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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
41351-41400 / 86044 show all | |||||||||||||||
| hfeng-pmm3 | INDEL | D16_PLUS | HG002compoundhet | homalt | 84.2105 | 100.0000 | 72.7273 | 76.0870 | 8 | 0 | 8 | 3 | 3 | 100.0000 | |
| gduggal-snapvard | INDEL | D6_15 | map_l100_m1_e0 | homalt | 57.6307 | 42.1875 | 90.9091 | 76.0870 | 27 | 37 | 30 | 3 | 3 | 100.0000 | |
| gduggal-snapvard | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 87.8412 | 97.4766 | 79.9394 | 76.0835 | 1352 | 35 | 1319 | 331 | 6 | 1.8127 | |
| hfeng-pmm3 | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | het | 96.6549 | 94.0260 | 99.4350 | 76.0811 | 362 | 23 | 352 | 2 | 1 | 50.0000 | |
| dgrover-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 99.7953 | 99.6169 | 99.9744 | 76.0807 | 3900 | 15 | 3900 | 1 | 1 | 100.0000 | |
| egarrison-hhga | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 98.4400 | 98.0595 | 98.8235 | 76.0788 | 758 | 15 | 756 | 9 | 1 | 11.1111 | |
| eyeh-varpipe | INDEL | I1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | hetalt | 91.7090 | 85.4430 | 98.9667 | 76.0780 | 270 | 46 | 862 | 9 | 9 | 100.0000 | |
| asubramanian-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 97.8328 | 99.0038 | 96.6891 | 76.0765 | 3876 | 39 | 3884 | 133 | 2 | 1.5038 | |
| rpoplin-dv42 | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_11to50 | het | 97.2294 | 97.7556 | 96.7089 | 76.0751 | 392 | 9 | 382 | 13 | 11 | 84.6154 | |
| jpowers-varprowl | SNP | ti | map_l125_m2_e0 | * | 97.7706 | 97.1809 | 98.3675 | 76.0737 | 29405 | 853 | 29405 | 488 | 165 | 33.8115 | |
| hfeng-pmm3 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | hetalt | 98.2533 | 96.5665 | 100.0000 | 76.0711 | 225 | 8 | 229 | 0 | 0 | ||
| jli-custom | SNP | tv | map_l150_m0_e0 | het | 98.0858 | 97.3268 | 98.8567 | 76.0708 | 2767 | 76 | 2767 | 32 | 7 | 21.8750 | |
| bgallagher-sentieon | SNP | * | map_l125_m2_e0 | hetalt | 96.5517 | 93.3333 | 100.0000 | 76.0684 | 28 | 2 | 28 | 0 | 0 | ||
| bgallagher-sentieon | SNP | * | map_l125_m2_e1 | hetalt | 96.5517 | 93.3333 | 100.0000 | 76.0684 | 28 | 2 | 28 | 0 | 0 | ||
| bgallagher-sentieon | SNP | tv | map_l125_m2_e0 | hetalt | 96.5517 | 93.3333 | 100.0000 | 76.0684 | 28 | 2 | 28 | 0 | 0 | ||
| bgallagher-sentieon | SNP | tv | map_l125_m2_e1 | hetalt | 96.5517 | 93.3333 | 100.0000 | 76.0684 | 28 | 2 | 28 | 0 | 0 | ||
| gduggal-snapvard | INDEL | I16_PLUS | map_l100_m1_e0 | * | 13.7405 | 7.6923 | 64.2857 | 76.0684 | 2 | 24 | 18 | 10 | 8 | 80.0000 | |
| bgallagher-sentieon | INDEL | D16_PLUS | HG002complexvar | homalt | 98.6254 | 99.3080 | 97.9522 | 76.0621 | 287 | 2 | 287 | 6 | 5 | 83.3333 | |
| jpowers-varprowl | SNP | tv | map_l100_m2_e1 | het | 96.9210 | 97.1703 | 96.6729 | 76.0613 | 15487 | 451 | 15487 | 533 | 100 | 18.7617 | |
| bgallagher-sentieon | SNP | tv | map_l150_m1_e0 | * | 98.9592 | 99.3402 | 98.5810 | 76.0604 | 10840 | 72 | 10838 | 156 | 25 | 16.0256 | |
| rpoplin-dv42 | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 98.0545 | 99.2126 | 96.9231 | 76.0589 | 126 | 1 | 126 | 4 | 3 | 75.0000 | |
| mlin-fermikit | INDEL | I16_PLUS | lowcmp_SimpleRepeat_triTR_11to50 | het | 90.9091 | 93.7500 | 88.2353 | 76.0563 | 15 | 1 | 15 | 2 | 2 | 100.0000 | |
| jpowers-varprowl | INDEL | I16_PLUS | lowcmp_SimpleRepeat_triTR_11to50 | het | 72.7273 | 75.0000 | 70.5882 | 76.0563 | 12 | 4 | 12 | 5 | 5 | 100.0000 | |
| hfeng-pmm3 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 99.9083 | 99.8168 | 100.0000 | 76.0545 | 545 | 1 | 545 | 0 | 0 | ||
| ciseli-custom | SNP | * | map_l125_m1_e0 | * | 80.8628 | 76.5085 | 85.7426 | 76.0516 | 34679 | 10648 | 34610 | 5755 | 1482 | 25.7515 | |
| mlin-fermikit | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 86.7858 | 90.4797 | 83.3817 | 76.0514 | 1226 | 129 | 1149 | 229 | 205 | 89.5197 | |
| rpoplin-dv42 | SNP | ti | map_l150_m2_e1 | het | 98.9954 | 98.8167 | 99.1746 | 76.0502 | 12861 | 154 | 12857 | 107 | 68 | 63.5514 | |
| raldana-dualsentieon | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | het | 73.4719 | 85.9184 | 64.1753 | 76.0494 | 421 | 69 | 249 | 139 | 136 | 97.8417 | |
| gduggal-bwaplat | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | homalt | 86.8534 | 76.7619 | 100.0000 | 76.0472 | 403 | 122 | 406 | 0 | 0 | ||
| gduggal-snapvard | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 9.3373 | 5.7895 | 24.1150 | 76.0466 | 77 | 1253 | 109 | 343 | 228 | 66.4723 | |
| ckim-gatk | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 99.4089 | 99.5877 | 99.2308 | 76.0442 | 48072 | 199 | 47859 | 371 | 265 | 71.4286 | |
| jpowers-varprowl | SNP | ti | map_l100_m0_e0 | het | 96.5732 | 95.9308 | 97.2242 | 76.0435 | 13414 | 569 | 13415 | 383 | 137 | 35.7702 | |
| jli-custom | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 99.7293 | 99.8915 | 99.5676 | 76.0425 | 921 | 1 | 921 | 4 | 2 | 50.0000 | |
| astatham-gatk | SNP | ti | map_l125_m2_e1 | * | 91.2494 | 84.0525 | 99.7941 | 76.0425 | 25694 | 4875 | 25690 | 53 | 29 | 54.7170 | |
| ltrigg-rtg2 | SNP | * | map_l250_m2_e0 | het | 95.8350 | 92.1448 | 99.8331 | 76.0408 | 4786 | 408 | 4786 | 8 | 1 | 12.5000 | |
| gduggal-snapplat | SNP | tv | map_l150_m2_e1 | homalt | 92.2034 | 85.5346 | 100.0000 | 76.0404 | 3536 | 598 | 3535 | 0 | 0 | ||
| asubramanian-gatk | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 99.0476 | 98.1132 | 100.0000 | 76.0369 | 52 | 1 | 52 | 0 | 0 | ||
| dgrover-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 99.7912 | 100.0000 | 99.5833 | 76.0359 | 478 | 0 | 478 | 2 | 2 | 100.0000 | |
| gduggal-snapfb | SNP | ti | map_l125_m0_e0 | * | 95.4780 | 94.9616 | 96.0000 | 76.0355 | 12119 | 643 | 12120 | 505 | 265 | 52.4752 | |
| ckim-dragen | INDEL | D6_15 | HG002compoundhet | homalt | 12.7321 | 100.0000 | 6.7989 | 76.0353 | 24 | 0 | 24 | 329 | 328 | 99.6960 | |
| ckim-vqsr | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 99.6927 | 99.4381 | 99.9487 | 76.0337 | 3893 | 22 | 3893 | 2 | 2 | 100.0000 | |
| ckim-dragen | SNP | ti | map_l100_m1_e0 | hetalt | 100.0000 | 100.0000 | 100.0000 | 76.0331 | 29 | 0 | 29 | 0 | 0 | ||
| jlack-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 96.1165 | 94.7368 | 97.5369 | 76.0331 | 198 | 11 | 198 | 5 | 4 | 80.0000 | |
| ckim-isaac | INDEL | * | HG002compoundhet | homalt | 60.3591 | 67.2012 | 54.7816 | 76.0328 | 461 | 225 | 464 | 383 | 372 | 97.1279 | |
| hfeng-pmm2 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 99.1817 | 98.5900 | 99.7805 | 76.0326 | 909 | 13 | 909 | 2 | 1 | 50.0000 | |
| asubramanian-gatk | INDEL | I16_PLUS | lowcmp_SimpleRepeat_quadTR_11to50 | * | 97.2940 | 95.6186 | 99.0291 | 76.0326 | 371 | 17 | 408 | 4 | 3 | 75.0000 | |
| ckim-vqsr | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.6856 | 99.9087 | 99.4636 | 76.0319 | 21879 | 20 | 21879 | 118 | 117 | 99.1525 | |
| gduggal-bwavard | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 64.2663 | 78.7037 | 54.3046 | 76.0317 | 85 | 23 | 82 | 69 | 42 | 60.8696 | |
| jlack-gatk | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | * | 94.7368 | 90.3346 | 99.5902 | 76.0314 | 243 | 26 | 243 | 1 | 0 | 0.0000 | |
| hfeng-pmm1 | SNP | * | map_l150_m2_e1 | het | 99.1153 | 98.7674 | 99.4657 | 76.0302 | 20112 | 251 | 20106 | 108 | 27 | 25.0000 | |