.557 -1.282 -1.727 0.718
  83. Tarim_EMBA1 1.752 -1.583 -0.986 -2.002 0.091
  84. A:
  85. scale 2.236 2.236 2.236 2.236 2.236
  86. Russia_HG_Samara 2.236 0.000 0.000 0.000 0.000
  87. Georgia_Kotias.SG 0.000 2.236 0.000 0.000 0.000
  88. Tajikistan_C_Sarazm 0.000 0.000 2.236 0.000 0.000
  89. Germany_EN_LBK 0.000 0.000 0.000 2.236 0.000
  90. Ukraine_N 0.000 0.000 0.000 0.000 2.236
  91.  
  92.  
  93. best coefficients: 0.441 0.179 0.209 0.111 0.059
  94. totmean: 0.441 0.179 0.209 0.111 0.059
  95. boot mean: 0.442 0.180 0.208 0.111 0.058
  96. std. errors: 0.038 0.028 0.036 0.014 0.030
  97.  
  98. error covariance (* 1,000,000)
  99. 1410 368 -915 197 -1059
  100. 368 783 -847 -28 -276
  101. -915 -847 1302 -159 619
  102. 197 -28 -159 186 -196
  103. -1059 -276 619 -196 913
  104.  
  105.  
  106. summ: Russia_Samara_EBA_Yamnaya 5 0.150256 0.442 0.180 0.208 0.111 0.058 1410 368 -915 197 -1059 ...
  107. 783 -847 -28 -276 1302 ...
  108. -159 619 186 -196 913
  109.  
  110. fixed pat wt dof chisq tail prob
  111. 00000 0 7 10.742 0.150256 0.441 0.179 0.209 0.111 0.059
  112. 00001 1 8 14.637 0.0665971 0.509 0.198 0.170 0.124 0.000
  113. 00010 1 8 80.216 4.42303e-14 0.384 0.231 0.256 0.000 0.129
  114. 00100 1 8 35.779 1.92757e-05 0.598 0.319 0.000 0.134 -0.051 infeasible
  115. 01000 1 8 80.509 3.86149e-14 0.318 0.000 0.433 0.104 0.145
  116. 10000 1 8 177.000 0 0.000 -0.062 0.653 0.045 0.364 infeasible
  117. 00011 2 9 99.358 2.12188e-17 0.549 0.345 0.106 0.000 0.000
  118. 00101 2 9 45.126 8.74305e-07 0.547 0.332 0.000 0.121 0.000
  119. 00110 2 9 107.404 4.96051e-19 0.558 0.434 0.000 0.000 0.008
  120. 01001 2 9 74.435 2.04291e-12 0.495 0.000 0.362 0.142 0.000
  121. 01010 2 9 134.917 1.15316e-24 0.222 0.000 0.540 0.000 0.238
  122. 01100 2 9 190.247 0 1.164 0.000 0.000 0.299 -0.463 infeasible
  123. 10001 2 9 389.822 0 0.000 -3.383 3.772 0.610 0.000 infeasible
  124. 10010 2 9 724.200 0 0.000 0.249 0.368 0.000 0.383
  125. 10100 2 9 547.476 0 0.000 0.624 0.000 -0.045 0.421 infeasible
  126. 11000 2 9 184.422 0 0.000 0.000 0.595 0.041 0.364
  127. 00111 3 10 106.804 2.34935e-18 0.568 0.432 0.000 0.000 0.000
  128. 01011 3 10 178.359 0 0.531 0.000 0.469 0.000 0.000
  129. 01101 3 10 330.387 0 0.734 0.000 0.000 0.266 0.000
  130. 01110 3 10 347.751 0 1.981 0.000 0.000 0.000 -0.981 infeasible
  131. 10011 3 10 427.715 0 0.000 -4.195 5.195 0.000 0.000 infeasible
  132. 10101 3 10 1102.704 0 0.000 1.285 0.000 -0.285 0.000 infeasible
  133. 10110 3 10 559.148 0 0.000 0.593 0.000 0.000 0.407
  134. 11001 3 10 960.473 0 0.000 0.000 0.904 0.096 0.000
  135. 11010 3 10 187.206 0 0.000 0.000 0.621 0.000 0.379
  136. 11100 3 10 2364.856 0 0.000 0.000 0.000 0.335 0.665
  137. 01111 4 11 583.675 0 1.000 0.000 0.000 0.000 0.000
  138. 10111 4 11 1189.591 0 0.000 1.000 0.000 0.000 0.000
  139. 11011 4 11 990.473 0 0.000 0.000 1.000 0.000 0.000
  140. 11101 4 11 5218.938 0 0.000 0.000 0.000 1.000 0.000
  141. 11110 4 11 3074.779 0 0.000 0.000 0.000 0.000 1.000
  142. best pat: 00000 0.150256 - -
  143. best pat: 00001 0.0665971 chi(nested): 3.895 p-value for nested model: 0.0484381
  144. best pat: 00101 8.74305e-07 chi(nested): 30.489 p-value for nested model: 3.35724e-08
  145. best pat: 00111 2.34935e-18 chi(nested): 61.678 p-value for nested model: 4.04544e-15
  146. best pat: 01111 4.34112e-118 chi(nested): 476.871 p-value for nested model: 1.02693e-105
  147.  
  148. coeffs: 0.441 0.179 0.209 0.111 0.059
  149.  
  150. ## dscore:: f_4(Base, Fit, Rbase, right2)
  151. ## genstat:: f_4(Base, Fit, right1, right2)
  152.  
  153. details: Russia_HG_Samara Serbia_IronGates_Mesolithic 0.014765 10.546054
  154. details: Georgia_Kotias.SG Serbia_IronGates_Mesolithic -0.022853 -16.687912
  155. details: Tajikistan_C_Sarazm Serbia_IronGates_Mesolithic -0.024167 -22.120535
  156. details: Germany_EN_LBK Serbia_IronGates_Mesolithic -0.006866 -8.282240
  157. details: Ukraine_N Serbia_IronGates_Mesolithic 0.035374 42.430817
  158. dscore: Serbia_IronGates_Mesolithic f4: -0.001315 Z: -1.556158
  159.  
  160. details: Russia_HG_Samara Iran_GanjDareh_N -0.007068 -5.195432
  161. details: Georgia_Kotias.SG Iran_GanjDareh_N 0.005176 4.101718
  162. details: Tajikistan_C_Sarazm Iran_GanjDareh_N 0.009852 8.907819
  163. details: Germany_EN_LBK Iran_GanjDareh_N -0.006970 -9.145991
  164. details: Ukraine_N Iran_GanjDareh_N -0.006065 -7.816298
  165. dscore: Iran_GanjDareh_N f4: -0.001260 Z: -1.585732
  166.  
  167. details: Russia_HG_Samara Sunghir 0.004153 2.885002
  168. details: Georgia_Kotias.SG Sunghir -0.007443 -5.483072
  169. details: Tajikistan_C_Sarazm Sunghir -0.008409 -6.831974
  170. details: Germany_EN_LBK Sunghir -0.002435 -2.962904
  171. details: Ukraine_N Sunghir 0.008073 9.882591
  172. dscore: Sunghir f4: -0.001057 Z: -1.217219
  173.  
  174. details: Russia_HG_Samara China_YR_MN 0.002919 1.979495
  175. details: Georgia_Kotias.SG China_YR_MN -0.006009 -4.321181
  176. details: Tajikistan_C_Sarazm China_YR_MN -0.002338 -1.898860
  177. details: Germany_EN_LBK China_YR_MN -0.007678 -9.345003
  178. details: Ukraine_N China_YR_MN 0.003053 3.772553
  179. dscore: China_YR_MN f4: -0.000954 Z: -1.103497
  180.  
  181. details: Russia_HG_Samara Turkey_N -0.004157 -3.372694
  182. details: Georgia_Kotias.SG Turkey_N -0.004882 -4.107325
  183. details: Tajikistan_C_Sarazm Turkey_N -0.007777 -8.388653
  184. details: Germany_EN_LBK Turkey_N 0.025452 34.345337
  185. details: Ukraine_N Turkey_N 0.003982 5.520084
  186. dscore: Turkey_N f4: -0.001265 Z: -1.757082
  187.  
  188. details: Russia_HG_Samara Georgia_Satsurblia.SG -0.010135 -5.447308
  189. details: Georgia_Kotias.SG Georgia_Satsurblia.SG 0.029914 14.002921
  190. details: Tajikistan_C_Sarazm Georgia_Satsurblia.SG -0.002221 -1.426447
  191. details: Germany_EN_LBK Georgia_Satsurblia.SG -0.010809 -10.228589
  192. details: Ukraine_N Georgia_Satsurblia.SG -0.010556 -10.018276
  193. dscore: Georgia_Satsurblia.SG f4: -0.001398 Z: -1.222699
  194.  
  195. details: Russia_HG_Samara Russia_Yana_UP.SG 0.005091 3.376222
  196. details: Georgia_Kotias.SG Russia_Yana_UP.SG -0.008214 -5.787946
  197. details: Tajikistan_C_Sarazm Russia_Yana_UP.SG -0.008557 -6.577524
  198. details: Germany_EN_LBK Russia_Yana_UP.SG -0.006877 -8.183082
  199. details: Ukraine_N Russia_Yana_UP.SG 0.005088 5.993939
  200. dscore: Russia_Yana_UP.SG f4: -0.001484 Z: -1.662747
  201.  
  202. details: Russia_HG_Samara Russia_Shamanka_Eneolithic.SG 0.005040 3.807964
  203. details: Georgia_Kotias.SG Russia_Shamanka_Eneolithic.SG -0.007387 -5.823081
  204. details: Tajikistan_C_Sarazm Russia_Shamanka_Eneolithic.SG -0.004557 -4.044659
  205. details: Germany_EN_LBK Russia_Shamanka_Eneolithic.SG -0.010750 -14.562522
  206. details: Ukraine_N Russia_Shamanka_Eneolithic.SG 0.002039 2.646830
  207. dscore: Russia_Shamanka_Eneolithic.SG f4: -0.001133 Z: -1.441984
  208.  
  209. details: Russia_HG_Samara ONG.SG 0.001913 1.303844
  210. details: Georgia_Kotias.SG ONG.SG -0.005649 -4.094569
  211. details: Tajikistan_C_Sarazm ONG.SG -0.002506 -2.034593
  212. details: Germany_EN_LBK ONG.SG -0.007431 -9.597912
  213. details: Ukraine_N ONG.SG 0.000500 0.626770
  214. dscore: ONG.SG f4: -0.001492 Z: -1.640840
  215.  
  216. details: Russia_HG_Samara WSHG 0.023136 13.213357
  217. details: Georgia_Kotias.SG WSHG -0.026164 -16.643721
  218. details: Tajikistan_C_Sarazm WSHG -0.013455 -9.498954
  219. details: Germany_EN_LBK WSHG -0.029170 -29.289642
  220. details: Ukraine_N WSHG 0.008654 8.917625
  221. dscore: WSHG f4: -0.000047 Z: -0.044915
  222.  
  223. details: Russia_HG_Samara Tarim_EMBA1 0.019709 11.286019
  224. details: Georgia_Kotias.SG Tarim_EMBA1 -0.026594 -16.615247
  225. details: Tajikistan_C_Sarazm Tarim_EMBA1 -0.010346 -6.970369
  226. details: Germany_EN_LBK Tarim_EMBA1 -0.033807 -35.410950
  227. details: Ukraine_N Tarim_EMBA1 0.001099 1.141999
  228. dscore: Tarim_EMBA1 f4: -0.001948 Z: -1.857483
  229.  
  230. gendstat: Mbuti.DG Serbia_IronGates_Mesolithic -1.556
  231. gendstat: Mbuti.DG Iran_GanjDareh_N -1.586
  232. gendstat: Mbuti.DG Sunghir -1.217
  233. gendstat: Mbuti.DG China_YR_MN -1.103
  234. gendstat: Mbuti.DG Turkey_N -1.757
  235. gendstat: Mbuti.DG Georgia_Satsurblia.SG -1.223
  236. gendstat: Mbuti.DG Russia_Yana_UP.SG -1.663
  237. gendstat: Mbuti.DG Russia_Shamanka_Eneolithic.SG -1.442
  238. gendstat: Mbuti.DG ONG.SG -1.641
  239. gendstat: Mbuti.DG WSHG -0.045
  240. gendstat: Mbuti.DG Tarim_EMBA1 -1.857
  241. gendstat: Serbia_IronGates_Mesolithic Iran_GanjDareh_N 0.065
  242. gendstat: Serbia_IronGates_Mesolithic Sunghir 0.344
  243. gendstat: Serbia_IronGates_Mesolithic China_YR_MN 0.410
  244. gendstat: Serbia_IronGates_Mesolithic Turkey_N 0.080
  245. gendstat: Serbia_IronGates_Mesolithic Georgia_Satsurblia.SG -0.072
  246. gendstat: Serbia_IronGates_Mesolithic Russia_Yana_UP.SG -0.210
  247. gendstat: Serbia_IronGates_Mesolithic Russia_Shamanka_Eneolithic.SG 0.229
  248. gendstat: Serbia_IronGates_Mesolithic ONG.SG -0.200
  249. gendstat: Serbia_IronGates_Mesolithic WSHG 1.346
  250. gendstat: Serbia_IronGates_Mesolithic Tarim_EMBA1 -0.666
  251. gendstat: Iran_GanjDareh_N Sunghir 0.239
  252. gendstat: Iran_GanjDareh_N China_YR_MN 0.357
  253. gendstat: Iran_GanjDareh_N Turkey_N -0.007
  254. gendstat: Iran_GanjDareh_N Georgia_Satsurblia.SG -0.129
  255. gendstat: Iran_GanjDareh_N Russia_Yana_UP.SG -0.244
  256. gendstat: Iran_GanjDareh_N Russia_Shamanka_Eneolithic.SG 0.161
  257. gendstat: Iran_GanjDareh_N ONG.SG -0.265
  258. gendstat: Iran_GanjDareh_N WSHG 1.217
  259. gendstat: Iran_GanjDareh_N Tarim_EMBA1 -0.700
  260. gendstat: Sunghir China_YR_MN 0.118
  261. gendstat: Sunghir Turkey_N -0.281
  262. gendstat: Sunghir Georgia_Satsurblia.SG -0.299
  263. gendstat: Sunghir Russia_Yana_UP.SG -0.502
  264. gendstat: Sunghir Russia_Shamanka_Eneolithic.SG -0.098
  265. gendstat: Sunghir ONG.SG -0.500
  266. gendstat: Sunghir WSHG 1.007
  267. gendstat: Sunghir Tarim_EMBA1 -0.919
  268. gendstat: China_YR_MN Turkey_N -0.378
  269. gendstat: China_YR_MN Georgia_Satsurblia.SG -0.374
  270. gendstat: China_YR_MN Russia_Yana_UP.SG -0.592
  271. gendstat: China_YR_MN Russia_Shamanka_Eneolithic.SG -0.315
  272. gendstat: China_YR_MN ONG.SG -0.664
  273. gendstat: China_YR_MN WSHG 0.895
  274. gendstat: China_YR_MN Tarim_EMBA1 -1.035
  275. gendstat: Turkey_N Georgia_Satsurblia.SG -0.129
  276. gendstat: Turkey_N Russia_Yana_UP.SG -0.273
  277. gendstat: Turkey_N Russia_Shamanka_Eneolithic.SG 0.183
  278. gendstat: Turkey_N ONG.SG -0.276
  279. gendstat: Turkey_N WSHG 1.254
  280. gendstat: Turkey_N Tarim_EMBA1 -0.726
  281. gendstat: Georgia_Satsurblia.SG Russia_Yana_UP.SG -0.072
  282. gendstat: Georgia_Satsurblia.SG Russia_Shamanka_Eneolithic.SG 0.235
  283. gendstat: Georgia_Satsurblia.SG ONG.SG -0.079
  284. gendstat: Georgia_Satsurblia.SG WSHG 1.031
  285. gendstat: Georgia_Satsurblia.SG Tarim_EMBA1 -0.431
  286. gendstat: Russia_Yana_UP.SG Russia_Shamanka_Eneolithic.SG 0.422
  287. gendstat: Russia_Yana_UP.SG ONG.SG -0.009
  288. gendstat: Russia_Yana_UP.SG WSHG 1.394
  289. gendstat: Russia_Yana_UP.SG Tarim_EMBA1 -0.474
  290. gendstat: Russia_Shamanka_Eneolithic.SG ONG.SG -0.496
  291. gendstat: Russia_Shamanka_Eneolithic.SG WSHG 1.186
  292. gendstat: Russia_Shamanka_Eneolithic.SG Tarim_EMBA1 -0.967
  293. gendstat: ONG.SG WSHG 1.373
  294. gendstat: ONG.SG Tarim_EMBA1 -0.460
  295. gendstat: WSHG Tarim_EMBA1 -2.277
  296.  
  297. removing /tmp/fsx.13438
  298. ##end of qpAdm: 61.284 seconds cpu 0.844 Mbytes in use
  299.  
Advertisement
Add Comment
Please, Sign In to add comment
Public Pastes
We use cookies for various purposes including analytics. By continuing to use Pastebin, you agree to our use of cookies as described in the Cookies Policy.  OK, I Understand
Not a member of Pastebin yet?
Sign Up, it unlocks many cool features!