Results: Wilcoxon-Rank-Sum Wilcoxon-median t-test t-test-mean mean1 (std) mean2 (std) median1 median2 ######Matthews###### --->fabia-------beagle1--: 3.96e-18 0.749768 2.82e-71 0.743288 0.737874 ( 0.151700) -0.005414 ( 0.004998) 0.754397 -0.005796 --->fabia-------beagle2--: 3.96e-18 0.747090 4.12e-71 0.740654 0.737874 ( 0.151700) -0.002780 ( 0.004658) 0.754397 -0.003496 --->fabia-------plink----: 3.96e-18 0.718442 3.4e-69 0.712201 0.737874 ( 0.151700) 0.025674 ( 0.011187) 0.754397 0.024793 --->fabia-------germline1: 3.96e-18 0.748790 4.93e-71 0.741213 0.737874 ( 0.151700) -0.003339 ( 0.004752) 0.754397 -0.002932 --->fabia-------germline2: 3.96e-18 0.745386 2.4e-71 0.738225 0.737874 ( 0.151700) -0.000351 ( 0.010889) 0.754397 -0.004378 --->fabia-------dash-----: 3.96e-18 0.754234 4.01e-71 0.746728 0.737874 ( 0.151700) -0.008853 ( 0.006891) 0.754397 -0.008671 --->beagle1-----beagle2--: 1.28e-09 -0.002687 3.89e-11 -0.002634 -0.005414 ( 0.004998) -0.002780 ( 0.004658) -0.005796 -0.003496 --->beagle1-----plink----: 4.33e-18 -0.031113 6.7e-44 -0.031088 -0.005414 ( 0.004998) 0.025674 ( 0.011187) -0.005796 0.024793 --->beagle1-----germline1: 6.68e-04 -0.002463 2.77e-03 -0.002075 -0.005414 ( 0.004998) -0.003339 ( 0.004752) -0.005796 -0.002932 --->beagle1-----germline2: 2.79e-05 -0.002953 3.83e-05 -0.005063 -0.005414 ( 0.004998) -0.000351 ( 0.010889) -0.005796 -0.004378 --->beagle1-----dash-----: 3.33e-04 0.003024 1.14e-04 0.003439 -0.005414 ( 0.004998) -0.008853 ( 0.006891) -0.005796 -0.008671 --->beagle2-----plink----: 4.89e-18 -0.028413 5.44e-41 -0.028453 -0.002780 ( 0.004658) 0.025674 ( 0.011187) -0.003496 0.024793 --->beagle2-----germline1: 6.79e-01 0.000291 3.98e-01 0.000559 -0.002780 ( 0.004658) -0.003339 ( 0.004752) -0.003496 -0.002932 --->beagle2-----germline2: 7.85e-01 -0.000210 4.33e-02 -0.002429 -0.002780 ( 0.004658) -0.000351 ( 0.010889) -0.003496 -0.004378 --->beagle2-----dash-----: 2.08e-09 0.005740 1.31e-10 0.006074 -0.002780 ( 0.004658) -0.008853 ( 0.006891) -0.003496 -0.008671 --->plink-------germline1: 4.46e-18 0.028668 1.6e-41 0.029012 0.025674 ( 0.011187) -0.003339 ( 0.004752) 0.024793 -0.002932 --->plink-------germline2: 4.68e-16 0.027109 7.07e-30 0.026024 0.025674 ( 0.011187) -0.000351 ( 0.010889) 0.024793 -0.004378 --->plink-------dash-----: 4.08e-18 0.034047 7.04e-44 0.034527 0.025674 ( 0.011187) -0.008853 ( 0.006891) 0.024793 -0.008671 --->germline1---germline2: 9.74e-01 1.23e-05 2.29e-02 -0.002988 -0.003339 ( 0.004752) -0.000351 ( 0.010889) -0.002932 -0.004378 --->germline1---dash-----: 7.45e-17 0.005311 2.71e-22 0.005515 -0.003339 ( 0.004752) -0.008853 ( 0.006891) -0.002932 -0.008671 --->germline2---dash-----: 5.86e-10 0.005671 3.41e-08 0.008502 -0.000351 ( 0.010889) -0.008853 ( 0.006891) -0.004378 -0.008671 ######F1###### --->fabia-------beagle1--: 3.96e-18 0.732549 1.57e-69 0.726874 0.728169 ( 0.154617) 0.001295 ( 0.000579) 0.747041 0.001246 --->fabia-------beagle2--: 3.96e-18 0.732660 1.57e-69 0.726814 0.728169 ( 0.154617) 0.001355 ( 0.000924) 0.747041 0.001171 --->fabia-------plink----: 3.96e-18 0.727501 3.31e-69 0.721913 0.728169 ( 0.154617) 0.006256 ( 0.001871) 0.747041 0.006190 --->fabia-------germline1: 3.96e-18 0.731941 1.75e-69 0.726285 0.728169 ( 0.154617) 0.001883 ( 8.95e-05) 0.747041 0.001877 --->fabia-------germline2: 3.96e-18 0.732353 1.06e-69 0.726526 0.728169 ( 0.154617) 0.001643 ( 0.004477) 0.747041 0.000000 --->fabia-------dash-----: 3.96e-18 0.732018 1.74e-69 0.726348 0.728169 ( 0.154617) 0.001820 ( 0.000103) 0.747041 0.001816 --->beagle1-----beagle2--: 1e+00 0.000000 1e+00 0.000000 0.001295 ( 0.000579) 0.001355 ( 0.000924) 0.001246 0.001171 --->beagle1-----plink----: 4.2e-18 -0.004968 4.58e-44 -0.004961 0.001295 ( 0.000579) 0.006256 ( 0.001871) 0.001246 0.006190 --->beagle1-----germline1: 5.52e-13 -0.000632 7.18e-17 -0.000588 0.001295 ( 0.000579) 0.001883 ( 8.95e-05) 0.001246 0.001877 --->beagle1-----germline2: 3.94e-04 0.001085 4.4e-01 -0.000348 0.001295 ( 0.000579) 0.001643 ( 0.004477) 0.001246 0.000000 --->beagle1-----dash-----: 1.05e-11 -0.000532 2.7e-14 -0.000525 0.001295 ( 0.000579) 0.001820 ( 0.000103) 0.001246 0.001816 --->beagle2-----plink----: 5.04e-18 -0.004910 1.05e-40 -0.004901 0.001355 ( 0.000924) 0.006256 ( 0.001871) 0.001171 0.006190 --->beagle2-----germline1: 3.51e-07 -0.000596 1.57e-07 -0.000528 0.001355 ( 0.000924) 0.001883 ( 8.95e-05) 0.001171 0.001877 --->beagle2-----germline2: 7.69e-04 0.001035 5.31e-01 -0.000288 0.001355 ( 0.000924) 0.001643 ( 0.004477) 0.001171 0.000000 --->beagle2-----dash-----: 3.43e-06 -0.000535 3.27e-06 -0.000465 0.001355 ( 0.000924) 0.001820 ( 0.000103) 0.001171 0.001816 --->plink-------germline1: 4.2e-18 0.004294 6.65e-42 0.004373 0.006256 ( 0.001871) 0.001883 ( 8.95e-05) 0.006190 0.001877 --->plink-------germline2: 3.82e-12 0.005495 2.18e-15 0.004613 0.006256 ( 0.001871) 0.001643 ( 0.004477) 0.006190 0.000000 --->plink-------dash-----: 4.2e-18 0.004360 2.81e-42 0.004436 0.006256 ( 0.001871) 0.001820 ( 0.000103) 0.006190 0.001816 --->germline1---germline2: 2.66e-04 0.001839 5.93e-01 0.000241 0.001883 ( 8.95e-05) 0.001643 ( 0.004477) 0.001877 0.000000 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 0.001883 ( 8.95e-05) 0.001820 ( 0.000103) 0.001877 0.001816 --->germline2---dash-----: 3.2e-04 -0.001779 6.94e-01 -0.000178 0.001643 ( 0.004477) 0.001820 ( 0.000103) 0.000000 0.001816 ######accuracy###### --->fabia-------beagle1--: 3.96e-18 0.224228 3.19e-116 0.224203 0.999727 ( 0.000188) 0.775524 ( 0.015789) 0.999772 0.775176 --->fabia-------beagle2--: 3.96e-18 0.087732 1.52e-94 0.087697 0.999727 ( 0.000188) 0.912030 ( 0.010261) 0.999772 0.911561 --->fabia-------plink----: 3.96e-18 0.116888 6.3e-123 0.116461 0.999727 ( 0.000188) 0.883265 ( 0.007000) 0.999772 0.882448 --->fabia-------germline1: 3.96e-18 0.959479 4.74e-166 0.955612 0.999727 ( 0.000188) 0.044114 ( 0.021049) 0.999772 0.039991 --->fabia-------germline2: 3.96e-18 0.020781 3.92e-78 0.020314 0.999727 ( 0.000188) 0.979412 ( 0.003490) 0.999772 0.978959 --->fabia-------dash-----: 3.96e-18 0.964695 3.36e-166 0.960831 0.999727 ( 0.000188) 0.038896 ( 0.021090) 0.999772 0.034816 --->beagle1-----beagle2--: 3.96e-18 -0.136233 1.19e-115 -0.136506 0.775524 ( 0.015789) 0.912030 ( 0.010261) 0.775176 0.911561 --->beagle1-----plink----: 3.96e-18 -0.107702 8.35e-84 -0.107742 0.775524 ( 0.015789) 0.883265 ( 0.007000) 0.775176 0.882448 --->beagle1-----germline1: 3.96e-18 0.733651 1.88e-148 0.731409 0.775524 ( 0.015789) 0.044114 ( 0.021049) 0.775176 0.039991 --->beagle1-----germline2: 3.96e-18 -0.203960 2.72e-111 -0.203889 0.775524 ( 0.015789) 0.979412 ( 0.003490) 0.775176 0.978959 --->beagle1-----dash-----: 3.96e-18 0.738888 1.58e-148 0.736627 0.775524 ( 0.015789) 0.038896 ( 0.021090) 0.775176 0.034816 --->beagle2-----plink----: 3.96e-18 0.028797 1.22e-41 0.028764 0.912030 ( 0.010261) 0.883265 ( 0.007000) 0.911561 0.882448 --->beagle2-----germline1: 3.96e-18 0.870875 1.59e-159 0.867915 0.912030 ( 0.010261) 0.044114 ( 0.021049) 0.911561 0.039991 --->beagle2-----germline2: 3.96e-18 -0.067302 1.33e-80 -0.067383 0.912030 ( 0.010261) 0.979412 ( 0.003490) 0.911561 0.978959 --->beagle2-----dash-----: 3.96e-18 0.876026 1.57e-159 0.873133 0.912030 ( 0.010261) 0.038896 ( 0.021090) 0.911561 0.034816 --->plink-------germline1: 3.96e-18 0.842067 1.85e-161 0.839151 0.883265 ( 0.007000) 0.044114 ( 0.021049) 0.882448 0.039991 --->plink-------germline2: 3.96e-18 -0.096254 8.7e-114 -0.096147 0.883265 ( 0.007000) 0.979412 ( 0.003490) 0.882448 0.978959 --->plink-------dash-----: 3.96e-18 0.847299 1.33e-161 0.844369 0.883265 ( 0.007000) 0.038896 ( 0.021090) 0.882448 0.034816 --->germline1---germline2: 3.96e-18 -0.938752 3.46e-169 -0.935298 0.044114 ( 0.021049) 0.979412 ( 0.003490) 0.039991 0.978959 --->germline1---dash-----: 3.96e-18 0.005212 2.27e-74 0.005218 0.044114 ( 0.021049) 0.038896 ( 0.021090) 0.039991 0.034816 --->germline2---dash-----: 3.96e-18 0.943939 2.85e-169 0.940516 0.979412 ( 0.003490) 0.038896 ( 0.021090) 0.978959 0.034816 ######FPR###### --->fabia-------beagle1--: 3.96e-18 -0.223751 4.36e-116 -0.223740 0.000135 ( 0.000162) 0.223874 ( 0.015813) 6.21e-05 0.224198 --->fabia-------beagle2--: 3.96e-18 -0.087034 3.52e-94 -0.087016 0.000135 ( 0.000162) 0.087151 ( 0.010277) 6.21e-05 0.087607 --->fabia-------plink----: 3.96e-18 -0.116538 1.33e-122 -0.116117 0.000135 ( 0.000162) 0.116251 ( 0.007026) 6.21e-05 0.117046 --->fabia-------germline1: 3.96e-18 -0.960451 4.85e-166 -0.956611 0.000135 ( 0.000162) 0.956746 ( 0.021085) 6.21e-05 0.960854 --->fabia-------germline2: 4.33e-18 -0.019960 1.46e-76 -0.019527 0.000135 ( 0.000162) 0.019661 ( 0.003494) 6.21e-05 0.020134 --->fabia-------dash-----: 3.96e-18 -0.965689 3.48e-166 -0.961809 0.000135 ( 0.000162) 0.961944 ( 0.021129) 6.21e-05 0.966037 --->beagle1-----beagle2--: 3.96e-18 0.136440 1.22e-115 0.136724 0.223874 ( 0.015813) 0.087151 ( 0.010277) 0.224198 0.087607 --->beagle1-----plink----: 3.96e-18 0.107598 1.07e-83 0.107623 0.223874 ( 0.015813) 0.116251 ( 0.007026) 0.224198 0.117046 --->beagle1-----germline1: 3.96e-18 -0.735121 1.94e-148 -0.732871 0.223874 ( 0.015813) 0.956746 ( 0.021085) 0.224198 0.960854 --->beagle1-----germline2: 3.96e-18 0.204318 2.64e-111 0.204213 0.223874 ( 0.015813) 0.019661 ( 0.003494) 0.224198 0.020134 --->beagle1-----dash-----: 3.96e-18 -0.740327 1.63e-148 -0.738069 0.223874 ( 0.015813) 0.961944 ( 0.021129) 0.224198 0.966037 --->beagle2-----plink----: 3.96e-18 -0.029147 5.37e-42 -0.029101 0.087151 ( 0.010277) 0.116251 ( 0.007026) 0.087607 0.117046 --->beagle2-----germline1: 3.96e-18 -0.872549 1.64e-159 -0.869595 0.087151 ( 0.010277) 0.956746 ( 0.021085) 0.087607 0.960854 --->beagle2-----germline2: 3.96e-18 0.067393 1.2e-80 0.067489 0.087151 ( 0.010277) 0.019661 ( 0.003494) 0.087607 0.020134 --->beagle2-----dash-----: 3.96e-18 -0.877692 1.63e-159 -0.874793 0.087151 ( 0.010277) 0.961944 ( 0.021129) 0.087607 0.966037 --->plink-------germline1: 3.96e-18 -0.843407 1.98e-161 -0.840495 0.116251 ( 0.007026) 0.956746 ( 0.021085) 0.117046 0.960854 --->plink-------germline2: 3.96e-18 0.096690 7.85e-114 0.096590 0.116251 ( 0.007026) 0.019661 ( 0.003494) 0.117046 0.020134 --->plink-------dash-----: 3.96e-18 -0.848624 1.45e-161 -0.845692 0.116251 ( 0.007026) 0.961944 ( 0.021129) 0.117046 0.966037 --->germline1---germline2: 3.96e-18 0.940564 3.42e-169 0.937085 0.956746 ( 0.021085) 0.019661 ( 0.003494) 0.960854 0.020134 --->germline1---dash-----: 3.96e-18 -0.005152 4.33e-74 -0.005198 0.956746 ( 0.021085) 0.961944 ( 0.021129) 0.960854 0.966037 --->germline2---dash-----: 3.96e-18 -0.945745 2.86e-169 -0.942282 0.019661 ( 0.003494) 0.961944 ( 0.021129) 0.020134 0.966037 ######FDR###### --->fabia-------beagle1--: 3.96e-18 -0.783589 7.76e-57 -0.782346 0.217004 ( 0.227609) 0.999350 ( 0.000291) 0.167328 0.999375 --->fabia-------beagle2--: 3.96e-18 -0.783791 7.82e-57 -0.782311 0.217004 ( 0.227609) 0.999315 ( 0.000467) 0.167328 0.999409 --->fabia-------plink----: 3.96e-18 -0.781434 1.08e-56 -0.779843 0.217004 ( 0.227609) 0.996846 ( 0.000943) 0.167328 0.996878 --->fabia-------germline1: 3.96e-18 -0.783315 8.03e-57 -0.782054 0.217004 ( 0.227609) 0.999057 ( 4.48e-05) 0.167328 0.999061 --->fabia-------germline2: 8.35e-18 -0.783256 1.17e-46 -0.762136 0.217004 ( 0.227609) 0.979140 ( 0.140601) 0.167328 1.000000 --->fabia-------dash-----: 3.96e-18 -0.783339 8e-57 -0.782085 0.217004 ( 0.227609) 0.999089 ( 5.17e-05) 0.167328 0.999091 --->beagle1-----beagle2--: 1e+00 0.000000 1e+00 0.000000 0.999350 ( 0.000291) 0.999315 ( 0.000467) 0.999375 0.999409 --->beagle1-----plink----: 4.2e-18 0.002501 4e-44 0.002504 0.999350 ( 0.000291) 0.996846 ( 0.000943) 0.999375 0.996878 --->beagle1-----germline1: 6.92e-13 0.000299 1.23e-16 0.000292 0.999350 ( 0.000291) 0.999057 ( 4.48e-05) 0.999375 0.999061 --->beagle1-----germline2: 3.1e-03 -0.000494 1.54e-01 0.020210 0.999350 ( 0.000291) 0.979140 ( 0.140601) 0.999375 1.000000 --->beagle1-----dash-----: 1.3e-11 0.000270 4.5e-14 0.000261 0.999350 ( 0.000291) 0.999089 ( 5.17e-05) 0.999375 0.999091 --->beagle2-----plink----: 5.04e-18 0.002477 1.2e-40 0.002469 0.999315 ( 0.000467) 0.996846 ( 0.000943) 0.999409 0.996878 --->beagle2-----germline1: 6.93e-07 0.000283 3.83e-07 0.000257 0.999315 ( 0.000467) 0.999057 ( 4.48e-05) 0.999409 0.999061 --->beagle2-----germline2: 5.64e-03 -0.000473 1.54e-01 0.020175 0.999315 ( 0.000467) 0.979140 ( 0.140601) 0.999409 1.000000 --->beagle2-----dash-----: 7.05e-06 0.000246 7.26e-06 0.000226 0.999315 ( 0.000467) 0.999089 ( 5.17e-05) 0.999409 0.999091 --->plink-------germline1: 4.2e-18 -0.002179 5.05e-42 -0.002211 0.996846 ( 0.000943) 0.999057 ( 4.48e-05) 0.996878 0.999061 --->plink-------germline2: 4.13e-10 -0.002680 2.11e-01 0.017706 0.996846 ( 0.000943) 0.979140 ( 0.140601) 0.996878 1.000000 --->plink-------dash-----: 4.2e-18 -0.002212 2.15e-42 -0.002243 0.996846 ( 0.000943) 0.999089 ( 5.17e-05) 0.996878 0.999091 --->germline1---germline2: 2.49e-03 -0.000922 1.6e-01 0.019918 0.999057 ( 4.48e-05) 0.979140 ( 0.140601) 0.999061 1.000000 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 0.999057 ( 4.48e-05) 0.999089 ( 5.17e-05) 0.999061 0.999091 --->germline2---dash-----: 2.55e-03 0.000882 1.59e-01 -0.019949 0.979140 ( 0.140601) 0.999089 ( 5.17e-05) 1.000000 0.999091 ######specifity###### --->fabia-------beagle1--: 3.96e-18 0.223761 4.36e-116 0.223740 0.999865 ( 0.000162) 0.776126 ( 0.015813) 0.999938 0.775802 --->fabia-------beagle2--: 3.96e-18 0.087086 3.52e-94 0.087016 0.999865 ( 0.000162) 0.912849 ( 0.010277) 0.999938 0.912393 --->fabia-------plink----: 3.96e-18 0.116517 1.33e-122 0.116117 0.999865 ( 0.000162) 0.883749 ( 0.007026) 0.999938 0.882954 --->fabia-------germline1: 3.96e-18 0.960484 4.85e-166 0.956611 0.999865 ( 0.000162) 0.043254 ( 0.021085) 0.999938 0.039146 --->fabia-------germline2: 4.33e-18 0.019984 1.46e-76 0.019527 0.999865 ( 0.000162) 0.980339 ( 0.003494) 0.999938 0.979866 --->fabia-------dash-----: 3.96e-18 0.965688 3.48e-166 0.961809 0.999865 ( 0.000162) 0.038056 ( 0.021129) 0.999938 0.033963 --->beagle1-----beagle2--: 3.96e-18 -0.136447 1.22e-115 -0.136724 0.776126 ( 0.015813) 0.912849 ( 0.010277) 0.775802 0.912393 --->beagle1-----plink----: 3.96e-18 -0.107621 1.07e-83 -0.107623 0.776126 ( 0.015813) 0.883749 ( 0.007026) 0.775802 0.882954 --->beagle1-----germline1: 3.96e-18 0.735149 1.94e-148 0.732871 0.776126 ( 0.015813) 0.043254 ( 0.021085) 0.775802 0.039146 --->beagle1-----germline2: 3.96e-18 -0.204318 2.64e-111 -0.204213 0.776126 ( 0.015813) 0.980339 ( 0.003494) 0.775802 0.979866 --->beagle1-----dash-----: 3.96e-18 0.740340 1.63e-148 0.738069 0.776126 ( 0.015813) 0.038056 ( 0.021129) 0.775802 0.033963 --->beagle2-----plink----: 3.96e-18 0.029153 5.37e-42 0.029101 0.912849 ( 0.010277) 0.883749 ( 0.007026) 0.912393 0.882954 --->beagle2-----germline1: 3.96e-18 0.872549 1.64e-159 0.869595 0.912849 ( 0.010277) 0.043254 ( 0.021085) 0.912393 0.039146 --->beagle2-----germline2: 3.96e-18 -0.067420 1.2e-80 -0.067489 0.912849 ( 0.010277) 0.980339 ( 0.003494) 0.912393 0.979866 --->beagle2-----dash-----: 3.96e-18 0.877708 1.63e-159 0.874793 0.912849 ( 0.010277) 0.038056 ( 0.021129) 0.912393 0.033963 --->plink-------germline1: 3.96e-18 0.843420 1.98e-161 0.840495 0.883749 ( 0.007026) 0.043254 ( 0.021085) 0.882954 0.039146 --->plink-------germline2: 3.96e-18 -0.096694 7.85e-114 -0.096590 0.883749 ( 0.007026) 0.980339 ( 0.003494) 0.882954 0.979866 --->plink-------dash-----: 3.96e-18 0.848623 1.45e-161 0.845692 0.883749 ( 0.007026) 0.038056 ( 0.021129) 0.882954 0.033963 --->germline1---germline2: 3.96e-18 -0.940541 3.42e-169 -0.937085 0.043254 ( 0.021085) 0.980339 ( 0.003494) 0.039146 0.979866 --->germline1---dash-----: 3.96e-18 0.005152 4.32e-74 0.005198 0.043254 ( 0.021085) 0.038056 ( 0.021129) 0.039146 0.033963 --->germline2---dash-----: 3.96e-18 0.945715 2.86e-169 0.942282 0.980339 ( 0.003494) 0.038056 ( 0.021129) 0.979866 0.033963 ######sensitivity###### --->fabia-------beagle1--: 3.96e-18 0.565861 1.58e-60 0.562390 0.713544 ( 0.141430) 0.151154 ( 0.066761) 0.723627 0.145233 --->fabia-------beagle2--: 3.96e-18 0.657641 3.05e-68 0.651820 0.713544 ( 0.141430) 0.061724 ( 0.041824) 0.723627 0.058129 --->fabia-------plink----: 1.57e-17 0.334834 6.04e-33 0.331280 0.713544 ( 0.141430) 0.382264 ( 0.118684) 0.723627 0.369712 --->fabia-------germline1: 7.9e-18 -0.212696 3.41e-28 -0.222716 0.713544 ( 0.141430) 0.936260 ( 0.034020) 0.723627 0.942057 --->fabia-------germline2: 3.96e-18 0.702553 3.03e-70 0.695341 0.713544 ( 0.141430) 0.018203 ( 0.049944) 0.723627 0.000000 --->fabia-------dash-----: 1.12e-16 -0.189927 3.64e-23 -0.196320 0.713544 ( 0.141430) 0.909864 ( 0.044628) 0.723627 0.914495 --->beagle1-----beagle2--: 1.24e-17 0.089672 1.14e-34 0.089430 0.151154 ( 0.066761) 0.061724 ( 0.041824) 0.145233 0.058129 --->beagle1-----plink----: 2.24e-17 -0.232205 4.65e-30 -0.231110 0.151154 ( 0.066761) 0.382264 ( 0.118684) 0.145233 0.369712 --->beagle1-----germline1: 3.96e-18 -0.789869 1.2e-101 -0.785106 0.151154 ( 0.066761) 0.936260 ( 0.034020) 0.145233 0.942057 --->beagle1-----germline2: 5.36e-17 0.135499 4.06e-30 0.132951 0.151154 ( 0.066761) 0.018203 ( 0.049944) 0.145233 0.000000 --->beagle1-----dash-----: 3.96e-18 -0.762792 6.53e-97 -0.758710 0.151154 ( 0.066761) 0.909864 ( 0.044628) 0.145233 0.914495 --->beagle2-----plink----: 4.08e-18 -0.318625 2.79e-44 -0.320539 0.061724 ( 0.041824) 0.382264 ( 0.118684) 0.058129 0.369712 --->beagle2-----germline1: 3.96e-18 -0.878979 8.58e-120 -0.874536 0.061724 ( 0.041824) 0.936260 ( 0.034020) 0.058129 0.942057 --->beagle2-----germline2: 4.93e-10 0.050177 9.96e-10 0.043521 0.061724 ( 0.041824) 0.018203 ( 0.049944) 0.058129 0.000000 --->beagle2-----dash-----: 3.96e-18 -0.852125 1.72e-112 -0.848140 0.061724 ( 0.041824) 0.909864 ( 0.044628) 0.058129 0.914495 --->plink-------germline1: 3.96e-18 -0.557092 8.74e-67 -0.553996 0.382264 ( 0.118684) 0.936260 ( 0.034020) 0.369712 0.942057 --->plink-------germline2: 3.96e-18 0.363793 1.09e-48 0.364061 0.382264 ( 0.118684) 0.018203 ( 0.049944) 0.369712 0.000000 --->plink-------dash-----: 3.96e-18 -0.532053 1.3e-62 -0.527600 0.382264 ( 0.118684) 0.909864 ( 0.044628) 0.369712 0.914495 --->germline1---germline2: 3.96e-18 0.932189 5.9e-116 0.918057 0.936260 ( 0.034020) 0.018203 ( 0.049944) 0.942057 0.000000 --->germline1---dash-----: 1.11e-14 0.025699 2.02e-17 0.026396 0.936260 ( 0.034020) 0.909864 ( 0.044628) 0.942057 0.914495 --->germline2---dash-----: 3.96e-18 -0.905472 4.41e-110 -0.891661 0.018203 ( 0.049944) 0.909864 ( 0.044628) 0.000000 0.914495 ######trueN###### --->fabia-------beagle1--: 3.96e-18 12234463 4.37e-189 12233881 2e+07 ( 3251) 7753782 ( 157968) 2e+07 7750698 --->fabia-------beagle2--: 3.96e-18 10868311 1.76e-202 10867960 2e+07 ( 3251) 9119703 ( 102633) 2e+07 9115098 --->fabia-------plink----: 3.96e-18 11162804 1.03e-219 11158685 2e+07 ( 3251) 8828977 ( 70220) 2e+07 8820704 --->fabia-------germline1: 3.96e-18 19594075 8.59e-197 19555536 2e+07 ( 3251) 432127 ( 210656) 2e+07 391084 --->fabia-------germline2: 3.96e-18 10198500 9.17e-246 10193715 2e+07 ( 3251) 9793948 ( 34942) 2e+07 9789246 --->fabia-------dash-----: 3.96e-18 19646049 8.11e-197 19607463 2e+07 ( 3251) 380199 ( 211092) 2e+07 339307 --->beagle1-----beagle2--: 3.96e-18 -1363256 1.22e-115 -1365921 7753782 ( 157968) 9119703 ( 102633) 7750698 9115098 --->beagle1-----plink----: 3.96e-18 -1075118 1.07e-83 -1075195 7753782 ( 157968) 8828977 ( 70220) 7750698 8820704 --->beagle1-----germline1: 3.96e-18 7344137 1.92e-148 7321655 7753782 ( 157968) 432127 ( 210656) 7750698 391084 --->beagle1-----germline2: 3.96e-18 -2041150 2.64e-111 -2040166 7753782 ( 157968) 9793948 ( 34942) 7750698 9789246 --->beagle1-----dash-----: 3.96e-18 7396234 1.61e-148 7373583 7753782 ( 157968) 380199 ( 211092) 7750698 339307 --->beagle2-----plink----: 3.96e-18 291040 5.37e-42 290725 9119703 ( 102633) 8828977 ( 70220) 9115098 8820704 --->beagle2-----germline1: 3.96e-18 8717063 1.6e-159 8687576 9119703 ( 102633) 432127 ( 210656) 9115098 391084 --->beagle2-----germline2: 3.96e-18 -673207 1.21e-80 -674245 9119703 ( 102633) 9793948 ( 34942) 9115098 9789246 --->beagle2-----dash-----: 3.96e-18 8768579 1.6e-159 8739504 9119703 ( 102633) 380199 ( 211092) 9115098 339307 --->plink-------germline1: 3.96e-18 8426105 1.96e-161 8396851 8828977 ( 70220) 432127 ( 210656) 8820704 391084 --->plink-------germline2: 3.96e-18 -966153 7.84e-114 -964970 8828977 ( 70220) 9793948 ( 34942) 8820704 9789246 --->plink-------dash-----: 3.96e-18 8478128 1.43e-161 8448778 8828977 ( 70220) 380199 ( 211092) 8820704 339307 --->germline1---germline2: 3.96e-18 -9396353 3.35e-169 -9361821 432127 ( 210656) 9793948 ( 34942) 391084 9789246 --->germline1---dash-----: 3.96e-18 51870 4.32e-74 51928 432127 ( 210656) 380199 ( 211092) 391084 339307 --->germline2---dash-----: 3.96e-18 9448209 2.8e-169 9413749 9793948 ( 34942) 380199 ( 211092) 9789246 339307 ######falseP###### --->fabia-------beagle1--: 3.96e-18 -2234454 4.47e-116 -2233897 2690 ( 3230) 2236587 ( 157975) 1242 2239870 --->fabia-------beagle2--: 3.96e-18 -868315 4.19e-94 -867976 2690 ( 3230) 870667 ( 102670) 1242 875217 --->fabia-------plink----: 3.96e-18 -1162802 2.05e-122 -1158702 2690 ( 3230) 1161392 ( 70185) 1242 1169291 --->fabia-------germline1: 3.96e-18 -9594087 5.18e-166 -9555552 2690 ( 3230) 9558243 ( 210608) 1242 9599256 --->fabia-------germline2: 4.33e-18 -198521 4.6e-76 -193732 2690 ( 3230) 196422 ( 34907) 1242 201147 --->fabia-------dash-----: 3.96e-18 -9646095 3.72e-166 -9607480 2690 ( 3230) 9610170 ( 211043) 1242 9651113 --->beagle1-----beagle2--: 3.96e-18 1363260 1.22e-115 1365921 2236587 ( 157975) 870667 ( 102670) 2239870 875217 --->beagle1-----plink----: 3.96e-18 1075108 1.07e-83 1075195 2236587 ( 157975) 1161392 ( 70185) 2239870 1169291 --->beagle1-----germline1: 3.96e-18 -7344136 1.92e-148 -7321655 2236587 ( 157975) 9558243 ( 210608) 2239870 9599256 --->beagle1-----germline2: 3.96e-18 2041159 2.64e-111 2040166 2236587 ( 157975) 196422 ( 34907) 2239870 201147 --->beagle1-----dash-----: 3.96e-18 -7396234 1.61e-148 -7373583 2236587 ( 157975) 9610170 ( 211043) 2239870 9651113 --->beagle2-----plink----: 3.96e-18 -291028 5.37e-42 -290725 870667 ( 102670) 1161392 ( 70185) 875217 1169291 --->beagle2-----germline1: 3.96e-18 -8717063 1.6e-159 -8687576 870667 ( 102670) 9558243 ( 210608) 875217 9599256 --->beagle2-----germline2: 3.96e-18 673207 1.21e-80 674245 870667 ( 102670) 196422 ( 34907) 875217 201147 --->beagle2-----dash-----: 3.96e-18 -8768615 1.6e-159 -8739504 870667 ( 102670) 9610170 ( 211043) 875217 9651113 --->plink-------germline1: 3.96e-18 -8426092 1.96e-161 -8396851 1161392 ( 70185) 9558243 ( 210608) 1169291 9599256 --->plink-------germline2: 3.96e-18 966153 7.84e-114 964970 1161392 ( 70185) 196422 ( 34907) 1169291 201147 --->plink-------dash-----: 3.96e-18 -8478128 1.43e-161 -8448778 1161392 ( 70185) 9610170 ( 211043) 1169291 9651113 --->germline1---germline2: 3.96e-18 9396350 3.35e-169 9361821 9558243 ( 210608) 196422 ( 34907) 9599256 201147 --->germline1---dash-----: 3.96e-18 -51874 4.32e-74 -51928 9558243 ( 210608) 9610170 ( 211043) 9599256 9651113 --->germline2---dash-----: 3.96e-18 -9448210 2.8e-169 -9413749 196422 ( 34907) 9610170 ( 211043) 201147 9651113 ######falseN###### --->fabia-------beagle1--: 3.96e-18 -5418 8.33e-61 -5402 2775 ( 1406) 8177 ( 732) 2570 8166 --->fabia-------beagle2--: 3.96e-18 -6307 1.41e-68 -6263 2775 ( 1406) 9038 ( 550) 2570 9038 --->fabia-------plink----: 1.52e-17 -3199 8.75e-33 -3179 2775 ( 1406) 5954 ( 1185) 2570 5988 --->fabia-------germline1: 7.9e-18 2063 1.32e-27 2161 2775 ( 1406) 614 ( 323) 2570 554 --->fabia-------germline2: 3.95e-18 -6737 5.76e-71 -6679 2775 ( 1406) 9454 ( 569) 2570 9536 --->fabia-------dash-----: 1.18e-16 1839 9.38e-23 1907 2775 ( 1406) 868 ( 426) 2570 829 --->beagle1-----beagle2--: 1.24e-17 -863 1.84e-34 -861 8177 ( 732) 9038 ( 550) 8166 9038 --->beagle1-----plink----: 2.17e-17 2228 4.34e-30 2223 8177 ( 732) 5954 ( 1185) 8166 5988 --->beagle1-----germline1: 3.96e-18 7579 4.26e-98 7563 8177 ( 732) 614 ( 323) 8166 554 --->beagle1-----germline2: 5.69e-17 -1302 5.2e-30 -1277 8177 ( 732) 9454 ( 569) 8166 9536 --->beagle1-----dash-----: 3.96e-18 7321 4.72e-94 7309 8177 ( 732) 868 ( 426) 8166 829 --->beagle2-----plink----: 4.08e-18 3062 1.84e-44 3084 9038 ( 550) 5954 ( 1185) 9038 5988 --->beagle2-----germline1: 3.96e-18 8448 1.24e-112 8425 9038 ( 550) 614 ( 323) 9038 554 --->beagle2-----germline2: 5.1e-10 -481 1.2e-09 -416 9038 ( 550) 9454 ( 569) 9038 9536 --->beagle2-----dash-----: 3.96e-18 8190 3.45e-107 8170 9038 ( 550) 868 ( 426) 9038 829 --->plink-------germline1: 3.96e-18 5374 9.56e-66 5341 5954 ( 1185) 614 ( 323) 5988 554 --->plink-------germline2: 3.96e-18 -3492 6.11e-49 -3500 5954 ( 1185) 9454 ( 569) 5988 9536 --->plink-------dash-----: 3.96e-18 5123 9e-62 5086 5954 ( 1185) 868 ( 426) 5988 829 --->germline1---germline2: 3.96e-18 -8931 6.67e-112 -8840 614 ( 323) 9454 ( 569) 554 9536 --->germline1---dash-----: 1.05e-14 -247 2.44e-17 -254 614 ( 323) 868 ( 426) 554 829 --->germline2---dash-----: 3.96e-18 8677 4.62e-107 8586 9454 ( 569) 868 ( 426) 9536 829 ######trueP###### --->fabia-------beagle1--: 3.96e-18 5437 5.66e-61 5419 6872 ( 1337) 1454 ( 644) 6975 1402 --->fabia-------beagle2--: 3.96e-18 6319 1.04e-68 6280 6872 ( 1337) 592 ( 399) 6975 538 --->fabia-------plink----: 1.46e-17 3219 5.03e-33 3196 6872 ( 1337) 3676 ( 1132) 6975 3578 --->fabia-------germline1: 7.9e-18 -2046 2.4e-27 -2145 6872 ( 1337) 9017 ( 450) 6975 9016 --->fabia-------germline2: 3.95e-18 6755 4.07e-71 6696 6872 ( 1337) 176 ( 486) 6975 0 --->fabia-------dash-----: 1.29e-16 -1817 1.67e-22 -1890 6872 ( 1337) 8763 ( 522) 6975 8780 --->beagle1-----beagle2--: 1.24e-17 863 1.84e-34 861 1454 ( 644) 592 ( 399) 1402 538 --->beagle1-----plink----: 2.17e-17 -2228 4.34e-30 -2223 1454 ( 644) 3676 ( 1132) 1402 3578 --->beagle1-----germline1: 3.96e-18 -7579 4.26e-98 -7563 1454 ( 644) 9017 ( 450) 1402 9016 --->beagle1-----germline2: 5.69e-17 1302 5.2e-30 1277 1454 ( 644) 176 ( 486) 1402 0 --->beagle1-----dash-----: 3.96e-18 -7321 4.72e-94 -7309 1454 ( 644) 8763 ( 522) 1402 8780 --->beagle2-----plink----: 4.08e-18 -3062 1.84e-44 -3084 592 ( 399) 3676 ( 1132) 538 3578 --->beagle2-----germline1: 3.96e-18 -8448 1.24e-112 -8425 592 ( 399) 9017 ( 450) 538 9016 --->beagle2-----germline2: 5.1e-10 481 1.2e-09 416 592 ( 399) 176 ( 486) 538 0 --->beagle2-----dash-----: 3.96e-18 -8190 3.45e-107 -8170 592 ( 399) 8763 ( 522) 538 8780 --->plink-------germline1: 3.96e-18 -5373 9.56e-66 -5341 3676 ( 1132) 9017 ( 450) 3578 9016 --->plink-------germline2: 3.96e-18 3492 6.11e-49 3500 3676 ( 1132) 176 ( 486) 3578 0 --->plink-------dash-----: 3.96e-18 -5123 9e-62 -5086 3676 ( 1132) 8763 ( 522) 3578 8780 --->germline1---germline2: 3.96e-18 8931 6.67e-112 8840 9017 ( 450) 176 ( 486) 9016 0 --->germline1---dash-----: 1.05e-14 247 2.44e-17 254 9017 ( 450) 8763 ( 522) 9016 8780 --->germline2---dash-----: 3.96e-18 -8677 4.62e-107 -8586 176 ( 486) 8763 ( 522) 0 8780 ######MatthewsSnps###### --->fabia-------beagle1--: 1e+00 0.000000 1e+00 0.000000 0.625945 ( 0.142458) 0.000000 ( 0.000000) 0.619402 0.000000 --->fabia-------beagle2--: 3.96e-18 0.624674 1.51e-66 0.625115 0.625945 ( 0.142458) 0.000829 ( 0.009101) 0.619402 0.000000 --->fabia-------plink----: 3.96e-18 0.625268 9.54e-67 0.625784 0.625945 ( 0.142458) 0.000161 ( 0.000704) 0.619402 0.000000 --->fabia-------germline1: 3.96e-18 0.602440 3.15e-62 0.603673 0.625945 ( 0.142458) 0.022272 ( 0.047035) 0.619402 0.029515 --->fabia-------germline2: 3.96e-18 0.628177 7.04e-59 0.625289 0.625945 ( 0.142458) 0.000656 ( 0.120686) 0.619402 -0.048583 --->fabia-------dash-----: 3.96e-18 0.602440 3.15e-62 0.603673 0.625945 ( 0.142458) 0.022272 ( 0.047035) 0.619402 0.029515 --->beagle1-----beagle2--: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.000829 ( 0.009101) 0.000000 0.000000 --->beagle1-----plink----: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.000161 ( 0.000704) 0.000000 0.000000 --->beagle1-----germline1: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.022272 ( 0.047035) 0.000000 0.029515 --->beagle1-----germline2: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.000656 ( 0.120686) 0.000000 -0.048583 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.022272 ( 0.047035) 0.000000 0.029515 --->beagle2-----plink----: 1e+00 0.000000 4.66e-01 0.000669 0.000829 ( 0.009101) 0.000161 ( 0.000704) 0.000000 0.000000 --->beagle2-----germline1: 4.18e-13 -0.029177 2.02e-05 -0.021442 0.000829 ( 0.009101) 0.022272 ( 0.047035) 0.000000 0.029515 --->beagle2-----germline2: 3.2e-04 0.047887 9.89e-01 0.000174 0.000829 ( 0.009101) 0.000656 ( 0.120686) 0.000000 -0.048583 --->beagle2-----dash-----: 4.18e-13 -0.029177 2.02e-05 -0.021442 0.000829 ( 0.009101) 0.022272 ( 0.047035) 0.000000 0.029515 --->plink-------germline1: 4.63e-14 -0.029175 8.41e-06 -0.022111 0.000161 ( 0.000704) 0.022272 ( 0.047035) 0.000000 0.029515 --->plink-------germline2: 3.29e-04 0.048087 9.67e-01 -0.000495 0.000161 ( 0.000704) 0.000656 ( 0.120686) 0.000000 -0.048583 --->plink-------dash-----: 4.63e-14 -0.029175 8.41e-06 -0.022111 0.000161 ( 0.000704) 0.022272 ( 0.047035) 0.000000 0.029515 --->germline1---germline2: 9.32e-05 0.077236 1.45e-01 0.021616 0.022272 ( 0.047035) 0.000656 ( 0.120686) 0.029515 -0.048583 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 0.022272 ( 0.047035) 0.022272 ( 0.047035) 0.029515 0.029515 --->germline2---dash-----: 9.32e-05 -0.077246 1.45e-01 -0.021616 0.000656 ( 0.120686) 0.022272 ( 0.047035) -0.048583 0.029515 ######F1Snps###### --->fabia-------beagle1--: 3.96e-18 0.476952 6.09e-59 0.477492 0.649457 ( 0.133842) 0.171965 ( 0.009445) 0.652501 0.173850 --->fabia-------beagle2--: 3.96e-18 0.476922 6.12e-59 0.477462 0.649457 ( 0.133842) 0.171995 ( 0.009437) 0.652501 0.173850 --->fabia-------plink----: 3.96e-18 0.476952 6.09e-59 0.477491 0.649457 ( 0.133842) 0.171966 ( 0.009445) 0.652501 0.173850 --->fabia-------germline1: 3.96e-18 0.475636 1.22e-58 0.476200 0.649457 ( 0.133842) 0.173257 ( 0.010285) 0.652501 0.174990 --->fabia-------germline2: 3.96e-18 0.611643 2.69e-64 0.612935 0.649457 ( 0.133842) 0.036523 ( 0.090379) 0.652501 0.000000 --->fabia-------dash-----: 3.96e-18 0.475636 1.22e-58 0.476200 0.649457 ( 0.133842) 0.173257 ( 0.010285) 0.652501 0.174990 --->beagle1-----beagle2--: 1e+00 0.000000 1e+00 0.000000 0.171965 ( 0.009445) 0.171995 ( 0.009437) 0.173850 0.173850 --->beagle1-----plink----: 1e+00 0.000000 1e+00 0.000000 0.171965 ( 0.009445) 0.171966 ( 0.009445) 0.173850 0.173850 --->beagle1-----germline1: 6.1e-13 -0.001318 7.56e-04 -0.001292 0.171965 ( 0.009445) 0.173257 ( 0.010285) 0.173850 0.174990 --->beagle1-----germline2: 1.18e-15 0.169656 6.09e-27 0.135443 0.171965 ( 0.009445) 0.036523 ( 0.090379) 0.173850 0.000000 --->beagle1-----dash-----: 6.1e-13 -0.001318 7.56e-04 -0.001292 0.171965 ( 0.009445) 0.173257 ( 0.010285) 0.173850 0.174990 --->beagle2-----plink----: 1e+00 0.000000 1e+00 0.000000 0.171995 ( 0.009437) 0.171966 ( 0.009445) 0.173850 0.173850 --->beagle2-----germline1: 1.18e-11 -0.001283 1.36e-03 -0.001262 0.171995 ( 0.009437) 0.173257 ( 0.010285) 0.173850 0.174990 --->beagle2-----germline2: 1.18e-15 0.169773 6.56e-27 0.135472 0.171995 ( 0.009437) 0.036523 ( 0.090379) 0.173850 0.000000 --->beagle2-----dash-----: 1.18e-11 -0.001283 1.36e-03 -0.001262 0.171995 ( 0.009437) 0.173257 ( 0.010285) 0.173850 0.174990 --->plink-------germline1: 6.75e-13 -0.001317 7.61e-04 -0.001291 0.171966 ( 0.009445) 0.173257 ( 0.010285) 0.173850 0.174990 --->plink-------germline2: 1.18e-15 0.169656 6.09e-27 0.135443 0.171966 ( 0.009445) 0.036523 ( 0.090379) 0.173850 0.000000 --->plink-------dash-----: 6.75e-13 -0.001317 7.61e-04 -0.001291 0.171966 ( 0.009445) 0.173257 ( 0.010285) 0.173850 0.174990 --->germline1---germline2: 1.15e-15 0.171264 7.6e-27 0.136735 0.173257 ( 0.010285) 0.036523 ( 0.090379) 0.174990 0.000000 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 0.173257 ( 0.010285) 0.173257 ( 0.010285) 0.174990 0.174990 --->germline2---dash-----: 1.15e-15 -0.171290 7.6e-27 -0.136735 0.036523 ( 0.090379) 0.173257 ( 0.010285) 0.000000 0.174990 ######accuracySnps###### --->fabia-------beagle1--: 3.96e-18 0.823157 3.86e-124 0.819426 0.913526 ( 0.048865) 0.094100 ( 0.005624) 0.923250 0.095200 --->fabia-------beagle2--: 3.96e-18 0.821784 6.87e-124 0.818197 0.913526 ( 0.048865) 0.095329 ( 0.008638) 0.923250 0.095400 --->fabia-------plink----: 3.96e-18 0.823133 3.85e-124 0.819421 0.913526 ( 0.048865) 0.094105 ( 0.005624) 0.923250 0.095200 --->fabia-------germline1: 3.96e-18 0.814523 4.1e-116 0.807962 0.913526 ( 0.048865) 0.105564 ( 0.020713) 0.923250 0.103200 --->fabia-------germline2: 1.74e-06 0.030247 2e-06 0.025712 0.913526 ( 0.048865) 0.887814 ( 0.012279) 0.923250 0.883900 --->fabia-------dash-----: 3.96e-18 0.814523 4.1e-116 0.807962 0.913526 ( 0.048865) 0.105564 ( 0.020713) 0.923250 0.103200 --->beagle1-----beagle2--: 1e+00 0.000000 4.28e-02 -0.001229 0.094100 ( 0.005624) 0.095329 ( 0.008638) 0.095200 0.095400 --->beagle1-----plink----: 1e+00 0.000000 1e+00 0.000000 0.094100 ( 0.005624) 0.094105 ( 0.005624) 0.095200 0.095200 --->beagle1-----germline1: 1.21e-17 -0.008348 8.49e-08 -0.011464 0.094100 ( 0.005624) 0.105564 ( 0.020713) 0.095200 0.103200 --->beagle1-----germline2: 3.95e-18 -0.791631 8.33e-171 -0.793714 0.094100 ( 0.005624) 0.887814 ( 0.012279) 0.095200 0.883900 --->beagle1-----dash-----: 1.21e-17 -0.008348 8.49e-08 -0.011464 0.094100 ( 0.005624) 0.105564 ( 0.020713) 0.095200 0.103200 --->beagle2-----plink----: 1e+00 0.000000 4.37e-02 0.001224 0.095329 ( 0.008638) 0.094105 ( 0.005624) 0.095400 0.095200 --->beagle2-----germline1: 6.83e-14 -0.008189 3.93e-06 -0.010235 0.095329 ( 0.008638) 0.105564 ( 0.020713) 0.095400 0.103200 --->beagle2-----germline2: 3.95e-18 -0.791051 5.22e-167 -0.792485 0.095329 ( 0.008638) 0.887814 ( 0.012279) 0.095400 0.883900 --->beagle2-----dash-----: 6.83e-14 -0.008189 3.93e-06 -0.010235 0.095329 ( 0.008638) 0.105564 ( 0.020713) 0.095400 0.103200 --->plink-------germline1: 1.23e-17 -0.008344 8.59e-08 -0.011459 0.094105 ( 0.005624) 0.105564 ( 0.020713) 0.095200 0.103200 --->plink-------germline2: 3.95e-18 -0.791615 8.29e-171 -0.793709 0.094105 ( 0.005624) 0.887814 ( 0.012279) 0.095200 0.883900 --->plink-------dash-----: 1.23e-17 -0.008344 8.59e-08 -0.011459 0.094105 ( 0.005624) 0.105564 ( 0.020713) 0.095200 0.103200 --->germline1---germline2: 3.95e-18 -0.781846 3.37e-150 -0.782250 0.105564 ( 0.020713) 0.887814 ( 0.012279) 0.103200 0.883900 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 0.105564 ( 0.020713) 0.105564 ( 0.020713) 0.103200 0.103200 --->germline2---dash-----: 3.95e-18 0.781813 3.37e-150 0.782250 0.887814 ( 0.012279) 0.105564 ( 0.020713) 0.883900 0.103200 ######FPRSnps###### --->fabia-------beagle1--: 3.96e-18 -0.172214 8.56e-124 -0.171452 0.013293 ( 0.010325) 0.184745 ( 0.001104) 0.011836 0.184506 --->fabia-------beagle2--: 3.96e-18 -0.171891 2.33e-123 -0.171178 0.013293 ( 0.010325) 0.184471 ( 0.001829) 0.011836 0.184497 --->fabia-------plink----: 3.96e-18 -0.172209 8.52e-124 -0.171451 0.013293 ( 0.010325) 0.184744 ( 0.001104) 0.011836 0.184506 --->fabia-------germline1: 3.96e-18 -0.170342 5.66e-116 -0.169037 0.013293 ( 0.010325) 0.182330 ( 0.004322) 0.011836 0.182840 --->fabia-------germline2: 6.92e-13 0.008166 5.35e-14 0.009171 0.013293 ( 0.010325) 0.004122 ( 0.001261) 0.011836 0.004526 --->fabia-------dash-----: 3.96e-18 -0.170342 5.66e-116 -0.169037 0.013293 ( 0.010325) 0.182330 ( 0.004322) 0.011836 0.182840 --->beagle1-----beagle2--: 1e+00 0.000000 4.38e-02 0.000274 0.184745 ( 0.001104) 0.184471 ( 0.001829) 0.184506 0.184497 --->beagle1-----plink----: 1e+00 0.000000 1e+00 0.000000 0.184745 ( 0.001104) 0.184744 ( 0.001104) 0.184506 0.184506 --->beagle1-----germline1: 3.96e-18 0.001710 6.87e-08 0.002415 0.184745 ( 0.001104) 0.182330 ( 0.004322) 0.184506 0.182840 --->beagle1-----germline2: 3.96e-18 0.180325 1.38e-203 0.180623 0.184745 ( 0.001104) 0.004122 ( 0.001261) 0.184506 0.004526 --->beagle1-----dash-----: 3.96e-18 0.001710 6.87e-08 0.002415 0.184745 ( 0.001104) 0.182330 ( 0.004322) 0.184506 0.182840 --->beagle2-----plink----: 1e+00 0.000000 4.46e-02 -0.000273 0.184471 ( 0.001829) 0.184744 ( 0.001104) 0.184497 0.184506 --->beagle2-----germline1: 2.52e-14 0.001699 4.42e-06 0.002141 0.184471 ( 0.001829) 0.182330 ( 0.004322) 0.184497 0.182840 --->beagle2-----germline2: 3.96e-18 0.180237 1.54e-191 0.180349 0.184471 ( 0.001829) 0.004122 ( 0.001261) 0.184497 0.004526 --->beagle2-----dash-----: 2.52e-14 0.001699 4.42e-06 0.002141 0.184471 ( 0.001829) 0.182330 ( 0.004322) 0.184497 0.182840 --->plink-------germline1: 3.96e-18 0.001709 6.95e-08 0.002414 0.184744 ( 0.001104) 0.182330 ( 0.004322) 0.184506 0.182840 --->plink-------germline2: 3.96e-18 0.180325 1.38e-203 0.180622 0.184744 ( 0.001104) 0.004122 ( 0.001261) 0.184506 0.004526 --->plink-------dash-----: 3.96e-18 0.001709 6.95e-08 0.002414 0.184744 ( 0.001104) 0.182330 ( 0.004322) 0.184506 0.182840 --->germline1---germline2: 3.96e-18 0.178477 2.98e-163 0.178208 0.182330 ( 0.004322) 0.004122 ( 0.001261) 0.182840 0.004526 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 0.182330 ( 0.004322) 0.182330 ( 0.004322) 0.182840 0.182840 --->germline2---dash-----: 3.96e-18 -0.178440 2.98e-163 -0.178208 0.004122 ( 0.001261) 0.182330 ( 0.004322) 0.004526 0.182840 ######FDRSnps###### --->fabia-------beagle1--: 3.96e-18 -0.492490 6.55e-43 -0.504807 0.401093 ( 0.212320) 0.905900 ( 0.005624) 0.427805 0.904800 --->fabia-------beagle2--: 3.96e-18 -0.492588 6.56e-43 -0.504778 0.401093 ( 0.212320) 0.905871 ( 0.005626) 0.427805 0.904800 --->fabia-------plink----: 3.96e-18 -0.492490 6.55e-43 -0.504806 0.401093 ( 0.212320) 0.905900 ( 0.005624) 0.427805 0.904800 --->fabia-------germline1: 3.96e-18 -0.491737 8.41e-43 -0.503991 0.401093 ( 0.212320) 0.905084 ( 0.006126) 0.427805 0.904116 --->fabia-------germline2: 2.16e-17 -0.510653 1.09e-31 -0.505570 0.401093 ( 0.212320) 0.906664 ( 0.230576) 0.427805 1.000000 --->fabia-------dash-----: 3.96e-18 -0.491737 8.41e-43 -0.503991 0.401093 ( 0.212320) 0.905084 ( 0.006126) 0.427805 0.904116 --->beagle1-----beagle2--: 1e+00 0.000000 1e+00 0.000000 0.905900 ( 0.005624) 0.905871 ( 0.005626) 0.904800 0.904800 --->beagle1-----plink----: 1e+00 0.000000 1e+00 0.000000 0.905900 ( 0.005624) 0.905900 ( 0.005624) 0.904800 0.904800 --->beagle1-----germline1: 3.08e-13 0.000758 3.38e-04 0.000816 0.905900 ( 0.005624) 0.905084 ( 0.006126) 0.904800 0.904116 --->beagle1-----germline2: 3.29e-04 -0.092429 9.74e-01 -0.000764 0.905900 ( 0.005624) 0.906664 ( 0.230576) 0.904800 1.000000 --->beagle1-----dash-----: 3.08e-13 0.000758 3.38e-04 0.000816 0.905900 ( 0.005624) 0.905084 ( 0.006126) 0.904800 0.904116 --->beagle2-----plink----: 1e+00 0.000000 1e+00 0.000000 0.905871 ( 0.005626) 0.905900 ( 0.005624) 0.904800 0.904800 --->beagle2-----germline1: 6.67e-12 0.000766 7.26e-04 0.000787 0.905871 ( 0.005626) 0.905084 ( 0.006126) 0.904800 0.904116 --->beagle2-----germline2: 3.29e-04 -0.092486 9.73e-01 -0.000793 0.905871 ( 0.005626) 0.906664 ( 0.230576) 0.904800 1.000000 --->beagle2-----dash-----: 6.67e-12 0.000766 7.26e-04 0.000787 0.905871 ( 0.005626) 0.905084 ( 0.006126) 0.904800 0.904116 --->plink-------germline1: 3.08e-13 0.000758 3.4e-04 0.000815 0.905900 ( 0.005624) 0.905084 ( 0.006126) 0.904800 0.904116 --->plink-------germline2: 3.29e-04 -0.092429 9.74e-01 -0.000764 0.905900 ( 0.005624) 0.906664 ( 0.230576) 0.904800 1.000000 --->plink-------dash-----: 3.08e-13 0.000758 3.4e-04 0.000815 0.905900 ( 0.005624) 0.905084 ( 0.006126) 0.904800 0.904116 --->germline1---germline2: 3.29e-04 -0.093419 9.46e-01 -0.001579 0.905084 ( 0.006126) 0.906664 ( 0.230576) 0.904116 1.000000 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 0.905084 ( 0.006126) 0.905084 ( 0.006126) 0.904116 0.904116 --->germline2---dash-----: 3.29e-04 0.093439 9.46e-01 0.001579 0.906664 ( 0.230576) 0.905084 ( 0.006126) 1.000000 0.904116 ######specifitySnps###### --->fabia-------beagle1--: 1e+00 0.000000 1e+00 0.000000 0.171452 ( 0.010117) 0.000000 ( 0.000000) 0.172290 0.000000 --->fabia-------beagle2--: 3.96e-18 0.171905 2.33e-123 0.171178 0.171452 ( 0.010117) 0.000274 ( 0.001340) 0.172290 0.000000 --->fabia-------plink----: 3.96e-18 0.172216 8.52e-124 0.171451 0.171452 ( 0.010117) 1.02e-06 ( 4.47e-06) 0.172290 0.000000 --->fabia-------germline1: 3.96e-18 0.170309 5.66e-116 0.169037 0.171452 ( 0.010117) 0.002415 ( 0.004140) 0.172290 0.001683 --->fabia-------germline2: 6.92e-13 -0.008172 5.35e-14 -0.009171 0.171452 ( 0.010117) 0.180623 ( 0.001663) 0.172290 0.180166 --->fabia-------dash-----: 3.96e-18 0.170309 5.66e-116 0.169037 0.171452 ( 0.010117) 0.002415 ( 0.004140) 0.172290 0.001683 --->beagle1-----beagle2--: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.000274 ( 0.001340) 0.000000 0.000000 --->beagle1-----plink----: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 1.02e-06 ( 4.47e-06) 0.000000 0.000000 --->beagle1-----germline1: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.002415 ( 0.004140) 0.000000 0.001683 --->beagle1-----germline2: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.180623 ( 0.001663) 0.000000 0.180166 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.002415 ( 0.004140) 0.000000 0.001683 --->beagle2-----plink----: 1e+00 0.000000 4.46e-02 0.000273 0.000274 ( 0.001340) 1.02e-06 ( 4.47e-06) 0.000000 0.000000 --->beagle2-----germline1: 2.52e-14 -0.001654 4.42e-06 -0.002141 0.000274 ( 0.001340) 0.002415 ( 0.004140) 0.000000 0.001683 --->beagle2-----germline2: 3.96e-18 -0.180219 1.54e-191 -0.180349 0.000274 ( 0.001340) 0.180623 ( 0.001663) 0.000000 0.180166 --->beagle2-----dash-----: 2.52e-14 -0.001654 4.42e-06 -0.002141 0.000274 ( 0.001340) 0.002415 ( 0.004140) 0.000000 0.001683 --->plink-------germline1: 3.96e-18 -0.001713 6.95e-08 -0.002414 1.02e-06 ( 4.47e-06) 0.002415 ( 0.004140) 0.000000 0.001683 --->plink-------germline2: 3.96e-18 -0.180345 1.38e-203 -0.180622 1.02e-06 ( 4.47e-06) 0.180623 ( 0.001663) 0.000000 0.180166 --->plink-------dash-----: 3.96e-18 -0.001713 6.95e-08 -0.002414 1.02e-06 ( 4.47e-06) 0.002415 ( 0.004140) 0.000000 0.001683 --->germline1---germline2: 3.96e-18 -0.178440 2.98e-163 -0.178208 0.002415 ( 0.004140) 0.180623 ( 0.001663) 0.001683 0.180166 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 0.002415 ( 0.004140) 0.002415 ( 0.004140) 0.001683 0.001683 --->germline2---dash-----: 3.96e-18 0.178480 2.98e-163 0.178208 0.180623 ( 0.001663) 0.002415 ( 0.004140) 0.180166 0.001683 ######sensitivitySnps###### --->fabia-------beagle1--: 3.96e-18 -0.213105 8.2e-37 -0.219964 0.755569 ( 0.120010) 0.975533 ( 0.053617) 0.758362 1.000000 --->fabia-------beagle2--: 4.08e-18 -0.212511 3.64e-36 -0.218824 0.755569 ( 0.120010) 0.974392 ( 0.053698) 0.758362 1.000000 --->fabia-------plink----: 3.96e-18 -0.213105 8.2e-37 -0.219964 0.755569 ( 0.120010) 0.975533 ( 0.053617) 0.758362 1.000000 --->fabia-------germline1: 3.96e-18 -0.209786 2.42e-35 -0.216013 0.755569 ( 0.120010) 0.971582 ( 0.055682) 0.758362 1.000000 --->fabia-------germline2: 3.96e-18 0.738052 9.55e-77 0.733585 0.755569 ( 0.120010) 0.021984 ( 0.054465) 0.758362 0.000000 --->fabia-------dash-----: 3.96e-18 -0.209786 2.42e-35 -0.216013 0.755569 ( 0.120010) 0.971582 ( 0.055682) 0.758362 1.000000 --->beagle1-----beagle2--: 1e+00 0.000000 1.61e-01 0.001140 0.975533 ( 0.053617) 0.974392 ( 0.053698) 1.000000 1.000000 --->beagle1-----plink----: 1e+00 0.000000 1e+00 0.000000 0.975533 ( 0.053617) 0.975533 ( 0.053617) 1.000000 1.000000 --->beagle1-----germline1: 1e+00 0.000000 1.96e-02 0.003951 0.975533 ( 0.053617) 0.971582 ( 0.055682) 1.000000 1.000000 --->beagle1-----germline2: 2.85e-19 0.978905 7.1e-110 0.953549 0.975533 ( 0.053617) 0.021984 ( 0.054465) 1.000000 0.000000 --->beagle1-----dash-----: 1e+00 0.000000 1.96e-02 0.003951 0.975533 ( 0.053617) 0.971582 ( 0.055682) 1.000000 1.000000 --->beagle2-----plink----: 1e+00 0.000000 1.61e-01 -0.001140 0.974392 ( 0.053698) 0.975533 ( 0.053617) 1.000000 1.000000 --->beagle2-----germline1: 1e+00 0.000000 1.37e-01 0.002810 0.974392 ( 0.053698) 0.971582 ( 0.055682) 1.000000 1.000000 --->beagle2-----germline2: 3.24e-19 0.974307 2.38e-109 0.952408 0.974392 ( 0.053698) 0.021984 ( 0.054465) 1.000000 0.000000 --->beagle2-----dash-----: 1e+00 0.000000 1.37e-01 0.002810 0.974392 ( 0.053698) 0.971582 ( 0.055682) 1.000000 1.000000 --->plink-------germline1: 1e+00 0.000000 1.96e-02 0.003951 0.975533 ( 0.053617) 0.971582 ( 0.055682) 1.000000 1.000000 --->plink-------germline2: 2.85e-19 0.978905 7.1e-110 0.953549 0.975533 ( 0.053617) 0.021984 ( 0.054465) 1.000000 0.000000 --->plink-------dash-----: 1e+00 0.000000 1.96e-02 0.003951 0.975533 ( 0.053617) 0.971582 ( 0.055682) 1.000000 1.000000 --->germline1---germline2: 3.67e-19 0.967591 2.31e-107 0.949598 0.971582 ( 0.055682) 0.021984 ( 0.054465) 1.000000 0.000000 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 0.971582 ( 0.055682) 0.971582 ( 0.055682) 1.000000 1.000000 --->germline2---dash-----: 3.67e-19 -0.967591 2.31e-107 -0.949598 0.021984 ( 0.054465) 0.971582 ( 0.055682) 0.000000 1.000000 ######trueNSnps###### --->fabia-------beagle1--: 1e+00 0 1e+00 0 8407 ( 496) 0 ( 0) 8450 0 --->fabia-------beagle2--: 3.96e-18 8429 2.19e-123 8394 8407 ( 496) 13.4 ( 65.7) 8450 0 --->fabia-------plink----: 3.95e-18 8443 7.93e-124 8407 8407 ( 496) 0.05 ( 0.219) 8450 0 --->fabia-------germline1: 3.96e-18 8352 5.24e-116 8289 8407 ( 496) 118 ( 203) 8450 82.5 --->fabia-------germline2: 6.92e-13 -402 5.37e-14 -450 8407 ( 496) 8857 ( 83) 8450 8839 --->fabia-------dash-----: 3.96e-18 8352 5.24e-116 8289 8407 ( 496) 118 ( 203) 8450 82.5 --->beagle1-----beagle2--: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 13.420000 (65.710596) 0.000000 0.000000 --->beagle1-----plink----: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.050000 ( 0.219043) 0.000000 0.000000 --->beagle1-----germline1: 1e+00 0 1e+00 0 0 ( 0) 118 ( 203) 0 82.5 --->beagle1-----germline2: 1e+00 0 1e+00 0 0 ( 0) 8857 ( 83) 0 8839 --->beagle1-----dash-----: 1e+00 0 1e+00 0 0 ( 0) 118 ( 203) 0 82.5 --->beagle2-----plink----: 1e+00 0.000000 4.46e-02 13.370000 13.420000 (65.710596) 0.050000 ( 0.219043) 0.000000 0.000000 --->beagle2-----germline1: 2.46e-14 -82 4.43e-06 -105 13.4 ( 65.7) 118 ( 203) 0 82.5 --->beagle2-----germline2: 3.95e-18 -8841 4.72e-191 -8843 13.4 ( 65.7) 8857 ( 83) 0 8839 --->beagle2-----dash-----: 2.46e-14 -82 4.43e-06 -105 13.4 ( 65.7) 118 ( 203) 0 82.5 --->plink-------germline1: 3.92e-18 -83.5 6.99e-08 -118 0.05 ( 0.219) 118 ( 203) 0 82.5 --->plink-------germline2: 3.95e-18 -8845 7.72e-203 -8857 0.05 ( 0.219) 8857 ( 83) 0 8839 --->plink-------dash-----: 3.92e-18 -83.5 6.99e-08 -118 0.05 ( 0.219) 118 ( 203) 0 82.5 --->germline1---germline2: 3.95e-18 -8753 2.87e-163 -8738 118 ( 203) 8857 ( 83) 82.5 8839 --->germline1---dash-----: 1e+00 0 1e+00 0 118 ( 203) 118 ( 203) 82.5 82.5 --->germline2---dash-----: 3.95e-18 8753 2.87e-163 8738 8857 ( 83) 118 ( 203) 8839 82.5 ######falsePSnps###### --->fabia-------beagle1--: 3.96e-18 -8443 7.97e-124 -8407 652 ( 506) 9059 ( 56.2) 580 9048 --->fabia-------beagle2--: 3.96e-18 -8429 2.19e-123 -8394 652 ( 506) 9046 ( 91.1) 580 9046 --->fabia-------plink----: 3.95e-18 -8443 7.93e-124 -8407 652 ( 506) 9059 ( 56.2) 580 9048 --->fabia-------germline1: 3.96e-18 -8352 5.24e-116 -8289 652 ( 506) 8941 ( 212) 580 8968 --->fabia-------germline2: 6.92e-13 402 5.37e-14 450 652 ( 506) 202 ( 61.8) 580 222 --->fabia-------dash-----: 3.96e-18 -8352 5.24e-116 -8289 652 ( 506) 8941 ( 212) 580 8968 --->beagle1-----beagle2--: 1e+00 0 4.38e-02 13.4 9059 ( 56.2) 9046 ( 91.1) 9048 9046 --->beagle1-----plink----: 1e+00 0 2.46e-02 0.05 9059 ( 56.2) 9059 ( 56.2) 9048 9048 --->beagle1-----germline1: 3.91e-18 83.5 6.91e-08 118 9059 ( 56.2) 8941 ( 212) 9048 8968 --->beagle1-----germline2: 3.95e-18 8845 7.75e-203 8857 9059 ( 56.2) 202 ( 61.8) 9048 222 --->beagle1-----dash-----: 3.91e-18 83.5 6.91e-08 118 9059 ( 56.2) 8941 ( 212) 9048 8968 --->beagle2-----plink----: 1e+00 0 4.46e-02 -13.4 9046 ( 91.1) 9059 ( 56.2) 9046 9048 --->beagle2-----germline1: 2.46e-14 82 4.43e-06 105 9046 ( 91.1) 8941 ( 212) 9046 8968 --->beagle2-----germline2: 3.95e-18 8841 4.72e-191 8843 9046 ( 91.1) 202 ( 61.8) 9046 222 --->beagle2-----dash-----: 2.46e-14 82 4.43e-06 105 9046 ( 91.1) 8941 ( 212) 9046 8968 --->plink-------germline1: 3.92e-18 83.5 6.99e-08 118 9059 ( 56.2) 8941 ( 212) 9048 8968 --->plink-------germline2: 3.95e-18 8845 7.72e-203 8857 9059 ( 56.2) 202 ( 61.8) 9048 222 --->plink-------dash-----: 3.92e-18 83.5 6.99e-08 118 9059 ( 56.2) 8941 ( 212) 9048 8968 --->germline1---germline2: 3.95e-18 8753 2.87e-163 8738 8941 ( 212) 202 ( 61.8) 8968 222 --->germline1---dash-----: 1e+00 0 1e+00 0 8941 ( 212) 8941 ( 212) 8968 8968 --->germline2---dash-----: 3.95e-18 -8753 2.87e-163 -8738 202 ( 61.8) 8941 ( 212) 222 8968 ######falseNSnps###### --->fabia-------beagle1--: 1e+00 0 1e+00 0 213 ( 107) 0 ( 0) 204 0 --->fabia-------beagle2--: 4.08e-18 205 1.41e-35 212 213 ( 107) 1.13 ( 8.02) 204 0 --->fabia-------plink----: 1e+00 0 1e+00 0 213 ( 107) 0 ( 0) 204 0 --->fabia-------germline1: 3.95e-18 202 8.49e-35 209 213 ( 107) 3.79 ( 16) 204 0 --->fabia-------germline2: 3.95e-18 -712 9.97e-78 -707 213 ( 107) 920 ( 77.6) 204 938 --->fabia-------dash-----: 3.95e-18 202 8.49e-35 209 213 ( 107) 3.79 ( 16) 204 0 --->beagle1-----beagle2--: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 1.130000 ( 8.021001) 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) 3.790000 (15.973017) 0.000000 0.000000 --->beagle1-----germline2: 1e+00 0 1e+00 0 0 ( 0) 920 ( 77.6) 0 938 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 3.790000 (15.973017) 0.000000 0.000000 --->beagle2-----plink----: 1e+00 0.000000 1e+00 0.000000 1.130000 ( 8.021001) 0.000000 ( 0.000000) 0.000000 0.000000 --->beagle2-----germline1: 1e+00 0.000000 1.45e-01 -2.660000 1.130000 ( 8.021001) 3.790000 (15.973017) 0.000000 0.000000 --->beagle2-----germline2: 3.95e-18 -930 3.45e-108 -919 1.13 ( 8.02) 920 ( 77.6) 0 938 --->beagle2-----dash-----: 1e+00 0.000000 1.45e-01 -2.660000 1.130000 ( 8.021001) 3.790000 (15.973017) 0.000000 0.000000 --->plink-------germline1: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 3.790000 (15.973017) 0.000000 0.000000 --->plink-------germline2: 1e+00 0 1e+00 0 0 ( 0) 920 ( 77.6) 0 938 --->plink-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 3.790000 (15.973017) 0.000000 0.000000 --->germline1---germline2: 3.95e-18 -928 5.94e-106 -916 3.79 ( 16) 920 ( 77.6) 0 938 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 3.790000 (15.973017) 3.790000 (15.973017) 0.000000 0.000000 --->germline2---dash-----: 3.95e-18 928 5.94e-106 916 920 ( 77.6) 3.79 ( 16) 938 0 ######truePSnps###### --->fabia-------beagle1--: 3.95e-18 -205 3.18e-36 -213 728 ( 113) 941 ( 56.2) 732 952 --->fabia-------beagle2--: 4.08e-18 -205 1.41e-35 -212 728 ( 113) 940 ( 55.8) 732 950 --->fabia-------plink----: 3.95e-18 -205 3.18e-36 -213 728 ( 113) 941 ( 56.2) 732 952 --->fabia-------germline1: 3.95e-18 -202 8.49e-35 -209 728 ( 113) 937 ( 58.4) 732 948 --->fabia-------germline2: 3.95e-18 712 9.97e-78 707 728 ( 113) 21.3 ( 52.8) 732 0 --->fabia-------dash-----: 3.95e-18 -202 8.49e-35 -209 728 ( 113) 937 ( 58.4) 732 948 --->beagle1-----beagle2--: 1e+00 0 1.62e-01 1.13 941 ( 56.2) 940 ( 55.8) 952 950 --->beagle1-----plink----: 1e+00 0 1e+00 0 941 ( 56.2) 941 ( 56.2) 952 952 --->beagle1-----germline1: 1e+00 0 1.96e-02 3.79 941 ( 56.2) 937 ( 58.4) 952 948 --->beagle1-----germline2: 3.95e-18 931 1.81e-108 920 941 ( 56.2) 21.3 ( 52.8) 952 0 --->beagle1-----dash-----: 1e+00 0 1.96e-02 3.79 941 ( 56.2) 937 ( 58.4) 952 948 --->beagle2-----plink----: 1e+00 0 1.62e-01 -1.13 940 ( 55.8) 941 ( 56.2) 950 952 --->beagle2-----germline1: 1e+00 0 1.45e-01 2.66 940 ( 55.8) 937 ( 58.4) 950 948 --->beagle2-----germline2: 3.95e-18 930 3.45e-108 919 940 ( 55.8) 21.3 ( 52.8) 950 0 --->beagle2-----dash-----: 1e+00 0 1.45e-01 2.66 940 ( 55.8) 937 ( 58.4) 950 948 --->plink-------germline1: 1e+00 0 1.96e-02 3.79 941 ( 56.2) 937 ( 58.4) 952 948 --->plink-------germline2: 3.95e-18 931 1.81e-108 920 941 ( 56.2) 21.3 ( 52.8) 952 0 --->plink-------dash-----: 1e+00 0 1.96e-02 3.79 941 ( 56.2) 937 ( 58.4) 952 948 --->germline1---germline2: 3.95e-18 928 5.94e-106 916 937 ( 58.4) 21.3 ( 52.8) 948 0 --->germline1---dash-----: 1e+00 0 1e+00 0 937 ( 58.4) 937 ( 58.4) 948 948 --->germline2---dash-----: 3.95e-18 -928 5.94e-106 -916 21.3 ( 52.8) 937 ( 58.4) 0 948 ######MatthewsSample###### --->fabia-------beagle1--: 3.96e-18 0.765097 9.05e-75 0.766663 0.755852 ( 0.142457) -0.010810 ( 0.034265) 0.718205 -0.014422 --->fabia-------beagle2--: 3.96e-18 0.761959 2.07e-75 0.759872 0.755852 ( 0.142457) -0.004020 ( 0.029254) 0.718205 -0.005205 --->fabia-------plink----: 3.96e-18 0.751819 7.47e-73 0.752266 0.755852 ( 0.142457) 0.003586 ( 0.028148) 0.718205 0.012114 --->fabia-------germline1: 1e+00 0.000000 1e+00 0.000000 0.755852 ( 0.142457) 0.000000 ( 0.000000) 0.718205 0.000000 --->fabia-------germline2: 3.96e-18 0.759080 1.16e-71 0.759350 0.755852 ( 0.142457) -0.003498 ( 0.033420) 0.718205 0.001531 --->fabia-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.755852 ( 0.142457) 0.000000 ( 0.000000) 0.718205 0.000000 --->beagle1-----beagle2--: 2.65e-02 -0.007429 4.78e-02 -0.006791 -0.010810 ( 0.034265) -0.004020 ( 0.029254) -0.014422 -0.005205 --->beagle1-----plink----: 1.57e-04 -0.018213 2.49e-03 -0.014397 -0.010810 ( 0.034265) 0.003586 ( 0.028148) -0.014422 0.012114 --->beagle1-----germline1: 1e+00 0.000000 1e+00 0.000000 -0.010810 ( 0.034265) 0.000000 ( 0.000000) -0.014422 0.000000 --->beagle1-----germline2: 8.91e-02 -0.007966 1.15e-01 -0.007313 -0.010810 ( 0.034265) -0.003498 ( 0.033420) -0.014422 0.001531 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 -0.010810 ( 0.034265) 0.000000 ( 0.000000) -0.014422 0.000000 --->beagle2-----plink----: 3.38e-03 -0.011590 6.18e-02 -0.007606 -0.004020 ( 0.029254) 0.003586 ( 0.028148) -0.005205 0.012114 --->beagle2-----germline1: 1e+00 0.000000 1e+00 0.000000 -0.004020 ( 0.029254) 0.000000 ( 0.000000) -0.005205 0.000000 --->beagle2-----germline2: 5.69e-01 -0.002644 9.09e-01 -0.000522 -0.004020 ( 0.029254) -0.003498 ( 0.033420) -0.005205 0.001531 --->beagle2-----dash-----: 1e+00 0.000000 1e+00 0.000000 -0.004020 ( 0.029254) 0.000000 ( 0.000000) -0.005205 0.000000 --->plink-------germline1: 1e+00 0.000000 1e+00 0.000000 0.003586 ( 0.028148) 0.000000 ( 0.000000) 0.012114 0.000000 --->plink-------germline2: 5.35e-02 0.007148 8.29e-02 0.007084 0.003586 ( 0.028148) -0.003498 ( 0.033420) 0.012114 0.001531 --->plink-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.003586 ( 0.028148) 0.000000 ( 0.000000) 0.012114 0.000000 --->germline1---germline2: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) -0.003498 ( 0.033420) 0.000000 0.001531 --->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 -0.003498 ( 0.033420) 0.000000 ( 0.000000) 0.001531 0.000000 ######F1Sample###### --->fabia-------beagle1--: 3.96e-18 0.651199 5.87e-65 0.650759 0.738296 ( 0.155520) 0.087537 ( 0.009970) 0.697267 0.086963 --->fabia-------beagle2--: 3.96e-18 0.658730 1.04e-65 0.657037 0.738296 ( 0.155520) 0.081259 ( 0.016745) 0.697267 0.082158 --->fabia-------plink----: 3.96e-18 0.644577 2.14e-64 0.645040 0.738296 ( 0.155520) 0.093256 ( 0.002063) 0.697267 0.093690 --->fabia-------germline1: 3.95e-18 0.644797 2.09e-64 0.645149 0.738296 ( 0.155520) 0.093148 ( 0.001836) 0.697267 0.093422 --->fabia-------germline2: 3.96e-18 0.646513 1.25e-64 0.647867 0.738296 ( 0.155520) 0.090430 ( 0.013732) 0.697267 0.092787 --->fabia-------dash-----: 3.95e-18 0.644797 2.09e-64 0.645149 0.738296 ( 0.155520) 0.093148 ( 0.001836) 0.697267 0.093422 --->beagle1-----beagle2--: 9.06e-05 0.006450 7.66e-05 0.006278 0.087537 ( 0.009970) 0.081259 ( 0.016745) 0.086963 0.082158 --->beagle1-----plink----: 1.57e-06 -0.005886 2.12e-07 -0.005719 0.087537 ( 0.009970) 0.093256 ( 0.002063) 0.086963 0.093690 --->beagle1-----germline1: 1.69e-06 -0.005775 2.84e-07 -0.005611 0.087537 ( 0.009970) 0.093148 ( 0.001836) 0.086963 0.093422 --->beagle1-----germline2: 1.06e-04 -0.004574 1.19e-01 -0.002893 0.087537 ( 0.009970) 0.090430 ( 0.013732) 0.086963 0.092787 --->beagle1-----dash-----: 1.69e-06 -0.005775 2.84e-07 -0.005611 0.087537 ( 0.009970) 0.093148 ( 0.001836) 0.086963 0.093422 --->beagle2-----plink----: 2.8e-09 -0.012193 1.31e-10 -0.011997 0.081259 ( 0.016745) 0.093256 ( 0.002063) 0.082158 0.093690 --->beagle2-----germline1: 2.74e-09 -0.012049 1.79e-10 -0.011889 0.081259 ( 0.016745) 0.093148 ( 0.001836) 0.082158 0.093422 --->beagle2-----germline2: 3.45e-07 -0.010934 1.4e-04 -0.009171 0.081259 ( 0.016745) 0.090430 ( 0.013732) 0.082158 0.092787 --->beagle2-----dash-----: 2.74e-09 -0.012049 1.79e-10 -0.011889 0.081259 ( 0.016745) 0.093148 ( 0.001836) 0.082158 0.093422 --->plink-------germline1: 5.71e-08 0.000268 6.49e-02 0.000108 0.093256 ( 0.002063) 0.093148 ( 0.001836) 0.093690 0.093422 --->plink-------germline2: 6.26e-02 0.000791 4.12e-02 0.002826 0.093256 ( 0.002063) 0.090430 ( 0.013732) 0.093690 0.092787 --->plink-------dash-----: 5.71e-08 0.000268 6.49e-02 0.000108 0.093256 ( 0.002063) 0.093148 ( 0.001836) 0.093690 0.093422 --->germline1---germline2: 1.08e-01 0.000688 5.03e-02 0.002718 0.093148 ( 0.001836) 0.090430 ( 0.013732) 0.093422 0.092787 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 0.093148 ( 0.001836) 0.093148 ( 0.001836) 0.093422 0.093422 --->germline2---dash-----: 1.08e-01 -7e-04 5.03e-02 -0.002718 0.090430 ( 0.013732) 0.093148 ( 0.001836) 0.092787 0.093422 ######accuracySample###### --->fabia-------beagle1--: 3.95e-18 0.613471 2.38e-127 0.613025 0.980965 ( 0.013680) 0.367940 ( 0.028628) 0.981500 0.366500 --->fabia-------beagle2--: 3.95e-18 0.293991 1.83e-98 0.293695 0.980965 ( 0.013680) 0.687270 ( 0.026579) 0.981500 0.685000 --->fabia-------plink----: 3.94e-18 0.929449 1.29e-183 0.929155 0.980965 ( 0.013680) 0.051810 ( 0.002616) 0.981500 0.052000 --->fabia-------germline1: 3.94e-18 0.932505 1.56e-183 0.932115 0.980965 ( 0.013680) 0.048850 ( 0.001009) 0.981500 0.049000 --->fabia-------germline2: 3.95e-18 0.859910 3.23e-83 0.836305 0.980965 ( 0.013680) 0.144660 ( 0.125239) 0.981500 0.118500 --->fabia-------dash-----: 3.94e-18 0.932505 1.56e-183 0.932115 0.980965 ( 0.013680) 0.048850 ( 0.001009) 0.981500 0.049000 --->beagle1-----beagle2--: 3.95e-18 -0.319479 1.23e-119 -0.319330 0.367940 ( 0.028628) 0.687270 ( 0.026579) 0.366500 0.685000 --->beagle1-----plink----: 3.94e-18 0.315040 4.29e-105 0.316130 0.367940 ( 0.028628) 0.051810 ( 0.002616) 0.366500 0.052000 --->beagle1-----germline1: 3.94e-18 0.318043 8.21e-106 0.319090 0.367940 ( 0.028628) 0.048850 ( 0.001009) 0.366500 0.049000 --->beagle1-----germline2: 1.29e-15 0.242040 4.38e-32 0.223280 0.367940 ( 0.028628) 0.144660 ( 0.125239) 0.366500 0.118500 --->beagle1-----dash-----: 3.94e-18 0.318043 8.21e-106 0.319090 0.367940 ( 0.028628) 0.048850 ( 0.001009) 0.366500 0.049000 --->beagle2-----plink----: 3.94e-18 0.635500 3.68e-138 0.635460 0.687270 ( 0.026579) 0.051810 ( 0.002616) 0.685000 0.052000 --->beagle2-----germline1: 3.94e-18 0.638480 1.06e-138 0.638420 0.687270 ( 0.026579) 0.048850 ( 0.001009) 0.685000 0.049000 --->beagle2-----germline2: 4.33e-18 0.563543 4.62e-65 0.542610 0.687270 ( 0.026579) 0.144660 ( 0.125239) 0.685000 0.118500 --->beagle2-----dash-----: 3.94e-18 0.638480 1.06e-138 0.638420 0.687270 ( 0.026579) 0.048850 ( 0.001009) 0.685000 0.049000 --->plink-------germline1: 1e-16 0.002972 3.58e-23 0.002960 0.051810 ( 0.002616) 0.048850 ( 0.001009) 0.052000 0.049000 --->plink-------germline2: 3.95e-18 -0.070013 3.6e-11 -0.092850 0.051810 ( 0.002616) 0.144660 ( 0.125239) 0.052000 0.118500 --->plink-------dash-----: 1e-16 0.002972 3.58e-23 0.002960 0.051810 ( 0.002616) 0.048850 ( 0.001009) 0.052000 0.049000 --->germline1---germline2: 3.95e-18 -0.072958 1.31e-11 -0.095810 0.048850 ( 0.001009) 0.144660 ( 0.125239) 0.049000 0.118500 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 0.048850 ( 0.001009) 0.048850 ( 0.001009) 0.049000 0.049000 --->germline2---dash-----: 3.95e-18 0.072958 1.31e-11 0.095810 0.144660 ( 0.125239) 0.048850 ( 0.001009) 0.118500 0.049000 ######FPRSample###### --->fabia-------beagle1--: 3.96e-18 -0.120488 1.08e-124 -0.120392 0.003556 ( 0.002751) 0.123947 ( 0.005979) 0.003417 0.124141 --->fabia-------beagle2--: 3.96e-18 -0.052635 6.58e-92 -0.052551 0.003556 ( 0.002751) 0.056107 ( 0.005545) 0.003417 0.056465 --->fabia-------plink----: 3.95e-18 -0.188078 5.67e-184 -0.187980 0.003556 ( 0.002751) 0.191535 ( 0.000516) 0.003417 0.191515 --->fabia-------germline1: 3.95e-18 -0.188698 8.36e-184 -0.188596 0.003556 ( 0.002751) 0.192152 ( 0.000204) 0.003417 0.192121 --->fabia-------germline2: 4.33e-18 -0.173281 8.1e-81 -0.168147 0.003556 ( 0.002751) 0.171703 ( 0.026671) 0.003417 0.177273 --->fabia-------dash-----: 3.95e-18 -0.188698 8.36e-184 -0.188596 0.003556 ( 0.002751) 0.192152 ( 0.000204) 0.003417 0.192121 --->beagle1-----beagle2--: 3.95e-18 0.067805 2.95e-122 0.067840 0.123947 ( 0.005979) 0.056107 ( 0.005545) 0.124141 0.056465 --->beagle1-----plink----: 3.95e-18 -0.067377 4.04e-106 -0.067588 0.123947 ( 0.005979) 0.191535 ( 0.000516) 0.124141 0.191515 --->beagle1-----germline1: 3.95e-18 -0.068077 7.42e-107 -0.068204 0.123947 ( 0.005979) 0.192152 ( 0.000204) 0.124141 0.192121 --->beagle1-----germline2: 1.29e-15 -0.051860 4.42e-32 -0.047756 0.123947 ( 0.005979) 0.171703 ( 0.026671) 0.124141 0.177273 --->beagle1-----dash-----: 3.95e-18 -0.068077 7.42e-107 -0.068204 0.123947 ( 0.005979) 0.192152 ( 0.000204) 0.124141 0.192121 --->beagle2-----plink----: 3.95e-18 -0.135312 5e-139 -0.135428 0.056107 ( 0.005545) 0.191535 ( 0.000516) 0.056465 0.191515 --->beagle2-----germline1: 3.95e-18 -0.135986 1.17e-139 -0.136044 0.056107 ( 0.005545) 0.192152 ( 0.000204) 0.056465 0.192121 --->beagle2-----germline2: 4.33e-18 -0.120005 5.22e-65 -0.115596 0.056107 ( 0.005545) 0.171703 ( 0.026671) 0.056465 0.177273 --->beagle2-----dash-----: 3.95e-18 -0.135986 1.17e-139 -0.136044 0.056107 ( 0.005545) 0.192152 ( 0.000204) 0.056465 0.192121 --->plink-------germline1: 3.48e-17 -0.000558 1.57e-24 -0.000616 0.191535 ( 0.000516) 0.192152 ( 0.000204) 0.191515 0.192121 --->plink-------germline2: 3.95e-18 0.014907 3.21e-11 0.019832 0.191535 ( 0.000516) 0.171703 ( 0.026671) 0.191515 0.177273 --->plink-------dash-----: 3.48e-17 -0.000558 1.57e-24 -0.000616 0.191535 ( 0.000516) 0.192152 ( 0.000204) 0.191515 0.192121 --->germline1---germline2: 3.95e-18 0.015522 1.21e-11 0.020448 0.192152 ( 0.000204) 0.171703 ( 0.026671) 0.192121 0.177273 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 0.192152 ( 0.000204) 0.192152 ( 0.000204) 0.192121 0.192121 --->germline2---dash-----: 3.95e-18 -0.015552 1.21e-11 -0.020448 0.171703 ( 0.026671) 0.192152 ( 0.000204) 0.177273 0.192121 ######FDRSample###### --->fabia-------beagle1--: 3.96e-18 -0.582886 2.48e-48 -0.587150 0.365754 ( 0.213011) 0.952904 ( 0.005353) 0.424408 0.953196 --->fabia-------beagle2--: 3.96e-18 -0.584024 1.88e-48 -0.586751 0.365754 ( 0.213011) 0.952506 ( 0.009750) 0.424408 0.952483 --->fabia-------plink----: 3.95e-18 -0.580564 4.02e-48 -0.585332 0.365754 ( 0.213011) 0.951086 ( 0.001127) 0.424408 0.950853 --->fabia-------germline1: 3.95e-18 -0.580663 3.95e-48 -0.585396 0.365754 ( 0.213011) 0.951150 ( 0.001009) 0.424408 0.951000 --->fabia-------germline2: 1.09e-16 -0.575853 1.29e-38 -0.566598 0.365754 ( 0.213011) 0.932352 ( 0.133885) 0.424408 0.951038 --->fabia-------dash-----: 3.95e-18 -0.580663 3.95e-48 -0.585396 0.365754 ( 0.213011) 0.951150 ( 0.001009) 0.424408 0.951000 --->beagle1-----beagle2--: 7.32e-01 0.000354 6.52e-01 0.000399 0.952904 ( 0.005353) 0.952506 ( 0.009750) 0.953196 0.952483 --->beagle1-----plink----: 2.67e-03 0.001883 1.3e-03 0.001818 0.952904 ( 0.005353) 0.951086 ( 0.001127) 0.953196 0.950853 --->beagle1-----germline1: 3.07e-03 0.001855 1.77e-03 0.001754 0.952904 ( 0.005353) 0.951150 ( 0.001009) 0.953196 0.951000 --->beagle1-----germline2: 2.1e-03 0.001867 1.25e-01 0.020552 0.952904 ( 0.005353) 0.932352 ( 0.133885) 0.953196 0.951038 --->beagle1-----dash-----: 3.07e-03 0.001855 1.77e-03 0.001754 0.952904 ( 0.005353) 0.951150 ( 0.001009) 0.953196 0.951000 --->beagle2-----plink----: 9.3e-02 0.001519 1.47e-01 0.001420 0.952506 ( 0.009750) 0.951086 ( 0.001127) 0.952483 0.950853 --->beagle2-----germline1: 1.12e-01 0.001450 1.66e-01 0.001356 0.952506 ( 0.009750) 0.951150 ( 0.001009) 0.952483 0.951000 --->beagle2-----germline2: 8.53e-02 0.001765 1.32e-01 0.020153 0.952506 ( 0.009750) 0.932352 ( 0.133885) 0.952483 0.951038 --->beagle2-----dash-----: 1.12e-01 0.001450 1.66e-01 0.001356 0.952506 ( 0.009750) 0.951150 ( 0.001009) 0.952483 0.951000 --->plink-------germline1: 5.59e-08 -0.000110 1e+00 0.000000 0.951086 ( 0.001127) 0.951150 ( 0.001009) 0.950853 0.951000 --->plink-------germline2: 8.08e-01 -3.7e-05 1.65e-01 0.018734 0.951086 ( 0.001127) 0.932352 ( 0.133885) 0.950853 0.951038 --->plink-------dash-----: 5.59e-08 -0.000110 1e+00 0.000000 0.951086 ( 0.001127) 0.951150 ( 0.001009) 0.950853 0.951000 --->germline1---germline2: 1e+00 0.000000 1.63e-01 0.018798 0.951150 ( 0.001009) 0.932352 ( 0.133885) 0.951000 0.951038 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 0.951150 ( 0.001009) 0.951150 ( 0.001009) 0.951000 0.951000 --->germline2---dash-----: 1e+00 0.000000 1.63e-01 -0.018798 0.932352 ( 0.133885) 0.951150 ( 0.001009) 0.951038 0.951000 ######specifitySample###### --->fabia-------beagle1--: 3.96e-18 0.124364 5.17e-126 0.124276 0.192480 ( 0.002750) 0.068204 ( 0.005980) 0.192663 0.067980 --->fabia-------beagle2--: 3.96e-18 0.056503 6.83e-95 0.056436 0.192480 ( 0.002750) 0.136044 ( 0.005545) 0.192663 0.135657 --->fabia-------plink----: 3.95e-18 0.191952 6.28e-185 0.191864 0.192480 ( 0.002750) 0.000616 ( 0.000451) 0.192663 0.000606 --->fabia-------germline1: 1e+00 0.000000 1e+00 0.000000 0.192480 ( 0.002750) 0.000000 ( 0.000000) 0.192663 0.000000 --->fabia-------germline2: 4.33e-18 0.177151 8.64e-82 0.172032 0.192480 ( 0.002750) 0.020448 ( 0.026658) 0.192663 0.015051 --->fabia-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.192480 ( 0.002750) 0.000000 ( 0.000000) 0.192663 0.000000 --->beagle1-----beagle2--: 3.96e-18 -0.067868 2.95e-122 -0.067840 0.068204 ( 0.005980) 0.136044 ( 0.005545) 0.067980 0.135657 --->beagle1-----plink----: 3.95e-18 0.067412 4.04e-106 0.067588 0.068204 ( 0.005980) 0.000616 ( 0.000451) 0.067980 0.000606 --->beagle1-----germline1: 1e+00 0.000000 1e+00 0.000000 0.068204 ( 0.005980) 0.000000 ( 0.000000) 0.067980 0.000000 --->beagle1-----germline2: 1.29e-15 0.051860 4.42e-32 0.047756 0.068204 ( 0.005980) 0.020448 ( 0.026658) 0.067980 0.015051 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.068204 ( 0.005980) 0.000000 ( 0.000000) 0.067980 0.000000 --->beagle2-----plink----: 3.95e-18 0.135298 5e-139 0.135428 0.136044 ( 0.005545) 0.000616 ( 0.000451) 0.135657 0.000606 --->beagle2-----germline1: 1e+00 0.000000 1e+00 0.000000 0.136044 ( 0.005545) 0.000000 ( 0.000000) 0.135657 0.000000 --->beagle2-----germline2: 4.33e-18 0.120009 5.22e-65 0.115596 0.136044 ( 0.005545) 0.020448 ( 0.026658) 0.135657 0.015051 --->beagle2-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.136044 ( 0.005545) 0.000000 ( 0.000000) 0.135657 0.000000 --->plink-------germline1: 1e+00 0.000000 1e+00 0.000000 0.000616 ( 0.000451) 0.000000 ( 0.000000) 0.000606 0.000000 --->plink-------germline2: 3.95e-18 -0.014899 3.21e-11 -0.019832 0.000616 ( 0.000451) 0.020448 ( 0.026658) 0.000606 0.015051 --->plink-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.000616 ( 0.000451) 0.000000 ( 0.000000) 0.000606 0.000000 --->germline1---germline2: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.020448 ( 0.026658) 0.000000 0.015051 --->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 0.020448 ( 0.026658) 0.000000 ( 0.000000) 0.015051 0.000000 ######sensitivitySample###### --->fabia-------beagle1--: 4.51e-18 0.339964 1.15e-45 0.328400 0.935000 ( 0.098365) 0.606600 ( 0.076439) 0.980000 0.600000 --->fabia-------beagle2--: 3.77e-18 0.669938 1.31e-78 0.658000 0.935000 ( 0.098365) 0.277000 ( 0.063652) 0.980000 0.260000 --->fabia-------plink----: 1e+00 0.000000 9.42e-05 -0.040200 0.935000 ( 0.098365) 0.975200 ( 0.022224) 0.980000 0.980000 --->fabia-------germline1: 1e+00 0.000000 4.94e-05 -0.042000 0.935000 ( 0.098365) 0.977000 ( 0.020176) 0.980000 0.980000 --->fabia-------germline2: 6.16e-05 0.069989 4.27e-04 0.066200 0.935000 ( 0.098365) 0.868800 ( 0.141602) 0.980000 0.900000 --->fabia-------dash-----: 1e+00 0.000000 4.94e-05 -0.042000 0.935000 ( 0.098365) 0.977000 ( 0.020176) 0.980000 0.980000 --->beagle1-----beagle2--: 3.85e-18 0.329998 2.05e-70 0.329600 0.606600 ( 0.076439) 0.277000 ( 0.063652) 0.600000 0.260000 --->beagle1-----plink----: 3.75e-18 -0.370053 1.66e-68 -0.368600 0.606600 ( 0.076439) 0.975200 ( 0.022224) 0.600000 0.980000 --->beagle1-----germline1: 3.75e-18 -0.370000 2.67e-69 -0.370400 0.606600 ( 0.076439) 0.977000 ( 0.020176) 0.600000 0.980000 --->beagle1-----germline2: 1.26e-15 -0.279940 6.83e-28 -0.262200 0.606600 ( 0.076439) 0.868800 ( 0.141602) 0.600000 0.900000 --->beagle1-----dash-----: 3.75e-18 -0.370000 2.67e-69 -0.370400 0.606600 ( 0.076439) 0.977000 ( 0.020176) 0.600000 0.980000 --->beagle2-----plink----: 3.53e-18 -0.699964 2.98e-103 -0.698200 0.277000 ( 0.063652) 0.975200 ( 0.022224) 0.260000 0.980000 --->beagle2-----germline1: 3.5e-18 -0.700012 4.46e-104 -0.700000 0.277000 ( 0.063652) 0.977000 ( 0.020176) 0.260000 0.980000 --->beagle2-----germline2: 4.6e-18 -0.610031 5.4e-59 -0.591800 0.277000 ( 0.063652) 0.868800 ( 0.141602) 0.260000 0.900000 --->beagle2-----dash-----: 3.5e-18 -0.700012 4.46e-104 -0.700000 0.277000 ( 0.063652) 0.977000 ( 0.020176) 0.260000 0.980000 --->plink-------germline1: 1e+00 0.000000 2.3e-03 -0.001800 0.975200 ( 0.022224) 0.977000 ( 0.020176) 0.980000 0.980000 --->plink-------germline2: 7.82e-18 0.080062 2.4e-11 0.106400 0.975200 ( 0.022224) 0.868800 ( 0.141602) 0.980000 0.900000 --->plink-------dash-----: 1e+00 0.000000 2.3e-03 -0.001800 0.975200 ( 0.022224) 0.977000 ( 0.020176) 0.980000 0.980000 --->germline1---germline2: 7.78e-18 0.089975 1.69e-11 0.108200 0.977000 ( 0.020176) 0.868800 ( 0.141602) 0.980000 0.900000 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 0.977000 ( 0.020176) 0.977000 ( 0.020176) 0.980000 0.980000 --->germline2---dash-----: 7.78e-18 -0.089975 1.69e-11 -0.108200 0.868800 ( 0.141602) 0.977000 ( 0.020176) 0.900000 0.980000 ######trueNSample###### --->fabia-------beagle1--: 3.95e-18 1578 1.35e-156 1578 1915 ( 27.4) 338 ( 29.6) 1917 336 --->fabia-------beagle2--: 3.95e-18 1242 4.42e-148 1242 1915 ( 27.4) 673 ( 27.4) 1917 672 --->fabia-------plink----: 3.94e-18 1913 5.78e-185 1912 1915 ( 27.4) 3.05 ( 2.23) 1917 3 --->fabia-------germline1: 1e+00 0 1e+00 0 1915 ( 27.4) 0 ( 0) 1917 0 --->fabia-------germline2: 3.95e-18 1838 1.43e-112 1814 1915 ( 27.4) 101 ( 132) 1917 74.5 --->fabia-------dash-----: 1e+00 0 1e+00 0 1915 ( 27.4) 0 ( 0) 1917 0 --->beagle1-----beagle2--: 3.93e-18 -336 2.95e-122 -336 338 ( 29.6) 673 ( 27.4) 336 672 --->beagle1-----plink----: 3.94e-18 334 4.04e-106 335 338 ( 29.6) 3.05 ( 2.23) 336 3 --->beagle1-----germline1: 1e+00 0 1e+00 0 338 ( 29.6) 0 ( 0) 336 0 --->beagle1-----germline2: 1.29e-15 257 4.42e-32 236 338 ( 29.6) 101 ( 132) 336 74.5 --->beagle1-----dash-----: 1e+00 0 1e+00 0 338 ( 29.6) 0 ( 0) 336 0 --->beagle2-----plink----: 3.94e-18 670 5e-139 670 673 ( 27.4) 3.05 ( 2.23) 672 3 --->beagle2-----germline1: 1e+00 0 1e+00 0 673 ( 27.4) 0 ( 0) 672 0 --->beagle2-----germline2: 4.32e-18 594 5.22e-65 572 673 ( 27.4) 101 ( 132) 672 74.5 --->beagle2-----dash-----: 1e+00 0 1e+00 0 673 ( 27.4) 0 ( 0) 672 0 --->plink-------germline1: 1e+00 0 1e+00 0 3.05 ( 2.23) 0 ( 0) 3 0 --->plink-------germline2: 3.95e-18 -74 3.21e-11 -98.2 3.05 ( 2.23) 101 ( 132) 3 74.5 --->plink-------dash-----: 1e+00 0 1e+00 0 3.05 ( 2.23) 0 ( 0) 3 0 --->germline1---germline2: 1e+00 0 1e+00 0 0 ( 0) 101 ( 132) 0 74.5 --->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 0 101 ( 132) 0 ( 0) 74.5 0 ######falsePSample###### --->fabia-------beagle1--: 3.95e-18 -579 1.38e-113 -578 35.4 ( 27.4) 614 ( 29.6) 34 614 --->fabia-------beagle2--: 3.94e-18 -243 1.84e-78 -242 35.4 ( 27.4) 278 ( 27.4) 34 280 --->fabia-------plink----: 3.94e-18 -914 3.54e-153 -913 35.4 ( 27.4) 948 ( 2.55) 34 948 --->fabia-------germline1: 3.94e-18 -917 5.25e-153 -916 35.4 ( 27.4) 951 ( 1.01) 34 951 --->fabia-------germline2: 4.32e-18 -839 1.27e-78 -815 35.4 ( 27.4) 850 ( 132) 34 878 --->fabia-------dash-----: 3.94e-18 -917 5.25e-153 -916 35.4 ( 27.4) 951 ( 1.01) 34 951 --->beagle1-----beagle2--: 3.93e-18 336 2.95e-122 336 614 ( 29.6) 278 ( 27.4) 614 280 --->beagle1-----plink----: 3.94e-18 -334 4.04e-106 -335 614 ( 29.6) 948 ( 2.55) 614 948 --->beagle1-----germline1: 3.94e-18 -337 7.42e-107 -338 614 ( 29.6) 951 ( 1.01) 614 951 --->beagle1-----germline2: 1.29e-15 -257 4.42e-32 -236 614 ( 29.6) 850 ( 132) 614 878 --->beagle1-----dash-----: 3.94e-18 -337 7.42e-107 -338 614 ( 29.6) 951 ( 1.01) 614 951 --->beagle2-----plink----: 3.94e-18 -670 5e-139 -670 278 ( 27.4) 948 ( 2.55) 280 948 --->beagle2-----germline1: 3.94e-18 -673 1.17e-139 -673 278 ( 27.4) 951 ( 1.01) 280 951 --->beagle2-----germline2: 4.32e-18 -594 5.22e-65 -572 278 ( 27.4) 850 ( 132) 280 878 --->beagle2-----dash-----: 3.94e-18 -673 1.17e-139 -673 278 ( 27.4) 951 ( 1.01) 280 951 --->plink-------germline1: 2.69e-17 -3 1.56e-24 -3.05 948 ( 2.55) 951 ( 1.01) 948 951 --->plink-------germline2: 3.95e-18 74 3.21e-11 98.2 948 ( 2.55) 850 ( 132) 948 878 --->plink-------dash-----: 2.69e-17 -3 1.56e-24 -3.05 948 ( 2.55) 951 ( 1.01) 948 951 --->germline1---germline2: 3.95e-18 77 1.21e-11 101 951 ( 1.01) 850 ( 132) 951 878 --->germline1---dash-----: 1e+00 0 1e+00 0 951 ( 1.01) 951 ( 1.01) 951 951 --->germline2---dash-----: 3.95e-18 -77 1.21e-11 -101 850 ( 132) 951 ( 1.01) 878 951 ######falseNSample###### --->fabia-------beagle1--: 5.03e-18 -16.5 4.6e-44 -15.8 2.69 ( 4.88) 18.5 ( 3.96) 0 19 --->fabia-------beagle2--: 3.72e-18 -33 6.24e-78 -32.3 2.69 ( 4.88) 35 ( 3.28) 0 35 --->fabia-------plink----: 1e+00 0.000000 5.73e-07 2.600000 2.690000 ( 4.879756) 0.090000 ( 0.287623) 0.000000 0.000000 --->fabia-------germline1: 1e+00 0.000000 1e+00 0.000000 2.690000 ( 4.879756) 0.000000 ( 0.000000) 0.000000 0.000000 --->fabia-------germline2: 1.5e-03 -3 3.47e-03 -2.72 2.69 ( 4.88) 5.41 ( 7.12) 0 4 --->fabia-------dash-----: 1e+00 0.000000 1e+00 0.000000 2.690000 ( 4.879756) 0.000000 ( 0.000000) 0.000000 0.000000 --->beagle1-----beagle2--: 3.61e-18 -16.5 2.05e-70 -16.5 18.5 ( 3.96) 35 ( 3.28) 19 35 --->beagle1-----plink----: 3.69e-18 18.5 1.66e-68 18.4 18.5 ( 3.96) 0.09 ( 0.288) 19 0 --->beagle1-----germline1: 1e+00 0 1e+00 0 18.5 ( 3.96) 0 ( 0) 19 0 --->beagle1-----germline2: 1.24e-15 14 6.83e-28 13.1 18.5 ( 3.96) 5.41 ( 7.12) 19 4 --->beagle1-----dash-----: 1e+00 0 1e+00 0 18.5 ( 3.96) 0 ( 0) 19 0 --->beagle2-----plink----: 3.44e-18 35 2.98e-103 34.9 35 ( 3.28) 0.09 ( 0.288) 35 0 --->beagle2-----germline1: 1e+00 0 1e+00 0 35 ( 3.28) 0 ( 0) 35 0 --->beagle2-----germline2: 4.38e-18 30.5 5.4e-59 29.6 35 ( 3.28) 5.41 ( 7.12) 35 4 --->beagle2-----dash-----: 1e+00 0 1e+00 0 35 ( 3.28) 0 ( 0) 35 0 --->plink-------germline1: 1e+00 0.000000 1e+00 0.000000 0.090000 ( 0.287623) 0.000000 ( 0.000000) 0.000000 0.000000 --->plink-------germline2: 7.3e-18 -4 2.4e-11 -5.32 0.09 ( 0.288) 5.41 ( 7.12) 0 4 --->plink-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.090000 ( 0.287623) 0.000000 ( 0.000000) 0.000000 0.000000 --->germline1---germline2: 1e+00 0 1e+00 0 0 ( 0) 5.41 ( 7.12) 0 4 --->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 5.41 ( 7.12) 0 ( 0) 4 0 ######truePSample###### --->fabia-------beagle1--: 4.5e-18 17 1.15e-45 16.4 46.8 ( 4.92) 30.3 ( 3.82) 49 30 --->fabia-------beagle2--: 3.76e-18 33.5 1.31e-78 32.9 46.8 ( 4.92) 13.8 ( 3.18) 49 13 --->fabia-------plink----: 1e+00 0 9.42e-05 -2.01 46.8 ( 4.92) 48.8 ( 1.11) 49 49 --->fabia-------germline1: 1e+00 0 4.94e-05 -2.1 46.8 ( 4.92) 48.9 ( 1.01) 49 49 --->fabia-------germline2: 9.03e-05 3.5 4.27e-04 3.31 46.8 ( 4.92) 43.4 ( 7.08) 49 45 --->fabia-------dash-----: 1e+00 0 4.94e-05 -2.1 46.8 ( 4.92) 48.9 ( 1.01) 49 49 --->beagle1-----beagle2--: 3.61e-18 16.5 2.05e-70 16.5 30.3 ( 3.82) 13.8 ( 3.18) 30 13 --->beagle1-----plink----: 3.69e-18 -18.5 1.66e-68 -18.4 30.3 ( 3.82) 48.8 ( 1.11) 30 49 --->beagle1-----germline1: 3.68e-18 -18.5 2.67e-69 -18.5 30.3 ( 3.82) 48.9 ( 1.01) 30 49 --->beagle1-----germline2: 1.24e-15 -14 6.83e-28 -13.1 30.3 ( 3.82) 43.4 ( 7.08) 30 45 --->beagle1-----dash-----: 3.68e-18 -18.5 2.67e-69 -18.5 30.3 ( 3.82) 48.9 ( 1.01) 30 49 --->beagle2-----plink----: 3.44e-18 -35 2.98e-103 -34.9 13.8 ( 3.18) 48.8 ( 1.11) 13 49 --->beagle2-----germline1: 3.48e-18 -35 4.46e-104 -35 13.8 ( 3.18) 48.9 ( 1.01) 13 49 --->beagle2-----germline2: 4.38e-18 -30.5 5.4e-59 -29.6 13.8 ( 3.18) 43.4 ( 7.08) 13 45 --->beagle2-----dash-----: 3.48e-18 -35 4.46e-104 -35 13.8 ( 3.18) 48.9 ( 1.01) 13 49 --->plink-------germline1: 1e+00 0 2.3e-03 -0.09 48.8 ( 1.11) 48.9 ( 1.01) 49 49 --->plink-------germline2: 7.3e-18 4 2.4e-11 5.32 48.8 ( 1.11) 43.4 ( 7.08) 49 45 --->plink-------dash-----: 1e+00 0 2.3e-03 -0.09 48.8 ( 1.11) 48.9 ( 1.01) 49 49 --->germline1---germline2: 7.28e-18 4.5 1.69e-11 5.41 48.9 ( 1.01) 43.4 ( 7.08) 49 45 --->germline1---dash-----: 1e+00 0 1e+00 0 48.9 ( 1.01) 48.9 ( 1.01) 49 49 --->germline2---dash-----: 7.28e-18 -4.5 1.69e-11 -5.41 43.4 ( 7.08) 48.9 ( 1.01) 45 49