Results: Wilcoxon-Rank-Sum Wilcoxon-median t-test t-test-mean mean1 (std) mean2 (std) median1 median2 ######Matthews###### --->fabia-------beagle1--: 9.75e-18 0.153283 4.99e-33 0.151627 0.958980 ( 0.046083) 0.807352 ( 0.069270) 0.975720 0.808645 --->fabia-------beagle2--: 3.84e-11 0.054302 2.8e-07 0.067686 0.958980 ( 0.046083) 0.891294 ( 0.110972) 0.975720 0.915022 --->fabia-------plink----: 3.96e-18 0.959941 3.01e-132 0.951090 0.958980 ( 0.046083) 0.007890 ( 0.000240) 0.975720 0.007907 --->fabia-------germline1: 3.96e-18 0.490625 1.6e-65 0.497243 0.958980 ( 0.046083) 0.461737 ( 0.110609) 0.975720 0.463979 --->fabia-------germline2: 3.96e-18 0.773980 3.17e-122 0.767435 0.958980 ( 0.046083) 0.191545 ( 0.013605) 0.975720 0.190181 --->fabia-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.958980 ( 0.046083) 0.000000 ( 0.000000) 0.975720 0.000000 --->beagle1-----beagle2--: 8.17e-13 -0.098932 3.09e-11 -0.083941 0.807352 ( 0.069270) 0.891294 ( 0.110972) 0.808645 0.915022 --->beagle1-----plink----: 3.96e-18 0.801270 2.29e-107 0.799462 0.807352 ( 0.069270) 0.007890 ( 0.000240) 0.808645 0.007907 --->beagle1-----germline1: 3.96e-18 0.341888 1.44e-46 0.345616 0.807352 ( 0.069270) 0.461737 ( 0.110609) 0.808645 0.463979 --->beagle1-----germline2: 3.96e-18 0.617539 2.53e-94 0.615807 0.807352 ( 0.069270) 0.191545 ( 0.013605) 0.808645 0.190181 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.807352 ( 0.069270) 0.000000 ( 0.000000) 0.808645 0.000000 --->beagle2-----plink----: 4.08e-18 0.900446 1.44e-91 0.883403 0.891294 ( 0.110972) 0.007890 ( 0.000240) 0.915022 0.007907 --->beagle2-----germline1: 5.57e-17 0.432616 5.61e-48 0.429557 0.891294 ( 0.110972) 0.461737 ( 0.110609) 0.915022 0.463979 --->beagle2-----germline2: 4.08e-18 0.717210 2.92e-81 0.699748 0.891294 ( 0.110972) 0.191545 ( 0.013605) 0.915022 0.190181 --->beagle2-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.891294 ( 0.110972) 0.000000 ( 0.000000) 0.915022 0.000000 --->plink-------germline1: 4.33e-18 -0.456009 5.47e-64 -0.453847 0.007890 ( 0.000240) 0.461737 ( 0.110609) 0.007907 0.463979 --->plink-------germline2: 3.96e-18 -0.183331 2.21e-114 -0.183655 0.007890 ( 0.000240) 0.191545 ( 0.013605) 0.007907 0.190181 --->plink-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.007890 ( 0.000240) 0.000000 ( 0.000000) 0.007907 0.000000 --->germline1---germline2: 5.68e-18 0.271424 1.44e-45 0.270192 0.461737 ( 0.110609) 0.191545 ( 0.013605) 0.463979 0.190181 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 0.461737 ( 0.110609) 0.000000 ( 0.000000) 0.463979 0.000000 --->germline2---dash-----: 1e+00 0.000000 1e+00 0.000000 0.191545 ( 0.013605) 0.000000 ( 0.000000) 0.190181 0.000000 ######F1###### --->fabia-------beagle1--: 1.03e-17 0.163347 3.11e-32 0.161783 0.957224 ( 0.049114) 0.795442 ( 0.076699) 0.975427 0.802958 --->fabia-------beagle2--: 8.21e-11 0.055076 3.99e-07 0.068903 0.957224 ( 0.049114) 0.888321 ( 0.113932) 0.975427 0.914229 --->fabia-------plink----: 3.96e-18 0.966694 9.11e-130 0.956818 0.957224 ( 0.049114) 0.000406 ( 1.95e-05) 0.975427 0.000410 --->fabia-------germline1: 3.96e-18 0.570532 1.06e-69 0.571904 0.957224 ( 0.049114) 0.385320 ( 0.115623) 0.975427 0.375102 --->fabia-------germline2: 3.96e-18 0.887871 4.85e-126 0.879342 0.957224 ( 0.049114) 0.077883 ( 0.009511) 0.975427 0.077778 --->fabia-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.957224 ( 0.049114) 0.000000 ( 0.000000) 0.975427 0.000000 --->beagle1-----beagle2--: 1.19e-12 -0.107832 9.24e-12 -0.092880 0.795442 ( 0.076699) 0.888321 ( 0.113932) 0.802958 0.914229 --->beagle1-----plink----: 3.96e-18 0.797855 8.84e-103 0.795036 0.795442 ( 0.076699) 0.000406 ( 1.95e-05) 0.802958 0.000410 --->beagle1-----germline1: 4.08e-18 0.413430 3.37e-50 0.410121 0.795442 ( 0.076699) 0.385320 ( 0.115623) 0.802958 0.375102 --->beagle1-----germline2: 3.96e-18 0.719635 1.92e-97 0.717559 0.795442 ( 0.076699) 0.077883 ( 0.009511) 0.802958 0.077778 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.795442 ( 0.076699) 0.000000 ( 0.000000) 0.802958 0.000000 --->beagle2-----plink----: 4.08e-18 0.906031 1.15e-90 0.887916 0.888321 ( 0.113932) 0.000406 ( 1.95e-05) 0.914229 0.000410 --->beagle2-----germline1: 1.31e-17 0.513287 1.69e-52 0.503001 0.888321 ( 0.113932) 0.385320 ( 0.115623) 0.914229 0.375102 --->beagle2-----germline2: 4.08e-18 0.828687 1.12e-86 0.810439 0.888321 ( 0.113932) 0.077883 ( 0.009511) 0.914229 0.077778 --->beagle2-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.888321 ( 0.113932) 0.000000 ( 0.000000) 0.914229 0.000000 --->plink-------germline1: 4.33e-18 -0.379644 1.42e-55 -0.384915 0.000406 ( 1.95e-05) 0.385320 ( 0.115623) 0.000410 0.375102 --->plink-------germline2: 3.96e-18 -0.077311 1.41e-92 -0.077477 0.000406 ( 1.95e-05) 0.077883 ( 0.009511) 0.000410 0.077778 --->plink-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.000406 ( 1.95e-05) 0.000000 ( 0.000000) 0.000410 0.000000 --->germline1---germline2: 4.6e-18 0.301151 3.82e-48 0.307438 0.385320 ( 0.115623) 0.077883 ( 0.009511) 0.375102 0.077778 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 0.385320 ( 0.115623) 0.000000 ( 0.000000) 0.375102 0.000000 --->germline2---dash-----: 1e+00 0.000000 1e+00 0.000000 0.077883 ( 0.009511) 0.000000 ( 0.000000) 0.077778 0.000000 ######accuracy###### --->fabia-------beagle1--: 1e+00 0.000000 1e+00 0.000000 0.999994 ( 6.62e-06) 0.999929 ( 3.27e-05) 0.999997 0.999936 --->fabia-------beagle2--: 1e+00 0.000000 1e+00 0.000000 0.999994 ( 6.62e-06) 0.999971 ( 2.07e-05) 0.999997 0.999975 --->fabia-------plink----: 3.96e-18 0.692834 3.77e-201 0.692894 0.999994 ( 6.62e-06) 0.307100 ( 0.006753) 0.999997 0.306307 --->fabia-------germline1: 3.96e-18 0.000407 7.84e-51 0.000408 0.999994 ( 6.62e-06) 0.999586 ( 0.000138) 0.999997 0.999590 --->fabia-------germline2: 3.96e-18 0.003038 5.37e-94 0.003055 0.999994 ( 6.62e-06) 0.996940 ( 0.000363) 0.999997 0.996969 --->fabia-------dash-----: 3.95e-18 0.000148 7.74e-119 0.000135 0.999994 ( 6.62e-06) 0.999859 ( 6.44e-06) 0.999997 0.999858 --->beagle1-----beagle2--: 1e+00 0.000000 1e+00 0.000000 0.999929 ( 3.27e-05) 0.999971 ( 2.07e-05) 0.999936 0.999975 --->beagle1-----plink----: 3.96e-18 0.692773 4.26e-201 0.692829 0.999929 ( 3.27e-05) 0.307100 ( 0.006753) 0.999936 0.306307 --->beagle1-----germline1: 4.08e-18 0.000352 5.06e-42 0.000343 0.999929 ( 3.27e-05) 0.999586 ( 0.000138) 0.999936 0.999590 --->beagle1-----germline2: 3.96e-18 0.002974 3.22e-92 0.002990 0.999929 ( 3.27e-05) 0.996940 ( 0.000363) 0.999936 0.996969 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.999929 ( 3.27e-05) 0.999859 ( 6.44e-06) 0.999936 0.999858 --->beagle2-----plink----: 3.96e-18 0.692809 3.8e-201 0.692871 0.999971 ( 2.07e-05) 0.307100 ( 0.006753) 0.999975 0.306307 --->beagle2-----germline1: 3.96e-18 0.000387 6.13e-48 0.000385 0.999971 ( 2.07e-05) 0.999586 ( 0.000138) 0.999975 0.999590 --->beagle2-----germline2: 3.96e-18 0.003013 1.43e-93 0.003031 0.999971 ( 2.07e-05) 0.996940 ( 0.000363) 0.999975 0.996969 --->beagle2-----dash-----: 4.08e-18 5.78e-05 3.54e-73 0.000112 0.999971 ( 2.07e-05) 0.999859 ( 6.44e-06) 0.999975 0.999858 --->plink-------germline1: 3.96e-18 -0.692418 3.02e-201 -0.692486 0.307100 ( 0.006753) 0.999586 ( 0.000138) 0.306307 0.999590 --->plink-------germline2: 3.96e-18 -0.689780 1.34e-201 -0.689840 0.307100 ( 0.006753) 0.996940 ( 0.000363) 0.306307 0.996969 --->plink-------dash-----: 3.96e-18 -0.692736 3.95e-201 -0.692759 0.307100 ( 0.006753) 0.999859 ( 6.44e-06) 0.306307 0.999858 --->germline1---germline2: 3.96e-18 0.002633 1.06e-91 0.002647 0.999586 ( 0.000138) 0.996940 ( 0.000363) 0.999590 0.996969 --->germline1---dash-----: 1.4e-17 -0.000264 9.13e-36 -0.000273 0.999586 ( 0.000138) 0.999859 ( 6.44e-06) 0.999590 0.999858 --->germline2---dash-----: 3.96e-18 -0.002909 4.98e-92 -0.002920 0.996940 ( 0.000363) 0.999859 ( 6.44e-06) 0.996969 0.999858 ######FPR###### --->fabia-------beagle1--: 1e+00 0.000000 1e+00 0.000000 1.04e-06 ( 4.5e-06) 6.28e-05 ( 3.24e-05) 0.000000 5.76e-05 --->fabia-------beagle2--: 1e+00 0.000000 1e+00 0.000000 1.04e-06 ( 4.5e-06) 1.31e-05 ( 7.88e-06) 0.000000 1.17e-05 --->fabia-------plink----: 3.96e-18 -0.692969 3.74e-201 -0.692996 1.04e-06 ( 4.5e-06) 0.692997 ( 0.006754) 0.000000 0.693790 --->fabia-------germline1: 3.96e-18 -0.000396 2.58e-49 -0.000393 1.04e-06 ( 4.5e-06) 0.000394 ( 0.000138) 0.000000 0.000394 --->fabia-------germline2: 3.96e-18 -0.003037 8.1e-94 -0.003047 1.04e-06 ( 4.5e-06) 0.003048 ( 0.000363) 0.000000 0.003018 --->fabia-------dash-----: 1e+00 0.000000 1e+00 0.000000 1.04e-06 ( 4.5e-06) 0.000000 ( 0.000000) 0.000000 0.000000 --->beagle1-----beagle2--: 1e+00 0.000000 1e+00 0.000000 6.28e-05 ( 3.24e-05) 1.31e-05 ( 7.88e-06) 5.76e-05 1.17e-05 --->beagle1-----plink----: 3.96e-18 -0.692910 4.23e-201 -0.692935 6.28e-05 ( 3.24e-05) 0.692997 ( 0.006754) 5.76e-05 0.693790 --->beagle1-----germline1: 4.08e-18 -0.000342 8.4e-41 -0.000332 6.28e-05 ( 3.24e-05) 0.000394 ( 0.000138) 5.76e-05 0.000394 --->beagle1-----germline2: 3.96e-18 -0.002976 3.8e-92 -0.002985 6.28e-05 ( 3.24e-05) 0.003048 ( 0.000363) 5.76e-05 0.003018 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 6.28e-05 ( 3.24e-05) 0.000000 ( 0.000000) 5.76e-05 0.000000 --->beagle2-----plink----: 3.96e-18 -0.692961 3.76e-201 -0.692984 1.31e-05 ( 7.88e-06) 0.692997 ( 0.006754) 1.17e-05 0.693790 --->beagle2-----germline1: 3.96e-18 -0.000377 2.03e-48 -0.000381 1.31e-05 ( 7.88e-06) 0.000394 ( 0.000138) 1.17e-05 0.000394 --->beagle2-----germline2: 3.96e-18 -0.003025 8.64e-94 -0.003035 1.31e-05 ( 7.88e-06) 0.003048 ( 0.000363) 1.17e-05 0.003018 --->beagle2-----dash-----: 1e+00 0.000000 1e+00 0.000000 1.31e-05 ( 7.88e-06) 0.000000 ( 0.000000) 1.17e-05 0.000000 --->plink-------germline1: 3.96e-18 0.692574 2.88e-201 0.692603 0.692997 ( 0.006754) 0.000394 ( 0.000138) 0.693790 0.000394 --->plink-------germline2: 3.96e-18 0.689897 1.32e-201 0.689950 0.692997 ( 0.006754) 0.003048 ( 0.000363) 0.693790 0.003018 --->plink-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.692997 ( 0.006754) 0.000000 ( 0.000000) 0.693790 0.000000 --->germline1---germline2: 3.96e-18 -0.002639 4.45e-92 -0.002653 0.000394 ( 0.000138) 0.003048 ( 0.000363) 0.000394 0.003018 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 0.000394 ( 0.000138) 0.000000 ( 0.000000) 0.000394 0.000000 --->germline2---dash-----: 1e+00 0.000000 1e+00 0.000000 0.003048 ( 0.000363) 0.000000 ( 0.000000) 0.003018 0.000000 ######FDR###### --->fabia-------beagle1--: 4.33e-18 -0.295480 2.59e-44 -0.292771 0.011693 ( 0.048246) 0.304464 ( 0.107945) 0.000000 0.296184 --->fabia-------beagle2--: 4.28e-14 -0.083434 3.23e-11 -0.086726 0.011693 ( 0.048246) 0.098419 ( 0.102420) 0.000000 0.085968 --->fabia-------plink----: 3.95e-18 -0.999762 6.52e-132 -0.988104 0.011693 ( 0.048246) 0.999797 ( 9.75e-06) 0.000000 0.999795 --->fabia-------germline1: 3.95e-18 -0.749334 1.78e-83 -0.733782 0.011693 ( 0.048246) 0.745475 ( 0.099120) 0.000000 0.759769 --->fabia-------germline2: 3.96e-18 -0.958526 6.73e-130 -0.947595 0.011693 ( 0.048246) 0.959288 ( 0.005176) 0.000000 0.959385 --->fabia-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.011693 ( 0.048246) 0.000000 ( 0.000000) 0.000000 0.000000 --->beagle1-----beagle2--: 5.44e-16 0.221319 3.2e-27 0.206044 0.304464 ( 0.107945) 0.098419 ( 0.102420) 0.296184 0.085968 --->beagle1-----plink----: 3.96e-18 -0.695823 1.24e-82 -0.695333 0.304464 ( 0.107945) 0.999797 ( 9.75e-06) 0.296184 0.999795 --->beagle1-----germline1: 4.08e-18 -0.444641 3.45e-50 -0.441011 0.304464 ( 0.107945) 0.745475 ( 0.099120) 0.296184 0.759769 --->beagle1-----germline2: 3.96e-18 -0.655100 8.62e-80 -0.654824 0.304464 ( 0.107945) 0.959288 ( 0.005176) 0.296184 0.959385 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.304464 ( 0.107945) 0.000000 ( 0.000000) 0.296184 0.000000 --->beagle2-----plink----: 4.08e-18 -0.912200 8.1e-96 -0.901378 0.098419 ( 0.102420) 0.999797 ( 9.75e-06) 0.085968 0.999795 --->beagle2-----germline1: 4.2e-18 -0.665132 1.01e-67 -0.647056 0.098419 ( 0.102420) 0.745475 ( 0.099120) 0.085968 0.759769 --->beagle2-----germline2: 4.08e-18 -0.871159 7.42e-94 -0.860869 0.098419 ( 0.102420) 0.959288 ( 0.005176) 0.085968 0.959385 --->beagle2-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.098419 ( 0.102420) 0.000000 ( 0.000000) 0.085968 0.000000 --->plink-------germline1: 4.33e-18 0.243687 1.55e-45 0.254322 0.999797 ( 9.75e-06) 0.745475 ( 0.099120) 0.999795 0.759769 --->plink-------germline2: 3.96e-18 0.040418 7e-91 0.040509 0.999797 ( 9.75e-06) 0.959288 ( 0.005176) 0.999795 0.959385 --->plink-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.999797 ( 9.75e-06) 0.000000 ( 0.000000) 0.999795 0.000000 --->germline1---germline2: 4.33e-18 -0.202699 6.44e-40 -0.213813 0.745475 ( 0.099120) 0.959288 ( 0.005176) 0.759769 0.959385 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 0.745475 ( 0.099120) 0.000000 ( 0.000000) 0.759769 0.000000 --->germline2---dash-----: 1e+00 0.000000 1e+00 0.000000 0.959288 ( 0.005176) 0.000000 ( 0.000000) 0.959385 0.000000 ######specifity###### --->fabia-------beagle1--: 1e+00 0.000000 1e+00 0.000000 0.999999 ( 4.49e-06) 0.999937 ( 3.24e-05) 1.000000 0.999942 --->fabia-------beagle2--: 1e+00 0.000000 1e+00 0.000000 0.999999 ( 4.49e-06) 0.999987 ( 7.87e-06) 1.000000 0.999988 --->fabia-------plink----: 3.96e-18 0.692938 3.74e-201 0.692996 0.999999 ( 4.49e-06) 0.307003 ( 0.006754) 1.000000 0.306210 --->fabia-------germline1: 3.95e-18 0.000396 2.58e-49 0.000393 0.999999 ( 4.49e-06) 0.999606 ( 0.000138) 1.000000 0.999606 --->fabia-------germline2: 3.96e-18 0.003032 8.1e-94 0.003047 0.999999 ( 4.49e-06) 0.996952 ( 0.000363) 1.000000 0.996982 --->fabia-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.999999 ( 4.49e-06) 1.000000 ( 0.000000) 1.000000 1.000000 --->beagle1-----beagle2--: 1e+00 0.000000 1e+00 0.000000 0.999937 ( 3.24e-05) 0.999987 ( 7.87e-06) 0.999942 0.999988 --->beagle1-----plink----: 3.96e-18 0.692924 4.23e-201 0.692935 0.999937 ( 3.24e-05) 0.307003 ( 0.006754) 0.999942 0.306210 --->beagle1-----germline1: 4.08e-18 0.000342 8.42e-41 0.000332 0.999937 ( 3.24e-05) 0.999606 ( 0.000138) 0.999942 0.999606 --->beagle1-----germline2: 3.96e-18 0.002973 3.8e-92 0.002985 0.999937 ( 3.24e-05) 0.996952 ( 0.000363) 0.999942 0.996982 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.999937 ( 3.24e-05) 1.000000 ( 0.000000) 0.999942 1.000000 --->beagle2-----plink----: 3.96e-18 0.692925 3.76e-201 0.692984 0.999987 ( 7.87e-06) 0.307003 ( 0.006754) 0.999988 0.306210 --->beagle2-----germline1: 3.96e-18 0.000377 2.04e-48 0.000381 0.999987 ( 7.87e-06) 0.999606 ( 0.000138) 0.999988 0.999606 --->beagle2-----germline2: 3.96e-18 0.003020 8.63e-94 0.003035 0.999987 ( 7.87e-06) 0.996952 ( 0.000363) 0.999988 0.996982 --->beagle2-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.999987 ( 7.87e-06) 1.000000 ( 0.000000) 0.999988 1.000000 --->plink-------germline1: 3.96e-18 -0.692539 2.88e-201 -0.692603 0.307003 ( 0.006754) 0.999606 ( 0.000138) 0.306210 0.999606 --->plink-------germline2: 3.96e-18 -0.689888 1.32e-201 -0.689950 0.307003 ( 0.006754) 0.996952 ( 0.000363) 0.306210 0.996982 --->plink-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.307003 ( 0.006754) 1.000000 ( 0.000000) 0.306210 1.000000 --->germline1---germline2: 3.96e-18 0.002640 4.45e-92 0.002653 0.999606 ( 0.000138) 0.996952 ( 0.000363) 0.999606 0.996982 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 0.999606 ( 0.000138) 1.000000 ( 0.000000) 0.999606 1.000000 --->germline2---dash-----: 1e+00 0.000000 1e+00 0.000000 0.996952 ( 0.000363) 1.000000 ( 0.000000) 0.996982 1.000000 ######sensitivity###### --->fabia-------beagle1--: 5.93e-01 -0.005302 3.08e-01 -0.010608 0.933206 ( 0.078628) 0.943814 ( 0.059495) 0.966536 0.959296 --->fabia-------beagle2--: 6.41e-02 0.026232 1.15e-02 0.046026 0.933206 ( 0.078628) 0.887180 ( 0.150652) 0.966536 0.953389 --->fabia-------plink----: 5.78e-18 -0.052481 2.1e-13 -0.066776 0.933206 ( 0.078628) 0.999982 ( 0.000181) 0.966536 1.000000 --->fabia-------germline1: 9.69e-07 0.054676 1.09e-04 0.073453 0.933206 ( 0.078628) 0.859753 ( 0.162707) 0.966536 0.901221 --->fabia-------germline2: 3.2e-04 0.035464 3e-03 0.025339 0.933206 ( 0.078628) 0.907867 ( 0.033261) 0.966536 0.908713 --->fabia-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.933206 ( 0.078628) 0.000000 ( 0.000000) 0.966536 0.000000 --->beagle1-----beagle2--: 1.23e-06 0.146152 5.41e-06 0.056634 0.943814 ( 0.059495) 0.887180 ( 0.150652) 0.959296 0.953389 --->beagle1-----plink----: 3.87e-17 -0.050139 1.81e-15 -0.056167 0.943814 ( 0.059495) 0.999982 ( 0.000181) 0.959296 1.000000 --->beagle1-----germline1: 1.11e-08 0.055278 5.97e-06 0.084061 0.943814 ( 0.059495) 0.859753 ( 0.162707) 0.959296 0.901221 --->beagle1-----germline2: 1.21e-06 0.042550 1.16e-06 0.035947 0.943814 ( 0.059495) 0.907867 ( 0.033261) 0.959296 0.908713 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.943814 ( 0.059495) 0.000000 ( 0.000000) 0.959296 0.000000 --->beagle2-----plink----: 3.87e-17 -0.102099 2.95e-11 -0.112802 0.887180 ( 0.150652) 0.999982 ( 0.000181) 0.953389 1.000000 --->beagle2-----germline1: 1.1e-01 0.024355 2.16e-01 0.027427 0.887180 ( 0.150652) 0.859753 ( 0.162707) 0.953389 0.901221 --->beagle2-----germline2: 8.73e-01 0.002366 1.83e-01 -0.020687 0.887180 ( 0.150652) 0.907867 ( 0.033261) 0.953389 0.908713 --->beagle2-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.887180 ( 0.150652) 0.000000 ( 0.000000) 0.953389 0.000000 --->plink-------germline1: 3.96e-18 0.100432 1.12e-13 0.140229 0.999982 ( 0.000181) 0.859753 ( 0.162707) 1.000000 0.901221 --->plink-------germline2: 3.96e-18 0.093022 2.05e-48 0.092115 0.999982 ( 0.000181) 0.907867 ( 0.033261) 1.000000 0.908713 --->plink-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.999982 ( 0.000181) 0.000000 ( 0.000000) 1.000000 0.000000 --->germline1---germline2: 1e+00 0.000000 1.68e-03 -0.048114 0.859753 ( 0.162707) 0.907867 ( 0.033261) 0.901221 0.908713 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 0.859753 ( 0.162707) 0.000000 ( 0.000000) 0.901221 0.000000 --->germline2---dash-----: 1e+00 0.000000 1e+00 0.000000 0.907867 ( 0.033261) 0.000000 ( 0.000000) 0.908713 0.000000 ######trueN###### --->fabia-------beagle1--: 3.96e-18 2e+08 0e+00 2e+08 4e+08 ( 2016) 2e+08 ( 6577) 4e+08 2e+08 --->fabia-------beagle2--: 3.96e-18 2e+08 0e+00 2e+08 4e+08 ( 2016) 2e+08 ( 2061) 4e+08 2e+08 --->fabia-------plink----: 3.96e-18 3.39e+08 1.45e-239 3.39e+08 4e+08 ( 2016) 61391906 ( 1350495) 4e+08 61233458 --->fabia-------germline1: 3.95e-18 2e+08 0e+00 2e+08 4e+08 ( 2016) 2e+08 ( 27533) 4e+08 2e+08 --->fabia-------germline2: 3.96e-18 2.01e+08 0e+00 2.01e+08 4e+08 ( 2016) 1.99e+08 ( 72589) 4e+08 1.99e+08 --->fabia-------dash-----: 3.33e-21 2e+08 0e+00 2e+08 4e+08 ( 2016) 2e+08 ( 1287) 4e+08 2e+08 --->beagle1-----beagle2--: 3.87e-17 -10019 7.91e-28 -9940 2e+08 ( 6577) 2e+08 ( 2061) 2e+08 2e+08 --->beagle1-----plink----: 3.96e-18 1.39e+08 4.27e-201 1.39e+08 2e+08 ( 6577) 61391906 ( 1350495) 2e+08 61233458 --->beagle1-----germline1: 4.08e-18 66360 8.4e-41 66324 2e+08 ( 6577) 2e+08 ( 27533) 2e+08 2e+08 --->beagle1-----germline2: 3.96e-18 593692 3.8e-92 596919 2e+08 ( 6577) 1.99e+08 ( 72589) 2e+08 1.99e+08 --->beagle1-----dash-----: 3.96e-18 -12013 1.72e-35 -12551 2e+08 ( 6577) 2e+08 ( 1287) 2e+08 2e+08 --->beagle2-----plink----: 3.96e-18 1.39e+08 3.8e-201 1.39e+08 2e+08 ( 2061) 61391906 ( 1350495) 2e+08 61233458 --->beagle2-----germline1: 3.96e-18 76008 2.03e-48 76264 2e+08 ( 2061) 2e+08 ( 27533) 2e+08 2e+08 --->beagle2-----germline2: 3.96e-18 603862 8.64e-94 606859 2e+08 ( 2061) 1.99e+08 ( 72589) 2e+08 1.99e+08 --->beagle2-----dash-----: 3.96e-18 -2515 2.58e-30 -2611 2e+08 ( 2061) 2e+08 ( 1287) 2e+08 2e+08 --->plink-------germline1: 3.96e-18 -1.38e+08 2.91e-201 -1.39e+08 61391906 ( 1350495) 2e+08 ( 27533) 61233458 2e+08 --->plink-------germline2: 3.96e-18 -1.38e+08 1.34e-201 -1.38e+08 61391906 ( 1350495) 1.99e+08 ( 72589) 61233458 1.99e+08 --->plink-------dash-----: 3.96e-18 -1.39e+08 3.82e-201 -1.39e+08 61391906 ( 1350495) 2e+08 ( 1287) 61233458 2e+08 --->germline1---germline2: 3.95e-18 527387 4.45e-92 530595 2e+08 ( 27533) 1.99e+08 ( 72589) 2e+08 1.99e+08 --->germline1---dash-----: 3.95e-18 -78689 1.46e-49 -78875 2e+08 ( 27533) 2e+08 ( 1287) 2e+08 2e+08 --->germline2---dash-----: 3.96e-18 -606415 8.05e-94 -609470 1.99e+08 ( 72589) 2e+08 ( 1287) 1.99e+08 2e+08 ######falseP###### --->fabia-------beagle1--: 5.51e-18 -11707 6.02e-33 -12135 415 ( 1798) 12551 ( 6472) 0 11524 --->fabia-------beagle2--: 3.87e-13 -2379 1.04e-13 -2196 415 ( 1798) 2611 ( 1575) 0 2332 --->fabia-------plink----: 3.96e-18 -1.39e+08 3.74e-201 -1.39e+08 415 ( 1798) 1.39e+08 ( 1350698) 0 1.39e+08 --->fabia-------germline1: 3.95e-18 -78199 4.97e-49 -78459 415 ( 1798) 78875 ( 27643) 0 78708 --->fabia-------germline2: 3.96e-18 -606004 8.27e-94 -609054 415 ( 1798) 609470 ( 72589) 0 603536 --->fabia-------dash-----: 1e+00 0.000000 1e+00 0.000000 415.420000 (1798.355170) 0.000000 ( 0.000000) 0.000000 0.000000 --->beagle1-----beagle2--: 3.87e-17 10019 7.91e-28 9940 12551 ( 6472) 2611 ( 1575) 11524 2332 --->beagle1-----plink----: 3.96e-18 -1.39e+08 4.27e-201 -1.39e+08 12551 ( 6472) 1.39e+08 ( 1350698) 11524 1.39e+08 --->beagle1-----germline1: 4.08e-18 -66358 8.4e-41 -66324 12551 ( 6472) 78875 ( 27643) 11524 78708 --->beagle1-----germline2: 3.96e-18 -593700 3.8e-92 -596919 12551 ( 6472) 609470 ( 72589) 11524 603536 --->beagle1-----dash-----: 1e+00 0 1e+00 0 12551 ( 6472) 0 ( 0) 11524 0 --->beagle2-----plink----: 3.96e-18 -1.39e+08 3.8e-201 -1.39e+08 2611 ( 1575) 1.39e+08 ( 1350698) 2332 1.39e+08 --->beagle2-----germline1: 3.96e-18 -76007 2.03e-48 -76264 2611 ( 1575) 78875 ( 27643) 2332 78708 --->beagle2-----germline2: 3.96e-18 -603859 8.64e-94 -606859 2611 ( 1575) 609470 ( 72589) 2332 603536 --->beagle2-----dash-----: 1e+00 0 1e+00 0 2611 ( 1575) 0 ( 0) 2332 0 --->plink-------germline1: 3.96e-18 1.38e+08 2.91e-201 1.39e+08 1.39e+08 ( 1350698) 78875 ( 27643) 1.39e+08 78708 --->plink-------germline2: 3.96e-18 1.38e+08 1.34e-201 1.38e+08 1.39e+08 ( 1350698) 609470 ( 72589) 1.39e+08 603536 --->plink-------dash-----: 1e+00 0 1e+00 0 1.39e+08 ( 1350698) 0 ( 0) 1.39e+08 0 --->germline1---germline2: 3.95e-18 -527388 4.45e-92 -530595 78875 ( 27643) 609470 ( 72589) 78708 603536 --->germline1---dash-----: 1e+00 0 1e+00 0 78875 ( 27643) 0 ( 0) 78708 0 --->germline2---dash-----: 1e+00 0 1e+00 0 609470 ( 72589) 0 ( 0) 603536 0 ######falseN###### --->fabia-------beagle1--: 5.64e-01 156 2.76e-01 317 1889 ( 2223) 1572 ( 1646) 957 1152 --->fabia-------beagle2--: 6.61e-02 -728 1.22e-02 -1273 1889 ( 2223) 3162 ( 4200) 957 1347 --->fabia-------plink----: 5.77e-18 1497 2.07e-13 1888 1889 ( 2223) 0.52 ( 5.1) 957 0 --->fabia-------germline1: 1.16e-06 -1539 6.97e-05 -1959 1889 ( 2223) 3847 ( 4094) 957 2775 --->fabia-------germline2: 3.68e-04 -993 3.6e-03 -699 1889 ( 2223) 2588 ( 928) 957 2574 --->fabia-------dash-----: 3.95e-18 -26649 5.84e-103 -26233 1889 ( 2223) 28122 ( 1287) 957 28392 --->beagle1-----beagle2--: 1.23e-06 -4146 5.24e-06 -1590 1572 ( 1646) 3162 ( 4200) 1152 1347 --->beagle1-----plink----: 3.87e-17 1428 1.06e-15 1571 1572 ( 1646) 0.52 ( 5.1) 1152 0 --->beagle1-----germline1: 9.65e-09 -1569 1.73e-06 -2275 1572 ( 1646) 3847 ( 4094) 1152 2775 --->beagle1-----germline2: 1.15e-06 -1198 7.82e-07 -1016 1572 ( 1646) 2588 ( 928) 1152 2574 --->beagle1-----dash-----: 3.96e-18 -26935 2.2e-110 -26550 1572 ( 1646) 28122 ( 1287) 1152 28392 --->beagle2-----plink----: 3.87e-17 2833 2.42e-11 3162 3162 ( 4200) 0.52 ( 5.1) 1347 0 --->beagle2-----germline1: 1.17e-01 -697 2.41e-01 -685 3162 ( 4200) 3847 ( 4094) 1347 2775 --->beagle2-----germline2: 8.96e-01 -52.1 1.86e-01 575 3162 ( 4200) 2588 ( 928) 1347 2574 --->beagle2-----dash-----: 5.78e-18 -25515 3.61e-77 -24960 3162 ( 4200) 28122 ( 1287) 1347 28392 --->plink-------germline1: 3.96e-18 -2832 2.27e-15 -3847 0.52 ( 5.1) 3847 ( 4094) 0 2775 --->plink-------germline2: 3.96e-18 -2604 1.2e-48 -2587 0.52 ( 5.1) 2588 ( 928) 0 2574 --->plink-------dash-----: 3.95e-18 -28398 1.06e-134 -28121 0.52 ( 5.1) 28122 ( 1287) 0 28392 --->germline1---germline2: 1e+00 0 1.07e-03 1260 3847 ( 4094) 2588 ( 928) 2775 2574 --->germline1---dash-----: 6.97e-18 -25601 9.11e-73 -24274 3847 ( 4094) 28122 ( 1287) 2775 28392 --->germline2---dash-----: 3.29e-18 -25684 1.22e-122 -25534 2588 ( 928) 28122 ( 1287) 2574 28392 ######trueP###### --->fabia-------beagle1--: 9.04e-01 -34.5 6.84e-01 -128 26422 ( 2399) 26550 ( 2143) 27006 27193 --->fabia-------beagle2--: 2.72e-02 894 5.68e-03 1462 26422 ( 2399) 24960 ( 4415) 27006 26774 --->fabia-------plink----: 3.97e-14 -1386 5.04e-10 -1699 26422 ( 2399) 28121 ( 1287) 27006 28392 --->fabia-------germline1: 4.02e-07 1686 1.88e-05 2147 26422 ( 2399) 24274 ( 4773) 27006 25587 --->fabia-------germline2: 1.37e-04 1113 7.63e-04 888 26422 ( 2399) 25534 ( 1548) 27006 25771 --->fabia-------dash-----: 1e+00 0 1e+00 0 26422 ( 2399) 0 ( 0) 27006 0 --->beagle1-----beagle2--: 1.23e-06 4145 5.24e-06 1590 26550 ( 2143) 24960 ( 4415) 27193 26774 --->beagle1-----plink----: 3.87e-17 -1428 1.06e-15 -1571 26550 ( 2143) 28121 ( 1287) 27193 28392 --->beagle1-----germline1: 9.65e-09 1570 1.73e-06 2275 26550 ( 2143) 24274 ( 4773) 27193 25587 --->beagle1-----germline2: 1.15e-06 1198 7.82e-07 1016 26550 ( 2143) 25534 ( 1548) 27193 25771 --->beagle1-----dash-----: 1e+00 0 1e+00 0 26550 ( 2143) 0 ( 0) 27193 0 --->beagle2-----plink----: 3.87e-17 -2833 2.42e-11 -3162 24960 ( 4415) 28121 ( 1287) 26774 28392 --->beagle2-----germline1: 1.17e-01 697 2.41e-01 685 24960 ( 4415) 24274 ( 4773) 26774 25587 --->beagle2-----germline2: 8.96e-01 52.3 1.86e-01 -575 24960 ( 4415) 25534 ( 1548) 26774 25771 --->beagle2-----dash-----: 1e+00 0 1e+00 0 24960 ( 4415) 0 ( 0) 26774 0 --->plink-------germline1: 3.96e-18 2832 2.27e-15 3847 28121 ( 1287) 24274 ( 4773) 28392 25587 --->plink-------germline2: 3.96e-18 2604 1.2e-48 2587 28121 ( 1287) 25534 ( 1548) 28392 25771 --->plink-------dash-----: 1e+00 0 1e+00 0 28121 ( 1287) 0 ( 0) 28392 0 --->germline1---germline2: 1e+00 0 1.07e-03 -1260 24274 ( 4773) 25534 ( 1548) 25587 25771 --->germline1---dash-----: 1e+00 0 1e+00 0 24274 ( 4773) 0 ( 0) 25587 0 --->germline2---dash-----: 1e+00 0 1e+00 0 25534 ( 1548) 0 ( 0) 25771 0 ######MatthewsSnps###### --->fabia-------beagle1--: 6.6e-18 0.259701 2.65e-38 0.253081 0.950157 ( 0.065757) 0.697076 ( 0.104739) 0.974002 0.698562 --->fabia-------beagle2--: 2.21e-06 0.041530 1.49e-03 0.041445 0.950157 ( 0.065757) 0.908712 ( 0.103941) 0.974002 0.926264 --->fabia-------plink----: 3.96e-18 0.964729 5.64e-117 0.950114 0.950157 ( 0.065757) 4.32e-05 ( 0.000119) 0.974002 0.000000 --->fabia-------germline1: 3.96e-18 0.650143 4.88e-81 0.644669 0.950157 ( 0.065757) 0.305489 ( 0.080224) 0.974002 0.298851 --->fabia-------germline2: 3.96e-18 0.878952 1.89e-111 0.865815 0.950157 ( 0.065757) 0.084342 ( 0.014717) 0.974002 0.085949 --->fabia-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.950157 ( 0.065757) 0.000000 ( 0.000000) 0.974002 0.000000 --->beagle1-----beagle2--: 3.42e-15 -0.241130 3.05e-28 -0.211636 0.697076 ( 0.104739) 0.908712 ( 0.103941) 0.698562 0.926264 --->beagle1-----plink----: 3.96e-18 0.692441 5.32e-84 0.697033 0.697076 ( 0.104739) 4.32e-05 ( 0.000119) 0.698562 0.000000 --->beagle1-----germline1: 4.08e-18 0.390288 2.25e-49 0.391588 0.697076 ( 0.104739) 0.305489 ( 0.080224) 0.698562 0.298851 --->beagle1-----germline2: 3.96e-18 0.607444 1.61e-77 0.612734 0.697076 ( 0.104739) 0.084342 ( 0.014717) 0.698562 0.085949 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.697076 ( 0.104739) 0.000000 ( 0.000000) 0.698562 0.000000 --->beagle2-----plink----: 4.08e-18 0.920109 1.59e-95 0.908669 0.908712 ( 0.103941) 4.32e-05 ( 0.000119) 0.926264 0.000000 --->beagle2-----germline1: 4.33e-18 0.614568 3.02e-67 0.603223 0.908712 ( 0.103941) 0.305489 ( 0.080224) 0.926264 0.298851 --->beagle2-----germline2: 4.08e-18 0.834776 7.75e-91 0.824370 0.908712 ( 0.103941) 0.084342 ( 0.014717) 0.926264 0.085949 --->beagle2-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.908712 ( 0.103941) 0.000000 ( 0.000000) 0.926264 0.000000 --->plink-------germline1: 4.08e-18 -0.301721 6.29e-61 -0.305445 4.32e-05 ( 0.000119) 0.305489 ( 0.080224) 0.000000 0.298851 --->plink-------germline2: 3.96e-18 -0.084892 9.1e-78 -0.084299 4.32e-05 ( 0.000119) 0.084342 ( 0.014717) 0.000000 0.085949 --->plink-------dash-----: 1e+00 0.000000 1e+00 0.000000 4.32e-05 ( 0.000119) 0.000000 ( 0.000000) 0.000000 0.000000 --->germline1---germline2: 7.9e-18 0.216809 2.4e-48 0.221147 0.305489 ( 0.080224) 0.084342 ( 0.014717) 0.298851 0.085949 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 0.305489 ( 0.080224) 0.000000 ( 0.000000) 0.298851 0.000000 --->germline2---dash-----: 1e+00 0.000000 1e+00 0.000000 0.084342 ( 0.014717) 0.000000 ( 0.000000) 0.085949 0.000000 ######F1Snps###### --->fabia-------beagle1--: 6.41e-18 0.291571 2.53e-37 0.286084 0.948427 ( 0.070735) 0.662343 ( 0.124514) 0.974277 0.666800 --->fabia-------beagle2--: 2.8e-06 0.042836 1.73e-03 0.041595 0.948427 ( 0.070735) 0.906831 ( 0.103548) 0.974277 0.925512 --->fabia-------plink----: 3.96e-18 0.918452 1.25e-111 0.902331 0.948427 ( 0.070735) 0.046096 ( 0.001423) 0.974277 0.046269 --->fabia-------germline1: 3.96e-18 0.739482 3.21e-86 0.728848 0.948427 ( 0.070735) 0.219579 ( 0.078554) 0.974277 0.205742 --->fabia-------germline2: 3.96e-18 0.904065 8.25e-111 0.888161 0.948427 ( 0.070735) 0.060266 ( 0.004179) 0.974277 0.060114 --->fabia-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.948427 ( 0.070735) 0.000000 ( 0.000000) 0.974277 0.000000 --->beagle1-----beagle2--: 3.32e-15 -0.276347 6.92e-30 -0.244488 0.662343 ( 0.124514) 0.906831 ( 0.103548) 0.666800 0.925512 --->beagle1-----plink----: 3.96e-18 0.612328 1.05e-71 0.616247 0.662343 ( 0.124514) 0.046096 ( 0.001423) 0.666800 0.046269 --->beagle1-----germline1: 4.08e-18 0.443846 5.27e-50 0.442764 0.662343 ( 0.124514) 0.219579 ( 0.078554) 0.666800 0.205742 --->beagle1-----germline2: 3.96e-18 0.597384 1.31e-70 0.602077 0.662343 ( 0.124514) 0.060266 ( 0.004179) 0.666800 0.060114 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.662343 ( 0.124514) 0.000000 ( 0.000000) 0.666800 0.000000 --->beagle2-----plink----: 4.08e-18 0.872567 1.99e-93 0.860736 0.906831 ( 0.103548) 0.046096 ( 0.001423) 0.925512 0.046269 --->beagle2-----germline1: 4.08e-18 0.702506 1.46e-73 0.687252 0.906831 ( 0.103548) 0.219579 ( 0.078554) 0.925512 0.205742 --->beagle2-----germline2: 4.08e-18 0.858143 9.72e-93 0.846565 0.906831 ( 0.103548) 0.060266 ( 0.004179) 0.925512 0.060114 --->beagle2-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.906831 ( 0.103548) 0.000000 ( 0.000000) 0.925512 0.000000 --->plink-------germline1: 4.08e-18 -0.165496 3.91e-40 -0.173483 0.046096 ( 0.001423) 0.219579 ( 0.078554) 0.046269 0.205742 --->plink-------germline2: 3.96e-18 -0.014069 6.64e-59 -0.014170 0.046096 ( 0.001423) 0.060266 ( 0.004179) 0.046269 0.060114 --->plink-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.046096 ( 0.001423) 0.000000 ( 0.000000) 0.046269 0.000000 --->germline1---germline2: 4.08e-18 0.151059 2.1e-37 0.159313 0.219579 ( 0.078554) 0.060266 ( 0.004179) 0.205742 0.060114 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 0.219579 ( 0.078554) 0.000000 ( 0.000000) 0.205742 0.000000 --->germline2---dash-----: 1e+00 0.000000 1e+00 0.000000 0.060266 ( 0.004179) 0.000000 ( 0.000000) 0.060114 0.000000 ######accuracySnps###### --->fabia-------beagle1--: 6.8e-18 0.023389 8.52e-30 0.024003 0.997432 ( 0.004351) 0.973429 ( 0.014159) 0.998803 0.976622 --->fabia-------beagle2--: 6.67e-08 0.002536 6.45e-04 0.002214 0.997432 ( 0.004351) 0.995219 ( 0.004266) 0.998803 0.996152 --->fabia-------plink----: 3.95e-18 0.974767 6.06e-234 0.973840 0.997432 ( 0.004351) 0.023593 ( 0.000744) 0.998803 0.023683 --->fabia-------germline1: 3.96e-18 0.173563 6.27e-51 0.173369 0.997432 ( 0.004351) 0.824063 ( 0.058215) 0.998803 0.825503 --->fabia-------germline2: 3.96e-18 0.725108 4.93e-120 0.724610 0.997432 ( 0.004351) 0.272823 ( 0.046406) 0.998803 0.270992 --->fabia-------dash-----: 4.2e-18 0.021963 3.61e-70 0.021025 0.997432 ( 0.004351) 0.976408 ( 0.000743) 0.998803 0.976317 --->beagle1-----beagle2--: 1.77e-16 -0.023068 5.73e-28 -0.021789 0.973429 ( 0.014159) 0.995219 ( 0.004266) 0.976622 0.996152 --->beagle1-----plink----: 3.96e-18 0.950536 4.99e-183 0.949837 0.973429 ( 0.014159) 0.023593 ( 0.000744) 0.976622 0.023683 --->beagle1-----germline1: 4.08e-18 0.149510 8.64e-44 0.149366 0.973429 ( 0.014159) 0.824063 ( 0.058215) 0.976622 0.825503 --->beagle1-----germline2: 3.96e-18 0.701226 2.24e-116 0.700607 0.973429 ( 0.014159) 0.272823 ( 0.046406) 0.976622 0.270992 --->beagle1-----dash-----: 1.35e-01 -0.002258 3.91e-02 -0.002978 0.973429 ( 0.014159) 0.976408 ( 0.000743) 0.976622 0.976317 --->beagle2-----plink----: 3.96e-18 0.972153 3.72e-235 0.971626 0.995219 ( 0.004266) 0.023593 ( 0.000744) 0.996152 0.023683 --->beagle2-----germline1: 3.96e-18 0.171377 1.21e-50 0.171156 0.995219 ( 0.004266) 0.824063 ( 0.058215) 0.996152 0.825503 --->beagle2-----germline2: 3.96e-18 0.723305 1.73e-120 0.722396 0.995219 ( 0.004266) 0.272823 ( 0.046406) 0.996152 0.270992 --->beagle2-----dash-----: 4.74e-18 0.019395 6.14e-66 0.018811 0.995219 ( 0.004266) 0.976408 ( 0.000743) 0.996152 0.976317 --->plink-------germline1: 3.95e-18 -0.800079 7.79e-115 -0.800470 0.023593 ( 0.000744) 0.824063 ( 0.058215) 0.023683 0.825503 --->plink-------germline2: 3.95e-18 -0.248513 5.12e-75 -0.249230 0.023593 ( 0.000744) 0.272823 ( 0.046406) 0.023683 0.270992 --->plink-------dash-----: 3.95e-18 -0.952630 6.64e-280 -0.952815 0.023593 ( 0.000744) 0.976408 ( 0.000743) 0.023683 0.976317 --->germline1---germline2: 3.96e-18 0.549582 9.16e-97 0.551240 0.824063 ( 0.058215) 0.272823 ( 0.046406) 0.825503 0.270992 --->germline1---dash-----: 3.96e-18 -0.152625 2.82e-46 -0.152345 0.824063 ( 0.058215) 0.976408 ( 0.000743) 0.825503 0.976317 --->germline2---dash-----: 3.96e-18 -0.704311 4.99e-119 -0.703585 0.272823 ( 0.046406) 0.976408 ( 0.000743) 0.270992 0.976317 ######FPRSnps###### --->fabia-------beagle1--: 5.51e-18 -0.025676 1.24e-31 -0.026194 0.001018 ( 0.004324) 0.027212 ( 0.014498) 0.000000 0.023935 --->fabia-------beagle2--: 2.46e-12 -0.004071 2.35e-09 -0.003636 0.001018 ( 0.004324) 0.004653 ( 0.003026) 0.000000 0.003942 --->fabia-------plink----: 2.51e-20 -1.000000 4.77e-236 -0.998981 0.001018 ( 0.004324) 0.999999 ( 1.87e-06) 0.000000 1.000000 --->fabia-------germline1: 3.96e-18 -0.178168 8.12e-51 -0.177808 0.001018 ( 0.004324) 0.178826 ( 0.059708) 0.000000 0.178498 --->fabia-------germline2: 3.96e-18 -0.743608 6.09e-120 -0.743364 0.001018 ( 0.004324) 0.744382 ( 0.047630) 0.000000 0.745524 --->fabia-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.001018 ( 0.004324) 0.000000 ( 0.000000) 0.000000 0.000000 --->beagle1-----beagle2--: 1.77e-16 0.023982 1.83e-28 0.022558 0.027212 ( 0.014498) 0.004653 ( 0.003026) 0.023935 0.003942 --->beagle1-----plink----: 3.96e-18 -0.973470 6.9e-183 -0.972788 0.027212 ( 0.014498) 0.999999 ( 1.87e-06) 0.023935 1.000000 --->beagle1-----germline1: 4.2e-18 -0.151944 1.98e-43 -0.151614 0.027212 ( 0.014498) 0.178826 ( 0.059708) 0.023935 0.178498 --->beagle1-----germline2: 3.96e-18 -0.717802 2.81e-116 -0.717171 0.027212 ( 0.014498) 0.744382 ( 0.047630) 0.023935 0.745524 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.027212 ( 0.014498) 0.000000 ( 0.000000) 0.023935 0.000000 --->beagle2-----plink----: 3.96e-18 -0.995629 3.12e-251 -0.995346 0.004653 ( 0.003026) 0.999999 ( 1.87e-06) 0.003942 1.000000 --->beagle2-----germline1: 3.96e-18 -0.174254 1.38e-50 -0.174173 0.004653 ( 0.003026) 0.178826 ( 0.059708) 0.003942 0.178498 --->beagle2-----germline2: 3.96e-18 -0.740780 1.9e-120 -0.739729 0.004653 ( 0.003026) 0.744382 ( 0.047630) 0.003942 0.745524 --->beagle2-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.004653 ( 0.003026) 0.000000 ( 0.000000) 0.003942 0.000000 --->plink-------germline1: 3.96e-18 0.820551 7.48e-115 0.821173 0.999999 ( 1.87e-06) 0.178826 ( 0.059708) 1.000000 0.178498 --->plink-------germline2: 3.96e-18 0.255004 5.32e-75 0.255617 0.999999 ( 1.87e-06) 0.744382 ( 0.047630) 1.000000 0.745524 --->plink-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.999999 ( 1.87e-06) 0.000000 ( 0.000000) 1.000000 0.000000 --->germline1---germline2: 3.96e-18 -0.563853 5.11e-97 -0.565556 0.178826 ( 0.059708) 0.744382 ( 0.047630) 0.178498 0.745524 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 0.178826 ( 0.059708) 0.000000 ( 0.000000) 0.178498 0.000000 --->germline2---dash-----: 1e+00 0.000000 1e+00 0.000000 0.744382 ( 0.047630) 0.000000 ( 0.000000) 0.745524 0.000000 ######FDRSnps###### --->fabia-------beagle1--: 4.46e-18 -0.485759 1.91e-47 -0.466613 0.024751 ( 0.095893) 0.491365 ( 0.147422) 0.000000 0.499838 --->fabia-------beagle2--: 1.33e-12 -0.140896 1.88e-13 -0.135185 0.024751 ( 0.095893) 0.159937 ( 0.116436) 0.000000 0.138648 --->fabia-------plink----: 3.95e-18 -0.976219 6.45e-101 -0.951656 0.024751 ( 0.095893) 0.976408 ( 0.000743) 0.000000 0.976317 --->fabia-------germline1: 3.95e-18 -0.876008 1.31e-88 -0.848287 0.024751 ( 0.095893) 0.873038 ( 0.057287) 0.000000 0.884575 --->fabia-------germline2: 3.96e-18 -0.968579 1.81e-100 -0.944160 0.024751 ( 0.095893) 0.968911 ( 0.002216) 0.000000 0.968988 --->fabia-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.024751 ( 0.095893) 0.000000 ( 0.000000) 0.000000 0.000000 --->beagle1-----beagle2--: 6.72e-16 0.372998 6.55e-35 0.331428 0.491365 ( 0.147422) 0.159937 ( 0.116436) 0.499838 0.138648 --->beagle1-----plink----: 3.96e-18 -0.473248 3.95e-55 -0.485043 0.491365 ( 0.147422) 0.976408 ( 0.000743) 0.499838 0.976317 --->beagle1-----germline1: 4.08e-18 -0.374096 3.39e-42 -0.381673 0.491365 ( 0.147422) 0.873038 ( 0.057287) 0.499838 0.884575 --->beagle1-----germline2: 3.96e-18 -0.465274 1.83e-54 -0.477547 0.491365 ( 0.147422) 0.968911 ( 0.002216) 0.499838 0.968988 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.491365 ( 0.147422) 0.000000 ( 0.000000) 0.499838 0.000000 --->beagle2-----plink----: 4.08e-18 -0.827644 3.15e-86 -0.816471 0.159937 ( 0.116436) 0.976408 ( 0.000743) 0.138648 0.976317 --->beagle2-----germline1: 4.08e-18 -0.726575 3.58e-76 -0.713101 0.159937 ( 0.116436) 0.873038 ( 0.057287) 0.138648 0.884575 --->beagle2-----germline2: 4.08e-18 -0.819842 7.3e-86 -0.808975 0.159937 ( 0.116436) 0.968911 ( 0.002216) 0.138648 0.968988 --->beagle2-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.159937 ( 0.116436) 0.000000 ( 0.000000) 0.138648 0.000000 --->plink-------germline1: 4.08e-18 0.095893 3.99e-33 0.103370 0.976408 ( 0.000743) 0.873038 ( 0.057287) 0.976317 0.884575 --->plink-------germline2: 3.96e-18 0.007430 7.66e-59 0.007496 0.976408 ( 0.000743) 0.968911 ( 0.002216) 0.976317 0.968988 --->plink-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.976408 ( 0.000743) 0.000000 ( 0.000000) 0.976317 0.000000 --->germline1---germline2: 4.08e-18 -0.088229 7.06e-31 -0.095873 0.873038 ( 0.057287) 0.968911 ( 0.002216) 0.884575 0.968988 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 0.873038 ( 0.057287) 0.000000 ( 0.000000) 0.884575 0.000000 --->germline2---dash-----: 1e+00 0.000000 1e+00 0.000000 0.968911 ( 0.002216) 0.000000 ( 0.000000) 0.968988 0.000000 ######specifitySnps###### --->fabia-------beagle1--: 5.51e-18 0.025670 1.24e-31 0.026194 0.998982 ( 0.004324) 0.972788 ( 0.014498) 1.000000 0.976065 --->fabia-------beagle2--: 2.46e-12 0.004079 2.35e-09 0.003636 0.998982 ( 0.004324) 0.995347 ( 0.003026) 1.000000 0.996058 --->fabia-------plink----: 2.55e-20 1.000000 4.77e-236 0.998981 0.998982 ( 0.004324) 6.66e-07 ( 1.88e-06) 1.000000 0.000000 --->fabia-------germline1: 3.96e-18 0.178180 8.12e-51 0.177808 0.998982 ( 0.004324) 0.821174 ( 0.059708) 1.000000 0.821502 --->fabia-------germline2: 3.96e-18 0.743614 6.09e-120 0.743364 0.998982 ( 0.004324) 0.255618 ( 0.047630) 1.000000 0.254476 --->fabia-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.998982 ( 0.004324) 1.000000 ( 0.000000) 1.000000 1.000000 --->beagle1-----beagle2--: 1.77e-16 -0.024003 1.83e-28 -0.022558 0.972788 ( 0.014498) 0.995347 ( 0.003026) 0.976065 0.996058 --->beagle1-----plink----: 3.96e-18 0.973468 6.9e-183 0.972788 0.972788 ( 0.014498) 6.66e-07 ( 1.88e-06) 0.976065 0.000000 --->beagle1-----germline1: 4.2e-18 0.151941 1.98e-43 0.151614 0.972788 ( 0.014498) 0.821174 ( 0.059708) 0.976065 0.821502 --->beagle1-----germline2: 3.96e-18 0.717821 2.81e-116 0.717171 0.972788 ( 0.014498) 0.255618 ( 0.047630) 0.976065 0.254476 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.972788 ( 0.014498) 1.000000 ( 0.000000) 0.976065 1.000000 --->beagle2-----plink----: 3.96e-18 0.995660 3.12e-251 0.995346 0.995347 ( 0.003026) 6.66e-07 ( 1.88e-06) 0.996058 0.000000 --->beagle2-----germline1: 3.96e-18 0.174303 1.38e-50 0.174173 0.995347 ( 0.003026) 0.821174 ( 0.059708) 0.996058 0.821502 --->beagle2-----germline2: 3.96e-18 0.740748 1.9e-120 0.739729 0.995347 ( 0.003026) 0.255618 ( 0.047630) 0.996058 0.254476 --->beagle2-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.995347 ( 0.003026) 1.000000 ( 0.000000) 0.996058 1.000000 --->plink-------germline1: 3.96e-18 -0.820557 7.48e-115 -0.821173 6.66e-07 ( 1.88e-06) 0.821174 ( 0.059708) 0.000000 0.821502 --->plink-------germline2: 3.96e-18 -0.254973 5.32e-75 -0.255617 6.66e-07 ( 1.88e-06) 0.255618 ( 0.047630) 0.000000 0.254476 --->plink-------dash-----: 1e+00 0.000000 1e+00 0.000000 6.66e-07 ( 1.88e-06) 1.000000 ( 0.000000) 0.000000 1.000000 --->germline1---germline2: 3.96e-18 0.563837 5.11e-97 0.565556 0.821174 ( 0.059708) 0.255618 ( 0.047630) 0.821502 0.254476 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 0.821174 ( 0.059708) 1.000000 ( 0.000000) 0.821502 1.000000 --->germline2---dash-----: 1e+00 0.000000 1e+00 0.000000 0.255618 ( 0.047630) 1.000000 ( 0.000000) 0.254476 1.000000 ######sensitivitySnps###### --->fabia-------beagle1--: 1e+00 0.000000 1e+00 0.000000 0.933218 ( 0.078638) 1.000000 ( 0.000000) 0.966536 1.000000 --->fabia-------beagle2--: 1.64e-16 -0.052531 4.07e-05 -0.056782 0.933218 ( 0.078638) 0.990000 ( 0.100000) 0.966536 1.000000 --->fabia-------plink----: 1e+00 0.000000 1e+00 0.000000 0.933218 ( 0.078638) 1.000000 ( 0.000000) 0.966536 1.000000 --->fabia-------germline1: 1.9e-01 -0.010692 4.76e-01 -0.009492 0.933218 ( 0.078638) 0.942710 ( 0.107248) 0.966536 0.970077 --->fabia-------germline2: 4.18e-10 -0.041180 1.07e-08 -0.051814 0.933218 ( 0.078638) 0.985032 ( 0.031028) 0.966536 1.000000 --->fabia-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.933218 ( 0.078638) 0.000000 ( 0.000000) 0.966536 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) 0.942710 ( 0.107248) 1.000000 0.970077 --->beagle1-----germline2: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 0.985032 ( 0.031028) 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: 4.65e-12 0.068040 2.22e-03 0.047290 0.990000 ( 0.100000) 0.942710 ( 0.107248) 1.000000 0.970077 --->beagle2-----germline2: 1e+00 0.000000 6.41e-01 0.004968 0.990000 ( 0.100000) 0.985032 ( 0.031028) 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) 0.942710 ( 0.107248) 1.000000 0.970077 --->plink-------germline2: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 0.985032 ( 0.031028) 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: 7.79e-10 -0.066973 1.23e-04 -0.042322 0.942710 ( 0.107248) 0.985032 ( 0.031028) 0.970077 1.000000 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 0.942710 ( 0.107248) 0.000000 ( 0.000000) 0.970077 0.000000 --->germline2---dash-----: 1e+00 0.000000 1e+00 0.000000 0.985032 ( 0.031028) 0.000000 ( 0.000000) 1.000000 0.000000 ######trueNSnps###### --->fabia-------beagle1--: 5.51e-18 5014 1.26e-31 5115 195083 ( 860) 189967 ( 2822) 195250 190616 --->fabia-------beagle2--: 2.46e-12 799 2.35e-09 710 195083 ( 860) 194373 ( 597) 195250 194486 --->fabia-------plink----: 3.95e-18 195246 2.98e-235 195083 195083 ( 860) 0.13 ( 0.367) 195250 0 --->fabia-------germline1: 3.95e-18 34795 8.02e-51 34722 195083 ( 860) 160360 ( 11662) 195250 160376 --->fabia-------germline2: 3.96e-18 145213 5.94e-120 145165 195083 ( 860) 49918 ( 9301) 195250 49702 --->fabia-------dash-----: 1e+00 0 2.05e-02 -199 195083 ( 860) 195282 ( 149) 195250 195264 --->beagle1-----beagle2--: 1.77e-16 -4686 1.84e-28 -4405 189967 ( 2822) 194373 ( 597) 190616 194486 --->beagle1-----plink----: 3.96e-18 190104 4.99e-183 189967 189967 ( 2822) 0.13 ( 0.367) 190616 0 --->beagle1-----germline1: 4.2e-18 29671 1.96e-43 29607 189967 ( 2822) 160360 ( 11662) 190616 160376 --->beagle1-----germline2: 3.96e-18 140168 2.66e-116 140050 189967 ( 2822) 49918 ( 9301) 190616 49702 --->beagle1-----dash-----: 3.96e-18 -5178 2.24e-34 -5314 189967 ( 2822) 195282 ( 149) 190616 195264 --->beagle2-----plink----: 3.96e-18 194431 8.4e-251 194373 194373 ( 597) 0.13 ( 0.367) 194486 0 --->beagle2-----germline1: 3.96e-18 34037 1.36e-50 34012 194373 ( 597) 160360 ( 11662) 194486 160376 --->beagle2-----germline2: 3.96e-18 144665 1.84e-120 144455 194373 ( 597) 49918 ( 9301) 194486 49702 --->beagle2-----dash-----: 3.96e-18 -849 5.56e-28 -909 194373 ( 597) 195282 ( 149) 194486 195264 --->plink-------germline1: 3.95e-18 -160264 7.61e-115 -160360 0.13 ( 0.367) 160360 ( 11662) 0 160376 --->plink-------germline2: 3.95e-18 -49800 5.32e-75 -49917 0.13 ( 0.367) 49918 ( 9301) 0 49702 --->plink-------dash-----: 3.95e-18 -195262 9.37e-311 -195281 0.13 ( 0.367) 195282 ( 149) 0 195264 --->germline1---germline2: 3.95e-18 110099 5.11e-97 110443 160360 ( 11662) 49918 ( 9301) 160376 49702 --->germline1---dash-----: 3.95e-18 -35044 1.95e-51 -34921 160360 ( 11662) 195282 ( 149) 160376 195264 --->germline2---dash-----: 3.96e-18 -145508 2.46e-120 -145364 49918 ( 9301) 195282 ( 149) 49702 195264 ######falsePSnps###### --->fabia-------beagle1--: 5.51e-18 -5014 1.26e-31 -5115 199 ( 844) 5314 ( 2832) 0 4676 --->fabia-------beagle2--: 2.46e-12 -799 2.35e-09 -710 199 ( 844) 909 ( 591) 0 770 --->fabia-------plink----: 3.95e-18 -195246 2.98e-235 -195083 199 ( 844) 195281 ( 149) 0 195264 --->fabia-------germline1: 3.95e-18 -34793 8.02e-51 -34722 199 ( 844) 34921 ( 11658) 0 34856 --->fabia-------germline2: 3.96e-18 -145213 5.94e-120 -145165 199 ( 844) 145364 ( 9299) 0 145610 --->fabia-------dash-----: 1e+00 0.000000 1e+00 0.000000 198.770000 (844.308968) 0.000000 ( 0.000000) 0.000000 0.000000 --->beagle1-----beagle2--: 1.77e-16 4686 1.84e-28 4405 5314 ( 2832) 909 ( 591) 4676 770 --->beagle1-----plink----: 3.96e-18 -190104 4.99e-183 -189967 5314 ( 2832) 195281 ( 149) 4676 195264 --->beagle1-----germline1: 4.2e-18 -29670 1.96e-43 -29607 5314 ( 2832) 34921 ( 11658) 4676 34856 --->beagle1-----germline2: 3.96e-18 -140167 2.66e-116 -140050 5314 ( 2832) 145364 ( 9299) 4676 145610 --->beagle1-----dash-----: 1e+00 0 1e+00 0 5314 ( 2832) 0 ( 0) 4676 0 --->beagle2-----plink----: 3.96e-18 -194431 8.4e-251 -194373 909 ( 591) 195281 ( 149) 770 195264 --->beagle2-----germline1: 3.96e-18 -34037 1.36e-50 -34012 909 ( 591) 34921 ( 11658) 770 34856 --->beagle2-----germline2: 3.96e-18 -144665 1.84e-120 -144455 909 ( 591) 145364 ( 9299) 770 145610 --->beagle2-----dash-----: 1e+00 0 1e+00 0 909 ( 591) 0 ( 0) 770 0 --->plink-------germline1: 3.95e-18 160265 7.61e-115 160360 195281 ( 149) 34921 ( 11658) 195264 34856 --->plink-------germline2: 3.95e-18 49800 5.32e-75 49917 195281 ( 149) 145364 ( 9299) 195264 145610 --->plink-------dash-----: 1e+00 0 1e+00 0 195281 ( 149) 0 ( 0) 195264 0 --->germline1---germline2: 3.95e-18 -110098 5.11e-97 -110443 34921 ( 11658) 145364 ( 9299) 34856 145610 --->germline1---dash-----: 1e+00 0 1e+00 0 34921 ( 11658) 0 ( 0) 34856 0 --->germline2---dash-----: 1e+00 0 1e+00 0 145364 ( 9299) 0 ( 0) 145610 0 ######falseNSnps###### --->fabia-------beagle1--: 1e+00 0 1e+00 0 315 ( 370) 0 ( 0) 160 0 --->fabia-------beagle2--: 1.64e-16 250 4.42e-05 267 315 ( 370) 47.4 ( 474) 160 0 --->fabia-------plink----: 1e+00 0 1e+00 0 315 ( 370) 0 ( 0) 160 0 --->fabia-------germline1: 1.88e-01 50.5 4.15e-01 48.6 315 ( 370) 266 ( 468) 160 144 --->fabia-------germline2: 4.62e-10 194 1.19e-08 243 315 ( 370) 71.5 ( 148) 160 0 --->fabia-------dash-----: 3.95e-18 -4472 2.37e-105 -4404 315 ( 370) 4718 ( 149) 160 4736 --->beagle1-----beagle2--: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 47.440000 (474.400000) 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 1e+00 0 0 ( 0) 266 ( 468) 0 144 --->beagle1-----germline2: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 71.450000 (148.363284) 0.000000 0.000000 --->beagle1-----dash-----: 1e+00 0 1e+00 0 0 ( 0) 4718 ( 149) 0 4736 --->beagle2-----plink----: 1e+00 0.000000 1e+00 0.000000 47.440000 (474.400000) 0.000000 ( 0.000000) 0.000000 0.000000 --->beagle2-----germline1: 4.74e-12 -323 1.9e-03 -219 47.4 ( 474) 266 ( 468) 0 144 --->beagle2-----germline2: 1e+00 0.000000 6.35e-01 -24.010000 47.440000 (474.400000) 71.450000 (148.363284) 0.000000 0.000000 --->beagle2-----dash-----: 5.78e-18 -4738 8.29e-99 -4671 47.4 ( 474) 4718 ( 149) 0 4736 --->plink-------germline1: 1e+00 0 1e+00 0 0 ( 0) 266 ( 468) 0 144 --->plink-------germline2: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 71.450000 (148.363284) 0.000000 0.000000 --->plink-------dash-----: 1e+00 0 1e+00 0 0 ( 0) 4718 ( 149) 0 4736 --->germline1---germline2: 7.79e-10 314 5.06e-05 195 266 ( 468) 71.5 ( 148) 144 0 --->germline1---dash-----: 5.06e-18 -4491 2.68e-94 -4452 266 ( 468) 4718 ( 149) 144 4736 --->germline2---dash-----: 3.95e-18 -4684 1.29e-139 -4647 71.5 ( 148) 4718 ( 149) 0 4736 ######truePSnps###### --->fabia-------beagle1--: 8.45e-18 -251 2.06e-13 -315 4404 ( 400) 4718 ( 149) 4501 4736 --->fabia-------beagle2--: 1.64e-16 -250 4.42e-05 -267 4404 ( 400) 4671 ( 495) 4501 4732 --->fabia-------plink----: 8.45e-18 -251 2.06e-13 -315 4404 ( 400) 4718 ( 149) 4501 4736 --->fabia-------germline1: 1.88e-01 -50.5 4.15e-01 -48.6 4404 ( 400) 4452 ( 524) 4501 4590 --->fabia-------germline2: 4.62e-10 -194 1.19e-08 -243 4404 ( 400) 4647 ( 190) 4501 4712 --->fabia-------dash-----: 1e+00 0 1e+00 0 4404 ( 400) 0 ( 0) 4501 0 --->beagle1-----beagle2--: 1e+00 0 3.2e-01 47.4 4718 ( 149) 4671 ( 495) 4736 4732 --->beagle1-----plink----: 1e+00 0 1e+00 0 4718 ( 149) 4718 ( 149) 4736 4736 --->beagle1-----germline1: 3.64e-13 327 1.32e-07 266 4718 ( 149) 4452 ( 524) 4736 4590 --->beagle1-----germline2: 1.83e-06 228 5.28e-06 71.5 4718 ( 149) 4647 ( 190) 4736 4712 --->beagle1-----dash-----: 1e+00 0 1e+00 0 4718 ( 149) 0 ( 0) 4736 0 --->beagle2-----plink----: 1e+00 0 3.2e-01 -47.4 4671 ( 495) 4718 ( 149) 4732 4736 --->beagle2-----germline1: 4.74e-12 323 1.9e-03 219 4671 ( 495) 4452 ( 524) 4732 4590 --->beagle2-----germline2: 2.21e-05 220 6.35e-01 24 4671 ( 495) 4647 ( 190) 4732 4712 --->beagle2-----dash-----: 1e+00 0 1e+00 0 4671 ( 495) 0 ( 0) 4732 0 --->plink-------germline1: 3.64e-13 327 1.32e-07 266 4718 ( 149) 4452 ( 524) 4736 4590 --->plink-------germline2: 1.83e-06 228 5.28e-06 71.5 4718 ( 149) 4647 ( 190) 4736 4712 --->plink-------dash-----: 1e+00 0 1e+00 0 4718 ( 149) 0 ( 0) 4736 0 --->germline1---germline2: 7.79e-10 -314 5.06e-05 -195 4452 ( 524) 4647 ( 190) 4590 4712 --->germline1---dash-----: 1e+00 0 1e+00 0 4452 ( 524) 0 ( 0) 4590 0 --->germline2---dash-----: 1e+00 0 1e+00 0 4647 ( 190) 0 ( 0) 4712 0 ######MatthewsSample###### --->fabia-------beagle1--: 6.13e-17 0.241355 3.71e-39 0.219992 0.995224 ( 0.024090) 0.775231 ( 0.104578) 1.000000 0.773037 --->fabia-------beagle2--: 1e+00 0.000000 1.51e-04 0.046753 0.995224 ( 0.024090) 0.948470 ( 0.117762) 1.000000 1.000000 --->fabia-------plink----: 1e+00 0.000000 1e+00 0.000000 0.995224 ( 0.024090) 0.000000 ( 0.000000) 1.000000 0.000000 --->fabia-------germline1: 3.87e-18 0.512154 5.84e-65 0.511270 0.995224 ( 0.024090) 0.483954 ( 0.119213) 1.000000 0.480360 --->fabia-------germline2: 3.93e-18 0.821853 6.41e-147 0.818023 0.995224 ( 0.024090) 0.177200 ( 0.011734) 1.000000 0.179353 --->fabia-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.995224 ( 0.024090) 0.000000 ( 0.000000) 1.000000 0.000000 --->beagle1-----beagle2--: 5.42e-15 -0.199021 2.76e-20 -0.173239 0.775231 ( 0.104578) 0.948470 ( 0.117762) 0.773037 1.000000 --->beagle1-----plink----: 1e+00 0.000000 1e+00 0.000000 0.775231 ( 0.104578) 0.000000 ( 0.000000) 0.773037 0.000000 --->beagle1-----germline1: 7.37e-18 0.289218 1.86e-33 0.291278 0.775231 ( 0.104578) 0.483954 ( 0.119213) 0.773037 0.480360 --->beagle1-----germline2: 3.95e-18 0.595394 3.66e-77 0.598031 0.775231 ( 0.104578) 0.177200 ( 0.011734) 0.773037 0.179353 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.775231 ( 0.104578) 0.000000 ( 0.000000) 0.773037 0.000000 --->beagle2-----plink----: 1e+00 0.000000 1e+00 0.000000 0.948470 ( 0.117762) 0.000000 ( 0.000000) 1.000000 0.000000 --->beagle2-----germline1: 3.67e-17 0.470685 5.13e-48 0.464517 0.948470 ( 0.117762) 0.483954 ( 0.119213) 1.000000 0.480360 --->beagle2-----germline2: 4.07e-18 0.782206 2.34e-83 0.771270 0.948470 ( 0.117762) 0.177200 ( 0.011734) 1.000000 0.179353 --->beagle2-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.948470 ( 0.117762) 0.000000 ( 0.000000) 1.000000 0.000000 --->plink-------germline1: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.483954 ( 0.119213) 0.000000 0.480360 --->plink-------germline2: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.177200 ( 0.011734) 0.000000 0.179353 --->plink-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.000000 ( 0.000000) 0.000000 0.000000 --->germline1---germline2: 5.68e-18 0.309210 4.7e-46 0.306753 0.483954 ( 0.119213) 0.177200 ( 0.011734) 0.480360 0.179353 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 0.483954 ( 0.119213) 0.000000 ( 0.000000) 0.480360 0.000000 --->germline2---dash-----: 1e+00 0.000000 1e+00 0.000000 0.177200 ( 0.011734) 0.000000 ( 0.000000) 0.179353 0.000000 ######F1Sample###### --->fabia-------beagle1--: 5.85e-17 0.266704 8.36e-38 0.244316 0.994945 ( 0.025542) 0.750629 ( 0.121014) 1.000000 0.750000 --->fabia-------beagle2--: 1e+00 0.000000 1.11e-04 0.049260 0.994945 ( 0.025542) 0.945685 ( 0.121420) 1.000000 1.000000 --->fabia-------plink----: 4.68e-22 0.988023 5.69e-159 0.983096 0.994945 ( 0.025542) 0.011849 ( 0.000390) 1.000000 0.011928 --->fabia-------germline1: 3.86e-18 0.601324 1.02e-69 0.594290 0.994945 ( 0.025542) 0.400655 ( 0.122214) 1.000000 0.387097 --->fabia-------germline2: 3.93e-18 0.927469 6.67e-153 0.923043 0.994945 ( 0.025542) 0.071902 ( 0.007732) 1.000000 0.073171 --->fabia-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.994945 ( 0.025542) 0.000000 ( 0.000000) 1.000000 0.000000 --->beagle1-----beagle2--: 6.63e-15 -0.218514 5.54e-21 -0.195056 0.750629 ( 0.121014) 0.945685 ( 0.121420) 0.750000 1.000000 --->beagle1-----plink----: 2.95e-18 0.738105 2.12e-80 0.738780 0.750629 ( 0.121014) 0.011849 ( 0.000390) 0.750000 0.011928 --->beagle1-----germline1: 7.14e-18 0.353443 1.42e-36 0.349974 0.750629 ( 0.121014) 0.400655 ( 0.122214) 0.750000 0.387097 --->beagle1-----germline2: 3.95e-18 0.679203 1.3e-76 0.678727 0.750629 ( 0.121014) 0.071902 ( 0.007732) 0.750000 0.073171 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.750629 ( 0.121014) 0.000000 ( 0.000000) 0.750000 0.000000 --->beagle2-----plink----: 3.2e-19 0.942627 4.01e-90 0.933836 0.945685 ( 0.121420) 0.011849 ( 0.000390) 1.000000 0.011928 --->beagle2-----germline1: 9.23e-18 0.560197 9.06e-53 0.545030 0.945685 ( 0.121420) 0.400655 ( 0.122214) 1.000000 0.387097 --->beagle2-----germline2: 4.07e-18 0.884713 2.1e-87 0.873784 0.945685 ( 0.121420) 0.071902 ( 0.007732) 1.000000 0.073171 --->beagle2-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.945685 ( 0.121420) 0.000000 ( 0.000000) 1.000000 0.000000 --->plink-------germline1: 4.21e-18 -0.382419 8.48e-54 -0.388806 0.011849 ( 0.000390) 0.400655 ( 0.122214) 0.011928 0.387097 --->plink-------germline2: 3.93e-18 -0.060211 3.79e-91 -0.060053 0.011849 ( 0.000390) 0.071902 ( 0.007732) 0.011928 0.073171 --->plink-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.011849 ( 0.000390) 0.000000 ( 0.000000) 0.011928 0.000000 --->germline1---germline2: 4.6e-18 0.321999 8.73e-48 0.328753 0.400655 ( 0.122214) 0.071902 ( 0.007732) 0.387097 0.073171 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 0.400655 ( 0.122214) 0.000000 ( 0.000000) 0.387097 0.000000 --->germline2---dash-----: 1e+00 0.000000 1e+00 0.000000 0.071902 ( 0.007732) 0.000000 ( 0.000000) 0.073171 0.000000 ######accuracySample###### --->fabia-------beagle1--: 5.91e-17 0.004476 1.53e-29 0.004275 0.999965 ( 0.000178) 0.995690 ( 0.002688) 1.000000 0.996000 --->fabia-------beagle2--: 1e+00 0.000000 4.35e-06 0.000505 0.999965 ( 0.000178) 0.999460 ( 0.001039) 1.000000 1.000000 --->fabia-------plink----: 4.68e-22 0.994000 0e+00 0.994005 0.999965 ( 0.000178) 0.005960 ( 0.000197) 1.000000 0.006000 --->fabia-------germline1: 3.82e-18 0.018000 2.29e-49 0.017975 0.999965 ( 0.000178) 0.981990 ( 0.006303) 1.000000 0.982000 --->fabia-------germline2: 3.93e-18 0.154466 1.55e-95 0.155605 0.999965 ( 0.000178) 0.844360 ( 0.017775) 1.000000 0.848000 --->fabia-------dash-----: 4.66e-22 0.006000 1.65e-136 0.005925 0.999965 ( 0.000178) 0.994040 ( 0.000197) 1.000000 0.994000 --->beagle1-----beagle2--: 1.99e-16 -0.003983 4.48e-24 -0.003770 0.995690 ( 0.002688) 0.999460 ( 0.001039) 0.996000 1.000000 --->beagle1-----plink----: 2.88e-18 0.989962 4.53e-256 0.989730 0.995690 ( 0.002688) 0.005960 ( 0.000197) 0.996000 0.006000 --->beagle1-----germline1: 9.35e-18 0.014034 1.87e-35 0.013700 0.995690 ( 0.002688) 0.981990 ( 0.006303) 0.996000 0.982000 --->beagle1-----germline2: 3.93e-18 0.150069 3.21e-93 0.151330 0.995690 ( 0.002688) 0.844360 ( 0.017775) 0.996000 0.848000 --->beagle1-----dash-----: 6.21e-08 0.002480 2e-08 0.001650 0.995690 ( 0.002688) 0.994040 ( 0.000197) 0.996000 0.994000 --->beagle2-----plink----: 2.73e-19 0.993551 4.34e-297 0.993500 0.999460 ( 0.001039) 0.005960 ( 0.000197) 1.000000 0.006000 --->beagle2-----germline1: 3.85e-18 0.017481 2.26e-47 0.017470 0.999460 ( 0.001039) 0.981990 ( 0.006303) 1.000000 0.982000 --->beagle2-----germline2: 3.92e-18 0.153973 2.11e-95 0.155100 0.999460 ( 0.001039) 0.844360 ( 0.017775) 1.000000 0.848000 --->beagle2-----dash-----: 3.11e-19 0.005530 2.04e-72 0.005420 0.999460 ( 0.001039) 0.994040 ( 0.000197) 1.000000 0.994000 --->plink-------germline1: 3.82e-18 -0.976000 5.79e-219 -0.976030 0.005960 ( 0.000197) 0.981990 ( 0.006303) 0.006000 0.982000 --->plink-------germline2: 3.93e-18 -0.839510 9.57e-168 -0.838400 0.005960 ( 0.000197) 0.844360 ( 0.017775) 0.006000 0.848000 --->plink-------dash-----: 9.7e-23 -0.988000 0e+00 -0.988080 0.005960 ( 0.000197) 0.994040 ( 0.000197) 0.006000 0.994000 --->germline1---germline2: 3.92e-18 0.136548 2.66e-92 0.137630 0.981990 ( 0.006303) 0.844360 ( 0.017775) 0.982000 0.848000 --->germline1---dash-----: 2.1e-17 -0.012444 7.08e-35 -0.012050 0.981990 ( 0.006303) 0.994040 ( 0.000197) 0.982000 0.994000 --->germline2---dash-----: 3.92e-18 -0.148475 6.21e-94 -0.149680 0.844360 ( 0.017775) 0.994040 ( 0.000197) 0.848000 0.994000 ######FPRSample###### --->fabia-------beagle1--: 5.66e-17 -0.004466 3.99e-29 -0.004241 3.51e-05 ( 0.000178) 0.004276 ( 0.002703) 0.000000 0.004024 --->fabia-------beagle2--: 1e+00 0.000000 1e+00 0.000000 3.51e-05 ( 0.000178) 6.04e-05 ( 0.000345) 0.000000 0.000000 --->fabia-------plink----: 4.68e-22 -1.000002 0e+00 -1.000005 3.51e-05 ( 0.000178) 1.000040 ( 0.000198) 0.000000 1.000000 --->fabia-------germline1: 3.78e-18 -0.017650 6.52e-49 -0.017721 3.51e-05 ( 0.000178) 0.017757 ( 0.006284) 0.000000 0.018109 --->fabia-------germline2: 3.93e-18 -0.155428 1.55e-95 -0.156544 3.51e-05 ( 0.000178) 0.156579 ( 0.017882) 0.000000 0.152918 --->fabia-------dash-----: 1e+00 0.000000 1e+00 0.000000 3.51e-05 ( 0.000178) 0.000000 ( 0.000000) 0.000000 0.000000 --->beagle1-----beagle2--: 5.49e-17 0.004030 2.86e-28 0.004215 0.004276 ( 0.002703) 6.04e-05 ( 0.000345) 0.004024 0.000000 --->beagle1-----plink----: 2.87e-18 -0.995947 5.49e-256 -0.995765 0.004276 ( 0.002703) 1.000040 ( 0.000198) 0.004024 1.000000 --->beagle1-----germline1: 6.91e-18 -0.013597 8.67e-35 -0.013481 0.004276 ( 0.002703) 0.017757 ( 0.006284) 0.004024 0.018109 --->beagle1-----germline2: 3.95e-18 -0.150915 3.34e-93 -0.152304 0.004276 ( 0.002703) 0.156579 ( 0.017882) 0.004024 0.152918 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.004276 ( 0.002703) 0.000000 ( 0.000000) 0.004024 0.000000 --->beagle2-----plink----: 3.23e-22 -1.000036 0e+00 -0.999980 6.04e-05 ( 0.000345) 1.000040 ( 0.000198) 0.000000 1.000000 --->beagle2-----germline1: 3.77e-18 -0.017645 7.64e-49 -0.017696 6.04e-05 ( 0.000345) 0.017757 ( 0.006284) 0.000000 0.018109 --->beagle2-----germline2: 3.93e-18 -0.155421 1.22e-95 -0.156519 6.04e-05 ( 0.000345) 0.156579 ( 0.017882) 0.000000 0.152918 --->beagle2-----dash-----: 1e+00 0.000000 1e+00 0.000000 6.04e-05 ( 0.000345) 0.000000 ( 0.000000) 0.000000 0.000000 --->plink-------germline1: 3.76e-18 0.982372 2.2e-219 0.982284 1.000040 ( 0.000198) 0.017757 ( 0.006284) 1.000000 0.018109 --->plink-------germline2: 3.93e-18 0.844571 9.57e-168 0.843461 1.000040 ( 0.000198) 0.156579 ( 0.017882) 1.000000 0.152918 --->plink-------dash-----: 1e+00 0.000000 1e+00 0.000000 1.000040 ( 0.000198) 0.000000 ( 0.000000) 1.000000 0.000000 --->germline1---germline2: 3.95e-18 -0.137851 1.12e-92 -0.138823 0.017757 ( 0.006284) 0.156579 ( 0.017882) 0.018109 0.152918 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 0.017757 ( 0.006284) 0.000000 ( 0.000000) 0.018109 0.000000 --->germline2---dash-----: 1e+00 0.000000 1e+00 0.000000 0.156579 ( 0.017882) 0.000000 ( 0.000000) 0.152918 0.000000 ######FDRSample###### --->fabia-------beagle1--: 6.08e-17 -0.400037 4.84e-42 -0.370952 0.008929 ( 0.044939) 0.379880 ( 0.162288) 0.000000 0.400000 --->fabia-------beagle2--: 1e+00 0.000000 6.01e-01 -0.006071 0.008929 ( 0.044939) 0.015000 ( 0.105529) 0.000000 0.000000 --->fabia-------plink----: 4.68e-22 -0.993961 8.06e-135 -0.985111 0.008929 ( 0.044939) 0.994040 ( 0.000197) 0.000000 0.994000 --->fabia-------germline1: 3.84e-18 -0.748204 7.53e-83 -0.730557 0.008929 ( 0.044939) 0.739485 ( 0.101353) 0.000000 0.755000 --->fabia-------germline2: 3.93e-18 -0.962381 9.5e-133 -0.953763 0.008929 ( 0.044939) 0.962692 ( 0.004157) 0.000000 0.962025 --->fabia-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.008929 ( 0.044939) 0.000000 ( 0.000000) 0.000000 0.000000 --->beagle1-----beagle2--: 8.15e-16 0.400034 2.13e-35 0.364880 0.379880 ( 0.162288) 0.015000 ( 0.105529) 0.400000 0.000000 --->beagle1-----plink----: 3.01e-18 -0.599840 1.09e-60 -0.614160 0.379880 ( 0.162288) 0.994040 ( 0.000197) 0.400000 0.994000 --->beagle1-----germline1: 8.07e-18 -0.356216 1.51e-33 -0.359605 0.379880 ( 0.162288) 0.739485 ( 0.101353) 0.400000 0.755000 --->beagle1-----germline2: 3.95e-18 -0.568263 1.7e-58 -0.582811 0.379880 ( 0.162288) 0.962692 ( 0.004157) 0.400000 0.962025 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.379880 ( 0.162288) 0.000000 ( 0.000000) 0.400000 0.000000 --->beagle2-----plink----: 3.35e-22 -0.994006 4.68e-98 -0.979040 0.015000 ( 0.105529) 0.994040 ( 0.000197) 0.000000 0.994000 --->beagle2-----germline1: 4.07e-18 -0.748296 8.34e-70 -0.724485 0.015000 ( 0.105529) 0.739485 ( 0.101353) 0.000000 0.755000 --->beagle2-----germline2: 4.05e-18 -0.962265 9.77e-97 -0.947692 0.015000 ( 0.105529) 0.962692 ( 0.004157) 0.000000 0.962025 --->beagle2-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.015000 ( 0.105529) 0.000000 ( 0.000000) 0.000000 0.000000 --->plink-------germline1: 4.2e-18 0.244042 9.58e-45 0.254555 0.994040 ( 0.000197) 0.739485 ( 0.101353) 0.994000 0.755000 --->plink-------germline2: 3.93e-18 0.031440 7.32e-90 0.031348 0.994040 ( 0.000197) 0.962692 ( 0.004157) 0.994000 0.962025 --->plink-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.994040 ( 0.000197) 0.000000 ( 0.000000) 0.994000 0.000000 --->germline1---germline2: 4.46e-18 -0.211926 2.88e-40 -0.223207 0.739485 ( 0.101353) 0.962692 ( 0.004157) 0.755000 0.962025 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 0.739485 ( 0.101353) 0.000000 ( 0.000000) 0.755000 0.000000 --->germline2---dash-----: 1e+00 0.000000 1e+00 0.000000 0.962692 ( 0.004157) 0.000000 ( 0.000000) 0.962025 0.000000 ######specifitySample###### --->fabia-------beagle1--: 5.53e-17 0.004064 9.47e-29 0.004200 0.999965 ( 0.000178) 0.995765 ( 0.002710) 1.000000 0.995976 --->fabia-------beagle2--: 1e+00 0.000000 1e+00 0.000000 0.999965 ( 0.000178) 0.999980 ( 0.000404) 1.000000 1.000000 --->fabia-------plink----: 1e+00 0.000000 1e+00 0.000000 0.999965 ( 0.000178) 0.000000 ( 0.000000) 1.000000 0.000000 --->fabia-------germline1: 3.78e-18 0.017642 5.99e-49 0.017681 0.999965 ( 0.000178) 0.982284 ( 0.006264) 1.000000 0.981891 --->fabia-------germline2: 3.93e-18 0.155379 1.57e-95 0.156504 0.999965 ( 0.000178) 0.843461 ( 0.017880) 1.000000 0.847082 --->fabia-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.999965 ( 0.000178) 1.000040 ( 0.000198) 1.000000 1.000000 --->beagle1-----beagle2--: 5.74e-17 -0.004029 2.86e-28 -0.004215 0.995765 ( 0.002710) 0.999980 ( 0.000404) 0.995976 1.000000 --->beagle1-----plink----: 1e+00 0.000000 1e+00 0.000000 0.995765 ( 0.002710) 0.000000 ( 0.000000) 0.995976 0.000000 --->beagle1-----germline1: 6.78e-18 0.013588 8.67e-35 0.013481 0.995765 ( 0.002710) 0.982284 ( 0.006264) 0.995976 0.981891 --->beagle1-----germline2: 3.94e-18 0.150952 3.34e-93 0.152304 0.995765 ( 0.002710) 0.843461 ( 0.017880) 0.995976 0.847082 --->beagle1-----dash-----: 5.69e-17 -0.004506 7.52e-29 -0.004276 0.995765 ( 0.002710) 1.000040 ( 0.000198) 0.995976 1.000000 --->beagle2-----plink----: 1e+00 0.000000 1e+00 0.000000 0.999980 ( 0.000404) 0.000000 ( 0.000000) 1.000000 0.000000 --->beagle2-----germline1: 3.77e-18 0.017614 7.64e-49 0.017696 0.999980 ( 0.000404) 0.982284 ( 0.006264) 1.000000 0.981891 --->beagle2-----germline2: 3.93e-18 0.155364 1.22e-95 0.156519 0.999980 ( 0.000404) 0.843461 ( 0.017880) 1.000000 0.847082 --->beagle2-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.999980 ( 0.000404) 1.000040 ( 0.000198) 1.000000 1.000000 --->plink-------germline1: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.982284 ( 0.006264) 0.000000 0.981891 --->plink-------germline2: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.843461 ( 0.017880) 0.000000 0.847082 --->plink-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 1.000040 ( 0.000198) 0.000000 1.000000 --->germline1---germline2: 3.95e-18 0.137869 1.12e-92 0.138823 0.982284 ( 0.006264) 0.843461 ( 0.017880) 0.981891 0.847082 --->germline1---dash-----: 3.75e-18 -0.017645 3.46e-49 -0.017757 0.982284 ( 0.006264) 1.000040 ( 0.000198) 0.981891 1.000000 --->germline2---dash-----: 3.93e-18 -0.155363 1.33e-95 -0.156579 0.843461 ( 0.017880) 1.000040 ( 0.000198) 0.847082 1.000000 ######sensitivitySample###### --->fabia-------beagle1--: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 0.983333 ( 0.060395) 1.000000 1.000000 --->fabia-------beagle2--: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 0.913333 ( 0.154397) 1.000000 1.000000 --->fabia-------plink----: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 0.993333 ( 0.032824) 1.000000 1.000000 --->fabia-------germline1: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 0.933333 ( 0.178848) 1.000000 1.000000 --->fabia-------germline2: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 0.993333 ( 0.032824) 1.000000 1.000000 --->fabia-------dash-----: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 0.000000 ( 0.000000) 1.000000 0.000000 --->beagle1-----beagle2--: 1e+00 0.000000 2.67e-06 0.070000 0.983333 ( 0.060395) 0.913333 ( 0.154397) 1.000000 1.000000 --->beagle1-----plink----: 1e+00 0.000000 1.36e-02 -0.010000 0.983333 ( 0.060395) 0.993333 ( 0.032824) 1.000000 1.000000 --->beagle1-----germline1: 1e+00 0.000000 7.37e-03 0.050000 0.983333 ( 0.060395) 0.933333 ( 0.178848) 1.000000 1.000000 --->beagle1-----germline2: 1e+00 0.000000 1.36e-02 -0.010000 0.983333 ( 0.060395) 0.993333 ( 0.032824) 1.000000 1.000000 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.983333 ( 0.060395) 0.000000 ( 0.000000) 1.000000 0.000000 --->beagle2-----plink----: 1e+00 0.000000 3.79e-07 -0.080000 0.913333 ( 0.154397) 0.993333 ( 0.032824) 1.000000 1.000000 --->beagle2-----germline1: 1e+00 0.000000 3.76e-01 -0.020000 0.913333 ( 0.154397) 0.933333 ( 0.178848) 1.000000 1.000000 --->beagle2-----germline2: 1e+00 0.000000 3.79e-07 -0.080000 0.913333 ( 0.154397) 0.993333 ( 0.032824) 1.000000 1.000000 --->beagle2-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.913333 ( 0.154397) 0.000000 ( 0.000000) 1.000000 0.000000 --->plink-------germline1: 1e+00 0.000000 1.08e-03 0.060000 0.993333 ( 0.032824) 0.933333 ( 0.178848) 1.000000 1.000000 --->plink-------germline2: 1e+00 0.000000 1e+00 0.000000 0.993333 ( 0.032824) 0.993333 ( 0.032824) 1.000000 1.000000 --->plink-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.993333 ( 0.032824) 0.000000 ( 0.000000) 1.000000 0.000000 --->germline1---germline2: 1e+00 0.000000 1.08e-03 -0.060000 0.933333 ( 0.178848) 0.993333 ( 0.032824) 1.000000 1.000000 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 0.933333 ( 0.178848) 0.000000 ( 0.000000) 1.000000 0.000000 --->germline2---dash-----: 1e+00 0.000000 1e+00 0.000000 0.993333 ( 0.032824) 0.000000 ( 0.000000) 1.000000 0.000000 ######trueNSample###### --->fabia-------beagle1--: 2.74e-18 1004 6.44e-258 1004 1994 ( 0.355) 990 ( 2.69) 1994 990 --->fabia-------beagle2--: 1.31e-21 1000 0e+00 1000 1994 ( 0.355) 994 ( 0.402) 1994 994 --->fabia-------plink----: 1e+00 0 1e+00 0 1994 ( 0.355) 0 ( 0) 1994 0 --->fabia-------germline1: 3.77e-18 1018 1.12e-220 1018 1994 ( 0.355) 976 ( 6.23) 1994 976 --->fabia-------germline2: 3.92e-18 1154 2.04e-181 1156 1994 ( 0.355) 838 ( 17.8) 1994 842 --->fabia-------dash-----: 4.67e-22 1000 0e+00 1000 1994 ( 0.355) 994 ( 0.197) 1994 994 --->beagle1-----beagle2--: 5.49e-17 -4 2.86e-28 -4.19 990 ( 2.69) 994 ( 0.402) 990 994 --->beagle1-----plink----: 1e+00 0 1e+00 0 990 ( 2.69) 0 ( 0) 990 0 --->beagle1-----germline1: 6.95e-18 13.5 8.67e-35 13.4 990 ( 2.69) 976 ( 6.23) 990 976 --->beagle1-----germline2: 3.93e-18 150 3.34e-93 151 990 ( 2.69) 838 ( 17.8) 990 842 --->beagle1-----dash-----: 5.55e-17 -4.5 7.53e-29 -4.25 990 ( 2.69) 994 ( 0.197) 990 994 --->beagle2-----plink----: 1e+00 0 1e+00 0 994 ( 0.402) 0 ( 0) 994 0 --->beagle2-----germline1: 3.76e-18 17.5 7.64e-49 17.6 994 ( 0.402) 976 ( 6.23) 994 976 --->beagle2-----germline2: 3.92e-18 154 1.22e-95 156 994 ( 0.402) 838 ( 17.8) 994 842 --->beagle2-----dash-----: 1e+00 0 8.32e-02 -0.06 994 ( 0.402) 994 ( 0.197) 994 994 --->plink-------germline1: 1e+00 0 1e+00 0 0 ( 0) 976 ( 6.23) 0 976 --->plink-------germline2: 1e+00 0 1e+00 0 0 ( 0) 838 ( 17.8) 0 842 --->plink-------dash-----: 1e+00 0 1e+00 0 0 ( 0) 994 ( 0.197) 0 994 --->germline1---germline2: 3.92e-18 137 1.12e-92 138 976 ( 6.23) 838 ( 17.8) 976 842 --->germline1---dash-----: 3.75e-18 -17.5 3.46e-49 -17.6 976 ( 6.23) 994 ( 0.197) 976 994 --->germline2---dash-----: 3.93e-18 -154 1.33e-95 -156 838 ( 17.8) 994 ( 0.197) 842 994 ######falsePSample###### --->fabia-------beagle1--: 5.51e-17 -4.5 2.83e-29 -4.18 0.07 ( 0.355) 4.25 ( 2.69) 0 4 --->fabia-------beagle2--: 1e+00 0.000000 8.43e-01 0.010000 0.070000 ( 0.355477) 0.060000 ( 0.342893) 0.000000 0.000000 --->fabia-------plink----: 4.68e-22 -994 0e+00 -994 0.07 ( 0.355) 994 ( 0.197) 0 994 --->fabia-------germline1: 3.77e-18 -17.5 1.32e-48 -17.6 0.07 ( 0.355) 17.6 ( 6.25) 0 18 --->fabia-------germline2: 3.92e-18 -154 1.83e-95 -156 0.07 ( 0.355) 156 ( 17.8) 0 152 --->fabia-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.070000 ( 0.355477) 0.000000 ( 0.000000) 0.000000 0.000000 --->beagle1-----beagle2--: 5.49e-17 4 2.86e-28 4.19 4.25 ( 2.69) 0.06 ( 0.343) 4 0 --->beagle1-----plink----: 2.75e-18 -990 5.49e-256 -990 4.25 ( 2.69) 994 ( 0.197) 4 994 --->beagle1-----germline1: 6.95e-18 -13.5 8.67e-35 -13.4 4.25 ( 2.69) 17.6 ( 6.25) 4 18 --->beagle1-----germline2: 3.93e-18 -150 3.34e-93 -151 4.25 ( 2.69) 156 ( 17.8) 4 152 --->beagle1-----dash-----: 1e+00 0 1e+00 0 4.25 ( 2.69) 0 ( 0) 4 0 --->beagle2-----plink----: 3.23e-22 -994 0e+00 -994 0.06 ( 0.343) 994 ( 0.197) 0 994 --->beagle2-----germline1: 3.76e-18 -17.5 7.64e-49 -17.6 0.06 ( 0.343) 17.6 ( 6.25) 0 18 --->beagle2-----germline2: 3.92e-18 -154 1.22e-95 -156 0.06 ( 0.343) 156 ( 17.8) 0 152 --->beagle2-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.060000 ( 0.342893) 0.000000 ( 0.000000) 0.000000 0.000000 --->plink-------germline1: 3.75e-18 976 2.2e-219 976 994 ( 0.197) 17.6 ( 6.25) 994 18 --->plink-------germline2: 3.93e-18 840 9.57e-168 838 994 ( 0.197) 156 ( 17.8) 994 152 --->plink-------dash-----: 1e+00 0 1e+00 0 994 ( 0.197) 0 ( 0) 994 0 --->germline1---germline2: 3.92e-18 -137 1.12e-92 -138 17.6 ( 6.25) 156 ( 17.8) 18 152 --->germline1---dash-----: 1e+00 0 1e+00 0 17.6 ( 6.25) 0 ( 0) 18 0 --->germline2---dash-----: 1e+00 0 1e+00 0 156 ( 17.8) 0 ( 0) 152 0 ######falseNSample###### --->fabia-------beagle1--: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.060000 ( 0.238683) 0.000000 0.000000 --->fabia-------beagle2--: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.480000 ( 0.881688) 0.000000 0.000000 --->fabia-------plink----: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.000000 ( 0.000000) 0.000000 0.000000 --->fabia-------germline1: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.360000 ( 1.068559) 0.000000 0.000000 --->fabia-------germline2: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.000000 ( 0.000000) 0.000000 0.000000 --->fabia-------dash-----: 1e+00 0 1e+00 0 0 ( 0) 5.96 ( 0.197) 0 6 --->beagle1-----beagle2--: 1e+00 0.000000 2.67e-06 -0.420000 0.060000 ( 0.238683) 0.480000 ( 0.881688) 0.000000 0.000000 --->beagle1-----plink----: 1e+00 0.000000 1e+00 0.000000 0.060000 ( 0.238683) 0.000000 ( 0.000000) 0.000000 0.000000 --->beagle1-----germline1: 1e+00 0.000000 7.37e-03 -0.300000 0.060000 ( 0.238683) 0.360000 ( 1.068559) 0.000000 0.000000 --->beagle1-----germline2: 1e+00 0.000000 1e+00 0.000000 0.060000 ( 0.238683) 0.000000 ( 0.000000) 0.000000 0.000000 --->beagle1-----dash-----: 4.67e-22 -6 4.46e-122 -5.9 0.06 ( 0.239) 5.96 ( 0.197) 0 6 --->beagle2-----plink----: 1e+00 0.000000 1e+00 0.000000 0.480000 ( 0.881688) 0.000000 ( 0.000000) 0.000000 0.000000 --->beagle2-----germline1: 1e+00 0.000000 3.76e-01 0.120000 0.480000 ( 0.881688) 0.360000 ( 1.068559) 0.000000 0.000000 --->beagle2-----germline2: 1e+00 0.000000 1e+00 0.000000 0.480000 ( 0.881688) 0.000000 ( 0.000000) 0.000000 0.000000 --->beagle2-----dash-----: 3.15e-19 -5.5 4.64e-79 -5.48 0.48 ( 0.882) 5.96 ( 0.197) 0 6 --->plink-------germline1: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.360000 ( 1.068559) 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) 5.96 ( 0.197) 0 6 --->germline1---germline2: 1e+00 0.000000 1e+00 0.000000 0.360000 ( 1.068559) 0.000000 ( 0.000000) 0.000000 0.000000 --->germline1---dash-----: 2.56e-20 -6 7.75e-74 -5.6 0.36 ( 1.07) 5.96 ( 0.197) 0 6 --->germline2---dash-----: 1e+00 0 1e+00 0 0 ( 0) 5.96 ( 0.197) 0 6 ######truePSample###### --->fabia-------beagle1--: 1e+00 0 1e+00 0 6 ( 0) 5.9 ( 0.362) 6 6 --->fabia-------beagle2--: 1e+00 0 1e+00 0 6 ( 0) 5.48 ( 0.926) 6 6 --->fabia-------plink----: 1e+00 0 1e+00 0 6 ( 0) 5.96 ( 0.197) 6 6 --->fabia-------germline1: 1e+00 0 1e+00 0 6 ( 0) 5.6 ( 1.07) 6 6 --->fabia-------germline2: 1e+00 0 1e+00 0 6 ( 0) 5.96 ( 0.197) 6 6 --->fabia-------dash-----: 1e+00 0 1e+00 0 6 ( 0) 0 ( 0) 6 0 --->beagle1-----beagle2--: 1e+00 0 2.67e-06 0.42 5.9 ( 0.362) 5.48 ( 0.926) 6 6 --->beagle1-----plink----: 1e+00 0 1.36e-02 -0.06 5.9 ( 0.362) 5.96 ( 0.197) 6 6 --->beagle1-----germline1: 1e+00 0 7.37e-03 0.3 5.9 ( 0.362) 5.6 ( 1.07) 6 6 --->beagle1-----germline2: 1e+00 0 1.36e-02 -0.06 5.9 ( 0.362) 5.96 ( 0.197) 6 6 --->beagle1-----dash-----: 1e+00 0 1e+00 0 5.9 ( 0.362) 0 ( 0) 6 0 --->beagle2-----plink----: 1e+00 0 3.79e-07 -0.48 5.48 ( 0.926) 5.96 ( 0.197) 6 6 --->beagle2-----germline1: 1e+00 0 3.76e-01 -0.12 5.48 ( 0.926) 5.6 ( 1.07) 6 6 --->beagle2-----germline2: 1e+00 0 3.79e-07 -0.48 5.48 ( 0.926) 5.96 ( 0.197) 6 6 --->beagle2-----dash-----: 1e+00 0 1e+00 0 5.48 ( 0.926) 0 ( 0) 6 0 --->plink-------germline1: 1e+00 0 1.08e-03 0.36 5.96 ( 0.197) 5.6 ( 1.07) 6 6 --->plink-------germline2: 1e+00 0 1e+00 0 5.96 ( 0.197) 5.96 ( 0.197) 6 6 --->plink-------dash-----: 1e+00 0 1e+00 0 5.96 ( 0.197) 0 ( 0) 6 0 --->germline1---germline2: 1e+00 0 1.08e-03 -0.36 5.6 ( 1.07) 5.96 ( 0.197) 6 6 --->germline1---dash-----: 1e+00 0 1e+00 0 5.6 ( 1.07) 0 ( 0) 6 0 --->germline2---dash-----: 1e+00 0 1e+00 0 5.96 ( 0.197) 0 ( 0) 6 0