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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
75151-75200 / 86044 show all | |||||||||||||||
| asubramanian-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 98.5824 | 99.3478 | 97.8288 | 50.3389 | 4722 | 31 | 4731 | 105 | 95 | 90.4762 | |
| ndellapenna-hhga | INDEL | I1_5 | HG002compoundhet | het | 88.3547 | 89.0588 | 87.6616 | 81.8124 | 757 | 93 | 746 | 105 | 65 | 61.9048 | |
| qzeng-custom | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | het | 89.2573 | 89.3506 | 89.1641 | 59.4561 | 344 | 41 | 864 | 105 | 76 | 72.3810 | |
| mlin-fermikit | INDEL | * | map_l150_m2_e0 | homalt | 67.7201 | 62.3701 | 74.0741 | 84.8315 | 300 | 181 | 300 | 105 | 92 | 87.6190 | |
| jlack-gatk | INDEL | D1_5 | map_l150_m2_e1 | het | 90.3207 | 98.8506 | 83.1461 | 92.4567 | 516 | 6 | 518 | 105 | 4 | 3.8095 | |
| hfeng-pmm1 | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 96.8438 | 95.8592 | 97.8488 | 71.3186 | 4792 | 207 | 4776 | 105 | 68 | 64.7619 | |
| hfeng-pmm1 | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 96.8438 | 95.8592 | 97.8488 | 71.3186 | 4792 | 207 | 4776 | 105 | 68 | 64.7619 | |
| hfeng-pmm1 | INDEL | D1_5 | HG002compoundhet | * | 95.7858 | 92.7013 | 99.0826 | 62.4019 | 11342 | 893 | 11341 | 105 | 101 | 96.1905 | |
| hfeng-pmm1 | SNP | * | map_l150_m1_e0 | het | 99.0880 | 98.7264 | 99.4522 | 74.8794 | 19070 | 246 | 19064 | 105 | 27 | 25.7143 | |
| hfeng-pmm2 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 92.4568 | 90.6336 | 94.3548 | 75.3152 | 1974 | 204 | 1755 | 105 | 95 | 90.4762 | |
| egarrison-hhga | SNP | ti | map_siren | het | 99.5580 | 99.2867 | 99.8308 | 53.2460 | 61937 | 445 | 61938 | 105 | 38 | 36.1905 | |
| eyeh-varpipe | INDEL | * | map_l100_m2_e1 | het | 96.0818 | 95.5186 | 96.6518 | 82.4853 | 2238 | 105 | 3031 | 105 | 69 | 65.7143 | |
| egarrison-hhga | INDEL | I16_PLUS | * | homalt | 93.8558 | 94.3626 | 93.3544 | 58.5193 | 1473 | 88 | 1475 | 105 | 76 | 72.3810 | |
| ckim-vqsr | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 98.8419 | 99.1062 | 98.5790 | 59.3072 | 7318 | 66 | 7284 | 105 | 100 | 95.2381 | |
| cchapple-custom | INDEL | D1_5 | map_siren | het | 97.0834 | 98.5946 | 95.6177 | 79.2698 | 2245 | 32 | 2291 | 105 | 10 | 9.5238 | |
| cchapple-custom | INDEL | I16_PLUS | * | * | 97.5144 | 96.5971 | 98.4493 | 68.4041 | 6160 | 217 | 6666 | 105 | 85 | 80.9524 | |
| ckim-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 98.9033 | 99.2281 | 98.5807 | 59.2778 | 7327 | 57 | 7293 | 105 | 100 | 95.2381 | |
| ckim-dragen | INDEL | * | map_l100_m1_e0 | het | 96.2275 | 97.0917 | 95.3785 | 87.2966 | 2170 | 65 | 2167 | 105 | 9 | 8.5714 | |
| rpoplin-dv42 | SNP | tv | map_l150_m1_e0 | * | 98.9126 | 98.7903 | 99.0352 | 73.1204 | 10780 | 132 | 10778 | 105 | 61 | 58.0952 | |
| rpoplin-dv42 | SNP | tv | map_l150_m2_e0 | * | 98.9506 | 98.8287 | 99.0728 | 74.8529 | 11222 | 133 | 11220 | 105 | 61 | 58.0952 | |
| rpoplin-dv42 | SNP | tv | map_l150_m2_e1 | * | 98.9641 | 98.8437 | 99.0847 | 74.8658 | 11369 | 133 | 11367 | 105 | 61 | 58.0952 | |
| rpoplin-dv42 | SNP | ti | map_l150_m2_e0 | het | 99.0005 | 98.8200 | 99.1816 | 75.9652 | 12729 | 152 | 12725 | 105 | 68 | 64.7619 | |
| gduggal-snapvard | INDEL | C6_15 | lowcmp_SimpleRepeat_diTR_11to50 | * | 0.0000 | 0.0000 | 47.2362 | 89.5263 | 0 | 0 | 94 | 105 | 43 | 40.9524 | |
| gduggal-snapvard | SNP | tv | segdup | * | 97.9096 | 97.0933 | 98.7396 | 94.2289 | 8284 | 248 | 8226 | 105 | 33 | 31.4286 | |
| gduggal-snapfb | INDEL | D1_5 | HG002compoundhet | hetalt | 86.5070 | 78.1323 | 96.8926 | 76.7383 | 7982 | 2234 | 3274 | 105 | 84 | 80.0000 | |
| gduggal-snapfb | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 1.8692 | 100.0000 | 0.9434 | 71.7333 | 1 | 0 | 1 | 105 | 2 | 1.9048 | |
| gduggal-bwavard | INDEL | C16_PLUS | * | het | 0.0000 | 0.0000 | 27.5862 | 93.9734 | 0 | 0 | 40 | 105 | 8 | 7.6191 | |
| gduggal-bwaplat | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_11to50 | * | 82.4404 | 73.1758 | 94.3910 | 71.5718 | 1765 | 647 | 1767 | 105 | 26 | 24.7619 | |
| gduggal-bwafb | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 90.9017 | 87.1048 | 95.0448 | 58.1886 | 1405 | 208 | 2014 | 105 | 83 | 79.0476 | |
| gduggal-bwafb | SNP | ti | HG002complexvar | homalt | 99.8904 | 99.8351 | 99.9457 | 18.2578 | 193145 | 319 | 193159 | 105 | 88 | 83.8095 | |
| gduggal-bwavard | SNP | ti | HG002complexvar | homalt | 98.4467 | 96.9948 | 99.9428 | 17.4866 | 187650 | 5814 | 183526 | 105 | 78 | 74.2857 | |
| gduggal-bwavard | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 65.2610 | 83.5526 | 53.5398 | 93.1390 | 127 | 25 | 121 | 105 | 14 | 13.3333 | |
| gduggal-snapfb | INDEL | * | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 92.5726 | 90.3810 | 94.8730 | 43.3628 | 1945 | 207 | 1943 | 105 | 74 | 70.4762 | |
| gduggal-bwavard | INDEL | D6_15 | map_siren | * | 75.5000 | 73.4774 | 77.6371 | 87.1753 | 374 | 135 | 368 | 106 | 86 | 81.1321 | |
| gduggal-bwavard | INDEL | D6_15 | map_siren | het | 83.0604 | 98.2143 | 71.9577 | 88.5593 | 275 | 5 | 272 | 106 | 86 | 81.1321 | |
| eyeh-varpipe | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 93.4325 | 88.9626 | 98.3752 | 33.8873 | 6569 | 815 | 6418 | 106 | 80 | 75.4717 | |
| gduggal-bwaplat | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 79.0138 | 67.0974 | 96.0770 | 80.1746 | 2596 | 1273 | 2596 | 106 | 58 | 54.7170 | |
| gduggal-bwaplat | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 87.6933 | 79.6065 | 97.6088 | 41.6096 | 4329 | 1109 | 4327 | 106 | 105 | 99.0566 | |
| gduggal-bwaplat | SNP | ti | map_l125_m1_e0 | het | 79.9258 | 66.9495 | 99.1416 | 88.1040 | 12229 | 6037 | 12243 | 106 | 30 | 28.3019 | |
| dgrover-gatk | SNP | ti | HG002complexvar | * | 99.9530 | 99.9268 | 99.9791 | 17.5262 | 508064 | 372 | 508000 | 106 | 56 | 52.8302 | |
| mlin-fermikit | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 96.1180 | 95.8000 | 96.4382 | 69.3543 | 2874 | 126 | 2870 | 106 | 91 | 85.8491 | |
| mlin-fermikit | INDEL | * | map_l125_m0_e0 | * | 59.8688 | 47.8458 | 79.9622 | 82.3077 | 422 | 460 | 423 | 106 | 75 | 70.7547 | |
| ndellapenna-hhga | SNP | * | map_l100_m1_e0 | het | 99.0732 | 98.3928 | 99.7631 | 62.7556 | 44630 | 729 | 44632 | 106 | 41 | 38.6792 | |
| ndellapenna-hhga | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 78.8884 | 79.2818 | 78.4990 | 70.8284 | 287 | 75 | 387 | 106 | 100 | 94.3396 | |
| qzeng-custom | SNP | tv | lowcmp_SimpleRepeat_diTR_11to50 | * | 98.5273 | 99.1969 | 97.8668 | 72.2743 | 4817 | 39 | 4863 | 106 | 20 | 18.8679 | |
| jpowers-varprowl | SNP | * | segdup | homalt | 99.4812 | 99.9441 | 99.0225 | 89.9716 | 10737 | 6 | 10738 | 106 | 65 | 61.3208 | |
| jpowers-varprowl | SNP | tv | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 98.0622 | 99.8912 | 96.2989 | 47.9935 | 2755 | 3 | 2758 | 106 | 73 | 68.8679 | |
| ltrigg-rtg2 | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | het | 98.7792 | 98.5236 | 99.0362 | 55.6925 | 10944 | 164 | 10892 | 106 | 23 | 21.6981 | |
| jmaeng-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 98.6091 | 98.6593 | 98.5590 | 59.0674 | 7285 | 99 | 7250 | 106 | 103 | 97.1698 | |
| jmaeng-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 97.9872 | 99.1753 | 96.8273 | 68.0073 | 3247 | 27 | 3235 | 106 | 103 | 97.1698 | |