Results: Wilcoxon-Rank-Sum Wilcoxon-median t-test t-test-mean mean1 (std) mean2 (std) median1 median2 ######Matthews###### --->fabia-------beagle1--: 3.96e-18 0.479673 1.28e-63 0.478933 0.477511 ( 0.118302) -0.001421 ( 0.005207) 0.481083 -0.002108 --->fabia-------beagle2--: 3.96e-18 0.482095 9.06e-64 0.481045 0.477511 ( 0.118302) -0.003534 ( 0.003536) 0.481083 -0.003865 --->fabia-------plink----: 3.96e-18 0.467072 1.41e-62 0.466221 0.477511 ( 0.118302) 0.011290 ( 0.002561) 0.481083 0.011555 --->fabia-------germline1: 3.96e-18 0.493281 1.73e-64 0.492071 0.477511 ( 0.118302) -0.014559 ( 0.005708) 0.481083 -0.014676 --->fabia-------germline2: 3.96e-18 0.490143 3.07e-64 0.489430 0.477511 ( 0.118302) -0.011918 ( 0.004427) 0.481083 -0.011665 --->fabia-------dash-----: 3.96e-18 0.487336 8.91e-64 0.486357 0.477511 ( 0.118302) -0.008845 ( 0.003969) 0.481083 -0.009160 --->beagle1-----beagle2--: 1.57e-04 0.001727 1.33e-05 0.002112 -0.001421 ( 0.005207) -0.003534 ( 0.003536) -0.002108 -0.003865 --->beagle1-----plink----: 4.46e-18 -0.012841 1.36e-39 -0.012712 -0.001421 ( 0.005207) 0.011290 ( 0.002561) -0.002108 0.011555 --->beagle1-----germline1: 2.05e-17 0.013385 1.62e-31 0.013138 -0.001421 ( 0.005207) -0.014559 ( 0.005708) -0.002108 -0.014676 --->beagle1-----germline2: 2.6e-17 0.010702 8.33e-30 0.010497 -0.001421 ( 0.005207) -0.011918 ( 0.004427) -0.002108 -0.011665 --->beagle1-----dash-----: 6.03e-15 0.007443 4.11e-20 0.007424 -0.001421 ( 0.005207) -0.008845 ( 0.003969) -0.002108 -0.009160 --->beagle2-----plink----: 3.96e-18 -0.014869 4.41e-57 -0.014824 -0.003534 ( 0.003536) 0.011290 ( 0.002561) -0.003865 0.011555 --->beagle2-----germline1: 4.95e-17 0.011027 2.71e-29 0.011025 -0.003534 ( 0.003536) -0.014559 ( 0.005708) -0.003865 -0.014676 --->beagle2-----germline2: 3.7e-17 0.008373 8.47e-28 0.008384 -0.003534 ( 0.003536) -0.011918 ( 0.004427) -0.003865 -0.011665 --->beagle2-----dash-----: 6.35e-14 0.005358 6.93e-18 0.005312 -0.003534 ( 0.003536) -0.008845 ( 0.003969) -0.003865 -0.009160 --->plink-------germline1: 3.96e-18 0.025800 2.1e-66 0.025849 0.011290 ( 0.002561) -0.014559 ( 0.005708) 0.011555 -0.014676 --->plink-------germline2: 3.96e-18 0.023042 1.28e-69 0.023208 0.011290 ( 0.002561) -0.011918 ( 0.004427) 0.011555 -0.011665 --->plink-------dash-----: 3.96e-18 0.020110 2.22e-66 0.020136 0.011290 ( 0.002561) -0.008845 ( 0.003969) 0.011555 -0.009160 --->germline1---germline2: 1.07e-08 -0.002609 1.97e-09 -0.002641 -0.014559 ( 0.005708) -0.011918 ( 0.004427) -0.014676 -0.011665 --->germline1---dash-----: 1.04e-14 -0.005832 1.32e-20 -0.005714 -0.014559 ( 0.005708) -0.008845 ( 0.003969) -0.014676 -0.009160 --->germline2---dash-----: 3.64e-12 -0.003265 5.4e-15 -0.003073 -0.011918 ( 0.004427) -0.008845 ( 0.003969) -0.011665 -0.009160 ######F1###### --->fabia-------beagle1--: 3.96e-18 0.464171 9.97e-64 0.463460 0.469134 ( 0.114030) 0.005674 ( 0.002028) 0.468665 0.005536 --->fabia-------beagle2--: 3.96e-18 0.465339 7.38e-64 0.464857 0.469134 ( 0.114030) 0.004278 ( 0.001821) 0.468665 0.004109 --->fabia-------plink----: 3.96e-18 0.462916 1.43e-63 0.462458 0.469134 ( 0.114030) 0.006676 ( 0.000656) 0.468665 0.006600 --->fabia-------germline1: 3.96e-18 0.464631 1.04e-63 0.464288 0.469134 ( 0.114030) 0.004847 ( 0.000886) 0.468665 0.004834 --->fabia-------germline2: 3.96e-18 0.465618 9.07e-64 0.465168 0.469134 ( 0.114030) 0.003966 ( 0.001010) 0.468665 0.003998 --->fabia-------dash-----: 3.96e-18 0.466050 9.68e-64 0.465907 0.469134 ( 0.114030) 0.003227 ( 0.001333) 0.468665 0.002996 --->beagle1-----beagle2--: 4.31e-11 0.001255 7.14e-12 0.001396 0.005674 ( 0.002028) 0.004278 ( 0.001821) 0.005536 0.004109 --->beagle1-----plink----: 2.14e-07 -0.001109 2.7e-07 -0.001002 0.005674 ( 0.002028) 0.006676 ( 0.000656) 0.005536 0.006600 --->beagle1-----germline1: 5.31e-05 0.000798 3.21e-05 0.000827 0.005674 ( 0.002028) 0.004847 ( 0.000886) 0.005536 0.004834 --->beagle1-----germline2: 4.01e-12 0.001681 4.15e-14 0.001708 0.005674 ( 0.002028) 0.003966 ( 0.001010) 0.005536 0.003998 --->beagle1-----dash-----: 1.16e-14 0.002398 5.02e-19 0.002447 0.005674 ( 0.002028) 0.003227 ( 0.001333) 0.005536 0.002996 --->beagle2-----plink----: 2.72e-16 -0.002441 6.1e-26 -0.002398 0.004278 ( 0.001821) 0.006676 ( 0.000656) 0.004109 0.006600 --->beagle2-----germline1: 7.96e-04 -0.000624 2.02e-03 -0.000569 0.004278 ( 0.001821) 0.004847 ( 0.000886) 0.004109 0.004834 --->beagle2-----germline2: 1.19e-01 0.000275 8.69e-02 0.000312 0.004278 ( 0.001821) 0.003966 ( 0.001010) 0.004109 0.003998 --->beagle2-----dash-----: 2.45e-06 0.001040 3.74e-07 0.001050 0.004278 ( 0.001821) 0.003227 ( 0.001333) 0.004109 0.002996 --->plink-------germline1: 3.96e-18 0.001811 1.21e-53 0.001829 0.006676 ( 0.000656) 0.004847 ( 0.000886) 0.006600 0.004834 --->plink-------germline2: 3.96e-18 0.002693 2.53e-53 0.002710 0.006676 ( 0.000656) 0.003966 ( 0.001010) 0.006600 0.003998 --->plink-------dash-----: 4.08e-18 0.003505 4.68e-47 0.003449 0.006676 ( 0.000656) 0.003227 ( 0.001333) 0.006600 0.002996 --->germline1---germline2: 3.95e-16 0.000892 2.52e-26 0.000881 0.004847 ( 0.000886) 0.003966 ( 0.001010) 0.004834 0.003998 --->germline1---dash-----: 1.58e-16 0.001676 4.77e-27 0.001620 0.004847 ( 0.000886) 0.003227 ( 0.001333) 0.004834 0.002996 --->germline2---dash-----: 2.03e-10 0.000718 1.07e-11 0.000739 0.003966 ( 0.001010) 0.003227 ( 0.001333) 0.003998 0.002996 ######accuracy###### --->fabia-------beagle1--: 3.96e-18 0.090733 4.02e-120 0.090676 0.998456 ( 0.000430) 0.907780 ( 0.005845) 0.998534 0.907687 --->fabia-------beagle2--: 3.96e-18 0.047984 6.92e-114 0.047922 0.998456 ( 0.000430) 0.950534 ( 0.003537) 0.998534 0.950177 --->fabia-------plink----: 3.96e-18 0.933219 6.02e-214 0.932897 0.998456 ( 0.000430) 0.065558 ( 0.006751) 0.998534 0.064657 --->fabia-------germline1: 3.96e-18 0.540990 8e-128 0.541656 0.998456 ( 0.000430) 0.456799 ( 0.029149) 0.998534 0.459064 --->fabia-------germline2: 3.96e-18 0.245954 1.49e-90 0.246353 0.998456 ( 0.000430) 0.752103 ( 0.031754) 0.998534 0.751526 --->fabia-------dash-----: 3.96e-18 0.099782 1.26e-61 0.100557 0.998456 ( 0.000430) 0.897899 ( 0.026021) 0.998534 0.898367 --->beagle1-----beagle2--: 3.96e-18 -0.042921 1.07e-103 -0.042754 0.907780 ( 0.005845) 0.950534 ( 0.003537) 0.907687 0.950177 --->beagle1-----plink----: 3.96e-18 0.842165 3.46e-201 0.842221 0.907780 ( 0.005845) 0.065558 ( 0.006751) 0.907687 0.064657 --->beagle1-----germline1: 3.96e-18 0.450607 1.28e-120 0.450980 0.907780 ( 0.005845) 0.456799 ( 0.029149) 0.907687 0.459064 --->beagle1-----germline2: 3.96e-18 0.155328 1.7e-71 0.155677 0.907780 ( 0.005845) 0.752103 ( 0.031754) 0.907687 0.751526 --->beagle1-----dash-----: 8.06e-04 0.009035 2.96e-04 0.009881 0.907780 ( 0.005845) 0.897899 ( 0.026021) 0.907687 0.898367 --->beagle2-----plink----: 3.96e-18 0.885061 1.73e-212 0.884975 0.950534 ( 0.003537) 0.065558 ( 0.006751) 0.950177 0.064657 --->beagle2-----germline1: 3.96e-18 0.493336 4.1e-124 0.493734 0.950534 ( 0.003537) 0.456799 ( 0.029149) 0.950177 0.459064 --->beagle2-----germline2: 3.96e-18 0.198247 2.86e-81 0.198431 0.950534 ( 0.003537) 0.752103 ( 0.031754) 0.950177 0.751526 --->beagle2-----dash-----: 4.08e-18 0.051852 1.63e-36 0.052635 0.950534 ( 0.003537) 0.897899 ( 0.026021) 0.950177 0.898367 --->plink-------germline1: 3.96e-18 -0.391804 4.06e-114 -0.391241 0.065558 ( 0.006751) 0.456799 ( 0.029149) 0.064657 0.459064 --->plink-------germline2: 3.96e-18 -0.686733 5.44e-134 -0.686545 0.065558 ( 0.006751) 0.752103 ( 0.031754) 0.064657 0.751526 --->plink-------dash-----: 3.96e-18 -0.832927 9.54e-150 -0.832340 0.065558 ( 0.006751) 0.897899 ( 0.026021) 0.064657 0.898367 --->germline1---germline2: 3.96e-18 -0.295555 3.01e-137 -0.295304 0.456799 ( 0.029149) 0.752103 ( 0.031754) 0.459064 0.751526 --->germline1---dash-----: 3.96e-18 -0.441593 7.9e-138 -0.441099 0.456799 ( 0.029149) 0.897899 ( 0.026021) 0.459064 0.898367 --->germline2---dash-----: 3.96e-18 -0.145671 3.96e-113 -0.145796 0.752103 ( 0.031754) 0.897899 ( 0.026021) 0.751526 0.898367 ######FPR###### --->fabia-------beagle1--: 3.96e-18 -0.089047 3.25e-119 -0.088956 0.000629 ( 0.000375) 0.089585 ( 0.005852) 0.000603 0.089581 --->fabia-------beagle2--: 3.96e-18 -0.045979 7.32e-112 -0.045907 0.000629 ( 0.000375) 0.046536 ( 0.003564) 0.000603 0.046911 --->fabia-------plink----: 3.96e-18 -0.937116 9.31e-214 -0.936753 0.000629 ( 0.000375) 0.937382 ( 0.006790) 0.000603 0.938226 --->fabia-------germline1: 3.96e-18 -0.541784 1.2e-127 -0.542442 0.000629 ( 0.000375) 0.543071 ( 0.029307) 0.000603 0.540675 --->fabia-------germline2: 3.96e-18 -0.244954 3.48e-90 -0.245363 0.000629 ( 0.000375) 0.245992 ( 0.031900) 0.000603 0.246573 --->fabia-------dash-----: 3.96e-18 -0.098044 1.02e-60 -0.098771 0.000629 ( 0.000375) 0.099400 ( 0.026137) 0.000603 0.098440 --->beagle1-----beagle2--: 3.96e-18 0.043201 1.03e-103 0.043048 0.089585 ( 0.005852) 0.046536 ( 0.003564) 0.089581 0.046911 --->beagle1-----plink----: 3.96e-18 -0.847760 2e-201 -0.847798 0.089585 ( 0.005852) 0.937382 ( 0.006790) 0.089581 0.938226 --->beagle1-----germline1: 3.96e-18 -0.453120 1.44e-120 -0.453486 0.089585 ( 0.005852) 0.543071 ( 0.029307) 0.089581 0.540675 --->beagle1-----germline2: 3.96e-18 -0.156005 1.84e-71 -0.156407 0.089585 ( 0.005852) 0.245992 ( 0.031900) 0.089581 0.246573 --->beagle1-----dash-----: 9.01e-04 -0.009000 3.44e-04 -0.009816 0.089585 ( 0.005852) 0.099400 ( 0.026137) 0.089581 0.098440 --->beagle2-----plink----: 3.96e-18 -0.890899 1.97e-212 -0.890846 0.046536 ( 0.003564) 0.937382 ( 0.006790) 0.046911 0.938226 --->beagle2-----germline1: 3.96e-18 -0.496175 4.75e-124 -0.496535 0.046536 ( 0.003564) 0.543071 ( 0.029307) 0.046911 0.540675 --->beagle2-----germline2: 3.96e-18 -0.199300 2.99e-81 -0.199456 0.046536 ( 0.003564) 0.245992 ( 0.031900) 0.046911 0.246573 --->beagle2-----dash-----: 4.08e-18 -0.052149 1.7e-36 -0.052864 0.046536 ( 0.003564) 0.099400 ( 0.026137) 0.046911 0.098440 --->plink-------germline1: 3.96e-18 0.394923 2.62e-114 0.394311 0.937382 ( 0.006790) 0.543071 ( 0.029307) 0.938226 0.540675 --->plink-------germline2: 3.96e-18 0.691545 3.81e-134 0.691390 0.937382 ( 0.006790) 0.245992 ( 0.031900) 0.938226 0.246573 --->plink-------dash-----: 3.96e-18 0.838639 7.27e-150 0.837982 0.937382 ( 0.006790) 0.099400 ( 0.026137) 0.938226 0.098440 --->germline1---germline2: 3.96e-18 0.297345 3.06e-137 0.297079 0.543071 ( 0.029307) 0.245992 ( 0.031900) 0.540675 0.246573 --->germline1---dash-----: 3.96e-18 0.444206 1.01e-137 0.443671 0.543071 ( 0.029307) 0.099400 ( 0.026137) 0.540675 0.098440 --->germline2---dash-----: 3.96e-18 0.146466 4.85e-113 0.146592 0.245992 ( 0.031900) 0.099400 ( 0.026137) 0.246573 0.098440 ######FDR###### --->fabia-------beagle1--: 3.96e-18 -0.543644 1.2e-51 -0.550170 0.446891 ( 0.182832) 0.997060 ( 0.001057) 0.457662 0.997126 --->fabia-------beagle2--: 3.96e-18 -0.544425 1.09e-51 -0.550821 0.446891 ( 0.182832) 0.997711 ( 0.000981) 0.457662 0.997787 --->fabia-------plink----: 3.96e-18 -0.543093 1.33e-51 -0.549760 0.446891 ( 0.182832) 0.996651 ( 0.000330) 0.457662 0.996689 --->fabia-------germline1: 3.96e-18 -0.544154 1.15e-51 -0.550672 0.446891 ( 0.182832) 0.997562 ( 0.000447) 0.457662 0.997568 --->fabia-------germline2: 3.96e-18 -0.544679 1.06e-51 -0.551100 0.446891 ( 0.182832) 0.997991 ( 0.000513) 0.457662 0.997975 --->fabia-------dash-----: 3.96e-18 -0.544875 1.07e-51 -0.551440 0.446891 ( 0.182832) 0.998331 ( 0.000691) 0.457662 0.998454 --->beagle1-----beagle2--: 2.17e-09 -0.000572 4.79e-10 -0.000651 0.997060 ( 0.001057) 0.997711 ( 0.000981) 0.997126 0.997787 --->beagle1-----plink----: 1.05e-05 0.000468 3.5e-05 0.000410 0.997060 ( 0.001057) 0.996651 ( 0.000330) 0.997126 0.996689 --->beagle1-----germline1: 3.48e-06 -0.000481 1.65e-06 -0.000502 0.997060 ( 0.001057) 0.997562 ( 0.000447) 0.997126 0.997568 --->beagle1-----germline2: 9.12e-13 -0.000913 4.48e-15 -0.000930 0.997060 ( 0.001057) 0.997991 ( 0.000513) 0.997126 0.997975 --->beagle1-----dash-----: 1.01e-14 -0.001225 4.6e-19 -0.001271 0.997060 ( 0.001057) 0.998331 ( 0.000691) 0.997126 0.998454 --->beagle2-----plink----: 9.07e-15 0.001071 1.1e-20 0.001061 0.997711 ( 0.000981) 0.996651 ( 0.000330) 0.997787 0.996689 --->beagle2-----germline1: 8.65e-02 0.000170 1.21e-01 0.000149 0.997711 ( 0.000981) 0.997562 ( 0.000447) 0.997787 0.997568 --->beagle2-----germline2: 6.5e-03 -0.000261 4.45e-03 -0.000279 0.997711 ( 0.000981) 0.997991 ( 0.000513) 0.997787 0.997975 --->beagle2-----dash-----: 3.15e-07 -0.000647 2.56e-08 -0.000619 0.997711 ( 0.000981) 0.998331 ( 0.000691) 0.997787 0.998454 --->plink-------germline1: 4.08e-18 -0.000926 2.91e-53 -0.000912 0.996651 ( 0.000330) 0.997562 ( 0.000447) 0.996689 0.997568 --->plink-------germline2: 3.96e-18 -0.001335 2.06e-52 -0.001340 0.996651 ( 0.000330) 0.997991 ( 0.000513) 0.996689 0.997975 --->plink-------dash-----: 4.33e-18 -0.001708 5.82e-45 -0.001680 0.996651 ( 0.000330) 0.998331 ( 0.000691) 0.996689 0.998454 --->germline1---germline2: 6.21e-16 -0.000445 3.33e-25 -0.000428 0.997562 ( 0.000447) 0.997991 ( 0.000513) 0.997568 0.997975 --->germline1---dash-----: 5.54e-16 -0.000781 1.12e-24 -0.000769 0.997562 ( 0.000447) 0.998331 ( 0.000691) 0.997568 0.998454 --->germline2---dash-----: 6.03e-09 -0.000331 5.84e-10 -0.000340 0.997991 ( 0.000513) 0.998331 ( 0.000691) 0.997975 0.998454 ######specifity###### --->fabia-------beagle1--: 3.96e-18 0.089027 3.26e-119 0.088956 0.999371 ( 0.000375) 0.910415 ( 0.005852) 0.999397 0.910419 --->fabia-------beagle2--: 3.96e-18 0.045970 7.32e-112 0.045907 0.999371 ( 0.000375) 0.953464 ( 0.003564) 0.999397 0.953089 --->fabia-------plink----: 3.96e-18 0.937157 9.31e-214 0.936753 0.999371 ( 0.000375) 0.062618 ( 0.006790) 0.999397 0.061774 --->fabia-------germline1: 3.96e-18 0.541748 1.2e-127 0.542442 0.999371 ( 0.000375) 0.456929 ( 0.029307) 0.999397 0.459325 --->fabia-------germline2: 3.96e-18 0.244943 3.48e-90 0.245363 0.999371 ( 0.000375) 0.754008 ( 0.031900) 0.999397 0.753427 --->fabia-------dash-----: 3.96e-18 0.098034 1.02e-60 0.098771 0.999371 ( 0.000375) 0.900600 ( 0.026137) 0.999397 0.901560 --->beagle1-----beagle2--: 3.96e-18 -0.043206 1.03e-103 -0.043048 0.910415 ( 0.005852) 0.953464 ( 0.003564) 0.910419 0.953089 --->beagle1-----plink----: 3.96e-18 0.847741 2e-201 0.847798 0.910415 ( 0.005852) 0.062618 ( 0.006790) 0.910419 0.061774 --->beagle1-----germline1: 3.96e-18 0.453130 1.44e-120 0.453486 0.910415 ( 0.005852) 0.456929 ( 0.029307) 0.910419 0.459325 --->beagle1-----germline2: 3.96e-18 0.155982 1.84e-71 0.156407 0.910415 ( 0.005852) 0.754008 ( 0.031900) 0.910419 0.753427 --->beagle1-----dash-----: 9.01e-04 0.008986 3.44e-04 0.009816 0.910415 ( 0.005852) 0.900600 ( 0.026137) 0.910419 0.901560 --->beagle2-----plink----: 3.96e-18 0.890909 1.97e-212 0.890846 0.953464 ( 0.003564) 0.062618 ( 0.006790) 0.953089 0.061774 --->beagle2-----germline1: 3.96e-18 0.496175 4.75e-124 0.496535 0.953464 ( 0.003564) 0.456929 ( 0.029307) 0.953089 0.459325 --->beagle2-----germline2: 3.96e-18 0.199292 2.99e-81 0.199456 0.953464 ( 0.003564) 0.754008 ( 0.031900) 0.953089 0.753427 --->beagle2-----dash-----: 4.08e-18 0.052156 1.7e-36 0.052864 0.953464 ( 0.003564) 0.900600 ( 0.026137) 0.953089 0.901560 --->plink-------germline1: 3.96e-18 -0.394931 2.62e-114 -0.394311 0.062618 ( 0.006790) 0.456929 ( 0.029307) 0.061774 0.459325 --->plink-------germline2: 3.96e-18 -0.691544 3.81e-134 -0.691390 0.062618 ( 0.006790) 0.754008 ( 0.031900) 0.061774 0.753427 --->plink-------dash-----: 3.96e-18 -0.838665 7.27e-150 -0.837982 0.062618 ( 0.006790) 0.900600 ( 0.026137) 0.061774 0.901560 --->germline1---germline2: 3.96e-18 -0.297368 3.06e-137 -0.297079 0.456929 ( 0.029307) 0.754008 ( 0.031900) 0.459325 0.753427 --->germline1---dash-----: 3.96e-18 -0.444196 1.01e-137 -0.443671 0.456929 ( 0.029307) 0.900600 ( 0.026137) 0.459325 0.901560 --->germline2---dash-----: 3.96e-18 -0.146472 4.85e-113 -0.146592 0.754008 ( 0.031900) 0.900600 ( 0.026137) 0.753427 0.901560 ######sensitivity###### --->fabia-------beagle1--: 3.96e-18 0.340284 1.49e-55 0.340659 0.422731 ( 0.102901) 0.082072 ( 0.026585) 0.411205 0.078669 --->fabia-------beagle2--: 3.96e-18 0.388111 1.7e-61 0.389526 0.422731 ( 0.102901) 0.033205 ( 0.013724) 0.411205 0.031267 --->fabia-------plink----: 3.96e-18 -0.564396 1.27e-76 -0.563022 0.422731 ( 0.102901) 0.985754 ( 0.010429) 0.411205 0.989250 --->fabia-------germline1: 3.63e-01 0.011163 4.3e-01 0.009074 0.422731 ( 0.102901) 0.413657 ( 0.056145) 0.411205 0.416986 --->fabia-------germline2: 4.33e-18 0.270277 1.11e-42 0.268077 0.422731 ( 0.102901) 0.154654 ( 0.040658) 0.411205 0.154436 --->fabia-------dash-----: 3.96e-18 0.371360 9.46e-56 0.370510 0.422731 ( 0.102901) 0.052221 ( 0.025467) 0.411205 0.048553 --->beagle1-----beagle2--: 3.96e-18 0.047385 1.96e-39 0.048867 0.082072 ( 0.026585) 0.033205 ( 0.013724) 0.078669 0.031267 --->beagle1-----plink----: 3.96e-18 -0.904351 2.84e-150 -0.903682 0.082072 ( 0.026585) 0.985754 ( 0.010429) 0.078669 0.989250 --->beagle1-----germline1: 3.96e-18 -0.331003 8.78e-76 -0.331585 0.082072 ( 0.026585) 0.413657 ( 0.056145) 0.078669 0.416986 --->beagle1-----germline2: 1.44e-17 -0.070891 5.67e-29 -0.072582 0.082072 ( 0.026585) 0.154654 ( 0.040658) 0.078669 0.154436 --->beagle1-----dash-----: 3.11e-11 0.030876 1.08e-12 0.029851 0.082072 ( 0.026585) 0.052221 ( 0.025467) 0.078669 0.048553 --->beagle2-----plink----: 3.96e-18 -0.952905 3.84e-176 -0.952549 0.033205 ( 0.013724) 0.985754 ( 0.010429) 0.031267 0.989250 --->beagle2-----germline1: 3.96e-18 -0.381025 1.68e-83 -0.380452 0.033205 ( 0.013724) 0.413657 ( 0.056145) 0.031267 0.416986 --->beagle2-----germline2: 4.08e-18 -0.120586 5.55e-51 -0.121449 0.033205 ( 0.013724) 0.154654 ( 0.040658) 0.031267 0.154436 --->beagle2-----dash-----: 1.07e-09 -0.018096 2.77e-10 -0.019016 0.033205 ( 0.013724) 0.052221 ( 0.025467) 0.031267 0.048553 --->plink-------germline1: 3.96e-18 0.571051 7.17e-103 0.572096 0.985754 ( 0.010429) 0.413657 ( 0.056145) 0.989250 0.416986 --->plink-------germline2: 3.96e-18 0.831963 2.6e-132 0.831100 0.985754 ( 0.010429) 0.154654 ( 0.040658) 0.989250 0.154436 --->plink-------dash-----: 3.96e-18 0.934841 1.47e-155 0.933532 0.985754 ( 0.010429) 0.052221 ( 0.025467) 0.989250 0.048553 --->germline1---germline2: 3.96e-18 0.259820 1.31e-86 0.259003 0.413657 ( 0.056145) 0.154654 ( 0.040658) 0.416986 0.154436 --->germline1---dash-----: 3.96e-18 0.361382 1.56e-90 0.361436 0.413657 ( 0.056145) 0.052221 ( 0.025467) 0.416986 0.048553 --->germline2---dash-----: 3.96e-18 0.100395 1.09e-61 0.102433 0.154654 ( 0.040658) 0.052221 ( 0.025467) 0.154436 0.048553 ######trueN###### --->fabia-------beagle1--: 3.96e-18 10881068 7.56e-227 10880326 2e+07 ( 8029) 9075164 ( 58642) 2e+07 9074140 --->fabia-------beagle2--: 3.96e-18 10451847 1.4e-245 10451215 2e+07 ( 8029) 9504275 ( 35456) 2e+07 9500702 --->fabia-------plink----: 3.96e-18 19334721 7.6e-245 19331306 2e+07 ( 8029) 624183 ( 67695) 2e+07 615769 --->fabia-------germline1: 3.96e-18 15393904 1.03e-172 15400735 2e+07 ( 8029) 4554755 ( 292411) 2e+07 4580026 --->fabia-------germline2: 3.96e-18 12435310 7.31e-160 12439408 2e+07 ( 8029) 7516081 ( 318300) 2e+07 7510564 --->fabia-------dash-----: 3.96e-18 1.1e+07 4.45e-163 1.1e+07 2e+07 ( 8029) 8977320 ( 260683) 2e+07 8981264 --->beagle1-----beagle2--: 3.96e-18 -430809 9.75e-104 -429111 9075164 ( 58642) 9504275 ( 35456) 9074140 9500702 --->beagle1-----plink----: 3.96e-18 8450407 2.24e-201 8450981 9075164 ( 58642) 624183 ( 67695) 9074140 615769 --->beagle1-----germline1: 3.96e-18 4516573 1.33e-120 4520409 9075164 ( 58642) 4554755 ( 292411) 9074140 4580026 --->beagle1-----germline2: 3.96e-18 1555248 1.82e-71 1559083 9075164 ( 58642) 7516081 ( 318300) 9074140 7510564 --->beagle1-----dash-----: 9.01e-04 89573 3.45e-04 97843 9075164 ( 58642) 8977320 ( 260683) 9074140 8981264 --->beagle2-----plink----: 3.96e-18 8880819 1.5e-212 8880092 9504275 ( 35456) 624183 ( 67695) 9500702 615769 --->beagle2-----germline1: 3.96e-18 4945715 4.32e-124 4949520 9504275 ( 35456) 4554755 ( 292411) 9500702 4580026 --->beagle2-----germline2: 3.96e-18 1986541 2.93e-81 1988194 9504275 ( 35456) 7516081 ( 318300) 9500702 7510564 --->beagle2-----dash-----: 4.08e-18 519656 1.7e-36 526954 9504275 ( 35456) 8977320 ( 260683) 9500702 8981264 --->plink-------germline1: 3.96e-18 -3936595 2.83e-114 -3930572 624183 ( 67695) 4554755 ( 292411) 615769 4580026 --->plink-------germline2: 3.96e-18 -6893558 4.13e-134 -6891898 624183 ( 67695) 7516081 ( 318300) 615769 7510564 --->plink-------dash-----: 3.96e-18 -8359288 7.54e-150 -8353138 624183 ( 67695) 8977320 ( 260683) 615769 8981264 --->germline1---germline2: 3.96e-18 -2964115 2.85e-137 -2961326 4554755 ( 292411) 7516081 ( 318300) 4580026 7510564 --->germline1---dash-----: 3.96e-18 -4427651 8.65e-138 -4422566 4554755 ( 292411) 8977320 ( 260683) 4580026 8981264 --->germline2---dash-----: 3.96e-18 -1460124 4.38e-113 -1461239 7516081 ( 318300) 8977320 ( 260683) 7510564 8981264 ######falseP###### --->fabia-------beagle1--: 3.96e-18 -881240 7.89e-119 -880432 12560 ( 7486) 892992 ( 58311) 12036 892868 --->fabia-------beagle2--: 3.96e-18 -451982 1.28e-110 -451321 12560 ( 7486) 463881 ( 35540) 12036 467624 --->fabia-------plink----: 3.96e-18 -9334835 1.55e-213 -9331413 12560 ( 7486) 9343973 ( 67594) 12036 9352389 --->fabia-------germline1: 3.96e-18 -5394019 1.03e-127 -5400841 12560 ( 7486) 5413401 ( 291840) 12036 5391178 --->fabia-------germline2: 3.96e-18 -2435413 3.71e-90 -2439514 12560 ( 7486) 2452075 ( 317907) 12036 2458336 --->fabia-------dash-----: 3.96e-18 -970611 1.54e-60 -978275 12560 ( 7486) 990836 ( 260535) 12036 980651 --->beagle1-----beagle2--: 3.96e-18 430810 9.75e-104 429111 892992 ( 58311) 463881 ( 35540) 892868 467624 --->beagle1-----plink----: 3.96e-18 -8450412 2.24e-201 -8450981 892992 ( 58311) 9343973 ( 67594) 892868 9352389 --->beagle1-----germline1: 3.96e-18 -4516571 1.33e-120 -4520409 892992 ( 58311) 5413401 ( 291840) 892868 5391178 --->beagle1-----germline2: 3.96e-18 -1555202 1.82e-71 -1559083 892992 ( 58311) 2452075 ( 317907) 892868 2458336 --->beagle1-----dash-----: 9.01e-04 -89561 3.45e-04 -97843 892992 ( 58311) 990836 ( 260535) 892868 980651 --->beagle2-----plink----: 3.96e-18 -8880817 1.5e-212 -8880092 463881 ( 35540) 9343973 ( 67594) 467624 9352389 --->beagle2-----germline1: 3.96e-18 -4945730 4.32e-124 -4949520 463881 ( 35540) 5413401 ( 291840) 467624 5391178 --->beagle2-----germline2: 3.96e-18 -1986483 2.93e-81 -1988194 463881 ( 35540) 2452075 ( 317907) 467624 2458336 --->beagle2-----dash-----: 4.08e-18 -519669 1.7e-36 -526954 463881 ( 35540) 990836 ( 260535) 467624 980651 --->plink-------germline1: 3.96e-18 3936579 2.83e-114 3930572 9343973 ( 67594) 5413401 ( 291840) 9352389 5391178 --->plink-------germline2: 3.96e-18 6893556 4.13e-134 6891898 9343973 ( 67594) 2452075 ( 317907) 9352389 2458336 --->plink-------dash-----: 3.96e-18 8359309 7.54e-150 8353138 9343973 ( 67594) 990836 ( 260535) 9352389 980651 --->germline1---germline2: 3.96e-18 2964090 2.85e-137 2961326 5413401 ( 291840) 2452075 ( 317907) 5391178 2458336 --->germline1---dash-----: 3.96e-18 4427667 8.65e-138 4422566 5413401 ( 291840) 990836 ( 260535) 5391178 980651 --->germline2---dash-----: 3.96e-18 1460104 4.38e-113 1461239 2452075 ( 317907) 990836 ( 260535) 2458336 980651 ######falseN###### --->fabia-------beagle1--: 3.96e-18 -10776 4.91e-50 -10886 18324 ( 3105) 29210 ( 2652) 18154 28794 --->fabia-------beagle2--: 3.96e-18 -12348 2.21e-54 -12455 18324 ( 3105) 30780 ( 2857) 18154 30309 --->fabia-------plink----: 3.96e-18 17853 4.1e-78 17882 18324 ( 3105) 442 ( 312) 18154 354 --->fabia-------germline1: 4.44e-01 -300 4.54e-01 -280 18324 ( 3105) 18604 ( 1914) 18154 18370 --->fabia-------germline2: 4.33e-18 -8518 2.42e-39 -8569 18324 ( 3105) 26893 ( 2595) 18154 26348 --->fabia-------dash-----: 3.96e-18 -11753 5.18e-50 -11851 18324 ( 3105) 30176 ( 2917) 18154 29558 --->beagle1-----beagle2--: 3.96e-18 -1486 4.38e-36 -1569 29210 ( 2652) 30780 ( 2857) 28794 30309 --->beagle1-----plink----: 3.96e-18 28724 4e-103 28768 29210 ( 2652) 442 ( 312) 28794 354 --->beagle1-----germline1: 3.96e-18 10605 1.27e-67 10607 29210 ( 2652) 18604 ( 1914) 28794 18370 --->beagle1-----germline2: 1.39e-17 2272 3.15e-29 2317 29210 ( 2652) 26893 ( 2595) 28794 26348 --->beagle1-----dash-----: 2.64e-11 -973 1.49e-12 -965 29210 ( 2652) 30176 ( 2917) 28794 29558 --->beagle2-----plink----: 3.96e-18 30234 1.94e-102 30337 30780 ( 2857) 442 ( 312) 30309 354 --->beagle2-----germline1: 3.96e-18 12177 1.88e-71 12176 30780 ( 2857) 18604 ( 1914) 30309 18370 --->beagle2-----germline2: 4.08e-18 3874 2.92e-49 3887 30780 ( 2857) 26893 ( 2595) 30309 26348 --->beagle2-----dash-----: 8.57e-10 576 1.18e-10 604 30780 ( 2857) 30176 ( 2917) 30309 29558 --->plink-------germline1: 3.96e-18 -18124 6.69e-98 -18161 442 ( 312) 18604 ( 1914) 354 18370 --->plink-------germline2: 3.96e-18 -26330 7.02e-101 -26451 442 ( 312) 26893 ( 2595) 354 26348 --->plink-------dash-----: 3.96e-18 -29570 7.19e-101 -29733 442 ( 312) 30176 ( 2917) 354 29558 --->germline1---germline2: 3.96e-18 -8245 2.27e-72 -8289 18604 ( 1914) 26893 ( 2595) 18370 26348 --->germline1---dash-----: 3.96e-18 -11511 6.87e-74 -11572 18604 ( 1914) 30176 ( 2917) 18370 29558 --->germline2---dash-----: 3.96e-18 -3221 4.66e-56 -3282 26893 ( 2595) 30176 ( 2917) 26348 29558 ######trueP###### --->fabia-------beagle1--: 3.96e-18 10883 3.23e-50 10993 13626 ( 4030) 2633 ( 981) 13327 2536 --->fabia-------beagle2--: 3.96e-18 12450 1.64e-54 12562 13626 ( 4030) 1064 ( 466) 13327 1017 --->fabia-------plink----: 3.96e-18 -17753 1.14e-77 -17775 13626 ( 4030) 31402 ( 3103) 13327 31024 --->fabia-------germline1: 2.95e-01 413 3.04e-01 386 13626 ( 4030) 13240 ( 2563) 13327 13490 --->fabia-------germline2: 4.33e-18 8630 1.29e-39 8675 13626 ( 4030) 4951 ( 1448) 13327 4976 --->fabia-------dash-----: 3.96e-18 11863 3.67e-50 11958 13626 ( 4030) 1668 ( 825) 13327 1548 --->beagle1-----beagle2--: 3.96e-18 1486 4.38e-36 1569 2633 ( 981) 1064 ( 466) 2536 1017 --->beagle1-----plink----: 3.96e-18 -28725 4e-103 -28768 2633 ( 981) 31402 ( 3103) 2536 31024 --->beagle1-----germline1: 3.96e-18 -10605 1.27e-67 -10607 2633 ( 981) 13240 ( 2563) 2536 13490 --->beagle1-----germline2: 1.39e-17 -2272 3.15e-29 -2317 2633 ( 981) 4951 ( 1448) 2536 4976 --->beagle1-----dash-----: 2.64e-11 973 1.49e-12 965 2633 ( 981) 1668 ( 825) 2536 1548 --->beagle2-----plink----: 3.96e-18 -30234 1.94e-102 -30337 1064 ( 466) 31402 ( 3103) 1017 31024 --->beagle2-----germline1: 3.96e-18 -12177 1.88e-71 -12176 1064 ( 466) 13240 ( 2563) 1017 13490 --->beagle2-----germline2: 4.08e-18 -3875 2.92e-49 -3887 1064 ( 466) 4951 ( 1448) 1017 4976 --->beagle2-----dash-----: 8.57e-10 -576 1.18e-10 -604 1064 ( 466) 1668 ( 825) 1017 1548 --->plink-------germline1: 3.96e-18 18124 6.69e-98 18161 31402 ( 3103) 13240 ( 2563) 31024 13490 --->plink-------germline2: 3.96e-18 26331 7.02e-101 26451 31402 ( 3103) 4951 ( 1448) 31024 4976 --->plink-------dash-----: 3.96e-18 29570 7.19e-101 29733 31402 ( 3103) 1668 ( 825) 31024 1548 --->germline1---germline2: 3.96e-18 8244 2.27e-72 8289 13240 ( 2563) 4951 ( 1448) 13490 4976 --->germline1---dash-----: 3.96e-18 11511 6.87e-74 11572 13240 ( 2563) 1668 ( 825) 13490 1548 --->germline2---dash-----: 3.96e-18 3221 4.66e-56 3282 4951 ( 1448) 1668 ( 825) 4976 1548 ######MatthewsSnps###### --->fabia-------beagle1--: 1e+00 0.000000 1e+00 0.000000 0.312560 ( 0.097104) 0.000000 ( 0.000000) 0.297748 0.000000 --->fabia-------beagle2--: 1e+00 0.000000 1e+00 0.000000 0.312560 ( 0.097104) 0.000000 ( 0.000000) 0.297748 0.000000 --->fabia-------plink----: 3.96e-18 0.303400 1.77e-53 0.305035 0.312560 ( 0.097104) 0.007524 ( 0.001840) 0.297748 0.006696 --->fabia-------germline1: 1e+00 0.000000 1e+00 0.000000 0.312560 ( 0.097104) 0.000000 ( 0.000000) 0.297748 0.000000 --->fabia-------germline2: 3.96e-18 0.310082 5.75e-54 0.311932 0.312560 ( 0.097104) 0.000628 ( 0.006278) 0.297748 0.000000 --->fabia-------dash-----: 3.96e-18 0.325202 5.78e-42 0.325556 0.312560 ( 0.097104) -0.012997 ( 0.117477) 0.297748 -0.003803 --->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) 0.007524 ( 0.001840) 0.000000 0.006696 --->beagle1-----germline1: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.000000 ( 0.000000) 0.000000 0.000000 --->beagle1-----germline2: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.000628 ( 0.006278) 0.000000 0.000000 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) -0.012997 ( 0.117477) 0.000000 -0.003803 --->beagle2-----plink----: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.007524 ( 0.001840) 0.000000 0.006696 --->beagle2-----germline1: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.000000 ( 0.000000) 0.000000 0.000000 --->beagle2-----germline2: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.000628 ( 0.006278) 0.000000 0.000000 --->beagle2-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) -0.012997 ( 0.117477) 0.000000 -0.003803 --->plink-------germline1: 1e+00 0.000000 1e+00 0.000000 0.007524 ( 0.001840) 0.000000 ( 0.000000) 0.006696 0.000000 --->plink-------germline2: 7.67e-17 0.007339 1.37e-18 0.006896 0.007524 ( 0.001840) 0.000628 ( 0.006278) 0.006696 0.000000 --->plink-------dash-----: 1.17e-01 0.019622 8.29e-02 0.020521 0.007524 ( 0.001840) -0.012997 ( 0.117477) 0.006696 -0.003803 --->germline1---germline2: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.000628 ( 0.006278) 0.000000 0.000000 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) -0.012997 ( 0.117477) 0.000000 -0.003803 --->germline2---dash-----: 3.18e-01 0.012774 2.46e-01 0.013624 0.000628 ( 0.006278) -0.012997 ( 0.117477) 0.000000 -0.003803 ######F1Snps###### --->fabia-------beagle1--: 3.96e-18 0.103191 4.38e-37 0.105129 0.532331 ( 0.066872) 0.427203 ( 0.036377) 0.527048 0.426436 --->fabia-------beagle2--: 3.96e-18 0.103191 4.38e-37 0.105129 0.532331 ( 0.066872) 0.427203 ( 0.036377) 0.527048 0.426436 --->fabia-------plink----: 3.96e-18 0.103152 4.52e-37 0.105075 0.532331 ( 0.066872) 0.427256 ( 0.036381) 0.527048 0.426520 --->fabia-------germline1: 3.96e-18 0.103191 4.38e-37 0.105129 0.532331 ( 0.066872) 0.427203 ( 0.036377) 0.527048 0.426436 --->fabia-------germline2: 3.96e-18 0.103154 4.58e-37 0.105089 0.532331 ( 0.066872) 0.427242 ( 0.036325) 0.527048 0.426436 --->fabia-------dash-----: 4.08e-18 0.125081 4.99e-40 0.126205 0.532331 ( 0.066872) 0.406126 ( 0.051934) 0.527048 0.416181 --->beagle1-----beagle2--: 1e+00 0.000000 1e+00 0.000000 0.427203 ( 0.036377) 0.427203 ( 0.036377) 0.426436 0.426436 --->beagle1-----plink----: 1e+00 0.000000 1e+00 0.000000 0.427203 ( 0.036377) 0.427256 ( 0.036381) 0.426436 0.426520 --->beagle1-----germline1: 1e+00 0.000000 1e+00 0.000000 0.427203 ( 0.036377) 0.427203 ( 0.036377) 0.426436 0.426436 --->beagle1-----germline2: 1e+00 0.000000 1e+00 0.000000 0.427203 ( 0.036377) 0.427242 ( 0.036325) 0.426436 0.426436 --->beagle1-----dash-----: 3.38e-07 0.019216 7.84e-08 0.021077 0.427203 ( 0.036377) 0.406126 ( 0.051934) 0.426436 0.416181 --->beagle2-----plink----: 1e+00 0.000000 1e+00 0.000000 0.427203 ( 0.036377) 0.427256 ( 0.036381) 0.426436 0.426520 --->beagle2-----germline1: 1e+00 0.000000 1e+00 0.000000 0.427203 ( 0.036377) 0.427203 ( 0.036377) 0.426436 0.426436 --->beagle2-----germline2: 1e+00 0.000000 1e+00 0.000000 0.427203 ( 0.036377) 0.427242 ( 0.036325) 0.426436 0.426436 --->beagle2-----dash-----: 3.38e-07 0.019216 7.84e-08 0.021077 0.427203 ( 0.036377) 0.406126 ( 0.051934) 0.426436 0.416181 --->plink-------germline1: 1e+00 0.000000 1e+00 0.000000 0.427256 ( 0.036381) 0.427203 ( 0.036377) 0.426520 0.426436 --->plink-------germline2: 1e+00 0.000000 1e+00 0.000000 0.427256 ( 0.036381) 0.427242 ( 0.036325) 0.426520 0.426436 --->plink-------dash-----: 3.26e-07 0.019261 7.32e-08 0.021130 0.427256 ( 0.036381) 0.406126 ( 0.051934) 0.426520 0.416181 --->germline1---germline2: 1e+00 0.000000 1e+00 0.000000 0.427203 ( 0.036377) 0.427242 ( 0.036325) 0.426436 0.426436 --->germline1---dash-----: 3.38e-07 0.019216 7.84e-08 0.021077 0.427203 ( 0.036377) 0.406126 ( 0.051934) 0.426436 0.416181 --->germline2---dash-----: 3.2e-07 0.019170 7.14e-08 0.021116 0.427242 ( 0.036325) 0.406126 ( 0.051934) 0.426436 0.416181 ######accuracySnps###### --->fabia-------beagle1--: 3.96e-18 0.351571 2.68e-74 0.352930 0.625221 ( 0.068545) 0.272291 ( 0.029336) 0.621900 0.271000 --->fabia-------beagle2--: 3.96e-18 0.351571 2.68e-74 0.352930 0.625221 ( 0.068545) 0.272291 ( 0.029336) 0.621900 0.271000 --->fabia-------plink----: 3.96e-18 0.351389 2.74e-74 0.352771 0.625221 ( 0.068545) 0.272450 ( 0.029337) 0.621900 0.271250 --->fabia-------germline1: 3.96e-18 0.351571 2.68e-74 0.352930 0.625221 ( 0.068545) 0.272291 ( 0.029336) 0.621900 0.271000 --->fabia-------germline2: 3.96e-18 0.351314 2.66e-74 0.352802 0.625221 ( 0.068545) 0.272419 ( 0.029190) 0.621900 0.271000 --->fabia-------dash-----: 3.96e-18 0.288645 5.04e-61 0.286880 0.625221 ( 0.068545) 0.338341 ( 0.047362) 0.621900 0.334800 --->beagle1-----beagle2--: 1e+00 0.000000 1e+00 0.000000 0.272291 ( 0.029336) 0.272291 ( 0.029336) 0.271000 0.271000 --->beagle1-----plink----: 1.6e-18 -0.000164 8.23e-38 -0.000159 0.272291 ( 0.029336) 0.272450 ( 0.029337) 0.271000 0.271250 --->beagle1-----germline1: 1e+00 0.000000 1e+00 0.000000 0.272291 ( 0.029336) 0.272291 ( 0.029336) 0.271000 0.271000 --->beagle1-----germline2: 1e+00 0.000000 3.2e-01 -0.000128 0.272291 ( 0.029336) 0.272419 ( 0.029190) 0.271000 0.271000 --->beagle1-----dash-----: 1.31e-17 -0.064652 2.65e-26 -0.066050 0.272291 ( 0.029336) 0.338341 ( 0.047362) 0.271000 0.334800 --->beagle2-----plink----: 1.6e-18 -0.000164 8.23e-38 -0.000159 0.272291 ( 0.029336) 0.272450 ( 0.029337) 0.271000 0.271250 --->beagle2-----germline1: 1e+00 0.000000 1e+00 0.000000 0.272291 ( 0.029336) 0.272291 ( 0.029336) 0.271000 0.271000 --->beagle2-----germline2: 1e+00 0.000000 3.2e-01 -0.000128 0.272291 ( 0.029336) 0.272419 ( 0.029190) 0.271000 0.271000 --->beagle2-----dash-----: 1.31e-17 -0.064652 2.65e-26 -0.066050 0.272291 ( 0.029336) 0.338341 ( 0.047362) 0.271000 0.334800 --->plink-------germline1: 1.6e-18 0.000164 8.23e-38 0.000159 0.272450 ( 0.029337) 0.272291 ( 0.029336) 0.271250 0.271000 --->plink-------germline2: 3.32e-17 0.000138 1e+00 0.000000 0.272450 ( 0.029337) 0.272419 ( 0.029190) 0.271250 0.271000 --->plink-------dash-----: 1.31e-17 -0.064517 3.06e-26 -0.065891 0.272450 ( 0.029337) 0.338341 ( 0.047362) 0.271250 0.334800 --->germline1---germline2: 1e+00 0.000000 3.2e-01 -0.000128 0.272291 ( 0.029336) 0.272419 ( 0.029190) 0.271000 0.271000 --->germline1---dash-----: 1.31e-17 -0.064652 2.65e-26 -0.066050 0.272291 ( 0.029336) 0.338341 ( 0.047362) 0.271000 0.334800 --->germline2---dash-----: 1.31e-17 -0.064663 1.56e-26 -0.065922 0.272419 ( 0.029190) 0.338341 ( 0.047362) 0.271000 0.334800 ######FPRSnps###### --->fabia-------beagle1--: 3.96e-18 -0.020964 2.22e-80 -0.020958 0.016017 ( 0.003571) 0.036975 ( 0.001445) 0.015884 0.037002 --->fabia-------beagle2--: 3.96e-18 -0.020964 2.22e-80 -0.020958 0.016017 ( 0.003571) 0.036975 ( 0.001445) 0.015884 0.037002 --->fabia-------plink----: 3.96e-18 -0.020951 2.26e-80 -0.020950 0.016017 ( 0.003571) 0.036967 ( 0.001445) 0.015884 0.036989 --->fabia-------germline1: 3.96e-18 -0.020964 2.22e-80 -0.020958 0.016017 ( 0.003571) 0.036975 ( 0.001445) 0.015884 0.037002 --->fabia-------germline2: 3.96e-18 -0.020964 2.22e-80 -0.020951 0.016017 ( 0.003571) 0.036968 ( 0.001437) 0.015884 0.037002 --->fabia-------dash-----: 3.96e-18 -0.015447 2.05e-60 -0.015363 0.016017 ( 0.003571) 0.031380 ( 0.002625) 0.015884 0.031296 --->beagle1-----beagle2--: 1e+00 0.000000 1e+00 0.000000 0.036975 ( 0.001445) 0.036975 ( 0.001445) 0.037002 0.037002 --->beagle1-----plink----: 1e+00 0.000000 1e+00 0.000000 0.036975 ( 0.001445) 0.036967 ( 0.001445) 0.037002 0.036989 --->beagle1-----germline1: 1e+00 0.000000 1e+00 0.000000 0.036975 ( 0.001445) 0.036975 ( 0.001445) 0.037002 0.037002 --->beagle1-----germline2: 1e+00 0.000000 1e+00 0.000000 0.036975 ( 0.001445) 0.036968 ( 0.001437) 0.037002 0.037002 --->beagle1-----dash-----: 3.96e-18 0.005561 3.52e-40 0.005595 0.036975 ( 0.001445) 0.031380 ( 0.002625) 0.037002 0.031296 --->beagle2-----plink----: 1e+00 0.000000 1e+00 0.000000 0.036975 ( 0.001445) 0.036967 ( 0.001445) 0.037002 0.036989 --->beagle2-----germline1: 1e+00 0.000000 1e+00 0.000000 0.036975 ( 0.001445) 0.036975 ( 0.001445) 0.037002 0.037002 --->beagle2-----germline2: 1e+00 0.000000 1e+00 0.000000 0.036975 ( 0.001445) 0.036968 ( 0.001437) 0.037002 0.037002 --->beagle2-----dash-----: 3.96e-18 0.005561 3.52e-40 0.005595 0.036975 ( 0.001445) 0.031380 ( 0.002625) 0.037002 0.031296 --->plink-------germline1: 1e+00 0.000000 1e+00 0.000000 0.036967 ( 0.001445) 0.036975 ( 0.001445) 0.036989 0.037002 --->plink-------germline2: 1e+00 0.000000 1e+00 0.000000 0.036967 ( 0.001445) 0.036968 ( 0.001437) 0.036989 0.037002 --->plink-------dash-----: 3.96e-18 0.005551 3.94e-40 0.005587 0.036967 ( 0.001445) 0.031380 ( 0.002625) 0.036989 0.031296 --->germline1---germline2: 1e+00 0.000000 1e+00 0.000000 0.036975 ( 0.001445) 0.036968 ( 0.001437) 0.037002 0.037002 --->germline1---dash-----: 3.96e-18 0.005561 3.52e-40 0.005595 0.036975 ( 0.001445) 0.031380 ( 0.002625) 0.037002 0.031296 --->germline2---dash-----: 3.96e-18 0.005584 2.01e-40 0.005588 0.036968 ( 0.001437) 0.031380 ( 0.002625) 0.037002 0.031296 ######FDRSnps###### --->fabia-------beagle1--: 3.96e-18 -0.133137 2.19e-43 -0.135725 0.591984 ( 0.070637) 0.727709 ( 0.029336) 0.596951 0.729000 --->fabia-------beagle2--: 3.96e-18 -0.133137 2.19e-43 -0.135725 0.591984 ( 0.070637) 0.727709 ( 0.029336) 0.596951 0.729000 --->fabia-------plink----: 3.96e-18 -0.133087 2.22e-43 -0.135681 0.591984 ( 0.070637) 0.727666 ( 0.029341) 0.596951 0.728932 --->fabia-------germline1: 3.96e-18 -0.133137 2.19e-43 -0.135725 0.591984 ( 0.070637) 0.727709 ( 0.029336) 0.596951 0.729000 --->fabia-------germline2: 3.96e-18 -0.133081 2.28e-43 -0.135694 0.591984 ( 0.070637) 0.727679 ( 0.029296) 0.596951 0.729000 --->fabia-------dash-----: 3.96e-18 -0.137319 1.73e-44 -0.138864 0.591984 ( 0.070637) 0.730848 ( 0.038171) 0.596951 0.727184 --->beagle1-----beagle2--: 1e+00 0.000000 1e+00 0.000000 0.727709 ( 0.029336) 0.727709 ( 0.029336) 0.729000 0.729000 --->beagle1-----plink----: 1e+00 0.000000 1e+00 0.000000 0.727709 ( 0.029336) 0.727666 ( 0.029341) 0.729000 0.728932 --->beagle1-----germline1: 1e+00 0.000000 1e+00 0.000000 0.727709 ( 0.029336) 0.727709 ( 0.029336) 0.729000 0.729000 --->beagle1-----germline2: 1e+00 0.000000 1e+00 0.000000 0.727709 ( 0.029336) 0.727679 ( 0.029296) 0.729000 0.729000 --->beagle1-----dash-----: 3.02e-01 -0.002378 1.69e-01 -0.003139 0.727709 ( 0.029336) 0.730848 ( 0.038171) 0.729000 0.727184 --->beagle2-----plink----: 1e+00 0.000000 1e+00 0.000000 0.727709 ( 0.029336) 0.727666 ( 0.029341) 0.729000 0.728932 --->beagle2-----germline1: 1e+00 0.000000 1e+00 0.000000 0.727709 ( 0.029336) 0.727709 ( 0.029336) 0.729000 0.729000 --->beagle2-----germline2: 1e+00 0.000000 1e+00 0.000000 0.727709 ( 0.029336) 0.727679 ( 0.029296) 0.729000 0.729000 --->beagle2-----dash-----: 3.02e-01 -0.002378 1.69e-01 -0.003139 0.727709 ( 0.029336) 0.730848 ( 0.038171) 0.729000 0.727184 --->plink-------germline1: 1e+00 0.000000 1e+00 0.000000 0.727666 ( 0.029341) 0.727709 ( 0.029336) 0.728932 0.729000 --->plink-------germline2: 1e+00 0.000000 1e+00 0.000000 0.727666 ( 0.029341) 0.727679 ( 0.029296) 0.728932 0.729000 --->plink-------dash-----: 2.89e-01 -0.002379 1.63e-01 -0.003182 0.727666 ( 0.029341) 0.730848 ( 0.038171) 0.728932 0.727184 --->germline1---germline2: 1e+00 0.000000 1e+00 0.000000 0.727709 ( 0.029336) 0.727679 ( 0.029296) 0.729000 0.729000 --->germline1---dash-----: 3.02e-01 -0.002378 1.69e-01 -0.003139 0.727709 ( 0.029336) 0.730848 ( 0.038171) 0.729000 0.727184 --->germline2---dash-----: 2.94e-01 -0.002359 1.63e-01 -0.003169 0.727679 ( 0.029296) 0.730848 ( 0.038171) 0.729000 0.727184 ######specifitySnps###### --->fabia-------beagle1--: 1e+00 0.000000 1e+00 0.000000 0.020958 ( 0.003433) 0.000000 ( 0.000000) 0.020859 0.000000 --->fabia-------beagle2--: 1e+00 0.000000 1e+00 0.000000 0.020958 ( 0.003433) 0.000000 ( 0.000000) 0.020859 0.000000 --->fabia-------plink----: 3.96e-18 0.020951 2.26e-80 0.020950 0.020958 ( 0.003433) 8.08e-06 ( 3.9e-06) 0.020859 5.09e-06 --->fabia-------germline1: 1e+00 0.000000 1e+00 0.000000 0.020958 ( 0.003433) 0.000000 ( 0.000000) 0.020859 0.000000 --->fabia-------germline2: 3.96e-18 0.020964 2.22e-80 0.020951 0.020958 ( 0.003433) 6.49e-06 ( 6.49e-05) 0.020859 0.000000 --->fabia-------dash-----: 3.96e-18 0.015447 2.05e-60 0.015363 0.020958 ( 0.003433) 0.005595 ( 0.002523) 0.020859 0.005397 --->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) 8.08e-06 ( 3.9e-06) 0.000000 5.09e-06 --->beagle1-----germline1: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.000000 ( 0.000000) 0.000000 0.000000 --->beagle1-----germline2: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 6.49e-06 ( 6.49e-05) 0.000000 0.000000 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.005595 ( 0.002523) 0.000000 0.005397 --->beagle2-----plink----: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 8.08e-06 ( 3.9e-06) 0.000000 5.09e-06 --->beagle2-----germline1: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.000000 ( 0.000000) 0.000000 0.000000 --->beagle2-----germline2: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 6.49e-06 ( 6.49e-05) 0.000000 0.000000 --->beagle2-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.005595 ( 0.002523) 0.000000 0.005397 --->plink-------germline1: 1e+00 0.000000 1e+00 0.000000 8.08e-06 ( 3.9e-06) 0.000000 ( 0.000000) 5.09e-06 0.000000 --->plink-------germline2: 1e+00 0.000000 1e+00 0.000000 8.08e-06 ( 3.9e-06) 6.49e-06 ( 6.49e-05) 5.09e-06 0.000000 --->plink-------dash-----: 3.96e-18 -0.005536 3.94e-40 -0.005587 8.08e-06 ( 3.9e-06) 0.005595 ( 0.002523) 5.09e-06 0.005397 --->germline1---germline2: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 6.49e-06 ( 6.49e-05) 0.000000 0.000000 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.005595 ( 0.002523) 0.000000 0.005397 --->germline2---dash-----: 3.96e-18 -0.005581 2.01e-40 -0.005588 6.49e-06 ( 6.49e-05) 0.005595 ( 0.002523) 0.000000 0.005397 ######sensitivitySnps###### --->fabia-------beagle1--: 3.96e-18 -0.187812 1.33e-51 -0.187686 0.664378 ( 0.071368) 0.852065 ( 0.053445) 0.669063 0.854331 --->fabia-------beagle2--: 3.96e-18 -0.187812 1.33e-51 -0.187686 0.664378 ( 0.071368) 0.852065 ( 0.053445) 0.669063 0.854331 --->fabia-------plink----: 3.96e-18 -0.187812 1.33e-51 -0.187686 0.664378 ( 0.071368) 0.852065 ( 0.053445) 0.669063 0.854331 --->fabia-------germline1: 3.96e-18 -0.187812 1.33e-51 -0.187686 0.664378 ( 0.071368) 0.852065 ( 0.053445) 0.669063 0.854331 --->fabia-------germline2: 3.96e-18 -0.187812 1.33e-51 -0.187686 0.664378 ( 0.071368) 0.852065 ( 0.053445) 0.669063 0.854331 --->fabia-------dash-----: 1.07e-05 -0.052187 8.3e-06 -0.047439 0.664378 ( 0.071368) 0.711817 ( 0.094153) 0.669063 0.717637 --->beagle1-----beagle2--: 1e+00 0.000000 1e+00 0.000000 0.852065 ( 0.053445) 0.852065 ( 0.053445) 0.854331 0.854331 --->beagle1-----plink----: 1e+00 0.000000 1e+00 0.000000 0.852065 ( 0.053445) 0.852065 ( 0.053445) 0.854331 0.854331 --->beagle1-----germline1: 1e+00 0.000000 1e+00 0.000000 0.852065 ( 0.053445) 0.852065 ( 0.053445) 0.854331 0.854331 --->beagle1-----germline2: 1e+00 0.000000 1e+00 0.000000 0.852065 ( 0.053445) 0.852065 ( 0.053445) 0.854331 0.854331 --->beagle1-----dash-----: 2.65e-17 0.141198 8.27e-28 0.140248 0.852065 ( 0.053445) 0.711817 ( 0.094153) 0.854331 0.717637 --->beagle2-----plink----: 1e+00 0.000000 1e+00 0.000000 0.852065 ( 0.053445) 0.852065 ( 0.053445) 0.854331 0.854331 --->beagle2-----germline1: 1e+00 0.000000 1e+00 0.000000 0.852065 ( 0.053445) 0.852065 ( 0.053445) 0.854331 0.854331 --->beagle2-----germline2: 1e+00 0.000000 1e+00 0.000000 0.852065 ( 0.053445) 0.852065 ( 0.053445) 0.854331 0.854331 --->beagle2-----dash-----: 2.65e-17 0.141198 8.27e-28 0.140248 0.852065 ( 0.053445) 0.711817 ( 0.094153) 0.854331 0.717637 --->plink-------germline1: 1e+00 0.000000 1e+00 0.000000 0.852065 ( 0.053445) 0.852065 ( 0.053445) 0.854331 0.854331 --->plink-------germline2: 1e+00 0.000000 1e+00 0.000000 0.852065 ( 0.053445) 0.852065 ( 0.053445) 0.854331 0.854331 --->plink-------dash-----: 2.65e-17 0.141198 8.27e-28 0.140248 0.852065 ( 0.053445) 0.711817 ( 0.094153) 0.854331 0.717637 --->germline1---germline2: 1e+00 0.000000 1e+00 0.000000 0.852065 ( 0.053445) 0.852065 ( 0.053445) 0.854331 0.854331 --->germline1---dash-----: 2.65e-17 0.141198 8.27e-28 0.140248 0.852065 ( 0.053445) 0.711817 ( 0.094153) 0.854331 0.717637 --->germline2---dash-----: 2.65e-17 0.141198 8.27e-28 0.140248 0.852065 ( 0.053445) 0.711817 ( 0.094153) 0.854331 0.717637 ######trueNSnps###### --->fabia-------beagle1--: 1e+00 0 1e+00 0 4125 ( 677) 0 ( 0) 4099 0 --->fabia-------beagle2--: 1e+00 0 1e+00 0 4125 ( 677) 0 ( 0) 4099 0 --->fabia-------plink----: 3.96e-18 4117 2.56e-80 4123 4125 ( 677) 1.59 ( 0.767) 4099 1 --->fabia-------germline1: 1e+00 0 1e+00 0 4125 ( 677) 0 ( 0) 4099 0 --->fabia-------germline2: 3.96e-18 4116 2.51e-80 4123 4125 ( 677) 1.28 ( 12.8) 4099 0 --->fabia-------dash-----: 3.96e-18 3035 1.98e-60 3023 4125 ( 677) 1101 ( 497) 4099 1060 --->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) 1.590000 ( 0.766667) 0.000000 1.000000 --->beagle1-----germline1: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.000000 ( 0.000000) 0.000000 0.000000 --->beagle1-----germline2: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 1.280000 (12.800000) 0.000000 0.000000 --->beagle1-----dash-----: 1e+00 0 1e+00 0 0 ( 0) 1101 ( 497) 0 1060 --->beagle2-----plink----: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 1.590000 ( 0.766667) 0.000000 1.000000 --->beagle2-----germline1: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.000000 ( 0.000000) 0.000000 0.000000 --->beagle2-----germline2: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 1.280000 (12.800000) 0.000000 0.000000 --->beagle2-----dash-----: 1e+00 0 1e+00 0 0 ( 0) 1101 ( 497) 0 1060 --->plink-------germline1: 1e+00 0.000000 1e+00 0.000000 1.590000 ( 0.766667) 0.000000 ( 0.000000) 1.000000 0.000000 --->plink-------germline2: 1.17e-17 1.499979 8.07e-01 0.310000 1.590000 ( 0.766667) 1.280000 (12.800000) 1.000000 0.000000 --->plink-------dash-----: 3.96e-18 -1093 4.35e-40 -1100 1.59 ( 0.767) 1101 ( 497) 1 1060 --->germline1---germline2: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 1.280000 (12.800000) 0.000000 0.000000 --->germline1---dash-----: 1e+00 0 1e+00 0 0 ( 0) 1101 ( 497) 0 1060 --->germline2---dash-----: 3.96e-18 -1094 2.22e-40 -1100 1.28 ( 12.8) 1101 ( 497) 0 1060 ######falsePSnps###### --->fabia-------beagle1--: 3.96e-18 -4118 2.52e-80 -4125 3152 ( 704) 7277 ( 293) 3128 7290 --->fabia-------beagle2--: 3.96e-18 -4118 2.52e-80 -4125 3152 ( 704) 7277 ( 293) 3128 7290 --->fabia-------plink----: 3.96e-18 -4117 2.56e-80 -4123 3152 ( 704) 7276 ( 293) 3128 7288 --->fabia-------germline1: 3.96e-18 -4118 2.52e-80 -4125 3152 ( 704) 7277 ( 293) 3128 7290 --->fabia-------germline2: 3.96e-18 -4117 2.51e-80 -4123 3152 ( 704) 7276 ( 292) 3128 7290 --->fabia-------dash-----: 3.96e-18 -3035 1.98e-60 -3023 3152 ( 704) 6176 ( 518) 3128 6166 --->beagle1-----beagle2--: 1e+00 0 1e+00 0 7277 ( 293) 7277 ( 293) 7290 7290 --->beagle1-----plink----: 5.14e-19 1.5 8.23e-38 1.59 7277 ( 293) 7276 ( 293) 7290 7288 --->beagle1-----germline1: 1e+00 0 1e+00 0 7277 ( 293) 7277 ( 293) 7290 7290 --->beagle1-----germline2: 1e+00 0 3.2e-01 1.28 7277 ( 293) 7276 ( 292) 7290 7290 --->beagle1-----dash-----: 3.96e-18 1094 3.88e-40 1101 7277 ( 293) 6176 ( 518) 7290 6166 --->beagle2-----plink----: 5.14e-19 1.5 8.23e-38 1.59 7277 ( 293) 7276 ( 293) 7290 7288 --->beagle2-----germline1: 1e+00 0 1e+00 0 7277 ( 293) 7277 ( 293) 7290 7290 --->beagle2-----germline2: 1e+00 0 3.2e-01 1.28 7277 ( 293) 7276 ( 292) 7290 7290 --->beagle2-----dash-----: 3.96e-18 1094 3.88e-40 1101 7277 ( 293) 6176 ( 518) 7290 6166 --->plink-------germline1: 5.14e-19 -1.5 8.23e-38 -1.59 7276 ( 293) 7277 ( 293) 7288 7290 --->plink-------germline2: 1.17e-17 -1.5 8.07e-01 -0.31 7276 ( 293) 7276 ( 292) 7288 7290 --->plink-------dash-----: 3.96e-18 1093 4.35e-40 1100 7276 ( 293) 6176 ( 518) 7288 6166 --->germline1---germline2: 1e+00 0 3.2e-01 1.28 7277 ( 293) 7276 ( 292) 7290 7290 --->germline1---dash-----: 3.96e-18 1094 3.88e-40 1101 7277 ( 293) 6176 ( 518) 7290 6166 --->germline2---dash-----: 3.96e-18 1094 2.22e-40 1100 7276 ( 292) 6176 ( 518) 7290 6166 ######falseNSnps###### --->fabia-------beagle1--: 1e+00 0 1e+00 0 595 ( 192) 0 ( 0) 601 0 --->fabia-------beagle2--: 1e+00 0 1e+00 0 595 ( 192) 0 ( 0) 601 0 --->fabia-------plink----: 1e+00 0 1e+00 0 595 ( 192) 0 ( 0) 601 0 --->fabia-------germline1: 1e+00 0 1e+00 0 595 ( 192) 0 ( 0) 601 0 --->fabia-------germline2: 1e+00 0 1e+00 0 595 ( 192) 0 ( 0) 601 0 --->fabia-------dash-----: 8.9e-06 170 4.6e-06 154 595 ( 192) 441 ( 275) 601 434 --->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) 0.000000 ( 0.000000) 0.000000 0.000000 --->beagle1-----germline2: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.000000 ( 0.000000) 0.000000 0.000000 --->beagle1-----dash-----: 1e+00 0 1e+00 0 0 ( 0) 441 ( 275) 0 434 --->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) 0.000000 ( 0.000000) 0.000000 0.000000 --->beagle2-----germline2: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.000000 ( 0.000000) 0.000000 0.000000 --->beagle2-----dash-----: 1e+00 0 1e+00 0 0 ( 0) 441 ( 275) 0 434 --->plink-------germline1: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.000000 ( 0.000000) 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) 441 ( 275) 0 434 --->germline1---germline2: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.000000 ( 0.000000) 0.000000 0.000000 --->germline1---dash-----: 1e+00 0 1e+00 0 0 ( 0) 441 ( 275) 0 434 --->germline2---dash-----: 1e+00 0 1e+00 0 0 ( 0) 441 ( 275) 0 434 ######truePSnps###### --->fabia-------beagle1--: 3.95e-18 -595 1.01e-52 -595 2128 ( 328) 2723 ( 293) 2122 2710 --->fabia-------beagle2--: 3.95e-18 -595 1.01e-52 -595 2128 ( 328) 2723 ( 293) 2122 2710 --->fabia-------plink----: 3.95e-18 -595 1.01e-52 -595 2128 ( 328) 2723 ( 293) 2122 2710 --->fabia-------germline1: 3.95e-18 -595 1.01e-52 -595 2128 ( 328) 2723 ( 293) 2122 2710 --->fabia-------germline2: 3.95e-18 -595 1.01e-52 -595 2128 ( 328) 2723 ( 293) 2122 2710 --->fabia-------dash-----: 8.9e-06 -170 4.6e-06 -154 2128 ( 328) 2282 ( 399) 2122 2310 --->beagle1-----beagle2--: 1e+00 0 1e+00 0 2723 ( 293) 2723 ( 293) 2710 2710 --->beagle1-----plink----: 1e+00 0 1e+00 0 2723 ( 293) 2723 ( 293) 2710 2710 --->beagle1-----germline1: 1e+00 0 1e+00 0 2723 ( 293) 2723 ( 293) 2710 2710 --->beagle1-----germline2: 1e+00 0 1e+00 0 2723 ( 293) 2723 ( 293) 2710 2710 --->beagle1-----dash-----: 2.65e-17 452 3.23e-29 441 2723 ( 293) 2282 ( 399) 2710 2310 --->beagle2-----plink----: 1e+00 0 1e+00 0 2723 ( 293) 2723 ( 293) 2710 2710 --->beagle2-----germline1: 1e+00 0 1e+00 0 2723 ( 293) 2723 ( 293) 2710 2710 --->beagle2-----germline2: 1e+00 0 1e+00 0 2723 ( 293) 2723 ( 293) 2710 2710 --->beagle2-----dash-----: 2.65e-17 452 3.23e-29 441 2723 ( 293) 2282 ( 399) 2710 2310 --->plink-------germline1: 1e+00 0 1e+00 0 2723 ( 293) 2723 ( 293) 2710 2710 --->plink-------germline2: 1e+00 0 1e+00 0 2723 ( 293) 2723 ( 293) 2710 2710 --->plink-------dash-----: 2.65e-17 452 3.23e-29 441 2723 ( 293) 2282 ( 399) 2710 2310 --->germline1---germline2: 1e+00 0 1e+00 0 2723 ( 293) 2723 ( 293) 2710 2710 --->germline1---dash-----: 2.65e-17 452 3.23e-29 441 2723 ( 293) 2282 ( 399) 2710 2310 --->germline2---dash-----: 2.65e-17 452 3.23e-29 441 2723 ( 293) 2282 ( 399) 2710 2310 ######MatthewsSample###### --->fabia-------beagle1--: 3.96e-18 0.488228 3.53e-76 0.487224 0.491400 ( 0.090625) 0.004177 ( 0.034725) 0.491761 0.002731 --->fabia-------beagle2--: 3.96e-18 0.495091 8.28e-75 0.493903 0.491400 ( 0.090625) -0.002502 ( 0.032470) 0.491761 0.000558 --->fabia-------plink----: 1e+00 0.000000 1e+00 0.000000 0.491400 ( 0.090625) 0.000000 ( 0.000000) 0.491761 0.000000 --->fabia-------germline1: 3.96e-18 0.492701 1.35e-72 0.490343 0.491400 ( 0.090625) 0.001058 ( 0.030950) 0.491761 -0.000862 --->fabia-------germline2: 3.96e-18 0.495967 7.86e-72 0.492182 0.491400 ( 0.090625) -0.000781 ( 0.032329) 0.491761 0.000618 --->fabia-------dash-----: 3.96e-18 0.498974 2.68e-71 0.494329 0.491400 ( 0.090625) -0.002928 ( 0.033876) 0.491761 -0.003220 --->beagle1-----beagle2--: 5.48e-02 0.006831 4.61e-02 0.006679 0.004177 ( 0.034725) -0.002502 ( 0.032470) 0.002731 0.000558 --->beagle1-----plink----: 1e+00 0.000000 1e+00 0.000000 0.004177 ( 0.034725) 0.000000 ( 0.000000) 0.002731 0.000000 --->beagle1-----germline1: 5.65e-01 0.002700 5.24e-01 0.003119 0.004177 ( 0.034725) 0.001058 ( 0.030950) 0.002731 -0.000862 --->beagle1-----germline2: 3.31e-01 0.005962 3.57e-01 0.004958 0.004177 ( 0.034725) -0.000781 ( 0.032329) 0.002731 0.000618 --->beagle1-----dash-----: 1.84e-01 0.007755 1.94e-01 0.007105 0.004177 ( 0.034725) -0.002928 ( 0.033876) 0.002731 -0.003220 --->beagle2-----plink----: 1e+00 0.000000 1e+00 0.000000 -0.002502 ( 0.032470) 0.000000 ( 0.000000) 0.000558 0.000000 --->beagle2-----germline1: 2.97e-01 -0.004810 4.69e-01 -0.003560 -0.002502 ( 0.032470) 0.001058 ( 0.030950) 0.000558 -0.000862 --->beagle2-----germline2: 1e+00 0.000000 7.56e-01 -0.001721 -0.002502 ( 0.032470) -0.000781 ( 0.032329) 0.000558 0.000618 --->beagle2-----dash-----: 9.36e-01 -0.000452 9.4e-01 0.000426 -0.002502 ( 0.032470) -0.002928 ( 0.033876) 0.000558 -0.003220 --->plink-------germline1: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.001058 ( 0.030950) 0.000000 -0.000862 --->plink-------germline2: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) -0.000781 ( 0.032329) 0.000000 0.000618 --->plink-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) -0.002928 ( 0.033876) 0.000000 -0.003220 --->germline1---germline2: 6.34e-01 0.001424 5.69e-01 0.001839 0.001058 ( 0.030950) -0.000781 ( 0.032329) -0.000862 0.000618 --->germline1---dash-----: 3.54e-01 0.003343 2.44e-01 0.003986 0.001058 ( 0.030950) -0.002928 ( 0.033876) -0.000862 -0.003220 --->germline2---dash-----: 5.67e-01 0.001107 2.75e-01 0.002147 -0.000781 ( 0.032329) -0.002928 ( 0.033876) 0.000618 -0.003220 ######F1Sample###### --->fabia-------beagle1--: 3.96e-18 0.282410 2.74e-59 0.280693 0.538160 ( 0.079310) 0.257466 ( 0.021538) 0.536701 0.258264 --->fabia-------beagle2--: 3.96e-18 0.361701 2.43e-67 0.360465 0.538160 ( 0.079310) 0.177695 ( 0.026689) 0.536701 0.178475 --->fabia-------plink----: 4.08e-18 0.234263 3.72e-50 0.232241 0.538160 ( 0.079310) 0.305918 ( 0.004803) 0.536701 0.305802 --->fabia-------germline1: 4.08e-18 0.235853 2.51e-50 0.234000 0.538160 ( 0.079310) 0.304159 ( 0.005955) 0.536701 0.304424 --->fabia-------germline2: 3.96e-18 0.245520 3.91e-51 0.242877 0.538160 ( 0.079310) 0.295282 ( 0.011213) 0.536701 0.296146 --->fabia-------dash-----: 4.08e-18 0.251439 2.24e-51 0.248196 0.538160 ( 0.079310) 0.289964 ( 0.013865) 0.536701 0.290715 --->beagle1-----beagle2--: 3.96e-18 0.079285 2.47e-54 0.079771 0.257466 ( 0.021538) 0.177695 ( 0.026689) 0.258264 0.178475 --->beagle1-----plink----: 3.96e-18 -0.048007 3.71e-40 -0.048452 0.257466 ( 0.021538) 0.305918 ( 0.004803) 0.258264 0.305802 --->beagle1-----germline1: 4.08e-18 -0.046278 1.03e-37 -0.046693 0.257466 ( 0.021538) 0.304159 ( 0.005955) 0.258264 0.304424 --->beagle1-----germline2: 1.93e-17 -0.037285 4.17e-26 -0.037816 0.257466 ( 0.021538) 0.295282 ( 0.011213) 0.258264 0.296146 --->beagle1-----dash-----: 4.98e-15 -0.032310 4.18e-20 -0.032498 0.257466 ( 0.021538) 0.289964 ( 0.013865) 0.258264 0.290715 --->beagle2-----plink----: 3.96e-18 -0.128211 8.02e-70 -0.128223 0.177695 ( 0.026689) 0.305918 ( 0.004803) 0.178475 0.305802 --->beagle2-----germline1: 3.96e-18 -0.126535 6.78e-68 -0.126464 0.177695 ( 0.026689) 0.304159 ( 0.005955) 0.178475 0.304424 --->beagle2-----germline2: 3.96e-18 -0.117755 5.29e-59 -0.117587 0.177695 ( 0.026689) 0.295282 ( 0.011213) 0.178475 0.296146 --->beagle2-----dash-----: 3.96e-18 -0.112230 5.47e-55 -0.112269 0.177695 ( 0.026689) 0.289964 ( 0.013865) 0.178475 0.290715 --->plink-------germline1: 3.66e-05 0.001804 3.67e-05 0.001759 0.305918 ( 0.004803) 0.304159 ( 0.005955) 0.305802 0.304424 --->plink-------germline2: 1.93e-14 0.010440 1.52e-18 0.010636 0.305918 ( 0.004803) 0.295282 ( 0.011213) 0.305802 0.296146 --->plink-------dash-----: 4.42e-16 0.015492 3.02e-22 0.015954 0.305918 ( 0.004803) 0.289964 ( 0.013865) 0.305802 0.290715 --->germline1---germline2: 3.46e-14 0.008643 1.64e-17 0.008877 0.304159 ( 0.005955) 0.295282 ( 0.011213) 0.304424 0.296146 --->germline1---dash-----: 2.11e-16 0.013677 3.82e-22 0.014195 0.304159 ( 0.005955) 0.289964 ( 0.013865) 0.304424 0.290715 --->germline2---dash-----: 9.45e-10 0.004602 3.92e-10 0.005318 0.295282 ( 0.011213) 0.289964 ( 0.013865) 0.296146 0.290715 ######accuracySample###### --->fabia-------beagle1--: 3.95e-18 0.348250 4.93e-109 0.348010 0.891890 ( 0.023512) 0.543880 ( 0.020189) 0.892750 0.547500 --->fabia-------beagle2--: 3.95e-18 0.187532 1.44e-85 0.187860 0.891890 ( 0.023512) 0.704030 ( 0.013977) 0.892750 0.704000 --->fabia-------plink----: 3.95e-18 0.711791 9.68e-148 0.711300 0.891890 ( 0.023512) 0.180590 ( 0.003349) 0.892750 0.180500 --->fabia-------germline1: 3.95e-18 0.685545 1.88e-144 0.685210 0.891890 ( 0.023512) 0.206680 ( 0.011021) 0.892750 0.204500 --->fabia-------germline2: 3.95e-18 0.592524 6.82e-136 0.591830 0.891890 ( 0.023512) 0.300060 ( 0.013078) 0.892750 0.300000 --->fabia-------dash-----: 3.95e-18 0.554777 1.16e-124 0.553270 0.891890 ( 0.023512) 0.338620 ( 0.024184) 0.892750 0.332500 --->beagle1-----beagle2--: 3.94e-18 -0.160017 1.04e-100 -0.160150 0.543880 ( 0.020189) 0.704030 ( 0.013977) 0.547500 0.704000 --->beagle1-----plink----: 3.94e-18 0.363950 7.9e-125 0.363290 0.543880 ( 0.020189) 0.180590 ( 0.003349) 0.547500 0.180500 --->beagle1-----germline1: 3.95e-18 0.337466 1.75e-115 0.337200 0.543880 ( 0.020189) 0.206680 ( 0.011021) 0.547500 0.204500 --->beagle1-----germline2: 3.94e-18 0.244007 1.22e-96 0.243820 0.543880 ( 0.020189) 0.300060 ( 0.013078) 0.547500 0.300000 --->beagle1-----dash-----: 3.95e-18 0.206928 3.39e-78 0.205260 0.543880 ( 0.020189) 0.338620 ( 0.024184) 0.547500 0.332500 --->beagle2-----plink----: 3.93e-18 0.523521 4.62e-155 0.523440 0.704030 ( 0.013977) 0.180590 ( 0.003349) 0.704000 0.180500 --->beagle2-----germline1: 3.94e-18 0.497978 2.23e-142 0.497350 0.704030 ( 0.013977) 0.206680 ( 0.011021) 0.704000 0.204500 --->beagle2-----germline2: 3.93e-18 0.404925 3.73e-126 0.403970 0.704030 ( 0.013977) 0.300060 ( 0.013078) 0.704000 0.300000 --->beagle2-----dash-----: 3.95e-18 0.366483 1.02e-106 0.365410 0.704030 ( 0.013977) 0.338620 ( 0.024184) 0.704000 0.332500 --->plink-------germline1: 3.92e-18 -0.025444 7.02e-43 -0.026090 0.180590 ( 0.003349) 0.206680 ( 0.011021) 0.180500 0.204500 --->plink-------germline2: 3.91e-18 -0.119496 4.69e-99 -0.119470 0.180590 ( 0.003349) 0.300060 ( 0.013078) 0.180500 0.300000 --->plink-------dash-----: 3.94e-18 -0.156533 1.01e-83 -0.158030 0.180590 ( 0.003349) 0.338620 ( 0.024184) 0.180500 0.332500 --->germline1---germline2: 3.92e-18 -0.093455 6.89e-99 -0.093380 0.206680 ( 0.011021) 0.300060 ( 0.013078) 0.204500 0.300000 --->germline1---dash-----: 3.95e-18 -0.131060 1.19e-82 -0.131940 0.206680 ( 0.011021) 0.338620 ( 0.024184) 0.204500 0.332500 --->germline2---dash-----: 3.94e-18 -0.037540 9.05e-38 -0.038560 0.300060 ( 0.013078) 0.338620 ( 0.024184) 0.300000 0.332500 ######FPRSample###### --->fabia-------beagle1--: 3.96e-18 -0.014124 1.17e-100 -0.014120 0.003792 ( 0.001038) 0.017912 ( 0.001016) 0.003857 0.017929 --->fabia-------beagle2--: 3.96e-18 -0.003633 1.67e-50 -0.003651 0.003792 ( 0.001038) 0.007444 ( 0.000648) 0.003857 0.007374 --->fabia-------plink----: 3.95e-18 -0.037607 3.57e-156 -0.037592 0.003792 ( 0.001038) 0.041384 ( 0.000169) 0.003857 0.041389 --->fabia-------germline1: 3.96e-18 -0.035912 9.06e-151 -0.035911 0.003792 ( 0.001038) 0.039704 ( 0.000635) 0.003857 0.039798 --->fabia-------germline2: 3.96e-18 -0.029880 1.65e-144 -0.029844 0.003792 ( 0.001038) 0.033636 ( 0.000580) 0.003857 0.033636 --->fabia-------dash-----: 3.96e-18 -0.027398 1.04e-123 -0.027315 0.003792 ( 0.001038) 0.031108 ( 0.001438) 0.003857 0.031414 --->beagle1-----beagle2--: 3.95e-18 0.010505 3.74e-111 0.010468 0.017912 ( 0.001016) 0.007444 ( 0.000648) 0.017929 0.007374 --->beagle1-----plink----: 3.95e-18 -0.023489 2.32e-136 -0.023472 0.017912 ( 0.001016) 0.041384 ( 0.000169) 0.017929 0.041389 --->beagle1-----germline1: 3.95e-18 -0.021793 2.08e-125 -0.021791 0.017912 ( 0.001016) 0.039704 ( 0.000635) 0.017929 0.039798 --->beagle1-----germline2: 3.95e-18 -0.015725 5.05e-110 -0.015724 0.017912 ( 0.001016) 0.033636 ( 0.000580) 0.017929 0.033636 --->beagle1-----dash-----: 3.95e-18 -0.013307 5.04e-84 -0.013195 0.017912 ( 0.001016) 0.031108 ( 0.001438) 0.017929 0.031414 --->beagle2-----plink----: 3.95e-18 -0.033986 1.86e-171 -0.033940 0.007444 ( 0.000648) 0.041384 ( 0.000169) 0.007374 0.041389 --->beagle2-----germline1: 3.95e-18 -0.032296 3.65e-155 -0.032260 0.007444 ( 0.000648) 0.039704 ( 0.000635) 0.007374 0.039798 --->beagle2-----germline2: 3.95e-18 -0.026225 6.12e-145 -0.026192 0.007444 ( 0.000648) 0.033636 ( 0.000580) 0.007374 0.033636 --->beagle2-----dash-----: 3.95e-18 -0.023753 3.97e-114 -0.023664 0.007444 ( 0.000648) 0.031108 ( 0.001438) 0.007374 0.031414 --->plink-------germline1: 3.94e-18 0.001653 3.91e-47 0.001681 0.041384 ( 0.000169) 0.039704 ( 0.000635) 0.041389 0.039798 --->plink-------germline2: 3.92e-18 0.007755 4.2e-116 0.007748 0.041384 ( 0.000169) 0.033636 ( 0.000580) 0.041389 0.033636 --->plink-------dash-----: 3.95e-18 0.010179 2.03e-87 0.010277 0.041384 ( 0.000169) 0.031108 ( 0.001438) 0.041389 0.031414 --->germline1---germline2: 3.93e-18 0.006035 1.8e-110 0.006067 0.039704 ( 0.000635) 0.033636 ( 0.000580) 0.039798 0.033636 --->germline1---dash-----: 3.95e-18 0.008513 1.16e-85 0.008596 0.039704 ( 0.000635) 0.031108 ( 0.001438) 0.039798 0.031414 --->germline2---dash-----: 3.95e-18 0.002443 1.63e-39 0.002529 0.033636 ( 0.000580) 0.031108 ( 0.001438) 0.033636 0.031414 ######FDRSample###### --->fabia-------beagle1--: 3.96e-18 -0.277216 1.49e-56 -0.278595 0.538965 ( 0.084190) 0.817560 ( 0.015145) 0.540821 0.816009 --->fabia-------beagle2--: 3.96e-18 -0.279994 2.62e-54 -0.282381 0.538965 ( 0.084190) 0.821345 ( 0.026910) 0.540821 0.820225 --->fabia-------plink----: 3.96e-18 -0.279693 1.61e-55 -0.280445 0.538965 ( 0.084190) 0.819410 ( 0.003349) 0.540821 0.819500 --->fabia-------germline1: 3.96e-18 -0.279620 1.91e-55 -0.280320 0.538965 ( 0.084190) 0.819285 ( 0.003938) 0.540821 0.819416 --->fabia-------germline2: 3.96e-18 -0.279815 3.48e-55 -0.280566 0.538965 ( 0.084190) 0.819531 ( 0.007220) 0.540821 0.819211 --->fabia-------dash-----: 3.96e-18 -0.280925 5.16e-55 -0.281125 0.538965 ( 0.084190) 0.820089 ( 0.008675) 0.540821 0.819711 --->beagle1-----beagle2--: 9.99e-02 -0.003980 1.05e-01 -0.003785 0.817560 ( 0.015145) 0.821345 ( 0.026910) 0.816009 0.820225 --->beagle1-----plink----: 1.71e-01 -0.002156 2.26e-01 -0.001850 0.817560 ( 0.015145) 0.819410 ( 0.003349) 0.816009 0.819500 --->beagle1-----germline1: 1.93e-01 -0.002060 2.72e-01 -0.001725 0.817560 ( 0.015145) 0.819285 ( 0.003938) 0.816009 0.819416 --->beagle1-----germline2: 1.83e-01 -0.002420 2.72e-01 -0.001971 0.817560 ( 0.015145) 0.819531 ( 0.007220) 0.816009 0.819211 --->beagle1-----dash-----: 1.32e-01 -0.002968 1.79e-01 -0.002529 0.817560 ( 0.015145) 0.820089 ( 0.008675) 0.816009 0.819711 --->beagle2-----plink----: 4.65e-01 0.002069 4.73e-01 0.001935 0.821345 ( 0.026910) 0.819410 ( 0.003349) 0.820225 0.819500 --->beagle2-----germline1: 4.44e-01 0.002185 4.54e-01 0.002060 0.821345 ( 0.026910) 0.819285 ( 0.003938) 0.820225 0.819416 --->beagle2-----germline2: 4.99e-01 0.002221 5.47e-01 0.001815 0.821345 ( 0.026910) 0.819531 ( 0.007220) 0.820225 0.819211 --->beagle2-----dash-----: 6.17e-01 0.001626 6.85e-01 0.001256 0.821345 ( 0.026910) 0.820089 ( 0.008675) 0.820225 0.819711 --->plink-------germline1: 1e+00 0.000000 6.09e-01 0.000125 0.819410 ( 0.003349) 0.819285 ( 0.003938) 0.819500 0.819416 --->plink-------germline2: 9.68e-01 -1.67e-07 8.42e-01 -0.000121 0.819410 ( 0.003349) 0.819531 ( 0.007220) 0.819500 0.819211 --->plink-------dash-----: 5.74e-01 -0.000467 3.75e-01 -0.000679 0.819410 ( 0.003349) 0.820089 ( 0.008675) 0.819500 0.819711 --->germline1---germline2: 8.06e-01 -0.000125 6.37e-01 -0.000246 0.819285 ( 0.003938) 0.819531 ( 0.007220) 0.819416 0.819211 --->germline1---dash-----: 4.12e-01 -0.000491 2.38e-01 -0.000804 0.819285 ( 0.003938) 0.820089 ( 0.008675) 0.819416 0.819711 --->germline2---dash-----: 5.37e-01 -0.000281 2.08e-01 -0.000559 0.819531 ( 0.007220) 0.820089 ( 0.008675) 0.819211 0.819711 ######specifitySample###### --->fabia-------beagle1--: 3.96e-18 0.018216 8.28e-111 0.018209 0.041681 ( 0.001049) 0.023472 ( 0.001033) 0.041658 0.023485 --->fabia-------beagle2--: 3.96e-18 0.007714 2.68e-80 0.007741 0.041681 ( 0.001049) 0.033940 ( 0.000660) 0.041658 0.034015 --->fabia-------plink----: 1e+00 0.000000 1e+00 0.000000 0.041681 ( 0.001049) 0.000000 ( 0.000000) 0.041658 0.000000 --->fabia-------germline1: 3.96e-18 0.040002 5.13e-155 0.040001 0.041681 ( 0.001049) 0.001681 ( 0.000628) 0.041658 0.001591 --->fabia-------germline2: 3.96e-18 0.033949 5.96e-150 0.033933 0.041681 ( 0.001049) 0.007748 ( 0.000547) 0.041658 0.007778 --->fabia-------dash-----: 3.96e-18 0.031486 9.91e-130 0.031405 0.041681 ( 0.001049) 0.010277 ( 0.001424) 0.041658 0.009975 --->beagle1-----beagle2--: 3.95e-18 -0.010455 3.74e-111 -0.010468 0.023472 ( 0.001033) 0.033940 ( 0.000660) 0.023485 0.034015 --->beagle1-----plink----: 1e+00 0.000000 1e+00 0.000000 0.023472 ( 0.001033) 0.000000 ( 0.000000) 0.023485 0.000000 --->beagle1-----germline1: 3.95e-18 0.021793 2.08e-125 0.021791 0.023472 ( 0.001033) 0.001681 ( 0.000628) 0.023485 0.001591 --->beagle1-----germline2: 3.95e-18 0.015727 5.05e-110 0.015724 0.023472 ( 0.001033) 0.007748 ( 0.000547) 0.023485 0.007778 --->beagle1-----dash-----: 3.95e-18 0.013301 5.04e-84 0.013195 0.023472 ( 0.001033) 0.010277 ( 0.001424) 0.023485 0.009975 --->beagle2-----plink----: 1e+00 0.000000 1e+00 0.000000 0.033940 ( 0.000660) 0.000000 ( 0.000000) 0.034015 0.000000 --->beagle2-----germline1: 3.95e-18 0.032281 3.65e-155 0.032260 0.033940 ( 0.000660) 0.001681 ( 0.000628) 0.034015 0.001591 --->beagle2-----germline2: 3.95e-18 0.026224 6.12e-145 0.026192 0.033940 ( 0.000660) 0.007748 ( 0.000547) 0.034015 0.007778 --->beagle2-----dash-----: 3.95e-18 0.023742 3.97e-114 0.023664 0.033940 ( 0.000660) 0.010277 ( 0.001424) 0.034015 0.009975 --->plink-------germline1: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.001681 ( 0.000628) 0.000000 0.001591 --->plink-------germline2: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.007748 ( 0.000547) 0.000000 0.007778 --->plink-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.010277 ( 0.001424) 0.000000 0.009975 --->germline1---germline2: 3.93e-18 -0.006035 1.8e-110 -0.006067 0.001681 ( 0.000628) 0.007748 ( 0.000547) 0.001591 0.007778 --->germline1---dash-----: 3.95e-18 -0.008549 1.16e-85 -0.008596 0.001681 ( 0.000628) 0.010277 ( 0.001424) 0.001591 0.009975 --->germline2---dash-----: 3.95e-18 -0.002439 1.63e-39 -0.002529 0.007748 ( 0.000547) 0.010277 ( 0.001424) 0.007778 0.009975 ######sensitivitySample###### --->fabia-------beagle1--: 4.32e-18 0.229966 2.51e-42 0.228650 0.624300 ( 0.094214) 0.395650 ( 0.038558) 0.625000 0.395000 --->fabia-------beagle2--: 3.94e-18 0.465060 8.24e-72 0.464250 0.624300 ( 0.094214) 0.160050 ( 0.025589) 0.625000 0.160000 --->fabia-------plink----: 3.94e-18 -0.277496 6.46e-49 -0.278650 0.624300 ( 0.094214) 0.902950 ( 0.016744) 0.625000 0.902500 --->fabia-------germline1: 3.94e-18 -0.240064 3.51e-43 -0.242700 0.624300 ( 0.094214) 0.867000 ( 0.022652) 0.625000 0.865000 --->fabia-------germline2: 3.65e-14 -0.109991 7.68e-18 -0.108950 0.624300 ( 0.094214) 0.733250 ( 0.029894) 0.625000 0.735000 --->fabia-------dash-----: 2.63e-05 -0.049971 1.01e-05 -0.051400 0.624300 ( 0.094214) 0.675700 ( 0.045361) 0.625000 0.680000 --->beagle1-----beagle2--: 3.91e-18 0.234938 1.49e-84 0.235600 0.395650 ( 0.038558) 0.160050 ( 0.025589) 0.395000 0.160000 --->beagle1-----plink----: 3.87e-18 -0.507589 4.75e-111 -0.507300 0.395650 ( 0.038558) 0.902950 ( 0.016744) 0.395000 0.902500 --->beagle1-----germline1: 3.9e-18 -0.470036 4.28e-104 -0.471350 0.395650 ( 0.038558) 0.867000 ( 0.022652) 0.395000 0.865000 --->beagle1-----germline2: 3.9e-18 -0.337469 2.46e-83 -0.337600 0.395650 ( 0.038558) 0.733250 ( 0.029894) 0.395000 0.735000 --->beagle1-----dash-----: 3.94e-18 -0.282477 3.09e-65 -0.280050 0.395650 ( 0.038558) 0.675700 ( 0.045361) 0.395000 0.680000 --->beagle2-----plink----: 3.83e-18 -0.742518 2.13e-140 -0.742900 0.160050 ( 0.025589) 0.902950 ( 0.016744) 0.160000 0.902500 --->beagle2-----germline1: 3.89e-18 -0.707464 6.4e-133 -0.706950 0.160050 ( 0.025589) 0.867000 ( 0.022652) 0.160000 0.865000 --->beagle2-----germline2: 3.91e-18 -0.574999 2.07e-112 -0.573200 0.160050 ( 0.025589) 0.733250 ( 0.029894) 0.160000 0.735000 --->beagle2-----dash-----: 3.93e-18 -0.517531 4.59e-96 -0.515650 0.160050 ( 0.025589) 0.675700 ( 0.045361) 0.160000 0.680000 --->plink-------germline1: 3.61e-18 0.035004 9.12e-40 0.035950 0.902950 ( 0.016744) 0.867000 ( 0.022652) 0.902500 0.865000 --->plink-------germline2: 3.76e-18 0.169974 6.49e-84 0.169700 0.902950 ( 0.016744) 0.733250 ( 0.029894) 0.902500 0.735000 --->plink-------dash-----: 3.91e-18 0.224937 2.21e-74 0.227250 0.902950 ( 0.016744) 0.675700 ( 0.045361) 0.902500 0.680000 --->germline1---germline2: 3.75e-18 0.134969 1.13e-74 0.133750 0.867000 ( 0.022652) 0.733250 ( 0.029894) 0.865000 0.735000 --->germline1---dash-----: 3.91e-18 0.189980 1.98e-71 0.191300 0.867000 ( 0.022652) 0.675700 ( 0.045361) 0.865000 0.680000 --->germline2---dash-----: 3.88e-18 0.054974 5.56e-34 0.057550 0.733250 ( 0.029894) 0.675700 ( 0.045361) 0.735000 0.680000 ######trueNSample###### --->fabia-------beagle1--: 3.95e-18 1194 5.01e-142 1194 1659 ( 41.7) 465 ( 20.5) 1658 465 --->fabia-------beagle2--: 3.95e-18 987 2.2e-135 987 1659 ( 41.7) 672 ( 13.1) 1658 674 --->fabia-------plink----: 1e+00 0 1e+00 0 1659 ( 41.7) 0 ( 0) 1658 0 --->fabia-------germline1: 3.95e-18 1626 1.74e-159 1626 1659 ( 41.7) 33.3 ( 12.4) 1658 31.5 --->fabia-------germline2: 3.94e-18 1506 7.38e-157 1506 1659 ( 41.7) 153 ( 10.8) 1658 154 --->fabia-------dash-----: 3.95e-18 1456 1.68e-150 1455 1659 ( 41.7) 203 ( 28.2) 1658 198 --->beagle1-----beagle2--: 3.93e-18 -207 3.74e-111 -207 465 ( 20.5) 672 ( 13.1) 465 674 --->beagle1-----plink----: 1e+00 0 1e+00 0 465 ( 20.5) 0 ( 0) 465 0 --->beagle1-----germline1: 3.94e-18 431 2.08e-125 431 465 ( 20.5) 33.3 ( 12.4) 465 31.5 --->beagle1-----germline2: 3.94e-18 311 5.05e-110 311 465 ( 20.5) 153 ( 10.8) 465 154 --->beagle1-----dash-----: 3.94e-18 263 5.04e-84 261 465 ( 20.5) 203 ( 28.2) 465 198 --->beagle2-----plink----: 1e+00 0 1e+00 0 672 ( 13.1) 0 ( 0) 674 0 --->beagle2-----germline1: 3.93e-18 639 3.65e-155 639 672 ( 13.1) 33.3 ( 12.4) 674 31.5 --->beagle2-----germline2: 3.94e-18 519 6.12e-145 519 672 ( 13.1) 153 ( 10.8) 674 154 --->beagle2-----dash-----: 3.94e-18 470 3.97e-114 469 672 ( 13.1) 203 ( 28.2) 674 198 --->plink-------germline1: 1e+00 0 1e+00 0 0 ( 0) 33.3 ( 12.4) 0 31.5 --->plink-------germline2: 1e+00 0 1e+00 0 0 ( 0) 153 ( 10.8) 0 154 --->plink-------dash-----: 1e+00 0 1e+00 0 0 ( 0) 203 ( 28.2) 0 198 --->germline1---germline2: 3.88e-18 -120 1.8e-110 -120 33.3 ( 12.4) 153 ( 10.8) 31.5 154 --->germline1---dash-----: 3.94e-18 -169 1.16e-85 -170 33.3 ( 12.4) 203 ( 28.2) 31.5 198 --->germline2---dash-----: 3.93e-18 -48.5 1.63e-39 -50.1 153 ( 10.8) 203 ( 28.2) 154 198 ######falsePSample###### --->fabia-------beagle1--: 3.95e-18 -203 1.38e-67 -204 151 ( 41.3) 355 ( 20.1) 154 355 --->fabia-------beagle2--: 4.13e-01 4 4.2e-01 3.55 151 ( 41.3) 147 ( 12.8) 154 146 --->fabia-------plink----: 3.95e-18 -668 7.44e-122 -668 151 ( 41.3) 819 ( 3.35) 154 820 --->fabia-------germline1: 3.94e-18 -635 1.16e-119 -635 151 ( 41.3) 786 ( 12.6) 154 788 --->fabia-------germline2: 3.95e-18 -515 2.53e-111 -515 151 ( 41.3) 666 ( 11.5) 154 666 --->fabia-------dash-----: 3.95e-18 -466 6.06e-102 -465 151 ( 41.3) 616 ( 28.5) 154 622 --->beagle1-----beagle2--: 3.93e-18 207 3.74e-111 207 355 ( 20.1) 147 ( 12.8) 355 146 --->beagle1-----plink----: 3.94e-18 -465 2.32e-136 -465 355 ( 20.1) 819 ( 3.35) 355 820 --->beagle1-----germline1: 3.94e-18 -431 2.08e-125 -431 355 ( 20.1) 786 ( 12.6) 355 788 --->beagle1-----germline2: 3.94e-18 -311 5.05e-110 -311 355 ( 20.1) 666 ( 11.5) 355 666 --->beagle1-----dash-----: 3.94e-18 -263 5.04e-84 -261 355 ( 20.1) 616 ( 28.5) 355 622 --->beagle2-----plink----: 3.91e-18 -673 1.86e-171 -672 147 ( 12.8) 819 ( 3.35) 146 820 --->beagle2-----germline1: 3.93e-18 -639 3.65e-155 -639 147 ( 12.8) 786 ( 12.6) 146 788 --->beagle2-----germline2: 3.94e-18 -519 6.12e-145 -519 147 ( 12.8) 666 ( 11.5) 146 666 --->beagle2-----dash-----: 3.94e-18 -470 3.97e-114 -469 147 ( 12.8) 616 ( 28.5) 146 622 --->plink-------germline1: 3.91e-18 32.5 3.91e-47 33.3 819 ( 3.35) 786 ( 12.6) 820 788 --->plink-------germline2: 3.9e-18 153 4.2e-116 153 819 ( 3.35) 666 ( 11.5) 820 666 --->plink-------dash-----: 3.95e-18 202 2.03e-87 203 819 ( 3.35) 616 ( 28.5) 820 622 --->germline1---germline2: 3.88e-18 120 1.8e-110 120 786 ( 12.6) 666 ( 11.5) 788 666 --->germline1---dash-----: 3.94e-18 169 1.16e-85 170 786 ( 12.6) 616 ( 28.5) 788 622 --->germline2---dash-----: 3.93e-18 48.5 1.63e-39 50.1 666 ( 11.5) 616 ( 28.5) 666 622 ######falseNSample###### --->fabia-------beagle1--: 1.02e-17 -36.5 2.2e-35 -36.2 65.3 ( 19) 101 ( 8.06) 67 102 --->fabia-------beagle2--: 3.94e-18 -83.5 1.16e-68 -83.3 65.3 ( 19) 149 ( 5.95) 67 148 --->fabia-------plink----: 1e+00 0 1e+00 0 65.3 ( 19) 0 ( 0) 67 0 --->fabia-------germline1: 3.94e-18 57.5 1.37e-51 58.1 65.3 ( 19) 7.19 ( 3.28) 67 7 --->fabia-------germline2: 1.12e-17 31 7.82e-29 31.3 65.3 ( 19) 33.9 ( 5.11) 67 34 --->fabia-------dash-----: 7.41e-13 19.5 3.2e-15 19.8 65.3 ( 19) 45.5 ( 8.6) 67 45 --->beagle1-----beagle2--: 3.85e-18 -47 1.49e-84 -47.1 101 ( 8.06) 149 ( 5.95) 102 148 --->beagle1-----plink----: 1e+00 0 1e+00 0 101 ( 8.06) 0 ( 0) 102 0 --->beagle1-----germline1: 3.87e-18 94 4.28e-104 94.3 101 ( 8.06) 7.19 ( 3.28) 102 7 --->beagle1-----germline2: 3.88e-18 67.5 2.46e-83 67.5 101 ( 8.06) 33.9 ( 5.11) 102 34 --->beagle1-----dash-----: 3.92e-18 56.5 3.09e-65 56 101 ( 8.06) 45.5 ( 8.6) 102 45 --->beagle2-----plink----: 1e+00 0 1e+00 0 149 ( 5.95) 0 ( 0) 148 0 --->beagle2-----germline1: 3.87e-18 141 6.4e-133 141 149 ( 5.95) 7.19 ( 3.28) 148 7 --->beagle2-----germline2: 3.89e-18 115 2.07e-112 115 149 ( 5.95) 33.9 ( 5.11) 148 34 --->beagle2-----dash-----: 3.91e-18 104 4.59e-96 103 149 ( 5.95) 45.5 ( 8.6) 148 45 --->plink-------germline1: 1e+00 0 1e+00 0 0 ( 0) 7.19 ( 3.28) 0 7 --->plink-------germline2: 1e+00 0 1e+00 0 0 ( 0) 33.9 ( 5.11) 0 34 --->plink-------dash-----: 1e+00 0 1e+00 0 0 ( 0) 45.5 ( 8.6) 0 45 --->germline1---germline2: 3.75e-18 -27 1.13e-74 -26.8 7.19 ( 3.28) 33.9 ( 5.11) 7 34 --->germline1---dash-----: 3.87e-18 -38 1.98e-71 -38.3 7.19 ( 3.28) 45.5 ( 8.6) 7 45 --->germline2---dash-----: 3.79e-18 -11 5.56e-34 -11.5 33.9 ( 5.11) 45.5 ( 8.6) 34 45 ######truePSample###### --->fabia-------beagle1--: 4.3e-18 46 2.51e-42 45.7 125 ( 18.8) 79.1 ( 7.71) 125 79 --->fabia-------beagle2--: 3.93e-18 93 8.24e-72 92.8 125 ( 18.8) 32 ( 5.12) 125 32 --->fabia-------plink----: 3.94e-18 -55.5 6.46e-49 -55.7 125 ( 18.8) 181 ( 3.35) 125 180 --->fabia-------germline1: 3.94e-18 -48 3.51e-43 -48.5 125 ( 18.8) 173 ( 4.53) 125 173 --->fabia-------germline2: 3.45e-14 -22 7.68e-18 -21.8 125 ( 18.8) 147 ( 5.98) 125 147 --->fabia-------dash-----: 2.71e-05 -10 1.01e-05 -10.3 125 ( 18.8) 135 ( 9.07) 125 136 --->beagle1-----beagle2--: 3.85e-18 47 1.49e-84 47.1 79.1 ( 7.71) 32 ( 5.12) 79 32 --->beagle1-----plink----: 3.85e-18 -102 4.75e-111 -101 79.1 ( 7.71) 181 ( 3.35) 79 180 --->beagle1-----germline1: 3.87e-18 -94 4.28e-104 -94.3 79.1 ( 7.71) 173 ( 4.53) 79 173 --->beagle1-----germline2: 3.88e-18 -67.5 2.46e-83 -67.5 79.1 ( 7.71) 147 ( 5.98) 79 147 --->beagle1-----dash-----: 3.92e-18 -56.5 3.09e-65 -56 79.1 ( 7.71) 135 ( 9.07) 79 136 --->beagle2-----plink----: 3.82e-18 -149 2.13e-140 -149 32 ( 5.12) 181 ( 3.35) 32 180 --->beagle2-----germline1: 3.87e-18 -141 6.4e-133 -141 32 ( 5.12) 173 ( 4.53) 32 173 --->beagle2-----germline2: 3.89e-18 -115 2.07e-112 -115 32 ( 5.12) 147 ( 5.98) 32 147 --->beagle2-----dash-----: 3.91e-18 -104 4.59e-96 -103 32 ( 5.12) 135 ( 9.07) 32 136 --->plink-------germline1: 3.58e-18 7 9.12e-40 7.19 181 ( 3.35) 173 ( 4.53) 180 173 --->plink-------germline2: 3.76e-18 34 6.49e-84 33.9 181 ( 3.35) 147 ( 5.98) 180 147 --->plink-------dash-----: 3.87e-18 45 2.21e-74 45.5 181 ( 3.35) 135 ( 9.07) 180 136 --->germline1---germline2: 3.75e-18 27 1.13e-74 26.8 173 ( 4.53) 147 ( 5.98) 173 147 --->germline1---dash-----: 3.87e-18 38 1.98e-71 38.3 173 ( 4.53) 135 ( 9.07) 173 136 --->germline2---dash-----: 3.79e-18 11 5.56e-34 11.5 147 ( 5.98) 135 ( 9.07) 147 136