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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
31201-31250 / 86044 show all | |||||||||||||||
| ckim-isaac | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | homalt | 93.9237 | 90.0875 | 98.1013 | 46.7116 | 309 | 34 | 310 | 6 | 1 | 16.6667 | |
| ckim-isaac | INDEL | I1_5 | map_l100_m2_e1 | het | 89.3559 | 81.3580 | 99.0977 | 86.3869 | 659 | 151 | 659 | 6 | 1 | 16.6667 | |
| egarrison-hhga | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 99.4422 | 99.5809 | 99.3038 | 58.0347 | 4277 | 18 | 4279 | 30 | 5 | 16.6667 | |
| egarrison-hhga | SNP | ti | lowcmp_SimpleRepeat_triTR_11to50 | * | 99.6923 | 99.5392 | 99.8459 | 28.7987 | 3888 | 18 | 3888 | 6 | 1 | 16.6667 | |
| eyeh-varpipe | INDEL | C1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 0.0000 | 0.0000 | 53.8462 | 93.6585 | 0 | 0 | 7 | 6 | 1 | 16.6667 | |
| ckim-vqsr | INDEL | D6_15 | map_l100_m0_e0 | * | 95.6938 | 97.0874 | 94.3396 | 91.8147 | 100 | 3 | 100 | 6 | 1 | 16.6667 | |
| ckim-vqsr | INDEL | D6_15 | map_l100_m0_e0 | het | 94.4000 | 98.3333 | 90.7692 | 93.0851 | 59 | 1 | 59 | 6 | 1 | 16.6667 | |
| ckim-vqsr | INDEL | I1_5 | map_l100_m0_e0 | * | 97.3193 | 96.8692 | 97.7737 | 89.6605 | 526 | 17 | 527 | 12 | 2 | 16.6667 | |
| ckim-vqsr | INDEL | I1_5 | map_l150_m1_e0 | * | 96.6092 | 95.6522 | 97.5855 | 92.5754 | 484 | 22 | 485 | 12 | 2 | 16.6667 | |
| ckim-vqsr | INDEL | I1_5 | map_l150_m2_e0 | * | 96.5943 | 95.5684 | 97.6424 | 93.2903 | 496 | 23 | 497 | 12 | 2 | 16.6667 | |
| ckim-vqsr | INDEL | I1_5 | map_l150_m2_e1 | * | 96.5736 | 95.4802 | 97.6923 | 93.3153 | 507 | 24 | 508 | 12 | 2 | 16.6667 | |
| gduggal-bwavard | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 91.6710 | 91.9194 | 91.4238 | 85.3408 | 8395 | 738 | 8283 | 777 | 129 | 16.6023 | |
| gduggal-bwavard | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 91.6710 | 91.9194 | 91.4238 | 85.3408 | 8395 | 738 | 8283 | 777 | 129 | 16.6023 | |
| gduggal-bwavard | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 93.5454 | 91.9051 | 95.2453 | 77.4805 | 28622 | 2521 | 28425 | 1419 | 235 | 16.5610 | |
| gduggal-bwavard | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 93.5454 | 91.9051 | 95.2453 | 77.4805 | 28622 | 2521 | 28425 | 1419 | 235 | 16.5610 | |
| dgrover-gatk | SNP | tv | map_l100_m2_e0 | het | 99.3042 | 99.5246 | 99.0848 | 72.9235 | 15702 | 75 | 15698 | 145 | 24 | 16.5517 | |
| bgallagher-sentieon | SNP | * | map_l125_m2_e0 | * | 99.2735 | 99.4499 | 99.0978 | 72.9518 | 46466 | 257 | 46460 | 423 | 70 | 16.5485 | |
| gduggal-snapplat | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 50.4391 | 35.8961 | 84.7921 | 83.3242 | 677 | 1209 | 775 | 139 | 23 | 16.5468 | |
| gduggal-snapplat | INDEL | * | map_l150_m1_e0 | het | 79.4298 | 74.1520 | 85.5164 | 95.0714 | 634 | 221 | 679 | 115 | 19 | 16.5217 | |
| ckim-gatk | SNP | ti | map_l150_m0_e0 | * | 72.8820 | 58.1733 | 97.5459 | 92.0553 | 4573 | 3288 | 4571 | 115 | 19 | 16.5217 | |
| bgallagher-sentieon | SNP | * | map_l125_m2_e1 | * | 99.2798 | 99.4555 | 99.1048 | 72.9953 | 46945 | 257 | 46939 | 424 | 70 | 16.5094 | |
| gduggal-snapvard | SNP | ti | * | * | 99.1158 | 98.9272 | 99.3052 | 22.3384 | 2063143 | 22374 | 2054412 | 14373 | 2372 | 16.5032 | |
| gduggal-bwavard | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 93.4281 | 91.8537 | 95.0573 | 78.9460 | 41979 | 3723 | 41502 | 2158 | 356 | 16.4968 | |
| gduggal-bwavard | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 93.4281 | 91.8537 | 95.0573 | 78.9460 | 41979 | 3723 | 41502 | 2158 | 356 | 16.4968 | |
| hfeng-pmm3 | SNP | ti | map_l125_m1_e0 | * | 99.5837 | 99.4989 | 99.6687 | 69.3283 | 29188 | 147 | 29184 | 97 | 16 | 16.4948 | |
| ciseli-custom | SNP | ti | * | * | 98.3062 | 98.8974 | 97.7221 | 19.7040 | 2062524 | 22994 | 2057571 | 47963 | 7893 | 16.4564 | |
| dgrover-gatk | SNP | tv | map_l100_m2_e1 | het | 99.3081 | 99.5294 | 99.0878 | 72.9526 | 15863 | 75 | 15859 | 146 | 24 | 16.4384 | |
| ltrigg-rtg2 | SNP | * | map_l100_m2_e0 | * | 99.2235 | 98.6534 | 99.8003 | 56.1674 | 72968 | 996 | 72965 | 146 | 24 | 16.4384 | |
| cchapple-custom | SNP | tv | map_l150_m1_e0 | * | 96.2415 | 96.9483 | 95.5449 | 77.7956 | 10579 | 333 | 10573 | 493 | 81 | 16.4300 | |
| cchapple-custom | SNP | tv | map_l150_m1_e0 | het | 95.1002 | 97.0775 | 93.2019 | 81.0524 | 6743 | 203 | 6759 | 493 | 81 | 16.4300 | |
| mlin-fermikit | SNP | * | HG002complexvar | het | 98.1632 | 96.4217 | 99.9688 | 17.2653 | 448843 | 16657 | 448744 | 140 | 23 | 16.4286 | |
| gduggal-bwaplat | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 75.0708 | 63.2962 | 92.2274 | 85.6453 | 795 | 461 | 795 | 67 | 11 | 16.4179 | |
| qzeng-custom | SNP | ti | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 98.8622 | 99.1709 | 98.5554 | 65.0606 | 17703 | 148 | 17874 | 262 | 43 | 16.4122 | |
| gduggal-snapfb | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 81.4700 | 91.7896 | 73.2362 | 71.7064 | 5601 | 501 | 6436 | 2352 | 386 | 16.4116 | |
| gduggal-snapfb | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 84.4875 | 91.0761 | 78.7879 | 71.3873 | 694 | 68 | 702 | 189 | 31 | 16.4021 | |
| ciseli-custom | INDEL | C6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 0.0000 | 0.0000 | 19.7368 | 95.1157 | 0 | 0 | 15 | 61 | 10 | 16.3934 | |
| ghariani-varprowl | SNP | * | map_siren | * | 98.7774 | 99.3373 | 98.2237 | 61.6367 | 145259 | 969 | 145263 | 2627 | 430 | 16.3685 | |
| gduggal-snapfb | INDEL | D1_5 | map_l125_m2_e1 | * | 96.0083 | 96.7156 | 95.3112 | 86.9753 | 1119 | 38 | 1118 | 55 | 9 | 16.3636 | |
| gduggal-snapvard | INDEL | D1_5 | map_l250_m2_e0 | * | 80.1166 | 97.8261 | 67.8363 | 95.0015 | 180 | 4 | 232 | 110 | 18 | 16.3636 | |
| gduggal-snapplat | INDEL | * | map_l150_m0_e0 | het | 78.1739 | 73.9003 | 82.9721 | 96.4230 | 252 | 89 | 268 | 55 | 9 | 16.3636 | |
| ltrigg-rtg1 | SNP | * | map_l150_m2_e1 | het | 98.4558 | 97.2204 | 99.7229 | 66.1731 | 19797 | 566 | 19797 | 55 | 9 | 16.3636 | |
| mlin-fermikit | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 86.4488 | 81.0811 | 92.5776 | 87.3872 | 690 | 161 | 686 | 55 | 9 | 16.3636 | |
| gduggal-snapvard | INDEL | D1_5 | map_l250_m1_e0 | * | 79.8265 | 97.6608 | 67.5000 | 94.8077 | 167 | 4 | 216 | 104 | 17 | 16.3462 | |
| bgallagher-sentieon | SNP | ti | map_l100_m2_e0 | * | 99.4612 | 99.5466 | 99.3760 | 66.3096 | 48739 | 222 | 48732 | 306 | 50 | 16.3399 | |
| bgallagher-sentieon | SNP | ti | map_l125_m0_e0 | het | 98.6693 | 99.1771 | 98.1668 | 78.4213 | 8195 | 68 | 8193 | 153 | 25 | 16.3399 | |
| cchapple-custom | SNP | tv | map_l150_m2_e0 | * | 96.3013 | 97.0233 | 95.5899 | 79.4079 | 11017 | 338 | 11011 | 508 | 83 | 16.3386 | |
| cchapple-custom | SNP | tv | map_l150_m2_e0 | het | 95.1992 | 97.1870 | 93.2911 | 82.3459 | 7048 | 204 | 7064 | 508 | 83 | 16.3386 | |
| jmaeng-gatk | INDEL | I16_PLUS | * | het | 97.7761 | 97.3878 | 98.1675 | 76.4716 | 2647 | 71 | 2625 | 49 | 8 | 16.3265 | |
| hfeng-pmm3 | SNP | * | map_l100_m1_e0 | * | 99.6620 | 99.5870 | 99.7371 | 63.4436 | 72104 | 299 | 72093 | 190 | 31 | 16.3158 | |
| cchapple-custom | SNP | ti | * | het | 99.8339 | 99.8795 | 99.7883 | 21.7295 | 1280346 | 1545 | 1280384 | 2716 | 443 | 16.3108 | |