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b/web/gemma/output/HLC_output.assoc.txt index 2590adca..d10b9137 100644 --- a/web/gemma/output/HLC_output.assoc.txt +++ b/web/gemma/output/HLC_output.assoc.txt @@ -1,273350 +1,273350 @@ chr rs ps n_miss allele1 allele0 af beta se l_remle p_wald -0 rs1155740 0 18 T C 0.274 -2.932864e+01 5.090527e+01 1.887754e+01 5.648245e-01 -0 rs1169469 0 16 T C 0.105 -3.842245e+00 7.407000e+01 1.850572e+01 9.586541e-01 -0 rs11775 0 19 G A 0.327 -2.285852e+01 4.823620e+01 1.811797e+01 6.358237e-01 -0 rs1368258 0 13 T C 0.343 8.200373e+01 4.955034e+01 1.850921e+01 9.867123e-02 -0 rs1414747 0 17 A C 0.446 1.644110e+01 4.430128e+01 1.836472e+01 7.107330e-01 -0 rs1459037 0 7 G A 0.290 -3.180213e+01 4.939313e+01 1.795147e+01 5.200153e-01 -0 rs150775 0 20 T G 0.061 4.546454e+00 9.500576e+01 1.847425e+01 9.618547e-01 -0 rs1538704 0 6 G A 0.292 -4.511488e+01 4.704953e+01 1.855053e+01 3.381642e-01 -0 rs1578301 0 0 C T 0.447 -1.335758e+01 4.570123e+01 1.857779e+01 7.702148e-01 -0 rs16907085 0 1 G A 0.124 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150518260 16 T C 0.236 -8.622611e+01 3.491918e+02 1.492596e+00 8.050812e-01 +23 rs1554914 150549224 9 G T 0.233 2.407349e+02 3.523384e+02 1.415294e+00 4.948216e-01 +23 rs6627452 150564760 14 A G 0.350 -6.605843e+01 3.080976e+02 1.407714e+00 8.303322e-01 +23 rs12839777 150571582 13 A G 0.292 -2.718031e+02 3.258020e+02 1.568886e+00 4.046041e-01 +23 rs5970100 150576381 17 A C 0.080 4.667135e+02 5.568858e+02 1.119021e+00 4.024582e-01 +23 rs5969818 150583736 10 C G 0.079 3.771094e+02 5.621897e+02 1.182218e+00 5.027207e-01 +23 rs5925036 150608736 14 A G 0.213 2.895545e+02 3.567176e+02 1.402990e+00 4.174072e-01 +23 3883889 150688242 12 T A 0.087 1.817912e+02 5.632847e+02 1.281868e+00 7.470554e-01 +23 3883890 150688297 7 T A 0.090 -3.005985e+02 5.258287e+02 1.533086e+00 5.678504e-01 +23 rs12843815 150692967 13 T C 0.403 -3.643431e+02 3.048683e+02 1.584031e+00 2.327209e-01 +23 rs6627483 150709289 7 T C 0.118 -1.774045e+02 4.729994e+02 1.500504e+00 7.078009e-01 +23 rs933191 150767597 2 G A 0.111 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8.575516e-01 +23 rs12845949 151688319 21 A G 0.284 -1.011003e+02 3.268018e+02 1.334796e+00 7.571972e-01 +23 rs5970391 151712954 6 T G 0.493 1.669590e+02 2.918648e+02 1.256621e+00 5.675959e-01 +23 rs6526138 151718162 20 A G 0.299 1.121662e+02 3.284373e+02 1.402478e+00 7.328849e-01 +23 rs5925239 151729952 2 C T 0.213 1.750042e+02 3.487526e+02 1.398059e+00 6.160677e-01 +23 rs5969921 151731439 20 C T 0.134 -8.675578e+00 4.624357e+02 1.402951e+00 9.850409e-01 +23 rs2071257 151759270 3 G T 0.204 -1.875519e+02 3.604521e+02 1.378771e+00 6.031086e-01 +23 rs10126824 151778651 8 T C 0.085 -4.540913e+02 5.384163e+02 1.337699e+00 3.994885e-01 +23 rs5925268 151808635 21 T C 0.267 -1.992814e+02 3.316334e+02 1.311576e+00 5.482212e-01 +23 rs12560037 151839176 19 T C 0.331 -3.782045e+02 3.092107e+02 1.408205e+00 2.219588e-01 +23 rs2382883 151873256 3 A G 0.065 5.332619e+02 5.749897e+02 1.010210e+00 3.542305e-01 +23 rs6627738 151900925 14 C T 0.059 5.159894e+02 6.112936e+02 1.099143e+00 3.990916e-01 +23 rs4828744 151925407 4 G A 0.070 6.633532e+02 5.537957e+02 8.364750e-01 2.316507e-01 +23 rs4828747 151929154 8 C T 0.074 8.191338e+02 5.461813e+02 6.878073e-01 1.344224e-01 +23 rs2008144 151966996 4 A G 0.069 6.653272e+02 5.622074e+02 8.150273e-01 2.373045e-01 +23 rs5925336 151987489 20 T C 0.189 5.057982e+02 3.782736e+02 1.091805e+00 1.818978e-01 +23 rs1894342 151987996 11 G A 0.066 7.920495e+02 5.760390e+02 7.318519e-01 1.698581e-01 +23 rs1557505 151992064 2 G A 0.181 4.906312e+02 3.758148e+02 1.107522e+00 1.924245e-01 +23 rs5924813 151995603 7 C T 0.060 1.050542e+03 6.060025e+02 5.676362e-01 8.372142e-02 +23 rs2012435 152010745 2 T C 0.068 7.649911e+02 5.614145e+02 7.160548e-01 1.737259e-01 +23 rs2012436 152010777 2 G C 0.068 7.649911e+02 5.614145e+02 7.160548e-01 1.737259e-01 +23 rs5925368 152033116 13 G A 0.056 4.850721e+02 6.443881e+02 1.060616e+00 4.520085e-01 +23 rs6627772 152053967 5 A G 0.327 -7.348535e+02 3.037732e+02 1.913365e+00 1.597861e-02 +23 rs995423 152085362 13 A T 0.488 -2.302553e+01 2.949064e+02 1.418232e+00 9.378032e-01 +23 rs1894354 152089815 0 T C 0.177 -8.651713e+01 3.852254e+02 1.493356e+00 8.224075e-01 +23 rs5986911 152351829 6 T A 0.036 -6.052153e+02 8.346069e+02 1.458641e+00 4.687590e-01 +23 rs5945145 152351894 5 C T 0.405 2.556045e+00 2.973697e+02 1.405507e+00 9.931459e-01 +23 rs4898424 152360329 16 G T 0.274 8.014956e+01 3.346344e+02 1.358128e+00 8.108226e-01 +23 rs4898428 152397543 12 A G 0.134 -5.622230e+02 4.425575e+02 1.452369e+00 2.046388e-01 +23 rs3761536 152427138 16 A T 0.178 -2.451683e+02 3.896597e+02 1.624546e+00 5.295654e-01 +23 rs5987140 152521101 20 C T 0.111 3.357028e+01 4.930577e+02 1.405850e+00 9.457493e-01 +23 rs2266887 152760433 8 T G 0.203 4.527955e+02 3.696201e+02 1.055914e+00 2.212426e-01 +23 rs7884370 152843727 5 G A 0.041 6.650459e+02 7.275102e+02 1.254241e+00 3.611618e-01 +23 rs1734791 152851766 13 T A 0.158 1.818275e+01 4.075201e+02 1.393589e+00 9.644327e-01 +23 rs766420 153075250 6 C G 0.220 -1.161442e+02 3.563688e+02 1.374410e+00 7.446527e-01 +23 rs766419 153075507 6 C T 0.219 -2.020163e+02 3.563200e+02 1.364275e+00 5.710461e-01 +23 rs2239467 153076140 14 G A 0.224 -1.279868e+02 3.576258e+02 1.367731e+00 7.206114e-01 +23 rs4898494 153174968 5 T A 0.108 4.589111e+02 4.725147e+02 1.486027e+00 3.319961e-01 +23 rs4898348 153450097 18 T C 0.231 1.085220e+03 3.552855e+02 1.654826e+00 2.396195e-03 +23 rs5945109 153471452 8 G A 0.377 5.977579e+02 3.064267e+02 1.532848e+00 5.174515e-02 +23 rs5945122 153737610 8 C A 0.135 3.680298e+01 4.337705e+02 1.429719e+00 9.324251e-01 +23 rs2051161 153849554 3 G C 0.383 7.052883e+02 3.026393e+02 1.477207e+00 2.024911e-02 +23 3885427 154017791 18 G A 0.232 -2.548193e+02 3.451999e+02 1.424038e+00 4.608131e-01 +23 rs475025 154048640 3 G A 0.243 -2.337655e+02 3.345153e+02 1.458479e+00 4.850476e-01 +23 rs6420603 154316683 14 G A 0.029 -1.355348e+02 8.962687e+02 1.416665e+00 8.798730e-01 +23 rs574386 154411192 9 C T 0.240 -3.510010e+02 3.367436e+02 1.408866e+00 2.978471e-01 diff --git a/web/gemma/output/HLC_output.log.txt b/web/gemma/output/HLC_output.log.txt index f7c9f5d2..773e86c4 100644 --- a/web/gemma/output/HLC_output.log.txt +++ b/web/gemma/output/HLC_output.log.txt @@ -10,19 +10,19 @@ ## number of phenotypes = 1 ## number of total SNPs = 358499 ## number of analyzed SNPs = 273349 -## REMLE log-likelihood in the null model = -3351.61 -## MLE log-likelihood in the null model = -3357.96 -## pve estimate in the null model = 0.858988 -## se(pve) in the null model = 0.0889649 -## vg estimate in the null model = 1.0633e+06 -## ve estimate in the null model = 57733.1 -## beta estimate in the null model = 620.978 -## se(beta) = 11.6278 +## REMLE log-likelihood in the null model = -4252.51 +## MLE log-likelihood in the null model = -4261.76 +## pve estimate in the null model = 0.314624 +## se(pve) in the null model = 0.403683 +## vg estimate in the null model = 2.61389e+07 +## ve estimate in the null model = 1.88332e+07 +## beta estimate in the null model = 5107.48 +## se(beta) = 210.014 ## ## Computation Time: -## total computation time = 2.67033 min +## total computation time = 2.61417 min ## computation time break down: -## time on eigen-decomposition = 0.00183333 min -## time on calculating UtX = 0.399833 min -## time on optimization = 2.12417 min +## time on eigen-decomposition = 0.00166667 min +## time on calculating UtX = 0.412 min +## time on optimization = 2.03567 min ## -- cgit v1.2.3