PrecisionFDA
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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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
29301-29350 / 86044 show all | |||||||||||||||
| gduggal-snapvard | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 96.3822 | 94.6628 | 98.1651 | 78.9575 | 2288 | 129 | 2247 | 42 | 19 | 45.2381 | |
| ckim-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 96.6974 | 94.6626 | 98.8216 | 55.5793 | 3689 | 208 | 3690 | 44 | 37 | 84.0909 | |
| hfeng-pmm2 | INDEL | D6_15 | HG002complexvar | * | 96.9573 | 94.6624 | 99.3663 | 56.8597 | 5019 | 283 | 5018 | 32 | 26 | 81.2500 | |
| dgrover-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 97.0365 | 94.6613 | 99.5340 | 28.2145 | 6791 | 383 | 6835 | 32 | 30 | 93.7500 | |
| jpowers-varprowl | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 88.7392 | 94.6612 | 83.5145 | 64.2718 | 461 | 26 | 461 | 91 | 89 | 97.8022 | |
| ckim-dragen | INDEL | I16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 96.2963 | 94.6602 | 97.9899 | 88.0409 | 195 | 11 | 195 | 4 | 2 | 50.0000 | |
| cchapple-custom | INDEL | D6_15 | map_l100_m2_e0 | het | 93.8735 | 94.6565 | 93.1034 | 84.7712 | 124 | 7 | 189 | 14 | 7 | 50.0000 | |
| raldana-dualsentieon | INDEL | D6_15 | map_l100_m2_e0 | het | 95.7529 | 94.6565 | 96.8750 | 86.7632 | 124 | 7 | 124 | 4 | 1 | 25.0000 | |
| jli-custom | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 97.2341 | 94.6563 | 99.9563 | 27.5665 | 4517 | 255 | 4570 | 2 | 2 | 100.0000 | |
| egarrison-hhga | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 96.8401 | 94.6563 | 99.1270 | 30.3647 | 4517 | 255 | 4542 | 40 | 38 | 95.0000 | |
| jpowers-varprowl | INDEL | * | map_siren | het | 92.1013 | 94.6539 | 89.6827 | 84.2292 | 4267 | 241 | 4268 | 491 | 415 | 84.5214 | |
| ltrigg-rtg2 | SNP | * | map_l250_m2_e1 | * | 97.1847 | 94.6538 | 99.8547 | 80.7686 | 7560 | 427 | 7560 | 11 | 4 | 36.3636 | |
| hfeng-pmm2 | INDEL | * | lowcmp_SimpleRepeat_quadTR_51to200 | * | 96.6238 | 94.6516 | 98.6800 | 66.1797 | 2513 | 142 | 2467 | 33 | 25 | 75.7576 | |
| dgrover-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 97.0680 | 94.6510 | 99.6117 | 25.8826 | 7662 | 433 | 7696 | 30 | 29 | 96.6667 | |
| ckim-dragen | INDEL | I1_5 | map_l125_m1_e0 | het | 95.2424 | 94.6502 | 95.8420 | 88.2223 | 460 | 26 | 461 | 20 | 3 | 15.0000 | |
| ltrigg-rtg2 | SNP | ti | map_l250_m1_e0 | * | 97.1749 | 94.6495 | 99.8389 | 79.6190 | 4334 | 245 | 4337 | 7 | 4 | 57.1429 | |
| asubramanian-gatk | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 96.7294 | 94.6488 | 98.9035 | 60.3171 | 14592 | 825 | 15424 | 171 | 158 | 92.3977 | |
| jpowers-varprowl | SNP | * | map_l150_m0_e0 | het | 94.6235 | 94.6474 | 94.5997 | 86.3683 | 7515 | 425 | 7515 | 429 | 135 | 31.4685 | |
| ndellapenna-hhga | SNP | ti | map_l250_m0_e0 | het | 96.8767 | 94.6467 | 99.2144 | 92.7117 | 884 | 50 | 884 | 7 | 2 | 28.5714 | |
| mlin-fermikit | SNP | ti | HG002compoundhet | hetalt | 97.2493 | 94.6459 | 100.0000 | 20.8092 | 548 | 31 | 548 | 0 | 0 | ||
| asubramanian-gatk | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 96.9885 | 94.6447 | 99.4513 | 62.5582 | 5620 | 318 | 6163 | 34 | 32 | 94.1176 | |
| gduggal-snapvard | SNP | ti | map_l150_m0_e0 | * | 89.0696 | 94.6444 | 84.1150 | 85.4263 | 7440 | 421 | 7371 | 1392 | 107 | 7.6868 | |
| ckim-dragen | INDEL | I1_5 | map_siren | hetalt | 97.2477 | 94.6429 | 100.0000 | 86.4277 | 106 | 6 | 106 | 0 | 0 | ||
| cchapple-custom | INDEL | D6_15 | map_siren | het | 94.8724 | 94.6429 | 95.1031 | 81.6462 | 265 | 15 | 369 | 19 | 8 | 42.1053 | |
| cchapple-custom | INDEL | I1_5 | map_siren | hetalt | 0.0000 | 94.6429 | 0.0000 | 0.0000 | 106 | 6 | 0 | 0 | 0 | ||
| jlack-gatk | INDEL | I1_5 | map_siren | hetalt | 97.2477 | 94.6429 | 100.0000 | 87.9682 | 106 | 6 | 106 | 0 | 0 | ||
| asubramanian-gatk | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_51to200 | * | 95.7178 | 94.6429 | 96.8174 | 68.4294 | 583 | 33 | 578 | 19 | 17 | 89.4737 | |
| ltrigg-rtg1 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 97.0481 | 94.6421 | 99.5798 | 42.9211 | 10510 | 595 | 10663 | 45 | 44 | 97.7778 | |
| raldana-dualsentieon | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 95.8304 | 94.6417 | 97.0494 | 60.1686 | 3038 | 172 | 3026 | 92 | 90 | 97.8261 | |
| gduggal-snapfb | SNP | tv | map_l250_m0_e0 | * | 93.9650 | 94.6405 | 93.2990 | 94.3329 | 724 | 41 | 724 | 52 | 12 | 23.0769 | |
| bgallagher-sentieon | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 97.2324 | 94.6386 | 99.9724 | 29.4827 | 3601 | 204 | 3625 | 1 | 1 | 100.0000 | |
| gduggal-snapfb | INDEL | I1_5 | HG002complexvar | * | 93.5109 | 94.6378 | 92.4106 | 55.4813 | 31574 | 1789 | 31902 | 2620 | 888 | 33.8931 | |
| gduggal-snapfb | SNP | ti | map_l150_m1_e0 | homalt | 97.0877 | 94.6363 | 99.6694 | 78.6440 | 6934 | 393 | 6935 | 23 | 14 | 60.8696 | |
| astatham-gatk | INDEL | D1_5 | map_l150_m2_e1 | het | 95.2826 | 94.6360 | 95.9381 | 90.5225 | 494 | 28 | 496 | 21 | 3 | 14.2857 | |
| egarrison-hhga | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | * | 94.8171 | 94.6358 | 94.9992 | 46.8433 | 11238 | 637 | 11246 | 592 | 535 | 90.3716 | |
| ghariani-varprowl | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 62.8376 | 94.6349 | 47.0342 | 60.4447 | 16863 | 956 | 16945 | 19082 | 18800 | 98.5222 | |
| astatham-gatk | INDEL | D1_5 | map_l125_m2_e0 | het | 95.7656 | 94.6335 | 96.9251 | 88.4193 | 723 | 41 | 725 | 23 | 3 | 13.0435 | |
| ckim-isaac | SNP | ti | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 96.7656 | 94.6334 | 98.9961 | 51.3619 | 16893 | 958 | 17059 | 173 | 13 | 7.5145 | |
| hfeng-pmm1 | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 96.8585 | 94.6327 | 99.1916 | 50.2361 | 2821 | 160 | 2822 | 23 | 18 | 78.2609 | |
| gduggal-snapplat | SNP | tv | map_l100_m2_e0 | het | 94.7121 | 94.6314 | 94.7930 | 82.9183 | 14930 | 847 | 14928 | 820 | 395 | 48.1707 | |
| bgallagher-sentieon | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 95.4289 | 94.6309 | 96.2406 | 77.3424 | 141 | 8 | 128 | 5 | 3 | 60.0000 | |
| ckim-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 95.4149 | 94.6309 | 96.2121 | 77.5128 | 141 | 8 | 127 | 5 | 3 | 60.0000 | |
| ckim-vqsr | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 95.4149 | 94.6309 | 96.2121 | 77.5128 | 141 | 8 | 127 | 5 | 3 | 60.0000 | |
| ckim-isaac | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 97.1734 | 94.6284 | 99.8591 | 48.1340 | 19114 | 1085 | 19138 | 27 | 18 | 66.6667 | |
| ndellapenna-hhga | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 96.0220 | 94.6281 | 97.4576 | 65.7475 | 229 | 13 | 230 | 6 | 3 | 50.0000 | |
| jpowers-varprowl | INDEL | I1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | homalt | 94.7458 | 94.6281 | 94.8637 | 60.4149 | 916 | 52 | 905 | 49 | 36 | 73.4694 | |
| jli-custom | INDEL | * | lowcmp_SimpleRepeat_quadTR_51to200 | het | 95.9472 | 94.6281 | 97.3036 | 80.6048 | 916 | 52 | 830 | 23 | 15 | 65.2174 | |
| hfeng-pmm3 | INDEL | I16_PLUS | HG002complexvar | hetalt | 96.8227 | 94.6269 | 99.1228 | 69.7613 | 317 | 18 | 339 | 3 | 3 | 100.0000 | |
| cchapple-custom | INDEL | D6_15 | HG002compoundhet | het | 96.2282 | 94.6262 | 97.8854 | 30.8078 | 810 | 46 | 9860 | 213 | 202 | 94.8357 | |
| gduggal-bwavard | INDEL | D6_15 | HG002compoundhet | het | 22.7477 | 94.6262 | 12.9278 | 37.5915 | 810 | 46 | 816 | 5496 | 5446 | 99.0902 | |