PrecisionFDA
Truth Challenge
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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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
53051-53100 / 86044 show all | |||||||||||||||
| gduggal-bwafb | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 93.1414 | 92.1902 | 94.1126 | 70.7669 | 1086 | 92 | 1087 | 68 | 66 | 97.0588 | |
| mlin-fermikit | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 86.3348 | 92.1922 | 81.1772 | 59.7644 | 5160 | 437 | 5158 | 1196 | 1175 | 98.2441 | |
| eyeh-varpipe | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | homalt | 94.1583 | 92.1965 | 96.2054 | 74.5165 | 319 | 27 | 431 | 17 | 17 | 100.0000 | |
| gduggal-snapfb | SNP | * | map_l250_m2_e1 | homalt | 95.5941 | 92.2001 | 99.2475 | 92.8509 | 2506 | 212 | 2506 | 19 | 10 | 52.6316 | |
| gduggal-snapfb | SNP | ti | map_l250_m0_e0 | homalt | 95.6005 | 92.2018 | 99.2593 | 96.2789 | 402 | 34 | 402 | 3 | 2 | 66.6667 | |
| ckim-gatk | INDEL | I16_PLUS | HG002compoundhet | * | 94.2299 | 92.2072 | 96.3432 | 52.0122 | 1976 | 167 | 1976 | 75 | 75 | 100.0000 | |
| gduggal-snapplat | SNP | * | tech_badpromoters | het | 91.0256 | 92.2078 | 89.8734 | 77.4286 | 71 | 6 | 71 | 8 | 0 | 0.0000 | |
| ltrigg-rtg1 | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | het | 94.1694 | 92.2078 | 96.2162 | 75.6258 | 355 | 30 | 356 | 14 | 2 | 14.2857 | |
| jmaeng-gatk | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 95.9181 | 92.2078 | 99.9396 | 36.0371 | 1633 | 138 | 1655 | 1 | 1 | 100.0000 | |
| anovak-vg | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 90.9171 | 92.2101 | 89.6598 | 73.7675 | 28717 | 2426 | 29308 | 3380 | 1164 | 34.4379 | |
| anovak-vg | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 90.9171 | 92.2101 | 89.6598 | 73.7675 | 28717 | 2426 | 29308 | 3380 | 1164 | 34.4379 | |
| ghariani-varprowl | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 66.9076 | 92.2101 | 52.5013 | 83.8765 | 1018 | 86 | 1039 | 940 | 100 | 10.6383 | |
| ltrigg-rtg2 | SNP | * | map_l250_m2_e1 | het | 95.8720 | 92.2112 | 99.8355 | 76.2366 | 4854 | 410 | 4854 | 8 | 1 | 12.5000 | |
| gduggal-snapplat | SNP | * | map_l100_m2_e0 | homalt | 95.9129 | 92.2138 | 99.9212 | 63.8760 | 25380 | 2143 | 25364 | 20 | 15 | 75.0000 | |
| ckim-isaac | SNP | tv | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 94.2766 | 92.2164 | 96.4310 | 62.9827 | 1398 | 118 | 1405 | 52 | 20 | 38.4615 | |
| gduggal-snapvard | INDEL | * | map_l150_m0_e0 | * | 82.1730 | 92.2179 | 74.1015 | 92.7012 | 474 | 40 | 701 | 245 | 50 | 20.4082 | |
| ltrigg-rtg1 | INDEL | * | map_l150_m0_e0 | * | 95.2820 | 92.2179 | 98.5567 | 87.0112 | 474 | 40 | 478 | 7 | 2 | 28.5714 | |
| egarrison-hhga | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 91.2797 | 92.2197 | 90.3587 | 46.2002 | 403 | 34 | 403 | 43 | 19 | 44.1860 | |
| ndellapenna-hhga | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 87.8953 | 92.2197 | 83.9583 | 47.5410 | 403 | 34 | 403 | 77 | 45 | 58.4416 | |
| ckim-vqsr | INDEL | D16_PLUS | map_l100_m2_e0 | * | 90.2174 | 92.2222 | 88.2979 | 95.8952 | 83 | 7 | 83 | 11 | 4 | 36.3636 | |
| hfeng-pmm1 | INDEL | D16_PLUS | map_l100_m2_e0 | * | 89.7297 | 92.2222 | 87.3684 | 93.0250 | 83 | 7 | 83 | 12 | 2 | 16.6667 | |
| hfeng-pmm2 | INDEL | D16_PLUS | map_l100_m2_e0 | * | 88.2979 | 92.2222 | 84.6939 | 93.9840 | 83 | 7 | 83 | 15 | 3 | 20.0000 | |
| jmaeng-gatk | INDEL | D16_PLUS | map_l100_m2_e0 | * | 89.2473 | 92.2222 | 86.4583 | 95.4717 | 83 | 7 | 83 | 13 | 4 | 30.7692 | |
| bgallagher-sentieon | INDEL | D16_PLUS | map_l100_m2_e0 | * | 87.3684 | 92.2222 | 83.0000 | 94.8823 | 83 | 7 | 83 | 17 | 4 | 23.5294 | |
| ckim-gatk | INDEL | D16_PLUS | map_l100_m2_e0 | * | 89.7297 | 92.2222 | 87.3684 | 95.8533 | 83 | 7 | 83 | 12 | 4 | 33.3333 | |
| anovak-vg | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 89.4551 | 92.2272 | 86.8448 | 82.4170 | 6348 | 535 | 6760 | 1024 | 420 | 41.0156 | |
| cchapple-custom | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 94.5231 | 92.2277 | 96.9357 | 58.1370 | 3726 | 314 | 10281 | 325 | 271 | 83.3846 | |
| gduggal-snapplat | SNP | ti | map_l125_m1_e0 | * | 94.1774 | 92.2277 | 96.2113 | 79.7747 | 27055 | 2280 | 27070 | 1066 | 586 | 54.9719 | |
| cchapple-custom | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 94.7350 | 92.2280 | 97.3822 | 89.6054 | 356 | 30 | 372 | 10 | 1 | 10.0000 | |
| gduggal-bwaplat | SNP | ti | HG002compoundhet | hetalt | 95.9569 | 92.2280 | 100.0000 | 21.9941 | 534 | 45 | 532 | 0 | 0 | ||
| astatham-gatk | INDEL | I1_5 | map_l150_m2_e0 | het | 95.1641 | 92.2330 | 98.2877 | 91.7561 | 285 | 24 | 287 | 5 | 0 | 0.0000 | |
| egarrison-hhga | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 93.8354 | 92.2330 | 95.4944 | 66.5970 | 760 | 64 | 763 | 36 | 33 | 91.6667 | |
| ckim-gatk | INDEL | I16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 95.0000 | 92.2330 | 97.9381 | 88.2850 | 190 | 16 | 190 | 4 | 2 | 50.0000 | |
| rpoplin-dv42 | INDEL | I1_5 | HG002compoundhet | het | 81.6272 | 92.2353 | 73.2075 | 84.1151 | 784 | 66 | 776 | 284 | 279 | 98.2394 | |
| gduggal-bwaplat | SNP | ti | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 95.7591 | 92.2386 | 99.5591 | 69.5815 | 1129 | 95 | 1129 | 5 | 5 | 100.0000 | |
| gduggal-bwavard | INDEL | * | map_l250_m2_e1 | homalt | 94.6903 | 92.2414 | 97.2727 | 93.4368 | 107 | 9 | 107 | 3 | 2 | 66.6667 | |
| cchapple-custom | INDEL | I6_15 | map_l100_m2_e0 | * | 92.9049 | 92.2414 | 93.5780 | 88.1907 | 107 | 9 | 102 | 7 | 2 | 28.5714 | |
| cchapple-custom | INDEL | I6_15 | map_l100_m2_e1 | * | 92.9336 | 92.2414 | 93.6364 | 88.3103 | 107 | 9 | 103 | 7 | 2 | 28.5714 | |
| egarrison-hhga | INDEL | I6_15 | map_l100_m2_e0 | * | 95.1111 | 92.2414 | 98.1651 | 85.7516 | 107 | 9 | 107 | 2 | 2 | 100.0000 | |
| egarrison-hhga | INDEL | I6_15 | map_l100_m2_e1 | * | 94.6903 | 92.2414 | 97.2727 | 85.9335 | 107 | 9 | 107 | 3 | 2 | 66.6667 | |
| ghariani-varprowl | INDEL | * | map_l250_m2_e1 | homalt | 93.8596 | 92.2414 | 95.5357 | 94.7955 | 107 | 9 | 107 | 5 | 2 | 40.0000 | |
| ltrigg-rtg2 | INDEL | I6_15 | map_l100_m2_e0 | * | 95.9641 | 92.2414 | 100.0000 | 81.9298 | 107 | 9 | 103 | 0 | 0 | ||
| ltrigg-rtg2 | INDEL | I6_15 | map_l100_m2_e1 | * | 95.9641 | 92.2414 | 100.0000 | 82.3328 | 107 | 9 | 103 | 0 | 0 | ||
| ltrigg-rtg1 | INDEL | I6_15 | map_l100_m2_e0 | * | 95.5192 | 92.2414 | 99.0385 | 81.8815 | 107 | 9 | 103 | 1 | 0 | 0.0000 | |
| ltrigg-rtg1 | INDEL | I6_15 | map_l100_m2_e1 | * | 95.5234 | 92.2414 | 99.0476 | 82.1124 | 107 | 9 | 104 | 1 | 0 | 0.0000 | |
| jpowers-varprowl | INDEL | * | map_l250_m2_e1 | homalt | 94.2731 | 92.2414 | 96.3964 | 94.4995 | 107 | 9 | 107 | 4 | 2 | 50.0000 | |
| gduggal-snapfb | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 28.4364 | 92.2444 | 16.8091 | 77.5112 | 785 | 66 | 846 | 4187 | 78 | 1.8629 | |
| ckim-vqsr | INDEL | I6_15 | HG002compoundhet | hetalt | 95.9547 | 92.2455 | 99.9747 | 28.2465 | 7875 | 662 | 7916 | 2 | 2 | 100.0000 | |
| jlack-gatk | INDEL | D16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 92.9210 | 92.2462 | 93.6058 | 72.7642 | 1963 | 165 | 1947 | 133 | 117 | 87.9699 | |
| ghariani-varprowl | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 60.3322 | 92.2485 | 44.8239 | 74.0840 | 1678 | 141 | 1693 | 2084 | 2043 | 98.0326 | |