Results: Wilcoxon-Rank-Sum Wilcoxon-median t-test t-test-mean mean1 (std) mean2 (std) median1 median2 ######Matthews###### --->fabia-------beagle1--: 3.92e-17 0.491670 1.21e-27 0.501612 0.507608 ( 0.332524) 0.005995 ( 0.008292) 0.461977 0.006398 --->fabia-------beagle2--: 1.17e-17 0.493017 1.2e-27 0.500806 0.507608 ( 0.332524) 0.006802 ( 0.011579) 0.461977 0.003054 --->fabia-------plink----: 1.88e-16 0.493721 2.28e-27 0.501491 0.507608 ( 0.332524) 0.006117 ( 0.010193) 0.461977 0.005638 --->fabia-------germline1: 2.52e-17 0.498490 8.31e-28 0.508474 0.507608 ( 0.332524) -0.000866 ( 0.003988) 0.461977 0.000285 --->fabia-------germline2: 3.96e-18 0.498872 8.75e-28 0.507076 0.507608 ( 0.332524) 0.000532 ( 0.011198) 0.461977 -0.001552 --->fabia-------dash-----: 7.9e-18 0.501779 6.21e-28 0.511130 0.507608 ( 0.332524) -0.003522 ( 0.005800) 0.461977 -0.001774 --->beagle1-----beagle2--: 1.07e-01 -0.001106 3.26e-01 -0.000807 0.005995 ( 0.008292) 0.006802 ( 0.011579) 0.006398 0.003054 --->beagle1-----plink----: 7.9e-01 0.000408 9.28e-01 -0.000121 0.005995 ( 0.008292) 0.006117 ( 0.010193) 0.006398 0.005638 --->beagle1-----germline1: 7.71e-09 0.006749 1.14e-10 0.006861 0.005995 ( 0.008292) -0.000866 ( 0.003988) 0.006398 0.000285 --->beagle1-----germline2: 2.28e-08 0.006722 1.88e-04 0.005463 0.005995 ( 0.008292) 0.000532 ( 0.011198) 0.006398 -0.001552 --->beagle1-----dash-----: 1.81e-11 0.009463 2.05e-14 0.009518 0.005995 ( 0.008292) -0.003522 ( 0.005800) 0.006398 -0.001774 --->beagle2-----plink----: 6.99e-01 0.000547 6.71e-01 0.000685 0.006802 ( 0.011579) 0.006117 ( 0.010193) 0.003054 0.005638 --->beagle2-----germline1: 8.41e-06 0.007240 1.73e-08 0.007668 0.006802 ( 0.011579) -0.000866 ( 0.003988) 0.003054 0.000285 --->beagle2-----germline2: 6.68e-04 0.005663 1.32e-04 0.006270 0.006802 ( 0.011579) 0.000532 ( 0.011198) 0.003054 -0.001552 --->beagle2-----dash-----: 8.66e-10 0.009439 5.89e-12 0.010324 0.006802 ( 0.011579) -0.003522 ( 0.005800) 0.003054 -0.001774 --->plink-------germline1: 2.02e-07 0.006099 1.59e-08 0.006983 0.006117 ( 0.010193) -0.000866 ( 0.003988) 0.005638 0.000285 --->plink-------germline2: 9.26e-06 0.005486 1.66e-04 0.005585 0.006117 ( 0.010193) 0.000532 ( 0.011198) 0.005638 -0.001552 --->plink-------dash-----: 1.95e-11 0.009065 1.28e-12 0.009639 0.006117 ( 0.010193) -0.003522 ( 0.005800) 0.005638 -0.001774 --->germline1---germline2: 1.1e-02 0.001130 2.72e-01 -0.001398 -0.000866 ( 0.003988) 0.000532 ( 0.011198) 0.000285 -0.001552 --->germline1---dash-----: 4.12e-11 0.002215 3.3e-08 0.002656 -0.000866 ( 0.003988) -0.003522 ( 0.005800) 0.000285 -0.001774 --->germline2---dash-----: 1.26e-02 0.001790 2.64e-03 0.004054 0.000532 ( 0.011198) -0.003522 ( 0.005800) -0.001552 -0.001774 ######F1###### --->fabia-------beagle1--: 3.14e-16 0.496737 4.11e-24 0.464951 0.465427 ( 0.345322) 0.000476 ( 0.000343) 0.372326 0.000470 --->fabia-------beagle2--: 1e-15 0.551744 4.17e-24 0.464704 0.465427 ( 0.345322) 0.000723 ( 0.000848) 0.372326 0.000436 --->fabia-------plink----: 3.01e-16 0.490435 4.27e-24 0.464838 0.465427 ( 0.345322) 0.000589 ( 6e-04) 0.372326 0.000559 --->fabia-------germline1: 3.52e-16 0.469794 4.05e-24 0.465198 0.465427 ( 0.345322) 0.000229 ( 2.74e-05) 0.372326 0.000234 --->fabia-------germline2: 2.55e-15 0.570089 4.04e-24 0.465107 0.465427 ( 0.345322) 0.000320 ( 0.001777) 0.372326 0.000000 --->fabia-------dash-----: 3.52e-16 0.469821 4.05e-24 0.465209 0.465427 ( 0.345322) 0.000218 ( 3.16e-05) 0.372326 0.000225 --->beagle1-----beagle2--: 1e+00 0.000000 2.3e-04 -0.000247 0.000476 ( 0.000343) 0.000723 ( 0.000848) 0.000470 0.000436 --->beagle1-----plink----: 1e+00 0.000000 1.12e-01 -0.000113 0.000476 ( 0.000343) 0.000589 ( 6e-04) 0.000470 0.000559 --->beagle1-----germline1: 5.33e-09 0.000248 1.27e-10 0.000247 0.000476 ( 0.000343) 0.000229 ( 2.74e-05) 0.000470 0.000234 --->beagle1-----germline2: 1.83e-10 0.000575 3.94e-01 0.000156 0.000476 ( 0.000343) 0.000320 ( 0.001777) 0.000470 0.000000 --->beagle1-----dash-----: 2.92e-09 0.000257 3.34e-11 0.000258 0.000476 ( 0.000343) 0.000218 ( 3.16e-05) 0.000470 0.000225 --->beagle2-----plink----: 3.08e-01 0.000148 2.22e-01 0.000134 0.000723 ( 0.000848) 0.000589 ( 6e-04) 0.000436 0.000559 --->beagle2-----germline1: 1.91e-05 0.000443 6.88e-08 0.000494 0.000723 ( 0.000848) 0.000229 ( 2.74e-05) 0.000436 0.000234 --->beagle2-----germline2: 4.64e-06 0.001268 4.15e-02 0.000403 0.000723 ( 0.000848) 0.000320 ( 0.001777) 0.000436 0.000000 --->beagle2-----dash-----: 1.71e-05 0.000446 4.01e-08 0.000505 0.000723 ( 0.000848) 0.000218 ( 3.16e-05) 0.000436 0.000225 --->plink-------germline1: 1.5e-07 0.000293 3.81e-08 0.000360 0.000589 ( 6e-04) 0.000229 ( 2.74e-05) 0.000559 0.000234 --->plink-------germline2: 4.37e-08 0.000772 1.42e-01 0.000269 0.000589 ( 6e-04) 0.000320 ( 0.001777) 0.000559 0.000000 --->plink-------dash-----: 1.07e-07 0.000344 1.63e-08 0.000371 0.000589 ( 6e-04) 0.000218 ( 3.16e-05) 0.000559 0.000225 --->germline1---germline2: 2.38e-13 0.000226 1e+00 0.000000 0.000229 ( 2.74e-05) 0.000320 ( 0.001777) 0.000234 0.000000 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 0.000229 ( 2.74e-05) 0.000218 ( 3.16e-05) 0.000234 0.000225 --->germline2---dash-----: 2.38e-13 -0.000214 5.69e-01 0.000102 0.000320 ( 0.001777) 0.000218 ( 3.16e-05) 0.000000 0.000225 ######accuracy###### --->fabia-------beagle1--: 3.96e-18 0.222685 1.66e-113 0.222245 0.999855 ( 0.000150) 0.777610 ( 0.016645) 0.999905 0.777373 --->fabia-------beagle2--: 3.96e-18 0.085607 2.27e-91 0.085469 0.999855 ( 0.000150) 0.914386 ( 0.010748) 0.999905 0.914270 --->fabia-------plink----: 3.96e-18 0.116437 2.53e-122 0.116577 0.999855 ( 0.000150) 0.883278 ( 0.007088) 0.999905 0.883855 --->fabia-------germline1: 3.96e-18 0.960729 6.11e-157 0.954518 0.999855 ( 0.000150) 0.045337 ( 0.026021) 0.999905 0.038931 --->fabia-------germline2: 3.96e-18 0.020545 1.21e-103 0.020436 0.999855 ( 0.000150) 0.979419 ( 0.001932) 0.999905 0.979296 --->fabia-------dash-----: 3.96e-18 0.965868 5.32e-157 0.959622 0.999855 ( 0.000150) 0.040233 ( 0.026124) 0.999905 0.033954 --->beagle1-----beagle2--: 3.96e-18 -0.136852 6.67e-116 -0.136776 0.777610 ( 0.016645) 0.914386 ( 0.010748) 0.777373 0.914270 --->beagle1-----plink----: 3.96e-18 -0.105560 1.77e-86 -0.105668 0.777610 ( 0.016645) 0.883278 ( 0.007088) 0.777373 0.883855 --->beagle1-----germline1: 3.96e-18 0.734759 1.84e-144 0.732273 0.777610 ( 0.016645) 0.045337 ( 0.026021) 0.777373 0.038931 --->beagle1-----germline2: 3.96e-18 -0.202065 6.19e-109 -0.201809 0.777610 ( 0.016645) 0.979419 ( 0.001932) 0.777373 0.979296 --->beagle1-----dash-----: 3.96e-18 0.739843 1.66e-144 0.737378 0.777610 ( 0.016645) 0.040233 ( 0.026124) 0.777373 0.033954 --->beagle2-----plink----: 3.96e-18 0.031414 2.83e-53 0.031108 0.914386 ( 0.010748) 0.883278 ( 0.007088) 0.914270 0.883855 --->beagle2-----germline1: 3.96e-18 0.872749 3.03e-155 0.869049 0.914386 ( 0.010748) 0.045337 ( 0.026021) 0.914270 0.038931 --->beagle2-----germline2: 3.96e-18 -0.065115 7.44e-80 -0.065033 0.914386 ( 0.010748) 0.979419 ( 0.001932) 0.914270 0.979296 --->beagle2-----dash-----: 3.96e-18 0.877829 3.18e-155 0.874153 0.914386 ( 0.010748) 0.040233 ( 0.026124) 0.914270 0.033954 --->plink-------germline1: 3.96e-18 0.842596 1.2e-154 0.837941 0.883278 ( 0.007088) 0.045337 ( 0.026021) 0.883855 0.038931 --->plink-------germline2: 3.96e-18 -0.096022 1.81e-114 -0.096141 0.883278 ( 0.007088) 0.979419 ( 0.001932) 0.883855 0.979296 --->plink-------dash-----: 3.96e-18 0.847740 1.19e-154 0.843045 0.883278 ( 0.007088) 0.040233 ( 0.026124) 0.883855 0.033954 --->germline1---germline2: 3.96e-18 -0.940246 4.03e-157 -0.934083 0.045337 ( 0.026021) 0.979419 ( 0.001932) 0.038931 0.979296 --->germline1---dash-----: 3.96e-18 0.005057 1.18e-68 0.005104 0.045337 ( 0.026021) 0.040233 ( 0.026124) 0.038931 0.033954 --->germline2---dash-----: 3.96e-18 0.945358 3.54e-157 0.939187 0.979419 ( 0.001932) 0.040233 ( 0.026124) 0.979296 0.033954 ######FPR###### --->fabia-------beagle1--: 3.96e-18 -0.222649 1.64e-113 -0.222225 0.000127 ( 0.000150) 0.222352 ( 0.016645) 7.42e-05 0.222629 --->fabia-------beagle2--: 3.96e-18 -0.085546 2.34e-91 -0.085411 0.000127 ( 0.000150) 0.085538 ( 0.010746) 7.42e-05 0.085679 --->fabia-------plink----: 3.96e-18 -0.116386 2.85e-122 -0.116527 0.000127 ( 0.000150) 0.116654 ( 0.007092) 7.42e-05 0.116103 --->fabia-------germline1: 3.96e-18 -0.960881 6.19e-157 -0.954640 0.000127 ( 0.000150) 0.954767 ( 0.026026) 7.42e-05 0.961178 --->fabia-------germline2: 3.96e-18 -0.020451 1.88e-103 -0.020343 0.000127 ( 0.000150) 0.020470 ( 0.001929) 7.42e-05 0.020586 --->fabia-------dash-----: 3.96e-18 -0.966012 5.39e-157 -0.959740 0.000127 ( 0.000150) 0.959868 ( 0.026128) 7.42e-05 0.966154 --->beagle1-----beagle2--: 3.96e-18 0.136890 6.63e-116 0.136814 0.222352 ( 0.016645) 0.085538 ( 0.010746) 0.222629 0.085679 --->beagle1-----plink----: 3.96e-18 0.105584 1.65e-86 0.105698 0.222352 ( 0.016645) 0.116654 ( 0.007092) 0.222629 0.116103 --->beagle1-----germline1: 3.96e-18 -0.734935 1.85e-144 -0.732415 0.222352 ( 0.016645) 0.954767 ( 0.026026) 0.222629 0.961178 --->beagle1-----germline2: 3.96e-18 0.202160 5.86e-109 0.201882 0.222352 ( 0.016645) 0.020470 ( 0.001929) 0.222629 0.020586 --->beagle1-----dash-----: 3.96e-18 -0.739930 1.66e-144 -0.737516 0.222352 ( 0.016645) 0.959868 ( 0.026128) 0.222629 0.966154 --->beagle2-----plink----: 3.96e-18 -0.031381 2.6e-53 -0.031116 0.085538 ( 0.010746) 0.116654 ( 0.007092) 0.085679 0.116103 --->beagle2-----germline1: 3.96e-18 -0.872975 3.08e-155 -0.869229 0.085538 ( 0.010746) 0.954767 ( 0.026026) 0.085679 0.961178 --->beagle2-----germline2: 3.96e-18 0.065139 6.88e-80 0.065068 0.085538 ( 0.010746) 0.020470 ( 0.001929) 0.085679 0.020586 --->beagle2-----dash-----: 3.96e-18 -0.878023 3.23e-155 -0.874330 0.085538 ( 0.010746) 0.959868 ( 0.026128) 0.085679 0.966154 --->plink-------germline1: 3.96e-18 -0.842734 1.2e-154 -0.838113 0.116654 ( 0.007092) 0.954767 ( 0.026026) 0.116103 0.961178 --->plink-------germline2: 3.96e-18 0.096060 1.84e-114 0.096184 0.116654 ( 0.007092) 0.020470 ( 0.001929) 0.116103 0.020586 --->plink-------dash-----: 3.96e-18 -0.847907 1.19e-154 -0.843214 0.116654 ( 0.007092) 0.959868 ( 0.026128) 0.116103 0.966154 --->germline1---germline2: 3.96e-18 0.940455 4.01e-157 0.934297 0.954767 ( 0.026026) 0.020470 ( 0.001929) 0.961178 0.020586 --->germline1---dash-----: 3.96e-18 -0.005051 1.33e-68 -0.005100 0.954767 ( 0.026026) 0.959868 ( 0.026128) 0.961178 0.966154 --->germline2---dash-----: 3.96e-18 -0.945570 3.51e-157 -0.939398 0.020470 ( 0.001929) 0.959868 ( 0.026128) 0.020586 0.966154 ######FDR###### --->fabia-------beagle1--: 1.97e-17 -0.568573 4.71e-23 -0.530144 0.469618 ( 0.409039) 0.999762 ( 0.000172) 0.643879 0.999765 --->fabia-------beagle2--: 5.49e-17 -0.577962 4.78e-23 -0.530020 0.469618 ( 0.409039) 0.999638 ( 0.000425) 0.643879 0.999782 --->fabia-------plink----: 1.91e-17 -0.568009 4.76e-23 -0.530087 0.469618 ( 0.409039) 0.999705 ( 0.000301) 0.643879 0.999720 --->fabia-------germline1: 1.17e-17 -0.558830 4.66e-23 -0.530268 0.469618 ( 0.409039) 0.999885 ( 1.37e-05) 0.643879 0.999883 --->fabia-------germline2: 4.24e-17 -0.584778 4.69e-23 -0.530221 0.469618 ( 0.409039) 0.999839 ( 0.000894) 0.643879 1.000000 --->fabia-------dash-----: 1.17e-17 -0.558855 4.65e-23 -0.530273 0.469618 ( 0.409039) 0.999891 ( 1.58e-05) 0.643879 0.999888 --->beagle1-----beagle2--: 1e+00 0.000000 2.25e-04 0.000124 0.999762 ( 0.000172) 0.999638 ( 0.000425) 0.999765 0.999782 --->beagle1-----plink----: 1e+00 0.000000 1e+00 0.000000 0.999762 ( 0.000172) 0.999705 ( 0.000301) 0.999765 0.999720 --->beagle1-----germline1: 5.38e-09 -9.8e-05 1.26e-10 -0.000124 0.999762 ( 0.000172) 0.999885 ( 1.37e-05) 0.999765 0.999883 --->beagle1-----germline2: 1.83e-10 -0.000264 1e+00 0.000000 0.999762 ( 0.000172) 0.999839 ( 0.000894) 0.999765 1.000000 --->beagle1-----dash-----: 2.92e-09 -0.000104 3.3e-11 -0.000129 0.999762 ( 0.000172) 0.999891 ( 1.58e-05) 0.999765 0.999888 --->beagle2-----plink----: 1e+00 0.000000 1e+00 0.000000 0.999638 ( 0.000425) 0.999705 ( 0.000301) 0.999782 0.999720 --->beagle2-----germline1: 1.88e-05 -0.000194 6.79e-08 -0.000248 0.999638 ( 0.000425) 0.999885 ( 1.37e-05) 0.999782 0.999883 --->beagle2-----germline2: 4.64e-06 -0.000638 4.31e-02 -0.000201 0.999638 ( 0.000425) 0.999839 ( 0.000894) 0.999782 1.000000 --->beagle2-----dash-----: 1.71e-05 -0.000203 3.96e-08 -0.000253 0.999638 ( 0.000425) 0.999891 ( 1.58e-05) 0.999782 0.999888 --->plink-------germline1: 1.5e-07 -0.000140 3.76e-08 -0.000180 0.999705 ( 0.000301) 0.999885 ( 1.37e-05) 0.999720 0.999883 --->plink-------germline2: 4.37e-08 -0.000370 1.46e-01 -0.000134 0.999705 ( 0.000301) 0.999839 ( 0.000894) 0.999720 1.000000 --->plink-------dash-----: 1.07e-07 -0.000143 1.61e-08 -0.000186 0.999705 ( 0.000301) 0.999891 ( 1.58e-05) 0.999720 0.999888 --->germline1---germline2: 2.38e-13 -8.4e-05 1e+00 0.000000 0.999885 ( 1.37e-05) 0.999839 ( 0.000894) 0.999883 1.000000 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 0.999885 ( 1.37e-05) 0.999891 ( 1.58e-05) 0.999883 0.999888 --->germline2---dash-----: 2.38e-13 7.66e-05 1e+00 0.000000 0.999839 ( 0.000894) 0.999891 ( 1.58e-05) 1.000000 0.999888 ######specifity###### --->fabia-------beagle1--: 3.96e-18 0.222662 1.64e-113 0.222225 0.999873 ( 0.000150) 0.777648 ( 0.016645) 0.999926 0.777371 --->fabia-------beagle2--: 3.96e-18 0.085544 2.34e-91 0.085411 0.999873 ( 0.000150) 0.914462 ( 0.010746) 0.999926 0.914321 --->fabia-------plink----: 3.96e-18 0.116386 2.85e-122 0.116527 0.999873 ( 0.000150) 0.883346 ( 0.007092) 0.999926 0.883897 --->fabia-------germline1: 3.96e-18 0.960863 6.19e-157 0.954640 0.999873 ( 0.000150) 0.045233 ( 0.026026) 0.999926 0.038822 --->fabia-------germline2: 3.96e-18 0.020449 1.88e-103 0.020343 0.999873 ( 0.000150) 0.979530 ( 0.001929) 0.999926 0.979414 --->fabia-------dash-----: 3.96e-18 0.965986 5.39e-157 0.959740 0.999873 ( 0.000150) 0.040132 ( 0.026128) 0.999926 0.033846 --->beagle1-----beagle2--: 3.96e-18 -0.136893 6.63e-116 -0.136814 0.777648 ( 0.016645) 0.914462 ( 0.010746) 0.777371 0.914321 --->beagle1-----plink----: 3.96e-18 -0.105598 1.65e-86 -0.105698 0.777648 ( 0.016645) 0.883346 ( 0.007092) 0.777371 0.883897 --->beagle1-----germline1: 3.96e-18 0.734901 1.85e-144 0.732415 0.777648 ( 0.016645) 0.045233 ( 0.026026) 0.777371 0.038822 --->beagle1-----germline2: 3.96e-18 -0.202144 5.86e-109 -0.201882 0.777648 ( 0.016645) 0.979530 ( 0.001929) 0.777371 0.979414 --->beagle1-----dash-----: 3.96e-18 0.739932 1.66e-144 0.737516 0.777648 ( 0.016645) 0.040132 ( 0.026128) 0.777371 0.033846 --->beagle2-----plink----: 3.96e-18 0.031371 2.6e-53 0.031116 0.914462 ( 0.010746) 0.883346 ( 0.007092) 0.914321 0.883897 --->beagle2-----germline1: 3.96e-18 0.872984 3.08e-155 0.869229 0.914462 ( 0.010746) 0.045233 ( 0.026026) 0.914321 0.038822 --->beagle2-----germline2: 3.96e-18 -0.065135 6.88e-80 -0.065068 0.914462 ( 0.010746) 0.979530 ( 0.001929) 0.914321 0.979414 --->beagle2-----dash-----: 3.96e-18 0.878009 3.23e-155 0.874330 0.914462 ( 0.010746) 0.040132 ( 0.026128) 0.914321 0.033846 --->plink-------germline1: 3.96e-18 0.842760 1.2e-154 0.838113 0.883346 ( 0.007092) 0.045233 ( 0.026026) 0.883897 0.038822 --->plink-------germline2: 3.96e-18 -0.096061 1.84e-114 -0.096184 0.883346 ( 0.007092) 0.979530 ( 0.001929) 0.883897 0.979414 --->plink-------dash-----: 3.96e-18 0.847901 1.19e-154 0.843214 0.883346 ( 0.007092) 0.040132 ( 0.026128) 0.883897 0.033846 --->germline1---germline2: 3.96e-18 -0.940455 4.01e-157 -0.934297 0.045233 ( 0.026026) 0.979530 ( 0.001929) 0.038822 0.979414 --->germline1---dash-----: 3.96e-18 0.005053 1.33e-68 0.005100 0.045233 ( 0.026026) 0.040132 ( 0.026128) 0.038822 0.033846 --->germline2---dash-----: 3.96e-18 0.945570 3.51e-157 0.939398 0.979530 ( 0.001929) 0.040132 ( 0.026128) 0.979414 0.033846 ######sensitivity###### --->fabia-------beagle1--: 1.46e-07 0.259624 1.25e-08 0.235427 0.688202 ( 0.349078) 0.452775 ( 0.315485) 0.861385 0.500000 --->fabia-------beagle2--: 4.71e-14 0.516827 3.45e-20 0.429241 0.688202 ( 0.349078) 0.258961 ( 0.293670) 0.861385 0.166667 --->fabia-------plink----: 8.27e-11 0.432538 2.49e-13 0.386507 0.688202 ( 0.349078) 0.301695 ( 0.306466) 0.861385 0.282467 --->fabia-------germline1: 1.23e-10 -0.185640 2.81e-10 -0.251872 0.688202 ( 0.349078) 0.940074 ( 0.080527) 0.861385 0.962302 --->fabia-------germline2: 2.74e-15 0.833486 2.11e-33 0.661448 0.688202 ( 0.349078) 0.026754 ( 0.139614) 0.861385 0.000000 --->fabia-------dash-----: 3.38e-07 -0.149541 5.12e-08 -0.212725 0.688202 ( 0.349078) 0.900927 ( 0.101536) 0.861385 0.931960 --->beagle1-----beagle2--: 1.06e-10 0.333378 9.64e-13 0.193814 0.452775 ( 0.315485) 0.258961 ( 0.293670) 0.500000 0.166667 --->beagle1-----plink----: 7.26e-04 0.175316 9.04e-04 0.151080 0.452775 ( 0.315485) 0.301695 ( 0.306466) 0.500000 0.282467 --->beagle1-----germline1: 5.56e-17 -0.500055 2.61e-26 -0.487299 0.452775 ( 0.315485) 0.940074 ( 0.080527) 0.500000 0.962302 --->beagle1-----germline2: 3.74e-14 0.500490 9.33e-22 0.426021 0.452775 ( 0.315485) 0.026754 ( 0.139614) 0.500000 0.000000 --->beagle1-----dash-----: 3.38e-16 -0.451309 4.53e-23 -0.448152 0.452775 ( 0.315485) 0.900927 ( 0.101536) 0.500000 0.931960 --->beagle2-----plink----: 6.14e-01 -0.039434 3.3e-01 -0.042734 0.258961 ( 0.293670) 0.301695 ( 0.306466) 0.166667 0.282467 --->beagle2-----germline1: 5.94e-18 -0.706588 2.17e-39 -0.681113 0.258961 ( 0.293670) 0.940074 ( 0.080527) 0.166667 0.962302 --->beagle2-----germline2: 4.82e-09 0.428245 6.5e-11 0.232207 0.258961 ( 0.293670) 0.026754 ( 0.139614) 0.166667 0.000000 --->beagle2-----dash-----: 9.34e-18 -0.666675 1.8e-36 -0.641966 0.258961 ( 0.293670) 0.900927 ( 0.101536) 0.166667 0.931960 --->plink-------germline1: 1.93e-17 -0.662501 3.84e-36 -0.638378 0.301695 ( 0.306466) 0.940074 ( 0.080527) 0.282467 0.962302 --->plink-------germline2: 2.08e-11 0.398835 1.47e-13 0.274942 0.301695 ( 0.306466) 0.026754 ( 0.139614) 0.282467 0.000000 --->plink-------dash-----: 2.06e-17 -0.626692 9.48e-34 -0.599231 0.301695 ( 0.306466) 0.900927 ( 0.101536) 0.282467 0.931960 --->germline1---germline2: 6.82e-18 0.953506 1.08e-73 0.913320 0.940074 ( 0.080527) 0.026754 ( 0.139614) 0.962302 0.000000 --->germline1---dash-----: 1.23e-06 0.078716 8.11e-07 0.039147 0.940074 ( 0.080527) 0.900927 ( 0.101536) 0.962302 0.931960 --->germline2---dash-----: 7.96e-18 -0.910348 2.15e-70 -0.874173 0.026754 ( 0.139614) 0.900927 ( 0.101536) 0.000000 0.931960 ######trueN###### --->fabia-------beagle1--: 3.96e-18 12225209 1.29e-186 12220717 2e+07 ( 3001) 7775577 ( 166435) 2e+07 7772788 --->fabia-------beagle2--: 3.96e-18 10854261 3.51e-200 10852737 2e+07 ( 3001) 9143558 ( 107453) 2e+07 9142090 --->fabia-------plink----: 3.96e-18 11162412 3.79e-219 11163860 2e+07 ( 3001) 8832434 ( 70930) 2e+07 8837866 --->fabia-------germline1: 3.96e-18 19606090 9.84e-188 19544019 2e+07 ( 3001) 452275 ( 260227) 2e+07 388174 --->fabia-------germline2: 3.96e-18 10203276 2.83e-271 10202132 2e+07 ( 3001) 9794163 ( 19298) 2e+07 9792956 --->fabia-------dash-----: 3.96e-18 19657689 1.12e-187 19595017 2e+07 ( 3001) 401278 ( 261250) 2e+07 338422 --->beagle1-----beagle2--: 3.96e-18 -1368613 6.64e-116 -1367980 7775577 ( 166435) 9143558 ( 107453) 7772788 9142090 --->beagle1-----plink----: 3.96e-18 -1055938 1.65e-86 -1056857 7775577 ( 166435) 8832434 ( 70930) 7772788 8837866 --->beagle1-----germline1: 3.96e-18 7348118 1.84e-144 7323302 7775577 ( 166435) 452275 ( 260227) 7772788 388174 --->beagle1-----germline2: 3.96e-18 -2021359 5.87e-109 -2018586 7775577 ( 166435) 9794163 ( 19298) 7772788 9792956 --->beagle1-----dash-----: 3.96e-18 7398751 1.66e-144 7374300 7775577 ( 166435) 401278 ( 261250) 7772788 338422 --->beagle2-----plink----: 3.96e-18 313876 2.6e-53 311123 9143558 ( 107453) 8832434 ( 70930) 9142090 8837866 --->beagle2-----germline1: 3.96e-18 8728422 3.07e-155 8691282 9143558 ( 107453) 452275 ( 260227) 9142090 388174 --->beagle2-----germline2: 3.96e-18 -651344 6.88e-80 -650605 9143558 ( 107453) 9794163 ( 19298) 9142090 9792956 --->beagle2-----dash-----: 3.96e-18 8778962 3.22e-155 8742280 9143558 ( 107453) 401278 ( 261250) 9142090 338422 --->plink-------germline1: 3.96e-18 8426513 1.2e-154 8380159 8832434 ( 70930) 452275 ( 260227) 8837866 388174 --->plink-------germline2: 3.96e-18 -960502 1.83e-114 -961728 8832434 ( 70930) 9794163 ( 19298) 8837866 9792956 --->plink-------dash-----: 3.96e-18 8477988 1.19e-154 8431157 8832434 ( 70930) 401278 ( 261250) 8837866 338422 --->germline1---germline2: 3.96e-18 -9403562 4e-157 -9341888 452275 ( 260227) 9794163 ( 19298) 388174 9792956 --->germline1---dash-----: 3.96e-18 50506 1.33e-68 50998 452275 ( 260227) 401278 ( 261250) 388174 338422 --->germline2---dash-----: 3.96e-18 9454594 3.5e-157 9392885 9794163 ( 19298) 401278 ( 261250) 9792956 338422 ######falseP###### --->fabia-------beagle1--: 3.96e-18 -2225216 2.07e-113 -2220719 2542 ( 2994) 2223262 ( 166435) 1484 2226030 --->fabia-------beagle2--: 3.96e-18 -854260 3.78e-91 -852739 2542 ( 2994) 855281 ( 107449) 1484 856686 --->fabia-------plink----: 3.96e-18 -1162411 5.12e-122 -1163862 2542 ( 2994) 1166404 ( 70914) 1484 1160880 --->fabia-------germline1: 3.96e-18 -9606088 6.28e-157 -9544021 2542 ( 2994) 9546564 ( 260219) 1484 9610683 --->fabia-------germline2: 3.96e-18 -203257 7.15e-103 -202134 2542 ( 2994) 204676 ( 19288) 1484 205830 --->fabia-------dash-----: 3.96e-18 -9657687 5.47e-157 -9595019 2542 ( 2994) 9597561 ( 261241) 1484 9660446 --->beagle1-----beagle2--: 3.96e-18 1368617 6.64e-116 1367980 2223262 ( 166435) 855281 ( 107449) 2226030 856686 --->beagle1-----plink----: 3.96e-18 1055938 1.65e-86 1056857 2223262 ( 166435) 1166404 ( 70914) 2226030 1160880 --->beagle1-----germline1: 3.96e-18 -7348115 1.84e-144 -7323302 2223262 ( 166435) 9546564 ( 260219) 2226030 9610683 --->beagle1-----germline2: 3.96e-18 2021376 5.87e-109 2018586 2223262 ( 166435) 204676 ( 19288) 2226030 205830 --->beagle1-----dash-----: 3.96e-18 -7398752 1.66e-144 -7374300 2223262 ( 166435) 9597561 ( 261241) 2226030 9660446 --->beagle2-----plink----: 3.96e-18 -313882 2.6e-53 -311123 855281 ( 107449) 1166404 ( 70914) 856686 1160880 --->beagle2-----germline1: 3.96e-18 -8728431 3.07e-155 -8691282 855281 ( 107449) 9546564 ( 260219) 856686 9610683 --->beagle2-----germline2: 3.96e-18 651346 6.88e-80 650605 855281 ( 107449) 204676 ( 19288) 856686 205830 --->beagle2-----dash-----: 3.96e-18 -8778959 3.22e-155 -8742280 855281 ( 107449) 9597561 ( 261241) 856686 9660446 --->plink-------germline1: 3.96e-18 -8426508 1.2e-154 -8380159 1166404 ( 70914) 9546564 ( 260219) 1160880 9610683 --->plink-------germline2: 3.96e-18 960499 1.83e-114 961728 1166404 ( 70914) 204676 ( 19288) 1160880 205830 --->plink-------dash-----: 3.96e-18 -8478016 1.19e-154 -8431157 1166404 ( 70914) 9597561 ( 261241) 1160880 9660446 --->germline1---germline2: 3.96e-18 9403560 4e-157 9341888 9546564 ( 260219) 204676 ( 19288) 9610683 205830 --->germline1---dash-----: 3.96e-18 -50505 1.33e-68 -50998 9546564 ( 260219) 9597561 ( 261241) 9610683 9660446 --->germline2---dash-----: 3.96e-18 -9454600 3.5e-157 -9392885 204676 ( 19288) 9597561 ( 261241) 205830 9660446 ######falseN###### --->fabia-------beagle1--: 9.91e-08 -302 8.83e-09 -277 359 ( 400) 636 ( 373) 165 624 --->fabia-------beagle2--: 4.4e-14 -606 4.12e-20 -501 359 ( 400) 860 ( 344) 165 960 --->fabia-------plink----: 7.88e-11 -505 1.51e-13 -457 359 ( 400) 816 ( 370) 165 850 --->fabia-------germline1: 1.29e-10 216 2.88e-10 290 359 ( 400) 68.6 ( 88.8) 165 42 --->fabia-------germline2: 2.08e-15 -963 1.59e-32 -773 359 ( 400) 1131 ( 185) 165 1152 --->fabia-------dash-----: 3.03e-07 172 5.79e-08 245 359 ( 400) 114 ( 115) 165 78 --->beagle1-----beagle2--: 1.14e-10 -391 1.21e-12 -224 636 ( 373) 860 ( 344) 624 960 --->beagle1-----plink----: 5.8e-04 -207 7.64e-04 -180 636 ( 373) 816 ( 370) 624 850 --->beagle1-----germline1: 5.78e-17 584 5.84e-26 568 636 ( 373) 68.6 ( 88.8) 624 42 --->beagle1-----germline2: 4.53e-14 -614 1.51e-21 -495 636 ( 373) 1131 ( 185) 624 1152 --->beagle1-----dash-----: 3.02e-16 526 9.6e-23 522 636 ( 373) 114 ( 115) 624 78 --->beagle2-----plink----: 6.08e-01 35 3.87e-01 44.3 860 ( 344) 816 ( 370) 960 850 --->beagle2-----germline1: 6.15e-18 815 3.36e-39 791 860 ( 344) 68.6 ( 88.8) 960 42 --->beagle2-----germline2: 5.86e-09 -528 4.69e-11 -271 860 ( 344) 1131 ( 185) 960 1152 --->beagle2-----dash-----: 9.41e-18 776 4.02e-36 746 860 ( 344) 114 ( 115) 960 78 --->plink-------germline1: 1.97e-17 777 2.49e-35 747 816 ( 370) 68.6 ( 88.8) 850 42 --->plink-------germline2: 2e-11 -451 1.57e-13 -315 816 ( 370) 1131 ( 185) 850 1152 --->plink-------dash-----: 2.13e-17 733 4.65e-33 702 816 ( 370) 114 ( 115) 850 78 --->germline1---germline2: 8.45e-18 -1107 2.25e-70 -1063 68.6 ( 88.8) 1131 ( 185) 42 1152 --->germline1---dash-----: 1.14e-06 -90 7.44e-07 -45 68.6 ( 88.8) 114 ( 115) 42 78 --->germline2---dash-----: 8.45e-18 1055 5.18e-67 1018 1131 ( 185) 114 ( 115) 1152 78 ######trueP###### --->fabia-------beagle1--: 8.13e-08 302 5.71e-09 279 805 ( 414) 525 ( 370) 960 571 --->fabia-------beagle2--: 3.38e-14 606 1.79e-20 503 805 ( 414) 301 ( 340) 960 189 --->fabia-------plink----: 5.88e-11 505 8.93e-14 459 805 ( 414) 346 ( 352) 960 330 --->fabia-------germline1: 1.29e-10 -215 2.79e-10 -288 805 ( 414) 1093 ( 129) 960 1121 --->fabia-------germline2: 2.73e-15 969 6.55e-33 774 805 ( 414) 30.3 ( 159) 960 0 --->fabia-------dash-----: 3.03e-07 -172 5.9e-08 -243 805 ( 414) 1048 ( 150) 960 1080 --->beagle1-----beagle2--: 1.14e-10 391 1.21e-12 224 525 ( 370) 301 ( 340) 571 189 --->beagle1-----plink----: 5.8e-04 207 7.64e-04 180 525 ( 370) 346 ( 352) 571 330 --->beagle1-----germline1: 5.78e-17 -584 5.84e-26 -568 525 ( 370) 1093 ( 129) 571 1121 --->beagle1-----germline2: 4.53e-14 614 1.51e-21 495 525 ( 370) 30.3 ( 159) 571 0 --->beagle1-----dash-----: 3.02e-16 -526 9.6e-23 -522 525 ( 370) 1048 ( 150) 571 1080 --->beagle2-----plink----: 6.08e-01 -35 3.87e-01 -44.3 301 ( 340) 346 ( 352) 189 330 --->beagle2-----germline1: 6.15e-18 -816 3.36e-39 -791 301 ( 340) 1093 ( 129) 189 1121 --->beagle2-----germline2: 5.86e-09 528 4.69e-11 271 301 ( 340) 30.3 ( 159) 189 0 --->beagle2-----dash-----: 9.41e-18 -776 4.02e-36 -746 301 ( 340) 1048 ( 150) 189 1080 --->plink-------germline1: 1.97e-17 -777 2.49e-35 -747 346 ( 352) 1093 ( 129) 330 1121 --->plink-------germline2: 2e-11 451 1.57e-13 315 346 ( 352) 30.3 ( 159) 330 0 --->plink-------dash-----: 2.13e-17 -733 4.65e-33 -702 346 ( 352) 1048 ( 150) 330 1080 --->germline1---germline2: 8.45e-18 1107 2.25e-70 1063 1093 ( 129) 30.3 ( 159) 1121 0 --->germline1---dash-----: 1.14e-06 90 7.44e-07 45 1093 ( 129) 1048 ( 150) 1121 1080 --->germline2---dash-----: 8.45e-18 -1055 5.18e-67 -1018 30.3 ( 159) 1048 ( 150) 0 1080 ######MatthewsSnps###### --->fabia-------beagle1--: 1e+00 0.000000 1e+00 0.000000 0.393513 ( 0.237658) 0.000000 ( 0.000000) 0.389988 0.000000 --->fabia-------beagle2--: 1.1e-17 0.387411 3.15e-30 0.392760 0.393513 ( 0.237658) 0.000753 ( 0.004569) 0.389988 0.000000 --->fabia-------plink----: 1.1e-17 0.387920 2.81e-30 0.393373 0.393513 ( 0.237658) 0.000140 ( 0.000423) 0.389988 0.000000 --->fabia-------germline1: 1.03e-17 0.371239 1.79e-28 0.382700 0.393513 ( 0.237658) 0.010813 ( 0.042002) 0.389988 0.012698 --->fabia-------germline2: 3.62e-16 0.386159 7.03e-26 0.386652 0.393513 ( 0.237658) 0.006861 ( 0.145472) 0.389988 -0.021414 --->fabia-------dash-----: 1.03e-17 0.371230 1.85e-28 0.382755 0.393513 ( 0.237658) 0.010758 ( 0.042569) 0.389988 0.012698 --->beagle1-----beagle2--: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.000753 ( 0.004569) 0.000000 0.000000 --->beagle1-----plink----: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.000140 ( 0.000423) 0.000000 0.000000 --->beagle1-----germline1: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.010813 ( 0.042002) 0.000000 0.012698 --->beagle1-----germline2: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.006861 ( 0.145472) 0.000000 -0.021414 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.010758 ( 0.042569) 0.000000 0.012698 --->beagle2-----plink----: 1e+00 0.000000 1.76e-01 0.000613 0.000753 ( 0.004569) 0.000140 ( 0.000423) 0.000000 0.000000 --->beagle2-----germline1: 1.15e-15 -0.012674 1.86e-02 -0.010060 0.000753 ( 0.004569) 0.010813 ( 0.042002) 0.000000 0.012698 --->beagle2-----germline2: 2.38e-13 0.021493 6.74e-01 -0.006108 0.000753 ( 0.004569) 0.006861 ( 0.145472) 0.000000 -0.021414 --->beagle2-----dash-----: 1.15e-15 -0.012661 2.08e-02 -0.010005 0.000753 ( 0.004569) 0.010758 ( 0.042569) 0.000000 0.012698 --->plink-------germline1: 7.67e-17 -0.012542 1.26e-02 -0.010673 0.000140 ( 0.000423) 0.010813 ( 0.042002) 0.000000 0.012698 --->plink-------germline2: 2.38e-13 0.021517 6.45e-01 -0.006721 0.000140 ( 0.000423) 0.006861 ( 0.145472) 0.000000 -0.021414 --->plink-------dash-----: 7.67e-17 -0.012531 1.43e-02 -0.010618 0.000140 ( 0.000423) 0.010758 ( 0.042569) 0.000000 0.012698 --->germline1---germline2: 2.38e-13 0.034233 8.14e-01 0.003953 0.010813 ( 0.042002) 0.006861 ( 0.145472) 0.012698 -0.021414 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 0.010813 ( 0.042002) 0.010758 ( 0.042569) 0.012698 0.012698 --->germline2---dash-----: 2.38e-13 -0.034241 8.17e-01 -0.003897 0.006861 ( 0.145472) 0.010758 ( 0.042569) -0.021414 0.012698 ######F1Snps###### --->fabia-------beagle1--: 1.03e-17 0.286553 7.89e-24 0.312998 0.351036 ( 0.235254) 0.038039 ( 0.002711) 0.314676 0.037869 --->fabia-------beagle2--: 1.03e-17 0.286398 7.93e-24 0.312958 0.351036 ( 0.235254) 0.038079 ( 0.002730) 0.314676 0.038039 --->fabia-------plink----: 1.03e-17 0.286553 7.89e-24 0.312997 0.351036 ( 0.235254) 0.038039 ( 0.002711) 0.314676 0.037869 --->fabia-------germline1: 1.03e-17 0.285938 9.17e-24 0.312517 0.351036 ( 0.235254) 0.038519 ( 0.003127) 0.314676 0.038737 --->fabia-------germline2: 7.82e-15 0.325092 3.29e-21 0.323391 0.351036 ( 0.235254) 0.027645 ( 0.141604) 0.314676 0.000000 --->fabia-------dash-----: 1.03e-17 0.285938 9.17e-24 0.312519 0.351036 ( 0.235254) 0.038517 ( 0.003135) 0.314676 0.038737 --->beagle1-----beagle2--: 1e+00 0.000000 1e+00 0.000000 0.038039 ( 0.002711) 0.038079 ( 0.002730) 0.037869 0.038039 --->beagle1-----plink----: 1e+00 0.000000 1e+00 0.000000 0.038039 ( 0.002711) 0.038039 ( 0.002711) 0.037869 0.037869 --->beagle1-----germline1: 7.67e-17 -0.000323 2.06e-03 -0.000480 0.038039 ( 0.002711) 0.038519 ( 0.003127) 0.037869 0.038737 --->beagle1-----germline2: 2.37e-13 0.037903 4.65e-01 0.010393 0.038039 ( 0.002711) 0.027645 ( 0.141604) 0.037869 0.000000 --->beagle1-----dash-----: 7.67e-17 -0.000269 2.33e-03 -0.000479 0.038039 ( 0.002711) 0.038517 ( 0.003135) 0.037869 0.038737 --->beagle2-----plink----: 1e+00 0.000000 1e+00 0.000000 0.038079 ( 0.002730) 0.038039 ( 0.002711) 0.038039 0.037869 --->beagle2-----germline1: 1.32e-14 -0.000295 4.75e-03 -0.000440 0.038079 ( 0.002730) 0.038519 ( 0.003127) 0.038039 0.038737 --->beagle2-----germline2: 2.37e-13 0.037962 4.64e-01 0.010433 0.038079 ( 0.002730) 0.027645 ( 0.141604) 0.038039 0.000000 --->beagle2-----dash-----: 1.32e-14 -0.000302 5.28e-03 -0.000438 0.038079 ( 0.002730) 0.038517 ( 0.003135) 0.038039 0.038737 --->plink-------germline1: 7.67e-17 -0.000322 2.08e-03 -0.000480 0.038039 ( 0.002711) 0.038519 ( 0.003127) 0.037869 0.038737 --->plink-------germline2: 2.37e-13 0.037903 4.65e-01 0.010394 0.038039 ( 0.002711) 0.027645 ( 0.141604) 0.037869 0.000000 --->plink-------dash-----: 7.67e-17 -0.000269 2.34e-03 -0.000478 0.038039 ( 0.002711) 0.038517 ( 0.003135) 0.037869 0.038737 --->germline1---germline2: 2.38e-13 0.038550 4.47e-01 0.010874 0.038519 ( 0.003127) 0.027645 ( 0.141604) 0.038737 0.000000 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 0.038519 ( 0.003127) 0.038517 ( 0.003135) 0.038737 0.038737 --->germline2---dash-----: 2.38e-13 -0.038549 4.47e-01 -0.010872 0.027645 ( 0.141604) 0.038517 ( 0.003135) 0.000000 0.038737 ######accuracySnps###### --->fabia-------beagle1--: 3.96e-18 0.916217 3.84e-132 0.912975 0.932365 ( 0.044429) 0.019390 ( 0.001409) 0.938000 0.019300 --->fabia-------beagle2--: 3.96e-18 0.915087 1.45e-131 0.911962 0.932365 ( 0.044429) 0.020403 ( 0.007141) 0.938000 0.019400 --->fabia-------plink----: 3.96e-18 0.916189 3.8e-132 0.912965 0.932365 ( 0.044429) 0.019400 ( 0.001408) 0.938000 0.019300 --->fabia-------germline1: 3.96e-18 0.904506 4.36e-121 0.898421 0.932365 ( 0.044429) 0.033944 ( 0.026847) 0.938000 0.027500 --->fabia-------germline2: 7.38e-07 -0.023737 4.99e-08 -0.026425 0.932365 ( 0.044429) 0.958790 ( 0.006398) 0.938000 0.958000 --->fabia-------dash-----: 3.96e-18 0.904488 4.39e-121 0.898418 0.932365 ( 0.044429) 0.033947 ( 0.026849) 0.938000 0.027500 --->beagle1-----beagle2--: 1e+00 0.000000 1.5e-01 -0.001013 0.019390 ( 0.001409) 0.020403 ( 0.007141) 0.019300 0.019400 --->beagle1-----plink----: 1e+00 0.000000 1e+00 0.000000 0.019390 ( 0.001409) 0.019400 ( 0.001408) 0.019300 0.019300 --->beagle1-----germline1: 4.07e-18 -0.008132 4.59e-07 -0.014554 0.019390 ( 0.001409) 0.033944 ( 0.026847) 0.019300 0.027500 --->beagle1-----germline2: 3.95e-18 -0.938480 6.8e-213 -0.939400 0.019390 ( 0.001409) 0.958790 ( 0.006398) 0.019300 0.958000 --->beagle1-----dash-----: 4.07e-18 -0.008163 4.58e-07 -0.014557 0.019390 ( 0.001409) 0.033947 ( 0.026849) 0.019300 0.027500 --->beagle2-----plink----: 1e+00 0.000000 1.53e-01 0.001003 0.020403 ( 0.007141) 0.019400 ( 0.001408) 0.019400 0.019300 --->beagle2-----germline1: 8.93e-16 -0.008146 2.93e-06 -0.013541 0.020403 ( 0.007141) 0.033944 ( 0.026847) 0.019400 0.027500 --->beagle2-----germline2: 3.95e-18 -0.938150 7.31e-203 -0.938387 0.020403 ( 0.007141) 0.958790 ( 0.006398) 0.019400 0.958000 --->beagle2-----dash-----: 8.93e-16 -0.008104 2.92e-06 -0.013544 0.020403 ( 0.007141) 0.033947 ( 0.026849) 0.019400 0.027500 --->plink-------germline1: 4.07e-18 -0.008147 4.68e-07 -0.014544 0.019400 ( 0.001408) 0.033944 ( 0.026847) 0.019300 0.027500 --->plink-------germline2: 3.95e-18 -0.938464 6.26e-213 -0.939390 0.019400 ( 0.001408) 0.958790 ( 0.006398) 0.019300 0.958000 --->plink-------dash-----: 4.07e-18 -0.008137 4.66e-07 -0.014547 0.019400 ( 0.001408) 0.033947 ( 0.026849) 0.019300 0.027500 --->germline1---germline2: 3.94e-18 -0.929799 2.74e-153 -0.924846 0.033944 ( 0.026847) 0.958790 ( 0.006398) 0.027500 0.958000 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 0.033944 ( 0.026847) 0.033947 ( 0.026849) 0.027500 0.027500 --->germline2---dash-----: 3.94e-18 0.929760 2.77e-153 0.924843 0.958790 ( 0.006398) 0.033947 ( 0.026849) 0.958000 0.027500 ######FPRSnps###### --->fabia-------beagle1--: 1e+00 0.000000 1e+00 0.000000 0.063664 ( 0.045493) 1.000000 ( 0.000000) 0.059060 1.000000 --->fabia-------beagle2--: 3.94e-18 -0.938237 1.76e-131 -0.935303 0.063664 ( 0.045493) 0.998967 ( 0.007118) 0.059060 1.000000 --->fabia-------plink----: 3.94e-18 -0.939407 3.97e-132 -0.936326 0.063664 ( 0.045493) 0.999990 ( 3.07e-05) 0.059060 1.000000 --->fabia-------germline1: 3.96e-18 -0.927747 5.97e-121 -0.921448 0.063664 ( 0.045493) 0.985112 ( 0.027447) 0.059060 0.991742 --->fabia-------germline2: 9.59e-13 0.037874 2.23e-14 0.040821 0.063664 ( 0.045493) 0.022842 ( 0.003418) 0.059060 0.023277 --->fabia-------dash-----: 3.96e-18 -0.927720 5.99e-121 -0.921444 0.063664 ( 0.045493) 0.985108 ( 0.027449) 0.059060 0.991742 --->beagle1-----beagle2--: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 0.998967 ( 0.007118) 1.000000 1.000000 --->beagle1-----plink----: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 0.999990 ( 3.07e-05) 1.000000 1.000000 --->beagle1-----germline1: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 0.985112 ( 0.027447) 1.000000 0.991742 --->beagle1-----germline2: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 0.022842 ( 0.003418) 1.000000 0.023277 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 0.985108 ( 0.027449) 1.000000 0.991742 --->beagle2-----plink----: 1e+00 0.000000 1.53e-01 -0.001023 0.998967 ( 0.007118) 0.999990 ( 3.07e-05) 1.000000 1.000000 --->beagle2-----germline1: 8.7e-16 0.008273 2.66e-06 0.013854 0.998967 ( 0.007118) 0.985112 ( 0.027447) 1.000000 0.991742 --->beagle2-----germline2: 3.96e-18 0.976585 4.51e-213 0.976124 0.998967 ( 0.007118) 0.022842 ( 0.003418) 1.000000 0.023277 --->beagle2-----dash-----: 8.7e-16 0.008282 2.65e-06 0.013859 0.998967 ( 0.007118) 0.985108 ( 0.027449) 1.000000 0.991742 --->plink-------germline1: 3.96e-18 0.008303 4.21e-07 0.014877 0.999990 ( 3.07e-05) 0.985112 ( 0.027447) 1.000000 0.991742 --->plink-------germline2: 3.96e-18 0.976758 2.85e-245 0.977147 0.999990 ( 3.07e-05) 0.022842 ( 0.003418) 1.000000 0.023277 --->plink-------dash-----: 3.96e-18 0.008306 4.19e-07 0.014882 0.999990 ( 3.07e-05) 0.985108 ( 0.027449) 1.000000 0.991742 --->germline1---germline2: 3.95e-18 0.968405 3.41e-155 0.962270 0.985112 ( 0.027447) 0.022842 ( 0.003418) 0.991742 0.023277 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 0.985112 ( 0.027447) 0.985108 ( 0.027449) 0.991742 0.991742 --->germline2---dash-----: 3.95e-18 -0.968344 3.43e-155 -0.962266 0.022842 ( 0.003418) 0.985108 ( 0.027449) 0.023277 0.991742 ######FDRSnps###### --->fabia-------beagle1--: 7.44e-18 -0.198781 1.55e-16 -0.255315 0.725295 ( 0.257220) 0.980610 ( 0.001409) 0.801095 0.980700 --->fabia-------beagle2--: 7.44e-18 -0.198751 1.56e-16 -0.255294 0.725295 ( 0.257220) 0.980589 ( 0.001418) 0.801095 0.980612 --->fabia-------plink----: 7.44e-18 -0.198812 1.55e-16 -0.255314 0.725295 ( 0.257220) 0.980610 ( 0.001409) 0.801095 0.980700 --->fabia-------germline1: 7.44e-18 -0.198549 1.66e-16 -0.255064 0.725295 ( 0.257220) 0.980359 ( 0.001621) 0.801095 0.980249 --->fabia-------germline2: 2.98e-14 -0.216166 8.45e-14 -0.249526 0.725295 ( 0.257220) 0.974821 ( 0.129676) 0.801095 1.000000 --->fabia-------dash-----: 7.44e-18 -0.198549 1.66e-16 -0.255065 0.725295 ( 0.257220) 0.980360 ( 0.001625) 0.801095 0.980249 --->beagle1-----beagle2--: 1e+00 0.000000 1e+00 0.000000 0.980610 ( 0.001409) 0.980589 ( 0.001418) 0.980700 0.980612 --->beagle1-----plink----: 1e+00 0.000000 1e+00 0.000000 0.980610 ( 0.001409) 0.980610 ( 0.001409) 0.980700 0.980700 --->beagle1-----germline1: 7.67e-17 0.000175 1.82e-03 0.000251 0.980610 ( 0.001409) 0.980359 ( 0.001621) 0.980700 0.980249 --->beagle1-----germline2: 2.37e-13 -0.019324 6.57e-01 0.005789 0.980610 ( 0.001409) 0.974821 ( 0.129676) 0.980700 1.000000 --->beagle1-----dash-----: 7.67e-17 0.000134 2.05e-03 0.000250 0.980610 ( 0.001409) 0.980360 ( 0.001625) 0.980700 0.980249 --->beagle2-----plink----: 1e+00 0.000000 1e+00 0.000000 0.980589 ( 0.001418) 0.980610 ( 0.001409) 0.980612 0.980700 --->beagle2-----germline1: 1.32e-14 0.000183 4.26e-03 0.000230 0.980589 ( 0.001418) 0.980359 ( 0.001621) 0.980612 0.980249 --->beagle2-----germline2: 2.37e-13 -0.019333 6.58e-01 0.005768 0.980589 ( 0.001418) 0.974821 ( 0.129676) 0.980612 1.000000 --->beagle2-----dash-----: 1.32e-14 0.000147 4.73e-03 0.000229 0.980589 ( 0.001418) 0.980360 ( 0.001625) 0.980612 0.980249 --->plink-------germline1: 7.67e-17 0.000175 1.83e-03 0.000251 0.980610 ( 0.001409) 0.980359 ( 0.001621) 0.980700 0.980249 --->plink-------germline2: 2.37e-13 -0.019324 6.57e-01 0.005788 0.980610 ( 0.001409) 0.974821 ( 0.129676) 0.980700 1.000000 --->plink-------dash-----: 7.67e-17 0.000134 2.07e-03 0.000250 0.980610 ( 0.001409) 0.980360 ( 0.001625) 0.980700 0.980249 --->germline1---germline2: 2.38e-13 -0.019671 6.71e-01 0.005538 0.980359 ( 0.001621) 0.974821 ( 0.129676) 0.980249 1.000000 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 0.980359 ( 0.001621) 0.980360 ( 0.001625) 0.980249 0.980249 --->germline2---dash-----: 2.38e-13 0.019631 6.71e-01 -0.005539 0.974821 ( 0.129676) 0.980360 ( 0.001625) 1.000000 0.980249 ######specifitySnps###### --->fabia-------beagle1--: 1e+00 0.000000 1e+00 0.000000 0.936336 ( 0.045493) 0.000000 ( 0.000000) 0.940940 0.000000 --->fabia-------beagle2--: 3.94e-18 0.938237 1.76e-131 0.935303 0.936336 ( 0.045493) 0.001033 ( 0.007118) 0.940940 0.000000 --->fabia-------plink----: 3.94e-18 0.939407 3.97e-132 0.936326 0.936336 ( 0.045493) 1.02e-05 ( 3.07e-05) 0.940940 0.000000 --->fabia-------germline1: 3.96e-18 0.927742 5.97e-121 0.921448 0.936336 ( 0.045493) 0.014888 ( 0.027447) 0.940940 0.008258 --->fabia-------germline2: 9.59e-13 -0.037910 2.23e-14 -0.040821 0.936336 ( 0.045493) 0.977158 ( 0.003418) 0.940940 0.976723 --->fabia-------dash-----: 3.96e-18 0.927742 5.99e-121 0.921444 0.936336 ( 0.045493) 0.014892 ( 0.027449) 0.940940 0.008258 --->beagle1-----beagle2--: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.001033 ( 0.007118) 0.000000 0.000000 --->beagle1-----plink----: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 1.02e-05 ( 3.07e-05) 0.000000 0.000000 --->beagle1-----germline1: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.014888 ( 0.027447) 0.000000 0.008258 --->beagle1-----germline2: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.977158 ( 0.003418) 0.000000 0.976723 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.014892 ( 0.027449) 0.000000 0.008258 --->beagle2-----plink----: 1e+00 0.000000 1.53e-01 0.001023 0.001033 ( 0.007118) 1.02e-05 ( 3.07e-05) 0.000000 0.000000 --->beagle2-----germline1: 8.7e-16 -0.008269 2.66e-06 -0.013854 0.001033 ( 0.007118) 0.014888 ( 0.027447) 0.000000 0.008258 --->beagle2-----germline2: 3.96e-18 -0.976609 4.51e-213 -0.976124 0.001033 ( 0.007118) 0.977158 ( 0.003418) 0.000000 0.976723 --->beagle2-----dash-----: 8.7e-16 -0.008276 2.65e-06 -0.013859 0.001033 ( 0.007118) 0.014892 ( 0.027449) 0.000000 0.008258 --->plink-------germline1: 3.96e-18 -0.008293 4.21e-07 -0.014877 1.02e-05 ( 3.07e-05) 0.014888 ( 0.027447) 0.000000 0.008258 --->plink-------germline2: 3.96e-18 -0.976751 2.85e-245 -0.977147 1.02e-05 ( 3.07e-05) 0.977158 ( 0.003418) 0.000000 0.976723 --->plink-------dash-----: 3.96e-18 -0.008302 4.19e-07 -0.014882 1.02e-05 ( 3.07e-05) 0.014892 ( 0.027449) 0.000000 0.008258 --->germline1---germline2: 3.96e-18 -0.968344 3.41e-155 -0.962270 0.014888 ( 0.027447) 0.977158 ( 0.003418) 0.008258 0.976723 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 0.014888 ( 0.027447) 0.014892 ( 0.027449) 0.008258 0.008258 --->germline2---dash-----: 3.96e-18 0.968405 3.43e-155 0.962266 0.977158 ( 0.003418) 0.014892 ( 0.027449) 0.976723 0.008258 ######sensitivitySnps###### --->fabia-------beagle1--: 1e+00 0.000000 1e+00 0.000000 0.729031 ( 0.303538) 1.000000 ( 0.000000) 0.863142 1.000000 --->fabia-------beagle2--: 1e+00 0.000000 1e+00 0.000000 0.729031 ( 0.303538) 1.000000 ( 0.000000) 0.863142 1.000000 --->fabia-------plink----: 1e+00 0.000000 1e+00 0.000000 0.729031 ( 0.303538) 1.000000 ( 0.000000) 0.863142 1.000000 --->fabia-------germline1: 1.74e-16 -0.233570 6.45e-14 -0.268200 0.729031 ( 0.303538) 0.997232 ( 0.027684) 0.863142 1.000000 --->fabia-------germline2: 6.24e-17 0.792004 7.31e-39 0.698272 0.729031 ( 0.303538) 0.030760 ( 0.156920) 0.863142 0.000000 --->fabia-------dash-----: 1.79e-16 -0.233548 6.6e-14 -0.268144 0.729031 ( 0.303538) 0.997175 ( 0.028249) 0.863142 1.000000 --->beagle1-----beagle2--: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 1.000000 ( 0.000000) 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) 0.997232 ( 0.027684) 1.000000 1.000000 --->beagle1-----germline2: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 0.030760 ( 0.156920) 1.000000 0.000000 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 0.997175 ( 0.028249) 1.000000 1.000000 --->beagle2-----plink----: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 1.000000 ( 0.000000) 1.000000 1.000000 --->beagle2-----germline1: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 0.997232 ( 0.027684) 1.000000 1.000000 --->beagle2-----germline2: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 0.030760 ( 0.156920) 1.000000 0.000000 --->beagle2-----dash-----: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 0.997175 ( 0.028249) 1.000000 1.000000 --->plink-------germline1: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 0.997232 ( 0.027684) 1.000000 1.000000 --->plink-------germline2: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 0.030760 ( 0.156920) 1.000000 0.000000 --->plink-------dash-----: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 0.997175 ( 0.028249) 1.000000 1.000000 --->germline1---germline2: 1.1e-22 1.000000 3.85e-77 0.966472 0.997232 ( 0.027684) 0.030760 ( 0.156920) 1.000000 0.000000 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 0.997232 ( 0.027684) 0.997175 ( 0.028249) 1.000000 1.000000 --->germline2---dash-----: 1.09e-22 -1.000000 4.64e-77 -0.966415 0.030760 ( 0.156920) 0.997175 ( 0.028249) 0.000000 1.000000 ######trueNSnps###### --->fabia-------beagle1--: 1e+00 0 1e+00 0 9182 ( 445) 0 ( 0) 9226 0 --->fabia-------beagle2--: 3.96e-18 9202 1.53e-131 9172 9182 ( 445) 10.1 ( 69.8) 9226 0 --->fabia-------plink----: 3.96e-18 9213 3.41e-132 9182 9182 ( 445) 0.1 ( 0.302) 9226 0 --->fabia-------germline1: 3.96e-18 9097 4.96e-121 9036 9182 ( 445) 146 ( 269) 9226 81 --->fabia-------germline2: 9.47e-13 -372 2.24e-14 -400 9182 ( 445) 9582 ( 37.7) 9226 9580 --->fabia-------dash-----: 3.96e-18 9097 4.98e-121 9036 9182 ( 445) 146 ( 269) 9226 81 --->beagle1-----beagle2--: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 10.130000 (69.783454) 0.000000 0.000000 --->beagle1-----plink----: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.100000 ( 0.301511) 0.000000 0.000000 --->beagle1-----germline1: 1e+00 0 1e+00 0 0 ( 0) 146 ( 269) 0 81 --->beagle1-----germline2: 1e+00 0 1e+00 0 0 ( 0) 9582 ( 37.7) 0 9580 --->beagle1-----dash-----: 1e+00 0 1e+00 0 0 ( 0) 146 ( 269) 0 81 --->beagle2-----plink----: 1e+00 0.000000 1.53e-01 10.030000 10.130000 (69.783454) 0.100000 ( 0.301511) 0.000000 0.000000 --->beagle2-----germline1: 8.67e-16 -81 2.68e-06 -136 10.1 ( 69.8) 146 ( 269) 0 81 --->beagle2-----germline2: 3.94e-18 -9577 1.04e-211 -9572 10.1 ( 69.8) 9582 ( 37.7) 0 9580 --->beagle2-----dash-----: 8.67e-16 -81 2.66e-06 -136 10.1 ( 69.8) 146 ( 269) 0 81 --->plink-------germline1: 3.94e-18 -81.5 4.23e-07 -146 0.1 ( 0.302) 146 ( 269) 0 81 --->plink-------germline2: 3.94e-18 -9578 3.27e-240 -9582 0.1 ( 0.302) 9582 ( 37.7) 0 9580 --->plink-------dash-----: 3.94e-18 -81.5 4.21e-07 -146 0.1 ( 0.302) 146 ( 269) 0 81 --->germline1---germline2: 3.93e-18 -9494 2.59e-155 -9436 146 ( 269) 9582 ( 37.7) 81 9580 --->germline1---dash-----: 1e+00 0 1.03e-01 -0.04 146 ( 269) 146 ( 269) 81 81 --->germline2---dash-----: 3.93e-18 9494 2.61e-155 9436 9582 ( 37.7) 146 ( 269) 9580 81 ######falsePSnps###### --->fabia-------beagle1--: 3.96e-18 -9213 3.44e-132 -9182 624 ( 446) 9806 ( 14.1) 579 9807 --->fabia-------beagle2--: 3.96e-18 -9202 1.53e-131 -9172 624 ( 446) 9796 ( 71.4) 579 9806 --->fabia-------plink----: 3.96e-18 -9213 3.41e-132 -9182 624 ( 446) 9806 ( 14.1) 579 9807 --->fabia-------germline1: 3.96e-18 -9097 4.96e-121 -9036 624 ( 446) 9660 ( 268) 579 9725 --->fabia-------germline2: 9.47e-13 372 2.24e-14 400 624 ( 446) 224 ( 33.5) 579 228 --->fabia-------dash-----: 3.96e-18 -9097 4.98e-121 -9036 624 ( 446) 9660 ( 268) 579 9725 --->beagle1-----beagle2--: 1e+00 0 1.5e-01 10.1 9806 ( 14.1) 9796 ( 71.4) 9807 9806 --->beagle1-----plink----: 1e+00 0 1.27e-03 0.1 9806 ( 14.1) 9806 ( 14.1) 9807 9807 --->beagle1-----germline1: 3.94e-18 81.5 4.16e-07 146 9806 ( 14.1) 9660 ( 268) 9807 9725 --->beagle1-----germline2: 3.94e-18 9578 3.76e-240 9582 9806 ( 14.1) 224 ( 33.5) 9807 228 --->beagle1-----dash-----: 3.94e-18 81.5 4.14e-07 146 9806 ( 14.1) 9660 ( 268) 9807 9725 --->beagle2-----plink----: 1e+00 0 1.53e-01 -10 9796 ( 71.4) 9806 ( 14.1) 9806 9807 --->beagle2-----germline1: 8.67e-16 81 2.68e-06 136 9796 ( 71.4) 9660 ( 268) 9806 9725 --->beagle2-----germline2: 3.94e-18 9577 1.04e-211 9572 9796 ( 71.4) 224 ( 33.5) 9806 228 --->beagle2-----dash-----: 8.67e-16 81 2.66e-06 136 9796 ( 71.4) 9660 ( 268) 9806 9725 --->plink-------germline1: 3.94e-18 81.5 4.23e-07 146 9806 ( 14.1) 9660 ( 268) 9807 9725 --->plink-------germline2: 3.94e-18 9578 3.27e-240 9582 9806 ( 14.1) 224 ( 33.5) 9807 228 --->plink-------dash-----: 3.94e-18 81.5 4.21e-07 146 9806 ( 14.1) 9660 ( 268) 9807 9725 --->germline1---germline2: 3.93e-18 9494 2.59e-155 9436 9660 ( 268) 224 ( 33.5) 9725 228 --->germline1---dash-----: 1e+00 0 1.03e-01 0.04 9660 ( 268) 9660 ( 268) 9725 9725 --->germline2---dash-----: 3.93e-18 -9494 2.61e-155 -9436 224 ( 33.5) 9660 ( 268) 228 9725 ######falseNSnps###### --->fabia-------beagle1--: 1e+00 0 1e+00 0 52 ( 57.8) 0 ( 0) 26 0 --->fabia-------beagle2--: 1e+00 0 1e+00 0 52 ( 57.8) 0 ( 0) 26 0 --->fabia-------plink----: 1e+00 0 1e+00 0 52 ( 57.8) 0 ( 0) 26 0 --->fabia-------germline1: 1.68e-16 45.5 4.23e-14 51.5 52 ( 57.8) 0.49 ( 4.9) 26 0 --->fabia-------germline2: 6.22e-17 -154 2.65e-38 -136 52 ( 57.8) 188 ( 33.7) 26 192 --->fabia-------dash-----: 1.71e-16 45.5 4.33e-14 51.5 52 ( 57.8) 0.5 ( 5) 26 0 --->beagle1-----beagle2--: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.000000 ( 0.000000) 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) 0.490000 ( 4.900000) 0.000000 0.000000 --->beagle1-----germline2: 1e+00 0 1e+00 0 0 ( 0) 188 ( 33.7) 0 192 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.500000 ( 5.000000) 0.000000 0.000000 --->beagle2-----plink----: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.000000 ( 0.000000) 0.000000 0.000000 --->beagle2-----germline1: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.490000 ( 4.900000) 0.000000 0.000000 --->beagle2-----germline2: 1e+00 0 1e+00 0 0 ( 0) 188 ( 33.7) 0 192 --->beagle2-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.500000 ( 5.000000) 0.000000 0.000000 --->plink-------germline1: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.490000 ( 4.900000) 0.000000 0.000000 --->plink-------germline2: 1e+00 0 1e+00 0 0 ( 0) 188 ( 33.7) 0 192 --->plink-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.500000 ( 5.000000) 0.000000 0.000000 --->germline1---germline2: 8.38e-18 -194 9.58e-74 -188 0.49 ( 4.9) 188 ( 33.7) 0 192 --->germline1---dash-----: 1e+00 0.000000 3.2e-01 -0.010000 0.490000 ( 4.900000) 0.500000 ( 5.000000) 0.000000 0.000000 --->germline2---dash-----: 5.91e-18 194 1.11e-73 188 188 ( 33.7) 0.5 ( 5) 192 0 ######truePSnps###### --->fabia-------beagle1--: 3.85e-17 -46.5 1.69e-14 -52 142 ( 60.1) 194 ( 14.1) 162 193 --->fabia-------beagle2--: 3.85e-17 -46.5 1.69e-14 -52 142 ( 60.1) 194 ( 14.1) 162 193 --->fabia-------plink----: 3.85e-17 -46.5 1.69e-14 -52 142 ( 60.1) 194 ( 14.1) 162 193 --->fabia-------germline1: 1.68e-16 -45.5 4.23e-14 -51.5 142 ( 60.1) 193 ( 15.5) 162 193 --->fabia-------germline2: 6.22e-17 154 2.65e-38 136 142 ( 60.1) 5.79 ( 29.6) 162 0 --->fabia-------dash-----: 1.71e-16 -45.5 4.33e-14 -51.5 142 ( 60.1) 193 ( 15.5) 162 193 --->beagle1-----beagle2--: 1e+00 0 1e+00 0 194 ( 14.1) 194 ( 14.1) 193 193 --->beagle1-----plink----: 1e+00 0 1e+00 0 194 ( 14.1) 194 ( 14.1) 193 193 --->beagle1-----germline1: 1e+00 0 3.2e-01 0.49 194 ( 14.1) 193 ( 15.5) 193 193 --->beagle1-----germline2: 5.73e-18 194 1.28e-76 188 194 ( 14.1) 5.79 ( 29.6) 193 0 --->beagle1-----dash-----: 1e+00 0 3.2e-01 0.5 194 ( 14.1) 193 ( 15.5) 193 193 --->beagle2-----plink----: 1e+00 0 1e+00 0 194 ( 14.1) 194 ( 14.1) 193 193 --->beagle2-----germline1: 1e+00 0 3.2e-01 0.49 194 ( 14.1) 193 ( 15.5) 193 193 --->beagle2-----germline2: 5.73e-18 194 1.28e-76 188 194 ( 14.1) 5.79 ( 29.6) 193 0 --->beagle2-----dash-----: 1e+00 0 3.2e-01 0.5 194 ( 14.1) 193 ( 15.5) 193 193 --->plink-------germline1: 1e+00 0 3.2e-01 0.49 194 ( 14.1) 193 ( 15.5) 193 193 --->plink-------germline2: 5.73e-18 194 1.28e-76 188 194 ( 14.1) 5.79 ( 29.6) 193 0 --->plink-------dash-----: 1e+00 0 3.2e-01 0.5 194 ( 14.1) 193 ( 15.5) 193 193 --->germline1---germline2: 8.38e-18 194 9.58e-74 188 193 ( 15.5) 5.79 ( 29.6) 193 0 --->germline1---dash-----: 1e+00 0 3.2e-01 0.01 193 ( 15.5) 193 ( 15.5) 193 193 --->germline2---dash-----: 5.91e-18 -194 1.11e-73 -188 5.79 ( 29.6) 193 ( 15.5) 0 193 ######MatthewsSample###### --->fabia-------beagle1--: 8.14e-18 0.369086 6.27e-31 0.395772 0.411373 ( 0.239858) 0.015601 ( 0.037222) 0.363649 0.026988 --->fabia-------beagle2--: 7.67e-18 0.357527 4.56e-30 0.386430 0.411373 ( 0.239858) 0.024944 ( 0.045460) 0.363649 0.018676 --->fabia-------plink----: 1.52e-17 0.380563 2.93e-31 0.409581 0.411373 ( 0.239858) 0.001792 ( 0.023724) 0.363649 0.004262 --->fabia-------germline1: 1e+00 0.000000 1e+00 0.000000 0.411373 ( 0.239858) 0.000000 ( 0.000000) 0.363649 0.000000 --->fabia-------germline2: 8.91e-18 0.383249 4.39e-31 0.413398 0.411373 ( 0.239858) -0.002025 ( 0.034452) 0.363649 0.015962 --->fabia-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.411373 ( 0.239858) 0.000000 ( 0.000000) 0.363649 0.000000 --->beagle1-----beagle2--: 2.99e-03 -0.010744 1.18e-02 -0.009342 0.015601 ( 0.037222) 0.024944 ( 0.045460) 0.026988 0.018676 --->beagle1-----plink----: 2.76e-03 0.012897 3.68e-03 0.013809 0.015601 ( 0.037222) 0.001792 ( 0.023724) 0.026988 0.004262 --->beagle1-----germline1: 1e+00 0.000000 1e+00 0.000000 0.015601 ( 0.037222) 0.000000 ( 0.000000) 0.026988 0.000000 --->beagle1-----germline2: 7.96e-04 0.018199 7.1e-04 0.017626 0.015601 ( 0.037222) -0.002025 ( 0.034452) 0.026988 0.015962 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.015601 ( 0.037222) 0.000000 ( 0.000000) 0.026988 0.000000 --->beagle2-----plink----: 4.25e-05 0.019657 3.21e-05 0.023152 0.024944 ( 0.045460) 0.001792 ( 0.023724) 0.018676 0.004262 --->beagle2-----germline1: 1e+00 0.000000 1e+00 0.000000 0.024944 ( 0.045460) 0.000000 ( 0.000000) 0.018676 0.000000 --->beagle2-----germline2: 5.46e-05 0.025446 1.36e-05 0.026969 0.024944 ( 0.045460) -0.002025 ( 0.034452) 0.018676 0.015962 --->beagle2-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.024944 ( 0.045460) 0.000000 ( 0.000000) 0.018676 0.000000 --->plink-------germline1: 1e+00 0.000000 1e+00 0.000000 0.001792 ( 0.023724) 0.000000 ( 0.000000) 0.004262 0.000000 --->plink-------germline2: 2.46e-01 0.004088 3.76e-01 0.003817 0.001792 ( 0.023724) -0.002025 ( 0.034452) 0.004262 0.015962 --->plink-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.001792 ( 0.023724) 0.000000 ( 0.000000) 0.004262 0.000000 --->germline1---germline2: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) -0.002025 ( 0.034452) 0.000000 0.015962 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.000000 ( 0.000000) 0.000000 0.000000 --->germline2---dash-----: 1e+00 0.000000 1e+00 0.000000 -0.002025 ( 0.034452) 0.000000 ( 0.000000) 0.015962 0.000000 ######F1Sample###### --->fabia-------beagle1--: 1.52e-17 0.253657 1.49e-20 0.305228 0.318897 ( 0.259932) 0.013669 ( 0.004297) 0.237647 0.014793 --->fabia-------beagle2--: 1.72e-17 0.252822 2.75e-20 0.301163 0.318897 ( 0.259932) 0.017734 ( 0.010995) 0.237647 0.016260 --->fabia-------plink----: 1.52e-17 0.255554 1.3e-20 0.306969 0.318897 ( 0.259932) 0.011928 ( 0.000282) 0.237647 0.011964 --->fabia-------germline1: 1.5e-17 0.255597 1.3e-20 0.306989 0.318897 ( 0.259932) 0.011909 ( 0.000198) 0.237647 0.011928 --->fabia-------germline2: 1.52e-17 0.254741 1.31e-20 0.307029 0.318897 ( 0.259932) 0.011868 ( 0.001444) 0.237647 0.012442 --->fabia-------dash-----: 1.5e-17 0.255597 1.3e-20 0.306989 0.318897 ( 0.259932) 0.011909 ( 0.000198) 0.237647 0.011928 --->beagle1-----beagle2--: 7.31e-05 -0.003989 1.47e-05 -0.004065 0.013669 ( 0.004297) 0.017734 ( 0.010995) 0.014793 0.016260 --->beagle1-----plink----: 6.8e-05 0.001873 1.05e-04 0.001741 0.013669 ( 0.004297) 0.011928 ( 0.000282) 0.014793 0.011964 --->beagle1-----germline1: 4.86e-05 0.001902 8.12e-05 0.001761 0.013669 ( 0.004297) 0.011909 ( 0.000198) 0.014793 0.011928 --->beagle1-----germline2: 1.34e-04 0.001996 1.21e-04 0.001801 0.013669 ( 0.004297) 0.011868 ( 0.001444) 0.014793 0.012442 --->beagle1-----dash-----: 4.86e-05 0.001902 8.12e-05 0.001761 0.013669 ( 0.004297) 0.011909 ( 0.000198) 0.014793 0.011928 --->beagle2-----plink----: 6.94e-06 0.005404 7.86e-07 0.005806 0.017734 ( 0.010995) 0.011928 ( 0.000282) 0.016260 0.011964 --->beagle2-----germline1: 5.79e-06 0.005394 7.03e-07 0.005826 0.017734 ( 0.010995) 0.011909 ( 0.000198) 0.016260 0.011928 --->beagle2-----germline2: 5.53e-06 0.005512 8.44e-07 0.005866 0.017734 ( 0.010995) 0.011868 ( 0.001444) 0.016260 0.012442 --->beagle2-----dash-----: 5.79e-06 0.005394 7.03e-07 0.005826 0.017734 ( 0.010995) 0.011909 ( 0.000198) 0.016260 0.011928 --->plink-------germline1: 1e+00 0.000000 1e+00 0.000000 0.011928 ( 0.000282) 0.011909 ( 0.000198) 0.011964 0.011928 --->plink-------germline2: 6.94e-01 5.22e-05 1e+00 0.000000 0.011928 ( 0.000282) 0.011868 ( 0.001444) 0.011964 0.012442 --->plink-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.011928 ( 0.000282) 0.011909 ( 0.000198) 0.011964 0.011928 --->germline1---germline2: 8.03e-01 2.96e-05 1e+00 0.000000 0.011909 ( 0.000198) 0.011868 ( 0.001444) 0.011928 0.012442 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 0.011909 ( 0.000198) 0.011909 ( 0.000198) 0.011928 0.011928 --->germline2---dash-----: 8.03e-01 -2.99e-05 1e+00 0.000000 0.011868 ( 0.001444) 0.011909 ( 0.000198) 0.012442 0.011928 ######accuracySample###### --->fabia-------beagle1--: 3.95e-18 0.623533 1.72e-124 0.622170 0.981960 ( 0.012267) 0.359790 ( 0.031572) 0.984250 0.362000 --->fabia-------beagle2--: 3.95e-18 0.271228 6.58e-90 0.270490 0.981960 ( 0.012267) 0.711470 ( 0.029893) 0.984250 0.708500 --->fabia-------plink----: 3.94e-18 0.972982 1.34e-188 0.972690 0.981960 ( 0.012267) 0.009270 ( 0.002034) 0.984250 0.009000 --->fabia-------germline1: 3.92e-18 0.976262 2.86e-190 0.975970 0.981960 ( 0.012267) 0.005990 ( 1e-04) 0.984250 0.006000 --->fabia-------germline2: 3.95e-18 0.903512 1.81e-133 0.898540 0.981960 ( 0.012267) 0.083420 ( 0.041630) 0.984250 0.075000 --->fabia-------dash-----: 3.92e-18 0.976262 2.86e-190 0.975970 0.981960 ( 0.012267) 0.005990 ( 1e-04) 0.984250 0.006000 --->beagle1-----beagle2--: 3.95e-18 -0.351512 2.1e-121 -0.351680 0.359790 ( 0.031572) 0.711470 ( 0.029893) 0.362000 0.708500 --->beagle1-----plink----: 3.94e-18 0.348987 1.93e-106 0.350520 0.359790 ( 0.031572) 0.009270 ( 0.002034) 0.362000 0.009000 --->beagle1-----germline1: 3.94e-18 0.351956 4.25e-106 0.353800 0.359790 ( 0.031572) 0.005990 ( 1e-04) 0.362000 0.006000 --->beagle1-----germline2: 3.95e-18 0.279081 1.4e-73 0.276370 0.359790 ( 0.031572) 0.083420 ( 0.041630) 0.362000 0.075000 --->beagle1-----dash-----: 3.94e-18 0.351956 4.25e-106 0.353800 0.359790 ( 0.031572) 0.005990 ( 1e-04) 0.362000 0.006000 --->beagle2-----plink----: 3.95e-18 0.701025 2e-138 0.702200 0.711470 ( 0.029893) 0.009270 ( 0.002034) 0.708500 0.009000 --->beagle2-----germline1: 3.95e-18 0.704480 5.48e-138 0.705480 0.711470 ( 0.029893) 0.005990 ( 1e-04) 0.708500 0.006000 --->beagle2-----germline2: 3.95e-18 0.630461 3.77e-110 0.628050 0.711470 ( 0.029893) 0.083420 ( 0.041630) 0.708500 0.075000 --->beagle2-----dash-----: 3.95e-18 0.704480 5.48e-138 0.705480 0.711470 ( 0.029893) 0.005990 ( 1e-04) 0.708500 0.006000 --->plink-------germline1: 4.25e-17 0.003453 1.39e-29 0.003280 0.009270 ( 0.002034) 0.005990 ( 1e-04) 0.009000 0.006000 --->plink-------germline2: 3.95e-18 -0.068506 2.56e-32 -0.074150 0.009270 ( 0.002034) 0.083420 ( 0.041630) 0.009000 0.075000 --->plink-------dash-----: 4.25e-17 0.003453 1.39e-29 0.003280 0.009270 ( 0.002034) 0.005990 ( 1e-04) 0.009000 0.006000 --->germline1---germline2: 3.95e-18 -0.072054 4.55e-34 -0.077430 0.005990 ( 1e-04) 0.083420 ( 0.041630) 0.006000 0.075000 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 0.005990 ( 1e-04) 0.005990 ( 1e-04) 0.006000 0.006000 --->germline2---dash-----: 3.95e-18 0.072020 4.55e-34 0.077430 0.083420 ( 0.041630) 0.005990 ( 1e-04) 0.075000 0.006000 ######FPRSample###### --->fabia-------beagle1--: 3.96e-18 -0.626013 1.79e-124 -0.624682 0.017823 ( 0.012465) 0.642505 ( 0.031760) 0.015797 0.641851 --->fabia-------beagle2--: 3.96e-18 -0.269702 1.93e-89 -0.269028 0.017823 ( 0.012465) 0.286851 ( 0.030100) 0.015797 0.289235 --->fabia-------plink----: 3.95e-18 -0.979175 3.56e-188 -0.978877 0.017823 ( 0.012465) 0.996700 ( 0.002038) 0.015797 0.996982 --->fabia-------germline1: 3.92e-18 -0.982499 7.48e-190 -0.982187 0.017823 ( 0.012465) 1.000010 ( 0.000101) 0.015797 1.000000 --->fabia-------germline2: 3.96e-18 -0.909007 2.76e-133 -0.903796 0.017823 ( 0.012465) 0.921620 ( 0.042021) 0.015797 0.929577 --->fabia-------dash-----: 3.92e-18 -0.982499 7.48e-190 -0.982187 0.017823 ( 0.012465) 1.000010 ( 0.000101) 0.015797 1.000000 --->beagle1-----beagle2--: 3.95e-18 0.355631 1.61e-121 0.355654 0.642505 ( 0.031760) 0.286851 ( 0.030100) 0.641851 0.289235 --->beagle1-----plink----: 3.95e-18 -0.352606 1.21e-106 -0.354195 0.642505 ( 0.031760) 0.996700 ( 0.002038) 0.641851 0.996982 --->beagle1-----germline1: 3.94e-18 -0.355673 2.73e-106 -0.357505 0.642505 ( 0.031760) 1.000010 ( 0.000101) 0.641851 1.000000 --->beagle1-----germline2: 3.95e-18 -0.281713 1.55e-73 -0.279115 0.642505 ( 0.031760) 0.921620 ( 0.042021) 0.641851 0.929577 --->beagle1-----dash-----: 3.94e-18 -0.355673 2.73e-106 -0.357505 0.642505 ( 0.031760) 1.000010 ( 0.000101) 0.641851 1.000000 --->beagle2-----plink----: 3.95e-18 -0.708709 1.33e-138 -0.709849 0.286851 ( 0.030100) 0.996700 ( 0.002038) 0.289235 0.996982 --->beagle2-----germline1: 3.95e-18 -0.711801 3.71e-138 -0.713159 0.286851 ( 0.030100) 1.000010 ( 0.000101) 0.289235 1.000000 --->beagle2-----germline2: 3.95e-18 -0.637347 4.8e-110 -0.634769 0.286851 ( 0.030100) 0.921620 ( 0.042021) 0.289235 0.929577 --->beagle2-----dash-----: 3.95e-18 -0.711801 3.71e-138 -0.713159 0.286851 ( 0.030100) 1.000010 ( 0.000101) 0.289235 1.000000 --->plink-------germline1: 4.27e-17 -0.003494 8.14e-30 -0.003310 0.996700 ( 0.002038) 1.000010 ( 0.000101) 0.996982 1.000000 --->plink-------germline2: 3.95e-18 0.069480 2.05e-32 0.075080 0.996700 ( 0.002038) 0.921620 ( 0.042021) 0.996982 0.929577 --->plink-------dash-----: 4.27e-17 -0.003494 8.14e-30 -0.003310 0.996700 ( 0.002038) 1.000010 ( 0.000101) 0.996982 1.000000 --->germline1---germline2: 3.94e-18 0.072971 3.61e-34 0.078390 1.000010 ( 0.000101) 0.921620 ( 0.042021) 1.000000 0.929577 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 1.000010 ( 0.000101) 1.000010 ( 0.000101) 1.000000 1.000000 --->germline2---dash-----: 3.94e-18 -0.072958 3.61e-34 -0.078390 0.921620 ( 0.042021) 1.000010 ( 0.000101) 0.929577 1.000000 ######FDRSample###### --->fabia-------beagle1--: 1.17e-17 -0.156659 8.59e-14 -0.231335 0.761767 ( 0.267121) 0.993101 ( 0.002169) 0.862051 0.992537 --->fabia-------beagle2--: 1.35e-17 -0.155721 1.25e-13 -0.229178 0.761767 ( 0.267121) 0.990945 ( 0.005619) 0.862051 0.991667 --->fabia-------plink----: 1.16e-17 -0.156933 7.64e-14 -0.232233 0.761767 ( 0.267121) 0.994000 ( 0.000142) 0.862051 0.993982 --->fabia-------germline1: 1.15e-17 -0.156985 7.63e-14 -0.232243 0.761767 ( 0.267121) 0.994010 ( 1e-04) 0.862051 0.994000 --->fabia-------germline2: 1.17e-17 -0.156637 7.7e-14 -0.232261 0.761767 ( 0.267121) 0.994027 ( 0.000727) 0.862051 0.993740 --->fabia-------dash-----: 1.15e-17 -0.156985 7.63e-14 -0.232243 0.761767 ( 0.267121) 0.994010 ( 1e-04) 0.862051 0.994000 --->beagle1-----beagle2--: 4.45e-05 0.002102 7.57e-06 0.002157 0.993101 ( 0.002169) 0.990945 ( 0.005619) 0.992537 0.991667 --->beagle1-----plink----: 5e-05 -0.000948 7.55e-05 -0.000899 0.993101 ( 0.002169) 0.994000 ( 0.000142) 0.992537 0.993982 --->beagle1-----germline1: 3.4e-05 -0.000962 5.77e-05 -0.000909 0.993101 ( 0.002169) 0.994010 ( 1e-04) 0.992537 0.994000 --->beagle1-----germline2: 1.1e-04 -0.001004 9.25e-05 -0.000926 0.993101 ( 0.002169) 0.994027 ( 0.000727) 0.992537 0.993740 --->beagle1-----dash-----: 3.4e-05 -0.000962 5.77e-05 -0.000909 0.993101 ( 0.002169) 0.994010 ( 1e-04) 0.992537 0.994000 --->beagle2-----plink----: 3.6e-06 -0.002830 4.01e-07 -0.003055 0.990945 ( 0.005619) 0.994000 ( 0.000142) 0.991667 0.993982 --->beagle2-----germline1: 3.15e-06 -0.002844 3.58e-07 -0.003065 0.990945 ( 0.005619) 0.994010 ( 1e-04) 0.991667 0.994000 --->beagle2-----germline2: 2.8e-06 -0.002895 4.43e-07 -0.003083 0.990945 ( 0.005619) 0.994027 ( 0.000727) 0.991667 0.993740 --->beagle2-----dash-----: 3.15e-06 -0.002844 3.58e-07 -0.003065 0.990945 ( 0.005619) 0.994010 ( 1e-04) 0.991667 0.994000 --->plink-------germline1: 1e+00 0.000000 1e+00 0.000000 0.994000 ( 0.000142) 0.994010 ( 1e-04) 0.993982 0.994000 --->plink-------germline2: 7.19e-01 -5.11e-05 1e+00 0.000000 0.994000 ( 0.000142) 0.994027 ( 0.000727) 0.993982 0.993740 --->plink-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.994000 ( 0.000142) 0.994010 ( 1e-04) 0.993982 0.994000 --->germline1---germline2: 8.35e-01 -3.91e-05 1e+00 0.000000 0.994010 ( 1e-04) 0.994027 ( 0.000727) 0.994000 0.993740 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 0.994010 ( 1e-04) 0.994010 ( 1e-04) 0.994000 0.994000 --->germline2---dash-----: 8.35e-01 3.91e-05 1e+00 0.000000 0.994027 ( 0.000727) 0.994010 ( 1e-04) 0.993740 0.994000 ######specifitySample###### --->fabia-------beagle1--: 3.96e-18 0.626010 1.83e-124 0.624672 0.982177 ( 0.012465) 0.357505 ( 0.031763) 0.984203 0.358149 --->fabia-------beagle2--: 3.96e-18 0.269722 2e-89 0.269018 0.982177 ( 0.012465) 0.713159 ( 0.030105) 0.984203 0.710765 --->fabia-------plink----: 3.95e-18 0.979120 4e-188 0.978867 0.982177 ( 0.012465) 0.003310 ( 0.002029) 0.984203 0.003018 --->fabia-------germline1: 1e+00 0.000000 1e+00 0.000000 0.982177 ( 0.012465) 0.000000 ( 0.000000) 0.984203 0.000000 --->fabia-------germline2: 3.96e-18 0.908985 2.86e-133 0.903786 0.982177 ( 0.012465) 0.078390 ( 0.042032) 0.984203 0.070423 --->fabia-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.982177 ( 0.012465) 0.000000 ( 0.000000) 0.984203 0.000000 --->beagle1-----beagle2--: 3.95e-18 -0.355582 1.61e-121 -0.355654 0.357505 ( 0.031763) 0.713159 ( 0.030105) 0.358149 0.710765 --->beagle1-----plink----: 3.95e-18 0.352588 1.21e-106 0.354195 0.357505 ( 0.031763) 0.003310 ( 0.002029) 0.358149 0.003018 --->beagle1-----germline1: 1e+00 0.000000 1e+00 0.000000 0.357505 ( 0.031763) 0.000000 ( 0.000000) 0.358149 0.000000 --->beagle1-----germline2: 3.96e-18 0.281753 1.55e-73 0.279115 0.357505 ( 0.031763) 0.078390 ( 0.042032) 0.358149 0.070423 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.357505 ( 0.031763) 0.000000 ( 0.000000) 0.358149 0.000000 --->beagle2-----plink----: 3.95e-18 0.708717 1.33e-138 0.709849 0.713159 ( 0.030105) 0.003310 ( 0.002029) 0.710765 0.003018 --->beagle2-----germline1: 1e+00 0.000000 1e+00 0.000000 0.713159 ( 0.030105) 0.000000 ( 0.000000) 0.710765 0.000000 --->beagle2-----germline2: 3.96e-18 0.637341 4.8e-110 0.634769 0.713159 ( 0.030105) 0.078390 ( 0.042032) 0.710765 0.070423 --->beagle2-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.713159 ( 0.030105) 0.000000 ( 0.000000) 0.710765 0.000000 --->plink-------germline1: 1e+00 0.000000 1e+00 0.000000 0.003310 ( 0.002029) 0.000000 ( 0.000000) 0.003018 0.000000 --->plink-------germline2: 3.95e-18 -0.069488 2.05e-32 -0.075080 0.003310 ( 0.002029) 0.078390 ( 0.042032) 0.003018 0.070423 --->plink-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.003310 ( 0.002029) 0.000000 ( 0.000000) 0.003018 0.000000 --->germline1---germline2: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.078390 ( 0.042032) 0.000000 0.070423 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.000000 ( 0.000000) 0.000000 0.000000 --->germline2---dash-----: 1e+00 0.000000 1e+00 0.000000 0.078390 ( 0.042032) 0.000000 ( 0.000000) 0.070423 0.000000 ######sensitivitySample###### --->fabia-------beagle1--: 3.47e-06 0.250001 1.52e-06 0.171667 0.910000 ( 0.287623) 0.738333 ( 0.229984) 1.000000 0.833333 --->fabia-------beagle2--: 1.4e-15 0.500019 4.98e-25 0.478333 0.910000 ( 0.287623) 0.431667 ( 0.264951) 1.000000 0.333333 --->fabia-------plink----: 1e+00 0.000000 3.49e-03 -0.086667 0.910000 ( 0.287623) 0.996667 ( 0.023451) 1.000000 1.000000 --->fabia-------germline1: 1e+00 0.000000 2.84e-03 -0.088333 0.910000 ( 0.287623) 0.998333 ( 0.016667) 1.000000 1.000000 --->fabia-------germline2: 1e+00 0.000000 8.28e-01 -0.006667 0.910000 ( 0.287623) 0.916667 ( 0.112367) 1.000000 1.000000 --->fabia-------dash-----: 1e+00 0.000000 2.84e-03 -0.088333 0.910000 ( 0.287623) 0.998333 ( 0.016667) 1.000000 1.000000 --->beagle1-----beagle2--: 4.78e-16 0.333406 1.64e-25 0.306667 0.738333 ( 0.229984) 0.431667 ( 0.264951) 0.833333 0.333333 --->beagle1-----plink----: 1.16e-13 -0.333381 3.18e-19 -0.258333 0.738333 ( 0.229984) 0.996667 ( 0.023451) 0.833333 1.000000 --->beagle1-----germline1: 9.68e-14 -0.333375 1.21e-19 -0.260000 0.738333 ( 0.229984) 0.998333 ( 0.016667) 0.833333 1.000000 --->beagle1-----germline2: 3.46e-08 -0.250079 5.14e-10 -0.178333 0.738333 ( 0.229984) 0.916667 ( 0.112367) 0.833333 1.000000 --->beagle1-----dash-----: 9.68e-14 -0.333375 1.21e-19 -0.260000 0.738333 ( 0.229984) 0.998333 ( 0.016667) 0.833333 1.000000 --->beagle2-----plink----: 6.23e-18 -0.583297 1.54e-38 -0.565000 0.431667 ( 0.264951) 0.996667 ( 0.023451) 0.333333 1.000000 --->beagle2-----germline1: 6.18e-18 -0.583316 6.57e-39 -0.566667 0.431667 ( 0.264951) 0.998333 ( 0.016667) 0.333333 1.000000 --->beagle2-----germline2: 1.48e-16 -0.500014 1.85e-29 -0.485000 0.431667 ( 0.264951) 0.916667 ( 0.112367) 0.333333 1.000000 --->beagle2-----dash-----: 6.18e-18 -0.583316 6.57e-39 -0.566667 0.431667 ( 0.264951) 0.998333 ( 0.016667) 0.333333 1.000000 --->plink-------germline1: 1e+00 0.000000 3.2e-01 -0.001667 0.996667 ( 0.023451) 0.998333 ( 0.016667) 1.000000 1.000000 --->plink-------germline2: 1e+00 0.000000 1.72e-10 0.080000 0.996667 ( 0.023451) 0.916667 ( 0.112367) 1.000000 1.000000 --->plink-------dash-----: 1e+00 0.000000 3.2e-01 -0.001667 0.996667 ( 0.023451) 0.998333 ( 0.016667) 1.000000 1.000000 --->germline1---germline2: 1e+00 0.000000 3.8e-11 0.081667 0.998333 ( 0.016667) 0.916667 ( 0.112367) 1.000000 1.000000 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 0.998333 ( 0.016667) 0.998333 ( 0.016667) 1.000000 1.000000 --->germline2---dash-----: 1e+00 0.000000 3.8e-11 -0.081667 0.916667 ( 0.112367) 0.998333 ( 0.016667) 1.000000 1.000000 ######trueNSample###### --->fabia-------beagle1--: 3.95e-18 1604 7.42e-157 1603 1958 ( 24.9) 355 ( 31.6) 1962 356 --->fabia-------beagle2--: 3.95e-18 1250 3.37e-146 1250 1958 ( 24.9) 709 ( 29.9) 1962 706 --->fabia-------plink----: 3.94e-18 1956 4.36e-189 1955 1958 ( 24.9) 3.29 ( 2.02) 1962 3 --->fabia-------germline1: 1e+00 0 1e+00 0 1958 ( 24.9) 0 ( 0) 1962 0 --->fabia-------germline2: 3.95e-18 1885 5.53e-161 1881 1958 ( 24.9) 77.9 ( 41.8) 1962 70 --->fabia-------dash-----: 1e+00 0 1e+00 0 1958 ( 24.9) 0 ( 0) 1962 0 --->beagle1-----beagle2--: 3.94e-18 -353 1.61e-121 -354 355 ( 31.6) 709 ( 29.9) 356 706 --->beagle1-----plink----: 3.94e-18 350 1.21e-106 352 355 ( 31.6) 3.29 ( 2.02) 356 3 --->beagle1-----germline1: 1e+00 0 1e+00 0 355 ( 31.6) 0 ( 0) 356 0 --->beagle1-----germline2: 3.95e-18 280 1.55e-73 277 355 ( 31.6) 77.9 ( 41.8) 356 70 --->beagle1-----dash-----: 1e+00 0 1e+00 0 355 ( 31.6) 0 ( 0) 356 0 --->beagle2-----plink----: 3.95e-18 704 1.33e-138 706 709 ( 29.9) 3.29 ( 2.02) 706 3 --->beagle2-----germline1: 1e+00 0 1e+00 0 709 ( 29.9) 0 ( 0) 706 0 --->beagle2-----germline2: 3.95e-18 634 4.8e-110 631 709 ( 29.9) 77.9 ( 41.8) 706 70 --->beagle2-----dash-----: 1e+00 0 1e+00 0 709 ( 29.9) 0 ( 0) 706 0 --->plink-------germline1: 1e+00 0 1e+00 0 3.29 ( 2.02) 0 ( 0) 3 0 --->plink-------germline2: 3.94e-18 -69 2.05e-32 -74.6 3.29 ( 2.02) 77.9 ( 41.8) 3 70 --->plink-------dash-----: 1e+00 0 1e+00 0 3.29 ( 2.02) 0 ( 0) 3 0 --->germline1---germline2: 1e+00 0 1e+00 0 0 ( 0) 77.9 ( 41.8) 0 70 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.000000 ( 0.000000) 0.000000 0.000000 --->germline2---dash-----: 1e+00 0 1e+00 0 77.9 ( 41.8) 0 ( 0) 70 0 ######falsePSample###### --->fabia-------beagle1--: 3.95e-18 -604 6.25e-115 -603 35.5 ( 24.9) 639 ( 31.6) 31.5 638 --->fabia-------beagle2--: 3.95e-18 -250 1.44e-77 -250 35.5 ( 24.9) 285 ( 29.9) 31.5 288 --->fabia-------plink----: 3.94e-18 -956 2.51e-158 -955 35.5 ( 24.9) 991 ( 2.03) 31.5 991 --->fabia-------germline1: 3.92e-18 -959 4.12e-159 -958 35.5 ( 24.9) 994 ( 0.1) 31.5 994 --->fabia-------germline2: 3.95e-18 -885 2.01e-128 -881 35.5 ( 24.9) 916 ( 41.8) 31.5 924 --->fabia-------dash-----: 3.92e-18 -959 4.12e-159 -958 35.5 ( 24.9) 994 ( 0.1) 31.5 994 --->beagle1-----beagle2--: 3.94e-18 353 1.61e-121 354 639 ( 31.6) 285 ( 29.9) 638 288 --->beagle1-----plink----: 3.94e-18 -350 1.21e-106 -352 639 ( 31.6) 991 ( 2.03) 638 991 --->beagle1-----germline1: 3.94e-18 -353 2.73e-106 -355 639 ( 31.6) 994 ( 0.1) 638 994 --->beagle1-----germline2: 3.95e-18 -280 1.55e-73 -277 639 ( 31.6) 916 ( 41.8) 638 924 --->beagle1-----dash-----: 3.94e-18 -353 2.73e-106 -355 639 ( 31.6) 994 ( 0.1) 638 994 --->beagle2-----plink----: 3.95e-18 -704 1.33e-138 -706 285 ( 29.9) 991 ( 2.03) 288 991 --->beagle2-----germline1: 3.95e-18 -708 3.71e-138 -709 285 ( 29.9) 994 ( 0.1) 288 994 --->beagle2-----germline2: 3.95e-18 -634 4.8e-110 -631 285 ( 29.9) 916 ( 41.8) 288 924 --->beagle2-----dash-----: 3.95e-18 -708 3.71e-138 -709 285 ( 29.9) 994 ( 0.1) 288 994 --->plink-------germline1: 4.18e-17 -3.5 8.14e-30 -3.29 991 ( 2.03) 994 ( 0.1) 991 994 --->plink-------germline2: 3.94e-18 69 2.05e-32 74.6 991 ( 2.03) 916 ( 41.8) 991 924 --->plink-------dash-----: 4.18e-17 -3.5 8.14e-30 -3.29 991 ( 2.03) 994 ( 0.1) 991 994 --->germline1---germline2: 3.94e-18 72.5 3.61e-34 77.9 994 ( 0.1) 916 ( 41.8) 994 924 --->germline1---dash-----: 1e+00 0 1e+00 0 994 ( 0.1) 994 ( 0.1) 994 994 --->germline2---dash-----: 3.94e-18 -72.5 3.61e-34 -77.9 916 ( 41.8) 994 ( 0.1) 924 994 ######falseNSample###### --->fabia-------beagle1--: 2.6e-06 -1.500012 1.73e-06 -1.020000 0.540000 ( 1.725741) 1.560000 ( 1.373045) 0.000000 1.000000 --->fabia-------beagle2--: 1.28e-15 -3 5.68e-25 -2.86 0.54 ( 1.73) 3.4 ( 1.59) 0 4 --->fabia-------plink----: 1e+00 0.000000 2.84e-03 0.530000 0.540000 ( 1.725741) 0.010000 ( 0.100000) 0.000000 0.000000 --->fabia-------germline1: 1e+00 0.000000 1e+00 0.000000 0.540000 ( 1.725741) 0.000000 ( 0.000000) 0.000000 0.000000 --->fabia-------germline2: 1e+00 0.000000 7.85e-01 0.050000 0.540000 ( 1.725741) 0.490000 ( 0.658971) 0.000000 0.000000 --->fabia-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.540000 ( 1.725741) 0.000000 ( 0.000000) 0.000000 0.000000 --->beagle1-----beagle2--: 2.59e-16 -2 1.64e-25 -1.84 1.56 ( 1.37) 3.4 ( 1.59) 1 4 --->beagle1-----plink----: 1.16e-13 2.000013 3.18e-19 1.550000 1.560000 ( 1.373045) 0.010000 ( 0.100000) 1.000000 0.000000 --->beagle1-----germline1: 1e+00 0.000000 1e+00 0.000000 1.560000 ( 1.373045) 0.000000 ( 0.000000) 1.000000 0.000000 --->beagle1-----germline2: 1.51e-08 1.500031 5.14e-10 1.070000 1.560000 ( 1.373045) 0.490000 ( 0.658971) 1.000000 0.000000 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 1.560000 ( 1.373045) 0.000000 ( 0.000000) 1.000000 0.000000 --->beagle2-----plink----: 6.19e-18 3.5 1.54e-38 3.39 3.4 ( 1.59) 0.01 ( 0.1) 4 0 --->beagle2-----germline1: 1e+00 0 1e+00 0 3.4 ( 1.59) 0 ( 0) 4 0 --->beagle2-----germline2: 1.62e-16 3 1.85e-29 2.91 3.4 ( 1.59) 0.49 ( 0.659) 4 0 --->beagle2-----dash-----: 1e+00 0 1e+00 0 3.4 ( 1.59) 0 ( 0) 4 0 --->plink-------germline1: 1e+00 0.000000 1e+00 0.000000 0.010000 ( 0.100000) 0.000000 ( 0.000000) 0.000000 0.000000 --->plink-------germline2: 1e+00 0.000000 1.72e-10 -0.480000 0.010000 ( 0.100000) 0.490000 ( 0.658971) 0.000000 0.000000 --->plink-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.010000 ( 0.100000) 0.000000 ( 0.000000) 0.000000 0.000000 --->germline1---germline2: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.490000 ( 0.658971) 0.000000 0.000000 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.000000 ( 0.000000) 0.000000 0.000000 --->germline2---dash-----: 1e+00 0.000000 1e+00 0.000000 0.490000 ( 0.658971) 0.000000 ( 0.000000) 0.000000 0.000000 ######truePSample###### --->fabia-------beagle1--: 2.48e-06 1.5 1.52e-06 1.03 5.46 ( 1.73) 4.43 ( 1.38) 6 5 --->fabia-------beagle2--: 1.26e-15 3 4.98e-25 2.87 5.46 ( 1.73) 2.59 ( 1.59) 6 2 --->fabia-------plink----: 1e+00 0 3.49e-03 -0.52 5.46 ( 1.73) 5.98 ( 0.141) 6 6 --->fabia-------germline1: 1e+00 0 2.84e-03 -0.53 5.46 ( 1.73) 5.99 ( 0.1) 6 6 --->fabia-------germline2: 1e+00 0 8.28e-01 -0.04 5.46 ( 1.73) 5.5 ( 0.674) 6 6 --->fabia-------dash-----: 1e+00 0 2.84e-03 -0.53 5.46 ( 1.73) 5.99 ( 0.1) 6 6 --->beagle1-----beagle2--: 2.59e-16 2 1.64e-25 1.84 4.43 ( 1.38) 2.59 ( 1.59) 5 2 --->beagle1-----plink----: 1.16e-13 -2 3.18e-19 -1.55 4.43 ( 1.38) 5.98 ( 0.141) 5 6 --->beagle1-----germline1: 9.68e-14 -2 1.21e-19 -1.56 4.43 ( 1.38) 5.99 ( 0.1) 5 6 --->beagle1-----germline2: 1.51e-08 -1.5 5.14e-10 -1.07 4.43 ( 1.38) 5.5 ( 0.674) 5 6 --->beagle1-----dash-----: 9.68e-14 -2 1.21e-19 -1.56 4.43 ( 1.38) 5.99 ( 0.1) 5 6 --->beagle2-----plink----: 6.19e-18 -3.5 1.54e-38 -3.39 2.59 ( 1.59) 5.98 ( 0.141) 2 6 --->beagle2-----germline1: 6.18e-18 -3.5 6.57e-39 -3.4 2.59 ( 1.59) 5.99 ( 0.1) 2 6 --->beagle2-----germline2: 1.62e-16 -3 1.85e-29 -2.91 2.59 ( 1.59) 5.5 ( 0.674) 2 6 --->beagle2-----dash-----: 6.18e-18 -3.5 6.57e-39 -3.4 2.59 ( 1.59) 5.99 ( 0.1) 2 6 --->plink-------germline1: 1e+00 0 3.2e-01 -0.01 5.98 ( 0.141) 5.99 ( 0.1) 6 6 --->plink-------germline2: 1e+00 0 1.72e-10 0.48 5.98 ( 0.141) 5.5 ( 0.674) 6 6 --->plink-------dash-----: 1e+00 0 3.2e-01 -0.01 5.98 ( 0.141) 5.99 ( 0.1) 6 6 --->germline1---germline2: 1e+00 0 3.8e-11 0.49 5.99 ( 0.1) 5.5 ( 0.674) 6 6 --->germline1---dash-----: 1e+00 0 1e+00 0 5.99 ( 0.1) 5.99 ( 0.1) 6 6 --->germline2---dash-----: 1e+00 0 3.8e-11 -0.49 5.5 ( 0.674) 5.99 ( 0.1) 6 6