Results: Wilcoxon-Rank-Sum Wilcoxon-median t-test t-test-mean mean1 (std) mean2 (std) median1 median2 ######Matthews###### --->fabia-------beagle1--: 8.48e-10 0.152630 1.45e-14 0.166970 0.206884 ( 0.185865) 0.039914 ( 0.008218) 0.247180 0.041687 --->fabia-------beagle2--: 1.1e-09 0.144556 1.72e-13 0.156736 0.206884 ( 0.185865) 0.050148 ( 0.020047) 0.247180 0.057504 --->fabia-------plink----: 8.66e-10 0.190907 9.42e-19 0.203430 0.206884 ( 0.185865) 0.003454 ( 0.000376) 0.247180 0.003447 --->fabia-------germline1: 9.35e-13 0.189731 4.88e-19 0.203973 0.206884 ( 0.185865) 0.002912 ( 0.007017) 0.247180 0.003605 --->fabia-------germline2: 1.4e-15 0.190835 1.88e-19 0.208425 0.206884 ( 0.185865) -0.001541 ( 0.007739) 0.247180 -0.004203 --->fabia-------dash-----: 6.75e-16 0.195269 2.1e-19 0.208929 0.206884 ( 0.185865) -0.002045 ( 0.006737) 0.247180 -0.004068 --->beagle1-----beagle2--: 2.43e-07 -0.015425 9.64e-10 -0.010233 0.039914 ( 0.008218) 0.050148 ( 0.020047) 0.041687 0.057504 --->beagle1-----plink----: 4.33e-18 0.037890 1.03e-67 0.036460 0.039914 ( 0.008218) 0.003454 ( 0.000376) 0.041687 0.003447 --->beagle1-----germline1: 4.2e-18 0.037755 2.8e-62 0.037003 0.039914 ( 0.008218) 0.002912 ( 0.007017) 0.041687 0.003605 --->beagle1-----germline2: 4.2e-18 0.042924 1.84e-61 0.041455 0.039914 ( 0.008218) -0.001541 ( 0.007739) 0.041687 -0.004203 --->beagle1-----dash-----: 4.74e-18 0.044153 1.12e-62 0.041959 0.039914 ( 0.008218) -0.002045 ( 0.006737) 0.041687 -0.004068 --->beagle2-----plink----: 2.45e-17 0.052561 4.81e-42 0.046694 0.050148 ( 0.020047) 0.003454 ( 0.000376) 0.057504 0.003447 --->beagle2-----germline1: 1.99e-17 0.052083 1.64e-41 0.047236 0.050148 ( 0.020047) 0.002912 ( 0.007017) 0.057504 0.003605 --->beagle2-----germline2: 1.03e-17 0.056457 1.3e-43 0.051689 0.050148 ( 0.020047) -0.001541 ( 0.007739) 0.057504 -0.004203 --->beagle2-----dash-----: 7.22e-18 0.058380 1.59e-43 0.052193 0.050148 ( 0.020047) -0.002045 ( 0.006737) 0.057504 -0.004068 --->plink-------germline1: 6.12e-01 0.000367 4.31e-01 0.000542 0.003454 ( 0.000376) 0.002912 ( 0.007017) 0.003447 0.003605 --->plink-------germline2: 2.47e-08 0.006183 2.62e-09 0.004995 0.003454 ( 0.000376) -0.001541 ( 0.007739) 0.003447 -0.004203 --->plink-------dash-----: 4.28e-13 0.007173 6.89e-13 0.005499 0.003454 ( 0.000376) -0.002045 ( 0.006737) 0.003447 -0.004068 --->germline1---germline2: 5.6e-07 0.004393 6.28e-08 0.004453 0.002912 ( 0.007017) -0.001541 ( 0.007739) 0.003605 -0.004203 --->germline1---dash-----: 2.78e-08 0.005266 4.15e-08 0.004957 0.002912 ( 0.007017) -0.002045 ( 0.006737) 0.003605 -0.004068 --->germline2---dash-----: 3.87e-01 -0.000561 4.36e-01 0.000504 -0.001541 ( 0.007739) -0.002045 ( 0.006737) -0.004203 -0.004068 ######F1###### --->fabia-------beagle1--: 6.29e-10 0.121936 1.69e-15 0.140745 0.144534 ( 0.149010) 0.003788 ( 0.000874) 0.133690 0.003889 --->fabia-------beagle2--: 1.78e-10 0.128390 3.75e-15 0.138097 0.144534 ( 0.149010) 0.006437 ( 0.002630) 0.133690 0.007140 --->fabia-------plink----: 8.66e-10 0.124654 5.62e-16 0.144143 0.144534 ( 0.149010) 0.000390 ( 5.62e-05) 0.133690 0.000390 --->fabia-------germline1: 6.29e-10 0.125384 5.63e-16 0.144091 0.144534 ( 0.149010) 0.000443 ( 0.000213) 0.133690 0.000469 --->fabia-------germline2: 1.38e-11 0.160657 5.34e-16 0.144236 0.144534 ( 0.149010) 0.000298 ( 0.000402) 0.133690 0.000150 --->fabia-------dash-----: 1.64e-12 0.192423 5.19e-16 0.144333 0.144534 ( 0.149010) 0.000201 ( 0.000609) 0.133690 0.000000 --->beagle1-----beagle2--: 1.44e-14 -0.003199 5.31e-23 -0.002648 0.003788 ( 0.000874) 0.006437 ( 0.002630) 0.003889 0.007140 --->beagle1-----plink----: 4.33e-18 0.003463 1.38e-63 0.003398 0.003788 ( 0.000874) 0.000390 ( 5.62e-05) 0.003889 0.000390 --->beagle1-----germline1: 4.33e-18 0.003457 3.33e-65 0.003345 0.003788 ( 0.000874) 0.000443 ( 0.000213) 0.003889 0.000469 --->beagle1-----germline2: 4.33e-18 0.003553 1.7e-63 0.003491 0.003788 ( 0.000874) 0.000298 ( 0.000402) 0.003889 0.000150 --->beagle1-----dash-----: 4.74e-18 0.003698 2.58e-58 0.003587 0.003788 ( 0.000874) 0.000201 ( 0.000609) 0.003889 0.000000 --->beagle2-----plink----: 1.48e-17 0.006549 7.87e-42 0.006046 0.006437 ( 0.002630) 0.000390 ( 5.62e-05) 0.007140 0.000390 --->beagle2-----germline1: 1.48e-17 0.006521 7.03e-42 0.005994 0.006437 ( 0.002630) 0.000443 ( 0.000213) 0.007140 0.000469 --->beagle2-----germline2: 1.66e-17 0.006722 2e-42 0.006139 0.006437 ( 0.002630) 0.000298 ( 0.000402) 0.007140 0.000150 --->beagle2-----dash-----: 3.52e-17 0.006888 1.03e-41 0.006236 0.006437 ( 0.002630) 0.000201 ( 0.000609) 0.007140 0.000000 --->plink-------germline1: 1e+00 0.000000 1e+00 0.000000 0.000390 ( 5.62e-05) 0.000443 ( 0.000213) 0.000390 0.000469 --->plink-------germline2: 4.06e-04 0.000145 1e+00 0.000000 0.000390 ( 5.62e-05) 0.000298 ( 0.000402) 0.000390 0.000150 --->plink-------dash-----: 1.44e-08 0.000348 2.03e-03 0.000190 0.000390 ( 5.62e-05) 0.000201 ( 0.000609) 0.000390 0.000000 --->germline1---germline2: 5.74e-06 0.000185 3.12e-05 0.000145 0.000443 ( 0.000213) 0.000298 ( 0.000402) 0.000469 0.000150 --->germline1---dash-----: 3.56e-10 0.000297 5.99e-05 0.000242 0.000443 ( 0.000213) 0.000201 ( 0.000609) 0.000469 0.000000 --->germline2---dash-----: 5.22e-04 0.000222 1e+00 0.000000 0.000298 ( 0.000402) 0.000201 ( 0.000609) 0.000150 0.000000 ######accuracy###### --->fabia-------beagle1--: 3.96e-18 0.090349 3.84e-121 0.090426 0.999260 ( 0.000378) 0.908833 ( 0.005629) 0.999265 0.909327 --->fabia-------beagle2--: 3.96e-18 0.047169 1.52e-109 0.047152 0.999260 ( 0.000378) 0.952108 ( 0.003840) 0.999265 0.952182 --->fabia-------plink----: 3.96e-18 0.936662 1.16e-211 0.936564 0.999260 ( 0.000378) 0.062695 ( 0.007152) 0.999265 0.062363 --->fabia-------germline1: 3.96e-18 0.542415 1.74e-121 0.542294 0.999260 ( 0.000378) 0.456966 ( 0.033737) 0.999265 0.460484 --->fabia-------germline2: 3.96e-18 0.246665 2.7e-84 0.247973 0.999260 ( 0.000378) 0.751287 ( 0.036981) 0.999265 0.752756 --->fabia-------dash-----: 3.96e-18 0.099756 2.58e-56 0.101470 0.999260 ( 0.000378) 0.897790 ( 0.029886) 0.999265 0.899960 --->beagle1-----beagle2--: 3.96e-18 -0.043250 2.47e-107 -0.043274 0.908833 ( 0.005629) 0.952108 ( 0.003840) 0.909327 0.952182 --->beagle1-----plink----: 3.96e-18 0.845849 4.58e-200 0.846138 0.908833 ( 0.005629) 0.062695 ( 0.007152) 0.909327 0.062363 --->beagle1-----germline1: 3.96e-18 0.451876 1.94e-113 0.451868 0.908833 ( 0.005629) 0.456966 ( 0.033737) 0.909327 0.460484 --->beagle1-----germline2: 3.96e-18 0.156063 3.89e-65 0.157547 0.908833 ( 0.005629) 0.751287 ( 0.036981) 0.909327 0.752756 --->beagle1-----dash-----: 1.7e-03 0.008885 4.49e-04 0.011043 0.908833 ( 0.005629) 0.897790 ( 0.029886) 0.909327 0.899960 --->beagle2-----plink----: 3.96e-18 0.889271 7.39e-207 0.889412 0.952108 ( 0.003840) 0.062695 ( 0.007152) 0.952182 0.062363 --->beagle2-----germline1: 3.96e-18 0.495146 4.24e-118 0.495142 0.952108 ( 0.003840) 0.456966 ( 0.033737) 0.952182 0.460484 --->beagle2-----germline2: 3.96e-18 0.199366 9.04e-76 0.200821 0.952108 ( 0.003840) 0.751287 ( 0.036981) 0.952182 0.752756 --->beagle2-----dash-----: 4.08e-18 0.052378 2.58e-33 0.054318 0.952108 ( 0.003840) 0.897790 ( 0.029886) 0.952182 0.899960 --->plink-------germline1: 3.96e-18 -0.394129 7.63e-109 -0.394270 0.062695 ( 0.007152) 0.456966 ( 0.033737) 0.062363 0.460484 --->plink-------germline2: 3.96e-18 -0.689722 2.13e-128 -0.688591 0.062695 ( 0.007152) 0.751287 ( 0.036981) 0.062363 0.752756 --->plink-------dash-----: 3.96e-18 -0.836276 5.67e-145 -0.835095 0.062695 ( 0.007152) 0.897790 ( 0.029886) 0.062363 0.899960 --->germline1---germline2: 3.96e-18 -0.294426 9.19e-138 -0.294321 0.456966 ( 0.033737) 0.751287 ( 0.036981) 0.460484 0.752756 --->germline1---dash-----: 3.96e-18 -0.441018 1.13e-137 -0.440824 0.456966 ( 0.033737) 0.897790 ( 0.029886) 0.460484 0.899960 --->germline2---dash-----: 3.96e-18 -0.146028 6.68e-109 -0.146504 0.751287 ( 0.036981) 0.897790 ( 0.029886) 0.752756 0.899960 ######FPR###### --->fabia-------beagle1--: 3.96e-18 -0.090353 3.72e-121 -0.090475 0.000698 ( 0.000370) 0.091173 ( 0.005630) 0.000695 0.090691 --->fabia-------beagle2--: 3.96e-18 -0.047187 1.54e-109 -0.047174 0.000698 ( 0.000370) 0.047872 ( 0.003842) 0.000695 0.047739 --->fabia-------plink----: 3.96e-18 -0.936845 1.09e-211 -0.936778 0.000698 ( 0.000370) 0.937476 ( 0.007153) 0.000695 0.937808 --->fabia-------germline1: 3.96e-18 -0.542530 1.78e-121 -0.542374 0.000698 ( 0.000370) 0.543072 ( 0.033759) 0.000695 0.539577 --->fabia-------germline2: 3.96e-18 -0.246648 2.84e-84 -0.247916 0.000698 ( 0.000370) 0.248614 ( 0.036999) 0.000695 0.247132 --->fabia-------dash-----: 3.96e-18 -0.099641 2.87e-56 -0.101358 0.000698 ( 0.000370) 0.102056 ( 0.029896) 0.000695 0.099880 --->beagle1-----beagle2--: 3.96e-18 0.043276 2.43e-107 0.043301 0.091173 ( 0.005630) 0.047872 ( 0.003842) 0.090691 0.047739 --->beagle1-----plink----: 3.96e-18 -0.846012 4.67e-200 -0.846303 0.091173 ( 0.005630) 0.937476 ( 0.007153) 0.090691 0.937808 --->beagle1-----germline1: 3.96e-18 -0.451915 2.08e-113 -0.451899 0.091173 ( 0.005630) 0.543072 ( 0.033759) 0.090691 0.539577 --->beagle1-----germline2: 3.96e-18 -0.155983 4.37e-65 -0.157441 0.091173 ( 0.005630) 0.248614 ( 0.036999) 0.090691 0.247132 --->beagle1-----dash-----: 1.96e-03 -0.008719 5.39e-04 -0.010883 0.091173 ( 0.005630) 0.102056 ( 0.029896) 0.090691 0.099880 --->beagle2-----plink----: 3.96e-18 -0.889433 7.09e-207 -0.889604 0.047872 ( 0.003842) 0.937476 ( 0.007153) 0.047739 0.937808 --->beagle2-----germline1: 3.96e-18 -0.495171 4.54e-118 -0.495199 0.047872 ( 0.003842) 0.543072 ( 0.033759) 0.047739 0.539577 --->beagle2-----germline2: 3.96e-18 -0.199251 9.93e-76 -0.200742 0.047872 ( 0.003842) 0.248614 ( 0.036999) 0.047739 0.247132 --->beagle2-----dash-----: 4.08e-18 -0.052195 3.21e-33 -0.054184 0.047872 ( 0.003842) 0.102056 ( 0.029896) 0.047739 0.099880 --->plink-------germline1: 3.96e-18 0.394261 7.84e-109 0.394405 0.937476 ( 0.007153) 0.543072 ( 0.033759) 0.937808 0.539577 --->plink-------germline2: 3.96e-18 0.689996 2.15e-128 0.688862 0.937476 ( 0.007153) 0.248614 ( 0.036999) 0.937808 0.247132 --->plink-------dash-----: 3.96e-18 0.836596 5.69e-145 0.835420 0.937476 ( 0.007153) 0.102056 ( 0.029896) 0.937808 0.099880 --->germline1---germline2: 3.96e-18 0.294543 9.62e-138 0.294458 0.543072 ( 0.033759) 0.248614 ( 0.036999) 0.539577 0.247132 --->germline1---dash-----: 3.96e-18 0.441178 1.18e-137 0.441016 0.543072 ( 0.033759) 0.102056 ( 0.029896) 0.539577 0.099880 --->germline2---dash-----: 3.96e-18 0.146075 6.86e-109 0.146558 0.248614 ( 0.036999) 0.102056 ( 0.029896) 0.247132 0.099880 ######FDR###### --->fabia-------beagle1--: 6.29e-10 -0.072303 4.92e-14 -0.085733 0.912369 ( 0.097693) 0.998102 ( 0.000438) 0.927347 0.998051 --->fabia-------beagle2--: 1.78e-10 -0.073469 9.14e-14 -0.084400 0.912369 ( 0.097693) 0.996769 ( 0.001321) 0.927347 0.996416 --->fabia-------plink----: 8.66e-10 -0.073149 2.12e-14 -0.087436 0.912369 ( 0.097693) 0.999805 ( 2.81e-05) 0.927347 0.999805 --->fabia-------germline1: 6.29e-10 -0.073964 2.12e-14 -0.087410 0.912369 ( 0.097693) 0.999778 ( 0.000106) 0.927347 0.999766 --->fabia-------germline2: 1.38e-11 -0.090754 2.04e-14 -0.087482 0.912369 ( 0.097693) 0.999851 ( 0.000201) 0.927347 0.999925 --->fabia-------dash-----: 1.64e-12 -0.111520 2e-14 -0.087530 0.912369 ( 0.097693) 0.999899 ( 0.000305) 0.927347 1.000000 --->beagle1-----beagle2--: 1.4e-14 0.001605 4.78e-23 0.001333 0.998102 ( 0.000438) 0.996769 ( 0.001321) 0.998051 0.996416 --->beagle1-----plink----: 4.33e-18 -0.001736 1.49e-63 -0.001703 0.998102 ( 0.000438) 0.999805 ( 2.81e-05) 0.998051 0.999805 --->beagle1-----germline1: 4.33e-18 -0.001711 3.57e-65 -0.001677 0.998102 ( 0.000438) 0.999778 ( 0.000106) 0.998051 0.999766 --->beagle1-----germline2: 4.33e-18 -0.001781 1.76e-63 -0.001749 0.998102 ( 0.000438) 0.999851 ( 0.000201) 0.998051 0.999925 --->beagle1-----dash-----: 4.74e-18 -0.001849 2.73e-58 -0.001797 0.998102 ( 0.000438) 0.999899 ( 0.000305) 0.998051 1.000000 --->beagle2-----plink----: 1.48e-17 -0.003267 8.24e-42 -0.003036 0.996769 ( 0.001321) 0.999805 ( 2.81e-05) 0.996416 0.999805 --->beagle2-----germline1: 1.48e-17 -0.003269 7.34e-42 -0.003010 0.996769 ( 0.001321) 0.999778 ( 0.000106) 0.996416 0.999766 --->beagle2-----germline2: 1.66e-17 -0.003391 2.09e-42 -0.003082 0.996769 ( 0.001321) 0.999851 ( 0.000201) 0.996416 0.999925 --->beagle2-----dash-----: 3.52e-17 -0.003468 1.08e-41 -0.003130 0.996769 ( 0.001321) 0.999899 ( 0.000305) 0.996416 1.000000 --->plink-------germline1: 1e+00 0.000000 1e+00 0.000000 0.999805 ( 2.81e-05) 0.999778 ( 0.000106) 0.999805 0.999766 --->plink-------germline2: 4.08e-04 -6.31e-05 1e+00 0.000000 0.999805 ( 2.81e-05) 0.999851 ( 0.000201) 0.999805 0.999925 --->plink-------dash-----: 1.5e-08 -0.000120 1e+00 0.000000 0.999805 ( 2.81e-05) 0.999899 ( 0.000305) 0.999805 1.000000 --->germline1---germline2: 5.84e-06 -6.59e-05 1e+00 0.000000 0.999778 ( 0.000106) 0.999851 ( 0.000201) 0.999766 0.999925 --->germline1---dash-----: 3.64e-10 -0.000154 6.32e-05 -0.000121 0.999778 ( 0.000106) 0.999899 ( 0.000305) 0.999766 1.000000 --->germline2---dash-----: 1e+00 0.000000 1e+00 0.000000 0.999851 ( 0.000201) 0.999899 ( 0.000305) 0.999925 1.000000 ######specifity###### --->fabia-------beagle1--: 3.96e-18 0.090361 3.72e-121 0.090475 0.999302 ( 0.000370) 0.908827 ( 0.005630) 0.999305 0.909309 --->fabia-------beagle2--: 3.96e-18 0.047187 1.54e-109 0.047174 0.999302 ( 0.000370) 0.952128 ( 0.003842) 0.999305 0.952261 --->fabia-------plink----: 3.96e-18 0.936836 1.09e-211 0.936778 0.999302 ( 0.000370) 0.062524 ( 0.007153) 0.999305 0.062192 --->fabia-------germline1: 3.96e-18 0.542518 1.78e-121 0.542374 0.999302 ( 0.000370) 0.456928 ( 0.033759) 0.999305 0.460423 --->fabia-------germline2: 3.96e-18 0.246609 2.84e-84 0.247916 0.999302 ( 0.000370) 0.751386 ( 0.036999) 0.999305 0.752868 --->fabia-------dash-----: 3.96e-18 0.099660 2.87e-56 0.101358 0.999302 ( 0.000370) 0.897944 ( 0.029896) 0.999305 0.900120 --->beagle1-----beagle2--: 3.96e-18 -0.043274 2.43e-107 -0.043301 0.908827 ( 0.005630) 0.952128 ( 0.003842) 0.909309 0.952261 --->beagle1-----plink----: 3.96e-18 0.846014 4.67e-200 0.846303 0.908827 ( 0.005630) 0.062524 ( 0.007153) 0.909309 0.062192 --->beagle1-----germline1: 3.96e-18 0.451902 2.08e-113 0.451899 0.908827 ( 0.005630) 0.456928 ( 0.033759) 0.909309 0.460423 --->beagle1-----germline2: 3.96e-18 0.155965 4.37e-65 0.157441 0.908827 ( 0.005630) 0.751386 ( 0.036999) 0.909309 0.752868 --->beagle1-----dash-----: 1.96e-03 0.008743 5.39e-04 0.010883 0.908827 ( 0.005630) 0.897944 ( 0.029896) 0.909309 0.900120 --->beagle2-----plink----: 3.96e-18 0.889450 7.09e-207 0.889604 0.952128 ( 0.003842) 0.062524 ( 0.007153) 0.952261 0.062192 --->beagle2-----germline1: 3.96e-18 0.495165 4.54e-118 0.495199 0.952128 ( 0.003842) 0.456928 ( 0.033759) 0.952261 0.460423 --->beagle2-----germline2: 3.96e-18 0.199217 9.93e-76 0.200742 0.952128 ( 0.003842) 0.751386 ( 0.036999) 0.952261 0.752868 --->beagle2-----dash-----: 4.08e-18 0.052236 3.21e-33 0.054184 0.952128 ( 0.003842) 0.897944 ( 0.029896) 0.952261 0.900120 --->plink-------germline1: 3.96e-18 -0.394272 7.84e-109 -0.394405 0.062524 ( 0.007153) 0.456928 ( 0.033759) 0.062192 0.460423 --->plink-------germline2: 3.96e-18 -0.689983 2.15e-128 -0.688862 0.062524 ( 0.007153) 0.751386 ( 0.036999) 0.062192 0.752868 --->plink-------dash-----: 3.96e-18 -0.836593 5.69e-145 -0.835420 0.062524 ( 0.007153) 0.897944 ( 0.029896) 0.062192 0.900120 --->germline1---germline2: 3.96e-18 -0.294518 9.62e-138 -0.294458 0.456928 ( 0.033759) 0.751386 ( 0.036999) 0.460423 0.752868 --->germline1---dash-----: 3.96e-18 -0.441210 1.18e-137 -0.441016 0.456928 ( 0.033759) 0.897944 ( 0.029896) 0.460423 0.900120 --->germline2---dash-----: 3.96e-18 -0.146076 6.86e-109 -0.146558 0.751386 ( 0.036999) 0.897944 ( 0.029896) 0.752868 0.900120 ######sensitivity###### --->fabia-------beagle1--: 2.21e-14 -0.488130 1.22e-14 -0.412420 0.528168 ( 0.430796) 0.940588 ( 0.165033) 0.722820 1.000000 --->fabia-------beagle2--: 1.34e-09 -0.355152 9.44e-09 -0.310473 0.528168 ( 0.430796) 0.838641 ( 0.307421) 0.722820 1.000000 --->fabia-------plink----: 3.54e-18 -0.521877 9.49e-19 -0.471329 0.528168 ( 0.430796) 0.999497 ( 0.003589) 0.722820 1.000000 --->fabia-------germline1: 3.46e-02 -0.107379 1.6e-02 -0.111985 0.528168 ( 0.430796) 0.640152 ( 0.266516) 0.722820 0.666667 --->fabia-------germline2: 7.72e-09 0.391129 2.23e-10 0.333321 0.528168 ( 0.430796) 0.194847 ( 0.246212) 0.722820 0.107671 --->fabia-------dash-----: 3.29e-12 0.774364 9.33e-18 0.472708 0.528168 ( 0.430796) 0.055460 ( 0.145972) 0.722820 0.000000 --->beagle1-----beagle2--: 1e+00 0.000000 1.45e-05 0.101947 0.940588 ( 0.165033) 0.838641 ( 0.307421) 1.000000 1.000000 --->beagle1-----plink----: 1e+00 0.000000 5.62e-04 -0.058909 0.940588 ( 0.165033) 0.999497 ( 0.003589) 1.000000 1.000000 --->beagle1-----germline1: 3.1e-13 0.311348 4.2e-16 0.300435 0.940588 ( 0.165033) 0.640152 ( 0.266516) 1.000000 0.666667 --->beagle1-----germline2: 5.8e-18 0.789477 5.24e-44 0.745740 0.940588 ( 0.165033) 0.194847 ( 0.246212) 1.000000 0.107671 --->beagle1-----dash-----: 1.74e-18 0.951076 6.6e-62 0.885127 0.940588 ( 0.165033) 0.055460 ( 0.145972) 1.000000 0.000000 --->beagle2-----plink----: 1e+00 0.000000 9.57e-07 -0.160856 0.838641 ( 0.307421) 0.999497 ( 0.003589) 1.000000 1.000000 --->beagle2-----germline1: 2.7e-06 0.239272 4.21e-06 0.198488 0.838641 ( 0.307421) 0.640152 ( 0.266516) 1.000000 0.666667 --->beagle2-----germline2: 2.53e-16 0.718135 2.22e-29 0.643794 0.838641 ( 0.307421) 0.194847 ( 0.246212) 1.000000 0.107671 --->beagle2-----dash-----: 2.88e-17 0.916442 1.42e-40 0.783181 0.838641 ( 0.307421) 0.055460 ( 0.145972) 1.000000 0.000000 --->plink-------germline1: 3.86e-17 0.370402 3.57e-24 0.359345 0.999497 ( 0.003589) 0.640152 ( 0.266516) 1.000000 0.666667 --->plink-------germline2: 2.41e-18 0.833400 6.91e-55 0.804650 0.999497 ( 0.003589) 0.194847 ( 0.246212) 1.000000 0.107671 --->plink-------dash-----: 1.38e-19 0.994158 7.67e-83 0.944037 0.999497 ( 0.003589) 0.055460 ( 0.145972) 1.000000 0.000000 --->germline1---germline2: 3.87e-17 0.466983 2.19e-31 0.445305 0.640152 ( 0.266516) 0.194847 ( 0.246212) 0.666667 0.107671 --->germline1---dash-----: 8.45e-18 0.602474 2.57e-40 0.584692 0.640152 ( 0.266516) 0.055460 ( 0.145972) 0.666667 0.000000 --->germline2---dash-----: 5.26e-11 0.231448 1.09e-10 0.139387 0.194847 ( 0.246212) 0.055460 ( 0.145972) 0.107671 0.000000 ######trueN###### --->fabia-------beagle1--: 3.96e-18 10896937 1.51e-227 10897600 2e+07 ( 7412) 9086608 ( 56284) 2e+07 9091288 --->fabia-------beagle2--: 3.96e-18 10464772 7.9e-242 10464674 2e+07 ( 7412) 9519534 ( 38421) 2e+07 9520691 --->fabia-------plink----: 3.96e-18 19359344 7.7e-243 19359083 2e+07 ( 7412) 625124 ( 71519) 2e+07 621808 --->fabia-------germline1: 3.96e-18 15418105 2.73e-166 15415760 2e+07 ( 7412) 4568448 ( 337529) 2e+07 4603468 --->fabia-------germline2: 3.96e-18 12459488 2.83e-153 12471722 2e+07 ( 7412) 7512486 ( 369921) 2e+07 7527409 --->fabia-------dash-----: 3.96e-18 1.1e+07 4.84e-157 1.1e+07 2e+07 ( 7412) 8977795 ( 298888) 2e+07 9e+06 --->beagle1-----beagle2--: 3.96e-18 -432580 2.43e-107 -432926 9086608 ( 56284) 9519534 ( 38421) 9091288 9520691 --->beagle1-----plink----: 3.96e-18 8458484 4.66e-200 8461484 9086608 ( 56284) 625124 ( 71519) 9091288 621808 --->beagle1-----germline1: 3.96e-18 4518444 2.07e-113 4518160 9086608 ( 56284) 4568448 ( 337529) 9091288 4603468 --->beagle1-----germline2: 3.96e-18 1559615 4.38e-65 1574122 9086608 ( 56284) 7512486 ( 369921) 9091288 7527409 --->beagle1-----dash-----: 1.96e-03 87037 5.39e-04 108813 9086608 ( 56284) 8977795 ( 298888) 9091288 9e+06 --->beagle2-----plink----: 3.96e-18 8892946 7.13e-207 8894410 9519534 ( 38421) 625124 ( 71519) 9520691 621808 --->beagle2-----germline1: 3.96e-18 4950624 4.54e-118 4951086 9519534 ( 38421) 4568448 ( 337529) 9520691 4603468 --->beagle2-----germline2: 3.96e-18 1992133 9.94e-76 2007048 9519534 ( 38421) 7512486 ( 369921) 9520691 7527409 --->beagle2-----dash-----: 4.08e-18 522122 3.22e-33 541739 9519534 ( 38421) 8977795 ( 298888) 9520691 9e+06 --->plink-------germline1: 3.96e-18 -3942209 7.86e-109 -3943324 625124 ( 71519) 4568448 ( 337529) 621808 4603468 --->plink-------germline2: 3.96e-18 -6898666 2.15e-128 -6887362 625124 ( 71519) 7512486 ( 369921) 621808 7527409 --->plink-------dash-----: 3.96e-18 -8364455 5.66e-145 -8352671 625124 ( 71519) 8977795 ( 298888) 621808 9e+06 --->germline1---germline2: 3.96e-18 -2945011 9.55e-138 -2944038 4568448 ( 337529) 7512486 ( 369921) 4603468 7527409 --->germline1---dash-----: 3.96e-18 -4410993 1.17e-137 -4409347 4568448 ( 337529) 8977795 ( 298888) 4603468 9e+06 --->germline2---dash-----: 3.96e-18 -1460291 6.83e-109 -1465309 7512486 ( 369921) 8977795 ( 298888) 7527409 9e+06 ######falseP###### --->fabia-------beagle1--: 3.96e-18 -896947 2.73e-120 -897603 13958 ( 7402) 911561 ( 56290) 13909 906728 --->fabia-------beagle2--: 3.96e-18 -464772 4.5e-108 -464677 13958 ( 7402) 478635 ( 38416) 13909 477293 --->fabia-------plink----: 3.96e-18 -9359343 1.36e-211 -9359086 13958 ( 7402) 9373045 ( 71522) 13909 9376368 --->fabia-------germline1: 3.96e-18 -5418078 2.19e-121 -5415763 13958 ( 7402) 5429721 ( 337520) 13909 5394712 --->fabia-------germline2: 3.96e-18 -2459467 3.91e-84 -2471725 13958 ( 7402) 2485683 ( 369924) 13909 2470899 --->fabia-------dash-----: 3.96e-18 -989773 5.78e-56 -1006415 13958 ( 7402) 1020374 ( 298908) 13909 998617 --->beagle1-----beagle2--: 3.96e-18 432587 2.43e-107 432926 911561 ( 56290) 478635 ( 38416) 906728 477293 --->beagle1-----plink----: 3.96e-18 -8458487 4.66e-200 -8461484 911561 ( 56290) 9373045 ( 71522) 906728 9376368 --->beagle1-----germline1: 3.96e-18 -4518445 2.07e-113 -4518160 911561 ( 56290) 5429721 ( 337520) 906728 5394712 --->beagle1-----germline2: 3.96e-18 -1559607 4.38e-65 -1574122 911561 ( 56290) 2485683 ( 369924) 906728 2470899 --->beagle1-----dash-----: 1.96e-03 -87045 5.39e-04 -108813 911561 ( 56290) 1020374 ( 298908) 906728 998617 --->beagle2-----plink----: 3.96e-18 -8892943 7.13e-207 -8894410 478635 ( 38416) 9373045 ( 71522) 477293 9376368 --->beagle2-----germline1: 3.96e-18 -4950627 4.54e-118 -4951086 478635 ( 38416) 5429721 ( 337520) 477293 5394712 --->beagle2-----germline2: 3.96e-18 -1992131 9.94e-76 -2007048 478635 ( 38416) 2485683 ( 369924) 477293 2470899 --->beagle2-----dash-----: 4.08e-18 -522143 3.22e-33 -541739 478635 ( 38416) 1020374 ( 298908) 477293 998617 --->plink-------germline1: 3.96e-18 3942163 7.86e-109 3943324 9373045 ( 71522) 5429721 ( 337520) 9376368 5394712 --->plink-------germline2: 3.96e-18 6898684 2.15e-128 6887362 9373045 ( 71522) 2485683 ( 369924) 9376368 2470899 --->plink-------dash-----: 3.96e-18 8364463 5.66e-145 8352671 9373045 ( 71522) 1020374 ( 298908) 9376368 998617 --->germline1---germline2: 3.96e-18 2945014 9.55e-138 2944038 5429721 ( 337520) 2485683 ( 369924) 5394712 2470899 --->germline1---dash-----: 3.96e-18 4410980 1.17e-137 4409347 5429721 ( 337520) 1020374 ( 298908) 5394712 998617 --->germline2---dash-----: 3.96e-18 1460291 6.83e-109 1465309 2485683 ( 369924) 1020374 ( 298908) 2470899 998617 ######falseN###### --->fabia-------beagle1--: 2.82e-14 803 1.21e-14 739 843 ( 775) 105 ( 269) 498 0 --->fabia-------beagle2--: 2.45e-09 585 9.83e-09 557 843 ( 775) 287 ( 549) 498 0 --->fabia-------plink----: 5.78e-18 906 1.37e-18 842 843 ( 775) 0.92 ( 6.42) 498 0 --->fabia-------germline1: 3.09e-02 198 9.59e-03 221 843 ( 775) 623 ( 435) 498 608 --->fabia-------germline2: 1.08e-08 -730 6.42e-10 -608 843 ( 775) 1451 ( 457) 498 1548 --->fabia-------dash-----: 4.28e-12 -1388 8.17e-17 -882 843 ( 775) 1726 ( 357) 498 1770 --->beagle1-----beagle2--: 1e+00 0.000000 1.95e-05 -182.100000 104.760000 (269.080707) 286.860000 (548.750169) 0.000000 0.000000 --->beagle1-----plink----: 1e+00 0.000000 2.07e-04 103.840000 104.760000 (269.080707) 0.920000 ( 6.417589) 0.000000 0.000000 --->beagle1-----germline1: 1.99e-13 -539 7.4e-17 -518 105 ( 269) 623 ( 435) 0 608 --->beagle1-----germline2: 6.4e-18 -1413 4.95e-44 -1347 105 ( 269) 1451 ( 457) 0 1548 --->beagle1-----dash-----: 4.74e-18 -1686 1.24e-57 -1621 105 ( 269) 1726 ( 357) 0 1770 --->beagle2-----plink----: 1e+00 0.000000 1.05e-06 285.940000 286.860000 (548.750169) 0.920000 ( 6.417589) 0.000000 0.000000 --->beagle2-----germline1: 2.68e-06 -417 9.94e-06 -336 287 ( 549) 623 ( 435) 0 608 --->beagle2-----germline2: 2.78e-16 -1292 7.45e-29 -1165 287 ( 549) 1451 ( 457) 0 1548 --->beagle2-----dash-----: 5.84e-17 -1638 1.93e-38 -1439 287 ( 549) 1726 ( 357) 0 1770 --->plink-------germline1: 3.87e-17 -648 7.75e-26 -622 0.92 ( 6.42) 623 ( 435) 0 608 --->plink-------germline2: 3.95e-18 -1492 1.02e-53 -1450 0.92 ( 6.42) 1451 ( 457) 0 1548 --->plink-------dash-----: 3.95e-18 -1751 1.12e-70 -1725 0.92 ( 6.42) 1726 ( 357) 0 1770 --->germline1---germline2: 3.87e-17 -858 3.22e-29 -829 623 ( 435) 1451 ( 457) 608 1548 --->germline1---dash-----: 8.46e-18 -1120 2.29e-35 -1103 623 ( 435) 1726 ( 357) 608 1770 --->germline2---dash-----: 5.28e-11 -431 7.71e-10 -274 1451 ( 457) 1726 ( 357) 1548 1770 ######trueP###### --->fabia-------beagle1--: 2.9e-14 -798 1.21e-14 -736 991 ( 835) 1727 ( 383) 1317 1776 --->fabia-------beagle2--: 2.56e-09 -583 1.02e-08 -554 991 ( 835) 1544 ( 618) 1317 1738 --->fabia-------plink----: 5.78e-18 -898 1.33e-18 -840 991 ( 835) 1830 ( 263) 1317 1815 --->fabia-------germline1: 3.4e-02 -194 1.05e-02 -218 991 ( 835) 1209 ( 590) 1317 1252 --->fabia-------germline2: 9.72e-09 733 4.81e-10 611 991 ( 835) 380 ( 517) 1317 192 --->fabia-------dash-----: 4.03e-12 1405 5.61e-17 885 991 ( 835) 106 ( 298) 1317 0 --->beagle1-----beagle2--: 1.94e-05 736 1.95e-05 182 1727 ( 383) 1544 ( 618) 1776 1738 --->beagle1-----plink----: 1.3e-06 -211 2.07e-04 -104 1727 ( 383) 1830 ( 263) 1776 1815 --->beagle1-----germline1: 1.99e-13 539 7.4e-17 518 1727 ( 383) 1209 ( 590) 1776 1252 --->beagle1-----germline2: 6.4e-18 1413 4.95e-44 1347 1727 ( 383) 380 ( 517) 1776 192 --->beagle1-----dash-----: 4.74e-18 1686 1.24e-57 1621 1727 ( 383) 106 ( 298) 1776 0 --->beagle2-----plink----: 6.04e-09 -432 1.05e-06 -286 1544 ( 618) 1830 ( 263) 1738 1815 --->beagle2-----germline1: 2.68e-06 417 9.94e-06 336 1544 ( 618) 1209 ( 590) 1738 1252 --->beagle2-----germline2: 2.78e-16 1292 7.45e-29 1165 1544 ( 618) 380 ( 517) 1738 192 --->beagle2-----dash-----: 5.84e-17 1638 1.93e-38 1439 1544 ( 618) 106 ( 298) 1738 0 --->plink-------germline1: 3.87e-17 648 7.75e-26 622 1830 ( 263) 1209 ( 590) 1815 1252 --->plink-------germline2: 3.95e-18 1492 1.02e-53 1450 1830 ( 263) 380 ( 517) 1815 192 --->plink-------dash-----: 3.95e-18 1751 1.12e-70 1725 1830 ( 263) 106 ( 298) 1815 0 --->germline1---germline2: 3.87e-17 858 3.22e-29 829 1209 ( 590) 380 ( 517) 1252 192 --->germline1---dash-----: 8.46e-18 1120 2.29e-35 1103 1209 ( 590) 106 ( 298) 1252 0 --->germline2---dash-----: 5.28e-11 431 7.71e-10 274 380 ( 517) 106 ( 298) 192 0 ######MatthewsSnps###### --->fabia-------beagle1--: 1e+00 0.000000 1e+00 0.000000 0.115113 ( 0.114754) 0.000000 ( 0.000000) 0.152304 0.000000 --->fabia-------beagle2--: 1e+00 0.000000 1e+00 0.000000 0.115113 ( 0.114754) 0.000000 ( 0.000000) 0.152304 0.000000 --->fabia-------plink----: 6.05e-12 0.133551 2.34e-16 0.112954 0.115113 ( 0.114754) 0.002159 ( 0.000571) 0.152304 0.001888 --->fabia-------germline1: 1e+00 0.000000 1e+00 0.000000 0.115113 ( 0.114754) 0.000000 ( 0.000000) 0.152304 0.000000 --->fabia-------germline2: 5.63e-12 0.135374 2.35e-16 0.114163 0.115113 ( 0.114754) 0.000950 ( 0.004174) 0.152304 0.000000 --->fabia-------dash-----: 4.22e-10 0.123124 1.77e-10 0.134193 0.115113 ( 0.114754) -0.019079 ( 0.157554) 0.152304 0.054030 --->beagle1-----beagle2--: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.000000 ( 0.000000) 0.000000 0.000000 --->beagle1-----plink----: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.002159 ( 0.000571) 0.000000 0.001888 --->beagle1-----germline1: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.000000 ( 0.000000) 0.000000 0.000000 --->beagle1-----germline2: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.000950 ( 0.004174) 0.000000 0.000000 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) -0.019079 ( 0.157554) 0.000000 0.054030 --->beagle2-----plink----: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.002159 ( 0.000571) 0.000000 0.001888 --->beagle2-----germline1: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.000000 ( 0.000000) 0.000000 0.000000 --->beagle2-----germline2: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.000950 ( 0.004174) 0.000000 0.000000 --->beagle2-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) -0.019079 ( 0.157554) 0.000000 0.054030 --->plink-------germline1: 1e+00 0.000000 1e+00 0.000000 0.002159 ( 0.000571) 0.000000 ( 0.000000) 0.001888 0.000000 --->plink-------germline2: 2.65e-12 0.002059 5.83e-03 0.001209 0.002159 ( 0.000571) 0.000950 ( 0.004174) 0.001888 0.000000 --->plink-------dash-----: 3.35e-01 -0.027865 1.81e-01 0.021238 0.002159 ( 0.000571) -0.019079 ( 0.157554) 0.001888 0.054030 --->germline1---germline2: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.000950 ( 0.004174) 0.000000 0.000000 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) -0.019079 ( 0.157554) 0.000000 0.054030 --->germline2---dash-----: 3.11e-01 -0.029527 2.06e-01 0.020029 0.000950 ( 0.004174) -0.019079 ( 0.157554) 0.000000 0.054030 ######F1Snps###### --->fabia-------beagle1--: 5.56e-11 0.044763 1.43e-14 0.040276 0.099572 ( 0.047479) 0.059296 ( 0.008187) 0.107083 0.058724 --->fabia-------beagle2--: 5.56e-11 0.044763 1.43e-14 0.040276 0.099572 ( 0.047479) 0.059296 ( 0.008187) 0.107083 0.058724 --->fabia-------plink----: 5.56e-11 0.044764 1.44e-14 0.040267 0.099572 ( 0.047479) 0.059305 ( 0.008188) 0.107083 0.058735 --->fabia-------germline1: 5.56e-11 0.044763 1.43e-14 0.040276 0.099572 ( 0.047479) 0.059296 ( 0.008187) 0.107083 0.058724 --->fabia-------germline2: 6.09e-11 0.044786 1.54e-14 0.040242 0.099572 ( 0.047479) 0.059329 ( 0.008167) 0.107083 0.058724 --->fabia-------dash-----: 3.28e-11 0.047983 1.1e-14 0.043807 0.099572 ( 0.047479) 0.055764 ( 0.024915) 0.107083 0.062954 --->beagle1-----beagle2--: 1e+00 0.000000 1e+00 0.000000 0.059296 ( 0.008187) 0.059296 ( 0.008187) 0.058724 0.058724 --->beagle1-----plink----: 1e+00 0.000000 1e+00 0.000000 0.059296 ( 0.008187) 0.059305 ( 0.008188) 0.058724 0.058735 --->beagle1-----germline1: 1e+00 0.000000 1e+00 0.000000 0.059296 ( 0.008187) 0.059296 ( 0.008187) 0.058724 0.058724 --->beagle1-----germline2: 1e+00 0.000000 1e+00 0.000000 0.059296 ( 0.008187) 0.059329 ( 0.008167) 0.058724 0.058724 --->beagle1-----dash-----: 3.08e-01 -0.003200 1.31e-01 0.003532 0.059296 ( 0.008187) 0.055764 ( 0.024915) 0.058724 0.062954 --->beagle2-----plink----: 1e+00 0.000000 1e+00 0.000000 0.059296 ( 0.008187) 0.059305 ( 0.008188) 0.058724 0.058735 --->beagle2-----germline1: 1e+00 0.000000 1e+00 0.000000 0.059296 ( 0.008187) 0.059296 ( 0.008187) 0.058724 0.058724 --->beagle2-----germline2: 1e+00 0.000000 1e+00 0.000000 0.059296 ( 0.008187) 0.059329 ( 0.008167) 0.058724 0.058724 --->beagle2-----dash-----: 3.08e-01 -0.003200 1.31e-01 0.003532 0.059296 ( 0.008187) 0.055764 ( 0.024915) 0.058724 0.062954 --->plink-------germline1: 1e+00 0.000000 1e+00 0.000000 0.059305 ( 0.008188) 0.059296 ( 0.008187) 0.058735 0.058724 --->plink-------germline2: 1e+00 0.000000 1e+00 0.000000 0.059305 ( 0.008188) 0.059329 ( 0.008167) 0.058735 0.058724 --->plink-------dash-----: 3.08e-01 -0.003189 1.3e-01 0.003541 0.059305 ( 0.008188) 0.055764 ( 0.024915) 0.058735 0.062954 --->germline1---germline2: 1e+00 0.000000 1e+00 0.000000 0.059296 ( 0.008187) 0.059329 ( 0.008167) 0.058724 0.058724 --->germline1---dash-----: 3.08e-01 -0.003200 1.31e-01 0.003532 0.059296 ( 0.008187) 0.055764 ( 0.024915) 0.058724 0.062954 --->germline2---dash-----: 3.13e-01 -0.003182 1.27e-01 0.003565 0.059329 ( 0.008167) 0.055764 ( 0.024915) 0.058724 0.062954 ######accuracySnps###### --->fabia-------beagle1--: 3.96e-18 0.532642 2.27e-83 0.531683 0.562255 ( 0.081297) 0.030572 ( 0.004353) 0.562400 0.030250 --->fabia-------beagle2--: 3.96e-18 0.532642 2.27e-83 0.531683 0.562255 ( 0.081297) 0.030572 ( 0.004353) 0.562400 0.030250 --->fabia-------plink----: 3.96e-18 0.532417 2.32e-83 0.531526 0.562255 ( 0.081297) 0.030729 ( 0.004360) 0.562400 0.030450 --->fabia-------germline1: 3.96e-18 0.532642 2.27e-83 0.531683 0.562255 ( 0.081297) 0.030572 ( 0.004353) 0.562400 0.030250 --->fabia-------germline2: 3.96e-18 0.531862 3.51e-83 0.531043 0.562255 ( 0.081297) 0.031212 ( 0.004741) 0.562400 0.030850 --->fabia-------dash-----: 3.96e-18 0.386746 2.98e-56 0.385227 0.562255 ( 0.081297) 0.177028 ( 0.080253) 0.562400 0.166000 --->beagle1-----beagle2--: 1e+00 0.000000 1e+00 0.000000 0.030572 ( 0.004353) 0.030572 ( 0.004353) 0.030250 0.030250 --->beagle1-----plink----: 2.61e-18 -0.000180 4.54e-35 -0.000157 0.030572 ( 0.004353) 0.030729 ( 0.004360) 0.030250 0.030450 --->beagle1-----germline1: 1e+00 0.000000 1e+00 0.000000 0.030572 ( 0.004353) 0.030572 ( 0.004353) 0.030250 0.030250 --->beagle1-----germline2: 1e+00 0.000000 2.46e-02 -0.000640 0.030572 ( 0.004353) 0.031212 ( 0.004741) 0.030250 0.030850 --->beagle1-----dash-----: 3.93e-18 -0.140824 2.74e-33 -0.146456 0.030572 ( 0.004353) 0.177028 ( 0.080253) 0.030250 0.166000 --->beagle2-----plink----: 2.61e-18 -0.000180 4.54e-35 -0.000157 0.030572 ( 0.004353) 0.030729 ( 0.004360) 0.030250 0.030450 --->beagle2-----germline1: 1e+00 0.000000 1e+00 0.000000 0.030572 ( 0.004353) 0.030572 ( 0.004353) 0.030250 0.030250 --->beagle2-----germline2: 1e+00 0.000000 2.46e-02 -0.000640 0.030572 ( 0.004353) 0.031212 ( 0.004741) 0.030250 0.030850 --->beagle2-----dash-----: 3.93e-18 -0.140824 2.74e-33 -0.146456 0.030572 ( 0.004353) 0.177028 ( 0.080253) 0.030250 0.166000 --->plink-------germline1: 2.61e-18 0.000180 4.54e-35 0.000157 0.030729 ( 0.004360) 0.030572 ( 0.004353) 0.030450 0.030250 --->plink-------germline2: 2.14e-12 0.000130 8.92e-02 -0.000483 0.030729 ( 0.004360) 0.031212 ( 0.004741) 0.030450 0.030850 --->plink-------dash-----: 3.95e-18 -0.140726 2.99e-33 -0.146299 0.030729 ( 0.004360) 0.177028 ( 0.080253) 0.030450 0.166000 --->germline1---germline2: 1e+00 0.000000 2.46e-02 -0.000640 0.030572 ( 0.004353) 0.031212 ( 0.004741) 0.030250 0.030850 --->germline1---dash-----: 3.93e-18 -0.140824 2.74e-33 -0.146456 0.030572 ( 0.004353) 0.177028 ( 0.080253) 0.030250 0.166000 --->germline2---dash-----: 3.93e-18 -0.140756 3.38e-33 -0.145816 0.031212 ( 0.004741) 0.177028 ( 0.080253) 0.030850 0.166000 ######FPRSnps###### --->fabia-------beagle1--: 1e+00 0.000000 1e+00 0.000000 0.444492 ( 0.083480) 1.000000 ( 0.000000) 0.443830 1.000000 --->fabia-------beagle2--: 1e+00 0.000000 1e+00 0.000000 0.444492 ( 0.083480) 1.000000 ( 0.000000) 0.443830 1.000000 --->fabia-------plink----: 3.96e-18 -0.556267 5.48e-84 -0.555346 0.444492 ( 0.083480) 0.999838 ( 8.47e-05) 0.443830 0.999896 --->fabia-------germline1: 1e+00 0.000000 1e+00 0.000000 0.444492 ( 0.083480) 1.000000 ( 0.000000) 0.443830 1.000000 --->fabia-------germline2: 3.96e-18 -0.555972 7.71e-84 -0.554850 0.444492 ( 0.083480) 0.999342 ( 0.002882) 0.443830 1.000000 --->fabia-------dash-----: 3.96e-18 -0.400507 2.04e-56 -0.398162 0.444492 ( 0.083480) 0.842654 ( 0.084578) 0.443830 0.852867 --->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) 0.999838 ( 8.47e-05) 1.000000 0.999896 --->beagle1-----germline1: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 1.000000 ( 0.000000) 1.000000 1.000000 --->beagle1-----germline2: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 0.999342 ( 0.002882) 1.000000 1.000000 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 0.842654 ( 0.084578) 1.000000 0.852867 --->beagle2-----plink----: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 0.999838 ( 8.47e-05) 1.000000 0.999896 --->beagle2-----germline1: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 1.000000 ( 0.000000) 1.000000 1.000000 --->beagle2-----germline2: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 0.999342 ( 0.002882) 1.000000 1.000000 --->beagle2-----dash-----: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 0.842654 ( 0.084578) 1.000000 0.852867 --->plink-------germline1: 1e+00 0.000000 1e+00 0.000000 0.999838 ( 8.47e-05) 1.000000 ( 0.000000) 0.999896 1.000000 --->plink-------germline2: 2.62e-12 -0.000136 8.95e-02 0.000496 0.999838 ( 8.47e-05) 0.999342 ( 0.002882) 0.999896 1.000000 --->plink-------dash-----: 3.96e-18 0.151700 4.77e-34 0.157184 0.999838 ( 8.47e-05) 0.842654 ( 0.084578) 0.999896 0.852867 --->germline1---germline2: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 0.999342 ( 0.002882) 1.000000 1.000000 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 0.842654 ( 0.084578) 1.000000 0.852867 --->germline2---dash-----: 3.96e-18 0.151402 5.52e-34 0.156688 0.999342 ( 0.002882) 0.842654 ( 0.084578) 1.000000 0.852867 ######FDRSnps###### --->fabia-------beagle1--: 1.18e-11 -0.024989 2.45e-15 -0.022848 0.946580 ( 0.025938) 0.969428 ( 0.004353) 0.943018 0.969750 --->fabia-------beagle2--: 1.18e-11 -0.024989 2.45e-15 -0.022848 0.946580 ( 0.025938) 0.969428 ( 0.004353) 0.943018 0.969750 --->fabia-------plink----: 1.18e-11 -0.024979 2.48e-15 -0.022844 0.946580 ( 0.025938) 0.969423 ( 0.004354) 0.943018 0.969744 --->fabia-------germline1: 1.18e-11 -0.024989 2.45e-15 -0.022848 0.946580 ( 0.025938) 0.969428 ( 0.004353) 0.943018 0.969750 --->fabia-------germline2: 1.27e-11 -0.024960 2.65e-15 -0.022831 0.946580 ( 0.025938) 0.969410 ( 0.004343) 0.943018 0.969750 --->fabia-------dash-----: 1.47e-11 -0.026460 2.52e-15 -0.024498 0.946580 ( 0.025938) 0.971077 ( 0.012974) 0.943018 0.967414 --->beagle1-----beagle2--: 1e+00 0.000000 1e+00 0.000000 0.969428 ( 0.004353) 0.969428 ( 0.004353) 0.969750 0.969750 --->beagle1-----plink----: 1e+00 0.000000 1e+00 0.000000 0.969428 ( 0.004353) 0.969423 ( 0.004354) 0.969750 0.969744 --->beagle1-----germline1: 1e+00 0.000000 1e+00 0.000000 0.969428 ( 0.004353) 0.969428 ( 0.004353) 0.969750 0.969750 --->beagle1-----germline2: 1e+00 0.000000 1e+00 0.000000 0.969428 ( 0.004353) 0.969410 ( 0.004343) 0.969750 0.969750 --->beagle1-----dash-----: 2.75e-01 0.001762 1.74e-01 -0.001649 0.969428 ( 0.004353) 0.971077 ( 0.012974) 0.969750 0.967414 --->beagle2-----plink----: 1e+00 0.000000 1e+00 0.000000 0.969428 ( 0.004353) 0.969423 ( 0.004354) 0.969750 0.969744 --->beagle2-----germline1: 1e+00 0.000000 1e+00 0.000000 0.969428 ( 0.004353) 0.969428 ( 0.004353) 0.969750 0.969750 --->beagle2-----germline2: 1e+00 0.000000 1e+00 0.000000 0.969428 ( 0.004353) 0.969410 ( 0.004343) 0.969750 0.969750 --->beagle2-----dash-----: 2.75e-01 0.001762 1.74e-01 -0.001649 0.969428 ( 0.004353) 0.971077 ( 0.012974) 0.969750 0.967414 --->plink-------germline1: 1e+00 0.000000 1e+00 0.000000 0.969423 ( 0.004354) 0.969428 ( 0.004353) 0.969744 0.969750 --->plink-------germline2: 1e+00 0.000000 1e+00 0.000000 0.969423 ( 0.004354) 0.969410 ( 0.004343) 0.969744 0.969750 --->plink-------dash-----: 2.75e-01 0.001755 1.73e-01 -0.001654 0.969423 ( 0.004354) 0.971077 ( 0.012974) 0.969744 0.967414 --->germline1---germline2: 1e+00 0.000000 1e+00 0.000000 0.969428 ( 0.004353) 0.969410 ( 0.004343) 0.969750 0.969750 --->germline1---dash-----: 2.75e-01 0.001762 1.74e-01 -0.001649 0.969428 ( 0.004353) 0.971077 ( 0.012974) 0.969750 0.967414 --->germline2---dash-----: 2.8e-01 0.001753 1.69e-01 -0.001667 0.969410 ( 0.004343) 0.971077 ( 0.012974) 0.969750 0.967414 ######specifitySnps###### --->fabia-------beagle1--: 1e+00 0.000000 1e+00 0.000000 0.555508 ( 0.083480) 0.000000 ( 0.000000) 0.556170 0.000000 --->fabia-------beagle2--: 1e+00 0.000000 1e+00 0.000000 0.555508 ( 0.083480) 0.000000 ( 0.000000) 0.556170 0.000000 --->fabia-------plink----: 3.96e-18 0.556279 5.48e-84 0.555346 0.555508 ( 0.083480) 0.000162 ( 8.47e-05) 0.556170 0.000104 --->fabia-------germline1: 1e+00 0.000000 1e+00 0.000000 0.555508 ( 0.083480) 0.000000 ( 0.000000) 0.556170 0.000000 --->fabia-------germline2: 3.96e-18 0.555979 7.71e-84 0.554850 0.555508 ( 0.083480) 0.000658 ( 0.002882) 0.556170 0.000000 --->fabia-------dash-----: 3.96e-18 0.400551 2.04e-56 0.398162 0.555508 ( 0.083480) 0.157346 ( 0.084578) 0.556170 0.147133 --->beagle1-----beagle2--: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.000000 ( 0.000000) 0.000000 0.000000 --->beagle1-----plink----: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.000162 ( 8.47e-05) 0.000000 0.000104 --->beagle1-----germline1: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.000000 ( 0.000000) 0.000000 0.000000 --->beagle1-----germline2: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.000658 ( 0.002882) 0.000000 0.000000 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.157346 ( 0.084578) 0.000000 0.147133 --->beagle2-----plink----: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.000162 ( 8.47e-05) 0.000000 0.000104 --->beagle2-----germline1: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.000000 ( 0.000000) 0.000000 0.000000 --->beagle2-----germline2: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.000658 ( 0.002882) 0.000000 0.000000 --->beagle2-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.157346 ( 0.084578) 0.000000 0.147133 --->plink-------germline1: 1e+00 0.000000 1e+00 0.000000 0.000162 ( 8.47e-05) 0.000000 ( 0.000000) 0.000104 0.000000 --->plink-------germline2: 2.65e-12 0.000113 8.95e-02 -0.000496 0.000162 ( 8.47e-05) 0.000658 ( 0.002882) 0.000104 0.000000 --->plink-------dash-----: 3.96e-18 -0.151736 4.77e-34 -0.157184 0.000162 ( 8.47e-05) 0.157346 ( 0.084578) 0.000104 0.147133 --->germline1---germline2: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.000658 ( 0.002882) 0.000000 0.000000 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.157346 ( 0.084578) 0.000000 0.147133 --->germline2---dash-----: 3.96e-18 -0.151435 5.52e-34 -0.156688 0.000658 ( 0.002882) 0.157346 ( 0.084578) 0.000000 0.147133 ######sensitivitySnps###### --->fabia-------beagle1--: 1e+00 0.000000 1e+00 0.000000 0.768680 ( 0.317912) 1.000000 ( 0.000000) 0.934603 1.000000 --->fabia-------beagle2--: 1e+00 0.000000 1e+00 0.000000 0.768680 ( 0.317912) 1.000000 ( 0.000000) 0.934603 1.000000 --->fabia-------plink----: 1e+00 0.000000 1e+00 0.000000 0.768680 ( 0.317912) 1.000000 ( 0.000000) 0.934603 1.000000 --->fabia-------germline1: 1e+00 0.000000 1e+00 0.000000 0.768680 ( 0.317912) 1.000000 ( 0.000000) 0.934603 1.000000 --->fabia-------germline2: 1e+00 0.000000 1e+00 0.000000 0.768680 ( 0.317912) 1.000000 ( 0.000000) 0.934603 1.000000 --->fabia-------dash-----: 4e-01 -0.038719 5.34e-01 -0.026408 0.768680 ( 0.317912) 0.795088 ( 0.340769) 0.934603 1.000000 --->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) 1.000000 ( 0.000000) 1.000000 1.000000 --->beagle1-----germline1: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 1.000000 ( 0.000000) 1.000000 1.000000 --->beagle1-----germline2: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 1.000000 ( 0.000000) 1.000000 1.000000 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 0.795088 ( 0.340769) 1.000000 1.000000 --->beagle2-----plink----: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 1.000000 ( 0.000000) 1.000000 1.000000 --->beagle2-----germline1: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 1.000000 ( 0.000000) 1.000000 1.000000 --->beagle2-----germline2: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 1.000000 ( 0.000000) 1.000000 1.000000 --->beagle2-----dash-----: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 0.795088 ( 0.340769) 1.000000 1.000000 --->plink-------germline1: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 1.000000 ( 0.000000) 1.000000 1.000000 --->plink-------germline2: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 1.000000 ( 0.000000) 1.000000 1.000000 --->plink-------dash-----: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 0.795088 ( 0.340769) 1.000000 1.000000 --->germline1---germline2: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 1.000000 ( 0.000000) 1.000000 1.000000 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 0.795088 ( 0.340769) 1.000000 1.000000 --->germline2---dash-----: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 0.795088 ( 0.340769) 1.000000 1.000000 ######trueNSnps###### --->fabia-------beagle1--: 1e+00 0 1e+00 0 5385 ( 809) 0 ( 0) 5386 0 --->fabia-------beagle2--: 1e+00 0 1e+00 0 5385 ( 809) 0 ( 0) 5386 0 --->fabia-------plink----: 3.96e-18 5392 5.4e-84 5384 5385 ( 809) 1.57 ( 0.82) 5386 1 --->fabia-------germline1: 1e+00 0 1e+00 0 5385 ( 809) 0 ( 0) 5386 0 --->fabia-------germline2: 3.96e-18 5387 7.48e-84 5379 5385 ( 809) 6.4 ( 28) 5386 0 --->fabia-------dash-----: 3.96e-18 3881 1.76e-56 3859 5385 ( 809) 1526 ( 821) 5386 1420 --->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) 1.570000 ( 0.819645) 0.000000 1.000000 --->beagle1-----germline1: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.000000 ( 0.000000) 0.000000 0.000000 --->beagle1-----germline2: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 6.400000 (28.037493) 0.000000 0.000000 --->beagle1-----dash-----: 1e+00 0 1e+00 0 0 ( 0) 1526 ( 821) 0 1420 --->beagle2-----plink----: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 1.570000 ( 0.819645) 0.000000 1.000000 --->beagle2-----germline1: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.000000 ( 0.000000) 0.000000 0.000000 --->beagle2-----germline2: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 6.400000 (28.037493) 0.000000 0.000000 --->beagle2-----dash-----: 1e+00 0 1e+00 0 0 ( 0) 1526 ( 821) 0 1420 --->plink-------germline1: 1e+00 0.000000 1e+00 0.000000 1.570000 ( 0.819645) 0.000000 ( 0.000000) 1.000000 0.000000 --->plink-------germline2: 7.32e-13 1.499973 8.92e-02 -4.830000 1.570000 ( 0.819645) 6.400000 (28.037493) 1.000000 0.000000 --->plink-------dash-----: 3.95e-18 -1471 5.14e-34 -1524 1.57 ( 0.82) 1526 ( 821) 1 1420 --->germline1---germline2: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 6.400000 (28.037493) 0.000000 0.000000 --->germline1---dash-----: 1e+00 0 1e+00 0 0 ( 0) 1526 ( 821) 0 1420 --->germline2---dash-----: 3.92e-18 -1472 5.93e-34 -1519 6.4 ( 28) 1526 ( 821) 0 1420 ######falsePSnps###### --->fabia-------beagle1--: 3.96e-18 -5393 5.28e-84 -5385 4309 ( 811) 9694 ( 43.5) 4307 9698 --->fabia-------beagle2--: 3.96e-18 -5393 5.28e-84 -5385 4309 ( 811) 9694 ( 43.5) 4307 9698 --->fabia-------plink----: 3.96e-18 -5392 5.4e-84 -5384 4309 ( 811) 9693 ( 43.6) 4307 9696 --->fabia-------germline1: 3.96e-18 -5393 5.28e-84 -5385 4309 ( 811) 9694 ( 43.5) 4307 9698 --->fabia-------germline2: 3.96e-18 -5387 7.48e-84 -5379 4309 ( 811) 9688 ( 47.4) 4307 9692 --->fabia-------dash-----: 3.96e-18 -3881 1.76e-56 -3859 4309 ( 811) 8169 ( 817) 4307 8265 --->beagle1-----beagle2--: 1e+00 0 1e+00 0 9694 ( 43.5) 9694 ( 43.5) 9698 9698 --->beagle1-----plink----: 3.51e-19 1.5 4.54e-35 1.57 9694 ( 43.5) 9693 ( 43.6) 9698 9696 --->beagle1-----germline1: 1e+00 0 1e+00 0 9694 ( 43.5) 9694 ( 43.5) 9698 9698 --->beagle1-----germline2: 1e+00 0 2.46e-02 6.4 9694 ( 43.5) 9688 ( 47.4) 9698 9692 --->beagle1-----dash-----: 3.92e-18 1472 4.72e-34 1526 9694 ( 43.5) 8169 ( 817) 9698 8265 --->beagle2-----plink----: 3.51e-19 1.5 4.54e-35 1.57 9694 ( 43.5) 9693 ( 43.6) 9698 9696 --->beagle2-----germline1: 1e+00 0 1e+00 0 9694 ( 43.5) 9694 ( 43.5) 9698 9698 --->beagle2-----germline2: 1e+00 0 2.46e-02 6.4 9694 ( 43.5) 9688 ( 47.4) 9698 9692 --->beagle2-----dash-----: 3.92e-18 1472 4.72e-34 1526 9694 ( 43.5) 8169 ( 817) 9698 8265 --->plink-------germline1: 3.51e-19 -1.5 4.54e-35 -1.57 9693 ( 43.6) 9694 ( 43.5) 9696 9698 --->plink-------germline2: 7.32e-13 -1.5 8.92e-02 4.83 9693 ( 43.6) 9688 ( 47.4) 9696 9692 --->plink-------dash-----: 3.95e-18 1471 5.14e-34 1524 9693 ( 43.6) 8169 ( 817) 9696 8265 --->germline1---germline2: 1e+00 0 2.46e-02 6.4 9694 ( 43.5) 9688 ( 47.4) 9698 9692 --->germline1---dash-----: 3.92e-18 1472 4.72e-34 1526 9694 ( 43.5) 8169 ( 817) 9698 8265 --->germline2---dash-----: 3.92e-18 1472 5.93e-34 1519 9688 ( 47.4) 8169 ( 817) 9692 8265 ######falseNSnps###### --->fabia-------beagle1--: 1e+00 0 1e+00 0 68.3 ( 93.4) 0 ( 0) 20 0 --->fabia-------beagle2--: 1e+00 0 1e+00 0 68.3 ( 93.4) 0 ( 0) 20 0 --->fabia-------plink----: 1e+00 0 1e+00 0 68.3 ( 93.4) 0 ( 0) 20 0 --->fabia-------germline1: 1e+00 0 1e+00 0 68.3 ( 93.4) 0 ( 0) 20 0 --->fabia-------germline2: 1e+00 0 1e+00 0 68.3 ( 93.4) 0 ( 0) 20 0 --->fabia-------dash-----: 4.13e-01 12 5.89e-01 7.1 68.3 ( 93.4) 61.2 ( 102) 20 0 --->beagle1-----beagle2--: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.000000 ( 0.000000) 0.000000 0.000000 --->beagle1-----plink----: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.000000 ( 0.000000) 0.000000 0.000000 --->beagle1-----germline1: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.000000 ( 0.000000) 0.000000 0.000000 --->beagle1-----germline2: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.000000 ( 0.000000) 0.000000 0.000000 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 61.180000 (102.128893) 0.000000 0.000000 --->beagle2-----plink----: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.000000 ( 0.000000) 0.000000 0.000000 --->beagle2-----germline1: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.000000 ( 0.000000) 0.000000 0.000000 --->beagle2-----germline2: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.000000 ( 0.000000) 0.000000 0.000000 --->beagle2-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 61.180000 (102.128893) 0.000000 0.000000 --->plink-------germline1: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.000000 ( 0.000000) 0.000000 0.000000 --->plink-------germline2: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.000000 ( 0.000000) 0.000000 0.000000 --->plink-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 61.180000 (102.128893) 0.000000 0.000000 --->germline1---germline2: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.000000 ( 0.000000) 0.000000 0.000000 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 61.180000 (102.128893) 0.000000 0.000000 --->germline2---dash-----: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 61.180000 (102.128893) 0.000000 0.000000 ######truePSnps###### --->fabia-------beagle1--: 2.48e-13 -83 6.89e-11 -68.3 237 ( 106) 306 ( 43.5) 266 302 --->fabia-------beagle2--: 2.48e-13 -83 6.89e-11 -68.3 237 ( 106) 306 ( 43.5) 266 302 --->fabia-------plink----: 2.48e-13 -83 6.89e-11 -68.3 237 ( 106) 306 ( 43.5) 266 302 --->fabia-------germline1: 2.48e-13 -83 6.89e-11 -68.3 237 ( 106) 306 ( 43.5) 266 302 --->fabia-------germline2: 2.48e-13 -83 6.89e-11 -68.3 237 ( 106) 306 ( 43.5) 266 302 --->fabia-------dash-----: 4.13e-01 -12 5.89e-01 -7.1 237 ( 106) 245 ( 112) 266 284 --->beagle1-----beagle2--: 1e+00 0 1e+00 0 306 ( 43.5) 306 ( 43.5) 302 302 --->beagle1-----plink----: 1e+00 0 1e+00 0 306 ( 43.5) 306 ( 43.5) 302 302 --->beagle1-----germline1: 1e+00 0 1e+00 0 306 ( 43.5) 306 ( 43.5) 302 302 --->beagle1-----germline2: 1e+00 0 1e+00 0 306 ( 43.5) 306 ( 43.5) 302 302 --->beagle1-----dash-----: 3.82e-07 179 3.39e-08 61.2 306 ( 43.5) 245 ( 112) 302 284 --->beagle2-----plink----: 1e+00 0 1e+00 0 306 ( 43.5) 306 ( 43.5) 302 302 --->beagle2-----germline1: 1e+00 0 1e+00 0 306 ( 43.5) 306 ( 43.5) 302 302 --->beagle2-----germline2: 1e+00 0 1e+00 0 306 ( 43.5) 306 ( 43.5) 302 302 --->beagle2-----dash-----: 3.82e-07 179 3.39e-08 61.2 306 ( 43.5) 245 ( 112) 302 284 --->plink-------germline1: 1e+00 0 1e+00 0 306 ( 43.5) 306 ( 43.5) 302 302 --->plink-------germline2: 1e+00 0 1e+00 0 306 ( 43.5) 306 ( 43.5) 302 302 --->plink-------dash-----: 3.82e-07 179 3.39e-08 61.2 306 ( 43.5) 245 ( 112) 302 284 --->germline1---germline2: 1e+00 0 1e+00 0 306 ( 43.5) 306 ( 43.5) 302 302 --->germline1---dash-----: 3.82e-07 179 3.39e-08 61.2 306 ( 43.5) 245 ( 112) 302 284 --->germline2---dash-----: 3.82e-07 179 3.39e-08 61.2 306 ( 43.5) 245 ( 112) 302 284 ######MatthewsSample###### --->fabia-------beagle1--: 2.92e-03 0.041060 1.02e-04 0.034976 0.117044 ( 0.086320) 0.082067 ( 0.018617) 0.159516 0.087118 --->fabia-------beagle2--: 5.17e-01 -0.004220 6.9e-02 -0.017886 0.117044 ( 0.086320) 0.134929 ( 0.053223) 0.159516 0.156860 --->fabia-------plink----: 1e+00 0.000000 1e+00 0.000000 0.117044 ( 0.086320) 0.000000 ( 0.000000) 0.159516 0.000000 --->fabia-------germline1: 1.1e-14 0.120940 1.17e-23 0.113745 0.117044 ( 0.086320) 0.003299 ( 0.026671) 0.159516 0.014352 --->fabia-------germline2: 6.37e-15 0.125766 8.06e-24 0.119936 0.117044 ( 0.086320) -0.002892 ( 0.034596) 0.159516 0.003282 --->fabia-------dash-----: 8.36e-15 0.124241 4.5e-23 0.119484 0.117044 ( 0.086320) -0.002441 ( 0.032156) 0.159516 0.000874 --->beagle1-----beagle2--: 3.07e-12 -0.065832 6.97e-22 -0.052862 0.082067 ( 0.018617) 0.134929 ( 0.053223) 0.087118 0.156860 --->beagle1-----plink----: 1e+00 0.000000 1e+00 0.000000 0.082067 ( 0.018617) 0.000000 ( 0.000000) 0.087118 0.000000 --->beagle1-----germline1: 5.04e-18 0.073774 1.37e-42 0.078768 0.082067 ( 0.018617) 0.003299 ( 0.026671) 0.087118 0.014352 --->beagle1-----germline2: 7.22e-18 0.084781 6.98e-39 0.084960 0.082067 ( 0.018617) -0.002892 ( 0.034596) 0.087118 0.003282 --->beagle1-----dash-----: 9.46e-18 0.085672 3.94e-40 0.084508 0.082067 ( 0.018617) -0.002441 ( 0.032156) 0.087118 0.000874 --->beagle2-----plink----: 1e+00 0.000000 1e+00 0.000000 0.134929 ( 0.053223) 0.000000 ( 0.000000) 0.156860 0.000000 --->beagle2-----germline1: 1.88e-17 0.140123 1.02e-38 0.131630 0.134929 ( 0.053223) 0.003299 ( 0.026671) 0.156860 0.014352 --->beagle2-----germline2: 1.48e-17 0.145838 8.56e-38 0.137821 0.134929 ( 0.053223) -0.002892 ( 0.034596) 0.156860 0.003282 --->beagle2-----dash-----: 1.67e-17 0.147501 1.88e-37 0.137370 0.134929 ( 0.053223) -0.002441 ( 0.032156) 0.156860 0.000874 --->plink-------germline1: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.003299 ( 0.026671) 0.000000 0.014352 --->plink-------germline2: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) -0.002892 ( 0.034596) 0.000000 0.003282 --->plink-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) -0.002441 ( 0.032156) 0.000000 0.000874 --->germline1---germline2: 5.95e-01 0.008331 1.27e-01 0.006191 0.003299 ( 0.026671) -0.002892 ( 0.034596) 0.014352 0.003282 --->germline1---dash-----: 1.16e-01 0.004038 1.39e-01 0.005740 0.003299 ( 0.026671) -0.002441 ( 0.032156) 0.014352 0.000874 --->germline2---dash-----: 1.78e-01 -0.004768 7.97e-01 -0.000451 -0.002892 ( 0.034596) -0.002441 ( 0.032156) 0.003282 0.000874 ######F1Sample###### --->fabia-------beagle1--: 7.1e-09 0.020457 1.43e-08 0.019885 0.045894 ( 0.032268) 0.026009 ( 0.003435) 0.055173 0.026726 --->fabia-------beagle2--: 1.74e-02 -0.006537 3.18e-02 -0.007808 0.045894 ( 0.032268) 0.053701 ( 0.016745) 0.055173 0.059613 --->fabia-------plink----: 1.37e-12 0.034192 7.33e-18 0.033985 0.045894 ( 0.032268) 0.011909 ( 0.000198) 0.055173 0.011928 --->fabia-------germline1: 9.83e-13 0.034295 7.56e-18 0.033875 0.045894 ( 0.032268) 0.012019 ( 0.000810) 0.055173 0.012333 --->fabia-------germline2: 7.85e-13 0.034706 3.68e-18 0.034203 0.045894 ( 0.032268) 0.011691 ( 0.002567) 0.055173 0.012151 --->fabia-------dash-----: 8.05e-13 0.035046 5.66e-18 0.034244 0.045894 ( 0.032268) 0.011650 ( 0.002869) 0.055173 0.012007 --->beagle1-----beagle2--: 3.38e-17 -0.031377 1.3e-34 -0.027692 0.026009 ( 0.003435) 0.053701 ( 0.016745) 0.026726 0.059613 --->beagle1-----plink----: 4.59e-18 0.014675 4.15e-64 0.014101 0.026009 ( 0.003435) 0.011909 ( 0.000198) 0.026726 0.011928 --->beagle1-----germline1: 4.6e-18 0.014494 1.61e-62 0.013990 0.026009 ( 0.003435) 0.012019 ( 0.000810) 0.026726 0.012333 --->beagle1-----germline2: 4.46e-18 0.014645 1.73e-55 0.014318 0.026009 ( 0.003435) 0.011691 ( 0.002567) 0.026726 0.012151 --->beagle1-----dash-----: 4.6e-18 0.014763 2.32e-53 0.014359 0.026009 ( 0.003435) 0.011650 ( 0.002869) 0.026726 0.012007 --->beagle2-----plink----: 1.66e-17 0.046020 1.69e-44 0.041793 0.053701 ( 0.016745) 0.011909 ( 0.000198) 0.059613 0.011928 --->beagle2-----germline1: 1.67e-17 0.045933 3.12e-44 0.041682 0.053701 ( 0.016745) 0.012019 ( 0.000810) 0.059613 0.012333 --->beagle2-----germline2: 1.39e-17 0.046077 1.18e-43 0.042010 0.053701 ( 0.016745) 0.011691 ( 0.002567) 0.059613 0.012151 --->beagle2-----dash-----: 1.44e-17 0.046084 4.66e-43 0.042051 0.053701 ( 0.016745) 0.011650 ( 0.002869) 0.059613 0.012007 --->plink-------germline1: 2.55e-03 -0.000375 1.69e-01 -0.000110 0.011909 ( 0.000198) 0.012019 ( 0.000810) 0.011928 0.012333 --->plink-------germline2: 3.56e-01 -0.000145 3.94e-01 0.000217 0.011909 ( 0.000198) 0.011691 ( 0.002567) 0.011928 0.012151 --->plink-------dash-----: 1e+00 0.000000 3.66e-01 0.000259 0.011909 ( 0.000198) 0.011650 ( 0.002869) 0.011928 0.012007 --->germline1---germline2: 7.41e-02 0.000275 1.96e-01 0.000328 0.012019 ( 0.000810) 0.011691 ( 0.002567) 0.012333 0.012151 --->germline1---dash-----: 5.28e-01 0.000391 1.95e-01 0.000369 0.012019 ( 0.000810) 0.011650 ( 0.002869) 0.012333 0.012007 --->germline2---dash-----: 6.46e-01 -0.000256 1e+00 0.000000 0.011691 ( 0.002567) 0.011650 ( 0.002869) 0.012151 0.012007 ######accuracySample###### --->fabia-------beagle1--: 3.95e-18 0.341756 1.29e-109 0.342270 0.910120 ( 0.021817) 0.567850 ( 0.020706) 0.909500 0.567000 --->fabia-------beagle2--: 3.95e-18 0.091526 9.2e-61 0.092980 0.910120 ( 0.021817) 0.817140 ( 0.014154) 0.909500 0.817000 --->fabia-------plink----: 3.95e-18 0.903791 3.55e-162 0.904130 0.910120 ( 0.021817) 0.005990 ( 1e-04) 0.909500 0.006000 --->fabia-------germline1: 3.95e-18 0.865290 1.41e-153 0.865370 0.910120 ( 0.021817) 0.044750 ( 0.014143) 0.909500 0.045000 --->fabia-------germline2: 3.95e-18 0.720022 3.5e-147 0.720150 0.910120 ( 0.021817) 0.189970 ( 0.011899) 0.909500 0.190000 --->fabia-------dash-----: 3.95e-18 0.660456 1.75e-116 0.657450 0.910120 ( 0.021817) 0.252670 ( 0.039464) 0.909500 0.244000 --->beagle1-----beagle2--: 3.94e-18 -0.248960 1.95e-108 -0.249290 0.567850 ( 0.020706) 0.817140 ( 0.014154) 0.567000 0.817000 --->beagle1-----plink----: 3.94e-18 0.561550 5.61e-144 0.561860 0.567850 ( 0.020706) 0.005990 ( 1e-04) 0.567000 0.006000 --->beagle1-----germline1: 3.95e-18 0.522989 9.27e-131 0.523100 0.567850 ( 0.020706) 0.044750 ( 0.014143) 0.567000 0.045000 --->beagle1-----germline2: 3.94e-18 0.377072 6.07e-117 0.377880 0.567850 ( 0.020706) 0.189970 ( 0.011899) 0.567000 0.190000 --->beagle1-----dash-----: 3.95e-18 0.318516 2.84e-83 0.315180 0.567850 ( 0.020706) 0.252670 ( 0.039464) 0.567000 0.244000 --->beagle2-----plink----: 3.92e-18 0.811025 4.32e-176 0.811150 0.817140 ( 0.014154) 0.005990 ( 1e-04) 0.817000 0.006000 --->beagle2-----germline1: 3.94e-18 0.772664 8.42e-164 0.772390 0.817140 ( 0.014154) 0.044750 ( 0.014143) 0.817000 0.045000 --->beagle2-----germline2: 3.94e-18 0.627500 3.84e-155 0.627170 0.817140 ( 0.014154) 0.189970 ( 0.011899) 0.817000 0.190000 --->beagle2-----dash-----: 3.95e-18 0.568548 2.77e-115 0.564470 0.817140 ( 0.014154) 0.252670 ( 0.039464) 0.817000 0.244000 --->plink-------germline1: 3.92e-18 -0.038537 5.32e-48 -0.038760 0.005990 ( 1e-04) 0.044750 ( 0.014143) 0.006000 0.045000 --->plink-------germline2: 3.88e-18 -0.184023 7.73e-120 -0.183980 0.005990 ( 1e-04) 0.189970 ( 0.011899) 0.006000 0.190000 --->plink-------dash-----: 3.95e-18 -0.240973 2.27e-81 -0.246680 0.005990 ( 1e-04) 0.252670 ( 0.039464) 0.006000 0.244000 --->germline1---germline2: 3.91e-18 -0.145006 7.39e-118 -0.145220 0.044750 ( 0.014143) 0.189970 ( 0.011899) 0.045000 0.190000 --->germline1---dash-----: 3.94e-18 -0.203025 1.4e-81 -0.207920 0.044750 ( 0.014143) 0.252670 ( 0.039464) 0.045000 0.244000 --->germline2---dash-----: 3.94e-18 -0.057971 9.15e-36 -0.062700 0.189970 ( 0.011899) 0.252670 ( 0.039464) 0.190000 0.244000 ######FPRSample###### --->fabia-------beagle1--: 3.96e-18 -0.344867 1.54e-109 -0.345284 0.089243 ( 0.021986) 0.434527 ( 0.020856) 0.090522 0.435614 --->fabia-------beagle2--: 3.96e-18 -0.092576 5.25e-61 -0.093906 0.089243 ( 0.021986) 0.183149 ( 0.014223) 0.090522 0.183099 --->fabia-------plink----: 3.95e-18 -0.910456 3.72e-162 -0.910767 0.089243 ( 0.021986) 1.000010 ( 0.000101) 0.090522 1.000000 --->fabia-------germline1: 3.96e-18 -0.871563 8.37e-154 -0.871592 0.089243 ( 0.021986) 0.960835 ( 0.014266) 0.090522 0.959759 --->fabia-------germline2: 3.96e-18 -0.724410 3.97e-147 -0.724470 0.089243 ( 0.021986) 0.813712 ( 0.011811) 0.090522 0.812877 --->fabia-------dash-----: 3.96e-18 -0.664170 2.95e-116 -0.661009 0.089243 ( 0.021986) 0.750252 ( 0.039986) 0.090522 0.759054 --->beagle1-----beagle2--: 3.95e-18 0.251081 2.5e-108 0.251378 0.434527 ( 0.020856) 0.183149 ( 0.014223) 0.435614 0.183099 --->beagle1-----plink----: 3.94e-18 -0.565325 6.06e-144 -0.565483 0.434527 ( 0.020856) 1.000010 ( 0.000101) 0.435614 1.000000 --->beagle1-----germline1: 3.95e-18 -0.526206 1.49e-130 -0.526308 0.434527 ( 0.020856) 0.960835 ( 0.014266) 0.435614 0.959759 --->beagle1-----germline2: 3.95e-18 -0.378284 7.19e-117 -0.379185 0.434527 ( 0.020856) 0.813712 ( 0.011811) 0.435614 0.812877 --->beagle1-----dash-----: 3.95e-18 -0.319357 8.42e-83 -0.315724 0.434527 ( 0.020856) 0.750252 ( 0.039986) 0.435614 0.759054 --->beagle2-----plink----: 3.92e-18 -0.816901 3.48e-176 -0.816861 0.183149 ( 0.014223) 1.000010 ( 0.000101) 0.183099 1.000000 --->beagle2-----germline1: 3.95e-18 -0.778137 1.8e-163 -0.777686 0.183149 ( 0.014223) 0.960835 ( 0.014266) 0.183099 0.959759 --->beagle2-----germline2: 3.95e-18 -0.630759 7.17e-156 -0.630563 0.183149 ( 0.014223) 0.813712 ( 0.011811) 0.183099 0.812877 --->beagle2-----dash-----: 3.95e-18 -0.571479 6.33e-115 -0.567103 0.183149 ( 0.014223) 0.750252 ( 0.039986) 0.183099 0.759054 --->plink-------germline1: 3.92e-18 0.038779 4.47e-48 0.039175 1.000010 ( 0.000101) 0.960835 ( 0.014266) 1.000000 0.959759 --->plink-------germline2: 3.9e-18 0.186563 1.09e-120 0.186298 1.000010 ( 0.000101) 0.813712 ( 0.011811) 1.000000 0.812877 --->plink-------dash-----: 3.94e-18 0.243942 2.43e-81 0.249759 1.000010 ( 0.000101) 0.750252 ( 0.039986) 1.000000 0.759054 --->germline1---germline2: 3.93e-18 0.147360 2.09e-118 0.147123 0.960835 ( 0.014266) 0.813712 ( 0.011811) 0.959759 0.812877 --->germline1---dash-----: 3.95e-18 0.205774 1.8e-81 0.210583 0.960835 ( 0.014266) 0.750252 ( 0.039986) 0.959759 0.759054 --->germline2---dash-----: 3.95e-18 0.058400 1.09e-35 0.063461 0.813712 ( 0.011811) 0.750252 ( 0.039986) 0.812877 0.759054 ######FDRSample###### --->fabia-------beagle1--: 4.07e-09 -0.010892 8.56e-09 -0.010602 0.976215 ( 0.016895) 0.986817 ( 0.001744) 0.971631 0.986456 --->fabia-------beagle2--: 1.86e-02 0.003369 3.88e-02 0.003931 0.976215 ( 0.016895) 0.972284 ( 0.008651) 0.971631 0.969231 --->fabia-------plink----: 7.14e-13 -0.017879 7.31e-18 -0.017795 0.976215 ( 0.016895) 0.994010 ( 1e-04) 0.971631 0.994000 --->fabia-------germline1: 9.59e-13 -0.017966 7.59e-18 -0.017738 0.976215 ( 0.016895) 0.993953 ( 0.000408) 0.971631 0.993795 --->fabia-------germline2: 7.65e-13 -0.018106 3.79e-18 -0.017897 0.976215 ( 0.016895) 0.994111 ( 0.001293) 0.971631 0.993880 --->fabia-------dash-----: 6.75e-13 -0.018248 5.79e-18 -0.017914 0.976215 ( 0.016895) 0.994128 ( 0.001446) 0.971631 0.993942 --->beagle1-----beagle2--: 3.29e-17 0.016405 4.54e-35 0.014533 0.986817 ( 0.001744) 0.972284 ( 0.008651) 0.986456 0.969231 --->beagle1-----plink----: 4.59e-18 -0.007485 2.72e-64 -0.007193 0.986817 ( 0.001744) 0.994010 ( 1e-04) 0.986456 0.994000 --->beagle1-----germline1: 4.6e-18 -0.007399 1.01e-62 -0.007136 0.986817 ( 0.001744) 0.993953 ( 0.000408) 0.986456 0.993795 --->beagle1-----germline2: 4.46e-18 -0.007478 9.84e-56 -0.007295 0.986817 ( 0.001744) 0.994111 ( 0.001293) 0.986456 0.993880 --->beagle1-----dash-----: 4.6e-18 -0.007486 1.35e-53 -0.007312 0.986817 ( 0.001744) 0.994128 ( 0.001446) 0.986456 0.993942 --->beagle2-----plink----: 1.52e-17 -0.023848 9.85e-45 -0.021726 0.972284 ( 0.008651) 0.994010 ( 1e-04) 0.969231 0.994000 --->beagle2-----germline1: 1.67e-17 -0.023817 1.79e-44 -0.021669 0.972284 ( 0.008651) 0.993953 ( 0.000408) 0.969231 0.993795 --->beagle2-----germline2: 1.39e-17 -0.023903 6.75e-44 -0.021827 0.972284 ( 0.008651) 0.994111 ( 0.001293) 0.969231 0.993880 --->beagle2-----dash-----: 1.35e-17 -0.023919 2.63e-43 -0.021844 0.972284 ( 0.008651) 0.994128 ( 0.001446) 0.969231 0.993942 --->plink-------germline1: 2.55e-03 0.000216 1e+00 0.000000 0.994010 ( 1e-04) 0.993953 ( 0.000408) 0.994000 0.993795 --->plink-------germline2: 3.43e-01 0.000116 4.31e-01 -0.000101 0.994010 ( 1e-04) 0.994111 ( 0.001293) 0.994000 0.993880 --->plink-------dash-----: 1e+00 0.000000 4.12e-01 -0.000118 0.994010 ( 1e-04) 0.994128 ( 0.001446) 0.994000 0.993942 --->germline1---germline2: 1e+00 0.000000 2.15e-01 -0.000158 0.993953 ( 0.000408) 0.994111 ( 0.001293) 0.993795 0.993880 --->germline1---dash-----: 5.42e-01 -0.000159 2.21e-01 -0.000175 0.993953 ( 0.000408) 0.994128 ( 0.001446) 0.993795 0.993942 --->germline2---dash-----: 1e+00 0.000000 1e+00 0.000000 0.994111 ( 0.001293) 0.994128 ( 0.001446) 0.993880 0.993942 ######specifitySample###### --->fabia-------beagle1--: 3.96e-18 0.344834 1.56e-109 0.345274 0.910757 ( 0.021986) 0.565483 ( 0.020861) 0.909478 0.564386 --->fabia-------beagle2--: 3.96e-18 0.092612 5.33e-61 0.093896 0.910757 ( 0.021986) 0.816861 ( 0.014229) 0.909478 0.816901 --->fabia-------plink----: 1e+00 0.000000 1e+00 0.000000 0.910757 ( 0.021986) 0.000000 ( 0.000000) 0.909478 0.000000 --->fabia-------germline1: 3.96e-18 0.871509 8.48e-154 0.871582 0.910757 ( 0.021986) 0.039175 ( 0.014274) 0.909478 0.040241 --->fabia-------germline2: 3.96e-18 0.724360 4.01e-147 0.724459 0.910757 ( 0.021986) 0.186298 ( 0.011819) 0.909478 0.187123 --->fabia-------dash-----: 3.96e-18 0.664190 2.94e-116 0.660999 0.910757 ( 0.021986) 0.249759 ( 0.039984) 0.909478 0.241449 --->beagle1-----beagle2--: 3.95e-18 -0.251028 2.5e-108 -0.251378 0.565483 ( 0.020861) 0.816861 ( 0.014229) 0.564386 0.816901 --->beagle1-----plink----: 1e+00 0.000000 1e+00 0.000000 0.565483 ( 0.020861) 0.000000 ( 0.000000) 0.564386 0.000000 --->beagle1-----germline1: 3.96e-18 0.526202 1.49e-130 0.526308 0.565483 ( 0.020861) 0.039175 ( 0.014274) 0.564386 0.040241 --->beagle1-----germline2: 3.95e-18 0.378272 7.19e-117 0.379185 0.565483 ( 0.020861) 0.186298 ( 0.011819) 0.564386 0.187123 --->beagle1-----dash-----: 3.95e-18 0.319353 8.42e-83 0.315724 0.565483 ( 0.020861) 0.249759 ( 0.039984) 0.564386 0.241449 --->beagle2-----plink----: 1e+00 0.000000 1e+00 0.000000 0.816861 ( 0.014229) 0.000000 ( 0.000000) 0.816901 0.000000 --->beagle2-----germline1: 3.96e-18 0.778154 1.8e-163 0.777686 0.816861 ( 0.014229) 0.039175 ( 0.014274) 0.816901 0.040241 --->beagle2-----germline2: 3.95e-18 0.630730 7.17e-156 0.630563 0.816861 ( 0.014229) 0.186298 ( 0.011819) 0.816901 0.187123 --->beagle2-----dash-----: 3.95e-18 0.571452 6.33e-115 0.567103 0.816861 ( 0.014229) 0.249759 ( 0.039984) 0.816901 0.241449 --->plink-------germline1: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.039175 ( 0.014274) 0.000000 0.040241 --->plink-------germline2: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.186298 ( 0.011819) 0.000000 0.187123 --->plink-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.249759 ( 0.039984) 0.000000 0.241449 --->germline1---germline2: 3.95e-18 -0.147382 2.09e-118 -0.147123 0.039175 ( 0.014274) 0.186298 ( 0.011819) 0.040241 0.187123 --->germline1---dash-----: 3.96e-18 -0.205739 1.8e-81 -0.210584 0.039175 ( 0.014274) 0.249759 ( 0.039984) 0.040241 0.241449 --->germline2---dash-----: 3.95e-18 -0.058379 1.09e-35 -0.063461 0.186298 ( 0.011819) 0.249759 ( 0.039984) 0.187123 0.241449 ######sensitivitySample###### --->fabia-------beagle1--: 1e+00 0.000000 3.7e-08 -0.261667 0.698333 ( 0.437249) 0.960000 ( 0.118729) 1.000000 1.000000 --->fabia-------beagle2--: 1e+00 0.000000 8.59e-04 -0.165000 0.698333 ( 0.437249) 0.863333 ( 0.269451) 1.000000 1.000000 --->fabia-------plink----: 1e+00 0.000000 5.27e-10 -0.300000 0.698333 ( 0.437249) 0.998333 ( 0.016667) 1.000000 1.000000 --->fabia-------germline1: 1e+00 0.000000 7.06e-09 -0.270000 0.698333 ( 0.437249) 0.968333 ( 0.065713) 1.000000 1.000000 --->fabia-------germline2: 8.68e-02 -0.166597 3.23e-02 -0.100000 0.698333 ( 0.437249) 0.798333 ( 0.174552) 1.000000 0.833333 --->fabia-------dash-----: 6e-01 -0.083307 4.44e-01 -0.036667 0.698333 ( 0.437249) 0.735000 ( 0.186670) 1.000000 0.666667 --->beagle1-----beagle2--: 1e+00 0.000000 1.05e-05 0.096667 0.960000 ( 0.118729) 0.863333 ( 0.269451) 1.000000 1.000000 --->beagle1-----plink----: 1e+00 0.000000 1.6e-03 -0.038333 0.960000 ( 0.118729) 0.998333 ( 0.016667) 1.000000 1.000000 --->beagle1-----germline1: 1e+00 0.000000 5.5e-01 -0.008333 0.960000 ( 0.118729) 0.968333 ( 0.065713) 1.000000 1.000000 --->beagle1-----germline2: 1.14e-09 0.249964 1.64e-11 0.161667 0.960000 ( 0.118729) 0.798333 ( 0.174552) 1.000000 0.833333 --->beagle1-----dash-----: 6.16e-12 0.250010 2.58e-16 0.225000 0.960000 ( 0.118729) 0.735000 ( 0.186670) 1.000000 0.666667 --->beagle2-----plink----: 1e+00 0.000000 2.44e-06 -0.135000 0.863333 ( 0.269451) 0.998333 ( 0.016667) 1.000000 1.000000 --->beagle2-----germline1: 1e+00 0.000000 3.57e-04 -0.105000 0.863333 ( 0.269451) 0.968333 ( 0.065713) 1.000000 1.000000 --->beagle2-----germline2: 3.41e-03 0.166700 5.33e-02 0.065000 0.863333 ( 0.269451) 0.798333 ( 0.174552) 1.000000 0.833333 --->beagle2-----dash-----: 4.59e-05 0.249995 4.16e-04 0.128333 0.863333 ( 0.269451) 0.735000 ( 0.186670) 1.000000 0.666667 --->plink-------germline1: 1e+00 0.000000 9.8e-06 0.030000 0.998333 ( 0.016667) 0.968333 ( 0.065713) 1.000000 1.000000 --->plink-------germline2: 1.16e-13 0.250014 3.75e-20 0.200000 0.998333 ( 0.016667) 0.798333 ( 0.174552) 1.000000 0.833333 --->plink-------dash-----: 2.24e-15 0.333328 1.21e-25 0.263333 0.998333 ( 0.016667) 0.735000 ( 0.186670) 1.000000 0.666667 --->germline1---germline2: 6.21e-12 0.250045 3.52e-16 0.170000 0.968333 ( 0.065713) 0.798333 ( 0.174552) 1.000000 0.833333 --->germline1---dash-----: 2.99e-14 0.333290 4.23e-22 0.233333 0.968333 ( 0.065713) 0.735000 ( 0.186670) 1.000000 0.666667 --->germline2---dash-----: 8.17e-07 0.166729 1.5e-08 0.063333 0.798333 ( 0.174552) 0.735000 ( 0.186670) 0.833333 0.666667 ######trueNSample###### --->fabia-------beagle1--: 3.94e-18 1253 5.24e-144 1254 1816 ( 43.8) 562 ( 20.7) 1814 561 --->fabia-------beagle2--: 3.95e-18 1002 3.01e-136 1004 1816 ( 43.8) 812 ( 14.1) 1814 812 --->fabia-------plink----: 1e+00 0 1e+00 0 1816 ( 43.8) 0 ( 0) 1814 0 --->fabia-------germline1: 3.95e-18 1777 8.91e-160 1777 1816 ( 43.8) 38.9 ( 14.2) 1814 40 --->fabia-------germline2: 3.95e-18 1631 3.39e-156 1631 1816 ( 43.8) 185 ( 11.7) 1814 186 --->fabia-------dash-----: 3.95e-18 1569 5.31e-142 1568 1816 ( 43.8) 248 ( 39.7) 1814 240 --->beagle1-----beagle2--: 3.93e-18 -250 2.5e-108 -250 562 ( 20.7) 812 ( 14.1) 561 812 --->beagle1-----plink----: 1e+00 0 1e+00 0 562 ( 20.7) 0 ( 0) 561 0 --->beagle1-----germline1: 3.94e-18 523 1.49e-130 523 562 ( 20.7) 38.9 ( 14.2) 561 40 --->beagle1-----germline2: 3.94e-18 376 7.19e-117 377 562 ( 20.7) 185 ( 11.7) 561 186 --->beagle1-----dash-----: 3.95e-18 317 8.42e-83 314 562 ( 20.7) 248 ( 39.7) 561 240 --->beagle2-----plink----: 1e+00 0 1e+00 0 812 ( 14.1) 0 ( 0) 812 0 --->beagle2-----germline1: 3.93e-18 773 1.8e-163 773 812 ( 14.1) 38.9 ( 14.2) 812 40 --->beagle2-----germline2: 3.93e-18 627 7.17e-156 627 812 ( 14.1) 185 ( 11.7) 812 186 --->beagle2-----dash-----: 3.94e-18 568 6.33e-115 564 812 ( 14.1) 248 ( 39.7) 812 240 --->plink-------germline1: 1e+00 0 1e+00 0 0 ( 0) 38.9 ( 14.2) 0 40 --->plink-------germline2: 1e+00 0 1e+00 0 0 ( 0) 185 ( 11.7) 0 186 --->plink-------dash-----: 1e+00 0 1e+00 0 0 ( 0) 248 ( 39.7) 0 240 --->germline1---germline2: 3.9e-18 -146 2.09e-118 -146 38.9 ( 14.2) 185 ( 11.7) 40 186 --->germline1---dash-----: 3.94e-18 -205 1.8e-81 -209 38.9 ( 14.2) 248 ( 39.7) 40 240 --->germline2---dash-----: 3.93e-18 -58 1.09e-35 -63.1 185 ( 11.7) 248 ( 39.7) 186 240 ######falsePSample###### --->fabia-------beagle1--: 3.94e-18 -253 5.22e-76 -254 178 ( 43.8) 432 ( 20.7) 180 433 --->fabia-------beagle2--: 6.78e-01 -1.5 3.57e-01 -4.1 178 ( 43.8) 182 ( 14.1) 180 182 --->fabia-------plink----: 3.95e-18 -815 8.19e-128 -816 178 ( 43.8) 994 ( 0.1) 180 994 --->fabia-------germline1: 3.95e-18 -777 2.85e-124 -777 178 ( 43.8) 955 ( 14.2) 180 954 --->fabia-------germline2: 3.95e-18 -631 1.87e-115 -631 178 ( 43.8) 809 ( 11.7) 180 808 --->fabia-------dash-----: 3.95e-18 -569 1.54e-98 -568 178 ( 43.8) 746 ( 39.7) 180 754 --->beagle1-----beagle2--: 3.93e-18 250 2.5e-108 250 432 ( 20.7) 182 ( 14.1) 433 182 --->beagle1-----plink----: 3.94e-18 -562 6.06e-144 -562 432 ( 20.7) 994 ( 0.1) 433 994 --->beagle1-----germline1: 3.94e-18 -523 1.49e-130 -523 432 ( 20.7) 955 ( 14.2) 433 954 --->beagle1-----germline2: 3.94e-18 -376 7.19e-117 -377 432 ( 20.7) 809 ( 11.7) 433 808 --->beagle1-----dash-----: 3.95e-18 -317 8.42e-83 -314 432 ( 20.7) 746 ( 39.7) 433 754 --->beagle2-----plink----: 3.92e-18 -812 3.48e-176 -812 182 ( 14.1) 994 ( 0.1) 182 994 --->beagle2-----germline1: 3.93e-18 -773 1.8e-163 -773 182 ( 14.1) 955 ( 14.2) 182 954 --->beagle2-----germline2: 3.93e-18 -627 7.17e-156 -627 182 ( 14.1) 809 ( 11.7) 182 808 --->beagle2-----dash-----: 3.94e-18 -568 6.33e-115 -564 182 ( 14.1) 746 ( 39.7) 182 754 --->plink-------germline1: 3.92e-18 38.5 4.47e-48 38.9 994 ( 0.1) 955 ( 14.2) 994 954 --->plink-------germline2: 3.9e-18 185 1.09e-120 185 994 ( 0.1) 809 ( 11.7) 994 808 --->plink-------dash-----: 3.94e-18 242 2.43e-81 248 994 ( 0.1) 746 ( 39.7) 994 754 --->germline1---germline2: 3.9e-18 146 2.09e-118 146 955 ( 14.2) 809 ( 11.7) 954 808 --->germline1---dash-----: 3.94e-18 205 1.8e-81 209 955 ( 14.2) 746 ( 39.7) 954 754 --->germline2---dash-----: 3.93e-18 58 1.09e-35 63.1 809 ( 11.7) 746 ( 39.7) 808 754 ######falseNSample###### --->fabia-------beagle1--: 1e+00 0.000000 3.5e-08 1.580000 1.810000 ( 2.623495) 0.230000 ( 0.708605) 0.000000 0.000000 --->fabia-------beagle2--: 1e+00 0.000000 8.04e-04 1.000000 1.810000 ( 2.623495) 0.810000 ( 1.618673) 0.000000 0.000000 --->fabia-------plink----: 1e+00 0.000000 1e+00 0.000000 1.810000 ( 2.623495) 0.000000 ( 0.000000) 0.000000 0.000000 --->fabia-------germline1: 1e+00 0.000000 6.71e-09 1.630000 1.810000 ( 2.623495) 0.180000 ( 0.386123) 0.000000 0.000000 --->fabia-------germline2: 7.05e-02 0.999995 3e-02 0.610000 1.810000 ( 2.623495) 1.200000 ( 1.034750) 0.000000 1.000000 --->fabia-------dash-----: 4.81e-01 0.5 4.25e-01 0.23 1.81 ( 2.62) 1.58 ( 1.11) 0 2 --->beagle1-----beagle2--: 1e+00 0.000000 1.05e-05 -0.580000 0.230000 ( 0.708605) 0.810000 ( 1.618673) 0.000000 0.000000 --->beagle1-----plink----: 1e+00 0.000000 1e+00 0.000000 0.230000 ( 0.708605) 0.000000 ( 0.000000) 0.000000 0.000000 --->beagle1-----germline1: 1e+00 0.000000 5.5e-01 0.050000 0.230000 ( 0.708605) 0.180000 ( 0.386123) 0.000000 0.000000 --->beagle1-----germline2: 4.75e-10 -1.499920 1.64e-11 -0.970000 0.230000 ( 0.708605) 1.200000 ( 1.034750) 0.000000 1.000000 --->beagle1-----dash-----: 3.2e-12 -1.5 2.58e-16 -1.35 0.23 ( 0.709) 1.58 ( 1.11) 0 2 --->beagle2-----plink----: 1e+00 0.000000 1e+00 0.000000 0.810000 ( 1.618673) 0.000000 ( 0.000000) 0.000000 0.000000 --->beagle2-----germline1: 1e+00 0.000000 3.57e-04 0.630000 0.810000 ( 1.618673) 0.180000 ( 0.386123) 0.000000 0.000000 --->beagle2-----germline2: 2.69e-03 -1.000055 5.33e-02 -0.390000 0.810000 ( 1.618673) 1.200000 ( 1.034750) 0.000000 1.000000 --->beagle2-----dash-----: 4.99e-05 -1.5 4.16e-04 -0.77 0.81 ( 1.62) 1.58 ( 1.11) 0 2 --->plink-------germline1: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.180000 ( 0.386123) 0.000000 0.000000 --->plink-------germline2: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 1.200000 ( 1.034750) 0.000000 1.000000 --->plink-------dash-----: 1e+00 0 1e+00 0 0 ( 0) 1.58 ( 1.11) 0 2 --->germline1---germline2: 3.9e-12 -1.500009 3.52e-16 -1.020000 0.180000 ( 0.386123) 1.200000 ( 1.034750) 0.000000 1.000000 --->germline1---dash-----: 2.21e-14 -2 4.23e-22 -1.4 0.18 ( 0.386) 1.58 ( 1.11) 0 2 --->germline2---dash-----: 2.6e-07 -1 1.5e-08 -0.38 1.2 ( 1.03) 1.58 ( 1.11) 1 2 ######truePSample###### --->fabia-------beagle1--: 1e+00 0 3.7e-08 -1.57 4.19 ( 2.62) 5.76 ( 0.712) 6 6 --->fabia-------beagle2--: 1e+00 0 8.59e-04 -0.99 4.19 ( 2.62) 5.18 ( 1.62) 6 6 --->fabia-------plink----: 1e+00 0 5.27e-10 -1.8 4.19 ( 2.62) 5.99 ( 0.1) 6 6 --->fabia-------germline1: 1e+00 0 7.06e-09 -1.62 4.19 ( 2.62) 5.81 ( 0.394) 6 6 --->fabia-------germline2: 7.76e-02 -1 3.23e-02 -0.6 4.19 ( 2.62) 4.79 ( 1.05) 6 5 --->fabia-------dash-----: 5.19e-01 -0.5 4.44e-01 -0.22 4.19 ( 2.62) 4.41 ( 1.12) 6 4 --->beagle1-----beagle2--: 1e+00 0 1.05e-05 0.58 5.76 ( 0.712) 5.18 ( 1.62) 6 6 --->beagle1-----plink----: 1e+00 0 1.6e-03 -0.23 5.76 ( 0.712) 5.99 ( 0.1) 6 6 --->beagle1-----germline1: 1e+00 0 5.5e-01 -0.05 5.76 ( 0.712) 5.81 ( 0.394) 6 6 --->beagle1-----germline2: 4.75e-10 1.5 1.64e-11 0.97 5.76 ( 0.712) 4.79 ( 1.05) 6 5 --->beagle1-----dash-----: 3.2e-12 1.5 2.58e-16 1.35 5.76 ( 0.712) 4.41 ( 1.12) 6 4 --->beagle2-----plink----: 1e+00 0 2.44e-06 -0.81 5.18 ( 1.62) 5.99 ( 0.1) 6 6 --->beagle2-----germline1: 1e+00 0 3.57e-04 -0.63 5.18 ( 1.62) 5.81 ( 0.394) 6 6 --->beagle2-----germline2: 2.69e-03 1 5.33e-02 0.39 5.18 ( 1.62) 4.79 ( 1.05) 6 5 --->beagle2-----dash-----: 4.99e-05 1.5 4.16e-04 0.77 5.18 ( 1.62) 4.41 ( 1.12) 6 4 --->plink-------germline1: 1e+00 0 9.8e-06 0.18 5.99 ( 0.1) 5.81 ( 0.394) 6 6 --->plink-------germline2: 1.16e-13 1.5 3.75e-20 1.2 5.99 ( 0.1) 4.79 ( 1.05) 6 5 --->plink-------dash-----: 2.24e-15 2 1.21e-25 1.58 5.99 ( 0.1) 4.41 ( 1.12) 6 4 --->germline1---germline2: 3.9e-12 1.5 3.52e-16 1.02 5.81 ( 0.394) 4.79 ( 1.05) 6 5 --->germline1---dash-----: 2.21e-14 2 4.23e-22 1.4 5.81 ( 0.394) 4.41 ( 1.12) 6 4 --->germline2---dash-----: 2.6e-07 1 1.5e-08 0.38 4.79 ( 1.05) 4.41 ( 1.12) 5 4