Results: Wilcoxon-Rank-Sum Wilcoxon-median t-test t-test-mean mean1 (std) mean2 (std) median1 median2 ######Matthews###### --->fabia-------beagle1--: 3.03e-14 0.145692 2.49e-10 0.134410 0.946744 ( 0.176098) 0.812334 ( 0.142124) 0.987953 0.835387 --->fabia-------beagle2--: 4.59e-15 0.194705 5.21e-15 0.188513 0.946744 ( 0.176098) 0.758231 ( 0.164632) 0.987953 0.764933 --->fabia-------plink----: 3.96e-18 0.918145 9.04e-75 0.885013 0.946744 ( 0.176098) 0.061730 ( 0.013041) 0.987953 0.063947 --->fabia-------germline1: 3.18e-10 0.028494 6.58e-03 0.041414 0.946744 ( 0.176098) 0.905329 ( 0.210175) 0.987953 0.965656 --->fabia-------germline2: 1.46e-09 0.029037 6.92e-02 0.028957 0.946744 ( 0.176098) 0.917787 ( 0.168133) 0.987953 0.965656 --->fabia-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.946744 ( 0.176098) 0.000000 ( 0.000000) 0.987953 0.000000 --->beagle1-----beagle2--: 3.95e-05 0.075624 1.58e-05 0.054103 0.812334 ( 0.142124) 0.758231 ( 0.164632) 0.835387 0.764933 --->beagle1-----plink----: 3.96e-18 0.764192 2.02e-75 0.750604 0.812334 ( 0.142124) 0.061730 ( 0.013041) 0.835387 0.063947 --->beagle1-----germline1: 1.33e-11 -0.111975 4.02e-05 -0.092995 0.812334 ( 0.142124) 0.905329 ( 0.210175) 0.835387 0.965656 --->beagle1-----germline2: 8.9e-13 -0.114376 6.33e-08 -0.105453 0.812334 ( 0.142124) 0.917787 ( 0.168133) 0.835387 0.965656 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.812334 ( 0.142124) 0.000000 ( 0.000000) 0.835387 0.000000 --->beagle2-----plink----: 3.96e-18 0.709383 7.17e-66 0.696501 0.758231 ( 0.164632) 0.061730 ( 0.013041) 0.764933 0.063947 --->beagle2-----germline1: 2.99e-12 -0.166839 3.12e-08 -0.147098 0.758231 ( 0.164632) 0.905329 ( 0.210175) 0.764933 0.965656 --->beagle2-----germline2: 1.5e-13 -0.166775 1.43e-11 -0.159556 0.758231 ( 0.164632) 0.917787 ( 0.168133) 0.764933 0.965656 --->beagle2-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.758231 ( 0.164632) 0.000000 ( 0.000000) 0.764933 0.000000 --->plink-------germline1: 4.6e-18 -0.883286 2.75e-65 -0.843599 0.061730 ( 0.013041) 0.905329 ( 0.210175) 0.063947 0.965656 --->plink-------germline2: 3.96e-18 -0.882731 1.87e-75 -0.856057 0.061730 ( 0.013041) 0.917787 ( 0.168133) 0.063947 0.965656 --->plink-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.061730 ( 0.013041) 0.000000 ( 0.000000) 0.063947 0.000000 --->germline1---germline2: 1e+00 0.000000 3.7e-01 -0.012458 0.905329 ( 0.210175) 0.917787 ( 0.168133) 0.965656 0.965656 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 0.905329 ( 0.210175) 0.000000 ( 0.000000) 0.965656 0.000000 --->germline2---dash-----: 1e+00 0.000000 1e+00 0.000000 0.917787 ( 0.168133) 0.000000 ( 0.000000) 0.965656 0.000000 ######F1###### --->fabia-------beagle1--: 4.09e-14 0.154949 1.25e-10 0.141767 0.945329 ( 0.179118) 0.803563 ( 0.146734) 0.987881 0.827594 --->fabia-------beagle2--: 4.86e-15 0.219305 1.01e-15 0.217311 0.945329 ( 0.179118) 0.728019 ( 0.190532) 0.987881 0.742618 --->fabia-------plink----: 1.24e-17 0.974736 2.94e-74 0.937221 0.945329 ( 0.179118) 0.008108 ( 0.001760) 0.987881 0.008333 --->fabia-------germline1: 3.57e-10 0.029310 8.16e-03 0.041300 0.945329 ( 0.179118) 0.904029 ( 0.210041) 0.987881 0.965070 --->fabia-------germline2: 1.63e-09 0.029873 7.31e-02 0.029330 0.945329 ( 0.179118) 0.915999 ( 0.168584) 0.987881 0.965070 --->fabia-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.945329 ( 0.179118) 0.000000 ( 0.000000) 0.987881 0.000000 --->beagle1-----beagle2--: 8.23e-07 0.099961 3.5e-07 0.075544 0.803563 ( 0.146734) 0.728019 ( 0.190532) 0.827594 0.742618 --->beagle1-----plink----: 5.78e-18 0.811069 1.42e-75 0.795455 0.803563 ( 0.146734) 0.008108 ( 0.001760) 0.827594 0.008333 --->beagle1-----germline1: 1.61e-11 -0.119665 1.17e-05 -0.100467 0.803563 ( 0.146734) 0.904029 ( 0.210041) 0.827594 0.965070 --->beagle1-----germline2: 9.37e-13 -0.121421 1.68e-08 -0.112437 0.803563 ( 0.146734) 0.915999 ( 0.168584) 0.827594 0.965070 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.803563 ( 0.146734) 0.000000 ( 0.000000) 0.827594 0.000000 --->beagle2-----plink----: 5.78e-18 0.739725 1.07e-60 0.719911 0.728019 ( 0.190532) 0.008108 ( 0.001760) 0.742618 0.008333 --->beagle2-----germline1: 3.05e-12 -0.191089 1.67e-09 -0.176011 0.728019 ( 0.190532) 0.904029 ( 0.210041) 0.742618 0.965070 --->beagle2-----germline2: 1.54e-13 -0.191447 1.44e-12 -0.187981 0.728019 ( 0.190532) 0.915999 ( 0.168584) 0.742618 0.965070 --->beagle2-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.728019 ( 0.190532) 0.000000 ( 0.000000) 0.742618 0.000000 --->plink-------germline1: 1.87e-17 -0.938657 8.1e-66 -0.895922 0.008108 ( 0.001760) 0.904029 ( 0.210041) 0.008333 0.965070 --->plink-------germline2: 1.24e-17 -0.937523 1.76e-75 -0.907892 0.008108 ( 0.001760) 0.915999 ( 0.168584) 0.008333 0.965070 --->plink-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.008108 ( 0.001760) 0.000000 ( 0.000000) 0.008333 0.000000 --->germline1---germline2: 1e+00 0.000000 3.9e-01 -0.011970 0.904029 ( 0.210041) 0.915999 ( 0.168584) 0.965070 0.965070 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 0.904029 ( 0.210041) 0.000000 ( 0.000000) 0.965070 0.000000 --->germline2---dash-----: 1e+00 0.000000 1e+00 0.000000 0.915999 ( 0.168584) 0.000000 ( 0.000000) 0.965070 0.000000 ######accuracy###### --->fabia-------beagle1--: 1e+00 0.000000 1e+00 0.000000 0.999996 ( 1.53e-05) 0.999968 ( 2.08e-05) 0.999999 0.999970 --->fabia-------beagle2--: 1e+00 0.000000 1e+00 0.000000 0.999996 ( 1.53e-05) 0.999963 ( 2.02e-05) 0.999999 0.999963 --->fabia-------plink----: 3.96e-18 0.022437 1.71e-118 0.022399 0.999996 ( 1.53e-05) 0.977597 ( 0.001496) 0.999999 0.977534 --->fabia-------germline1: 1e+00 0.000000 1e+00 0.000000 0.999996 ( 1.53e-05) 0.999989 ( 1.14e-05) 0.999999 0.999993 --->fabia-------germline2: 1e+00 0.000000 1e+00 0.000000 0.999996 ( 1.53e-05) 0.999989 ( 1.17e-05) 0.999999 0.999993 --->fabia-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.999996 ( 1.53e-05) 0.999907 ( 1.2e-05) 0.999999 0.999905 --->beagle1-----beagle2--: 1e+00 0.000000 1e+00 0.000000 0.999968 ( 2.08e-05) 0.999963 ( 2.02e-05) 0.999970 0.999963 --->beagle1-----plink----: 3.96e-18 0.022409 1.96e-118 0.022371 0.999968 ( 2.08e-05) 0.977597 ( 0.001496) 0.999970 0.977534 --->beagle1-----germline1: 1e+00 0.000000 1e+00 0.000000 0.999968 ( 2.08e-05) 0.999989 ( 1.14e-05) 0.999970 0.999993 --->beagle1-----germline2: 1e+00 0.000000 1e+00 0.000000 0.999968 ( 2.08e-05) 0.999989 ( 1.17e-05) 0.999970 0.999993 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.999968 ( 2.08e-05) 0.999907 ( 1.2e-05) 0.999970 0.999905 --->beagle2-----plink----: 3.96e-18 0.022408 1.85e-118 0.022366 0.999963 ( 2.02e-05) 0.977597 ( 0.001496) 0.999963 0.977534 --->beagle2-----germline1: 1e+00 0.000000 1e+00 0.000000 0.999963 ( 2.02e-05) 0.999989 ( 1.14e-05) 0.999963 0.999993 --->beagle2-----germline2: 1e+00 0.000000 1e+00 0.000000 0.999963 ( 2.02e-05) 0.999989 ( 1.17e-05) 0.999963 0.999993 --->beagle2-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.999963 ( 2.02e-05) 0.999907 ( 1.2e-05) 0.999963 0.999905 --->plink-------germline1: 3.96e-18 -0.022407 1.99e-118 -0.022392 0.977597 ( 0.001496) 0.999989 ( 1.14e-05) 0.977534 0.999993 --->plink-------germline2: 3.96e-18 -0.022405 1.79e-118 -0.022392 0.977597 ( 0.001496) 0.999989 ( 1.17e-05) 0.977534 0.999993 --->plink-------dash-----: 3.96e-18 -0.022323 2.58e-118 -0.022310 0.977597 ( 0.001496) 0.999907 ( 1.2e-05) 0.977534 0.999905 --->germline1---germline2: 1e+00 0.000000 1e+00 0.000000 0.999989 ( 1.14e-05) 0.999989 ( 1.17e-05) 0.999993 0.999993 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 0.999989 ( 1.14e-05) 0.999907 ( 1.2e-05) 0.999993 0.999905 --->germline2---dash-----: 1e+00 0.000000 1e+00 0.000000 0.999989 ( 1.17e-05) 0.999907 ( 1.2e-05) 0.999993 0.999905 ######FPR###### --->fabia-------beagle1--: 1e+00 0.000000 1e+00 0.000000 1.54e-06 ( 1.5e-05) 1.04e-05 ( 1.42e-05) 0.000000 2.08e-06 --->fabia-------beagle2--: 1e+00 0.000000 1e+00 0.000000 1.54e-06 ( 1.5e-05) 1.22e-06 ( 2.97e-06) 0.000000 0.000000 --->fabia-------plink----: 3.96e-18 -0.022415 1.76e-118 -0.022402 1.54e-06 ( 1.5e-05) 0.022404 ( 0.001497) 0.000000 0.022468 --->fabia-------germline1: 1e+00 0.000000 1e+00 0.000000 1.54e-06 ( 1.5e-05) 1.39e-07 ( 5.76e-07) 0.000000 0.000000 --->fabia-------germline2: 1e+00 0.000000 1e+00 0.000000 1.54e-06 ( 1.5e-05) 1.84e-06 ( 9.81e-06) 0.000000 0.000000 --->fabia-------dash-----: 1e+00 0.000000 1e+00 0.000000 1.54e-06 ( 1.5e-05) 0.000000 ( 0.000000) 0.000000 0.000000 --->beagle1-----beagle2--: 1e+00 0.000000 1e+00 0.000000 1.04e-05 ( 1.42e-05) 1.22e-06 ( 2.97e-06) 2.08e-06 0.000000 --->beagle1-----plink----: 3.96e-18 -0.022452 1.89e-118 -0.022393 1.04e-05 ( 1.42e-05) 0.022404 ( 0.001497) 2.08e-06 0.022468 --->beagle1-----germline1: 1e+00 0.000000 1e+00 0.000000 1.04e-05 ( 1.42e-05) 1.39e-07 ( 5.76e-07) 2.08e-06 0.000000 --->beagle1-----germline2: 1e+00 0.000000 1e+00 0.000000 1.04e-05 ( 1.42e-05) 1.84e-06 ( 9.81e-06) 2.08e-06 0.000000 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 1.04e-05 ( 1.42e-05) 0.000000 ( 0.000000) 2.08e-06 0.000000 --->beagle2-----plink----: 3.96e-18 -0.022415 1.78e-118 -0.022402 1.22e-06 ( 2.97e-06) 0.022404 ( 0.001497) 0.000000 0.022468 --->beagle2-----germline1: 1e+00 0.000000 1e+00 0.000000 1.22e-06 ( 2.97e-06) 1.39e-07 ( 5.76e-07) 0.000000 0.000000 --->beagle2-----germline2: 1e+00 0.000000 1e+00 0.000000 1.22e-06 ( 2.97e-06) 1.84e-06 ( 9.81e-06) 0.000000 0.000000 --->beagle2-----dash-----: 1e+00 0.000000 1e+00 0.000000 1.22e-06 ( 2.97e-06) 0.000000 ( 0.000000) 0.000000 0.000000 --->plink-------germline1: 3.96e-18 0.022443 1.78e-118 0.022403 0.022404 ( 0.001497) 1.39e-07 ( 5.76e-07) 0.022468 0.000000 --->plink-------germline2: 3.96e-18 0.022438 1.78e-118 0.022402 0.022404 ( 0.001497) 1.84e-06 ( 9.81e-06) 0.022468 0.000000 --->plink-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.022404 ( 0.001497) 0.000000 ( 0.000000) 0.022468 0.000000 --->germline1---germline2: 1e+00 0.000000 1e+00 0.000000 1.39e-07 ( 5.76e-07) 1.84e-06 ( 9.81e-06) 0.000000 0.000000 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 1.39e-07 ( 5.76e-07) 0.000000 ( 0.000000) 0.000000 0.000000 --->germline2---dash-----: 1e+00 0.000000 1e+00 0.000000 1.84e-06 ( 9.81e-06) 0.000000 ( 0.000000) 0.000000 0.000000 ######FDR###### --->fabia-------beagle1--: 1.7e-11 -0.144567 1.54e-07 -0.105291 0.008548 ( 0.076988) 0.113839 ( 0.164066) 0.000000 0.024819 --->fabia-------beagle2--: 1e+00 0.000000 1.71e-01 -0.017936 0.008548 ( 0.076988) 0.026484 ( 0.103088) 0.000000 0.000000 --->fabia-------plink----: 3.95e-18 -0.995764 7.35e-112 -0.987381 0.008548 ( 0.076988) 0.995929 ( 0.000884) 0.000000 0.995816 --->fabia-------germline1: 1e+00 0.000000 3.63e-01 0.007055 0.008548 ( 0.076988) 0.001493 ( 0.005952) 0.000000 0.000000 --->fabia-------germline2: 1e+00 0.000000 6.47e-01 -0.004765 0.008548 ( 0.076988) 0.013313 ( 0.068132) 0.000000 0.000000 --->fabia-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.008548 ( 0.076988) 0.000000 ( 0.000000) 0.000000 0.000000 --->beagle1-----beagle2--: 4.87e-07 0.146751 1.11e-08 0.087355 0.113839 ( 0.164066) 0.026484 ( 0.103088) 0.024819 0.000000 --->beagle1-----plink----: 5.78e-18 -0.899345 4.03e-75 -0.882090 0.113839 ( 0.164066) 0.995929 ( 0.000884) 0.024819 0.995816 --->beagle1-----germline1: 8.23e-13 0.144936 5.67e-10 0.112346 0.113839 ( 0.164066) 0.001493 ( 0.005952) 0.024819 0.000000 --->beagle1-----germline2: 5.25e-11 0.138072 3.39e-08 0.100526 0.113839 ( 0.164066) 0.013313 ( 0.068132) 0.024819 0.000000 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.113839 ( 0.164066) 0.000000 ( 0.000000) 0.024819 0.000000 --->beagle2-----plink----: 5.78e-18 -0.989893 8.16e-99 -0.969445 0.026484 ( 0.103088) 0.995929 ( 0.000884) 0.000000 0.995816 --->beagle2-----germline1: 1e+00 0.000000 1.72e-02 0.024990 0.026484 ( 0.103088) 0.001493 ( 0.005952) 0.000000 0.000000 --->beagle2-----germline2: 1e+00 0.000000 2.98e-01 0.013171 0.026484 ( 0.103088) 0.013313 ( 0.068132) 0.000000 0.000000 --->beagle2-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.026484 ( 0.103088) 0.000000 ( 0.000000) 0.000000 0.000000 --->plink-------germline1: 3.95e-18 0.995704 2.66e-221 0.994436 0.995929 ( 0.000884) 0.001493 ( 0.005952) 0.995816 0.000000 --->plink-------germline2: 3.95e-18 0.995689 7.28e-117 0.982616 0.995929 ( 0.000884) 0.013313 ( 0.068132) 0.995816 0.000000 --->plink-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.995929 ( 0.000884) 0.000000 ( 0.000000) 0.995816 0.000000 --->germline1---germline2: 1e+00 0.000000 8.33e-02 -0.011820 0.001493 ( 0.005952) 0.013313 ( 0.068132) 0.000000 0.000000 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 0.001493 ( 0.005952) 0.000000 ( 0.000000) 0.000000 0.000000 --->germline2---dash-----: 1e+00 0.000000 1e+00 0.000000 0.013313 ( 0.068132) 0.000000 ( 0.000000) 0.000000 0.000000 ######specifity###### --->fabia-------beagle1--: 1e+00 0.000000 1e+00 0.000000 0.999998 ( 1.5e-05) 0.999990 ( 1.42e-05) 1.000000 0.999998 --->fabia-------beagle2--: 1e+00 0.000000 1e+00 0.000000 0.999998 ( 1.5e-05) 0.999999 ( 2.97e-06) 1.000000 1.000000 --->fabia-------plink----: 3.96e-18 0.022440 1.76e-118 0.022402 0.999998 ( 1.5e-05) 0.977596 ( 0.001497) 1.000000 0.977532 --->fabia-------germline1: 1e+00 0.000000 1e+00 0.000000 0.999998 ( 1.5e-05) 1.000000 ( 5.74e-07) 1.000000 1.000000 --->fabia-------germline2: 1e+00 0.000000 1e+00 0.000000 0.999998 ( 1.5e-05) 0.999998 ( 9.81e-06) 1.000000 1.000000 --->fabia-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.999998 ( 1.5e-05) 1.000000 ( 0.000000) 1.000000 1.000000 --->beagle1-----beagle2--: 1e+00 0.000000 1e+00 0.000000 0.999990 ( 1.42e-05) 0.999999 ( 2.97e-06) 0.999998 1.000000 --->beagle1-----plink----: 3.96e-18 0.022429 1.89e-118 0.022393 0.999990 ( 1.42e-05) 0.977596 ( 0.001497) 0.999998 0.977532 --->beagle1-----germline1: 1e+00 0.000000 1e+00 0.000000 0.999990 ( 1.42e-05) 1.000000 ( 5.74e-07) 0.999998 1.000000 --->beagle1-----germline2: 1e+00 0.000000 1e+00 0.000000 0.999990 ( 1.42e-05) 0.999998 ( 9.81e-06) 0.999998 1.000000 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.999990 ( 1.42e-05) 1.000000 ( 0.000000) 0.999998 1.000000 --->beagle2-----plink----: 3.96e-18 0.022441 1.78e-118 0.022402 0.999999 ( 2.97e-06) 0.977596 ( 0.001497) 1.000000 0.977532 --->beagle2-----germline1: 1e+00 0.000000 1e+00 0.000000 0.999999 ( 2.97e-06) 1.000000 ( 5.74e-07) 1.000000 1.000000 --->beagle2-----germline2: 1e+00 0.000000 1e+00 0.000000 0.999999 ( 2.97e-06) 0.999998 ( 9.81e-06) 1.000000 1.000000 --->beagle2-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.999999 ( 2.97e-06) 1.000000 ( 0.000000) 1.000000 1.000000 --->plink-------germline1: 3.96e-18 -0.022416 1.78e-118 -0.022403 0.977596 ( 0.001497) 1.000000 ( 5.74e-07) 0.977532 1.000000 --->plink-------germline2: 3.96e-18 -0.022415 1.78e-118 -0.022402 0.977596 ( 0.001497) 0.999998 ( 9.81e-06) 0.977532 1.000000 --->plink-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.977596 ( 0.001497) 1.000000 ( 0.000000) 0.977532 1.000000 --->germline1---germline2: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 5.74e-07) 0.999998 ( 9.81e-06) 1.000000 1.000000 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 5.74e-07) 1.000000 ( 0.000000) 1.000000 1.000000 --->germline2---dash-----: 1e+00 0.000000 1e+00 0.000000 0.999998 ( 9.81e-06) 1.000000 ( 0.000000) 1.000000 1.000000 ######sensitivity###### --->fabia-------beagle1--: 1.02e-14 0.182942 2.35e-13 0.178529 0.935414 ( 0.170574) 0.756885 ( 0.176549) 0.976514 0.809317 --->fabia-------beagle2--: 1.34e-15 0.335206 2.36e-21 0.323321 0.935414 ( 0.170574) 0.612094 ( 0.225735) 0.976514 0.615978 --->fabia-------plink----: 2.4e-16 -0.030214 3.2e-02 -0.024251 0.935414 ( 0.170574) 0.959665 ( 0.196891) 0.976514 1.000000 --->fabia-------germline1: 4.24e-11 0.056213 6.03e-06 0.070639 0.935414 ( 0.170574) 0.864775 ( 0.204872) 0.976514 0.933850 --->fabia-------germline2: 2.53e-10 0.054810 8.77e-04 0.052902 0.935414 ( 0.170574) 0.882512 ( 0.163364) 0.976514 0.934577 --->fabia-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.935414 ( 0.170574) 0.000000 ( 0.000000) 0.976514 0.000000 --->beagle1-----beagle2--: 5.29e-12 0.217197 1.29e-15 0.144791 0.756885 ( 0.176549) 0.612094 ( 0.225735) 0.809317 0.615978 --->beagle1-----plink----: 1.77e-14 -0.210148 7.53e-15 -0.202780 0.756885 ( 0.176549) 0.959665 ( 0.196891) 0.809317 1.000000 --->beagle1-----germline1: 6.81e-09 -0.120028 1.35e-05 -0.107891 0.756885 ( 0.176549) 0.864775 ( 0.204872) 0.809317 0.933850 --->beagle1-----germline2: 2.46e-10 -0.126769 2.71e-08 -0.125627 0.756885 ( 0.176549) 0.882512 ( 0.163364) 0.809317 0.934577 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.756885 ( 0.176549) 0.000000 ( 0.000000) 0.809317 0.000000 --->beagle2-----plink----: 3.68e-15 -0.365674 7e-22 -0.347572 0.612094 ( 0.225735) 0.959665 ( 0.196891) 0.615978 1.000000 --->beagle2-----germline1: 1.85e-12 -0.274585 1.57e-13 -0.252682 0.612094 ( 0.225735) 0.864775 ( 0.204872) 0.615978 0.933850 --->beagle2-----germline2: 4.43e-14 -0.281923 7.11e-17 -0.270418 0.612094 ( 0.225735) 0.882512 ( 0.163364) 0.615978 0.934577 --->beagle2-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.612094 ( 0.225735) 0.000000 ( 0.000000) 0.615978 0.000000 --->plink-------germline1: 1.81e-17 0.097861 1.11e-14 0.094890 0.959665 ( 0.196891) 0.864775 ( 0.204872) 1.000000 0.933850 --->plink-------germline2: 2.4e-16 0.096194 2.21e-09 0.077153 0.959665 ( 0.196891) 0.882512 ( 0.163364) 1.000000 0.934577 --->plink-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.959665 ( 0.196891) 0.000000 ( 0.000000) 1.000000 0.000000 --->germline1---germline2: 1e+00 0.000000 1.6e-01 -0.017736 0.864775 ( 0.204872) 0.882512 ( 0.163364) 0.933850 0.934577 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 0.864775 ( 0.204872) 0.000000 ( 0.000000) 0.933850 0.000000 --->germline2---dash-----: 1e+00 0.000000 1e+00 0.000000 0.882512 ( 0.163364) 0.000000 ( 0.000000) 0.934577 0.000000 ######trueN###### --->fabia-------beagle1--: 3.06e-18 2e+08 0e+00 2e+08 4e+08 ( 6472) 2e+08 ( 3724) 4e+08 2e+08 --->fabia-------beagle2--: 7.05e-19 2e+08 0e+00 2e+08 4e+08 ( 6472) 2e+08 ( 2125) 4e+08 2e+08 --->fabia-------plink----: 3.96e-18 2.04e+08 1.14e-282 2.04e+08 4e+08 ( 6472) 1.96e+08 ( 299345) 4e+08 1.95e+08 --->fabia-------germline1: 5.86e-21 2e+08 0e+00 2e+08 4e+08 ( 6472) 2e+08 ( 2412) 4e+08 2e+08 --->fabia-------germline2: 9.91e-21 2e+08 0e+00 2e+08 4e+08 ( 6472) 2e+08 ( 3154) 4e+08 2e+08 --->fabia-------dash-----: 4.03e-23 2e+08 0e+00 2e+08 4e+08 ( 6472) 2e+08 ( 2402) 4e+08 2e+08 --->beagle1-----beagle2--: 5.47e-08 -4768 3.87e-09 -1841 2e+08 ( 3724) 2e+08 ( 2125) 2e+08 2e+08 --->beagle1-----plink----: 3.96e-18 4485461 1.89e-118 4478214 2e+08 ( 3724) 1.96e+08 ( 299345) 2e+08 1.95e+08 --->beagle1-----germline1: 8.59e-13 -2846 8.52e-11 -2058 2e+08 ( 3724) 2e+08 ( 2412) 2e+08 2e+08 --->beagle1-----germline2: 5.16e-10 -2453 3.24e-07 -1718 2e+08 ( 3724) 2e+08 ( 3154) 2e+08 2e+08 --->beagle1-----dash-----: 5.33e-13 -2937 6.06e-11 -2086 2e+08 ( 3724) 2e+08 ( 2402) 2e+08 2e+08 --->beagle2-----plink----: 3.96e-18 4487104 1.78e-118 4480055 2e+08 ( 2125) 1.96e+08 ( 299345) 2e+08 1.95e+08 --->beagle2-----germline1: 1.07e-06 -306 4.6e-04 -217 2e+08 ( 2125) 2e+08 ( 2412) 2e+08 2e+08 --->beagle2-----germline2: 1.31e-04 -266 5.55e-01 124 2e+08 ( 2125) 2e+08 ( 3154) 2e+08 2e+08 --->beagle2-----dash-----: 1.16e-08 -415 7.82e-05 -245 2e+08 ( 2125) 2e+08 ( 2402) 2e+08 2e+08 --->plink-------germline1: 3.96e-18 -4487286 1.78e-118 -4480272 1.96e+08 ( 299345) 2e+08 ( 2412) 1.95e+08 2e+08 --->plink-------germline2: 3.96e-18 -4486975 1.77e-118 -4479932 1.96e+08 ( 299345) 2e+08 ( 3154) 1.95e+08 2e+08 --->plink-------dash-----: 3.96e-18 -4487360 1.78e-118 -4480300 1.96e+08 ( 299345) 2e+08 ( 2402) 1.95e+08 2e+08 --->germline1---germline2: 1e+00 0 8.43e-02 341 2e+08 ( 2412) 2e+08 ( 3154) 2e+08 2e+08 --->germline1---dash-----: 1e+00 0 1.75e-02 -27.9 2e+08 ( 2412) 2e+08 ( 2402) 2e+08 2e+08 --->germline2---dash-----: 1e+00 0 6.34e-02 -368 2e+08 ( 3154) 2e+08 ( 2402) 2e+08 2e+08 ######falseP###### --->fabia-------beagle1--: 2.43e-11 -2814 3.39e-02 -1468 618 ( 5994) 2086 ( 2842) 0 415 --->fabia-------beagle2--: 1e+00 0.000000 5.39e-01 372.920000 617.700000 (5994.357551) 244.780000 (593.873292) 0.000000 0.000000 --->fabia-------plink----: 3.96e-18 -4486862 1.76e-118 -4479682 618 ( 5994) 4480300 ( 299319) 0 4493151 --->fabia-------germline1: 1e+00 0.000000 3.28e-01 589.840000 617.700000 (5994.357551) 27.860000 (115.247386) 0.000000 0.000000 --->fabia-------germline2: 1e+00 0.000000 6.95e-01 249.300000 617.700000 (5994.357551) 368.400000 (1962.084009) 0.000000 0.000000 --->fabia-------dash-----: 1e+00 0.000000 1e+00 0.000000 617.700000 (5994.357551) 0.000000 ( 0.000000) 0.000000 0.000000 --->beagle1-----beagle2--: 5.47e-08 4768 3.87e-09 1841 2086 ( 2842) 245 ( 594) 415 0 --->beagle1-----plink----: 3.96e-18 -4485522 1.89e-118 -4478214 2086 ( 2842) 4480300 ( 299319) 415 4493151 --->beagle1-----germline1: 8.59e-13 2846 8.52e-11 2058 2086 ( 2842) 27.9 ( 115) 415 0 --->beagle1-----germline2: 5.16e-10 2452 3.24e-07 1718 2086 ( 2842) 368 ( 1962) 415 0 --->beagle1-----dash-----: 1e+00 0 1e+00 0 2086 ( 2842) 0 ( 0) 415 0 --->beagle2-----plink----: 3.96e-18 -4487097 1.78e-118 -4480055 245 ( 594) 4480300 ( 299319) 0 4493151 --->beagle2-----germline1: 1e+00 0.000000 4.6e-04 216.920000 244.780000 (593.873292) 27.860000 (115.247386) 0.000000 0.000000 --->beagle2-----germline2: 1e+00 0.000000 5.55e-01 -123.620000 244.780000 (593.873292) 368.400000 (1962.084009) 0.000000 0.000000 --->beagle2-----dash-----: 1e+00 0.000000 1e+00 0.000000 244.780000 (593.873292) 0.000000 ( 0.000000) 0.000000 0.000000 --->plink-------germline1: 3.96e-18 4487297 1.78e-118 4480272 4480300 ( 299319) 27.9 ( 115) 4493151 0 --->plink-------germline2: 3.96e-18 4486976 1.77e-118 4479932 4480300 ( 299319) 368 ( 1962) 4493151 0 --->plink-------dash-----: 1e+00 0 1e+00 0 4480300 ( 299319) 0 ( 0) 4493151 0 --->germline1---germline2: 1e+00 0.000000 8.43e-02 -340.540000 27.860000 (115.247386) 368.400000 (1962.084009) 0.000000 0.000000 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 27.860000 (115.247386) 0.000000 ( 0.000000) 0.000000 0.000000 --->germline2---dash-----: 1e+00 0.000000 1e+00 0.000000 368.400000 (1962.084009) 0.000000 ( 0.000000) 0.000000 0.000000 ######falseN###### --->fabia-------beagle1--: 4.23e-15 -3446 4.76e-18 -3499 864 ( 1541) 4363 ( 2945) 449 3609 --->fabia-------beagle2--: 2.01e-16 -6343 3.87e-25 -6250 864 ( 1541) 7114 ( 4138) 449 7018 --->fabia-------plink----: 2.39e-16 575 9.1e-05 550 864 ( 1541) 314 ( 1730) 449 0 --->fabia-------germline1: 3.89e-11 -1067 2.25e-07 -1239 864 ( 1541) 2103 ( 2295) 449 1271 --->fabia-------germline2: 2.39e-10 -1043 4.53e-06 -979 864 ( 1541) 1843 ( 1349) 449 1259 --->fabia-------dash-----: 1.24e-17 -18393 1.74e-74 -17691 864 ( 1541) 18555 ( 2402) 449 19046 --->beagle1-----beagle2--: 5.29e-12 -4121 1.48e-15 -2751 4363 ( 2945) 7114 ( 4138) 3609 7018 --->beagle1-----plink----: 2.71e-15 4002 1.2e-20 4049 4363 ( 2945) 314 ( 1730) 3609 0 --->beagle1-----germline1: 3.23e-09 2286 3.43e-08 2260 4363 ( 2945) 2103 ( 2295) 3609 1271 --->beagle1-----germline2: 1.34e-10 2411 8.71e-12 2520 4363 ( 2945) 1843 ( 1349) 3609 1259 --->beagle1-----dash-----: 5.78e-18 -14635 1.44e-62 -14192 4363 ( 2945) 18555 ( 2402) 3609 19046 --->beagle2-----plink----: 1.69e-16 6965 1.62e-26 6800 7114 ( 4138) 314 ( 1730) 7018 0 --->beagle2-----germline1: 1.9e-13 5224 8.36e-17 5011 7114 ( 4138) 2103 ( 2295) 7018 1271 --->beagle2-----germline2: 6.78e-15 5325 1.6e-20 5271 7114 ( 4138) 1843 ( 1349) 7018 1259 --->beagle2-----dash-----: 5.78e-18 -11618 1.11e-46 -11441 7114 ( 4138) 18555 ( 2402) 7018 19046 --->plink-------germline1: 1.81e-17 -1845 5.08e-16 -1789 314 ( 1730) 2103 ( 2295) 0 1271 --->plink-------germline2: 2.4e-16 -1804 8.37e-15 -1529 314 ( 1730) 1843 ( 1349) 0 1259 --->plink-------dash-----: 1.81e-17 -19047 7.71e-71 -18241 314 ( 1730) 18555 ( 2402) 0 19046 --->germline1---germline2: 1e+00 0 1.6e-01 260 2103 ( 2295) 1843 ( 1349) 1271 1259 --->germline1---dash-----: 5.59e-18 -17000 5e-65 -16452 2103 ( 2295) 18555 ( 2402) 1271 19046 --->germline2---dash-----: 2.79e-18 -17000 2.07e-74 -16712 1843 ( 1349) 18555 ( 2402) 1259 19046 ######trueP###### --->fabia-------beagle1--: 4.23e-15 3446 4.76e-18 3499 17691 ( 3337) 14192 ( 3579) 18555 15313 --->fabia-------beagle2--: 2.01e-16 6343 3.87e-25 6250 17691 ( 3337) 11441 ( 4325) 18555 11517 --->fabia-------plink----: 2.39e-16 -575 9.1e-05 -550 17691 ( 3337) 18241 ( 3758) 18555 19046 --->fabia-------germline1: 3.89e-11 1067 2.25e-07 1239 17691 ( 3337) 16452 ( 3905) 18555 17988 --->fabia-------germline2: 2.39e-10 1043 4.53e-06 979 17691 ( 3337) 16712 ( 3158) 18555 17988 --->fabia-------dash-----: 1e+00 0 1e+00 0 17691 ( 3337) 0 ( 0) 18555 0 --->beagle1-----beagle2--: 5.29e-12 4121 1.48e-15 2751 14192 ( 3579) 11441 ( 4325) 15313 11517 --->beagle1-----plink----: 2.71e-15 -4002 1.2e-20 -4049 14192 ( 3579) 18241 ( 3758) 15313 19046 --->beagle1-----germline1: 3.23e-09 -2286 3.43e-08 -2260 14192 ( 3579) 16452 ( 3905) 15313 17988 --->beagle1-----germline2: 1.34e-10 -2412 8.71e-12 -2520 14192 ( 3579) 16712 ( 3158) 15313 17988 --->beagle1-----dash-----: 1e+00 0 1e+00 0 14192 ( 3579) 0 ( 0) 15313 0 --->beagle2-----plink----: 1.69e-16 -6966 1.62e-26 -6800 11441 ( 4325) 18241 ( 3758) 11517 19046 --->beagle2-----germline1: 1.9e-13 -5223 8.36e-17 -5011 11441 ( 4325) 16452 ( 3905) 11517 17988 --->beagle2-----germline2: 6.78e-15 -5326 1.6e-20 -5271 11441 ( 4325) 16712 ( 3158) 11517 17988 --->beagle2-----dash-----: 1e+00 0 1e+00 0 11441 ( 4325) 0 ( 0) 11517 0 --->plink-------germline1: 1.81e-17 1845 5.08e-16 1789 18241 ( 3758) 16452 ( 3905) 19046 17988 --->plink-------germline2: 2.4e-16 1804 8.37e-15 1529 18241 ( 3758) 16712 ( 3158) 19046 17988 --->plink-------dash-----: 1e+00 0 1e+00 0 18241 ( 3758) 0 ( 0) 19046 0 --->germline1---germline2: 1e+00 0 1.6e-01 -260 16452 ( 3905) 16712 ( 3158) 17988 17988 --->germline1---dash-----: 1e+00 0 1e+00 0 16452 ( 3905) 0 ( 0) 17988 0 --->germline2---dash-----: 1e+00 0 1e+00 0 16712 ( 3158) 0 ( 0) 17988 0 ######MatthewsSnps###### --->fabia-------beagle1--: 3.03e-14 0.148267 1.94e-10 0.137579 0.945492 ( 0.177199) 0.807913 ( 0.144748) 0.987360 0.829559 --->fabia-------beagle2--: 5.41e-15 0.200814 2.35e-15 0.193993 0.945492 ( 0.177199) 0.751499 ( 0.166651) 0.987360 0.756845 --->fabia-------plink----: 8.72e-18 0.978387 1.62e-74 0.941701 0.945492 ( 0.177199) 0.003791 ( 0.007294) 0.987360 0.000000 --->fabia-------germline1: 3.18e-10 0.029826 6.14e-03 0.042189 0.945492 ( 0.177199) 0.903303 ( 0.209832) 0.987360 0.964011 --->fabia-------germline2: 1.59e-09 0.029652 8.14e-02 0.027836 0.945492 ( 0.177199) 0.917656 ( 0.167509) 0.987360 0.964191 --->fabia-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.945492 ( 0.177199) 0.000000 ( 0.000000) 0.987360 0.000000 --->beagle1-----beagle2--: 3.85e-05 0.077511 1.44e-05 0.056414 0.807913 ( 0.144748) 0.751499 ( 0.166651) 0.829559 0.756845 --->beagle1-----plink----: 4.08e-18 0.819234 2.64e-76 0.804122 0.807913 ( 0.144748) 0.003791 ( 0.007294) 0.829559 0.000000 --->beagle1-----germline1: 1.33e-11 -0.113246 3.37e-05 -0.095390 0.807913 ( 0.144748) 0.903303 ( 0.209832) 0.829559 0.964011 --->beagle1-----germline2: 1.01e-12 -0.115055 5.39e-08 -0.109743 0.807913 ( 0.144748) 0.917656 ( 0.167509) 0.829559 0.964191 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.807913 ( 0.144748) 0.000000 ( 0.000000) 0.829559 0.000000 --->beagle2-----plink----: 4.08e-18 0.759333 1.23e-67 0.747708 0.751499 ( 0.166651) 0.003791 ( 0.007294) 0.756845 0.000000 --->beagle2-----germline1: 3.07e-12 -0.171767 1.56e-08 -0.151804 0.751499 ( 0.166651) 0.903303 ( 0.209832) 0.756845 0.964011 --->beagle2-----germline2: 1.58e-13 -0.173763 5.78e-12 -0.166157 0.751499 ( 0.166651) 0.917656 ( 0.167509) 0.756845 0.964191 --->beagle2-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.751499 ( 0.166651) 0.000000 ( 0.000000) 0.756845 0.000000 --->plink-------germline1: 1.87e-17 -0.944520 9.2e-66 -0.899512 0.003791 ( 0.007294) 0.903303 ( 0.209832) 0.000000 0.964011 --->plink-------germline2: 8.72e-18 -0.943628 1.41e-75 -0.913865 0.003791 ( 0.007294) 0.917656 ( 0.167509) 0.000000 0.964191 --->plink-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.003791 ( 0.007294) 0.000000 ( 0.000000) 0.000000 0.000000 --->germline1---germline2: 1e+00 0.000000 2.95e-01 -0.014353 0.903303 ( 0.209832) 0.917656 ( 0.167509) 0.964011 0.964191 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 0.903303 ( 0.209832) 0.000000 ( 0.000000) 0.964011 0.000000 --->germline2---dash-----: 1e+00 0.000000 1e+00 0.000000 0.917656 ( 0.167509) 0.000000 ( 0.000000) 0.964191 0.000000 ######F1Snps###### --->fabia-------beagle1--: 4.09e-14 0.150133 2.1e-10 0.138614 0.945329 ( 0.179118) 0.806715 ( 0.145754) 0.987881 0.832466 --->fabia-------beagle2--: 4.86e-15 0.219305 1.01e-15 0.217311 0.945329 ( 0.179118) 0.728019 ( 0.190532) 0.987881 0.742618 --->fabia-------plink----: 4.74e-18 0.891153 2.44e-72 0.856613 0.945329 ( 0.179118) 0.088716 ( 0.011338) 0.987881 0.090934 --->fabia-------germline1: 3.57e-10 0.029310 8.16e-03 0.041300 0.945329 ( 0.179118) 0.904029 ( 0.210041) 0.987881 0.965070 --->fabia-------germline2: 1.78e-09 0.029198 9.57e-02 0.026949 0.945329 ( 0.179118) 0.918380 ( 0.167673) 0.987881 0.965275 --->fabia-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.945329 ( 0.179118) 0.000000 ( 0.000000) 0.987881 0.000000 --->beagle1-----beagle2--: 2.96e-07 0.100977 1.91e-07 0.078696 0.806715 ( 0.145754) 0.728019 ( 0.190532) 0.832466 0.742618 --->beagle1-----plink----: 4.08e-18 0.731772 9.14e-73 0.717999 0.806715 ( 0.145754) 0.088716 ( 0.011338) 0.832466 0.090934 --->beagle1-----germline1: 1.61e-11 -0.116034 2.17e-05 -0.097315 0.806715 ( 0.145754) 0.904029 ( 0.210041) 0.832466 0.965070 --->beagle1-----germline2: 1.01e-12 -0.117588 2.97e-08 -0.111666 0.806715 ( 0.145754) 0.918380 ( 0.167673) 0.832466 0.965275 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.806715 ( 0.145754) 0.000000 ( 0.000000) 0.832466 0.000000 --->beagle2-----plink----: 4.08e-18 0.655257 1.96e-56 0.639302 0.728019 ( 0.190532) 0.088716 ( 0.011338) 0.742618 0.090934 --->beagle2-----germline1: 3.05e-12 -0.191089 1.67e-09 -0.176011 0.728019 ( 0.190532) 0.904029 ( 0.210041) 0.742618 0.965070 --->beagle2-----germline2: 1.54e-13 -0.193808 1.14e-12 -0.190362 0.728019 ( 0.190532) 0.918380 ( 0.167673) 0.742618 0.965275 --->beagle2-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.728019 ( 0.190532) 0.000000 ( 0.000000) 0.742618 0.000000 --->plink-------germline1: 6.22e-18 -0.854478 1.4e-63 -0.815313 0.088716 ( 0.011338) 0.904029 ( 0.210041) 0.090934 0.965070 --->plink-------germline2: 4.74e-18 -0.854510 3.76e-74 -0.829664 0.088716 ( 0.011338) 0.918380 ( 0.167673) 0.090934 0.965275 --->plink-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.088716 ( 0.011338) 0.000000 ( 0.000000) 0.090934 0.000000 --->germline1---germline2: 1e+00 0.000000 2.95e-01 -0.014351 0.904029 ( 0.210041) 0.918380 ( 0.167673) 0.965070 0.965275 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 0.904029 ( 0.210041) 0.000000 ( 0.000000) 0.965070 0.000000 --->germline2---dash-----: 1e+00 0.000000 1e+00 0.000000 0.918380 ( 0.167673) 0.000000 ( 0.000000) 0.965275 0.000000 ######accuracySnps###### --->fabia-------beagle1--: 3.39e-15 0.013000 7.48e-09 0.012019 0.996295 ( 0.015342) 0.984276 ( 0.010000) 0.998850 0.985020 --->fabia-------beagle2--: 1.48e-15 0.015912 1.86e-13 0.014692 0.996295 ( 0.015342) 0.981603 ( 0.010080) 0.998850 0.981397 --->fabia-------plink----: 3.96e-18 0.949977 9.96e-177 0.948513 0.996295 ( 0.015342) 0.047782 ( 0.006745) 0.998850 0.047793 --->fabia-------germline1: 3.26e-10 0.002616 3.04e-01 0.001623 0.996295 ( 0.015342) 0.994672 ( 0.005711) 0.998850 0.996735 --->fabia-------germline2: 1.56e-09 0.002622 3.46e-01 0.001524 0.996295 ( 0.015342) 0.994771 ( 0.005181) 0.998850 0.996747 --->fabia-------dash-----: 2.4e-16 0.045879 9.96e-45 0.042683 0.996295 ( 0.015342) 0.953611 ( 0.006006) 0.998850 0.952385 --->beagle1-----beagle2--: 1.55e-02 0.003930 5.52e-03 0.002673 0.984276 ( 0.010000) 0.981603 ( 0.010080) 0.985020 0.981397 --->beagle1-----plink----: 3.96e-18 0.936763 8.52e-188 0.936494 0.984276 ( 0.010000) 0.047782 ( 0.006745) 0.985020 0.047793 --->beagle1-----germline1: 7.66e-13 -0.010062 4.58e-14 -0.010396 0.984276 ( 0.010000) 0.994672 ( 0.005711) 0.985020 0.996735 --->beagle1-----germline2: 5.25e-13 -0.010083 1.19e-14 -0.010495 0.984276 ( 0.010000) 0.994771 ( 0.005181) 0.985020 0.996747 --->beagle1-----dash-----: 4.89e-18 0.031539 7.55e-48 0.030665 0.984276 ( 0.010000) 0.953611 ( 0.006006) 0.985020 0.952385 --->beagle2-----plink----: 3.96e-18 0.933237 6.31e-187 0.933821 0.981603 ( 0.010080) 0.047782 ( 0.006745) 0.981397 0.047793 --->beagle2-----germline1: 4.88e-14 -0.013408 3.99e-18 -0.013069 0.981603 ( 0.010080) 0.994672 ( 0.005711) 0.981397 0.996735 --->beagle2-----germline2: 3.75e-14 -0.013420 4.2e-19 -0.013168 0.981603 ( 0.010080) 0.994771 ( 0.005181) 0.981397 0.996747 --->beagle2-----dash-----: 5.04e-18 0.028270 3.85e-45 0.027992 0.981603 ( 0.010080) 0.953611 ( 0.006006) 0.981397 0.952385 --->plink-------germline1: 3.96e-18 -0.947257 9.34e-212 -0.946890 0.047782 ( 0.006745) 0.994672 ( 0.005711) 0.047793 0.996735 --->plink-------germline2: 3.96e-18 -0.947372 2.91e-208 -0.946989 0.047782 ( 0.006745) 0.994771 ( 0.005181) 0.047793 0.996747 --->plink-------dash-----: 3.95e-18 -0.904361 6.05e-187 -0.905830 0.047782 ( 0.006745) 0.953611 ( 0.006006) 0.047793 0.952385 --->germline1---germline2: 1e+00 0.000000 1e+00 0.000000 0.994672 ( 0.005711) 0.994771 ( 0.005181) 0.996735 0.996747 --->germline1---dash-----: 1.53e-17 0.042554 4.51e-65 0.041061 0.994672 ( 0.005711) 0.953611 ( 0.006006) 0.996735 0.952385 --->germline2---dash-----: 7.31e-18 0.042541 1.44e-69 0.041159 0.994771 ( 0.005181) 0.953611 ( 0.006006) 0.996747 0.952385 ######FPRSnps###### --->fabia-------beagle1--: 2.43e-11 -0.006816 5.04e-02 -0.003484 0.001620 ( 0.015721) 0.005104 ( 0.006764) 0.000000 0.001089 --->fabia-------beagle2--: 1e+00 0.000000 5.36e-01 0.000984 0.001620 ( 0.015721) 0.000636 ( 0.001519) 0.000000 0.000000 --->fabia-------plink----: 2.84e-19 -0.999940 3.92e-179 -0.996920 0.001620 ( 0.015721) 0.998540 ( 0.003660) 0.000000 1.000000 --->fabia-------germline1: 1e+00 0.000000 3.28e-01 0.001547 0.001620 ( 0.015721) 7.32e-05 ( 0.000303) 0.000000 0.000000 --->fabia-------germline2: 1e+00 0.000000 5.54e-01 0.000968 0.001620 ( 0.015721) 0.000652 ( 0.004125) 0.000000 0.000000 --->fabia-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.001620 ( 0.015721) 0.000000 ( 0.000000) 0.000000 0.000000 --->beagle1-----beagle2--: 5.47e-08 0.011688 2.37e-09 0.004467 0.005104 ( 0.006764) 0.000636 ( 0.001519) 0.001089 0.000000 --->beagle1-----plink----: 3.53e-18 -0.994069 4.44e-211 -0.993437 0.005104 ( 0.006764) 0.998540 ( 0.003660) 0.001089 1.000000 --->beagle1-----germline1: 8.59e-13 0.006851 3.11e-11 0.005031 0.005104 ( 0.006764) 7.32e-05 ( 0.000303) 0.001089 0.000000 --->beagle1-----germline2: 1.31e-10 0.006422 9.09e-08 0.004452 0.005104 ( 0.006764) 0.000652 ( 0.004125) 0.001089 0.000000 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.005104 ( 0.006764) 0.000000 ( 0.000000) 0.001089 0.000000 --->beagle2-----plink----: 2.54e-18 -0.999063 4.21e-239 -0.997904 0.000636 ( 0.001519) 0.998540 ( 0.003660) 0.000000 1.000000 --->beagle2-----germline1: 1e+00 0.000000 3.83e-04 0.000563 0.000636 ( 0.001519) 7.32e-05 ( 0.000303) 0.000000 0.000000 --->beagle2-----germline2: 1e+00 0.000000 1e+00 0.000000 0.000636 ( 0.001519) 0.000652 ( 0.004125) 0.000000 0.000000 --->beagle2-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.000636 ( 0.001519) 0.000000 ( 0.000000) 0.000000 0.000000 --->plink-------germline1: 8.48e-19 0.999833 3.13e-243 0.998467 0.998540 ( 0.003660) 7.32e-05 ( 0.000303) 1.000000 0.000000 --->plink-------germline2: 8.48e-19 0.999799 3.59e-225 0.997888 0.998540 ( 0.003660) 0.000652 ( 0.004125) 1.000000 0.000000 --->plink-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.998540 ( 0.003660) 0.000000 ( 0.000000) 1.000000 0.000000 --->germline1---germline2: 1e+00 0.000000 1.6e-01 -0.000579 7.32e-05 ( 0.000303) 0.000652 ( 0.004125) 0.000000 0.000000 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 7.32e-05 ( 0.000303) 0.000000 ( 0.000000) 0.000000 0.000000 --->germline2---dash-----: 1e+00 0.000000 1e+00 0.000000 0.000652 ( 0.004125) 0.000000 ( 0.000000) 0.000000 0.000000 ######FDRSnps###### --->fabia-------beagle1--: 1.7e-11 -0.138401 2.37e-07 -0.100740 0.008548 ( 0.076988) 0.109288 ( 0.158729) 0.000000 0.024819 --->fabia-------beagle2--: 1e+00 0.000000 1.71e-01 -0.017936 0.008548 ( 0.076988) 0.026484 ( 0.103088) 0.000000 0.000000 --->fabia-------plink----: 3.95e-18 -0.952320 7.87e-110 -0.945000 0.008548 ( 0.076988) 0.953548 ( 0.006012) 0.000000 0.952368 --->fabia-------germline1: 1e+00 0.000000 3.63e-01 0.007055 0.008548 ( 0.076988) 0.001493 ( 0.005952) 0.000000 0.000000 --->fabia-------germline2: 1e+00 0.000000 9.36e-01 -0.000765 0.008548 ( 0.076988) 0.009313 ( 0.055832) 0.000000 0.000000 --->fabia-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.008548 ( 0.076988) 0.000000 ( 0.000000) 0.000000 0.000000 --->beagle1-----beagle2--: 4.87e-07 0.140169 1.33e-08 0.082804 0.109288 ( 0.158729) 0.026484 ( 0.103088) 0.024819 0.000000 --->beagle1-----plink----: 4.08e-18 -0.854698 3.42e-75 -0.844260 0.109288 ( 0.158729) 0.953548 ( 0.006012) 0.024819 0.952368 --->beagle1-----germline1: 8.23e-13 0.139203 7.29e-10 0.107795 0.109288 ( 0.158729) 0.001493 ( 0.005952) 0.024819 0.000000 --->beagle1-----germline2: 5.06e-11 0.133103 3.76e-08 0.099975 0.109288 ( 0.158729) 0.009313 ( 0.055832) 0.024819 0.000000 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.109288 ( 0.158729) 0.000000 ( 0.000000) 0.024819 0.000000 --->beagle2-----plink----: 4.08e-18 -0.946440 1.51e-98 -0.927064 0.026484 ( 0.103088) 0.953548 ( 0.006012) 0.000000 0.952368 --->beagle2-----germline1: 1e+00 0.000000 1.72e-02 0.024990 0.026484 ( 0.103088) 0.001493 ( 0.005952) 0.000000 0.000000 --->beagle2-----germline2: 1e+00 0.000000 1.51e-01 0.017171 0.026484 ( 0.103088) 0.009313 ( 0.055832) 0.000000 0.000000 --->beagle2-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.026484 ( 0.103088) 0.000000 ( 0.000000) 0.000000 0.000000 --->plink-------germline1: 3.95e-18 0.952199 8.82e-204 0.952054 0.953548 ( 0.006012) 0.001493 ( 0.005952) 0.952368 0.000000 --->plink-------germline2: 3.95e-18 0.952172 2.56e-123 0.944235 0.953548 ( 0.006012) 0.009313 ( 0.055832) 0.952368 0.000000 --->plink-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.953548 ( 0.006012) 0.000000 ( 0.000000) 0.952368 0.000000 --->germline1---germline2: 1e+00 0.000000 1.58e-01 -0.007820 0.001493 ( 0.005952) 0.009313 ( 0.055832) 0.000000 0.000000 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 0.001493 ( 0.005952) 0.000000 ( 0.000000) 0.000000 0.000000 --->germline2---dash-----: 1e+00 0.000000 1e+00 0.000000 0.009313 ( 0.055832) 0.000000 ( 0.000000) 0.000000 0.000000 ######specifitySnps###### --->fabia-------beagle1--: 2.43e-11 0.006797 5.04e-02 0.003484 0.998380 ( 0.015721) 0.994896 ( 0.006764) 1.000000 0.998911 --->fabia-------beagle2--: 1e+00 0.000000 5.36e-01 -0.000984 0.998380 ( 0.015721) 0.999364 ( 0.001519) 1.000000 1.000000 --->fabia-------plink----: 2.85e-19 0.999940 3.92e-179 0.996920 0.998380 ( 0.015721) 0.001460 ( 0.003660) 1.000000 0.000000 --->fabia-------germline1: 1e+00 0.000000 3.28e-01 -0.001547 0.998380 ( 0.015721) 0.999927 ( 0.000303) 1.000000 1.000000 --->fabia-------germline2: 1e+00 0.000000 5.54e-01 -0.000968 0.998380 ( 0.015721) 0.999348 ( 0.004125) 1.000000 1.000000 --->fabia-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.998380 ( 0.015721) 1.000000 ( 0.000000) 1.000000 1.000000 --->beagle1-----beagle2--: 5.47e-08 -0.011650 2.37e-09 -0.004467 0.994896 ( 0.006764) 0.999364 ( 0.001519) 0.998911 1.000000 --->beagle1-----plink----: 3.53e-18 0.994069 4.44e-211 0.993437 0.994896 ( 0.006764) 0.001460 ( 0.003660) 0.998911 0.000000 --->beagle1-----germline1: 8.59e-13 -0.006833 3.11e-11 -0.005031 0.994896 ( 0.006764) 0.999927 ( 0.000303) 0.998911 1.000000 --->beagle1-----germline2: 1.31e-10 -0.006431 9.09e-08 -0.004452 0.994896 ( 0.006764) 0.999348 ( 0.004125) 0.998911 1.000000 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.994896 ( 0.006764) 1.000000 ( 0.000000) 0.998911 1.000000 --->beagle2-----plink----: 2.54e-18 0.999063 4.21e-239 0.997904 0.999364 ( 0.001519) 0.001460 ( 0.003660) 1.000000 0.000000 --->beagle2-----germline1: 1e+00 0.000000 3.83e-04 -0.000563 0.999364 ( 0.001519) 0.999927 ( 0.000303) 1.000000 1.000000 --->beagle2-----germline2: 1e+00 0.000000 1e+00 0.000000 0.999364 ( 0.001519) 0.999348 ( 0.004125) 1.000000 1.000000 --->beagle2-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.999364 ( 0.001519) 1.000000 ( 0.000000) 1.000000 1.000000 --->plink-------germline1: 8.49e-19 -0.999833 3.13e-243 -0.998467 0.001460 ( 0.003660) 0.999927 ( 0.000303) 0.000000 1.000000 --->plink-------germline2: 8.49e-19 -0.999799 3.59e-225 -0.997888 0.001460 ( 0.003660) 0.999348 ( 0.004125) 0.000000 1.000000 --->plink-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.001460 ( 0.003660) 1.000000 ( 0.000000) 0.000000 1.000000 --->germline1---germline2: 1e+00 0.000000 1.6e-01 0.000579 0.999927 ( 0.000303) 0.999348 ( 0.004125) 1.000000 1.000000 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 0.999927 ( 0.000303) 1.000000 ( 0.000000) 1.000000 1.000000 --->germline2---dash-----: 1e+00 0.000000 1e+00 0.000000 0.999348 ( 0.004125) 1.000000 ( 0.000000) 1.000000 1.000000 ######sensitivitySnps###### --->fabia-------beagle1--: 1.02e-14 0.181983 3.11e-13 0.177453 0.935414 ( 0.170574) 0.757961 ( 0.176977) 0.976514 0.809317 --->fabia-------beagle2--: 1.34e-15 0.335206 2.36e-21 0.323321 0.935414 ( 0.170574) 0.612094 ( 0.225735) 0.976514 0.615978 --->fabia-------plink----: 1e+00 0.000000 1e+00 0.000000 0.935414 ( 0.170574) 1.000000 ( 0.000000) 0.976514 1.000000 --->fabia-------germline1: 4.24e-11 0.056213 6.03e-06 0.070639 0.935414 ( 0.170574) 0.864775 ( 0.204872) 0.976514 0.933850 --->fabia-------germline2: 2.53e-10 0.054810 8.77e-04 0.052902 0.935414 ( 0.170574) 0.882512 ( 0.163364) 0.976514 0.934577 --->fabia-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.935414 ( 0.170574) 0.000000 ( 0.000000) 0.976514 0.000000 --->beagle1-----beagle2--: 3.61e-12 0.212632 1.78e-15 0.145867 0.757961 ( 0.176977) 0.612094 ( 0.225735) 0.809317 0.615978 --->beagle1-----plink----: 1e+00 0.000000 1e+00 0.000000 0.757961 ( 0.176977) 1.000000 ( 0.000000) 0.809317 1.000000 --->beagle1-----germline1: 1.03e-08 -0.119195 1.65e-05 -0.106815 0.757961 ( 0.176977) 0.864775 ( 0.204872) 0.809317 0.933850 --->beagle1-----germline2: 3.85e-10 -0.125523 3.62e-08 -0.124551 0.757961 ( 0.176977) 0.882512 ( 0.163364) 0.809317 0.934577 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.757961 ( 0.176977) 0.000000 ( 0.000000) 0.809317 0.000000 --->beagle2-----plink----: 1e+00 0.000000 1e+00 0.000000 0.612094 ( 0.225735) 1.000000 ( 0.000000) 0.615978 1.000000 --->beagle2-----germline1: 1.85e-12 -0.274585 1.57e-13 -0.252682 0.612094 ( 0.225735) 0.864775 ( 0.204872) 0.615978 0.933850 --->beagle2-----germline2: 4.43e-14 -0.281923 7.11e-17 -0.270418 0.612094 ( 0.225735) 0.882512 ( 0.163364) 0.615978 0.934577 --->beagle2-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.612094 ( 0.225735) 0.000000 ( 0.000000) 0.615978 0.000000 --->plink-------germline1: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 0.864775 ( 0.204872) 1.000000 0.933850 --->plink-------germline2: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 0.882512 ( 0.163364) 1.000000 0.934577 --->plink-------dash-----: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 0.000000 ( 0.000000) 1.000000 0.000000 --->germline1---germline2: 1e+00 0.000000 1.6e-01 -0.017736 0.864775 ( 0.204872) 0.882512 ( 0.163364) 0.933850 0.934577 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 0.864775 ( 0.204872) 0.000000 ( 0.000000) 0.933850 0.000000 --->germline2---dash-----: 1e+00 0.000000 1e+00 0.000000 0.882512 ( 0.163364) 0.000000 ( 0.000000) 0.934577 0.000000 ######trueNSnps###### --->fabia-------beagle1--: 2.43e-11 1297 5.03e-02 665 190413 ( 3236) 189749 ( 1758) 190475 190320 --->fabia-------beagle2--: 1.4e-06 179 5.39e-01 -186 190413 ( 3236) 190600 ( 1062) 190475 190438 --->fabia-------plink----: 3.95e-18 190418 2.99e-176 190135 190413 ( 3236) 279 ( 699) 190475 0 --->fabia-------germline1: 1e+00 0 3.28e-01 -295 190413 ( 3236) 190708 ( 1206) 190475 190474 --->fabia-------germline2: 1e+00 0 5.54e-01 -185 190413 ( 3236) 190598 ( 1454) 190475 190471 --->fabia-------dash-----: 1e+00 0 3.05e-01 -309 190413 ( 3236) 190722 ( 1201) 190475 190477 --->beagle1-----beagle2--: 5.47e-08 -2223 2.36e-09 -851 189749 ( 1758) 190600 ( 1062) 190320 190438 --->beagle1-----plink----: 3.96e-18 189436 8.22e-201 189470 189749 ( 1758) 279 ( 699) 190320 0 --->beagle1-----germline1: 8.59e-13 -1303 3.05e-11 -959 189749 ( 1758) 190708 ( 1206) 190320 190474 --->beagle1-----germline2: 1.31e-10 -1230 8.93e-08 -849 189749 ( 1758) 190598 ( 1454) 190320 190471 --->beagle1-----dash-----: 5.33e-13 -1346 2.18e-11 -973 189749 ( 1758) 190722 ( 1201) 190320 190477 --->beagle2-----plink----: 3.95e-18 190338 1.14e-218 190321 190600 ( 1062) 279 ( 699) 190438 0 --->beagle2-----germline1: 1.07e-06 -153 4.6e-04 -108 190600 ( 1062) 190708 ( 1206) 190438 190474 --->beagle2-----germline2: 2.85e-05 -143 9.83e-01 1.81 190600 ( 1062) 190598 ( 1454) 190438 190471 --->beagle2-----dash-----: 1.16e-08 -207 7.82e-05 -122 190600 ( 1062) 190722 ( 1201) 190438 190477 --->plink-------germline1: 3.95e-18 -190408 8.99e-215 -190430 279 ( 699) 190708 ( 1206) 0 190474 --->plink-------germline2: 3.95e-18 -190407 6.26e-208 -190319 279 ( 699) 190598 ( 1454) 0 190471 --->plink-------dash-----: 3.95e-18 -190422 7.22e-215 -190444 279 ( 699) 190722 ( 1201) 0 190477 --->germline1---germline2: 1e+00 0 1.6e-01 110 190708 ( 1206) 190598 ( 1454) 190474 190471 --->germline1---dash-----: 1e+00 0 1.75e-02 -13.9 190708 ( 1206) 190722 ( 1201) 190474 190477 --->germline2---dash-----: 1e+00 0 1.17e-01 -124 190598 ( 1454) 190722 ( 1201) 190471 190477 ######falsePSnps###### --->fabia-------beagle1--: 2.43e-11 -1297 5.03e-02 -665 309 ( 2997) 973 ( 1289) 0 208 --->fabia-------beagle2--: 1e+00 0.000000 5.39e-01 186.460000 308.850000 (2997.178776) 122.390000 (296.936646) 0.000000 0.000000 --->fabia-------plink----: 3.95e-18 -190418 2.99e-176 -190135 309 ( 2997) 190444 ( 1349) 0 190442 --->fabia-------germline1: 1e+00 0.000000 3.28e-01 294.920000 308.850000 (2997.178776) 13.930000 (57.623693) 0.000000 0.000000 --->fabia-------germline2: 1e+00 0.000000 5.54e-01 184.650000 308.850000 (2997.178776) 124.200000 (785.810384) 0.000000 0.000000 --->fabia-------dash-----: 1e+00 0.000000 1e+00 0.000000 308.850000 (2997.178776) 0.000000 ( 0.000000) 0.000000 0.000000 --->beagle1-----beagle2--: 5.47e-08 2225 2.36e-09 851 973 ( 1289) 122 ( 297) 208 0 --->beagle1-----plink----: 3.96e-18 -189436 8.22e-201 -189470 973 ( 1289) 190444 ( 1349) 208 190442 --->beagle1-----germline1: 8.59e-13 1302 3.05e-11 959 973 ( 1289) 13.9 ( 57.6) 208 0 --->beagle1-----germline2: 1.31e-10 1230 8.93e-08 849 973 ( 1289) 124 ( 786) 208 0 --->beagle1-----dash-----: 1e+00 0 1e+00 0 973 ( 1289) 0 ( 0) 208 0 --->beagle2-----plink----: 3.95e-18 -190338 1.14e-218 -190321 122 ( 297) 190444 ( 1349) 0 190442 --->beagle2-----germline1: 1e+00 0.000000 4.6e-04 108.460000 122.390000 (296.936646) 13.930000 (57.623693) 0.000000 0.000000 --->beagle2-----germline2: 1e+00 0.000000 9.83e-01 -1.810000 122.390000 (296.936646) 124.200000 (785.810384) 0.000000 0.000000 --->beagle2-----dash-----: 1e+00 0.000000 1e+00 0.000000 122.390000 (296.936646) 0.000000 ( 0.000000) 0.000000 0.000000 --->plink-------germline1: 3.95e-18 190408 8.99e-215 190430 190444 ( 1349) 13.9 ( 57.6) 190442 0 --->plink-------germline2: 3.95e-18 190407 6.26e-208 190319 190444 ( 1349) 124 ( 786) 190442 0 --->plink-------dash-----: 1e+00 0 1e+00 0 190444 ( 1349) 0 ( 0) 190442 0 --->germline1---germline2: 1e+00 0.000000 1.6e-01 -110.270000 13.930000 (57.623693) 124.200000 (785.810384) 0.000000 0.000000 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 13.930000 (57.623693) 0.000000 ( 0.000000) 0.000000 0.000000 --->germline2---dash-----: 1e+00 0.000000 1e+00 0.000000 124.200000 (785.810384) 0.000000 ( 0.000000) 0.000000 0.000000 ######falseNSnps###### --->fabia-------beagle1--: 4.23e-15 -1714 6.89e-18 -1739 432 ( 771) 2171 ( 1476) 224 1804 --->fabia-------beagle2--: 2.01e-16 -3171 3.87e-25 -3125 432 ( 771) 3557 ( 2069) 224 3509 --->fabia-------plink----: 1e+00 0 1e+00 0 432 ( 771) 0 ( 0) 224 0 --->fabia-------germline1: 3.89e-11 -534 2.25e-07 -619 432 ( 771) 1052 ( 1148) 224 636 --->fabia-------germline2: 2.39e-10 -522 4.53e-06 -489 432 ( 771) 922 ( 675) 224 630 --->fabia-------dash-----: 1.24e-17 -9196 1.74e-74 -8846 432 ( 771) 9278 ( 1201) 224 9523 --->beagle1-----beagle2--: 3.61e-12 -2021 2.02e-15 -1386 2171 ( 1476) 3557 ( 2069) 1804 3509 --->beagle1-----plink----: 1e+00 0 1e+00 0 2171 ( 1476) 0 ( 0) 1804 0 --->beagle1-----germline1: 4.92e-09 1134 4.62e-08 1120 2171 ( 1476) 1052 ( 1148) 1804 636 --->beagle1-----germline2: 2.12e-10 1192 1.34e-11 1250 2171 ( 1476) 922 ( 675) 1804 630 --->beagle1-----dash-----: 5.78e-18 -7330 1.59e-62 -7106 2171 ( 1476) 9278 ( 1201) 1804 9523 --->beagle2-----plink----: 1e+00 0 1e+00 0 3557 ( 2069) 0 ( 0) 3509 0 --->beagle2-----germline1: 1.9e-13 2612 8.36e-17 2505 3557 ( 2069) 1052 ( 1148) 3509 636 --->beagle2-----germline2: 6.78e-15 2663 1.6e-20 2635 3557 ( 2069) 922 ( 675) 3509 630 --->beagle2-----dash-----: 5.78e-18 -5809 1.11e-46 -5721 3557 ( 2069) 9278 ( 1201) 3509 9523 --->plink-------germline1: 1e+00 0 1e+00 0 0 ( 0) 1052 ( 1148) 0 636 --->plink-------germline2: 1e+00 0 1e+00 0 0 ( 0) 922 ( 675) 0 630 --->plink-------dash-----: 1e+00 0 1e+00 0 0 ( 0) 9278 ( 1201) 0 9523 --->germline1---germline2: 1e+00 0 1.6e-01 130 1052 ( 1148) 922 ( 675) 636 630 --->germline1---dash-----: 5.59e-18 -8500 5e-65 -8226 1052 ( 1148) 9278 ( 1201) 636 9523 --->germline2---dash-----: 2.79e-18 -8500 2.07e-74 -8356 922 ( 675) 9278 ( 1201) 630 9523 ######truePSnps###### --->fabia-------beagle1--: 4.23e-15 1714 6.89e-18 1739 8846 ( 1669) 7106 ( 1794) 9278 7656 --->fabia-------beagle2--: 2.01e-16 3172 3.87e-25 3125 8846 ( 1669) 5721 ( 2163) 9278 5758 --->fabia-------plink----: 3.95e-18 -313 1.86e-07 -432 8846 ( 1669) 9278 ( 1201) 9278 9523 --->fabia-------germline1: 3.89e-11 534 2.25e-07 619 8846 ( 1669) 8226 ( 1953) 9278 8994 --->fabia-------germline2: 2.39e-10 522 4.53e-06 489 8846 ( 1669) 8356 ( 1579) 9278 8994 --->fabia-------dash-----: 1e+00 0 1e+00 0 8846 ( 1669) 0 ( 0) 9278 0 --->beagle1-----beagle2--: 3.61e-12 2020 2.02e-15 1386 7106 ( 1794) 5721 ( 2163) 7656 5758 --->beagle1-----plink----: 3.96e-18 -2071 1.19e-26 -2171 7106 ( 1794) 9278 ( 1201) 7656 9523 --->beagle1-----germline1: 4.92e-09 -1134 4.62e-08 -1120 7106 ( 1794) 8226 ( 1953) 7656 8994 --->beagle1-----germline2: 2.12e-10 -1192 1.34e-11 -1250 7106 ( 1794) 8356 ( 1579) 7656 8994 --->beagle1-----dash-----: 1e+00 0 1e+00 0 7106 ( 1794) 0 ( 0) 7656 0 --->beagle2-----plink----: 3.96e-18 -3516 1.75e-31 -3557 5721 ( 2163) 9278 ( 1201) 5758 9523 --->beagle2-----germline1: 1.9e-13 -2612 8.36e-17 -2505 5721 ( 2163) 8226 ( 1953) 5758 8994 --->beagle2-----germline2: 6.78e-15 -2663 1.6e-20 -2635 5721 ( 2163) 8356 ( 1579) 5758 8994 --->beagle2-----dash-----: 1e+00 0 1e+00 0 5721 ( 2163) 0 ( 0) 5758 0 --->plink-------germline1: 3.95e-18 958 7.29e-15 1052 9278 ( 1201) 8226 ( 1953) 9523 8994 --->plink-------germline2: 3.95e-18 938 1.64e-24 922 9278 ( 1201) 8356 ( 1579) 9523 8994 --->plink-------dash-----: 1e+00 0 1e+00 0 9278 ( 1201) 0 ( 0) 9523 0 --->germline1---germline2: 1e+00 0 1.6e-01 -130 8226 ( 1953) 8356 ( 1579) 8994 8994 --->germline1---dash-----: 1e+00 0 1e+00 0 8226 ( 1953) 0 ( 0) 8994 0 --->germline2---dash-----: 1e+00 0 1e+00 0 8356 ( 1579) 0 ( 0) 8994 0 ######MatthewsSample###### --->fabia-------beagle1--: 1e+00 0.000000 2.39e-04 0.081412 0.970000 ( 0.171447) 0.888588 ( 0.172335) 1.000000 1.000000 --->fabia-------beagle2--: 1e+00 0.000000 1.59e-01 -0.019980 0.970000 ( 0.171447) 0.989980 ( 0.100200) 1.000000 1.000000 --->fabia-------plink----: 4.45e-18 0.951648 5.15e-77 0.923536 0.970000 ( 0.171447) 0.046464 ( 0.011173) 1.000000 0.048114 --->fabia-------germline1: 1e+00 0.000000 1.58e-01 0.020000 0.970000 ( 0.171447) 0.950000 ( 0.219043) 1.000000 1.000000 --->fabia-------germline2: 1e+00 0.000000 5.6e-01 0.008808 0.970000 ( 0.171447) 0.961192 ( 0.177183) 1.000000 1.000000 --->fabia-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.970000 ( 0.171447) 0.000000 ( 0.000000) 1.000000 0.000000 --->beagle1-----beagle2--: 1e+00 0.000000 5.45e-10 -0.101392 0.888588 ( 0.172335) 0.989980 ( 0.100200) 1.000000 1.000000 --->beagle1-----plink----: 4.07e-18 0.806942 2.04e-71 0.842124 0.888588 ( 0.172335) 0.046464 ( 0.011173) 1.000000 0.048114 --->beagle1-----germline1: 1e+00 0.000000 1.48e-02 -0.061412 0.888588 ( 0.172335) 0.950000 ( 0.219043) 1.000000 1.000000 --->beagle1-----germline2: 1e+00 0.000000 9.41e-04 -0.072604 0.888588 ( 0.172335) 0.961192 ( 0.177183) 1.000000 1.000000 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.888588 ( 0.172335) 0.000000 ( 0.000000) 1.000000 0.000000 --->beagle2-----plink----: 4.06e-18 0.951775 2e-100 0.943516 0.989980 ( 0.100200) 0.046464 ( 0.011173) 1.000000 0.048114 --->beagle2-----germline1: 1e+00 0.000000 4.5e-02 0.039980 0.989980 ( 0.100200) 0.950000 ( 0.219043) 1.000000 1.000000 --->beagle2-----germline2: 1e+00 0.000000 5.5e-02 0.028788 0.989980 ( 0.100200) 0.961192 ( 0.177183) 1.000000 1.000000 --->beagle2-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.989980 ( 0.100200) 0.000000 ( 0.000000) 1.000000 0.000000 --->plink-------germline1: 5.66e-18 -0.951556 1.35e-65 -0.903536 0.046464 ( 0.011173) 0.950000 ( 0.219043) 0.048114 1.000000 --->plink-------germline2: 4.73e-18 -0.951515 1.9e-74 -0.914728 0.046464 ( 0.011173) 0.961192 ( 0.177183) 0.048114 1.000000 --->plink-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.046464 ( 0.011173) 0.000000 ( 0.000000) 0.048114 0.000000 --->germline1---germline2: 1e+00 0.000000 4.59e-01 -0.011192 0.950000 ( 0.219043) 0.961192 ( 0.177183) 1.000000 1.000000 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 0.950000 ( 0.219043) 0.000000 ( 0.000000) 1.000000 0.000000 --->germline2---dash-----: 1e+00 0.000000 1e+00 0.000000 0.961192 ( 0.177183) 0.000000 ( 0.000000) 1.000000 0.000000 ######F1Sample###### --->fabia-------beagle1--: 1e+00 0.000000 6.73e-05 0.095810 0.970000 ( 0.171447) 0.874190 ( 0.190183) 1.000000 1.000000 --->fabia-------beagle2--: 1e+00 0.000000 1.58e-01 -0.020000 0.970000 ( 0.171447) 0.990000 ( 0.100000) 1.000000 1.000000 --->fabia-------plink----: 6.32e-18 0.991366 5.16e-77 0.961550 0.970000 ( 0.171447) 0.008450 ( 0.001142) 1.000000 0.008584 --->fabia-------germline1: 1e+00 0.000000 1.58e-01 0.020000 0.970000 ( 0.171447) 0.950000 ( 0.219043) 1.000000 1.000000 --->fabia-------germline2: 1e+00 0.000000 5.15e-01 0.010000 0.970000 ( 0.171447) 0.960000 ( 0.179036) 1.000000 1.000000 --->fabia-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.970000 ( 0.171447) 0.000000 ( 0.000000) 1.000000 0.000000 --->beagle1-----beagle2--: 1e+00 0.000000 6.06e-10 -0.115810 0.874190 ( 0.190183) 0.990000 ( 0.100000) 1.000000 1.000000 --->beagle1-----plink----: 4.07e-18 0.825109 3.18e-68 0.865740 0.874190 ( 0.190183) 0.008450 ( 0.001142) 1.000000 0.008584 --->beagle1-----germline1: 1e+00 0.000000 4.5e-03 -0.075810 0.874190 ( 0.190183) 0.950000 ( 0.219043) 1.000000 1.000000 --->beagle1-----germline2: 1e+00 0.000000 3.06e-04 -0.085810 0.874190 ( 0.190183) 0.960000 ( 0.179036) 1.000000 1.000000 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.874190 ( 0.190183) 0.000000 ( 0.000000) 1.000000 0.000000 --->beagle2-----plink----: 4.06e-18 0.991388 1.22e-100 0.981550 0.990000 ( 0.100000) 0.008450 ( 0.001142) 1.000000 0.008584 --->beagle2-----germline1: 1e+00 0.000000 4.49e-02 0.040000 0.990000 ( 0.100000) 0.950000 ( 0.219043) 1.000000 1.000000 --->beagle2-----germline2: 1e+00 0.000000 4.9e-02 0.030000 0.990000 ( 0.100000) 0.960000 ( 0.179036) 1.000000 1.000000 --->beagle2-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.990000 ( 0.100000) 0.000000 ( 0.000000) 1.000000 0.000000 --->plink-------germline1: 7.82e-18 -0.991356 5.54e-66 -0.941550 0.008450 ( 0.001142) 0.950000 ( 0.219043) 0.008584 1.000000 --->plink-------germline2: 4.73e-18 -0.991313 1.06e-74 -0.951550 0.008450 ( 0.001142) 0.960000 ( 0.179036) 0.008584 1.000000 --->plink-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.008450 ( 0.001142) 0.000000 ( 0.000000) 0.008584 0.000000 --->germline1---germline2: 1e+00 0.000000 5.15e-01 -0.010000 0.950000 ( 0.219043) 0.960000 ( 0.179036) 1.000000 1.000000 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 0.950000 ( 0.219043) 0.000000 ( 0.000000) 1.000000 0.000000 --->germline2---dash-----: 1e+00 0.000000 1e+00 0.000000 0.960000 ( 0.179036) 0.000000 ( 0.000000) 1.000000 0.000000 ######accuracySample###### --->fabia-------beagle1--: 1e+00 0.000000 3.65e-09 0.000740 0.999970 ( 0.000171) 0.999230 ( 0.001145) 1.000000 1.000000 --->fabia-------beagle2--: 1e+00 0.000000 1e+00 0.000000 0.999970 ( 0.000171) 0.999960 ( 4e-04) 1.000000 1.000000 --->fabia-------plink----: 3.94e-18 0.461034 3.54e-129 0.461200 0.999970 ( 0.000171) 0.538770 ( 0.024009) 1.000000 0.539000 --->fabia-------germline1: 1e+00 0.000000 1e+00 0.000000 0.999970 ( 0.000171) 0.999900 ( 0.000438) 1.000000 1.000000 --->fabia-------germline2: 1e+00 0.000000 1e+00 0.000000 0.999970 ( 0.000171) 0.999880 ( 0.000477) 1.000000 1.000000 --->fabia-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.999970 ( 0.000171) 0.998000 ( 0.000000) 1.000000 0.998000 --->beagle1-----beagle2--: 1e+00 0.000000 1.71e-09 -0.000730 0.999230 ( 0.001145) 0.999960 ( 4e-04) 1.000000 1.000000 --->beagle1-----plink----: 3.94e-18 0.460460 3.71e-129 0.460460 0.999230 ( 0.001145) 0.538770 ( 0.024009) 1.000000 0.539000 --->beagle1-----germline1: 1e+00 0.000000 1.16e-07 -0.000670 0.999230 ( 0.001145) 0.999900 ( 0.000438) 1.000000 1.000000 --->beagle1-----germline2: 1e+00 0.000000 1.5e-07 -0.000650 0.999230 ( 0.001145) 0.999880 ( 0.000477) 1.000000 1.000000 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.999230 ( 0.001145) 0.998000 ( 0.000000) 1.000000 0.998000 --->beagle2-----plink----: 3.94e-18 0.461047 3.16e-129 0.461190 0.999960 ( 4e-04) 0.538770 ( 0.024009) 1.000000 0.539000 --->beagle2-----germline1: 1e+00 0.000000 1e+00 0.000000 0.999960 ( 4e-04) 0.999900 ( 0.000438) 1.000000 1.000000 --->beagle2-----germline2: 1e+00 0.000000 1e+00 0.000000 0.999960 ( 4e-04) 0.999880 ( 0.000477) 1.000000 1.000000 --->beagle2-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.999960 ( 4e-04) 0.998000 ( 0.000000) 1.000000 0.998000 --->plink-------germline1: 3.94e-18 -0.460948 4.17e-129 -0.461130 0.538770 ( 0.024009) 0.999900 ( 0.000438) 0.539000 1.000000 --->plink-------germline2: 3.94e-18 -0.460961 3.7e-129 -0.461110 0.538770 ( 0.024009) 0.999880 ( 0.000477) 0.539000 1.000000 --->plink-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.538770 ( 0.024009) 0.998000 ( 0.000000) 0.539000 0.998000 --->germline1---germline2: 1e+00 0.000000 1e+00 0.000000 0.999900 ( 0.000438) 0.999880 ( 0.000477) 1.000000 1.000000 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 0.999900 ( 0.000438) 0.998000 ( 0.000000) 1.000000 0.998000 --->germline2---dash-----: 1e+00 0.000000 1e+00 0.000000 0.999880 ( 0.000477) 0.998000 ( 0.000000) 1.000000 0.998000 ######FPRSample###### --->fabia-------beagle1--: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.000752 ( 0.001107) 0.000000 0.000000 --->fabia-------beagle2--: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 2e-05 ( 2e-04) 0.000000 0.000000 --->fabia-------plink----: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.462114 ( 0.024052) 0.000000 0.461924 --->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) 6.01e-05 ( 0.000344) 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 1.71e-09 0.000731 0.000752 ( 0.001107) 2e-05 ( 2e-04) 0.000000 0.000000 --->beagle1-----plink----: 3.95e-18 -0.461417 3.92e-129 -0.461363 0.000752 ( 0.001107) 0.462114 ( 0.024052) 0.000000 0.461924 --->beagle1-----germline1: 1e+00 0.000000 1e+00 0.000000 0.000752 ( 0.001107) 0.000000 ( 0.000000) 0.000000 0.000000 --->beagle1-----germline2: 1e+00 0.000000 6.99e-09 0.000691 0.000752 ( 0.001107) 6.01e-05 ( 0.000344) 0.000000 0.000000 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.000752 ( 0.001107) 0.000000 ( 0.000000) 0.000000 0.000000 --->beagle2-----plink----: 3.94e-18 -0.461954 3.34e-129 -0.462094 2e-05 ( 2e-04) 0.462114 ( 0.024052) 0.000000 0.461924 --->beagle2-----germline1: 1e+00 0.000000 1e+00 0.000000 2e-05 ( 2e-04) 0.000000 ( 0.000000) 0.000000 0.000000 --->beagle2-----germline2: 1e+00 0.000000 1e+00 0.000000 2e-05 ( 2e-04) 6.01e-05 ( 0.000344) 0.000000 0.000000 --->beagle2-----dash-----: 1e+00 0.000000 1e+00 0.000000 2e-05 ( 2e-04) 0.000000 ( 0.000000) 0.000000 0.000000 --->plink-------germline1: 1e+00 0.000000 1e+00 0.000000 0.462114 ( 0.024052) 0.000000 ( 0.000000) 0.461924 0.000000 --->plink-------germline2: 3.94e-18 0.461903 3.7e-129 0.462054 0.462114 ( 0.024052) 6.01e-05 ( 0.000344) 0.461924 0.000000 --->plink-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.462114 ( 0.024052) 0.000000 ( 0.000000) 0.461924 0.000000 --->germline1---germline2: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 6.01e-05 ( 0.000344) 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 6.01e-05 ( 0.000344) 0.000000 ( 0.000000) 0.000000 0.000000 ######FDRSample###### --->fabia-------beagle1--: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.180667 ( 0.259680) 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) 0.995757 ( 0.000574) 0.000000 0.995690 --->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) 0.015000 ( 0.085723) 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 4.6e-10 0.170667 0.180667 ( 0.259680) 0.010000 ( 0.100000) 0.000000 0.000000 --->beagle1-----plink----: 4.07e-18 -0.745893 2.91e-53 -0.815090 0.180667 ( 0.259680) 0.995757 ( 0.000574) 0.000000 0.995690 --->beagle1-----germline1: 1e+00 0.000000 1e+00 0.000000 0.180667 ( 0.259680) 0.000000 ( 0.000000) 0.000000 0.000000 --->beagle1-----germline2: 1e+00 0.000000 7.16e-09 0.165667 0.180667 ( 0.259680) 0.015000 ( 0.085723) 0.000000 0.000000 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.180667 ( 0.259680) 0.000000 ( 0.000000) 0.000000 0.000000 --->beagle2-----plink----: 4.06e-18 -0.995716 9.88e-101 -0.985757 0.010000 ( 0.100000) 0.995757 ( 0.000574) 0.000000 0.995690 --->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 7.07e-01 -0.005000 0.010000 ( 0.100000) 0.015000 ( 0.085723) 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 0.995757 ( 0.000574) 0.000000 ( 0.000000) 0.995690 0.000000 --->plink-------germline2: 3.95e-18 0.995674 5.59e-107 0.980757 0.995757 ( 0.000574) 0.015000 ( 0.085723) 0.995690 0.000000 --->plink-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.995757 ( 0.000574) 0.000000 ( 0.000000) 0.995690 0.000000 --->germline1---germline2: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.015000 ( 0.085723) 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 0.015000 ( 0.085723) 0.000000 ( 0.000000) 0.000000 0.000000 ######specifitySample###### --->fabia-------beagle1--: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 0.999248 ( 0.001107) 1.000000 1.000000 --->fabia-------beagle2--: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 0.999980 ( 2e-04) 1.000000 1.000000 --->fabia-------plink----: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 0.537886 ( 0.024052) 1.000000 0.538076 --->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) 0.999940 ( 0.000344) 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 1.71e-09 -0.000731 0.999248 ( 0.001107) 0.999980 ( 2e-04) 1.000000 1.000000 --->beagle1-----plink----: 3.94e-18 0.461370 3.92e-129 0.461363 0.999248 ( 0.001107) 0.537886 ( 0.024052) 1.000000 0.538076 --->beagle1-----germline1: 1e+00 0.000000 1e+00 0.000000 0.999248 ( 0.001107) 1.000000 ( 0.000000) 1.000000 1.000000 --->beagle1-----germline2: 1e+00 0.000000 6.99e-09 -0.000691 0.999248 ( 0.001107) 0.999940 ( 0.000344) 1.000000 1.000000 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.999248 ( 0.001107) 1.000000 ( 0.000000) 1.000000 1.000000 --->beagle2-----plink----: 3.94e-18 0.461939 3.34e-129 0.462094 0.999980 ( 2e-04) 0.537886 ( 0.024052) 1.000000 0.538076 --->beagle2-----germline1: 1e+00 0.000000 1e+00 0.000000 0.999980 ( 2e-04) 1.000000 ( 0.000000) 1.000000 1.000000 --->beagle2-----germline2: 1e+00 0.000000 1e+00 0.000000 0.999980 ( 2e-04) 0.999940 ( 0.000344) 1.000000 1.000000 --->beagle2-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.999980 ( 2e-04) 1.000000 ( 0.000000) 1.000000 1.000000 --->plink-------germline1: 1e+00 0.000000 1e+00 0.000000 0.537886 ( 0.024052) 1.000000 ( 0.000000) 0.538076 1.000000 --->plink-------germline2: 3.94e-18 -0.461861 3.7e-129 -0.462054 0.537886 ( 0.024052) 0.999940 ( 0.000344) 0.538076 1.000000 --->plink-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.537886 ( 0.024052) 1.000000 ( 0.000000) 0.538076 1.000000 --->germline1---germline2: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 0.999940 ( 0.000344) 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 0.999940 ( 0.000344) 1.000000 ( 0.000000) 1.000000 1.000000 ######sensitivitySample###### --->fabia-------beagle1--: 1e+00 0.000000 1.58e-01 -0.020000 0.970000 ( 0.171447) 0.990000 ( 0.100000) 1.000000 1.000000 --->fabia-------beagle2--: 1e+00 0.000000 1.58e-01 -0.020000 0.970000 ( 0.171447) 0.990000 ( 0.100000) 1.000000 1.000000 --->fabia-------plink----: 1e+00 0.000000 4.17e-01 -0.010000 0.970000 ( 0.171447) 0.980000 ( 0.121439) 1.000000 1.000000 --->fabia-------germline1: 1e+00 0.000000 1.58e-01 0.020000 0.970000 ( 0.171447) 0.950000 ( 0.219043) 1.000000 1.000000 --->fabia-------germline2: 1e+00 0.000000 1e+00 0.000000 0.970000 ( 0.171447) 0.970000 ( 0.171447) 1.000000 1.000000 --->fabia-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.970000 ( 0.171447) 0.000000 ( 0.000000) 1.000000 0.000000 --->beagle1-----beagle2--: 1e+00 0.000000 1e+00 0.000000 0.990000 ( 0.100000) 0.990000 ( 0.100000) 1.000000 1.000000 --->beagle1-----plink----: 1e+00 0.000000 4.17e-01 0.010000 0.990000 ( 0.100000) 0.980000 ( 0.121439) 1.000000 1.000000 --->beagle1-----germline1: 1e+00 0.000000 4.49e-02 0.040000 0.990000 ( 0.100000) 0.950000 ( 0.219043) 1.000000 1.000000 --->beagle1-----germline2: 1e+00 0.000000 1.58e-01 0.020000 0.990000 ( 0.100000) 0.970000 ( 0.171447) 1.000000 1.000000 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.990000 ( 0.100000) 0.000000 ( 0.000000) 1.000000 0.000000 --->beagle2-----plink----: 1e+00 0.000000 4.17e-01 0.010000 0.990000 ( 0.100000) 0.980000 ( 0.121439) 1.000000 1.000000 --->beagle2-----germline1: 1e+00 0.000000 4.49e-02 0.040000 0.990000 ( 0.100000) 0.950000 ( 0.219043) 1.000000 1.000000 --->beagle2-----germline2: 1e+00 0.000000 1.58e-01 0.020000 0.990000 ( 0.100000) 0.970000 ( 0.171447) 1.000000 1.000000 --->beagle2-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.990000 ( 0.100000) 0.000000 ( 0.000000) 1.000000 0.000000 --->plink-------germline1: 1e+00 0.000000 5.74e-02 0.030000 0.980000 ( 0.121439) 0.950000 ( 0.219043) 1.000000 1.000000 --->plink-------germline2: 1e+00 0.000000 5.3e-01 0.010000 0.980000 ( 0.121439) 0.970000 ( 0.171447) 1.000000 1.000000 --->plink-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.980000 ( 0.121439) 0.000000 ( 0.000000) 1.000000 0.000000 --->germline1---germline2: 1e+00 0.000000 1.58e-01 -0.020000 0.950000 ( 0.219043) 0.970000 ( 0.171447) 1.000000 1.000000 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 0.950000 ( 0.219043) 0.000000 ( 0.000000) 1.000000 0.000000 --->germline2---dash-----: 1e+00 0.000000 1e+00 0.000000 0.970000 ( 0.171447) 0.000000 ( 0.000000) 1.000000 0.000000 ######trueNSample###### --->fabia-------beagle1--: 1e+00 0 1e+00 0 1998 ( 0) 997 ( 1.1) 1998 998 --->fabia-------beagle2--: 1e+00 0 1e+00 0 1998 ( 0) 998 ( 0.2) 1998 998 --->fabia-------plink----: 1e+00 0 1e+00 0 1998 ( 0) 537 ( 24) 1998 537 --->fabia-------germline1: 1e+00 0 1e+00 0 1998 ( 0) 998 ( 0) 1998 998 --->fabia-------germline2: 1e+00 0 1e+00 0 1998 ( 0) 998 ( 0.343) 1998 998 --->fabia-------dash-----: 1e+00 0 1e+00 0 1998 ( 0) 998 ( 0) 1998 998 --->beagle1-----beagle2--: 1e+00 0 1.71e-09 -0.73 997 ( 1.1) 998 ( 0.2) 998 998 --->beagle1-----plink----: 3.94e-18 460 3.92e-129 460 997 ( 1.1) 537 ( 24) 998 537 --->beagle1-----germline1: 1e+00 0 1e+00 0 997 ( 1.1) 998 ( 0) 998 998 --->beagle1-----germline2: 1e+00 0 6.99e-09 -0.69 997 ( 1.1) 998 ( 0.343) 998 998 --->beagle1-----dash-----: 1e+00 0 1e+00 0 997 ( 1.1) 998 ( 0) 998 998 --->beagle2-----plink----: 3.94e-18 461 3.34e-129 461 998 ( 0.2) 537 ( 24) 998 537 --->beagle2-----germline1: 1e+00 0 1e+00 0 998 ( 0.2) 998 ( 0) 998 998 --->beagle2-----germline2: 1e+00 0 3.2e-01 0.04 998 ( 0.2) 998 ( 0.343) 998 998 --->beagle2-----dash-----: 1e+00 0 1e+00 0 998 ( 0.2) 998 ( 0) 998 998 --->plink-------germline1: 1e+00 0 1e+00 0 537 ( 24) 998 ( 0) 537 998 --->plink-------germline2: 3.94e-18 -461 3.7e-129 -461 537 ( 24) 998 ( 0.343) 537 998 --->plink-------dash-----: 1e+00 0 1e+00 0 537 ( 24) 998 ( 0) 537 998 --->germline1---germline2: 1e+00 0 1e+00 0 998 ( 0) 998 ( 0.343) 998 998 --->germline1---dash-----: 1e+00 0 1e+00 0 998 ( 0) 998 ( 0) 998 998 --->germline2---dash-----: 1e+00 0 1e+00 0 998 ( 0.343) 998 ( 0) 998 998 ######falsePSample###### --->fabia-------beagle1--: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.750000 ( 1.104399) 0.000000 0.000000 --->fabia-------beagle2--: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.020000 ( 0.200000) 0.000000 0.000000 --->fabia-------plink----: 1e+00 0 1e+00 0 0 ( 0) 461 ( 24) 0 461 --->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) 0.060000 ( 0.342893) 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 1.71e-09 0.730000 0.750000 ( 1.104399) 0.020000 ( 0.200000) 0.000000 0.000000 --->beagle1-----plink----: 3.94e-18 -460 3.92e-129 -460 0.75 ( 1.1) 461 ( 24) 0 461 --->beagle1-----germline1: 1e+00 0.000000 1e+00 0.000000 0.750000 ( 1.104399) 0.000000 ( 0.000000) 0.000000 0.000000 --->beagle1-----germline2: 1e+00 0.000000 6.99e-09 0.690000 0.750000 ( 1.104399) 0.060000 ( 0.342893) 0.000000 0.000000 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.750000 ( 1.104399) 0.000000 ( 0.000000) 0.000000 0.000000 --->beagle2-----plink----: 3.94e-18 -461 3.34e-129 -461 0.02 ( 0.2) 461 ( 24) 0 461 --->beagle2-----germline1: 1e+00 0.000000 1e+00 0.000000 0.020000 ( 0.200000) 0.000000 ( 0.000000) 0.000000 0.000000 --->beagle2-----germline2: 1e+00 0.000000 3.2e-01 -0.040000 0.020000 ( 0.200000) 0.060000 ( 0.342893) 0.000000 0.000000 --->beagle2-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.020000 ( 0.200000) 0.000000 ( 0.000000) 0.000000 0.000000 --->plink-------germline1: 1e+00 0 1e+00 0 461 ( 24) 0 ( 0) 461 0 --->plink-------germline2: 3.94e-18 461 3.7e-129 461 461 ( 24) 0.06 ( 0.343) 461 0 --->plink-------dash-----: 1e+00 0 1e+00 0 461 ( 24) 0 ( 0) 461 0 --->germline1---germline2: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.060000 ( 0.342893) 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 0.060000 ( 0.342893) 0.000000 ( 0.000000) 0.000000 0.000000 ######falseNSample###### --->fabia-------beagle1--: 1e+00 0.000000 1.58e-01 0.040000 0.060000 ( 0.342893) 0.020000 ( 0.200000) 0.000000 0.000000 --->fabia-------beagle2--: 1e+00 0.000000 1.58e-01 0.040000 0.060000 ( 0.342893) 0.020000 ( 0.200000) 0.000000 0.000000 --->fabia-------plink----: 1e+00 0.000000 4.17e-01 0.020000 0.060000 ( 0.342893) 0.040000 ( 0.242878) 0.000000 0.000000 --->fabia-------germline1: 1e+00 0.000000 1.58e-01 -0.040000 0.060000 ( 0.342893) 0.100000 ( 0.438086) 0.000000 0.000000 --->fabia-------germline2: 1e+00 0.000000 1e+00 0.000000 0.060000 ( 0.342893) 0.060000 ( 0.342893) 0.000000 0.000000 --->fabia-------dash-----: 1e+00 0 1e+00 0 0.06 ( 0.343) 2 ( 0) 0 2 --->beagle1-----beagle2--: 1e+00 0.000000 1e+00 0.000000 0.020000 ( 0.200000) 0.020000 ( 0.200000) 0.000000 0.000000 --->beagle1-----plink----: 1e+00 0.000000 4.17e-01 -0.020000 0.020000 ( 0.200000) 0.040000 ( 0.242878) 0.000000 0.000000 --->beagle1-----germline1: 1e+00 0.000000 4.49e-02 -0.080000 0.020000 ( 0.200000) 0.100000 ( 0.438086) 0.000000 0.000000 --->beagle1-----germline2: 1e+00 0.000000 1.58e-01 -0.040000 0.020000 ( 0.200000) 0.060000 ( 0.342893) 0.000000 0.000000 --->beagle1-----dash-----: 1e+00 0 1e+00 0 0.02 ( 0.2) 2 ( 0) 0 2 --->beagle2-----plink----: 1e+00 0.000000 4.17e-01 -0.020000 0.020000 ( 0.200000) 0.040000 ( 0.242878) 0.000000 0.000000 --->beagle2-----germline1: 1e+00 0.000000 4.49e-02 -0.080000 0.020000 ( 0.200000) 0.100000 ( 0.438086) 0.000000 0.000000 --->beagle2-----germline2: 1e+00 0.000000 1.58e-01 -0.040000 0.020000 ( 0.200000) 0.060000 ( 0.342893) 0.000000 0.000000 --->beagle2-----dash-----: 1e+00 0 1e+00 0 0.02 ( 0.2) 2 ( 0) 0 2 --->plink-------germline1: 1e+00 0.000000 5.74e-02 -0.060000 0.040000 ( 0.242878) 0.100000 ( 0.438086) 0.000000 0.000000 --->plink-------germline2: 1e+00 0.000000 5.3e-01 -0.020000 0.040000 ( 0.242878) 0.060000 ( 0.342893) 0.000000 0.000000 --->plink-------dash-----: 1e+00 0 1e+00 0 0.04 ( 0.243) 2 ( 0) 0 2 --->germline1---germline2: 1e+00 0.000000 1.58e-01 0.040000 0.100000 ( 0.438086) 0.060000 ( 0.342893) 0.000000 0.000000 --->germline1---dash-----: 1e+00 0 1e+00 0 0.1 ( 0.438) 2 ( 0) 0 2 --->germline2---dash-----: 1e+00 0 1e+00 0 0.06 ( 0.343) 2 ( 0) 0 2 ######truePSample###### --->fabia-------beagle1--: 1e+00 0 1.58e-01 -0.04 1.94 ( 0.343) 1.98 ( 0.2) 2 2 --->fabia-------beagle2--: 1e+00 0 1.58e-01 -0.04 1.94 ( 0.343) 1.98 ( 0.2) 2 2 --->fabia-------plink----: 1e+00 0 4.17e-01 -0.02 1.94 ( 0.343) 1.96 ( 0.243) 2 2 --->fabia-------germline1: 1e+00 0 1.58e-01 0.04 1.94 ( 0.343) 1.9 ( 0.438) 2 2 --->fabia-------germline2: 1e+00 0 1e+00 0 1.94 ( 0.343) 1.94 ( 0.343) 2 2 --->fabia-------dash-----: 1e+00 0 1e+00 0 1.94 ( 0.343) 0 ( 0) 2 0 --->beagle1-----beagle2--: 1e+00 0 1e+00 0 1.98 ( 0.2) 1.98 ( 0.2) 2 2 --->beagle1-----plink----: 1e+00 0 4.17e-01 0.02 1.98 ( 0.2) 1.96 ( 0.243) 2 2 --->beagle1-----germline1: 1e+00 0 4.49e-02 0.08 1.98 ( 0.2) 1.9 ( 0.438) 2 2 --->beagle1-----germline2: 1e+00 0 1.58e-01 0.04 1.98 ( 0.2) 1.94 ( 0.343) 2 2 --->beagle1-----dash-----: 1e+00 0 1e+00 0 1.98 ( 0.2) 0 ( 0) 2 0 --->beagle2-----plink----: 1e+00 0 4.17e-01 0.02 1.98 ( 0.2) 1.96 ( 0.243) 2 2 --->beagle2-----germline1: 1e+00 0 4.49e-02 0.08 1.98 ( 0.2) 1.9 ( 0.438) 2 2 --->beagle2-----germline2: 1e+00 0 1.58e-01 0.04 1.98 ( 0.2) 1.94 ( 0.343) 2 2 --->beagle2-----dash-----: 1e+00 0 1e+00 0 1.98 ( 0.2) 0 ( 0) 2 0 --->plink-------germline1: 1e+00 0 5.74e-02 0.06 1.96 ( 0.243) 1.9 ( 0.438) 2 2 --->plink-------germline2: 1e+00 0 5.3e-01 0.02 1.96 ( 0.243) 1.94 ( 0.343) 2 2 --->plink-------dash-----: 1e+00 0 1e+00 0 1.96 ( 0.243) 0 ( 0) 2 0 --->germline1---germline2: 1e+00 0 1.58e-01 -0.04 1.9 ( 0.438) 1.94 ( 0.343) 2 2 --->germline1---dash-----: 1e+00 0 1e+00 0 1.9 ( 0.438) 0 ( 0) 2 0 --->germline2---dash-----: 1e+00 0 1e+00 0 1.94 ( 0.343) 0 ( 0) 2 0