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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
17951-18000 / 86044 show all | |||||||||||||||
| hfeng-pmm3 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 99.5273 | 99.6634 | 99.3915 | 39.2247 | 4737 | 16 | 4737 | 29 | 28 | 96.5517 | |
| hfeng-pmm3 | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 99.6691 | 99.7378 | 99.6004 | 35.1764 | 7228 | 19 | 7228 | 29 | 28 | 96.5517 | |
| hfeng-pmm3 | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 96.4527 | 93.8414 | 99.2135 | 55.2222 | 3657 | 240 | 3658 | 29 | 24 | 82.7586 | |
| hfeng-pmm3 | SNP | tv | HG002complexvar | het | 99.7826 | 99.5854 | 99.9807 | 20.9857 | 150106 | 625 | 150027 | 29 | 6 | 20.6897 | |
| eyeh-varpipe | SNP | tv | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 96.5573 | 98.6641 | 94.5386 | 64.0244 | 517 | 7 | 502 | 29 | 9 | 31.0345 | |
| eyeh-varpipe | SNP | tv | map_l250_m0_e0 | * | 97.7391 | 99.2157 | 96.3057 | 94.5189 | 759 | 6 | 756 | 29 | 3 | 10.3448 | |
| gduggal-bwafb | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 84.6329 | 76.2619 | 95.0680 | 66.4957 | 559 | 174 | 559 | 29 | 29 | 100.0000 | |
| gduggal-bwafb | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | het | 75.3138 | 61.2245 | 97.8261 | 47.4389 | 300 | 190 | 1305 | 29 | 26 | 89.6552 | |
| gduggal-bwavard | INDEL | I6_15 | map_l100_m1_e0 | * | 71.7489 | 70.1754 | 73.3945 | 86.6585 | 80 | 34 | 80 | 29 | 19 | 65.5172 | |
| gduggal-bwavard | INDEL | I6_15 | map_l100_m2_e0 | * | 72.2467 | 70.6897 | 73.8739 | 87.7212 | 82 | 34 | 82 | 29 | 19 | 65.5172 | |
| gduggal-bwavard | INDEL | I6_15 | map_l100_m2_e1 | * | 72.2467 | 70.6897 | 73.8739 | 87.9870 | 82 | 34 | 82 | 29 | 19 | 65.5172 | |
| gduggal-bwavard | SNP | * | map_l100_m1_e0 | homalt | 98.6152 | 97.3744 | 99.8881 | 60.4751 | 26294 | 709 | 25878 | 29 | 23 | 79.3103 | |
| gduggal-snapfb | INDEL | * | map_l150_m0_e0 | het | 90.4453 | 89.4428 | 91.4706 | 88.9359 | 305 | 36 | 311 | 29 | 6 | 20.6897 | |
| gduggal-bwaplat | INDEL | * | map_l100_m2_e1 | * | 80.6558 | 68.1044 | 98.8790 | 92.5655 | 2558 | 1198 | 2558 | 29 | 11 | 37.9310 | |
| gduggal-bwaplat | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 72.7369 | 58.3764 | 96.4677 | 87.8568 | 791 | 564 | 792 | 29 | 21 | 72.4138 | |
| gduggal-bwaplat | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_51to200 | * | 37.5839 | 24.1033 | 85.2792 | 74.6461 | 168 | 529 | 168 | 29 | 9 | 31.0345 | |
| gduggal-bwaplat | INDEL | D6_15 | HG002complexvar | hetalt | 82.3891 | 72.0632 | 96.1691 | 62.5248 | 730 | 283 | 728 | 29 | 27 | 93.1034 | |
| gduggal-bwavard | INDEL | C6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 0.0000 | 0.0000 | 59.7222 | 96.2284 | 0 | 0 | 43 | 29 | 12 | 41.3793 | |
| gduggal-bwavard | INDEL | D1_5 | map_l250_m0_e0 | * | 73.9496 | 95.6522 | 60.2740 | 97.1350 | 44 | 2 | 44 | 29 | 2 | 6.8966 | |
| gduggal-bwavard | INDEL | D1_5 | map_l250_m0_e0 | het | 69.4737 | 100.0000 | 53.2258 | 97.1702 | 33 | 0 | 33 | 29 | 2 | 6.8966 | |
| gduggal-bwaplat | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 83.2726 | 71.7728 | 99.1604 | 47.4357 | 3425 | 1347 | 3425 | 29 | 27 | 93.1034 | |
| gduggal-bwaplat | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 82.8931 | 71.4423 | 98.7151 | 55.3864 | 2229 | 891 | 2228 | 29 | 26 | 89.6552 | |
| gduggal-bwaplat | SNP | * | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 88.1535 | 79.4790 | 98.9534 | 72.5834 | 2746 | 709 | 2742 | 29 | 25 | 86.2069 | |
| gduggal-bwafb | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 87.7698 | 86.2191 | 89.3773 | 67.9201 | 244 | 39 | 244 | 29 | 29 | 100.0000 | |
| gduggal-bwafb | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 63.9411 | 49.6269 | 89.8601 | 54.0931 | 266 | 270 | 257 | 29 | 29 | 100.0000 | |
| gduggal-bwafb | SNP | ti | lowcmp_SimpleRepeat_triTR_11to50 | het | 99.1968 | 99.5561 | 98.8400 | 40.7302 | 2467 | 11 | 2471 | 29 | 6 | 20.6897 | |
| 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 | |
| ndellapenna-hhga | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 92.2061 | 92.0844 | 92.3280 | 55.4245 | 349 | 30 | 349 | 29 | 16 | 55.1724 | |
| ndellapenna-hhga | INDEL | I16_PLUS | * | hetalt | 89.6769 | 82.4118 | 98.3466 | 51.6538 | 1729 | 369 | 1725 | 29 | 24 | 82.7586 | |
| ltrigg-rtg2 | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 87.8760 | 79.8693 | 97.6669 | 68.5714 | 1222 | 308 | 1214 | 29 | 21 | 72.4138 | |
| ltrigg-rtg2 | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 87.8760 | 79.8693 | 97.6669 | 68.5714 | 1222 | 308 | 1214 | 29 | 21 | 72.4138 | |
| ltrigg-rtg2 | INDEL | I1_5 | * | hetalt | 98.3546 | 97.0076 | 99.7395 | 72.4903 | 10860 | 335 | 11105 | 29 | 29 | 100.0000 | |
| qzeng-custom | INDEL | C16_PLUS | map_l100_m1_e0 | * | 0.0000 | 0.0000 | 77.1654 | 0 | 0 | 0 | 29 | 0 | 0.0000 | ||
| qzeng-custom | INDEL | C16_PLUS | map_l100_m2_e0 | * | 0.0000 | 0.0000 | 79.5775 | 0 | 0 | 0 | 29 | 0 | 0.0000 | ||
| qzeng-custom | INDEL | C16_PLUS | map_l100_m2_e1 | * | 0.0000 | 0.0000 | 79.8611 | 0 | 0 | 0 | 29 | 0 | 0.0000 | ||
| qzeng-custom | SNP | * | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 99.6848 | 99.5401 | 99.8300 | 56.5387 | 17098 | 79 | 17030 | 29 | 9 | 31.0345 | |
| qzeng-custom | SNP | * | map_l150_m0_e0 | homalt | 74.2731 | 59.5011 | 98.8021 | 79.7981 | 2433 | 1656 | 2392 | 29 | 29 | 100.0000 | |
| raldana-dualsentieon | INDEL | * | map_l150_m2_e1 | * | 97.2377 | 96.5254 | 97.9606 | 88.6503 | 1389 | 50 | 1393 | 29 | 5 | 17.2414 | |
| mlin-fermikit | INDEL | I16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 67.2776 | 57.7670 | 80.5369 | 88.2492 | 119 | 87 | 120 | 29 | 23 | 79.3103 | |
| mlin-fermikit | INDEL | I1_5 | map_l150_m2_e0 | * | 61.4412 | 46.8208 | 89.3382 | 85.2734 | 243 | 276 | 243 | 29 | 25 | 86.2069 | |
| mlin-fermikit | INDEL | I1_5 | map_l150_m2_e1 | * | 61.8989 | 47.2693 | 89.6429 | 85.3403 | 251 | 280 | 251 | 29 | 25 | 86.2069 | |
| ndellapenna-hhga | SNP | * | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 98.8830 | 98.6107 | 99.1567 | 58.6659 | 3407 | 48 | 3410 | 29 | 25 | 86.2069 | |
| ndellapenna-hhga | SNP | * | map_l250_m1_e0 | het | 97.4601 | 95.6257 | 99.3663 | 87.5048 | 4547 | 208 | 4547 | 29 | 14 | 48.2759 | |
| ndellapenna-hhga | SNP | ti | map_l125_m0_e0 | * | 98.8454 | 97.9392 | 99.7685 | 71.9216 | 12499 | 263 | 12499 | 29 | 16 | 55.1724 | |
| ndellapenna-hhga | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 96.4386 | 95.2569 | 97.6499 | 83.7824 | 1205 | 60 | 1205 | 29 | 20 | 68.9655 | |
| qzeng-custom | INDEL | * | map_l100_m0_e0 | homalt | 82.8374 | 73.4774 | 94.9301 | 85.9563 | 374 | 135 | 543 | 29 | 6 | 20.6897 | |
| qzeng-custom | INDEL | * | map_l125_m2_e0 | homalt | 83.6240 | 73.9187 | 96.2629 | 86.5020 | 564 | 199 | 747 | 29 | 11 | 37.9310 | |
| qzeng-custom | INDEL | * | map_l125_m2_e1 | homalt | 83.8858 | 74.2894 | 96.3291 | 86.5211 | 575 | 199 | 761 | 29 | 11 | 37.9310 | |
| ltrigg-rtg2 | SNP | ti | map_l125_m1_e0 | het | 98.5415 | 97.2791 | 99.8371 | 55.5647 | 17769 | 497 | 17770 | 29 | 4 | 13.7931 | |
| ltrigg-rtg2 | SNP | tv | map_l125_m1_e0 | * | 98.9355 | 98.0707 | 99.8157 | 58.1812 | 15707 | 309 | 15707 | 29 | 5 | 17.2414 | |