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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
27151-27200 / 86044 show all | |||||||||||||||
| jli-custom | INDEL | D6_15 | map_l125_m2_e0 | het | 97.1429 | 95.7746 | 98.5507 | 90.4300 | 68 | 3 | 68 | 1 | 0 | 0.0000 | |
| jli-custom | INDEL | D6_15 | map_l125_m2_e1 | het | 97.1429 | 95.7746 | 98.5507 | 90.6631 | 68 | 3 | 68 | 1 | 0 | 0.0000 | |
| jli-custom | INDEL | I1_5 | map_l150_m2_e1 | homalt | 99.2701 | 100.0000 | 98.5507 | 87.4469 | 204 | 0 | 204 | 3 | 2 | 66.6667 | |
| hfeng-pmm2 | INDEL | I1_5 | map_l150_m2_e1 | homalt | 99.2701 | 100.0000 | 98.5507 | 87.4545 | 204 | 0 | 204 | 3 | 2 | 66.6667 | |
| hfeng-pmm1 | INDEL | I1_5 | map_l150_m2_e1 | homalt | 99.2701 | 100.0000 | 98.5507 | 87.7078 | 204 | 0 | 204 | 3 | 2 | 66.6667 | |
| jlack-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 98.8242 | 99.0991 | 98.5507 | 72.0171 | 1320 | 12 | 1292 | 19 | 15 | 78.9474 | |
| hfeng-pmm3 | INDEL | I1_5 | map_l150_m2_e1 | homalt | 99.2701 | 100.0000 | 98.5507 | 86.9318 | 204 | 0 | 204 | 3 | 2 | 66.6667 | |
| hfeng-pmm3 | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 89.7690 | 82.4242 | 98.5507 | 91.0273 | 136 | 29 | 136 | 2 | 0 | 0.0000 | |
| jlack-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 98.7893 | 99.0291 | 98.5507 | 71.3594 | 816 | 8 | 816 | 12 | 4 | 33.3333 | |
| gduggal-bwafb | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_51to200 | het | 63.6016 | 46.9512 | 98.5507 | 57.2314 | 77 | 87 | 204 | 3 | 3 | 100.0000 | |
| gduggal-bwaplat | SNP | * | tech_badpromoters | het | 93.1507 | 88.3117 | 98.5507 | 74.5387 | 68 | 9 | 68 | 1 | 0 | 0.0000 | |
| gduggal-bwaplat | SNP | tv | map_l250_m0_e0 | het | 38.3099 | 23.7762 | 98.5507 | 99.1755 | 136 | 436 | 136 | 2 | 0 | 0.0000 | |
| eyeh-varpipe | INDEL | I1_5 | map_l150_m2_e1 | homalt | 99.0279 | 99.5098 | 98.5507 | 88.2373 | 203 | 1 | 340 | 5 | 5 | 100.0000 | |
| eyeh-varpipe | SNP | * | lowcmp_SimpleRepeat_homopolymer_6to10 | hetalt | 99.2701 | 100.0000 | 98.5507 | 78.2334 | 5 | 0 | 68 | 1 | 0 | 0.0000 | |
| ltrigg-rtg1 | INDEL | C1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 0.0000 | 0.0000 | 98.5507 | 98.0976 | 0 | 0 | 68 | 1 | 0 | 0.0000 | |
| ltrigg-rtg1 | INDEL | D16_PLUS | map_siren | het | 93.2340 | 88.4615 | 98.5507 | 87.7876 | 69 | 9 | 68 | 1 | 0 | 0.0000 | |
| ltrigg-rtg1 | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 98.0769 | 97.6077 | 98.5507 | 70.1299 | 204 | 5 | 204 | 3 | 0 | 0.0000 | |
| ltrigg-rtg2 | INDEL | C1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 0.0000 | 0.0000 | 98.5507 | 98.0274 | 0 | 0 | 68 | 1 | 0 | 0.0000 | |
| jmaeng-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_triTR_51to200 | * | 97.5038 | 96.4789 | 98.5507 | 46.5116 | 137 | 5 | 136 | 2 | 1 | 50.0000 | |
| hfeng-pmm1 | INDEL | D16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 98.0433 | 97.5410 | 98.5507 | 69.5460 | 476 | 12 | 476 | 7 | 4 | 57.1429 | |
| bgallagher-sentieon | SNP | ti | map_l150_m2_e0 | het | 98.8935 | 99.2392 | 98.5502 | 79.6724 | 12783 | 98 | 12779 | 188 | 30 | 15.9574 | |
| bgallagher-sentieon | SNP | ti | map_l150_m2_e1 | het | 98.8973 | 99.2470 | 98.5500 | 79.7478 | 12917 | 98 | 12913 | 190 | 30 | 15.7895 | |
| gduggal-snapplat | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 92.5093 | 87.1670 | 98.5493 | 64.5442 | 1963 | 289 | 1970 | 29 | 7 | 24.1379 | |
| gduggal-snapfb | SNP | tv | map_l250_m2_e1 | homalt | 95.8740 | 93.3404 | 98.5491 | 93.5115 | 883 | 63 | 883 | 13 | 5 | 38.4615 | |
| hfeng-pmm1 | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 97.3392 | 96.1587 | 98.5491 | 67.9366 | 5382 | 215 | 5366 | 79 | 71 | 89.8734 | |
| ckim-dragen | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.2414 | 99.9435 | 98.5491 | 72.6182 | 3535 | 2 | 3532 | 52 | 52 | 100.0000 | |
| ckim-isaac | INDEL | * | map_l125_m1_e0 | * | 77.9687 | 64.4993 | 98.5486 | 87.4682 | 1359 | 748 | 1358 | 20 | 8 | 40.0000 | |
| ckim-gatk | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 98.3167 | 98.0869 | 98.5475 | 60.4971 | 15740 | 307 | 15741 | 232 | 216 | 93.1034 | |
| gduggal-snapvard | INDEL | * | map_l125_m2_e0 | homalt | 92.4285 | 87.0249 | 98.5475 | 81.2093 | 664 | 99 | 882 | 13 | 11 | 84.6154 | |
| jli-custom | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 98.5605 | 98.5736 | 98.5474 | 69.9656 | 1313 | 19 | 1289 | 19 | 14 | 73.6842 | |
| gduggal-bwaplat | INDEL | * | map_l100_m2_e1 | het | 83.4646 | 72.3858 | 98.5474 | 93.4041 | 1696 | 647 | 1696 | 25 | 8 | 32.0000 | |
| bgallagher-sentieon | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 99.0051 | 99.4671 | 98.5473 | 71.4531 | 28559 | 153 | 28559 | 421 | 23 | 5.4632 | |
| bgallagher-sentieon | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 99.0051 | 99.4671 | 98.5473 | 71.4531 | 28559 | 153 | 28559 | 421 | 23 | 5.4632 | |
| cchapple-custom | INDEL | D6_15 | * | * | 97.8623 | 97.1869 | 98.5472 | 48.1960 | 25358 | 734 | 26658 | 393 | 348 | 88.5496 | |
| dgrover-gatk | INDEL | I16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 97.6602 | 96.7890 | 98.5472 | 85.8707 | 422 | 14 | 407 | 6 | 4 | 66.6667 | |
| raldana-dualsentieon | SNP | tv | map_l250_m2_e1 | * | 98.1230 | 97.7023 | 98.5472 | 88.2575 | 2849 | 67 | 2849 | 42 | 3 | 7.1429 | |
| bgallagher-sentieon | SNP | ti | map_l150_m1_e0 | het | 98.8799 | 99.2158 | 98.5462 | 78.5485 | 12273 | 97 | 12269 | 181 | 29 | 16.0221 | |
| ckim-isaac | INDEL | D6_15 | * | homalt | 92.2382 | 86.6899 | 98.5453 | 37.3467 | 5484 | 842 | 5487 | 81 | 30 | 37.0370 | |
| ltrigg-rtg1 | SNP | * | segdup | * | 99.0787 | 99.6188 | 98.5445 | 88.0967 | 27960 | 107 | 27963 | 413 | 51 | 12.3487 | |
| raldana-dualsentieon | SNP | * | map_l150_m0_e0 | * | 98.5116 | 98.4791 | 98.5442 | 78.4632 | 11849 | 183 | 11846 | 175 | 7 | 4.0000 | |
| ckim-vqsr | SNP | ti | map_l150_m0_e0 | * | 60.7533 | 43.9130 | 98.5441 | 93.9394 | 3452 | 4409 | 3452 | 51 | 0 | 0.0000 | |
| dgrover-gatk | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | het | 98.9340 | 99.3274 | 98.5437 | 62.8374 | 15654 | 106 | 15496 | 229 | 203 | 88.6463 | |
| dgrover-gatk | INDEL | I1_5 | map_l150_m2_e1 | homalt | 99.0244 | 99.5098 | 98.5437 | 88.6501 | 203 | 1 | 203 | 3 | 2 | 66.6667 | |
| ckim-gatk | INDEL | I1_5 | map_l150_m2_e1 | homalt | 99.0244 | 99.5098 | 98.5437 | 88.9009 | 203 | 1 | 203 | 3 | 2 | 66.6667 | |
| ndellapenna-hhga | INDEL | I1_5 | map_l150_m2_e1 | homalt | 99.0244 | 99.5098 | 98.5437 | 88.9840 | 203 | 1 | 203 | 3 | 1 | 33.3333 | |
| ndellapenna-hhga | SNP | ti | HG002complexvar | hetalt | 98.3051 | 98.0676 | 98.5437 | 41.1429 | 203 | 4 | 203 | 3 | 3 | 100.0000 | |
| mlin-fermikit | INDEL | I16_PLUS | HG002complexvar | hetalt | 71.7549 | 56.4179 | 98.5437 | 70.9450 | 189 | 146 | 203 | 3 | 2 | 66.6667 | |
| hfeng-pmm2 | INDEL | I16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 97.5416 | 96.5596 | 98.5437 | 84.5866 | 421 | 15 | 406 | 6 | 0 | 0.0000 | |
| ltrigg-rtg1 | SNP | tv | lowcmp_SimpleRepeat_quadTR_11to50 | het | 98.9815 | 99.4242 | 98.5428 | 38.7768 | 4662 | 27 | 4666 | 69 | 1 | 1.4493 | |
| ckim-gatk | SNP | ti | segdup | * | 98.9344 | 99.3295 | 98.5425 | 92.9771 | 19406 | 131 | 19404 | 287 | 8 | 2.7875 | |