Results: Wilcoxon-Rank-Sum Wilcoxon-median t-test t-test-mean mean1 (std) mean2 (std) median1 median2 ######Matthews###### --->fabia-------beagle1--: 3.96e-18 0.485149 8.25e-54 0.487258 0.493336 ( 0.153874) 0.006078 ( 0.012020) 0.476888 0.004084 --->fabia-------beagle2--: 3.96e-18 0.493335 2.57e-54 0.495948 0.493336 ( 0.153874) -0.002612 ( 0.006777) 0.476888 -0.004764 --->fabia-------plink----: 3.96e-18 0.481527 1.95e-53 0.483920 0.493336 ( 0.153874) 0.009416 ( 0.001473) 0.476888 0.009632 --->fabia-------germline1: 3.96e-18 0.482420 9.96e-54 0.483944 0.493336 ( 0.153874) 0.009392 ( 0.008578) 0.476888 0.009015 --->fabia-------germline2: 3.96e-18 0.488781 4.64e-54 0.491403 0.493336 ( 0.153874) 0.001933 ( 0.008639) 0.476888 0.002196 --->fabia-------dash-----: 3.96e-18 0.494418 1.17e-54 0.496836 0.493336 ( 0.153874) -0.003500 ( 0.007615) 0.476888 -0.004890 --->beagle1-----beagle2--: 3.58e-11 0.007655 2.95e-12 0.008689 0.006078 ( 0.012020) -0.002612 ( 0.006777) 0.004084 -0.004764 --->beagle1-----plink----: 3.19e-03 -0.003862 6.6e-03 -0.003338 0.006078 ( 0.012020) 0.009416 ( 0.001473) 0.004084 0.009632 --->beagle1-----germline1: 1.01e-02 -0.003651 1.83e-02 -0.003315 0.006078 ( 0.012020) 0.009392 ( 0.008578) 0.004084 0.009015 --->beagle1-----germline2: 7.99e-03 0.003751 3.31e-03 0.004145 0.006078 ( 0.012020) 0.001933 ( 0.008639) 0.004084 0.002196 --->beagle1-----dash-----: 4.42e-09 0.009058 3.98e-10 0.009577 0.006078 ( 0.012020) -0.003500 ( 0.007615) 0.004084 -0.004890 --->beagle2-----plink----: 1.72e-16 -0.013208 1.87e-32 -0.012027 -0.002612 ( 0.006777) 0.009416 ( 0.001473) -0.004764 0.009632 --->beagle2-----germline1: 1.35e-13 -0.012289 3.48e-18 -0.012004 -0.002612 ( 0.006777) 0.009392 ( 0.008578) -0.004764 0.009015 --->beagle2-----germline2: 8.56e-05 -0.004929 7.36e-05 -0.004544 -0.002612 ( 0.006777) 0.001933 ( 0.008639) -0.004764 0.002196 --->beagle2-----dash-----: 2.66e-01 0.001206 3.78e-01 0.000888 -0.002612 ( 0.006777) -0.003500 ( 0.007615) -0.004764 -0.004890 --->plink-------germline1: 7.43e-01 0.000271 1e+00 0.000000 0.009416 ( 0.001473) 0.009392 ( 0.008578) 0.009632 0.009015 --->plink-------germline2: 3.46e-12 0.007460 8.77e-14 0.007483 0.009416 ( 0.001473) 0.001933 ( 0.008639) 0.009632 0.002196 --->plink-------dash-----: 2.17e-16 0.013693 2.54e-30 0.012915 0.009416 ( 0.001473) -0.003500 ( 0.007615) 0.009632 -0.004890 --->germline1---germline2: 1.29e-14 0.007254 1.82e-18 0.007459 0.009392 ( 0.008578) 0.001933 ( 0.008639) 0.009015 0.002196 --->germline1---dash-----: 1.63e-16 0.012708 1.11e-24 0.012892 0.009392 ( 0.008578) -0.003500 ( 0.007615) 0.009015 -0.004890 --->germline2---dash-----: 1.51e-10 0.005271 7.34e-12 0.005433 0.001933 ( 0.008639) -0.003500 ( 0.007615) 0.002196 -0.004890 ######F1###### --->fabia-------beagle1--: 3.96e-18 0.469938 2.65e-52 0.474087 0.478502 ( 0.155223) 0.004416 ( 0.003017) 0.470669 0.003864 --->fabia-------beagle2--: 3.96e-18 0.472559 1.98e-52 0.476492 0.478502 ( 0.155223) 0.002011 ( 0.002265) 0.470669 0.001359 --->fabia-------plink----: 3.96e-18 0.471259 2.52e-52 0.475339 0.478502 ( 0.155223) 0.003164 ( 0.000332) 0.470669 0.003112 --->fabia-------germline1: 3.96e-18 0.470911 2.57e-52 0.474842 0.478502 ( 0.155223) 0.003660 ( 0.000902) 0.470669 0.003561 --->fabia-------germline2: 3.96e-18 0.471228 2.43e-52 0.475249 0.478502 ( 0.155223) 0.003253 ( 0.001360) 0.470669 0.003219 --->fabia-------dash-----: 3.96e-18 0.472509 1.77e-52 0.476348 0.478502 ( 0.155223) 0.002154 ( 0.001928) 0.470669 0.001753 --->beagle1-----beagle2--: 8.26e-13 0.002169 3.13e-13 0.002405 0.004416 ( 0.003017) 0.002011 ( 0.002265) 0.003864 0.001359 --->beagle1-----plink----: 3.33e-04 0.001098 4.54e-05 0.001252 0.004416 ( 0.003017) 0.003164 ( 0.000332) 0.003864 0.003112 --->beagle1-----germline1: 2.4e-02 0.000625 1.07e-02 0.000755 0.004416 ( 0.003017) 0.003660 ( 0.000902) 0.003864 0.003561 --->beagle1-----germline2: 5.82e-04 0.001047 1.68e-04 0.001162 0.004416 ( 0.003017) 0.003253 ( 0.001360) 0.003864 0.003219 --->beagle1-----dash-----: 6.55e-09 0.002084 6.35e-10 0.002261 0.004416 ( 0.003017) 0.002154 ( 0.001928) 0.003864 0.001753 --->beagle2-----plink----: 3.64e-07 -0.001569 1.73e-06 -0.001153 0.002011 ( 0.002265) 0.003164 ( 0.000332) 0.001359 0.003112 --->beagle2-----germline1: 3.38e-09 -0.001997 6.56e-10 -0.001649 0.002011 ( 0.002265) 0.003660 ( 0.000902) 0.001359 0.003561 --->beagle2-----germline2: 2.07e-06 -0.001568 5.39e-06 -0.001242 0.002011 ( 0.002265) 0.003253 ( 0.001360) 0.001359 0.003219 --->beagle2-----dash-----: 4.08e-01 -0.000243 6.22e-01 -0.000144 0.002011 ( 0.002265) 0.002154 ( 0.001928) 0.001359 0.001753 --->plink-------germline1: 2.48e-10 -0.000485 1e-11 -0.000496 0.003164 ( 0.000332) 0.003660 ( 0.000902) 0.003112 0.003561 --->plink-------germline2: 4.86e-01 -7.2e-05 1e+00 0.000000 0.003164 ( 0.000332) 0.003253 ( 0.001360) 0.003112 0.003219 --->plink-------dash-----: 2.57e-08 0.001267 3.22e-07 0.001009 0.003164 ( 0.000332) 0.002154 ( 0.001928) 0.003112 0.001753 --->germline1---germline2: 1.04e-05 0.000378 1.17e-05 0.000407 0.003660 ( 0.000902) 0.003253 ( 0.001360) 0.003561 0.003219 --->germline1---dash-----: 6.35e-12 0.001678 8.65e-14 0.001506 0.003660 ( 0.000902) 0.002154 ( 0.001928) 0.003561 0.001753 --->germline2---dash-----: 9.63e-11 0.001170 1.18e-11 0.001099 0.003253 ( 0.001360) 0.002154 ( 0.001928) 0.003219 0.001753 ######accuracy###### --->fabia-------beagle1--: 3.96e-18 0.090379 2.45e-125 0.090592 0.998988 ( 0.000399) 0.908396 ( 0.005061) 0.999030 0.908920 --->fabia-------beagle2--: 3.96e-18 0.047672 2.94e-109 0.047656 0.998988 ( 0.000399) 0.951331 ( 0.003859) 0.999030 0.951079 --->fabia-------plink----: 3.96e-18 0.936183 1.85e-219 0.936233 0.998988 ( 0.000399) 0.062755 ( 0.006016) 0.999030 0.062811 --->fabia-------germline1: 3.96e-18 0.538987 1.23e-128 0.538570 0.998988 ( 0.000399) 0.460418 ( 0.028403) 0.999030 0.457578 --->fabia-------germline2: 3.96e-18 0.244680 8.17e-87 0.244098 0.998988 ( 0.000399) 0.754890 ( 0.034333) 0.999030 0.754294 --->fabia-------dash-----: 3.96e-18 0.098179 8.71e-57 0.098466 0.998988 ( 0.000399) 0.900521 ( 0.028711) 0.999030 0.899073 --->beagle1-----beagle2--: 3.96e-18 -0.042750 7.35e-109 -0.042935 0.908396 ( 0.005061) 0.951331 ( 0.003859) 0.908920 0.951079 --->beagle1-----plink----: 3.96e-18 0.845759 7.09e-203 0.845641 0.908396 ( 0.005061) 0.062755 ( 0.006016) 0.908920 0.062811 --->beagle1-----germline1: 3.96e-18 0.448470 7.14e-122 0.447978 0.908396 ( 0.005061) 0.460418 ( 0.028403) 0.908920 0.457578 --->beagle1-----germline2: 3.96e-18 0.154099 3.13e-68 0.153506 0.908396 ( 0.005061) 0.754890 ( 0.034333) 0.908920 0.754294 --->beagle1-----dash-----: 8.15e-03 0.007828 6.53e-03 0.007874 0.908396 ( 0.005061) 0.900521 ( 0.028711) 0.908920 0.899073 --->beagle2-----plink----: 3.96e-18 0.888449 3.61e-211 0.888577 0.951331 ( 0.003859) 0.062755 ( 0.006016) 0.951079 0.062811 --->beagle2-----germline1: 3.96e-18 0.491314 5.05e-126 0.490914 0.951331 ( 0.003859) 0.460418 ( 0.028403) 0.951079 0.457578 --->beagle2-----germline2: 3.96e-18 0.196925 2.64e-78 0.196442 0.951331 ( 0.003859) 0.754890 ( 0.034333) 0.951079 0.754294 --->beagle2-----dash-----: 9.46e-18 0.050618 1.07e-32 0.050810 0.951331 ( 0.003859) 0.900521 ( 0.028711) 0.951079 0.899073 --->plink-------germline1: 3.96e-18 -0.397406 8.68e-117 -0.397663 0.062755 ( 0.006016) 0.460418 ( 0.028403) 0.062811 0.457578 --->plink-------germline2: 3.96e-18 -0.691752 1.44e-131 -0.692135 0.062755 ( 0.006016) 0.754890 ( 0.034333) 0.062811 0.754294 --->plink-------dash-----: 3.96e-18 -0.838423 9.3e-147 -0.837767 0.062755 ( 0.006016) 0.900521 ( 0.028711) 0.062811 0.899073 --->germline1---germline2: 3.96e-18 -0.294573 1.67e-131 -0.294472 0.460418 ( 0.028403) 0.754890 ( 0.034333) 0.457578 0.754294 --->germline1---dash-----: 3.96e-18 -0.440100 2.08e-136 -0.440104 0.460418 ( 0.028403) 0.900521 ( 0.028711) 0.457578 0.899073 --->germline2---dash-----: 3.96e-18 -0.145614 3.33e-112 -0.145632 0.754890 ( 0.034333) 0.900521 ( 0.028711) 0.754294 0.899073 ######FPR###### --->fabia-------beagle1--: 3.96e-18 -0.089477 5.92e-125 -0.089732 0.000720 ( 0.000378) 0.090451 ( 0.005067) 0.000658 0.089836 --->fabia-------beagle2--: 3.96e-18 -0.046596 1.06e-108 -0.046577 0.000720 ( 0.000378) 0.047297 ( 0.003836) 0.000658 0.047449 --->fabia-------plink----: 3.96e-18 -0.937861 2.21e-219 -0.937922 0.000720 ( 0.000378) 0.938642 ( 0.006046) 0.000658 0.938584 --->fabia-------germline1: 3.96e-18 -0.539572 1.53e-128 -0.539169 0.000720 ( 0.000378) 0.539889 ( 0.028497) 0.000658 0.542831 --->fabia-------germline2: 3.96e-18 -0.244226 1.25e-86 -0.243664 0.000720 ( 0.000378) 0.244383 ( 0.034417) 0.000658 0.245043 --->fabia-------dash-----: 3.96e-18 -0.097267 2.64e-56 -0.097520 0.000720 ( 0.000378) 0.098240 ( 0.028769) 0.000658 0.099485 --->beagle1-----beagle2--: 3.96e-18 0.042956 4.28e-109 0.043154 0.090451 ( 0.005067) 0.047297 ( 0.003836) 0.089836 0.047449 --->beagle1-----plink----: 3.96e-18 -0.848299 7e-203 -0.848190 0.090451 ( 0.005067) 0.938642 ( 0.006046) 0.089836 0.938584 --->beagle1-----germline1: 3.96e-18 -0.449963 7.86e-122 -0.449437 0.090451 ( 0.005067) 0.539889 ( 0.028497) 0.089836 0.542831 --->beagle1-----germline2: 3.96e-18 -0.154602 3.23e-68 -0.153932 0.090451 ( 0.005067) 0.244383 ( 0.034417) 0.089836 0.245043 --->beagle1-----dash-----: 8.84e-03 -0.007727 7.26e-03 -0.007789 0.090451 ( 0.005067) 0.098240 ( 0.028769) 0.089836 0.099485 --->beagle2-----plink----: 3.96e-18 -0.891244 3.44e-211 -0.891345 0.047297 ( 0.003836) 0.938642 ( 0.006046) 0.047449 0.938584 --->beagle2-----germline1: 3.96e-18 -0.493025 5.25e-126 -0.492592 0.047297 ( 0.003836) 0.539889 ( 0.028497) 0.047449 0.542831 --->beagle2-----germline2: 3.96e-18 -0.197616 2.52e-78 -0.197086 0.047297 ( 0.003836) 0.244383 ( 0.034417) 0.047449 0.245043 --->beagle2-----dash-----: 9.46e-18 -0.050751 1.04e-32 -0.050943 0.047297 ( 0.003836) 0.098240 ( 0.028769) 0.047449 0.099485 --->plink-------germline1: 3.96e-18 0.398450 8.61e-117 0.398753 0.938642 ( 0.006046) 0.539889 ( 0.028497) 0.938584 0.542831 --->plink-------germline2: 3.96e-18 0.693889 1.32e-131 0.694258 0.938642 ( 0.006046) 0.244383 ( 0.034417) 0.938584 0.245043 --->plink-------dash-----: 3.96e-18 0.841128 8.41e-147 0.840401 0.938642 ( 0.006046) 0.098240 ( 0.028769) 0.938584 0.099485 --->germline1---germline2: 3.96e-18 0.295620 1.62e-131 0.295505 0.539889 ( 0.028497) 0.244383 ( 0.034417) 0.542831 0.245043 --->germline1---dash-----: 3.96e-18 0.441634 2.27e-136 0.441649 0.539889 ( 0.028497) 0.098240 ( 0.028769) 0.542831 0.099485 --->germline2---dash-----: 3.96e-18 0.146128 3.56e-112 0.146143 0.244383 ( 0.034417) 0.098240 ( 0.028769) 0.245043 0.099485 ######FDR###### --->fabia-------beagle1--: 3.96e-18 -0.400985 4.72e-43 -0.415121 0.582634 ( 0.173337) 0.997755 ( 0.001535) 0.609329 0.998035 --->fabia-------beagle2--: 3.96e-18 -0.402183 4.19e-43 -0.416328 0.582634 ( 0.173337) 0.998963 ( 0.001168) 0.609329 0.999297 --->fabia-------plink----: 3.96e-18 -0.401479 4.76e-43 -0.415781 0.582634 ( 0.173337) 0.998416 ( 0.000166) 0.609329 0.998441 --->fabia-------germline1: 3.96e-18 -0.401195 4.84e-43 -0.415531 0.582634 ( 0.173337) 0.998165 ( 0.000453) 0.609329 0.998215 --->fabia-------germline2: 3.96e-18 -0.401455 4.71e-43 -0.415729 0.582634 ( 0.173337) 0.998363 ( 0.000685) 0.609329 0.998380 --->fabia-------dash-----: 3.96e-18 -0.401952 4.12e-43 -0.416270 0.582634 ( 0.173337) 0.998904 ( 0.000983) 0.609329 0.999108 --->beagle1-----beagle2--: 1.59e-12 -0.001079 6.32e-13 -0.001207 0.997755 ( 0.001535) 0.998963 ( 0.001168) 0.998035 0.999297 --->beagle1-----plink----: 2e-04 -0.000584 2.49e-05 -0.000661 0.997755 ( 0.001535) 0.998416 ( 0.000166) 0.998035 0.998441 --->beagle1-----germline1: 1.54e-02 -0.000331 6.6e-03 -0.000410 0.997755 ( 0.001535) 0.998165 ( 0.000453) 0.998035 0.998215 --->beagle1-----germline2: 3.95e-04 -0.000545 1.1e-04 -0.000608 0.997755 ( 0.001535) 0.998363 ( 0.000685) 0.998035 0.998380 --->beagle1-----dash-----: 6.28e-09 -0.001065 6.39e-10 -0.001149 0.997755 ( 0.001535) 0.998904 ( 0.000983) 0.998035 0.999108 --->beagle2-----plink----: 1.11e-06 0.000763 9.12e-06 0.000547 0.998963 ( 0.001168) 0.998416 ( 0.000166) 0.999297 0.998441 --->beagle2-----germline1: 9.84e-09 0.000980 4.3e-09 0.000798 0.998963 ( 0.001168) 0.998165 ( 0.000453) 0.999297 0.998215 --->beagle2-----germline2: 3.72e-06 0.000751 1.65e-05 6e-04 0.998963 ( 0.001168) 0.998363 ( 0.000685) 0.999297 0.998380 --->beagle2-----dash-----: 4.57e-01 0.000122 1e+00 0.000000 0.998963 ( 0.001168) 0.998904 ( 0.000983) 0.999297 0.999108 --->plink-------germline1: 1.94e-10 0.000238 7.82e-12 0.000251 0.998416 ( 0.000166) 0.998165 ( 0.000453) 0.998441 0.998215 --->plink-------germline2: 1e+00 0.000000 1e+00 0.000000 0.998416 ( 0.000166) 0.998363 ( 0.000685) 0.998441 0.998380 --->plink-------dash-----: 6.06e-08 -0.000606 1.06e-06 -0.000489 0.998416 ( 0.000166) 0.998904 ( 0.000983) 0.998441 0.999108 --->germline1---germline2: 1.53e-05 -0.000190 2.12e-05 -0.000198 0.998165 ( 0.000453) 0.998363 ( 0.000685) 0.998215 0.998380 --->germline1---dash-----: 1.37e-11 -0.000819 4.1e-13 -0.000739 0.998165 ( 0.000453) 0.998904 ( 0.000983) 0.998215 0.999108 --->germline2---dash-----: 2.12e-10 -0.000557 4.06e-11 -0.000541 0.998363 ( 0.000685) 0.998904 ( 0.000983) 0.998380 0.999108 ######specifity###### --->fabia-------beagle1--: 3.96e-18 0.089517 5.92e-125 0.089732 0.999280 ( 0.000378) 0.909549 ( 0.005067) 0.999341 0.910164 --->fabia-------beagle2--: 3.96e-18 0.046585 1.06e-108 0.046577 0.999280 ( 0.000378) 0.952703 ( 0.003836) 0.999341 0.952551 --->fabia-------plink----: 3.96e-18 0.937856 2.21e-219 0.937922 0.999280 ( 0.000378) 0.061358 ( 0.006046) 0.999341 0.061416 --->fabia-------germline1: 3.96e-18 0.539568 1.53e-128 0.539169 0.999280 ( 0.000378) 0.460111 ( 0.028497) 0.999341 0.457169 --->fabia-------germline2: 3.96e-18 0.244221 1.25e-86 0.243664 0.999280 ( 0.000378) 0.755617 ( 0.034417) 0.999341 0.754957 --->fabia-------dash-----: 3.96e-18 0.097228 2.64e-56 0.097520 0.999280 ( 0.000378) 0.901760 ( 0.028769) 0.999341 0.900515 --->beagle1-----beagle2--: 3.96e-18 -0.042956 4.28e-109 -0.043154 0.909549 ( 0.005067) 0.952703 ( 0.003836) 0.910164 0.952551 --->beagle1-----plink----: 3.96e-18 0.848294 7e-203 0.848190 0.909549 ( 0.005067) 0.061358 ( 0.006046) 0.910164 0.061416 --->beagle1-----germline1: 3.96e-18 0.449969 7.86e-122 0.449437 0.909549 ( 0.005067) 0.460111 ( 0.028497) 0.910164 0.457169 --->beagle1-----germline2: 3.96e-18 0.154595 3.23e-68 0.153932 0.909549 ( 0.005067) 0.755617 ( 0.034417) 0.910164 0.754957 --->beagle1-----dash-----: 8.84e-03 0.007730 7.26e-03 0.007789 0.909549 ( 0.005067) 0.901760 ( 0.028769) 0.910164 0.900515 --->beagle2-----plink----: 3.96e-18 0.891241 3.44e-211 0.891344 0.952703 ( 0.003836) 0.061358 ( 0.006046) 0.952551 0.061416 --->beagle2-----germline1: 3.96e-18 0.493042 5.25e-126 0.492592 0.952703 ( 0.003836) 0.460111 ( 0.028497) 0.952551 0.457169 --->beagle2-----germline2: 3.96e-18 0.197623 2.52e-78 0.197086 0.952703 ( 0.003836) 0.755617 ( 0.034417) 0.952551 0.754957 --->beagle2-----dash-----: 9.46e-18 0.050723 1.04e-32 0.050943 0.952703 ( 0.003836) 0.901760 ( 0.028769) 0.952551 0.900515 --->plink-------germline1: 3.96e-18 -0.398451 8.61e-117 -0.398753 0.061358 ( 0.006046) 0.460111 ( 0.028497) 0.061416 0.457169 --->plink-------germline2: 3.96e-18 -0.693910 1.32e-131 -0.694258 0.061358 ( 0.006046) 0.755617 ( 0.034417) 0.061416 0.754957 --->plink-------dash-----: 3.96e-18 -0.841143 8.41e-147 -0.840401 0.061358 ( 0.006046) 0.901760 ( 0.028769) 0.061416 0.900515 --->germline1---germline2: 3.96e-18 -0.295622 1.62e-131 -0.295505 0.460111 ( 0.028497) 0.755617 ( 0.034417) 0.457169 0.754957 --->germline1---dash-----: 3.96e-18 -0.441667 2.27e-136 -0.441649 0.460111 ( 0.028497) 0.901760 ( 0.028769) 0.457169 0.900515 --->germline2---dash-----: 3.96e-18 -0.146126 3.56e-112 -0.146143 0.755617 ( 0.034417) 0.901760 ( 0.028769) 0.754957 0.900515 ######sensitivity###### --->fabia-------beagle1--: 4.6e-18 0.474546 3.24e-41 0.468037 0.603192 ( 0.183728) 0.135155 ( 0.088989) 0.608348 0.119661 --->fabia-------beagle2--: 3.96e-18 0.575409 2.86e-52 0.570258 0.603192 ( 0.183728) 0.032934 ( 0.037557) 0.608348 0.022063 --->fabia-------plink----: 3.96e-18 -0.389204 2.79e-39 -0.394048 0.603192 ( 0.183728) 0.997240 ( 0.008359) 0.608348 1.000000 --->fabia-------germline1: 1.04e-02 -0.056073 8.21e-03 -0.054379 0.603192 ( 0.183728) 0.657571 ( 0.112239) 0.608348 0.662269 --->fabia-------germline2: 1.1e-17 0.338807 1.41e-30 0.339215 0.603192 ( 0.183728) 0.263977 ( 0.099185) 0.608348 0.269769 --->fabia-------dash-----: 3.96e-18 0.533568 8.76e-50 0.533185 0.603192 ( 0.183728) 0.070007 ( 0.059100) 0.608348 0.052157 --->beagle1-----beagle2--: 1.24e-17 0.098637 4.88e-23 0.102221 0.135155 ( 0.088989) 0.032934 ( 0.037557) 0.119661 0.022063 --->beagle1-----plink----: 3.96e-18 -0.865660 8.92e-100 -0.862085 0.135155 ( 0.088989) 0.997240 ( 0.008359) 0.119661 1.000000 --->beagle1-----germline1: 3.96e-18 -0.528520 1.09e-60 -0.522416 0.135155 ( 0.088989) 0.657571 ( 0.112239) 0.119661 0.662269 --->beagle1-----germline2: 3.87e-13 -0.132329 7.97e-17 -0.128822 0.135155 ( 0.088989) 0.263977 ( 0.099185) 0.119661 0.269769 --->beagle1-----dash-----: 1.34e-07 0.063494 2.13e-08 0.065148 0.135155 ( 0.088989) 0.070007 ( 0.059100) 0.119661 0.052157 --->beagle2-----plink----: 3.92e-18 -0.970939 2.16e-141 -0.964305 0.032934 ( 0.037557) 0.997240 ( 0.008359) 0.022063 1.000000 --->beagle2-----germline1: 3.96e-18 -0.629186 7.11e-74 -0.624637 0.032934 ( 0.037557) 0.657571 ( 0.112239) 0.022063 0.662269 --->beagle2-----germline2: 4.46e-18 -0.234029 1.44e-39 -0.231043 0.032934 ( 0.037557) 0.263977 ( 0.099185) 0.022063 0.269769 --->beagle2-----dash-----: 2.25e-06 -0.032541 5.75e-07 -0.037072 0.032934 ( 0.037557) 0.070007 ( 0.059100) 0.022063 0.052157 --->plink-------germline1: 3.96e-18 0.336848 8.2e-52 0.339669 0.997240 ( 0.008359) 0.657571 ( 0.112239) 1.000000 0.662269 --->plink-------germline2: 3.96e-18 0.729824 5.16e-88 0.733263 0.997240 ( 0.008359) 0.263977 ( 0.099185) 1.000000 0.269769 --->plink-------dash-----: 3.95e-18 0.934198 2.34e-119 0.927233 0.997240 ( 0.008359) 0.070007 ( 0.059100) 1.000000 0.052157 --->germline1---germline2: 3.96e-18 0.391348 1.7e-69 0.393594 0.657571 ( 0.112239) 0.263977 ( 0.099185) 0.662269 0.269769 --->germline1---dash-----: 3.96e-18 0.587265 1.43e-76 0.587564 0.657571 ( 0.112239) 0.070007 ( 0.059100) 0.662269 0.052157 --->germline2---dash-----: 3.96e-18 0.193467 2.76e-46 0.193970 0.263977 ( 0.099185) 0.070007 ( 0.059100) 0.269769 0.052157 ######trueN###### --->fabia-------beagle1--: 3.96e-18 10886406 2.35e-231 10888733 2e+07 ( 7553) 9081921 ( 50779) 2e+07 9088137 --->fabia-------beagle2--: 3.96e-18 10457756 3.19e-241 10457832 2e+07 ( 7553) 9512823 ( 38626) 2e+07 9510262 --->fabia-------plink----: 3.96e-18 19357466 4.61e-251 19357983 2e+07 ( 7553) 612671 ( 60380) 2e+07 613277 --->fabia-------germline1: 3.96e-18 15380297 1.19e-173 15376397 2e+07 ( 7553) 4594257 ( 284653) 2e+07 4565050 --->fabia-------germline2: 3.96e-18 12430985 2.35e-156 12425752 2e+07 ( 7553) 7544903 ( 343784) 2e+07 7538606 --->fabia-------dash-----: 3.96e-18 1.1e+07 1.1e-158 1.1e+07 2e+07 ( 7553) 9e+06 ( 287330) 2e+07 8990075 --->beagle1-----beagle2--: 3.96e-18 -428985 4.3e-109 -430901 9081921 ( 50779) 9512823 ( 38626) 9088137 9510262 --->beagle1-----plink----: 3.96e-18 8470204 6.68e-203 8469250 9081921 ( 50779) 612671 ( 60380) 9088137 613277 --->beagle1-----germline1: 3.96e-18 4492753 7.67e-122 4487664 9081921 ( 50779) 4594257 ( 284653) 9088137 4565050 --->beagle1-----germline2: 3.96e-18 1543480 3.24e-68 1537019 9081921 ( 50779) 7544903 ( 343784) 9088137 7538606 --->beagle1-----dash-----: 8.84e-03 77098 7.26e-03 77769 9081921 ( 50779) 9e+06 ( 287330) 9088137 8990075 --->beagle2-----plink----: 3.96e-18 8899030 3.38e-211 8900152 9512823 ( 38626) 612671 ( 60380) 9510262 613277 --->beagle2-----germline1: 3.96e-18 4922740 5.12e-126 4918565 9512823 ( 38626) 4594257 ( 284653) 9510262 4565050 --->beagle2-----germline2: 3.96e-18 1973636 2.52e-78 1967920 9512823 ( 38626) 7544903 ( 343784) 9510262 7538606 --->beagle2-----dash-----: 9.46e-18 506770 1.04e-32 508670 9512823 ( 38626) 9e+06 ( 287330) 9510262 8990075 --->plink-------germline1: 3.96e-18 -3978518 8.84e-117 -3981586 612671 ( 60380) 4594257 ( 284653) 613277 4565050 --->plink-------germline2: 3.96e-18 -6928366 1.36e-131 -6932231 612671 ( 60380) 7544903 ( 343784) 613277 7538606 --->plink-------dash-----: 3.96e-18 -8398337 8.47e-147 -8391481 612671 ( 60380) 9e+06 ( 287330) 613277 8990075 --->germline1---germline2: 3.96e-18 -2951709 1.61e-131 -2950645 4594257 ( 284653) 7544903 ( 343784) 4565050 7538606 --->germline1---dash-----: 3.96e-18 -4409944 2.16e-136 -4409895 4594257 ( 284653) 9e+06 ( 287330) 4565050 8990075 --->germline2---dash-----: 3.96e-18 -1459008 3.43e-112 -1459250 7544903 ( 343784) 9e+06 ( 287330) 7538606 8990075 ######falseP###### --->fabia-------beagle1--: 3.96e-18 -886509 1.07e-123 -888781 14384 ( 7549) 903165 ( 50575) 13160 897023 --->fabia-------beagle2--: 3.96e-18 -457797 7.16e-107 -457880 14384 ( 7549) 472264 ( 38287) 13160 473861 --->fabia-------plink----: 3.96e-18 -9357466 8.4e-220 -9358031 14384 ( 7549) 9372415 ( 60169) 13160 9371891 --->fabia-------germline1: 3.96e-18 -5380375 1.6e-128 -5376445 14384 ( 7549) 5390829 ( 284446) 13160 5420430 --->fabia-------germline2: 3.96e-18 -2430941 1.61e-86 -2425800 14384 ( 7549) 2440184 ( 343633) 13160 2446864 --->fabia-------dash-----: 3.96e-18 -962642 5.04e-56 -966550 14384 ( 7549) 980934 ( 287269) 13160 993190 --->beagle1-----beagle2--: 3.96e-18 428986 4.3e-109 430901 903165 ( 50575) 472264 ( 38287) 897023 473861 --->beagle1-----plink----: 3.96e-18 -8470204 6.68e-203 -8469250 903165 ( 50575) 9372415 ( 60169) 897023 9371891 --->beagle1-----germline1: 3.96e-18 -4492753 7.67e-122 -4487664 903165 ( 50575) 5390829 ( 284446) 897023 5420430 --->beagle1-----germline2: 3.96e-18 -1543548 3.24e-68 -1537019 903165 ( 50575) 2440184 ( 343633) 897023 2446864 --->beagle1-----dash-----: 8.84e-03 -77087 7.26e-03 -77769 903165 ( 50575) 980934 ( 287269) 897023 993190 --->beagle2-----plink----: 3.96e-18 -8899028 3.38e-211 -8900152 472264 ( 38287) 9372415 ( 60169) 473861 9371891 --->beagle2-----germline1: 3.96e-18 -4922744 5.12e-126 -4918565 472264 ( 38287) 5390829 ( 284446) 473861 5420430 --->beagle2-----germline2: 3.96e-18 -1973627 2.52e-78 -1967920 472264 ( 38287) 2440184 ( 343633) 473861 2446864 --->beagle2-----dash-----: 9.46e-18 -506768 1.04e-32 -508670 472264 ( 38287) 980934 ( 287269) 473861 993190 --->plink-------germline1: 3.96e-18 3978522 8.84e-117 3981586 9372415 ( 60169) 5390829 ( 284446) 9371891 5420430 --->plink-------germline2: 3.96e-18 6928349 1.36e-131 6932231 9372415 ( 60169) 2440184 ( 343633) 9371891 2446864 --->plink-------dash-----: 3.96e-18 8398359 8.47e-147 8391481 9372415 ( 60169) 980934 ( 287269) 9371891 993190 --->germline1---germline2: 3.96e-18 2951713 1.61e-131 2950645 5390829 ( 284446) 2440184 ( 343633) 5420430 2446864 --->germline1---dash-----: 3.96e-18 4409932 2.16e-136 4409895 5390829 ( 284446) 980934 ( 287269) 5420430 993190 --->germline2---dash-----: 3.96e-18 1458999 3.43e-112 1459250 2440184 ( 343633) 980934 ( 287269) 2446864 993190 ######falseN###### --->fabia-------beagle1--: 4.6e-18 -7086 1.02e-39 -7010 5866 ( 2631) 12876 ( 1738) 5720 12850 --->fabia-------beagle2--: 3.96e-18 -8532 2.45e-48 -8558 5866 ( 2631) 14424 ( 1613) 5720 14298 --->fabia-------plink----: 3.96e-18 5761 2.44e-40 5826 5866 ( 2631) 39.4 ( 116) 5720 0 --->fabia-------germline1: 9.87e-03 875 4.4e-03 872 5866 ( 2631) 4994 ( 1378) 5720 4978 --->fabia-------germline2: 1.1e-17 -5065 4.11e-30 -5053 5866 ( 2631) 10919 ( 1492) 5720 10970 --->fabia-------dash-----: 3.96e-18 -7952 1.31e-46 -7986 5866 ( 2631) 13852 ( 1556) 5720 13713 --->beagle1-----beagle2--: 1.24e-17 -1463 6.09e-22 -1547 12876 ( 1738) 14424 ( 1613) 12850 14298 --->beagle1-----plink----: 3.96e-18 12804 4.65e-88 12837 12876 ( 1738) 39.4 ( 116) 12850 0 --->beagle1-----germline1: 3.96e-18 7876 2.31e-53 7882 12876 ( 1738) 4994 ( 1378) 12850 4978 --->beagle1-----germline2: 1.89e-13 1977 1.08e-16 1957 12876 ( 1738) 10919 ( 1492) 12850 10970 --->beagle1-----dash-----: 1.78e-07 -915 2.87e-08 -976 12876 ( 1738) 13852 ( 1556) 12850 13713 --->beagle2-----plink----: 3.96e-18 14343 5.25e-96 14384 14424 ( 1613) 39.4 ( 116) 14298 0 --->beagle2-----germline1: 3.96e-18 9373 1.56e-60 9429 14424 ( 1613) 4994 ( 1378) 14298 4978 --->beagle2-----germline2: 4.6e-18 3495 1.68e-36 3505 14424 ( 1613) 10919 ( 1492) 14298 10970 --->beagle2-----dash-----: 1.98e-06 484 5.55e-07 572 14424 ( 1613) 13852 ( 1556) 14298 13713 --->plink-------germline1: 3.96e-18 -4939 2.24e-58 -4955 39.4 ( 116) 4994 ( 1378) 0 4978 --->plink-------germline2: 3.96e-18 -10873 4.15e-87 -10879 39.4 ( 116) 10919 ( 1492) 0 10970 --->plink-------dash-----: 3.96e-18 -13762 1.84e-95 -13812 39.4 ( 116) 13852 ( 1556) 0 13713 --->germline1---germline2: 3.96e-18 -5846 3.65e-59 -5925 4994 ( 1378) 10919 ( 1492) 4978 10970 --->germline1---dash-----: 3.96e-18 -8764 4.08e-62 -8858 4994 ( 1378) 13852 ( 1556) 4978 13713 --->germline2---dash-----: 3.96e-18 -2878 1.12e-41 -2933 10919 ( 1492) 13852 ( 1556) 10970 13713 ######trueP###### --->fabia-------beagle1--: 4.6e-18 7135 6.91e-40 7058 9096 ( 3100) 2038 ( 1401) 8772 1802 --->fabia-------beagle2--: 3.96e-18 8592 1.73e-48 8606 9096 ( 3100) 490 ( 561) 8772 328 --->fabia-------plink----: 3.96e-18 -5735 8.16e-40 -5778 9096 ( 3100) 14874 ( 1574) 8772 14664 --->fabia-------germline1: 1.4e-02 -826 7.09e-03 -824 9096 ( 3100) 9920 ( 2470) 8772 9850 --->fabia-------germline2: 1.07e-17 5108 2.06e-30 5101 9096 ( 3100) 3995 ( 1694) 8772 4055 --->fabia-------dash-----: 3.96e-18 8007 9.1e-47 8034 9096 ( 3100) 1062 ( 944) 8772 754 --->beagle1-----beagle2--: 1.24e-17 1463 6.09e-22 1547 2038 ( 1401) 490 ( 561) 1802 328 --->beagle1-----plink----: 3.96e-18 -12804 4.65e-88 -12837 2038 ( 1401) 14874 ( 1574) 1802 14664 --->beagle1-----germline1: 3.96e-18 -7876 2.31e-53 -7882 2038 ( 1401) 9920 ( 2470) 1802 9850 --->beagle1-----germline2: 1.89e-13 -1977 1.08e-16 -1957 2038 ( 1401) 3995 ( 1694) 1802 4055 --->beagle1-----dash-----: 1.78e-07 915 2.87e-08 976 2038 ( 1401) 1062 ( 944) 1802 754 --->beagle2-----plink----: 3.96e-18 -14343 5.25e-96 -14384 490 ( 561) 14874 ( 1574) 328 14664 --->beagle2-----germline1: 3.96e-18 -9372 1.56e-60 -9429 490 ( 561) 9920 ( 2470) 328 9850 --->beagle2-----germline2: 4.6e-18 -3495 1.68e-36 -3505 490 ( 561) 3995 ( 1694) 328 4055 --->beagle2-----dash-----: 1.98e-06 -484 5.55e-07 -572 490 ( 561) 1062 ( 944) 328 754 --->plink-------germline1: 3.96e-18 4939 2.24e-58 4955 14874 ( 1574) 9920 ( 2470) 14664 9850 --->plink-------germline2: 3.96e-18 10874 4.15e-87 10879 14874 ( 1574) 3995 ( 1694) 14664 4055 --->plink-------dash-----: 3.96e-18 13762 1.84e-95 13812 14874 ( 1574) 1062 ( 944) 14664 754 --->germline1---germline2: 3.96e-18 5846 3.65e-59 5925 9920 ( 2470) 3995 ( 1694) 9850 4055 --->germline1---dash-----: 3.96e-18 8764 4.08e-62 8858 9920 ( 2470) 1062 ( 944) 9850 754 --->germline2---dash-----: 3.96e-18 2878 1.12e-41 2933 3995 ( 1694) 1062 ( 944) 4055 754 ######MatthewsSnps###### --->fabia-------beagle1--: 1e+00 0.000000 1e+00 0.000000 0.252735 ( 0.117474) 0.000000 ( 0.000000) 0.266222 0.000000 --->fabia-------beagle2--: 1e+00 0.000000 1e+00 0.000000 0.252735 ( 0.117474) 0.000000 ( 0.000000) 0.266222 0.000000 --->fabia-------plink----: 1.24e-17 0.253296 2.35e-38 0.247469 0.252735 ( 0.117474) 0.005266 ( 0.001598) 0.266222 0.004447 --->fabia-------germline1: 1e+00 0.000000 1e+00 0.000000 0.252735 ( 0.117474) 0.000000 ( 0.000000) 0.266222 0.000000 --->fabia-------germline2: 1.17e-17 0.256712 6.53e-39 0.251351 0.252735 ( 0.117474) 0.001384 ( 0.007918) 0.266222 0.000000 --->fabia-------dash-----: 6.63e-17 0.237273 8.17e-23 0.248180 0.252735 ( 0.117474) 0.004555 ( 0.161669) 0.266222 0.047629 --->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) 0.005266 ( 0.001598) 0.000000 0.004447 --->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) 0.001384 ( 0.007918) 0.000000 0.000000 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.004555 ( 0.161669) 0.000000 0.047629 --->beagle2-----plink----: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.005266 ( 0.001598) 0.000000 0.004447 --->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) 0.001384 ( 0.007918) 0.000000 0.000000 --->beagle2-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.004555 ( 0.161669) 0.000000 0.047629 --->plink-------germline1: 1e+00 0.000000 1e+00 0.000000 0.005266 ( 0.001598) 0.000000 ( 0.000000) 0.004447 0.000000 --->plink-------germline2: 1.88e-14 0.005091 7.27e-06 0.003882 0.005266 ( 0.001598) 0.001384 ( 0.007918) 0.004447 0.000000 --->plink-------dash-----: 6.74e-01 -0.008217 9.65e-01 0.000711 0.005266 ( 0.001598) 0.004555 ( 0.161669) 0.004447 0.047629 --->germline1---germline2: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.001384 ( 0.007918) 0.000000 0.000000 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.004555 ( 0.161669) 0.000000 0.047629 --->germline2---dash-----: 4.82e-01 -0.012595 8.45e-01 -0.003171 0.001384 ( 0.007918) 0.004555 ( 0.161669) 0.000000 0.047629 ######F1Snps###### --->fabia-------beagle1--: 6.63e-17 0.112472 1.02e-29 0.111445 0.356350 ( 0.079106) 0.244905 ( 0.027725) 0.360373 0.247536 --->fabia-------beagle2--: 6.63e-17 0.112472 1.02e-29 0.111445 0.356350 ( 0.079106) 0.244905 ( 0.027725) 0.360373 0.247536 --->fabia-------plink----: 6.63e-17 0.112410 1.05e-29 0.111405 0.356350 ( 0.079106) 0.244945 ( 0.027725) 0.360373 0.247612 --->fabia-------germline1: 6.63e-17 0.112472 1.02e-29 0.111445 0.356350 ( 0.079106) 0.244905 ( 0.027725) 0.360373 0.247536 --->fabia-------germline2: 6.63e-17 0.112327 1.06e-29 0.111360 0.356350 ( 0.079106) 0.244989 ( 0.027739) 0.360373 0.247536 --->fabia-------dash-----: 6.44e-17 0.116219 9.75e-27 0.116344 0.356350 ( 0.079106) 0.240006 ( 0.046683) 0.360373 0.239724 --->beagle1-----beagle2--: 1e+00 0.000000 1e+00 0.000000 0.244905 ( 0.027725) 0.244905 ( 0.027725) 0.247536 0.247536 --->beagle1-----plink----: 1e+00 0.000000 1e+00 0.000000 0.244905 ( 0.027725) 0.244945 ( 0.027725) 0.247536 0.247612 --->beagle1-----germline1: 1e+00 0.000000 1e+00 0.000000 0.244905 ( 0.027725) 0.244905 ( 0.027725) 0.247536 0.247536 --->beagle1-----germline2: 1e+00 0.000000 1e+00 0.000000 0.244905 ( 0.027725) 0.244989 ( 0.027739) 0.247536 0.247536 --->beagle1-----dash-----: 6.17e-01 0.002434 2.57e-01 0.004899 0.244905 ( 0.027725) 0.240006 ( 0.046683) 0.247536 0.239724 --->beagle2-----plink----: 1e+00 0.000000 1e+00 0.000000 0.244905 ( 0.027725) 0.244945 ( 0.027725) 0.247536 0.247612 --->beagle2-----germline1: 1e+00 0.000000 1e+00 0.000000 0.244905 ( 0.027725) 0.244905 ( 0.027725) 0.247536 0.247536 --->beagle2-----germline2: 1e+00 0.000000 1e+00 0.000000 0.244905 ( 0.027725) 0.244989 ( 0.027739) 0.247536 0.247536 --->beagle2-----dash-----: 6.17e-01 0.002434 2.57e-01 0.004899 0.244905 ( 0.027725) 0.240006 ( 0.046683) 0.247536 0.239724 --->plink-------germline1: 1e+00 0.000000 1e+00 0.000000 0.244945 ( 0.027725) 0.244905 ( 0.027725) 0.247612 0.247536 --->plink-------germline2: 1e+00 0.000000 1e+00 0.000000 0.244945 ( 0.027725) 0.244989 ( 0.027739) 0.247612 0.247536 --->plink-------dash-----: 6.12e-01 0.002441 2.53e-01 0.004939 0.244945 ( 0.027725) 0.240006 ( 0.046683) 0.247612 0.239724 --->germline1---germline2: 1e+00 0.000000 1e+00 0.000000 0.244905 ( 0.027725) 0.244989 ( 0.027739) 0.247536 0.247536 --->germline1---dash-----: 6.17e-01 0.002434 2.57e-01 0.004899 0.244905 ( 0.027725) 0.240006 ( 0.046683) 0.247536 0.239724 --->germline2---dash-----: 6.07e-01 0.002473 2.49e-01 0.004983 0.244989 ( 0.027739) 0.240006 ( 0.046683) 0.247536 0.239724 ######accuracySnps###### --->fabia-------beagle1--: 3.96e-18 0.448804 1.96e-76 0.447677 0.587497 ( 0.083357) 0.139820 ( 0.017925) 0.604050 0.141250 --->fabia-------beagle2--: 3.96e-18 0.448804 1.96e-76 0.447677 0.587497 ( 0.083357) 0.139820 ( 0.017925) 0.604050 0.141250 --->fabia-------plink----: 3.96e-18 0.448659 2.1e-76 0.447489 0.587497 ( 0.083357) 0.140008 ( 0.017909) 0.604050 0.141500 --->fabia-------germline1: 3.96e-18 0.448804 1.96e-76 0.447677 0.587497 ( 0.083357) 0.139820 ( 0.017925) 0.604050 0.141250 --->fabia-------germline2: 3.96e-18 0.448597 1.93e-76 0.447293 0.587497 ( 0.083357) 0.140204 ( 0.018087) 0.604050 0.141650 --->fabia-------dash-----: 3.96e-18 0.320608 2.37e-52 0.323657 0.587497 ( 0.083357) 0.263840 ( 0.067613) 0.604050 0.269550 --->beagle1-----beagle2--: 1e+00 0.000000 1e+00 0.000000 0.139820 ( 0.017925) 0.139820 ( 0.017925) 0.141250 0.141250 --->beagle1-----plink----: 2.68e-18 -0.000193 4.85e-26 -0.000188 0.139820 ( 0.017925) 0.140008 ( 0.017909) 0.141250 0.141500 --->beagle1-----germline1: 1e+00 0.000000 1e+00 0.000000 0.139820 ( 0.017925) 0.139820 ( 0.017925) 0.141250 0.141250 --->beagle1-----germline2: 1e+00 0.000000 8.32e-02 -0.000384 0.139820 ( 0.017925) 0.140204 ( 0.018087) 0.141250 0.141650 --->beagle1-----dash-----: 7.44e-18 -0.124838 8.45e-33 -0.124020 0.139820 ( 0.017925) 0.263840 ( 0.067613) 0.141250 0.269550 --->beagle2-----plink----: 2.68e-18 -0.000193 4.85e-26 -0.000188 0.139820 ( 0.017925) 0.140008 ( 0.017909) 0.141250 0.141500 --->beagle2-----germline1: 1e+00 0.000000 1e+00 0.000000 0.139820 ( 0.017925) 0.139820 ( 0.017925) 0.141250 0.141250 --->beagle2-----germline2: 1e+00 0.000000 8.32e-02 -0.000384 0.139820 ( 0.017925) 0.140204 ( 0.018087) 0.141250 0.141650 --->beagle2-----dash-----: 7.44e-18 -0.124838 8.45e-33 -0.124020 0.139820 ( 0.017925) 0.263840 ( 0.067613) 0.141250 0.269550 --->plink-------germline1: 2.68e-18 0.000193 4.85e-26 0.000188 0.140008 ( 0.017909) 0.139820 ( 0.017925) 0.141500 0.141250 --->plink-------germline2: 1.45e-14 0.000139 3.77e-01 -0.000196 0.140008 ( 0.017909) 0.140204 ( 0.018087) 0.141500 0.141650 --->plink-------dash-----: 7.44e-18 -0.124604 9.53e-33 -0.123832 0.140008 ( 0.017909) 0.263840 ( 0.067613) 0.141500 0.269550 --->germline1---germline2: 1e+00 0.000000 8.32e-02 -0.000384 0.139820 ( 0.017925) 0.140204 ( 0.018087) 0.141250 0.141650 --->germline1---dash-----: 7.44e-18 -0.124838 8.45e-33 -0.124020 0.139820 ( 0.017925) 0.263840 ( 0.067613) 0.141250 0.269550 --->germline2---dash-----: 7.44e-18 -0.124618 1.15e-32 -0.123636 0.140204 ( 0.018087) 0.263840 ( 0.067613) 0.141650 0.269550 ######FPRSnps###### --->fabia-------beagle1--: 3.96e-18 -0.097781 6.36e-79 -0.097857 0.079482 ( 0.017159) 0.177340 ( 0.003337) 0.076091 0.176885 --->fabia-------beagle2--: 3.96e-18 -0.097781 6.36e-79 -0.097857 0.079482 ( 0.017159) 0.177340 ( 0.003337) 0.076091 0.176885 --->fabia-------plink----: 3.96e-18 -0.097750 6.81e-79 -0.097819 0.079482 ( 0.017159) 0.177301 ( 0.003334) 0.076091 0.176844 --->fabia-------germline1: 3.96e-18 -0.097781 6.36e-79 -0.097857 0.079482 ( 0.017159) 0.177340 ( 0.003337) 0.076091 0.176885 --->fabia-------germline2: 3.96e-18 -0.097764 6.15e-79 -0.097778 0.079482 ( 0.017159) 0.177260 ( 0.003381) 0.076091 0.176785 --->fabia-------dash-----: 3.96e-18 -0.067302 1.31e-52 -0.067547 0.079482 ( 0.017159) 0.147030 ( 0.014232) 0.076091 0.148848 --->beagle1-----beagle2--: 1e+00 0.000000 1e+00 0.000000 0.177340 ( 0.003337) 0.177340 ( 0.003337) 0.176885 0.176885 --->beagle1-----plink----: 1e+00 0.000000 1e+00 0.000000 0.177340 ( 0.003337) 0.177301 ( 0.003334) 0.176885 0.176844 --->beagle1-----germline1: 1e+00 0.000000 1e+00 0.000000 0.177340 ( 0.003337) 0.177340 ( 0.003337) 0.176885 0.176885 --->beagle1-----germline2: 1e+00 0.000000 1e+00 0.000000 0.177340 ( 0.003337) 0.177260 ( 0.003381) 0.176885 0.176785 --->beagle1-----dash-----: 3.96e-18 0.029921 7.93e-39 0.030310 0.177340 ( 0.003337) 0.147030 ( 0.014232) 0.176885 0.148848 --->beagle2-----plink----: 1e+00 0.000000 1e+00 0.000000 0.177340 ( 0.003337) 0.177301 ( 0.003334) 0.176885 0.176844 --->beagle2-----germline1: 1e+00 0.000000 1e+00 0.000000 0.177340 ( 0.003337) 0.177340 ( 0.003337) 0.176885 0.176885 --->beagle2-----germline2: 1e+00 0.000000 1e+00 0.000000 0.177340 ( 0.003337) 0.177260 ( 0.003381) 0.176885 0.176785 --->beagle2-----dash-----: 3.96e-18 0.029921 7.93e-39 0.030310 0.177340 ( 0.003337) 0.147030 ( 0.014232) 0.176885 0.148848 --->plink-------germline1: 1e+00 0.000000 1e+00 0.000000 0.177301 ( 0.003334) 0.177340 ( 0.003337) 0.176844 0.176885 --->plink-------germline2: 1e+00 0.000000 1e+00 0.000000 0.177301 ( 0.003334) 0.177260 ( 0.003381) 0.176844 0.176785 --->plink-------dash-----: 3.96e-18 0.029884 8.92e-39 0.030271 0.177301 ( 0.003334) 0.147030 ( 0.014232) 0.176844 0.148848 --->germline1---germline2: 1e+00 0.000000 1e+00 0.000000 0.177340 ( 0.003337) 0.177260 ( 0.003381) 0.176885 0.176785 --->germline1---dash-----: 3.96e-18 0.029921 7.93e-39 0.030310 0.177340 ( 0.003337) 0.147030 ( 0.014232) 0.176885 0.148848 --->germline2---dash-----: 3.96e-18 0.029824 9.97e-39 0.030231 0.177260 ( 0.003381) 0.147030 ( 0.014232) 0.176785 0.148848 ######FDRSnps###### --->fabia-------beagle1--: 1.13e-17 -0.090827 5.45e-33 -0.091353 0.768827 ( 0.058864) 0.860180 ( 0.017925) 0.768565 0.858750 --->fabia-------beagle2--: 1.13e-17 -0.090827 5.45e-33 -0.091353 0.768827 ( 0.058864) 0.860180 ( 0.017925) 0.768565 0.858750 --->fabia-------plink----: 1.13e-17 -0.090796 5.58e-33 -0.091327 0.768827 ( 0.058864) 0.860154 ( 0.017926) 0.768565 0.858701 --->fabia-------germline1: 1.13e-17 -0.090827 5.45e-33 -0.091353 0.768827 ( 0.058864) 0.860180 ( 0.017925) 0.768565 0.858750 --->fabia-------germline2: 1.13e-17 -0.090785 5.57e-33 -0.091298 0.768827 ( 0.058864) 0.860125 ( 0.017935) 0.768565 0.858750 --->fabia-------dash-----: 1.03e-17 -0.089323 2.25e-29 -0.090639 0.768827 ( 0.058864) 0.859466 ( 0.028428) 0.768565 0.860043 --->beagle1-----beagle2--: 1e+00 0.000000 1e+00 0.000000 0.860180 ( 0.017925) 0.860180 ( 0.017925) 0.858750 0.858750 --->beagle1-----plink----: 1e+00 0.000000 1e+00 0.000000 0.860180 ( 0.017925) 0.860154 ( 0.017926) 0.858750 0.858701 --->beagle1-----germline1: 1e+00 0.000000 1e+00 0.000000 0.860180 ( 0.017925) 0.860180 ( 0.017925) 0.858750 0.858750 --->beagle1-----germline2: 1e+00 0.000000 1e+00 0.000000 0.860180 ( 0.017925) 0.860125 ( 0.017935) 0.858750 0.858750 --->beagle1-----dash-----: 4.22e-01 0.001942 7.76e-01 0.000714 0.860180 ( 0.017925) 0.859466 ( 0.028428) 0.858750 0.860043 --->beagle2-----plink----: 1e+00 0.000000 1e+00 0.000000 0.860180 ( 0.017925) 0.860154 ( 0.017926) 0.858750 0.858701 --->beagle2-----germline1: 1e+00 0.000000 1e+00 0.000000 0.860180 ( 0.017925) 0.860180 ( 0.017925) 0.858750 0.858750 --->beagle2-----germline2: 1e+00 0.000000 1e+00 0.000000 0.860180 ( 0.017925) 0.860125 ( 0.017935) 0.858750 0.858750 --->beagle2-----dash-----: 4.22e-01 0.001942 7.76e-01 0.000714 0.860180 ( 0.017925) 0.859466 ( 0.028428) 0.858750 0.860043 --->plink-------germline1: 1e+00 0.000000 1e+00 0.000000 0.860154 ( 0.017926) 0.860180 ( 0.017925) 0.858701 0.858750 --->plink-------germline2: 1e+00 0.000000 1e+00 0.000000 0.860154 ( 0.017926) 0.860125 ( 0.017935) 0.858701 0.858750 --->plink-------dash-----: 4.28e-01 0.001922 7.84e-01 0.000688 0.860154 ( 0.017926) 0.859466 ( 0.028428) 0.858701 0.860043 --->germline1---germline2: 1e+00 0.000000 1e+00 0.000000 0.860180 ( 0.017925) 0.860125 ( 0.017935) 0.858750 0.858750 --->germline1---dash-----: 4.22e-01 0.001942 7.76e-01 0.000714 0.860180 ( 0.017925) 0.859466 ( 0.028428) 0.858750 0.860043 --->germline2---dash-----: 4.36e-01 0.001901 7.93e-01 0.000659 0.860125 ( 0.017935) 0.859466 ( 0.028428) 0.858750 0.860043 ######specifitySnps###### --->fabia-------beagle1--: 1e+00 0.000000 1e+00 0.000000 0.097857 ( 0.016597) 0.000000 ( 0.000000) 0.100765 0.000000 --->fabia-------beagle2--: 1e+00 0.000000 1e+00 0.000000 0.097857 ( 0.016597) 0.000000 ( 0.000000) 0.100765 0.000000 --->fabia-------plink----: 3.96e-18 0.097733 6.81e-79 0.097819 0.097857 ( 0.016597) 3.88e-05 ( 2.69e-05) 0.100765 2.07e-05 --->fabia-------germline1: 1e+00 0.000000 1e+00 0.000000 0.097857 ( 0.016597) 0.000000 ( 0.000000) 0.100765 0.000000 --->fabia-------germline2: 3.96e-18 0.097755 6.15e-79 0.097778 0.097857 ( 0.016597) 7.9e-05 ( 0.000452) 0.100765 0.000000 --->fabia-------dash-----: 3.96e-18 0.067310 1.31e-52 0.067547 0.097857 ( 0.016597) 0.030310 ( 0.014199) 0.100765 0.028967 --->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) 3.88e-05 ( 2.69e-05) 0.000000 2.07e-05 --->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) 7.9e-05 ( 0.000452) 0.000000 0.000000 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.030310 ( 0.014199) 0.000000 0.028967 --->beagle2-----plink----: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 3.88e-05 ( 2.69e-05) 0.000000 2.07e-05 --->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) 7.9e-05 ( 0.000452) 0.000000 0.000000 --->beagle2-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.030310 ( 0.014199) 0.000000 0.028967 --->plink-------germline1: 1e+00 0.000000 1e+00 0.000000 3.88e-05 ( 2.69e-05) 0.000000 ( 0.000000) 2.07e-05 0.000000 --->plink-------germline2: 1e+00 0.000000 1e+00 0.000000 3.88e-05 ( 2.69e-05) 7.9e-05 ( 0.000452) 2.07e-05 0.000000 --->plink-------dash-----: 3.96e-18 -0.029865 8.92e-39 -0.030271 3.88e-05 ( 2.69e-05) 0.030310 ( 0.014199) 2.07e-05 0.028967 --->germline1---germline2: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 7.9e-05 ( 0.000452) 0.000000 0.000000 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.030310 ( 0.014199) 0.000000 0.028967 --->germline2---dash-----: 3.96e-18 -0.029829 9.97e-39 -0.030231 7.9e-05 ( 0.000452) 0.030310 ( 0.014199) 0.000000 0.028967 ######sensitivitySnps###### --->fabia-------beagle1--: 3.96e-18 -0.164525 4.07e-23 -0.182452 0.752986 ( 0.145958) 0.935438 ( 0.087546) 0.772090 0.994408 --->fabia-------beagle2--: 3.96e-18 -0.164525 4.07e-23 -0.182452 0.752986 ( 0.145958) 0.935438 ( 0.087546) 0.772090 0.994408 --->fabia-------plink----: 3.96e-18 -0.164525 4.07e-23 -0.182452 0.752986 ( 0.145958) 0.935438 ( 0.087546) 0.772090 0.994408 --->fabia-------germline1: 3.96e-18 -0.164525 4.07e-23 -0.182452 0.752986 ( 0.145958) 0.935438 ( 0.087546) 0.772090 0.994408 --->fabia-------germline2: 3.96e-18 -0.164525 4.07e-23 -0.182452 0.752986 ( 0.145958) 0.935438 ( 0.087546) 0.772090 0.994408 --->fabia-------dash-----: 1.99e-01 -0.025788 1.49e-01 -0.027724 0.752986 ( 0.145958) 0.780710 ( 0.156570) 0.772090 0.785504 --->beagle1-----beagle2--: 1e+00 0.000000 1e+00 0.000000 0.935438 ( 0.087546) 0.935438 ( 0.087546) 0.994408 0.994408 --->beagle1-----plink----: 1e+00 0.000000 1e+00 0.000000 0.935438 ( 0.087546) 0.935438 ( 0.087546) 0.994408 0.994408 --->beagle1-----germline1: 1e+00 0.000000 1e+00 0.000000 0.935438 ( 0.087546) 0.935438 ( 0.087546) 0.994408 0.994408 --->beagle1-----germline2: 1e+00 0.000000 1e+00 0.000000 0.935438 ( 0.087546) 0.935438 ( 0.087546) 0.994408 0.994408 --->beagle1-----dash-----: 3.64e-13 0.207289 2.59e-16 0.154728 0.935438 ( 0.087546) 0.780710 ( 0.156570) 0.994408 0.785504 --->beagle2-----plink----: 1e+00 0.000000 1e+00 0.000000 0.935438 ( 0.087546) 0.935438 ( 0.087546) 0.994408 0.994408 --->beagle2-----germline1: 1e+00 0.000000 1e+00 0.000000 0.935438 ( 0.087546) 0.935438 ( 0.087546) 0.994408 0.994408 --->beagle2-----germline2: 1e+00 0.000000 1e+00 0.000000 0.935438 ( 0.087546) 0.935438 ( 0.087546) 0.994408 0.994408 --->beagle2-----dash-----: 3.64e-13 0.207289 2.59e-16 0.154728 0.935438 ( 0.087546) 0.780710 ( 0.156570) 0.994408 0.785504 --->plink-------germline1: 1e+00 0.000000 1e+00 0.000000 0.935438 ( 0.087546) 0.935438 ( 0.087546) 0.994408 0.994408 --->plink-------germline2: 1e+00 0.000000 1e+00 0.000000 0.935438 ( 0.087546) 0.935438 ( 0.087546) 0.994408 0.994408 --->plink-------dash-----: 3.64e-13 0.207289 2.59e-16 0.154728 0.935438 ( 0.087546) 0.780710 ( 0.156570) 0.994408 0.785504 --->germline1---germline2: 1e+00 0.000000 1e+00 0.000000 0.935438 ( 0.087546) 0.935438 ( 0.087546) 0.994408 0.994408 --->germline1---dash-----: 3.64e-13 0.207289 2.59e-16 0.154728 0.935438 ( 0.087546) 0.780710 ( 0.156570) 0.994408 0.785504 --->germline2---dash-----: 3.64e-13 0.207289 2.59e-16 0.154728 0.935438 ( 0.087546) 0.780710 ( 0.156570) 0.994408 0.785504 ######trueNSnps###### --->fabia-------beagle1--: 1e+00 0 1e+00 0 4746 ( 803) 0 ( 0) 4878 0 --->fabia-------beagle2--: 1e+00 0 1e+00 0 4746 ( 803) 0 ( 0) 4878 0 --->fabia-------plink----: 3.96e-18 4740 5.13e-79 4744 4746 ( 803) 1.88 ( 1.3) 4878 1 --->fabia-------germline1: 1e+00 0 1e+00 0 4746 ( 803) 0 ( 0) 4878 0 --->fabia-------germline2: 3.96e-18 4742 4.61e-79 4742 4746 ( 803) 3.84 ( 21.9) 4878 0 --->fabia-------dash-----: 3.96e-18 3260 9.82e-53 3275 4746 ( 803) 1471 ( 690) 4878 1408 --->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) 1.880000 ( 1.304847) 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) 1471 ( 690) 0 1408 --->beagle2-----plink----: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 1.880000 ( 1.304847) 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) 1471 ( 690) 0 1408 --->plink-------germline1: 1e+00 0.000000 1e+00 0.000000 1.880000 ( 1.304847) 0.000000 ( 0.000000) 1.000000 0.000000 --->plink-------germline2: 6.06e-15 1.500051 3.77e-01 -1.960000 1.880000 ( 1.304847) 3.840000 (21.945166) 1.000000 0.000000 --->plink-------dash-----: 3.95e-18 -1450 1e-38 -1469 1.88 ( 1.3) 1471 ( 690) 1 1408 --->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) 1471 ( 690) 0 1408 --->germline2---dash-----: 3.94e-18 -1447 1.12e-38 -1467 3.84 ( 21.9) 1471 ( 690) 0 1408 ######falsePSnps###### --->fabia-------beagle1--: 3.96e-18 -4743 4.79e-79 -4746 3856 ( 836) 8602 ( 179) 3695 8588 --->fabia-------beagle2--: 3.96e-18 -4743 4.79e-79 -4746 3856 ( 836) 8602 ( 179) 3695 8588 --->fabia-------plink----: 3.96e-18 -4740 5.13e-79 -4744 3856 ( 836) 8600 ( 179) 3695 8585 --->fabia-------germline1: 3.96e-18 -4743 4.79e-79 -4746 3856 ( 836) 8602 ( 179) 3695 8588 --->fabia-------germline2: 3.96e-18 -4742 4.61e-79 -4742 3856 ( 836) 8598 ( 181) 3695 8584 --->fabia-------dash-----: 3.96e-18 -3260 9.82e-53 -3275 3856 ( 836) 7131 ( 688) 3695 7214 --->beagle1-----beagle2--: 1e+00 0 1e+00 0 8602 ( 179) 8602 ( 179) 8588 8588 --->beagle1-----plink----: 7.75e-19 1.5 4.85e-26 1.88 8602 ( 179) 8600 ( 179) 8588 8585 --->beagle1-----germline1: 1e+00 0 1e+00 0 8602 ( 179) 8602 ( 179) 8588 8588 --->beagle1-----germline2: 1e+00 0 8.32e-02 3.84 8602 ( 179) 8598 ( 181) 8588 8584 --->beagle1-----dash-----: 3.94e-18 1452 8.91e-39 1471 8602 ( 179) 7131 ( 688) 8588 7214 --->beagle2-----plink----: 7.75e-19 1.5 4.85e-26 1.88 8602 ( 179) 8600 ( 179) 8588 8585 --->beagle2-----germline1: 1e+00 0 1e+00 0 8602 ( 179) 8602 ( 179) 8588 8588 --->beagle2-----germline2: 1e+00 0 8.32e-02 3.84 8602 ( 179) 8598 ( 181) 8588 8584 --->beagle2-----dash-----: 3.94e-18 1452 8.91e-39 1471 8602 ( 179) 7131 ( 688) 8588 7214 --->plink-------germline1: 7.75e-19 -1.5 4.85e-26 -1.88 8600 ( 179) 8602 ( 179) 8585 8588 --->plink-------germline2: 6.06e-15 -1.5 3.77e-01 1.96 8600 ( 179) 8598 ( 181) 8585 8584 --->plink-------dash-----: 3.95e-18 1450 1e-38 1469 8600 ( 179) 7131 ( 688) 8585 7214 --->germline1---germline2: 1e+00 0 8.32e-02 3.84 8602 ( 179) 8598 ( 181) 8588 8584 --->germline1---dash-----: 3.94e-18 1452 8.91e-39 1471 8602 ( 179) 7131 ( 688) 8588 7214 --->germline2---dash-----: 3.94e-18 1447 1.12e-38 1467 8598 ( 181) 7131 ( 688) 8584 7214 ######falseNSnps###### --->fabia-------beagle1--: 1e+00 0 1e+00 0 269 ( 206) 0 ( 0) 217 0 --->fabia-------beagle2--: 1e+00 0 1e+00 0 269 ( 206) 0 ( 0) 217 0 --->fabia-------plink----: 1e+00 0 1e+00 0 269 ( 206) 0 ( 0) 217 0 --->fabia-------germline1: 1e+00 0 1e+00 0 269 ( 206) 0 ( 0) 217 0 --->fabia-------germline2: 1e+00 0 1e+00 0 269 ( 206) 0 ( 0) 217 0 --->fabia-------dash-----: 2.26e-01 35.5 1.69e-01 38.6 269 ( 206) 230 ( 231) 217 200 --->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 1e+00 0 0 ( 0) 230 ( 231) 0 200 --->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 1e+00 0 0 ( 0) 230 ( 231) 0 200 --->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 1e+00 0 0 ( 0) 230 ( 231) 0 200 --->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 1e+00 0 0 ( 0) 230 ( 231) 0 200 --->germline2---dash-----: 1e+00 0 1e+00 0 0 ( 0) 230 ( 231) 0 200 ######truePSnps###### --->fabia-------beagle1--: 3.95e-18 -246 2.73e-23 -269 1129 ( 254) 1398 ( 179) 1154 1412 --->fabia-------beagle2--: 3.95e-18 -246 2.73e-23 -269 1129 ( 254) 1398 ( 179) 1154 1412 --->fabia-------plink----: 3.95e-18 -246 2.73e-23 -269 1129 ( 254) 1398 ( 179) 1154 1412 --->fabia-------germline1: 3.95e-18 -246 2.73e-23 -269 1129 ( 254) 1398 ( 179) 1154 1412 --->fabia-------germline2: 3.95e-18 -246 2.73e-23 -269 1129 ( 254) 1398 ( 179) 1154 1412 --->fabia-------dash-----: 2.26e-01 -35.5 1.69e-01 -38.6 1129 ( 254) 1168 ( 254) 1154 1179 --->beagle1-----beagle2--: 1e+00 0 1e+00 0 1398 ( 179) 1398 ( 179) 1412 1412 --->beagle1-----plink----: 1e+00 0 1e+00 0 1398 ( 179) 1398 ( 179) 1412 1412 --->beagle1-----germline1: 1e+00 0 1e+00 0 1398 ( 179) 1398 ( 179) 1412 1412 --->beagle1-----germline2: 1e+00 0 1e+00 0 1398 ( 179) 1398 ( 179) 1412 1412 --->beagle1-----dash-----: 3.63e-13 314 1.13e-16 230 1398 ( 179) 1168 ( 254) 1412 1179 --->beagle2-----plink----: 1e+00 0 1e+00 0 1398 ( 179) 1398 ( 179) 1412 1412 --->beagle2-----germline1: 1e+00 0 1e+00 0 1398 ( 179) 1398 ( 179) 1412 1412 --->beagle2-----germline2: 1e+00 0 1e+00 0 1398 ( 179) 1398 ( 179) 1412 1412 --->beagle2-----dash-----: 3.63e-13 314 1.13e-16 230 1398 ( 179) 1168 ( 254) 1412 1179 --->plink-------germline1: 1e+00 0 1e+00 0 1398 ( 179) 1398 ( 179) 1412 1412 --->plink-------germline2: 1e+00 0 1e+00 0 1398 ( 179) 1398 ( 179) 1412 1412 --->plink-------dash-----: 3.63e-13 314 1.13e-16 230 1398 ( 179) 1168 ( 254) 1412 1179 --->germline1---germline2: 1e+00 0 1e+00 0 1398 ( 179) 1398 ( 179) 1412 1412 --->germline1---dash-----: 3.63e-13 314 1.13e-16 230 1398 ( 179) 1168 ( 254) 1412 1179 --->germline2---dash-----: 3.63e-13 314 1.13e-16 230 1398 ( 179) 1168 ( 254) 1412 1179 ######MatthewsSample###### --->fabia-------beagle1--: 3.96e-18 0.332677 9.04e-50 0.333122 0.347155 ( 0.108591) 0.014033 ( 0.037732) 0.357449 0.012743 --->fabia-------beagle2--: 3.96e-18 0.350531 2.72e-53 0.351062 0.347155 ( 0.108591) -0.003907 ( 0.035367) 0.357449 -0.007450 --->fabia-------plink----: 1e+00 0.000000 1e+00 0.000000 0.347155 ( 0.108591) 0.000000 ( 0.000000) 0.357449 0.000000 --->fabia-------germline1: 3.96e-18 0.335132 3.58e-51 0.336460 0.347155 ( 0.108591) 0.010695 ( 0.024069) 0.357449 0.010333 --->fabia-------germline2: 3.96e-18 0.336304 1.22e-52 0.337335 0.347155 ( 0.108591) 0.009820 ( 0.025777) 0.357449 0.011982 --->fabia-------dash-----: 3.96e-18 0.336516 4.37e-52 0.339454 0.347155 ( 0.108591) 0.007700 ( 0.031652) 0.357449 0.007249 --->beagle1-----beagle2--: 1.58e-05 0.018038 1.41e-06 0.017939 0.014033 ( 0.037732) -0.003907 ( 0.035367) 0.012743 -0.007450 --->beagle1-----plink----: 1e+00 0.000000 1e+00 0.000000 0.014033 ( 0.037732) 0.000000 ( 0.000000) 0.012743 0.000000 --->beagle1-----germline1: 5.35e-01 0.002740 4.55e-01 0.003338 0.014033 ( 0.037732) 0.010695 ( 0.024069) 0.012743 0.010333 --->beagle1-----germline2: 4.63e-01 0.003673 4.15e-01 0.004213 0.014033 ( 0.037732) 0.009820 ( 0.025777) 0.012743 0.011982 --->beagle1-----dash-----: 2.97e-01 0.005539 2.49e-01 0.006332 0.014033 ( 0.037732) 0.007700 ( 0.031652) 0.012743 0.007249 --->beagle2-----plink----: 1e+00 0.000000 1e+00 0.000000 -0.003907 ( 0.035367) 0.000000 ( 0.000000) -0.007450 0.000000 --->beagle2-----germline1: 8.37e-04 -0.015044 5.6e-04 -0.014602 -0.003907 ( 0.035367) 0.010695 ( 0.024069) -0.007450 0.010333 --->beagle2-----germline2: 6.57e-03 -0.014145 5.37e-03 -0.013727 -0.003907 ( 0.035367) 0.009820 ( 0.025777) -0.007450 0.011982 --->beagle2-----dash-----: 3.2e-02 -0.012784 3.55e-02 -0.011607 -0.003907 ( 0.035367) 0.007700 ( 0.031652) -0.007450 0.007249 --->plink-------germline1: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.010695 ( 0.024069) 0.000000 0.010333 --->plink-------germline2: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.009820 ( 0.025777) 0.000000 0.011982 --->plink-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.007700 ( 0.031652) 0.000000 0.007249 --->germline1---germline2: 8.84e-01 0.000479 7.52e-01 0.000875 0.010695 ( 0.024069) 0.009820 ( 0.025777) 0.010333 0.011982 --->germline1---dash-----: 5.6e-01 0.002180 3.9e-01 0.002994 0.010695 ( 0.024069) 0.007700 ( 0.031652) 0.010333 0.007249 --->germline2---dash-----: 6.29e-01 0.000938 2.95e-01 0.002119 0.009820 ( 0.025777) 0.007700 ( 0.031652) 0.011982 0.007249 ######F1Sample###### --->fabia-------beagle1--: 3.96e-18 0.201427 2.83e-39 0.204259 0.298494 ( 0.092134) 0.094236 ( 0.016916) 0.308063 0.094155 --->fabia-------beagle2--: 3.96e-18 0.221265 1.57e-42 0.224110 0.298494 ( 0.092134) 0.074384 ( 0.025642) 0.308063 0.072235 --->fabia-------plink----: 3.96e-18 0.201638 2.6e-40 0.205146 0.298494 ( 0.092134) 0.093348 ( 0.001809) 0.308063 0.093422 --->fabia-------germline1: 3.96e-18 0.200912 3.82e-40 0.204509 0.298494 ( 0.092134) 0.093986 ( 0.002784) 0.308063 0.094246 --->fabia-------germline2: 3.96e-18 0.200487 2.73e-40 0.204267 0.298494 ( 0.092134) 0.094228 ( 0.005043) 0.308063 0.094960 --->fabia-------dash-----: 3.96e-18 0.200691 2.71e-40 0.204991 0.298494 ( 0.092134) 0.093504 ( 0.007692) 0.308063 0.094123 --->beagle1-----beagle2--: 1.18e-11 0.019859 6.1e-15 0.019852 0.094236 ( 0.016916) 0.074384 ( 0.025642) 0.094155 0.072235 --->beagle1-----plink----: 6.91e-01 0.000756 5.95e-01 0.000888 0.094236 ( 0.016916) 0.093348 ( 0.001809) 0.094155 0.093422 --->beagle1-----germline1: 1e+00 0.000000 8.82e-01 0.000250 0.094236 ( 0.016916) 0.093986 ( 0.002784) 0.094155 0.094246 --->beagle1-----germline2: 9.47e-01 -9.14e-05 1e+00 0.000000 0.094236 ( 0.016916) 0.094228 ( 0.005043) 0.094155 0.094960 --->beagle1-----dash-----: 1e+00 0.000000 7.12e-01 0.000732 0.094236 ( 0.016916) 0.093504 ( 0.007692) 0.094155 0.094123 --->beagle2-----plink----: 1.72e-09 -0.019500 3.07e-11 -0.018964 0.074384 ( 0.025642) 0.093348 ( 0.001809) 0.072235 0.093422 --->beagle2-----germline1: 6.39e-10 -0.020172 8.34e-12 -0.019601 0.074384 ( 0.025642) 0.093986 ( 0.002784) 0.072235 0.094246 --->beagle2-----germline2: 2.98e-09 -0.020484 5.17e-11 -0.019843 0.074384 ( 0.025642) 0.094228 ( 0.005043) 0.072235 0.094960 --->beagle2-----dash-----: 2.03e-08 -0.019811 1.51e-09 -0.019119 0.074384 ( 0.025642) 0.093504 ( 0.007692) 0.072235 0.094123 --->plink-------germline1: 1.65e-03 -0.000707 1.95e-03 -0.000638 0.093348 ( 0.001809) 0.093986 ( 0.002784) 0.093422 0.094246 --->plink-------germline2: 6.12e-02 -0.000977 8.13e-02 -0.000880 0.093348 ( 0.001809) 0.094228 ( 0.005043) 0.093422 0.094960 --->plink-------dash-----: 7.27e-01 -0.000235 8.35e-01 -0.000156 0.093348 ( 0.001809) 0.093504 ( 0.007692) 0.093422 0.094123 --->germline1---germline2: 3.95e-01 -0.000389 6.01e-01 -0.000242 0.093986 ( 0.002784) 0.094228 ( 0.005043) 0.094246 0.094960 --->germline1---dash-----: 7.45e-01 0.000213 5.1e-01 0.000482 0.093986 ( 0.002784) 0.093504 ( 0.007692) 0.094246 0.094123 --->germline2---dash-----: 3.33e-01 0.000420 1.39e-01 0.000724 0.094228 ( 0.005043) 0.093504 ( 0.007692) 0.094960 0.094123 ######accuracySample###### --->fabia-------beagle1--: 3.95e-18 0.346701 2.87e-104 0.347715 0.907375 ( 0.024952) 0.559660 ( 0.020412) 0.904250 0.560000 --->fabia-------beagle2--: 3.95e-18 0.121493 5.97e-67 0.121995 0.907375 ( 0.024952) 0.785380 ( 0.015289) 0.904250 0.786000 --->fabia-------plink----: 3.95e-18 0.858215 5.05e-154 0.858415 0.907375 ( 0.024952) 0.048960 ( 0.000994) 0.904250 0.049000 --->fabia-------germline1: 3.95e-18 0.821974 1.75e-148 0.821955 0.907375 ( 0.024952) 0.085420 ( 0.012569) 0.904250 0.085500 --->fabia-------germline2: 3.95e-18 0.689226 6.04e-142 0.689325 0.907375 ( 0.024952) 0.218050 ( 0.012099) 0.904250 0.218000 --->fabia-------dash-----: 3.95e-18 0.631508 6.22e-112 0.627245 0.907375 ( 0.024952) 0.280130 ( 0.043979) 0.904250 0.268500 --->beagle1-----beagle2--: 3.94e-18 -0.225490 7.71e-111 -0.225720 0.559660 ( 0.020412) 0.785380 ( 0.015289) 0.560000 0.786000 --->beagle1-----plink----: 3.92e-18 0.511511 1.61e-140 0.510700 0.559660 ( 0.020412) 0.048960 ( 0.000994) 0.560000 0.049000 --->beagle1-----germline1: 3.95e-18 0.475026 1.8e-129 0.474240 0.559660 ( 0.020412) 0.085420 ( 0.012569) 0.560000 0.085500 --->beagle1-----germline2: 3.95e-18 0.342021 1.16e-114 0.341610 0.559660 ( 0.020412) 0.218050 ( 0.012099) 0.560000 0.218000 --->beagle1-----dash-----: 3.95e-18 0.285507 4.91e-77 0.279530 0.559660 ( 0.020412) 0.280130 ( 0.043979) 0.560000 0.268500 --->beagle2-----plink----: 3.93e-18 0.736522 8.15e-169 0.736420 0.785380 ( 0.015289) 0.048960 ( 0.000994) 0.786000 0.049000 --->beagle2-----germline1: 3.94e-18 0.699559 1.62e-156 0.699960 0.785380 ( 0.015289) 0.085420 ( 0.012569) 0.786000 0.085500 --->beagle2-----germline2: 3.93e-18 0.566986 2.39e-146 0.567330 0.785380 ( 0.015289) 0.218050 ( 0.012099) 0.786000 0.218000 --->beagle2-----dash-----: 3.95e-18 0.510964 2.3e-105 0.505250 0.785380 ( 0.015289) 0.280130 ( 0.043979) 0.786000 0.268500 --->plink-------germline1: 3.92e-18 -0.036489 1.93e-50 -0.036460 0.048960 ( 0.000994) 0.085420 ( 0.012569) 0.049000 0.085500 --->plink-------germline2: 3.91e-18 -0.169441 2.33e-115 -0.169090 0.048960 ( 0.000994) 0.218050 ( 0.012099) 0.049000 0.218000 --->plink-------dash-----: 3.94e-18 -0.223457 4.44e-74 -0.231170 0.048960 ( 0.000994) 0.280130 ( 0.043979) 0.049000 0.268500 --->germline1---germline2: 3.92e-18 -0.133455 6.2e-111 -0.132630 0.085420 ( 0.012569) 0.218050 ( 0.012099) 0.085500 0.218000 --->germline1---dash-----: 3.95e-18 -0.187997 2.1e-71 -0.194710 0.085420 ( 0.012569) 0.280130 ( 0.043979) 0.085500 0.268500 --->germline2---dash-----: 3.94e-18 -0.054967 1.58e-30 -0.062080 0.218050 ( 0.012099) 0.280130 ( 0.043979) 0.218000 0.268500 ######FPRSample###### --->fabia-------beagle1--: 3.96e-18 -0.066052 2.99e-103 -0.066265 0.017430 ( 0.004833) 0.083695 ( 0.004080) 0.017538 0.083333 --->fabia-------beagle2--: 3.96e-18 -0.017674 3.11e-55 -0.017780 0.017430 ( 0.004833) 0.035210 ( 0.003058) 0.017538 0.035152 --->fabia-------plink----: 3.95e-18 -0.174659 3.85e-156 -0.174699 0.017430 ( 0.004833) 0.192129 ( 0.000201) 0.017538 0.192121 --->fabia-------germline1: 3.96e-18 -0.167046 1.65e-149 -0.167026 0.017430 ( 0.004833) 0.184457 ( 0.002678) 0.017538 0.184343 --->fabia-------germline2: 3.96e-18 -0.138805 1.26e-142 -0.138867 0.017430 ( 0.004833) 0.156297 ( 0.002531) 0.017538 0.156162 --->fabia-------dash-----: 3.96e-18 -0.126658 8.87e-110 -0.125618 0.017430 ( 0.004833) 0.143048 ( 0.009421) 0.017538 0.145960 --->beagle1-----beagle2--: 3.95e-18 0.048398 4.11e-113 0.048485 0.083695 ( 0.004080) 0.035210 ( 0.003058) 0.083333 0.035152 --->beagle1-----plink----: 3.95e-18 -0.108608 4.03e-143 -0.108434 0.083695 ( 0.004080) 0.192129 ( 0.000201) 0.083333 0.192121 --->beagle1-----germline1: 3.96e-18 -0.100977 1.28e-130 -0.100762 0.083695 ( 0.004080) 0.184457 ( 0.002678) 0.083333 0.184343 --->beagle1-----germline2: 3.96e-18 -0.072750 9.2e-117 -0.072602 0.083695 ( 0.004080) 0.156297 ( 0.002531) 0.083333 0.156162 --->beagle1-----dash-----: 3.96e-18 -0.060766 6.7e-77 -0.059354 0.083695 ( 0.004080) 0.143048 ( 0.009421) 0.083333 0.145960 --->beagle2-----plink----: 3.95e-18 -0.156952 1.27e-171 -0.156919 0.035210 ( 0.003058) 0.192129 ( 0.000201) 0.035152 0.192121 --->beagle2-----germline1: 3.96e-18 -0.149145 2.47e-157 -0.149246 0.035210 ( 0.003058) 0.184457 ( 0.002678) 0.035152 0.184343 --->beagle2-----germline2: 3.95e-18 -0.120963 1.48e-148 -0.121087 0.035210 ( 0.003058) 0.156297 ( 0.002531) 0.035152 0.156162 --->beagle2-----dash-----: 3.96e-18 -0.109198 1.8e-105 -0.107838 0.035210 ( 0.003058) 0.143048 ( 0.009421) 0.035152 0.145960 --->plink-------germline1: 3.94e-18 0.007652 6.14e-50 0.007673 0.192129 ( 0.000201) 0.184457 ( 0.002678) 0.192121 0.184343 --->plink-------germline2: 3.93e-18 0.035918 4.71e-116 0.035832 0.192129 ( 0.000201) 0.156297 ( 0.002531) 0.192121 0.156162 --->plink-------dash-----: 3.95e-18 0.047353 1.02e-73 0.049081 0.192129 ( 0.000201) 0.143048 ( 0.009421) 0.192121 0.145960 --->germline1---germline2: 3.92e-18 0.028237 2.06e-113 0.028160 0.184457 ( 0.002678) 0.156297 ( 0.002531) 0.184343 0.156162 --->germline1---dash-----: 3.95e-18 0.039784 3.71e-71 0.041408 0.184457 ( 0.002678) 0.143048 ( 0.009421) 0.184343 0.145960 --->germline2---dash-----: 3.95e-18 0.011689 1.65e-30 0.013248 0.156297 ( 0.002531) 0.143048 ( 0.009421) 0.156162 0.145960 ######FDRSample###### --->fabia-------beagle1--: 3.96e-18 -0.132135 4.88e-37 -0.135613 0.811978 ( 0.065606) 0.947591 ( 0.009435) 0.814533 0.947724 --->fabia-------beagle2--: 3.96e-18 -0.137838 3.88e-38 -0.140796 0.811978 ( 0.065606) 0.952773 ( 0.016327) 0.814533 0.954648 --->fabia-------plink----: 3.96e-18 -0.135658 1.45e-38 -0.139062 0.811978 ( 0.065606) 0.951040 ( 0.000994) 0.814533 0.951000 --->fabia-------germline1: 3.96e-18 -0.135249 2.05e-38 -0.138633 0.811978 ( 0.065606) 0.950610 ( 0.001494) 0.814533 0.950515 --->fabia-------germline2: 3.96e-18 -0.134570 2.1e-38 -0.138075 0.811978 ( 0.065606) 0.950053 ( 0.002678) 0.814533 0.949693 --->fabia-------dash-----: 3.96e-18 -0.134651 2.3e-38 -0.138188 0.811978 ( 0.065606) 0.950165 ( 0.004065) 0.814533 0.950035 --->beagle1-----beagle2--: 5.39e-04 -0.005187 2.25e-04 -0.005183 0.947591 ( 0.009435) 0.952773 ( 0.016327) 0.947724 0.954648 --->beagle1-----plink----: 3.8e-04 -0.003405 3.31e-04 -0.003449 0.947591 ( 0.009435) 0.951040 ( 0.000994) 0.947724 0.951000 --->beagle1-----germline1: 2.2e-03 -0.002974 1.65e-03 -0.003020 0.947591 ( 0.009435) 0.950610 ( 0.001494) 0.947724 0.950515 --->beagle1-----germline2: 2.76e-02 -0.002372 1.91e-02 -0.002462 0.947591 ( 0.009435) 0.950053 ( 0.002678) 0.947724 0.949693 --->beagle1-----dash-----: 2.91e-02 -0.002493 1.98e-02 -0.002575 0.947591 ( 0.009435) 0.950165 ( 0.004065) 0.947724 0.950035 --->beagle2-----plink----: 2.27e-01 0.002085 2.86e-01 0.001733 0.952773 ( 0.016327) 0.951040 ( 0.000994) 0.954648 0.951000 --->beagle2-----germline1: 1.48e-01 0.002555 1.82e-01 0.002163 0.952773 ( 0.016327) 0.950610 ( 0.001494) 0.954648 0.950515 --->beagle2-----germline2: 1.01e-01 0.002971 1.12e-01 0.002721 0.952773 ( 0.016327) 0.950053 ( 0.002678) 0.954648 0.949693 --->beagle2-----dash-----: 1.47e-01 0.003049 1.47e-01 0.002608 0.952773 ( 0.016327) 0.950165 ( 0.004065) 0.954648 0.950035 --->plink-------germline1: 1.06e-04 0.000481 8.56e-05 0.000430 0.951040 ( 0.000994) 0.950610 ( 0.001494) 0.951000 0.950515 --->plink-------germline2: 2.77e-04 0.001042 3.04e-04 0.000987 0.951040 ( 0.000994) 0.950053 ( 0.002678) 0.951000 0.949693 --->plink-------dash-----: 2.81e-02 0.000919 2.86e-02 0.000875 0.951040 ( 0.000994) 0.950165 ( 0.004065) 0.951000 0.950035 --->germline1---germline2: 1.29e-02 0.000654 2.45e-02 0.000558 0.950610 ( 0.001494) 0.950053 ( 0.002678) 0.950515 0.949693 --->germline1---dash-----: 1.44e-01 0.000590 2.49e-01 0.000445 0.950610 ( 0.001494) 0.950165 ( 0.004065) 0.950515 0.950035 --->germline2---dash-----: 8.95e-01 2.32e-05 6.6e-01 -0.000113 0.950053 ( 0.002678) 0.950165 ( 0.004065) 0.949693 0.950035 ######specifitySample###### --->fabia-------beagle1--: 3.96e-18 0.069990 8.6e-106 0.070168 0.178602 ( 0.004838) 0.108434 ( 0.004078) 0.178442 0.108788 --->fabia-------beagle2--: 3.96e-18 0.021583 2.65e-63 0.021683 0.178602 ( 0.004838) 0.156919 ( 0.003040) 0.178442 0.156869 --->fabia-------plink----: 1e+00 0.000000 1e+00 0.000000 0.178602 ( 0.004838) 0.000000 ( 0.000000) 0.178442 0.000000 --->fabia-------germline1: 3.96e-18 0.170921 1.28e-150 0.170929 0.178602 ( 0.004838) 0.007673 ( 0.002663) 0.178442 0.007778 --->fabia-------germline2: 3.96e-18 0.142715 6.85e-144 0.142770 0.178602 ( 0.004838) 0.035832 ( 0.002533) 0.178442 0.035960 --->fabia-------dash-----: 3.96e-18 0.130575 4.88e-111 0.129521 0.178602 ( 0.004838) 0.049081 ( 0.009432) 0.178442 0.046061 --->beagle1-----beagle2--: 3.95e-18 -0.048416 4.12e-113 -0.048485 0.108434 ( 0.004078) 0.156919 ( 0.003040) 0.108788 0.156869 --->beagle1-----plink----: 1e+00 0.000000 1e+00 0.000000 0.108434 ( 0.004078) 0.000000 ( 0.000000) 0.108788 0.000000 --->beagle1-----germline1: 3.96e-18 0.100996 1.28e-130 0.100762 0.108434 ( 0.004078) 0.007673 ( 0.002663) 0.108788 0.007778 --->beagle1-----germline2: 3.95e-18 0.072738 9.2e-117 0.072602 0.108434 ( 0.004078) 0.035832 ( 0.002533) 0.108788 0.035960 --->beagle1-----dash-----: 3.96e-18 0.060804 6.7e-77 0.059354 0.108434 ( 0.004078) 0.049081 ( 0.009432) 0.108788 0.046061 --->beagle2-----plink----: 1e+00 0.000000 1e+00 0.000000 0.156919 ( 0.003040) 0.000000 ( 0.000000) 0.156869 0.000000 --->beagle2-----germline1: 3.96e-18 0.149147 2.47e-157 0.149246 0.156919 ( 0.003040) 0.007673 ( 0.002663) 0.156869 0.007778 --->beagle2-----germline2: 3.95e-18 0.120993 1.48e-148 0.121087 0.156919 ( 0.003040) 0.035832 ( 0.002533) 0.156869 0.035960 --->beagle2-----dash-----: 3.95e-18 0.109231 1.8e-105 0.107838 0.156919 ( 0.003040) 0.049081 ( 0.009432) 0.156869 0.046061 --->plink-------germline1: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.007673 ( 0.002663) 0.000000 0.007778 --->plink-------germline2: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.035832 ( 0.002533) 0.000000 0.035960 --->plink-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.049081 ( 0.009432) 0.000000 0.046061 --->germline1---germline2: 3.95e-18 -0.028244 2.06e-113 -0.028160 0.007673 ( 0.002663) 0.035832 ( 0.002533) 0.007778 0.035960 --->germline1---dash-----: 3.95e-18 -0.039722 3.71e-71 -0.041408 0.007673 ( 0.002663) 0.049081 ( 0.009432) 0.007778 0.046061 --->germline2---dash-----: 3.95e-18 -0.011651 1.65e-30 -0.013248 0.035832 ( 0.002533) 0.049081 ( 0.009432) 0.035960 0.046061 ######sensitivitySample###### --->fabia-------beagle1--: 2.07e-16 0.309939 2.34e-26 0.295000 0.753200 ( 0.185543) 0.458200 ( 0.084667) 0.790000 0.460000 --->fabia-------beagle2--: 3.93e-18 0.589941 1.86e-52 0.580600 0.753200 ( 0.185543) 0.172600 ( 0.061012) 0.790000 0.180000 --->fabia-------plink----: 5e-15 -0.260028 2.35e-21 -0.226000 0.753200 ( 0.185543) 0.979200 ( 0.019882) 0.790000 0.980000 --->fabia-------germline1: 1.3e-13 -0.209996 1.94e-17 -0.195600 0.753200 ( 0.185543) 0.948800 ( 0.032576) 0.790000 0.960000 --->fabia-------germline2: 6.68e-03 -0.059925 1.77e-03 -0.060400 0.753200 ( 0.185543) 0.813600 ( 0.047472) 0.790000 0.820000 --->fabia-------dash-----: 6.11e-01 0.010068 6.35e-01 0.009600 0.753200 ( 0.185543) 0.743600 ( 0.084250) 0.790000 0.760000 --->beagle1-----beagle2--: 3.81e-18 0.289981 8.59e-62 0.285600 0.458200 ( 0.084667) 0.172600 ( 0.061012) 0.460000 0.180000 --->beagle1-----plink----: 3.8e-18 -0.520063 1.27e-81 -0.521000 0.458200 ( 0.084667) 0.979200 ( 0.019882) 0.460000 0.980000 --->beagle1-----germline1: 3.86e-18 -0.489988 4.57e-76 -0.490600 0.458200 ( 0.084667) 0.948800 ( 0.032576) 0.460000 0.960000 --->beagle1-----germline2: 3.91e-18 -0.359921 7.11e-56 -0.355400 0.458200 ( 0.084667) 0.813600 ( 0.047472) 0.460000 0.820000 --->beagle1-----dash-----: 5.91e-18 -0.290051 9.59e-40 -0.285400 0.458200 ( 0.084667) 0.743600 ( 0.084250) 0.460000 0.760000 --->beagle2-----plink----: 3.66e-18 -0.809987 1.61e-113 -0.806600 0.172600 ( 0.061012) 0.979200 ( 0.019882) 0.180000 0.980000 --->beagle2-----germline1: 3.72e-18 -0.779990 1.25e-107 -0.776200 0.172600 ( 0.061012) 0.948800 ( 0.032576) 0.180000 0.960000 --->beagle2-----germline2: 3.83e-18 -0.640022 2.94e-90 -0.641000 0.172600 ( 0.061012) 0.813600 ( 0.047472) 0.180000 0.820000 --->beagle2-----dash-----: 3.9e-18 -0.579986 3.68e-72 -0.571000 0.172600 ( 0.061012) 0.743600 ( 0.084250) 0.180000 0.760000 --->plink-------germline1: 5.08e-14 0.039927 1.09e-20 0.030400 0.979200 ( 0.019882) 0.948800 ( 0.032576) 0.980000 0.960000 --->plink-------germline2: 3.57e-18 0.169995 2.07e-57 0.165600 0.979200 ( 0.019882) 0.813600 ( 0.047472) 0.980000 0.820000 --->plink-------dash-----: 3.77e-18 0.230082 1.38e-49 0.235600 0.979200 ( 0.019882) 0.743600 ( 0.084250) 0.980000 0.760000 --->germline1---germline2: 3.48e-18 0.130038 2.91e-54 0.135200 0.948800 ( 0.032576) 0.813600 ( 0.047472) 0.960000 0.820000 --->germline1---dash-----: 3.79e-18 0.199999 1.4e-46 0.205200 0.948800 ( 0.032576) 0.743600 ( 0.084250) 0.960000 0.760000 --->germline2---dash-----: 1.62e-16 0.070020 5.28e-21 0.070000 0.813600 ( 0.047472) 0.743600 ( 0.084250) 0.820000 0.760000 ######trueNSample###### --->fabia-------beagle1--: 3.95e-18 1240 2.2e-138 1240 1777 ( 48.1) 537 ( 20.2) 1776 538 --->fabia-------beagle2--: 3.94e-18 1001 3.53e-132 1000 1777 ( 48.1) 777 ( 15) 1776 776 --->fabia-------plink----: 1e+00 0 1e+00 0 1777 ( 48.1) 0 ( 0) 1776 0 --->fabia-------germline1: 3.95e-18 1739 2.59e-155 1739 1777 ( 48.1) 38 ( 13.2) 1776 38.5 --->fabia-------germline2: 3.95e-18 1599 3.68e-152 1600 1777 ( 48.1) 177 ( 12.5) 1776 178 --->fabia-------dash-----: 3.95e-18 1536 3.31e-138 1534 1777 ( 48.1) 243 ( 46.7) 1776 228 --->beagle1-----beagle2--: 3.93e-18 -240 4.11e-113 -240 537 ( 20.2) 777 ( 15) 538 776 --->beagle1-----plink----: 1e+00 0 1e+00 0 537 ( 20.2) 0 ( 0) 538 0 --->beagle1-----germline1: 3.94e-18 500 1.28e-130 499 537 ( 20.2) 38 ( 13.2) 538 38.5 --->beagle1-----germline2: 3.93e-18 360 9.2e-117 359 537 ( 20.2) 177 ( 12.5) 538 178 --->beagle1-----dash-----: 3.95e-18 301 6.7e-77 294 537 ( 20.2) 243 ( 46.7) 538 228 --->beagle2-----plink----: 1e+00 0 1e+00 0 777 ( 15) 0 ( 0) 776 0 --->beagle2-----germline1: 3.94e-18 738 2.47e-157 739 777 ( 15) 38 ( 13.2) 776 38.5 --->beagle2-----germline2: 3.93e-18 599 1.48e-148 599 777 ( 15) 177 ( 12.5) 776 178 --->beagle2-----dash-----: 3.94e-18 541 1.8e-105 534 777 ( 15) 243 ( 46.7) 776 228 --->plink-------germline1: 1e+00 0 1e+00 0 0 ( 0) 38 ( 13.2) 0 38.5 --->plink-------germline2: 1e+00 0 1e+00 0 0 ( 0) 177 ( 12.5) 0 178 --->plink-------dash-----: 1e+00 0 1e+00 0 0 ( 0) 243 ( 46.7) 0 228 --->germline1---germline2: 3.9e-18 -140 2.06e-113 -139 38 ( 13.2) 177 ( 12.5) 38.5 178 --->germline1---dash-----: 3.94e-18 -197 3.71e-71 -205 38 ( 13.2) 243 ( 46.7) 38.5 228 --->germline2---dash-----: 3.93e-18 -57.5 1.65e-30 -65.6 177 ( 12.5) 243 ( 46.7) 178 228 ######falsePSample###### --->fabia-------beagle1--: 3.95e-18 -240 8.47e-69 -241 173 ( 48.1) 414 ( 20.2) 174 412 --->fabia-------beagle2--: 8.27e-01 -1 8.6e-01 -0.86 173 ( 48.1) 174 ( 15.1) 174 174 --->fabia-------plink----: 3.95e-18 -777 1.04e-121 -778 173 ( 48.1) 951 ( 0.994) 174 951 --->fabia-------germline1: 3.95e-18 -740 1.34e-118 -740 173 ( 48.1) 913 ( 13.3) 174 912 --->fabia-------germline2: 3.95e-18 -600 4.13e-110 -600 173 ( 48.1) 774 ( 12.5) 174 773 --->fabia-------dash-----: 3.95e-18 -536 3.36e-93 -535 173 ( 48.1) 708 ( 46.6) 174 722 --->beagle1-----beagle2--: 3.93e-18 240 4.11e-113 240 414 ( 20.2) 174 ( 15.1) 412 174 --->beagle1-----plink----: 3.93e-18 -538 4.03e-143 -537 414 ( 20.2) 951 ( 0.994) 412 951 --->beagle1-----germline1: 3.94e-18 -500 1.28e-130 -499 414 ( 20.2) 913 ( 13.3) 412 912 --->beagle1-----germline2: 3.93e-18 -360 9.2e-117 -359 414 ( 20.2) 774 ( 12.5) 412 773 --->beagle1-----dash-----: 3.95e-18 -301 6.7e-77 -294 414 ( 20.2) 708 ( 46.6) 412 722 --->beagle2-----plink----: 3.93e-18 -777 1.27e-171 -777 174 ( 15.1) 951 ( 0.994) 174 951 --->beagle2-----germline1: 3.94e-18 -738 2.47e-157 -739 174 ( 15.1) 913 ( 13.3) 174 912 --->beagle2-----germline2: 3.93e-18 -599 1.48e-148 -599 174 ( 15.1) 774 ( 12.5) 174 773 --->beagle2-----dash-----: 3.94e-18 -541 1.8e-105 -534 174 ( 15.1) 708 ( 46.6) 174 722 --->plink-------germline1: 3.92e-18 37.5 6.14e-50 38 951 ( 0.994) 913 ( 13.3) 951 912 --->plink-------germline2: 3.9e-18 178 4.71e-116 177 951 ( 0.994) 774 ( 12.5) 951 773 --->plink-------dash-----: 3.93e-18 234 1.02e-73 243 951 ( 0.994) 708 ( 46.6) 951 722 --->germline1---germline2: 3.9e-18 140 2.06e-113 139 913 ( 13.3) 774 ( 12.5) 912 773 --->germline1---dash-----: 3.94e-18 197 3.71e-71 205 913 ( 13.3) 708 ( 46.6) 912 722 --->germline2---dash-----: 3.93e-18 57.5 1.65e-30 65.6 774 ( 12.5) 708 ( 46.6) 773 722 ######falseNSample###### --->fabia-------beagle1--: 3.95e-16 -15 4.45e-25 -14.2 11.8 ( 9.38) 26.1 ( 4.14) 10 26 --->fabia-------beagle2--: 3.88e-18 -29 1.77e-51 -28.5 11.8 ( 9.38) 40.3 ( 3.03) 10 41 --->fabia-------plink----: 1e+00 0 1e+00 0 11.8 ( 9.38) 0 ( 0) 10 0 --->fabia-------germline1: 5.45e-14 11.5 1.9e-18 10.3 11.8 ( 9.38) 1.52 ( 1.28) 10 1 --->fabia-------germline2: 1.34e-03 3.5 3.25e-04 3.54 11.8 ( 9.38) 8.28 ( 2.37) 10 8 --->fabia-------dash-----: 9.44e-01 -5.65e-06 9.69e-01 0.04 11.8 ( 9.38) 11.8 ( 4.13) 10 11.5 --->beagle1-----beagle2--: 3.62e-18 -14.5 8.59e-62 -14.3 26.1 ( 4.14) 40.3 ( 3.03) 26 41 --->beagle1-----plink----: 1e+00 0 1e+00 0 26.1 ( 4.14) 0 ( 0) 26 0 --->beagle1-----germline1: 3.74e-18 24.5 4.57e-76 24.5 26.1 ( 4.14) 1.52 ( 1.28) 26 1 --->beagle1-----germline2: 3.8e-18 18 7.11e-56 17.8 26.1 ( 4.14) 8.28 ( 2.37) 26 8 --->beagle1-----dash-----: 5.97e-18 14.5 9.59e-40 14.3 26.1 ( 4.14) 11.8 ( 4.13) 26 11.5 --->beagle2-----plink----: 1e+00 0 1e+00 0 40.3 ( 3.03) 0 ( 0) 41 0 --->beagle2-----germline1: 3.6e-18 39 1.25e-107 38.8 40.3 ( 3.03) 1.52 ( 1.28) 41 1 --->beagle2-----germline2: 3.7e-18 32 2.94e-90 32 40.3 ( 3.03) 8.28 ( 2.37) 41 8 --->beagle2-----dash-----: 3.83e-18 29 3.68e-72 28.6 40.3 ( 3.03) 11.8 ( 4.13) 41 11.5 --->plink-------germline1: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 1.520000 ( 1.282989) 0.000000 1.000000 --->plink-------germline2: 1e+00 0 1e+00 0 0 ( 0) 8.28 ( 2.37) 0 8 --->plink-------dash-----: 1e+00 0 1e+00 0 0 ( 0) 11.8 ( 4.13) 0 11.5 --->germline1---germline2: 3.23e-18 -6.5 2.91e-54 -6.76 1.52 ( 1.28) 8.28 ( 2.37) 1 8 --->germline1---dash-----: 3.67e-18 -10 1.4e-46 -10.3 1.52 ( 1.28) 11.8 ( 4.13) 1 11.5 --->germline2---dash-----: 1.39e-16 -3.5 5.28e-21 -3.5 8.28 ( 2.37) 11.8 ( 4.13) 8 11.5 ######truePSample###### --->fabia-------beagle1--: 1.7e-16 15.5 2.34e-26 14.8 37.7 ( 9.28) 22.9 ( 4.23) 39.5 23 --->fabia-------beagle2--: 3.9e-18 29.5 1.86e-52 29 37.7 ( 9.28) 8.63 ( 3.05) 39.5 9 --->fabia-------plink----: 5.36e-15 -13 2.35e-21 -11.3 37.7 ( 9.28) 49 ( 0.994) 39.5 49 --->fabia-------germline1: 1.29e-13 -10.5 1.94e-17 -9.78 37.7 ( 9.28) 47.4 ( 1.63) 39.5 48 --->fabia-------germline2: 5.99e-03 -3 1.77e-03 -3.02 37.7 ( 9.28) 40.7 ( 2.37) 39.5 41 --->fabia-------dash-----: 6.03e-01 0.5 6.35e-01 0.48 37.7 ( 9.28) 37.2 ( 4.21) 39.5 38 --->beagle1-----beagle2--: 3.62e-18 14.5 8.59e-62 14.3 22.9 ( 4.23) 8.63 ( 3.05) 23 9 --->beagle1-----plink----: 3.72e-18 -26 1.27e-81 -26.1 22.9 ( 4.23) 49 ( 0.994) 23 49 --->beagle1-----germline1: 3.74e-18 -24.5 4.57e-76 -24.5 22.9 ( 4.23) 47.4 ( 1.63) 23 48 --->beagle1-----germline2: 3.8e-18 -18 7.11e-56 -17.8 22.9 ( 4.23) 40.7 ( 2.37) 23 41 --->beagle1-----dash-----: 5.97e-18 -14.5 9.59e-40 -14.3 22.9 ( 4.23) 37.2 ( 4.21) 23 38 --->beagle2-----plink----: 3.58e-18 -40.5 1.61e-113 -40.3 8.63 ( 3.05) 49 ( 0.994) 9 49 --->beagle2-----germline1: 3.6e-18 -39 1.25e-107 -38.8 8.63 ( 3.05) 47.4 ( 1.63) 9 48 --->beagle2-----germline2: 3.7e-18 -32 2.94e-90 -32 8.63 ( 3.05) 40.7 ( 2.37) 9 41 --->beagle2-----dash-----: 3.83e-18 -29 3.68e-72 -28.6 8.63 ( 3.05) 37.2 ( 4.21) 9 38 --->plink-------germline1: 3.61e-14 2 1.09e-20 1.52 49 ( 0.994) 47.4 ( 1.63) 49 48 --->plink-------germline2: 3.4e-18 8.5 2.07e-57 8.28 49 ( 0.994) 40.7 ( 2.37) 49 41 --->plink-------dash-----: 3.7e-18 11.5 1.38e-49 11.8 49 ( 0.994) 37.2 ( 4.21) 49 38 --->germline1---germline2: 3.23e-18 6.5 2.91e-54 6.76 47.4 ( 1.63) 40.7 ( 2.37) 48 41 --->germline1---dash-----: 3.67e-18 10 1.4e-46 10.3 47.4 ( 1.63) 37.2 ( 4.21) 48 38 --->germline2---dash-----: 1.39e-16 3.5 5.28e-21 3.5 40.7 ( 2.37) 37.2 ( 4.21) 41 38