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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
33051-33100 / 86044 show all | |||||||||||||||
| ltrigg-rtg1 | INDEL | D6_15 | map_l150_m1_e0 | homalt | 98.0392 | 96.1538 | 100.0000 | 86.0465 | 25 | 1 | 24 | 0 | 0 | ||
| jmaeng-gatk | INDEL | D6_15 | map_l125_m1_e0 | hetalt | 97.2973 | 94.7368 | 100.0000 | 86.0465 | 18 | 1 | 18 | 0 | 0 | ||
| gduggal-bwafb | INDEL | D1_5 | map_l125_m2_e0 | het | 97.4578 | 97.7749 | 97.1429 | 86.0457 | 747 | 17 | 748 | 22 | 0 | 0.0000 | |
| rpoplin-dv42 | INDEL | D1_5 | map_l125_m2_e1 | het | 98.1180 | 98.0519 | 98.1842 | 86.0452 | 755 | 15 | 757 | 14 | 3 | 21.4286 | |
| raldana-dualsentieon | INDEL | I1_5 | HG002compoundhet | het | 88.2507 | 86.4706 | 90.1055 | 86.0431 | 735 | 115 | 683 | 75 | 74 | 98.6667 | |
| hfeng-pmm1 | INDEL | I1_5 | map_l125_m2_e0 | * | 98.5925 | 98.0163 | 99.1755 | 86.0408 | 840 | 17 | 842 | 7 | 2 | 28.5714 | |
| ltrigg-rtg1 | INDEL | * | map_l150_m2_e0 | * | 96.6549 | 94.3892 | 99.0320 | 86.0395 | 1329 | 79 | 1330 | 13 | 3 | 23.0769 | |
| ghariani-varprowl | INDEL | D16_PLUS | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 72.5832 | 98.0769 | 57.6087 | 86.0395 | 51 | 1 | 53 | 39 | 20 | 51.2821 | |
| egarrison-hhga | INDEL | I1_5 | map_l125_m1_e0 | * | 98.7342 | 98.6747 | 98.7937 | 86.0391 | 819 | 11 | 819 | 10 | 2 | 20.0000 | |
| cchapple-custom | INDEL | C6_15 | HG002compoundhet | het | 0.0000 | 0.0000 | 88.0342 | 86.0382 | 0 | 0 | 103 | 14 | 5 | 35.7143 | |
| ciseli-custom | SNP | tv | map_l150_m0_e0 | * | 72.3723 | 66.6267 | 79.2023 | 86.0382 | 2781 | 1393 | 2780 | 730 | 179 | 24.5205 | |
| hfeng-pmm2 | INDEL | I1_5 | HG002compoundhet | homalt | 80.1471 | 99.3921 | 67.1458 | 86.0378 | 327 | 2 | 327 | 160 | 159 | 99.3750 | |
| mlin-fermikit | SNP | * | segdup | homalt | 98.6182 | 98.6689 | 98.5676 | 86.0366 | 10600 | 143 | 10597 | 154 | 135 | 87.6623 | |
| mlin-fermikit | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 85.1852 | 100.0000 | 74.1935 | 86.0360 | 23 | 0 | 23 | 8 | 8 | 100.0000 | |
| hfeng-pmm3 | INDEL | I6_15 | map_l100_m2_e0 | het | 94.0171 | 90.1639 | 98.2143 | 86.0349 | 55 | 6 | 55 | 1 | 1 | 100.0000 | |
| hfeng-pmm1 | INDEL | I16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 96.4427 | 100.0000 | 93.1298 | 86.0341 | 122 | 0 | 122 | 9 | 9 | 100.0000 | |
| jli-custom | INDEL | D1_5 | map_l125_m2_e0 | * | 98.6439 | 98.6002 | 98.6877 | 86.0337 | 1127 | 16 | 1128 | 15 | 5 | 33.3333 | |
| mlin-fermikit | INDEL | I6_15 | map_l100_m1_e0 | homalt | 68.9655 | 60.6061 | 80.0000 | 86.0335 | 20 | 13 | 20 | 5 | 5 | 100.0000 | |
| anovak-vg | INDEL | D6_15 | map_l100_m2_e1 | het | 75.1170 | 75.5556 | 74.6835 | 86.0301 | 102 | 33 | 118 | 40 | 23 | 57.5000 | |
| gduggal-bwavard | INDEL | D6_15 | map_l150_m1_e0 | homalt | 86.9565 | 76.9231 | 100.0000 | 86.0294 | 20 | 6 | 19 | 0 | 0 | ||
| ltrigg-rtg2 | INDEL | I6_15 | map_l100_m1_e0 | hetalt | 95.2381 | 90.9091 | 100.0000 | 86.0294 | 20 | 2 | 19 | 0 | 0 | ||
| ltrigg-rtg1 | INDEL | * | map_l150_m2_e1 | * | 96.6561 | 94.3711 | 99.0545 | 86.0293 | 1358 | 81 | 1362 | 13 | 3 | 23.0769 | |
| mlin-fermikit | INDEL | * | map_l150_m0_e0 | * | 55.2333 | 42.6070 | 78.4946 | 86.0290 | 219 | 295 | 219 | 60 | 41 | 68.3333 | |
| egarrison-hhga | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 93.2051 | 91.0693 | 95.4433 | 86.0265 | 775 | 76 | 775 | 37 | 12 | 32.4324 | |
| ltrigg-rtg1 | SNP | tv | map_l250_m1_e0 | homalt | 99.6487 | 99.4159 | 99.8826 | 86.0259 | 851 | 5 | 851 | 1 | 1 | 100.0000 | |
| ckim-isaac | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 81.8034 | 73.8226 | 91.7189 | 86.0200 | 674 | 239 | 731 | 66 | 8 | 12.1212 | |
| jli-custom | INDEL | * | map_l125_m1_e0 | het | 98.3481 | 98.0524 | 98.6456 | 86.0194 | 1309 | 26 | 1311 | 18 | 4 | 22.2222 | |
| rpoplin-dv42 | INDEL | D6_15 | map_l100_m2_e1 | * | 94.8905 | 94.5455 | 95.2381 | 86.0143 | 260 | 15 | 260 | 13 | 7 | 53.8462 | |
| gduggal-snapplat | SNP | tv | map_l150_m2_e1 | * | 92.0738 | 89.4279 | 94.8810 | 86.0143 | 10286 | 1216 | 10287 | 555 | 293 | 52.7928 | |
| asubramanian-gatk | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | hetalt | 100.0000 | 100.0000 | 100.0000 | 86.0140 | 18 | 0 | 20 | 0 | 0 | ||
| gduggal-bwaplat | SNP | ti | map_l100_m0_e0 | * | 72.8908 | 57.5582 | 99.3581 | 86.0136 | 12531 | 9240 | 12537 | 81 | 26 | 32.0988 | |
| jli-custom | SNP | ti | map_l250_m1_e0 | * | 98.2684 | 97.2920 | 99.2647 | 86.0135 | 4455 | 124 | 4455 | 33 | 18 | 54.5455 | |
| jpowers-varprowl | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 95.8792 | 96.9561 | 94.8260 | 86.0126 | 4109 | 129 | 4142 | 226 | 11 | 4.8673 | |
| bgallagher-sentieon | INDEL | D1_5 | map_l125_m2_e0 | homalt | 99.4505 | 99.4505 | 99.4505 | 86.0108 | 362 | 2 | 362 | 2 | 2 | 100.0000 | |
| bgallagher-sentieon | INDEL | D1_5 | map_l125_m2_e1 | homalt | 99.4624 | 99.4624 | 99.4624 | 86.0098 | 370 | 2 | 370 | 2 | 2 | 100.0000 | |
| gduggal-snapplat | SNP | tv | map_l150_m2_e0 | * | 92.0132 | 89.3351 | 94.8569 | 86.0094 | 10144 | 1211 | 10144 | 550 | 292 | 53.0909 | |
| ghariani-varprowl | INDEL | I16_PLUS | map_l100_m2_e0 | het | 76.9231 | 83.3333 | 71.4286 | 86.0000 | 15 | 3 | 15 | 6 | 4 | 66.6667 | |
| anovak-vg | INDEL | C1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 0.0000 | 0.0000 | 86.0000 | 0 | 0 | 0 | 7 | 0 | 0.0000 | ||
| ciseli-custom | SNP | tv | lowcmp_SimpleRepeat_triTR_51to200 | * | 13.3333 | 100.0000 | 7.1429 | 86.0000 | 1 | 0 | 1 | 13 | 0 | 0.0000 | |
| ltrigg-rtg2 | INDEL | D16_PLUS | map_l100_m2_e0 | het | 91.2052 | 87.5000 | 95.2381 | 86.0000 | 42 | 6 | 40 | 2 | 1 | 50.0000 | |
| jlack-gatk | SNP | * | map_l250_m1_e0 | homalt | 98.5442 | 97.5639 | 99.5443 | 85.9993 | 2403 | 60 | 2403 | 11 | 8 | 72.7273 | |
| rpoplin-dv42 | INDEL | D6_15 | map_l100_m2_e0 | homalt | 97.6744 | 96.9231 | 98.4375 | 85.9956 | 63 | 2 | 63 | 1 | 0 | 0.0000 | |
| bgallagher-sentieon | INDEL | * | map_l100_m2_e0 | * | 98.3285 | 98.6461 | 98.0129 | 85.9953 | 3643 | 50 | 3650 | 74 | 17 | 22.9730 | |
| ckim-vqsr | INDEL | D1_5 | map_siren | het | 97.8636 | 97.4967 | 98.2332 | 85.9953 | 2220 | 57 | 2224 | 40 | 2 | 5.0000 | |
| rpoplin-dv42 | INDEL | D6_15 | map_siren | het | 96.0854 | 96.4286 | 95.7447 | 85.9911 | 270 | 10 | 270 | 12 | 5 | 41.6667 | |
| hfeng-pmm2 | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_51to200 | het | 95.7107 | 95.7317 | 95.6897 | 85.9903 | 157 | 7 | 111 | 5 | 5 | 100.0000 | |
| eyeh-varpipe | INDEL | C6_15 | HG002compoundhet | * | 0.0000 | 0.0000 | 65.6489 | 85.9893 | 0 | 0 | 86 | 45 | 39 | 86.6667 | |
| gduggal-bwafb | INDEL | * | map_l125_m1_e0 | * | 96.9083 | 95.7760 | 98.0676 | 85.9889 | 2018 | 89 | 2030 | 40 | 8 | 20.0000 | |
| asubramanian-gatk | SNP | ti | map_l100_m2_e1 | het | 65.2727 | 48.4981 | 99.7873 | 85.9875 | 15015 | 15945 | 15011 | 32 | 12 | 37.5000 | |
| jpowers-varprowl | INDEL | D6_15 | map_l150_m2_e1 | homalt | 86.2745 | 75.8621 | 100.0000 | 85.9873 | 22 | 7 | 22 | 0 | 0 | ||