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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
18651-18700 / 86044 show all | |||||||||||||||
| rpoplin-dv42 | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.1559 | 98.4882 | 99.8328 | 57.1769 | 3583 | 55 | 3583 | 6 | 4 | 66.6667 | |
| jmaeng-gatk | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 98.8577 | 98.4881 | 99.2301 | 73.8561 | 93021 | 1428 | 92930 | 721 | 622 | 86.2691 | |
| jlack-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 98.0315 | 98.4878 | 97.5794 | 54.7750 | 6578 | 101 | 6571 | 163 | 149 | 91.4110 | |
| asubramanian-gatk | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 98.8815 | 98.4877 | 99.2784 | 83.9265 | 2605 | 40 | 2614 | 19 | 9 | 47.3684 | |
| gduggal-snapvard | INDEL | I1_5 | map_l100_m2_e0 | het | 89.8150 | 98.4868 | 82.5468 | 88.8499 | 781 | 12 | 1102 | 233 | 108 | 46.3519 | |
| jli-custom | INDEL | I1_5 | map_l100_m2_e0 | het | 99.1120 | 98.4868 | 99.7452 | 83.3439 | 781 | 12 | 783 | 2 | 0 | 0.0000 | |
| egarrison-hhga | INDEL | I1_5 | map_l100_m2_e0 | het | 98.5489 | 98.4868 | 98.6111 | 85.1044 | 781 | 12 | 781 | 11 | 1 | 9.0909 | |
| dgrover-gatk | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | * | 99.0861 | 98.4860 | 99.6935 | 62.3159 | 1301 | 20 | 1301 | 4 | 2 | 50.0000 | |
| hfeng-pmm2 | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 99.2012 | 98.4859 | 99.9268 | 62.0594 | 1366 | 21 | 1366 | 1 | 0 | 0.0000 | |
| ltrigg-rtg1 | SNP | * | map_l125_m2_e1 | * | 99.1279 | 98.4852 | 99.7790 | 64.7783 | 46487 | 715 | 46495 | 103 | 28 | 27.1845 | |
| ltrigg-rtg1 | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_11to50 | hetalt | 99.1302 | 98.4848 | 99.7840 | 42.2693 | 455 | 7 | 462 | 1 | 1 | 100.0000 | |
| jlack-gatk | INDEL | * | map_l150_m1_e0 | homalt | 98.5915 | 98.4848 | 98.6985 | 88.1613 | 455 | 7 | 455 | 6 | 3 | 50.0000 | |
| astatham-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | het | 97.2266 | 98.4848 | 96.0000 | 75.7282 | 325 | 5 | 312 | 13 | 7 | 53.8462 | |
| ndellapenna-hhga | INDEL | * | map_l150_m1_e0 | homalt | 98.5915 | 98.4848 | 98.6985 | 87.6408 | 455 | 7 | 455 | 6 | 4 | 66.6667 | |
| ckim-vqsr | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | het | 97.3783 | 98.4848 | 96.2963 | 75.6574 | 325 | 5 | 312 | 12 | 6 | 50.0000 | |
| ckim-dragen | INDEL | I1_5 | map_l150_m1_e0 | homalt | 98.2317 | 98.4848 | 97.9798 | 85.9375 | 195 | 3 | 194 | 4 | 3 | 75.0000 | |
| ckim-gatk | INDEL | * | map_l150_m2_e1 | het | 94.3211 | 98.4848 | 90.4950 | 93.9981 | 910 | 14 | 914 | 96 | 6 | 6.2500 | |
| ckim-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | het | 97.2266 | 98.4848 | 96.0000 | 75.6006 | 325 | 5 | 312 | 13 | 7 | 53.8462 | |
| cchapple-custom | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 98.6739 | 98.4848 | 98.8636 | 88.6158 | 65 | 1 | 87 | 1 | 0 | 0.0000 | |
| hfeng-pmm1 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | hetalt | 99.2366 | 98.4848 | 100.0000 | 80.0604 | 130 | 2 | 132 | 0 | 0 | ||
| ghariani-varprowl | INDEL | I1_5 | map_l250_m2_e0 | het | 90.2778 | 98.4848 | 83.3333 | 97.8793 | 65 | 1 | 65 | 13 | 3 | 23.0769 | |
| ghariani-varprowl | INDEL | I1_5 | map_l250_m2_e1 | het | 90.2778 | 98.4848 | 83.3333 | 97.9517 | 65 | 1 | 65 | 13 | 3 | 23.0769 | |
| gduggal-snapfb | INDEL | I1_5 | map_l150_m1_e0 | homalt | 97.9836 | 98.4848 | 97.4874 | 91.7152 | 195 | 3 | 194 | 5 | 3 | 60.0000 | |
| anovak-vg | SNP | ti | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 98.3610 | 98.4844 | 98.2380 | 45.9412 | 6173 | 95 | 6300 | 113 | 46 | 40.7080 | |
| ciseli-custom | SNP | ti | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 97.0190 | 98.4844 | 95.5966 | 46.9536 | 6173 | 95 | 6209 | 286 | 37 | 12.9371 | |
| ndellapenna-hhga | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 98.3782 | 98.4839 | 98.2727 | 72.8894 | 21567 | 332 | 21563 | 379 | 204 | 53.8259 | |
| gduggal-bwafb | SNP | * | map_l150_m0_e0 | homalt | 99.1750 | 98.4837 | 99.8760 | 78.3354 | 4027 | 62 | 4027 | 5 | 4 | 80.0000 | |
| astatham-gatk | SNP | tv | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 99.1039 | 98.4828 | 99.7328 | 68.8838 | 1493 | 23 | 1493 | 4 | 1 | 25.0000 | |
| ghariani-varprowl | SNP | * | map_l100_m0_e0 | * | 97.6658 | 98.4806 | 96.8644 | 74.2691 | 32342 | 499 | 32344 | 1047 | 227 | 21.6810 | |
| ghariani-varprowl | SNP | tv | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 94.4227 | 98.4802 | 90.6863 | 72.2353 | 17301 | 267 | 17390 | 1786 | 11 | 0.6159 | |
| qzeng-custom | INDEL | I1_5 | HG002compoundhet | homalt | 68.8793 | 98.4802 | 52.9605 | 78.9109 | 324 | 5 | 322 | 286 | 246 | 86.0140 | |
| jli-custom | SNP | ti | map_l150_m1_e0 | het | 98.8959 | 98.4802 | 99.3151 | 73.0550 | 12182 | 188 | 12180 | 84 | 29 | 34.5238 | |
| egarrison-hhga | INDEL | I1_5 | HG002compoundhet | homalt | 78.9281 | 98.4802 | 65.8537 | 81.8115 | 324 | 5 | 324 | 168 | 152 | 90.4762 | |
| eyeh-varpipe | INDEL | D1_5 | map_l100_m1_e0 | homalt | 97.4137 | 98.4797 | 96.3705 | 85.1515 | 583 | 9 | 770 | 29 | 24 | 82.7586 | |
| jlack-gatk | INDEL | D1_5 | map_l100_m1_e0 | homalt | 99.1497 | 98.4797 | 99.8288 | 81.5598 | 583 | 9 | 583 | 1 | 1 | 100.0000 | |
| hfeng-pmm3 | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 99.2339 | 98.4795 | 100.0000 | 52.7497 | 842 | 13 | 842 | 0 | 0 | ||
| ckim-dragen | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 99.0631 | 98.4795 | 99.6536 | 52.7550 | 842 | 13 | 863 | 3 | 1 | 33.3333 | |
| ckim-gatk | INDEL | * | map_l150_m1_e0 | het | 93.9968 | 98.4795 | 89.9044 | 93.5685 | 842 | 13 | 846 | 95 | 6 | 6.3158 | |
| jmaeng-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 98.0265 | 98.4792 | 97.5780 | 71.1859 | 17548 | 271 | 17163 | 426 | 391 | 91.7840 | |
| raldana-dualsentieon | SNP | * | map_l150_m0_e0 | * | 98.5116 | 98.4791 | 98.5442 | 78.4632 | 11849 | 183 | 11846 | 175 | 7 | 4.0000 | |
| hfeng-pmm2 | INDEL | * | map_l100_m1_e0 | het | 98.0433 | 98.4787 | 97.6117 | 85.3524 | 2201 | 34 | 2207 | 54 | 7 | 12.9630 | |
| cchapple-custom | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | het | 98.9656 | 98.4786 | 99.4574 | 53.6403 | 10939 | 169 | 15763 | 86 | 67 | 77.9070 | |
| cchapple-custom | SNP | ti | map_siren | * | 98.4477 | 98.4784 | 98.4171 | 57.2072 | 98828 | 1527 | 98796 | 1589 | 367 | 23.0963 | |
| hfeng-pmm3 | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 99.1881 | 98.4782 | 99.9083 | 59.9451 | 34880 | 539 | 34871 | 32 | 8 | 25.0000 | |
| ltrigg-rtg2 | INDEL | * | HG002complexvar | * | 98.9919 | 98.4780 | 99.5112 | 54.8986 | 75766 | 1171 | 75523 | 371 | 227 | 61.1860 | |
| ltrigg-rtg1 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 98.8593 | 98.4779 | 99.2436 | 74.6743 | 647 | 10 | 656 | 5 | 1 | 20.0000 | |
| hfeng-pmm2 | INDEL | D1_5 | HG002complexvar | * | 99.1842 | 98.4778 | 99.9009 | 57.1533 | 32217 | 498 | 32268 | 32 | 21 | 65.6250 | |
| jli-custom | INDEL | D1_5 | map_l100_m0_e0 | het | 98.1450 | 98.4772 | 97.8151 | 83.8007 | 582 | 9 | 582 | 13 | 3 | 23.0769 | |
| ltrigg-rtg2 | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | homalt | 98.9834 | 98.4772 | 99.4949 | 54.7945 | 194 | 3 | 197 | 1 | 1 | 100.0000 | |
| jmaeng-gatk | INDEL | D1_5 | map_l100_m0_e0 | het | 94.5649 | 98.4772 | 90.9516 | 90.5332 | 582 | 9 | 583 | 58 | 3 | 5.1724 | |