Results: Wilcoxon-Rank-Sum Wilcoxon-median t-test t-test-mean mean1 (std) mean2 (std) median1 median2 ######Matthews###### --->fabia-------beagle1--: 2.24e-17 0.491527 1.84e-23 0.573467 0.571449 ( 0.435958) -0.002017 ( 0.003133) 0.852796 -0.002976 --->fabia-------beagle2--: 6.63e-17 0.491423 1.97e-23 0.572866 0.571449 ( 0.435958) -0.001417 ( 0.003245) 0.852796 -0.002942 --->fabia-------plink----: 1.83e-12 0.480815 8.89e-23 0.562474 0.571449 ( 0.435958) 0.008976 ( 0.012713) 0.852796 0.002019 --->fabia-------germline1: 3.65e-14 0.488867 2.24e-23 0.571527 0.571449 ( 0.435958) -7.76e-05 ( 0.006731) 0.852796 0.003541 --->fabia-------germline2: 1.1e-17 0.489681 2.21e-23 0.571571 0.571449 ( 0.435958) -0.000122 ( 0.006968) 0.852796 -0.001034 --->fabia-------dash-----: 3.21e-15 0.489821 2.4e-23 0.571950 0.571449 ( 0.435958) -0.000501 ( 0.007605) 0.852796 -0.003544 --->beagle1-----beagle2--: 1e+00 0.000000 4.33e-02 -0.000601 -0.002017 ( 0.003133) -0.001417 ( 0.003245) -0.002976 -0.002942 --->beagle1-----plink----: 7.47e-13 -0.009620 2.63e-13 -0.010993 -0.002017 ( 0.003133) 0.008976 ( 0.012713) -0.002976 0.002019 --->beagle1-----germline1: 5.05e-03 -0.003333 1.74e-02 -0.001940 -0.002017 ( 0.003133) -7.76e-05 ( 0.006731) -0.002976 0.003541 --->beagle1-----germline2: 7.48e-04 -0.001273 1.62e-02 -0.001895 -0.002017 ( 0.003133) -0.000122 ( 0.006968) -0.002976 -0.001034 --->beagle1-----dash-----: 7.56e-01 0.000227 7.32e-02 -0.001517 -0.002017 ( 0.003133) -0.000501 ( 0.007605) -0.002976 -0.003544 --->beagle2-----plink----: 7.85e-13 -0.008961 2.62e-12 -0.010392 -0.001417 ( 0.003245) 0.008976 ( 0.012713) -0.002942 0.002019 --->beagle2-----germline1: 1.14e-02 -0.002528 9.89e-02 -0.001339 -0.001417 ( 0.003245) -7.76e-05 ( 0.006731) -0.002942 0.003541 --->beagle2-----germline2: 4.25e-06 -0.001337 1.04e-01 -0.001295 -0.001417 ( 0.003245) -0.000122 ( 0.006968) -0.002942 -0.001034 --->beagle2-----dash-----: 6.3e-03 0.000789 2.87e-01 -0.000916 -0.001417 ( 0.003245) -0.000501 ( 0.007605) -0.002942 -0.003544 --->plink-------germline1: 4.44e-07 0.008049 2.09e-08 0.009053 0.008976 ( 0.012713) -7.76e-05 ( 0.006731) 0.002019 0.003541 --->plink-------germline2: 2.09e-05 0.007468 8.66e-09 0.009098 0.008976 ( 0.012713) -0.000122 ( 0.006968) 0.002019 -0.001034 --->plink-------dash-----: 4.41e-11 0.008921 1.39e-09 0.009476 0.008976 ( 0.012713) -0.000501 ( 0.007605) 0.002019 -0.003544 --->germline1---germline2: 1.53e-01 0.002513 1e+00 0.000000 -7.76e-05 ( 0.006731) -0.000122 ( 0.006968) 0.003541 -0.001034 --->germline1---dash-----: 9.64e-02 0.002513 7.21e-01 0.000423 -7.76e-05 ( 0.006731) -0.000501 ( 0.007605) 0.003541 -0.003544 --->germline2---dash-----: 1.74e-03 0.002472 7.22e-01 0.000379 -0.000122 ( 0.006968) -0.000501 ( 0.007605) -0.001034 -0.003544 ######F1###### --->fabia-------beagle1--: 3.39e-12 0.563172 8.76e-23 0.561739 0.561868 ( 0.437731) 0.000129 ( 0.000118) 0.842105 9.27e-05 --->fabia-------beagle2--: 3.29e-13 0.861707 8.74e-23 0.561756 0.561868 ( 0.437731) 0.000112 ( 0.000218) 0.842105 0.000000 --->fabia-------plink----: 7.34e-13 0.654011 1.08e-22 0.560307 0.561868 ( 0.437731) 0.001560 ( 0.001942) 0.842105 0.000524 --->fabia-------germline1: 2.41e-11 0.489905 8.83e-23 0.561665 0.561868 ( 0.437731) 0.000203 ( 7.45e-05) 0.842105 0.000228 --->fabia-------germline2: 1.2e-12 0.908698 8.82e-23 0.561670 0.561868 ( 0.437731) 0.000198 ( 0.001436) 0.842105 0.000000 --->fabia-------dash-----: 3.17e-13 0.875436 8.86e-23 0.561688 0.561868 ( 0.437731) 0.000180 ( 0.000408) 0.842105 0.000000 --->beagle1-----beagle2--: 1e+00 0.000000 1e+00 0.000000 0.000129 ( 0.000118) 0.000112 ( 0.000218) 9.27e-05 0.000000 --->beagle1-----plink----: 5.26e-08 -0.001508 5.22e-11 -0.001432 0.000129 ( 0.000118) 0.001560 ( 0.001942) 9.27e-05 0.000524 --->beagle1-----germline1: 6.72e-06 -7.99e-05 1e+00 0.000000 0.000129 ( 0.000118) 0.000203 ( 7.45e-05) 9.27e-05 0.000228 --->beagle1-----germline2: 1e+00 0.000000 1e+00 0.000000 0.000129 ( 0.000118) 0.000198 ( 0.001436) 9.27e-05 0.000000 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.000129 ( 0.000118) 0.000180 ( 0.000408) 9.27e-05 0.000000 --->beagle2-----plink----: 4.34e-10 -0.002079 3.9e-11 -0.001448 0.000112 ( 0.000218) 0.001560 ( 0.001942) 0.000000 0.000524 --->beagle2-----germline1: 1.49e-06 -0.000163 1e+00 0.000000 0.000112 ( 0.000218) 0.000203 ( 7.45e-05) 0.000000 0.000228 --->beagle2-----germline2: 1e+00 0.000000 1e+00 0.000000 0.000112 ( 0.000218) 0.000198 ( 0.001436) 0.000000 0.000000 --->beagle2-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.000112 ( 0.000218) 0.000180 ( 0.000408) 0.000000 0.000000 --->plink-------germline1: 1.44e-05 0.001057 3.62e-10 0.001358 0.001560 ( 0.001942) 0.000203 ( 7.45e-05) 0.000524 0.000228 --->plink-------germline2: 6.66e-08 0.002747 1.75e-07 0.001362 0.001560 ( 0.001942) 0.000198 ( 0.001436) 0.000524 0.000000 --->plink-------dash-----: 1.4e-09 0.002219 2.07e-10 0.001380 0.001560 ( 0.001942) 0.000180 ( 0.000408) 0.000524 0.000000 --->germline1---germline2: 1.88e-15 0.000213 1e+00 0.000000 0.000203 ( 7.45e-05) 0.000198 ( 0.001436) 0.000228 0.000000 --->germline1---dash-----: 2.49e-04 0.000185 1e+00 0.000000 0.000203 ( 7.45e-05) 0.000180 ( 0.000408) 0.000228 0.000000 --->germline2---dash-----: 1e+00 0.000000 1e+00 0.000000 0.000198 ( 0.001436) 0.000180 ( 0.000408) 0.000000 0.000000 ######accuracy###### --->fabia-------beagle1--: 3.96e-18 0.224663 8.31e-117 0.225507 0.999954 ( 6.87e-05) 0.774447 ( 0.015658) 0.999986 0.777270 --->fabia-------beagle2--: 3.96e-18 0.087220 2.42e-98 0.087640 0.999954 ( 6.87e-05) 0.912314 ( 0.009382) 0.999986 0.913126 --->fabia-------plink----: 3.96e-18 0.017084 4.56e-112 0.017094 0.999954 ( 6.87e-05) 0.982860 ( 0.001325) 0.999986 0.982844 --->fabia-------germline1: 3.96e-18 0.777301 2.7e-136 0.777373 0.999954 ( 6.87e-05) 0.222581 ( 0.034279) 0.999986 0.219788 --->fabia-------germline2: 4.08e-18 0.010249 2.54e-58 0.009979 0.999954 ( 6.87e-05) 0.989975 ( 0.002789) 0.999986 0.989578 --->fabia-------dash-----: 3.96e-18 0.125503 5.11e-65 0.126468 0.999954 ( 6.87e-05) 0.873486 ( 0.030024) 0.999986 0.874362 --->beagle1-----beagle2--: 3.96e-18 -0.137475 2.16e-117 -0.137867 0.774447 ( 0.015658) 0.912314 ( 0.009382) 0.777270 0.913126 --->beagle1-----plink----: 3.96e-18 -0.207727 4.45e-113 -0.208413 0.774447 ( 0.015658) 0.982860 ( 0.001325) 0.777270 0.982844 --->beagle1-----germline1: 3.96e-18 0.551166 3.57e-115 0.551866 0.774447 ( 0.015658) 0.222581 ( 0.034279) 0.777270 0.219788 --->beagle1-----germline2: 3.96e-18 -0.214923 2.57e-114 -0.215528 0.774447 ( 0.015658) 0.989975 ( 0.002789) 0.777270 0.989578 --->beagle1-----dash-----: 3.96e-18 -0.101071 1.75e-52 -0.099038 0.774447 ( 0.015658) 0.873486 ( 0.030024) 0.777270 0.874362 --->beagle2-----plink----: 3.96e-18 -0.070180 1.65e-88 -0.070546 0.912314 ( 0.009382) 0.982860 ( 0.001325) 0.913126 0.982844 --->beagle2-----germline1: 3.96e-18 0.689770 5.81e-128 0.689733 0.912314 ( 0.009382) 0.222581 ( 0.034279) 0.913126 0.219788 --->beagle2-----germline2: 3.96e-18 -0.077416 7.99e-92 -0.077661 0.912314 ( 0.009382) 0.989975 ( 0.002789) 0.913126 0.989578 --->beagle2-----dash-----: 1.77e-16 0.037304 2.99e-22 0.038829 0.912314 ( 0.009382) 0.873486 ( 0.030024) 0.913126 0.874362 --->plink-------germline1: 3.96e-18 0.760140 2.82e-135 0.760279 0.982860 ( 0.001325) 0.222581 ( 0.034279) 0.982844 0.219788 --->plink-------germline2: 4.04e-17 -0.006924 2.31e-42 -0.007115 0.982860 ( 0.001325) 0.989975 ( 0.002789) 0.982844 0.989578 --->plink-------dash-----: 3.96e-18 0.108230 1.96e-59 0.109375 0.982860 ( 0.001325) 0.873486 ( 0.030024) 0.982844 0.874362 --->germline1---germline2: 3.96e-18 -0.767339 2.22e-136 -0.767394 0.222581 ( 0.034279) 0.989975 ( 0.002789) 0.219788 0.989578 --->germline1---dash-----: 3.96e-18 -0.651854 4.74e-108 -0.650904 0.222581 ( 0.034279) 0.873486 ( 0.030024) 0.219788 0.874362 --->germline2---dash-----: 3.96e-18 0.115135 4.71e-61 0.116489 0.989975 ( 0.002789) 0.873486 ( 0.030024) 0.989578 0.874362 ######FPR###### --->fabia-------beagle1--: 3.96e-18 -0.224572 8.45e-117 -0.225464 2.42e-05 ( 6.41e-05) 0.225488 ( 0.015659) 0.000000 0.222679 --->fabia-------beagle2--: 3.96e-18 -0.087136 2.51e-98 -0.087573 2.42e-05 ( 6.41e-05) 0.087598 ( 0.009382) 0.000000 0.086781 --->fabia-------plink----: 3.96e-18 -0.017024 7.87e-112 -0.017029 2.42e-05 ( 6.41e-05) 0.017053 ( 0.001327) 0.000000 0.017070 --->fabia-------germline1: 3.96e-18 -0.777399 2.73e-136 -0.777450 2.42e-05 ( 6.41e-05) 0.777475 ( 0.034286) 0.000000 0.780285 --->fabia-------germline2: 5.96e-18 -0.010206 4.81e-58 -0.009900 2.42e-05 ( 6.41e-05) 0.009925 ( 0.002789) 0.000000 0.010320 --->fabia-------dash-----: 3.96e-18 -0.125418 5.41e-65 -0.126412 2.42e-05 ( 6.41e-05) 0.126437 ( 0.030027) 0.000000 0.125573 --->beagle1-----beagle2--: 3.96e-18 0.137492 2.15e-117 0.137891 0.225488 ( 0.015659) 0.087598 ( 0.009382) 0.222679 0.086781 --->beagle1-----plink----: 3.96e-18 0.207754 4.42e-113 0.208435 0.225488 ( 0.015659) 0.017053 ( 0.001327) 0.222679 0.017070 --->beagle1-----germline1: 3.96e-18 -0.551271 3.56e-115 -0.551987 0.225488 ( 0.015659) 0.777475 ( 0.034286) 0.222679 0.780285 --->beagle1-----germline2: 3.96e-18 0.214995 2.56e-114 0.215563 0.225488 ( 0.015659) 0.009925 ( 0.002789) 0.222679 0.010320 --->beagle1-----dash-----: 3.96e-18 0.101096 1.75e-52 0.099051 0.225488 ( 0.015659) 0.126437 ( 0.030027) 0.222679 0.125573 --->beagle2-----plink----: 3.96e-18 0.070175 1.68e-88 0.070545 0.087598 ( 0.009382) 0.017053 ( 0.001327) 0.086781 0.017070 --->beagle2-----germline1: 3.96e-18 -0.689947 5.8e-128 -0.689877 0.087598 ( 0.009382) 0.777475 ( 0.034286) 0.086781 0.780285 --->beagle2-----germline2: 3.96e-18 0.077473 7.99e-92 0.077673 0.087598 ( 0.009382) 0.009925 ( 0.002789) 0.086781 0.010320 --->beagle2-----dash-----: 1.77e-16 -0.037281 2.98e-22 -0.038839 0.087598 ( 0.009382) 0.126437 ( 0.030027) 0.086781 0.125573 --->plink-------germline1: 3.96e-18 -0.760295 2.82e-135 -0.760422 0.017053 ( 0.001327) 0.777475 ( 0.034286) 0.017070 0.780285 --->plink-------germline2: 4.04e-17 0.006932 1.95e-42 0.007128 0.017053 ( 0.001327) 0.009925 ( 0.002789) 0.017070 0.010320 --->plink-------dash-----: 3.96e-18 -0.108258 1.99e-59 -0.109384 0.017053 ( 0.001327) 0.126437 ( 0.030027) 0.017070 0.125573 --->germline1---germline2: 3.96e-18 0.767464 2.23e-136 0.767550 0.777475 ( 0.034286) 0.009925 ( 0.002789) 0.780285 0.010320 --->germline1---dash-----: 3.96e-18 0.652011 4.71e-108 0.651038 0.777475 ( 0.034286) 0.126437 ( 0.030027) 0.780285 0.125573 --->germline2---dash-----: 3.96e-18 -0.115156 4.71e-61 -0.116512 0.009925 ( 0.002789) 0.126437 ( 0.030027) 0.010320 0.125573 ######FDR###### --->fabia-------beagle1--: 6.88e-18 -0.999883 8.47e-51 -0.880537 0.119399 ( 0.298848) 0.999936 ( 5.9e-05) 0.000000 0.999954 --->fabia-------beagle2--: 2.4e-18 -0.999904 8.44e-51 -0.880545 0.119399 ( 0.298848) 0.999944 ( 0.000109) 0.000000 1.000000 --->fabia-------plink----: 5.66e-18 -0.998926 9.31e-51 -0.879816 0.119399 ( 0.298848) 0.999215 ( 0.000977) 0.000000 0.999736 --->fabia-------germline1: 6.22e-18 -0.999878 8.51e-51 -0.880500 0.119399 ( 0.298848) 0.999899 ( 3.73e-05) 0.000000 0.999886 --->fabia-------germline2: 8.93e-20 -1.000000 3.04e-44 -0.860500 0.119399 ( 0.298848) 0.979899 ( 0.140693) 0.000000 1.000000 --->fabia-------dash-----: 8.19e-19 -0.999917 8.48e-51 -0.880511 0.119399 ( 0.298848) 0.999910 ( 0.000204) 0.000000 1.000000 --->beagle1-----beagle2--: 1e+00 0.000000 1e+00 0.000000 0.999936 ( 5.9e-05) 0.999944 ( 0.000109) 0.999954 1.000000 --->beagle1-----plink----: 5.26e-08 0.000735 5.16e-11 0.000721 0.999936 ( 5.9e-05) 0.999215 ( 0.000977) 0.999954 0.999736 --->beagle1-----germline1: 1e+00 0.000000 1e+00 0.000000 0.999936 ( 5.9e-05) 0.999899 ( 3.73e-05) 0.999954 0.999886 --->beagle1-----germline2: 1e+00 0.000000 1.58e-01 0.020037 0.999936 ( 5.9e-05) 0.979899 ( 0.140693) 0.999954 1.000000 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.999936 ( 5.9e-05) 0.999910 ( 0.000204) 0.999954 1.000000 --->beagle2-----plink----: 4.34e-10 0.001063 3.86e-11 0.000729 0.999944 ( 0.000109) 0.999215 ( 0.000977) 1.000000 0.999736 --->beagle2-----germline1: 1.52e-06 7.76e-05 1e+00 0.000000 0.999944 ( 0.000109) 0.999899 ( 3.73e-05) 1.000000 0.999886 --->beagle2-----germline2: 1e+00 0.000000 1.57e-01 0.020045 0.999944 ( 0.000109) 0.979899 ( 0.140693) 1.000000 1.000000 --->beagle2-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.999944 ( 0.000109) 0.999910 ( 0.000204) 1.000000 1.000000 --->plink-------germline1: 1.44e-05 -0.000577 3.53e-10 -0.000684 0.999215 ( 0.000977) 0.999899 ( 3.73e-05) 0.999736 0.999886 --->plink-------germline2: 4.64e-06 -0.001349 1.73e-01 0.019316 0.999215 ( 0.000977) 0.979899 ( 0.140693) 0.999736 1.000000 --->plink-------dash-----: 1.37e-09 -0.001103 2.03e-10 -0.000695 0.999215 ( 0.000977) 0.999910 ( 0.000204) 0.999736 1.000000 --->germline1---germline2: 3.45e-13 -9.5e-05 1.58e-01 0.020000 0.999899 ( 3.73e-05) 0.979899 ( 0.140693) 0.999886 1.000000 --->germline1---dash-----: 2.54e-04 -9.61e-05 1e+00 0.000000 0.999899 ( 3.73e-05) 0.999910 ( 0.000204) 0.999886 1.000000 --->germline2---dash-----: 1e+00 0.000000 1.58e-01 -0.020011 0.979899 ( 0.140693) 0.999910 ( 0.000204) 1.000000 1.000000 ######specifity###### --->fabia-------beagle1--: 3.96e-18 0.224614 8.45e-117 0.225464 0.999976 ( 6.41e-05) 0.774512 ( 0.015659) 1.000000 0.777321 --->fabia-------beagle2--: 3.96e-18 0.087157 2.51e-98 0.087573 0.999976 ( 6.41e-05) 0.912402 ( 0.009382) 1.000000 0.913219 --->fabia-------plink----: 3.96e-18 0.017024 7.87e-112 0.017029 0.999976 ( 6.41e-05) 0.982947 ( 0.001327) 1.000000 0.982930 --->fabia-------germline1: 3.96e-18 0.777377 2.73e-136 0.777450 0.999976 ( 6.41e-05) 0.222525 ( 0.034286) 1.000000 0.219715 --->fabia-------germline2: 5.96e-18 0.010204 4.81e-58 0.009900 0.999976 ( 6.41e-05) 0.990075 ( 0.002789) 1.000000 0.989680 --->fabia-------dash-----: 3.96e-18 0.125425 5.41e-65 0.126412 0.999976 ( 6.41e-05) 0.873563 ( 0.030027) 1.000000 0.874427 --->beagle1-----beagle2--: 3.96e-18 -0.137493 2.15e-117 -0.137890 0.774512 ( 0.015659) 0.912402 ( 0.009382) 0.777321 0.913219 --->beagle1-----plink----: 3.96e-18 -0.207748 4.42e-113 -0.208435 0.774512 ( 0.015659) 0.982947 ( 0.001327) 0.777321 0.982930 --->beagle1-----germline1: 3.96e-18 0.551289 3.56e-115 0.551987 0.774512 ( 0.015659) 0.222525 ( 0.034286) 0.777321 0.219715 --->beagle1-----germline2: 3.96e-18 -0.215004 2.56e-114 -0.215563 0.774512 ( 0.015659) 0.990075 ( 0.002789) 0.777321 0.989680 --->beagle1-----dash-----: 3.96e-18 -0.101075 1.75e-52 -0.099051 0.774512 ( 0.015659) 0.873563 ( 0.030027) 0.777321 0.874427 --->beagle2-----plink----: 3.96e-18 -0.070178 1.68e-88 -0.070545 0.912402 ( 0.009382) 0.982947 ( 0.001327) 0.913219 0.982930 --->beagle2-----germline1: 3.96e-18 0.689931 5.8e-128 0.689877 0.912402 ( 0.009382) 0.222525 ( 0.034286) 0.913219 0.219715 --->beagle2-----germline2: 3.96e-18 -0.077426 7.99e-92 -0.077673 0.912402 ( 0.009382) 0.990075 ( 0.002789) 0.913219 0.989680 --->beagle2-----dash-----: 1.77e-16 0.037285 2.98e-22 0.038839 0.912402 ( 0.009382) 0.873563 ( 0.030027) 0.913219 0.874427 --->plink-------germline1: 3.96e-18 0.760293 2.82e-135 0.760422 0.982947 ( 0.001327) 0.222525 ( 0.034286) 0.982930 0.219715 --->plink-------germline2: 4.04e-17 -0.006937 1.95e-42 -0.007128 0.982947 ( 0.001327) 0.990075 ( 0.002789) 0.982930 0.989680 --->plink-------dash-----: 3.96e-18 0.108265 1.99e-59 0.109384 0.982947 ( 0.001327) 0.873563 ( 0.030027) 0.982930 0.874427 --->germline1---germline2: 3.96e-18 -0.767457 2.23e-136 -0.767550 0.222525 ( 0.034286) 0.990075 ( 0.002789) 0.219715 0.989680 --->germline1---dash-----: 3.96e-18 -0.652018 4.71e-108 -0.651038 0.222525 ( 0.034286) 0.873563 ( 0.030027) 0.219715 0.874427 --->germline2---dash-----: 3.96e-18 0.115139 4.71e-61 0.116512 0.990075 ( 0.002789) 0.873563 ( 0.030027) 0.989680 0.874427 ######sensitivity###### --->fabia-------beagle1--: 3.86e-12 0.481887 9.15e-17 0.434056 0.576005 ( 0.422162) 0.141949 ( 0.128287) 0.827728 0.100000 --->fabia-------beagle2--: 3.53e-13 0.785460 1.03e-21 0.528462 0.576005 ( 0.422162) 0.047543 ( 0.089822) 0.827728 0.000000 --->fabia-------plink----: 2.3e-12 0.662441 5.75e-15 0.442332 0.576005 ( 0.422162) 0.133673 ( 0.164829) 0.827728 0.044006 --->fabia-------germline1: 1.94e-04 -0.164512 1.08e-04 -0.199340 0.576005 ( 0.422162) 0.775346 ( 0.278712) 0.827728 0.918062 --->fabia-------germline2: 1.2e-12 0.874169 5.99e-24 0.567871 0.576005 ( 0.422162) 0.008134 ( 0.071531) 0.827728 0.000000 --->fabia-------dash-----: 8.02e-11 0.788622 5.02e-15 0.468134 0.576005 ( 0.422162) 0.107872 ( 0.251027) 0.827728 0.000000 --->beagle1-----beagle2--: 2.25e-11 0.150016 4.67e-14 0.094406 0.141949 ( 0.128287) 0.047543 ( 0.089822) 0.100000 0.000000 --->beagle1-----plink----: 4.1e-01 0.017256 6.88e-01 0.008276 0.141949 ( 0.128287) 0.133673 ( 0.164829) 0.100000 0.044006 --->beagle1-----germline1: 2.99e-17 -0.689322 7.52e-35 -0.633397 0.141949 ( 0.128287) 0.775346 ( 0.278712) 0.100000 0.918062 --->beagle1-----germline2: 1.7e-12 0.193600 1.94e-14 0.133815 0.141949 ( 0.128287) 0.008134 ( 0.071531) 0.100000 0.000000 --->beagle1-----dash-----: 1.28e-02 0.100040 2.39e-01 0.034077 0.141949 ( 0.128287) 0.107872 ( 0.251027) 0.100000 0.000000 --->beagle2-----plink----: 1.94e-05 -0.136127 1e-05 -0.086130 0.047543 ( 0.089822) 0.133673 ( 0.164829) 0.000000 0.044006 --->beagle2-----germline1: 6.01e-18 -0.789124 3.18e-42 -0.727803 0.047543 ( 0.089822) 0.775346 ( 0.278712) 0.000000 0.918062 --->beagle2-----germline2: 1e+00 0.000000 1.2e-03 0.039409 0.047543 ( 0.089822) 0.008134 ( 0.071531) 0.000000 0.000000 --->beagle2-----dash-----: 1e+00 0.000000 3.05e-02 -0.060329 0.047543 ( 0.089822) 0.107872 ( 0.251027) 0.000000 0.000000 --->plink-------germline1: 2.15e-17 -0.676030 5.91e-35 -0.641672 0.133673 ( 0.164829) 0.775346 ( 0.278712) 0.044006 0.918062 --->plink-------germline2: 5.39e-09 0.238608 2.87e-10 0.125539 0.133673 ( 0.164829) 0.008134 ( 0.071531) 0.044006 0.000000 --->plink-------dash-----: 1.59e-02 0.130657 3.73e-01 0.025802 0.133673 ( 0.164829) 0.107872 ( 0.251027) 0.044006 0.000000 --->germline1---germline2: 7.51e-18 0.852042 1.28e-46 0.767212 0.775346 ( 0.278712) 0.008134 ( 0.071531) 0.918062 0.000000 --->germline1---dash-----: 7.76e-16 0.725444 5.98e-28 0.667474 0.775346 ( 0.278712) 0.107872 ( 0.251027) 0.918062 0.000000 --->germline2---dash-----: 1e+00 0.000000 2.76e-04 -0.099738 0.008134 ( 0.071531) 0.107872 ( 0.251027) 0.000000 0.000000 ######trueN###### --->fabia-------beagle1--: 3.96e-18 12245395 1.78e-189 12254166 2e+07 ( 1289) 7744330 ( 156574) 2e+07 7772482 --->fabia-------beagle2--: 3.96e-18 10871112 2.05e-206 10875401 2e+07 ( 1289) 9123094 ( 93827) 2e+07 9131214 --->fabia-------plink----: 3.96e-18 10169993 2.19e-287 10170027 2e+07 ( 1289) 9828468 ( 13257) 2e+07 9828154 --->fabia-------germline1: 3.96e-18 17772811 8.01e-172 17773468 2e+07 ( 1289) 2225027 ( 342828) 2e+07 2196930 --->fabia-------germline2: 3.96e-18 10101434 3.53e-255 10098752 2e+07 ( 1289) 9899743 ( 27892) 2e+07 9895784 --->fabia-------dash-----: 3.96e-18 11253890 6.88e-158 11263752 2e+07 ( 1289) 8734743 ( 3e+05) 2e+07 8743353 --->beagle1-----beagle2--: 3.96e-18 -1374882 2.15e-117 -1378764 7744330 ( 156574) 9123094 ( 93827) 7772482 9131214 --->beagle1-----plink----: 3.96e-18 -2077151 4.41e-113 -2084139 7744330 ( 156574) 9828468 ( 13257) 7772482 9828154 --->beagle1-----germline1: 3.96e-18 5512225 3.56e-115 5519302 7744330 ( 156574) 2225027 ( 342828) 7772482 2196930 --->beagle1-----germline2: 3.96e-18 -2149500 2.56e-114 -2155414 7744330 ( 156574) 9899743 ( 27892) 7772482 9895784 --->beagle1-----dash-----: 3.96e-18 -1010915 1.75e-52 -990414 7744330 ( 156574) 8734743 ( 3e+05) 7772482 8743353 --->beagle2-----plink----: 3.96e-18 -701931 1.68e-88 -705374 9123094 ( 93827) 9828468 ( 13257) 9131214 9828154 --->beagle2-----germline1: 3.96e-18 6898525 5.81e-128 6898067 9123094 ( 93827) 2225027 ( 342828) 9131214 2196930 --->beagle2-----germline2: 3.96e-18 -774483 7.98e-92 -776649 9123094 ( 93827) 9899743 ( 27892) 9131214 9895784 --->beagle2-----dash-----: 1.77e-16 373033 2.98e-22 388351 9123094 ( 93827) 8734743 ( 3e+05) 9131214 8743353 --->plink-------germline1: 3.96e-18 7601877 2.83e-135 7603441 9828468 ( 13257) 2225027 ( 342828) 9828154 2196930 --->plink-------germline2: 4.04e-17 -69460 1.95e-42 -71275 9828468 ( 13257) 9899743 ( 27892) 9828154 9895784 --->plink-------dash-----: 3.96e-18 1082490 1.98e-59 1093725 9828468 ( 13257) 8734743 ( 3e+05) 9828154 8743353 --->germline1---germline2: 3.96e-18 -7673877 2.23e-136 -7674716 2225027 ( 342828) 9899743 ( 27892) 2196930 9895784 --->germline1---dash-----: 3.96e-18 -6519390 4.72e-108 -6509716 2225027 ( 342828) 8734743 ( 3e+05) 2196930 8743353 --->germline2---dash-----: 3.96e-18 1151579 4.7e-61 1165000 9899743 ( 27892) 8734743 ( 3e+05) 9895784 8743353 ######falseP###### --->fabia-------beagle1--: 3.96e-18 -2245420 8.85e-117 -2254166 484 ( 1282) 2254650 ( 156572) 0 2226578 --->fabia-------beagle2--: 3.96e-18 -871112 2.53e-98 -875401 484 ( 1282) 875886 ( 93809) 0 867720 --->fabia-------plink----: 3.96e-18 -169993 1.3e-111 -170027 484 ( 1282) 170512 ( 13269) 0 170676 --->fabia-------germline1: 3.96e-18 -7772799 2.67e-136 -7773468 484 ( 1282) 7773953 ( 342830) 0 7802070 --->fabia-------germline2: 5.96e-18 -101652 7.58e-58 -98752 484 ( 1282) 99237 ( 27884) 0 103190 --->fabia-------dash-----: 3.96e-18 -1253897 5.58e-65 -1263752 484 ( 1282) 1264236 ( 3e+05) 0 1255602 --->beagle1-----beagle2--: 3.96e-18 1374891 2.15e-117 1378764 2254650 ( 156572) 875886 ( 93809) 2226578 867720 --->beagle1-----plink----: 3.96e-18 2077150 4.41e-113 2084139 2254650 ( 156572) 170512 ( 13269) 2226578 170676 --->beagle1-----germline1: 3.96e-18 -5512248 3.56e-115 -5519302 2254650 ( 156572) 7773953 ( 342830) 2226578 7802070 --->beagle1-----germline2: 3.96e-18 2149517 2.56e-114 2155414 2254650 ( 156572) 99237 ( 27884) 2226578 103190 --->beagle1-----dash-----: 3.96e-18 1010911 1.75e-52 990414 2254650 ( 156572) 1264236 ( 3e+05) 2226578 1255602 --->beagle2-----plink----: 3.96e-18 701932 1.68e-88 705374 875886 ( 93809) 170512 ( 13269) 867720 170676 --->beagle2-----germline1: 3.96e-18 -6898511 5.81e-128 -6898067 875886 ( 93809) 7773953 ( 342830) 867720 7802070 --->beagle2-----germline2: 3.96e-18 774486 7.98e-92 776649 875886 ( 93809) 99237 ( 27884) 867720 103190 --->beagle2-----dash-----: 1.77e-16 -373033 2.98e-22 -388351 875886 ( 93809) 1264236 ( 3e+05) 867720 1255602 --->plink-------germline1: 3.96e-18 -7601874 2.83e-135 -7603441 170512 ( 13269) 7773953 ( 342830) 170676 7802070 --->plink-------germline2: 4.04e-17 69457 1.95e-42 71275 170512 ( 13269) 99237 ( 27884) 170676 103190 --->plink-------dash-----: 3.96e-18 -1082483 1.98e-59 -1093725 170512 ( 13269) 1264236 ( 3e+05) 170676 1255602 --->germline1---germline2: 3.96e-18 7673879 2.23e-136 7674716 7773953 ( 342830) 99237 ( 27884) 7802070 103190 --->germline1---dash-----: 3.96e-18 6519395 4.72e-108 6509716 7773953 ( 342830) 1264236 ( 3e+05) 7802070 1255602 --->germline2---dash-----: 3.96e-18 -1151564 4.7e-61 -1165000 99237 ( 27884) 1264236 ( 3e+05) 103190 1255602 ######falseN###### --->fabia-------beagle1--: 4.35e-12 -491 1.04e-16 -444 432 ( 436) 876 ( 166) 200 891 --->fabia-------beagle2--: 3.41e-13 -795 1.53e-21 -539 432 ( 436) 971 ( 138) 200 1000 --->fabia-------plink----: 1.84e-12 -667 3.89e-15 -455 432 ( 436) 887 ( 205) 200 898 --->fabia-------germline1: 2.07e-04 165 1.34e-04 200 432 ( 436) 232 ( 289) 200 80.5 --->fabia-------germline2: 1.19e-12 -885 8.16e-24 -580 432 ( 436) 1012 ( 135) 200 1030 --->fabia-------dash-----: 4.25e-10 -795 8.93e-15 -475 432 ( 436) 907 ( 274) 200 995 --->beagle1-----beagle2--: 3.57e-11 -153 4.57e-14 -95.1 876 ( 166) 971 ( 138) 891 1000 --->beagle1-----plink----: 4.01e-01 -18 6.13e-01 -10.6 876 ( 166) 887 ( 205) 891 898 --->beagle1-----germline1: 2.75e-17 698 1.14e-34 644 876 ( 166) 232 ( 289) 891 80.5 --->beagle1-----germline2: 2.39e-12 -184 4.85e-14 -136 876 ( 166) 1012 ( 135) 891 1030 --->beagle1-----dash-----: 1.15e-02 -105 3.18e-01 -30.7 876 ( 166) 907 ( 274) 891 995 --->beagle2-----plink----: 2.56e-05 132 1.77e-05 84.5 971 ( 138) 887 ( 205) 1000 898 --->beagle2-----germline1: 6.03e-18 795 6.56e-42 739 971 ( 138) 232 ( 289) 1000 80.5 --->beagle2-----germline2: 3.25e-05 -111 1.39e-03 -40.6 971 ( 138) 1012 ( 135) 1000 1030 --->beagle2-----dash-----: 2.4e-01 63.7 3.09e-02 64.4 971 ( 138) 907 ( 274) 1000 995 --->plink-------germline1: 2.11e-17 692 1.15e-34 654 887 ( 205) 232 ( 289) 898 80.5 --->plink-------germline2: 5.71e-09 -240 3.66e-10 -125 887 ( 205) 1012 ( 135) 898 1030 --->plink-------dash-----: 1.87e-02 -129 5.19e-01 -20.1 887 ( 205) 907 ( 274) 898 995 --->germline1---germline2: 8.45e-18 -845 1.36e-45 -779 232 ( 289) 1012 ( 135) 80.5 1030 --->germline1---dash-----: 2.04e-15 -746 6.54e-27 -674 232 ( 289) 907 ( 274) 80.5 995 --->germline2---dash-----: 1.4e-04 422 3.31e-04 105 1012 ( 135) 907 ( 274) 1030 995 ######trueP###### --->fabia-------beagle1--: 4.35e-12 491 1.04e-16 444 588 ( 433) 144 ( 133) 820 105 --->fabia-------beagle2--: 3.41e-13 795 1.53e-21 539 588 ( 433) 49 ( 94) 820 0 --->fabia-------plink----: 1.84e-12 667 3.89e-15 455 588 ( 433) 134 ( 165) 820 47.5 --->fabia-------germline1: 2.07e-04 -165 1.34e-04 -200 588 ( 433) 788 ( 292) 820 892 --->fabia-------germline2: 1.19e-12 885 8.16e-24 580 588 ( 433) 8.47 ( 74.4) 820 0 --->fabia-------dash-----: 4.25e-10 795 8.93e-15 475 588 ( 433) 113 ( 269) 820 0 --->beagle1-----beagle2--: 3.57e-11 153 4.57e-14 95.1 144 ( 133) 49 ( 94) 105 0 --->beagle1-----plink----: 4.01e-01 18 6.13e-01 10.6 144 ( 133) 134 ( 165) 105 47.5 --->beagle1-----germline1: 2.75e-17 -698 1.14e-34 -644 144 ( 133) 788 ( 292) 105 892 --->beagle1-----germline2: 2.39e-12 184 4.85e-14 136 144 ( 133) 8.47 ( 74.4) 105 0 --->beagle1-----dash-----: 1.15e-02 105 3.18e-01 30.7 144 ( 133) 113 ( 269) 105 0 --->beagle2-----plink----: 2.56e-05 -132 1.77e-05 -84.5 49 ( 94) 134 ( 165) 0 47.5 --->beagle2-----germline1: 6.03e-18 -795 6.56e-42 -739 49 ( 94) 788 ( 292) 0 892 --->beagle2-----germline2: 1e+00 0.000000 1.39e-03 40.580000 49.050000 (93.993593) 8.470000 (74.406399) 0.000000 0.000000 --->beagle2-----dash-----: 1e+00 0.000000 3.09e-02 -64.400000 49.050000 (93.993593) 113.450000 (268.674050) 0.000000 0.000000 --->plink-------germline1: 2.11e-17 -692 1.15e-34 -654 134 ( 165) 788 ( 292) 47.5 892 --->plink-------germline2: 5.71e-09 240 3.66e-10 125 134 ( 165) 8.47 ( 74.4) 47.5 0 --->plink-------dash-----: 1.87e-02 129 5.19e-01 20.1 134 ( 165) 113 ( 269) 47.5 0 --->germline1---germline2: 8.45e-18 845 1.36e-45 779 788 ( 292) 8.47 ( 74.4) 892 0 --->germline1---dash-----: 2.04e-15 746 6.54e-27 674 788 ( 292) 113 ( 269) 892 0 --->germline2---dash-----: 1e+00 0.000000 3.31e-04 -104.980000 8.470000 (74.406399) 113.450000 (268.674050) 0.000000 0.000000 ######MatthewsSnps###### --->fabia-------beagle1--: 1e+00 0.000000 1e+00 0.000000 0.384533 ( 0.260954) 0.000000 ( 0.000000) 0.321873 0.000000 --->fabia-------beagle2--: 9.18e-18 0.347961 1.12e-26 0.384366 0.384533 ( 0.260954) 0.000167 ( 0.001674) 0.321873 0.000000 --->fabia-------plink----: 9.18e-18 0.343587 6.99e-26 0.377269 0.384533 ( 0.260954) 0.007264 ( 0.033317) 0.321873 0.013794 --->fabia-------germline1: 1e-17 0.346045 2.22e-25 0.378970 0.384533 ( 0.260954) 0.005563 ( 0.070973) 0.321873 0.046807 --->fabia-------germline2: 3.73e-16 0.353403 7.7e-24 0.381287 0.384533 ( 0.260954) 0.003246 ( 0.100374) 0.321873 -0.010906 --->fabia-------dash-----: 3.59e-17 0.353617 4.4e-25 0.388222 0.384533 ( 0.260954) -0.003688 ( 0.079844) 0.321873 -0.035987 --->beagle1-----beagle2--: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.000167 ( 0.001674) 0.000000 0.000000 --->beagle1-----plink----: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.007264 ( 0.033317) 0.000000 0.013794 --->beagle1-----germline1: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.005563 ( 0.070973) 0.000000 0.046807 --->beagle1-----germline2: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.003246 ( 0.100374) 0.000000 -0.010906 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) -0.003688 ( 0.079844) 0.000000 -0.035987 --->beagle2-----plink----: 3.11e-11 -0.013805 3.56e-02 -0.007097 0.000167 ( 0.001674) 0.007264 ( 0.033317) 0.000000 0.013794 --->beagle2-----germline1: 1.94e-01 -0.019601 4.5e-01 -0.005396 0.000167 ( 0.001674) 0.005563 ( 0.070973) 0.000000 0.046807 --->beagle2-----germline2: 1.29e-15 0.010853 7.6e-01 -0.003079 0.000167 ( 0.001674) 0.003246 ( 0.100374) 0.000000 -0.010906 --->beagle2-----dash-----: 2.62e-04 0.035071 6.31e-01 0.003856 0.000167 ( 0.001674) -0.003688 ( 0.079844) 0.000000 -0.035987 --->plink-------germline1: 3.35e-01 -0.008782 8.37e-01 0.001701 0.007264 ( 0.033317) 0.005563 ( 0.070973) 0.013794 0.046807 --->plink-------germline2: 2.54e-10 0.024477 7.01e-01 0.004018 0.007264 ( 0.033317) 0.003246 ( 0.100374) 0.013794 -0.010906 --->plink-------dash-----: 3.47e-04 0.043426 1.93e-01 0.010953 0.007264 ( 0.033317) -0.003688 ( 0.079844) 0.013794 -0.035987 --->germline1---germline2: 8.78e-02 0.028874 8.52e-01 0.002317 0.005563 ( 0.070973) 0.003246 ( 0.100374) 0.046807 -0.010906 --->germline1---dash-----: 4.52e-02 0.032059 4.64e-01 0.009251 0.005563 ( 0.070973) -0.003688 ( 0.079844) 0.046807 -0.035987 --->germline2---dash-----: 2.33e-03 0.024579 6.01e-01 0.006935 0.003246 ( 0.100374) -0.003688 ( 0.079844) -0.010906 -0.035987 ######F1Snps###### --->fabia-------beagle1--: 9.18e-18 0.243168 1.65e-18 0.299592 0.319786 ( 0.276453) 0.020193 ( 0.002229) 0.221390 0.020390 --->fabia-------beagle2--: 9.18e-18 0.243157 1.65e-18 0.299587 0.319786 ( 0.276453) 0.020199 ( 0.002224) 0.221390 0.020390 --->fabia-------plink----: 9.18e-18 0.243046 1.72e-18 0.299375 0.319786 ( 0.276453) 0.020411 ( 0.002481) 0.221390 0.020604 --->fabia-------germline1: 1.16e-17 0.244300 1.79e-18 0.299115 0.319786 ( 0.276453) 0.020671 ( 0.007470) 0.221390 0.023643 --->fabia-------germline2: 5.77e-15 0.276963 5.13e-17 0.305985 0.319786 ( 0.276453) 0.013801 ( 0.098959) 0.221390 0.000000 --->fabia-------dash-----: 1.28e-16 0.262303 2.74e-18 0.302383 0.319786 ( 0.276453) 0.017403 ( 0.039156) 0.221390 0.000000 --->beagle1-----beagle2--: 1e+00 0.000000 1e+00 0.000000 0.020193 ( 0.002229) 0.020199 ( 0.002224) 0.020390 0.020390 --->beagle1-----plink----: 9.41e-11 -0.000408 2.77e-02 -0.000218 0.020193 ( 0.002229) 0.020411 ( 0.002481) 0.020390 0.020604 --->beagle1-----germline1: 1.56e-01 -0.001903 5.13e-01 -0.000477 0.020193 ( 0.002229) 0.020671 ( 0.007470) 0.020390 0.023643 --->beagle1-----germline2: 1.27e-15 0.020178 5.2e-01 0.006392 0.020193 ( 0.002229) 0.013801 ( 0.098959) 0.020390 0.000000 --->beagle1-----dash-----: 1.82e-04 0.018635 4.76e-01 0.002791 0.020193 ( 0.002229) 0.017403 ( 0.039156) 0.020390 0.000000 --->beagle2-----plink----: 9.85e-11 -0.000408 3.17e-02 -0.000212 0.020199 ( 0.002224) 0.020411 ( 0.002481) 0.020390 0.020604 --->beagle2-----germline1: 1.7e-01 -0.001884 5.18e-01 -0.000472 0.020199 ( 0.002224) 0.020671 ( 0.007470) 0.020390 0.023643 --->beagle2-----germline2: 1.27e-15 0.020151 5.19e-01 0.006398 0.020199 ( 0.002224) 0.013801 ( 0.098959) 0.020390 0.000000 --->beagle2-----dash-----: 1.79e-04 0.018635 4.75e-01 0.002796 0.020199 ( 0.002224) 0.017403 ( 0.039156) 0.020390 0.000000 --->plink-------germline1: 2.03e-01 -0.001648 7.29e-01 -0.000260 0.020411 ( 0.002481) 0.020671 ( 0.007470) 0.020604 0.023643 --->plink-------germline2: 1.29e-15 0.020403 5.05e-01 0.006610 0.020411 ( 0.002481) 0.013801 ( 0.098959) 0.020604 0.000000 --->plink-------dash-----: 1.24e-04 0.018480 4.41e-01 0.003008 0.020411 ( 0.002481) 0.017403 ( 0.039156) 0.020604 0.000000 --->germline1---germline2: 1.88e-15 0.021875 4.91e-01 0.006870 0.020671 ( 0.007470) 0.013801 ( 0.098959) 0.023643 0.000000 --->germline1---dash-----: 2.26e-04 0.016883 4.42e-01 0.003268 0.020671 ( 0.007470) 0.017403 ( 0.039156) 0.023643 0.000000 --->germline2---dash-----: 1e+00 0.000000 7.41e-01 -0.003602 0.013801 ( 0.098959) 0.017403 ( 0.039156) 0.000000 0.000000 ######accuracySnps###### --->fabia-------beagle1--: 3.95e-18 0.928907 2.95e-128 0.926100 0.936301 ( 0.049325) 0.010201 ( 0.001137) 0.939900 0.010300 --->fabia-------beagle2--: 3.95e-18 0.928560 6.62e-128 0.925804 0.936301 ( 0.049325) 0.010497 ( 0.003065) 0.939900 0.010300 --->fabia-------plink----: 3.96e-18 0.907747 3.21e-124 0.904649 0.936301 ( 0.049325) 0.031652 ( 0.009595) 0.939900 0.031000 --->fabia-------germline1: 3.96e-18 0.724213 9.92e-110 0.721843 0.936301 ( 0.049325) 0.214458 ( 0.034541) 0.939900 0.212850 --->fabia-------germline2: 2.35e-11 -0.039179 2.38e-13 -0.042439 0.936301 ( 0.049325) 0.978740 ( 0.003536) 0.939900 0.978350 --->fabia-------dash-----: 1.25e-14 0.075677 1.25e-20 0.073434 0.936301 ( 0.049325) 0.862867 ( 0.031238) 0.939900 0.862400 --->beagle1-----beagle2--: 1e+00 0.000000 3.2e-01 -0.000296 0.010201 ( 0.001137) 0.010497 ( 0.003065) 0.010300 0.010300 --->beagle1-----plink----: 3.95e-18 -0.020999 1.9e-40 -0.021451 0.010201 ( 0.001137) 0.031652 ( 0.009595) 0.010300 0.031000 --->beagle1-----germline1: 3.96e-18 -0.204321 4.72e-79 -0.204257 0.010201 ( 0.001137) 0.214458 ( 0.034541) 0.010300 0.212850 --->beagle1-----germline2: 3.95e-18 -0.968253 1.51e-237 -0.968539 0.010201 ( 0.001137) 0.978740 ( 0.003536) 0.010300 0.978350 --->beagle1-----dash-----: 3.95e-18 -0.853758 8.18e-144 -0.852666 0.010201 ( 0.001137) 0.862867 ( 0.031238) 0.010300 0.862400 --->beagle2-----plink----: 4.07e-18 -0.020752 8.46e-39 -0.021155 0.010497 ( 0.003065) 0.031652 ( 0.009595) 0.010300 0.031000 --->beagle2-----germline1: 3.96e-18 -0.203964 4.31e-79 -0.203961 0.010497 ( 0.003065) 0.214458 ( 0.034541) 0.010300 0.212850 --->beagle2-----germline2: 3.95e-18 -0.968172 4.92e-229 -0.968243 0.010497 ( 0.003065) 0.978740 ( 0.003536) 0.010300 0.978350 --->beagle2-----dash-----: 3.95e-18 -0.853413 5.91e-144 -0.852370 0.010497 ( 0.003065) 0.862867 ( 0.031238) 0.010300 0.862400 --->plink-------germline1: 3.96e-18 -0.182867 1.35e-71 -0.182806 0.031652 ( 0.009595) 0.214458 ( 0.034541) 0.031000 0.212850 --->plink-------germline2: 3.95e-18 -0.947422 3.54e-198 -0.947088 0.031652 ( 0.009595) 0.978740 ( 0.003536) 0.031000 0.978350 --->plink-------dash-----: 3.96e-18 -0.832419 5.18e-144 -0.831215 0.031652 ( 0.009595) 0.862867 ( 0.031238) 0.031000 0.862400 --->germline1---germline2: 3.96e-18 -0.764470 5.6e-136 -0.764282 0.214458 ( 0.034541) 0.978740 ( 0.003536) 0.212850 0.978350 --->germline1---dash-----: 3.96e-18 -0.649517 8.42e-107 -0.648409 0.214458 ( 0.034541) 0.862867 ( 0.031238) 0.212850 0.862400 --->germline2---dash-----: 3.95e-18 0.115687 1.85e-59 0.115873 0.978740 ( 0.003536) 0.862867 ( 0.031238) 0.978350 0.862400 ######FPRSnps###### --->fabia-------beagle1--: 1e+00 0.000000 1e+00 0.000000 0.061855 ( 0.049735) 1.000000 ( 0.000000) 0.055699 1.000000 --->fabia-------beagle2--: 3.81e-18 -0.940980 5.06e-128 -0.937846 0.061855 ( 0.049735) 0.999701 ( 0.002987) 0.055699 1.000000 --->fabia-------plink----: 3.96e-18 -0.918917 2.82e-124 -0.916362 0.061855 ( 0.049735) 0.978216 ( 0.009706) 0.055699 0.977897 --->fabia-------germline1: 3.96e-18 -0.732166 6.27e-110 -0.729852 0.061855 ( 0.049735) 0.791707 ( 0.034862) 0.055699 0.793412 --->fabia-------germline2: 1.32e-14 0.047275 8.46e-17 0.050531 0.061855 ( 0.049735) 0.011324 ( 0.002794) 0.055699 0.011472 --->fabia-------dash-----: 1.22e-13 -0.070790 2.25e-18 -0.067608 0.061855 ( 0.049735) 0.129463 ( 0.031138) 0.055699 0.129332 --->beagle1-----beagle2--: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 0.999701 ( 0.002987) 1.000000 1.000000 --->beagle1-----plink----: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 0.978216 ( 0.009706) 1.000000 0.977897 --->beagle1-----germline1: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 0.791707 ( 0.034862) 1.000000 0.793412 --->beagle1-----germline2: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 0.011324 ( 0.002794) 1.000000 0.011472 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 0.129463 ( 0.031138) 1.000000 0.129332 --->beagle2-----plink----: 4.08e-18 0.021136 5.9e-39 0.021485 0.999701 ( 0.002987) 0.978216 ( 0.009706) 1.000000 0.977897 --->beagle2-----germline1: 3.96e-18 0.207511 1.55e-79 0.207994 0.999701 ( 0.002987) 0.791707 ( 0.034862) 1.000000 0.793412 --->beagle2-----germline2: 3.96e-18 0.988520 1.9e-237 0.988378 0.999701 ( 0.002987) 0.011324 ( 0.002794) 1.000000 0.011472 --->beagle2-----dash-----: 3.95e-18 0.870760 2.09e-145 0.870238 0.999701 ( 0.002987) 0.129463 ( 0.031138) 1.000000 0.129332 --->plink-------germline1: 3.96e-18 0.186685 5.11e-72 0.186510 0.978216 ( 0.009706) 0.791707 ( 0.034862) 0.977897 0.793412 --->plink-------germline2: 3.96e-18 0.967230 3e-199 0.966893 0.978216 ( 0.009706) 0.011324 ( 0.002794) 0.977897 0.011472 --->plink-------dash-----: 3.96e-18 0.850207 1.64e-145 0.848753 0.978216 ( 0.009706) 0.129463 ( 0.031138) 0.977897 0.129332 --->germline1---germline2: 3.96e-18 0.781288 1.96e-136 0.780383 0.791707 ( 0.034862) 0.011324 ( 0.002794) 0.793412 0.011472 --->germline1---dash-----: 3.96e-18 0.663422 1.25e-107 0.662244 0.791707 ( 0.034862) 0.129463 ( 0.031138) 0.793412 0.129332 --->germline2---dash-----: 3.96e-18 -0.117295 3.86e-60 -0.118140 0.011324 ( 0.002794) 0.129463 ( 0.031138) 0.011472 0.129332 ######FDRSnps###### --->fabia-------beagle1--: 9.18e-18 -0.152259 3.02e-12 -0.271938 0.717861 ( 0.341928) 0.989799 ( 0.001137) 0.872668 0.989700 --->fabia-------beagle2--: 9.18e-18 -0.152259 3.02e-12 -0.271936 0.717861 ( 0.341928) 0.989796 ( 0.001135) 0.872668 0.989700 --->fabia-------plink----: 9.18e-18 -0.152222 3.07e-12 -0.271826 0.717861 ( 0.341928) 0.989687 ( 0.001264) 0.872668 0.989591 --->fabia-------germline1: 1.1e-17 -0.153986 3.14e-12 -0.271669 0.717861 ( 0.341928) 0.989530 ( 0.003788) 0.872668 0.988037 --->fabia-------germline2: 5.73e-15 -0.173862 4.34e-11 -0.268645 0.717861 ( 0.341928) 0.986505 ( 0.095674) 0.872668 1.000000 --->fabia-------dash-----: 1.28e-16 -0.164521 3.46e-12 -0.272694 0.717861 ( 0.341928) 0.990555 ( 0.021227) 0.872668 1.000000 --->beagle1-----beagle2--: 1e+00 0.000000 1e+00 0.000000 0.989799 ( 0.001137) 0.989796 ( 0.001135) 0.989700 0.989700 --->beagle1-----plink----: 8.79e-11 0.000206 2.46e-02 0.000112 0.989799 ( 0.001137) 0.989687 ( 0.001264) 0.989700 0.989591 --->beagle1-----germline1: 1.47e-01 0.000991 4.67e-01 0.000269 0.989799 ( 0.001137) 0.989530 ( 0.003788) 0.989700 0.988037 --->beagle1-----germline2: 1.27e-15 -0.010157 7.31e-01 0.003294 0.989799 ( 0.001137) 0.986505 ( 0.095674) 0.989700 1.000000 --->beagle1-----dash-----: 6.27e-04 -0.009399 7.22e-01 -0.000756 0.989799 ( 0.001137) 0.990555 ( 0.021227) 0.989700 1.000000 --->beagle2-----plink----: 9.2e-11 0.000206 2.83e-02 0.000110 0.989796 ( 0.001135) 0.989687 ( 0.001264) 0.989700 0.989591 --->beagle2-----germline1: 1.65e-01 0.000992 4.72e-01 0.000266 0.989796 ( 0.001135) 0.989530 ( 0.003788) 0.989700 0.988037 --->beagle2-----germline2: 1.27e-15 -0.010163 7.32e-01 0.003291 0.989796 ( 0.001135) 0.986505 ( 0.095674) 0.989700 1.000000 --->beagle2-----dash-----: 6.27e-04 -0.009405 7.21e-01 -0.000758 0.989796 ( 0.001135) 0.990555 ( 0.021227) 0.989700 1.000000 --->plink-------germline1: 1.91e-01 0.000874 6.8e-01 0.000157 0.989687 ( 0.001264) 0.989530 ( 0.003788) 0.989591 0.988037 --->plink-------germline2: 1.29e-15 -0.010305 7.4e-01 0.003181 0.989687 ( 0.001264) 0.986505 ( 0.095674) 0.989591 1.000000 --->plink-------dash-----: 5.32e-04 -0.009323 6.82e-01 -0.000868 0.989687 ( 0.001264) 0.990555 ( 0.021227) 0.989591 1.000000 --->germline1---germline2: 1.88e-15 -0.011092 7.53e-01 0.003025 0.989530 ( 0.003788) 0.986505 ( 0.095674) 0.988037 1.000000 --->germline1---dash-----: 6.04e-04 -0.008529 6.54e-01 -0.001025 0.989530 ( 0.003788) 0.990555 ( 0.021227) 0.988037 1.000000 --->germline2---dash-----: 1e+00 0.000000 6.84e-01 -0.004049 0.986505 ( 0.095674) 0.990555 ( 0.021227) 1.000000 1.000000 ######specifitySnps###### --->fabia-------beagle1--: 1e+00 0.000000 1e+00 0.000000 0.938145 ( 0.049735) 0.000000 ( 0.000000) 0.944301 0.000000 --->fabia-------beagle2--: 3.81e-18 0.940980 5.06e-128 0.937846 0.938145 ( 0.049735) 0.000299 ( 0.002987) 0.944301 0.000000 --->fabia-------plink----: 3.96e-18 0.918884 2.82e-124 0.916362 0.938145 ( 0.049735) 0.021783 ( 0.009706) 0.944301 0.022103 --->fabia-------germline1: 3.96e-18 0.732188 6.27e-110 0.729852 0.938145 ( 0.049735) 0.208293 ( 0.034862) 0.944301 0.206588 --->fabia-------germline2: 1.34e-14 -0.047288 8.46e-17 -0.050531 0.938145 ( 0.049735) 0.988676 ( 0.002794) 0.944301 0.988528 --->fabia-------dash-----: 1.22e-13 0.070756 2.25e-18 0.067608 0.938145 ( 0.049735) 0.870537 ( 0.031138) 0.944301 0.870668 --->beagle1-----beagle2--: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.000299 ( 0.002987) 0.000000 0.000000 --->beagle1-----plink----: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.021783 ( 0.009706) 0.000000 0.022103 --->beagle1-----germline1: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.208293 ( 0.034862) 0.000000 0.206588 --->beagle1-----germline2: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.988676 ( 0.002794) 0.000000 0.988528 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.870537 ( 0.031138) 0.000000 0.870668 --->beagle2-----plink----: 4.08e-18 -0.021130 5.9e-39 -0.021485 0.000299 ( 0.002987) 0.021783 ( 0.009706) 0.000000 0.022103 --->beagle2-----germline1: 3.96e-18 -0.207512 1.55e-79 -0.207994 0.000299 ( 0.002987) 0.208293 ( 0.034862) 0.000000 0.206588 --->beagle2-----germline2: 3.96e-18 -0.988527 1.9e-237 -0.988378 0.000299 ( 0.002987) 0.988676 ( 0.002794) 0.000000 0.988528 --->beagle2-----dash-----: 3.95e-18 -0.870749 2.09e-145 -0.870238 0.000299 ( 0.002987) 0.870537 ( 0.031138) 0.000000 0.870668 --->plink-------germline1: 3.96e-18 -0.186716 5.11e-72 -0.186510 0.021783 ( 0.009706) 0.208293 ( 0.034862) 0.022103 0.206588 --->plink-------germline2: 3.96e-18 -0.967210 3e-199 -0.966893 0.021783 ( 0.009706) 0.988676 ( 0.002794) 0.022103 0.988528 --->plink-------dash-----: 3.96e-18 -0.850208 1.64e-145 -0.848753 0.021783 ( 0.009706) 0.870537 ( 0.031138) 0.022103 0.870668 --->germline1---germline2: 3.96e-18 -0.781286 1.96e-136 -0.780383 0.208293 ( 0.034862) 0.988676 ( 0.002794) 0.206588 0.988528 --->germline1---dash-----: 3.96e-18 -0.663451 1.25e-107 -0.662244 0.208293 ( 0.034862) 0.870537 ( 0.031138) 0.206588 0.870668 --->germline2---dash-----: 3.96e-18 0.117306 3.86e-60 0.118140 0.988676 ( 0.002794) 0.870537 ( 0.031138) 0.988528 0.870668 ######sensitivitySnps###### --->fabia-------beagle1--: 1e+00 0.000000 1e+00 0.000000 0.767301 ( 0.268710) 1.000000 ( 0.000000) 0.859254 1.000000 --->fabia-------beagle2--: 1e+00 0.000000 1e+00 0.000000 0.767301 ( 0.268710) 1.000000 ( 0.000000) 0.859254 1.000000 --->fabia-------plink----: 1.85e-15 -0.184595 1.33e-12 -0.221525 0.767301 ( 0.268710) 0.988826 ( 0.046931) 0.859254 1.000000 --->fabia-------germline1: 1.06e-01 -0.064860 2.02e-01 -0.047986 0.767301 ( 0.268710) 0.815287 ( 0.284086) 0.859254 1.000000 --->fabia-------germline2: 8.19e-17 0.841586 2.9e-47 0.753024 0.767301 ( 0.268710) 0.014277 ( 0.104007) 0.859254 0.000000 --->fabia-------dash-----: 3.21e-15 0.770292 2.02e-30 0.652859 0.767301 ( 0.268710) 0.114441 ( 0.262315) 0.859254 0.000000 --->beagle1-----beagle2--: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 1.000000 ( 0.000000) 1.000000 1.000000 --->beagle1-----plink----: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 0.988826 ( 0.046931) 1.000000 1.000000 --->beagle1-----germline1: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 0.815287 ( 0.284086) 1.000000 1.000000 --->beagle1-----germline2: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 0.014277 ( 0.104007) 1.000000 0.000000 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 0.114441 ( 0.262315) 1.000000 0.000000 --->beagle2-----plink----: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 0.988826 ( 0.046931) 1.000000 1.000000 --->beagle2-----germline1: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 0.815287 ( 0.284086) 1.000000 1.000000 --->beagle2-----germline2: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 0.014277 ( 0.104007) 1.000000 0.000000 --->beagle2-----dash-----: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 0.114441 ( 0.262315) 1.000000 0.000000 --->plink-------germline1: 1e+00 0.000000 5.51e-08 0.173539 0.988826 ( 0.046931) 0.815287 ( 0.284086) 1.000000 1.000000 --->plink-------germline2: 1.32e-21 1.000000 4.47e-95 0.974549 0.988826 ( 0.046931) 0.014277 ( 0.104007) 1.000000 0.000000 --->plink-------dash-----: 2.52e-19 0.994974 1e-55 0.874384 0.988826 ( 0.046931) 0.114441 ( 0.262315) 1.000000 0.000000 --->germline1---germline2: 1.25e-18 0.886850 2.04e-46 0.801010 0.815287 ( 0.284086) 0.014277 ( 0.104007) 1.000000 0.000000 --->germline1---dash-----: 2.33e-16 0.761963 4.17e-28 0.700846 0.815287 ( 0.284086) 0.114441 ( 0.262315) 1.000000 0.000000 --->germline2---dash-----: 1e+00 0.000000 7.51e-04 -0.100165 0.014277 ( 0.104007) 0.114441 ( 0.262315) 0.000000 0.000000 ######trueNSnps###### --->fabia-------beagle1--: 1e+00 0 1e+00 0 9286 ( 491) 0 ( 0) 9342 0 --->fabia-------beagle2--: 3.96e-18 9313 4.15e-128 9283 9286 ( 491) 2.96 ( 29.6) 9342 0 --->fabia-------plink----: 3.96e-18 9098 2.37e-124 9070 9286 ( 491) 216 ( 96.1) 9342 219 --->fabia-------germline1: 3.96e-18 7248 5.73e-110 7224 9286 ( 491) 2062 ( 345) 9342 2044 --->fabia-------germline2: 1.3e-14 -468 8.54e-17 -500 9286 ( 491) 9786 ( 30) 9342 9784 --->fabia-------dash-----: 1.21e-13 700 2.26e-18 669 9286 ( 491) 8617 ( 311) 9342 8617 --->beagle1-----beagle2--: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 2.960000 (29.600000) 0.000000 0.000000 --->beagle1-----plink----: 1e+00 0 1e+00 0 0 ( 0) 216 ( 96.1) 0 219 --->beagle1-----germline1: 1e+00 0 1e+00 0 0 ( 0) 2062 ( 345) 0 2044 --->beagle1-----germline2: 1e+00 0 1e+00 0 0 ( 0) 9786 ( 30) 0 9784 --->beagle1-----dash-----: 1e+00 0 1e+00 0 0 ( 0) 8617 ( 311) 0 8617 --->beagle2-----plink----: 4.07e-18 -209 5.92e-39 -213 2.96 ( 29.6) 216 ( 96.1) 0 219 --->beagle2-----germline1: 3.96e-18 -2054 1.55e-79 -2059 2.96 ( 29.6) 2062 ( 345) 0 2044 --->beagle2-----germline2: 3.93e-18 -9784 1.59e-236 -9783 2.96 ( 29.6) 9786 ( 30) 0 9784 --->beagle2-----dash-----: 3.95e-18 -8623 4.57e-145 -8614 2.96 ( 29.6) 8617 ( 311) 0 8617 --->plink-------germline1: 3.96e-18 -1848 5.09e-72 -1846 216 ( 96.1) 2062 ( 345) 219 2044 --->plink-------germline2: 3.95e-18 -9574 2.87e-199 -9570 216 ( 96.1) 9786 ( 30) 219 9784 --->plink-------dash-----: 3.96e-18 -8414 3.54e-145 -8401 216 ( 96.1) 8617 ( 311) 219 8617 --->germline1---germline2: 3.95e-18 -7732 2.09e-136 -7724 2062 ( 345) 9786 ( 30) 2044 9784 --->germline1---dash-----: 3.96e-18 -6568 1.5e-107 -6555 2062 ( 345) 8617 ( 311) 2044 8617 --->germline2---dash-----: 3.95e-18 1161 3.51e-60 1169 9786 ( 30) 8617 ( 311) 9784 8617 ######falsePSnps###### --->fabia-------beagle1--: 3.96e-18 -9316 1.82e-128 -9286 612 ( 492) 9898 ( 11.4) 551 9897 --->fabia-------beagle2--: 3.96e-18 -9313 4.15e-128 -9283 612 ( 492) 9895 ( 30.7) 551 9897 --->fabia-------plink----: 3.96e-18 -9098 2.37e-124 -9070 612 ( 492) 9682 ( 96) 551 9689 --->fabia-------germline1: 3.96e-18 -7248 5.73e-110 -7224 612 ( 492) 7836 ( 345) 551 7852 --->fabia-------germline2: 1.3e-14 468 8.54e-17 500 612 ( 492) 112 ( 27.7) 551 114 --->fabia-------dash-----: 1.21e-13 -700 2.26e-18 -669 612 ( 492) 1281 ( 308) 551 1280 --->beagle1-----beagle2--: 1e+00 0 3.2e-01 2.96 9898 ( 11.4) 9895 ( 30.7) 9897 9897 --->beagle1-----plink----: 3.95e-18 212 1.3e-40 216 9898 ( 11.4) 9682 ( 96) 9897 9689 --->beagle1-----germline1: 3.96e-18 2058 1.78e-79 2062 9898 ( 11.4) 7836 ( 345) 9897 7852 --->beagle1-----germline2: 3.93e-18 9785 7.79e-251 9786 9898 ( 11.4) 112 ( 27.7) 9897 114 --->beagle1-----dash-----: 3.95e-18 8625 6.42e-145 8617 9898 ( 11.4) 1281 ( 308) 9897 1280 --->beagle2-----plink----: 4.07e-18 209 5.92e-39 213 9895 ( 30.7) 9682 ( 96) 9897 9689 --->beagle2-----germline1: 3.96e-18 2054 1.55e-79 2059 9895 ( 30.7) 7836 ( 345) 9897 7852 --->beagle2-----germline2: 3.93e-18 9784 1.59e-236 9783 9895 ( 30.7) 112 ( 27.7) 9897 114 --->beagle2-----dash-----: 3.95e-18 8623 4.57e-145 8614 9895 ( 30.7) 1281 ( 308) 9897 1280 --->plink-------germline1: 3.96e-18 1848 5.09e-72 1846 9682 ( 96) 7836 ( 345) 9689 7852 --->plink-------germline2: 3.95e-18 9574 2.87e-199 9570 9682 ( 96) 112 ( 27.7) 9689 114 --->plink-------dash-----: 3.96e-18 8414 3.54e-145 8401 9682 ( 96) 1281 ( 308) 9689 1280 --->germline1---germline2: 3.95e-18 7732 2.09e-136 7724 7836 ( 345) 112 ( 27.7) 7852 114 --->germline1---dash-----: 3.96e-18 6568 1.5e-107 6555 7836 ( 345) 1281 ( 308) 7852 1280 --->germline2---dash-----: 3.95e-18 -1161 3.51e-60 -1169 112 ( 27.7) 1281 ( 308) 114 1280 ######falseNSnps###### --->fabia-------beagle1--: 1e+00 0 1e+00 0 24.7 ( 30.9) 0 ( 0) 13 0 --->fabia-------beagle2--: 1e+00 0 1e+00 0 24.7 ( 30.9) 0 ( 0) 13 0 --->fabia-------plink----: 2.06e-15 19 2.46e-11 23.6 24.7 ( 30.9) 1.11 ( 4.8) 13 0 --->fabia-------germline1: 9.37e-02 7 1.65e-01 5.58 24.7 ( 30.9) 19.1 ( 29.4) 13 0 --->fabia-------germline2: 8.22e-17 -84.5 7.75e-46 -75.8 24.7 ( 30.9) 101 ( 15.5) 13 103 --->fabia-------dash-----: 1.15e-14 -76.5 7.51e-29 -65.3 24.7 ( 30.9) 90 ( 28.5) 13 99.5 --->beagle1-----beagle2--: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.000000 ( 0.000000) 0.000000 0.000000 --->beagle1-----plink----: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 1.110000 ( 4.796663) 0.000000 0.000000 --->beagle1-----germline1: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 19.110000 (29.449801) 0.000000 0.000000 --->beagle1-----germline2: 1e+00 0 1e+00 0 0 ( 0) 101 ( 15.5) 0 103 --->beagle1-----dash-----: 1e+00 0 1e+00 0 0 ( 0) 90 ( 28.5) 0 99.5 --->beagle2-----plink----: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 1.110000 ( 4.796663) 0.000000 0.000000 --->beagle2-----germline1: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 19.110000 (29.449801) 0.000000 0.000000 --->beagle2-----germline2: 1e+00 0 1e+00 0 0 ( 0) 101 ( 15.5) 0 103 --->beagle2-----dash-----: 1e+00 0 1e+00 0 0 ( 0) 90 ( 28.5) 0 99.5 --->plink-------germline1: 1e+00 0.000000 5.22e-08 -18.000000 1.110000 ( 4.796663) 19.110000 (29.449801) 0.000000 0.000000 --->plink-------germline2: 3.91e-18 -101 1.28e-80 -99.4 1.11 ( 4.8) 101 ( 15.5) 0 103 --->plink-------dash-----: 8.39e-18 -96 5.04e-53 -88.9 1.11 ( 4.8) 90 ( 28.5) 0 99.5 --->germline1---germline2: 1.23e-17 -89 3.74e-45 -81.4 19.1 ( 29.4) 101 ( 15.5) 0 103 --->germline1---dash-----: 2.71e-15 -78 5.17e-27 -70.9 19.1 ( 29.4) 90 ( 28.5) 0 99.5 --->germline2---dash-----: 5.18e-04 44.5 8.52e-04 10.5 101 ( 15.5) 90 ( 28.5) 103 99.5 ######truePSnps###### --->fabia-------beagle1--: 1.76e-16 -20 2.44e-12 -24.7 77.3 ( 28.3) 102 ( 11.4) 87 103 --->fabia-------beagle2--: 1.76e-16 -20 2.44e-12 -24.7 77.3 ( 28.3) 102 ( 11.4) 87 103 --->fabia-------plink----: 2.06e-15 -19 2.46e-11 -23.6 77.3 ( 28.3) 101 ( 12.4) 87 103 --->fabia-------germline1: 9.37e-02 -7 1.65e-01 -5.58 77.3 ( 28.3) 82.9 ( 30) 87 95 --->fabia-------germline2: 8.22e-17 84.5 7.75e-46 75.8 77.3 ( 28.3) 1.49 ( 10.8) 87 0 --->fabia-------dash-----: 1.15e-14 76.5 7.51e-29 65.3 77.3 ( 28.3) 12 ( 28) 87 0 --->beagle1-----beagle2--: 1e+00 0 1e+00 0 102 ( 11.4) 102 ( 11.4) 103 103 --->beagle1-----plink----: 1e+00 0 2.27e-02 1.11 102 ( 11.4) 101 ( 12.4) 103 103 --->beagle1-----germline1: 3.69e-08 48 3.45e-09 19.1 102 ( 11.4) 82.9 ( 30) 103 95 --->beagle1-----germline2: 3.9e-18 102 5.83e-83 101 102 ( 11.4) 1.49 ( 10.8) 103 0 --->beagle1-----dash-----: 8.38e-18 97 1.74e-53 90 102 ( 11.4) 12 ( 28) 103 0 --->beagle2-----plink----: 1e+00 0 2.27e-02 1.11 102 ( 11.4) 101 ( 12.4) 103 103 --->beagle2-----germline1: 3.69e-08 48 3.45e-09 19.1 102 ( 11.4) 82.9 ( 30) 103 95 --->beagle2-----germline2: 3.9e-18 102 5.83e-83 101 102 ( 11.4) 1.49 ( 10.8) 103 0 --->beagle2-----dash-----: 8.38e-18 97 1.74e-53 90 102 ( 11.4) 12 ( 28) 103 0 --->plink-------germline1: 3.72e-07 37 5.22e-08 18 101 ( 12.4) 82.9 ( 30) 103 95 --->plink-------germline2: 3.91e-18 101 1.28e-80 99.4 101 ( 12.4) 1.49 ( 10.8) 103 0 --->plink-------dash-----: 8.39e-18 96 5.04e-53 88.9 101 ( 12.4) 12 ( 28) 103 0 --->germline1---germline2: 1.23e-17 89 3.74e-45 81.4 82.9 ( 30) 1.49 ( 10.8) 95 0 --->germline1---dash-----: 2.71e-15 78 5.17e-27 70.9 82.9 ( 30) 12 ( 28) 95 0 --->germline2---dash-----: 1e+00 0.000000 8.52e-04 -10.530000 1.490000 (10.842765) 12.020000 (27.984115) 0.000000 0.000000 ######MatthewsSample###### --->fabia-------beagle1--: 6.8e-18 0.537258 5.66e-36 0.552826 0.548692 ( 0.278035) -0.004135 ( 0.034540) 0.481119 -0.005085 --->fabia-------beagle2--: 7.44e-18 0.531811 2.64e-35 0.547823 0.548692 ( 0.278035) 0.000868 ( 0.032793) 0.481119 -0.001850 --->fabia-------plink----: 6.22e-18 0.529530 5.25e-36 0.543886 0.548692 ( 0.278035) 0.004806 ( 0.031388) 0.481119 0.012173 --->fabia-------germline1: 1e+00 0.000000 1e+00 0.000000 0.548692 ( 0.278035) 0.000000 ( 0.000000) 0.481119 0.000000 --->fabia-------germline2: 7.44e-18 0.531628 3.9e-36 0.546563 0.548692 ( 0.278035) 0.002128 ( 0.032050) 0.481119 0.013016 --->fabia-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.548692 ( 0.278035) 0.000000 ( 0.000000) 0.481119 0.000000 --->beagle1-----beagle2--: 7.86e-02 -0.007446 1.51e-01 -0.005003 -0.004135 ( 0.034540) 0.000868 ( 0.032793) -0.005085 -0.001850 --->beagle1-----plink----: 6.66e-02 -0.008772 5.76e-02 -0.008940 -0.004135 ( 0.034540) 0.004806 ( 0.031388) -0.005085 0.012173 --->beagle1-----germline1: 1e+00 0.000000 1e+00 0.000000 -0.004135 ( 0.034540) 0.000000 ( 0.000000) -0.005085 0.000000 --->beagle1-----germline2: 9.92e-02 -0.008069 1.99e-01 -0.006263 -0.004135 ( 0.034540) 0.002128 ( 0.032050) -0.005085 0.013016 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 -0.004135 ( 0.034540) 0.000000 ( 0.000000) -0.005085 0.000000 --->beagle2-----plink----: 3.65e-01 -0.004831 4.21e-01 -0.003937 0.000868 ( 0.032793) 0.004806 ( 0.031388) -0.001850 0.012173 --->beagle2-----germline1: 1e+00 0.000000 1e+00 0.000000 0.000868 ( 0.032793) 0.000000 ( 0.000000) -0.001850 0.000000 --->beagle2-----germline2: 4.61e-01 -0.003824 7.94e-01 -0.001260 0.000868 ( 0.032793) 0.002128 ( 0.032050) -0.001850 0.013016 --->beagle2-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.000868 ( 0.032793) 0.000000 ( 0.000000) -0.001850 0.000000 --->plink-------germline1: 1e+00 0.000000 1e+00 0.000000 0.004806 ( 0.031388) 0.000000 ( 0.000000) 0.012173 0.000000 --->plink-------germline2: 8.51e-01 0.000905 5.56e-01 0.002677 0.004806 ( 0.031388) 0.002128 ( 0.032050) 0.012173 0.013016 --->plink-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.004806 ( 0.031388) 0.000000 ( 0.000000) 0.012173 0.000000 --->germline1---germline2: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.002128 ( 0.032050) 0.000000 0.013016 --->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 0.002128 ( 0.032050) 0.000000 ( 0.000000) 0.013016 0.000000 ######F1Sample###### --->fabia-------beagle1--: 7.44e-18 0.446576 4.36e-27 0.460777 0.479864 ( 0.308624) 0.019087 ( 0.005033) 0.380987 0.018913 --->fabia-------beagle2--: 7.9e-18 0.444440 5.88e-27 0.460355 0.479864 ( 0.308624) 0.019509 ( 0.009883) 0.380987 0.018838 --->fabia-------plink----: 7.44e-18 0.445744 4.76e-27 0.459668 0.479864 ( 0.308624) 0.020196 ( 0.002986) 0.380987 0.020858 --->fabia-------germline1: 1e+00 0.000000 1e+00 0.000000 0.479864 ( 0.308624) 0.019802 ( 0.000000) 0.380987 0.019802 --->fabia-------germline2: 7.44e-18 0.445731 4.2e-27 0.460324 0.479864 ( 0.308624) 0.019540 ( 0.003434) 0.380987 0.020212 --->fabia-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.479864 ( 0.308624) 0.019802 ( 0.000000) 0.380987 0.019802 --->beagle1-----beagle2--: 1e+00 0.000000 6.31e-01 -0.000422 0.019087 ( 0.005033) 0.019509 ( 0.009883) 0.018913 0.018838 --->beagle1-----plink----: 7.8e-02 -0.001111 5.85e-02 -0.001109 0.019087 ( 0.005033) 0.020196 ( 0.002986) 0.018913 0.020858 --->beagle1-----germline1: 1e+00 0.000000 1e+00 0.000000 0.019087 ( 0.005033) 0.019802 ( 0.000000) 0.018913 0.019802 --->beagle1-----germline2: 3.74e-01 -0.000515 4.51e-01 -0.000453 0.019087 ( 0.005033) 0.019540 ( 0.003434) 0.018913 0.020212 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.019087 ( 0.005033) 0.019802 ( 0.000000) 0.018913 0.019802 --->beagle2-----plink----: 5.15e-01 -0.000760 5.24e-01 -0.000687 0.019509 ( 0.009883) 0.020196 ( 0.002986) 0.018838 0.020858 --->beagle2-----germline1: 1e+00 0.000000 1e+00 0.000000 0.019509 ( 0.009883) 0.019802 ( 0.000000) 0.018838 0.019802 --->beagle2-----germline2: 7.71e-01 -0.000270 1e+00 0.000000 0.019509 ( 0.009883) 0.019540 ( 0.003434) 0.018838 0.020212 --->beagle2-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.019509 ( 0.009883) 0.019802 ( 0.000000) 0.018838 0.019802 --->plink-------germline1: 1e+00 0.000000 1e+00 0.000000 0.020196 ( 0.002986) 0.019802 ( 0.000000) 0.020858 0.019802 --->plink-------germline2: 2.63e-01 0.000429 1.55e-01 0.000657 0.020196 ( 0.002986) 0.019540 ( 0.003434) 0.020858 0.020212 --->plink-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.020196 ( 0.002986) 0.019802 ( 0.000000) 0.020858 0.019802 --->germline1---germline2: 1e+00 0.000000 1e+00 0.000000 0.019802 ( 0.000000) 0.019540 ( 0.003434) 0.019802 0.020212 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 0.019802 ( 0.000000) 0.019802 ( 0.000000) 0.019802 0.019802 --->germline2---dash-----: 1e+00 0.000000 1e+00 0.000000 0.019540 ( 0.003434) 0.019802 ( 0.000000) 0.020212 0.019802 ######accuracySample###### --->fabia-------beagle1--: 3.95e-18 0.627950 5.82e-128 0.628030 0.982880 ( 0.014887) 0.354850 ( 0.028686) 0.984500 0.357000 --->fabia-------beagle2--: 3.95e-18 0.279725 8.65e-97 0.280430 0.982880 ( 0.014887) 0.702450 ( 0.026695) 0.984500 0.702000 --->fabia-------plink----: 3.95e-18 0.792255 5.83e-141 0.791040 0.982880 ( 0.014887) 0.191840 ( 0.025470) 0.984500 0.190500 --->fabia-------germline1: 1e+00 0.000000 1e+00 0.000000 0.982880 ( 0.014887) 0.010000 ( 0.000000) 0.984500 0.010000 --->fabia-------germline2: 4.2e-18 0.903764 1.42e-69 0.860950 0.982880 ( 0.014887) 0.121930 ( 0.183542) 0.984500 0.070000 --->fabia-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.982880 ( 0.014887) 0.010000 ( 0.000000) 0.984500 0.010000 --->beagle1-----beagle2--: 3.95e-18 -0.347028 6.26e-130 -0.347600 0.354850 ( 0.028686) 0.702450 ( 0.026695) 0.357000 0.702000 --->beagle1-----plink----: 3.95e-18 0.165040 5.91e-64 0.163010 0.354850 ( 0.028686) 0.191840 ( 0.025470) 0.357000 0.190500 --->beagle1-----germline1: 1e+00 0.000000 1e+00 0.000000 0.354850 ( 0.028686) 0.010000 ( 0.000000) 0.357000 0.010000 --->beagle1-----germline2: 1.43e-12 0.275038 2.1e-22 0.232920 0.354850 ( 0.028686) 0.121930 ( 0.183542) 0.357000 0.070000 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.354850 ( 0.028686) 0.010000 ( 0.000000) 0.357000 0.010000 --->beagle2-----plink----: 3.95e-18 0.511462 4.45e-114 0.510610 0.702450 ( 0.026695) 0.191840 ( 0.025470) 0.702000 0.190500 --->beagle2-----germline1: 1e+00 0.000000 1e+00 0.000000 0.702450 ( 0.026695) 0.010000 ( 0.000000) 0.702000 0.010000 --->beagle2-----germline2: 6.03e-18 0.622452 1.58e-53 0.580520 0.702450 ( 0.026695) 0.121930 ( 0.183542) 0.702000 0.070000 --->beagle2-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.702450 ( 0.026695) 0.010000 ( 0.000000) 0.702000 0.010000 --->plink-------germline1: 1e+00 0.000000 1e+00 0.000000 0.191840 ( 0.025470) 0.010000 ( 0.000000) 0.190500 0.010000 --->plink-------germline2: 9.24e-10 0.112923 2.7e-04 0.069910 0.191840 ( 0.025470) 0.121930 ( 0.183542) 0.190500 0.070000 --->plink-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.191840 ( 0.025470) 0.010000 ( 0.000000) 0.190500 0.010000 --->germline1---germline2: 1e+00 0.000000 1e+00 0.000000 0.010000 ( 0.000000) 0.121930 ( 0.183542) 0.010000 0.070000 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 0.010000 ( 0.000000) 0.010000 ( 0.000000) 0.010000 0.010000 --->germline2---dash-----: 1e+00 0.000000 1e+00 0.000000 0.121930 ( 0.183542) 0.010000 ( 0.000000) 0.070000 0.010000 ######FPRSample###### --->fabia-------beagle1--: 3.96e-18 -0.631217 1.21e-127 -0.631055 0.016854 ( 0.014924) 0.647909 ( 0.029183) 0.014824 0.646465 --->fabia-------beagle2--: 3.96e-18 -0.275865 1.31e-95 -0.276610 0.016854 ( 0.014924) 0.293465 ( 0.027330) 0.014824 0.293434 --->fabia-------plink----: 3.96e-18 -0.799018 1.06e-140 -0.797782 0.016854 ( 0.014924) 0.814636 ( 0.025933) 0.014824 0.815152 --->fabia-------germline1: 1e+00 0.000000 1e+00 0.000000 0.016854 ( 0.014924) 1.000000 ( 0.000000) 0.014824 1.000000 --->fabia-------germline2: 4.33e-18 -0.912626 4.12e-69 -0.869004 0.016854 ( 0.014924) 0.885859 ( 0.187308) 0.014824 0.939394 --->fabia-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.016854 ( 0.014924) 1.000000 ( 0.000000) 0.014824 1.000000 --->beagle1-----beagle2--: 3.95e-18 0.354004 4.93e-130 0.354444 0.647909 ( 0.029183) 0.293465 ( 0.027330) 0.646465 0.293434 --->beagle1-----plink----: 3.95e-18 -0.168748 3.31e-64 -0.166727 0.647909 ( 0.029183) 0.814636 ( 0.025933) 0.646465 0.815152 --->beagle1-----germline1: 1e+00 0.000000 1e+00 0.000000 0.647909 ( 0.029183) 1.000000 ( 0.000000) 0.646465 1.000000 --->beagle1-----germline2: 1.43e-12 -0.280858 1.83e-22 -0.237950 0.647909 ( 0.029183) 0.885859 ( 0.187308) 0.646465 0.939394 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.647909 ( 0.029183) 1.000000 ( 0.000000) 0.646465 1.000000 --->beagle2-----plink----: 3.95e-18 -0.521741 4.35e-114 -0.521172 0.293465 ( 0.027330) 0.814636 ( 0.025933) 0.293434 0.815152 --->beagle2-----germline1: 1e+00 0.000000 1e+00 0.000000 0.293465 ( 0.027330) 1.000000 ( 0.000000) 0.293434 1.000000 --->beagle2-----germline2: 6.03e-18 -0.634861 1.49e-53 -0.592394 0.293465 ( 0.027330) 0.885859 ( 0.187308) 0.293434 0.939394 --->beagle2-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.293465 ( 0.027330) 1.000000 ( 0.000000) 0.293434 1.000000 --->plink-------germline1: 1e+00 0.000000 1e+00 0.000000 0.814636 ( 0.025933) 1.000000 ( 0.000000) 0.815152 1.000000 --->plink-------germline2: 9.24e-10 -0.114679 2.73e-04 -0.071222 0.814636 ( 0.025933) 0.885859 ( 0.187308) 0.815152 0.939394 --->plink-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.814636 ( 0.025933) 1.000000 ( 0.000000) 0.815152 1.000000 --->germline1---germline2: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 0.885859 ( 0.187308) 1.000000 0.939394 --->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 0.885859 ( 0.187308) 1.000000 ( 0.000000) 0.939394 1.000000 ######FDRSample###### --->fabia-------beagle1--: 7.44e-18 -0.315707 1.88e-19 -0.371958 0.618351 ( 0.329947) 0.990309 ( 0.002556) 0.764673 0.990392 --->fabia-------beagle2--: 7.44e-18 -0.315469 2.14e-19 -0.371561 0.618351 ( 0.329947) 0.989912 ( 0.005110) 0.764673 0.990275 --->fabia-------plink----: 7.44e-18 -0.315074 1.98e-19 -0.371426 0.618351 ( 0.329947) 0.989778 ( 0.001512) 0.764673 0.989449 --->fabia-------germline1: 1e+00 0.000000 1e+00 0.000000 0.618351 ( 0.329947) 0.990000 ( 0.000000) 0.764673 0.990000 --->fabia-------germline2: 6.95e-16 -0.300049 4.57e-16 -0.351761 0.618351 ( 0.329947) 0.970113 ( 0.139289) 0.764673 0.989775 --->fabia-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.618351 ( 0.329947) 0.990000 ( 0.000000) 0.764673 0.990000 --->beagle1-----beagle2--: 3.11e-01 0.000475 3.84e-01 0.000396 0.990309 ( 0.002556) 0.989912 ( 0.005110) 0.990392 0.990275 --->beagle1-----plink----: 9.17e-02 0.000527 7.4e-02 0.000531 0.990309 ( 0.002556) 0.989778 ( 0.001512) 0.990392 0.989449 --->beagle1-----germline1: 1e+00 0.000000 1e+00 0.000000 0.990309 ( 0.002556) 0.990000 ( 0.000000) 0.990392 0.990000 --->beagle1-----germline2: 1.63e-01 0.000460 1.51e-01 0.020196 0.990309 ( 0.002556) 0.970113 ( 0.139289) 0.990392 0.989775 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.990309 ( 0.002556) 0.990000 ( 0.000000) 0.990392 0.990000 --->beagle2-----plink----: 7.79e-01 0.000176 8.09e-01 0.000135 0.989912 ( 0.005110) 0.989778 ( 0.001512) 0.990275 0.989449 --->beagle2-----germline1: 1e+00 0.000000 1e+00 0.000000 0.989912 ( 0.005110) 0.990000 ( 0.000000) 0.990275 0.990000 --->beagle2-----germline2: 6.54e-01 0.000238 1.59e-01 0.019800 0.989912 ( 0.005110) 0.970113 ( 0.139289) 0.990275 0.989775 --->beagle2-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.989912 ( 0.005110) 0.990000 ( 0.000000) 0.990275 0.990000 --->plink-------germline1: 1e+00 0.000000 1e+00 0.000000 0.989778 ( 0.001512) 0.990000 ( 0.000000) 0.989449 0.990000 --->plink-------germline2: 6.3e-01 -0.000101 1.61e-01 0.019665 0.989778 ( 0.001512) 0.970113 ( 0.139289) 0.989449 0.989775 --->plink-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.989778 ( 0.001512) 0.990000 ( 0.000000) 0.989449 0.990000 --->germline1---germline2: 1e+00 0.000000 1e+00 0.000000 0.990000 ( 0.000000) 0.970113 ( 0.139289) 0.990000 0.989775 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 0.990000 ( 0.000000) 0.990000 ( 0.000000) 0.990000 0.990000 --->germline2---dash-----: 1e+00 0.000000 1e+00 0.000000 0.970113 ( 0.139289) 0.990000 ( 0.000000) 0.989775 0.990000 ######specifitySample###### --->fabia-------beagle1--: 3.96e-18 0.631238 1.21e-127 0.631055 0.983146 ( 0.014924) 0.352091 ( 0.029183) 0.985176 0.353535 --->fabia-------beagle2--: 3.96e-18 0.275896 1.31e-95 0.276610 0.983146 ( 0.014924) 0.706535 ( 0.027330) 0.985176 0.706566 --->fabia-------plink----: 3.96e-18 0.799019 1.06e-140 0.797782 0.983146 ( 0.014924) 0.185364 ( 0.025933) 0.985176 0.184848 --->fabia-------germline1: 1e+00 0.000000 1e+00 0.000000 0.983146 ( 0.014924) 0.000000 ( 0.000000) 0.985176 0.000000 --->fabia-------germline2: 4.33e-18 0.912624 4.12e-69 0.869004 0.983146 ( 0.014924) 0.114141 ( 0.187308) 0.985176 0.060606 --->fabia-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.983146 ( 0.014924) 0.000000 ( 0.000000) 0.985176 0.000000 --->beagle1-----beagle2--: 3.95e-18 -0.353998 4.93e-130 -0.354444 0.352091 ( 0.029183) 0.706535 ( 0.027330) 0.353535 0.706566 --->beagle1-----plink----: 3.95e-18 0.168752 3.31e-64 0.166727 0.352091 ( 0.029183) 0.185364 ( 0.025933) 0.353535 0.184848 --->beagle1-----germline1: 1e+00 0.000000 1e+00 0.000000 0.352091 ( 0.029183) 0.000000 ( 0.000000) 0.353535 0.000000 --->beagle1-----germline2: 1.43e-12 0.280853 1.83e-22 0.237950 0.352091 ( 0.029183) 0.114141 ( 0.187308) 0.353535 0.060606 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.352091 ( 0.029183) 0.000000 ( 0.000000) 0.353535 0.000000 --->beagle2-----plink----: 3.95e-18 0.521747 4.35e-114 0.521172 0.706535 ( 0.027330) 0.185364 ( 0.025933) 0.706566 0.184848 --->beagle2-----germline1: 1e+00 0.000000 1e+00 0.000000 0.706535 ( 0.027330) 0.000000 ( 0.000000) 0.706566 0.000000 --->beagle2-----germline2: 6.03e-18 0.634870 1.49e-53 0.592394 0.706535 ( 0.027330) 0.114141 ( 0.187308) 0.706566 0.060606 --->beagle2-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.706535 ( 0.027330) 0.000000 ( 0.000000) 0.706566 0.000000 --->plink-------germline1: 1e+00 0.000000 1e+00 0.000000 0.185364 ( 0.025933) 0.000000 ( 0.000000) 0.184848 0.000000 --->plink-------germline2: 9.24e-10 0.114667 2.73e-04 0.071222 0.185364 ( 0.025933) 0.114141 ( 0.187308) 0.184848 0.060606 --->plink-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.185364 ( 0.025933) 0.000000 ( 0.000000) 0.184848 0.000000 --->germline1---germline2: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.114141 ( 0.187308) 0.000000 0.060606 --->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 0.114141 ( 0.187308) 0.000000 ( 0.000000) 0.060606 0.000000 ######sensitivitySample###### --->fabia-------beagle1--: 7e-11 0.350059 6.73e-16 0.302000 0.930000 ( 0.252862) 0.628000 ( 0.167622) 1.000000 0.600000 --->fabia-------beagle2--: 2.92e-17 0.699944 1.85e-36 0.632000 0.930000 ( 0.252862) 0.298000 ( 0.154384) 1.000000 0.300000 --->fabia-------plink----: 3.45e-08 0.150013 4.59e-04 0.097000 0.930000 ( 0.252862) 0.833000 ( 0.125573) 1.000000 0.900000 --->fabia-------germline1: 1e+00 0.000000 1e+00 0.000000 0.930000 ( 0.252862) 1.000000 ( 0.000000) 1.000000 1.000000 --->fabia-------germline2: 1e+00 0.000000 2.7e-01 0.037000 0.930000 ( 0.252862) 0.893000 ( 0.204621) 1.000000 1.000000 --->fabia-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.930000 ( 0.252862) 1.000000 ( 0.000000) 1.000000 1.000000 --->beagle1-----beagle2--: 7.72e-18 0.349969 5.67e-37 0.330000 0.628000 ( 0.167622) 0.298000 ( 0.154384) 0.600000 0.300000 --->beagle1-----plink----: 1.3e-12 -0.249947 2.06e-16 -0.205000 0.628000 ( 0.167622) 0.833000 ( 0.125573) 0.600000 0.900000 --->beagle1-----germline1: 1e+00 0.000000 1e+00 0.000000 0.628000 ( 0.167622) 1.000000 ( 0.000000) 0.600000 1.000000 --->beagle1-----germline2: 6.57e-13 -0.300085 5.87e-18 -0.265000 0.628000 ( 0.167622) 0.893000 ( 0.204621) 0.600000 1.000000 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.628000 ( 0.167622) 1.000000 ( 0.000000) 0.600000 1.000000 --->beagle2-----plink----: 3.59e-18 -0.549941 9.34e-45 -0.535000 0.298000 ( 0.154384) 0.833000 ( 0.125573) 0.300000 0.900000 --->beagle2-----germline1: 1e+00 0.000000 1e+00 0.000000 0.298000 ( 0.154384) 1.000000 ( 0.000000) 0.300000 1.000000 --->beagle2-----germline2: 1.35e-17 -0.600048 4.77e-43 -0.595000 0.298000 ( 0.154384) 0.893000 ( 0.204621) 0.300000 1.000000 --->beagle2-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.298000 ( 0.154384) 1.000000 ( 0.000000) 0.300000 1.000000 --->plink-------germline1: 1e+00 0.000000 1e+00 0.000000 0.833000 ( 0.125573) 1.000000 ( 0.000000) 0.900000 1.000000 --->plink-------germline2: 5.09e-04 -0.100016 1.01e-02 -0.060000 0.833000 ( 0.125573) 0.893000 ( 0.204621) 0.900000 1.000000 --->plink-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.833000 ( 0.125573) 1.000000 ( 0.000000) 0.900000 1.000000 --->germline1---germline2: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 0.893000 ( 0.204621) 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 0.893000 ( 0.204621) 1.000000 ( 0.000000) 1.000000 1.000000 ######trueNSample###### --->fabia-------beagle1--: 3.95e-18 1608 2.26e-157 1608 1956 ( 29.7) 349 ( 28.9) 1960 350 --->fabia-------beagle2--: 3.94e-18 1257 2.21e-149 1257 1956 ( 29.7) 699 ( 27.1) 1960 700 --->fabia-------plink----: 3.95e-18 1775 5.39e-163 1773 1956 ( 29.7) 184 ( 25.7) 1960 183 --->fabia-------germline1: 1e+00 0 1e+00 0 1956 ( 29.7) 0 ( 0) 1960 0 --->fabia-------germline2: 3.95e-18 1885 5.28e-101 1843 1956 ( 29.7) 113 ( 185) 1960 60 --->fabia-------dash-----: 1e+00 0 1e+00 0 1956 ( 29.7) 0 ( 0) 1960 0 --->beagle1-----beagle2--: 3.92e-18 -350 4.93e-130 -351 349 ( 28.9) 699 ( 27.1) 350 700 --->beagle1-----plink----: 3.95e-18 167 3.31e-64 165 349 ( 28.9) 184 ( 25.7) 350 183 --->beagle1-----germline1: 1e+00 0 1e+00 0 349 ( 28.9) 0 ( 0) 350 0 --->beagle1-----germline2: 1.43e-12 278 1.83e-22 236 349 ( 28.9) 113 ( 185) 350 60 --->beagle1-----dash-----: 1e+00 0 1e+00 0 349 ( 28.9) 0 ( 0) 350 0 --->beagle2-----plink----: 3.95e-18 517 4.35e-114 516 699 ( 27.1) 184 ( 25.7) 700 183 --->beagle2-----germline1: 1e+00 0 1e+00 0 699 ( 27.1) 0 ( 0) 700 0 --->beagle2-----germline2: 6.03e-18 629 1.49e-53 586 699 ( 27.1) 113 ( 185) 700 60 --->beagle2-----dash-----: 1e+00 0 1e+00 0 699 ( 27.1) 0 ( 0) 700 0 --->plink-------germline1: 1e+00 0 1e+00 0 184 ( 25.7) 0 ( 0) 183 0 --->plink-------germline2: 9.33e-10 114 2.73e-04 70.5 184 ( 25.7) 113 ( 185) 183 60 --->plink-------dash-----: 1e+00 0 1e+00 0 184 ( 25.7) 0 ( 0) 183 0 --->germline1---germline2: 1e+00 0 1e+00 0 0 ( 0) 113 ( 185) 0 60 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.000000 ( 0.000000) 0.000000 0.000000 --->germline2---dash-----: 1e+00 0 1e+00 0 113 ( 185) 0 ( 0) 60 0 ######falsePSample###### --->fabia-------beagle1--: 3.95e-18 -608 1.21e-115 -608 33.5 ( 29.7) 641 ( 28.9) 29.5 640 --->fabia-------beagle2--: 3.94e-18 -257 1.24e-81 -257 33.5 ( 29.7) 291 ( 27.1) 29.5 290 --->fabia-------plink----: 3.95e-18 -775 2.37e-127 -773 33.5 ( 29.7) 806 ( 25.7) 29.5 807 --->fabia-------germline1: 1e+00 0 1e+00 0 33.5 ( 29.7) 990 ( 0) 29.5 990 --->fabia-------germline2: 4.33e-18 -885 3.61e-68 -843 33.5 ( 29.7) 877 ( 185) 29.5 930 --->fabia-------dash-----: 1e+00 0 1e+00 0 33.5 ( 29.7) 990 ( 0) 29.5 990 --->beagle1-----beagle2--: 3.92e-18 350 4.93e-130 351 641 ( 28.9) 291 ( 27.1) 640 290 --->beagle1-----plink----: 3.95e-18 -167 3.31e-64 -165 641 ( 28.9) 806 ( 25.7) 640 807 --->beagle1-----germline1: 1e+00 0 1e+00 0 641 ( 28.9) 990 ( 0) 640 990 --->beagle1-----germline2: 1.43e-12 -278 1.83e-22 -236 641 ( 28.9) 877 ( 185) 640 930 --->beagle1-----dash-----: 1e+00 0 1e+00 0 641 ( 28.9) 990 ( 0) 640 990 --->beagle2-----plink----: 3.95e-18 -517 4.35e-114 -516 291 ( 27.1) 806 ( 25.7) 290 807 --->beagle2-----germline1: 1e+00 0 1e+00 0 291 ( 27.1) 990 ( 0) 290 990 --->beagle2-----germline2: 6.03e-18 -629 1.49e-53 -586 291 ( 27.1) 877 ( 185) 290 930 --->beagle2-----dash-----: 1e+00 0 1e+00 0 291 ( 27.1) 990 ( 0) 290 990 --->plink-------germline1: 1e+00 0 1e+00 0 806 ( 25.7) 990 ( 0) 807 990 --->plink-------germline2: 9.33e-10 -114 2.73e-04 -70.5 806 ( 25.7) 877 ( 185) 807 930 --->plink-------dash-----: 1e+00 0 1e+00 0 806 ( 25.7) 990 ( 0) 807 990 --->germline1---germline2: 1e+00 0 1e+00 0 990 ( 0) 877 ( 185) 990 930 --->germline1---dash-----: 1e+00 0 1e+00 0 990 ( 0) 990 ( 0) 990 990 --->germline2---dash-----: 1e+00 0 1e+00 0 877 ( 185) 990 ( 0) 930 990 ######falseNSample###### --->fabia-------beagle1--: 7e-11 -3.5 6.73e-16 -3.02 0.7 ( 2.53) 3.72 ( 1.68) 0 4 --->fabia-------beagle2--: 2.94e-17 -7 1.85e-36 -6.32 0.7 ( 2.53) 7.02 ( 1.54) 0 7 --->fabia-------plink----: 3.45e-08 -1.500069 4.59e-04 -0.970000 0.700000 ( 2.528624) 1.670000 ( 1.255734) 0.000000 1.000000 --->fabia-------germline1: 1e+00 0.000000 1e+00 0.000000 0.700000 ( 2.528624) 0.000000 ( 0.000000) 0.000000 0.000000 --->fabia-------germline2: 1e+00 0.000000 2.7e-01 -0.370000 0.700000 ( 2.528624) 1.070000 ( 2.046209) 0.000000 0.000000 --->fabia-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.700000 ( 2.528624) 0.000000 ( 0.000000) 0.000000 0.000000 --->beagle1-----beagle2--: 5.39e-18 -3.5 5.67e-37 -3.3 3.72 ( 1.68) 7.02 ( 1.54) 4 7 --->beagle1-----plink----: 8.74e-13 2.5 2.06e-16 2.05 3.72 ( 1.68) 1.67 ( 1.26) 4 1 --->beagle1-----germline1: 1e+00 0 1e+00 0 3.72 ( 1.68) 0 ( 0) 4 0 --->beagle1-----germline2: 1.06e-12 3 5.87e-18 2.65 3.72 ( 1.68) 1.07 ( 2.05) 4 0 --->beagle1-----dash-----: 1e+00 0 1e+00 0 3.72 ( 1.68) 0 ( 0) 4 0 --->beagle2-----plink----: 3.2e-18 5.5 9.34e-45 5.35 7.02 ( 1.54) 1.67 ( 1.26) 7 1 --->beagle2-----germline1: 1e+00 0 1e+00 0 7.02 ( 1.54) 0 ( 0) 7 0 --->beagle2-----germline2: 1.16e-17 6 4.77e-43 5.95 7.02 ( 1.54) 1.07 ( 2.05) 7 0 --->beagle2-----dash-----: 1e+00 0 1e+00 0 7.02 ( 1.54) 0 ( 0) 7 0 --->plink-------germline1: 1e+00 0.000000 1e+00 0.000000 1.670000 ( 1.255734) 0.000000 ( 0.000000) 1.000000 0.000000 --->plink-------germline2: 5.35e-04 1.000030 1.01e-02 0.600000 1.670000 ( 1.255734) 1.070000 ( 2.046209) 1.000000 0.000000 --->plink-------dash-----: 1e+00 0.000000 1e+00 0.000000 1.670000 ( 1.255734) 0.000000 ( 0.000000) 1.000000 0.000000 --->germline1---germline2: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 1.070000 ( 2.046209) 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 1.070000 ( 2.046209) 0.000000 ( 0.000000) 0.000000 0.000000 ######truePSample###### --->fabia-------beagle1--: 7e-11 3.5 6.73e-16 3.02 9.3 ( 2.53) 6.28 ( 1.68) 10 6 --->fabia-------beagle2--: 2.94e-17 7 1.85e-36 6.32 9.3 ( 2.53) 2.98 ( 1.54) 10 3 --->fabia-------plink----: 3.45e-08 1.5 4.59e-04 0.97 9.3 ( 2.53) 8.33 ( 1.26) 10 9 --->fabia-------germline1: 1e+00 0 1e+00 0 9.3 ( 2.53) 10 ( 0) 10 10 --->fabia-------germline2: 1e+00 0 2.7e-01 0.37 9.3 ( 2.53) 8.93 ( 2.05) 10 10 --->fabia-------dash-----: 1e+00 0 1e+00 0 9.3 ( 2.53) 10 ( 0) 10 10 --->beagle1-----beagle2--: 5.39e-18 3.5 5.67e-37 3.3 6.28 ( 1.68) 2.98 ( 1.54) 6 3 --->beagle1-----plink----: 8.74e-13 -2.5 2.06e-16 -2.05 6.28 ( 1.68) 8.33 ( 1.26) 6 9 --->beagle1-----germline1: 1e+00 0 1e+00 0 6.28 ( 1.68) 10 ( 0) 6 10 --->beagle1-----germline2: 1.06e-12 -3 5.87e-18 -2.65 6.28 ( 1.68) 8.93 ( 2.05) 6 10 --->beagle1-----dash-----: 1e+00 0 1e+00 0 6.28 ( 1.68) 10 ( 0) 6 10 --->beagle2-----plink----: 3.2e-18 -5.5 9.34e-45 -5.35 2.98 ( 1.54) 8.33 ( 1.26) 3 9 --->beagle2-----germline1: 1e+00 0 1e+00 0 2.98 ( 1.54) 10 ( 0) 3 10 --->beagle2-----germline2: 1.16e-17 -6 4.77e-43 -5.95 2.98 ( 1.54) 8.93 ( 2.05) 3 10 --->beagle2-----dash-----: 1e+00 0 1e+00 0 2.98 ( 1.54) 10 ( 0) 3 10 --->plink-------germline1: 1e+00 0 1e+00 0 8.33 ( 1.26) 10 ( 0) 9 10 --->plink-------germline2: 5.35e-04 -1 1.01e-02 -0.6 8.33 ( 1.26) 8.93 ( 2.05) 9 10 --->plink-------dash-----: 1e+00 0 1e+00 0 8.33 ( 1.26) 10 ( 0) 9 10 --->germline1---germline2: 1e+00 0 1e+00 0 10 ( 0) 8.93 ( 2.05) 10 10 --->germline1---dash-----: 1e+00 0 1e+00 0 10 ( 0) 10 ( 0) 10 10 --->germline2---dash-----: 1e+00 0 1e+00 0 8.93 ( 2.05) 10 ( 0) 10 10