From 759a7a23b0ea848b8c8ffe2804841322254d8696 Mon Sep 17 00:00:00 2001 From: Zachary Sloan Date: Mon, 5 May 2014 17:09:24 +0000 Subject: Committing a bunch of changes related to integrating GEMMA and adding the correlation matrix page --- wqflask/output/HLC_output.assoc.txt | 273350 ++++++++++++++++++++++++++++++++ wqflask/output/HLC_output.log.txt | 28 + wqflask/output/HLC_output1.assoc.txt | 273350 ++++++++++++++++++++++++++++++++ wqflask/output/HLC_output1.log.txt | 28 + 4 files changed, 546756 insertions(+) create mode 100755 wqflask/output/HLC_output.assoc.txt create mode 100755 wqflask/output/HLC_output.log.txt create mode 100755 wqflask/output/HLC_output1.assoc.txt create mode 100755 wqflask/output/HLC_output1.log.txt (limited to 'wqflask/output') diff --git a/wqflask/output/HLC_output.assoc.txt b/wqflask/output/HLC_output.assoc.txt new file mode 100755 index 00000000..962ee30a --- /dev/null +++ b/wqflask/output/HLC_output.assoc.txt @@ -0,0 +1,273350 @@ +chr rs ps n_miss allele1 allele0 af beta se l_remle p_wald +0 rs1155740 0 18 T C 0.274 -8.927624e+01 1.026031e+02 1.643091e+01 3.847300e-01 +0 rs1169469 0 16 T C 0.105 9.200707e+01 1.491476e+02 1.583560e+01 5.376401e-01 +0 rs11775 0 19 G A 0.327 -1.489315e+02 9.702455e+01 1.590665e+01 1.255308e-01 +0 rs1368258 0 13 T C 0.343 8.160595e+01 1.001130e+02 1.609552e+01 4.154496e-01 +0 rs1414747 0 17 A C 0.446 9.248497e+01 8.917807e+01 1.569481e+01 3.002873e-01 +0 rs1459037 0 7 G A 0.290 -9.386644e-01 9.966103e+01 1.591604e+01 9.924896e-01 +0 rs150775 0 20 T G 0.061 -2.146073e+02 1.912066e+02 1.593540e+01 2.623327e-01 +0 rs1538704 0 6 G A 0.292 -5.174857e+01 9.488451e+01 1.577911e+01 5.857750e-01 +0 rs1578301 0 0 C T 0.447 3.293481e+01 9.209531e+01 1.595064e+01 7.208078e-01 +0 rs16907085 0 1 G A 0.124 1.249005e+02 1.392221e+02 1.599469e+01 3.701568e-01 +0 rs16992891 0 3 T C 0.333 -6.977747e+01 9.374774e+01 1.599852e+01 4.570997e-01 +0 rs17566573 0 20 A G 0.195 1.370863e+02 1.163727e+02 1.591232e+01 2.394583e-01 +0 rs2229935 0 1 T C 0.275 -2.270192e+02 1.006232e+02 1.573053e+01 2.456991e-02 +0 rs2230394 0 5 T C 0.098 2.579272e+02 1.549294e+02 1.577268e+01 9.668865e-02 +0 rs2230395 0 1 C A 0.101 2.609912e+02 1.525609e+02 1.573474e+01 8.785997e-02 +0 rs2387949 0 8 A G 0.119 1.002418e+02 1.333433e+02 1.586741e+01 4.526132e-01 +0 rs2565615 0 21 T A 0.498 1.478314e+02 9.398838e+01 1.598875e+01 1.164932e-01 +0 rs2886026 0 5 G A 0.435 -8.558085e+01 9.199129e+01 1.601461e+01 3.527363e-01 +0 rs2886027 0 18 A G 0.436 -7.448537e+01 9.355173e+01 1.599255e+01 4.263635e-01 +0 rs2903177 0 11 G A 0.050 2.461875e+02 1.950445e+02 1.790120e+01 2.075648e-01 +0 rs2903407 0 1 G A 0.130 3.776679e+01 1.343046e+02 1.585527e+01 7.786919e-01 +0 rs3818890 0 7 A G 0.044 -2.784716e+02 2.209028e+02 1.597487e+01 2.081422e-01 +0 rs3885710 0 2 C T 0.029 -4.563270e+02 2.583355e+02 1.605043e+01 7.804452e-02 +0 rs3923989 0 3 G A 0.208 -6.478366e+00 1.096655e+02 1.594977e+01 9.529210e-01 +0 rs3928422 0 15 T C 0.476 1.178778e+02 8.911709e+01 1.635353e+01 1.866367e-01 +0 rs3929758 0 0 C A 0.276 -1.082620e+01 9.917858e+01 1.597915e+01 9.131282e-01 +0 rs3963196 0 6 C G 0.110 -1.223485e+02 1.457098e+02 1.581492e+01 4.015641e-01 +0 rs3990898 0 19 T C 0.475 7.803269e+01 9.229887e+01 1.603365e+01 3.983437e-01 +0 rs4000844 0 3 C T 0.324 5.304427e+01 9.416013e+01 1.597918e+01 5.734998e-01 +0 rs449837 0 2 C T 0.120 -1.714379e+02 1.343282e+02 1.590009e+01 2.025601e-01 +0 rs5749531 0 6 C T 0.270 3.360770e+01 9.988338e+01 1.605925e+01 7.366830e-01 +0 rs828748 0 13 A T 0.469 1.313925e+02 8.669709e+01 1.582815e+01 1.303802e-01 +0 rs9620258 0 18 T C 0.465 5.493139e+00 9.410155e+01 1.595825e+01 9.534777e-01 +0 rs9625253 0 2 C G 0.166 -2.965483e+01 1.168450e+02 1.595882e+01 7.997757e-01 +1 rs4040617 819184 0 G A 0.129 -1.461435e+02 1.322900e+02 1.593512e+01 2.699056e-01 +1 rs4075116 1043551 3 G A 0.303 -1.213767e+02 9.411141e+01 1.594662e+01 1.978516e-01 +1 rs10907175 1170649 2 C A 0.104 -3.134470e+02 1.436499e+02 1.604784e+01 2.965499e-02 +1 rs6603781 1198553 9 A G 0.104 2.969327e+01 1.566109e+02 1.598022e+01 8.497139e-01 +1 rs6685064 1251214 1 T C 0.072 -2.344562e+01 1.712186e+02 1.600270e+01 8.911479e-01 +1 rs1695824 1450836 7 G T 0.242 9.504432e+01 1.052646e+02 1.570121e+01 3.670860e-01 +1 rs3766180 1563419 10 G A 0.294 -4.599604e+01 9.459196e+01 1.598563e+01 6.270353e-01 +1 rs6603791 1586207 5 G A 0.315 -2.993825e+01 9.426220e+01 1.599451e+01 7.509397e-01 +1 rs2281173 1720353 8 A G 0.094 3.187159e+01 1.490880e+02 1.595439e+01 8.308235e-01 +1 rs1107910 1724482 11 G A 0.444 -9.931061e+01 8.821614e+01 1.590374e+01 2.609005e-01 +1 rs2272908 1753640 6 T C 0.499 6.396691e+01 8.345319e+01 1.591206e+01 4.438041e-01 +1 rs3737628 1755093 7 T C 0.496 7.778926e+01 8.489332e+01 1.594231e+01 3.600198e-01 +1 rs9786963 1791187 11 T C 0.055 1.753881e+02 1.868894e+02 1.587395e+01 3.485413e-01 +1 rs10907187 1791215 2 A G 0.280 -1.286666e+02 9.769479e+01 1.591722e+01 1.885394e-01 +1 rs7511905 1825947 1 A C 0.055 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2849319 15 A G 0.257 -3.677836e+01 1.068850e+02 1.606365e+01 7.309466e-01 +1 rs10752728 2867410 18 T A 0.244 9.541699e+00 1.099327e+02 1.594323e+01 9.308747e-01 +1 rs897635 2869430 13 T A 0.245 5.943079e+01 1.083927e+02 1.586006e+01 5.837796e-01 +1 rs1869972 2874394 14 A G 0.324 2.014784e+01 9.851490e+01 1.569545e+01 8.380485e-01 +1 rs2606414 2890304 7 T C 0.301 9.059183e+01 1.003563e+02 1.592671e+01 3.671953e-01 +1 rs6659552 2902616 8 C G 0.245 -9.022798e+01 1.035073e+02 1.614374e+01 3.838609e-01 +1 rs10909855 2931544 4 T C 0.128 8.116666e+01 1.414506e+02 1.587561e+01 5.663956e-01 +1 rs17391750 2932527 12 A G 0.112 4.928324e+01 1.531817e+02 1.593942e+01 7.478149e-01 +1 rs6661908 2973490 2 A G 0.189 3.057703e+01 1.204009e+02 1.590374e+01 7.996492e-01 +1 694027 2973527 13 T G 0.174 -7.397515e+01 1.271141e+02 1.599071e+01 5.609032e-01 +1 rs10489588 2974990 1 T C 0.207 1.052888e+01 1.159417e+02 1.595444e+01 9.276849e-01 +1 rs9661525 2975996 7 G T 0.187 -5.255146e+00 1.213005e+02 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0.089 2.055264e+02 1.493543e+02 1.607623e+01 1.695154e-01 +1 rs6424068 3151081 5 G A 0.098 -2.107664e+02 1.461064e+02 1.608679e+01 1.498826e-01 +1 rs12075867 3161112 7 C T 0.071 2.760800e+02 1.673623e+02 1.613321e+01 9.976474e-02 +1 rs6424069 3170186 11 C T 0.167 1.675145e+01 1.134130e+02 1.596866e+01 8.826471e-01 +1 rs10797384 3170981 8 G A 0.147 -3.372327e+00 1.188302e+02 1.594750e+01 9.773729e-01 +1 rs2455109 3176124 9 A T 0.152 -1.050287e+02 1.234787e+02 1.606042e+01 3.954812e-01 +1 rs12409315 3252414 2 G A 0.074 -2.911243e+01 1.665530e+02 1.594227e+01 8.613249e-01 +1 rs6687835 3260330 18 T C 0.330 -1.659438e+01 9.943326e+01 1.594046e+01 8.675363e-01 +1 rs2500274 3260365 8 C T 0.070 1.324913e+02 1.833809e+02 1.594159e+01 4.703892e-01 +1 rs2493310 3317578 2 C T 0.161 -1.019941e+02 1.210278e+02 1.605296e+01 3.998518e-01 +1 rs2493275 3331190 2 T C 0.102 -1.948896e+01 1.470670e+02 1.590708e+01 8.946377e-01 +1 rs17822581 3337752 14 G A 0.191 1.332508e+01 1.166758e+02 1.592635e+01 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8.178030e+01 1.581850e+01 5.988899e-01 +23 rs12560037 151839176 19 T C 0.331 -9.374265e+01 7.608673e+01 1.598719e+01 2.186117e-01 +23 rs2382883 151873256 3 A G 0.065 4.962433e+01 1.434923e+02 1.593669e+01 7.296396e-01 +23 rs6627738 151900925 14 C T 0.059 1.454160e+02 1.509728e+02 1.586812e+01 3.359982e-01 +23 rs4828744 151925407 4 G A 0.070 8.377843e+01 1.389327e+02 1.593464e+01 5.468208e-01 +23 rs4828747 151929154 8 C T 0.074 1.066877e+02 1.371978e+02 1.594889e+01 4.372258e-01 +23 rs2008144 151966996 4 A G 0.069 7.890449e+01 1.409684e+02 1.592538e+01 5.759572e-01 +23 rs5925336 151987489 20 T C 0.189 4.454084e+01 9.338956e+01 1.596915e+01 6.336528e-01 +23 rs1894342 151987996 11 G A 0.066 1.193728e+02 1.450988e+02 1.591428e+01 4.111400e-01 +23 rs1557505 151992064 2 G A 0.181 4.253441e+01 9.270232e+01 1.597832e+01 6.465923e-01 +23 rs5924813 151995603 7 C T 0.060 1.789484e+02 1.516085e+02 1.575204e+01 2.385282e-01 +23 rs2012435 152010745 2 T C 0.068 1.011081e+02 1.414283e+02 1.590293e+01 4.750588e-01 +23 rs2012436 152010777 2 G C 0.068 1.011081e+02 1.414283e+02 1.590293e+01 4.750588e-01 +23 rs5925368 152033116 13 G A 0.056 5.376141e+01 1.609354e+02 1.591488e+01 7.385023e-01 +23 rs6627772 152053967 5 A G 0.327 -1.864113e+02 7.490601e+01 1.562485e+01 1.320654e-02 +23 rs995423 152085362 13 A T 0.488 -6.090244e+01 7.253517e+01 1.593372e+01 4.015900e-01 +23 rs1894354 152089815 0 T C 0.177 -4.725626e+01 9.573306e+01 1.615418e+01 6.218258e-01 +23 rs5986911 152351829 6 T A 0.036 -2.349732e+02 2.052692e+02 1.608473e+01 2.529747e-01 +23 rs5945145 152351894 5 C T 0.405 -2.296156e+01 7.337206e+01 1.600948e+01 7.544745e-01 +23 rs4898424 152360329 16 G T 0.274 4.684036e+00 8.221131e+01 1.594832e+01 9.545914e-01 +23 rs4898428 152397543 12 A G 0.134 -5.955819e+01 1.092205e+02 1.596693e+01 5.858318e-01 +23 rs3761536 152427138 16 A T 0.178 -2.681676e+00 9.622300e+01 1.595431e+01 9.777794e-01 +23 rs5987140 152521101 20 C T 0.111 5.193335e+01 1.213441e+02 1.595543e+01 6.688794e-01 +23 rs2266887 152760433 8 T G 0.203 7.718603e+01 9.181158e+01 1.588840e+01 4.009886e-01 +23 rs7884370 152843727 5 G A 0.041 2.460087e+02 1.782285e+02 1.583888e+01 1.682200e-01 +23 rs1734791 152851766 13 T A 0.158 -1.149214e+01 1.001773e+02 1.603198e+01 9.087229e-01 +23 rs766420 153075250 6 C G 0.220 6.280638e+01 8.755395e+01 1.608354e+01 4.735554e-01 +23 rs766419 153075507 6 C T 0.219 4.411589e+01 8.756093e+01 1.602046e+01 6.146413e-01 +23 rs2239467 153076140 14 G A 0.224 5.717691e+01 8.783936e+01 1.606658e+01 5.154461e-01 +23 rs4898494 153174968 5 T A 0.108 2.427077e+02 1.155737e+02 1.590925e+01 3.631549e-02 +23 rs4898348 153450097 18 T C 0.231 2.775226e+02 8.732649e+01 1.621495e+01 1.591316e-03 +23 rs5945109 153471452 8 G A 0.377 1.691606e+02 7.536096e+01 1.619144e+01 2.530292e-02 +23 rs5945122 153737610 8 C A 0.135 1.924957e+01 1.071433e+02 1.598439e+01 8.575037e-01 +23 rs2051161 153849554 3 G C 0.383 1.635377e+02 7.466881e+01 1.599425e+01 2.905430e-02 +23 3885427 154017791 18 G A 0.232 -4.297558e+01 8.482810e+01 1.569159e+01 6.126845e-01 +23 rs475025 154048640 3 G A 0.243 -2.214191e+01 8.269887e+01 1.592490e+01 7.890283e-01 +23 rs6420603 154316683 14 G A 0.029 -8.620842e+01 2.205232e+02 1.595658e+01 6.960472e-01 +23 rs574386 154411192 9 C T 0.240 -4.051368e+01 8.233156e+01 1.565906e+01 6.229171e-01 diff --git a/wqflask/output/HLC_output.log.txt b/wqflask/output/HLC_output.log.txt new file mode 100755 index 00000000..bfa65d9a --- /dev/null +++ b/wqflask/output/HLC_output.log.txt @@ -0,0 +1,28 @@ +## +## GEMMA Version = 0.94 +## +## Command Line Input = -bfile /home/zas1024/gene/web/gemma/HLC -k ../web/gemma/output_HLC.cXX.txt -lmm 1 -o HLC_output +## +## Summary Statistics: +## number of total individuals = 427 +## number of analyzed individuals = 427 +## number of covariates = 1 +## number of phenotypes = 1 +## number of total SNPs = 358499 +## number of analyzed SNPs = 273349 +## REMLE log-likelihood in the null model = -3650.56 +## MLE log-likelihood in the null model = -3657.67 +## pve estimate in the null model = 0.840196 +## se(pve) in the null model = 0.106606 +## vg estimate in the null model = 4.2245e+06 +## ve estimate in the null model = 265756 +## beta estimate in the null model = 1202.14 +## se(beta) = 24.9475 +## +## Computation Time: +## total computation time = 2.68417 min +## computation time break down: +## time on eigen-decomposition = 0.00166667 min +## time on calculating UtX = 0.417 min +## time on optimization = 2.11733 min +## diff --git a/wqflask/output/HLC_output1.assoc.txt b/wqflask/output/HLC_output1.assoc.txt new file mode 100755 index 00000000..1b22ddae --- /dev/null +++ b/wqflask/output/HLC_output1.assoc.txt @@ -0,0 +1,273350 @@ +chr rs ps n_miss allele1 allele0 af beta se l_remle p_wald +0 rs1155740 0 18 T C 0.274 -3.846147e+01 1.015555e+02 1.000000e-05 7.050822e-01 +0 rs1169469 0 16 T C 0.105 5.815072e+01 1.450964e+02 1.000000e-05 6.887886e-01 +0 rs11775 0 19 G A 0.327 8.604462e+00 9.721899e+01 1.000000e-05 9.295162e-01 +0 rs1368258 0 13 T C 0.343 1.146921e+02 9.964327e+01 1.000000e-05 2.503682e-01 +0 rs1414747 0 17 A C 0.446 -1.154040e+02 8.829289e+01 1.000000e-05 1.918993e-01 +0 rs1459037 0 7 G A 0.290 1.934242e+02 1.002362e+02 1.000000e-05 5.431133e-02 +0 rs150775 0 20 T G 0.061 -2.008807e+02 1.914387e+02 1.000000e-05 2.946266e-01 +0 rs1538704 0 6 G A 0.292 7.925848e+01 9.452851e+01 1.000000e-05 4.022431e-01 +0 rs1578301 0 0 C T 0.447 1.299856e+02 9.151110e+01 1.000000e-05 1.562140e-01 +0 rs16907085 0 1 G A 0.124 -3.201286e+01 1.402721e+02 1.000000e-05 8.195852e-01 +0 rs16992891 0 3 T C 0.333 8.815026e+01 9.446301e+01 1.000000e-05 3.512608e-01 +0 rs17566573 0 20 A G 0.195 -8.067095e+00 1.161555e+02 1.000000e-05 9.446635e-01 +0 rs2229935 0 1 T C 0.275 2.764873e+01 1.009033e+02 1.000000e-05 7.842085e-01 +0 rs2230394 0 5 T C 0.098 1.520282e+01 1.544037e+02 1.000000e-05 9.216123e-01 +0 rs2230395 0 1 C A 0.101 2.300772e+01 1.523006e+02 1.000000e-05 8.799939e-01 +0 rs2387949 0 8 A G 0.119 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2.589765e-01 +0 rs4000844 0 3 C T 0.324 -1.048665e+02 9.338586e+01 1.000000e-05 2.620981e-01 +0 rs449837 0 2 C T 0.120 -1.185196e+02 1.341052e+02 1.000000e-05 3.773144e-01 +0 rs5749531 0 6 C T 0.270 -3.229884e+01 9.995633e+01 1.000000e-05 7.467561e-01 +0 rs828748 0 13 A T 0.469 7.801369e+01 8.657702e+01 1.000000e-05 3.680508e-01 +0 rs9620258 0 18 T C 0.465 -9.557191e+01 9.382411e+01 1.000000e-05 3.089589e-01 +0 rs9625253 0 2 C G 0.166 8.293478e+01 1.173460e+02 1.000000e-05 4.801067e-01 +1 rs4040617 819184 0 G A 0.129 -5.504185e+01 1.326897e+02 1.000000e-05 6.784858e-01 +1 rs4075116 1043551 3 G A 0.303 8.128329e+01 9.428207e+01 1.000000e-05 3.891028e-01 +1 rs10907175 1170649 2 C A 0.104 -8.582678e+01 1.452696e+02 1.000000e-05 5.549615e-01 +1 rs6603781 1198553 9 A G 0.104 -1.103367e+02 1.562992e+02 1.000000e-05 4.806167e-01 +1 rs6685064 1251214 1 T C 0.072 2.901623e+02 1.613102e+02 1.000000e-05 7.276223e-02 +1 rs1695824 1450836 7 G T 0.242 -1.005953e+01 1.036343e+02 1.000000e-05 9.227185e-01 +1 rs3766180 1563419 10 G A 0.294 -4.647770e+01 9.437970e+01 1.000000e-05 6.226524e-01 +1 rs6603791 1586207 5 G A 0.315 -3.868412e+01 9.358020e+01 1.000000e-05 6.795372e-01 +1 rs2281173 1720353 8 A G 0.094 -6.813679e+01 1.507539e+02 1.000000e-05 6.515186e-01 +1 rs1107910 1724482 11 G A 0.444 -3.493828e+01 8.920070e+01 1.000000e-05 6.954897e-01 +1 rs2272908 1753640 6 T C 0.499 1.224539e+02 8.410937e+01 1.000000e-05 1.461616e-01 +1 rs3737628 1755093 7 T C 0.496 1.295374e+02 8.555217e+01 1.000000e-05 1.307353e-01 +1 rs9786963 1791187 11 T C 0.055 -7.280974e+01 1.894840e+02 1.000000e-05 7.009833e-01 +1 rs10907187 1791215 2 A G 0.280 -1.000470e+02 9.865078e+01 1.000000e-05 3.110866e-01 +1 rs7511905 1825947 1 A C 0.055 -8.770608e+01 1.876744e+02 1.000000e-05 6.405025e-01 +1 rs6603803 1844849 1 G A 0.496 9.789304e+01 8.454704e+01 1.000000e-05 2.475743e-01 +1 rs6688000 1856083 17 A G 0.057 -8.194751e+01 1.880791e+02 1.000000e-05 6.632701e-01 +1 rs2803285 1920530 13 T C 0.164 -1.862255e+02 1.216022e+02 1.000000e-05 1.264067e-01 +1 rs7513222 2060062 4 A G 0.342 7.704131e+01 8.752531e+01 1.000000e-05 3.792390e-01 +1 rs3107146 2079745 10 T C 0.118 1.729165e+02 1.373630e+02 1.000000e-05 2.087830e-01 +1 rs385039 2109570 8 G A 0.289 -4.818158e+01 9.509152e+01 1.000000e-05 6.126377e-01 +1 rs3128309 2138039 13 A G 0.091 -2.463721e+01 1.536013e+02 1.000000e-05 8.726444e-01 +1 rs262680 2199310 21 A G 0.413 3.280966e+01 9.304218e+01 1.000000e-05 7.245391e-01 +1 rs16824948 2218381 6 T C 0.056 -1.498461e+02 2.007560e+02 1.000000e-05 4.558331e-01 +1 rs12084736 2221741 2 T C 0.061 2.087846e+02 1.877980e+02 1.000000e-05 2.668738e-01 +1 rs2132303 2255419 2 T C 0.135 -3.388608e+01 1.285913e+02 1.000000e-05 7.922794e-01 +1 rs1496555 2266412 1 A G 0.133 -8.103980e+01 1.266017e+02 1.000000e-05 5.224419e-01 +1 rs7527871 2313887 15 C A 0.161 -8.287130e+01 1.174210e+02 1.000000e-05 4.807228e-01 +1 rs2843130 2315474 3 C G 0.171 9.262793e+01 1.140174e+02 1.000000e-05 4.170161e-01 +1 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1.151801e+02 1.000000e-05 1.751974e-01 +1 rs6684865 2578390 14 A G 0.328 2.339101e+02 9.576759e+01 1.000000e-05 1.499334e-02 +1 rs3890745 2585785 3 G A 0.323 2.381309e+02 9.527544e+01 1.000000e-05 1.281681e-02 +1 rs2377041 2736484 16 A G 0.438 -1.029781e+02 9.437044e+01 1.000000e-05 2.757981e-01 +1 rs4648360 2746501 15 T C 0.453 -1.130038e+02 9.418411e+01 1.000000e-05 2.308784e-01 +1 rs729045 2777562 21 C T 0.451 1.515010e+02 9.289125e+01 1.000000e-05 1.036417e-01 +1 rs6680471 2777668 1 T C 0.471 -1.415055e+02 9.454016e+01 1.000000e-05 1.351938e-01 +1 rs12049543 2784531 7 A C 0.448 -1.138792e+02 8.910891e+01 1.000000e-05 2.019547e-01 +1 rs897631 2848523 0 C T 0.248 1.460503e+02 1.047909e+02 1.000000e-05 1.641271e-01 +1 rs897632 2849319 15 A G 0.257 1.512979e+02 1.054105e+02 1.000000e-05 1.519312e-01 +1 rs10752728 2867410 18 T A 0.244 1.639739e+02 1.078039e+02 1.000000e-05 1.289937e-01 +1 rs897635 2869430 13 T A 0.245 1.536742e+02 1.066348e+02 1.000000e-05 1.502855e-01 +1 rs1869972 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1.913828e-01 +23 rs5945122 153737610 8 C A 0.135 1.372704e+02 1.063033e+02 1.000000e-05 1.972982e-01 +23 rs2051161 153849554 3 G C 0.383 1.495907e+02 7.460626e+01 1.000000e-05 4.558928e-02 +23 3885427 154017791 18 G A 0.232 -1.535544e+01 8.490187e+01 1.000000e-05 8.565629e-01 +23 rs475025 154048640 3 G A 0.243 2.759141e+01 8.209993e+01 1.000000e-05 7.369831e-01 +23 rs6420603 154316683 14 G A 0.029 5.459859e+01 2.206449e+02 1.000000e-05 8.046795e-01 +23 rs574386 154411192 9 C T 0.240 1.393606e+01 8.303839e+01 1.000000e-05 8.667994e-01 diff --git a/wqflask/output/HLC_output1.log.txt b/wqflask/output/HLC_output1.log.txt new file mode 100755 index 00000000..e8461e91 --- /dev/null +++ b/wqflask/output/HLC_output1.log.txt @@ -0,0 +1,28 @@ +## +## GEMMA Version = 0.94 +## +## Command Line Input = -bfile /home/zas1024/gene/web/gemma/HLC -k ../web/gemma/output_HLC.cXX.txt -lmm 1 -o HLC_output1 +## +## Summary Statistics: +## number of total individuals = 427 +## number of analyzed individuals = 427 +## number of covariates = 1 +## number of phenotypes = 1 +## number of total SNPs = 358499 +## number of analyzed SNPs = 273349 +## REMLE log-likelihood in the null model = -3657.8 +## MLE log-likelihood in the null model = -3665.89 +## pve estimate in the null model = 3.30749e-06 +## se(pve) in the null model = nan +## vg estimate in the null model = 16.8101 +## ve estimate in the null model = 1.68101e+06 +## beta estimate in the null model = 890.587 +## se(beta) = 62.7439 +## +## Computation Time: +## total computation time = 1.857 min +## computation time break down: +## time on eigen-decomposition = 0.0015 min +## time on calculating UtX = 0.406 min +## time on optimization = 1.30517 min +## -- cgit v1.2.3