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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
44751-44800 / 86044 show all | |||||||||||||||
| dgrover-gatk | SNP | * | map_l125_m1_e0 | het | 99.1524 | 99.3097 | 98.9956 | 76.1623 | 28196 | 196 | 28190 | 286 | 55 | 19.2308 | |
| asubramanian-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 78.0641 | 95.8333 | 65.8537 | 76.1628 | 23 | 1 | 27 | 14 | 14 | 100.0000 | |
| ghariani-varprowl | INDEL | I16_PLUS | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 72.0930 | 68.8889 | 75.6098 | 76.1628 | 31 | 14 | 31 | 10 | 10 | 100.0000 | |
| gduggal-snapfb | SNP | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 52.4956 | 98.0106 | 35.8482 | 76.1642 | 2956 | 60 | 3022 | 5408 | 61 | 1.1280 | |
| gduggal-bwaplat | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 90.6304 | 83.9615 | 98.4500 | 76.1644 | 2094 | 400 | 2096 | 33 | 8 | 24.2424 | |
| ckim-dragen | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 96.0496 | 99.2794 | 93.0233 | 76.1666 | 1240 | 9 | 1240 | 93 | 84 | 90.3226 | |
| ckim-dragen | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 96.0496 | 99.2794 | 93.0233 | 76.1666 | 1240 | 9 | 1240 | 93 | 84 | 90.3226 | |
| eyeh-varpipe | INDEL | * | HG002complexvar | hetalt | 61.1209 | 45.5799 | 92.7426 | 76.1697 | 1686 | 2013 | 3642 | 285 | 277 | 97.1930 | |
| hfeng-pmm1 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 99.8165 | 99.6337 | 100.0000 | 76.1717 | 544 | 2 | 544 | 0 | 0 | ||
| mlin-fermikit | INDEL | I1_5 | map_l100_m0_e0 | * | 62.6026 | 49.1713 | 86.1290 | 76.1722 | 267 | 276 | 267 | 43 | 36 | 83.7209 | |
| gduggal-snapvard | SNP | tv | map_l100_m2_e0 | * | 94.5205 | 97.0079 | 92.1574 | 76.1726 | 24284 | 749 | 24195 | 2059 | 151 | 7.3337 | |
| mlin-fermikit | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_11to50 | het | 88.3380 | 89.7756 | 86.9458 | 76.1737 | 360 | 41 | 353 | 53 | 41 | 77.3585 | |
| dgrover-gatk | SNP | tv | map_l100_m0_e0 | het | 98.8895 | 99.2661 | 98.5157 | 76.1747 | 7169 | 53 | 7168 | 108 | 20 | 18.5185 | |
| gduggal-bwaplat | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 84.3152 | 73.5419 | 98.7866 | 76.1775 | 1387 | 499 | 1384 | 17 | 13 | 76.4706 | |
| ghariani-varprowl | SNP | tv | map_l100_m0_e0 | * | 97.0755 | 98.5204 | 95.6724 | 76.1776 | 10920 | 164 | 10921 | 494 | 87 | 17.6113 | |
| gduggal-snapfb | INDEL | D6_15 | map_l100_m2_e1 | het | 79.7221 | 68.1481 | 96.0317 | 76.1815 | 92 | 43 | 121 | 5 | 4 | 80.0000 | |
| gduggal-bwaplat | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 85.1218 | 75.0000 | 98.4018 | 76.1827 | 432 | 144 | 431 | 7 | 1 | 14.2857 | |
| raldana-dualsentieon | SNP | * | map_l125_m0_e0 | het | 98.3431 | 98.4365 | 98.2499 | 76.1833 | 12466 | 198 | 12463 | 222 | 2 | 0.9009 | |
| rpoplin-dv42 | INDEL | D1_5 | HG002compoundhet | het | 90.2551 | 96.8171 | 84.5262 | 76.1853 | 1673 | 55 | 1677 | 307 | 300 | 97.7199 | |
| gduggal-bwaplat | SNP | ti | map_l100_m0_e0 | homalt | 64.8122 | 47.9547 | 99.9463 | 76.1862 | 3728 | 4046 | 3722 | 2 | 2 | 100.0000 | |
| gduggal-bwafb | SNP | * | map_l125_m2_e1 | het | 98.4726 | 98.7517 | 98.1951 | 76.1869 | 29270 | 370 | 29270 | 538 | 123 | 22.8625 | |
| gduggal-bwavard | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 93.9379 | 89.0339 | 99.4135 | 76.1872 | 341 | 42 | 339 | 2 | 2 | 100.0000 | |
| ghariani-varprowl | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 97.2427 | 99.4993 | 95.0863 | 76.1894 | 16890 | 85 | 16913 | 874 | 433 | 49.5423 | |
| ghariani-varprowl | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 97.2427 | 99.4993 | 95.0863 | 76.1894 | 16890 | 85 | 16913 | 874 | 433 | 49.5423 | |
| gduggal-snapplat | SNP | * | lowcmp_SimpleRepeat_homopolymer_6to10 | hetalt | 100.0000 | 100.0000 | 100.0000 | 76.1905 | 5 | 0 | 5 | 0 | 0 | ||
| gduggal-snapplat | SNP | tv | lowcmp_SimpleRepeat_homopolymer_6to10 | hetalt | 100.0000 | 100.0000 | 100.0000 | 76.1905 | 5 | 0 | 5 | 0 | 0 | ||
| gduggal-snapfb | INDEL | I6_15 | map_siren | hetalt | 66.0377 | 62.5000 | 70.0000 | 76.1905 | 45 | 27 | 14 | 6 | 6 | 100.0000 | |
| gduggal-bwavard | INDEL | I1_5 | map_l125_m1_e0 | homalt | 97.5126 | 96.0245 | 99.0476 | 76.1905 | 314 | 13 | 312 | 3 | 1 | 33.3333 | |
| gduggal-snapfb | INDEL | D6_15 | map_l100_m2_e0 | het | 80.6053 | 69.4656 | 96.0000 | 76.1905 | 91 | 40 | 120 | 5 | 4 | 80.0000 | |
| eyeh-varpipe | INDEL | I16_PLUS | map_l125_m2_e0 | * | 41.1429 | 26.6667 | 90.0000 | 76.1905 | 4 | 11 | 9 | 1 | 1 | 100.0000 | |
| eyeh-varpipe | INDEL | I6_15 | map_l100_m2_e0 | het | 79.0220 | 72.1311 | 87.3684 | 76.1905 | 44 | 17 | 83 | 12 | 10 | 83.3333 | |
| eyeh-varpipe | SNP | tv | map_l150_m1_e0 | hetalt | 99.2248 | 100.0000 | 98.4615 | 76.1905 | 20 | 0 | 64 | 1 | 0 | 0.0000 | |
| gduggal-bwaplat | INDEL | D1_5 | tech_badpromoters | het | 76.9231 | 62.5000 | 100.0000 | 76.1905 | 5 | 3 | 5 | 0 | 0 | ||
| jmaeng-gatk | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | hetalt | 97.0588 | 94.2857 | 100.0000 | 76.1905 | 33 | 2 | 35 | 0 | 0 | ||
| mlin-fermikit | INDEL | D6_15 | map_l150_m1_e0 | hetalt | 61.5385 | 50.0000 | 80.0000 | 76.1905 | 4 | 4 | 4 | 1 | 0 | 0.0000 | |
| mlin-fermikit | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | hetalt | 81.3559 | 68.5714 | 100.0000 | 76.1905 | 24 | 11 | 25 | 0 | 0 | ||
| ckim-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 98.5365 | 98.0213 | 99.0571 | 76.1911 | 1932 | 39 | 1891 | 18 | 6 | 33.3333 | |
| ckim-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 98.5365 | 98.0213 | 99.0571 | 76.1911 | 1932 | 39 | 1891 | 18 | 6 | 33.3333 | |
| gduggal-bwavard | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 86.3098 | 85.7592 | 86.8676 | 76.1917 | 819 | 136 | 807 | 122 | 105 | 86.0656 | |
| jli-custom | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_11to50 | het | 98.9286 | 99.0462 | 98.8113 | 76.1938 | 1350 | 13 | 1330 | 16 | 10 | 62.5000 | |
| qzeng-custom | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | homalt | 98.7932 | 98.6450 | 98.9418 | 76.1965 | 364 | 5 | 374 | 4 | 1 | 25.0000 | |
| gduggal-snapfb | SNP | tv | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 89.5049 | 98.6984 | 81.8782 | 76.1990 | 1744 | 23 | 1735 | 384 | 49 | 12.7604 | |
| ltrigg-rtg1 | SNP | tv | map_l150_m0_e0 | homalt | 99.6981 | 99.4729 | 99.9244 | 76.2016 | 1321 | 7 | 1321 | 1 | 1 | 100.0000 | |
| ckim-vqsr | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 98.9555 | 98.7078 | 99.2044 | 76.2044 | 19326 | 253 | 19326 | 155 | 19 | 12.2581 | |
| ckim-vqsr | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 98.9555 | 98.7078 | 99.2044 | 76.2044 | 19326 | 253 | 19326 | 155 | 19 | 12.2581 | |
| dgrover-gatk | INDEL | I6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 92.1875 | 100.0000 | 85.5072 | 76.2069 | 59 | 0 | 59 | 10 | 10 | 100.0000 | |
| gduggal-snapvard | SNP | tv | map_l100_m2_e1 | * | 94.5392 | 97.0059 | 92.1948 | 76.2078 | 24526 | 757 | 24427 | 2068 | 154 | 7.4468 | |
| ckim-gatk | INDEL | I16_PLUS | * | het | 98.3735 | 98.3444 | 98.4027 | 76.2086 | 2673 | 45 | 2649 | 43 | 10 | 23.2558 | |
| gduggal-bwavard | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 97.0137 | 98.0306 | 96.0177 | 76.2105 | 896 | 18 | 868 | 36 | 5 | 13.8889 | |
| mlin-fermikit | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | hetalt | 89.5397 | 81.0606 | 100.0000 | 76.2115 | 107 | 25 | 108 | 0 | 0 | ||