Results: Wilcoxon-Rank-Sum Wilcoxon-median t-test t-test-mean mean1 (std) mean2 (std) median1 median2 ######Matthews###### --->fabia-------beagle1--: 6.26e-17 0.385242 1.67e-33 0.374313 0.956115 ( 0.107138) 0.581802 ( 0.171262) 0.981811 0.572800 --->fabia-------beagle2--: 1.75e-13 0.162551 2.88e-12 0.168257 0.956115 ( 0.107138) 0.787858 ( 0.177133) 0.981811 0.810899 --->fabia-------plink----: 4.08e-18 0.970164 3.32e-96 0.951550 0.956115 ( 0.107138) 0.004565 ( 0.000144) 0.981811 0.004563 --->fabia-------germline1: 4.08e-18 0.687264 1.37e-67 0.692738 0.956115 ( 0.107138) 0.263377 ( 0.101173) 0.981811 0.281638 --->fabia-------germline2: 4.08e-18 0.864755 5.27e-91 0.847462 0.956115 ( 0.107138) 0.108653 ( 0.010031) 0.981811 0.110034 --->fabia-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.956115 ( 0.107138) 0.000000 ( 0.000000) 0.981811 0.000000 --->beagle1-----beagle2--: 2.51e-13 -0.246113 2.48e-20 -0.206056 0.581802 ( 0.171262) 0.787858 ( 0.177133) 0.572800 0.810899 --->beagle1-----plink----: 3.96e-18 0.569662 4.68e-56 0.577237 0.581802 ( 0.171262) 0.004565 ( 0.000144) 0.572800 0.004563 --->beagle1-----germline1: 6.6e-18 0.309564 2.26e-30 0.318425 0.581802 ( 0.171262) 0.263377 ( 0.101173) 0.572800 0.281638 --->beagle1-----germline2: 3.96e-18 0.466479 1.93e-48 0.473149 0.581802 ( 0.171262) 0.108653 ( 0.010031) 0.572800 0.110034 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.581802 ( 0.171262) 0.000000 ( 0.000000) 0.572800 0.000000 --->beagle2-----plink----: 4.08e-18 0.796214 5.24e-67 0.783293 0.787858 ( 0.177133) 0.004565 ( 0.000144) 0.810899 0.004563 --->beagle2-----germline1: 6.22e-18 0.535666 1.54e-46 0.524481 0.787858 ( 0.177133) 0.263377 ( 0.101173) 0.810899 0.281638 --->beagle2-----germline2: 4.08e-18 0.692877 1.29e-61 0.679205 0.787858 ( 0.177133) 0.108653 ( 0.010031) 0.810899 0.110034 --->beagle2-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.787858 ( 0.177133) 0.000000 ( 0.000000) 0.810899 0.000000 --->plink-------germline1: 2.84e-17 -0.278757 2.02e-45 -0.258812 0.004565 ( 0.000144) 0.263377 ( 0.101173) 0.004563 0.281638 --->plink-------germline2: 3.96e-18 -0.104851 6.39e-103 -0.104088 0.004565 ( 0.000144) 0.108653 ( 0.010031) 0.004563 0.110034 --->plink-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.004565 ( 0.000144) 0.000000 ( 0.000000) 0.004563 0.000000 --->germline1---germline2: 2.84e-17 0.173112 3.52e-30 0.154724 0.263377 ( 0.101173) 0.108653 ( 0.010031) 0.281638 0.110034 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 0.263377 ( 0.101173) 0.000000 ( 0.000000) 0.281638 0.000000 --->germline2---dash-----: 1e+00 0.000000 1e+00 0.000000 0.108653 ( 0.010031) 0.000000 ( 0.000000) 0.110034 0.000000 ######F1###### --->fabia-------beagle1--: 3.81e-17 0.418198 1.65e-34 0.404128 0.954848 ( 0.108323) 0.550720 ( 0.181284) 0.981646 0.542914 --->fabia-------beagle2--: 1.42e-13 0.182900 5.84e-13 0.187875 0.954848 ( 0.108323) 0.766973 ( 0.194267) 0.981646 0.798511 --->fabia-------plink----: 4.08e-18 0.974055 7.04e-96 0.954711 0.954848 ( 0.108323) 0.000137 ( 2.84e-06) 0.981646 0.000137 --->fabia-------germline1: 4.08e-18 0.804059 1.31e-78 0.796096 0.954848 ( 0.108323) 0.158752 ( 0.070059) 0.981646 0.162951 --->fabia-------germline2: 4.08e-18 0.947143 1.22e-94 0.928159 0.954848 ( 0.108323) 0.026689 ( 0.003666) 0.981646 0.026816 --->fabia-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.954848 ( 0.108323) 0.000000 ( 0.000000) 0.981646 0.000000 --->beagle1-----beagle2--: 7.15e-13 -0.252114 1.57e-18 -0.216253 0.550720 ( 0.181284) 0.766973 ( 0.194267) 0.542914 0.798511 --->beagle1-----plink----: 3.96e-18 0.540143 5.66e-52 0.550583 0.550720 ( 0.181284) 0.000137 ( 2.84e-06) 0.542914 0.000137 --->beagle1-----germline1: 3.96e-18 0.381793 8.56e-38 0.391968 0.550720 ( 0.181284) 0.158752 ( 0.070059) 0.542914 0.162951 --->beagle1-----germline2: 3.96e-18 0.513619 4.12e-50 0.524031 0.550720 ( 0.181284) 0.026689 ( 0.003666) 0.542914 0.026816 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.550720 ( 0.181284) 0.000000 ( 0.000000) 0.542914 0.000000 --->beagle2-----plink----: 4.08e-18 0.779780 2.2e-62 0.766836 0.766973 ( 0.194267) 0.000137 ( 2.84e-06) 0.798511 0.000137 --->beagle2-----germline1: 4.74e-18 0.623268 1.37e-51 0.608221 0.766973 ( 0.194267) 0.158752 ( 0.070059) 0.798511 0.162951 --->beagle2-----germline2: 4.08e-18 0.752884 4.1e-61 0.740284 0.766973 ( 0.194267) 0.026689 ( 0.003666) 0.798511 0.026816 --->beagle2-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.766973 ( 0.194267) 0.000000 ( 0.000000) 0.798511 0.000000 --->plink-------germline1: 2.84e-17 -0.164215 6.24e-41 -0.158615 0.000137 ( 2.84e-06) 0.158752 ( 0.070059) 0.000137 0.162951 --->plink-------germline2: 3.96e-18 -0.026599 1.42e-87 -0.026552 0.000137 ( 2.84e-06) 0.026689 ( 0.003666) 0.000137 0.026816 --->plink-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.000137 ( 2.84e-06) 0.000000 ( 0.000000) 0.000137 0.000000 --->germline1---germline2: 2.84e-17 0.137206 1.41e-35 0.132063 0.158752 ( 0.070059) 0.026689 ( 0.003666) 0.162951 0.026816 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 0.158752 ( 0.070059) 0.000000 ( 0.000000) 0.162951 0.000000 --->germline2---dash-----: 1e+00 0.000000 1e+00 0.000000 0.026689 ( 0.003666) 0.000000 ( 0.000000) 0.026816 0.000000 ######accuracy###### --->fabia-------beagle1--: 1e+00 0.000000 1e+00 0.000000 0.999998 ( 3.32e-06) 0.999932 ( 3.89e-05) 0.999999 0.999938 --->fabia-------beagle2--: 1e+00 0.000000 1e+00 0.000000 0.999998 ( 3.32e-06) 0.999982 ( 1.41e-05) 0.999999 0.999983 --->fabia-------plink----: 3.96e-18 0.693482 2.44e-201 0.693266 0.999998 ( 3.32e-06) 0.306732 ( 0.006727) 0.999999 0.305190 --->fabia-------germline1: 3.96e-18 0.000417 2.42e-58 0.000419 0.999998 ( 3.32e-06) 0.999579 ( 0.000117) 0.999999 0.999583 --->fabia-------germline2: 3.96e-18 0.003070 4.61e-94 0.003084 0.999998 ( 3.32e-06) 0.996914 ( 0.000365) 0.999999 0.996949 --->fabia-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.999998 ( 3.32e-06) 0.999952 ( 8.36e-07) 0.999999 0.999952 --->beagle1-----beagle2--: 1e+00 0.000000 1e+00 0.000000 0.999932 ( 3.89e-05) 0.999982 ( 1.41e-05) 0.999938 0.999983 --->beagle1-----plink----: 3.96e-18 0.693418 2.42e-201 0.693200 0.999932 ( 3.89e-05) 0.306732 ( 0.006727) 0.999938 0.305190 --->beagle1-----germline1: 3.96e-18 0.000343 5.24e-50 0.000354 0.999932 ( 3.89e-05) 0.999579 ( 0.000117) 0.999938 0.999583 --->beagle1-----germline2: 3.96e-18 0.003008 2.81e-93 0.003018 0.999932 ( 3.89e-05) 0.996914 ( 0.000365) 0.999938 0.996949 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.999932 ( 3.89e-05) 0.999952 ( 8.36e-07) 0.999938 0.999952 --->beagle2-----plink----: 3.96e-18 0.693467 2.45e-201 0.693250 0.999982 ( 1.41e-05) 0.306732 ( 0.006727) 0.999983 0.305190 --->beagle2-----germline1: 3.96e-18 0.000402 1.17e-56 0.000404 0.999982 ( 1.41e-05) 0.999579 ( 0.000117) 0.999983 0.999583 --->beagle2-----germline2: 3.96e-18 0.003055 3.48e-94 0.003068 0.999982 ( 1.41e-05) 0.996914 ( 0.000365) 0.999983 0.996949 --->beagle2-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.999982 ( 1.41e-05) 0.999952 ( 8.36e-07) 0.999983 0.999952 --->plink-------germline1: 3.96e-18 -0.693044 3.31e-201 -0.692847 0.306732 ( 0.006727) 0.999579 ( 0.000117) 0.305190 0.999583 --->plink-------germline2: 3.96e-18 -0.690392 1.93e-201 -0.690182 0.306732 ( 0.006727) 0.996914 ( 0.000365) 0.305190 0.996949 --->plink-------dash-----: 3.96e-18 -0.693415 2.47e-201 -0.693221 0.306732 ( 0.006727) 0.999952 ( 8.36e-07) 0.305190 0.999952 --->germline1---germline2: 3.96e-18 0.002654 1e-89 0.002664 0.999579 ( 0.000117) 0.996914 ( 0.000365) 0.999583 0.996949 --->germline1---dash-----: 3.94e-18 -0.000341 7.96e-54 -0.000374 0.999579 ( 0.000117) 0.999952 ( 8.36e-07) 0.999583 0.999952 --->germline2---dash-----: 3.96e-18 -0.003026 2.08e-93 -0.003038 0.996914 ( 0.000365) 0.999952 ( 8.36e-07) 0.996949 0.999952 ######FPR###### --->fabia-------beagle1--: 1e+00 0.000000 1e+00 0.000000 2.83e-07 ( 1.82e-06) 5.7e-05 ( 3.81e-05) 0.000000 4.78e-05 --->fabia-------beagle2--: 1e+00 0.000000 1e+00 0.000000 2.83e-07 ( 1.82e-06) 2.96e-06 ( 7.64e-06) 0.000000 1.75e-07 --->fabia-------plink----: 3.96e-18 -0.693493 2.44e-201 -0.693301 2.83e-07 ( 1.82e-06) 0.693301 ( 0.006727) 0.000000 0.694843 --->fabia-------germline1: 3.95e-18 -0.000379 1.31e-57 -0.000411 2.83e-07 ( 1.82e-06) 0.000412 ( 0.000118) 0.000000 4e-04 --->fabia-------germline2: 3.96e-18 -0.003067 4.91e-94 -0.003080 2.83e-07 ( 1.82e-06) 0.003080 ( 0.000365) 0.000000 0.003042 --->fabia-------dash-----: 1e+00 0.000000 1e+00 0.000000 2.83e-07 ( 1.82e-06) 0.000000 ( 0.000000) 0.000000 0.000000 --->beagle1-----beagle2--: 1e+00 0.000000 1e+00 0.000000 5.7e-05 ( 3.81e-05) 2.96e-06 ( 7.64e-06) 4.78e-05 1.75e-07 --->beagle1-----plink----: 3.96e-18 -0.693433 2.46e-201 -0.693244 5.7e-05 ( 3.81e-05) 0.693301 ( 0.006727) 4.78e-05 0.694843 --->beagle1-----germline1: 3.96e-18 -0.000318 4.18e-50 -0.000355 5.7e-05 ( 3.81e-05) 0.000412 ( 0.000118) 4.78e-05 4e-04 --->beagle1-----germline2: 3.96e-18 -0.003012 3.12e-93 -0.003023 5.7e-05 ( 3.81e-05) 0.003080 ( 0.000365) 4.78e-05 0.003042 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 5.7e-05 ( 3.81e-05) 0.000000 ( 0.000000) 4.78e-05 0.000000 --->beagle2-----plink----: 3.96e-18 -0.693537 2.44e-201 -0.693298 2.96e-06 ( 7.64e-06) 0.693301 ( 0.006727) 1.75e-07 0.694843 --->beagle2-----germline1: 3.96e-18 -0.000377 2e-57 -0.000409 2.96e-06 ( 7.64e-06) 0.000412 ( 0.000118) 1.75e-07 4e-04 --->beagle2-----germline2: 3.96e-18 -0.003065 3.66e-94 -0.003077 2.96e-06 ( 7.64e-06) 0.003080 ( 0.000365) 1.75e-07 0.003042 --->beagle2-----dash-----: 1e+00 0.000000 1e+00 0.000000 2.96e-06 ( 7.64e-06) 0.000000 ( 0.000000) 1.75e-07 0.000000 --->plink-------germline1: 3.96e-18 0.693115 3.36e-201 0.692889 0.693301 ( 0.006727) 0.000412 ( 0.000118) 0.694843 4e-04 --->plink-------germline2: 3.96e-18 0.690438 1.93e-201 0.690221 0.693301 ( 0.006727) 0.003080 ( 0.000365) 0.694843 0.003042 --->plink-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.693301 ( 0.006727) 0.000000 ( 0.000000) 0.694843 0.000000 --->germline1---germline2: 3.96e-18 -0.002659 1.8e-89 -0.002668 0.000412 ( 0.000118) 0.003080 ( 0.000365) 4e-04 0.003042 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 0.000412 ( 0.000118) 0.000000 ( 0.000000) 4e-04 0.000000 --->germline2---dash-----: 1e+00 0.000000 1e+00 0.000000 0.003080 ( 0.000365) 0.000000 ( 0.000000) 0.003042 0.000000 ######FDR###### --->fabia-------beagle1--: 1.81e-17 -0.570029 2.56e-43 -0.531195 0.008540 ( 0.053055) 0.539735 ( 0.217338) 0.000000 0.576548 --->fabia-------beagle2--: 3.86e-08 -0.068571 5.22e-04 -0.059903 0.008540 ( 0.053055) 0.068443 ( 0.154941) 0.000000 0.004951 --->fabia-------plink----: 3.92e-18 -0.999841 5.58e-128 -0.991391 0.008540 ( 0.053055) 0.999932 ( 1.42e-06) 0.000000 0.999932 --->fabia-------germline1: 3.89e-18 -0.907872 1.08e-113 -0.902620 0.008540 ( 0.053055) 0.911160 ( 0.040987) 0.000000 0.910256 --->fabia-------germline2: 3.96e-18 -0.986334 2.58e-127 -0.977906 0.008540 ( 0.053055) 0.986447 ( 0.001883) 0.000000 0.986385 --->fabia-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.008540 ( 0.053055) 0.000000 ( 0.000000) 0.000000 0.000000 --->beagle1-----beagle2--: 1.49e-16 0.532137 4.77e-34 0.471292 0.539735 ( 0.217338) 0.068443 ( 0.154941) 0.576548 0.004951 --->beagle1-----plink----: 3.96e-18 -0.432738 1.53e-38 -0.460196 0.539735 ( 0.217338) 0.999932 ( 1.42e-06) 0.576548 0.999932 --->beagle1-----germline1: 3.96e-18 -0.342679 6.43e-31 -0.371425 0.539735 ( 0.217338) 0.911160 ( 0.040987) 0.576548 0.910256 --->beagle1-----germline2: 3.96e-18 -0.418963 1.68e-37 -0.446711 0.539735 ( 0.217338) 0.986447 ( 0.001883) 0.576548 0.986385 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.539735 ( 0.217338) 0.000000 ( 0.000000) 0.576548 0.000000 --->beagle2-----plink----: 4.07e-18 -0.975448 9.76e-80 -0.931488 0.068443 ( 0.154941) 0.999932 ( 1.42e-06) 0.004951 0.999932 --->beagle2-----germline1: 4.06e-18 -0.874652 1.78e-73 -0.842717 0.068443 ( 0.154941) 0.911160 ( 0.040987) 0.004951 0.910256 --->beagle2-----germline2: 4.08e-18 -0.961206 3.39e-79 -0.918003 0.068443 ( 0.154941) 0.986447 ( 0.001883) 0.004951 0.986385 --->beagle2-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.068443 ( 0.154941) 0.000000 ( 0.000000) 0.004951 0.000000 --->plink-------germline1: 2.84e-17 0.090631 2.42e-39 0.088771 0.999932 ( 1.42e-06) 0.911160 ( 0.040987) 0.999932 0.910256 --->plink-------germline2: 3.96e-18 0.013510 4.27e-87 0.013485 0.999932 ( 1.42e-06) 0.986447 ( 0.001883) 0.999932 0.986385 --->plink-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.999932 ( 1.42e-06) 0.000000 ( 0.000000) 0.999932 0.000000 --->germline1---germline2: 2.84e-17 -0.077010 1.49e-34 -0.075286 0.911160 ( 0.040987) 0.986447 ( 0.001883) 0.910256 0.986385 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 0.911160 ( 0.040987) 0.000000 ( 0.000000) 0.910256 0.000000 --->germline2---dash-----: 1e+00 0.000000 1e+00 0.000000 0.986447 ( 0.001883) 0.000000 ( 0.000000) 0.986385 0.000000 ######specifity###### --->fabia-------beagle1--: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 1.82e-06) 0.999943 ( 3.81e-05) 1.000000 0.999952 --->fabia-------beagle2--: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 1.82e-06) 0.999997 ( 7.64e-06) 1.000000 1.000000 --->fabia-------plink----: 3.96e-18 0.693517 2.44e-201 0.693301 1.000000 ( 1.82e-06) 0.306699 ( 0.006727) 1.000000 0.305157 --->fabia-------germline1: 3.94e-18 0.000380 1.31e-57 0.000411 1.000000 ( 1.82e-06) 0.999588 ( 0.000118) 1.000000 0.999600 --->fabia-------germline2: 3.96e-18 0.003066 4.92e-94 0.003080 1.000000 ( 1.82e-06) 0.996920 ( 0.000365) 1.000000 0.996958 --->fabia-------dash-----: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 1.82e-06) 1.000000 ( 0.000000) 1.000000 1.000000 --->beagle1-----beagle2--: 1e+00 0.000000 1e+00 0.000000 0.999943 ( 3.81e-05) 0.999997 ( 7.64e-06) 0.999952 1.000000 --->beagle1-----plink----: 3.96e-18 0.693466 2.46e-201 0.693244 0.999943 ( 3.81e-05) 0.306699 ( 0.006727) 0.999952 0.305157 --->beagle1-----germline1: 3.96e-18 0.000342 4.21e-50 0.000355 0.999943 ( 3.81e-05) 0.999588 ( 0.000118) 0.999952 0.999600 --->beagle1-----germline2: 3.96e-18 0.003012 3.13e-93 0.003023 0.999943 ( 3.81e-05) 0.996920 ( 0.000365) 0.999952 0.996958 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.999943 ( 3.81e-05) 1.000000 ( 0.000000) 0.999952 1.000000 --->beagle2-----plink----: 3.96e-18 0.693511 2.44e-201 0.693298 0.999997 ( 7.64e-06) 0.306699 ( 0.006727) 1.000000 0.305157 --->beagle2-----germline1: 3.95e-18 0.000407 2e-57 0.000409 0.999997 ( 7.64e-06) 0.999588 ( 0.000118) 1.000000 0.999600 --->beagle2-----germline2: 3.96e-18 0.003064 3.67e-94 0.003077 0.999997 ( 7.64e-06) 0.996920 ( 0.000365) 1.000000 0.996958 --->beagle2-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.999997 ( 7.64e-06) 1.000000 ( 0.000000) 1.000000 1.000000 --->plink-------germline1: 3.96e-18 -0.693084 3.36e-201 -0.692889 0.306699 ( 0.006727) 0.999588 ( 0.000118) 0.305157 0.999600 --->plink-------germline2: 3.96e-18 -0.690436 1.93e-201 -0.690221 0.306699 ( 0.006727) 0.996920 ( 0.000365) 0.305157 0.996958 --->plink-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.306699 ( 0.006727) 1.000000 ( 0.000000) 0.305157 1.000000 --->germline1---germline2: 3.96e-18 0.002658 1.8e-89 0.002668 0.999588 ( 0.000118) 0.996920 ( 0.000365) 0.999600 0.996958 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 0.999588 ( 0.000118) 1.000000 ( 0.000000) 0.999600 1.000000 --->germline2---dash-----: 1e+00 0.000000 1e+00 0.000000 0.996920 ( 0.000365) 1.000000 ( 0.000000) 0.996958 1.000000 ######sensitivity###### --->fabia-------beagle1--: 2.54e-10 0.151530 8.41e-11 0.160157 0.933338 ( 0.114671) 0.773180 ( 0.191099) 0.963954 0.804227 --->fabia-------beagle2--: 2.92e-12 0.244052 1.14e-14 0.243268 0.933338 ( 0.114671) 0.690069 ( 0.246952) 0.963954 0.697579 --->fabia-------plink----: 3.96e-18 -0.046931 1.34e-07 -0.065277 0.933338 ( 0.114671) 0.998615 ( 0.008738) 0.963954 1.000000 --->fabia-------germline1: 2.07e-10 0.070424 2.2e-05 0.137706 0.933338 ( 0.114671) 0.795632 ( 0.283235) 0.963954 0.881982 --->fabia-------germline2: 7.95e-10 0.066266 3.62e-05 0.055817 0.933338 ( 0.114671) 0.877520 ( 0.059670) 0.963954 0.881982 --->fabia-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.933338 ( 0.114671) 0.000000 ( 0.000000) 0.963954 0.000000 --->beagle1-----beagle2--: 5.64e-07 0.234063 8.58e-08 0.083111 0.773180 ( 0.191099) 0.690069 ( 0.246952) 0.804227 0.697579 --->beagle1-----plink----: 1.04e-16 -0.233534 1.43e-20 -0.225435 0.773180 ( 0.191099) 0.998615 ( 0.008738) 0.804227 1.000000 --->beagle1-----germline1: 1.89e-02 -0.061080 4.84e-01 -0.022452 0.773180 ( 0.191099) 0.795632 ( 0.283235) 0.804227 0.881982 --->beagle1-----germline2: 4.62e-06 -0.094570 4.35e-07 -0.104340 0.773180 ( 0.191099) 0.877520 ( 0.059670) 0.804227 0.881982 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.773180 ( 0.191099) 0.000000 ( 0.000000) 0.804227 0.000000 --->beagle2-----plink----: 1.04e-16 -0.331005 4.82e-22 -0.308545 0.690069 ( 0.246952) 0.998615 ( 0.008738) 0.697579 1.000000 --->beagle2-----germline1: 2.96e-04 -0.133638 3.62e-03 -0.105563 0.690069 ( 0.246952) 0.795632 ( 0.283235) 0.697579 0.881982 --->beagle2-----germline2: 8.66e-10 -0.181919 1.3e-11 -0.187451 0.690069 ( 0.246952) 0.877520 ( 0.059670) 0.697579 0.881982 --->beagle2-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.690069 ( 0.246952) 0.000000 ( 0.000000) 0.697579 0.000000 --->plink-------germline1: 1.11e-17 0.119621 1.42e-10 0.202983 0.998615 ( 0.008738) 0.795632 ( 0.283235) 1.000000 0.881982 --->plink-------germline2: 1.12e-17 0.119424 3.41e-36 0.121094 0.998615 ( 0.008738) 0.877520 ( 0.059670) 1.000000 0.881982 --->plink-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.998615 ( 0.008738) 0.000000 ( 0.000000) 1.000000 0.000000 --->germline1---germline2: 1e+00 0.000000 6.6e-04 -0.081888 0.795632 ( 0.283235) 0.877520 ( 0.059670) 0.881982 0.881982 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 0.795632 ( 0.283235) 0.000000 ( 0.000000) 0.881982 0.000000 --->germline2---dash-----: 1e+00 0.000000 1e+00 0.000000 0.877520 ( 0.059670) 0.000000 ( 0.000000) 0.881982 0.000000 ######trueN###### --->fabia-------beagle1--: 3.95e-18 2e+08 0e+00 2e+08 4e+08 ( 743) 2e+08 ( 7635) 4e+08 2e+08 --->fabia-------beagle2--: 1.95e-18 2e+08 0e+00 2e+08 4e+08 ( 743) 2e+08 ( 1534) 4e+08 2e+08 --->fabia-------plink----: 3.96e-18 3.39e+08 9.83e-240 3.39e+08 4e+08 ( 743) 61336874 ( 1345377) 4e+08 6.1e+07 --->fabia-------germline1: 3.94e-18 2e+08 0e+00 2e+08 4e+08 ( 743) 2e+08 ( 23506) 4e+08 2e+08 --->fabia-------germline2: 3.96e-18 2.01e+08 0e+00 2.01e+08 4e+08 ( 743) 1.99e+08 ( 72984) 4e+08 1.99e+08 --->fabia-------dash-----: 6.31e-23 2e+08 0e+00 2e+08 4e+08 ( 743) 2e+08 ( 168) 4e+08 2e+08 --->beagle1-----beagle2--: 1.77e-16 -11787 1.94e-25 -10815 2e+08 ( 7635) 2e+08 ( 1534) 2e+08 2e+08 --->beagle1-----plink----: 3.96e-18 1.39e+08 2.46e-201 1.39e+08 2e+08 ( 7635) 61336874 ( 1345377) 2e+08 6.1e+07 --->beagle1-----germline1: 3.96e-18 70301 4.18e-50 70921 2e+08 ( 7635) 2e+08 ( 23506) 2e+08 2e+08 --->beagle1-----germline2: 3.96e-18 601634 3.12e-93 604560 2e+08 ( 7635) 1.99e+08 ( 72984) 2e+08 1.99e+08 --->beagle1-----dash-----: 1.81e-17 -11562 3.62e-27 -11408 2e+08 ( 7635) 2e+08 ( 168) 2e+08 2e+08 --->beagle2-----plink----: 3.96e-18 1.39e+08 2.44e-201 1.39e+08 2e+08 ( 1534) 61336874 ( 1345377) 2e+08 6.1e+07 --->beagle2-----germline1: 3.95e-18 81136 2e-57 81736 2e+08 ( 1534) 2e+08 ( 23506) 2e+08 2e+08 --->beagle2-----germline2: 3.96e-18 612398 3.66e-94 615375 2e+08 ( 1534) 1.99e+08 ( 72984) 2e+08 1.99e+08 --->beagle2-----dash-----: 7.75e-11 -600 1.87e-04 -593 2e+08 ( 1534) 2e+08 ( 168) 2e+08 2e+08 --->plink-------germline1: 3.96e-18 -1.39e+08 3.36e-201 -1.39e+08 61336874 ( 1345377) 2e+08 ( 23506) 6.1e+07 2e+08 --->plink-------germline2: 3.96e-18 -1.38e+08 1.93e-201 -1.38e+08 61336874 ( 1345377) 1.99e+08 ( 72984) 6.1e+07 1.99e+08 --->plink-------dash-----: 3.96e-18 -1.39e+08 2.45e-201 -1.39e+08 61336874 ( 1345377) 2e+08 ( 168) 6.1e+07 2e+08 --->germline1---germline2: 3.96e-18 531463 1.8e-89 533639 2e+08 ( 23506) 1.99e+08 ( 72984) 2e+08 1.99e+08 --->germline1---dash-----: 3.94e-18 -81900 1.37e-57 -82329 2e+08 ( 23506) 2e+08 ( 168) 2e+08 2e+08 --->germline2---dash-----: 3.96e-18 -612850 5e-94 -615968 1.99e+08 ( 72984) 2e+08 ( 168) 1.99e+08 2e+08 ######falseP###### --->fabia-------beagle1--: 1.81e-17 -11398 4.16e-27 -11294 113 ( 728) 11408 ( 7622) 0 9558 --->fabia-------beagle2--: 5.72e-08 -549 6.64e-03 -480 113 ( 728) 593 ( 1528) 0 35 --->fabia-------plink----: 3.96e-18 -1.39e+08 2.43e-201 -1.39e+08 113 ( 728) 1.39e+08 ( 1345381) 0 1.39e+08 --->fabia-------germline1: 3.94e-18 -81700 1.29e-57 -82215 113 ( 728) 82329 ( 23502) 0 79904 --->fabia-------germline2: 3.96e-18 -612832 4.83e-94 -615855 113 ( 728) 615968 ( 73005) 0 608465 --->fabia-------dash-----: 1e+00 0.000000 1e+00 0.000000 113.260000 (728.489271) 0.000000 ( 0.000000) 0.000000 0.000000 --->beagle1-----beagle2--: 1.77e-16 11787 1.94e-25 10815 11408 ( 7622) 593 ( 1528) 9558 35 --->beagle1-----plink----: 3.96e-18 -1.39e+08 2.46e-201 -1.39e+08 11408 ( 7622) 1.39e+08 ( 1345381) 9558 1.39e+08 --->beagle1-----germline1: 3.96e-18 -70302 4.18e-50 -70921 11408 ( 7622) 82329 ( 23502) 9558 79904 --->beagle1-----germline2: 3.96e-18 -601626 3.12e-93 -604560 11408 ( 7622) 615968 ( 73005) 9558 608465 --->beagle1-----dash-----: 1e+00 0 1e+00 0 11408 ( 7622) 0 ( 0) 9558 0 --->beagle2-----plink----: 3.96e-18 -1.39e+08 2.44e-201 -1.39e+08 593 ( 1528) 1.39e+08 ( 1345381) 35 1.39e+08 --->beagle2-----germline1: 3.95e-18 -81142 2e-57 -81736 593 ( 1528) 82329 ( 23502) 35 79904 --->beagle2-----germline2: 3.96e-18 -612396 3.66e-94 -615375 593 ( 1528) 615968 ( 73005) 35 608465 --->beagle2-----dash-----: 1e+00 0 1e+00 0 593 ( 1528) 0 ( 0) 35 0 --->plink-------germline1: 3.96e-18 1.39e+08 3.36e-201 1.39e+08 1.39e+08 ( 1345381) 82329 ( 23502) 1.39e+08 79904 --->plink-------germline2: 3.96e-18 1.38e+08 1.93e-201 1.38e+08 1.39e+08 ( 1345381) 615968 ( 73005) 1.39e+08 608465 --->plink-------dash-----: 1e+00 0 1e+00 0 1.39e+08 ( 1345381) 0 ( 0) 1.39e+08 0 --->germline1---germline2: 3.96e-18 -531464 1.8e-89 -533639 82329 ( 23502) 615968 ( 73005) 79904 608465 --->germline1---dash-----: 1e+00 0 1e+00 0 82329 ( 23502) 0 ( 0) 79904 0 --->germline2---dash-----: 1e+00 0 1e+00 0 615968 ( 73005) 0 ( 0) 608465 0 ######falseN###### --->fabia-------beagle1--: 2.4e-10 -1438 8.99e-11 -1520 634 ( 1094) 2154 ( 1818) 341 1882 --->fabia-------beagle2--: 2.71e-12 -2313 1.26e-14 -2310 634 ( 1094) 2945 ( 2351) 341 2848 --->fabia-------plink----: 3.95e-18 448 1.45e-07 621 634 ( 1094) 13.4 ( 85.5) 341 0 --->fabia-------germline1: 2.1e-10 -670 2.16e-05 -1304 634 ( 1094) 1939 ( 2675) 341 1124 --->fabia-------germline2: 8.39e-10 -630 3.79e-05 -531 634 ( 1094) 1165 ( 567) 341 1124 --->fabia-------dash-----: 5.78e-18 -9061 4.15e-92 -8873 634 ( 1094) 9508 ( 168) 341 9510 --->beagle1-----beagle2--: 5.64e-07 -2236 8.32e-08 -790 2154 ( 1818) 2945 ( 2351) 1882 2848 --->beagle1-----plink----: 1.08e-16 2208 1.61e-20 2141 2154 ( 1818) 13.4 ( 85.5) 1882 0 --->beagle1-----germline1: 1.89e-02 580 4.79e-01 215 2154 ( 1818) 1939 ( 2675) 1882 1124 --->beagle1-----germline2: 4.89e-06 893 4.7e-07 989 2154 ( 1818) 1165 ( 567) 1882 1124 --->beagle1-----dash-----: 3.96e-18 -7486 5.24e-63 -7354 2154 ( 1818) 9508 ( 168) 1882 9510 --->beagle2-----plink----: 1.08e-16 3148 5.5e-22 2931 2945 ( 2351) 13.4 ( 85.5) 2848 0 --->beagle2-----germline1: 2.9e-04 1264 3.51e-03 1006 2945 ( 2351) 1939 ( 2675) 2848 1124 --->beagle2-----germline2: 9.05e-10 1722 1.44e-11 1780 2945 ( 2351) 1165 ( 567) 2848 1124 --->beagle2-----dash-----: 5.78e-18 -6641 1.55e-48 -6563 2945 ( 2351) 9508 ( 168) 2848 9510 --->plink-------germline1: 1.12e-17 -1141 1.23e-10 -1925 13.4 ( 85.5) 1939 ( 2675) 0 1124 --->plink-------germline2: 1.12e-17 -1138 3.47e-36 -1152 13.4 ( 85.5) 1165 ( 567) 0 1124 --->plink-------dash-----: 3.95e-18 -9506 1.35e-173 -9494 13.4 ( 85.5) 9508 ( 168) 0 9510 --->germline1---germline2: 1e+00 0 6.6e-04 774 1939 ( 2675) 1165 ( 567) 1124 1124 --->germline1---dash-----: 4.83e-18 -8400 5.79e-49 -7569 1939 ( 2675) 9508 ( 168) 1124 9510 --->germline2---dash-----: 2.13e-19 -8400 6.9e-117 -8343 1165 ( 567) 9508 ( 168) 1124 9510 ######trueP###### --->fabia-------beagle1--: 2.4e-10 1438 8.99e-11 1520 8873 ( 1100) 7354 ( 1835) 9084 7673 --->fabia-------beagle2--: 2.71e-12 2312 1.26e-14 2310 8873 ( 1100) 6563 ( 2363) 9084 6620 --->fabia-------plink----: 3.95e-18 -448 1.45e-07 -621 8873 ( 1100) 9494 ( 176) 9084 9505 --->fabia-------germline1: 2.1e-10 670 2.16e-05 1304 8873 ( 1100) 7569 ( 2694) 9084 8400 --->fabia-------germline2: 8.39e-10 630 3.79e-05 531 8873 ( 1100) 8343 ( 578) 9084 8400 --->fabia-------dash-----: 1e+00 0 1e+00 0 8873 ( 1100) 0 ( 0) 9084 0 --->beagle1-----beagle2--: 5.64e-07 2236 8.32e-08 790 7354 ( 1835) 6563 ( 2363) 7673 6620 --->beagle1-----plink----: 1.08e-16 -2209 1.61e-20 -2141 7354 ( 1835) 9494 ( 176) 7673 9505 --->beagle1-----germline1: 1.89e-02 -580 4.79e-01 -215 7354 ( 1835) 7569 ( 2694) 7673 8400 --->beagle1-----germline2: 4.89e-06 -893 4.7e-07 -989 7354 ( 1835) 8343 ( 578) 7673 8400 --->beagle1-----dash-----: 1e+00 0 1e+00 0 7354 ( 1835) 0 ( 0) 7673 0 --->beagle2-----plink----: 1.08e-16 -3148 5.5e-22 -2931 6563 ( 2363) 9494 ( 176) 6620 9505 --->beagle2-----germline1: 2.9e-04 -1264 3.51e-03 -1006 6563 ( 2363) 7569 ( 2694) 6620 8400 --->beagle2-----germline2: 9.05e-10 -1722 1.44e-11 -1780 6563 ( 2363) 8343 ( 578) 6620 8400 --->beagle2-----dash-----: 1e+00 0 1e+00 0 6563 ( 2363) 0 ( 0) 6620 0 --->plink-------germline1: 1.12e-17 1141 1.23e-10 1925 9494 ( 176) 7569 ( 2694) 9505 8400 --->plink-------germline2: 1.12e-17 1138 3.47e-36 1152 9494 ( 176) 8343 ( 578) 9505 8400 --->plink-------dash-----: 1e+00 0 1e+00 0 9494 ( 176) 0 ( 0) 9505 0 --->germline1---germline2: 1e+00 0 6.6e-04 -774 7569 ( 2694) 8343 ( 578) 8400 8400 --->germline1---dash-----: 1e+00 0 1e+00 0 7569 ( 2694) 0 ( 0) 8400 0 --->germline2---dash-----: 1e+00 0 1e+00 0 8343 ( 578) 0 ( 0) 8400 0 ######MatthewsSnps###### --->fabia-------beagle1--: 5.57e-17 0.380774 2.46e-33 0.370208 0.955347 ( 0.107537) 0.585139 ( 0.171019) 0.981382 0.570634 --->fabia-------beagle2--: 1.75e-13 0.165173 2.42e-12 0.171002 0.955347 ( 0.107537) 0.784345 ( 0.179721) 0.981382 0.807516 --->fabia-------plink----: 5.78e-18 0.974543 3.23e-96 0.955297 0.955347 ( 0.107537) 4.96e-05 ( 0.000131) 0.981382 0.000000 --->fabia-------germline1: 4.08e-18 0.698407 8.14e-67 0.702909 0.955347 ( 0.107537) 0.252438 ( 0.105765) 0.981382 0.271274 --->fabia-------germline2: 4.08e-18 0.892981 4.5e-92 0.876935 0.955347 ( 0.107537) 0.078412 ( 0.019657) 0.981382 0.081117 --->fabia-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.955347 ( 0.107537) 0.000000 ( 0.000000) 0.981382 0.000000 --->beagle1-----beagle2--: 5.4e-13 -0.238401 1.65e-19 -0.199206 0.585139 ( 0.171019) 0.784345 ( 0.179721) 0.570634 0.807516 --->beagle1-----plink----: 3.96e-18 0.579252 1.19e-56 0.585089 0.585139 ( 0.171019) 4.96e-05 ( 0.000131) 0.570634 0.000000 --->beagle1-----germline1: 5.35e-18 0.320108 1.37e-31 0.332701 0.585139 ( 0.171019) 0.252438 ( 0.105765) 0.570634 0.271274 --->beagle1-----germline2: 3.96e-18 0.501101 4.57e-51 0.506727 0.585139 ( 0.171019) 0.078412 ( 0.019657) 0.570634 0.081117 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.585139 ( 0.171019) 0.000000 ( 0.000000) 0.570634 0.000000 --->beagle2-----plink----: 4.08e-18 0.797177 1.82e-66 0.784295 0.784345 ( 0.179721) 4.96e-05 ( 0.000131) 0.807516 0.000000 --->beagle2-----germline1: 5.68e-18 0.542746 3.36e-47 0.531907 0.784345 ( 0.179721) 0.252438 ( 0.105765) 0.807516 0.271274 --->beagle2-----germline2: 4.08e-18 0.721009 2.37e-62 0.705933 0.784345 ( 0.179721) 0.078412 ( 0.019657) 0.807516 0.081117 --->beagle2-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.784345 ( 0.179721) 0.000000 ( 0.000000) 0.807516 0.000000 --->plink-------germline1: 1.17e-17 -0.269438 7.65e-43 -0.252389 4.96e-05 ( 0.000131) 0.252438 ( 0.105765) 0.000000 0.271274 --->plink-------germline2: 4.08e-18 -0.079477 8.51e-63 -0.078362 4.96e-05 ( 0.000131) 0.078412 ( 0.019657) 0.000000 0.081117 --->plink-------dash-----: 1e+00 0.000000 1e+00 0.000000 4.96e-05 ( 0.000131) 0.000000 ( 0.000000) 0.000000 0.000000 --->germline1---germline2: 8.13e-17 0.190833 3.45e-31 0.174026 0.252438 ( 0.105765) 0.078412 ( 0.019657) 0.271274 0.081117 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 0.252438 ( 0.105765) 0.000000 ( 0.000000) 0.271274 0.000000 --->germline2---dash-----: 1e+00 0.000000 1e+00 0.000000 0.078412 ( 0.019657) 0.000000 ( 0.000000) 0.081117 0.000000 ######F1Snps###### --->fabia-------beagle1--: 4.95e-17 0.399278 2.59e-34 0.385927 0.954848 ( 0.108323) 0.568921 ( 0.173208) 0.981646 0.554438 --->fabia-------beagle2--: 1.42e-13 0.182900 5.84e-13 0.187875 0.954848 ( 0.108323) 0.766973 ( 0.194267) 0.981646 0.798511 --->fabia-------plink----: 4.08e-18 0.927624 9.27e-94 0.908413 0.954848 ( 0.108323) 0.046435 ( 8e-04) 0.981646 0.046446 --->fabia-------germline1: 4.08e-18 0.780490 4.22e-77 0.772258 0.954848 ( 0.108323) 0.182590 ( 0.069298) 0.981646 0.184310 --->fabia-------germline2: 4.08e-18 0.913748 4.03e-93 0.895262 0.954848 ( 0.108323) 0.059586 ( 0.004656) 0.981646 0.059178 --->fabia-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.954848 ( 0.108323) 0.000000 ( 0.000000) 0.981646 0.000000 --->beagle1-----beagle2--: 2.23e-12 -0.230724 2.43e-17 -0.198052 0.568921 ( 0.173208) 0.766973 ( 0.194267) 0.554438 0.798511 --->beagle1-----plink----: 3.96e-18 0.513386 1.05e-51 0.522486 0.568921 ( 0.173208) 0.046435 ( 8e-04) 0.554438 0.046446 --->beagle1-----germline1: 3.96e-18 0.374229 4.74e-39 0.386331 0.568921 ( 0.173208) 0.182590 ( 0.069298) 0.554438 0.184310 --->beagle1-----germline2: 3.96e-18 0.500761 8.32e-51 0.509335 0.568921 ( 0.173208) 0.059586 ( 0.004656) 0.554438 0.059178 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.568921 ( 0.173208) 0.000000 ( 0.000000) 0.554438 0.000000 --->beagle2-----plink----: 4.08e-18 0.733685 7e-60 0.720538 0.766973 ( 0.194267) 0.046435 ( 8e-04) 0.798511 0.046446 --->beagle2-----germline1: 5.04e-18 0.597648 6.22e-51 0.584383 0.766973 ( 0.194267) 0.182590 ( 0.069298) 0.798511 0.184310 --->beagle2-----germline2: 4.08e-18 0.720572 2.95e-59 0.707387 0.766973 ( 0.194267) 0.059586 ( 0.004656) 0.798511 0.059178 --->beagle2-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.766973 ( 0.194267) 0.000000 ( 0.000000) 0.798511 0.000000 --->plink-------germline1: 1.17e-17 -0.140326 5.54e-36 -0.136154 0.046435 ( 8e-04) 0.182590 ( 0.069298) 0.046446 0.184310 --->plink-------germline2: 4.08e-18 -0.012999 1.48e-50 -0.013151 0.046435 ( 8e-04) 0.059586 ( 0.004656) 0.046446 0.059178 --->plink-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.046435 ( 8e-04) 0.000000 ( 0.000000) 0.046446 0.000000 --->germline1---germline2: 1.72e-17 0.126766 4.11e-33 0.123004 0.182590 ( 0.069298) 0.059586 ( 0.004656) 0.184310 0.059178 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 0.182590 ( 0.069298) 0.000000 ( 0.000000) 0.184310 0.000000 --->germline2---dash-----: 1e+00 0.000000 1e+00 0.000000 0.059586 ( 0.004656) 0.000000 ( 0.000000) 0.059178 0.000000 ######accuracySnps###### --->fabia-------beagle1--: 4.89e-18 0.028664 6.1e-31 0.029128 0.998131 ( 0.003318) 0.969003 ( 0.016903) 0.999147 0.970378 --->fabia-------beagle2--: 4.74e-13 0.006688 6.9e-14 0.006975 0.998131 ( 0.003318) 0.991156 ( 0.007036) 0.999147 0.991663 --->fabia-------plink----: 3.96e-18 0.974964 6.54e-246 0.974360 0.998131 ( 0.003318) 0.023771 ( 0.000419) 0.999147 0.023778 --->fabia-------germline1: 3.96e-18 0.182637 1.07e-62 0.182674 0.998131 ( 0.003318) 0.815456 ( 0.045706) 0.999147 0.814542 --->fabia-------germline2: 3.96e-18 0.729696 1.6e-118 0.729067 0.998131 ( 0.003318) 0.269063 ( 0.048488) 0.999147 0.262683 --->fabia-------dash-----: 5.78e-18 0.022627 2.03e-83 0.021900 0.998131 ( 0.003318) 0.976230 ( 0.000419) 0.999147 0.976225 --->beagle1-----beagle2--: 3.76e-16 -0.023267 2.48e-23 -0.022154 0.969003 ( 0.016903) 0.991156 ( 0.007036) 0.970378 0.991663 --->beagle1-----plink----: 3.96e-18 0.945747 5.49e-175 0.945232 0.969003 ( 0.016903) 0.023771 ( 0.000419) 0.970378 0.023778 --->beagle1-----germline1: 3.96e-18 0.152494 2.84e-55 0.153546 0.969003 ( 0.016903) 0.815456 ( 0.045706) 0.970378 0.814542 --->beagle1-----germline2: 3.96e-18 0.699807 2.4e-115 0.699939 0.969003 ( 0.016903) 0.269063 ( 0.048488) 0.970378 0.262683 --->beagle1-----dash-----: 2.17e-04 -0.006710 4.32e-05 -0.007228 0.969003 ( 0.016903) 0.976230 ( 0.000419) 0.970378 0.976225 --->beagle2-----plink----: 3.96e-18 0.967946 9.46e-214 0.967386 0.991156 ( 0.007036) 0.023771 ( 0.000419) 0.991663 0.023778 --->beagle2-----germline1: 3.96e-18 0.174834 3.95e-61 0.175700 0.991156 ( 0.007036) 0.815456 ( 0.045706) 0.991663 0.814542 --->beagle2-----germline2: 3.96e-18 0.723210 5.03e-119 0.722093 0.991156 ( 0.007036) 0.269063 ( 0.048488) 0.991663 0.262683 --->beagle2-----dash-----: 1.13e-17 0.015503 1.82e-38 0.014926 0.991156 ( 0.007036) 0.976230 ( 0.000419) 0.991663 0.976225 --->plink-------germline1: 3.96e-18 -0.791949 1e-124 -0.791686 0.023771 ( 0.000419) 0.815456 ( 0.045706) 0.023778 0.814542 --->plink-------germline2: 3.96e-18 -0.244559 1.39e-72 -0.245293 0.023771 ( 0.000419) 0.269063 ( 0.048488) 0.023778 0.262683 --->plink-------dash-----: 3.95e-18 -0.952423 1.52e-304 -0.952460 0.023771 ( 0.000419) 0.976230 ( 0.000419) 0.023778 0.976225 --->germline1---germline2: 3.96e-18 0.546228 7.25e-98 0.546393 0.815456 ( 0.045706) 0.269063 ( 0.048488) 0.814542 0.262683 --->germline1---dash-----: 3.95e-18 -0.160727 9.34e-58 -0.160774 0.815456 ( 0.045706) 0.976230 ( 0.000419) 0.814542 0.976225 --->germline2---dash-----: 3.96e-18 -0.707817 2.52e-117 -0.707167 0.269063 ( 0.048488) 0.976230 ( 0.000419) 0.262683 0.976225 ######FPRSnps###### --->fabia-------beagle1--: 1.81e-17 -0.026402 2.42e-28 -0.026131 0.000290 ( 0.001865) 0.026421 ( 0.017014) 0.000000 0.023753 --->fabia-------beagle2--: 1e+00 0.000000 6.64e-03 -0.001228 0.000290 ( 0.001865) 0.001518 ( 0.003912) 0.000000 8.96e-05 --->fabia-------plink----: 5.78e-21 -1.000000 3.17e-272 -0.999709 0.000290 ( 0.001865) 0.999999 ( 2.26e-06) 0.000000 1.000000 --->fabia-------germline1: 3.96e-18 -0.184631 3.62e-62 -0.184813 0.000290 ( 0.001865) 0.185103 ( 0.047181) 0.000000 0.186818 --->fabia-------germline2: 3.96e-18 -0.748158 1.17e-118 -0.747717 0.000290 ( 0.001865) 0.748007 ( 0.049669) 0.000000 0.753325 --->fabia-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.000290 ( 0.001865) 0.000000 ( 0.000000) 0.000000 0.000000 --->beagle1-----beagle2--: 1.77e-16 0.026796 1.84e-26 0.024903 0.026421 ( 0.017014) 0.001518 ( 0.003912) 0.023753 8.96e-05 --->beagle1-----plink----: 3.96e-18 -0.974341 4.79e-176 -0.973578 0.026421 ( 0.017014) 0.999999 ( 2.26e-06) 0.023753 1.000000 --->beagle1-----germline1: 3.96e-18 -0.157846 2.89e-55 -0.158682 0.026421 ( 0.017014) 0.185103 ( 0.047181) 0.023753 0.186818 --->beagle1-----germline2: 3.96e-18 -0.721451 4.32e-115 -0.721586 0.026421 ( 0.017014) 0.748007 ( 0.049669) 0.023753 0.753325 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.026421 ( 0.017014) 0.000000 ( 0.000000) 0.023753 0.000000 --->beagle2-----plink----: 2.34e-18 -0.999464 2.49e-240 -0.998481 0.001518 ( 0.003912) 0.999999 ( 2.26e-06) 8.96e-05 1.000000 --->beagle2-----germline1: 3.96e-18 -0.182895 6.37e-62 -0.183585 0.001518 ( 0.003912) 0.185103 ( 0.047181) 8.96e-05 0.186818 --->beagle2-----germline2: 3.96e-18 -0.747426 7.43e-119 -0.746489 0.001518 ( 0.003912) 0.748007 ( 0.049669) 8.96e-05 0.753325 --->beagle2-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.001518 ( 0.003912) 0.000000 ( 0.000000) 8.96e-05 0.000000 --->plink-------germline1: 3.96e-18 0.815231 1.32e-124 0.814896 0.999999 ( 2.26e-06) 0.185103 ( 0.047181) 1.000000 0.186818 --->plink-------germline2: 3.96e-18 0.251267 1.15e-72 0.251992 0.999999 ( 2.26e-06) 0.748007 ( 0.049669) 1.000000 0.753325 --->plink-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.999999 ( 2.26e-06) 0.000000 ( 0.000000) 1.000000 0.000000 --->germline1---germline2: 3.96e-18 -0.562738 4.25e-97 -0.562904 0.185103 ( 0.047181) 0.748007 ( 0.049669) 0.186818 0.753325 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 0.185103 ( 0.047181) 0.000000 ( 0.000000) 0.186818 0.000000 --->germline2---dash-----: 1e+00 0.000000 1e+00 0.000000 0.748007 ( 0.049669) 0.000000 ( 0.000000) 0.753325 0.000000 ######FDRSnps###### --->fabia-------beagle1--: 1.81e-17 -0.553366 1.56e-43 -0.513452 0.008540 ( 0.053055) 0.521993 ( 0.209010) 0.000000 0.566760 --->fabia-------beagle2--: 3.86e-08 -0.068571 5.22e-04 -0.059903 0.008540 ( 0.053055) 0.068443 ( 0.154941) 0.000000 0.004951 --->fabia-------plink----: 3.95e-18 -0.976177 6.03e-127 -0.967690 0.008540 ( 0.053055) 0.976230 ( 0.000419) 0.000000 0.976225 --->fabia-------germline1: 3.94e-18 -0.894532 4.74e-113 -0.888315 0.008540 ( 0.053055) 0.896855 ( 0.041313) 0.000000 0.897476 --->fabia-------germline2: 3.96e-18 -0.969189 1.32e-126 -0.960718 0.008540 ( 0.053055) 0.969259 ( 0.002458) 0.000000 0.969509 --->fabia-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.008540 ( 0.053055) 0.000000 ( 0.000000) 0.000000 0.000000 --->beagle1-----beagle2--: 1.59e-16 0.512726 8.98e-34 0.453550 0.521993 ( 0.209010) 0.068443 ( 0.154941) 0.566760 0.004951 --->beagle1-----plink----: 3.96e-18 -0.426851 1.84e-39 -0.454238 0.521993 ( 0.209010) 0.976230 ( 0.000419) 0.566760 0.976225 --->beagle1-----germline1: 3.96e-18 -0.344701 1.67e-32 -0.374863 0.521993 ( 0.209010) 0.896855 ( 0.041313) 0.566760 0.897476 --->beagle1-----germline2: 3.96e-18 -0.419397 6.33e-39 -0.447266 0.521993 ( 0.209010) 0.969259 ( 0.002458) 0.566760 0.969509 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.521993 ( 0.209010) 0.000000 ( 0.000000) 0.566760 0.000000 --->beagle2-----plink----: 4.08e-18 -0.951395 1.16e-78 -0.907787 0.068443 ( 0.154941) 0.976230 ( 0.000419) 0.004951 0.976225 --->beagle2-----germline1: 4.06e-18 -0.861282 1.19e-72 -0.828412 0.068443 ( 0.154941) 0.896855 ( 0.041313) 0.004951 0.897476 --->beagle2-----germline2: 4.08e-18 -0.943599 2.3e-78 -0.900816 0.068443 ( 0.154941) 0.969259 ( 0.002458) 0.004951 0.969509 --->beagle2-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.068443 ( 0.154941) 0.000000 ( 0.000000) 0.004951 0.000000 --->plink-------germline1: 1.17e-17 0.080447 3.26e-35 0.079375 0.976230 ( 0.000419) 0.896855 ( 0.041313) 0.976225 0.897476 --->plink-------germline2: 4.08e-18 0.006863 9.91e-51 0.006972 0.976230 ( 0.000419) 0.969259 ( 0.002458) 0.976225 0.969509 --->plink-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.976230 ( 0.000419) 0.000000 ( 0.000000) 0.976225 0.000000 --->germline1---germline2: 1.31e-17 -0.073214 1.24e-32 -0.072403 0.896855 ( 0.041313) 0.969259 ( 0.002458) 0.897476 0.969509 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 0.896855 ( 0.041313) 0.000000 ( 0.000000) 0.897476 0.000000 --->germline2---dash-----: 1e+00 0.000000 1e+00 0.000000 0.969259 ( 0.002458) 0.000000 ( 0.000000) 0.969509 0.000000 ######specifitySnps###### --->fabia-------beagle1--: 1.81e-17 0.026412 2.42e-28 0.026131 0.999710 ( 0.001865) 0.973579 ( 0.017014) 1.000000 0.976247 --->fabia-------beagle2--: 1e+00 0.000000 6.64e-03 0.001228 0.999710 ( 0.001865) 0.998482 ( 0.003912) 1.000000 0.999910 --->fabia-------plink----: 5.86e-21 1.000000 3.17e-272 0.999709 0.999710 ( 0.001865) 8.19e-07 ( 2.27e-06) 1.000000 0.000000 --->fabia-------germline1: 3.96e-18 0.184659 3.62e-62 0.184813 0.999710 ( 0.001865) 0.814897 ( 0.047181) 1.000000 0.813182 --->fabia-------germline2: 3.96e-18 0.748155 1.17e-118 0.747717 0.999710 ( 0.001865) 0.251993 ( 0.049669) 1.000000 0.246675 --->fabia-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.999710 ( 0.001865) 1.000000 ( 0.000000) 1.000000 1.000000 --->beagle1-----beagle2--: 1.77e-16 -0.026819 1.84e-26 -0.024903 0.973579 ( 0.017014) 0.998482 ( 0.003912) 0.976247 0.999910 --->beagle1-----plink----: 3.96e-18 0.974341 4.79e-176 0.973578 0.973579 ( 0.017014) 8.19e-07 ( 2.27e-06) 0.976247 0.000000 --->beagle1-----germline1: 3.96e-18 0.157818 2.89e-55 0.158682 0.973579 ( 0.017014) 0.814897 ( 0.047181) 0.976247 0.813182 --->beagle1-----germline2: 3.96e-18 0.721442 4.32e-115 0.721586 0.973579 ( 0.017014) 0.251993 ( 0.049669) 0.976247 0.246675 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.973579 ( 0.017014) 1.000000 ( 0.000000) 0.976247 1.000000 --->beagle2-----plink----: 2.35e-18 0.999463 2.49e-240 0.998481 0.998482 ( 0.003912) 8.19e-07 ( 2.27e-06) 0.999910 0.000000 --->beagle2-----germline1: 3.96e-18 0.182869 6.37e-62 0.183585 0.998482 ( 0.003912) 0.814897 ( 0.047181) 0.999910 0.813182 --->beagle2-----germline2: 3.96e-18 0.747435 7.43e-119 0.746489 0.998482 ( 0.003912) 0.251993 ( 0.049669) 0.999910 0.246675 --->beagle2-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.998482 ( 0.003912) 1.000000 ( 0.000000) 0.999910 1.000000 --->plink-------germline1: 3.96e-18 -0.815244 1.32e-124 -0.814896 8.19e-07 ( 2.27e-06) 0.814897 ( 0.047181) 0.000000 0.813182 --->plink-------germline2: 3.96e-18 -0.251239 1.15e-72 -0.251992 8.19e-07 ( 2.27e-06) 0.251993 ( 0.049669) 0.000000 0.246675 --->plink-------dash-----: 1e+00 0.000000 1e+00 0.000000 8.19e-07 ( 2.27e-06) 1.000000 ( 0.000000) 0.000000 1.000000 --->germline1---germline2: 3.96e-18 0.562735 4.25e-97 0.562904 0.814897 ( 0.047181) 0.251993 ( 0.049669) 0.813182 0.246675 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 0.814897 ( 0.047181) 1.000000 ( 0.000000) 0.813182 1.000000 --->germline2---dash-----: 1e+00 0.000000 1e+00 0.000000 0.251993 ( 0.049669) 1.000000 ( 0.000000) 0.246675 1.000000 ######sensitivitySnps###### --->fabia-------beagle1--: 9.86e-10 0.144448 4.71e-10 0.152521 0.933338 ( 0.114671) 0.780816 ( 0.191543) 0.963954 0.825123 --->fabia-------beagle2--: 2.92e-12 0.244052 1.14e-14 0.243268 0.933338 ( 0.114671) 0.690069 ( 0.246952) 0.963954 0.697579 --->fabia-------plink----: 1e+00 0.000000 1e+00 0.000000 0.933338 ( 0.114671) 1.000000 ( 0.000000) 0.963954 1.000000 --->fabia-------germline1: 8.28e-06 0.046178 1.08e-03 0.095260 0.933338 ( 0.114671) 0.838077 ( 0.252942) 0.963954 0.888983 --->fabia-------germline2: 6.8e-05 -0.021713 2.46e-03 -0.036898 0.933338 ( 0.114671) 0.970236 ( 0.042454) 0.963954 1.000000 --->fabia-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.933338 ( 0.114671) 0.000000 ( 0.000000) 0.963954 0.000000 --->beagle1-----beagle2--: 2.59e-07 0.242208 3.06e-08 0.090747 0.780816 ( 0.191543) 0.690069 ( 0.246952) 0.825123 0.697579 --->beagle1-----plink----: 1e+00 0.000000 1e+00 0.000000 0.780816 ( 0.191543) 1.000000 ( 0.000000) 0.825123 1.000000 --->beagle1-----germline1: 1.43e-03 -0.077874 5.34e-02 -0.057261 0.780816 ( 0.191543) 0.838077 ( 0.252942) 0.825123 0.888983 --->beagle1-----germline2: 1.9e-14 -0.192396 6.45e-16 -0.189420 0.780816 ( 0.191543) 0.970236 ( 0.042454) 0.825123 1.000000 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.780816 ( 0.191543) 0.000000 ( 0.000000) 0.825123 0.000000 --->beagle2-----plink----: 1e+00 0.000000 1e+00 0.000000 0.690069 ( 0.246952) 1.000000 ( 0.000000) 0.697579 1.000000 --->beagle2-----germline1: 4.18e-06 -0.163915 1.42e-05 -0.148008 0.690069 ( 0.246952) 0.838077 ( 0.252942) 0.697579 0.888983 --->beagle2-----germline2: 2.38e-15 -0.296668 2.61e-19 -0.280167 0.690069 ( 0.246952) 0.970236 ( 0.042454) 0.697579 1.000000 --->beagle2-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.690069 ( 0.246952) 0.000000 ( 0.000000) 0.697579 0.000000 --->plink-------germline1: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 0.838077 ( 0.252942) 1.000000 0.888983 --->plink-------germline2: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 0.970236 ( 0.042454) 1.000000 1.000000 --->plink-------dash-----: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 0.000000 ( 0.000000) 1.000000 0.000000 --->germline1---germline2: 1.71e-14 -0.081047 1.04e-06 -0.132159 0.838077 ( 0.252942) 0.970236 ( 0.042454) 0.888983 1.000000 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 0.838077 ( 0.252942) 0.000000 ( 0.000000) 0.888983 0.000000 --->germline2---dash-----: 1e+00 0.000000 1e+00 0.000000 0.970236 ( 0.042454) 0.000000 ( 0.000000) 1.000000 0.000000 ######trueNSnps###### --->fabia-------beagle1--: 1.81e-17 5159 2.41e-28 5102 195189 ( 372) 190087 ( 3328) 195242 190590 --->fabia-------beagle2--: 5.72e-08 274 6.64e-03 240 195189 ( 372) 194950 ( 767) 195242 195180 --->fabia-------plink----: 3.95e-18 195239 2.36e-271 195189 195189 ( 372) 0.16 ( 0.443) 195242 0 --->fabia-------germline1: 3.95e-18 36050 3.6e-62 36084 195189 ( 372) 159105 ( 9213) 195242 158805 --->fabia-------germline2: 3.96e-18 146074 1.25e-118 145989 195189 ( 372) 49200 ( 9696) 195242 48158 --->fabia-------dash-----: 1e+00 0 1.23e-01 -56.6 195189 ( 372) 195246 ( 83.8) 195242 195245 --->beagle1-----beagle2--: 1.77e-16 -5234 1.83e-26 -4862 190087 ( 3328) 194950 ( 767) 190590 195180 --->beagle1-----plink----: 3.96e-18 190249 5.8e-176 190087 190087 ( 3328) 0.16 ( 0.443) 190590 0 --->beagle1-----germline1: 3.96e-18 30814 2.88e-55 30982 190087 ( 3328) 159105 ( 9213) 190590 158805 --->beagle1-----germline2: 3.96e-18 140859 4.61e-115 140887 190087 ( 3328) 49200 ( 9696) 190590 48158 --->beagle1-----dash-----: 1.81e-17 -5204 2.75e-28 -5159 190087 ( 3328) 195246 ( 83.8) 190590 195245 --->beagle2-----plink----: 3.95e-18 195119 3.8e-240 194949 194950 ( 767) 0.16 ( 0.443) 195180 0 --->beagle2-----germline1: 3.96e-18 35711 6.33e-62 35844 194950 ( 767) 159105 ( 9213) 195180 158805 --->beagle2-----germline2: 3.96e-18 145930 7.92e-119 145749 194950 ( 767) 49200 ( 9696) 195180 48158 --->beagle2-----dash-----: 7.75e-11 -300 1.87e-04 -296 194950 ( 767) 195246 ( 83.8) 195180 195245 --->plink-------germline1: 3.96e-18 -159172 1.33e-124 -159105 0.16 ( 0.443) 159105 ( 9213) 0 158805 --->plink-------germline2: 3.95e-18 -49066 1.13e-72 -49200 0.16 ( 0.443) 49200 ( 9696) 0 48158 --->plink-------dash-----: 3.95e-18 -195242 0e+00 -195246 0.16 ( 0.443) 195246 ( 83.8) 0 195245 --->germline1---germline2: 3.96e-18 109879 4.4e-97 109905 159105 ( 9213) 49200 ( 9696) 158805 48158 --->germline1---dash-----: 3.95e-18 -36075 3.86e-62 -36141 159105 ( 9213) 195246 ( 83.8) 158805 195245 --->germline2---dash-----: 3.96e-18 -146182 1.04e-118 -146046 49200 ( 9696) 195246 ( 83.8) 48158 195245 ######falsePSnps###### --->fabia-------beagle1--: 1.81e-17 -5159 2.41e-28 -5102 56.6 ( 364) 5159 ( 3322) 0 4638 --->fabia-------beagle2--: 5.72e-08 -274 6.64e-03 -240 56.6 ( 364) 296 ( 764) 0 17.5 --->fabia-------plink----: 3.95e-18 -195239 2.36e-271 -195189 56.6 ( 364) 195246 ( 83.8) 0 195244 --->fabia-------germline1: 3.95e-18 -36050 3.6e-62 -36084 56.6 ( 364) 36141 ( 9211) 0 36484 --->fabia-------germline2: 3.96e-18 -146072 1.25e-118 -145989 56.6 ( 364) 146046 ( 9704) 0 147061 --->fabia-------dash-----: 1e+00 0.000000 1e+00 0.000000 56.630000 (364.244636) 0.000000 ( 0.000000) 0.000000 0.000000 --->beagle1-----beagle2--: 1.77e-16 5234 1.83e-26 4862 5159 ( 3322) 296 ( 764) 4638 17.5 --->beagle1-----plink----: 3.96e-18 -190249 5.8e-176 -190087 5159 ( 3322) 195246 ( 83.8) 4638 195244 --->beagle1-----germline1: 3.96e-18 -30814 2.88e-55 -30982 5159 ( 3322) 36141 ( 9211) 4638 36484 --->beagle1-----germline2: 3.96e-18 -140859 4.61e-115 -140887 5159 ( 3322) 146046 ( 9704) 4638 147061 --->beagle1-----dash-----: 1e+00 0 1e+00 0 5159 ( 3322) 0 ( 0) 4638 0 --->beagle2-----plink----: 3.95e-18 -195119 3.8e-240 -194949 296 ( 764) 195246 ( 83.8) 17.5 195244 --->beagle2-----germline1: 3.96e-18 -35711 6.33e-62 -35844 296 ( 764) 36141 ( 9211) 17.5 36484 --->beagle2-----germline2: 3.96e-18 -145932 7.92e-119 -145749 296 ( 764) 146046 ( 9704) 17.5 147061 --->beagle2-----dash-----: 1e+00 0 1e+00 0 296 ( 764) 0 ( 0) 17.5 0 --->plink-------germline1: 3.96e-18 159171 1.33e-124 159105 195246 ( 83.8) 36141 ( 9211) 195244 36484 --->plink-------germline2: 3.95e-18 49064 1.13e-72 49200 195246 ( 83.8) 146046 ( 9704) 195244 147061 --->plink-------dash-----: 1e+00 0 1e+00 0 195246 ( 83.8) 0 ( 0) 195244 0 --->germline1---germline2: 3.96e-18 -109879 4.4e-97 -109905 36141 ( 9211) 146046 ( 9704) 36484 147061 --->germline1---dash-----: 1e+00 0 1e+00 0 36141 ( 9211) 0 ( 0) 36484 0 --->germline2---dash-----: 1e+00 0 1e+00 0 146046 ( 9704) 0 ( 0) 147061 0 ######falseNSnps###### --->fabia-------beagle1--: 9.14e-10 -686 4.96e-10 -724 317 ( 547) 1041 ( 911) 170 839 --->fabia-------beagle2--: 2.71e-12 -1156 1.26e-14 -1155 317 ( 547) 1472 ( 1176) 170 1424 --->fabia-------plink----: 1e+00 0 1e+00 0 317 ( 547) 0 ( 0) 170 0 --->fabia-------germline1: 8.83e-06 -219 1.09e-03 -451 317 ( 547) 768 ( 1195) 170 522 --->fabia-------germline2: 7.1e-05 104 2.49e-03 176 317 ( 547) 142 ( 202) 170 0 --->fabia-------dash-----: 5.78e-18 -4530 4.15e-92 -4437 317 ( 547) 4754 ( 83.8) 170 4755 --->beagle1-----beagle2--: 2.59e-07 -1147 3e-08 -431 1041 ( 911) 1472 ( 1176) 839 1424 --->beagle1-----plink----: 1e+00 0 1e+00 0 1041 ( 911) 0 ( 0) 839 0 --->beagle1-----germline1: 1.45e-03 369 5.21e-02 273 1041 ( 911) 768 ( 1195) 839 522 --->beagle1-----germline2: 2.02e-14 911 6.98e-16 899 1041 ( 911) 142 ( 202) 839 0 --->beagle1-----dash-----: 3.96e-18 -3784 2.45e-63 -3713 1041 ( 911) 4754 ( 83.8) 839 4755 --->beagle2-----plink----: 1e+00 0 1e+00 0 1472 ( 1176) 0 ( 0) 1424 0 --->beagle2-----germline1: 4.11e-06 782 1.38e-05 704 1472 ( 1176) 768 ( 1195) 1424 522 --->beagle2-----germline2: 2.53e-15 1409 2.87e-19 1331 1472 ( 1176) 142 ( 202) 1424 0 --->beagle2-----dash-----: 5.78e-18 -3321 1.55e-48 -3282 1472 ( 1176) 4754 ( 83.8) 1424 4755 --->plink-------germline1: 1e+00 0 1e+00 0 0 ( 0) 768 ( 1195) 0 522 --->plink-------germline2: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 141.510000 (201.988073) 0.000000 0.000000 --->plink-------dash-----: 1e+00 0 1e+00 0 0 ( 0) 4754 ( 83.8) 0 4755 --->germline1---germline2: 1.71e-14 386 9.64e-07 627 768 ( 1195) 142 ( 202) 522 0 --->germline1---dash-----: 2.19e-17 -4328 2.43e-55 -3986 768 ( 1195) 4754 ( 83.8) 522 4755 --->germline2---dash-----: 3.95e-18 -4628 2.09e-133 -4612 142 ( 202) 4754 ( 83.8) 0 4755 ######truePSnps###### --->fabia-------beagle1--: 9.14e-10 686 4.96e-10 724 4437 ( 550) 3713 ( 919) 4542 3902 --->fabia-------beagle2--: 2.71e-12 1156 1.26e-14 1155 4437 ( 550) 3282 ( 1181) 4542 3310 --->fabia-------plink----: 3.95e-18 -233 8.04e-08 -317 4437 ( 550) 4754 ( 83.8) 4542 4755 --->fabia-------germline1: 8.83e-06 220 1.09e-03 451 4437 ( 550) 3986 ( 1204) 4542 4200 --->fabia-------germline2: 7.1e-05 -104 2.49e-03 -176 4437 ( 550) 4612 ( 218) 4542 4708 --->fabia-------dash-----: 1e+00 0 1e+00 0 4437 ( 550) 0 ( 0) 4542 0 --->beagle1-----beagle2--: 2.59e-07 1147 3e-08 431 3713 ( 919) 3282 ( 1181) 3902 3310 --->beagle1-----plink----: 1.21e-16 -1077 8.66e-20 -1041 3713 ( 919) 4754 ( 83.8) 3902 4755 --->beagle1-----germline1: 1.45e-03 -369 5.21e-02 -273 3713 ( 919) 3986 ( 1204) 3902 4200 --->beagle1-----germline2: 2.02e-14 -911 6.98e-16 -899 3713 ( 919) 4612 ( 218) 3902 4708 --->beagle1-----dash-----: 1e+00 0 1e+00 0 3713 ( 919) 0 ( 0) 3902 0 --->beagle2-----plink----: 8.28e-17 -1581 3.92e-22 -1472 3282 ( 1181) 4754 ( 83.8) 3310 4755 --->beagle2-----germline1: 4.11e-06 -782 1.38e-05 -704 3282 ( 1181) 3986 ( 1204) 3310 4200 --->beagle2-----germline2: 2.53e-15 -1409 2.87e-19 -1331 3282 ( 1181) 4612 ( 218) 3310 4708 --->beagle2-----dash-----: 1e+00 0 1e+00 0 3282 ( 1181) 0 ( 0) 3310 0 --->plink-------germline1: 8.28e-17 522 4.6e-09 768 4754 ( 83.8) 3986 ( 1204) 4755 4200 --->plink-------germline2: 1.71e-08 341 3.01e-10 142 4754 ( 83.8) 4612 ( 218) 4755 4708 --->plink-------dash-----: 1e+00 0 1e+00 0 4754 ( 83.8) 0 ( 0) 4755 0 --->germline1---germline2: 1.71e-14 -386 9.64e-07 -627 3986 ( 1204) 4612 ( 218) 4200 4708 --->germline1---dash-----: 1e+00 0 1e+00 0 3986 ( 1204) 0 ( 0) 4200 0 --->germline2---dash-----: 1e+00 0 1e+00 0 4612 ( 218) 0 ( 0) 4708 0 ######MatthewsSample###### --->fabia-------beagle1--: 1.01e-15 0.423877 3.56e-37 0.380399 0.981203 ( 0.111130) 0.600803 ( 0.157159) 1.000000 0.576192 --->fabia-------beagle2--: 1e+00 0.000000 6.68e-01 0.007205 0.981203 ( 0.111130) 0.973998 ( 0.121473) 1.000000 1.000000 --->fabia-------plink----: 1e+00 0.000000 1e+00 0.000000 0.981203 ( 0.111130) 0.000000 ( 0.000000) 1.000000 0.000000 --->fabia-------germline1: 4.12e-18 0.695489 4.8e-65 0.701585 0.981203 ( 0.111130) 0.279617 ( 0.108830) 1.000000 0.305655 --->fabia-------germline2: 4.05e-18 0.896569 5.17e-91 0.878136 0.981203 ( 0.111130) 0.103066 ( 0.006832) 1.000000 0.102955 --->fabia-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.981203 ( 0.111130) 0.000000 ( 0.000000) 1.000000 0.000000 --->beagle1-----beagle2--: 1.54e-15 -0.423883 1.46e-35 -0.373194 0.600803 ( 0.157159) 0.973998 ( 0.121473) 0.576192 1.000000 --->beagle1-----plink----: 1e+00 0.000000 1e+00 0.000000 0.600803 ( 0.157159) 0.000000 ( 0.000000) 0.576192 0.000000 --->beagle1-----germline1: 3.95e-18 0.300629 4.55e-31 0.321186 0.600803 ( 0.157159) 0.279617 ( 0.108830) 0.576192 0.305655 --->beagle1-----germline2: 3.95e-18 0.479648 1.69e-53 0.497737 0.600803 ( 0.157159) 0.103066 ( 0.006832) 0.576192 0.102955 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.600803 ( 0.157159) 0.000000 ( 0.000000) 0.576192 0.000000 --->beagle2-----plink----: 1e+00 0.000000 1e+00 0.000000 0.973998 ( 0.121473) 0.000000 ( 0.000000) 1.000000 0.000000 --->beagle2-----germline1: 4.13e-18 0.691979 8.15e-64 0.694381 0.973998 ( 0.121473) 0.279617 ( 0.108830) 1.000000 0.305655 --->beagle2-----germline2: 4.05e-18 0.895753 1.49e-87 0.870931 0.973998 ( 0.121473) 0.103066 ( 0.006832) 1.000000 0.102955 --->beagle2-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.973998 ( 0.121473) 0.000000 ( 0.000000) 1.000000 0.000000 --->plink-------germline1: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.279617 ( 0.108830) 0.000000 0.305655 --->plink-------germline2: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.103066 ( 0.006832) 0.000000 0.102955 --->plink-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.000000 ( 0.000000) 0.000000 0.000000 --->germline1---germline2: 2.84e-17 0.198780 3.99e-30 0.176551 0.279617 ( 0.108830) 0.103066 ( 0.006832) 0.305655 0.102955 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 0.279617 ( 0.108830) 0.000000 ( 0.000000) 0.305655 0.000000 --->germline2---dash-----: 1e+00 0.000000 1e+00 0.000000 0.103066 ( 0.006832) 0.000000 ( 0.000000) 0.102955 0.000000 ######F1Sample###### --->fabia-------beagle1--: 2.4e-16 0.499945 6e-38 0.451506 0.980000 ( 0.114298) 0.528494 ( 0.192034) 1.000000 0.500000 --->fabia-------beagle2--: 1e+00 0.000000 6.34e-01 0.008333 0.980000 ( 0.114298) 0.971667 ( 0.127690) 1.000000 1.000000 --->fabia-------plink----: 1e+00 0.000000 1e+00 0.000000 0.980000 ( 0.114298) 0.003992 ( 0.000000) 1.000000 0.003992 --->fabia-------germline1: 3.83e-18 0.825771 2.04e-76 0.815079 0.980000 ( 0.114298) 0.164921 ( 0.072457) 1.000000 0.173913 --->fabia-------germline2: 4.05e-18 0.974887 1.53e-93 0.955025 0.980000 ( 0.114298) 0.024975 ( 0.002752) 1.000000 0.024845 --->fabia-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.980000 ( 0.114298) 0.000000 ( 0.000000) 1.000000 0.000000 --->beagle1-----beagle2--: 3.98e-16 -0.499946 2.79e-36 -0.443173 0.528494 ( 0.192034) 0.971667 ( 0.127690) 0.500000 1.000000 --->beagle1-----plink----: 1e+00 0.000000 1e+00 0.000000 0.528494 ( 0.192034) 0.003992 ( 0.000000) 0.500000 0.003992 --->beagle1-----germline1: 3.95e-18 0.346330 8.27e-33 0.363573 0.528494 ( 0.192034) 0.164921 ( 0.072457) 0.500000 0.173913 --->beagle1-----germline2: 3.95e-18 0.480280 2.54e-46 0.503519 0.528494 ( 0.192034) 0.024975 ( 0.002752) 0.500000 0.024845 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.528494 ( 0.192034) 0.000000 ( 0.000000) 0.500000 0.000000 --->beagle2-----plink----: 1e+00 0.000000 1e+00 0.000000 0.971667 ( 0.127690) 0.003992 ( 0.000000) 1.000000 0.003992 --->beagle2-----germline1: 3.84e-18 0.822360 1.27e-74 0.806746 0.971667 ( 0.127690) 0.164921 ( 0.072457) 1.000000 0.173913 --->beagle2-----germline2: 4.05e-18 0.974568 9.86e-89 0.946691 0.971667 ( 0.127690) 0.024975 ( 0.002752) 1.000000 0.024845 --->beagle2-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.971667 ( 0.127690) 0.000000 ( 0.000000) 1.000000 0.000000 --->plink-------germline1: 1e+00 0.000000 1e+00 0.000000 0.003992 ( 0.000000) 0.164921 ( 0.072457) 0.003992 0.173913 --->plink-------germline2: 1e+00 0.000000 1e+00 0.000000 0.003992 ( 0.000000) 0.024975 ( 0.002752) 0.003992 0.024845 --->plink-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.003992 ( 0.000000) 0.000000 ( 0.000000) 0.003992 0.000000 --->germline1---germline2: 2.84e-17 0.145564 1.03e-35 0.139945 0.164921 ( 0.072457) 0.024975 ( 0.002752) 0.173913 0.024845 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 0.164921 ( 0.072457) 0.000000 ( 0.000000) 0.173913 0.000000 --->germline2---dash-----: 1e+00 0.000000 1e+00 0.000000 0.024975 ( 0.002752) 0.000000 ( 0.000000) 0.024845 0.000000 ######accuracySample###### --->fabia-------beagle1--: 5.72e-17 0.004529 1.31e-27 0.004510 0.999960 ( 0.000197) 0.995450 ( 0.002979) 1.000000 0.996000 --->fabia-------beagle2--: 1e+00 0.000000 9.63e-02 0.000120 0.999960 ( 0.000197) 0.999840 ( 0.000677) 1.000000 1.000000 --->fabia-------plink----: 1e+00 0.000000 1e+00 0.000000 0.999960 ( 0.000197) 0.002000 ( 0.000000) 1.000000 0.002000 --->fabia-------germline1: 3.69e-18 0.018966 2.66e-58 0.018900 0.999960 ( 0.000197) 0.981060 ( 0.005276) 1.000000 0.981500 --->fabia-------germline2: 3.93e-18 0.157490 6.15e-96 0.158050 0.999960 ( 0.000197) 0.841910 ( 0.017897) 1.000000 0.843000 --->fabia-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.999960 ( 0.000197) 0.998000 ( 0.000000) 1.000000 0.998000 --->beagle1-----beagle2--: 1.25e-16 -0.004535 3.44e-26 -0.004390 0.995450 ( 0.002979) 0.999840 ( 0.000677) 0.996000 1.000000 --->beagle1-----plink----: 1e+00 0.000000 1e+00 0.000000 0.995450 ( 0.002979) 0.002000 ( 0.000000) 0.996000 0.002000 --->beagle1-----germline1: 3.81e-18 0.014496 3.9e-43 0.014390 0.995450 ( 0.002979) 0.981060 ( 0.005276) 0.996000 0.981500 --->beagle1-----germline2: 3.93e-18 0.153044 3.15e-94 0.153540 0.995450 ( 0.002979) 0.841910 ( 0.017897) 0.996000 0.843000 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.995450 ( 0.002979) 0.998000 ( 0.000000) 0.996000 0.998000 --->beagle2-----plink----: 1e+00 0.000000 1e+00 0.000000 0.999840 ( 0.000677) 0.002000 ( 0.000000) 1.000000 0.002000 --->beagle2-----germline1: 3.68e-18 0.018972 5.29e-58 0.018780 0.999840 ( 0.000677) 0.981060 ( 0.005276) 1.000000 0.981500 --->beagle2-----germline2: 3.93e-18 0.157456 2.83e-96 0.157930 0.999840 ( 0.000677) 0.841910 ( 0.017897) 1.000000 0.843000 --->beagle2-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.999840 ( 0.000677) 0.998000 ( 0.000000) 1.000000 0.998000 --->plink-------germline1: 1e+00 0.000000 1e+00 0.000000 0.002000 ( 0.000000) 0.981060 ( 0.005276) 0.002000 0.981500 --->plink-------germline2: 1e+00 0.000000 1e+00 0.000000 0.002000 ( 0.000000) 0.841910 ( 0.017897) 0.002000 0.843000 --->plink-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.002000 ( 0.000000) 0.998000 ( 0.000000) 0.002000 0.998000 --->germline1---germline2: 3.93e-18 0.138976 1.19e-91 0.139150 0.981060 ( 0.005276) 0.841910 ( 0.017897) 0.981500 0.843000 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 0.981060 ( 0.005276) 0.998000 ( 0.000000) 0.981500 0.998000 --->germline2---dash-----: 1e+00 0.000000 1e+00 0.000000 0.841910 ( 0.017897) 0.998000 ( 0.000000) 0.843000 0.998000 ######FPRSample###### --->fabia-------beagle1--: 5.85e-17 -0.004570 1.04e-27 -0.004529 3e-05 ( 0.000172) 0.004559 ( 0.002985) 0.000000 0.004008 --->fabia-------beagle2--: 1e+00 0.000000 7.8e-02 -0.000110 3e-05 ( 0.000172) 0.000140 ( 0.000588) 0.000000 0.000000 --->fabia-------plink----: 1e+00 0.000000 1e+00 0.000000 3e-05 ( 0.000172) 1.000000 ( 0.000000) 0.000000 1.000000 --->fabia-------germline1: 3.66e-18 -0.018561 5.19e-58 -0.018727 3e-05 ( 0.000172) 0.018758 ( 0.005287) 0.000000 0.018036 --->fabia-------germline2: 3.93e-18 -0.157786 5.92e-96 -0.158377 3e-05 ( 0.000172) 0.158407 ( 0.017932) 0.000000 0.157315 --->fabia-------dash-----: 1e+00 0.000000 1e+00 0.000000 3e-05 ( 0.000172) 0.000000 ( 0.000000) 0.000000 0.000000 --->beagle1-----beagle2--: 1.25e-16 0.004547 1.76e-26 0.004419 0.004559 ( 0.002985) 0.000140 ( 0.000588) 0.004008 0.000000 --->beagle1-----plink----: 1e+00 0.000000 1e+00 0.000000 0.004559 ( 0.002985) 1.000000 ( 0.000000) 0.004008 1.000000 --->beagle1-----germline1: 3.94e-18 -0.014086 1.58e-42 -0.014198 0.004559 ( 0.002985) 0.018758 ( 0.005287) 0.004008 0.018036 --->beagle1-----germline2: 3.95e-18 -0.153366 3.15e-94 -0.153848 0.004559 ( 0.002985) 0.158407 ( 0.017932) 0.004008 0.157315 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.004559 ( 0.002985) 0.000000 ( 0.000000) 0.004008 0.000000 --->beagle2-----plink----: 1e+00 0.000000 1e+00 0.000000 0.000140 ( 0.000588) 1.000000 ( 0.000000) 0.000000 1.000000 --->beagle2-----germline1: 3.67e-18 -0.018510 6.72e-58 -0.018617 0.000140 ( 0.000588) 0.018758 ( 0.005287) 0.000000 0.018036 --->beagle2-----germline2: 3.93e-18 -0.157806 3.07e-96 -0.158267 0.000140 ( 0.000588) 0.158407 ( 0.017932) 0.000000 0.157315 --->beagle2-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.000140 ( 0.000588) 0.000000 ( 0.000000) 0.000000 0.000000 --->plink-------germline1: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 0.018758 ( 0.005287) 1.000000 0.018036 --->plink-------germline2: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 0.158407 ( 0.017932) 1.000000 0.157315 --->plink-------dash-----: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 0.000000 ( 0.000000) 1.000000 0.000000 --->germline1---germline2: 3.95e-18 -0.139286 2.16e-91 -0.139649 0.018758 ( 0.005287) 0.158407 ( 0.017932) 0.018036 0.157315 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 0.018758 ( 0.005287) 0.000000 ( 0.000000) 0.018036 0.000000 --->germline2---dash-----: 1e+00 0.000000 1e+00 0.000000 0.158407 ( 0.017932) 0.000000 ( 0.000000) 0.157315 0.000000 ######FDRSample###### --->fabia-------beagle1--: 5.85e-17 -0.657987 6.95e-47 -0.598354 0.015000 ( 0.085723) 0.613354 ( 0.216570) 0.000000 0.666667 --->fabia-------beagle2--: 1e+00 0.000000 2.27e-01 -0.021667 0.015000 ( 0.085723) 0.036667 ( 0.152753) 0.000000 0.000000 --->fabia-------plink----: 1e+00 0.000000 1e+00 0.000000 0.015000 ( 0.085723) 0.998000 ( 0.000000) 0.000000 0.998000 --->fabia-------germline1: 3.71e-18 -0.904589 8.21e-98 -0.893492 0.015000 ( 0.085723) 0.908492 ( 0.041930) 0.000000 0.904762 --->fabia-------germline2: 3.93e-18 -0.987316 1.36e-106 -0.972352 0.015000 ( 0.085723) 0.987352 ( 0.001411) 0.000000 0.987421 --->fabia-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.015000 ( 0.085723) 0.000000 ( 0.000000) 0.000000 0.000000 --->beagle1-----beagle2--: 1.45e-16 0.650024 7.1e-41 0.576688 0.613354 ( 0.216570) 0.036667 ( 0.152753) 0.666667 0.000000 --->beagle1-----plink----: 1e+00 0.000000 1e+00 0.000000 0.613354 ( 0.216570) 0.998000 ( 0.000000) 0.666667 0.998000 --->beagle1-----germline1: 3.94e-18 -0.261814 4.09e-24 -0.295138 0.613354 ( 0.216570) 0.908492 ( 0.041930) 0.666667 0.904762 --->beagle1-----germline2: 3.95e-18 -0.339160 1.28e-31 -0.373998 0.613354 ( 0.216570) 0.987352 ( 0.001411) 0.666667 0.987421 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.613354 ( 0.216570) 0.000000 ( 0.000000) 0.666667 0.000000 --->beagle2-----plink----: 1e+00 0.000000 1e+00 0.000000 0.036667 ( 0.152753) 0.998000 ( 0.000000) 0.000000 0.998000 --->beagle2-----germline1: 3.84e-18 -0.902433 1.86e-75 -0.871826 0.036667 ( 0.152753) 0.908492 ( 0.041930) 0.000000 0.904762 --->beagle2-----germline2: 4.05e-18 -0.987111 2.86e-81 -0.950686 0.036667 ( 0.152753) 0.987352 ( 0.001411) 0.000000 0.987421 --->beagle2-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.036667 ( 0.152753) 0.000000 ( 0.000000) 0.000000 0.000000 --->plink-------germline1: 1e+00 0.000000 1e+00 0.000000 0.998000 ( 0.000000) 0.908492 ( 0.041930) 0.998000 0.904762 --->plink-------germline2: 1e+00 0.000000 1e+00 0.000000 0.998000 ( 0.000000) 0.987352 ( 0.001411) 0.998000 0.987421 --->plink-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.998000 ( 0.000000) 0.000000 ( 0.000000) 0.998000 0.000000 --->germline1---germline2: 2.84e-17 -0.080717 9.04e-35 -0.078860 0.908492 ( 0.041930) 0.987352 ( 0.001411) 0.904762 0.987421 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 0.908492 ( 0.041930) 0.000000 ( 0.000000) 0.904762 0.000000 --->germline2---dash-----: 1e+00 0.000000 1e+00 0.000000 0.987352 ( 0.001411) 0.000000 ( 0.000000) 0.987421 0.000000 ######specifitySample###### --->fabia-------beagle1--: 5.85e-17 0.004570 1.04e-27 0.004529 0.999970 ( 0.000172) 0.995441 ( 0.002985) 1.000000 0.995992 --->fabia-------beagle2--: 1e+00 0.000000 7.8e-02 0.000110 0.999970 ( 0.000172) 0.999860 ( 0.000588) 1.000000 1.000000 --->fabia-------plink----: 1e+00 0.000000 1e+00 0.000000 0.999970 ( 0.000172) 0.000000 ( 0.000000) 1.000000 0.000000 --->fabia-------germline1: 3.66e-18 0.018608 5.19e-58 0.018727 0.999970 ( 0.000172) 0.981242 ( 0.005287) 1.000000 0.981964 --->fabia-------germline2: 3.93e-18 0.157771 5.92e-96 0.158377 0.999970 ( 0.000172) 0.841593 ( 0.017932) 1.000000 0.842685 --->fabia-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.999970 ( 0.000172) 1.000000 ( 0.000000) 1.000000 1.000000 --->beagle1-----beagle2--: 1.25e-16 -0.004547 1.76e-26 -0.004419 0.995441 ( 0.002985) 0.999860 ( 0.000588) 0.995992 1.000000 --->beagle1-----plink----: 1e+00 0.000000 1e+00 0.000000 0.995441 ( 0.002985) 0.000000 ( 0.000000) 0.995992 0.000000 --->beagle1-----germline1: 3.85e-18 0.014047 1.58e-42 0.014198 0.995441 ( 0.002985) 0.981242 ( 0.005287) 0.995992 0.981964 --->beagle1-----germline2: 3.94e-18 0.153367 3.15e-94 0.153848 0.995441 ( 0.002985) 0.841593 ( 0.017932) 0.995992 0.842685 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.995441 ( 0.002985) 1.000000 ( 0.000000) 0.995992 1.000000 --->beagle2-----plink----: 1e+00 0.000000 1e+00 0.000000 0.999860 ( 0.000588) 0.000000 ( 0.000000) 1.000000 0.000000 --->beagle2-----germline1: 3.63e-18 0.018478 6.72e-58 0.018617 0.999860 ( 0.000588) 0.981242 ( 0.005287) 1.000000 0.981964 --->beagle2-----germline2: 3.93e-18 0.157796 3.07e-96 0.158267 0.999860 ( 0.000588) 0.841593 ( 0.017932) 1.000000 0.842685 --->beagle2-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.999860 ( 0.000588) 1.000000 ( 0.000000) 1.000000 1.000000 --->plink-------germline1: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.981242 ( 0.005287) 0.000000 0.981964 --->plink-------germline2: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.841593 ( 0.017932) 0.000000 0.842685 --->plink-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 1.000000 ( 0.000000) 0.000000 1.000000 --->germline1---germline2: 3.94e-18 0.139286 2.16e-91 0.139649 0.981242 ( 0.005287) 0.841593 ( 0.017932) 0.981964 0.842685 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 0.981242 ( 0.005287) 1.000000 ( 0.000000) 0.981964 1.000000 --->germline2---dash-----: 1e+00 0.000000 1e+00 0.000000 0.841593 ( 0.017932) 1.000000 ( 0.000000) 0.842685 1.000000 ######sensitivitySample###### --->fabia-------beagle1--: 1e+00 0.000000 1e+00 0.000000 0.990000 ( 0.100000) 1.000000 ( 0.000000) 1.000000 1.000000 --->fabia-------beagle2--: 1e+00 0.000000 1e+00 0.000000 0.990000 ( 0.100000) 0.990000 ( 0.100000) 1.000000 1.000000 --->fabia-------plink----: 1e+00 0.000000 1e+00 0.000000 0.990000 ( 0.100000) 1.000000 ( 0.000000) 1.000000 1.000000 --->fabia-------germline1: 1e+00 0.000000 3.42e-03 0.100000 0.990000 ( 0.100000) 0.890000 ( 0.314466) 1.000000 1.000000 --->fabia-------germline2: 1e+00 0.000000 1e+00 0.000000 0.990000 ( 0.100000) 1.000000 ( 0.000000) 1.000000 1.000000 --->fabia-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.990000 ( 0.100000) 0.000000 ( 0.000000) 1.000000 0.000000 --->beagle1-----beagle2--: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 0.990000 ( 0.100000) 1.000000 1.000000 --->beagle1-----plink----: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 1.000000 ( 0.000000) 1.000000 1.000000 --->beagle1-----germline1: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 0.890000 ( 0.314466) 1.000000 1.000000 --->beagle1-----germline2: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 1.000000 ( 0.000000) 1.000000 1.000000 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 0.000000 ( 0.000000) 1.000000 0.000000 --->beagle2-----plink----: 1e+00 0.000000 1e+00 0.000000 0.990000 ( 0.100000) 1.000000 ( 0.000000) 1.000000 1.000000 --->beagle2-----germline1: 1e+00 0.000000 3.42e-03 0.100000 0.990000 ( 0.100000) 0.890000 ( 0.314466) 1.000000 1.000000 --->beagle2-----germline2: 1e+00 0.000000 1e+00 0.000000 0.990000 ( 0.100000) 1.000000 ( 0.000000) 1.000000 1.000000 --->beagle2-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.990000 ( 0.100000) 0.000000 ( 0.000000) 1.000000 0.000000 --->plink-------germline1: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 0.890000 ( 0.314466) 1.000000 1.000000 --->plink-------germline2: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 1.000000 ( 0.000000) 1.000000 1.000000 --->plink-------dash-----: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 0.000000 ( 0.000000) 1.000000 0.000000 --->germline1---germline2: 1e+00 0.000000 1e+00 0.000000 0.890000 ( 0.314466) 1.000000 ( 0.000000) 1.000000 1.000000 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 0.890000 ( 0.314466) 0.000000 ( 0.000000) 1.000000 0.000000 --->germline2---dash-----: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 0.000000 ( 0.000000) 1.000000 0.000000 ######trueNSample###### --->fabia-------beagle1--: 2.92e-18 1004 1.55e-252 1004 1998 ( 0.343) 993 ( 2.98) 1998 994 --->fabia-------beagle2--: 6.68e-22 1000 6.8e-315 1000 1998 ( 0.343) 998 ( 0.586) 1998 998 --->fabia-------plink----: 1e+00 0 1e+00 0 1998 ( 0.343) 0 ( 0) 1998 0 --->fabia-------germline1: 3.63e-18 1019 3.15e-228 1019 1998 ( 0.343) 979 ( 5.28) 1998 980 --->fabia-------germline2: 3.93e-18 1157 2.68e-181 1158 1998 ( 0.343) 840 ( 17.9) 1998 841 --->fabia-------dash-----: 1e+00 0 1e+00 0 1998 ( 0.343) 998 ( 0) 1998 998 --->beagle1-----beagle2--: 1.25e-16 -4.5 1.76e-26 -4.41 993 ( 2.98) 998 ( 0.586) 994 998 --->beagle1-----plink----: 1e+00 0 1e+00 0 993 ( 2.98) 0 ( 0) 994 0 --->beagle1-----germline1: 3.81e-18 14 1.58e-42 14.2 993 ( 2.98) 979 ( 5.28) 994 980 --->beagle1-----germline2: 3.93e-18 153 3.15e-94 154 993 ( 2.98) 840 ( 17.9) 994 841 --->beagle1-----dash-----: 1e+00 0 1e+00 0 993 ( 2.98) 998 ( 0) 994 998 --->beagle2-----plink----: 1e+00 0 1e+00 0 998 ( 0.586) 0 ( 0) 998 0 --->beagle2-----germline1: 3.63e-18 18.5 6.72e-58 18.6 998 ( 0.586) 979 ( 5.28) 998 980 --->beagle2-----germline2: 3.93e-18 157 3.07e-96 158 998 ( 0.586) 840 ( 17.9) 998 841 --->beagle2-----dash-----: 1e+00 0 1e+00 0 998 ( 0.586) 998 ( 0) 998 998 --->plink-------germline1: 1e+00 0 1e+00 0 0 ( 0) 979 ( 5.28) 0 980 --->plink-------germline2: 1e+00 0 1e+00 0 0 ( 0) 840 ( 17.9) 0 841 --->plink-------dash-----: 1e+00 0 1e+00 0 0 ( 0) 998 ( 0) 0 998 --->germline1---germline2: 3.93e-18 139 2.16e-91 139 979 ( 5.28) 840 ( 17.9) 980 841 --->germline1---dash-----: 1e+00 0 1e+00 0 979 ( 5.28) 998 ( 0) 980 998 --->germline2---dash-----: 1e+00 0 1e+00 0 840 ( 17.9) 998 ( 0) 841 998 ######falsePSample###### --->fabia-------beagle1--: 5.82e-17 -4.5 1.52e-27 -4.49 0.06 ( 0.343) 4.55 ( 2.98) 0 4 --->fabia-------beagle2--: 1e+00 0.000000 2.5e-01 -0.080000 0.060000 ( 0.342893) 0.140000 ( 0.586377) 0.000000 0.000000 --->fabia-------plink----: 1e+00 0 1e+00 0 0.06 ( 0.343) 998 ( 0) 0 998 --->fabia-------germline1: 3.63e-18 -18.5 7e-58 -18.7 0.06 ( 0.343) 18.7 ( 5.28) 0 18 --->fabia-------germline2: 3.93e-18 -157 6.27e-96 -158 0.06 ( 0.343) 158 ( 17.9) 0 157 --->fabia-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.060000 ( 0.342893) 0.000000 ( 0.000000) 0.000000 0.000000 --->beagle1-----beagle2--: 1.25e-16 4.5 1.76e-26 4.41 4.55 ( 2.98) 0.14 ( 0.586) 4 0 --->beagle1-----plink----: 1e+00 0 1e+00 0 4.55 ( 2.98) 998 ( 0) 4 998 --->beagle1-----germline1: 3.81e-18 -14 1.58e-42 -14.2 4.55 ( 2.98) 18.7 ( 5.28) 4 18 --->beagle1-----germline2: 3.93e-18 -153 3.15e-94 -154 4.55 ( 2.98) 158 ( 17.9) 4 157 --->beagle1-----dash-----: 1e+00 0 1e+00 0 4.55 ( 2.98) 0 ( 0) 4 0 --->beagle2-----plink----: 1e+00 0 1e+00 0 0.14 ( 0.586) 998 ( 0) 0 998 --->beagle2-----germline1: 3.63e-18 -18.5 6.72e-58 -18.6 0.14 ( 0.586) 18.7 ( 5.28) 0 18 --->beagle2-----germline2: 3.93e-18 -157 3.07e-96 -158 0.14 ( 0.586) 158 ( 17.9) 0 157 --->beagle2-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.140000 ( 0.586377) 0.000000 ( 0.000000) 0.000000 0.000000 --->plink-------germline1: 1e+00 0 1e+00 0 998 ( 0) 18.7 ( 5.28) 998 18 --->plink-------germline2: 1e+00 0 1e+00 0 998 ( 0) 158 ( 17.9) 998 157 --->plink-------dash-----: 1e+00 0 1e+00 0 998 ( 0) 0 ( 0) 998 0 --->germline1---germline2: 3.93e-18 -139 2.16e-91 -139 18.7 ( 5.28) 158 ( 17.9) 18 157 --->germline1---dash-----: 1e+00 0 1e+00 0 18.7 ( 5.28) 0 ( 0) 18 0 --->germline2---dash-----: 1e+00 0 1e+00 0 158 ( 17.9) 0 ( 0) 157 0 ######falseNSample###### --->fabia-------beagle1--: 1e+00 0.000000 1e+00 0.000000 0.020000 ( 0.200000) 0.000000 ( 0.000000) 0.000000 0.000000 --->fabia-------beagle2--: 1e+00 0.000000 1e+00 0.000000 0.020000 ( 0.200000) 0.020000 ( 0.200000) 0.000000 0.000000 --->fabia-------plink----: 1e+00 0.000000 1e+00 0.000000 0.020000 ( 0.200000) 0.000000 ( 0.000000) 0.000000 0.000000 --->fabia-------germline1: 1e+00 0.000000 3.42e-03 -0.200000 0.020000 ( 0.200000) 0.220000 ( 0.628932) 0.000000 0.000000 --->fabia-------germline2: 1e+00 0.000000 1e+00 0.000000 0.020000 ( 0.200000) 0.000000 ( 0.000000) 0.000000 0.000000 --->fabia-------dash-----: 1e+00 0 1e+00 0 0.02 ( 0.2) 2 ( 0) 0 2 --->beagle1-----beagle2--: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.020000 ( 0.200000) 0.000000 0.000000 --->beagle1-----plink----: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.000000 ( 0.000000) 0.000000 0.000000 --->beagle1-----germline1: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.220000 ( 0.628932) 0.000000 0.000000 --->beagle1-----germline2: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.000000 ( 0.000000) 0.000000 0.000000 --->beagle1-----dash-----: 1e+00 0 1e+00 0 0 ( 0) 2 ( 0) 0 2 --->beagle2-----plink----: 1e+00 0.000000 1e+00 0.000000 0.020000 ( 0.200000) 0.000000 ( 0.000000) 0.000000 0.000000 --->beagle2-----germline1: 1e+00 0.000000 3.42e-03 -0.200000 0.020000 ( 0.200000) 0.220000 ( 0.628932) 0.000000 0.000000 --->beagle2-----germline2: 1e+00 0.000000 1e+00 0.000000 0.020000 ( 0.200000) 0.000000 ( 0.000000) 0.000000 0.000000 --->beagle2-----dash-----: 1e+00 0 1e+00 0 0.02 ( 0.2) 2 ( 0) 0 2 --->plink-------germline1: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.220000 ( 0.628932) 0.000000 0.000000 --->plink-------germline2: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.000000 ( 0.000000) 0.000000 0.000000 --->plink-------dash-----: 1e+00 0 1e+00 0 0 ( 0) 2 ( 0) 0 2 --->germline1---germline2: 1e+00 0.000000 1e+00 0.000000 0.220000 ( 0.628932) 0.000000 ( 0.000000) 0.000000 0.000000 --->germline1---dash-----: 1e+00 0 1e+00 0 0.22 ( 0.629) 2 ( 0) 0 2 --->germline2---dash-----: 1e+00 0 1e+00 0 0 ( 0) 2 ( 0) 0 2 ######truePSample###### --->fabia-------beagle1--: 1e+00 0 1e+00 0 1.98 ( 0.2) 2 ( 0) 2 2 --->fabia-------beagle2--: 1e+00 0 1e+00 0 1.98 ( 0.2) 1.98 ( 0.2) 2 2 --->fabia-------plink----: 1e+00 0 1e+00 0 1.98 ( 0.2) 2 ( 0) 2 2 --->fabia-------germline1: 1e+00 0 3.42e-03 0.2 1.98 ( 0.2) 1.78 ( 0.629) 2 2 --->fabia-------germline2: 1e+00 0 1e+00 0 1.98 ( 0.2) 2 ( 0) 2 2 --->fabia-------dash-----: 1e+00 0 1e+00 0 1.98 ( 0.2) 0 ( 0) 2 0 --->beagle1-----beagle2--: 1e+00 0 1e+00 0 2 ( 0) 1.98 ( 0.2) 2 2 --->beagle1-----plink----: 1e+00 0 1e+00 0 2 ( 0) 2 ( 0) 2 2 --->beagle1-----germline1: 1e+00 0 1e+00 0 2 ( 0) 1.78 ( 0.629) 2 2 --->beagle1-----germline2: 1e+00 0 1e+00 0 2 ( 0) 2 ( 0) 2 2 --->beagle1-----dash-----: 1e+00 0 1e+00 0 2 ( 0) 0 ( 0) 2 0 --->beagle2-----plink----: 1e+00 0 1e+00 0 1.98 ( 0.2) 2 ( 0) 2 2 --->beagle2-----germline1: 1e+00 0 3.42e-03 0.2 1.98 ( 0.2) 1.78 ( 0.629) 2 2 --->beagle2-----germline2: 1e+00 0 1e+00 0 1.98 ( 0.2) 2 ( 0) 2 2 --->beagle2-----dash-----: 1e+00 0 1e+00 0 1.98 ( 0.2) 0 ( 0) 2 0 --->plink-------germline1: 1e+00 0 1e+00 0 2 ( 0) 1.78 ( 0.629) 2 2 --->plink-------germline2: 1e+00 0 1e+00 0 2 ( 0) 2 ( 0) 2 2 --->plink-------dash-----: 1e+00 0 1e+00 0 2 ( 0) 0 ( 0) 2 0 --->germline1---germline2: 1e+00 0 1e+00 0 1.78 ( 0.629) 2 ( 0) 2 2 --->germline1---dash-----: 1e+00 0 1e+00 0 1.78 ( 0.629) 0 ( 0) 2 0 --->germline2---dash-----: 1e+00 0 1e+00 0 2 ( 0) 0 ( 0) 2 0