Results: Wilcoxon-Rank-Sum Wilcoxon-median t-test t-test-mean mean1 (std) mean2 (std) median1 median2 ######Matthews###### --->fabia-------beagle1--: 3.96e-18 0.748959 1.12e-103 0.744564 0.736802 ( 0.070478) -0.007763 ( 0.003127) 0.736028 -0.007260 --->fabia-------beagle2--: 3.96e-18 0.745472 2.9e-103 0.740858 0.736802 ( 0.070478) -0.004057 ( 0.002822) 0.736028 -0.004276 --->fabia-------plink----: 3.96e-18 0.705886 2.13e-99 0.701650 0.736802 ( 0.070478) 0.035152 ( 0.011981) 0.736028 0.035084 --->fabia-------germline1: 3.96e-18 0.743095 2.23e-103 0.738523 0.736802 ( 0.070478) -0.001721 ( 0.006920) 0.736028 -0.001592 --->fabia-------germline2: 3.96e-18 0.742641 1.88e-102 0.738167 0.736802 ( 0.070478) -0.001366 ( 0.005768) 0.736028 -0.004324 --->fabia-------dash-----: 3.96e-18 0.743177 2.26e-102 0.738828 0.736802 ( 0.070478) -0.002026 ( 0.007657) 0.736028 -0.002950 --->beagle1-----beagle2--: 4.06e-16 -0.003635 9.19e-24 -0.003706 -0.007763 ( 0.003127) -0.004057 ( 0.002822) -0.007260 -0.004276 --->beagle1-----plink----: 3.96e-18 -0.042758 1.1e-56 -0.042914 -0.007763 ( 0.003127) 0.035152 ( 0.011981) -0.007260 0.035084 --->beagle1-----germline1: 1.85e-10 -0.006237 3.4e-12 -0.006041 -0.007763 ( 0.003127) -0.001721 ( 0.006920) -0.007260 -0.001592 --->beagle1-----germline2: 2.57e-16 -0.005341 5.46e-16 -0.006397 -0.007763 ( 0.003127) -0.001366 ( 0.005768) -0.007260 -0.004324 --->beagle1-----dash-----: 5.22e-09 -0.005402 2.49e-10 -0.005736 -0.007763 ( 0.003127) -0.002026 ( 0.007657) -0.007260 -0.002950 --->beagle2-----plink----: 3.96e-18 -0.038990 1.9e-53 -0.039209 -0.004057 ( 0.002822) 0.035152 ( 0.011981) -0.004276 0.035084 --->beagle2-----germline1: 1.39e-03 -0.002484 2.86e-03 -0.002336 -0.004057 ( 0.002822) -0.001721 ( 0.006920) -0.004276 -0.001592 --->beagle2-----germline2: 1e+00 0.000000 4.96e-05 -0.002691 -0.004057 ( 0.002822) -0.001366 ( 0.005768) -0.004276 -0.004324 --->beagle2-----dash-----: 4.27e-02 -0.001773 1.47e-02 -0.002030 -0.004057 ( 0.002822) -0.002026 ( 0.007657) -0.004276 -0.002950 --->plink-------germline1: 3.96e-18 0.036335 7.06e-49 0.036873 0.035152 ( 0.011981) -0.001721 ( 0.006920) 0.035084 -0.001592 --->plink-------germline2: 3.96e-18 0.036066 3.85e-50 0.036517 0.035152 ( 0.011981) -0.001366 ( 0.005768) 0.035084 -0.004324 --->plink-------dash-----: 4.6e-18 0.037298 6.48e-43 0.037178 0.035152 ( 0.011981) -0.002026 ( 0.007657) 0.035084 -0.002950 --->germline1---germline2: 7.61e-01 0.000315 6.93e-01 -0.000356 -0.001721 ( 0.006920) -0.001366 ( 0.005768) -0.001592 -0.004324 --->germline1---dash-----: 6.05e-01 0.000596 8.04e-01 0.000305 -0.001721 ( 0.006920) -0.002026 ( 0.007657) -0.001592 -0.002950 --->germline2---dash-----: 7.35e-01 0.000361 5.22e-01 0.000661 -0.001366 ( 0.005768) -0.002026 ( 0.007657) -0.004324 -0.002950 ######F1###### --->fabia-------beagle1--: 3.96e-18 0.709406 4.64e-96 0.705242 0.707908 ( 0.079708) 0.002666 ( 0.000512) 0.713563 0.002707 --->fabia-------beagle2--: 3.96e-18 0.709295 5.17e-96 0.705164 0.707908 ( 0.079708) 0.002744 ( 0.000803) 0.713563 0.002771 --->fabia-------plink----: 3.96e-18 0.686863 6.59e-94 0.683102 0.707908 ( 0.079708) 0.024806 ( 0.007294) 0.713563 0.024505 --->fabia-------germline1: 3.96e-18 0.708112 5.61e-96 0.704019 0.707908 ( 0.079708) 0.003889 ( 0.000328) 0.713563 0.003893 --->fabia-------germline2: 3.96e-18 0.709242 1.15e-95 0.705688 0.707908 ( 0.079708) 0.002220 ( 0.004287) 0.713563 0.000000 --->fabia-------dash-----: 3.96e-18 0.708423 7.62e-96 0.704457 0.707908 ( 0.079708) 0.003451 ( 0.001841) 0.713563 0.003172 --->beagle1-----beagle2--: 1e+00 0.000000 1e+00 0.000000 0.002666 ( 0.000512) 0.002744 ( 0.000803) 0.002707 0.002771 --->beagle1-----plink----: 3.96e-18 -0.021871 9.21e-52 -0.022140 0.002666 ( 0.000512) 0.024806 ( 0.007294) 0.002707 0.024505 --->beagle1-----germline1: 4.46e-18 -0.001213 5.58e-37 -0.001222 0.002666 ( 0.000512) 0.003889 ( 0.000328) 0.002707 0.003893 --->beagle1-----germline2: 9.97e-03 0.002097 3.07e-01 0.000447 0.002666 ( 0.000512) 0.002220 ( 0.004287) 0.002707 0.000000 --->beagle1-----dash-----: 4.11e-04 -0.000691 7.18e-05 -0.000785 0.002666 ( 0.000512) 0.003451 ( 0.001841) 0.002707 0.003172 --->beagle2-----plink----: 3.96e-18 -0.021868 1.73e-51 -0.022062 0.002744 ( 0.000803) 0.024806 ( 0.007294) 0.002771 0.024505 --->beagle2-----germline1: 1.52e-15 -0.001171 1.82e-23 -0.001145 0.002744 ( 0.000803) 0.003889 ( 0.000328) 0.002771 0.003893 --->beagle2-----germline2: 6.3e-03 0.001939 2.32e-01 0.000524 0.002744 ( 0.000803) 0.002220 ( 0.004287) 0.002771 0.000000 --->beagle2-----dash-----: 2.95e-03 -0.000645 6.56e-04 -0.000707 0.002744 ( 0.000803) 0.003451 ( 0.001841) 0.002771 0.003172 --->plink-------germline1: 3.96e-18 0.020656 7.06e-50 0.020918 0.024806 ( 0.007294) 0.003889 ( 0.000328) 0.024505 0.003893 --->plink-------germline2: 3.96e-18 0.022420 1.59e-49 0.022587 0.024806 ( 0.007294) 0.002220 ( 0.004287) 0.024505 0.000000 --->plink-------dash-----: 4.08e-18 0.021267 1.87e-47 0.021356 0.024806 ( 0.007294) 0.003451 ( 0.001841) 0.024505 0.003172 --->germline1---germline2: 7.74e-05 0.003519 1.9e-04 0.001669 0.003889 ( 0.000328) 0.002220 ( 0.004287) 0.003893 0.000000 --->germline1---dash-----: 1.3e-02 0.000515 2.95e-02 0.000438 0.003889 ( 0.000328) 0.003451 ( 0.001841) 0.003893 0.003172 --->germline2---dash-----: 5.12e-04 -0.002248 1.43e-02 -0.001231 0.002220 ( 0.004287) 0.003451 ( 0.001841) 0.000000 0.003172 ######accuracy###### --->fabia-------beagle1--: 3.96e-18 0.224349 7.86e-116 0.224676 0.999546 ( 0.000107) 0.774871 ( 0.015958) 0.999548 0.776215 --->fabia-------beagle2--: 3.96e-18 0.087928 2.78e-97 0.088072 0.999546 ( 0.000107) 0.911474 ( 0.009664) 0.999548 0.911824 --->fabia-------plink----: 3.96e-18 0.018297 9.28e-104 0.018307 0.999546 ( 0.000107) 0.981239 ( 0.001707) 0.999548 0.981385 --->fabia-------germline1: 3.96e-18 0.786842 5.13e-136 0.785803 0.999546 ( 0.000107) 0.213743 ( 0.034866) 0.999548 0.211732 --->fabia-------germline2: 3.96e-18 0.011493 9.37e-60 0.011306 0.999546 ( 0.000107) 0.988241 ( 0.003052) 0.999548 0.987990 --->fabia-------dash-----: 3.96e-18 0.125241 1.73e-64 0.124233 0.999546 ( 0.000107) 0.875313 ( 0.029886) 0.999548 0.884708 --->beagle1-----beagle2--: 3.96e-18 -0.136341 3.01e-119 -0.136603 0.774871 ( 0.015958) 0.911474 ( 0.009664) 0.776215 0.911824 --->beagle1-----plink----: 3.96e-18 -0.205872 3.53e-113 -0.206368 0.774871 ( 0.015958) 0.981239 ( 0.001707) 0.776215 0.981385 --->beagle1-----germline1: 3.96e-18 0.562772 5.41e-114 0.561128 0.774871 ( 0.015958) 0.213743 ( 0.034866) 0.776215 0.211732 --->beagle1-----germline2: 3.96e-18 -0.213102 3.86e-111 -0.213370 0.774871 ( 0.015958) 0.988241 ( 0.003052) 0.776215 0.987990 --->beagle1-----dash-----: 3.96e-18 -0.099051 1.21e-51 -0.100443 0.774871 ( 0.015958) 0.875313 ( 0.029886) 0.776215 0.884708 --->beagle2-----plink----: 3.96e-18 -0.069629 2.82e-89 -0.069765 0.911474 ( 0.009664) 0.981239 ( 0.001707) 0.911824 0.981385 --->beagle2-----germline1: 3.96e-18 0.698871 1.72e-127 0.697731 0.911474 ( 0.009664) 0.213743 ( 0.034866) 0.911824 0.211732 --->beagle2-----germline2: 3.96e-18 -0.076802 5.56e-87 -0.076767 0.911474 ( 0.009664) 0.988241 ( 0.003052) 0.911824 0.987990 --->beagle2-----dash-----: 1.19e-14 0.036513 7.09e-20 0.036161 0.911474 ( 0.009664) 0.875313 ( 0.029886) 0.911824 0.884708 --->plink-------germline1: 3.96e-18 0.768457 1.31e-134 0.767496 0.981239 ( 0.001707) 0.213743 ( 0.034866) 0.981385 0.211732 --->plink-------germline2: 1.77e-16 -0.007004 1.26e-35 -0.007002 0.981239 ( 0.001707) 0.988241 ( 0.003052) 0.981385 0.987990 --->plink-------dash-----: 3.96e-18 0.105435 3.68e-58 0.105926 0.981239 ( 0.001707) 0.875313 ( 0.029886) 0.981385 0.884708 --->germline1---germline2: 3.96e-18 -0.775392 6.4e-135 -0.774498 0.213743 ( 0.034866) 0.988241 ( 0.003052) 0.211732 0.987990 --->germline1---dash-----: 3.96e-18 -0.662200 1.61e-108 -0.661570 0.213743 ( 0.034866) 0.875313 ( 0.029886) 0.211732 0.884708 --->germline2---dash-----: 3.96e-18 0.112368 5.72e-61 0.112927 0.988241 ( 0.003052) 0.875313 ( 0.029886) 0.987990 0.884708 ######FPR###### --->fabia-------beagle1--: 3.96e-18 -0.223513 1.52e-115 -0.223871 1.52e-05 ( 3.84e-05) 0.223886 ( 0.016011) 0.000000 0.222529 --->fabia-------beagle2--: 3.96e-18 -0.086676 1.56e-96 -0.086815 1.52e-05 ( 3.84e-05) 0.086831 ( 0.009694) 0.000000 0.086542 --->fabia-------plink----: 3.96e-18 -0.016994 1.31e-100 -0.017028 1.52e-05 ( 3.84e-05) 0.017043 ( 0.001721) 0.000000 0.016833 --->fabia-------germline1: 3.96e-18 -0.788412 6.14e-136 -0.787353 1.52e-05 ( 3.84e-05) 0.787368 ( 0.035003) 0.000000 0.789477 --->fabia-------germline2: 5.78e-18 -0.010007 5.18e-54 -0.009787 1.52e-05 ( 3.84e-05) 0.009802 ( 0.003066) 0.000000 0.010066 --->fabia-------dash-----: 3.96e-18 -0.124193 5.32e-64 -0.123142 1.52e-05 ( 3.84e-05) 0.123157 ( 0.029977) 0.000000 0.113609 --->beagle1-----beagle2--: 3.96e-18 0.136800 3.15e-119 0.137055 0.223886 ( 0.016011) 0.086831 ( 0.009694) 0.222529 0.086542 --->beagle1-----plink----: 3.96e-18 0.206331 3.98e-113 0.206843 0.223886 ( 0.016011) 0.017043 ( 0.001721) 0.222529 0.016833 --->beagle1-----germline1: 3.96e-18 -0.565142 4.92e-114 -0.563482 0.223886 ( 0.016011) 0.787368 ( 0.035003) 0.222529 0.789477 --->beagle1-----germline2: 3.96e-18 0.213818 4.06e-111 0.214084 0.223886 ( 0.016011) 0.009802 ( 0.003066) 0.222529 0.010066 --->beagle1-----dash-----: 3.96e-18 0.099318 1.31e-51 0.100729 0.223886 ( 0.016011) 0.123157 ( 0.029977) 0.222529 0.113609 --->beagle2-----plink----: 3.96e-18 0.069608 3.58e-89 0.069788 0.086831 ( 0.009694) 0.017043 ( 0.001721) 0.086542 0.016833 --->beagle2-----germline1: 3.96e-18 -0.701698 1.6e-127 -0.700537 0.086831 ( 0.009694) 0.787368 ( 0.035003) 0.086542 0.789477 --->beagle2-----germline2: 3.96e-18 0.077036 5.74e-87 0.077029 0.086831 ( 0.009694) 0.009802 ( 0.003066) 0.086542 0.010066 --->beagle2-----dash-----: 1.19e-14 -0.036704 6.65e-20 -0.036327 0.086831 ( 0.009694) 0.123157 ( 0.029977) 0.086542 0.113609 --->plink-------germline1: 3.96e-18 -0.771304 1.29e-134 -0.770325 0.017043 ( 0.001721) 0.787368 ( 0.035003) 0.016833 0.789477 --->plink-------germline2: 1.33e-16 0.007245 1.49e-36 0.007241 0.017043 ( 0.001721) 0.009802 ( 0.003066) 0.016833 0.010066 --->plink-------dash-----: 3.96e-18 -0.105515 4.26e-58 -0.106114 0.017043 ( 0.001721) 0.123157 ( 0.029977) 0.016833 0.113609 --->germline1---germline2: 3.96e-18 0.778538 5.95e-135 0.777566 0.787368 ( 0.035003) 0.009802 ( 0.003066) 0.789477 0.010066 --->germline1---dash-----: 3.96e-18 0.664819 1.51e-108 0.664210 0.787368 ( 0.035003) 0.123157 ( 0.029977) 0.789477 0.113609 --->germline2---dash-----: 3.96e-18 -0.112814 5.67e-61 -0.113355 0.009802 ( 0.003066) 0.123157 ( 0.029977) 0.010066 0.113609 ######FDR###### --->fabia-------beagle1--: 3.96e-18 -0.998344 5.55e-120 -0.973406 0.025249 ( 0.062799) 0.998655 ( 0.000258) 0.000000 0.998635 --->fabia-------beagle2--: 3.96e-18 -0.998170 5.91e-120 -0.973347 0.025249 ( 0.062799) 0.998596 ( 0.000411) 0.000000 0.998585 --->fabia-------plink----: 3.96e-18 -0.984030 1e-118 -0.960899 0.025249 ( 0.062799) 0.986148 ( 0.004092) 0.000000 0.986420 --->fabia-------germline1: 3.96e-18 -0.997833 5.9e-120 -0.972802 0.025249 ( 0.062799) 0.998051 ( 0.000164) 0.000000 0.998048 --->fabia-------germline2: 1.09e-18 -0.997264 2.47e-93 -0.963411 0.025249 ( 0.062799) 0.988660 ( 0.099898) 0.000000 1.000000 --->fabia-------dash-----: 3.96e-18 -0.997254 5.9e-120 -0.972996 0.025249 ( 0.062799) 0.998245 ( 0.000937) 0.000000 0.998391 --->beagle1-----beagle2--: 1e+00 0.000000 1e+00 0.000000 0.998655 ( 0.000258) 0.998596 ( 0.000411) 0.998635 0.998585 --->beagle1-----plink----: 3.96e-18 0.012376 4.54e-52 0.012507 0.998655 ( 0.000258) 0.986148 ( 0.004092) 0.998635 0.986420 --->beagle1-----germline1: 4.74e-18 0.000630 2.45e-36 0.000604 0.998655 ( 0.000258) 0.998051 ( 0.000164) 0.998635 0.998048 --->beagle1-----germline2: 6.51e-02 -0.001009 3.19e-01 0.009995 0.998655 ( 0.000258) 0.988660 ( 0.099898) 0.998635 1.000000 --->beagle1-----dash-----: 3.25e-04 0.000390 4.7e-05 0.000410 0.998655 ( 0.000258) 0.998245 ( 0.000937) 0.998635 0.998391 --->beagle2-----plink----: 3.96e-18 0.012322 9.04e-52 0.012448 0.998596 ( 0.000411) 0.986148 ( 0.004092) 0.998585 0.986420 --->beagle2-----germline1: 6.73e-15 0.000565 1.29e-21 0.000545 0.998596 ( 0.000411) 0.998051 ( 0.000164) 0.998585 0.998048 --->beagle2-----germline2: 3.83e-02 -0.000944 3.22e-01 0.009936 0.998596 ( 0.000411) 0.988660 ( 0.099898) 0.998585 1.000000 --->beagle2-----dash-----: 3.9e-03 0.000312 8.82e-04 0.000351 0.998596 ( 0.000411) 0.998245 ( 0.000937) 0.998585 0.998391 --->plink-------germline1: 3.96e-18 -0.011780 2.04e-50 -0.011903 0.986148 ( 0.004092) 0.998051 ( 0.000164) 0.986420 0.998048 --->plink-------germline2: 7.67e-17 -0.012372 8.03e-01 -0.002513 0.986148 ( 0.004092) 0.988660 ( 0.099898) 0.986420 1.000000 --->plink-------dash-----: 3.96e-18 -0.012027 3.57e-48 -0.012097 0.986148 ( 0.004092) 0.998245 ( 0.000937) 0.986420 0.998391 --->germline1---germline2: 2.17e-03 -0.001699 3.49e-01 0.009391 0.998051 ( 0.000164) 0.988660 ( 0.099898) 0.998048 1.000000 --->germline1---dash-----: 2.72e-02 -0.000235 5.71e-02 -0.000194 0.998051 ( 0.000164) 0.998245 ( 0.000937) 0.998048 0.998391 --->germline2---dash-----: 9.02e-03 0.001068 3.4e-01 -0.009585 0.988660 ( 0.099898) 0.998245 ( 0.000937) 1.000000 0.998391 ######specifity###### --->fabia-------beagle1--: 3.96e-18 0.223543 1.52e-115 0.223871 0.999985 ( 3.84e-05) 0.776114 ( 0.016011) 1.000000 0.777471 --->fabia-------beagle2--: 3.96e-18 0.086710 1.56e-96 0.086815 0.999985 ( 3.84e-05) 0.913169 ( 0.009694) 1.000000 0.913458 --->fabia-------plink----: 3.96e-18 0.017016 1.31e-100 0.017028 0.999985 ( 3.84e-05) 0.982957 ( 0.001721) 1.000000 0.983167 --->fabia-------germline1: 3.96e-18 0.788429 6.14e-136 0.787353 0.999985 ( 3.84e-05) 0.212632 ( 0.035003) 1.000000 0.210523 --->fabia-------germline2: 5.78e-18 0.010008 5.18e-54 0.009787 0.999985 ( 3.84e-05) 0.990198 ( 0.003066) 1.000000 0.989934 --->fabia-------dash-----: 3.96e-18 0.124187 5.32e-64 0.123142 0.999985 ( 3.84e-05) 0.876843 ( 0.029977) 1.000000 0.886391 --->beagle1-----beagle2--: 3.96e-18 -0.136794 3.15e-119 -0.137055 0.776114 ( 0.016011) 0.913169 ( 0.009694) 0.777471 0.913458 --->beagle1-----plink----: 3.96e-18 -0.206292 3.98e-113 -0.206843 0.776114 ( 0.016011) 0.982957 ( 0.001721) 0.777471 0.983167 --->beagle1-----germline1: 3.96e-18 0.565170 4.92e-114 0.563482 0.776114 ( 0.016011) 0.212632 ( 0.035003) 0.777471 0.210523 --->beagle1-----germline2: 3.96e-18 -0.213814 4.06e-111 -0.214084 0.776114 ( 0.016011) 0.990198 ( 0.003066) 0.777471 0.989934 --->beagle1-----dash-----: 3.96e-18 -0.099308 1.31e-51 -0.100729 0.776114 ( 0.016011) 0.876843 ( 0.029977) 0.777471 0.886391 --->beagle2-----plink----: 3.96e-18 -0.069607 3.58e-89 -0.069788 0.913169 ( 0.009694) 0.982957 ( 0.001721) 0.913458 0.983167 --->beagle2-----germline1: 3.96e-18 0.701737 1.6e-127 0.700537 0.913169 ( 0.009694) 0.212632 ( 0.035003) 0.913458 0.210523 --->beagle2-----germline2: 3.96e-18 -0.077063 5.74e-87 -0.077029 0.913169 ( 0.009694) 0.990198 ( 0.003066) 0.913458 0.989934 --->beagle2-----dash-----: 1.19e-14 0.036714 6.65e-20 0.036327 0.913169 ( 0.009694) 0.876843 ( 0.029977) 0.913458 0.886391 --->plink-------germline1: 3.96e-18 0.771331 1.29e-134 0.770325 0.982957 ( 0.001721) 0.212632 ( 0.035003) 0.983167 0.210523 --->plink-------germline2: 1.33e-16 -0.007248 1.49e-36 -0.007241 0.982957 ( 0.001721) 0.990198 ( 0.003066) 0.983167 0.989934 --->plink-------dash-----: 3.96e-18 0.105476 4.26e-58 0.106114 0.982957 ( 0.001721) 0.876843 ( 0.029977) 0.983167 0.886391 --->germline1---germline2: 3.96e-18 -0.778494 5.95e-135 -0.777566 0.212632 ( 0.035003) 0.990198 ( 0.003066) 0.210523 0.989934 --->germline1---dash-----: 3.96e-18 -0.664823 1.51e-108 -0.664210 0.212632 ( 0.035003) 0.876843 ( 0.029977) 0.210523 0.886391 --->germline2---dash-----: 3.96e-18 0.112805 5.67e-61 0.113355 0.990198 ( 0.003066) 0.876843 ( 0.029977) 0.989934 0.886391 ######sensitivity###### --->fabia-------beagle1--: 3.96e-18 0.408994 4.72e-67 0.409175 0.560511 ( 0.089151) 0.151337 ( 0.031798) 0.560113 0.149702 --->fabia-------beagle2--: 3.96e-18 0.499734 1.52e-75 0.499373 0.560511 ( 0.089151) 0.061138 ( 0.018863) 0.560113 0.061368 --->fabia-------plink----: 3.96e-18 0.439828 1.93e-67 0.440832 0.560511 ( 0.089151) 0.119679 ( 0.035696) 0.560113 0.121667 --->fabia-------germline1: 6.6e-18 -0.210750 4e-34 -0.211083 0.560511 ( 0.089151) 0.771595 ( 0.074651) 0.560113 0.785410 --->fabia-------germline2: 3.96e-18 0.554352 8e-80 0.553780 0.560511 ( 0.089151) 0.006732 ( 0.013024) 0.560113 0.000000 --->fabia-------dash-----: 3.96e-18 0.456814 7.46e-62 0.452729 0.560511 ( 0.089151) 0.107783 ( 0.060577) 0.560113 0.095582 --->beagle1-----beagle2--: 3.96e-18 0.090069 1.1e-58 0.090198 0.151337 ( 0.031798) 0.061138 ( 0.018863) 0.149702 0.061368 --->beagle1-----plink----: 3.66e-08 0.030465 2.76e-09 0.031657 0.151337 ( 0.031798) 0.119679 ( 0.035696) 0.149702 0.121667 --->beagle1-----germline1: 3.96e-18 -0.622796 1.66e-90 -0.620258 0.151337 ( 0.031798) 0.771595 ( 0.074651) 0.149702 0.785410 --->beagle1-----germline2: 3.96e-18 0.144208 7.9e-64 0.144605 0.151337 ( 0.031798) 0.006732 ( 0.013024) 0.149702 0.000000 --->beagle1-----dash-----: 4.9e-08 0.046972 8.6e-09 0.043554 0.151337 ( 0.031798) 0.107783 ( 0.060577) 0.149702 0.095582 --->beagle2-----plink----: 9.13e-17 -0.058542 3.89e-26 -0.058541 0.061138 ( 0.018863) 0.119679 ( 0.035696) 0.061368 0.121667 --->beagle2-----germline1: 3.96e-18 -0.713810 2.95e-97 -0.710457 0.061138 ( 0.018863) 0.771595 ( 0.074651) 0.061368 0.785410 --->beagle2-----germline2: 4.89e-18 0.054690 1.59e-41 0.054406 0.061138 ( 0.018863) 0.006732 ( 0.013024) 0.061368 0.000000 --->beagle2-----dash-----: 8.66e-10 -0.043147 4.6e-11 -0.046644 0.061138 ( 0.018863) 0.107783 ( 0.060577) 0.061368 0.095582 --->plink-------germline1: 3.96e-18 -0.655167 5.29e-92 -0.651915 0.119679 ( 0.035696) 0.771595 ( 0.074651) 0.121667 0.785410 --->plink-------germline2: 3.96e-18 0.111735 2.91e-52 0.112948 0.119679 ( 0.035696) 0.006732 ( 0.013024) 0.121667 0.000000 --->plink-------dash-----: 5.27e-02 0.014630 1.14e-01 0.011897 0.119679 ( 0.035696) 0.107783 ( 0.060577) 0.121667 0.095582 --->germline1---germline2: 3.96e-18 0.767576 4.78e-102 0.764863 0.771595 ( 0.074651) 0.006732 ( 0.013024) 0.785410 0.000000 --->germline1---dash-----: 3.96e-18 0.668612 2.5e-78 0.663812 0.771595 ( 0.074651) 0.107783 ( 0.060577) 0.785410 0.095582 --->germline2---dash-----: 6.6e-18 -0.098339 7.82e-29 -0.101051 0.006732 ( 0.013024) 0.107783 ( 0.060577) 0.000000 0.095582 ######trueN###### --->fabia-------beagle1--: 3.96e-18 12230813 1.56e-188 12234045 2e+07 ( 928) 7745694 ( 159839) 2e+07 7758890 --->fabia-------beagle2--: 3.96e-18 10865029 5.63e-205 10866219 2e+07 ( 928) 9113520 ( 96770) 2e+07 9116674 --->fabia-------plink----: 3.96e-18 10169560 4.4e-276 10169730 2e+07 ( 928) 9810008 ( 17189) 2e+07 9811776 --->fabia-------germline1: 3.96e-18 17868371 3.51e-171 17857656 2e+07 ( 928) 2122083 ( 349280) 2e+07 2101117 --->fabia-------germline2: 3.96e-18 10099259 1.42e-251 10097467 2e+07 ( 928) 9882272 ( 30541) 2e+07 9879896 --->fabia-------dash-----: 3.96e-18 11239534 6.36e-158 11228758 2e+07 ( 928) 8750981 ( 299330) 2e+07 8846096 --->beagle1-----beagle2--: 3.96e-18 -1365397 3.11e-119 -1367826 7745694 ( 159839) 9113520 ( 96770) 7758890 9116674 --->beagle1-----plink----: 3.96e-18 -2059028 3.95e-113 -2064315 7745694 ( 159839) 9810008 ( 17189) 7758890 9811776 --->beagle1-----germline1: 3.96e-18 5640278 5.06e-114 5623611 7745694 ( 159839) 2122083 ( 349280) 7758890 2101117 --->beagle1-----germline2: 3.96e-18 -2133840 4.02e-111 -2136578 7745694 ( 159839) 9882272 ( 30541) 7758890 9879896 --->beagle1-----dash-----: 3.96e-18 -990960 1.31e-51 -1005287 7745694 ( 159839) 8750981 ( 299330) 7758890 8846096 --->beagle2-----plink----: 3.96e-18 -694887 3.58e-89 -696489 9113520 ( 96770) 9810008 ( 17189) 9116674 9811776 --->beagle2-----germline1: 3.96e-18 7e+06 1.67e-127 6991437 9113520 ( 96770) 2122083 ( 349280) 9116674 2101117 --->beagle2-----germline2: 3.96e-18 -768935 5.72e-87 -768753 9113520 ( 96770) 9882272 ( 30541) 9116674 9879896 --->beagle2-----dash-----: 1.19e-14 366267 6.65e-20 362539 9113520 ( 96770) 8750981 ( 299330) 9116674 8846096 --->plink-------germline1: 3.96e-18 7697794 1.35e-134 7687926 9810008 ( 17189) 2122083 ( 349280) 9811776 2101117 --->plink-------germline2: 1.33e-16 -72325 1.49e-36 -72264 9810008 ( 17189) 9882272 ( 30541) 9811776 9879896 --->plink-------dash-----: 3.96e-18 1052753 4.23e-58 1059028 9810008 ( 17189) 8750981 ( 299330) 9811776 8846096 --->germline1---germline2: 3.96e-18 -7769581 6.23e-135 -7760189 2122083 ( 349280) 9882272 ( 30541) 2101117 9879896 --->germline1---dash-----: 3.96e-18 -6634993 1.55e-108 -6628898 2122083 ( 349280) 8750981 ( 299330) 2101117 8846096 --->germline2---dash-----: 3.96e-18 1125570 5.63e-61 1131292 9882272 ( 30541) 8750981 ( 299330) 9879896 8846096 ######falseP###### --->fabia-------beagle1--: 3.96e-18 -2230830 1.56e-115 -2234100 304 ( 768) 2234404 ( 159778) 0 2220762 --->fabia-------beagle2--: 3.96e-18 -865074 1.68e-96 -866274 304 ( 768) 866578 ( 96741) 0 863722 --->fabia-------plink----: 3.96e-18 -169609 2.29e-100 -169786 304 ( 768) 170090 ( 17176) 0 167994 --->fabia-------germline1: 3.96e-18 -7868418 6.43e-136 -7857711 304 ( 768) 7858015 ( 349507) 0 7879344 --->fabia-------germline2: 5.78e-18 -99639 4.79e-54 -97522 304 ( 768) 97826 ( 30604) 0 1e+05 --->fabia-------dash-----: 3.96e-18 -1239607 5.35e-64 -1228813 304 ( 768) 1229117 ( 299152) 0 1133804 --->beagle1-----beagle2--: 3.96e-18 1365396 3.11e-119 1367826 2234404 ( 159778) 866578 ( 96741) 2220762 863722 --->beagle1-----plink----: 3.96e-18 2058998 3.95e-113 2064315 2234404 ( 159778) 170090 ( 17176) 2220762 167994 --->beagle1-----germline1: 3.96e-18 -5640220 5.06e-114 -5623611 2234404 ( 159778) 7858015 ( 349507) 2220762 7879344 --->beagle1-----germline2: 3.96e-18 2133825 4.02e-111 2136578 2234404 ( 159778) 97826 ( 30604) 2220762 1e+05 --->beagle1-----dash-----: 3.96e-18 990848 1.31e-51 1005287 2234404 ( 159778) 1229117 ( 299152) 2220762 1133804 --->beagle2-----plink----: 3.96e-18 694900 3.58e-89 696489 866578 ( 96741) 170090 ( 17176) 863722 167994 --->beagle2-----germline1: 3.96e-18 -7e+06 1.67e-127 -6991437 866578 ( 96741) 7858015 ( 349507) 863722 7879344 --->beagle2-----germline2: 3.96e-18 768909 5.72e-87 768753 866578 ( 96741) 97826 ( 30604) 863722 1e+05 --->beagle2-----dash-----: 1.19e-14 -366344 6.65e-20 -362539 866578 ( 96741) 1229117 ( 299152) 863722 1133804 --->plink-------germline1: 3.96e-18 -7697832 1.35e-134 -7687926 170090 ( 17176) 7858015 ( 349507) 167994 7879344 --->plink-------germline2: 1.33e-16 72316 1.49e-36 72264 170090 ( 17176) 97826 ( 30604) 167994 1e+05 --->plink-------dash-----: 3.96e-18 -1052730 4.23e-58 -1059028 170090 ( 17176) 1229117 ( 299152) 167994 1133804 --->germline1---germline2: 3.96e-18 7769561 6.23e-135 7760189 7858015 ( 349507) 97826 ( 30604) 7879344 1e+05 --->germline1---dash-----: 3.96e-18 6635010 1.55e-108 6628898 7858015 ( 349507) 1229117 ( 299152) 7879344 1133804 --->germline2---dash-----: 3.96e-18 -1125597 5.63e-61 -1131292 97826 ( 30604) 1229117 ( 299152) 1e+05 1133804 ######falseN###### --->fabia-------beagle1--: 3.96e-18 -8098 4.81e-67 -8116 8774 ( 1807) 16890 ( 755) 8805 16913 --->fabia-------beagle2--: 3.96e-18 -9917 1.46e-75 -9911 8774 ( 1807) 18684 ( 572) 8805 18724 --->fabia-------plink----: 3.96e-18 -8724 2.02e-67 -8746 8774 ( 1807) 17520 ( 830) 8805 17542 --->fabia-------germline1: 6.6e-18 4204 2.5e-34 4217 8774 ( 1807) 4557 ( 1529) 8805 4221 --->fabia-------germline2: 3.96e-18 -10995 9.21e-80 -10995 8774 ( 1807) 19769 ( 572) 8805 19826 --->fabia-------dash-----: 3.96e-18 -9047 3.68e-62 -8977 8774 ( 1807) 17751 ( 1198) 8805 17794 --->beagle1-----beagle2--: 3.96e-18 -1791 2.29e-58 -1795 16890 ( 755) 18684 ( 572) 16913 18724 --->beagle1-----plink----: 3.7e-08 -607 2.99e-09 -630 16890 ( 755) 17520 ( 830) 16913 17542 --->beagle1-----germline1: 3.96e-18 12379 5.6e-92 12333 16890 ( 755) 4557 ( 1529) 16913 4221 --->beagle1-----germline2: 3.96e-18 -2867 2.35e-63 -2879 16890 ( 755) 19769 ( 572) 16913 19826 --->beagle1-----dash-----: 4.81e-08 -936 1.03e-08 -861 16890 ( 755) 17751 ( 1198) 16913 17794 --->beagle2-----plink----: 9.4e-17 1163 4.05e-26 1165 18684 ( 572) 17520 ( 830) 18724 17542 --->beagle2-----germline1: 3.96e-18 14172 4.48e-99 14128 18684 ( 572) 4557 ( 1529) 18724 4221 --->beagle2-----germline2: 4.89e-18 -1088 2.28e-41 -1084 18684 ( 572) 19769 ( 572) 18724 19826 --->beagle2-----dash-----: 8.3e-10 863 4.79e-11 934 18684 ( 572) 17751 ( 1198) 18724 17794 --->plink-------germline1: 3.96e-18 13031 2.05e-93 12963 17520 ( 830) 4557 ( 1529) 17542 4221 --->plink-------germline2: 3.96e-18 -2219 5.28e-52 -2249 17520 ( 830) 19769 ( 572) 17542 19826 --->plink-------dash-----: 5.42e-02 -289 1.25e-01 -231 17520 ( 830) 17751 ( 1198) 17542 17794 --->germline1---germline2: 3.96e-18 -15264 1.11e-103 -15212 4557 ( 1529) 19769 ( 572) 4221 19826 --->germline1---dash-----: 3.96e-18 -13295 1.18e-79 -13194 4557 ( 1529) 17751 ( 1198) 4221 17794 --->germline2---dash-----: 6.6e-18 1959 1.5e-28 2018 19769 ( 572) 17751 ( 1198) 19826 17794 ######trueP###### --->fabia-------beagle1--: 3.96e-18 8149 4.03e-67 8171 11184 ( 1783) 3012 ( 640) 11224 2996 --->fabia-------beagle2--: 3.96e-18 9968 1.63e-75 9966 11184 ( 1783) 1217 ( 379) 11224 1226 --->fabia-------plink----: 3.96e-18 8776 2.71e-67 8802 11184 ( 1783) 2382 ( 715) 11224 2343 --->fabia-------germline1: 7.22e-18 -4156 1.06e-33 -4161 11184 ( 1783) 15345 ( 1422) 11224 15549 --->fabia-------germline2: 3.96e-18 11052 1.1e-79 11050 11184 ( 1783) 133 ( 257) 11224 0 --->fabia-------dash-----: 3.96e-18 9100 3.84e-62 9032 11184 ( 1783) 2151 ( 1223) 11224 1896 --->beagle1-----beagle2--: 3.96e-18 1791 2.29e-58 1795 3012 ( 640) 1217 ( 379) 2996 1226 --->beagle1-----plink----: 3.7e-08 607 2.99e-09 630 3012 ( 640) 2382 ( 715) 2996 2343 --->beagle1-----germline1: 3.96e-18 -12379 5.6e-92 -12333 3012 ( 640) 15345 ( 1422) 2996 15549 --->beagle1-----germline2: 3.96e-18 2866 2.35e-63 2879 3012 ( 640) 133 ( 257) 2996 0 --->beagle1-----dash-----: 4.81e-08 936 1.03e-08 861 3012 ( 640) 2151 ( 1223) 2996 1896 --->beagle2-----plink----: 9.4e-17 -1163 4.05e-26 -1165 1217 ( 379) 2382 ( 715) 1226 2343 --->beagle2-----germline1: 3.96e-18 -14172 4.48e-99 -14128 1217 ( 379) 15345 ( 1422) 1226 15549 --->beagle2-----germline2: 4.89e-18 1088 2.28e-41 1084 1217 ( 379) 133 ( 257) 1226 0 --->beagle2-----dash-----: 8.3e-10 -863 4.79e-11 -934 1217 ( 379) 2151 ( 1223) 1226 1896 --->plink-------germline1: 3.96e-18 -13031 2.05e-93 -12963 2382 ( 715) 15345 ( 1422) 2343 15549 --->plink-------germline2: 3.96e-18 2219 5.28e-52 2249 2382 ( 715) 133 ( 257) 2343 0 --->plink-------dash-----: 5.42e-02 289 1.25e-01 231 2382 ( 715) 2151 ( 1223) 2343 1896 --->germline1---germline2: 3.96e-18 15264 1.11e-103 15212 15345 ( 1422) 133 ( 257) 15549 0 --->germline1---dash-----: 3.96e-18 13294 1.18e-79 13194 15345 ( 1422) 2151 ( 1223) 15549 1896 --->germline2---dash-----: 6.6e-18 -1958 1.5e-28 -2018 133 ( 257) 2151 ( 1223) 0 1896 ######MatthewsSnps###### --->fabia-------beagle1--: 1e+00 0.000000 1e+00 0.000000 0.742408 ( 0.095085) 0.000000 ( 0.000000) 0.745367 0.000000 --->fabia-------beagle2--: 3.96e-18 0.745239 8.78e-91 0.742868 0.742408 ( 0.095085) -0.000460 ( 0.004599) 0.745367 0.000000 --->fabia-------plink----: 3.96e-18 0.727338 8.24e-87 0.725833 0.742408 ( 0.095085) 0.016575 ( 0.056035) 0.745367 0.035100 --->fabia-------germline1: 3.96e-18 0.733292 1.37e-76 0.730341 0.742408 ( 0.095085) 0.012066 ( 0.073475) 0.745367 0.014894 --->fabia-------germline2: 3.96e-18 0.753780 5.61e-78 0.747938 0.742408 ( 0.095085) -0.005530 ( 0.080368) 0.745367 -0.048373 --->fabia-------dash-----: 3.96e-18 0.743448 2.84e-78 0.744144 0.742408 ( 0.095085) -0.001736 ( 0.083341) 0.745367 -0.005619 --->beagle1-----beagle2--: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) -0.000460 ( 0.004599) 0.000000 0.000000 --->beagle1-----plink----: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.016575 ( 0.056035) 0.000000 0.035100 --->beagle1-----germline1: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.012066 ( 0.073475) 0.000000 0.014894 --->beagle1-----germline2: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) -0.005530 ( 0.080368) 0.000000 -0.048373 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) -0.001736 ( 0.083341) 0.000000 -0.005619 --->beagle2-----plink----: 2.09e-04 -0.024276 3.31e-03 -0.017035 -0.000460 ( 0.004599) 0.016575 ( 0.056035) 0.000000 0.035100 --->beagle2-----germline1: 6.71e-02 -0.014475 9.26e-02 -0.012526 -0.000460 ( 0.004599) 0.012066 ( 0.073475) 0.000000 0.014894 --->beagle2-----germline2: 3.32e-02 0.032630 5.29e-01 0.005070 -0.000460 ( 0.004599) -0.005530 ( 0.080368) 0.000000 -0.048373 --->beagle2-----dash-----: 7.45e-01 0.003028 8.79e-01 0.001276 -0.000460 ( 0.004599) -0.001736 ( 0.083341) 0.000000 -0.005619 --->plink-------germline1: 5.26e-01 0.006331 6.29e-01 0.004508 0.016575 ( 0.056035) 0.012066 ( 0.073475) 0.035100 0.014894 --->plink-------germline2: 4.16e-03 0.033766 3.07e-02 0.022105 0.016575 ( 0.056035) -0.005530 ( 0.080368) 0.035100 -0.048373 --->plink-------dash-----: 5.19e-02 0.020578 6.65e-02 0.018311 0.016575 ( 0.056035) -0.001736 ( 0.083341) 0.035100 -0.005619 --->germline1---germline2: 3.43e-02 0.026271 1.1e-01 0.017596 0.012066 ( 0.073475) -0.005530 ( 0.080368) 0.014894 -0.048373 --->germline1---dash-----: 2.19e-01 0.015624 3.04e-01 0.013803 0.012066 ( 0.073475) -0.001736 ( 0.083341) 0.014894 -0.005619 --->germline2---dash-----: 3.89e-01 -0.010011 7.58e-01 -0.003794 -0.005530 ( 0.080368) -0.001736 ( 0.083341) -0.048373 -0.005619 ######F1Snps###### --->fabia-------beagle1--: 3.96e-18 0.479127 1.18e-81 0.477905 0.787202 ( 0.076342) 0.309297 ( 0.014900) 0.785628 0.309526 --->fabia-------beagle2--: 3.96e-18 0.479298 1.14e-81 0.477967 0.787202 ( 0.076342) 0.309235 ( 0.014940) 0.785628 0.309526 --->fabia-------plink----: 3.96e-18 0.478741 3.28e-82 0.477494 0.787202 ( 0.076342) 0.309708 ( 0.015774) 0.785628 0.309911 --->fabia-------germline1: 3.96e-18 0.488232 1.83e-78 0.486073 0.787202 ( 0.076342) 0.301129 ( 0.026576) 0.785628 0.302601 --->fabia-------germline2: 3.96e-18 0.770897 6.37e-96 0.767876 0.787202 ( 0.076342) 0.019326 ( 0.034574) 0.785628 0.000000 --->fabia-------dash-----: 3.96e-18 0.641293 4.53e-81 0.641384 0.787202 ( 0.076342) 0.145818 ( 0.071290) 0.785628 0.132317 --->beagle1-----beagle2--: 1e+00 0.000000 1e+00 0.000000 0.309297 ( 0.014900) 0.309235 ( 0.014940) 0.309526 0.309526 --->beagle1-----plink----: 2.21e-02 -0.001238 4.91e-01 -0.000411 0.309297 ( 0.014900) 0.309708 ( 0.015774) 0.309526 0.309911 --->beagle1-----germline1: 2.58e-03 0.007534 9.21e-04 0.008169 0.309297 ( 0.014900) 0.301129 ( 0.026576) 0.309526 0.302601 --->beagle1-----germline2: 3.96e-18 0.297244 4.64e-88 0.289971 0.309297 ( 0.014900) 0.019326 ( 0.034574) 0.309526 0.000000 --->beagle1-----dash-----: 4.33e-18 0.165717 5.32e-42 0.163479 0.309297 ( 0.014900) 0.145818 ( 0.071290) 0.309526 0.132317 --->beagle2-----plink----: 2.02e-02 -0.001311 4.34e-01 -0.000473 0.309235 ( 0.014940) 0.309708 ( 0.015774) 0.309526 0.309911 --->beagle2-----germline1: 2.82e-03 0.007447 1.02e-03 0.008106 0.309235 ( 0.014940) 0.301129 ( 0.026576) 0.309526 0.302601 --->beagle2-----germline2: 3.96e-18 0.297050 4.55e-88 0.289909 0.309235 ( 0.014940) 0.019326 ( 0.034574) 0.309526 0.000000 --->beagle2-----dash-----: 4.33e-18 0.165689 5.71e-42 0.163417 0.309235 ( 0.014940) 0.145818 ( 0.071290) 0.309526 0.132317 --->plink-------germline1: 1.57e-03 0.008136 7.95e-04 0.008580 0.309708 ( 0.015774) 0.301129 ( 0.026576) 0.309911 0.302601 --->plink-------germline2: 3.96e-18 0.297579 2.37e-87 0.290382 0.309708 ( 0.015774) 0.019326 ( 0.034574) 0.309911 0.000000 --->plink-------dash-----: 4.46e-18 0.166068 5.7e-42 0.163891 0.309708 ( 0.015774) 0.145818 ( 0.071290) 0.309911 0.132317 --->germline1---germline2: 3.96e-18 0.286920 1.75e-81 0.281802 0.301129 ( 0.026576) 0.019326 ( 0.034574) 0.302601 0.000000 --->germline1---dash-----: 1.24e-17 0.157469 2.81e-34 0.155311 0.301129 ( 0.026576) 0.145818 ( 0.071290) 0.302601 0.132317 --->germline2---dash-----: 3.7e-17 -0.125958 1.39e-27 -0.126492 0.019326 ( 0.034574) 0.145818 ( 0.071290) 0.000000 0.132317 ######accuracySnps###### --->fabia-------beagle1--: 3.96e-18 0.736335 9.08e-127 0.733424 0.916455 ( 0.039190) 0.183031 ( 0.010426) 0.924150 0.183100 --->fabia-------beagle2--: 3.96e-18 0.736165 9.11e-127 0.733307 0.916455 ( 0.039190) 0.183148 ( 0.010442) 0.924150 0.183250 --->fabia-------plink----: 3.96e-18 0.722548 1.82e-124 0.719191 0.916455 ( 0.039190) 0.197264 ( 0.012475) 0.924150 0.198050 --->fabia-------germline1: 3.96e-18 0.606390 3.33e-108 0.604578 0.916455 ( 0.039190) 0.311877 ( 0.031120) 0.924150 0.311700 --->fabia-------germline2: 5.51e-18 0.110215 1.11e-45 0.107230 0.916455 ( 0.039190) 0.809225 ( 0.012930) 0.924150 0.809050 --->fabia-------dash-----: 3.95e-18 0.182399 7.11e-57 0.179819 0.916455 ( 0.039190) 0.736636 ( 0.031958) 0.924150 0.737350 --->beagle1-----beagle2--: 1e+00 0.000000 3.2e-01 -0.000117 0.183031 ( 0.010426) 0.183148 ( 0.010442) 0.183100 0.183250 --->beagle1-----plink----: 6.4e-18 -0.013366 9.84e-25 -0.014233 0.183031 ( 0.010426) 0.197264 ( 0.012475) 0.183100 0.198050 --->beagle1-----germline1: 3.96e-18 -0.128615 1.3e-67 -0.128846 0.183031 ( 0.010426) 0.311877 ( 0.031120) 0.183100 0.311700 --->beagle1-----germline2: 3.96e-18 -0.626262 3.67e-145 -0.626194 0.183031 ( 0.010426) 0.809225 ( 0.012930) 0.183100 0.809050 --->beagle1-----dash-----: 3.95e-18 -0.554810 2.29e-118 -0.553605 0.183031 ( 0.010426) 0.736636 ( 0.031958) 0.183100 0.737350 --->beagle2-----plink----: 6.4e-18 -0.013216 1.27e-24 -0.014116 0.183148 ( 0.010442) 0.197264 ( 0.012475) 0.183250 0.198050 --->beagle2-----germline1: 3.96e-18 -0.128484 1.46e-67 -0.128729 0.183148 ( 0.010442) 0.311877 ( 0.031120) 0.183250 0.311700 --->beagle2-----germline2: 3.96e-18 -0.626100 3.74e-145 -0.626077 0.183148 ( 0.010442) 0.809225 ( 0.012930) 0.183250 0.809050 --->beagle2-----dash-----: 3.95e-18 -0.554735 1.66e-118 -0.553488 0.183148 ( 0.010442) 0.736636 ( 0.031958) 0.183250 0.737350 --->plink-------germline1: 3.96e-18 -0.114126 4.53e-61 -0.114613 0.197264 ( 0.012475) 0.311877 ( 0.031120) 0.198050 0.311700 --->plink-------germline2: 3.96e-18 -0.612070 6.26e-145 -0.611961 0.197264 ( 0.012475) 0.809225 ( 0.012930) 0.198050 0.809050 --->plink-------dash-----: 3.96e-18 -0.540123 1.21e-117 -0.539372 0.197264 ( 0.012475) 0.736636 ( 0.031958) 0.198050 0.737350 --->germline1---germline2: 3.95e-18 -0.497668 7.16e-113 -0.497348 0.311877 ( 0.031120) 0.809225 ( 0.012930) 0.311700 0.809050 --->germline1---dash-----: 3.96e-18 -0.426937 8.12e-90 -0.424759 0.311877 ( 0.031120) 0.736636 ( 0.031958) 0.311700 0.737350 --->germline2---dash-----: 3.96e-18 0.071456 1.34e-42 0.072589 0.809225 ( 0.012930) 0.736636 ( 0.031958) 0.809050 0.737350 ######FPRSnps###### --->fabia-------beagle1--: 3.96e-18 -0.038966 6.37e-128 -0.038777 0.002484 ( 0.002053) 0.041260 ( 0.000523) 0.002189 0.041259 --->fabia-------beagle2--: 3.96e-18 -0.038956 5.49e-128 -0.038767 0.002484 ( 0.002053) 0.041251 ( 0.000528) 0.002189 0.041253 --->fabia-------plink----: 3.96e-18 -0.038103 4.1e-124 -0.037916 0.002484 ( 0.002053) 0.040400 ( 0.000620) 0.002189 0.040390 --->fabia-------germline1: 3.96e-18 -0.030650 1.39e-109 -0.030520 0.002484 ( 0.002053) 0.033003 ( 0.001647) 0.002189 0.033157 --->fabia-------germline2: 1.69e-14 0.001803 4.66e-16 0.001999 0.002484 ( 0.002053) 0.000485 ( 0.000205) 0.002189 0.000533 --->fabia-------dash-----: 4.74e-13 -0.002938 6.55e-18 -0.002730 0.002484 ( 0.002053) 0.005214 ( 0.001403) 0.002189 0.005200 --->beagle1-----beagle2--: 1e+00 0.000000 1e+00 0.000000 0.041260 ( 0.000523) 0.041251 ( 0.000528) 0.041259 0.041253 --->beagle1-----plink----: 3.96e-18 0.000812 3.56e-30 0.000860 0.041260 ( 0.000523) 0.040400 ( 0.000620) 0.041259 0.040390 --->beagle1-----germline1: 3.96e-18 0.008246 2.72e-77 0.008257 0.041260 ( 0.000523) 0.033003 ( 0.001647) 0.041259 0.033157 --->beagle1-----germline2: 3.96e-18 0.040784 7.43e-186 0.040775 0.041260 ( 0.000523) 0.000485 ( 0.000205) 0.041259 0.000533 --->beagle1-----dash-----: 3.96e-18 0.036091 9.69e-137 0.036047 0.041260 ( 0.000523) 0.005214 ( 0.001403) 0.041259 0.005200 --->beagle2-----plink----: 3.96e-18 0.000801 1.03e-29 0.000851 0.041251 ( 0.000528) 0.040400 ( 0.000620) 0.041253 0.040390 --->beagle2-----germline1: 3.96e-18 0.008233 4.04e-77 0.008247 0.041251 ( 0.000528) 0.033003 ( 0.001647) 0.041253 0.033157 --->beagle2-----germline2: 3.96e-18 0.040784 2.1e-185 0.040766 0.041251 ( 0.000528) 0.000485 ( 0.000205) 0.041253 0.000533 --->beagle2-----dash-----: 3.96e-18 0.036084 5.3e-137 0.036037 0.041251 ( 0.000528) 0.005214 ( 0.001403) 0.041253 0.005200 --->plink-------germline1: 3.96e-18 0.007387 4.05e-69 0.007397 0.040400 ( 0.000620) 0.033003 ( 0.001647) 0.040390 0.033157 --->plink-------germline2: 3.96e-18 0.039928 9.22e-179 0.039915 0.040400 ( 0.000620) 0.000485 ( 0.000205) 0.040390 0.000533 --->plink-------dash-----: 3.96e-18 0.035156 1.51e-135 0.035186 0.040400 ( 0.000620) 0.005214 ( 0.001403) 0.040390 0.005200 --->germline1---germline2: 3.96e-18 0.032523 2.55e-129 0.032518 0.033003 ( 0.001647) 0.000485 ( 0.000205) 0.033157 0.000533 --->germline1---dash-----: 3.96e-18 0.027840 1.34e-103 0.027790 0.033003 ( 0.001647) 0.005214 ( 0.001403) 0.033157 0.005200 --->germline2---dash-----: 3.96e-18 -0.004707 4.09e-56 -0.004729 0.000485 ( 0.000205) 0.005214 ( 0.001403) 0.000533 0.005200 ######FDRSnps###### --->fabia-------beagle1--: 3.96e-18 -0.598933 2.51e-65 -0.596694 0.220275 ( 0.141725) 0.816969 ( 0.010426) 0.222308 0.816900 --->fabia-------beagle2--: 3.96e-18 -0.598928 2.52e-65 -0.596723 0.220275 ( 0.141725) 0.816998 ( 0.010443) 0.222308 0.816900 --->fabia-------plink----: 3.96e-18 -0.597930 1.94e-65 -0.595883 0.220275 ( 0.141725) 0.816159 ( 0.010809) 0.222308 0.816375 --->fabia-------germline1: 3.96e-18 -0.597056 2.65e-64 -0.594634 0.220275 ( 0.141725) 0.814909 ( 0.017326) 0.222308 0.815057 --->fabia-------germline2: 2.59e-17 -0.669922 5.75e-34 -0.619348 0.220275 ( 0.141725) 0.839623 ( 0.288168) 0.222308 1.000000 --->fabia-------dash-----: 3.96e-18 -0.597989 4.56e-59 -0.597777 0.220275 ( 0.141725) 0.818052 ( 0.088222) 0.222308 0.834635 --->beagle1-----beagle2--: 1e+00 0.000000 1e+00 0.000000 0.816969 ( 0.010426) 0.816998 ( 0.010443) 0.816900 0.816900 --->beagle1-----plink----: 4.86e-04 0.001244 2.31e-02 0.000810 0.816969 ( 0.010426) 0.816159 ( 0.010809) 0.816900 0.816375 --->beagle1-----germline1: 1.06e-01 0.002299 1.53e-01 0.002060 0.816969 ( 0.010426) 0.814909 ( 0.017326) 0.816900 0.815057 --->beagle1-----germline2: 3.18e-02 -0.139582 4.36e-01 -0.022654 0.816969 ( 0.010426) 0.839623 ( 0.288168) 0.816900 1.000000 --->beagle1-----dash-----: 6.81e-01 -0.003290 9.01e-01 -0.001083 0.816969 ( 0.010426) 0.818052 ( 0.088222) 0.816900 0.834635 --->beagle2-----plink----: 4.5e-04 0.001259 1.99e-02 0.000840 0.816998 ( 0.010443) 0.816159 ( 0.010809) 0.816900 0.816375 --->beagle2-----germline1: 1.05e-01 0.002373 1.48e-01 0.002089 0.816998 ( 0.010443) 0.814909 ( 0.017326) 0.816900 0.815057 --->beagle2-----germline2: 3.18e-02 -0.139582 4.36e-01 -0.022625 0.816998 ( 0.010443) 0.839623 ( 0.288168) 0.816900 1.000000 --->beagle2-----dash-----: 6.84e-01 -0.003330 9.04e-01 -0.001054 0.816998 ( 0.010443) 0.818052 ( 0.088222) 0.816900 0.834635 --->plink-------germline1: 3.37e-01 0.001464 3.99e-01 0.001249 0.816159 ( 0.010809) 0.814909 ( 0.017326) 0.816375 0.815057 --->plink-------germline2: 2.76e-02 -0.142055 4.2e-01 -0.023464 0.816159 ( 0.010809) 0.839623 ( 0.288168) 0.816375 1.000000 --->plink-------dash-----: 6.05e-01 -0.004490 8.28e-01 -0.001894 0.816159 ( 0.010809) 0.818052 ( 0.088222) 0.816375 0.834635 --->germline1---germline2: 3.23e-02 -0.143705 3.96e-01 -0.024714 0.814909 ( 0.017326) 0.839623 ( 0.288168) 0.815057 1.000000 --->germline1---dash-----: 5.55e-01 -0.005524 7.38e-01 -0.003143 0.814909 ( 0.017326) 0.818052 ( 0.088222) 0.815057 0.834635 --->germline2---dash-----: 2.65e-02 0.108414 4.93e-01 0.021571 0.839623 ( 0.288168) 0.818052 ( 0.088222) 1.000000 0.834635 ######specifitySnps###### --->fabia-------beagle1--: 1e+00 0.000000 1e+00 0.000000 0.038777 ( 0.002078) 0.000000 ( 0.000000) 0.039053 0.000000 --->fabia-------beagle2--: 3.96e-18 0.038951 5.49e-128 0.038767 0.038777 ( 0.002078) 9.8e-06 ( 9.8e-05) 0.039053 0.000000 --->fabia-------plink----: 3.96e-18 0.038114 4.1e-124 0.037916 0.038777 ( 0.002078) 0.000860 ( 0.000521) 0.039053 0.000783 --->fabia-------germline1: 3.96e-18 0.030631 1.39e-109 0.030520 0.038777 ( 0.002078) 0.008257 ( 0.001456) 0.039053 0.008210 --->fabia-------germline2: 1.69e-14 -0.001812 4.66e-16 -0.001999 0.038777 ( 0.002078) 0.040775 ( 0.000567) 0.039053 0.040788 --->fabia-------dash-----: 4.74e-13 0.002928 6.55e-18 0.002730 0.038777 ( 0.002078) 0.036047 ( 0.001573) 0.039053 0.036020 --->beagle1-----beagle2--: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 9.8e-06 ( 9.8e-05) 0.000000 0.000000 --->beagle1-----plink----: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.000860 ( 0.000521) 0.000000 0.000783 --->beagle1-----germline1: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.008257 ( 0.001456) 0.000000 0.008210 --->beagle1-----germline2: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.040775 ( 0.000567) 0.000000 0.040788 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.036047 ( 0.001573) 0.000000 0.036020 --->beagle2-----plink----: 3.96e-18 -0.000803 1.03e-29 -0.000851 9.8e-06 ( 9.8e-05) 0.000860 ( 0.000521) 0.000000 0.000783 --->beagle2-----germline1: 3.96e-18 -0.008235 4.04e-77 -0.008247 9.8e-06 ( 9.8e-05) 0.008257 ( 0.001456) 0.000000 0.008210 --->beagle2-----germline2: 3.96e-18 -0.040784 2.1e-185 -0.040766 9.8e-06 ( 9.8e-05) 0.040775 ( 0.000567) 0.000000 0.040788 --->beagle2-----dash-----: 3.96e-18 -0.036084 5.3e-137 -0.036037 9.8e-06 ( 9.8e-05) 0.036047 ( 0.001573) 0.000000 0.036020 --->plink-------germline1: 3.96e-18 -0.007386 4.05e-69 -0.007397 0.000860 ( 0.000521) 0.008257 ( 0.001456) 0.000783 0.008210 --->plink-------germline2: 3.96e-18 -0.039938 9.22e-179 -0.039915 0.000860 ( 0.000521) 0.040775 ( 0.000567) 0.000783 0.040788 --->plink-------dash-----: 3.96e-18 -0.035156 1.51e-135 -0.035186 0.000860 ( 0.000521) 0.036047 ( 0.001573) 0.000783 0.036020 --->germline1---germline2: 3.96e-18 -0.032522 2.55e-129 -0.032518 0.008257 ( 0.001456) 0.040775 ( 0.000567) 0.008210 0.040788 --->germline1---dash-----: 3.96e-18 -0.027843 1.34e-103 -0.027790 0.008257 ( 0.001456) 0.036047 ( 0.001573) 0.008210 0.036020 --->germline2---dash-----: 3.96e-18 0.004716 4.09e-56 0.004729 0.040775 ( 0.000567) 0.036047 ( 0.001573) 0.040788 0.036020 ######sensitivitySnps###### --->fabia-------beagle1--: 3.96e-18 -0.170180 2.66e-57 -0.172064 0.744625 ( 0.059973) 0.916690 ( 0.047338) 0.750842 0.922441 --->fabia-------beagle2--: 3.96e-18 -0.169921 1.06e-57 -0.171669 0.744625 ( 0.059973) 0.916294 ( 0.047498) 0.750842 0.922441 --->fabia-------plink----: 3.96e-18 -0.157115 5.91e-50 -0.157966 0.744625 ( 0.059973) 0.902592 ( 0.051551) 0.750842 0.909639 --->fabia-------germline1: 9.38e-01 -0.000720 9.14e-01 0.000896 0.744625 ( 0.059973) 0.743730 ( 0.077915) 0.750842 0.760388 --->fabia-------germline2: 3.96e-18 0.736902 2.84e-108 0.735278 0.744625 ( 0.059973) 0.009347 ( 0.016798) 0.750842 0.000000 --->fabia-------dash-----: 3.96e-18 0.636668 5.37e-88 0.630237 0.744625 ( 0.059973) 0.114388 ( 0.060096) 0.750842 0.103904 --->beagle1-----beagle2--: 1e+00 0.000000 3.2e-01 0.000395 0.916690 ( 0.047338) 0.916294 ( 0.047498) 0.922441 0.922441 --->beagle1-----plink----: 1.68e-12 0.018632 3.75e-10 0.014098 0.916690 ( 0.047338) 0.902592 ( 0.051551) 0.922441 0.909639 --->beagle1-----germline1: 3.96e-18 0.170463 9.26e-44 0.172960 0.916690 ( 0.047338) 0.743730 ( 0.077915) 0.922441 0.760388 --->beagle1-----germline2: 3.96e-18 0.909603 2.39e-125 0.907342 0.916690 ( 0.047338) 0.009347 ( 0.016798) 0.922441 0.000000 --->beagle1-----dash-----: 3.96e-18 0.806330 2.65e-107 0.802301 0.916690 ( 0.047338) 0.114388 ( 0.060096) 0.922441 0.103904 --->beagle2-----plink----: 1.66e-11 0.018416 2.21e-09 0.013703 0.916294 ( 0.047498) 0.902592 ( 0.051551) 0.922441 0.909639 --->beagle2-----germline1: 3.96e-18 0.169899 1.54e-43 0.172565 0.916294 ( 0.047498) 0.743730 ( 0.077915) 0.922441 0.760388 --->beagle2-----germline2: 3.96e-18 0.909113 2.87e-125 0.906947 0.916294 ( 0.047498) 0.009347 ( 0.016798) 0.922441 0.000000 --->beagle2-----dash-----: 3.96e-18 0.805643 3.36e-107 0.801906 0.916294 ( 0.047498) 0.114388 ( 0.060096) 0.922441 0.103904 --->plink-------germline1: 4.46e-18 0.158401 8.06e-38 0.158862 0.902592 ( 0.051551) 0.743730 ( 0.077915) 0.909639 0.760388 --->plink-------germline2: 3.96e-18 0.895624 6.84e-121 0.893244 0.902592 ( 0.051551) 0.009347 ( 0.016798) 0.909639 0.000000 --->plink-------dash-----: 3.96e-18 0.792778 3.11e-105 0.788203 0.902592 ( 0.051551) 0.114388 ( 0.060096) 0.909639 0.103904 --->germline1---germline2: 3.96e-18 0.736884 1.12e-97 0.734382 0.743730 ( 0.077915) 0.009347 ( 0.016798) 0.760388 0.000000 --->germline1---dash-----: 3.96e-18 0.635047 3.74e-77 0.629341 0.743730 ( 0.077915) 0.114388 ( 0.060096) 0.760388 0.103904 --->germline2---dash-----: 8.14e-18 -0.102862 1.14e-29 -0.105041 0.009347 ( 0.016798) 0.114388 ( 0.060096) 0.000000 0.103904 ######trueNSnps###### --->fabia-------beagle1--: 1e+00 0 1e+00 0 7678 ( 411) 0 ( 0) 7732 0 --->fabia-------beagle2--: 3.96e-18 7713 5.46e-128 7676 7678 ( 411) 1.94 ( 19.4) 7732 0 --->fabia-------plink----: 3.96e-18 7546 4.03e-124 7508 7678 ( 411) 170 ( 103) 7732 155 --->fabia-------germline1: 3.96e-18 6068 1.48e-109 6043 7678 ( 411) 1635 ( 288) 7732 1626 --->fabia-------germline2: 1.66e-14 -355 4.68e-16 -396 7678 ( 411) 8074 ( 113) 7732 8076 --->fabia-------dash-----: 4.68e-13 580 6.56e-18 541 7678 ( 411) 7137 ( 312) 7732 7131 --->beagle1-----beagle2--: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 1.940000 (19.400000) 0.000000 0.000000 --->beagle1-----plink----: 1e+00 0 1e+00 0 0 ( 0) 170 ( 103) 0 155 --->beagle1-----germline1: 1e+00 0 1e+00 0 0 ( 0) 1635 ( 288) 0 1626 --->beagle1-----germline2: 1e+00 0 1e+00 0 0 ( 0) 8074 ( 113) 0 8076 --->beagle1-----dash-----: 1e+00 0 1e+00 0 0 ( 0) 7137 ( 312) 0 7131 --->beagle2-----plink----: 3.95e-18 -159 1.03e-29 -168 1.94 ( 19.4) 170 ( 103) 0 155 --->beagle2-----germline1: 3.96e-18 -1631 3.84e-77 -1633 1.94 ( 19.4) 1635 ( 288) 0 1626 --->beagle2-----germline2: 3.95e-18 -8072 3.7e-185 -8072 1.94 ( 19.4) 8074 ( 113) 0 8076 --->beagle2-----dash-----: 3.96e-18 -7144 6.57e-137 -7135 1.94 ( 19.4) 7137 ( 312) 0 7131 --->plink-------germline1: 3.95e-18 -1464 3.87e-69 -1465 170 ( 103) 1635 ( 288) 155 1626 --->plink-------germline2: 3.95e-18 -7906 1.18e-178 -7903 170 ( 103) 8074 ( 113) 155 8076 --->plink-------dash-----: 3.96e-18 -6967 1.81e-135 -6967 170 ( 103) 7137 ( 312) 155 7131 --->germline1---germline2: 3.96e-18 -6441 3.12e-129 -6439 1635 ( 288) 8074 ( 113) 1626 8076 --->germline1---dash-----: 3.96e-18 -5513 1.5e-103 -5502 1635 ( 288) 7137 ( 312) 1626 7131 --->germline2---dash-----: 3.95e-18 933 4e-56 936 8074 ( 113) 7137 ( 312) 8076 7131 ######falsePSnps###### --->fabia-------beagle1--: 3.96e-18 -7715 6.35e-128 -7678 492 ( 406) 8170 ( 104) 434 8169 --->fabia-------beagle2--: 3.96e-18 -7713 5.46e-128 -7676 492 ( 406) 8168 ( 105) 434 8168 --->fabia-------plink----: 3.96e-18 -7546 4.03e-124 -7508 492 ( 406) 7999 ( 123) 434 7996 --->fabia-------germline1: 3.96e-18 -6068 1.48e-109 -6043 492 ( 406) 6535 ( 327) 434 6566 --->fabia-------germline2: 1.66e-14 355 4.68e-16 396 492 ( 406) 96 ( 40.5) 434 106 --->fabia-------dash-----: 4.68e-13 -579 6.56e-18 -541 492 ( 406) 1032 ( 278) 434 1030 --->beagle1-----beagle2--: 1e+00 0 3.2e-01 1.94 8170 ( 104) 8168 ( 105) 8169 8168 --->beagle1-----plink----: 3.95e-18 161 3.56e-30 170 8170 ( 104) 7999 ( 123) 8169 7996 --->beagle1-----germline1: 3.96e-18 1633 2.59e-77 1635 8170 ( 104) 6535 ( 327) 8169 6566 --->beagle1-----germline2: 3.95e-18 8074 1.37e-185 8074 8170 ( 104) 96 ( 40.5) 8169 106 --->beagle1-----dash-----: 3.96e-18 7145 1.2e-136 7137 8170 ( 104) 1032 ( 278) 8169 1030 --->beagle2-----plink----: 3.95e-18 159 1.03e-29 168 8168 ( 105) 7999 ( 123) 8168 7996 --->beagle2-----germline1: 3.96e-18 1631 3.84e-77 1633 8168 ( 105) 6535 ( 327) 8168 6566 --->beagle2-----germline2: 3.95e-18 8072 3.7e-185 8072 8168 ( 105) 96 ( 40.5) 8168 106 --->beagle2-----dash-----: 3.96e-18 7144 6.57e-137 7135 8168 ( 105) 1032 ( 278) 8168 1030 --->plink-------germline1: 3.95e-18 1464 3.87e-69 1465 7999 ( 123) 6535 ( 327) 7996 6566 --->plink-------germline2: 3.95e-18 7906 1.18e-178 7903 7999 ( 123) 96 ( 40.5) 7996 106 --->plink-------dash-----: 3.96e-18 6967 1.81e-135 6967 7999 ( 123) 1032 ( 278) 7996 1030 --->germline1---germline2: 3.96e-18 6441 3.12e-129 6439 6535 ( 327) 96 ( 40.5) 6566 106 --->germline1---dash-----: 3.96e-18 5513 1.5e-103 5502 6535 ( 327) 1032 ( 278) 6566 1030 --->germline2---dash-----: 3.95e-18 -933 4e-56 -936 96 ( 40.5) 1032 ( 278) 106 1030 ######falseNSnps###### --->fabia-------beagle1--: 1e+00 0 1e+00 0 344 ( 99.3) 0 ( 0) 336 0 --->fabia-------beagle2--: 3.95e-18 339 1.84e-57 343 344 ( 99.3) 0.77 ( 7.7) 336 0 --->fabia-------plink----: 3.95e-18 314 7.39e-50 316 344 ( 99.3) 28 ( 39.8) 336 10.5 --->fabia-------germline1: 9.75e-01 0.5 8.67e-01 -2.78 344 ( 99.3) 346 ( 145) 336 322 --->fabia-------germline2: 3.95e-18 -1470 1.14e-106 -1468 344 ( 99.3) 1812 ( 113) 336 1803 --->fabia-------dash-----: 3.95e-18 -1267 2.44e-88 -1258 344 ( 99.3) 1601 ( 138) 336 1610 --->beagle1-----beagle2--: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.770000 ( 7.700000) 0.000000 0.000000 --->beagle1-----plink----: 1e+00 0 1e+00 0 0 ( 0) 28 ( 39.8) 0 10.5 --->beagle1-----germline1: 1e+00 0 1e+00 0 0 ( 0) 346 ( 145) 0 322 --->beagle1-----germline2: 1e+00 0 1e+00 0 0 ( 0) 1812 ( 113) 0 1803 --->beagle1-----dash-----: 1e+00 0 1e+00 0 0 ( 0) 1601 ( 138) 0 1610 --->beagle2-----plink----: 1.62e-11 -36.5 1.47e-09 -27.3 0.77 ( 7.7) 28 ( 39.8) 0 10.5 --->beagle2-----germline1: 3.95e-18 -339 9.95e-43 -346 0.77 ( 7.7) 346 ( 145) 0 322 --->beagle2-----germline2: 3.95e-18 -1811 3.74e-121 -1811 0.77 ( 7.7) 1812 ( 113) 0 1803 --->beagle2-----dash-----: 3.95e-18 -1603 1.74e-107 -1601 0.77 ( 7.7) 1601 ( 138) 0 1610 --->plink-------germline1: 4.46e-18 -316 2.69e-37 -318 28 ( 39.8) 346 ( 145) 10.5 322 --->plink-------germline2: 3.95e-18 -1786 3.98e-117 -1784 28 ( 39.8) 1812 ( 113) 10.5 1803 --->plink-------dash-----: 3.95e-18 -1578 3.2e-105 -1573 28 ( 39.8) 1601 ( 138) 10.5 1610 --->germline1---germline2: 3.95e-18 -1468 5.26e-99 -1465 346 ( 145) 1812 ( 113) 322 1803 --->germline1---dash-----: 3.95e-18 -1265 1.84e-78 -1255 346 ( 145) 1601 ( 138) 322 1610 --->germline2---dash-----: 8.14e-18 205 2.1e-29 210 1812 ( 113) 1601 ( 138) 1803 1610 ######truePSnps###### --->fabia-------beagle1--: 3.95e-18 -340 4.08e-57 -344 1487 ( 124) 1830 ( 104) 1476 1831 --->fabia-------beagle2--: 3.95e-18 -339 1.84e-57 -343 1487 ( 124) 1830 ( 105) 1476 1831 --->fabia-------plink----: 3.95e-18 -314 7.39e-50 -316 1487 ( 124) 1802 ( 113) 1476 1800 --->fabia-------germline1: 9.75e-01 -0.5 8.67e-01 2.78 1487 ( 124) 1484 ( 150) 1476 1496 --->fabia-------germline2: 3.95e-18 1470 1.14e-106 1468 1487 ( 124) 18.6 ( 33.3) 1476 0 --->fabia-------dash-----: 3.95e-18 1267 2.44e-88 1258 1487 ( 124) 229 ( 122) 1476 209 --->beagle1-----beagle2--: 1e+00 0 3.2e-01 0.77 1830 ( 104) 1830 ( 105) 1831 1831 --->beagle1-----plink----: 1.67e-12 37 2.48e-10 28 1830 ( 104) 1802 ( 113) 1831 1800 --->beagle1-----germline1: 3.95e-18 340 6.02e-43 346 1830 ( 104) 1484 ( 150) 1831 1496 --->beagle1-----germline2: 3.95e-18 1811 2.45e-121 1812 1830 ( 104) 18.6 ( 33.3) 1831 0 --->beagle1-----dash-----: 3.95e-18 1604 1.18e-107 1601 1830 ( 104) 229 ( 122) 1831 209 --->beagle2-----plink----: 1.62e-11 36.5 1.47e-09 27.3 1830 ( 105) 1802 ( 113) 1831 1800 --->beagle2-----germline1: 3.95e-18 339 9.95e-43 346 1830 ( 105) 1484 ( 150) 1831 1496 --->beagle2-----germline2: 3.95e-18 1811 3.74e-121 1811 1830 ( 105) 18.6 ( 33.3) 1831 0 --->beagle2-----dash-----: 3.95e-18 1603 1.74e-107 1601 1830 ( 105) 229 ( 122) 1831 209 --->plink-------germline1: 4.46e-18 316 2.69e-37 318 1802 ( 113) 1484 ( 150) 1800 1496 --->plink-------germline2: 3.95e-18 1786 3.98e-117 1784 1802 ( 113) 18.6 ( 33.3) 1800 0 --->plink-------dash-----: 3.95e-18 1578 3.2e-105 1573 1802 ( 113) 229 ( 122) 1800 209 --->germline1---germline2: 3.95e-18 1468 5.26e-99 1465 1484 ( 150) 18.6 ( 33.3) 1496 0 --->germline1---dash-----: 3.95e-18 1265 1.84e-78 1255 1484 ( 150) 229 ( 122) 1496 209 --->germline2---dash-----: 8.14e-18 -205 2.1e-29 -210 18.6 ( 33.3) 229 ( 122) 0 209 ######MatthewsSample###### --->fabia-------beagle1--: 3.96e-18 0.914885 2.04e-118 0.915289 0.902768 ( 0.056082) -0.012522 ( 0.031618) 0.907098 -0.014550 --->fabia-------beagle2--: 3.96e-18 0.909383 2.7e-113 0.910982 0.902768 ( 0.056082) -0.008214 ( 0.033013) 0.907098 -0.002677 --->fabia-------plink----: 3.96e-18 0.895206 2.69e-117 0.894449 0.902768 ( 0.056082) 0.008318 ( 0.030038) 0.907098 0.008420 --->fabia-------germline1: 1e+00 0.000000 1e+00 0.000000 0.902768 ( 0.056082) 0.000000 ( 0.000000) 0.907098 0.000000 --->fabia-------germline2: 3.96e-18 0.901181 3.85e-118 0.899174 0.902768 ( 0.056082) 0.003594 ( 0.029611) 0.907098 0.000761 --->fabia-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.902768 ( 0.056082) 0.000000 ( 0.000000) 0.907098 0.000000 --->beagle1-----beagle2--: 3.23e-01 -0.003084 1.55e-01 -0.004307 -0.012522 ( 0.031618) -0.008214 ( 0.033013) -0.014550 -0.002677 --->beagle1-----plink----: 2.29e-05 -0.021778 1.64e-05 -0.020840 -0.012522 ( 0.031618) 0.008318 ( 0.030038) -0.014550 0.008420 --->beagle1-----germline1: 1e+00 0.000000 1e+00 0.000000 -0.012522 ( 0.031618) 0.000000 ( 0.000000) -0.014550 0.000000 --->beagle1-----germline2: 6.41e-05 -0.020033 2.66e-04 -0.016116 -0.012522 ( 0.031618) 0.003594 ( 0.029611) -0.014550 0.000761 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 -0.012522 ( 0.031618) 0.000000 ( 0.000000) -0.014550 0.000000 --->beagle2-----plink----: 4.39e-03 -0.014463 1e-03 -0.016533 -0.008214 ( 0.033013) 0.008318 ( 0.030038) -0.002677 0.008420 --->beagle2-----germline1: 1e+00 0.000000 1e+00 0.000000 -0.008214 ( 0.033013) 0.000000 ( 0.000000) -0.002677 0.000000 --->beagle2-----germline2: 3.45e-03 -0.013070 7.7e-03 -0.011808 -0.008214 ( 0.033013) 0.003594 ( 0.029611) -0.002677 0.000761 --->beagle2-----dash-----: 1e+00 0.000000 1e+00 0.000000 -0.008214 ( 0.033013) 0.000000 ( 0.000000) -0.002677 0.000000 --->plink-------germline1: 1e+00 0.000000 1e+00 0.000000 0.008318 ( 0.030038) 0.000000 ( 0.000000) 0.008420 0.000000 --->plink-------germline2: 2.2e-01 0.005742 2.54e-01 0.004725 0.008318 ( 0.030038) 0.003594 ( 0.029611) 0.008420 0.000761 --->plink-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.008318 ( 0.030038) 0.000000 ( 0.000000) 0.008420 0.000000 --->germline1---germline2: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.003594 ( 0.029611) 0.000000 0.000761 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.000000 ( 0.000000) 0.000000 0.000000 --->germline2---dash-----: 1e+00 0.000000 1e+00 0.000000 0.003594 ( 0.029611) 0.000000 ( 0.000000) 0.000761 0.000000 ######F1Sample###### --->fabia-------beagle1--: 3.96e-18 0.633345 6.56e-109 0.632334 0.910341 ( 0.051943) 0.278007 ( 0.015699) 0.913069 0.275779 --->fabia-------beagle2--: 3.96e-18 0.693008 3.51e-107 0.692860 0.910341 ( 0.051943) 0.217481 ( 0.026487) 0.913069 0.220126 --->fabia-------plink----: 3.96e-18 0.611876 8.61e-108 0.610434 0.910341 ( 0.051943) 0.299907 ( 0.010856) 0.913069 0.300893 --->fabia-------germline1: 3.96e-18 0.604355 4.32e-107 0.602678 0.910341 ( 0.051943) 0.307663 ( 0.005484) 0.913069 0.307953 --->fabia-------germline2: 3.96e-18 0.612435 1.46e-98 0.613249 0.910341 ( 0.051943) 0.297091 ( 0.035503) 0.913069 0.304845 --->fabia-------dash-----: 3.96e-18 0.604355 4.32e-107 0.602678 0.910341 ( 0.051943) 0.307663 ( 0.005484) 0.913069 0.307953 --->beagle1-----beagle2--: 3.96e-18 0.060054 5.08e-50 0.060526 0.278007 ( 0.015699) 0.217481 ( 0.026487) 0.275779 0.220126 --->beagle1-----plink----: 7.5e-15 -0.022505 3.26e-21 -0.021900 0.278007 ( 0.015699) 0.299907 ( 0.010856) 0.275779 0.300893 --->beagle1-----germline1: 7.44e-18 -0.030075 1.05e-36 -0.029656 0.278007 ( 0.015699) 0.307663 ( 0.005484) 0.275779 0.307953 --->beagle1-----germline2: 2.41e-11 -0.024686 6.14e-07 -0.019084 0.278007 ( 0.015699) 0.297091 ( 0.035503) 0.275779 0.304845 --->beagle1-----dash-----: 7.44e-18 -0.030075 1.05e-36 -0.029656 0.278007 ( 0.015699) 0.307663 ( 0.005484) 0.275779 0.307953 --->beagle2-----plink----: 3.96e-18 -0.081463 1.62e-49 -0.082426 0.217481 ( 0.026487) 0.299907 ( 0.010856) 0.220126 0.300893 --->beagle2-----germline1: 3.96e-18 -0.089511 9.2e-57 -0.090182 0.217481 ( 0.026487) 0.307663 ( 0.005484) 0.220126 0.307953 --->beagle2-----germline2: 1.03e-16 -0.082714 9.57e-35 -0.079611 0.217481 ( 0.026487) 0.297091 ( 0.035503) 0.220126 0.304845 --->beagle2-----dash-----: 3.96e-18 -0.089511 9.2e-57 -0.090182 0.217481 ( 0.026487) 0.307663 ( 0.005484) 0.220126 0.307953 --->plink-------germline1: 3.84e-11 -0.007703 4.11e-13 -0.007756 0.299907 ( 0.010856) 0.307663 ( 0.005484) 0.300893 0.307953 --->plink-------germline2: 5.93e-02 -0.002927 4.42e-01 0.002816 0.299907 ( 0.010856) 0.297091 ( 0.035503) 0.300893 0.304845 --->plink-------dash-----: 3.84e-11 -0.007703 4.11e-13 -0.007756 0.299907 ( 0.010856) 0.307663 ( 0.005484) 0.300893 0.307953 --->germline1---germline2: 3.01e-08 0.003669 3.55e-03 0.010572 0.307663 ( 0.005484) 0.297091 ( 0.035503) 0.307953 0.304845 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 0.307663 ( 0.005484) 0.307663 ( 0.005484) 0.307953 0.307953 --->germline2---dash-----: 3.01e-08 -0.003681 3.55e-03 -0.010572 0.297091 ( 0.035503) 0.307663 ( 0.005484) 0.304845 0.307953 ######accuracySample###### --->fabia-------beagle1--: 3.95e-18 0.579213 6.96e-138 0.579325 0.981755 ( 0.011252) 0.402430 ( 0.021778) 0.982500 0.403000 --->fabia-------beagle2--: 3.95e-18 0.352212 5e-116 0.352215 0.981755 ( 0.011252) 0.629540 ( 0.020080) 0.982500 0.629000 --->fabia-------plink----: 3.95e-18 0.683497 1.49e-144 0.683105 0.981755 ( 0.011252) 0.298650 ( 0.020847) 0.982500 0.297500 --->fabia-------germline1: 3.94e-18 0.800493 4.09e-182 0.799945 0.981755 ( 0.011252) 0.181810 ( 0.003826) 0.982500 0.182000 --->fabia-------germline2: 3.95e-18 0.749971 1.68e-81 0.718565 0.981755 ( 0.011252) 0.263190 ( 0.116444) 0.982500 0.218500 --->fabia-------dash-----: 3.94e-18 0.800493 4.09e-182 0.799945 0.981755 ( 0.011252) 0.181810 ( 0.003826) 0.982500 0.182000 --->beagle1-----beagle2--: 3.95e-18 -0.227051 6.41e-117 -0.227110 0.402430 ( 0.021778) 0.629540 ( 0.020080) 0.403000 0.629000 --->beagle1-----plink----: 3.95e-18 0.103500 9.17e-60 0.103780 0.402430 ( 0.021778) 0.298650 ( 0.020847) 0.403000 0.297500 --->beagle1-----germline1: 3.94e-18 0.220500 3.21e-101 0.220620 0.402430 ( 0.021778) 0.181810 ( 0.003826) 0.403000 0.182000 --->beagle1-----germline2: 1.5e-12 0.169552 3.04e-20 0.139240 0.402430 ( 0.021778) 0.263190 ( 0.116444) 0.403000 0.218500 --->beagle1-----dash-----: 3.94e-18 0.220500 3.21e-101 0.220620 0.402430 ( 0.021778) 0.181810 ( 0.003826) 0.403000 0.182000 --->beagle2-----plink----: 3.95e-18 0.331443 4.63e-110 0.330890 0.629540 ( 0.020080) 0.298650 ( 0.020847) 0.629000 0.297500 --->beagle2-----germline1: 3.93e-18 0.447488 4.46e-134 0.447730 0.629540 ( 0.020080) 0.181810 ( 0.003826) 0.629000 0.182000 --->beagle2-----germline2: 5.19e-18 0.395975 2.95e-52 0.366350 0.629540 ( 0.020080) 0.263190 ( 0.116444) 0.629000 0.218500 --->beagle2-----dash-----: 3.93e-18 0.447488 4.46e-134 0.447730 0.629540 ( 0.020080) 0.181810 ( 0.003826) 0.629000 0.182000 --->plink-------germline1: 3.94e-18 0.116417 2.69e-77 0.116840 0.298650 ( 0.020847) 0.181810 ( 0.003826) 0.297500 0.182000 --->plink-------germline2: 2.47e-06 0.065953 3e-03 0.035460 0.298650 ( 0.020847) 0.263190 ( 0.116444) 0.297500 0.218500 --->plink-------dash-----: 3.94e-18 0.116417 2.69e-77 0.116840 0.298650 ( 0.020847) 0.181810 ( 0.003826) 0.297500 0.182000 --->germline1---germline2: 3.95e-18 -0.049963 3.42e-10 -0.081380 0.181810 ( 0.003826) 0.263190 ( 0.116444) 0.182000 0.218500 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 0.181810 ( 0.003826) 0.181810 ( 0.003826) 0.182000 0.182000 --->germline2---dash-----: 3.95e-18 0.049963 3.42e-10 0.081380 0.263190 ( 0.116444) 0.181810 ( 0.003826) 0.218500 0.182000 ######FPRSample###### --->fabia-------beagle1--: 3.96e-18 -0.026126 2.45e-127 -0.026140 0.000674 ( 0.000536) 0.026814 ( 0.001269) 0.000616 0.026717 --->fabia-------beagle2--: 3.96e-18 -0.011452 1.73e-94 -0.011463 0.000674 ( 0.000536) 0.012137 ( 0.001133) 0.000616 0.012096 --->fabia-------plink----: 3.96e-18 -0.033173 7.35e-137 -0.033156 0.000674 ( 0.000536) 0.033830 ( 0.001280) 0.000616 0.033838 --->fabia-------germline1: 3.95e-18 -0.040671 4.31e-185 -0.040649 0.000674 ( 0.000536) 0.041323 ( 0.000193) 0.000616 0.041313 --->fabia-------germline2: 4.08e-18 -0.037384 5.81e-70 -0.035405 0.000674 ( 0.000536) 0.036079 ( 0.007538) 0.000616 0.039015 --->fabia-------dash-----: 3.95e-18 -0.040671 4.31e-185 -0.040649 0.000674 ( 0.000536) 0.041323 ( 0.000193) 0.000616 0.041313 --->beagle1-----beagle2--: 3.95e-18 0.014689 2.67e-128 0.014677 0.026814 ( 0.001269) 0.012137 ( 0.001133) 0.026717 0.012096 --->beagle1-----plink----: 3.95e-18 -0.007029 1.4e-66 -0.007016 0.026814 ( 0.001269) 0.033830 ( 0.001280) 0.026717 0.033838 --->beagle1-----germline1: 3.95e-18 -0.014506 1.02e-106 -0.014509 0.026814 ( 0.001269) 0.041323 ( 0.000193) 0.026717 0.041313 --->beagle1-----germline2: 8.57e-13 -0.011221 4.05e-21 -0.009265 0.026814 ( 0.001269) 0.036079 ( 0.007538) 0.026717 0.039015 --->beagle1-----dash-----: 3.95e-18 -0.014506 1.02e-106 -0.014509 0.026814 ( 0.001269) 0.041323 ( 0.000193) 0.026717 0.041313 --->beagle2-----plink----: 3.95e-18 -0.021710 1.75e-118 -0.021693 0.012137 ( 0.001133) 0.033830 ( 0.001280) 0.012096 0.033838 --->beagle2-----germline1: 3.95e-18 -0.029188 2.68e-141 -0.029186 0.012137 ( 0.001133) 0.041323 ( 0.000193) 0.012096 0.041313 --->beagle2-----germline2: 5.19e-18 -0.025904 5.84e-53 -0.023942 0.012137 ( 0.001133) 0.036079 ( 0.007538) 0.012096 0.039015 --->beagle2-----dash-----: 3.95e-18 -0.029188 2.68e-141 -0.029186 0.012137 ( 0.001133) 0.041323 ( 0.000193) 0.012096 0.041313 --->plink-------germline1: 3.95e-18 -0.007464 4.47e-79 -0.007492 0.033830 ( 0.001280) 0.041323 ( 0.000193) 0.033838 0.041313 --->plink-------germline2: 2.53e-06 -0.004146 3.69e-03 -0.002249 0.033830 ( 0.001280) 0.036079 ( 0.007538) 0.033838 0.039015 --->plink-------dash-----: 3.95e-18 -0.007464 4.47e-79 -0.007492 0.033830 ( 0.001280) 0.041323 ( 0.000193) 0.033838 0.041313 --->germline1---germline2: 3.95e-18 0.003235 3.95e-10 0.005243 0.041323 ( 0.000193) 0.036079 ( 0.007538) 0.041313 0.039015 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 0.041323 ( 0.000193) 0.041323 ( 0.000193) 0.041313 0.041313 --->germline2---dash-----: 3.95e-18 -0.003224 3.95e-10 -0.005243 0.036079 ( 0.007538) 0.041323 ( 0.000193) 0.039015 0.041313 ######FDRSample###### --->fabia-------beagle1--: 3.96e-18 -0.703066 1.36e-92 -0.701413 0.120398 ( 0.086111) 0.821811 ( 0.010012) 0.114476 0.823651 --->fabia-------beagle2--: 3.96e-18 -0.704517 2.77e-90 -0.702828 0.120398 ( 0.086111) 0.823226 ( 0.020377) 0.114476 0.820766 --->fabia-------plink----: 3.96e-18 -0.697485 3.05e-92 -0.696358 0.120398 ( 0.086111) 0.816756 ( 0.006820) 0.114476 0.816149 --->fabia-------germline1: 3.96e-18 -0.699332 3.1e-92 -0.697792 0.120398 ( 0.086111) 0.818190 ( 0.003826) 0.114476 0.818000 --->fabia-------germline2: 4.08e-18 -0.697354 4.49e-78 -0.689025 0.120398 ( 0.086111) 0.809423 ( 0.081979) 0.114476 0.817676 --->fabia-------dash-----: 3.96e-18 -0.699332 3.1e-92 -0.697792 0.120398 ( 0.086111) 0.818190 ( 0.003826) 0.114476 0.818000 --->beagle1-----beagle2--: 5.44e-01 -0.001003 3.96e-01 -0.001415 0.821811 ( 0.010012) 0.823226 ( 0.020377) 0.823651 0.820766 --->beagle1-----plink----: 1.19e-05 0.005386 1.63e-05 0.005055 0.821811 ( 0.010012) 0.816756 ( 0.006820) 0.823651 0.816149 --->beagle1-----germline1: 1.1e-04 0.004006 1.36e-04 0.003621 0.821811 ( 0.010012) 0.818190 ( 0.003826) 0.823651 0.818000 --->beagle1-----germline2: 3.78e-05 0.005073 1.43e-01 0.012388 0.821811 ( 0.010012) 0.809423 ( 0.081979) 0.823651 0.817676 --->beagle1-----dash-----: 1.1e-04 0.004006 1.36e-04 0.003621 0.821811 ( 0.010012) 0.818190 ( 0.003826) 0.823651 0.818000 --->beagle2-----plink----: 1.12e-02 0.005628 3.55e-03 0.006470 0.823226 ( 0.020377) 0.816756 ( 0.006820) 0.820766 0.816149 --->beagle2-----germline1: 3.64e-02 0.004360 1.31e-02 0.005036 0.823226 ( 0.020377) 0.818190 ( 0.003826) 0.820766 0.818000 --->beagle2-----germline2: 1.65e-02 0.005646 1.1e-01 0.013803 0.823226 ( 0.020377) 0.809423 ( 0.081979) 0.820766 0.817676 --->beagle2-----dash-----: 3.64e-02 0.004360 1.31e-02 0.005036 0.823226 ( 0.020377) 0.818190 ( 0.003826) 0.820766 0.818000 --->plink-------germline1: 1.13e-02 -0.001416 9.51e-03 -0.001434 0.816756 ( 0.006820) 0.818190 ( 0.003826) 0.816149 0.818000 --->plink-------germline2: 3.93e-01 -0.000587 3.74e-01 0.007333 0.816756 ( 0.006820) 0.809423 ( 0.081979) 0.816149 0.817676 --->plink-------dash-----: 1.13e-02 -0.001416 9.51e-03 -0.001434 0.816756 ( 0.006820) 0.818190 ( 0.003826) 0.816149 0.818000 --->germline1---germline2: 1.43e-01 0.000449 2.87e-01 0.008767 0.818190 ( 0.003826) 0.809423 ( 0.081979) 0.818000 0.817676 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 0.818190 ( 0.003826) 0.818190 ( 0.003826) 0.818000 0.818000 --->germline2---dash-----: 1.43e-01 -0.000459 2.87e-01 -0.008767 0.809423 ( 0.081979) 0.818190 ( 0.003826) 0.817676 0.818000 ######specifitySample###### --->fabia-------beagle1--: 3.96e-18 0.030266 1.63e-133 0.030280 0.044788 ( 0.000546) 0.014509 ( 0.001276) 0.044862 0.014596 --->fabia-------beagle2--: 3.96e-18 0.015605 1.71e-107 0.015603 0.044788 ( 0.000546) 0.029186 ( 0.001145) 0.044862 0.029242 --->fabia-------plink----: 3.96e-18 0.037315 2.12e-142 0.037296 0.044788 ( 0.000546) 0.007492 ( 0.001266) 0.044862 0.007500 --->fabia-------germline1: 1e+00 0.000000 1e+00 0.000000 0.044788 ( 0.000546) 0.000000 ( 0.000000) 0.044862 0.000000 --->fabia-------germline2: 3.96e-18 0.041533 1.73e-74 0.039545 0.044788 ( 0.000546) 0.005243 ( 0.007545) 0.044862 0.002197 --->fabia-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.044788 ( 0.000546) 0.000000 ( 0.000000) 0.044862 0.000000 --->beagle1-----beagle2--: 3.95e-18 -0.014712 2.67e-128 -0.014677 0.014509 ( 0.001276) 0.029186 ( 0.001145) 0.014596 0.029242 --->beagle1-----plink----: 3.96e-18 0.007029 1.4e-66 0.007016 0.014509 ( 0.001276) 0.007492 ( 0.001266) 0.014596 0.007500 --->beagle1-----germline1: 1e+00 0.000000 1e+00 0.000000 0.014509 ( 0.001276) 0.000000 ( 0.000000) 0.014596 0.000000 --->beagle1-----germline2: 8.46e-13 0.011213 4.05e-21 0.009265 0.014509 ( 0.001276) 0.005243 ( 0.007545) 0.014596 0.002197 --->beagle1-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.014509 ( 0.001276) 0.000000 ( 0.000000) 0.014596 0.000000 --->beagle2-----plink----: 3.96e-18 0.021717 1.75e-118 0.021693 0.029186 ( 0.001145) 0.007492 ( 0.001266) 0.029242 0.007500 --->beagle2-----germline1: 1e+00 0.000000 1e+00 0.000000 0.029186 ( 0.001145) 0.000000 ( 0.000000) 0.029242 0.000000 --->beagle2-----germline2: 5.19e-18 0.025904 5.84e-53 0.023942 0.029186 ( 0.001145) 0.005243 ( 0.007545) 0.029242 0.002197 --->beagle2-----dash-----: 1e+00 0.000000 1e+00 0.000000 0.029186 ( 0.001145) 0.000000 ( 0.000000) 0.029242 0.000000 --->plink-------germline1: 1e+00 0.000000 1e+00 0.000000 0.007492 ( 0.001266) 0.000000 ( 0.000000) 0.007500 0.000000 --->plink-------germline2: 2.49e-06 0.004146 3.69e-03 0.002249 0.007492 ( 0.001266) 0.005243 ( 0.007545) 0.007500 0.002197 --->plink-------dash-----: 1e+00 0.000000 1e+00 0.000000 0.007492 ( 0.001266) 0.000000 ( 0.000000) 0.007500 0.000000 --->germline1---germline2: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.005243 ( 0.007545) 0.000000 0.002197 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.000000 ( 0.000000) 0.000000 0.000000 --->germline2---dash-----: 1e+00 0.000000 1e+00 0.000000 0.005243 ( 0.007545) 0.000000 ( 0.000000) 0.002197 0.000000 ######sensitivitySample###### --->fabia-------beagle1--: 3.92e-18 0.330071 1.28e-73 0.328850 0.904650 ( 0.047414) 0.575800 ( 0.044465) 0.910000 0.575000 --->fabia-------beagle2--: 3.93e-18 0.649990 3.73e-103 0.646350 0.904650 ( 0.047414) 0.258300 ( 0.039976) 0.910000 0.260000 --->fabia-------plink----: 4.11e-18 0.155048 1.75e-46 0.153150 0.904650 ( 0.047414) 0.751500 ( 0.040735) 0.910000 0.755000 --->fabia-------germline1: 1e+00 0.000000 3.7e-01 -0.004400 0.904650 ( 0.047414) 0.909050 ( 0.019131) 0.910000 0.910000 --->fabia-------germline2: 6.96e-11 0.072524 1.7e-08 0.107800 0.904650 ( 0.047414) 0.796850 ( 0.167072) 0.910000 0.860000 --->fabia-------dash-----: 1e+00 0.000000 3.7e-01 -0.004400 0.904650 ( 0.047414) 0.909050 ( 0.019131) 0.910000 0.910000 --->beagle1-----beagle2--: 3.92e-18 0.317521 1.39e-100 0.317500 0.575800 ( 0.044465) 0.258300 ( 0.039976) 0.575000 0.260000 --->beagle1-----plink----: 5.75e-18 -0.179967 3.34e-55 -0.175700 0.575800 ( 0.044465) 0.751500 ( 0.040735) 0.575000 0.755000 --->beagle1-----germline1: 3.92e-18 -0.332574 2.02e-91 -0.333250 0.575800 ( 0.044465) 0.909050 ( 0.019131) 0.575000 0.910000 --->beagle1-----germline2: 8.54e-14 -0.259997 2.82e-23 -0.221050 0.575800 ( 0.044465) 0.796850 ( 0.167072) 0.575000 0.860000 --->beagle1-----dash-----: 3.92e-18 -0.332574 2.02e-91 -0.333250 0.575800 ( 0.044465) 0.909050 ( 0.019131) 0.575000 0.910000 --->beagle2-----plink----: 3.92e-18 -0.495067 1.59e-99 -0.493200 0.258300 ( 0.039976) 0.751500 ( 0.040735) 0.260000 0.755000 --->beagle2-----germline1: 3.88e-18 -0.650024 7.51e-121 -0.650750 0.258300 ( 0.039976) 0.909050 ( 0.019131) 0.260000 0.910000 --->beagle2-----germline2: 4.99e-18 -0.577593 7.29e-54 -0.538550 0.258300 ( 0.039976) 0.796850 ( 0.167072) 0.260000 0.860000 --->beagle2-----dash-----: 3.88e-18 -0.650024 7.51e-121 -0.650750 0.258300 ( 0.039976) 0.909050 ( 0.019131) 0.260000 0.910000 --->plink-------germline1: 3.88e-18 -0.157500 5.02e-65 -0.157550 0.751500 ( 0.040735) 0.909050 ( 0.019131) 0.755000 0.910000 --->plink-------germline2: 5.65e-06 -0.084932 8.91e-03 -0.045350 0.751500 ( 0.040735) 0.796850 ( 0.167072) 0.755000 0.860000 --->plink-------dash-----: 3.88e-18 -0.157500 5.02e-65 -0.157550 0.751500 ( 0.040735) 0.909050 ( 0.019131) 0.755000 0.910000 --->germline1---germline2: 5.62e-18 0.069960 9.32e-10 0.112200 0.909050 ( 0.019131) 0.796850 ( 0.167072) 0.910000 0.860000 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 0.909050 ( 0.019131) 0.909050 ( 0.019131) 0.910000 0.910000 --->germline2---dash-----: 5.62e-18 -0.069960 9.32e-10 -0.112200 0.796850 ( 0.167072) 0.909050 ( 0.019131) 0.860000 0.910000 ######trueNSample###### --->fabia-------beagle1--: 3.95e-18 1495 4.35e-164 1495 1783 ( 21.7) 287 ( 25.3) 1786 289 --->fabia-------beagle2--: 3.94e-18 1205 1.44e-155 1205 1783 ( 21.7) 578 ( 22.7) 1786 579 --->fabia-------plink----: 3.95e-18 1635 1.21e-167 1634 1783 ( 21.7) 148 ( 25.1) 1786 148 --->fabia-------germline1: 1e+00 0 1e+00 0 1783 ( 21.7) 0 ( 0) 1786 0 --->fabia-------germline2: 3.95e-18 1716 5.69e-107 1679 1783 ( 21.7) 104 ( 149) 1786 43.5 --->fabia-------dash-----: 1e+00 0 1e+00 0 1783 ( 21.7) 0 ( 0) 1786 0 --->beagle1-----beagle2--: 3.93e-18 -291 2.67e-128 -291 287 ( 25.3) 578 ( 22.7) 289 579 --->beagle1-----plink----: 3.94e-18 139 1.4e-66 139 287 ( 25.3) 148 ( 25.1) 289 148 --->beagle1-----germline1: 1e+00 0 1e+00 0 287 ( 25.3) 0 ( 0) 289 0 --->beagle1-----germline2: 8.45e-13 222 4.05e-21 183 287 ( 25.3) 104 ( 149) 289 43.5 --->beagle1-----dash-----: 1e+00 0 1e+00 0 287 ( 25.3) 0 ( 0) 289 0 --->beagle2-----plink----: 3.95e-18 430 1.75e-118 430 578 ( 22.7) 148 ( 25.1) 579 148 --->beagle2-----germline1: 1e+00 0 1e+00 0 578 ( 22.7) 0 ( 0) 579 0 --->beagle2-----germline2: 5.18e-18 512 5.84e-53 474 578 ( 22.7) 104 ( 149) 579 43.5 --->beagle2-----dash-----: 1e+00 0 1e+00 0 578 ( 22.7) 0 ( 0) 579 0 --->plink-------germline1: 1e+00 0 1e+00 0 148 ( 25.1) 0 ( 0) 148 0 --->plink-------germline2: 2.55e-06 82 3.69e-03 44.5 148 ( 25.1) 104 ( 149) 148 43.5 --->plink-------dash-----: 1e+00 0 1e+00 0 148 ( 25.1) 0 ( 0) 148 0 --->germline1---germline2: 1e+00 0 1e+00 0 0 ( 0) 104 ( 149) 0 43.5 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.000000 ( 0.000000) 0.000000 0.000000 --->germline2---dash-----: 1e+00 0 1e+00 0 104 ( 149) 0 ( 0) 43.5 0 ######falsePSample###### --->fabia-------beagle1--: 3.95e-18 -504 1.25e-117 -504 26.8 ( 21.3) 531 ( 25.1) 24.5 529 --->fabia-------beagle2--: 3.94e-18 -214 8.64e-82 -213 26.8 ( 21.3) 240 ( 22.4) 24.5 240 --->fabia-------plink----: 3.95e-18 -644 2.38e-127 -643 26.8 ( 21.3) 670 ( 25.4) 24.5 670 --->fabia-------germline1: 3.94e-18 -793 1.69e-156 -791 26.8 ( 21.3) 818 ( 3.83) 24.5 818 --->fabia-------germline2: 4.07e-18 -725 1.93e-69 -688 26.8 ( 21.3) 714 ( 149) 24.5 772 --->fabia-------dash-----: 3.94e-18 -793 1.69e-156 -791 26.8 ( 21.3) 818 ( 3.83) 24.5 818 --->beagle1-----beagle2--: 3.93e-18 291 2.67e-128 291 531 ( 25.1) 240 ( 22.4) 529 240 --->beagle1-----plink----: 3.94e-18 -139 1.4e-66 -139 531 ( 25.1) 670 ( 25.4) 529 670 --->beagle1-----germline1: 3.94e-18 -287 1.02e-106 -287 531 ( 25.1) 818 ( 3.83) 529 818 --->beagle1-----germline2: 8.45e-13 -222 4.05e-21 -183 531 ( 25.1) 714 ( 149) 529 772 --->beagle1-----dash-----: 3.94e-18 -287 1.02e-106 -287 531 ( 25.1) 818 ( 3.83) 529 818 --->beagle2-----plink----: 3.95e-18 -430 1.75e-118 -430 240 ( 22.4) 670 ( 25.4) 240 670 --->beagle2-----germline1: 3.94e-18 -578 2.68e-141 -578 240 ( 22.4) 818 ( 3.83) 240 818 --->beagle2-----germline2: 5.18e-18 -512 5.84e-53 -474 240 ( 22.4) 714 ( 149) 240 772 --->beagle2-----dash-----: 3.94e-18 -578 2.68e-141 -578 240 ( 22.4) 818 ( 3.83) 240 818 --->plink-------germline1: 3.94e-18 -148 4.47e-79 -148 670 ( 25.4) 818 ( 3.83) 670 818 --->plink-------germline2: 2.55e-06 -82 3.69e-03 -44.5 670 ( 25.4) 714 ( 149) 670 772 --->plink-------dash-----: 3.94e-18 -148 4.47e-79 -148 670 ( 25.4) 818 ( 3.83) 670 818 --->germline1---germline2: 3.94e-18 64 3.95e-10 104 818 ( 3.83) 714 ( 149) 818 772 --->germline1---dash-----: 1e+00 0 1e+00 0 818 ( 3.83) 818 ( 3.83) 818 818 --->germline2---dash-----: 3.94e-18 -64 3.95e-10 -104 714 ( 149) 818 ( 3.83) 772 818 ######falseNSample###### --->fabia-------beagle1--: 3.91e-18 -57.5 3.19e-70 -57 9.66 ( 8.82) 66.7 ( 8.4) 9 66 --->fabia-------beagle2--: 3.91e-18 -121 1.54e-101 -120 9.66 ( 8.82) 130 ( 8.23) 9 130 --->fabia-------plink----: 7.36e-18 -22 3.46e-36 -21.9 9.66 ( 8.82) 31.5 ( 7.48) 9 31.5 --->fabia-------germline1: 1e+00 0 1e+00 0 9.66 ( 8.82) 0 ( 0) 9 0 --->fabia-------germline2: 2.28e-03 -6 3.68e-04 -12.8 9.66 ( 8.82) 22.4 ( 33.2) 9 9.5 --->fabia-------dash-----: 1e+00 0 1e+00 0 9.66 ( 8.82) 0 ( 0) 9 0 --->beagle1-----beagle2--: 3.86e-18 -63.5 1.39e-100 -63.5 66.7 ( 8.4) 130 ( 8.23) 66 130 --->beagle1-----plink----: 5.72e-18 36 3.34e-55 35.1 66.7 ( 8.4) 31.5 ( 7.48) 66 31.5 --->beagle1-----germline1: 1e+00 0 1e+00 0 66.7 ( 8.4) 0 ( 0) 66 0 --->beagle1-----germline2: 8.98e-14 52 2.82e-23 44.2 66.7 ( 8.4) 22.4 ( 33.2) 66 9.5 --->beagle1-----dash-----: 1e+00 0 1e+00 0 66.7 ( 8.4) 0 ( 0) 66 0 --->beagle2-----plink----: 3.9e-18 99 1.59e-99 98.6 130 ( 8.23) 31.5 ( 7.48) 130 31.5 --->beagle2-----germline1: 1e+00 0 1e+00 0 130 ( 8.23) 0 ( 0) 130 0 --->beagle2-----germline2: 4.98e-18 116 7.29e-54 108 130 ( 8.23) 22.4 ( 33.2) 130 9.5 --->beagle2-----dash-----: 1e+00 0 1e+00 0 130 ( 8.23) 0 ( 0) 130 0 --->plink-------germline1: 1e+00 0 1e+00 0 31.5 ( 7.48) 0 ( 0) 31.5 0 --->plink-------germline2: 5.56e-06 17 8.91e-03 9.07 31.5 ( 7.48) 22.4 ( 33.2) 31.5 9.5 --->plink-------dash-----: 1e+00 0 1e+00 0 31.5 ( 7.48) 0 ( 0) 31.5 0 --->germline1---germline2: 1e+00 0 1e+00 0 0 ( 0) 22.4 ( 33.2) 0 9.5 --->germline1---dash-----: 1e+00 0.000000 1e+00 0.000000 0.000000 ( 0.000000) 0.000000 ( 0.000000) 0.000000 0.000000 --->germline2---dash-----: 1e+00 0 1e+00 0 22.4 ( 33.2) 0 ( 0) 9.5 0 ######truePSample###### --->fabia-------beagle1--: 3.9e-18 66 1.28e-73 65.8 181 ( 9.48) 115 ( 8.89) 182 115 --->fabia-------beagle2--: 3.92e-18 130 3.73e-103 129 181 ( 9.48) 51.7 ( 8) 182 52 --->fabia-------plink----: 4.08e-18 31 1.75e-46 30.6 181 ( 9.48) 150 ( 8.15) 182 151 --->fabia-------germline1: 1e+00 0 3.7e-01 -0.88 181 ( 9.48) 182 ( 3.83) 182 182 --->fabia-------germline2: 6.1e-11 14.5 1.7e-08 21.6 181 ( 9.48) 159 ( 33.4) 182 172 --->fabia-------dash-----: 1e+00 0 3.7e-01 -0.88 181 ( 9.48) 182 ( 3.83) 182 182 --->beagle1-----beagle2--: 3.86e-18 63.5 1.39e-100 63.5 115 ( 8.89) 51.7 ( 8) 115 52 --->beagle1-----plink----: 5.72e-18 -36 3.34e-55 -35.1 115 ( 8.89) 150 ( 8.15) 115 151 --->beagle1-----germline1: 3.89e-18 -66.5 2.02e-91 -66.7 115 ( 8.89) 182 ( 3.83) 115 182 --->beagle1-----germline2: 8.98e-14 -52 2.82e-23 -44.2 115 ( 8.89) 159 ( 33.4) 115 172 --->beagle1-----dash-----: 3.89e-18 -66.5 2.02e-91 -66.7 115 ( 8.89) 182 ( 3.83) 115 182 --->beagle2-----plink----: 3.9e-18 -99 1.59e-99 -98.6 51.7 ( 8) 150 ( 8.15) 52 151 --->beagle2-----germline1: 3.87e-18 -130 7.51e-121 -130 51.7 ( 8) 182 ( 3.83) 52 182 --->beagle2-----germline2: 4.98e-18 -116 7.29e-54 -108 51.7 ( 8) 159 ( 33.4) 52 172 --->beagle2-----dash-----: 3.87e-18 -130 7.51e-121 -130 51.7 ( 8) 182 ( 3.83) 52 182 --->plink-------germline1: 3.87e-18 -31.5 5.02e-65 -31.5 150 ( 8.15) 182 ( 3.83) 151 182 --->plink-------germline2: 5.56e-06 -17 8.91e-03 -9.07 150 ( 8.15) 159 ( 33.4) 151 172 --->plink-------dash-----: 3.87e-18 -31.5 5.02e-65 -31.5 150 ( 8.15) 182 ( 3.83) 151 182 --->germline1---germline2: 5.61e-18 14 9.32e-10 22.4 182 ( 3.83) 159 ( 33.4) 182 172 --->germline1---dash-----: 1e+00 0 1e+00 0 182 ( 3.83) 182 ( 3.83) 182 182 --->germline2---dash-----: 5.61e-18 -14 9.32e-10 -22.4 159 ( 33.4) 182 ( 3.83) 172 182