PrecisionFDA
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Explore HG002 comparison results
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| Entry | Type | Subtype | Subset | Genotype | F-score | Recall | Precision | Frac_NA | Truth TP | Truth FN | Query TP | Query FP | FP gt | % FP ma | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
80851-80900 / 86044 show all | |||||||||||||||
| jmaeng-gatk | INDEL | D1_5 | * | * | 99.3810 | 99.3322 | 99.4300 | 61.6387 | 145765 | 980 | 145820 | 836 | 338 | 40.4306 | |
| raldana-dualsentieon | INDEL | I1_5 | * | hetalt | 95.4134 | 91.2372 | 99.9903 | 60.4923 | 10214 | 981 | 10271 | 1 | 1 | 100.0000 | |
| hfeng-pmm2 | INDEL | * | HG002complexvar | het | 98.8368 | 97.8772 | 99.8154 | 56.6580 | 45231 | 981 | 44870 | 83 | 50 | 60.2410 | |
| gduggal-snapfb | INDEL | D6_15 | * | homalt | 84.4844 | 84.4926 | 84.4762 | 53.3817 | 5345 | 981 | 5322 | 978 | 974 | 99.5910 | |
| cchapple-custom | SNP | * | map_l100_m2_e0 | het | 96.8591 | 97.8857 | 95.8537 | 73.9797 | 45418 | 981 | 45473 | 1967 | 406 | 20.6406 | |
| anovak-vg | INDEL | * | map_l100_m1_e0 | * | 72.2354 | 72.6157 | 71.8590 | 84.0163 | 2604 | 982 | 2671 | 1046 | 628 | 60.0382 | |
| hfeng-pmm1 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 96.9479 | 94.1155 | 99.9561 | 40.9419 | 15722 | 983 | 15944 | 7 | 6 | 85.7143 | |
| hfeng-pmm1 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 96.9479 | 94.1155 | 99.9561 | 40.9419 | 15722 | 983 | 15944 | 7 | 6 | 85.7143 | |
| eyeh-varpipe | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 38.1941 | 23.9567 | 94.1423 | 64.6972 | 310 | 984 | 450 | 28 | 28 | 100.0000 | |
| hfeng-pmm2 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 96.9418 | 94.1095 | 99.9498 | 41.0630 | 15721 | 984 | 15938 | 8 | 7 | 87.5000 | |
| hfeng-pmm2 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 96.9418 | 94.1095 | 99.9498 | 41.0630 | 15721 | 984 | 15938 | 8 | 7 | 87.5000 | |
| cchapple-custom | SNP | * | map_l100_m2_e1 | het | 96.8714 | 97.9018 | 95.8624 | 74.0033 | 45914 | 984 | 45967 | 1984 | 408 | 20.5645 | |
| gduggal-snapvard | SNP | * | map_l100_m1_e0 | homalt | 98.0408 | 96.3523 | 99.7895 | 60.4906 | 26018 | 985 | 25605 | 54 | 41 | 75.9259 | |
| rpoplin-dv42 | SNP | * | HG002complexvar | * | 99.9179 | 99.8694 | 99.9664 | 18.9545 | 753396 | 985 | 753221 | 253 | 214 | 84.5850 | |
| mlin-fermikit | SNP | ti | map_l250_m0_e0 | * | 41.9162 | 28.1022 | 82.4411 | 81.5488 | 385 | 985 | 385 | 82 | 72 | 87.8049 | |
| jlack-gatk | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 91.4681 | 90.2214 | 92.7497 | 68.5930 | 9088 | 985 | 8942 | 699 | 645 | 92.2747 | |
| gduggal-snapplat | INDEL | I1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 75.1306 | 62.9044 | 93.2559 | 77.8634 | 1672 | 986 | 1687 | 122 | 15 | 12.2951 | |
| ckim-isaac | INDEL | D6_15 | * | het | 91.7291 | 91.4941 | 91.9653 | 44.9050 | 10606 | 986 | 10084 | 881 | 656 | 74.4608 | |
| qzeng-custom | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 75.3156 | 74.9046 | 75.7313 | 50.0285 | 2943 | 986 | 3314 | 1062 | 550 | 51.7891 | |
| gduggal-snapplat | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 18.3177 | 25.9009 | 14.1693 | 78.4001 | 345 | 987 | 365 | 2211 | 26 | 1.1759 | |
| anovak-vg | INDEL | D1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 96.3676 | 96.1079 | 96.6286 | 54.1432 | 24372 | 987 | 24047 | 839 | 436 | 51.9666 | |
| asubramanian-gatk | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | * | 97.2439 | 97.3027 | 97.1852 | 57.6417 | 35605 | 987 | 38256 | 1108 | 730 | 65.8845 | |
| asubramanian-gatk | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 98.9428 | 98.4681 | 99.4221 | 74.5651 | 63444 | 987 | 63485 | 369 | 305 | 82.6558 | |
| gduggal-bwaplat | INDEL | D16_PLUS | * | het | 80.5941 | 68.7559 | 97.3566 | 80.9524 | 2172 | 987 | 2173 | 59 | 43 | 72.8814 | |
| ciseli-custom | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 30.3983 | 25.0379 | 38.6792 | 58.6745 | 330 | 988 | 328 | 520 | 491 | 94.4231 | |
| anovak-vg | INDEL | I16_PLUS | HG002complexvar | * | 33.1975 | 24.5225 | 51.3699 | 42.4631 | 321 | 988 | 300 | 284 | 225 | 79.2254 | |
| eyeh-varpipe | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 83.2366 | 80.6994 | 85.9386 | 73.3453 | 4131 | 988 | 5091 | 833 | 775 | 93.0372 | |
| ltrigg-rtg2 | SNP | * | map_l100_m1_e0 | * | 99.2192 | 98.6340 | 99.8113 | 53.5259 | 71414 | 989 | 71410 | 135 | 22 | 16.2963 | |
| gduggal-snapplat | SNP | * | map_l150_m0_e0 | het | 89.5077 | 87.5441 | 91.5613 | 90.3664 | 6951 | 989 | 6955 | 641 | 350 | 54.6022 | |
| gduggal-snapplat | SNP | ti | HG002compoundhet | het | 78.6871 | 89.5844 | 70.1534 | 57.2786 | 8515 | 990 | 8645 | 3678 | 282 | 7.6672 | |
| gduggal-bwaplat | SNP | ti | lowcmp_SimpleRepeat_diTR_11to50 | * | 87.8326 | 79.5328 | 98.0666 | 79.9980 | 3847 | 990 | 3855 | 76 | 43 | 56.5789 | |
| jmaeng-gatk | INDEL | I1_5 | HG002compoundhet | * | 94.6029 | 91.9877 | 97.3711 | 66.5483 | 11366 | 990 | 11371 | 307 | 304 | 99.0228 | |
| gduggal-bwafb | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 93.3120 | 87.8747 | 99.4664 | 36.3431 | 7182 | 991 | 2237 | 12 | 12 | 100.0000 | |
| eyeh-varpipe | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 98.1071 | 97.0183 | 99.2207 | 69.5547 | 32245 | 991 | 32847 | 258 | 171 | 66.2791 | |
| gduggal-bwavard | INDEL | D6_15 | HG002complexvar | hetalt | 0.0000 | 2.1718 | 0.0000 | 0.0000 | 22 | 991 | 0 | 0 | 0 | ||
| ghariani-varprowl | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | * | 47.5210 | 44.6987 | 50.7237 | 69.1756 | 801 | 991 | 806 | 783 | 771 | 98.4674 | |
| mlin-fermikit | SNP | ti | map_l250_m2_e0 | homalt | 54.3759 | 43.3391 | 72.9548 | 76.3218 | 758 | 991 | 758 | 281 | 257 | 91.4591 | |
| hfeng-pmm2 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 98.0631 | 96.8992 | 99.2554 | 50.7827 | 31000 | 992 | 30924 | 232 | 217 | 93.5345 | |
| gduggal-snapplat | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 60.1656 | 43.9300 | 95.4373 | 42.4088 | 778 | 993 | 753 | 36 | 29 | 80.5556 | |
| anovak-vg | INDEL | I1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 41.7184 | 27.7293 | 84.1930 | 71.7265 | 381 | 993 | 1518 | 285 | 107 | 37.5439 | |
| mlin-fermikit | INDEL | * | HG002complexvar | homalt | 95.7600 | 96.3222 | 95.2043 | 55.1307 | 26033 | 994 | 25927 | 1306 | 1267 | 97.0138 | |
| jmaeng-gatk | INDEL | * | * | het | 99.3015 | 99.4880 | 99.1156 | 62.5254 | 193139 | 994 | 192770 | 1720 | 614 | 35.6977 | |
| gduggal-snapplat | INDEL | * | map_l100_m1_e0 | * | 79.9637 | 72.2811 | 89.4737 | 91.2096 | 2592 | 994 | 2822 | 332 | 38 | 11.4458 | |
| gduggal-bwaplat | INDEL | D16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 68.7500 | 53.2425 | 97.0034 | 79.7187 | 1133 | 995 | 1133 | 35 | 29 | 82.8571 | |
| eyeh-varpipe | INDEL | I6_15 | * | homalt | 77.6886 | 84.0359 | 72.2329 | 34.4939 | 5243 | 996 | 5273 | 2027 | 2012 | 99.2600 | |
| ghariani-varprowl | INDEL | D6_15 | HG002complexvar | hetalt | 0.0000 | 1.6782 | 0.0000 | 0.0000 | 17 | 996 | 0 | 0 | 0 | ||
| ltrigg-rtg2 | SNP | * | map_l100_m2_e0 | * | 99.2235 | 98.6534 | 99.8003 | 56.1674 | 72968 | 996 | 72965 | 146 | 24 | 16.4384 | |
| ltrigg-rtg2 | SNP | * | map_l100_m2_e1 | * | 99.2263 | 98.6673 | 99.7916 | 56.2116 | 73741 | 996 | 73738 | 154 | 24 | 15.5844 | |
| qzeng-custom | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | * | 56.1509 | 52.5940 | 60.2239 | 47.9612 | 1105 | 996 | 1614 | 1066 | 694 | 65.1032 | |
| bgallagher-sentieon | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 96.1489 | 92.9019 | 99.6311 | 33.4986 | 13036 | 996 | 13232 | 49 | 48 | 97.9592 | |