Results: Wilcoxon-Rank-Sum Wilcoxon-median t-test t-test-mean mean1 (std) mean2 (std) median1 median2 ######Matthews###### --->fabia-------beagle1--: 6.87e-02 0.013558 8.2e-02 -0.015684 0.948242 ( 0.088355) 0.963926 ( 0.016765) 0.990670 0.967953 --->fabia-------beagle2--: 4.48e-02 0.018635 4.07e-01 -0.007442 0.948242 ( 0.088355) 0.955684 ( 0.022975) 0.990670 0.957554 --->fabia-------plink----: 3.96e-18 0.827160 2.1e-96 0.794300 0.948242 ( 0.088355) 0.153942 ( 0.009897) 0.990670 0.155618 --->fabia-------germline1: 8.51e-01 0.000798 6.81e-04 -0.031008 0.948242 ( 0.088355) 0.979250 ( 0.008592) 0.990670 0.976611 --->fabia-------germline2: 8.08e-01 0.001136 8.53e-04 -0.030523 0.948242 ( 0.088355) 0.978765 ( 0.009116) 0.990670 0.976597 --->fabia-------dash-----: 4.91e-01 0.003181 1.7e-03 -0.028564 0.948242 ( 0.088355) 0.976806 ( 0.009090) 0.990670 0.974495 --->beagle1-----beagle2--: 3.95e-04 0.009488 2.16e-04 0.008242 0.963926 ( 0.016765) 0.955684 ( 0.022975) 0.967953 0.957554 --->beagle1-----plink----: 3.96e-18 0.810959 2.44e-167 0.809984 0.963926 ( 0.016765) 0.153942 ( 0.009897) 0.967953 0.155618 --->beagle1-----germline1: 2.9e-11 -0.014376 8.04e-13 -0.015324 0.963926 ( 0.016765) 0.979250 ( 0.008592) 0.967953 0.976611 --->beagle1-----germline2: 1.15e-10 -0.013941 4.95e-12 -0.014838 0.963926 ( 0.016765) 0.978765 ( 0.009116) 0.967953 0.976597 --->beagle1-----dash-----: 7.34e-08 -0.012095 1.66e-09 -0.012879 0.963926 ( 0.016765) 0.976806 ( 0.009090) 0.967953 0.974495 --->beagle2-----plink----: 3.96e-18 0.802997 9.83e-154 0.801742 0.955684 ( 0.022975) 0.153942 ( 0.009897) 0.957554 0.155618 --->beagle2-----germline1: 8.92e-14 -0.022336 4.36e-16 -0.023566 0.955684 ( 0.022975) 0.979250 ( 0.008592) 0.957554 0.976611 --->beagle2-----germline2: 1.22e-13 -0.021782 9.38e-16 -0.023080 0.955684 ( 0.022975) 0.978765 ( 0.009116) 0.957554 0.976597 --->beagle2-----dash-----: 1.08e-11 -0.020085 1.81e-13 -0.021121 0.955684 ( 0.022975) 0.976806 ( 0.009090) 0.957554 0.974495 --->plink-------germline1: 3.96e-18 -0.823970 3.98e-183 -0.825308 0.153942 ( 0.009897) 0.979250 ( 0.008592) 0.155618 0.976611 --->plink-------germline2: 3.96e-18 -0.823574 2.99e-182 -0.824822 0.153942 ( 0.009897) 0.978765 ( 0.009116) 0.155618 0.976597 --->plink-------dash-----: 3.96e-18 -0.821322 2.18e-180 -0.822863 0.153942 ( 0.009897) 0.976806 ( 0.009090) 0.155618 0.974495 --->germline1---germline2: 1e+00 0.000000 3.2e-01 0.000485 0.979250 ( 0.008592) 0.978765 ( 0.009116) 0.976611 0.976597 --->germline1---dash-----: 3.92e-08 0.005666 3.03e-09 0.002444 0.979250 ( 0.008592) 0.976806 ( 0.009090) 0.976611 0.974495 --->germline2---dash-----: 4.68e-07 0.005486 2.55e-03 0.001959 0.978765 ( 0.009116) 0.976806 ( 0.009090) 0.976597 0.974495 ######F1###### --->fabia-------beagle1--: 7.13e-02 0.013476 4.77e-02 -0.020051 0.943671 ( 0.099199) 0.963722 ( 0.016950) 0.990629 0.967686 --->fabia-------beagle2--: 4.59e-02 0.018702 2.53e-01 -0.011504 0.943671 ( 0.099199) 0.955175 ( 0.023617) 0.990629 0.957549 --->fabia-------plink----: 3.96e-18 0.933188 7.98e-97 0.896161 0.943671 ( 0.099199) 0.047509 ( 0.005461) 0.990629 0.048339 --->fabia-------germline1: 8.65e-01 0.000761 5.62e-04 -0.035390 0.943671 ( 0.099199) 0.979061 ( 0.008747) 0.990629 0.976379 --->fabia-------germline2: 8.19e-01 0.001035 6.9e-04 -0.034896 0.943671 ( 0.099199) 0.978567 ( 0.009284) 0.990629 0.976351 --->fabia-------dash-----: 5.08e-01 0.003178 1.32e-03 -0.032850 0.943671 ( 0.099199) 0.976521 ( 0.009286) 0.990629 0.974184 --->beagle1-----beagle2--: 3.68e-04 0.009811 1.89e-04 0.008547 0.963722 ( 0.016950) 0.955175 ( 0.023617) 0.967686 0.957549 --->beagle1-----plink----: 3.96e-18 0.917505 1.13e-174 0.916212 0.963722 ( 0.016950) 0.047509 ( 0.005461) 0.967686 0.048339 --->beagle1-----germline1: 4.31e-11 -0.014371 1.24e-12 -0.015339 0.963722 ( 0.016950) 0.979061 ( 0.008747) 0.967686 0.976379 --->beagle1-----germline2: 1.7e-10 -0.013920 7.68e-12 -0.014845 0.963722 ( 0.016950) 0.978567 ( 0.009284) 0.967686 0.976351 --->beagle1-----dash-----: 9.58e-08 -0.011986 3.01e-09 -0.012800 0.963722 ( 0.016950) 0.976521 ( 0.009286) 0.967686 0.974184 --->beagle2-----plink----: 3.96e-18 0.909502 2.59e-159 0.907666 0.955175 ( 0.023617) 0.047509 ( 0.005461) 0.957549 0.048339 --->beagle2-----germline1: 1.02e-13 -0.022516 8.1e-16 -0.023886 0.955175 ( 0.023617) 0.979061 ( 0.008747) 0.957549 0.976379 --->beagle2-----germline2: 1.42e-13 -0.022039 1.8e-15 -0.023392 0.955175 ( 0.023617) 0.978567 ( 0.009284) 0.957549 0.976351 --->beagle2-----dash-----: 1.65e-11 -0.020299 3.49e-13 -0.021346 0.955175 ( 0.023617) 0.976521 ( 0.009286) 0.957549 0.974184 --->plink-------germline1: 3.96e-18 -0.930765 3.88e-198 -0.931551 0.047509 ( 0.005461) 0.979061 ( 0.008747) 0.048339 0.976379 --->plink-------germline2: 3.96e-18 -0.930260 1.9e-196 -0.931057 0.047509 ( 0.005461) 0.978567 ( 0.009284) 0.048339 0.976351 --->plink-------dash-----: 3.96e-18 -0.927649 1.02e-194 -0.929012 0.047509 ( 0.005461) 0.976521 ( 0.009286) 0.048339 0.974184 --->germline1---germline2: 1e+00 0.000000 3.2e-01 0.000494 0.979061 ( 0.008747) 0.978567 ( 0.009284) 0.976379 0.976351 --->germline1---dash-----: 3.14e-08 0.005884 2.38e-09 0.002540 0.979061 ( 0.008747) 0.976521 ( 0.009286) 0.976379 0.974184 --->germline2---dash-----: 3.84e-07 0.005704 2.09e-03 0.002046 0.978567 ( 0.009284) 0.976521 ( 0.009286) 0.976351 0.974184 ######accuracy###### --->fabia-------beagle1--: 1e+00 0.000000 1e+00 0.000000 0.999959 ( 8.4e-05) 0.999960 ( 1.9e-05) 0.999995 0.999964 --->fabia-------beagle2--: 1e+00 0.000000 1e+00 0.000000 0.999959 ( 8.4e-05) 0.999952 ( 2.3e-05) 0.999995 0.999953 --->fabia-------plink----: 3.96e-18 0.022331 9.66e-107 0.022439 0.999959 ( 8.4e-05) 0.977520 ( 0.001966) 0.999995 0.977652 --->fabia-------germline1: 1e+00 0.000000 1e+00 0.000000 0.999959 ( 8.4e-05) 0.999977 ( 8.93e-06) 0.999995 0.999974 --->fabia-------germline2: 1e+00 0.000000 1e+00 0.000000 0.999959 ( 8.4e-05) 0.999977 ( 9.85e-06) 0.999995 0.999974 --->fabia-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.999959 ( 8.4e-05) 0.999975 ( 9.7e-06) 0.999995 0.999972 --->beagle1-----beagle2--: 1e+00 0.000000 1e+00 0.000000 0.999960 ( 1.9e-05) 0.999952 ( 2.3e-05) 0.999964 0.999953 --->beagle1-----plink----: 3.96e-18 0.022336 6.05e-107 0.022440 0.999960 ( 1.9e-05) 0.977520 ( 0.001966) 0.999964 0.977652 --->beagle1-----germline1: 1e+00 0.000000 1e+00 0.000000 0.999960 ( 1.9e-05) 0.999977 ( 8.93e-06) 0.999964 0.999974 --->beagle1-----germline2: 1e+00 0.000000 1e+00 0.000000 0.999960 ( 1.9e-05) 0.999977 ( 9.85e-06) 0.999964 0.999974 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.999960 ( 1.9e-05) 0.999975 ( 9.7e-06) 0.999964 0.999972 --->beagle2-----plink----: 3.96e-18 0.022328 7.19e-107 0.022432 0.999952 ( 2.3e-05) 0.977520 ( 0.001966) 0.999953 0.977652 --->beagle2-----germline1: 1e+00 0.000000 1e+00 0.000000 0.999952 ( 2.3e-05) 0.999977 ( 8.93e-06) 0.999953 0.999974 --->beagle2-----germline2: 1e+00 0.000000 1e+00 0.000000 0.999952 ( 2.3e-05) 0.999977 ( 9.85e-06) 0.999953 0.999974 --->beagle2-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.999952 ( 2.3e-05) 0.999975 ( 9.7e-06) 0.999953 0.999972 --->plink-------germline1: 3.96e-18 -0.022352 6.8e-107 -0.022458 0.977520 ( 0.001966) 0.999977 ( 8.93e-06) 0.977652 0.999974 --->plink-------germline2: 3.96e-18 -0.022352 6.64e-107 -0.022457 0.977520 ( 0.001966) 0.999977 ( 9.85e-06) 0.977652 0.999974 --->plink-------dash-----: 3.96e-18 -0.022349 6.96e-107 -0.022455 0.977520 ( 0.001966) 0.999975 ( 9.7e-06) 0.977652 0.999972 --->germline1---germline2: 1e+00 0.000000 1e+00 0.000000 0.999977 ( 8.93e-06) 0.999977 ( 9.85e-06) 0.999974 0.999974 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 0.999977 ( 8.93e-06) 0.999975 ( 9.7e-06) 0.999974 0.999972 --->germline2---dash-----: 1e+00 0.000000 1e+00 0.000000 0.999977 ( 9.85e-06) 0.999975 ( 9.7e-06) 0.999974 0.999972 ######FPR###### --->fabia-------beagle1--: 1e+00 0.000000 1e+00 0.000000 3.62e-05 ( 8.48e-05) 2.17e-05 ( 1.58e-05) 0.000000 1.79e-05 --->fabia-------beagle2--: 1e+00 0.000000 1e+00 0.000000 3.62e-05 ( 8.48e-05) 1.23e-05 ( 7.83e-06) 0.000000 1.03e-05 --->fabia-------plink----: 3.96e-18 -0.022350 9.26e-107 -0.022457 3.62e-05 ( 8.48e-05) 0.022493 ( 0.001967) 0.000000 0.022360 --->fabia-------germline1: 1e+00 0.000000 1e+00 0.000000 3.62e-05 ( 8.48e-05) 1.74e-06 ( 2.48e-06) 0.000000 9.11e-07 --->fabia-------germline2: 1e+00 0.000000 1e+00 0.000000 3.62e-05 ( 8.48e-05) 2.34e-06 ( 6.33e-06) 0.000000 9.51e-07 --->fabia-------dash-----: 1e+00 0.000000 1e+00 0.000000 3.62e-05 ( 8.48e-05) 4.6e-07 ( 1.1e-06) 0.000000 0.000000 --->beagle1-----beagle2--: 1e+00 0.000000 1e+00 0.000000 2.17e-05 ( 1.58e-05) 1.23e-05 ( 7.83e-06) 1.79e-05 1.03e-05 --->beagle1-----plink----: 3.96e-18 -0.022369 5.39e-107 -0.022471 2.17e-05 ( 1.58e-05) 0.022493 ( 0.001967) 1.79e-05 0.022360 --->beagle1-----germline1: 1e+00 0.000000 1e+00 0.000000 2.17e-05 ( 1.58e-05) 1.74e-06 ( 2.48e-06) 1.79e-05 9.11e-07 --->beagle1-----germline2: 1e+00 0.000000 1e+00 0.000000 2.17e-05 ( 1.58e-05) 2.34e-06 ( 6.33e-06) 1.79e-05 9.51e-07 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 2.17e-05 ( 1.58e-05) 4.6e-07 ( 1.1e-06) 1.79e-05 0.000000 --->beagle2-----plink----: 3.96e-18 -0.022378 5.76e-107 -0.022480 1.23e-05 ( 7.83e-06) 0.022493 ( 0.001967) 1.03e-05 0.022360 --->beagle2-----germline1: 1e+00 0.000000 1e+00 0.000000 1.23e-05 ( 7.83e-06) 1.74e-06 ( 2.48e-06) 1.03e-05 9.11e-07 --->beagle2-----germline2: 1e+00 0.000000 1e+00 0.000000 1.23e-05 ( 7.83e-06) 2.34e-06 ( 6.33e-06) 1.03e-05 9.51e-07 --->beagle2-----dash-----: 1e+00 0.000000 1e+00 0.000000 1.23e-05 ( 7.83e-06) 4.6e-07 ( 1.1e-06) 1.03e-05 0.000000 --->plink-------germline1: 3.96e-18 0.022387 5.76e-107 0.022491 0.022493 ( 0.001967) 1.74e-06 ( 2.48e-06) 0.022360 9.11e-07 --->plink-------germline2: 3.96e-18 0.022387 5.62e-107 0.022490 0.022493 ( 0.001967) 2.34e-06 ( 6.33e-06) 0.022360 9.51e-07 --->plink-------dash-----: 3.96e-18 0.022389 5.67e-107 0.022492 0.022493 ( 0.001967) 4.6e-07 ( 1.1e-06) 0.022360 0.000000 --->germline1---germline2: 1e+00 0.000000 1e+00 0.000000 1.74e-06 ( 2.48e-06) 2.34e-06 ( 6.33e-06) 9.11e-07 9.51e-07 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 1.74e-06 ( 2.48e-06) 4.6e-07 ( 1.1e-06) 9.11e-07 0.000000 --->germline2---dash-----: 1e+00 0.000000 1e+00 0.000000 2.34e-06 ( 6.33e-06) 4.6e-07 ( 1.1e-06) 9.51e-07 0.000000 ######FDR###### --->fabia-------beagle1--: 4.63e-02 -0.019137 2e-02 0.037288 0.075411 ( 0.155975) 0.038123 ( 0.026323) 0.000000 0.031599 --->fabia-------beagle2--: 7.86e-02 -0.012649 1.04e-03 0.052309 0.075411 ( 0.155975) 0.023102 ( 0.014495) 0.000000 0.019452 --->fabia-------plink----: 3.96e-18 -0.973974 5.44e-78 -0.900249 0.075411 ( 0.155975) 0.975659 ( 0.002848) 0.000000 0.975232 --->fabia-------germline1: 2.69e-01 0.056117 1.13e-05 0.072215 0.075411 ( 0.155975) 0.003196 ( 0.004529) 0.000000 0.001633 --->fabia-------germline2: 3.19e-01 0.055137 1.56e-05 0.071263 0.075411 ( 0.155975) 0.004148 ( 0.010250) 0.000000 0.001727 --->fabia-------dash-----: 1e+00 0.000000 6.16e-06 0.074510 0.075411 ( 0.155975) 0.000901 ( 0.002276) 0.000000 0.000000 --->beagle1-----beagle2--: 9.16e-09 0.017002 7.92e-09 0.015021 0.038123 ( 0.026323) 0.023102 ( 0.014495) 0.031599 0.019452 --->beagle1-----plink----: 3.96e-18 -0.939924 1.26e-156 -0.937536 0.038123 ( 0.026323) 0.975659 ( 0.002848) 0.031599 0.975232 --->beagle1-----germline1: 7.01e-18 0.033061 1.48e-23 0.034927 0.038123 ( 0.026323) 0.003196 ( 0.004529) 0.031599 0.001633 --->beagle1-----germline2: 4.54e-17 0.032230 6.75e-22 0.033975 0.038123 ( 0.026323) 0.004148 ( 0.010250) 0.031599 0.001727 --->beagle1-----dash-----: 3.96e-18 0.035109 6.28e-26 0.037222 0.038123 ( 0.026323) 0.000901 ( 0.002276) 0.031599 0.000000 --->beagle2-----plink----: 3.96e-18 -0.954233 2.09e-183 -0.952557 0.023102 ( 0.014495) 0.975659 ( 0.002848) 0.019452 0.975232 --->beagle2-----germline1: 1.2e-17 0.017764 8.11e-24 0.019906 0.023102 ( 0.014495) 0.003196 ( 0.004529) 0.019452 0.001633 --->beagle2-----germline2: 1.67e-16 0.017291 3.82e-21 0.018954 0.023102 ( 0.014495) 0.004148 ( 0.010250) 0.019452 0.001727 --->beagle2-----dash-----: 3.96e-18 0.020262 2.71e-28 0.022201 0.023102 ( 0.014495) 0.000901 ( 0.002276) 0.019452 0.000000 --->plink-------germline1: 3.96e-18 0.972842 2.25e-226 0.972464 0.975659 ( 0.002848) 0.003196 ( 0.004529) 0.975232 0.001633 --->plink-------germline2: 3.96e-18 0.972690 1.06e-196 0.971511 0.975659 ( 0.002848) 0.004148 ( 0.010250) 0.975232 0.001727 --->plink-------dash-----: 3.96e-18 0.974671 3.28e-251 0.974758 0.975659 ( 0.002848) 0.000901 ( 0.002276) 0.975232 0.000000 --->germline1---germline2: 1e+00 0.000000 3.2e-01 -0.000952 0.003196 ( 0.004529) 0.004148 ( 0.010250) 0.001633 0.001727 --->germline1---dash-----: 2.52e-08 0.004620 1.56e-07 0.002294 0.003196 ( 0.004529) 0.000901 ( 0.002276) 0.001633 0.000000 --->germline2---dash-----: 1.71e-08 0.004808 1.83e-03 0.003247 0.004148 ( 0.010250) 0.000901 ( 0.002276) 0.001727 0.000000 ######specifity###### --->fabia-------beagle1--: 1e+00 0.000000 1e+00 0.000000 0.999964 ( 8.48e-05) 0.999978 ( 1.58e-05) 1.000000 0.999982 --->fabia-------beagle2--: 1e+00 0.000000 1e+00 0.000000 0.999964 ( 8.48e-05) 0.999988 ( 7.82e-06) 1.000000 0.999990 --->fabia-------plink----: 3.96e-18 0.022351 9.26e-107 0.022457 0.999964 ( 8.48e-05) 0.977507 ( 0.001967) 1.000000 0.977640 --->fabia-------germline1: 1e+00 0.000000 1e+00 0.000000 0.999964 ( 8.48e-05) 0.999998 ( 2.48e-06) 1.000000 0.999999 --->fabia-------germline2: 1e+00 0.000000 1e+00 0.000000 0.999964 ( 8.48e-05) 0.999998 ( 6.33e-06) 1.000000 0.999999 --->fabia-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.999964 ( 8.48e-05) 1.000000 ( 1.11e-06) 1.000000 1.000000 --->beagle1-----beagle2--: 1e+00 0.000000 1e+00 0.000000 0.999978 ( 1.58e-05) 0.999988 ( 7.82e-06) 0.999982 0.999990 --->beagle1-----plink----: 3.96e-18 0.022370 5.39e-107 0.022471 0.999978 ( 1.58e-05) 0.977507 ( 0.001967) 0.999982 0.977640 --->beagle1-----germline1: 1e+00 0.000000 1e+00 0.000000 0.999978 ( 1.58e-05) 0.999998 ( 2.48e-06) 0.999982 0.999999 --->beagle1-----germline2: 1e+00 0.000000 1e+00 0.000000 0.999978 ( 1.58e-05) 0.999998 ( 6.33e-06) 0.999982 0.999999 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.999978 ( 1.58e-05) 1.000000 ( 1.11e-06) 0.999982 1.000000 --->beagle2-----plink----: 3.96e-18 0.022378 5.76e-107 0.022480 0.999988 ( 7.82e-06) 0.977507 ( 0.001967) 0.999990 0.977640 --->beagle2-----germline1: 1e+00 0.000000 1e+00 0.000000 0.999988 ( 7.82e-06) 0.999998 ( 2.48e-06) 0.999990 0.999999 --->beagle2-----germline2: 1e+00 0.000000 1e+00 0.000000 0.999988 ( 7.82e-06) 0.999998 ( 6.33e-06) 0.999990 0.999999 --->beagle2-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.999988 ( 7.82e-06) 1.000000 ( 1.11e-06) 0.999990 1.000000 --->plink-------germline1: 3.96e-18 -0.022385 5.76e-107 -0.022491 0.977507 ( 0.001967) 0.999998 ( 2.48e-06) 0.977640 0.999999 --->plink-------germline2: 3.96e-18 -0.022385 5.62e-107 -0.022490 0.977507 ( 0.001967) 0.999998 ( 6.33e-06) 0.977640 0.999999 --->plink-------dash-----: 3.96e-18 -0.022387 5.67e-107 -0.022492 0.977507 ( 0.001967) 1.000000 ( 1.11e-06) 0.977640 1.000000 --->germline1---germline2: 1e+00 0.000000 1e+00 0.000000 0.999998 ( 2.48e-06) 0.999998 ( 6.33e-06) 0.999999 0.999999 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 0.999998 ( 2.48e-06) 1.000000 ( 1.11e-06) 0.999999 1.000000 --->germline2---dash-----: 1e+00 0.000000 1e+00 0.000000 0.999998 ( 6.33e-06) 1.000000 ( 1.11e-06) 0.999999 1.000000 ######sensitivity###### --->fabia-------beagle1--: 5.09e-06 0.015267 2.77e-05 0.015101 0.981566 ( 0.025131) 0.966466 ( 0.026622) 0.992095 0.973832 --->fabia-------beagle2--: 2.52e-14 0.043873 1.48e-16 0.045981 0.981566 ( 0.025131) 0.935585 ( 0.043908) 0.992095 0.944016 --->fabia-------plink----: 8.28e-17 -0.013966 6.36e-11 -0.018393 0.981566 ( 0.025131) 0.999959 ( 0.000394) 0.992095 1.000000 --->fabia-------germline1: 1.3e-09 0.020920 3.08e-11 0.019447 0.981566 ( 0.025131) 0.962119 ( 0.017394) 0.992095 0.960341 --->fabia-------germline2: 1.3e-09 0.020920 3.08e-11 0.019447 0.981566 ( 0.025131) 0.962119 ( 0.017394) 0.992095 0.960341 --->fabia-------dash-----: 2.07e-12 0.028537 2.71e-16 0.026435 0.981566 ( 0.025131) 0.955132 ( 0.018494) 0.992095 0.950035 --->beagle1-----beagle2--: 5.33e-13 0.040692 5.5e-15 0.030881 0.966466 ( 0.026622) 0.935585 ( 0.043908) 0.973832 0.944016 --->beagle1-----plink----: 3.96e-18 -0.029810 3.13e-22 -0.033494 0.966466 ( 0.026622) 0.999959 ( 0.000394) 0.973832 1.000000 --->beagle1-----germline1: 5.79e-02 0.006229 1.7e-01 0.004346 0.966466 ( 0.026622) 0.962119 ( 0.017394) 0.973832 0.960341 --->beagle1-----germline2: 5.79e-02 0.006229 1.7e-01 0.004346 0.966466 ( 0.026622) 0.962119 ( 0.017394) 0.973832 0.960341 --->beagle1-----dash-----: 3.25e-04 0.012999 5.75e-04 0.011334 0.966466 ( 0.026622) 0.955132 ( 0.018494) 0.973832 0.950035 --->beagle2-----plink----: 3.96e-18 -0.060766 1.59e-26 -0.064374 0.935585 ( 0.043908) 0.999959 ( 0.000394) 0.944016 1.000000 --->beagle2-----germline1: 1.04e-06 -0.024271 1.34e-07 -0.026534 0.935585 ( 0.043908) 0.962119 ( 0.017394) 0.944016 0.960341 --->beagle2-----germline2: 1.04e-06 -0.024271 1.34e-07 -0.026534 0.935585 ( 0.043908) 0.962119 ( 0.017394) 0.944016 0.960341 --->beagle2-----dash-----: 3.25e-04 -0.018075 7.17e-05 -0.019547 0.935585 ( 0.043908) 0.955132 ( 0.018494) 0.944016 0.950035 --->plink-------germline1: 3.96e-18 0.038463 1.69e-39 0.037840 0.999959 ( 0.000394) 0.962119 ( 0.017394) 1.000000 0.960341 --->plink-------germline2: 3.96e-18 0.038463 1.69e-39 0.037840 0.999959 ( 0.000394) 0.962119 ( 0.017394) 1.000000 0.960341 --->plink-------dash-----: 3.95e-18 0.047747 1.94e-43 0.044828 0.999959 ( 0.000394) 0.955132 ( 0.018494) 1.000000 0.950035 --->germline1---germline2: 1e+00 0.000000 1e+00 0.000000 0.962119 ( 0.017394) 0.962119 ( 0.017394) 0.960341 0.960341 --->germline1---dash-----: 2.52e-08 0.014854 8.36e-11 0.006988 0.962119 ( 0.017394) 0.955132 ( 0.018494) 0.960341 0.950035 --->germline2---dash-----: 2.52e-08 0.014854 8.36e-11 0.006988 0.962119 ( 0.017394) 0.955132 ( 0.018494) 0.960341 0.950035 ######trueN###### --->fabia-------beagle1--: 3.96e-18 2e+08 0e+00 2e+08 4e+08 ( 35920) 2e+08 ( 11071) 4e+08 2e+08 --->fabia-------beagle2--: 3.96e-18 2e+08 0e+00 2e+08 4e+08 ( 35920) 2e+08 ( 10618) 4e+08 2e+08 --->fabia-------plink----: 3.96e-18 2.04e+08 1.08e-270 2.04e+08 4e+08 ( 35920) 1.95e+08 ( 393691) 4e+08 1.95e+08 --->fabia-------germline1: 2.81e-18 2e+08 0e+00 2e+08 4e+08 ( 35920) 2e+08 ( 10461) 4e+08 2e+08 --->fabia-------germline2: 2.9e-18 2e+08 0e+00 2e+08 4e+08 ( 35920) 2e+08 ( 10570) 4e+08 2e+08 --->fabia-------dash-----: 5.77e-19 2e+08 0e+00 2e+08 4e+08 ( 35920) 2e+08 ( 10395) 4e+08 2e+08 --->beagle1-----beagle2--: 1.15e-12 -2629 3.96e-09 -1863 2e+08 ( 11071) 2e+08 ( 10618) 2e+08 2e+08 --->beagle1-----plink----: 3.96e-18 4471671 5.4e-107 4491709 2e+08 ( 11071) 1.95e+08 ( 393691) 2e+08 1.95e+08 --->beagle1-----germline1: 7.67e-18 -3705 3e-22 -3983 2e+08 ( 11071) 2e+08 ( 10461) 2e+08 2e+08 --->beagle1-----germline2: 5.73e-17 -3611 1.62e-20 -3863 2e+08 ( 11071) 2e+08 ( 10570) 2e+08 2e+08 --->beagle1-----dash-----: 3.96e-18 -3917 2.4e-24 -4238 2e+08 ( 11071) 2e+08 ( 10395) 2e+08 2e+08 --->beagle2-----plink----: 3.96e-18 4473101 5.77e-107 4493572 2e+08 ( 10618) 1.95e+08 ( 393691) 2e+08 1.95e+08 --->beagle2-----germline1: 1.62e-17 -1889 2.46e-23 -2120 2e+08 ( 10618) 2e+08 ( 10461) 2e+08 2e+08 --->beagle2-----germline2: 2.57e-16 -1833 8.61e-20 -2000 2e+08 ( 10618) 2e+08 ( 10570) 2e+08 2e+08 --->beagle2-----dash-----: 3.96e-18 -2160 7.91e-28 -2375 2e+08 ( 10618) 2e+08 ( 10395) 2e+08 2e+08 --->plink-------germline1: 3.96e-18 -4475142 5.77e-107 -4495693 1.95e+08 ( 393691) 2e+08 ( 10461) 1.95e+08 2e+08 --->plink-------germline2: 3.96e-18 -4475142 5.63e-107 -4495573 1.95e+08 ( 393691) 2e+08 ( 10570) 1.95e+08 2e+08 --->plink-------dash-----: 3.96e-18 -4475584 5.68e-107 -4495948 1.95e+08 ( 393691) 2e+08 ( 10395) 1.95e+08 2e+08 --->germline1---germline2: 1e+00 0 3.2e-01 120 2e+08 ( 10461) 2e+08 ( 10570) 2e+08 2e+08 --->germline1---dash-----: 2.52e-08 -508 1.99e-07 -255 2e+08 ( 10461) 2e+08 ( 10395) 2e+08 2e+08 --->germline2---dash-----: 1.71e-08 -530 3.65e-03 -375 2e+08 ( 10570) 2e+08 ( 10395) 2e+08 2e+08 ######falseP###### --->fabia-------beagle1--: 4.67e-02 -2146 3.53e-03 10160 14490 ( 33925) 4330 ( 3163) 0 3570 --->fabia-------beagle2--: 7.86e-02 -1319 5.65e-04 12023 14490 ( 33925) 2467 ( 1564) 0 2052 --->fabia-------plink----: 3.96e-18 -4458986 1.79e-106 -4481549 14490 ( 33925) 4496039 ( 393156) 0 4469541 --->fabia-------germline1: 2.83e-01 7318 6.68e-05 14143 14490 ( 33925) 347 ( 496) 0 182 --->fabia-------germline2: 3.34e-01 7182 7.86e-05 14023 14490 ( 33925) 467 ( 1266) 0 190 --->fabia-------dash-----: 1e+00 0.000000 4.99e-05 14398.400000 14490.310000 (33924.536882) 91.910000 (220.721320) 0.000000 0.000000 --->beagle1-----beagle2--: 1.15e-12 2629 3.96e-09 1863 4330 ( 3163) 2467 ( 1564) 3570 2052 --->beagle1-----plink----: 3.96e-18 -4471673 5.4e-107 -4491709 4330 ( 3163) 4496039 ( 393156) 3570 4469541 --->beagle1-----germline1: 7.67e-18 3705 3e-22 3983 4330 ( 3163) 347 ( 496) 3570 182 --->beagle1-----germline2: 5.73e-17 3611 1.62e-20 3863 4330 ( 3163) 467 ( 1266) 3570 190 --->beagle1-----dash-----: 3.96e-18 3917 2.4e-24 4238 4330 ( 3163) 91.9 ( 221) 3570 0 --->beagle2-----plink----: 3.96e-18 -4473141 5.77e-107 -4493572 2467 ( 1564) 4496039 ( 393156) 2052 4469541 --->beagle2-----germline1: 1.62e-17 1889 2.46e-23 2120 2467 ( 1564) 347 ( 496) 2052 182 --->beagle2-----germline2: 2.57e-16 1833 8.61e-20 2000 2467 ( 1564) 467 ( 1266) 2052 190 --->beagle2-----dash-----: 3.96e-18 2161 7.91e-28 2375 2467 ( 1564) 91.9 ( 221) 2052 0 --->plink-------germline1: 3.96e-18 4475140 5.77e-107 4495693 4496039 ( 393156) 347 ( 496) 4469541 182 --->plink-------germline2: 3.96e-18 4475142 5.63e-107 4495573 4496039 ( 393156) 467 ( 1266) 4469541 190 --->plink-------dash-----: 3.96e-18 4475578 5.68e-107 4495948 4496039 ( 393156) 91.9 ( 221) 4469541 0 --->germline1---germline2: 1e+00 0 3.2e-01 -120 347 ( 496) 467 ( 1266) 182 190 --->germline1---dash-----: 2.52e-08 508 1.99e-07 255 347 ( 496) 91.9 ( 221) 182 0 --->germline2---dash-----: 1.71e-08 530 3.65e-03 375 467 ( 1266) 91.9 ( 221) 190 0 ######falseN###### --->fabia-------beagle1--: 2.69e-06 -1720 7.03e-06 -1743 1972 ( 2571) 3716 ( 2980) 909 2976 --->fabia-------beagle2--: 1.36e-14 -4812 4.15e-17 -5153 1972 ( 2571) 7125 ( 4815) 909 6143 --->fabia-------plink----: 8.28e-17 1583 1.22e-11 1968 1972 ( 2571) 4.64 ( 44.8) 909 0 --->fabia-------germline1: 1.01e-09 -2380 2e-11 -2202 1972 ( 2571) 4175 ( 1840) 909 4444 --->fabia-------germline2: 1.01e-09 -2380 2e-11 -2202 1972 ( 2571) 4175 ( 1840) 909 4444 --->fabia-------dash-----: 1.79e-12 -3225 1.69e-16 -2997 1972 ( 2571) 4969 ( 2031) 909 5619 --->beagle1-----beagle2--: 5.33e-13 -4631 5.3e-16 -3410 3716 ( 2980) 7125 ( 4815) 2976 6143 --->beagle1-----plink----: 3.96e-18 3314 5.84e-22 3711 3716 ( 2980) 4.64 ( 44.8) 2976 0 --->beagle1-----germline1: 5.68e-02 -679 1.89e-01 -459 3716 ( 2980) 4175 ( 1840) 2976 4444 --->beagle1-----germline2: 5.68e-02 -679 1.89e-01 -459 3716 ( 2980) 4175 ( 1840) 2976 4444 --->beagle1-----dash-----: 2.64e-04 -1439 5.79e-04 -1253 3716 ( 2980) 4969 ( 2031) 2976 5619 --->beagle2-----plink----: 3.96e-18 6747 8.87e-27 7121 7125 ( 4815) 4.64 ( 44.8) 6143 0 --->beagle2-----germline1: 9.52e-07 2682 8.4e-08 2951 7125 ( 4815) 4175 ( 1840) 6143 4444 --->beagle2-----germline2: 9.52e-07 2682 8.4e-08 2951 7125 ( 4815) 4175 ( 1840) 6143 4444 --->beagle2-----dash-----: 2.73e-04 2019 5.92e-05 2156 7125 ( 4815) 4969 ( 2031) 6143 5619 --->plink-------germline1: 3.96e-18 -4240 5.69e-41 -4170 4.64 ( 44.8) 4175 ( 1840) 0 4444 --->plink-------germline2: 3.96e-18 -4240 5.69e-41 -4170 4.64 ( 44.8) 4175 ( 1840) 0 4444 --->plink-------dash-----: 3.95e-18 -5281 9.25e-44 -4965 4.64 ( 44.8) 4969 ( 2031) 0 5619 --->germline1---germline2: 1e+00 0 1e+00 0 4175 ( 1840) 4175 ( 1840) 4444 4444 --->germline1---dash-----: 2.52e-08 -1687 9.06e-11 -795 4175 ( 1840) 4969 ( 2031) 4444 5619 --->germline2---dash-----: 2.52e-08 -1687 9.06e-11 -795 4175 ( 1840) 4969 ( 2031) 4444 5619 ######trueP###### --->fabia-------beagle1--: 2.09e-06 1788 8.87e-06 1932 109758 ( 10865) 107826 ( 10700) 112692 110961 --->fabia-------beagle2--: 1.16e-14 4956 5.43e-17 5342 109758 ( 10865) 104416 ( 11126) 112692 107042 --->fabia-------plink----: 1.6e-15 -1551 4.64e-07 -1779 109758 ( 10865) 111537 ( 10431) 112692 113976 --->fabia-------germline1: 9.45e-10 2401 1.48e-09 2391 109758 ( 10865) 107367 ( 10495) 112692 109261 --->fabia-------germline2: 9.45e-10 2401 1.48e-09 2391 109758 ( 10865) 107367 ( 10495) 112692 109261 --->fabia-------dash-----: 1.66e-12 3255 5.47e-14 3186 109758 ( 10865) 106573 ( 10359) 112692 108000 --->beagle1-----beagle2--: 5.33e-13 4631 5.3e-16 3410 107826 ( 10700) 104416 ( 11126) 110961 107042 --->beagle1-----plink----: 3.96e-18 -3314 5.84e-22 -3711 107826 ( 10700) 111537 ( 10431) 110961 113976 --->beagle1-----germline1: 5.68e-02 678 1.89e-01 459 107826 ( 10700) 107367 ( 10495) 110961 109261 --->beagle1-----germline2: 5.68e-02 678 1.89e-01 459 107826 ( 10700) 107367 ( 10495) 110961 109261 --->beagle1-----dash-----: 2.64e-04 1439 5.79e-04 1253 107826 ( 10700) 106573 ( 10359) 110961 108000 --->beagle2-----plink----: 3.96e-18 -6746 8.87e-27 -7121 104416 ( 11126) 111537 ( 10431) 107042 113976 --->beagle2-----germline1: 9.52e-07 -2683 8.4e-08 -2951 104416 ( 11126) 107367 ( 10495) 107042 109261 --->beagle2-----germline2: 9.52e-07 -2683 8.4e-08 -2951 104416 ( 11126) 107367 ( 10495) 107042 109261 --->beagle2-----dash-----: 2.73e-04 -2019 5.92e-05 -2156 104416 ( 11126) 106573 ( 10359) 107042 108000 --->plink-------germline1: 3.96e-18 4240 5.69e-41 4170 111537 ( 10431) 107367 ( 10495) 113976 109261 --->plink-------germline2: 3.96e-18 4240 5.69e-41 4170 111537 ( 10431) 107367 ( 10495) 113976 109261 --->plink-------dash-----: 3.95e-18 5281 9.25e-44 4965 111537 ( 10431) 106573 ( 10359) 113976 108000 --->germline1---germline2: 1e+00 0 1e+00 0 107367 ( 10495) 107367 ( 10495) 109261 109261 --->germline1---dash-----: 2.52e-08 1687 9.06e-11 795 107367 ( 10495) 106573 ( 10359) 109261 108000 --->germline2---dash-----: 2.52e-08 1687 9.06e-11 795 107367 ( 10495) 106573 ( 10359) 109261 108000 ######MatthewsSnps###### --->fabia-------beagle1--: 2.86e-01 0.009042 4.91e-03 -0.044669 0.911735 ( 0.152101) 0.956404 ( 0.032361) 0.989704 0.969065 --->fabia-------beagle2--: 9.41e-01 0.000372 5.8e-05 -0.063277 0.911735 ( 0.152101) 0.975013 ( 0.015220) 0.989704 0.978685 --->fabia-------plink----: 3.96e-18 0.972404 3.86e-79 0.906203 0.911735 ( 0.152101) 0.005532 ( 0.010293) 0.989704 0.000000 --->fabia-------germline1: 4.42e-01 -0.003015 1.44e-05 -0.069611 0.911735 ( 0.152101) 0.981346 ( 0.010664) 0.989704 0.980636 --->fabia-------germline2: 4.42e-01 -0.003015 1.44e-05 -0.069611 0.911735 ( 0.152101) 0.981346 ( 0.010664) 0.989704 0.980636 --->fabia-------dash-----: 8.08e-01 0.001461 5.96e-05 -0.064133 0.911735 ( 0.152101) 0.975868 ( 0.011190) 0.989704 0.972249 --->beagle1-----beagle2--: 1.71e-08 -0.042363 2.66e-08 -0.018608 0.956404 ( 0.032361) 0.975013 ( 0.015220) 0.969065 0.978685 --->beagle1-----plink----: 3.96e-18 0.954278 1.65e-143 0.950872 0.956404 ( 0.032361) 0.005532 ( 0.010293) 0.969065 0.000000 --->beagle1-----germline1: 4.04e-10 -0.021577 6.02e-11 -0.024942 0.956404 ( 0.032361) 0.981346 ( 0.010664) 0.969065 0.980636 --->beagle1-----germline2: 4.04e-10 -0.021577 6.02e-11 -0.024942 0.956404 ( 0.032361) 0.981346 ( 0.010664) 0.969065 0.980636 --->beagle1-----dash-----: 2.55e-05 -0.016341 3.19e-07 -0.019464 0.956404 ( 0.032361) 0.975868 ( 0.011190) 0.969065 0.972249 --->beagle2-----plink----: 3.96e-18 0.972458 3.59e-168 0.969481 0.975013 ( 0.015220) 0.005532 ( 0.010293) 0.978685 0.000000 --->beagle2-----germline1: 6.5e-03 -0.006147 1.36e-03 -0.006333 0.975013 ( 0.015220) 0.981346 ( 0.010664) 0.978685 0.980636 --->beagle2-----germline2: 6.5e-03 -0.006147 1.36e-03 -0.006333 0.975013 ( 0.015220) 0.981346 ( 0.010664) 0.978685 0.980636 --->beagle2-----dash-----: 6.14e-01 0.001063 6.64e-01 -0.000855 0.975013 ( 0.015220) 0.975868 ( 0.011190) 0.978685 0.972249 --->plink-------germline1: 3.96e-18 -0.976991 5.25e-182 -0.975814 0.005532 ( 0.010293) 0.981346 ( 0.010664) 0.000000 0.980636 --->plink-------germline2: 3.96e-18 -0.976991 5.25e-182 -0.975814 0.005532 ( 0.010293) 0.981346 ( 0.010664) 0.000000 0.980636 --->plink-------dash-----: 3.95e-18 -0.970862 6.27e-180 -0.970336 0.005532 ( 0.010293) 0.975868 ( 0.011190) 0.000000 0.972249 --->germline1---germline2: 1e+00 0.000000 1e+00 0.000000 0.981346 ( 0.010664) 0.981346 ( 0.010664) 0.980636 0.980636 --->germline1---dash-----: 2.46e-07 0.015882 3.2e-09 0.005478 0.981346 ( 0.010664) 0.975868 ( 0.011190) 0.980636 0.972249 --->germline2---dash-----: 2.46e-07 0.015882 3.2e-09 0.005478 0.981346 ( 0.010664) 0.975868 ( 0.011190) 0.980636 0.972249 ######F1Snps###### --->fabia-------beagle1--: 2.89e-01 0.008297 3.13e-03 -0.047767 0.911610 ( 0.154849) 0.959376 ( 0.030825) 0.990629 0.971643 --->fabia-------beagle2--: 9.57e-01 0.000287 4.58e-05 -0.065397 0.911610 ( 0.154849) 0.977007 ( 0.014228) 0.990629 0.980448 --->fabia-------plink----: 3.96e-18 0.810310 2.6e-70 0.741165 0.911610 ( 0.154849) 0.170445 ( 0.014968) 0.990629 0.173613 --->fabia-------germline1: 4.3e-01 -0.002920 1.3e-05 -0.071246 0.911610 ( 0.154849) 0.982856 ( 0.010001) 0.990629 0.982474 --->fabia-------germline2: 4.3e-01 -0.002920 1.3e-05 -0.071246 0.911610 ( 0.154849) 0.982856 ( 0.010001) 0.990629 0.982474 --->fabia-------dash-----: 8.22e-01 0.001300 4.84e-05 -0.066119 0.911610 ( 0.154849) 0.977729 ( 0.010475) 0.990629 0.974329 --->beagle1-----beagle2--: 1.71e-08 -0.040047 3.08e-08 -0.017630 0.959376 ( 0.030825) 0.977007 ( 0.014228) 0.971643 0.980448 --->beagle1-----plink----: 3.96e-18 0.791941 7.65e-139 0.788931 0.959376 ( 0.030825) 0.170445 ( 0.014968) 0.971643 0.173613 --->beagle1-----germline1: 4.61e-10 -0.020115 7.42e-11 -0.023479 0.959376 ( 0.030825) 0.982856 ( 0.010001) 0.971643 0.982474 --->beagle1-----germline2: 4.61e-10 -0.020115 7.42e-11 -0.023479 0.959376 ( 0.030825) 0.982856 ( 0.010001) 0.971643 0.982474 --->beagle1-----dash-----: 2.97e-05 -0.015333 3.5e-07 -0.018352 0.959376 ( 0.030825) 0.977729 ( 0.010475) 0.971643 0.974329 --->beagle2-----plink----: 3.96e-18 0.806890 1.73e-163 0.806561 0.977007 ( 0.014228) 0.170445 ( 0.014968) 0.980448 0.173613 --->beagle2-----germline1: 7.06e-03 -0.005639 1.48e-03 -0.005849 0.977007 ( 0.014228) 0.982856 ( 0.010001) 0.980448 0.982474 --->beagle2-----germline2: 7.06e-03 -0.005639 1.48e-03 -0.005849 0.977007 ( 0.014228) 0.982856 ( 0.010001) 0.980448 0.982474 --->beagle2-----dash-----: 5.79e-01 0.001079 6.94e-01 -0.000722 0.977007 ( 0.014228) 0.977729 ( 0.010475) 0.980448 0.974329 --->plink-------germline1: 3.96e-18 -0.810762 2.73e-173 -0.812410 0.170445 ( 0.014968) 0.982856 ( 0.010001) 0.173613 0.982474 --->plink-------germline2: 3.96e-18 -0.810762 2.73e-173 -0.812410 0.170445 ( 0.014968) 0.982856 ( 0.010001) 0.173613 0.982474 --->plink-------dash-----: 3.95e-18 -0.804584 1.86e-169 -0.807284 0.170445 ( 0.014968) 0.977729 ( 0.010475) 0.173613 0.974329 --->germline1---germline2: 1e+00 0.000000 1e+00 0.000000 0.982856 ( 0.010001) 0.982856 ( 0.010001) 0.982474 0.982474 --->germline1---dash-----: 2.26e-07 0.014843 2.86e-09 0.005127 0.982856 ( 0.010001) 0.977729 ( 0.010475) 0.982474 0.974329 --->germline2---dash-----: 2.26e-07 0.014843 2.86e-09 0.005127 0.982856 ( 0.010001) 0.977729 ( 0.010475) 0.982474 0.974329 ######accuracySnps###### --->fabia-------beagle1--: 2.65e-01 0.001670 7.74e-04 -0.018122 0.973852 ( 0.051822) 0.991973 ( 0.006489) 0.998228 0.994490 --->fabia-------beagle2--: 8.07e-01 0.000226 5.19e-05 -0.021770 0.973852 ( 0.051822) 0.995621 ( 0.002786) 0.998228 0.996345 --->fabia-------plink----: 3.96e-18 0.900374 5.29e-123 0.879441 0.973852 ( 0.051822) 0.094411 ( 0.009157) 0.998228 0.095190 --->fabia-------germline1: 5.19e-01 -0.000437 2.32e-05 -0.023057 0.973852 ( 0.051822) 0.996909 ( 0.001702) 0.998228 0.996953 --->fabia-------germline2: 5.19e-01 -0.000437 2.32e-05 -0.023057 0.973852 ( 0.051822) 0.996909 ( 0.001702) 0.998228 0.996953 --->fabia-------dash-----: 7.67e-01 0.000290 4.65e-05 -0.022142 0.973852 ( 0.051822) 0.995994 ( 0.001841) 0.998228 0.995318 --->beagle1-----beagle2--: 1.71e-08 -0.008218 5.34e-08 -0.003648 0.991973 ( 0.006489) 0.995621 ( 0.002786) 0.994490 0.996345 --->beagle1-----plink----: 3.96e-18 0.897204 2.71e-188 0.897562 0.991973 ( 0.006489) 0.094411 ( 0.009157) 0.994490 0.095190 --->beagle1-----germline1: 1.48e-10 -0.004060 8.19e-11 -0.004935 0.991973 ( 0.006489) 0.996909 ( 0.001702) 0.994490 0.996953 --->beagle1-----germline2: 1.48e-10 -0.004060 8.19e-11 -0.004935 0.991973 ( 0.006489) 0.996909 ( 0.001702) 0.994490 0.996953 --->beagle1-----dash-----: 6.99e-06 -0.003208 1.09e-07 -0.004020 0.991973 ( 0.006489) 0.995994 ( 0.001841) 0.994490 0.995318 --->beagle2-----plink----: 3.96e-18 0.900579 1.67e-195 0.901210 0.995621 ( 0.002786) 0.094411 ( 0.009157) 0.996345 0.095190 --->beagle2-----germline1: 1.89e-03 -0.001198 2.79e-04 -0.001287 0.995621 ( 0.002786) 0.996909 ( 0.001702) 0.996345 0.996953 --->beagle2-----germline2: 1.89e-03 -0.001198 2.79e-04 -0.001287 0.995621 ( 0.002786) 0.996909 ( 0.001702) 0.996345 0.996953 --->beagle2-----dash-----: 9.64e-01 1.53e-05 2.88e-01 -0.000372 0.995621 ( 0.002786) 0.995994 ( 0.001841) 0.996345 0.995318 --->plink-------germline1: 3.96e-18 -0.901435 8.57e-199 -0.902498 0.094411 ( 0.009157) 0.996909 ( 0.001702) 0.095190 0.996953 --->plink-------germline2: 3.96e-18 -0.901435 8.57e-199 -0.902498 0.094411 ( 0.009157) 0.996909 ( 0.001702) 0.095190 0.996953 --->plink-------dash-----: 3.95e-18 -0.900411 1.22e-197 -0.901583 0.094411 ( 0.009157) 0.995994 ( 0.001841) 0.095190 0.995318 --->germline1---germline2: 1e+00 0.000000 1e+00 0.000000 0.996909 ( 0.001702) 0.996909 ( 0.001702) 0.996953 0.996953 --->germline1---dash-----: 3.16e-07 0.002635 4.64e-09 0.000915 0.996909 ( 0.001702) 0.995994 ( 0.001841) 0.996953 0.995318 --->germline2---dash-----: 3.16e-07 0.002635 4.64e-09 0.000915 0.996909 ( 0.001702) 0.995994 ( 0.001841) 0.996953 0.995318 ######FPRSnps###### --->fabia-------beagle1--: 6.92e-02 -0.003991 2.27e-03 0.018188 0.027044 ( 0.057588) 0.008856 ( 0.007169) 0.000000 0.005943 --->fabia-------beagle2--: 9.57e-02 -0.002552 1.84e-04 0.022213 0.027044 ( 0.057588) 0.004831 ( 0.003082) 0.000000 0.004039 --->fabia-------plink----: 1.18e-18 -0.996920 1.9e-123 -0.971520 0.027044 ( 0.057588) 0.998564 ( 0.003389) 0.000000 1.000000 --->fabia-------germline1: 2.18e-01 0.020813 1.44e-05 0.026313 0.027044 ( 0.057588) 0.000731 ( 0.001141) 0.000000 0.000227 --->fabia-------germline2: 2.18e-01 0.020813 1.44e-05 0.026313 0.027044 ( 0.057588) 0.000731 ( 0.001141) 0.000000 0.000227 --->fabia-------dash-----: 1e+00 0.000000 9.33e-06 0.026924 0.027044 ( 0.057588) 0.000120 ( 0.000303) 0.000000 0.000000 --->beagle1-----beagle2--: 1.71e-08 0.009076 5.44e-08 0.004025 0.008856 ( 0.007169) 0.004831 ( 0.003082) 0.005943 0.004039 --->beagle1-----plink----: 3.96e-18 -0.990864 1.47e-207 -0.989707 0.008856 ( 0.007169) 0.998564 ( 0.003389) 0.005943 1.000000 --->beagle1-----germline1: 1.48e-17 0.007185 3.6e-19 0.008125 0.008856 ( 0.007169) 0.000731 ( 0.001141) 0.005943 0.000227 --->beagle1-----germline2: 1.48e-17 0.007185 3.6e-19 0.008125 0.008856 ( 0.007169) 0.000731 ( 0.001141) 0.005943 0.000227 --->beagle1-----dash-----: 3.96e-18 0.007750 1.3e-21 0.008736 0.008856 ( 0.007169) 0.000120 ( 0.000303) 0.005943 0.000000 --->beagle2-----plink----: 3.96e-18 -0.994755 8.19e-228 -0.993733 0.004831 ( 0.003082) 0.998564 ( 0.003389) 0.004039 1.000000 --->beagle2-----germline1: 1.03e-16 0.003684 5.07e-22 0.004100 0.004831 ( 0.003082) 0.000731 ( 0.001141) 0.004039 0.000227 --->beagle2-----germline2: 1.03e-16 0.003684 5.07e-22 0.004100 0.004831 ( 0.003082) 0.000731 ( 0.001141) 0.004039 0.000227 --->beagle2-----dash-----: 3.96e-18 0.004267 7.59e-28 0.004711 0.004831 ( 0.003082) 0.000120 ( 0.000303) 0.004039 0.000000 --->plink-------germline1: 3.29e-18 0.998871 1.88e-243 0.997832 0.998564 ( 0.003389) 0.000731 ( 0.001141) 1.000000 0.000227 --->plink-------germline2: 3.29e-18 0.998871 1.88e-243 0.997832 0.998564 ( 0.003389) 0.000731 ( 0.001141) 1.000000 0.000227 --->plink-------dash-----: 9.26e-19 0.999497 1.7e-246 0.998444 0.998564 ( 0.003389) 0.000120 ( 0.000303) 1.000000 0.000000 --->germline1---germline2: 1e+00 0.000000 1e+00 0.000000 0.000731 ( 0.001141) 0.000731 ( 0.001141) 0.000227 0.000227 --->germline1---dash-----: 1.75e-07 0.001454 3.8e-07 0.000611 0.000731 ( 0.001141) 0.000120 ( 0.000303) 0.000227 0.000000 --->germline2---dash-----: 1.75e-07 0.001454 3.8e-07 0.000611 0.000731 ( 0.001141) 0.000120 ( 0.000303) 0.000227 0.000000 ######FDRSnps###### --->fabia-------beagle1--: 6.36e-02 -0.036974 9.38e-02 0.038837 0.115294 ( 0.223211) 0.076457 ( 0.055218) 0.000000 0.055150 --->fabia-------beagle2--: 9.51e-02 -0.024271 1.85e-03 0.070710 0.115294 ( 0.223211) 0.044584 ( 0.026820) 0.000000 0.038354 --->fabia-------plink----: 3.96e-18 -0.904288 4.32e-58 -0.791475 0.115294 ( 0.223211) 0.906768 ( 0.008595) 0.000000 0.904942 --->fabia-------germline1: 2.13e-01 0.139079 4.64e-06 0.108321 0.115294 ( 0.223211) 0.006973 ( 0.010545) 0.000000 0.002158 --->fabia-------germline2: 2.13e-01 0.139079 4.64e-06 0.108321 0.115294 ( 0.223211) 0.006973 ( 0.010545) 0.000000 0.002158 --->fabia-------dash-----: 1e+00 0.000000 1.56e-06 0.114047 0.115294 ( 0.223211) 0.001247 ( 0.003206) 0.000000 0.000000 --->beagle1-----beagle2--: 1.71e-08 0.072629 2.21e-08 0.031873 0.076457 ( 0.055218) 0.044584 ( 0.026820) 0.055150 0.038354 --->beagle1-----plink----: 3.96e-18 -0.835938 7.22e-119 -0.830311 0.076457 ( 0.055218) 0.906768 ( 0.008595) 0.055150 0.904942 --->beagle1-----germline1: 1.52e-17 0.064363 1.56e-21 0.069484 0.076457 ( 0.055218) 0.006973 ( 0.010545) 0.055150 0.002158 --->beagle1-----germline2: 1.52e-17 0.064363 1.56e-21 0.069484 0.076457 ( 0.055218) 0.006973 ( 0.010545) 0.055150 0.002158 --->beagle1-----dash-----: 3.96e-18 0.069567 1.13e-24 0.075210 0.076457 ( 0.055218) 0.001247 ( 0.003206) 0.055150 0.000000 --->beagle2-----plink----: 3.96e-18 -0.865118 2.82e-151 -0.862184 0.044584 ( 0.026820) 0.906768 ( 0.008595) 0.038354 0.904942 --->beagle2-----germline1: 8.13e-17 0.034396 4.01e-23 0.037611 0.044584 ( 0.026820) 0.006973 ( 0.010545) 0.038354 0.002158 --->beagle2-----germline2: 8.13e-17 0.034396 4.01e-23 0.037611 0.044584 ( 0.026820) 0.006973 ( 0.010545) 0.038354 0.002158 --->beagle2-----dash-----: 3.96e-18 0.039723 1.19e-29 0.043337 0.044584 ( 0.026820) 0.001247 ( 0.003206) 0.038354 0.000000 --->plink-------germline1: 3.96e-18 0.900576 2.25e-181 0.899795 0.906768 ( 0.008595) 0.006973 ( 0.010545) 0.904942 0.002158 --->plink-------germline2: 3.96e-18 0.900576 2.25e-181 0.899795 0.906768 ( 0.008595) 0.006973 ( 0.010545) 0.904942 0.002158 --->plink-------dash-----: 3.95e-18 0.904668 4.85e-203 0.905521 0.906768 ( 0.008595) 0.001247 ( 0.003206) 0.904942 0.000000 --->germline1---germline2: 1e+00 0.000000 1e+00 0.000000 0.006973 ( 0.010545) 0.006973 ( 0.010545) 0.002158 0.002158 --->germline1---dash-----: 1.75e-07 0.013716 2.38e-07 0.005726 0.006973 ( 0.010545) 0.001247 ( 0.003206) 0.002158 0.000000 --->germline2---dash-----: 1.75e-07 0.013716 2.38e-07 0.005726 0.006973 ( 0.010545) 0.001247 ( 0.003206) 0.002158 0.000000 ######specifitySnps###### --->fabia-------beagle1--: 6.92e-02 0.003990 2.27e-03 -0.018188 0.972956 ( 0.057588) 0.991144 ( 0.007169) 1.000000 0.994057 --->fabia-------beagle2--: 9.57e-02 0.002529 1.84e-04 -0.022213 0.972956 ( 0.057588) 0.995169 ( 0.003082) 1.000000 0.995961 --->fabia-------plink----: 1.18e-18 0.996921 1.9e-123 0.971520 0.972956 ( 0.057588) 0.001436 ( 0.003389) 1.000000 0.000000 --->fabia-------germline1: 2.18e-01 -0.020830 1.44e-05 -0.026313 0.972956 ( 0.057588) 0.999269 ( 0.001141) 1.000000 0.999773 --->fabia-------germline2: 2.18e-01 -0.020830 1.44e-05 -0.026313 0.972956 ( 0.057588) 0.999269 ( 0.001141) 1.000000 0.999773 --->fabia-------dash-----: 1e+00 0.000000 9.33e-06 -0.026924 0.972956 ( 0.057588) 0.999880 ( 0.000303) 1.000000 1.000000 --->beagle1-----beagle2--: 1.71e-08 -0.009078 5.44e-08 -0.004025 0.991144 ( 0.007169) 0.995169 ( 0.003082) 0.994057 0.995961 --->beagle1-----plink----: 3.96e-18 0.990895 1.47e-207 0.989707 0.991144 ( 0.007169) 0.001436 ( 0.003389) 0.994057 0.000000 --->beagle1-----germline1: 1.48e-17 -0.007190 3.6e-19 -0.008125 0.991144 ( 0.007169) 0.999269 ( 0.001141) 0.994057 0.999773 --->beagle1-----germline2: 1.48e-17 -0.007190 3.6e-19 -0.008125 0.991144 ( 0.007169) 0.999269 ( 0.001141) 0.994057 0.999773 --->beagle1-----dash-----: 3.96e-18 -0.007726 1.3e-21 -0.008736 0.991144 ( 0.007169) 0.999880 ( 0.000303) 0.994057 1.000000 --->beagle2-----plink----: 3.96e-18 0.994753 8.19e-228 0.993733 0.995169 ( 0.003082) 0.001436 ( 0.003389) 0.995961 0.000000 --->beagle2-----germline1: 1.03e-16 -0.003683 5.07e-22 -0.004100 0.995169 ( 0.003082) 0.999269 ( 0.001141) 0.995961 0.999773 --->beagle2-----germline2: 1.03e-16 -0.003683 5.07e-22 -0.004100 0.995169 ( 0.003082) 0.999269 ( 0.001141) 0.995961 0.999773 --->beagle2-----dash-----: 3.96e-18 -0.004276 7.59e-28 -0.004711 0.995169 ( 0.003082) 0.999880 ( 0.000303) 0.995961 1.000000 --->plink-------germline1: 3.29e-18 -0.998871 1.88e-243 -0.997832 0.001436 ( 0.003389) 0.999269 ( 0.001141) 0.000000 0.999773 --->plink-------germline2: 3.29e-18 -0.998871 1.88e-243 -0.997832 0.001436 ( 0.003389) 0.999269 ( 0.001141) 0.000000 0.999773 --->plink-------dash-----: 9.26e-19 -0.999497 1.7e-246 -0.998444 0.001436 ( 0.003389) 0.999880 ( 0.000303) 0.000000 1.000000 --->germline1---germline2: 1e+00 0.000000 1e+00 0.000000 0.999269 ( 0.001141) 0.999269 ( 0.001141) 0.999773 0.999773 --->germline1---dash-----: 1.75e-07 -0.001472 3.8e-07 -0.000611 0.999269 ( 0.001141) 0.999880 ( 0.000303) 0.999773 1.000000 --->germline2---dash-----: 1.75e-07 -0.001472 3.8e-07 -0.000611 0.999269 ( 0.001141) 0.999880 ( 0.000303) 0.999773 1.000000 ######sensitivitySnps###### --->fabia-------beagle1--: 1e+00 0.000000 1e+00 0.000000 0.981660 ( 0.025067) 1.000000 ( 0.000000) 0.992095 1.000000 --->fabia-------beagle2--: 1e+00 0.000000 1e+00 0.000000 0.981660 ( 0.025067) 1.000000 ( 0.000000) 0.992095 1.000000 --->fabia-------plink----: 1e+00 0.000000 1e+00 0.000000 0.981660 ( 0.025067) 1.000000 ( 0.000000) 0.992095 1.000000 --->fabia-------germline1: 5.16e-03 0.007766 3.17e-03 0.008336 0.981660 ( 0.025067) 0.973324 ( 0.022512) 0.992095 0.982216 --->fabia-------germline2: 5.16e-03 0.007766 3.17e-03 0.008336 0.981660 ( 0.025067) 0.973324 ( 0.022512) 0.992095 0.982216 --->fabia-------dash-----: 1.05e-10 0.025389 2.32e-13 0.023819 0.981660 ( 0.025067) 0.957841 ( 0.021498) 0.992095 0.950260 --->beagle1-----beagle2--: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 1.000000 ( 0.000000) 1.000000 1.000000 --->beagle1-----plink----: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 1.000000 ( 0.000000) 1.000000 1.000000 --->beagle1-----germline1: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 0.973324 ( 0.022512) 1.000000 0.982216 --->beagle1-----germline2: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 0.973324 ( 0.022512) 1.000000 0.982216 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 0.957841 ( 0.021498) 1.000000 0.950260 --->beagle2-----plink----: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 1.000000 ( 0.000000) 1.000000 1.000000 --->beagle2-----germline1: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 0.973324 ( 0.022512) 1.000000 0.982216 --->beagle2-----germline2: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 0.973324 ( 0.022512) 1.000000 0.982216 --->beagle2-----dash-----: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 0.957841 ( 0.021498) 1.000000 0.950260 --->plink-------germline1: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 0.973324 ( 0.022512) 1.000000 0.982216 --->plink-------germline2: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 0.973324 ( 0.022512) 1.000000 0.982216 --->plink-------dash-----: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 0.957841 ( 0.021498) 1.000000 0.950260 --->germline1---germline2: 1e+00 0.000000 1e+00 0.000000 0.973324 ( 0.022512) 0.973324 ( 0.022512) 0.982216 0.982216 --->germline1---dash-----: 1.75e-07 0.042294 9.01e-11 0.015483 0.973324 ( 0.022512) 0.957841 ( 0.021498) 0.982216 0.950260 --->germline2---dash-----: 1.75e-07 0.042294 9.01e-11 0.015483 0.973324 ( 0.022512) 0.957841 ( 0.021498) 0.982216 0.950260 ######trueNSnps###### --->fabia-------beagle1--: 6.92e-02 727 2.25e-03 -3297 176476 ( 10606) 179773 ( 2225) 180950 179911 --->fabia-------beagle2--: 9.57e-02 464 1.82e-04 -4027 176476 ( 10606) 180502 ( 1843) 180950 180272 --->fabia-------plink----: 3.96e-18 180605 8.56e-123 176215 176476 ( 10606) 260 ( 614) 180950 0 --->fabia-------germline1: 2.18e-01 -3767 1.41e-05 -4770 176476 ( 10606) 181246 ( 1743) 180950 180928 --->fabia-------germline2: 2.18e-01 -3767 1.41e-05 -4770 176476 ( 10606) 181246 ( 1743) 180950 180928 --->fabia-------dash-----: 3.48e-04 -9846 9.14e-06 -4881 176476 ( 10606) 181356 ( 1708) 180950 180987 --->beagle1-----beagle2--: 1.71e-08 -1641 5.34e-08 -730 179773 ( 2225) 180502 ( 1843) 179911 180272 --->beagle1-----plink----: 3.96e-18 179438 2.71e-188 179512 179773 ( 2225) 260 ( 614) 179911 0 --->beagle1-----germline1: 1.48e-17 -1305 3.35e-19 -1473 179773 ( 2225) 181246 ( 1743) 179911 180928 --->beagle1-----germline2: 1.48e-17 -1305 3.35e-19 -1473 179773 ( 2225) 181246 ( 1743) 179911 180928 --->beagle1-----dash-----: 3.96e-18 -1401 1.2e-21 -1584 179773 ( 2225) 181356 ( 1708) 179911 180987 --->beagle2-----plink----: 3.96e-18 180118 1.67e-195 180242 180502 ( 1843) 260 ( 614) 180272 0 --->beagle2-----germline1: 1.02e-16 -668 4.48e-22 -743 180502 ( 1843) 181246 ( 1743) 180272 180928 --->beagle2-----germline2: 1.02e-16 -668 4.48e-22 -743 180502 ( 1843) 181246 ( 1743) 180272 180928 --->beagle2-----dash-----: 3.96e-18 -776 6.41e-28 -854 180502 ( 1843) 181356 ( 1708) 180272 180987 --->plink-------germline1: 3.95e-18 -180817 7.73e-199 -180985 260 ( 614) 181246 ( 1743) 0 180928 --->plink-------germline2: 3.95e-18 -180817 7.73e-199 -180985 260 ( 614) 181246 ( 1743) 0 180928 --->plink-------dash-----: 3.95e-18 -180922 1e-199 -181096 260 ( 614) 181356 ( 1708) 0 180987 --->germline1---germline2: 1e+00 0 1e+00 0 181246 ( 1743) 181246 ( 1743) 180928 180928 --->germline1---dash-----: 1.75e-07 -263 3.78e-07 -111 181246 ( 1743) 181356 ( 1708) 180928 180987 --->germline2---dash-----: 1.75e-07 -263 3.78e-07 -111 181246 ( 1743) 181356 ( 1708) 180928 180987 ######falsePSnps###### --->fabia-------beagle1--: 6.92e-02 -727 2.25e-03 3297 4903 ( 10428) 1605 ( 1298) 0 1102 --->fabia-------beagle2--: 9.57e-02 -464 1.82e-04 4027 4903 ( 10428) 876 ( 557) 0 731 --->fabia-------plink----: 3.96e-18 -180605 8.56e-123 -176215 4903 ( 10428) 181118 ( 1831) 0 180962 --->fabia-------germline1: 2.18e-01 3767 1.41e-05 4770 4903 ( 10428) 132 ( 207) 0 41 --->fabia-------germline2: 2.18e-01 3767 1.41e-05 4770 4903 ( 10428) 132 ( 207) 0 41 --->fabia-------dash-----: 1e+00 0.000000 9.14e-06 4880.870000 4902.710000 (10428.195309) 21.840000 (55.185220) 0.000000 0.000000 --->beagle1-----beagle2--: 1.71e-08 1641 5.34e-08 730 1605 ( 1298) 876 ( 557) 1102 731 --->beagle1-----plink----: 3.96e-18 -179438 2.71e-188 -179512 1605 ( 1298) 181118 ( 1831) 1102 180962 --->beagle1-----germline1: 1.48e-17 1304 3.35e-19 1473 1605 ( 1298) 132 ( 207) 1102 41 --->beagle1-----germline2: 1.48e-17 1304 3.35e-19 1473 1605 ( 1298) 132 ( 207) 1102 41 --->beagle1-----dash-----: 3.96e-18 1401 1.2e-21 1584 1605 ( 1298) 21.8 ( 55.2) 1102 0 --->beagle2-----plink----: 3.96e-18 -180118 1.67e-195 -180242 876 ( 557) 181118 ( 1831) 731 180962 --->beagle2-----germline1: 1.02e-16 668 4.48e-22 743 876 ( 557) 132 ( 207) 731 41 --->beagle2-----germline2: 1.02e-16 668 4.48e-22 743 876 ( 557) 132 ( 207) 731 41 --->beagle2-----dash-----: 3.96e-18 777 6.41e-28 854 876 ( 557) 21.8 ( 55.2) 731 0 --->plink-------germline1: 3.95e-18 180817 7.73e-199 180985 181118 ( 1831) 132 ( 207) 180962 41 --->plink-------germline2: 3.95e-18 180817 7.73e-199 180985 181118 ( 1831) 132 ( 207) 180962 41 --->plink-------dash-----: 3.95e-18 180922 1e-199 181096 181118 ( 1831) 21.8 ( 55.2) 180962 0 --->germline1---germline2: 1e+00 0 1e+00 0 132 ( 207) 132 ( 207) 41 41 --->germline1---dash-----: 1.75e-07 263 3.78e-07 111 132 ( 207) 21.8 ( 55.2) 41 0 --->germline2---dash-----: 1.75e-07 263 3.78e-07 111 132 ( 207) 21.8 ( 55.2) 41 0 ######falseNSnps###### --->fabia-------beagle1--: 1e+00 0 1e+00 0 327 ( 427) 0 ( 0) 152 0 --->fabia-------beagle2--: 1e+00 0 1e+00 0 327 ( 427) 0 ( 0) 152 0 --->fabia-------plink----: 1e+00 0 1e+00 0 327 ( 427) 0 ( 0) 152 0 --->fabia-------germline1: 4.76e-03 -146 2.77e-03 -159 327 ( 427) 486 ( 399) 152 319 --->fabia-------germline2: 4.76e-03 -146 2.77e-03 -159 327 ( 427) 486 ( 399) 152 319 --->fabia-------dash-----: 1.03e-10 -477 1.51e-13 -452 327 ( 427) 779 ( 395) 152 932 --->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 1e+00 0 0 ( 0) 486 ( 399) 0 319 --->beagle1-----germline2: 1e+00 0 1e+00 0 0 ( 0) 486 ( 399) 0 319 --->beagle1-----dash-----: 1e+00 0 1e+00 0 0 ( 0) 779 ( 395) 0 932 --->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 1e+00 0 0 ( 0) 486 ( 399) 0 319 --->beagle2-----germline2: 1e+00 0 1e+00 0 0 ( 0) 486 ( 399) 0 319 --->beagle2-----dash-----: 1e+00 0 1e+00 0 0 ( 0) 779 ( 395) 0 932 --->plink-------germline1: 1e+00 0 1e+00 0 0 ( 0) 486 ( 399) 0 319 --->plink-------germline2: 1e+00 0 1e+00 0 0 ( 0) 486 ( 399) 0 319 --->plink-------dash-----: 1e+00 0 1e+00 0 0 ( 0) 779 ( 395) 0 932 --->germline1---germline2: 1e+00 0 1e+00 0 486 ( 399) 486 ( 399) 319 319 --->germline1---dash-----: 1.75e-07 -800 9.63e-11 -294 486 ( 399) 779 ( 395) 319 932 --->germline2---dash-----: 1.75e-07 -800 9.63e-11 -294 486 ( 399) 779 ( 395) 319 932 ######truePSnps###### --->fabia-------beagle1--: 1.77e-16 -275 1.29e-11 -327 18295 ( 1811) 18622 ( 1715) 18782 18996 --->fabia-------beagle2--: 1.77e-16 -275 1.29e-11 -327 18295 ( 1811) 18622 ( 1715) 18782 18996 --->fabia-------plink----: 1.77e-16 -275 1.29e-11 -327 18295 ( 1811) 18622 ( 1715) 18782 18996 --->fabia-------germline1: 4.76e-03 146 2.77e-03 159 18295 ( 1811) 18136 ( 1778) 18782 18650 --->fabia-------germline2: 4.76e-03 146 2.77e-03 159 18295 ( 1811) 18136 ( 1778) 18782 18650 --->fabia-------dash-----: 1.03e-10 477 1.51e-13 452 18295 ( 1811) 17842 ( 1718) 18782 18000 --->beagle1-----beagle2--: 1e+00 0 1e+00 0 18622 ( 1715) 18622 ( 1715) 18996 18996 --->beagle1-----plink----: 1e+00 0 1e+00 0 18622 ( 1715) 18622 ( 1715) 18996 18996 --->beagle1-----germline1: 8.28e-17 549 2.27e-21 486 18622 ( 1715) 18136 ( 1778) 18996 18650 --->beagle1-----germline2: 8.28e-17 549 2.27e-21 486 18622 ( 1715) 18136 ( 1778) 18996 18650 --->beagle1-----dash-----: 5.78e-18 871 4.35e-36 779 18622 ( 1715) 17842 ( 1718) 18996 18000 --->beagle2-----plink----: 1e+00 0 1e+00 0 18622 ( 1715) 18622 ( 1715) 18996 18996 --->beagle2-----germline1: 8.28e-17 549 2.27e-21 486 18622 ( 1715) 18136 ( 1778) 18996 18650 --->beagle2-----germline2: 8.28e-17 549 2.27e-21 486 18622 ( 1715) 18136 ( 1778) 18996 18650 --->beagle2-----dash-----: 5.78e-18 871 4.35e-36 779 18622 ( 1715) 17842 ( 1718) 18996 18000 --->plink-------germline1: 8.28e-17 549 2.27e-21 486 18622 ( 1715) 18136 ( 1778) 18996 18650 --->plink-------germline2: 8.28e-17 549 2.27e-21 486 18622 ( 1715) 18136 ( 1778) 18996 18650 --->plink-------dash-----: 5.78e-18 871 4.35e-36 779 18622 ( 1715) 17842 ( 1718) 18996 18000 --->germline1---germline2: 1e+00 0 1e+00 0 18136 ( 1778) 18136 ( 1778) 18650 18650 --->germline1---dash-----: 1.75e-07 800 9.63e-11 294 18136 ( 1778) 17842 ( 1718) 18650 18000 --->germline2---dash-----: 1.75e-07 800 9.63e-11 294 18136 ( 1778) 17842 ( 1718) 18650 18000 ######MatthewsSample###### --->fabia-------beagle1--: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 0.953376 ( 0.076743) 1.000000 1.000000 --->fabia-------beagle2--: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 0.999124 ( 0.008759) 1.000000 1.000000 --->fabia-------plink----: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 0.083494 ( 0.005043) 1.000000 0.083588 --->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) 0.998652 ( 0.013485) 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 5.51e-08 -0.045749 0.953376 ( 0.076743) 0.999124 ( 0.008759) 1.000000 1.000000 --->beagle1-----plink----: 3.95e-18 0.908743 5.27e-107 0.869882 0.953376 ( 0.076743) 0.083494 ( 0.005043) 1.000000 0.083588 --->beagle1-----germline1: 1e+00 0.000000 1e+00 0.000000 0.953376 ( 0.076743) 1.000000 ( 0.000000) 1.000000 1.000000 --->beagle1-----germline2: 1e+00 0.000000 9.9e-08 -0.045276 0.953376 ( 0.076743) 0.998652 ( 0.013485) 1.000000 1.000000 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.953376 ( 0.076743) 1.000000 ( 0.000000) 1.000000 1.000000 --->beagle2-----plink----: 3.94e-18 0.916420 5.02e-192 0.915630 0.999124 ( 0.008759) 0.083494 ( 0.005043) 1.000000 0.083588 --->beagle2-----germline1: 1e+00 0.000000 1e+00 0.000000 0.999124 ( 0.008759) 1.000000 ( 0.000000) 1.000000 1.000000 --->beagle2-----germline2: 1e+00 0.000000 7.7e-01 0.000473 0.999124 ( 0.008759) 0.998652 ( 0.013485) 1.000000 1.000000 --->beagle2-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.999124 ( 0.008759) 1.000000 ( 0.000000) 1.000000 1.000000 --->plink-------germline1: 1e+00 0.000000 1e+00 0.000000 0.083494 ( 0.005043) 1.000000 ( 0.000000) 0.083588 1.000000 --->plink-------germline2: 3.94e-18 -0.916299 4.95e-182 -0.915158 0.083494 ( 0.005043) 0.998652 ( 0.013485) 0.083588 1.000000 --->plink-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.083494 ( 0.005043) 1.000000 ( 0.000000) 0.083588 1.000000 --->germline1---germline2: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 0.998652 ( 0.013485) 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 0.998652 ( 0.013485) 1.000000 ( 0.000000) 1.000000 1.000000 ######F1Sample###### --->fabia-------beagle1--: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 0.949821 ( 0.083221) 1.000000 1.000000 --->fabia-------beagle2--: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 0.999091 ( 0.009091) 1.000000 1.000000 --->fabia-------plink----: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 0.025557 ( 0.001680) 1.000000 0.025559 --->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) 0.998571 ( 0.014286) 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 6.45e-08 -0.049270 0.949821 ( 0.083221) 0.999091 ( 0.009091) 1.000000 1.000000 --->beagle1-----plink----: 3.95e-18 0.971832 7.28e-106 0.924264 0.949821 ( 0.083221) 0.025557 ( 0.001680) 1.000000 0.025559 --->beagle1-----germline1: 1e+00 0.000000 1e+00 0.000000 0.949821 ( 0.083221) 1.000000 ( 0.000000) 1.000000 1.000000 --->beagle1-----germline2: 1e+00 0.000000 1.16e-07 -0.048751 0.949821 ( 0.083221) 0.998571 ( 0.014286) 1.000000 1.000000 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.949821 ( 0.083221) 1.000000 ( 0.000000) 1.000000 1.000000 --->beagle2-----plink----: 3.94e-18 0.974450 1.39e-200 0.973534 0.999091 ( 0.009091) 0.025557 ( 0.001680) 1.000000 0.025559 --->beagle2-----germline1: 1e+00 0.000000 1e+00 0.000000 0.999091 ( 0.009091) 1.000000 ( 0.000000) 1.000000 1.000000 --->beagle2-----germline2: 1e+00 0.000000 7.61e-01 0.000519 0.999091 ( 0.009091) 0.998571 ( 0.014286) 1.000000 1.000000 --->beagle2-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.999091 ( 0.009091) 1.000000 ( 0.000000) 1.000000 1.000000 --->plink-------germline1: 1e+00 0.000000 1e+00 0.000000 0.025557 ( 0.001680) 1.000000 ( 0.000000) 0.025559 1.000000 --->plink-------germline2: 3.94e-18 -0.974363 1.01e-183 -0.973015 0.025557 ( 0.001680) 0.998571 ( 0.014286) 0.025559 1.000000 --->plink-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.025557 ( 0.001680) 1.000000 ( 0.000000) 0.025559 1.000000 --->germline1---germline2: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 0.998571 ( 0.014286) 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 0.998571 ( 0.014286) 1.000000 ( 0.000000) 1.000000 1.000000 ######accuracySample###### --->fabia-------beagle1--: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 0.999260 ( 0.001268) 1.000000 1.000000 --->fabia-------beagle2--: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 0.999990 ( 1e-04) 1.000000 1.000000 --->fabia-------plink----: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 0.541340 ( 0.029074) 1.000000 0.542500 --->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) 0.999980 ( 2e-04) 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 1.18e-07 -0.000730 0.999260 ( 0.001268) 0.999990 ( 1e-04) 1.000000 1.000000 --->beagle1-----plink----: 3.94e-18 0.457018 6.86e-121 0.457920 0.999260 ( 0.001268) 0.541340 ( 0.029074) 1.000000 0.542500 --->beagle1-----germline1: 1e+00 0.000000 1e+00 0.000000 0.999260 ( 0.001268) 1.000000 ( 0.000000) 1.000000 1.000000 --->beagle1-----germline2: 1e+00 0.000000 2.31e-07 -0.000720 0.999260 ( 0.001268) 0.999980 ( 2e-04) 1.000000 1.000000 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.999260 ( 0.001268) 1.000000 ( 0.000000) 1.000000 1.000000 --->beagle2-----plink----: 3.94e-18 0.457999 1.08e-120 0.458650 0.999990 ( 1e-04) 0.541340 ( 0.029074) 1.000000 0.542500 --->beagle2-----germline1: 1e+00 0.000000 1e+00 0.000000 0.999990 ( 1e-04) 1.000000 ( 0.000000) 1.000000 1.000000 --->beagle2-----germline2: 1e+00 0.000000 1e+00 0.000000 0.999990 ( 1e-04) 0.999980 ( 2e-04) 1.000000 1.000000 --->beagle2-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.999990 ( 1e-04) 1.000000 ( 0.000000) 1.000000 1.000000 --->plink-------germline1: 1e+00 0.000000 1e+00 0.000000 0.541340 ( 0.029074) 1.000000 ( 0.000000) 0.542500 1.000000 --->plink-------germline2: 3.94e-18 -0.457941 9.41e-121 -0.458640 0.541340 ( 0.029074) 0.999980 ( 2e-04) 0.542500 1.000000 --->plink-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.541340 ( 0.029074) 1.000000 ( 0.000000) 0.542500 1.000000 --->germline1---germline2: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 0.999980 ( 2e-04) 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 0.999980 ( 2e-04) 1.000000 ( 0.000000) 1.000000 1.000000 ######FPRSample###### --->fabia-------beagle1--: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.000744 ( 0.001276) 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) 0.461429 ( 0.029249) 0.000000 0.460262 --->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) 2.01e-05 ( 0.000201) 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 0.000744 ( 0.001276) 0.000000 ( 0.000000) 0.000000 0.000000 --->beagle1-----plink----: 3.95e-18 -0.459769 6.86e-121 -0.460684 0.000744 ( 0.001276) 0.461429 ( 0.029249) 0.000000 0.460262 --->beagle1-----germline1: 1e+00 0.000000 1e+00 0.000000 0.000744 ( 0.001276) 0.000000 ( 0.000000) 0.000000 0.000000 --->beagle1-----germline2: 1e+00 0.000000 2.31e-07 0.000724 0.000744 ( 0.001276) 2.01e-05 ( 0.000201) 0.000000 0.000000 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.000744 ( 0.001276) 0.000000 ( 0.000000) 0.000000 0.000000 --->beagle2-----plink----: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.461429 ( 0.029249) 0.000000 0.460262 --->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) 2.01e-05 ( 0.000201) 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 0.461429 ( 0.029249) 0.000000 ( 0.000000) 0.460262 0.000000 --->plink-------germline2: 3.94e-18 0.460718 9.41e-121 0.461408 0.461429 ( 0.029249) 2.01e-05 ( 0.000201) 0.460262 0.000000 --->plink-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.461429 ( 0.029249) 0.000000 ( 0.000000) 0.460262 0.000000 --->germline1---germline2: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 2.01e-05 ( 0.000201) 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 2.01e-05 ( 0.000201) 0.000000 ( 0.000000) 0.000000 0.000000 ######FDRSample###### --->fabia-------beagle1--: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.084736 ( 0.138219) 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) 0.987056 ( 0.000861) 0.000000 0.987055 --->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) 0.002500 ( 0.025000) 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 0.084736 ( 0.138219) 0.000000 ( 0.000000) 0.000000 0.000000 --->beagle1-----plink----: 3.95e-18 -0.985708 3.06e-83 -0.902320 0.084736 ( 0.138219) 0.987056 ( 0.000861) 0.000000 0.987055 --->beagle1-----germline1: 1e+00 0.000000 1e+00 0.000000 0.084736 ( 0.138219) 0.000000 ( 0.000000) 0.000000 0.000000 --->beagle1-----germline2: 1e+00 0.000000 8.24e-08 0.082236 0.084736 ( 0.138219) 0.002500 ( 0.025000) 0.000000 0.000000 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.084736 ( 0.138219) 0.000000 ( 0.000000) 0.000000 0.000000 --->beagle2-----plink----: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.987056 ( 0.000861) 0.000000 0.987055 --->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) 0.002500 ( 0.025000) 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 0.987056 ( 0.000861) 0.000000 ( 0.000000) 0.987055 0.000000 --->plink-------germline2: 3.94e-18 0.987005 4.18e-160 0.984556 0.987056 ( 0.000861) 0.002500 ( 0.025000) 0.987055 0.000000 --->plink-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.987056 ( 0.000861) 0.000000 ( 0.000000) 0.987055 0.000000 --->germline1---germline2: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.002500 ( 0.025000) 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 0.002500 ( 0.025000) 0.000000 ( 0.000000) 0.000000 0.000000 ######specifitySample###### --->fabia-------beagle1--: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 0.999266 ( 0.001270) 1.000000 1.000000 --->fabia-------beagle2--: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 1.000010 ( 0.000101) 1.000000 1.000000 --->fabia-------plink----: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 0.538581 ( 0.029200) 1.000000 0.539738 --->fabia-------germline1: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 1.000010 ( 0.000101) 1.000000 1.000000 --->fabia-------germline2: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 0.999990 ( 0.000226) 1.000000 1.000000 --->fabia-------dash-----: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 1.000010 ( 0.000101) 1.000000 1.000000 --->beagle1-----beagle2--: 1e+00 0.000000 6.81e-08 -0.000744 0.999266 ( 0.001270) 1.000010 ( 0.000101) 1.000000 1.000000 --->beagle1-----plink----: 3.95e-18 0.459775 6.86e-121 0.460684 0.999266 ( 0.001270) 0.538581 ( 0.029200) 1.000000 0.539738 --->beagle1-----germline1: 1e+00 0.000000 6.81e-08 -0.000744 0.999266 ( 0.001270) 1.000010 ( 0.000101) 1.000000 1.000000 --->beagle1-----germline2: 1e+00 0.000000 2.31e-07 -0.000724 0.999266 ( 0.001270) 0.999990 ( 0.000226) 1.000000 1.000000 --->beagle1-----dash-----: 1e+00 0.000000 6.81e-08 -0.000744 0.999266 ( 0.001270) 1.000010 ( 0.000101) 1.000000 1.000000 --->beagle2-----plink----: 3.94e-18 0.460749 1e-120 0.461429 1.000010 ( 0.000101) 0.538581 ( 0.029200) 1.000000 0.539738 --->beagle2-----germline1: 1e+00 0.000000 1e+00 0.000000 1.000010 ( 0.000101) 1.000010 ( 0.000101) 1.000000 1.000000 --->beagle2-----germline2: 1e+00 0.000000 1e+00 0.000000 1.000010 ( 0.000101) 0.999990 ( 0.000226) 1.000000 1.000000 --->beagle2-----dash-----: 1e+00 0.000000 1e+00 0.000000 1.000010 ( 0.000101) 1.000010 ( 0.000101) 1.000000 1.000000 --->plink-------germline1: 3.94e-18 -0.460738 1e-120 -0.461429 0.538581 ( 0.029200) 1.000010 ( 0.000101) 0.539738 1.000000 --->plink-------germline2: 3.94e-18 -0.460705 9.41e-121 -0.461408 0.538581 ( 0.029200) 0.999990 ( 0.000226) 0.539738 1.000000 --->plink-------dash-----: 3.94e-18 -0.460738 1e-120 -0.461429 0.538581 ( 0.029200) 1.000010 ( 0.000101) 0.539738 1.000000 --->germline1---germline2: 1e+00 0.000000 1e+00 0.000000 1.000010 ( 0.000101) 0.999990 ( 0.000226) 1.000000 1.000000 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 1.000010 ( 0.000101) 1.000010 ( 0.000101) 1.000000 1.000000 --->germline2---dash-----: 1e+00 0.000000 1e+00 0.000000 0.999990 ( 0.000226) 1.000010 ( 0.000101) 1.000000 1.000000 ######sensitivitySample###### --->fabia-------beagle1--: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 0.998333 ( 0.016667) 1.000000 1.000000 --->fabia-------beagle2--: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 0.996667 ( 0.023451) 1.000000 1.000000 --->fabia-------plink----: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 0.998333 ( 0.016667) 1.000000 1.000000 --->fabia-------germline1: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 0.998333 ( 0.016667) 1.000000 1.000000 --->fabia-------germline2: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 0.998333 ( 0.016667) 1.000000 1.000000 --->fabia-------dash-----: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 0.998333 ( 0.016667) 1.000000 1.000000 --->beagle1-----beagle2--: 1e+00 0.000000 3.2e-01 0.001667 0.998333 ( 0.016667) 0.996667 ( 0.023451) 1.000000 1.000000 --->beagle1-----plink----: 1e+00 0.000000 1e+00 0.000000 0.998333 ( 0.016667) 0.998333 ( 0.016667) 1.000000 1.000000 --->beagle1-----germline1: 1e+00 0.000000 1e+00 0.000000 0.998333 ( 0.016667) 0.998333 ( 0.016667) 1.000000 1.000000 --->beagle1-----germline2: 1e+00 0.000000 1e+00 0.000000 0.998333 ( 0.016667) 0.998333 ( 0.016667) 1.000000 1.000000 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.998333 ( 0.016667) 0.998333 ( 0.016667) 1.000000 1.000000 --->beagle2-----plink----: 1e+00 0.000000 3.2e-01 -0.001667 0.996667 ( 0.023451) 0.998333 ( 0.016667) 1.000000 1.000000 --->beagle2-----germline1: 1e+00 0.000000 3.2e-01 -0.001667 0.996667 ( 0.023451) 0.998333 ( 0.016667) 1.000000 1.000000 --->beagle2-----germline2: 1e+00 0.000000 3.2e-01 -0.001667 0.996667 ( 0.023451) 0.998333 ( 0.016667) 1.000000 1.000000 --->beagle2-----dash-----: 1e+00 0.000000 3.2e-01 -0.001667 0.996667 ( 0.023451) 0.998333 ( 0.016667) 1.000000 1.000000 --->plink-------germline1: 1e+00 0.000000 1e+00 0.000000 0.998333 ( 0.016667) 0.998333 ( 0.016667) 1.000000 1.000000 --->plink-------germline2: 1e+00 0.000000 1e+00 0.000000 0.998333 ( 0.016667) 0.998333 ( 0.016667) 1.000000 1.000000 --->plink-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.998333 ( 0.016667) 0.998333 ( 0.016667) 1.000000 1.000000 --->germline1---germline2: 1e+00 0.000000 1e+00 0.000000 0.998333 ( 0.016667) 0.998333 ( 0.016667) 1.000000 1.000000 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 0.998333 ( 0.016667) 0.998333 ( 0.016667) 1.000000 1.000000 --->germline2---dash-----: 1e+00 0.000000 1e+00 0.000000 0.998333 ( 0.016667) 0.998333 ( 0.016667) 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 ( 0.1) 1994 994 --->fabia-------plink----: 1e+00 0 1e+00 0 1994 ( 0) 535 ( 29) 1994 536 --->fabia-------germline1: 1e+00 0 1e+00 0 1994 ( 0) 994 ( 0.1) 1994 994 --->fabia-------germline2: 1e+00 0 1e+00 0 1994 ( 0) 994 ( 0.225) 1994 994 --->fabia-------dash-----: 1e+00 0 1e+00 0 1994 ( 0) 994 ( 0.1) 1994 994 --->beagle1-----beagle2--: 1e+00 0 6.81e-08 -0.74 993 ( 1.26) 994 ( 0.1) 994 994 --->beagle1-----plink----: 3.94e-18 457 6.86e-121 458 993 ( 1.26) 535 ( 29) 994 536 --->beagle1-----germline1: 1e+00 0 6.81e-08 -0.74 993 ( 1.26) 994 ( 0.1) 994 994 --->beagle1-----germline2: 1e+00 0 2.31e-07 -0.72 993 ( 1.26) 994 ( 0.225) 994 994 --->beagle1-----dash-----: 1e+00 0 6.81e-08 -0.74 993 ( 1.26) 994 ( 0.1) 994 994 --->beagle2-----plink----: 3.94e-18 458 1e-120 459 994 ( 0.1) 535 ( 29) 994 536 --->beagle2-----germline1: 1e+00 0 1e+00 0 994 ( 0.1) 994 ( 0.1) 994 994 --->beagle2-----germline2: 1e+00 0 3.2e-01 0.02 994 ( 0.1) 994 ( 0.225) 994 994 --->beagle2-----dash-----: 1e+00 0 1e+00 0 994 ( 0.1) 994 ( 0.1) 994 994 --->plink-------germline1: 3.94e-18 -458 1e-120 -459 535 ( 29) 994 ( 0.1) 536 994 --->plink-------germline2: 3.94e-18 -458 9.41e-121 -459 535 ( 29) 994 ( 0.225) 536 994 --->plink-------dash-----: 3.94e-18 -458 1e-120 -459 535 ( 29) 994 ( 0.1) 536 994 --->germline1---germline2: 1e+00 0 3.2e-01 0.02 994 ( 0.1) 994 ( 0.225) 994 994 --->germline1---dash-----: 1e+00 0 1e+00 0 994 ( 0.1) 994 ( 0.1) 994 994 --->germline2---dash-----: 1e+00 0 3.2e-01 -0.02 994 ( 0.225) 994 ( 0.1) 994 994 ######falsePSample###### --->fabia-------beagle1--: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.740000 ( 1.268261) 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) 459 ( 29.1) 0 458 --->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) 0.020000 ( 0.200000) 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 0.740000 ( 1.268261) 0.000000 ( 0.000000) 0.000000 0.000000 --->beagle1-----plink----: 3.94e-18 -457 6.86e-121 -458 0.74 ( 1.27) 459 ( 29.1) 0 458 --->beagle1-----germline1: 1e+00 0.000000 1e+00 0.000000 0.740000 ( 1.268261) 0.000000 ( 0.000000) 0.000000 0.000000 --->beagle1-----germline2: 1e+00 0.000000 2.31e-07 0.720000 0.740000 ( 1.268261) 0.020000 ( 0.200000) 0.000000 0.000000 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.740000 ( 1.268261) 0.000000 ( 0.000000) 0.000000 0.000000 --->beagle2-----plink----: 1e+00 0 1e+00 0 0 ( 0) 459 ( 29.1) 0 458 --->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) 0.020000 ( 0.200000) 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 0 459 ( 29.1) 0 ( 0) 458 0 --->plink-------germline2: 3.94e-18 458 9.41e-121 459 459 ( 29.1) 0.02 ( 0.2) 458 0 --->plink-------dash-----: 1e+00 0 1e+00 0 459 ( 29.1) 0 ( 0) 458 0 --->germline1---germline2: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.020000 ( 0.200000) 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 0.020000 ( 0.200000) 0.000000 ( 0.000000) 0.000000 0.000000 ######falseNSample###### --->fabia-------beagle1--: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.000000 ( 0.000000) 0.000000 0.000000 --->fabia-------beagle2--: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.010000 ( 0.100000) 0.000000 0.000000 --->fabia-------plink----: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.000000 ( 0.000000) 0.000000 0.000000 --->fabia-------germline1: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.000000 ( 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 0.000000 ( 0.000000) 0.010000 ( 0.100000) 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 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.000000 ( 0.000000) 0.000000 0.000000 --->beagle2-----plink----: 1e+00 0.000000 1e+00 0.000000 0.010000 ( 0.100000) 0.000000 ( 0.000000) 0.000000 0.000000 --->beagle2-----germline1: 1e+00 0.000000 1e+00 0.000000 0.010000 ( 0.100000) 0.000000 ( 0.000000) 0.000000 0.000000 --->beagle2-----germline2: 1e+00 0.000000 1e+00 0.000000 0.010000 ( 0.100000) 0.000000 ( 0.000000) 0.000000 0.000000 --->beagle2-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.010000 ( 0.100000) 0.000000 ( 0.000000) 0.000000 0.000000 --->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 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.000000 ( 0.000000) 0.000000 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 ######truePSample###### --->fabia-------beagle1--: 1e+00 0 1e+00 0 6 ( 0) 5.99 ( 0.1) 6 6 --->fabia-------beagle2--: 1e+00 0 1e+00 0 6 ( 0) 5.98 ( 0.141) 6 6 --->fabia-------plink----: 1e+00 0 1e+00 0 6 ( 0) 5.99 ( 0.1) 6 6 --->fabia-------germline1: 1e+00 0 1e+00 0 6 ( 0) 5.99 ( 0.1) 6 6 --->fabia-------germline2: 1e+00 0 1e+00 0 6 ( 0) 5.99 ( 0.1) 6 6 --->fabia-------dash-----: 1e+00 0 1e+00 0 6 ( 0) 5.99 ( 0.1) 6 6 --->beagle1-----beagle2--: 1e+00 0 3.2e-01 0.01 5.99 ( 0.1) 5.98 ( 0.141) 6 6 --->beagle1-----plink----: 1e+00 0 1e+00 0 5.99 ( 0.1) 5.99 ( 0.1) 6 6 --->beagle1-----germline1: 1e+00 0 1e+00 0 5.99 ( 0.1) 5.99 ( 0.1) 6 6 --->beagle1-----germline2: 1e+00 0 1e+00 0 5.99 ( 0.1) 5.99 ( 0.1) 6 6 --->beagle1-----dash-----: 1e+00 0 1e+00 0 5.99 ( 0.1) 5.99 ( 0.1) 6 6 --->beagle2-----plink----: 1e+00 0 3.2e-01 -0.01 5.98 ( 0.141) 5.99 ( 0.1) 6 6 --->beagle2-----germline1: 1e+00 0 3.2e-01 -0.01 5.98 ( 0.141) 5.99 ( 0.1) 6 6 --->beagle2-----germline2: 1e+00 0 3.2e-01 -0.01 5.98 ( 0.141) 5.99 ( 0.1) 6 6 --->beagle2-----dash-----: 1e+00 0 3.2e-01 -0.01 5.98 ( 0.141) 5.99 ( 0.1) 6 6 --->plink-------germline1: 1e+00 0 1e+00 0 5.99 ( 0.1) 5.99 ( 0.1) 6 6 --->plink-------germline2: 1e+00 0 1e+00 0 5.99 ( 0.1) 5.99 ( 0.1) 6 6 --->plink-------dash-----: 1e+00 0 1e+00 0 5.99 ( 0.1) 5.99 ( 0.1) 6 6 --->germline1---germline2: 1e+00 0 1e+00 0 5.99 ( 0.1) 5.99 ( 0.1) 6 6 --->germline1---dash-----: 1e+00 0 1e+00 0 5.99 ( 0.1) 5.99 ( 0.1) 6 6 --->germline2---dash-----: 1e+00 0 1e+00 0 5.99 ( 0.1) 5.99 ( 0.1) 6 6