Results: Wilcoxon-Rank-Sum Wilcoxon-median t-test t-test-mean mean1 (std) mean2 (std) median1 median2 ######Matthews###### --->fabia-------beagle1--: 1.41e-01 0.015903 8.45e-02 -0.026351 0.913520 ( 0.149366) 0.939871 ( 0.030535) 0.976608 0.946509 --->fabia-------beagle2--: 2.72e-02 0.023903 2.56e-01 -0.017285 0.913520 ( 0.149366) 0.930805 ( 0.035824) 0.976608 0.937665 --->fabia-------plink----: 3.96e-18 0.850896 3.64e-77 0.803097 0.913520 ( 0.149366) 0.110423 ( 0.012464) 0.976608 0.111891 --->fabia-------germline1: 5.13e-01 0.004215 8.11e-02 -0.024519 0.913520 ( 0.149366) 0.938039 ( 0.136061) 0.976608 0.964175 --->fabia-------germline2: 5.13e-01 0.004227 7.45e-02 -0.025253 0.913520 ( 0.149366) 0.938773 ( 0.135905) 0.976608 0.964175 --->fabia-------dash-----: 2.69e-01 0.007507 1.68e-01 -0.019555 0.913520 ( 0.149366) 0.933075 ( 0.136887) 0.976608 0.963726 --->beagle1-----beagle2--: 1.88e-02 0.013594 1.84e-02 0.009066 0.939871 ( 0.030535) 0.930805 ( 0.035824) 0.946509 0.937665 --->beagle1-----plink----: 3.96e-18 0.831930 1.62e-145 0.829447 0.939871 ( 0.030535) 0.110423 ( 0.012464) 0.946509 0.111891 --->beagle1-----germline1: 4.68e-04 -0.014088 8.91e-01 0.001832 0.939871 ( 0.030535) 0.938039 ( 0.136061) 0.946509 0.964175 --->beagle1-----germline2: 2.03e-04 -0.014686 9.34e-01 0.001098 0.939871 ( 0.030535) 0.938773 ( 0.135905) 0.946509 0.964175 --->beagle1-----dash-----: 2.49e-02 -0.010611 6.12e-01 0.006796 0.939871 ( 0.030535) 0.933075 ( 0.136887) 0.946509 0.963726 --->beagle2-----plink----: 3.96e-18 0.822182 2.31e-136 0.820381 0.930805 ( 0.035824) 0.110423 ( 0.012464) 0.937665 0.111891 --->beagle2-----germline1: 2e-06 -0.023496 6.02e-01 -0.007234 0.930805 ( 0.035824) 0.938039 ( 0.136061) 0.937665 0.964175 --->beagle2-----germline2: 6.69e-07 -0.023882 5.65e-01 -0.007968 0.930805 ( 0.035824) 0.938773 ( 0.135905) 0.937665 0.964175 --->beagle2-----dash-----: 2.92e-04 -0.018995 8.7e-01 -0.002270 0.930805 ( 0.035824) 0.933075 ( 0.136887) 0.937665 0.963726 --->plink-------germline1: 4.2e-18 -0.846441 1.53e-83 -0.827615 0.110423 ( 0.012464) 0.938039 ( 0.136061) 0.111891 0.964175 --->plink-------germline2: 4.2e-18 -0.846645 1.24e-83 -0.828350 0.110423 ( 0.012464) 0.938773 ( 0.135905) 0.111891 0.964175 --->plink-------dash-----: 4.2e-18 -0.840915 5.71e-83 -0.822651 0.110423 ( 0.012464) 0.933075 ( 0.136887) 0.111891 0.963726 --->germline1---germline2: 1e+00 0.000000 3.2e-01 -0.000734 0.938039 ( 0.136061) 0.938773 ( 0.135905) 0.964175 0.964175 --->germline1---dash-----: 5.97e-05 0.010631 8.41e-03 0.004964 0.938039 ( 0.136061) 0.933075 ( 0.136887) 0.964175 0.963726 --->germline2---dash-----: 3.57e-05 0.011257 4.66e-03 0.005698 0.938773 ( 0.135905) 0.933075 ( 0.136887) 0.964175 0.963726 ######F1###### --->fabia-------beagle1--: 1.58e-01 0.015351 4.4e-02 -0.033941 0.905191 ( 0.163814) 0.939132 ( 0.031380) 0.976338 0.946016 --->fabia-------beagle2--: 3.23e-02 0.023757 1.46e-01 -0.024452 0.905191 ( 0.163814) 0.929642 ( 0.037017) 0.976338 0.937432 --->fabia-------plink----: 5.78e-18 0.938912 1.82e-75 0.880239 0.905191 ( 0.163814) 0.024952 ( 0.003207) 0.976338 0.025281 --->fabia-------germline1: 5.47e-01 0.004089 3.93e-02 -0.032029 0.905191 ( 0.163814) 0.937220 ( 0.136082) 0.976338 0.963864 --->fabia-------germline2: 5.47e-01 0.004069 3.61e-02 -0.032828 0.905191 ( 0.163814) 0.938019 ( 0.135890) 0.976338 0.963864 --->fabia-------dash-----: 2.91e-01 0.007512 9.11e-02 -0.026498 0.905191 ( 0.163814) 0.931689 ( 0.137135) 0.976338 0.963446 --->beagle1-----beagle2--: 1.7e-02 0.014486 1.83e-02 0.009489 0.939132 ( 0.031380) 0.929642 ( 0.037017) 0.946016 0.937432 --->beagle1-----plink----: 3.96e-18 0.917141 5.43e-148 0.914180 0.939132 ( 0.031380) 0.024952 ( 0.003207) 0.946016 0.025281 --->beagle1-----germline1: 7.12e-04 -0.014065 8.86e-01 0.001912 0.939132 ( 0.031380) 0.937220 ( 0.136082) 0.946016 0.963864 --->beagle1-----germline2: 3.12e-04 -0.014602 9.33e-01 0.001113 0.939132 ( 0.031380) 0.938019 ( 0.135890) 0.946016 0.963864 --->beagle1-----dash-----: 3.55e-02 -0.010203 5.8e-01 0.007443 0.939132 ( 0.031380) 0.931689 ( 0.137135) 0.946016 0.963446 --->beagle2-----plink----: 3.96e-18 0.906682 1.09e-139 0.904690 0.929642 ( 0.037017) 0.024952 ( 0.003207) 0.937432 0.025281 --->beagle2-----germline1: 3.37e-06 -0.023732 5.86e-01 -0.007577 0.929642 ( 0.037017) 0.937220 ( 0.136082) 0.937432 0.963864 --->beagle2-----germline2: 1.15e-06 -0.024307 5.47e-01 -0.008377 0.929642 ( 0.037017) 0.938019 ( 0.135890) 0.937432 0.963864 --->beagle2-----dash-----: 5.53e-04 -0.018742 8.83e-01 -0.002046 0.929642 ( 0.037017) 0.931689 ( 0.137135) 0.937432 0.963446 --->plink-------germline1: 5.96e-18 -0.933005 4.13e-85 -0.912268 0.024952 ( 0.003207) 0.937220 ( 0.136082) 0.025281 0.963864 --->plink-------germline2: 5.96e-18 -0.933215 3.3e-85 -0.913067 0.024952 ( 0.003207) 0.938019 ( 0.135890) 0.025281 0.963864 --->plink-------dash-----: 5.96e-18 -0.926937 1.64e-84 -0.906737 0.024952 ( 0.003207) 0.931689 ( 0.137135) 0.025281 0.963446 --->germline1---germline2: 1e+00 0.000000 3.2e-01 -0.000799 0.937220 ( 0.136082) 0.938019 ( 0.135890) 0.963864 0.963864 --->germline1---dash-----: 2.64e-05 0.011888 7.72e-03 0.005531 0.937220 ( 0.136082) 0.931689 ( 0.137135) 0.963864 0.963446 --->germline2---dash-----: 1.6e-05 0.012444 4.28e-03 0.006330 0.938019 ( 0.135890) 0.931689 ( 0.137135) 0.963864 0.963446 ######accuracy###### --->fabia-------beagle1--: 1e+00 0.000000 1e+00 0.000000 0.999964 ( 6.92e-05) 0.999965 ( 1.88e-05) 0.999993 0.999969 --->fabia-------beagle2--: 1e+00 0.000000 1e+00 0.000000 0.999964 ( 6.92e-05) 0.999962 ( 1.85e-05) 0.999993 0.999965 --->fabia-------plink----: 3.96e-18 0.021908 2.92e-120 0.021953 0.999964 ( 6.92e-05) 0.978011 ( 0.001411) 0.999993 0.978081 --->fabia-------germline1: 1e+00 0.000000 1e+00 0.000000 0.999964 ( 6.92e-05) 0.999973 ( 2.23e-05) 0.999993 0.999979 --->fabia-------germline2: 1e+00 0.000000 1e+00 0.000000 0.999964 ( 6.92e-05) 0.999974 ( 2.21e-05) 0.999993 0.999979 --->fabia-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.999964 ( 6.92e-05) 0.999971 ( 2.41e-05) 0.999993 0.999979 --->beagle1-----beagle2--: 1e+00 0.000000 1e+00 0.000000 0.999965 ( 1.88e-05) 0.999962 ( 1.85e-05) 0.999969 0.999965 --->beagle1-----plink----: 3.96e-18 0.021898 3.74e-120 0.021954 0.999965 ( 1.88e-05) 0.978011 ( 0.001411) 0.999969 0.978081 --->beagle1-----germline1: 1e+00 0.000000 1e+00 0.000000 0.999965 ( 1.88e-05) 0.999973 ( 2.23e-05) 0.999969 0.999979 --->beagle1-----germline2: 1e+00 0.000000 1e+00 0.000000 0.999965 ( 1.88e-05) 0.999974 ( 2.21e-05) 0.999969 0.999979 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.999965 ( 1.88e-05) 0.999971 ( 2.41e-05) 0.999969 0.999979 --->beagle2-----plink----: 3.96e-18 0.021896 4.58e-120 0.021952 0.999962 ( 1.85e-05) 0.978011 ( 0.001411) 0.999965 0.978081 --->beagle2-----germline1: 1e+00 0.000000 1e+00 0.000000 0.999962 ( 1.85e-05) 0.999973 ( 2.23e-05) 0.999965 0.999979 --->beagle2-----germline2: 1e+00 0.000000 1e+00 0.000000 0.999962 ( 1.85e-05) 0.999974 ( 2.21e-05) 0.999965 0.999979 --->beagle2-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.999962 ( 1.85e-05) 0.999971 ( 2.41e-05) 0.999965 0.999979 --->plink-------germline1: 3.96e-18 -0.021917 3.59e-120 -0.021963 0.978011 ( 0.001411) 0.999973 ( 2.23e-05) 0.978081 0.999979 --->plink-------germline2: 3.96e-18 -0.021919 3.55e-120 -0.021963 0.978011 ( 0.001411) 0.999974 ( 2.21e-05) 0.978081 0.999979 --->plink-------dash-----: 3.96e-18 -0.021918 3.85e-120 -0.021960 0.978011 ( 0.001411) 0.999971 ( 2.41e-05) 0.978081 0.999979 --->germline1---germline2: 1e+00 0.000000 1e+00 0.000000 0.999973 ( 2.23e-05) 0.999974 ( 2.21e-05) 0.999979 0.999979 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 0.999973 ( 2.23e-05) 0.999971 ( 2.41e-05) 0.999979 0.999979 --->germline2---dash-----: 1e+00 0.000000 1e+00 0.000000 0.999974 ( 2.21e-05) 0.999971 ( 2.41e-05) 0.999979 0.999979 ######FPR###### --->fabia-------beagle1--: 1e+00 0.000000 1e+00 0.000000 3.09e-05 ( 7.03e-05) 2.21e-05 ( 1.85e-05) 0.000000 1.65e-05 --->fabia-------beagle2--: 1e+00 0.000000 1e+00 0.000000 3.09e-05 ( 7.03e-05) 1.1e-05 ( 7.15e-06) 0.000000 9.37e-06 --->fabia-------plink----: 3.96e-18 -0.021930 2.68e-120 -0.021963 3.09e-05 ( 7.03e-05) 0.021994 ( 0.001411) 0.000000 0.021926 --->fabia-------germline1: 1e+00 0.000000 1e+00 0.000000 3.09e-05 ( 7.03e-05) 2.16e-06 ( 3.65e-06) 0.000000 3.08e-07 --->fabia-------germline2: 1e+00 0.000000 1e+00 0.000000 3.09e-05 ( 7.03e-05) 2.16e-06 ( 3.65e-06) 0.000000 3.08e-07 --->fabia-------dash-----: 1e+00 0.000000 1e+00 0.000000 3.09e-05 ( 7.03e-05) 6.98e-07 ( 1.86e-06) 0.000000 0.000000 --->beagle1-----beagle2--: 1e+00 0.000000 1e+00 0.000000 2.21e-05 ( 1.85e-05) 1.1e-05 ( 7.15e-06) 1.65e-05 9.37e-06 --->beagle1-----plink----: 3.96e-18 -0.021925 3.1e-120 -0.021972 2.21e-05 ( 1.85e-05) 0.021994 ( 0.001411) 1.65e-05 0.021926 --->beagle1-----germline1: 1e+00 0.000000 1e+00 0.000000 2.21e-05 ( 1.85e-05) 2.16e-06 ( 3.65e-06) 1.65e-05 3.08e-07 --->beagle1-----germline2: 1e+00 0.000000 1e+00 0.000000 2.21e-05 ( 1.85e-05) 2.16e-06 ( 3.65e-06) 1.65e-05 3.08e-07 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 2.21e-05 ( 1.85e-05) 6.98e-07 ( 1.86e-06) 1.65e-05 0.000000 --->beagle2-----plink----: 3.96e-18 -0.021939 3.36e-120 -0.021983 1.1e-05 ( 7.15e-06) 0.021994 ( 0.001411) 9.37e-06 0.021926 --->beagle2-----germline1: 1e+00 0.000000 1e+00 0.000000 1.1e-05 ( 7.15e-06) 2.16e-06 ( 3.65e-06) 9.37e-06 3.08e-07 --->beagle2-----germline2: 1e+00 0.000000 1e+00 0.000000 1.1e-05 ( 7.15e-06) 2.16e-06 ( 3.65e-06) 9.37e-06 3.08e-07 --->beagle2-----dash-----: 1e+00 0.000000 1e+00 0.000000 1.1e-05 ( 7.15e-06) 6.98e-07 ( 1.86e-06) 9.37e-06 0.000000 --->plink-------germline1: 3.96e-18 0.021937 3.46e-120 0.021992 0.021994 ( 0.001411) 2.16e-06 ( 3.65e-06) 0.021926 3.08e-07 --->plink-------germline2: 3.96e-18 0.021937 3.46e-120 0.021992 0.021994 ( 0.001411) 2.16e-06 ( 3.65e-06) 0.021926 3.08e-07 --->plink-------dash-----: 3.96e-18 0.021937 3.42e-120 0.021993 0.021994 ( 0.001411) 6.98e-07 ( 1.86e-06) 0.021926 0.000000 --->germline1---germline2: 1e+00 0.000000 1e+00 0.000000 2.16e-06 ( 3.65e-06) 2.16e-06 ( 3.65e-06) 3.08e-07 3.08e-07 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 2.16e-06 ( 3.65e-06) 6.98e-07 ( 1.86e-06) 3.08e-07 0.000000 --->germline2---dash-----: 1e+00 0.000000 1e+00 0.000000 2.16e-06 ( 3.65e-06) 6.98e-07 ( 1.86e-06) 3.08e-07 0.000000 ######FDR###### --->fabia-------beagle1--: 6.76e-02 -0.034636 1.46e-01 0.031027 0.103907 ( 0.201116) 0.072879 ( 0.053199) 0.000000 0.056589 --->fabia-------beagle2--: 2.89e-01 -0.016871 2.07e-03 0.063049 0.103907 ( 0.201116) 0.040858 ( 0.026198) 0.000000 0.035005 --->fabia-------plink----: 3.96e-18 -0.986236 9.35e-67 -0.883457 0.103907 ( 0.201116) 0.987364 ( 0.001631) 0.000000 0.987198 --->fabia-------germline1: 5.62e-02 0.101525 7.4e-06 0.096036 0.103907 ( 0.201116) 0.007871 ( 0.012701) 0.000000 0.001152 --->fabia-------germline2: 5.62e-02 0.101525 7.4e-06 0.096037 0.103907 ( 0.201116) 0.007870 ( 0.012701) 0.000000 0.001152 --->fabia-------dash-----: 1e+00 0.000000 2.05e-06 0.101293 0.103907 ( 0.201116) 0.002613 ( 0.006680) 0.000000 0.000000 --->beagle1-----beagle2--: 2.91e-12 0.035965 4.33e-10 0.032022 0.072879 ( 0.053199) 0.040858 ( 0.026198) 0.056589 0.035005 --->beagle1-----plink----: 3.96e-18 -0.921520 1.16e-124 -0.914484 0.072879 ( 0.053199) 0.987364 ( 0.001631) 0.056589 0.987198 --->beagle1-----germline1: 3.96e-18 0.058592 1.4e-22 0.065009 0.072879 ( 0.053199) 0.007871 ( 0.012701) 0.056589 0.001152 --->beagle1-----germline2: 3.96e-18 0.058592 1.39e-22 0.065010 0.072879 ( 0.053199) 0.007870 ( 0.012701) 0.056589 0.001152 --->beagle1-----dash-----: 3.96e-18 0.062749 1.56e-23 0.070266 0.072879 ( 0.053199) 0.002613 ( 0.006680) 0.056589 0.000000 --->beagle2-----plink----: 3.96e-18 -0.949728 3.86e-157 -0.946506 0.040858 ( 0.026198) 0.987364 ( 0.001631) 0.035005 0.987198 --->beagle2-----germline1: 1.03e-16 0.029549 4.2e-21 0.032987 0.040858 ( 0.026198) 0.007871 ( 0.012701) 0.035005 0.001152 --->beagle2-----germline2: 1.03e-16 0.029549 4.2e-21 0.032988 0.040858 ( 0.026198) 0.007870 ( 0.012701) 0.035005 0.001152 --->beagle2-----dash-----: 3.96e-18 0.035208 8.38e-27 0.038244 0.040858 ( 0.026198) 0.002613 ( 0.006680) 0.035005 0.000000 --->plink-------germline1: 3.96e-18 0.981875 5.11e-188 0.979493 0.987364 ( 0.001631) 0.007871 ( 0.012701) 0.987198 0.001152 --->plink-------germline2: 3.96e-18 0.981873 5.13e-188 0.979494 0.987364 ( 0.001631) 0.007870 ( 0.012701) 0.987198 0.001152 --->plink-------dash-----: 3.96e-18 0.986581 1.12e-214 0.984750 0.987364 ( 0.001631) 0.002613 ( 0.006680) 0.987198 0.000000 --->germline1---germline2: 1e+00 0.000000 1e+00 0.000000 0.007871 ( 0.012701) 0.007870 ( 0.012701) 0.001152 0.001152 --->germline1---dash-----: 1.75e-07 0.012075 9.09e-06 0.005257 0.007871 ( 0.012701) 0.002613 ( 0.006680) 0.001152 0.000000 --->germline2---dash-----: 1.29e-07 0.011618 9.13e-06 0.005256 0.007870 ( 0.012701) 0.002613 ( 0.006680) 0.001152 0.000000 ######specifity###### --->fabia-------beagle1--: 1e+00 0.000000 1e+00 0.000000 0.999969 ( 7.03e-05) 0.999978 ( 1.85e-05) 1.000000 0.999984 --->fabia-------beagle2--: 1e+00 0.000000 1e+00 0.000000 0.999969 ( 7.03e-05) 0.999989 ( 7.15e-06) 1.000000 0.999991 --->fabia-------plink----: 3.96e-18 0.021917 2.68e-120 0.021963 0.999969 ( 7.03e-05) 0.978006 ( 0.001411) 1.000000 0.978074 --->fabia-------germline1: 1e+00 0.000000 1e+00 0.000000 0.999969 ( 7.03e-05) 0.999998 ( 3.66e-06) 1.000000 1.000000 --->fabia-------germline2: 1e+00 0.000000 1e+00 0.000000 0.999969 ( 7.03e-05) 0.999998 ( 3.66e-06) 1.000000 1.000000 --->fabia-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.999969 ( 7.03e-05) 0.999999 ( 1.86e-06) 1.000000 1.000000 --->beagle1-----beagle2--: 1e+00 0.000000 1e+00 0.000000 0.999978 ( 1.85e-05) 0.999989 ( 7.15e-06) 0.999984 0.999991 --->beagle1-----plink----: 3.96e-18 0.021915 3.1e-120 0.021972 0.999978 ( 1.85e-05) 0.978006 ( 0.001411) 0.999984 0.978074 --->beagle1-----germline1: 1e+00 0.000000 1e+00 0.000000 0.999978 ( 1.85e-05) 0.999998 ( 3.66e-06) 0.999984 1.000000 --->beagle1-----germline2: 1e+00 0.000000 1e+00 0.000000 0.999978 ( 1.85e-05) 0.999998 ( 3.66e-06) 0.999984 1.000000 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.999978 ( 1.85e-05) 0.999999 ( 1.86e-06) 0.999984 1.000000 --->beagle2-----plink----: 3.96e-18 0.021929 3.36e-120 0.021983 0.999989 ( 7.15e-06) 0.978006 ( 0.001411) 0.999991 0.978074 --->beagle2-----germline1: 1e+00 0.000000 1e+00 0.000000 0.999989 ( 7.15e-06) 0.999998 ( 3.66e-06) 0.999991 1.000000 --->beagle2-----germline2: 1e+00 0.000000 1e+00 0.000000 0.999989 ( 7.15e-06) 0.999998 ( 3.66e-06) 0.999991 1.000000 --->beagle2-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.999989 ( 7.15e-06) 0.999999 ( 1.86e-06) 0.999991 1.000000 --->plink-------germline1: 3.96e-18 -0.021948 3.46e-120 -0.021992 0.978006 ( 0.001411) 0.999998 ( 3.66e-06) 0.978074 1.000000 --->plink-------germline2: 3.96e-18 -0.021948 3.46e-120 -0.021992 0.978006 ( 0.001411) 0.999998 ( 3.66e-06) 0.978074 1.000000 --->plink-------dash-----: 3.96e-18 -0.021949 3.42e-120 -0.021993 0.978006 ( 0.001411) 0.999999 ( 1.86e-06) 0.978074 1.000000 --->germline1---germline2: 1e+00 0.000000 1e+00 0.000000 0.999998 ( 3.66e-06) 0.999998 ( 3.66e-06) 1.000000 1.000000 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 0.999998 ( 3.66e-06) 0.999999 ( 1.86e-06) 1.000000 1.000000 --->germline2---dash-----: 1e+00 0.000000 1e+00 0.000000 0.999998 ( 3.66e-06) 0.999999 ( 1.86e-06) 1.000000 1.000000 ######sensitivity###### --->fabia-------beagle1--: 5.55e-03 0.014172 5.97e-01 0.005066 0.959238 ( 0.103476) 0.954173 ( 0.036753) 0.982912 0.955440 --->fabia-------beagle2--: 2.3e-11 0.060222 5.68e-06 0.054363 0.959238 ( 0.103476) 0.904875 ( 0.067275) 0.982912 0.921476 --->fabia-------plink----: 1.55e-15 -0.026646 1.81e-10 -0.029079 0.959238 ( 0.103476) 0.988318 ( 0.101211) 0.982912 1.000000 --->fabia-------germline1: 1.49e-10 0.045688 4.49e-06 0.053604 0.959238 ( 0.103476) 0.905635 ( 0.135250) 0.982912 0.938527 --->fabia-------germline2: 1.63e-10 0.045425 6e-06 0.052267 0.959238 ( 0.103476) 0.906971 ( 0.134485) 0.982912 0.938527 --->fabia-------dash-----: 1.85e-12 0.056575 6.14e-08 0.067638 0.959238 ( 0.103476) 0.891600 ( 0.138174) 0.982912 0.930859 --->beagle1-----beagle2--: 1.14e-10 0.087352 8.11e-14 0.049298 0.954173 ( 0.036753) 0.904875 ( 0.067275) 0.955440 0.921476 --->beagle1-----plink----: 4e-15 -0.042508 6.04e-04 -0.034145 0.954173 ( 0.036753) 0.988318 ( 0.101211) 0.955440 1.000000 --->beagle1-----germline1: 4.13e-07 0.031967 5.59e-04 0.048538 0.954173 ( 0.036753) 0.905635 ( 0.135250) 0.955440 0.938527 --->beagle1-----germline2: 4.85e-07 0.031060 7.36e-04 0.047202 0.954173 ( 0.036753) 0.906971 ( 0.134485) 0.955440 0.938527 --->beagle1-----dash-----: 2.27e-09 0.043667 2.03e-05 0.062572 0.954173 ( 0.036753) 0.891600 ( 0.138174) 0.955440 0.930859 --->beagle2-----plink----: 2.15e-15 -0.094041 1.51e-10 -0.083443 0.904875 ( 0.067275) 0.988318 ( 0.101211) 0.921476 1.000000 --->beagle2-----germline1: 7.58e-02 -0.016021 9.61e-01 -0.000760 0.904875 ( 0.067275) 0.905635 ( 0.135250) 0.921476 0.938527 --->beagle2-----germline2: 5.79e-02 -0.016668 8.91e-01 -0.002096 0.904875 ( 0.067275) 0.906971 ( 0.134485) 0.921476 0.938527 --->beagle2-----dash-----: 8.35e-01 -0.002212 3.95e-01 0.013275 0.904875 ( 0.067275) 0.891600 ( 0.138174) 0.921476 0.930859 --->plink-------germline1: 5.78e-18 0.070803 3.84e-16 0.082683 0.988318 ( 0.101211) 0.905635 ( 0.135250) 1.000000 0.938527 --->plink-------germline2: 5.78e-18 0.070750 3.74e-16 0.081347 0.988318 ( 0.101211) 0.906971 ( 0.134485) 1.000000 0.938527 --->plink-------dash-----: 5.78e-18 0.087132 5.33e-18 0.096717 0.988318 ( 0.101211) 0.891600 ( 0.138174) 1.000000 0.930859 --->germline1---germline2: 1e+00 0.000000 3.2e-01 -0.001336 0.905635 ( 0.135250) 0.906971 ( 0.134485) 0.938527 0.938527 --->germline1---dash-----: 1.75e-07 0.029384 7.7e-05 0.014035 0.905635 ( 0.135250) 0.891600 ( 0.138174) 0.938527 0.930859 --->germline2---dash-----: 1.19e-07 0.030294 4.54e-05 0.015371 0.906971 ( 0.134485) 0.891600 ( 0.138174) 0.938527 0.930859 ######trueN###### --->fabia-------beagle1--: 3.96e-18 2e+08 0e+00 2e+08 4e+08 ( 28212) 2e+08 ( 5123) 4e+08 2e+08 --->fabia-------beagle2--: 3.96e-18 2e+08 0e+00 2e+08 4e+08 ( 28212) 2e+08 ( 3785) 4e+08 2e+08 --->fabia-------plink----: 3.96e-18 2.04e+08 2.2e-285 2.04e+08 4e+08 ( 28212) 1.96e+08 ( 282204) 4e+08 1.96e+08 --->fabia-------germline1: 2.9e-18 2e+08 0e+00 2e+08 4e+08 ( 28212) 2e+08 ( 3761) 4e+08 2e+08 --->fabia-------germline2: 2.9e-18 2e+08 0e+00 2e+08 4e+08 ( 28212) 2e+08 ( 3761) 4e+08 2e+08 --->fabia-------dash-----: 1.27e-18 2e+08 0e+00 2e+08 4e+08 ( 28212) 2e+08 ( 3672) 4e+08 2e+08 --->beagle1-----beagle2--: 5.33e-13 -2659 6.66e-10 -2229 2e+08 ( 5123) 2e+08 ( 3785) 2e+08 2e+08 --->beagle1-----plink----: 3.96e-18 4382911 3.1e-120 4393104 2e+08 ( 5123) 1.96e+08 ( 282204) 2e+08 1.96e+08 --->beagle1-----germline1: 3.96e-18 -3426 1.98e-19 -3993 2e+08 ( 5123) 2e+08 ( 3761) 2e+08 2e+08 --->beagle1-----germline2: 3.96e-18 -3426 1.98e-19 -3993 2e+08 ( 5123) 2e+08 ( 3761) 2e+08 2e+08 --->beagle1-----dash-----: 3.96e-18 -3663 4.12e-20 -4286 2e+08 ( 5123) 2e+08 ( 3672) 2e+08 2e+08 --->beagle2-----plink----: 3.96e-18 4385706 3.36e-120 4395334 2e+08 ( 3785) 1.96e+08 ( 282204) 2e+08 1.96e+08 --->beagle2-----germline1: 1.49e-16 -1609 1.17e-20 -1764 2e+08 ( 3785) 2e+08 ( 3761) 2e+08 2e+08 --->beagle2-----germline2: 1.49e-16 -1609 1.17e-20 -1764 2e+08 ( 3785) 2e+08 ( 3761) 2e+08 2e+08 --->beagle2-----dash-----: 3.96e-18 -1911 2.69e-26 -2056 2e+08 ( 3785) 2e+08 ( 3672) 2e+08 2e+08 --->plink-------germline1: 3.96e-18 -4387426 3.46e-120 -4397097 1.96e+08 ( 282204) 2e+08 ( 3761) 1.96e+08 2e+08 --->plink-------germline2: 3.96e-18 -4387426 3.46e-120 -4397097 1.96e+08 ( 282204) 2e+08 ( 3761) 1.96e+08 2e+08 --->plink-------dash-----: 3.96e-18 -4387932 3.42e-120 -4397390 1.96e+08 ( 282204) 2e+08 ( 3672) 1.96e+08 2e+08 --->germline1---germline2: 1e+00 0 1e+00 0 2e+08 ( 3761) 2e+08 ( 3761) 2e+08 2e+08 --->germline1---dash-----: 1.75e-07 -655 1.76e-05 -292 2e+08 ( 3761) 2e+08 ( 3672) 2e+08 2e+08 --->germline2---dash-----: 1.75e-07 -655 1.76e-05 -292 2e+08 ( 3761) 2e+08 ( 3672) 2e+08 2e+08 ######falseP###### --->fabia-------beagle1--: 8.84e-02 -1953 6.53e-03 7943 12368 ( 28105) 4425 ( 3697) 0 3305 --->fabia-------beagle2--: 3.44e-01 -846 4.35e-04 10172 12368 ( 28105) 2196 ( 1430) 0 1874 --->fabia-------plink----: 3.96e-18 -4377623 2.72e-120 -4385161 12368 ( 28105) 4397529 ( 282203) 0 4383883 --->fabia-------germline1: 5.62e-02 7160 5.17e-05 11936 12368 ( 28105) 432 ( 730) 0 61.5 --->fabia-------germline2: 5.62e-02 7160 5.17e-05 11936 12368 ( 28105) 432 ( 730) 0 61.5 --->fabia-------dash-----: 1e+00 0.000000 3.27e-05 12228.540000 12368.010000 (28105.103096) 139.470000 (371.660007) 0.000000 0.000000 --->beagle1-----beagle2--: 5.33e-13 2659 6.66e-10 2229 4425 ( 3697) 2196 ( 1430) 3305 1874 --->beagle1-----plink----: 3.96e-18 -4382893 3.1e-120 -4393104 4425 ( 3697) 4397529 ( 282203) 3305 4383883 --->beagle1-----germline1: 3.96e-18 3424 1.98e-19 3993 4425 ( 3697) 432 ( 730) 3305 61.5 --->beagle1-----germline2: 3.96e-18 3424 1.98e-19 3993 4425 ( 3697) 432 ( 730) 3305 61.5 --->beagle1-----dash-----: 3.96e-18 3663 4.12e-20 4286 4425 ( 3697) 139 ( 372) 3305 0 --->beagle2-----plink----: 3.96e-18 -4385711 3.36e-120 -4395334 2196 ( 1430) 4397529 ( 282203) 1874 4383883 --->beagle2-----germline1: 1.49e-16 1608 1.17e-20 1764 2196 ( 1430) 432 ( 730) 1874 61.5 --->beagle2-----germline2: 1.49e-16 1608 1.17e-20 1764 2196 ( 1430) 432 ( 730) 1874 61.5 --->beagle2-----dash-----: 3.96e-18 1911 2.69e-26 2056 2196 ( 1430) 139 ( 372) 1874 0 --->plink-------germline1: 3.96e-18 4387442 3.46e-120 4397097 4397529 ( 282203) 432 ( 730) 4383883 61.5 --->plink-------germline2: 3.96e-18 4387442 3.46e-120 4397097 4397529 ( 282203) 432 ( 730) 4383883 61.5 --->plink-------dash-----: 3.96e-18 4387710 3.42e-120 4397390 4397529 ( 282203) 139 ( 372) 4383883 0 --->germline1---germline2: 1e+00 0 1e+00 0 432 ( 730) 432 ( 730) 61.5 61.5 --->germline1---dash-----: 1.75e-07 655 1.76e-05 292 432 ( 730) 139 ( 372) 61.5 0 --->germline2---dash-----: 1.75e-07 655 1.76e-05 292 432 ( 730) 139 ( 372) 61.5 0 ######falseN###### --->fabia-------beagle1--: 5.55e-03 -807 1.3e-01 -532 2027 ( 3322) 2559 ( 1984) 978 2510 --->fabia-------beagle2--: 2.02e-11 -3399 3.17e-10 -3325 2027 ( 3322) 5352 ( 3791) 978 4474 --->fabia-------plink----: 1.32e-15 1527 1.43e-11 1686 2027 ( 3322) 341 ( 2838) 978 0 --->fabia-------germline1: 1.47e-10 -2610 2.9e-08 -2844 2027 ( 3322) 4871 ( 4541) 978 3537 --->fabia-------germline2: 1.61e-10 -2584 3.74e-08 -2774 2027 ( 3322) 4801 ( 4477) 978 3537 --->fabia-------dash-----: 1.74e-12 -3222 1.59e-10 -3632 2027 ( 3322) 5659 ( 4856) 978 3966 --->beagle1-----beagle2--: 1.14e-10 -4950 7.23e-14 -2793 2559 ( 1984) 5352 ( 3791) 2510 4474 --->beagle1-----plink----: 3.37e-15 2418 1.66e-09 2218 2559 ( 1984) 341 ( 2838) 2510 0 --->beagle1-----germline1: 3.91e-07 -1823 1.78e-05 -2313 2559 ( 1984) 4871 ( 4541) 2510 3537 --->beagle1-----germline2: 4.68e-07 -1770 2.57e-05 -2243 2559 ( 1984) 4801 ( 4477) 2510 3537 --->beagle1-----dash-----: 2e-09 -2479 1.45e-07 -3100 2559 ( 1984) 5659 ( 4856) 2510 3966 --->beagle2-----plink----: 1.26e-15 5329 1.99e-17 5011 5352 ( 3791) 341 ( 2838) 4474 0 --->beagle2-----germline1: 7.8e-02 896 4.53e-01 481 5352 ( 3791) 4871 ( 4541) 4474 3537 --->beagle2-----germline2: 5.88e-02 951 3.85e-01 551 5352 ( 3791) 4801 ( 4477) 4474 3537 --->beagle2-----dash-----: 8.43e-01 120 6.39e-01 -307 5352 ( 3791) 5659 ( 4856) 4474 3966 --->plink-------germline1: 5.78e-18 -4032 1.29e-23 -4531 341 ( 2838) 4871 ( 4541) 0 3537 --->plink-------germline2: 5.78e-18 -4023 6.04e-24 -4461 341 ( 2838) 4801 ( 4477) 0 3537 --->plink-------dash-----: 5.78e-18 -4953 1.95e-24 -5318 341 ( 2838) 5659 ( 4856) 0 3966 --->germline1---germline2: 1e+00 0 3.2e-01 70 4871 ( 4541) 4801 ( 4477) 3537 3537 --->germline1---dash-----: 1.75e-07 -1681 4.34e-05 -788 4871 ( 4541) 5659 ( 4856) 3537 3966 --->germline2---dash-----: 1.19e-07 -1725 2.54e-05 -858 4801 ( 4477) 5659 ( 4856) 3537 3966 ######trueP###### --->fabia-------beagle1--: 5.55e-03 807 1.3e-01 532 54373 ( 6199) 53841 ( 4141) 55923 54648 --->fabia-------beagle2--: 2.02e-11 3399 3.17e-10 3325 54373 ( 6199) 51048 ( 5094) 55923 52400 --->fabia-------plink----: 1.32e-15 -1527 1.43e-11 -1686 54373 ( 6199) 56059 ( 6299) 55923 56994 --->fabia-------germline1: 1.47e-10 2610 2.9e-08 2844 54373 ( 6199) 51528 ( 7817) 55923 54000 --->fabia-------germline2: 1.61e-10 2584 3.74e-08 2774 54373 ( 6199) 51598 ( 7743) 55923 54000 --->fabia-------dash-----: 1.74e-12 3222 1.59e-10 3632 54373 ( 6199) 50741 ( 8026) 55923 53934 --->beagle1-----beagle2--: 1.14e-10 4949 7.23e-14 2793 53841 ( 4141) 51048 ( 5094) 54648 52400 --->beagle1-----plink----: 3.37e-15 -2418 1.66e-09 -2218 53841 ( 4141) 56059 ( 6299) 54648 56994 --->beagle1-----germline1: 3.91e-07 1824 1.78e-05 2313 53841 ( 4141) 51528 ( 7817) 54648 54000 --->beagle1-----germline2: 4.68e-07 1770 2.57e-05 2243 53841 ( 4141) 51598 ( 7743) 54648 54000 --->beagle1-----dash-----: 2e-09 2479 1.45e-07 3100 53841 ( 4141) 50741 ( 8026) 54648 53934 --->beagle2-----plink----: 1.26e-15 -5329 1.99e-17 -5011 51048 ( 5094) 56059 ( 6299) 52400 56994 --->beagle2-----germline1: 7.8e-02 -897 4.53e-01 -481 51048 ( 5094) 51528 ( 7817) 52400 54000 --->beagle2-----germline2: 5.88e-02 -951 3.85e-01 -551 51048 ( 5094) 51598 ( 7743) 52400 54000 --->beagle2-----dash-----: 8.43e-01 -121 6.39e-01 307 51048 ( 5094) 50741 ( 8026) 52400 53934 --->plink-------germline1: 5.78e-18 4032 1.29e-23 4531 56059 ( 6299) 51528 ( 7817) 56994 54000 --->plink-------germline2: 5.78e-18 4023 6.04e-24 4461 56059 ( 6299) 51598 ( 7743) 56994 54000 --->plink-------dash-----: 5.78e-18 4953 1.95e-24 5318 56059 ( 6299) 50741 ( 8026) 56994 53934 --->germline1---germline2: 1e+00 0 3.2e-01 -70 51528 ( 7817) 51598 ( 7743) 54000 54000 --->germline1---dash-----: 1.75e-07 1681 4.34e-05 788 51528 ( 7817) 50741 ( 8026) 54000 53934 --->germline2---dash-----: 1.19e-07 1725 2.54e-05 858 51598 ( 7743) 50741 ( 8026) 54000 53934 ######MatthewsSnps###### --->fabia-------beagle1--: 4.52e-01 0.009820 2.7e-02 -0.044533 0.882249 ( 0.189356) 0.926782 ( 0.057926) 0.975839 0.949026 --->fabia-------beagle2--: 2.92e-01 -0.012723 4.86e-05 -0.078402 0.882249 ( 0.189356) 0.960650 ( 0.022859) 0.975839 0.964977 --->fabia-------plink----: 4.08e-18 0.945860 5.43e-69 0.878276 0.882249 ( 0.189356) 0.003973 ( 0.007371) 0.975839 0.000000 --->fabia-------germline1: 9.65e-01 0.000328 1.11e-03 -0.059444 0.882249 ( 0.189356) 0.941692 ( 0.136369) 0.975839 0.966467 --->fabia-------germline2: 9.65e-01 0.000328 1.11e-03 -0.059444 0.882249 ( 0.189356) 0.941692 ( 0.136369) 0.975839 0.966467 --->fabia-------dash-----: 9.15e-01 -0.001286 2.85e-03 -0.054726 0.882249 ( 0.189356) 0.936975 ( 0.136341) 0.975839 0.965641 --->beagle1-----beagle2--: 5.3e-10 -0.063861 4.25e-09 -0.033869 0.926782 ( 0.057926) 0.960650 ( 0.022859) 0.949026 0.964977 --->beagle1-----plink----: 3.96e-18 0.932821 5.15e-121 0.922809 0.926782 ( 0.057926) 0.003973 ( 0.007371) 0.949026 0.000000 --->beagle1-----germline1: 3.78e-05 -0.022547 2.91e-01 -0.014911 0.926782 ( 0.057926) 0.941692 ( 0.136369) 0.949026 0.966467 --->beagle1-----germline2: 3.78e-05 -0.022547 2.91e-01 -0.014911 0.926782 ( 0.057926) 0.941692 ( 0.136369) 0.949026 0.966467 --->beagle1-----dash-----: 1.15e-03 -0.019648 4.71e-01 -0.010193 0.926782 ( 0.057926) 0.936975 ( 0.136341) 0.949026 0.965641 --->beagle2-----plink----: 3.96e-18 0.958725 3.44e-160 0.956678 0.960650 ( 0.022859) 0.003973 ( 0.007371) 0.964977 0.000000 --->beagle2-----germline1: 5.76e-01 0.001496 1.56e-01 0.018958 0.960650 ( 0.022859) 0.941692 ( 0.136369) 0.964977 0.966467 --->beagle2-----germline2: 5.76e-01 0.001496 1.56e-01 0.018958 0.960650 ( 0.022859) 0.941692 ( 0.136369) 0.964977 0.966467 --->beagle2-----dash-----: 6.61e-02 0.006299 7.78e-02 0.023675 0.960650 ( 0.022859) 0.936975 ( 0.136341) 0.964977 0.965641 --->plink-------germline1: 4.33e-18 -0.959070 1.78e-85 -0.937720 0.003973 ( 0.007371) 0.941692 ( 0.136369) 0.000000 0.966467 --->plink-------germline2: 4.33e-18 -0.959070 1.78e-85 -0.937720 0.003973 ( 0.007371) 0.941692 ( 0.136369) 0.000000 0.966467 --->plink-------dash-----: 4.33e-18 -0.955802 3.03e-85 -0.933002 0.003973 ( 0.007371) 0.936975 ( 0.136341) 0.000000 0.965641 --->germline1---germline2: 1e+00 0.000000 1e+00 0.000000 0.941692 ( 0.136369) 0.941692 ( 0.136369) 0.966467 0.966467 --->germline1---dash-----: 5.28e-03 0.020341 1.41e-02 0.004717 0.941692 ( 0.136369) 0.936975 ( 0.136341) 0.966467 0.965641 --->germline2---dash-----: 5.28e-03 0.020341 1.41e-02 0.004717 0.941692 ( 0.136369) 0.936975 ( 0.136341) 0.966467 0.965641 ######F1Snps###### --->fabia-------beagle1--: 4.63e-01 0.009588 1.69e-02 -0.051874 0.874702 ( 0.204255) 0.926576 ( 0.060655) 0.976684 0.950357 --->fabia-------beagle2--: 2.87e-01 -0.012755 3.19e-05 -0.086891 0.874702 ( 0.204255) 0.961593 ( 0.022853) 0.976684 0.966084 --->fabia-------plink----: 4.08e-18 0.864562 7.84e-62 0.784817 0.874702 ( 0.204255) 0.089885 ( 0.005646) 0.976684 0.090820 --->fabia-------germline1: 1e+00 -1.87e-06 5.61e-04 -0.068151 0.874702 ( 0.204255) 0.942853 ( 0.136511) 0.976684 0.967775 --->fabia-------germline2: 1e+00 -1.87e-06 5.61e-04 -0.068151 0.874702 ( 0.204255) 0.942853 ( 0.136511) 0.976684 0.967775 --->fabia-------dash-----: 8.79e-01 -0.001540 1.47e-03 -0.063151 0.874702 ( 0.204255) 0.937853 ( 0.136506) 0.976684 0.966677 --->beagle1-----beagle2--: 5.3e-10 -0.065883 6.5e-09 -0.035017 0.926576 ( 0.060655) 0.961593 ( 0.022853) 0.950357 0.966084 --->beagle1-----plink----: 3.96e-18 0.847623 1.71e-115 0.836692 0.926576 ( 0.060655) 0.089885 ( 0.005646) 0.950357 0.090820 --->beagle1-----germline1: 3.01e-05 -0.022680 2.52e-01 -0.016277 0.926576 ( 0.060655) 0.942853 ( 0.136511) 0.950357 0.967775 --->beagle1-----germline2: 3.01e-05 -0.022680 2.52e-01 -0.016277 0.926576 ( 0.060655) 0.942853 ( 0.136511) 0.950357 0.967775 --->beagle1-----dash-----: 1.21e-03 -0.019735 4.28e-01 -0.011277 0.926576 ( 0.060655) 0.937853 ( 0.136506) 0.950357 0.966677 --->beagle2-----plink----: 3.96e-18 0.873659 1.2e-160 0.871709 0.961593 ( 0.022853) 0.089885 ( 0.005646) 0.966084 0.090820 --->beagle2-----germline1: 6.1e-01 0.001402 1.6e-01 0.018741 0.961593 ( 0.022853) 0.942853 ( 0.136511) 0.966084 0.967775 --->beagle2-----germline2: 6.1e-01 0.001402 1.6e-01 0.018741 0.961593 ( 0.022853) 0.942853 ( 0.136511) 0.966084 0.967775 --->beagle2-----dash-----: 6.56e-02 0.006320 7.66e-02 0.023740 0.961593 ( 0.022853) 0.937853 ( 0.136506) 0.966084 0.966677 --->plink-------germline1: 4.33e-18 -0.874053 5.27e-83 -0.852968 0.089885 ( 0.005646) 0.942853 ( 0.136511) 0.090820 0.967775 --->plink-------germline2: 4.33e-18 -0.874053 5.27e-83 -0.852968 0.089885 ( 0.005646) 0.942853 ( 0.136511) 0.090820 0.967775 --->plink-------dash-----: 4.33e-18 -0.871776 9.45e-83 -0.847968 0.089885 ( 0.005646) 0.937853 ( 0.136506) 0.090820 0.966677 --->germline1---germline2: 1e+00 0.000000 1e+00 0.000000 0.942853 ( 0.136511) 0.942853 ( 0.136511) 0.967775 0.967775 --->germline1---dash-----: 3.27e-03 0.021342 1.01e-02 0.005000 0.942853 ( 0.136511) 0.937853 ( 0.136506) 0.967775 0.966677 --->germline2---dash-----: 3.27e-03 0.021342 1.01e-02 0.005000 0.942853 ( 0.136511) 0.937853 ( 0.136506) 0.967775 0.966677 ######accuracySnps###### --->fabia-------beagle1--: 3.89e-01 0.001129 3.19e-03 -0.011935 0.980206 ( 0.038307) 0.992141 ( 0.007475) 0.997830 0.995055 --->fabia-------beagle2--: 3.73e-01 -0.001051 5.6e-05 -0.016032 0.980206 ( 0.038307) 0.996238 ( 0.002260) 0.997830 0.996690 --->fabia-------plink----: 3.96e-18 0.945327 1.52e-139 0.931819 0.980206 ( 0.038307) 0.048387 ( 0.004594) 0.997830 0.047730 --->fabia-------germline1: 8.12e-01 -0.000242 7.17e-05 -0.015806 0.980206 ( 0.038307) 0.996012 ( 0.003752) 0.997830 0.996965 --->fabia-------germline2: 8.12e-01 -0.000242 7.17e-05 -0.015806 0.980206 ( 0.038307) 0.996012 ( 0.003752) 0.997830 0.996965 --->fabia-------dash-----: 6.07e-01 -0.000606 1.07e-04 -0.015449 0.980206 ( 0.038307) 0.995655 ( 0.003834) 0.997830 0.996897 --->beagle1-----beagle2--: 5.3e-10 -0.007145 3.94e-08 -0.004097 0.992141 ( 0.007475) 0.996238 ( 0.002260) 0.995055 0.996690 --->beagle1-----plink----: 3.96e-18 0.944840 1.57e-204 0.943754 0.992141 ( 0.007475) 0.048387 ( 0.004594) 0.995055 0.047730 --->beagle1-----germline1: 1.84e-06 -0.002675 7.43e-06 -0.003871 0.992141 ( 0.007475) 0.996012 ( 0.003752) 0.995055 0.996965 --->beagle1-----germline2: 1.84e-06 -0.002675 7.43e-06 -0.003871 0.992141 ( 0.007475) 0.996012 ( 0.003752) 0.995055 0.996965 --->beagle1-----dash-----: 8.2e-05 -0.002468 5.42e-05 -0.003514 0.992141 ( 0.007475) 0.995655 ( 0.003834) 0.995055 0.996897 --->beagle2-----plink----: 3.96e-18 0.948185 2.17e-227 0.947851 0.996238 ( 0.002260) 0.048387 ( 0.004594) 0.996690 0.047730 --->beagle2-----germline1: 8.27e-01 -5.93e-05 6.1e-01 0.000226 0.996238 ( 0.002260) 0.996012 ( 0.003752) 0.996690 0.996965 --->beagle2-----germline2: 8.27e-01 -5.93e-05 6.1e-01 0.000226 0.996238 ( 0.002260) 0.996012 ( 0.003752) 0.996690 0.996965 --->beagle2-----dash-----: 3.33e-01 0.000297 2.02e-01 0.000583 0.996238 ( 0.002260) 0.995655 ( 0.003834) 0.996690 0.996897 --->plink-------germline1: 3.95e-18 -0.948384 7.3e-238 -0.947625 0.048387 ( 0.004594) 0.996012 ( 0.003752) 0.047730 0.996965 --->plink-------germline2: 3.95e-18 -0.948384 7.3e-238 -0.947625 0.048387 ( 0.004594) 0.996012 ( 0.003752) 0.047730 0.996965 --->plink-------dash-----: 3.95e-18 -0.947923 3.23e-236 -0.947268 0.048387 ( 0.004594) 0.995655 ( 0.003834) 0.047730 0.996897 --->germline1---germline2: 1e+00 0.000000 1e+00 0.000000 0.996012 ( 0.003752) 0.996012 ( 0.003752) 0.996965 0.996965 --->germline1---dash-----: 1e+00 0.000000 4.18e-02 0.000357 0.996012 ( 0.003752) 0.995655 ( 0.003834) 0.996965 0.996897 --->germline2---dash-----: 1e+00 0.000000 4.18e-02 0.000357 0.996012 ( 0.003752) 0.995655 ( 0.003834) 0.996965 0.996897 ######FPRSnps###### --->fabia-------beagle1--: 9.99e-02 -0.003216 1.11e-02 0.010836 0.019081 ( 0.040629) 0.008245 ( 0.007845) 0.000000 0.005183 --->fabia-------beagle2--: 4.61e-01 -0.001592 3.01e-04 0.015135 0.019081 ( 0.040629) 0.003946 ( 0.002372) 0.000000 0.003476 --->fabia-------plink----: 1.45e-18 -0.993882 5.24e-139 -0.979463 0.019081 ( 0.040629) 0.998544 ( 0.003481) 0.000000 1.000000 --->fabia-------germline1: 1e+00 0.000000 2.25e-05 0.018195 0.019081 ( 0.040629) 0.000886 ( 0.001607) 0.000000 6.04e-05 --->fabia-------germline2: 1e+00 0.000000 2.25e-05 0.018195 0.019081 ( 0.040629) 0.000886 ( 0.001607) 0.000000 6.04e-05 --->fabia-------dash-----: 1e+00 0.000000 1.03e-05 0.018874 0.019081 ( 0.040629) 0.000207 ( 0.000590) 0.000000 0.000000 --->beagle1-----beagle2--: 5.3e-10 0.007527 3.92e-08 0.004299 0.008245 ( 0.007845) 0.003946 ( 0.002372) 0.005183 0.003476 --->beagle1-----plink----: 3.96e-18 -0.991668 4.79e-207 -0.990299 0.008245 ( 0.007845) 0.998544 ( 0.003481) 0.005183 1.000000 --->beagle1-----germline1: 4.33e-18 0.005776 4.87e-16 0.007359 0.008245 ( 0.007845) 0.000886 ( 0.001607) 0.005183 6.04e-05 --->beagle1-----germline2: 4.33e-18 0.005776 4.87e-16 0.007359 0.008245 ( 0.007845) 0.000886 ( 0.001607) 0.005183 6.04e-05 --->beagle1-----dash-----: 3.96e-18 0.006459 4.13e-17 0.008037 0.008245 ( 0.007845) 0.000207 ( 0.000590) 0.005183 0.000000 --->beagle2-----plink----: 3.96e-18 -0.995396 5.21e-237 -0.994598 0.003946 ( 0.002372) 0.998544 ( 0.003481) 0.003476 1.000000 --->beagle2-----germline1: 1.48e-15 0.002891 9.83e-20 0.003060 0.003946 ( 0.002372) 0.000886 ( 0.001607) 0.003476 6.04e-05 --->beagle2-----germline2: 1.48e-15 0.002891 9.83e-20 0.003060 0.003946 ( 0.002372) 0.000886 ( 0.001607) 0.003476 6.04e-05 --->beagle2-----dash-----: 3.96e-18 0.003499 8.71e-29 0.003738 0.003946 ( 0.002372) 0.000207 ( 0.000590) 0.003476 0.000000 --->plink-------germline1: 2.98e-18 0.998700 4.31e-241 0.997658 0.998544 ( 0.003481) 0.000886 ( 0.001607) 1.000000 6.04e-05 --->plink-------germline2: 2.98e-18 0.998700 4.31e-241 0.997658 0.998544 ( 0.003481) 0.000886 ( 0.001607) 1.000000 6.04e-05 --->plink-------dash-----: 1.75e-18 0.999507 3.98e-245 0.998337 0.998544 ( 0.003481) 0.000207 ( 0.000590) 1.000000 0.000000 --->germline1---germline2: 1e+00 0.000000 1e+00 0.000000 0.000886 ( 0.001607) 0.000886 ( 0.001607) 6.04e-05 6.04e-05 --->germline1---dash-----: 1e+00 0.000000 2.56e-05 0.000679 0.000886 ( 0.001607) 0.000207 ( 0.000590) 6.04e-05 0.000000 --->germline2---dash-----: 1e+00 0.000000 2.56e-05 0.000679 0.000886 ( 0.001607) 0.000207 ( 0.000590) 6.04e-05 0.000000 ######FDRSnps###### --->fabia-------beagle1--: 7.58e-02 -0.059463 7.29e-01 0.009555 0.140883 ( 0.253578) 0.131328 ( 0.098004) 0.000000 0.094589 --->fabia-------beagle2--: 4.24e-01 -0.030786 8.23e-03 0.067845 0.140883 ( 0.253578) 0.073039 ( 0.041566) 0.000000 0.065607 --->fabia-------plink----: 3.95e-18 -0.951670 4.25e-54 -0.812051 0.140883 ( 0.253578) 0.952934 ( 0.003037) 0.000000 0.952430 --->fabia-------germline1: 8.32e-02 0.173203 5.97e-06 0.123831 0.140883 ( 0.253578) 0.017053 ( 0.029101) 0.000000 0.001278 --->fabia-------germline2: 8.32e-02 0.173203 5.97e-06 0.123831 0.140883 ( 0.253578) 0.017053 ( 0.029101) 0.000000 0.001278 --->fabia-------dash-----: 1e+00 0.000000 4.39e-07 0.136724 0.140883 ( 0.253578) 0.004159 ( 0.011409) 0.000000 0.000000 --->beagle1-----beagle2--: 5.3e-10 0.111410 2.3e-09 0.058290 0.131328 ( 0.098004) 0.073039 ( 0.041566) 0.094589 0.065607 --->beagle1-----plink----: 3.96e-18 -0.836215 5.56e-94 -0.821606 0.131328 ( 0.098004) 0.952934 ( 0.003037) 0.094589 0.952430 --->beagle1-----germline1: 4.46e-18 0.101146 6.66e-21 0.114276 0.131328 ( 0.098004) 0.017053 ( 0.029101) 0.094589 0.001278 --->beagle1-----germline2: 4.46e-18 0.101146 6.66e-21 0.114276 0.131328 ( 0.098004) 0.017053 ( 0.029101) 0.094589 0.001278 --->beagle1-----dash-----: 3.96e-18 0.112730 7.87e-23 0.127169 0.131328 ( 0.098004) 0.004159 ( 0.011409) 0.094589 0.000000 --->beagle2-----plink----: 3.96e-18 -0.883326 3.69e-134 -0.879895 0.073039 ( 0.041566) 0.952934 ( 0.003037) 0.065607 0.952430 --->beagle2-----germline1: 1.18e-15 0.053130 2.74e-20 0.055986 0.073039 ( 0.041566) 0.017053 ( 0.029101) 0.065607 0.001278 --->beagle2-----germline2: 1.18e-15 0.053130 2.74e-20 0.055986 0.073039 ( 0.041566) 0.017053 ( 0.029101) 0.065607 0.001278 --->beagle2-----dash-----: 3.96e-18 0.064957 3.89e-30 0.068880 0.073039 ( 0.041566) 0.004159 ( 0.011409) 0.065607 0.000000 --->plink-------germline1: 3.96e-18 0.942662 1.04e-150 0.935881 0.952934 ( 0.003037) 0.017053 ( 0.029101) 0.952430 0.001278 --->plink-------germline2: 3.96e-18 0.942662 1.04e-150 0.935881 0.952934 ( 0.003037) 0.017053 ( 0.029101) 0.952430 0.001278 --->plink-------dash-----: 3.96e-18 0.951948 4.21e-190 0.948775 0.952934 ( 0.003037) 0.004159 ( 0.011409) 0.952430 0.000000 --->germline1---germline2: 1e+00 0.000000 1e+00 0.000000 0.017053 ( 0.029101) 0.017053 ( 0.029101) 0.001278 0.001278 --->germline1---dash-----: 2.7e-06 0.037885 9.96e-06 0.012894 0.017053 ( 0.029101) 0.004159 ( 0.011409) 0.001278 0.000000 --->germline2---dash-----: 2.7e-06 0.037885 9.96e-06 0.012894 0.017053 ( 0.029101) 0.004159 ( 0.011409) 0.001278 0.000000 ######specifitySnps###### --->fabia-------beagle1--: 9.99e-02 0.003227 1.11e-02 -0.010836 0.980919 ( 0.040629) 0.991755 ( 0.007845) 1.000000 0.994817 --->fabia-------beagle2--: 4.61e-01 0.001599 3.01e-04 -0.015135 0.980919 ( 0.040629) 0.996054 ( 0.002372) 1.000000 0.996524 --->fabia-------plink----: 1.45e-18 0.993882 5.24e-139 0.979463 0.980919 ( 0.040629) 0.001456 ( 0.003481) 1.000000 0.000000 --->fabia-------germline1: 1e+00 0.000000 2.25e-05 -0.018195 0.980919 ( 0.040629) 0.999114 ( 0.001607) 1.000000 0.999940 --->fabia-------germline2: 1e+00 0.000000 2.25e-05 -0.018195 0.980919 ( 0.040629) 0.999114 ( 0.001607) 1.000000 0.999940 --->fabia-------dash-----: 1e+00 0.000000 1.03e-05 -0.018874 0.980919 ( 0.040629) 0.999793 ( 0.000590) 1.000000 1.000000 --->beagle1-----beagle2--: 5.3e-10 -0.007501 3.92e-08 -0.004299 0.991755 ( 0.007845) 0.996054 ( 0.002372) 0.994817 0.996524 --->beagle1-----plink----: 3.96e-18 0.991670 4.79e-207 0.990299 0.991755 ( 0.007845) 0.001456 ( 0.003481) 0.994817 0.000000 --->beagle1-----germline1: 4.33e-18 -0.005776 4.87e-16 -0.007359 0.991755 ( 0.007845) 0.999114 ( 0.001607) 0.994817 0.999940 --->beagle1-----germline2: 4.33e-18 -0.005776 4.87e-16 -0.007359 0.991755 ( 0.007845) 0.999114 ( 0.001607) 0.994817 0.999940 --->beagle1-----dash-----: 3.96e-18 -0.006455 4.13e-17 -0.008037 0.991755 ( 0.007845) 0.999793 ( 0.000590) 0.994817 1.000000 --->beagle2-----plink----: 3.96e-18 0.995365 5.21e-237 0.994598 0.996054 ( 0.002372) 0.001456 ( 0.003481) 0.996524 0.000000 --->beagle2-----germline1: 1.48e-15 -0.002889 9.83e-20 -0.003060 0.996054 ( 0.002372) 0.999114 ( 0.001607) 0.996524 0.999940 --->beagle2-----germline2: 1.48e-15 -0.002889 9.83e-20 -0.003060 0.996054 ( 0.002372) 0.999114 ( 0.001607) 0.996524 0.999940 --->beagle2-----dash-----: 3.96e-18 -0.003494 8.71e-29 -0.003738 0.996054 ( 0.002372) 0.999793 ( 0.000590) 0.996524 1.000000 --->plink-------germline1: 2.98e-18 -0.998700 4.31e-241 -0.997658 0.001456 ( 0.003481) 0.999114 ( 0.001607) 0.000000 0.999940 --->plink-------germline2: 2.98e-18 -0.998700 4.31e-241 -0.997658 0.001456 ( 0.003481) 0.999114 ( 0.001607) 0.000000 0.999940 --->plink-------dash-----: 1.75e-18 -0.999507 3.98e-245 -0.998337 0.001456 ( 0.003481) 0.999793 ( 0.000590) 0.000000 1.000000 --->germline1---germline2: 1e+00 0.000000 1e+00 0.000000 0.999114 ( 0.001607) 0.999114 ( 0.001607) 0.999940 0.999940 --->germline1---dash-----: 1e+00 0.000000 2.56e-05 -0.000679 0.999114 ( 0.001607) 0.999793 ( 0.000590) 0.999940 1.000000 --->germline2---dash-----: 1e+00 0.000000 2.56e-05 -0.000679 0.999114 ( 0.001607) 0.999793 ( 0.000590) 0.999940 1.000000 ######sensitivitySnps###### --->fabia-------beagle1--: 1.21e-16 -0.027934 2.54e-04 -0.038944 0.961049 ( 0.102610) 0.999994 ( 6.41e-05) 0.983872 1.000000 --->fabia-------beagle2--: 1.69e-16 -0.027905 2.57e-04 -0.038919 0.961049 ( 0.102610) 0.999968 ( 0.000264) 0.983872 1.000000 --->fabia-------plink----: 1e+00 0.000000 1e+00 0.000000 0.961049 ( 0.102610) 1.000000 ( 0.000000) 0.983872 1.000000 --->fabia-------germline1: 3.32e-07 0.028402 1.32e-03 0.035943 0.961049 ( 0.102610) 0.925106 ( 0.137282) 0.983872 0.942577 --->fabia-------germline2: 3.32e-07 0.028402 1.32e-03 0.035943 0.961049 ( 0.102610) 0.925106 ( 0.137282) 0.983872 0.942577 --->fabia-------dash-----: 3.36e-11 0.047037 1.4e-06 0.057127 0.961049 ( 0.102610) 0.903922 ( 0.136746) 0.983872 0.939402 --->beagle1-----beagle2--: 1e+00 0.000000 1e+00 0.000000 0.999994 ( 6.41e-05) 0.999968 ( 0.000264) 1.000000 1.000000 --->beagle1-----plink----: 1e+00 0.000000 1e+00 0.000000 0.999994 ( 6.41e-05) 1.000000 ( 0.000000) 1.000000 1.000000 --->beagle1-----germline1: 2.59e-16 0.060102 3.62e-07 0.074888 0.999994 ( 6.41e-05) 0.925106 ( 0.137282) 1.000000 0.942577 --->beagle1-----germline2: 2.59e-16 0.060102 3.62e-07 0.074888 0.999994 ( 6.41e-05) 0.925106 ( 0.137282) 1.000000 0.942577 --->beagle1-----dash-----: 8.46e-18 0.068484 2.74e-10 0.096072 0.999994 ( 6.41e-05) 0.903922 ( 0.136746) 1.000000 0.939402 --->beagle2-----plink----: 1e+00 0.000000 1e+00 0.000000 0.999968 ( 0.000264) 1.000000 ( 0.000000) 1.000000 1.000000 --->beagle2-----germline1: 2.59e-16 0.060043 3.65e-07 0.074862 0.999968 ( 0.000264) 0.925106 ( 0.137282) 1.000000 0.942577 --->beagle2-----germline2: 2.59e-16 0.060043 3.65e-07 0.074862 0.999968 ( 0.000264) 0.925106 ( 0.137282) 1.000000 0.942577 --->beagle2-----dash-----: 8.46e-18 0.068484 2.76e-10 0.096046 0.999968 ( 0.000264) 0.903922 ( 0.136746) 1.000000 0.939402 --->plink-------germline1: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 0.925106 ( 0.137282) 1.000000 0.942577 --->plink-------germline2: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 0.925106 ( 0.137282) 1.000000 0.942577 --->plink-------dash-----: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 0.903922 ( 0.136746) 1.000000 0.939402 --->germline1---germline2: 1e+00 0.000000 1e+00 0.000000 0.925106 ( 0.137282) 0.925106 ( 0.137282) 0.942577 0.942577 --->germline1---dash-----: 2.7e-06 0.072951 1.55e-07 0.021184 0.925106 ( 0.137282) 0.903922 ( 0.136746) 0.942577 0.939402 --->germline2---dash-----: 2.7e-06 0.072951 1.55e-07 0.021184 0.925106 ( 0.137282) 0.903922 ( 0.136746) 0.942577 0.939402 ######trueNSnps###### --->fabia-------beagle1--: 9.99e-02 614 1.1e-02 -2066 186962 ( 7735) 189028 ( 1587) 190430 189608 --->fabia-------beagle2--: 4.61e-01 303 3e-04 -2886 186962 ( 7735) 189848 ( 728) 190430 189824 --->fabia-------plink----: 3.95e-18 189354 4.84e-139 186685 186962 ( 7735) 277 ( 663) 190430 0 --->fabia-------germline1: 7.39e-02 -2691 2.23e-05 -3469 186962 ( 7735) 190431 ( 699) 190430 190431 --->fabia-------germline2: 7.39e-02 -2691 2.23e-05 -3469 186962 ( 7735) 190431 ( 699) 190430 190431 --->fabia-------dash-----: 4.8e-04 -4729 1.02e-05 -3599 186962 ( 7735) 190561 ( 621) 190430 190481 --->beagle1-----beagle2--: 5.3e-10 -1438 3.9e-08 -820 189028 ( 1587) 189848 ( 728) 189608 189824 --->beagle1-----plink----: 3.96e-18 188964 1.57e-204 188751 189028 ( 1587) 277 ( 663) 189608 0 --->beagle1-----germline1: 4.33e-18 -1103 4.82e-16 -1403 189028 ( 1587) 190431 ( 699) 189608 190431 --->beagle1-----germline2: 4.33e-18 -1103 4.82e-16 -1403 189028 ( 1587) 190431 ( 699) 189608 190431 --->beagle1-----dash-----: 3.96e-18 -1230 4.08e-17 -1532 189028 ( 1587) 190561 ( 621) 189608 190481 --->beagle2-----plink----: 3.96e-18 189638 2.21e-227 189570 189848 ( 728) 277 ( 663) 189824 0 --->beagle2-----germline1: 1.48e-15 -551 9.96e-20 -583 189848 ( 728) 190431 ( 699) 189824 190431 --->beagle2-----germline2: 1.48e-15 -551 9.96e-20 -583 189848 ( 728) 190431 ( 699) 189824 190431 --->beagle2-----dash-----: 3.95e-18 -667 8.86e-29 -713 189848 ( 728) 190561 ( 621) 189824 190481 --->plink-------germline1: 3.95e-18 -190233 2.24e-228 -190154 277 ( 663) 190431 ( 699) 0 190431 --->plink-------germline2: 3.95e-18 -190233 2.24e-228 -190154 277 ( 663) 190431 ( 699) 0 190431 --->plink-------dash-----: 3.95e-18 -190391 4.8e-231 -190283 277 ( 663) 190561 ( 621) 0 190481 --->germline1---germline2: 1e+00 0 1e+00 0 190431 ( 699) 190431 ( 699) 190431 190431 --->germline1---dash-----: 2.7e-06 -369 2.56e-05 -129 190431 ( 699) 190561 ( 621) 190431 190481 --->germline2---dash-----: 2.7e-06 -369 2.56e-05 -129 190431 ( 699) 190561 ( 621) 190431 190481 ######falsePSnps###### --->fabia-------beagle1--: 9.99e-02 -614 1.1e-02 2066 3638 ( 7744) 1572 ( 1495) 0 989 --->fabia-------beagle2--: 4.61e-01 -303 3e-04 2886 3638 ( 7744) 752 ( 452) 0 662 --->fabia-------plink----: 3.95e-18 -189354 4.84e-139 -186685 3638 ( 7744) 190323 ( 919) 0 190454 --->fabia-------germline1: 7.39e-02 2691 2.23e-05 3469 3638 ( 7744) 169 ( 306) 0 11.5 --->fabia-------germline2: 7.39e-02 2691 2.23e-05 3469 3638 ( 7744) 169 ( 306) 0 11.5 --->fabia-------dash-----: 1e+00 0.000000 1.02e-05 3598.610000 3638.140000 (7744.112599) 39.530000 (112.487257) 0.000000 0.000000 --->beagle1-----beagle2--: 5.3e-10 1438 3.9e-08 820 1572 ( 1495) 752 ( 452) 989 662 --->beagle1-----plink----: 3.96e-18 -188965 1.57e-204 -188751 1572 ( 1495) 190323 ( 919) 989 190454 --->beagle1-----germline1: 4.33e-18 1103 4.82e-16 1403 1572 ( 1495) 169 ( 306) 989 11.5 --->beagle1-----germline2: 4.33e-18 1103 4.82e-16 1403 1572 ( 1495) 169 ( 306) 989 11.5 --->beagle1-----dash-----: 3.96e-18 1230 4.08e-17 1532 1572 ( 1495) 39.5 ( 112) 989 0 --->beagle2-----plink----: 3.96e-18 -189638 2.21e-227 -189570 752 ( 452) 190323 ( 919) 662 190454 --->beagle2-----germline1: 1.48e-15 551 9.96e-20 583 752 ( 452) 169 ( 306) 662 11.5 --->beagle2-----germline2: 1.48e-15 551 9.96e-20 583 752 ( 452) 169 ( 306) 662 11.5 --->beagle2-----dash-----: 3.95e-18 667 8.86e-29 713 752 ( 452) 39.5 ( 112) 662 0 --->plink-------germline1: 3.95e-18 190233 2.24e-228 190154 190323 ( 919) 169 ( 306) 190454 11.5 --->plink-------germline2: 3.95e-18 190233 2.24e-228 190154 190323 ( 919) 169 ( 306) 190454 11.5 --->plink-------dash-----: 3.95e-18 190391 4.8e-231 190283 190323 ( 919) 39.5 ( 112) 190454 0 --->germline1---germline2: 1e+00 0 1e+00 0 169 ( 306) 169 ( 306) 11.5 11.5 --->germline1---dash-----: 2.7e-06 369 2.56e-05 129 169 ( 306) 39.5 ( 112) 11.5 0 --->germline2---dash-----: 2.7e-06 369 2.56e-05 129 169 ( 306) 39.5 ( 112) 11.5 0 ######falseNSnps###### --->fabia-------beagle1--: 1.21e-16 264 3.76e-08 321 321 ( 537) 0.06 ( 0.6) 154 0 --->fabia-------beagle2--: 1.69e-16 264 3.87e-08 320 321 ( 537) 0.3 ( 2.47) 154 0 --->fabia-------plink----: 1e+00 0 1e+00 0 321 ( 537) 0 ( 0) 154 0 --->fabia-------germline1: 3.17e-07 -269 1.03e-04 -308 321 ( 537) 629 ( 773) 154 548 --->fabia-------germline2: 3.17e-07 -269 1.03e-04 -308 321 ( 537) 629 ( 773) 154 548 --->fabia-------dash-----: 2.85e-11 -446 6.41e-09 -509 321 ( 537) 829 ( 785) 154 578 --->beagle1-----beagle2--: 1e+00 0.000000 3.2e-01 -0.240000 0.060000 ( 0.600000) 0.300000 ( 2.467977) 0.000000 0.000000 --->beagle1-----plink----: 1e+00 0.000000 1e+00 0.000000 0.060000 ( 0.600000) 0.000000 ( 0.000000) 0.000000 0.000000 --->beagle1-----germline1: 2.59e-16 -571 1.22e-12 -629 0.06 ( 0.6) 629 ( 773) 0 548 --->beagle1-----germline2: 2.59e-16 -571 1.22e-12 -629 0.06 ( 0.6) 629 ( 773) 0 548 --->beagle1-----dash-----: 8.46e-18 -649 6.42e-18 -829 0.06 ( 0.6) 829 ( 785) 0 578 --->beagle2-----plink----: 1e+00 0.000000 1e+00 0.000000 0.300000 ( 2.467977) 0.000000 ( 0.000000) 0.000000 0.000000 --->beagle2-----germline1: 2.59e-16 -571 1.24e-12 -628 0.3 ( 2.47) 629 ( 773) 0 548 --->beagle2-----germline2: 2.59e-16 -571 1.24e-12 -628 0.3 ( 2.47) 629 ( 773) 0 548 --->beagle2-----dash-----: 8.46e-18 -649 6.44e-18 -829 0.3 ( 2.47) 829 ( 785) 0 578 --->plink-------germline1: 1e+00 0 1e+00 0 0 ( 0) 629 ( 773) 0 548 --->plink-------germline2: 1e+00 0 1e+00 0 0 ( 0) 629 ( 773) 0 548 --->plink-------dash-----: 1e+00 0 1e+00 0 0 ( 0) 829 ( 785) 0 578 --->germline1---germline2: 1e+00 0 1e+00 0 629 ( 773) 629 ( 773) 548 548 --->germline1---dash-----: 2.7e-06 -687 1.57e-07 -201 629 ( 773) 829 ( 785) 548 578 --->germline2---dash-----: 2.7e-06 -687 1.57e-07 -201 629 ( 773) 829 ( 785) 548 578 ######truePSnps###### --->fabia-------beagle1--: 1.21e-16 -265 3.76e-08 -321 9079 ( 1026) 9400 ( 605) 9334 9499 --->fabia-------beagle2--: 1.69e-16 -264 3.87e-08 -320 9079 ( 1026) 9400 ( 605) 9334 9499 --->fabia-------plink----: 1.21e-16 -265 3.74e-08 -321 9079 ( 1026) 9400 ( 605) 9334 9499 --->fabia-------germline1: 3.17e-07 269 1.03e-04 308 9079 ( 1026) 8771 ( 1314) 9334 9000 --->fabia-------germline2: 3.17e-07 269 1.03e-04 308 9079 ( 1026) 8771 ( 1314) 9334 9000 --->fabia-------dash-----: 2.85e-11 446 6.41e-09 509 9079 ( 1026) 8570 ( 1309) 9334 8989 --->beagle1-----beagle2--: 1e+00 0 3.2e-01 0.24 9400 ( 605) 9400 ( 605) 9499 9499 --->beagle1-----plink----: 1e+00 0 3.2e-01 -0.06 9400 ( 605) 9400 ( 605) 9499 9499 --->beagle1-----germline1: 2.59e-16 571 1.22e-12 629 9400 ( 605) 8771 ( 1314) 9499 9000 --->beagle1-----germline2: 2.59e-16 571 1.22e-12 629 9400 ( 605) 8771 ( 1314) 9499 9000 --->beagle1-----dash-----: 8.46e-18 649 6.42e-18 829 9400 ( 605) 8570 ( 1309) 9499 8989 --->beagle2-----plink----: 1e+00 0 2.27e-01 -0.3 9400 ( 605) 9400 ( 605) 9499 9499 --->beagle2-----germline1: 2.59e-16 571 1.24e-12 628 9400 ( 605) 8771 ( 1314) 9499 9000 --->beagle2-----germline2: 2.59e-16 571 1.24e-12 628 9400 ( 605) 8771 ( 1314) 9499 9000 --->beagle2-----dash-----: 8.46e-18 649 6.44e-18 829 9400 ( 605) 8570 ( 1309) 9499 8989 --->plink-------germline1: 2.59e-16 571 1.22e-12 629 9400 ( 605) 8771 ( 1314) 9499 9000 --->plink-------germline2: 2.59e-16 571 1.22e-12 629 9400 ( 605) 8771 ( 1314) 9499 9000 --->plink-------dash-----: 8.46e-18 649 6.38e-18 829 9400 ( 605) 8570 ( 1309) 9499 8989 --->germline1---germline2: 1e+00 0 1e+00 0 8771 ( 1314) 8771 ( 1314) 9000 9000 --->germline1---dash-----: 2.7e-06 687 1.57e-07 201 8771 ( 1314) 8570 ( 1309) 9000 8989 --->germline2---dash-----: 2.7e-06 687 1.57e-07 201 8771 ( 1314) 8570 ( 1309) 9000 8989 ######MatthewsSample###### --->fabia-------beagle1--: 1e+00 0.000000 7.57e-04 0.042957 0.989126 ( 0.100293) 0.946169 ( 0.076166) 1.000000 1.000000 --->fabia-------beagle2--: 1e+00 0.000000 7.55e-01 -0.002991 0.989126 ( 0.100293) 0.992117 ( 0.025192) 1.000000 1.000000 --->fabia-------plink----: 4.06e-18 0.914911 3.22e-100 0.905051 0.989126 ( 0.100293) 0.084075 ( 0.008537) 1.000000 0.085202 --->fabia-------germline1: 1e+00 0.000000 3.23e-01 0.010002 0.989126 ( 0.100293) 0.979124 ( 0.140852) 1.000000 1.000000 --->fabia-------germline2: 1e+00 0.000000 3.66e-01 0.009126 0.989126 ( 0.100293) 0.980000 ( 0.140705) 1.000000 1.000000 --->fabia-------dash-----: 1e+00 0.000000 2.49e-01 0.011846 0.989126 ( 0.100293) 0.977281 ( 0.141779) 1.000000 1.000000 --->beagle1-----beagle2--: 1e+00 0.000000 2.59e-07 -0.045948 0.946169 ( 0.076166) 0.992117 ( 0.025192) 1.000000 1.000000 --->beagle1-----plink----: 3.95e-18 0.850091 1.44e-106 0.862094 0.946169 ( 0.076166) 0.084075 ( 0.008537) 1.000000 0.085202 --->beagle1-----germline1: 1e+00 0.000000 3.37e-02 -0.032955 0.946169 ( 0.076166) 0.979124 ( 0.140852) 1.000000 1.000000 --->beagle1-----germline2: 1e+00 0.000000 2.89e-02 -0.033831 0.946169 ( 0.076166) 0.980000 ( 0.140705) 1.000000 1.000000 --->beagle1-----dash-----: 1e+00 0.000000 4.68e-02 -0.031112 0.946169 ( 0.076166) 0.977281 ( 0.141779) 1.000000 1.000000 --->beagle2-----plink----: 3.94e-18 0.914444 9.48e-158 0.908042 0.992117 ( 0.025192) 0.084075 ( 0.008537) 1.000000 0.085202 --->beagle2-----germline1: 1e+00 0.000000 3.49e-01 0.012993 0.992117 ( 0.025192) 0.979124 ( 0.140852) 1.000000 1.000000 --->beagle2-----germline2: 1e+00 0.000000 3.81e-01 0.012117 0.992117 ( 0.025192) 0.980000 ( 0.140705) 1.000000 1.000000 --->beagle2-----dash-----: 1e+00 0.000000 2.88e-01 0.014836 0.992117 ( 0.025192) 0.977281 ( 0.141779) 1.000000 1.000000 --->plink-------germline1: 4.31e-18 -0.914810 1.24e-83 -0.895049 0.084075 ( 0.008537) 0.979124 ( 0.140852) 0.085202 1.000000 --->plink-------germline2: 4.31e-18 -0.914903 1.01e-83 -0.895925 0.084075 ( 0.008537) 0.980000 ( 0.140705) 0.085202 1.000000 --->plink-------dash-----: 4.31e-18 -0.914792 3.16e-83 -0.893206 0.084075 ( 0.008537) 0.977281 ( 0.141779) 0.085202 1.000000 --->germline1---germline2: 1e+00 0.000000 3.2e-01 -0.000876 0.979124 ( 0.140852) 0.980000 ( 0.140705) 1.000000 1.000000 --->germline1---dash-----: 1e+00 0.000000 3.2e-01 0.001843 0.979124 ( 0.140852) 0.977281 ( 0.141779) 1.000000 1.000000 --->germline2---dash-----: 1e+00 0.000000 1.84e-01 0.002719 0.980000 ( 0.140705) 0.977281 ( 0.141779) 1.000000 1.000000 ######F1Sample###### --->fabia-------beagle1--: 1e+00 0.000000 4.01e-04 0.046745 0.989091 ( 0.100321) 0.942345 ( 0.082327) 1.000000 1.000000 --->fabia-------beagle2--: 1e+00 0.000000 7.75e-01 -0.002727 0.989091 ( 0.100321) 0.991818 ( 0.026148) 1.000000 1.000000 --->fabia-------plink----: 4.06e-18 0.973944 4.66e-100 0.963224 0.989091 ( 0.100321) 0.025867 ( 0.001764) 1.000000 0.026087 --->fabia-------germline1: 1e+00 0.000000 3.24e-01 0.010000 0.989091 ( 0.100321) 0.979091 ( 0.140868) 1.000000 1.000000 --->fabia-------germline2: 1e+00 0.000000 3.68e-01 0.009091 0.989091 ( 0.100321) 0.980000 ( 0.140705) 1.000000 1.000000 --->fabia-------dash-----: 1e+00 0.000000 2.45e-01 0.012000 0.989091 ( 0.100321) 0.977091 ( 0.141984) 1.000000 1.000000 --->beagle1-----beagle2--: 1e+00 0.000000 2.54e-07 -0.049473 0.942345 ( 0.082327) 0.991818 ( 0.026148) 1.000000 1.000000 --->beagle1-----plink----: 3.95e-18 0.903325 7.11e-106 0.916479 0.942345 ( 0.082327) 0.025867 ( 0.001764) 1.000000 0.026087 --->beagle1-----germline1: 1e+00 0.000000 2.05e-02 -0.036745 0.942345 ( 0.082327) 0.979091 ( 0.140868) 1.000000 1.000000 --->beagle1-----germline2: 1e+00 0.000000 1.73e-02 -0.037655 0.942345 ( 0.082327) 0.980000 ( 0.140705) 1.000000 1.000000 --->beagle1-----dash-----: 1e+00 0.000000 2.99e-02 -0.034745 0.942345 ( 0.082327) 0.977091 ( 0.141984) 1.000000 1.000000 --->beagle2-----plink----: 3.94e-18 0.973777 9.73e-158 0.965951 0.991818 ( 0.026148) 0.025867 ( 0.001764) 1.000000 0.026087 --->beagle2-----germline1: 1e+00 0.000000 3.59e-01 0.012727 0.991818 ( 0.026148) 0.979091 ( 0.140868) 1.000000 1.000000 --->beagle2-----germline2: 1e+00 0.000000 3.93e-01 0.011818 0.991818 ( 0.026148) 0.980000 ( 0.140705) 1.000000 1.000000 --->beagle2-----dash-----: 1e+00 0.000000 2.93e-01 0.014727 0.991818 ( 0.026148) 0.977091 ( 0.141984) 1.000000 1.000000 --->plink-------germline1: 4.31e-18 -0.973920 5.78e-85 -0.953224 0.025867 ( 0.001764) 0.979091 ( 0.140868) 0.026087 1.000000 --->plink-------germline2: 4.31e-18 -0.973950 4.71e-85 -0.954133 0.025867 ( 0.001764) 0.980000 ( 0.140705) 0.026087 1.000000 --->plink-------dash-----: 4.31e-18 -0.973900 1.56e-84 -0.951224 0.025867 ( 0.001764) 0.977091 ( 0.141984) 0.026087 1.000000 --->germline1---germline2: 1e+00 0.000000 3.2e-01 -0.000909 0.979091 ( 0.140868) 0.980000 ( 0.140705) 1.000000 1.000000 --->germline1---dash-----: 1e+00 0.000000 3.2e-01 0.002000 0.979091 ( 0.140868) 0.977091 ( 0.141984) 1.000000 1.000000 --->germline2---dash-----: 1e+00 0.000000 1.87e-01 0.002909 0.980000 ( 0.140705) 0.977091 ( 0.141984) 1.000000 1.000000 ######accuracySample###### --->fabia-------beagle1--: 1e+00 0.000000 1.06e-08 0.000805 0.999965 ( 0.000304) 0.999160 ( 0.001253) 1.000000 1.000000 --->fabia-------beagle2--: 1e+00 0.000000 1e+00 0.000000 0.999965 ( 0.000304) 0.999910 ( 0.000288) 1.000000 1.000000 --->fabia-------plink----: 3.94e-18 0.449554 3.78e-132 0.450595 0.999965 ( 0.000304) 0.549370 ( 0.021874) 1.000000 0.552000 --->fabia-------germline1: 1e+00 0.000000 1e+00 0.000000 0.999965 ( 0.000304) 0.999870 ( 0.000849) 1.000000 1.000000 --->fabia-------germline2: 1e+00 0.000000 1e+00 0.000000 0.999965 ( 0.000304) 0.999880 ( 0.000844) 1.000000 1.000000 --->fabia-------dash-----: 1e+00 0.000000 1.05e-01 0.000115 0.999965 ( 0.000304) 0.999850 ( 0.000869) 1.000000 1.000000 --->beagle1-----beagle2--: 1e+00 0.000000 1.37e-07 -0.000750 0.999160 ( 0.001253) 0.999910 ( 0.000288) 1.000000 1.000000 --->beagle1-----plink----: 3.94e-18 0.448541 3.99e-132 0.449790 0.999160 ( 0.001253) 0.549370 ( 0.021874) 1.000000 0.552000 --->beagle1-----germline1: 1e+00 0.000000 4.69e-06 -0.000710 0.999160 ( 0.001253) 0.999870 ( 0.000849) 1.000000 1.000000 --->beagle1-----germline2: 1e+00 0.000000 3.16e-06 -0.000720 0.999160 ( 0.001253) 0.999880 ( 0.000844) 1.000000 1.000000 --->beagle1-----dash-----: 1e+00 0.000000 1.09e-05 -0.000690 0.999160 ( 0.001253) 0.999850 ( 0.000869) 1.000000 1.000000 --->beagle2-----plink----: 3.94e-18 0.449507 3.88e-132 0.450540 0.999910 ( 0.000288) 0.549370 ( 0.021874) 1.000000 0.552000 --->beagle2-----germline1: 1e+00 0.000000 1e+00 0.000000 0.999910 ( 0.000288) 0.999870 ( 0.000849) 1.000000 1.000000 --->beagle2-----germline2: 1e+00 0.000000 1e+00 0.000000 0.999910 ( 0.000288) 0.999880 ( 0.000844) 1.000000 1.000000 --->beagle2-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.999910 ( 0.000288) 0.999850 ( 0.000869) 1.000000 1.000000 --->plink-------germline1: 3.94e-18 -0.449459 4.4e-132 -0.450500 0.549370 ( 0.021874) 0.999870 ( 0.000849) 0.552000 1.000000 --->plink-------germline2: 3.94e-18 -0.449487 4.41e-132 -0.450510 0.549370 ( 0.021874) 0.999880 ( 0.000844) 0.552000 1.000000 --->plink-------dash-----: 3.94e-18 -0.449449 4.95e-132 -0.450480 0.549370 ( 0.021874) 0.999850 ( 0.000869) 0.552000 1.000000 --->germline1---germline2: 1e+00 0.000000 1e+00 0.000000 0.999870 ( 0.000849) 0.999880 ( 0.000844) 1.000000 1.000000 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 0.999870 ( 0.000849) 0.999850 ( 0.000869) 1.000000 1.000000 --->germline2---dash-----: 1e+00 0.000000 1e+00 0.000000 0.999880 ( 0.000844) 0.999850 ( 0.000869) 1.000000 1.000000 ######FPRSample###### --->fabia-------beagle1--: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.000835 ( 0.001263) 0.000000 0.000000 --->fabia-------beagle2--: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.000000 ( 0.000000) 0.000000 0.000000 --->fabia-------plink----: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.453320 ( 0.022010) 0.000000 0.450201 --->fabia-------germline1: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.000000 ( 0.000000) 0.000000 0.000000 --->fabia-------germline2: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.000000 ( 0.000000) 0.000000 0.000000 --->fabia-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.000000 ( 0.000000) 0.000000 0.000000 --->beagle1-----beagle2--: 1e+00 0.000000 1e+00 0.000000 0.000835 ( 0.001263) 0.000000 ( 0.000000) 0.000000 0.000000 --->beagle1-----plink----: 3.95e-18 -0.451244 4.06e-132 -0.452485 0.000835 ( 0.001263) 0.453320 ( 0.022010) 0.000000 0.450201 --->beagle1-----germline1: 1e+00 0.000000 1e+00 0.000000 0.000835 ( 0.001263) 0.000000 ( 0.000000) 0.000000 0.000000 --->beagle1-----germline2: 1e+00 0.000000 1e+00 0.000000 0.000835 ( 0.001263) 0.000000 ( 0.000000) 0.000000 0.000000 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.000835 ( 0.001263) 0.000000 ( 0.000000) 0.000000 0.000000 --->beagle2-----plink----: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.453320 ( 0.022010) 0.000000 0.450201 --->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 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.000000 ( 0.000000) 0.000000 0.000000 --->plink-------germline1: 1e+00 0.000000 1e+00 0.000000 0.453320 ( 0.022010) 0.000000 ( 0.000000) 0.450201 0.000000 --->plink-------germline2: 1e+00 0.000000 1e+00 0.000000 0.453320 ( 0.022010) 0.000000 ( 0.000000) 0.450201 0.000000 --->plink-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.453320 ( 0.022010) 0.000000 ( 0.000000) 0.450201 0.000000 --->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 0.000000 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 0.000000 ( 0.000000) 0.000000 ( 0.000000) 0.000000 0.000000 ######FDRSample###### --->fabia-------beagle1--: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.096762 ( 0.137934) 0.000000 0.000000 --->fabia-------beagle2--: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.000000 ( 0.000000) 0.000000 0.000000 --->fabia-------plink----: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.986896 ( 0.000899) 0.000000 0.986784 --->fabia-------germline1: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.000000 ( 0.000000) 0.000000 0.000000 --->fabia-------germline2: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.000000 ( 0.000000) 0.000000 0.000000 --->fabia-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.000000 ( 0.000000) 0.000000 0.000000 --->beagle1-----beagle2--: 1e+00 0.000000 1e+00 0.000000 0.096762 ( 0.137934) 0.000000 ( 0.000000) 0.000000 0.000000 --->beagle1-----plink----: 3.95e-18 -0.862239 1.05e-82 -0.890134 0.096762 ( 0.137934) 0.986896 ( 0.000899) 0.000000 0.986784 --->beagle1-----germline1: 1e+00 0.000000 1e+00 0.000000 0.096762 ( 0.137934) 0.000000 ( 0.000000) 0.000000 0.000000 --->beagle1-----germline2: 1e+00 0.000000 1e+00 0.000000 0.096762 ( 0.137934) 0.000000 ( 0.000000) 0.000000 0.000000 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.096762 ( 0.137934) 0.000000 ( 0.000000) 0.000000 0.000000 --->beagle2-----plink----: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.986896 ( 0.000899) 0.000000 0.986784 --->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 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.000000 ( 0.000000) 0.000000 0.000000 --->plink-------germline1: 1e+00 0.000000 1e+00 0.000000 0.986896 ( 0.000899) 0.000000 ( 0.000000) 0.986784 0.000000 --->plink-------germline2: 1e+00 0.000000 1e+00 0.000000 0.986896 ( 0.000899) 0.000000 ( 0.000000) 0.986784 0.000000 --->plink-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.986896 ( 0.000899) 0.000000 ( 0.000000) 0.986784 0.000000 --->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 0.000000 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 0.000000 ( 0.000000) 0.000000 ( 0.000000) 0.000000 0.000000 ######specifitySample###### --->fabia-------beagle1--: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 0.999165 ( 0.001263) 1.000000 1.000000 --->fabia-------beagle2--: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 1.000000 ( 0.000000) 1.000000 1.000000 --->fabia-------plink----: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 0.546680 ( 0.022010) 1.000000 0.549799 --->fabia-------germline1: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 1.000000 ( 0.000000) 1.000000 1.000000 --->fabia-------germline2: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 1.000000 ( 0.000000) 1.000000 1.000000 --->fabia-------dash-----: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 1.000000 ( 0.000000) 1.000000 1.000000 --->beagle1-----beagle2--: 1e+00 0.000000 1e+00 0.000000 0.999165 ( 0.001263) 1.000000 ( 0.000000) 1.000000 1.000000 --->beagle1-----plink----: 3.94e-18 0.451209 4.06e-132 0.452485 0.999165 ( 0.001263) 0.546680 ( 0.022010) 1.000000 0.549799 --->beagle1-----germline1: 1e+00 0.000000 1e+00 0.000000 0.999165 ( 0.001263) 1.000000 ( 0.000000) 1.000000 1.000000 --->beagle1-----germline2: 1e+00 0.000000 1e+00 0.000000 0.999165 ( 0.001263) 1.000000 ( 0.000000) 1.000000 1.000000 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.999165 ( 0.001263) 1.000000 ( 0.000000) 1.000000 1.000000 --->beagle2-----plink----: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 0.546680 ( 0.022010) 1.000000 0.549799 --->beagle2-----germline1: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 1.000000 ( 0.000000) 1.000000 1.000000 --->beagle2-----germline2: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 1.000000 ( 0.000000) 1.000000 1.000000 --->beagle2-----dash-----: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 1.000000 ( 0.000000) 1.000000 1.000000 --->plink-------germline1: 1e+00 0.000000 1e+00 0.000000 0.546680 ( 0.022010) 1.000000 ( 0.000000) 0.549799 1.000000 --->plink-------germline2: 1e+00 0.000000 1e+00 0.000000 0.546680 ( 0.022010) 1.000000 ( 0.000000) 0.549799 1.000000 --->plink-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.546680 ( 0.022010) 1.000000 ( 0.000000) 0.549799 1.000000 --->germline1---germline2: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 1.000000 ( 0.000000) 1.000000 1.000000 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 1.000000 ( 0.000000) 1.000000 1.000000 --->germline2---dash-----: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 1.000000 ( 0.000000) 1.000000 1.000000 ######sensitivitySample###### --->fabia-------beagle1--: 1e+00 0.000000 2.41e-01 -0.010000 0.988333 ( 0.101213) 0.998333 ( 0.016667) 1.000000 1.000000 --->fabia-------beagle2--: 1e+00 0.000000 7.33e-01 0.003333 0.988333 ( 0.101213) 0.985000 ( 0.047937) 1.000000 1.000000 --->fabia-------plink----: 1e+00 0.000000 2.08e-01 -0.006667 0.988333 ( 0.101213) 0.995000 ( 0.050000) 1.000000 1.000000 --->fabia-------germline1: 1e+00 0.000000 3.33e-01 0.010000 0.988333 ( 0.101213) 0.978333 ( 0.141451) 1.000000 1.000000 --->fabia-------germline2: 1e+00 0.000000 4.14e-01 0.008333 0.988333 ( 0.101213) 0.980000 ( 0.140705) 1.000000 1.000000 --->fabia-------dash-----: 1e+00 0.000000 2.19e-01 0.013333 0.988333 ( 0.101213) 0.975000 ( 0.144823) 1.000000 1.000000 --->beagle1-----beagle2--: 1e+00 0.000000 4.16e-03 0.013333 0.998333 ( 0.016667) 0.985000 ( 0.047937) 1.000000 1.000000 --->beagle1-----plink----: 1e+00 0.000000 3.2e-01 0.003333 0.998333 ( 0.016667) 0.995000 ( 0.050000) 1.000000 1.000000 --->beagle1-----germline1: 1e+00 0.000000 1.28e-01 0.020000 0.998333 ( 0.016667) 0.978333 ( 0.141451) 1.000000 1.000000 --->beagle1-----germline2: 1e+00 0.000000 1.6e-01 0.018333 0.998333 ( 0.016667) 0.980000 ( 0.140705) 1.000000 1.000000 --->beagle1-----dash-----: 1e+00 0.000000 8.48e-02 0.023333 0.998333 ( 0.016667) 0.975000 ( 0.144823) 1.000000 1.000000 --->beagle2-----plink----: 1e+00 0.000000 8.32e-02 -0.010000 0.985000 ( 0.047937) 0.995000 ( 0.050000) 1.000000 1.000000 --->beagle2-----germline1: 1e+00 0.000000 6.35e-01 0.006667 0.985000 ( 0.047937) 0.978333 ( 0.141451) 1.000000 1.000000 --->beagle2-----germline2: 1e+00 0.000000 7.2e-01 0.005000 0.985000 ( 0.047937) 0.980000 ( 0.140705) 1.000000 1.000000 --->beagle2-----dash-----: 1e+00 0.000000 4.88e-01 0.010000 0.985000 ( 0.047937) 0.975000 ( 0.144823) 1.000000 1.000000 --->plink-------germline1: 1e+00 0.000000 1.41e-01 0.016667 0.995000 ( 0.050000) 0.978333 ( 0.141451) 1.000000 1.000000 --->plink-------germline2: 1e+00 0.000000 1.81e-01 0.015000 0.995000 ( 0.050000) 0.980000 ( 0.140705) 1.000000 1.000000 --->plink-------dash-----: 1e+00 0.000000 8.98e-02 0.020000 0.995000 ( 0.050000) 0.975000 ( 0.144823) 1.000000 1.000000 --->germline1---germline2: 1e+00 0.000000 3.2e-01 -0.001667 0.978333 ( 0.141451) 0.980000 ( 0.140705) 1.000000 1.000000 --->germline1---dash-----: 1e+00 0.000000 3.2e-01 0.003333 0.978333 ( 0.141451) 0.975000 ( 0.144823) 1.000000 1.000000 --->germline2---dash-----: 1e+00 0.000000 1.81e-01 0.005000 0.980000 ( 0.140705) 0.975000 ( 0.144823) 1.000000 1.000000 ######trueNSample###### --->fabia-------beagle1--: 1e+00 0 1e+00 0 1994 ( 0) 993 ( 1.26) 1994 994 --->fabia-------beagle2--: 1e+00 0 1e+00 0 1994 ( 0) 994 ( 0) 1994 994 --->fabia-------plink----: 1e+00 0 1e+00 0 1994 ( 0) 543 ( 21.9) 1994 546 --->fabia-------germline1: 1e+00 0 1e+00 0 1994 ( 0) 994 ( 0) 1994 994 --->fabia-------germline2: 1e+00 0 1e+00 0 1994 ( 0) 994 ( 0) 1994 994 --->fabia-------dash-----: 1e+00 0 1e+00 0 1994 ( 0) 994 ( 0) 1994 994 --->beagle1-----beagle2--: 1e+00 0 1e+00 0 993 ( 1.26) 994 ( 0) 994 994 --->beagle1-----plink----: 3.94e-18 449 4.06e-132 450 993 ( 1.26) 543 ( 21.9) 994 546 --->beagle1-----germline1: 1e+00 0 1e+00 0 993 ( 1.26) 994 ( 0) 994 994 --->beagle1-----germline2: 1e+00 0 1e+00 0 993 ( 1.26) 994 ( 0) 994 994 --->beagle1-----dash-----: 1e+00 0 1e+00 0 993 ( 1.26) 994 ( 0) 994 994 --->beagle2-----plink----: 1e+00 0 1e+00 0 994 ( 0) 543 ( 21.9) 994 546 --->beagle2-----germline1: 1e+00 0 1e+00 0 994 ( 0) 994 ( 0) 994 994 --->beagle2-----germline2: 1e+00 0 1e+00 0 994 ( 0) 994 ( 0) 994 994 --->beagle2-----dash-----: 1e+00 0 1e+00 0 994 ( 0) 994 ( 0) 994 994 --->plink-------germline1: 1e+00 0 1e+00 0 543 ( 21.9) 994 ( 0) 546 994 --->plink-------germline2: 1e+00 0 1e+00 0 543 ( 21.9) 994 ( 0) 546 994 --->plink-------dash-----: 1e+00 0 1e+00 0 543 ( 21.9) 994 ( 0) 546 994 --->germline1---germline2: 1e+00 0 1e+00 0 994 ( 0) 994 ( 0) 994 994 --->germline1---dash-----: 1e+00 0 1e+00 0 994 ( 0) 994 ( 0) 994 994 --->germline2---dash-----: 1e+00 0 1e+00 0 994 ( 0) 994 ( 0) 994 994 ######falsePSample###### --->fabia-------beagle1--: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.830000 ( 1.255734) 0.000000 0.000000 --->fabia-------beagle2--: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.000000 ( 0.000000) 0.000000 0.000000 --->fabia-------plink----: 1e+00 0 1e+00 0 0 ( 0) 451 ( 21.9) 0 448 --->fabia-------germline1: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.000000 ( 0.000000) 0.000000 0.000000 --->fabia-------germline2: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.000000 ( 0.000000) 0.000000 0.000000 --->fabia-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.000000 ( 0.000000) 0.000000 0.000000 --->beagle1-----beagle2--: 1e+00 0.000000 1e+00 0.000000 0.830000 ( 1.255734) 0.000000 ( 0.000000) 0.000000 0.000000 --->beagle1-----plink----: 3.94e-18 -449 4.06e-132 -450 0.83 ( 1.26) 451 ( 21.9) 0 448 --->beagle1-----germline1: 1e+00 0.000000 1e+00 0.000000 0.830000 ( 1.255734) 0.000000 ( 0.000000) 0.000000 0.000000 --->beagle1-----germline2: 1e+00 0.000000 1e+00 0.000000 0.830000 ( 1.255734) 0.000000 ( 0.000000) 0.000000 0.000000 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.830000 ( 1.255734) 0.000000 ( 0.000000) 0.000000 0.000000 --->beagle2-----plink----: 1e+00 0 1e+00 0 0 ( 0) 451 ( 21.9) 0 448 --->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 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.000000 ( 0.000000) 0.000000 0.000000 --->plink-------germline1: 1e+00 0 1e+00 0 451 ( 21.9) 0 ( 0) 448 0 --->plink-------germline2: 1e+00 0 1e+00 0 451 ( 21.9) 0 ( 0) 448 0 --->plink-------dash-----: 1e+00 0 1e+00 0 451 ( 21.9) 0 ( 0) 448 0 --->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 0.000000 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 0.000000 ( 0.000000) 0.000000 ( 0.000000) 0.000000 0.000000 ######falseNSample###### --->fabia-------beagle1--: 1e+00 0.000000 2.41e-01 0.060000 0.070000 ( 0.607279) 0.010000 ( 0.100000) 0.000000 0.000000 --->fabia-------beagle2--: 1e+00 0.000000 7.33e-01 -0.020000 0.070000 ( 0.607279) 0.090000 ( 0.287623) 0.000000 0.000000 --->fabia-------plink----: 1e+00 0.000000 2.08e-01 0.040000 0.070000 ( 0.607279) 0.030000 ( 0.300000) 0.000000 0.000000 --->fabia-------germline1: 1e+00 0.000000 3.33e-01 -0.060000 0.070000 ( 0.607279) 0.130000 ( 0.848707) 0.000000 0.000000 --->fabia-------germline2: 1e+00 0.000000 4.14e-01 -0.050000 0.070000 ( 0.607279) 0.120000 ( 0.844232) 0.000000 0.000000 --->fabia-------dash-----: 1e+00 0.000000 2.19e-01 -0.080000 0.070000 ( 0.607279) 0.150000 ( 0.868936) 0.000000 0.000000 --->beagle1-----beagle2--: 1e+00 0.000000 4.16e-03 -0.080000 0.010000 ( 0.100000) 0.090000 ( 0.287623) 0.000000 0.000000 --->beagle1-----plink----: 1e+00 0.000000 3.2e-01 -0.020000 0.010000 ( 0.100000) 0.030000 ( 0.300000) 0.000000 0.000000 --->beagle1-----germline1: 1e+00 0.000000 1.28e-01 -0.120000 0.010000 ( 0.100000) 0.130000 ( 0.848707) 0.000000 0.000000 --->beagle1-----germline2: 1e+00 0.000000 1.6e-01 -0.110000 0.010000 ( 0.100000) 0.120000 ( 0.844232) 0.000000 0.000000 --->beagle1-----dash-----: 1e+00 0.000000 8.48e-02 -0.140000 0.010000 ( 0.100000) 0.150000 ( 0.868936) 0.000000 0.000000 --->beagle2-----plink----: 1e+00 0.000000 8.32e-02 0.060000 0.090000 ( 0.287623) 0.030000 ( 0.300000) 0.000000 0.000000 --->beagle2-----germline1: 1e+00 0.000000 6.35e-01 -0.040000 0.090000 ( 0.287623) 0.130000 ( 0.848707) 0.000000 0.000000 --->beagle2-----germline2: 1e+00 0.000000 7.2e-01 -0.030000 0.090000 ( 0.287623) 0.120000 ( 0.844232) 0.000000 0.000000 --->beagle2-----dash-----: 1e+00 0.000000 4.88e-01 -0.060000 0.090000 ( 0.287623) 0.150000 ( 0.868936) 0.000000 0.000000 --->plink-------germline1: 1e+00 0.000000 1.41e-01 -0.100000 0.030000 ( 0.300000) 0.130000 ( 0.848707) 0.000000 0.000000 --->plink-------germline2: 1e+00 0.000000 1.81e-01 -0.090000 0.030000 ( 0.300000) 0.120000 ( 0.844232) 0.000000 0.000000 --->plink-------dash-----: 1e+00 0.000000 8.98e-02 -0.120000 0.030000 ( 0.300000) 0.150000 ( 0.868936) 0.000000 0.000000 --->germline1---germline2: 1e+00 0.000000 3.2e-01 0.010000 0.130000 ( 0.848707) 0.120000 ( 0.844232) 0.000000 0.000000 --->germline1---dash-----: 1e+00 0.000000 3.2e-01 -0.020000 0.130000 ( 0.848707) 0.150000 ( 0.868936) 0.000000 0.000000 --->germline2---dash-----: 1e+00 0.000000 1.81e-01 -0.030000 0.120000 ( 0.844232) 0.150000 ( 0.868936) 0.000000 0.000000 ######truePSample###### --->fabia-------beagle1--: 1e+00 0 2.41e-01 -0.06 5.93 ( 0.607) 5.99 ( 0.1) 6 6 --->fabia-------beagle2--: 1e+00 0 7.33e-01 0.02 5.93 ( 0.607) 5.91 ( 0.288) 6 6 --->fabia-------plink----: 1e+00 0 2.08e-01 -0.04 5.93 ( 0.607) 5.97 ( 0.3) 6 6 --->fabia-------germline1: 1e+00 0 3.33e-01 0.06 5.93 ( 0.607) 5.87 ( 0.849) 6 6 --->fabia-------germline2: 1e+00 0 4.14e-01 0.05 5.93 ( 0.607) 5.88 ( 0.844) 6 6 --->fabia-------dash-----: 1e+00 0 2.19e-01 0.08 5.93 ( 0.607) 5.85 ( 0.869) 6 6 --->beagle1-----beagle2--: 1e+00 0 4.16e-03 0.08 5.99 ( 0.1) 5.91 ( 0.288) 6 6 --->beagle1-----plink----: 1e+00 0 3.2e-01 0.02 5.99 ( 0.1) 5.97 ( 0.3) 6 6 --->beagle1-----germline1: 1e+00 0 1.28e-01 0.12 5.99 ( 0.1) 5.87 ( 0.849) 6 6 --->beagle1-----germline2: 1e+00 0 1.6e-01 0.11 5.99 ( 0.1) 5.88 ( 0.844) 6 6 --->beagle1-----dash-----: 1e+00 0 8.48e-02 0.14 5.99 ( 0.1) 5.85 ( 0.869) 6 6 --->beagle2-----plink----: 1e+00 0 8.32e-02 -0.06 5.91 ( 0.288) 5.97 ( 0.3) 6 6 --->beagle2-----germline1: 1e+00 0 6.35e-01 0.04 5.91 ( 0.288) 5.87 ( 0.849) 6 6 --->beagle2-----germline2: 1e+00 0 7.2e-01 0.03 5.91 ( 0.288) 5.88 ( 0.844) 6 6 --->beagle2-----dash-----: 1e+00 0 4.88e-01 0.06 5.91 ( 0.288) 5.85 ( 0.869) 6 6 --->plink-------germline1: 1e+00 0 1.41e-01 0.1 5.97 ( 0.3) 5.87 ( 0.849) 6 6 --->plink-------germline2: 1e+00 0 1.81e-01 0.09 5.97 ( 0.3) 5.88 ( 0.844) 6 6 --->plink-------dash-----: 1e+00 0 8.98e-02 0.12 5.97 ( 0.3) 5.85 ( 0.869) 6 6 --->germline1---germline2: 1e+00 0 3.2e-01 -0.01 5.87 ( 0.849) 5.88 ( 0.844) 6 6 --->germline1---dash-----: 1e+00 0 3.2e-01 0.02 5.87 ( 0.849) 5.85 ( 0.869) 6 6 --->germline2---dash-----: 1e+00 0 1.81e-01 0.03 5.88 ( 0.844) 5.85 ( 0.869) 6 6