RG701

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Jul 25th, 2021
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  1. /home/ubuntu/AdmixTools-master/bin/qpAdm: parameter file: qpAdm_parfile
  2. ### THE INPUT PARAMETERS
  3. ##PARAMETER NAME: VALUE
  4. genotypename: /home/ubuntu/DataSet1/data.geno
  5. snpname: /home/ubuntu/DataSet1/data.snp
  6. indivname: /home/ubuntu/DataSet1/data.ind
  7. popleft: pleftA.txt
  8. popright: pRightC.txt
  9. ## qpAdm version: 1201
  10. seed: 1428899685
  11. read 1073741824 bytes
  12. read 2147483648 bytes
  13. read 2859357147 bytes
  14. packed geno read OK
  15. end of inpack
  16.  
  17. left pops:
  18. Moldova_Cimmerian2.SG
  19. Russia_Srubnaya_Alakul.SG
  20. Russia_Shamanka_EBA.SG
  21. Turkmenistan_Gonur_BA_1
  22.  
  23. right pops:
  24. Cameroon_SMA.DG
  25. Turkey_Epipaleolithic
  26. Russia_MA1_HG.SG
  27. Israel_PPNB
  28. Russia_Kolyma_M.SG
  29. Iran_GanjDareh_N
  30. Brazil_LapaDoSanto_9600BP
  31. Russia_Kostenki14.SG
  32. China_Tianyuan
  33. Russia_HG_Tyumen
  34. Mongolia_North_N
  35. Georgia_Satsurblia.SG
  36. Italy_North_Villabruna_HG
  37. Serbia_EN_Starcevo
  38.  
  39. 0 Moldova_Cimmerian2.SG 1
  40. 1 Russia_Srubnaya_Alakul.SG 12
  41. 2 Russia_Shamanka_EBA.SG 5
  42. 3 Turkmenistan_Gonur_BA_1 19
  43. 4 Cameroon_SMA.DG 1
  44. 5 Turkey_Epipaleolithic 1
  45. 6 Russia_MA1_HG.SG 1
  46. 7 Israel_PPNB 1
  47. 8 Russia_Kolyma_M.SG 1
  48. 9 Iran_GanjDareh_N 8
  49. 10 Brazil_LapaDoSanto_9600BP 4
  50. 11 Russia_Kostenki14.SG 1
  51. 12 China_Tianyuan 1
  52. 13 Russia_HG_Tyumen 1
  53. 14 Mongolia_North_N 6
  54. 15 Georgia_Satsurblia.SG 1
  55. 16 Italy_North_Villabruna_HG 1
  56. 17 Serbia_EN_Starcevo 1
  57. jackknife block size: 0.050
  58. snps: 1150466 indivs: 66
  59. number of blocks for block jackknife: 714
  60. ## ncols: 1150466
  61. coverage: Moldova_Cimmerian2.SG 156329
  62. coverage: Russia_Srubnaya_Alakul.SG 1150047
  63. coverage: Russia_Shamanka_EBA.SG 1042830
  64. coverage: Turkmenistan_Gonur_BA_1 950812
  65. coverage: Cameroon_SMA.DG 1140138
  66. coverage: Turkey_Epipaleolithic 848431
  67. coverage: Russia_MA1_HG.SG 805960
  68. coverage: Israel_PPNB 737560
  69. coverage: Russia_Kolyma_M.SG 1149857
  70. coverage: Iran_GanjDareh_N 1057358
  71. coverage: Brazil_LapaDoSanto_9600BP 883139
  72. coverage: Russia_Kostenki14.SG 1048972
  73. coverage: China_Tianyuan 885079
  74. coverage: Russia_HG_Tyumen 805417
  75. coverage: Mongolia_North_N 1061245
  76. coverage: Georgia_Satsurblia.SG 801311
  77. coverage: Italy_North_Villabruna_HG 883779
  78. coverage: Serbia_EN_Starcevo 816289
  79. Effective number of blocks: 599.810
  80. numsnps used: 88657
  81. codimension 1
  82. f4info:
  83. f4rank: 2 dof: 11 chisq: 11.233 tail: 0.423976989 dofdiff: 13 chisqdiff: -11.233 taildiff: 1
  84. B:
  85. scale 1.000 1.000
  86. Turkey_Epipaleolithic -0.669 0.887
  87. Russia_MA1_HG.SG -0.106 1.107
  88. Israel_PPNB -0.998 0.457
  89. Russia_Kolyma_M.SG 1.579 0.392
  90. Iran_GanjDareh_N -0.555 -1.101
  91. Brazil_LapaDoSanto_9600BP 1.144 0.693
  92. Russia_Kostenki14.SG -0.195 0.726
  93. China_Tianyuan 1.092 0.333
  94. Russia_HG_Tyumen 0.341 1.594
  95. Mongolia_North_N 2.046 0.156
  96. Georgia_Satsurblia.SG -0.943 0.333
  97. Italy_North_Villabruna_HG -0.707 2.314
  98. Serbia_EN_Starcevo -0.718 0.514
  99. A:
  100. scale 811.382 2418.288
  101. Russia_Srubnaya_Alakul.SG -0.463 0.613
  102. Russia_Shamanka_EBA.SG 1.578 -0.103
  103. Turkmenistan_Gonur_BA_1 -0.545 -1.617
  104.  
  105.  
  106. full rank
  107. f4info:
  108. f4rank: 3 dof: 0 chisq: 0.000 tail: 1 dofdiff: 11 chisqdiff: 11.233 taildiff: 0.423976989
  109. B:
  110. scale 1407.887 507.649 877.680
  111. Turkey_Epipaleolithic 0.932 -0.674 -0.151
  112. Russia_MA1_HG.SG 0.486 -0.152 -0.643
  113. Israel_PPNB 0.623 -1.151 0.053
  114. Russia_Kolyma_M.SG -1.877 1.237 -1.660
  115. Iran_GanjDareh_N -0.187 -0.618 0.784
  116. Brazil_LapaDoSanto_9600BP -0.691 1.116 -1.125
  117. Russia_Kostenki14.SG -0.519 -0.545 -0.872
  118. China_Tianyuan -1.583 0.789 -1.344
  119. Russia_HG_Tyumen 0.620 0.413 -0.972
  120. Mongolia_North_N -1.961 1.883 -1.551
  121. Georgia_Satsurblia.SG 0.172 -1.183 -0.027
  122. Italy_North_Villabruna_HG 0.654 -1.035 -1.380
  123. Serbia_EN_Starcevo 0.089 -0.967 -0.322
  124. A:
  125. scale 1.732 1.732 1.732
  126. Russia_Srubnaya_Alakul.SG 1.732 0.000 0.000
  127. Russia_Shamanka_EBA.SG 0.000 1.732 0.000
  128. Turkmenistan_Gonur_BA_1 0.000 0.000 1.732
  129.  
  130.  
  131. best coefficients: 0.566 0.235 0.200
  132. Jackknife mean: 0.563858284 0.234802737 0.201338979
  133. std. errors: 0.108 0.032 0.103
  134.  
  135. error covariance (* 1,000,000)
  136. 11681 -985 -10696
  137. -985 1001 -16
  138. -10696 -16 10712
  139.  
  140.  
  141. summ: Moldova_Cimmerian2.SG 3 0.423977 0.564 0.235 0.201 11681 -985 -10696 1001 -16 ...
  142. 10712
  143.  
  144. fixed pat wt dof chisq tail prob
  145. 000 0 11 11.233 0.423977 0.566 0.235 0.200
  146. 001 1 12 15.029 0.239879 0.765 0.235 0.000
  147. 010 1 12 62.019 9.64887e-09 0.868 0.000 0.132
  148. 100 1 12 38.699 0.000117963 0.000 0.284 0.716
  149. 011 2 13 63.016 1.50824e-08 1.000 0.000 0.000
  150. 101 2 13 369.736 0 0.000 1.000 0.000
  151. 110 2 13 109.050 2.8669e-17 0.000 0.000 1.000
  152. best pat: 000 0.423977 - -
  153. best pat: 001 0.239879 chi(nested): 3.796 p-value for nested model: 0.0513807
  154. best pat: 011 1.50824e-08 chi(nested): 47.987 p-value for nested model: 4.29009e-12
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