Results: Wilcoxon-Rank-Sum Wilcoxon-median t-test t-test-mean mean1 (std) mean2 (std) median1 median2 ######Matthews###### --->fabia-------beagle1--: 5.77e-12 0.139727 4.15e-15 0.152831 0.152298 ( 0.164497) -0.000533 ( 0.005047) 0.134537 -0.002439 --->fabia-------beagle2--: 5.25e-13 0.139529 3.1e-15 0.153635 0.152298 ( 0.164497) -0.001338 ( 0.002799) 0.134537 -0.002639 --->fabia-------plink----: 2.76e-06 0.135472 1e-14 0.149636 0.152298 ( 0.164497) 0.002661 ( 0.001914) 0.134537 0.003157 --->fabia-------germline1: 3.05e-16 0.143625 1.42e-15 0.155583 0.152298 ( 0.164497) -0.003286 ( 0.004474) 0.134537 -0.003694 --->fabia-------germline2: 4.42e-16 0.142463 1.68e-15 0.155328 0.152298 ( 0.164497) -0.003030 ( 0.003761) 0.134537 -0.004077 --->fabia-------dash-----: 3.83e-16 0.140926 2.17e-15 0.154304 0.152298 ( 0.164497) -0.002006 ( 0.003192) 0.134537 -0.003390 --->beagle1-----beagle2--: 4.84e-01 -0.000462 1.23e-01 0.000804 -0.000533 ( 0.005047) -0.001338 ( 0.002799) -0.002439 -0.002639 --->beagle1-----plink----: 7.32e-11 -0.003856 1.44e-08 -0.003194 -0.000533 ( 0.005047) 0.002661 ( 0.001914) -0.002439 0.003157 --->beagle1-----germline1: 1.24e-04 0.002417 5.08e-05 0.002753 -0.000533 ( 0.005047) -0.003286 ( 0.004474) -0.002439 -0.003694 --->beagle1-----germline2: 1.42e-04 0.002176 1.44e-04 0.002497 -0.000533 ( 0.005047) -0.003030 ( 0.003761) -0.002439 -0.004077 --->beagle1-----dash-----: 7.59e-03 0.001012 1.62e-02 0.001473 -0.000533 ( 0.005047) -0.002006 ( 0.003192) -0.002439 -0.003390 --->beagle2-----plink----: 1.75e-13 -0.004677 1.77e-20 -0.003999 -0.001338 ( 0.002799) 0.002661 ( 0.001914) -0.002639 0.003157 --->beagle2-----germline1: 9.35e-04 0.001912 4.66e-04 0.001948 -0.001338 ( 0.002799) -0.003286 ( 0.004474) -0.002639 -0.003694 --->beagle2-----germline2: 1.27e-03 0.001742 7.59e-04 0.001693 -0.001338 ( 0.002799) -0.003030 ( 0.003761) -0.002639 -0.004077 --->beagle2-----dash-----: 3.99e-02 0.000957 1.24e-01 0.000669 -0.001338 ( 0.002799) -0.002006 ( 0.003192) -0.002639 -0.003390 --->plink-------germline1: 4e-15 0.005962 3.51e-21 0.005947 0.002661 ( 0.001914) -0.003286 ( 0.004474) 0.003157 -0.003694 --->plink-------germline2: 1.65e-15 0.005894 9.93e-24 0.005691 0.002661 ( 0.001914) -0.003030 ( 0.003761) 0.003157 -0.004077 --->plink-------dash-----: 4e-15 0.004986 2.87e-23 0.004667 0.002661 ( 0.001914) -0.002006 ( 0.003192) 0.003157 -0.003390 --->germline1---germline2: 3.97e-01 -0.000314 4.76e-01 -0.000255 -0.003286 ( 0.004474) -0.003030 ( 0.003761) -0.003694 -0.004077 --->germline1---dash-----: 4.16e-03 -0.001348 3.42e-03 -0.001280 -0.003286 ( 0.004474) -0.002006 ( 0.003192) -0.003694 -0.003390 --->germline2---dash-----: 2.97e-05 -0.001487 2.29e-03 -0.001024 -0.003030 ( 0.003761) -0.002006 ( 0.003192) -0.004077 -0.003390 ######F1###### --->fabia-------beagle1--: 2.54e-08 0.101506 1.8e-12 0.096610 0.096884 ( 0.119874) 0.000274 ( 0.000410) 0.066331 0.000125 --->fabia-------beagle2--: 3.79e-10 0.138046 1.71e-12 0.096716 0.096884 ( 0.119874) 0.000168 ( 0.000338) 0.066331 0.000000 --->fabia-------plink----: 7.89e-06 0.082351 1.83e-12 0.096548 0.096884 ( 0.119874) 0.000336 ( 5.66e-05) 0.066331 0.000328 --->fabia-------germline1: 5.84e-06 0.082566 1.76e-12 0.096641 0.096884 ( 0.119874) 0.000244 ( 0.000117) 0.066331 0.000237 --->fabia-------germline2: 3.51e-08 0.097833 1.72e-12 0.096701 0.096884 ( 0.119874) 0.000184 ( 0.000172) 0.066331 0.000145 --->fabia-------dash-----: 4.68e-10 0.136120 1.7e-12 0.096717 0.096884 ( 0.119874) 0.000168 ( 0.000264) 0.066331 0.000000 --->beagle1-----beagle2--: 4.64e-02 0.000126 2.45e-02 0.000106 0.000274 ( 0.000410) 0.000168 ( 0.000338) 0.000125 0.000000 --->beagle1-----plink----: 5.92e-03 -0.000149 1e+00 0.000000 0.000274 ( 0.000410) 0.000336 ( 5.66e-05) 0.000125 0.000328 --->beagle1-----germline1: 4.76e-01 -4.64e-05 1e+00 0.000000 0.000274 ( 0.000410) 0.000244 ( 0.000117) 0.000125 0.000237 --->beagle1-----germline2: 1e+00 0.000000 1e+00 0.000000 0.000274 ( 0.000410) 0.000184 ( 0.000172) 0.000125 0.000145 --->beagle1-----dash-----: 1.44e-02 0.000108 3.31e-02 0.000107 0.000274 ( 0.000410) 0.000168 ( 0.000264) 0.000125 0.000000 --->beagle2-----plink----: 9.35e-07 -0.000277 2.3e-06 -0.000168 0.000168 ( 0.000338) 0.000336 ( 5.66e-05) 0.000000 0.000328 --->beagle2-----germline1: 3.53e-03 -0.000116 1e+00 0.000000 0.000168 ( 0.000338) 0.000244 ( 0.000117) 0.000000 0.000237 --->beagle2-----germline2: 1.22e-01 -7.18e-05 1e+00 0.000000 0.000168 ( 0.000338) 0.000184 ( 0.000172) 0.000000 0.000145 --->beagle2-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.000168 ( 0.000338) 0.000168 ( 0.000264) 0.000000 0.000000 --->plink-------germline1: 1e+00 0.000000 1e+00 0.000000 0.000336 ( 5.66e-05) 0.000244 ( 0.000117) 0.000328 0.000237 --->plink-------germline2: 1.81e-11 0.000188 1.93e-14 0.000152 0.000336 ( 5.66e-05) 0.000184 ( 0.000172) 0.000328 0.000145 --->plink-------dash-----: 9.24e-10 0.000209 4.15e-09 0.000169 0.000336 ( 5.66e-05) 0.000168 ( 0.000264) 0.000328 0.000000 --->germline1---germline2: 1e+00 0.000000 1e+00 0.000000 0.000244 ( 0.000117) 0.000184 ( 0.000172) 0.000237 0.000145 --->germline1---dash-----: 1.32e-04 8.02e-05 1e+00 0.000000 0.000244 ( 0.000117) 0.000168 ( 0.000264) 0.000237 0.000000 --->germline2---dash-----: 3.11e-01 3.21e-05 1e+00 0.000000 0.000184 ( 0.000172) 0.000168 ( 0.000264) 0.000145 0.000000 ######accuracy###### --->fabia-------beagle1--: 3.96e-18 0.088398 2.79e-123 0.088546 0.999179 ( 0.000396) 0.910632 ( 0.005262) 0.999179 0.911033 --->fabia-------beagle2--: 3.96e-18 0.045508 2.35e-109 0.045584 0.999179 ( 0.000396) 0.953595 ( 0.003785) 0.999179 0.953625 --->fabia-------plink----: 3.96e-18 0.936389 3.52e-214 0.936379 0.999179 ( 0.000396) 0.062800 ( 0.006771) 0.999179 0.062751 --->fabia-------germline1: 3.96e-18 0.541060 4.39e-127 0.539402 0.999179 ( 0.000396) 0.459777 ( 0.029439) 0.999179 0.455839 --->fabia-------germline2: 3.96e-18 0.246308 1.23e-91 0.245961 0.999179 ( 0.000396) 0.753218 ( 0.030847) 0.999179 0.747955 --->fabia-------dash-----: 3.96e-18 0.100288 2.41e-62 0.100493 0.999179 ( 0.000396) 0.898685 ( 0.025513) 0.999179 0.899250 --->beagle1-----beagle2--: 3.96e-18 -0.042891 1.23e-105 -0.042962 0.910632 ( 0.005262) 0.953595 ( 0.003785) 0.911033 0.953625 --->beagle1-----plink----: 3.96e-18 0.848097 1.38e-202 0.847833 0.910632 ( 0.005262) 0.062800 ( 0.006771) 0.911033 0.062751 --->beagle1-----germline1: 3.96e-18 0.452128 1.44e-119 0.450856 0.910632 ( 0.005262) 0.459777 ( 0.029439) 0.911033 0.455839 --->beagle1-----germline2: 3.96e-18 0.157911 6.4e-73 0.157414 0.910632 ( 0.005262) 0.753218 ( 0.030847) 0.911033 0.747955 --->beagle1-----dash-----: 2.59e-05 0.011914 8.56e-06 0.011947 0.910632 ( 0.005262) 0.898685 ( 0.025513) 0.911033 0.899250 --->beagle2-----plink----: 3.96e-18 0.890818 6.97e-209 0.890795 0.953595 ( 0.003785) 0.062800 ( 0.006771) 0.953625 0.062751 --->beagle2-----germline1: 3.96e-18 0.495502 5.01e-123 0.493818 0.953595 ( 0.003785) 0.459777 ( 0.029439) 0.953625 0.455839 --->beagle2-----germline2: 3.96e-18 0.201265 4.14e-83 0.200377 0.953595 ( 0.003785) 0.753218 ( 0.030847) 0.953625 0.747955 --->beagle2-----dash-----: 4.46e-18 0.055207 1.58e-39 0.054909 0.953595 ( 0.003785) 0.898685 ( 0.025513) 0.953625 0.899250 --->plink-------germline1: 3.96e-18 -0.395976 7.28e-113 -0.396977 0.062800 ( 0.006771) 0.459777 ( 0.029439) 0.062751 0.455839 --->plink-------germline2: 3.96e-18 -0.690215 5.53e-134 -0.690418 0.062800 ( 0.006771) 0.753218 ( 0.030847) 0.062751 0.747955 --->plink-------dash-----: 3.96e-18 -0.836399 4.35e-149 -0.835886 0.062800 ( 0.006771) 0.898685 ( 0.025513) 0.062751 0.899250 --->germline1---germline2: 3.96e-18 -0.293331 1.3e-136 -0.293441 0.459777 ( 0.029439) 0.753218 ( 0.030847) 0.455839 0.747955 --->germline1---dash-----: 3.96e-18 -0.439336 3.68e-136 -0.438909 0.459777 ( 0.029439) 0.898685 ( 0.025513) 0.455839 0.899250 --->germline2---dash-----: 3.96e-18 -0.145267 3.55e-113 -0.145467 0.753218 ( 0.030847) 0.898685 ( 0.025513) 0.747955 0.899250 ######FPR###### --->fabia-------beagle1--: 3.96e-18 -0.088304 2.91e-123 -0.088457 0.000778 ( 0.000389) 0.089235 ( 0.005264) 0.000797 0.088821 --->fabia-------beagle2--: 3.96e-18 -0.045405 2.81e-109 -0.045479 0.000778 ( 0.000389) 0.046257 ( 0.003782) 0.000797 0.046224 --->fabia-------plink----: 3.96e-18 -0.936581 3.23e-214 -0.936570 0.000778 ( 0.000389) 0.937348 ( 0.006773) 0.000797 0.937409 --->fabia-------germline1: 3.96e-18 -0.541121 4.43e-127 -0.539438 0.000778 ( 0.000389) 0.540216 ( 0.029444) 0.000797 0.544152 --->fabia-------germline2: 3.96e-18 -0.246261 1.29e-91 -0.245907 0.000778 ( 0.000389) 0.246685 ( 0.030854) 0.000797 0.251960 --->fabia-------dash-----: 3.96e-18 -0.100205 2.65e-62 -0.100402 0.000778 ( 0.000389) 0.101180 ( 0.025516) 0.000797 0.100630 --->beagle1-----beagle2--: 3.96e-18 0.042906 1.25e-105 0.042978 0.089235 ( 0.005264) 0.046257 ( 0.003782) 0.088821 0.046224 --->beagle1-----plink----: 3.96e-18 -0.848334 1.37e-202 -0.848113 0.089235 ( 0.005264) 0.937348 ( 0.006773) 0.088821 0.937409 --->beagle1-----germline1: 3.96e-18 -0.452257 1.43e-119 -0.450981 0.089235 ( 0.005264) 0.540216 ( 0.029444) 0.088821 0.544152 --->beagle1-----germline2: 3.96e-18 -0.157942 6.46e-73 -0.157450 0.089235 ( 0.005264) 0.246685 ( 0.030854) 0.088821 0.251960 --->beagle1-----dash-----: 2.59e-05 -0.011916 8.63e-06 -0.011945 0.089235 ( 0.005264) 0.101180 ( 0.025516) 0.088821 0.100630 --->beagle2-----plink----: 3.96e-18 -0.891111 6.82e-209 -0.891091 0.046257 ( 0.003782) 0.937348 ( 0.006773) 0.046224 0.937409 --->beagle2-----germline1: 3.96e-18 -0.495623 4.95e-123 -0.493959 0.046257 ( 0.003782) 0.540216 ( 0.029444) 0.046224 0.544152 --->beagle2-----germline2: 3.96e-18 -0.201330 4.16e-83 -0.200428 0.046257 ( 0.003782) 0.246685 ( 0.030854) 0.046224 0.251960 --->beagle2-----dash-----: 4.46e-18 -0.055230 1.59e-39 -0.054923 0.046257 ( 0.003782) 0.101180 ( 0.025516) 0.046224 0.100630 --->plink-------germline1: 3.96e-18 0.396161 7.06e-113 0.397132 0.937348 ( 0.006773) 0.540216 ( 0.029444) 0.937409 0.544152 --->plink-------germline2: 3.96e-18 0.690434 5.41e-134 0.690663 0.937348 ( 0.006773) 0.246685 ( 0.030854) 0.937409 0.251960 --->plink-------dash-----: 3.96e-18 0.836706 4.2e-149 0.836168 0.937348 ( 0.006773) 0.101180 ( 0.025516) 0.937409 0.100630 --->germline1---germline2: 3.96e-18 0.293414 1.27e-136 0.293531 0.540216 ( 0.029444) 0.246685 ( 0.030854) 0.544152 0.251960 --->germline1---dash-----: 3.96e-18 0.439448 3.55e-136 0.439036 0.540216 ( 0.029444) 0.101180 ( 0.025516) 0.544152 0.100630 --->germline2---dash-----: 3.96e-18 0.145310 3.46e-113 0.145505 0.246685 ( 0.030854) 0.101180 ( 0.025516) 0.251960 0.100630 ######FDR###### --->fabia-------beagle1--: 2.54e-08 -0.056940 7.13e-11 -0.056665 0.943198 ( 0.077557) 0.999863 ( 0.000205) 0.964509 0.999938 --->fabia-------beagle2--: 3.79e-10 -0.077052 6.86e-11 -0.056718 0.943198 ( 0.077557) 0.999916 ( 0.000170) 0.964509 1.000000 --->fabia-------plink----: 7.89e-06 -0.045217 7.23e-11 -0.056634 0.943198 ( 0.077557) 0.999832 ( 2.83e-05) 0.964509 0.999836 --->fabia-------germline1: 5.84e-06 -0.045358 7.01e-11 -0.056680 0.943198 ( 0.077557) 0.999878 ( 5.84e-05) 0.964509 0.999881 --->fabia-------germline2: 3.51e-08 -0.054318 6.89e-11 -0.056710 0.943198 ( 0.077557) 0.999908 ( 8.6e-05) 0.964509 0.999927 --->fabia-------dash-----: 4.68e-10 -0.075594 6.83e-11 -0.056718 0.943198 ( 0.077557) 0.999916 ( 0.000132) 0.964509 1.000000 --->beagle1-----beagle2--: 1e+00 0.000000 1e+00 0.000000 0.999863 ( 0.000205) 0.999916 ( 0.000170) 0.999938 1.000000 --->beagle1-----plink----: 6.3e-03 4.1e-05 1e+00 0.000000 0.999863 ( 0.000205) 0.999832 ( 2.83e-05) 0.999938 0.999836 --->beagle1-----germline1: 1e+00 0.000000 1e+00 0.000000 0.999863 ( 0.000205) 0.999878 ( 5.84e-05) 0.999938 0.999881 --->beagle1-----germline2: 1e+00 0.000000 1e+00 0.000000 0.999863 ( 0.000205) 0.999908 ( 8.6e-05) 0.999938 0.999927 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.999863 ( 0.000205) 0.999916 ( 0.000132) 0.999938 1.000000 --->beagle2-----plink----: 1.12e-06 0.000153 1e+00 0.000000 0.999916 ( 0.000170) 0.999832 ( 2.83e-05) 1.000000 0.999836 --->beagle2-----germline1: 3.81e-03 5.37e-05 1e+00 0.000000 0.999916 ( 0.000170) 0.999878 ( 5.84e-05) 1.000000 0.999881 --->beagle2-----germline2: 1e+00 0.000000 1e+00 0.000000 0.999916 ( 0.000170) 0.999908 ( 8.6e-05) 1.000000 0.999927 --->beagle2-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.999916 ( 0.000170) 0.999916 ( 0.000132) 1.000000 1.000000 --->plink-------germline1: 1e+00 0.000000 1e+00 0.000000 0.999832 ( 2.83e-05) 0.999878 ( 5.84e-05) 0.999836 0.999881 --->plink-------germline2: 1e+00 0.000000 1e+00 0.000000 0.999832 ( 2.83e-05) 0.999908 ( 8.6e-05) 0.999836 0.999927 --->plink-------dash-----: 1.01e-09 -0.000131 1e+00 0.000000 0.999832 ( 2.83e-05) 0.999916 ( 0.000132) 0.999836 1.000000 --->germline1---germline2: 1e+00 0.000000 1e+00 0.000000 0.999878 ( 5.84e-05) 0.999908 ( 8.6e-05) 0.999881 0.999927 --->germline1---dash-----: 1.36e-04 -3.45e-05 1e+00 0.000000 0.999878 ( 5.84e-05) 0.999916 ( 0.000132) 0.999881 1.000000 --->germline2---dash-----: 1e+00 0.000000 1e+00 0.000000 0.999908 ( 8.6e-05) 0.999916 ( 0.000132) 0.999927 1.000000 ######specifity###### --->fabia-------beagle1--: 3.96e-18 0.088305 2.91e-123 0.088457 0.999222 ( 0.000389) 0.910765 ( 0.005264) 0.999203 0.911179 --->fabia-------beagle2--: 3.96e-18 0.045412 2.81e-109 0.045479 0.999222 ( 0.000389) 0.953743 ( 0.003782) 0.999203 0.953776 --->fabia-------plink----: 3.96e-18 0.936582 3.23e-214 0.936570 0.999222 ( 0.000389) 0.062652 ( 0.006773) 0.999203 0.062591 --->fabia-------germline1: 3.96e-18 0.541135 4.43e-127 0.539438 0.999222 ( 0.000389) 0.459784 ( 0.029444) 0.999203 0.455848 --->fabia-------germline2: 3.96e-18 0.246254 1.29e-91 0.245907 0.999222 ( 0.000389) 0.753315 ( 0.030854) 0.999203 0.748040 --->fabia-------dash-----: 3.96e-18 0.100202 2.65e-62 0.100402 0.999222 ( 0.000389) 0.898820 ( 0.025516) 0.999203 0.899370 --->beagle1-----beagle2--: 3.96e-18 -0.042905 1.25e-105 -0.042978 0.910765 ( 0.005264) 0.953743 ( 0.003782) 0.911179 0.953776 --->beagle1-----plink----: 3.96e-18 0.848337 1.37e-202 0.848113 0.910765 ( 0.005264) 0.062652 ( 0.006773) 0.911179 0.062591 --->beagle1-----germline1: 3.96e-18 0.452270 1.43e-119 0.450981 0.910765 ( 0.005264) 0.459784 ( 0.029444) 0.911179 0.455848 --->beagle1-----germline2: 3.96e-18 0.157949 6.46e-73 0.157450 0.910765 ( 0.005264) 0.753315 ( 0.030854) 0.911179 0.748040 --->beagle1-----dash-----: 2.59e-05 0.011909 8.63e-06 0.011945 0.910765 ( 0.005264) 0.898820 ( 0.025516) 0.911179 0.899370 --->beagle2-----plink----: 3.96e-18 0.891113 6.82e-209 0.891091 0.953743 ( 0.003782) 0.062652 ( 0.006773) 0.953776 0.062591 --->beagle2-----germline1: 3.96e-18 0.495630 4.95e-123 0.493959 0.953743 ( 0.003782) 0.459784 ( 0.029444) 0.953776 0.455848 --->beagle2-----germline2: 3.96e-18 0.201318 4.16e-83 0.200428 0.953743 ( 0.003782) 0.753315 ( 0.030854) 0.953776 0.748040 --->beagle2-----dash-----: 4.46e-18 0.055223 1.59e-39 0.054923 0.953743 ( 0.003782) 0.898820 ( 0.025516) 0.953776 0.899370 --->plink-------germline1: 3.96e-18 -0.396135 7.06e-113 -0.397132 0.062652 ( 0.006773) 0.459784 ( 0.029444) 0.062591 0.455848 --->plink-------germline2: 3.96e-18 -0.690454 5.41e-134 -0.690663 0.062652 ( 0.006773) 0.753315 ( 0.030854) 0.062591 0.748040 --->plink-------dash-----: 3.96e-18 -0.836706 4.2e-149 -0.836168 0.062652 ( 0.006773) 0.898820 ( 0.025516) 0.062591 0.899370 --->germline1---germline2: 3.96e-18 -0.293415 1.27e-136 -0.293531 0.459784 ( 0.029444) 0.753315 ( 0.030854) 0.455848 0.748040 --->germline1---dash-----: 3.96e-18 -0.439458 3.55e-136 -0.439036 0.459784 ( 0.029444) 0.898820 ( 0.025516) 0.455848 0.899370 --->germline2---dash-----: 3.96e-18 -0.145306 3.46e-113 -0.145505 0.753315 ( 0.030854) 0.898820 ( 0.025516) 0.748040 0.899370 ######sensitivity###### --->fabia-------beagle1--: 5.84e-08 0.407882 3.43e-12 0.363715 0.440839 ( 0.443335) 0.077124 ( 0.114615) 0.506187 0.034130 --->fabia-------beagle2--: 3.78e-10 0.728735 3.68e-15 0.417431 0.440839 ( 0.443335) 0.023408 ( 0.044870) 0.506187 0.000000 --->fabia-------plink----: 1.84e-17 -0.549476 8.37e-22 -0.547463 0.440839 ( 0.443335) 0.988303 ( 0.037101) 0.506187 1.000000 --->fabia-------germline1: 4.25e-01 0.034183 4.7e-01 0.032766 0.440839 ( 0.443335) 0.408074 ( 0.177375) 0.506187 0.400000 --->fabia-------germline2: 7.34e-08 0.339176 1.9e-09 0.297961 0.440839 ( 0.443335) 0.142878 ( 0.130914) 0.506187 0.100000 --->fabia-------dash-----: 4.67e-10 0.654773 2.6e-14 0.387980 0.440839 ( 0.443335) 0.052859 ( 0.076660) 0.506187 0.000000 --->beagle1-----beagle2--: 5.06e-08 0.113126 6.08e-06 0.053716 0.077124 ( 0.114615) 0.023408 ( 0.044870) 0.034130 0.000000 --->beagle1-----plink----: 2.9e-18 -0.928344 3.33e-91 -0.911179 0.077124 ( 0.114615) 0.988303 ( 0.037101) 0.034130 1.000000 --->beagle1-----germline1: 6.11e-17 -0.343583 1e-29 -0.330950 0.077124 ( 0.114615) 0.408074 ( 0.177375) 0.034130 0.400000 --->beagle1-----germline2: 1.67e-04 -0.081146 2.7e-04 -0.065754 0.077124 ( 0.114615) 0.142878 ( 0.130914) 0.034130 0.100000 --->beagle1-----dash-----: 1.29e-01 0.025462 8.26e-02 0.024265 0.077124 ( 0.114615) 0.052859 ( 0.076660) 0.034130 0.000000 --->beagle2-----plink----: 5.04e-19 -0.978341 2.34e-122 -0.964894 0.023408 ( 0.044870) 0.988303 ( 0.037101) 0.000000 1.000000 --->beagle2-----germline1: 4.58e-18 -0.385225 5.62e-38 -0.384666 0.023408 ( 0.044870) 0.408074 ( 0.177375) 0.000000 0.400000 --->beagle2-----germline2: 2.36e-11 -0.138287 3.44e-13 -0.119470 0.023408 ( 0.044870) 0.142878 ( 0.130914) 0.000000 0.100000 --->beagle2-----dash-----: 1e+00 0.000000 1.64e-03 -0.029451 0.023408 ( 0.044870) 0.052859 ( 0.076660) 0.000000 0.000000 --->plink-------germline1: 3.94e-18 0.579048 7.21e-54 0.580229 0.988303 ( 0.037101) 0.408074 ( 0.177375) 1.000000 0.400000 --->plink-------germline2: 3.36e-18 0.850052 4.03e-81 0.845425 0.988303 ( 0.037101) 0.142878 ( 0.130914) 1.000000 0.100000 --->plink-------dash-----: 1.3e-18 0.949962 2.03e-107 0.935443 0.988303 ( 0.037101) 0.052859 ( 0.076660) 1.000000 0.000000 --->germline1---germline2: 1.23e-17 0.270908 6.39e-35 0.265196 0.408074 ( 0.177375) 0.142878 ( 0.130914) 0.400000 0.100000 --->germline1---dash-----: 5.75e-18 0.354162 1.28e-39 0.355214 0.408074 ( 0.177375) 0.052859 ( 0.076660) 0.400000 0.000000 --->germline2---dash-----: 1.56e-12 0.116530 2.15e-13 0.090019 0.142878 ( 0.130914) 0.052859 ( 0.076660) 0.100000 0.000000 ######trueN###### --->fabia-------beagle1--: 3.96e-18 10875208 1.09e-230 10876643 2e+07 ( 7868) 9106199 ( 52652) 2e+07 9110332 --->fabia-------beagle2--: 3.96e-18 10445846 1.32e-243 10446933 2e+07 ( 7868) 9535909 ( 37841) 2e+07 9536249 --->fabia-------plink----: 3.96e-18 19356555 1.54e-245 19356420 2e+07 ( 7868) 626422 ( 67722) 2e+07 625800 --->fabia-------germline1: 3.96e-18 15402423 4.93e-172 15385732 2e+07 ( 7868) 4597110 ( 294396) 2e+07 4557726 --->fabia-------germline2: 3.96e-18 12455455 4.82e-161 12450891 2e+07 ( 7868) 7531951 ( 308516) 2e+07 7479267 --->fabia-------dash-----: 3.96e-18 1.1e+07 5.89e-164 1.1e+07 2e+07 ( 7868) 8986769 ( 255162) 2e+07 8992414 --->beagle1-----beagle2--: 3.96e-18 -429028 1.25e-105 -429710 9106199 ( 52652) 9535909 ( 37841) 9110332 9536249 --->beagle1-----plink----: 3.96e-18 8482260 1.37e-202 8479777 9106199 ( 52652) 626422 ( 67722) 9110332 625800 --->beagle1-----germline1: 3.96e-18 4522001 1.42e-119 4509090 9106199 ( 52652) 4597110 ( 294396) 9110332 4557726 --->beagle1-----germline2: 3.96e-18 1579409 6.46e-73 1574248 9106199 ( 52652) 7531951 ( 308516) 9110332 7479267 --->beagle1-----dash-----: 2.59e-05 118972 8.63e-06 119430 9106199 ( 52652) 8986769 ( 255162) 9110332 8992414 --->beagle2-----plink----: 3.96e-18 8909764 6.85e-209 8909487 9535909 ( 37841) 626422 ( 67722) 9536249 625800 --->beagle2-----germline1: 3.96e-18 4955428 4.94e-123 4938800 9535909 ( 37841) 4597110 ( 294396) 9536249 4557726 --->beagle2-----germline2: 3.96e-18 2013115 4.16e-83 2e+06 9535909 ( 37841) 7531951 ( 308516) 9536249 7479267 --->beagle2-----dash-----: 4.46e-18 552057 1.58e-39 549140 9535909 ( 37841) 8986769 ( 255162) 9536249 8992414 --->plink-------germline1: 3.96e-18 -3960695 7.07e-113 -3970688 626422 ( 67722) 4597110 ( 294396) 625800 4557726 --->plink-------germline2: 3.96e-18 -6903312 5.45e-134 -6905529 626422 ( 67722) 7531951 ( 308516) 625800 7479267 --->plink-------dash-----: 3.96e-18 -8365384 4.25e-149 -8360348 626422 ( 67722) 8986769 ( 255162) 625800 8992414 --->germline1---germline2: 3.96e-18 -2933741 1.29e-136 -2934841 4597110 ( 294396) 7531951 ( 308516) 4557726 7479267 --->germline1---dash-----: 3.96e-18 -4393785 3.58e-136 -4389660 4597110 ( 294396) 8986769 ( 255162) 4557726 8992414 --->germline2---dash-----: 3.96e-18 -1452938 3.48e-113 -1454818 7531951 ( 308516) 8986769 ( 255162) 7479267 8992414 ######falseP###### --->fabia-------beagle1--: 3.96e-18 -875207 1.71e-122 -876646 15562 ( 7775) 892208 ( 52635) 15933 888073 --->fabia-------beagle2--: 3.96e-18 -445845 2.98e-108 -446936 15562 ( 7775) 462498 ( 37812) 15933 462169 --->fabia-------plink----: 3.96e-18 -9356578 2.77e-214 -9356424 15562 ( 7775) 9371986 ( 67710) 15933 9372490 --->fabia-------germline1: 3.96e-18 -5402368 5.88e-127 -5385736 15562 ( 7775) 5401298 ( 294383) 15933 5440628 --->fabia-------germline2: 3.96e-18 -2455484 1.76e-91 -2450894 15562 ( 7775) 2466456 ( 308486) 15933 2519223 --->fabia-------dash-----: 3.96e-18 -993861 5.01e-62 -996076 15562 ( 7775) 1011638 ( 255115) 15933 1006156 --->beagle1-----beagle2--: 3.96e-18 429022 1.25e-105 429710 892208 ( 52635) 462498 ( 37812) 888073 462169 --->beagle1-----plink----: 3.96e-18 -8482243 1.37e-202 -8479777 892208 ( 52635) 9371986 ( 67710) 888073 9372490 --->beagle1-----germline1: 3.96e-18 -4521983 1.42e-119 -4509090 892208 ( 52635) 5401298 ( 294383) 888073 5440628 --->beagle1-----germline2: 3.96e-18 -1579475 6.46e-73 -1574248 892208 ( 52635) 2466456 ( 308486) 888073 2519223 --->beagle1-----dash-----: 2.59e-05 -118971 8.63e-06 -119430 892208 ( 52635) 1011638 ( 255115) 888073 1006156 --->beagle2-----plink----: 3.96e-18 -8909770 6.85e-209 -8909487 462498 ( 37812) 9371986 ( 67710) 462169 9372490 --->beagle2-----germline1: 3.96e-18 -4955431 4.94e-123 -4938800 462498 ( 37812) 5401298 ( 294383) 462169 5440628 --->beagle2-----germline2: 3.96e-18 -2013115 4.16e-83 -2e+06 462498 ( 37812) 2466456 ( 308486) 462169 2519223 --->beagle2-----dash-----: 4.46e-18 -552007 1.58e-39 -549140 462498 ( 37812) 1011638 ( 255115) 462169 1006156 --->plink-------germline1: 3.96e-18 3960731 7.07e-113 3970688 9371986 ( 67710) 5401298 ( 294383) 9372490 5440628 --->plink-------germline2: 3.96e-18 6903284 5.45e-134 6905529 9371986 ( 67710) 2466456 ( 308486) 9372490 2519223 --->plink-------dash-----: 3.96e-18 8365383 4.25e-149 8360348 9371986 ( 67710) 1011638 ( 255115) 9372490 1006156 --->germline1---germline2: 3.96e-18 2933700 1.29e-136 2934841 5401298 ( 294383) 2466456 ( 308486) 5440628 2519223 --->germline1---dash-----: 3.96e-18 4393789 3.58e-136 4389660 5401298 ( 294383) 1011638 ( 255115) 5440628 1006156 --->germline2---dash-----: 3.96e-18 1452961 3.48e-113 1454818 2466456 ( 308486) 1011638 ( 255115) 2519223 1006156 ######falseN###### --->fabia-------beagle1--: 6.18e-08 -688 3.91e-12 -607 862 ( 691) 1469 ( 299) 785 1464 --->fabia-------beagle2--: 3.79e-10 -1174 8.85e-15 -692 862 ( 691) 1554 ( 252) 785 1535 --->fabia-------plink----: 2.96e-17 845 1.81e-21 845 862 ( 691) 17.1 ( 53.9) 785 0 --->fabia-------germline1: 2.99e-01 -75.5 3.17e-01 -73.2 862 ( 691) 935 ( 294) 785 951 --->fabia-------germline2: 1.24e-07 -576 1.53e-09 -501 862 ( 691) 1363 ( 295) 785 1352 --->fabia-------dash-----: 5.86e-10 -1008 4.34e-14 -645 862 ( 691) 1507 ( 261) 785 1505 --->beagle1-----beagle2--: 5.46e-08 -176 1.23e-05 -85.7 1469 ( 299) 1554 ( 252) 1464 1535 --->beagle1-----plink----: 3.95e-18 1447 5.7e-70 1452 1469 ( 299) 17.1 ( 53.9) 1464 0 --->beagle1-----germline1: 7.55e-17 548 2.86e-28 533 1469 ( 299) 935 ( 294) 1464 951 --->beagle1-----germline2: 1.02e-04 123 3.95e-04 106 1469 ( 299) 1363 ( 295) 1464 1352 --->beagle1-----dash-----: 1.29e-01 -41.5 8.94e-02 -38.4 1469 ( 299) 1507 ( 261) 1464 1505 --->beagle2-----plink----: 3.95e-18 1528 2.97e-78 1537 1554 ( 252) 17.1 ( 53.9) 1535 0 --->beagle2-----germline1: 4.67e-18 615 1.08e-35 619 1554 ( 252) 935 ( 294) 1535 951 --->beagle2-----germline2: 1.21e-11 210 1.22e-12 191 1554 ( 252) 1363 ( 295) 1535 1352 --->beagle2-----dash-----: 2.02e-03 82 1.59e-03 47.3 1554 ( 252) 1507 ( 261) 1535 1505 --->plink-------germline1: 3.96e-18 -916 4.93e-52 -918 17.1 ( 53.9) 935 ( 294) 0 951 --->plink-------germline2: 3.95e-18 -1344 4.36e-67 -1346 17.1 ( 53.9) 1363 ( 295) 0 1352 --->plink-------dash-----: 3.95e-18 -1481 4.81e-76 -1490 17.1 ( 53.9) 1507 ( 261) 0 1505 --->germline1---germline2: 1.24e-17 -432 1.28e-32 -428 935 ( 294) 1363 ( 295) 951 1352 --->germline1---dash-----: 5.78e-18 -572 2.79e-37 -572 935 ( 294) 1507 ( 261) 951 1505 --->germline2---dash-----: 1.68e-12 -188 8.67e-13 -144 1363 ( 295) 1507 ( 261) 1352 1505 ######trueP###### --->fabia-------beagle1--: 6.18e-08 692 3.3e-12 610 734 ( 756) 124 ( 189) 697 54.5 --->fabia-------beagle2--: 3.79e-10 1175 7.37e-15 696 734 ( 756) 38 ( 73.6) 697 0 --->fabia-------plink----: 5.42e-17 -840 2.52e-21 -842 734 ( 756) 1575 ( 266) 697 1535 --->fabia-------germline1: 2.7e-01 80 2.95e-01 76.6 734 ( 756) 657 ( 312) 697 642 --->fabia-------germline2: 9.22e-08 585 1.28e-09 504 734 ( 756) 229 ( 222) 697 184 --->fabia-------dash-----: 4.68e-10 1043 3.51e-14 648 734 ( 756) 85.3 ( 128) 697 0 --->beagle1-----beagle2--: 5.46e-08 176 1.23e-05 85.7 124 ( 189) 38 ( 73.6) 54.5 0 --->beagle1-----plink----: 3.95e-18 -1447 5.7e-70 -1452 124 ( 189) 1575 ( 266) 54.5 1535 --->beagle1-----germline1: 7.55e-17 -548 2.86e-28 -533 124 ( 189) 657 ( 312) 54.5 642 --->beagle1-----germline2: 1.02e-04 -123 3.95e-04 -106 124 ( 189) 229 ( 222) 54.5 184 --->beagle1-----dash-----: 1.29e-01 41.5 8.94e-02 38.4 124 ( 189) 85.3 ( 128) 54.5 0 --->beagle2-----plink----: 3.95e-18 -1528 2.97e-78 -1537 38 ( 73.6) 1575 ( 266) 0 1535 --->beagle2-----germline1: 4.67e-18 -615 1.08e-35 -619 38 ( 73.6) 657 ( 312) 0 642 --->beagle2-----germline2: 1.21e-11 -210 1.22e-12 -191 38 ( 73.6) 229 ( 222) 0 184 --->beagle2-----dash-----: 1e+00 0.000000 1.59e-03 -47.310000 38.010000 (73.551809) 85.320000 (128.284869) 0.000000 0.000000 --->plink-------germline1: 3.96e-18 916 4.93e-52 918 1575 ( 266) 657 ( 312) 1535 642 --->plink-------germline2: 3.95e-18 1344 4.36e-67 1346 1575 ( 266) 229 ( 222) 1535 184 --->plink-------dash-----: 3.95e-18 1481 4.81e-76 1490 1575 ( 266) 85.3 ( 128) 1535 0 --->germline1---germline2: 1.24e-17 432 1.28e-32 428 657 ( 312) 229 ( 222) 642 184 --->germline1---dash-----: 5.78e-18 572 2.79e-37 572 657 ( 312) 85.3 ( 128) 642 0 --->germline2---dash-----: 1.68e-12 188 8.67e-13 144 229 ( 222) 85.3 ( 128) 184 0 ######MatthewsSnps###### --->fabia-------beagle1--: 1e+00 0.000000 1e+00 0.000000 0.076034 ( 0.093714) 0.000000 ( 0.000000) 0.110037 0.000000 --->fabia-------beagle2--: 1e+00 0.000000 1e+00 0.000000 0.076034 ( 0.093714) 0.000000 ( 0.000000) 0.110037 0.000000 --->fabia-------plink----: 8.85e-10 0.098067 3.14e-12 0.074357 0.076034 ( 0.093714) 0.001677 ( 0.000512) 0.110037 0.001495 --->fabia-------germline1: 1e+00 0.000000 1e+00 0.000000 0.076034 ( 0.093714) 0.000000 ( 0.000000) 0.110037 0.000000 --->fabia-------germline2: 5.03e-10 0.099026 1.63e-12 0.075597 0.076034 ( 0.093714) 0.000437 ( 0.002506) 0.110037 0.000000 --->fabia-------dash-----: 1.37e-06 0.063050 6.33e-06 0.063832 0.076034 ( 0.093714) 0.012202 ( 0.114202) 0.110037 0.050540 --->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) 0.001677 ( 0.000512) 0.000000 0.001495 --->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) 0.000437 ( 0.002506) 0.000000 0.000000 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.012202 ( 0.114202) 0.000000 0.050540 --->beagle2-----plink----: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.001677 ( 0.000512) 0.000000 0.001495 --->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) 0.000437 ( 0.002506) 0.000000 0.000000 --->beagle2-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.012202 ( 0.114202) 0.000000 0.050540 --->plink-------germline1: 1e+00 0.000000 1e+00 0.000000 0.001677 ( 0.000512) 0.000000 ( 0.000000) 0.001495 0.000000 --->plink-------germline2: 1.87e-14 0.001592 4.77e-06 0.001240 0.001677 ( 0.000512) 0.000437 ( 0.002506) 0.001495 0.000000 --->plink-------dash-----: 1.12e-05 -0.045573 3.59e-01 -0.010526 0.001677 ( 0.000512) 0.012202 ( 0.114202) 0.001495 0.050540 --->germline1---germline2: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.000437 ( 0.002506) 0.000000 0.000000 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.012202 ( 0.114202) 0.000000 0.050540 --->germline2---dash-----: 9.56e-06 -0.046940 3.05e-01 -0.011766 0.000437 ( 0.002506) 0.012202 ( 0.114202) 0.000000 0.050540 ######F1Snps###### --->fabia-------beagle1--: 2.86e-09 0.023877 1.8e-11 0.020697 0.052102 ( 0.028605) 0.031405 ( 0.004901) 0.056939 0.030527 --->fabia-------beagle2--: 2.86e-09 0.023877 1.8e-11 0.020697 0.052102 ( 0.028605) 0.031405 ( 0.004901) 0.056939 0.030527 --->fabia-------plink----: 2.86e-09 0.023861 1.82e-11 0.020691 0.052102 ( 0.028605) 0.031410 ( 0.004901) 0.056939 0.030536 --->fabia-------germline1: 2.86e-09 0.023877 1.8e-11 0.020697 0.052102 ( 0.028605) 0.031405 ( 0.004901) 0.056939 0.030527 --->fabia-------germline2: 2.86e-09 0.023811 1.84e-11 0.020685 0.052102 ( 0.028605) 0.031417 ( 0.004905) 0.056939 0.030527 --->fabia-------dash-----: 2.44e-08 0.021361 7.98e-10 0.019039 0.052102 ( 0.028605) 0.033063 ( 0.012727) 0.056939 0.034855 --->beagle1-----beagle2--: 1e+00 0.000000 1e+00 0.000000 0.031405 ( 0.004901) 0.031405 ( 0.004901) 0.030527 0.030527 --->beagle1-----plink----: 1e+00 0.000000 1e+00 0.000000 0.031405 ( 0.004901) 0.031410 ( 0.004901) 0.030527 0.030536 --->beagle1-----germline1: 1e+00 0.000000 1e+00 0.000000 0.031405 ( 0.004901) 0.031405 ( 0.004901) 0.030527 0.030527 --->beagle1-----germline2: 1e+00 0.000000 1e+00 0.000000 0.031405 ( 0.004901) 0.031417 ( 0.004905) 0.030527 0.030527 --->beagle1-----dash-----: 1.49e-05 -0.004587 1.6e-01 -0.001658 0.031405 ( 0.004901) 0.033063 ( 0.012727) 0.030527 0.034855 --->beagle2-----plink----: 1e+00 0.000000 1e+00 0.000000 0.031405 ( 0.004901) 0.031410 ( 0.004901) 0.030527 0.030536 --->beagle2-----germline1: 1e+00 0.000000 1e+00 0.000000 0.031405 ( 0.004901) 0.031405 ( 0.004901) 0.030527 0.030527 --->beagle2-----germline2: 1e+00 0.000000 1e+00 0.000000 0.031405 ( 0.004901) 0.031417 ( 0.004905) 0.030527 0.030527 --->beagle2-----dash-----: 1.49e-05 -0.004587 1.6e-01 -0.001658 0.031405 ( 0.004901) 0.033063 ( 0.012727) 0.030527 0.034855 --->plink-------germline1: 1e+00 0.000000 1e+00 0.000000 0.031410 ( 0.004901) 0.031405 ( 0.004901) 0.030536 0.030527 --->plink-------germline2: 1e+00 0.000000 1e+00 0.000000 0.031410 ( 0.004901) 0.031417 ( 0.004905) 0.030536 0.030527 --->plink-------dash-----: 1.49e-05 -0.004630 1.62e-01 -0.001653 0.031410 ( 0.004901) 0.033063 ( 0.012727) 0.030536 0.034855 --->germline1---germline2: 1e+00 0.000000 1e+00 0.000000 0.031405 ( 0.004901) 0.031417 ( 0.004905) 0.030527 0.030527 --->germline1---dash-----: 1.49e-05 -0.004587 1.6e-01 -0.001658 0.031405 ( 0.004901) 0.033063 ( 0.012727) 0.030527 0.034855 --->germline2---dash-----: 1.49e-05 -0.004581 1.63e-01 -0.001646 0.031417 ( 0.004905) 0.033063 ( 0.012727) 0.030527 0.034855 ######accuracySnps###### --->fabia-------beagle1--: 3.96e-18 0.528377 5.77e-81 0.532337 0.548296 ( 0.085594) 0.015959 ( 0.002532) 0.545750 0.015500 --->fabia-------beagle2--: 3.96e-18 0.528377 5.77e-81 0.532337 0.548296 ( 0.085594) 0.015959 ( 0.002532) 0.545750 0.015500 --->fabia-------plink----: 3.96e-18 0.528221 5.92e-81 0.532145 0.548296 ( 0.085594) 0.016151 ( 0.002518) 0.545750 0.015750 --->fabia-------germline1: 3.96e-18 0.528377 5.77e-81 0.532337 0.548296 ( 0.085594) 0.015959 ( 0.002532) 0.545750 0.015500 --->fabia-------germline2: 3.96e-18 0.527991 5.93e-81 0.531953 0.548296 ( 0.085594) 0.016343 ( 0.003379) 0.545750 0.015650 --->fabia-------dash-----: 3.96e-18 0.372037 5.33e-55 0.370619 0.548296 ( 0.085594) 0.177677 ( 0.073282) 0.545750 0.171100 --->beagle1-----beagle2--: 1e+00 0.000000 1e+00 0.000000 0.015959 ( 0.002532) 0.015959 ( 0.002532) 0.015500 0.015500 --->beagle1-----plink----: 1.7e-18 -0.000152 1.09e-27 -0.000192 0.015959 ( 0.002532) 0.016151 ( 0.002518) 0.015500 0.015750 --->beagle1-----germline1: 1e+00 0.000000 1e+00 0.000000 0.015959 ( 0.002532) 0.015959 ( 0.002532) 0.015500 0.015500 --->beagle1-----germline2: 1e+00 0.000000 8.32e-02 -0.000384 0.015959 ( 0.002532) 0.016343 ( 0.003379) 0.015500 0.015650 --->beagle1-----dash-----: 3.92e-18 -0.159996 5.72e-40 -0.161718 0.015959 ( 0.002532) 0.177677 ( 0.073282) 0.015500 0.171100 --->beagle2-----plink----: 1.7e-18 -0.000152 1.09e-27 -0.000192 0.015959 ( 0.002532) 0.016151 ( 0.002518) 0.015500 0.015750 --->beagle2-----germline1: 1e+00 0.000000 1e+00 0.000000 0.015959 ( 0.002532) 0.015959 ( 0.002532) 0.015500 0.015500 --->beagle2-----germline2: 1e+00 0.000000 8.32e-02 -0.000384 0.015959 ( 0.002532) 0.016343 ( 0.003379) 0.015500 0.015650 --->beagle2-----dash-----: 3.92e-18 -0.159996 5.72e-40 -0.161718 0.015959 ( 0.002532) 0.177677 ( 0.073282) 0.015500 0.171100 --->plink-------germline1: 1.7e-18 0.000152 1.09e-27 0.000192 0.016151 ( 0.002518) 0.015959 ( 0.002532) 0.015750 0.015500 --->plink-------germline2: 9.75e-15 0.000160 3.85e-01 -0.000192 0.016151 ( 0.002518) 0.016343 ( 0.003379) 0.015750 0.015650 --->plink-------dash-----: 3.95e-18 -0.159734 6.39e-40 -0.161526 0.016151 ( 0.002518) 0.177677 ( 0.073282) 0.015750 0.171100 --->germline1---germline2: 1e+00 0.000000 8.32e-02 -0.000384 0.015959 ( 0.002532) 0.016343 ( 0.003379) 0.015500 0.015650 --->germline1---dash-----: 3.92e-18 -0.159996 5.72e-40 -0.161718 0.015959 ( 0.002532) 0.177677 ( 0.073282) 0.015500 0.171100 --->germline2---dash-----: 3.92e-18 -0.159980 5.45e-40 -0.161334 0.016343 ( 0.003379) 0.177677 ( 0.073282) 0.015650 0.171100 ######FPRSnps###### --->fabia-------beagle1--: 1e+00 0.000000 1e+00 0.000000 0.455126 ( 0.087036) 1.000000 ( 0.000000) 0.459778 1.000000 --->fabia-------beagle2--: 1e+00 0.000000 1e+00 0.000000 0.455126 ( 0.087036) 1.000000 ( 0.000000) 0.459778 1.000000 --->fabia-------plink----: 3.96e-18 -0.541145 2.02e-81 -0.544679 0.455126 ( 0.087036) 0.999805 ( 0.000128) 0.459778 0.999898 --->fabia-------germline1: 1e+00 0.000000 1e+00 0.000000 0.455126 ( 0.087036) 1.000000 ( 0.000000) 0.459778 1.000000 --->fabia-------germline2: 3.96e-18 -0.540848 2.03e-81 -0.544484 0.455126 ( 0.087036) 0.999610 ( 0.002231) 0.459778 1.000000 --->fabia-------dash-----: 3.96e-18 -0.380253 2.84e-55 -0.378549 0.455126 ( 0.087036) 0.833675 ( 0.074368) 0.459778 0.841052 --->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) 0.999805 ( 0.000128) 1.000000 0.999898 --->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) 0.999610 ( 0.002231) 1.000000 1.000000 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 0.833675 ( 0.074368) 1.000000 0.841052 --->beagle2-----plink----: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 0.999805 ( 0.000128) 1.000000 0.999898 --->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) 0.999610 ( 0.002231) 1.000000 1.000000 --->beagle2-----dash-----: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 0.833675 ( 0.074368) 1.000000 0.841052 --->plink-------germline1: 1e+00 0.000000 1e+00 0.000000 0.999805 ( 0.000128) 1.000000 ( 0.000000) 0.999898 1.000000 --->plink-------germline2: 1.83e-14 -0.000189 3.85e-01 0.000195 0.999805 ( 0.000128) 0.999610 ( 0.002231) 0.999898 1.000000 --->plink-------dash-----: 3.96e-18 0.162576 1.92e-40 0.166130 0.999805 ( 0.000128) 0.833675 ( 0.074368) 0.999898 0.841052 --->germline1---germline2: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 0.999610 ( 0.002231) 1.000000 1.000000 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 0.833675 ( 0.074368) 1.000000 0.841052 --->germline2---dash-----: 3.96e-18 0.162677 1.65e-40 0.165934 0.999610 ( 0.002231) 0.833675 ( 0.074368) 1.000000 0.841052 ######FDRSnps###### --->fabia-------beagle1--: 1.22e-09 -0.012602 8.8e-12 -0.011097 0.972944 ( 0.015043) 0.984041 ( 0.002532) 0.970607 0.984500 --->fabia-------beagle2--: 1.22e-09 -0.012602 8.8e-12 -0.011097 0.972944 ( 0.015043) 0.984041 ( 0.002532) 0.970607 0.984500 --->fabia-------plink----: 1.25e-09 -0.012604 8.88e-12 -0.011094 0.972944 ( 0.015043) 0.984038 ( 0.002533) 0.970607 0.984495 --->fabia-------germline1: 1.22e-09 -0.012602 8.8e-12 -0.011097 0.972944 ( 0.015043) 0.984041 ( 0.002532) 0.970607 0.984500 --->fabia-------germline2: 1.3e-09 -0.012596 8.95e-12 -0.011091 0.972944 ( 0.015043) 0.984035 ( 0.002535) 0.970607 0.984500 --->fabia-------dash-----: 1.21e-08 -0.011296 4.13e-10 -0.010197 0.972944 ( 0.015043) 0.983141 ( 0.006522) 0.970607 0.982263 --->beagle1-----beagle2--: 1e+00 0.000000 1e+00 0.000000 0.984041 ( 0.002532) 0.984041 ( 0.002532) 0.984500 0.984500 --->beagle1-----plink----: 1e+00 0.000000 1e+00 0.000000 0.984041 ( 0.002532) 0.984038 ( 0.002533) 0.984500 0.984495 --->beagle1-----germline1: 1e+00 0.000000 1e+00 0.000000 0.984041 ( 0.002532) 0.984041 ( 0.002532) 0.984500 0.984500 --->beagle1-----germline2: 1e+00 0.000000 1e+00 0.000000 0.984041 ( 0.002532) 0.984035 ( 0.002535) 0.984500 0.984500 --->beagle1-----dash-----: 1.31e-05 0.002390 1.36e-01 9e-04 0.984041 ( 0.002532) 0.983141 ( 0.006522) 0.984500 0.982263 --->beagle2-----plink----: 1e+00 0.000000 1e+00 0.000000 0.984041 ( 0.002532) 0.984038 ( 0.002533) 0.984500 0.984495 --->beagle2-----germline1: 1e+00 0.000000 1e+00 0.000000 0.984041 ( 0.002532) 0.984041 ( 0.002532) 0.984500 0.984500 --->beagle2-----germline2: 1e+00 0.000000 1e+00 0.000000 0.984041 ( 0.002532) 0.984035 ( 0.002535) 0.984500 0.984500 --->beagle2-----dash-----: 1.31e-05 0.002390 1.36e-01 9e-04 0.984041 ( 0.002532) 0.983141 ( 0.006522) 0.984500 0.982263 --->plink-------germline1: 1e+00 0.000000 1e+00 0.000000 0.984038 ( 0.002533) 0.984041 ( 0.002532) 0.984495 0.984500 --->plink-------germline2: 1e+00 0.000000 1e+00 0.000000 0.984038 ( 0.002533) 0.984035 ( 0.002535) 0.984495 0.984500 --->plink-------dash-----: 1.31e-05 0.002387 1.37e-01 0.000897 0.984038 ( 0.002533) 0.983141 ( 0.006522) 0.984495 0.982263 --->germline1---germline2: 1e+00 0.000000 1e+00 0.000000 0.984041 ( 0.002532) 0.984035 ( 0.002535) 0.984500 0.984500 --->germline1---dash-----: 1.31e-05 0.002390 1.36e-01 9e-04 0.984041 ( 0.002532) 0.983141 ( 0.006522) 0.984500 0.982263 --->germline2---dash-----: 1.31e-05 0.002383 1.39e-01 0.000894 0.984035 ( 0.002535) 0.983141 ( 0.006522) 0.984500 0.982263 ######specifitySnps###### --->fabia-------beagle1--: 1e+00 0.000000 1e+00 0.000000 0.544874 ( 0.087036) 0.000000 ( 0.000000) 0.540222 0.000000 --->fabia-------beagle2--: 1e+00 0.000000 1e+00 0.000000 0.544874 ( 0.087036) 0.000000 ( 0.000000) 0.540222 0.000000 --->fabia-------plink----: 3.96e-18 0.541204 2.02e-81 0.544679 0.544874 ( 0.087036) 0.000195 ( 0.000128) 0.540222 0.000102 --->fabia-------germline1: 1e+00 0.000000 1e+00 0.000000 0.544874 ( 0.087036) 0.000000 ( 0.000000) 0.540222 0.000000 --->fabia-------germline2: 3.96e-18 0.540859 2.03e-81 0.544484 0.544874 ( 0.087036) 0.000390 ( 0.002231) 0.540222 0.000000 --->fabia-------dash-----: 3.96e-18 0.380234 2.84e-55 0.378549 0.544874 ( 0.087036) 0.166325 ( 0.074368) 0.540222 0.158948 --->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) 0.000195 ( 0.000128) 0.000000 0.000102 --->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) 0.000390 ( 0.002231) 0.000000 0.000000 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.166325 ( 0.074368) 0.000000 0.158948 --->beagle2-----plink----: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.000195 ( 0.000128) 0.000000 0.000102 --->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) 0.000390 ( 0.002231) 0.000000 0.000000 --->beagle2-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.166325 ( 0.074368) 0.000000 0.158948 --->plink-------germline1: 1e+00 0.000000 1e+00 0.000000 0.000195 ( 0.000128) 0.000000 ( 0.000000) 0.000102 0.000000 --->plink-------germline2: 1.87e-14 0.000165 3.85e-01 -0.000195 0.000195 ( 0.000128) 0.000390 ( 0.002231) 0.000102 0.000000 --->plink-------dash-----: 3.96e-18 -0.162552 1.92e-40 -0.166130 0.000195 ( 0.000128) 0.166325 ( 0.074368) 0.000102 0.158948 --->germline1---germline2: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.000390 ( 0.002231) 0.000000 0.000000 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.166325 ( 0.074368) 0.000000 0.158948 --->germline2---dash-----: 3.96e-18 -0.162703 1.65e-40 -0.165934 0.000390 ( 0.002231) 0.166325 ( 0.074368) 0.000000 0.158948 ######sensitivitySnps###### --->fabia-------beagle1--: 1e+00 0.000000 1e+00 0.000000 0.747939 ( 0.359563) 1.000000 ( 0.000000) 0.938296 1.000000 --->fabia-------beagle2--: 1e+00 0.000000 1e+00 0.000000 0.747939 ( 0.359563) 1.000000 ( 0.000000) 0.938296 1.000000 --->fabia-------plink----: 1e+00 0.000000 1e+00 0.000000 0.747939 ( 0.359563) 1.000000 ( 0.000000) 0.938296 1.000000 --->fabia-------germline1: 1e+00 0.000000 1e+00 0.000000 0.747939 ( 0.359563) 1.000000 ( 0.000000) 0.938296 1.000000 --->fabia-------germline2: 1e+00 0.000000 1e+00 0.000000 0.747939 ( 0.359563) 1.000000 ( 0.000000) 0.938296 1.000000 --->fabia-------dash-----: 5.09e-04 -0.197354 2.39e-03 -0.130606 0.747939 ( 0.359563) 0.878544 ( 0.296962) 0.938296 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) 0.878544 ( 0.296962) 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) 0.878544 ( 0.296962) 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) 0.878544 ( 0.296962) 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) 0.878544 ( 0.296962) 1.000000 1.000000 --->germline2---dash-----: 1e+00 0.000000 1e+00 0.000000 1.000000 ( 0.000000) 0.878544 ( 0.296962) 1.000000 1.000000 ######trueNSnps###### --->fabia-------beagle1--: 1e+00 0 1e+00 0 5362 ( 859) 0 ( 0) 5314 0 --->fabia-------beagle2--: 1e+00 0 1e+00 0 5362 ( 859) 0 ( 0) 5314 0 --->fabia-------plink----: 3.96e-18 5324 2.63e-81 5360 5362 ( 859) 1.92 ( 1.26) 5314 1 --->fabia-------germline1: 1e+00 0 1e+00 0 5362 ( 859) 0 ( 0) 5314 0 --->fabia-------germline2: 3.96e-18 5321 2.65e-81 5358 5362 ( 859) 3.84 ( 21.9) 5314 0 --->fabia-------dash-----: 3.96e-18 3742 3.06e-55 3725 5362 ( 859) 1637 ( 732) 5314 1556 --->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) 1.920000 ( 1.260752) 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) 3.840000 (21.945166) 0.000000 0.000000 --->beagle1-----dash-----: 1e+00 0 1e+00 0 0 ( 0) 1637 ( 732) 0 1556 --->beagle2-----plink----: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 1.920000 ( 1.260752) 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) 3.840000 (21.945166) 0.000000 0.000000 --->beagle2-----dash-----: 1e+00 0 1e+00 0 0 ( 0) 1637 ( 732) 0 1556 --->plink-------germline1: 1e+00 0.000000 1e+00 0.000000 1.920000 ( 1.260752) 0.000000 ( 0.000000) 1.000000 0.000000 --->plink-------germline2: 6.19e-15 1.500055 3.85e-01 -1.920000 1.920000 ( 1.260752) 3.840000 (21.945166) 1.000000 0.000000 --->plink-------dash-----: 3.94e-18 -1599 2.01e-40 -1635 1.92 ( 1.26) 1637 ( 732) 1 1556 --->germline1---germline2: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 3.840000 (21.945166) 0.000000 0.000000 --->germline1---dash-----: 1e+00 0 1e+00 0 0 ( 0) 1637 ( 732) 0 1556 --->germline2---dash-----: 3.89e-18 -1600 1.73e-40 -1633 3.84 ( 21.9) 1637 ( 732) 0 1556 ######falsePSnps###### --->fabia-------beagle1--: 3.96e-18 -5326 2.56e-81 -5362 4478 ( 855) 9840 ( 25.3) 4519 9845 --->fabia-------beagle2--: 3.96e-18 -5326 2.56e-81 -5362 4478 ( 855) 9840 ( 25.3) 4519 9845 --->fabia-------plink----: 3.96e-18 -5324 2.63e-81 -5360 4478 ( 855) 9838 ( 25.2) 4519 9842 --->fabia-------germline1: 3.96e-18 -5326 2.56e-81 -5362 4478 ( 855) 9840 ( 25.3) 4519 9845 --->fabia-------germline2: 3.96e-18 -5321 2.65e-81 -5358 4478 ( 855) 9837 ( 33.8) 4519 9844 --->fabia-------dash-----: 3.96e-18 -3741 3.06e-55 -3725 4478 ( 855) 8204 ( 732) 4519 8236 --->beagle1-----beagle2--: 1e+00 0 1e+00 0 9840 ( 25.3) 9840 ( 25.3) 9845 9845 --->beagle1-----plink----: 8.55e-19 1.5 1.09e-27 1.92 9840 ( 25.3) 9838 ( 25.2) 9845 9842 --->beagle1-----germline1: 1e+00 0 1e+00 0 9840 ( 25.3) 9840 ( 25.3) 9845 9845 --->beagle1-----germline2: 1e+00 0 8.32e-02 3.84 9840 ( 25.3) 9837 ( 33.8) 9845 9844 --->beagle1-----dash-----: 3.9e-18 1600 1.8e-40 1637 9840 ( 25.3) 8204 ( 732) 9845 8236 --->beagle2-----plink----: 8.55e-19 1.5 1.09e-27 1.92 9840 ( 25.3) 9838 ( 25.2) 9845 9842 --->beagle2-----germline1: 1e+00 0 1e+00 0 9840 ( 25.3) 9840 ( 25.3) 9845 9845 --->beagle2-----germline2: 1e+00 0 8.32e-02 3.84 9840 ( 25.3) 9837 ( 33.8) 9845 9844 --->beagle2-----dash-----: 3.9e-18 1600 1.8e-40 1637 9840 ( 25.3) 8204 ( 732) 9845 8236 --->plink-------germline1: 8.55e-19 -1.5 1.09e-27 -1.92 9838 ( 25.2) 9840 ( 25.3) 9842 9845 --->plink-------germline2: 6.19e-15 -1.5 3.85e-01 1.92 9838 ( 25.2) 9837 ( 33.8) 9842 9844 --->plink-------dash-----: 3.94e-18 1599 2.01e-40 1635 9838 ( 25.2) 8204 ( 732) 9842 8236 --->germline1---germline2: 1e+00 0 8.32e-02 3.84 9840 ( 25.3) 9837 ( 33.8) 9845 9844 --->germline1---dash-----: 3.9e-18 1600 1.8e-40 1637 9840 ( 25.3) 8204 ( 732) 9845 8236 --->germline2---dash-----: 3.89e-18 1600 1.73e-40 1633 9837 ( 33.8) 8204 ( 732) 9844 8236 ######falseNSnps###### --->fabia-------beagle1--: 1e+00 0 1e+00 0 38.8 ( 55.4) 0 ( 0) 10.5 0 --->fabia-------beagle2--: 1e+00 0 1e+00 0 38.8 ( 55.4) 0 ( 0) 10.5 0 --->fabia-------plink----: 1e+00 0 1e+00 0 38.8 ( 55.4) 0 ( 0) 10.5 0 --->fabia-------germline1: 1e+00 0 1e+00 0 38.8 ( 55.4) 0 ( 0) 10.5 0 --->fabia-------germline2: 1e+00 0 1e+00 0 38.8 ( 55.4) 0 ( 0) 10.5 0 --->fabia-------dash-----: 6.4e-04 31 4.73e-03 19.2 38.8 ( 55.4) 19.6 ( 48.5) 10.5 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) 19.600000 (48.501380) 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) 19.600000 (48.501380) 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) 19.600000 (48.501380) 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) 19.600000 (48.501380) 0.000000 0.000000 --->germline2---dash-----: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 19.600000 (48.501380) 0.000000 0.000000 ######truePSnps###### --->fabia-------beagle1--: 7.74e-12 -57.5 3.14e-10 -38.8 121 ( 62.1) 160 ( 25.3) 145 155 --->fabia-------beagle2--: 7.74e-12 -57.5 3.14e-10 -38.8 121 ( 62.1) 160 ( 25.3) 145 155 --->fabia-------plink----: 7.74e-12 -57.5 3.14e-10 -38.8 121 ( 62.1) 160 ( 25.3) 145 155 --->fabia-------germline1: 7.74e-12 -57.5 3.14e-10 -38.8 121 ( 62.1) 160 ( 25.3) 145 155 --->fabia-------germline2: 7.74e-12 -57.5 3.14e-10 -38.8 121 ( 62.1) 160 ( 25.3) 145 155 --->fabia-------dash-----: 6.4e-04 -31 4.73e-03 -19.2 121 ( 62.1) 140 ( 52.9) 145 150 --->beagle1-----beagle2--: 1e+00 0 1e+00 0 160 ( 25.3) 160 ( 25.3) 155 155 --->beagle1-----plink----: 1e+00 0 1e+00 0 160 ( 25.3) 160 ( 25.3) 155 155 --->beagle1-----germline1: 1e+00 0 1e+00 0 160 ( 25.3) 160 ( 25.3) 155 155 --->beagle1-----germline2: 1e+00 0 1e+00 0 160 ( 25.3) 160 ( 25.3) 155 155 --->beagle1-----dash-----: 1e+00 0 1.05e-04 19.6 160 ( 25.3) 140 ( 52.9) 155 150 --->beagle2-----plink----: 1e+00 0 1e+00 0 160 ( 25.3) 160 ( 25.3) 155 155 --->beagle2-----germline1: 1e+00 0 1e+00 0 160 ( 25.3) 160 ( 25.3) 155 155 --->beagle2-----germline2: 1e+00 0 1e+00 0 160 ( 25.3) 160 ( 25.3) 155 155 --->beagle2-----dash-----: 1e+00 0 1.05e-04 19.6 160 ( 25.3) 140 ( 52.9) 155 150 --->plink-------germline1: 1e+00 0 1e+00 0 160 ( 25.3) 160 ( 25.3) 155 155 --->plink-------germline2: 1e+00 0 1e+00 0 160 ( 25.3) 160 ( 25.3) 155 155 --->plink-------dash-----: 1e+00 0 1.05e-04 19.6 160 ( 25.3) 140 ( 52.9) 155 150 --->germline1---germline2: 1e+00 0 1e+00 0 160 ( 25.3) 160 ( 25.3) 155 155 --->germline1---dash-----: 1e+00 0 1.05e-04 19.6 160 ( 25.3) 140 ( 52.9) 155 150 --->germline2---dash-----: 1e+00 0 1.05e-04 19.6 160 ( 25.3) 140 ( 52.9) 155 150 ######MatthewsSample###### --->fabia-------beagle1--: 1.88e-14 0.142593 6.59e-22 0.145638 0.140876 ( 0.114768) -0.004762 ( 0.034063) 0.191195 -0.006090 --->fabia-------beagle2--: 2.45e-14 0.141084 1.37e-22 0.147503 0.140876 ( 0.114768) -0.006627 ( 0.028026) 0.191195 -0.013464 --->fabia-------plink----: 1e+00 0.000000 1e+00 0.000000 0.140876 ( 0.114768) 0.000000 ( 0.000000) 0.191195 0.000000 --->fabia-------germline1: 7.1e-13 0.131064 2.17e-20 0.137162 0.140876 ( 0.114768) 0.003714 ( 0.025201) 0.191195 0.016742 --->fabia-------germline2: 1.79e-12 0.132443 1.46e-19 0.138179 0.140876 ( 0.114768) 0.002697 ( 0.028921) 0.191195 -0.001015 --->fabia-------dash-----: 7.47e-13 0.132972 4.42e-20 0.140131 0.140876 ( 0.114768) 0.000745 ( 0.029469) 0.191195 0.002709 --->beagle1-----beagle2--: 9.93e-01 6.46e-06 6.03e-01 0.001865 -0.004762 ( 0.034063) -0.006627 ( 0.028026) -0.006090 -0.013464 --->beagle1-----plink----: 1e+00 0.000000 1e+00 0.000000 -0.004762 ( 0.034063) 0.000000 ( 0.000000) -0.006090 0.000000 --->beagle1-----germline1: 3.64e-02 -0.008572 4.77e-02 -0.008476 -0.004762 ( 0.034063) 0.003714 ( 0.025201) -0.006090 0.016742 --->beagle1-----germline2: 1.28e-01 -0.008329 1.49e-01 -0.007458 -0.004762 ( 0.034063) 0.002697 ( 0.028921) -0.006090 -0.001015 --->beagle1-----dash-----: 2.66e-01 -0.006123 2.88e-01 -0.005507 -0.004762 ( 0.034063) 0.000745 ( 0.029469) -0.006090 0.002709 --->beagle2-----plink----: 1e+00 0.000000 1e+00 0.000000 -0.006627 ( 0.028026) 0.000000 ( 0.000000) -0.013464 0.000000 --->beagle2-----germline1: 5.85e-03 -0.011444 7.25e-03 -0.010341 -0.006627 ( 0.028026) 0.003714 ( 0.025201) -0.013464 0.016742 --->beagle2-----germline2: 1.68e-02 -0.012363 4.9e-02 -0.009324 -0.006627 ( 0.028026) 0.002697 ( 0.028921) -0.013464 -0.001015 --->beagle2-----dash-----: 9.04e-02 -0.009207 1.31e-01 -0.007372 -0.006627 ( 0.028026) 0.000745 ( 0.029469) -0.013464 0.002709 --->plink-------germline1: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.003714 ( 0.025201) 0.000000 0.016742 --->plink-------germline2: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.002697 ( 0.028921) 0.000000 -0.001015 --->plink-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.000745 ( 0.029469) 0.000000 0.002709 --->germline1---germline2: 3.74e-01 -0.002062 7.64e-01 0.001018 0.003714 ( 0.025201) 0.002697 ( 0.028921) 0.016742 -0.001015 --->germline1---dash-----: 7.04e-01 0.001235 3.85e-01 0.002969 0.003714 ( 0.025201) 0.000745 ( 0.029469) 0.016742 0.002709 --->germline2---dash-----: 8.92e-01 0.000309 3.45e-01 0.001952 0.002697 ( 0.028921) 0.000745 ( 0.029469) -0.001015 0.002709 ######F1Sample###### --->fabia-------beagle1--: 3.75e-11 0.048301 2.77e-15 0.052243 0.070758 ( 0.055846) 0.018515 ( 0.007502) 0.081136 0.018182 --->fabia-------beagle2--: 2.65e-12 0.055136 3.54e-16 0.054483 0.070758 ( 0.055846) 0.016275 ( 0.011305) 0.081136 0.012508 --->fabia-------plink----: 9.6e-11 0.048648 8.72e-15 0.050995 0.070758 ( 0.055846) 0.019763 ( 0.000276) 0.081136 0.019802 --->fabia-------germline1: 1.1e-10 0.048424 9.77e-15 0.050884 0.070758 ( 0.055846) 0.019874 ( 0.001019) 0.081136 0.020346 --->fabia-------germline2: 7.66e-11 0.048703 1.46e-14 0.050791 0.070758 ( 0.055846) 0.019967 ( 0.002678) 0.081136 0.019608 --->fabia-------dash-----: 6.68e-11 0.048113 1.05e-14 0.050974 0.070758 ( 0.055846) 0.019783 ( 0.003317) 0.081136 0.020025 --->beagle1-----beagle2--: 8.96e-02 0.001934 4.83e-02 0.002240 0.018515 ( 0.007502) 0.016275 ( 0.011305) 0.018182 0.012508 --->beagle1-----plink----: 1.31e-01 -0.001358 9.91e-02 -0.001248 0.018515 ( 0.007502) 0.019763 ( 0.000276) 0.018182 0.019802 --->beagle1-----germline1: 9.44e-02 -0.001356 7.53e-02 -0.001359 0.018515 ( 0.007502) 0.019874 ( 0.001019) 0.018182 0.020346 --->beagle1-----germline2: 1.09e-01 -0.001531 9.96e-02 -0.001452 0.018515 ( 0.007502) 0.019967 ( 0.002678) 0.018182 0.019608 --->beagle1-----dash-----: 1.77e-01 -0.001259 1.67e-01 -0.001268 0.018515 ( 0.007502) 0.019783 ( 0.003317) 0.018182 0.020025 --->beagle2-----plink----: 1.56e-02 -0.003886 2.61e-03 -0.003488 0.016275 ( 0.011305) 0.019763 ( 0.000276) 0.012508 0.019802 --->beagle2-----germline1: 7.59e-03 -0.003994 2e-03 -0.003599 0.016275 ( 0.011305) 0.019874 ( 0.001019) 0.012508 0.020346 --->beagle2-----germline2: 4.25e-03 -0.004174 3.8e-03 -0.003692 0.016275 ( 0.011305) 0.019967 ( 0.002678) 0.012508 0.019608 --->beagle2-----dash-----: 7.82e-03 -0.003886 8.26e-03 -0.003509 0.016275 ( 0.011305) 0.019783 ( 0.003317) 0.012508 0.020025 --->plink-------germline1: 2.35e-01 -0.000232 2.71e-01 -0.000112 0.019763 ( 0.000276) 0.019874 ( 0.001019) 0.019802 0.020346 --->plink-------germline2: 5.15e-01 -0.000505 4.51e-01 -0.000204 0.019763 ( 0.000276) 0.019967 ( 0.002678) 0.019802 0.019608 --->plink-------dash-----: 7.82e-01 -0.000116 1e+00 0.000000 0.019763 ( 0.000276) 0.019783 ( 0.003317) 0.019802 0.020025 --->germline1---germline2: 3.02e-01 -0.000163 1e+00 0.000000 0.019874 ( 0.001019) 0.019967 ( 0.002678) 0.020346 0.019608 --->germline1---dash-----: 9.77e-01 -4.5e-07 1e+00 0.000000 0.019874 ( 0.001019) 0.019783 ( 0.003317) 0.020346 0.020025 --->germline2---dash-----: 9.68e-01 2.85e-06 4.25e-01 0.000184 0.019967 ( 0.002678) 0.019783 ( 0.003317) 0.019608 0.020025 ######accuracySample###### --->fabia-------beagle1--: 3.95e-18 0.343670 1.18e-98 0.342910 0.907680 ( 0.026829) 0.564770 ( 0.022998) 0.906250 0.569000 --->fabia-------beagle2--: 3.95e-18 0.095044 3.13e-51 0.095360 0.907680 ( 0.026829) 0.812320 ( 0.015878) 0.906250 0.813000 --->fabia-------plink----: 3.95e-18 0.897030 5.51e-153 0.897700 0.907680 ( 0.026829) 0.009980 ( 0.000141) 0.906250 0.010000 --->fabia-------germline1: 3.95e-18 0.859785 1.15e-149 0.859360 0.907680 ( 0.026829) 0.048320 ( 0.015617) 0.906250 0.045500 --->fabia-------germline2: 3.95e-18 0.715940 4.78e-142 0.716560 0.907680 ( 0.026829) 0.191120 ( 0.011977) 0.906250 0.192000 --->fabia-------dash-----: 3.95e-18 0.657317 5.88e-124 0.656050 0.907680 ( 0.026829) 0.251630 ( 0.036313) 0.906250 0.243000 --->beagle1-----beagle2--: 3.95e-18 -0.247040 4.11e-107 -0.247550 0.564770 ( 0.022998) 0.812320 ( 0.015878) 0.569000 0.813000 --->beagle1-----plink----: 3.93e-18 0.555948 6.21e-139 0.554790 0.564770 ( 0.022998) 0.009980 ( 0.000141) 0.569000 0.010000 --->beagle1-----germline1: 3.95e-18 0.517529 2.83e-126 0.516450 0.564770 ( 0.022998) 0.048320 ( 0.015617) 0.569000 0.045500 --->beagle1-----germline2: 3.95e-18 0.375000 3.96e-113 0.373650 0.564770 ( 0.022998) 0.191120 ( 0.011977) 0.569000 0.192000 --->beagle1-----dash-----: 3.95e-18 0.316507 3.26e-84 0.313140 0.564770 ( 0.022998) 0.251630 ( 0.036313) 0.569000 0.243000 --->beagle2-----plink----: 3.92e-18 0.802938 1.19e-170 0.802340 0.812320 ( 0.015878) 0.009980 ( 0.000141) 0.813000 0.010000 --->beagle2-----germline1: 3.95e-18 0.764510 4.23e-152 0.764000 0.812320 ( 0.015878) 0.048320 ( 0.015617) 0.813000 0.045500 --->beagle2-----germline2: 3.93e-18 0.621998 6.45e-147 0.621200 0.812320 ( 0.015878) 0.191120 ( 0.011977) 0.813000 0.192000 --->beagle2-----dash-----: 3.95e-18 0.565534 3.35e-113 0.560690 0.812320 ( 0.015878) 0.251630 ( 0.036313) 0.813000 0.243000 --->plink-------germline1: 3.91e-18 -0.036996 7.02e-44 -0.038340 0.009980 ( 0.000141) 0.048320 ( 0.015617) 0.010000 0.045500 --->plink-------germline2: 3.89e-18 -0.181472 6.62e-119 -0.181140 0.009980 ( 0.000141) 0.191120 ( 0.011977) 0.010000 0.192000 --->plink-------dash-----: 3.94e-18 -0.236962 5.2e-84 -0.241650 0.009980 ( 0.000141) 0.251630 ( 0.036313) 0.010000 0.243000 --->germline1---germline2: 3.94e-18 -0.143533 2.77e-111 -0.142800 0.048320 ( 0.015617) 0.191120 ( 0.011977) 0.045500 0.192000 --->germline1---dash-----: 3.94e-18 -0.198950 1.84e-83 -0.203310 0.048320 ( 0.015617) 0.251630 ( 0.036313) 0.045500 0.243000 --->germline2---dash-----: 3.94e-18 -0.056480 4.61e-38 -0.060510 0.191120 ( 0.011977) 0.251630 ( 0.036313) 0.192000 0.243000 ######FPRSample###### --->fabia-------beagle1--: 3.96e-18 -0.343261 1.43e-98 -0.342606 0.091070 ( 0.027009) 0.433677 ( 0.022940) 0.091709 0.429798 --->fabia-------beagle2--: 3.96e-18 -0.089589 1.94e-48 -0.089990 0.091070 ( 0.027009) 0.181061 ( 0.016019) 0.091709 0.179798 --->fabia-------plink----: 3.95e-18 -0.908300 3.1e-153 -0.908950 0.091070 ( 0.027009) 1.000020 ( 0.000142) 0.091709 1.000000 --->fabia-------germline1: 3.96e-18 -0.870131 6.31e-150 -0.869889 0.091070 ( 0.027009) 0.960960 ( 0.015984) 0.091709 0.963636 --->fabia-------germline2: 3.96e-18 -0.723729 2.67e-142 -0.724223 0.091070 ( 0.027009) 0.815293 ( 0.012065) 0.091709 0.814646 --->fabia-------dash-----: 3.96e-18 -0.663480 7.49e-124 -0.662404 0.091070 ( 0.027009) 0.753475 ( 0.036966) 0.091709 0.761616 --->beagle1-----beagle2--: 3.95e-18 0.252465 9.61e-108 0.252616 0.433677 ( 0.022940) 0.181061 ( 0.016019) 0.429798 0.179798 --->beagle1-----plink----: 3.94e-18 -0.567231 6.28e-140 -0.566343 0.433677 ( 0.022940) 1.000020 ( 0.000142) 0.429798 1.000000 --->beagle1-----germline1: 3.95e-18 -0.528320 7.73e-127 -0.527283 0.433677 ( 0.022940) 0.960960 ( 0.015984) 0.429798 0.963636 --->beagle1-----germline2: 3.95e-18 -0.382795 5.29e-114 -0.381616 0.433677 ( 0.022940) 0.815293 ( 0.012065) 0.429798 0.814646 --->beagle1-----dash-----: 3.95e-18 -0.323684 1.28e-84 -0.319798 0.433677 ( 0.022940) 0.753475 ( 0.036966) 0.429798 0.761616 --->beagle2-----plink----: 3.92e-18 -0.819692 3.73e-171 -0.818960 0.181061 ( 0.016019) 1.000020 ( 0.000142) 0.179798 1.000000 --->beagle2-----germline1: 3.95e-18 -0.780772 3.62e-152 -0.779899 0.181061 ( 0.016019) 0.960960 ( 0.015984) 0.179798 0.963636 --->beagle2-----germline2: 3.94e-18 -0.634927 9.92e-148 -0.634232 0.181061 ( 0.016019) 0.815293 ( 0.012065) 0.179798 0.814646 --->beagle2-----dash-----: 3.95e-18 -0.577291 1.45e-113 -0.572414 0.181061 ( 0.016019) 0.753475 ( 0.036966) 0.179798 0.761616 --->plink-------germline1: 3.91e-18 0.037374 1.03e-43 0.039061 1.000020 ( 0.000142) 0.960960 ( 0.015984) 1.000000 0.963636 --->plink-------germline2: 3.89e-18 0.184875 1.93e-119 0.184727 1.000020 ( 0.000142) 0.815293 ( 0.012065) 1.000000 0.814646 --->plink-------dash-----: 3.94e-18 0.241430 4.18e-84 0.246545 1.000020 ( 0.000142) 0.753475 ( 0.036966) 1.000000 0.761616 --->germline1---germline2: 3.94e-18 0.146514 4.65e-111 0.145667 0.960960 ( 0.015984) 0.815293 ( 0.012065) 0.963636 0.814646 --->germline1---dash-----: 3.95e-18 0.203037 1.65e-83 0.207485 0.960960 ( 0.015984) 0.753475 ( 0.036966) 0.963636 0.761616 --->germline2---dash-----: 3.94e-18 0.057591 4e-38 0.061818 0.815293 ( 0.012065) 0.753475 ( 0.036966) 0.814646 0.761616 ######FDRSample###### --->fabia-------beagle1--: 3.34e-11 -0.025795 4.02e-15 -0.028170 0.962358 ( 0.030366) 0.990528 ( 0.003839) 0.957716 0.990698 --->fabia-------beagle2--: 2.65e-12 -0.029054 8.6e-16 -0.029051 0.962358 ( 0.030366) 0.991409 ( 0.005972) 0.957716 0.993329 --->fabia-------plink----: 7.3e-11 -0.026207 9.72e-15 -0.027662 0.962358 ( 0.030366) 0.990020 ( 0.000141) 0.957716 0.990000 --->fabia-------germline1: 8.21e-11 -0.026123 1.09e-14 -0.027602 0.962358 ( 0.030366) 0.989960 ( 0.000515) 0.957716 0.989722 --->fabia-------germline2: 5.82e-11 -0.026232 1.62e-14 -0.027536 0.962358 ( 0.030366) 0.989894 ( 0.001355) 0.957716 0.990074 --->fabia-------dash-----: 5.07e-11 -0.026000 1.19e-14 -0.027619 0.962358 ( 0.030366) 0.989977 ( 0.001681) 0.957716 0.989861 --->beagle1-----beagle2--: 2.27e-01 -0.000725 1.37e-01 -0.000881 0.990528 ( 0.003839) 0.991409 ( 0.005972) 0.990698 0.993329 --->beagle1-----plink----: 1.94e-01 0.000533 1.88e-01 0.000508 0.990528 ( 0.003839) 0.990020 ( 0.000141) 0.990698 0.990000 --->beagle1-----germline1: 1.75e-01 0.000533 1.45e-01 0.000568 0.990528 ( 0.003839) 0.989960 ( 0.000515) 0.990698 0.989722 --->beagle1-----germline2: 1.56e-01 0.000650 1.59e-01 0.000634 0.990528 ( 0.003839) 0.989894 ( 0.001355) 0.990698 0.990074 --->beagle1-----dash-----: 2.47e-01 0.000557 2.39e-01 0.000551 0.990528 ( 0.003839) 0.989977 ( 0.001681) 0.990698 0.989861 --->beagle2-----plink----: 3.48e-02 0.001599 2.19e-02 0.001389 0.991409 ( 0.005972) 0.990020 ( 0.000141) 0.993329 0.990000 --->beagle2-----germline1: 3.46e-02 0.001692 1.73e-02 0.001449 0.991409 ( 0.005972) 0.989960 ( 0.000515) 0.993329 0.989722 --->beagle2-----germline2: 2.08e-02 0.001766 2.28e-02 0.001515 0.991409 ( 0.005972) 0.989894 ( 0.001355) 0.993329 0.990074 --->beagle2-----dash-----: 3.49e-02 0.001639 3.87e-02 0.001432 0.991409 ( 0.005972) 0.989977 ( 0.001681) 0.993329 0.989861 --->plink-------germline1: 2.04e-01 0.000131 1e+00 0.000000 0.990020 ( 0.000141) 0.989960 ( 0.000515) 0.990000 0.989722 --->plink-------germline2: 1e+00 0.000000 3.6e-01 0.000126 0.990020 ( 0.000141) 0.989894 ( 0.001355) 0.990000 0.990074 --->plink-------dash-----: 6.71e-01 0.000113 1e+00 0.000000 0.990020 ( 0.000141) 0.989977 ( 0.001681) 0.990000 0.989861 --->germline1---germline2: 2.01e-01 0.000141 1e+00 0.000000 0.989960 ( 0.000515) 0.989894 ( 0.001355) 0.989722 0.990074 --->germline1---dash-----: 8.41e-01 1.5e-05 1e+00 0.000000 0.989960 ( 0.000515) 0.989977 ( 0.001681) 0.989722 0.989861 --->germline2---dash-----: 9.57e-01 2.67e-05 1e+00 0.000000 0.989894 ( 0.001355) 0.989977 ( 0.001681) 0.990074 0.989861 ######specifitySample###### --->fabia-------beagle1--: 3.96e-18 0.343206 1.44e-98 0.342586 0.908930 ( 0.027009) 0.566343 ( 0.022941) 0.908291 0.570202 --->fabia-------beagle2--: 3.96e-18 0.089614 2.03e-48 0.089970 0.908930 ( 0.027009) 0.818960 ( 0.016037) 0.908291 0.820202 --->fabia-------plink----: 1e+00 0.000000 1e+00 0.000000 0.908930 ( 0.027009) 0.000000 ( 0.000000) 0.908291 0.000000 --->fabia-------germline1: 3.96e-18 0.870041 6.4e-150 0.869869 0.908930 ( 0.027009) 0.039061 ( 0.015988) 0.908291 0.036364 --->fabia-------germline2: 3.96e-18 0.723705 2.7e-142 0.724202 0.908930 ( 0.027009) 0.184727 ( 0.012066) 0.908291 0.185354 --->fabia-------dash-----: 3.96e-18 0.663425 7.34e-124 0.662384 0.908930 ( 0.027009) 0.246545 ( 0.036955) 0.908291 0.238384 --->beagle1-----beagle2--: 3.95e-18 -0.252452 9.61e-108 -0.252616 0.566343 ( 0.022941) 0.818960 ( 0.016037) 0.570202 0.820202 --->beagle1-----plink----: 1e+00 0.000000 1e+00 0.000000 0.566343 ( 0.022941) 0.000000 ( 0.000000) 0.570202 0.000000 --->beagle1-----germline1: 3.96e-18 0.528298 7.73e-127 0.527283 0.566343 ( 0.022941) 0.039061 ( 0.015988) 0.570202 0.036364 --->beagle1-----germline2: 3.95e-18 0.382787 5.29e-114 0.381616 0.566343 ( 0.022941) 0.184727 ( 0.012066) 0.570202 0.185354 --->beagle1-----dash-----: 3.95e-18 0.323705 1.28e-84 0.319798 0.566343 ( 0.022941) 0.246545 ( 0.036955) 0.570202 0.238384 --->beagle2-----plink----: 1e+00 0.000000 1e+00 0.000000 0.818960 ( 0.016037) 0.000000 ( 0.000000) 0.820202 0.000000 --->beagle2-----germline1: 3.95e-18 0.780786 3.62e-152 0.779899 0.818960 ( 0.016037) 0.039061 ( 0.015988) 0.820202 0.036364 --->beagle2-----germline2: 3.94e-18 0.634927 9.92e-148 0.634232 0.818960 ( 0.016037) 0.184727 ( 0.012066) 0.820202 0.185354 --->beagle2-----dash-----: 3.95e-18 0.577273 1.45e-113 0.572414 0.818960 ( 0.016037) 0.246545 ( 0.036955) 0.820202 0.238384 --->plink-------germline1: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.039061 ( 0.015988) 0.000000 0.036364 --->plink-------germline2: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.184727 ( 0.012066) 0.000000 0.185354 --->plink-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.246545 ( 0.036955) 0.000000 0.238384 --->germline1---germline2: 3.95e-18 -0.146543 4.65e-111 -0.145667 0.039061 ( 0.015988) 0.184727 ( 0.012066) 0.036364 0.185354 --->germline1---dash-----: 3.95e-18 -0.203043 1.65e-83 -0.207485 0.039061 ( 0.015988) 0.246545 ( 0.036955) 0.036364 0.238384 --->germline2---dash-----: 3.94e-18 -0.057591 4e-38 -0.061818 0.184727 ( 0.012066) 0.246545 ( 0.036955) 0.185354 0.238384 ######sensitivitySample###### --->fabia-------beagle1--: 1.25e-07 0.249965 3.95e-07 0.250000 0.659000 ( 0.444289) 0.409000 ( 0.165203) 1.000000 0.400000 --->fabia-------beagle2--: 1.28e-12 0.549960 4.13e-19 0.504000 0.659000 ( 0.444289) 0.155000 ( 0.107661) 1.000000 0.100000 --->fabia-------plink----: 1e+00 0.000000 1.71e-11 -0.339000 0.659000 ( 0.444289) 0.998000 ( 0.014071) 1.000000 1.000000 --->fabia-------germline1: 1e+00 0.000000 6.43e-10 -0.306000 0.659000 ( 0.444289) 0.965000 ( 0.053889) 1.000000 1.000000 --->fabia-------germline2: 3.44e-02 -0.249986 7.38e-04 -0.165000 0.659000 ( 0.444289) 0.824000 ( 0.111119) 1.000000 0.800000 --->fabia-------dash-----: 1.16e-01 -0.149998 4.72e-02 -0.096000 0.659000 ( 0.444289) 0.755000 ( 0.129782) 1.000000 0.800000 --->beagle1-----beagle2--: 1.07e-16 0.250057 3.6e-28 0.254000 0.409000 ( 0.165203) 0.155000 ( 0.107661) 0.400000 0.100000 --->beagle1-----plink----: 2.88e-18 -0.599978 2.53e-58 -0.589000 0.409000 ( 0.165203) 0.998000 ( 0.014071) 0.400000 1.000000 --->beagle1-----germline1: 4.22e-18 -0.550020 4.98e-54 -0.556000 0.409000 ( 0.165203) 0.965000 ( 0.053889) 0.400000 1.000000 --->beagle1-----germline2: 2.15e-17 -0.449954 2.04e-33 -0.415000 0.409000 ( 0.165203) 0.824000 ( 0.111119) 0.400000 0.800000 --->beagle1-----dash-----: 4.66e-16 -0.350066 4.28e-26 -0.346000 0.409000 ( 0.165203) 0.755000 ( 0.129782) 0.400000 0.800000 --->beagle2-----plink----: 2.06e-18 -0.849970 6.59e-91 -0.843000 0.155000 ( 0.107661) 0.998000 ( 0.014071) 0.100000 1.000000 --->beagle2-----germline1: 2.33e-18 -0.800011 3.06e-84 -0.810000 0.155000 ( 0.107661) 0.965000 ( 0.053889) 0.100000 1.000000 --->beagle2-----germline2: 3.31e-18 -0.700000 2.69e-60 -0.669000 0.155000 ( 0.107661) 0.824000 ( 0.111119) 0.100000 0.800000 --->beagle2-----dash-----: 3.59e-18 -0.600058 3.4e-52 -0.600000 0.155000 ( 0.107661) 0.755000 ( 0.129782) 0.100000 0.800000 --->plink-------germline1: 1e+00 0.000000 1.35e-08 0.033000 0.998000 ( 0.014071) 0.965000 ( 0.053889) 1.000000 1.000000 --->plink-------germline2: 1.52e-16 0.199949 3.62e-28 0.174000 0.998000 ( 0.014071) 0.824000 ( 0.111119) 1.000000 0.800000 --->plink-------dash-----: 2.08e-17 0.250018 6.31e-34 0.243000 0.998000 ( 0.014071) 0.755000 ( 0.129782) 1.000000 0.800000 --->germline1---germline2: 1.67e-15 0.150070 4.67e-22 0.141000 0.965000 ( 0.053889) 0.824000 ( 0.111119) 1.000000 0.800000 --->germline1---dash-----: 3.89e-17 0.200069 1.01e-29 0.210000 0.965000 ( 0.053889) 0.755000 ( 0.129782) 1.000000 0.800000 --->germline2---dash-----: 1e+00 0.000000 2.55e-11 0.069000 0.824000 ( 0.111119) 0.755000 ( 0.129782) 0.800000 0.800000 ######trueNSample###### --->fabia-------beagle1--: 3.95e-18 1249 7.39e-133 1248 1809 ( 53.7) 561 ( 22.7) 1808 564 --->fabia-------beagle2--: 3.95e-18 997 5.21e-125 998 1809 ( 53.7) 811 ( 15.9) 1808 812 --->fabia-------plink----: 1e+00 0 1e+00 0 1809 ( 53.7) 0 ( 0) 1808 0 --->fabia-------germline1: 3.95e-18 1770 1.75e-153 1770 1809 ( 53.7) 38.7 ( 15.8) 1808 36 --->fabia-------germline2: 3.95e-18 1625 3.97e-149 1626 1809 ( 53.7) 183 ( 11.9) 1808 184 --->fabia-------dash-----: 3.95e-18 1564 1.71e-145 1565 1809 ( 53.7) 244 ( 36.6) 1808 236 --->beagle1-----beagle2--: 3.94e-18 -250 9.61e-108 -250 561 ( 22.7) 811 ( 15.9) 564 812 --->beagle1-----plink----: 1e+00 0 1e+00 0 561 ( 22.7) 0 ( 0) 564 0 --->beagle1-----germline1: 3.94e-18 523 7.73e-127 522 561 ( 22.7) 38.7 ( 15.8) 564 36 --->beagle1-----germline2: 3.94e-18 379 5.29e-114 378 561 ( 22.7) 183 ( 11.9) 564 184 --->beagle1-----dash-----: 3.95e-18 320 1.28e-84 317 561 ( 22.7) 244 ( 36.6) 564 236 --->beagle2-----plink----: 1e+00 0 1e+00 0 811 ( 15.9) 0 ( 0) 812 0 --->beagle2-----germline1: 3.94e-18 773 3.62e-152 772 811 ( 15.9) 38.7 ( 15.8) 812 36 --->beagle2-----germline2: 3.93e-18 629 9.93e-148 628 811 ( 15.9) 183 ( 11.9) 812 184 --->beagle2-----dash-----: 3.94e-18 572 1.45e-113 567 811 ( 15.9) 244 ( 36.6) 812 236 --->plink-------germline1: 1e+00 0 1e+00 0 0 ( 0) 38.7 ( 15.8) 0 36 --->plink-------germline2: 1e+00 0 1e+00 0 0 ( 0) 183 ( 11.9) 0 184 --->plink-------dash-----: 1e+00 0 1e+00 0 0 ( 0) 244 ( 36.6) 0 236 --->germline1---germline2: 3.89e-18 -145 4.65e-111 -144 38.7 ( 15.8) 183 ( 11.9) 36 184 --->germline1---dash-----: 3.94e-18 -201 1.65e-83 -205 38.7 ( 15.8) 244 ( 36.6) 36 236 --->germline2---dash-----: 3.94e-18 -57 4e-38 -61.2 183 ( 11.9) 244 ( 36.6) 184 236 ######falsePSample###### --->fabia-------beagle1--: 3.95e-18 -249 1.55e-64 -248 181 ( 53.7) 429 ( 22.7) 182 426 --->fabia-------beagle2--: 6.86e-01 3 7.3e-01 1.98 181 ( 53.7) 179 ( 15.9) 182 178 --->fabia-------plink----: 3.95e-18 -808 1.06e-118 -809 181 ( 53.7) 990 ( 0.141) 182 990 --->fabia-------germline1: 3.95e-18 -770 8.79e-118 -770 181 ( 53.7) 951 ( 15.8) 182 954 --->fabia-------germline2: 3.95e-18 -625 3.25e-108 -626 181 ( 53.7) 807 ( 11.9) 182 806 --->fabia-------dash-----: 3.95e-18 -564 7.55e-102 -565 181 ( 53.7) 746 ( 36.6) 182 754 --->beagle1-----beagle2--: 3.94e-18 250 9.61e-108 250 429 ( 22.7) 179 ( 15.9) 426 178 --->beagle1-----plink----: 3.94e-18 -562 6.28e-140 -561 429 ( 22.7) 990 ( 0.141) 426 990 --->beagle1-----germline1: 3.94e-18 -523 7.73e-127 -522 429 ( 22.7) 951 ( 15.8) 426 954 --->beagle1-----germline2: 3.94e-18 -379 5.29e-114 -378 429 ( 22.7) 807 ( 11.9) 426 806 --->beagle1-----dash-----: 3.95e-18 -320 1.28e-84 -317 429 ( 22.7) 746 ( 36.6) 426 754 --->beagle2-----plink----: 3.92e-18 -811 3.73e-171 -811 179 ( 15.9) 990 ( 0.141) 178 990 --->beagle2-----germline1: 3.94e-18 -773 3.62e-152 -772 179 ( 15.9) 951 ( 15.8) 178 954 --->beagle2-----germline2: 3.93e-18 -629 9.93e-148 -628 179 ( 15.9) 807 ( 11.9) 178 806 --->beagle2-----dash-----: 3.94e-18 -572 1.45e-113 -567 179 ( 15.9) 746 ( 36.6) 178 754 --->plink-------germline1: 3.91e-18 37 1.03e-43 38.7 990 ( 0.141) 951 ( 15.8) 990 954 --->plink-------germline2: 3.89e-18 183 1.93e-119 183 990 ( 0.141) 807 ( 11.9) 990 806 --->plink-------dash-----: 3.94e-18 239 4.18e-84 244 990 ( 0.141) 746 ( 36.6) 990 754 --->germline1---germline2: 3.89e-18 145 4.65e-111 144 951 ( 15.8) 807 ( 11.9) 954 806 --->germline1---dash-----: 3.94e-18 201 1.65e-83 205 951 ( 15.8) 746 ( 36.6) 954 754 --->germline2---dash-----: 3.94e-18 57 4e-38 61.2 807 ( 11.9) 746 ( 36.6) 806 754 ######falseNSample###### --->fabia-------beagle1--: 1.87e-07 -2.5 4.4e-07 -2.48 3.41 ( 4.44) 5.89 ( 1.65) 0 6 --->fabia-------beagle2--: 1.56e-12 -5.5 4.26e-19 -5.02 3.41 ( 4.44) 8.43 ( 1.08) 0 8 --->fabia-------plink----: 1e+00 0.000000 1e+00 0.000000 3.410000 ( 4.442892) 0.000000 ( 0.000000) 0.000000 0.000000 --->fabia-------germline1: 1e+00 0.000000 4.61e-10 3.080000 3.410000 ( 4.442892) 0.330000 ( 0.532860) 0.000000 0.000000 --->fabia-------germline2: 2.64e-02 2.5 6.23e-04 1.67 3.41 ( 4.44) 1.74 ( 1.12) 0 2 --->fabia-------dash-----: 1.03e-01 1.5 4.24e-02 0.98 3.41 ( 4.44) 2.43 ( 1.31) 0 2 --->beagle1-----beagle2--: 7.86e-17 -2.5 3.6e-28 -2.54 5.89 ( 1.65) 8.43 ( 1.08) 6 8 --->beagle1-----plink----: 1e+00 0 1e+00 0 5.89 ( 1.65) 0 ( 0) 6 0 --->beagle1-----germline1: 4.1e-18 5.5 4.98e-54 5.56 5.89 ( 1.65) 0.33 ( 0.533) 6 0 --->beagle1-----germline2: 2.06e-17 4.5 2.04e-33 4.15 5.89 ( 1.65) 1.74 ( 1.12) 6 2 --->beagle1-----dash-----: 3.75e-16 3.5 4.28e-26 3.46 5.89 ( 1.65) 2.43 ( 1.31) 6 2 --->beagle2-----plink----: 1e+00 0 1e+00 0 8.43 ( 1.08) 0 ( 0) 8 0 --->beagle2-----germline1: 2.32e-18 8 3.06e-84 8.1 8.43 ( 1.08) 0.33 ( 0.533) 8 0 --->beagle2-----germline2: 2.87e-18 7 2.69e-60 6.69 8.43 ( 1.08) 1.74 ( 1.12) 8 2 --->beagle2-----dash-----: 2.97e-18 6 3.4e-52 6 8.43 ( 1.08) 2.43 ( 1.31) 8 2 --->plink-------germline1: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.330000 ( 0.532860) 0.000000 0.000000 --->plink-------germline2: 1e+00 0 1e+00 0 0 ( 0) 1.74 ( 1.12) 0 2 --->plink-------dash-----: 1e+00 0 1e+00 0 0 ( 0) 2.43 ( 1.31) 0 2 --->germline1---germline2: 1.3e-15 -1.5 4.67e-22 -1.41 0.33 ( 0.533) 1.74 ( 1.12) 0 2 --->germline1---dash-----: 2.82e-17 -2 1.01e-29 -2.1 0.33 ( 0.533) 2.43 ( 1.31) 0 2 --->germline2---dash-----: 1e+00 0 2.55e-11 -0.69 1.74 ( 1.12) 2.43 ( 1.31) 2 2 ######truePSample###### --->fabia-------beagle1--: 1.68e-07 2.5 3.95e-07 2.5 6.59 ( 4.44) 4.09 ( 1.65) 10 4 --->fabia-------beagle2--: 1.55e-12 5.5 4.13e-19 5.04 6.59 ( 4.44) 1.55 ( 1.08) 10 1 --->fabia-------plink----: 1e+00 0 1.71e-11 -3.39 6.59 ( 4.44) 9.98 ( 0.141) 10 10 --->fabia-------germline1: 1e+00 0 6.43e-10 -3.06 6.59 ( 4.44) 9.65 ( 0.539) 10 10 --->fabia-------germline2: 3.19e-02 -2.5 7.38e-04 -1.65 6.59 ( 4.44) 8.24 ( 1.11) 10 8 --->fabia-------dash-----: 1.03e-01 -1.5 4.72e-02 -0.96 6.59 ( 4.44) 7.55 ( 1.3) 10 8 --->beagle1-----beagle2--: 7.86e-17 2.5 3.6e-28 2.54 4.09 ( 1.65) 1.55 ( 1.08) 4 1 --->beagle1-----plink----: 2.85e-18 -6 2.53e-58 -5.89 4.09 ( 1.65) 9.98 ( 0.141) 4 10 --->beagle1-----germline1: 4.1e-18 -5.5 4.98e-54 -5.56 4.09 ( 1.65) 9.65 ( 0.539) 4 10 --->beagle1-----germline2: 2.06e-17 -4.5 2.04e-33 -4.15 4.09 ( 1.65) 8.24 ( 1.11) 4 8 --->beagle1-----dash-----: 3.75e-16 -3.5 4.28e-26 -3.46 4.09 ( 1.65) 7.55 ( 1.3) 4 8 --->beagle2-----plink----: 2.06e-18 -8.5 6.59e-91 -8.43 1.55 ( 1.08) 9.98 ( 0.141) 1 10 --->beagle2-----germline1: 2.32e-18 -8 3.06e-84 -8.1 1.55 ( 1.08) 9.65 ( 0.539) 1 10 --->beagle2-----germline2: 2.87e-18 -7 2.69e-60 -6.69 1.55 ( 1.08) 8.24 ( 1.11) 1 8 --->beagle2-----dash-----: 2.97e-18 -6 3.4e-52 -6 1.55 ( 1.08) 7.55 ( 1.3) 1 8 --->plink-------germline1: 1e+00 0 1.35e-08 0.33 9.98 ( 0.141) 9.65 ( 0.539) 10 10 --->plink-------germline2: 1.52e-16 2 3.62e-28 1.74 9.98 ( 0.141) 8.24 ( 1.11) 10 8 --->plink-------dash-----: 2.08e-17 2.5 6.31e-34 2.43 9.98 ( 0.141) 7.55 ( 1.3) 10 8 --->germline1---germline2: 1.3e-15 1.5 4.67e-22 1.41 9.65 ( 0.539) 8.24 ( 1.11) 10 8 --->germline1---dash-----: 2.82e-17 2 1.01e-29 2.1 9.65 ( 0.539) 7.55 ( 1.3) 10 8 --->germline2---dash-----: 1e+00 0 2.55e-11 0.69 8.24 ( 1.11) 7.55 ( 1.3) 8 8