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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
54651-54700 / 86044 show all | |||||||||||||||
| ckim-vqsr | SNP | ti | map_l100_m2_e0 | homalt | 61.7649 | 44.6884 | 99.9633 | 77.1942 | 8182 | 10127 | 8182 | 3 | 3 | 100.0000 | |
| ckim-vqsr | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 97.7528 | 96.0459 | 99.5215 | 32.8514 | 753 | 31 | 832 | 4 | 4 | 100.0000 | |
| ckim-vqsr | INDEL | D16_PLUS | map_l100_m0_e0 | * | 89.6552 | 92.8571 | 86.6667 | 97.1910 | 26 | 2 | 26 | 4 | 0 | 0.0000 | |
| ckim-vqsr | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 99.9182 | 99.9454 | 99.8909 | 51.3011 | 3664 | 2 | 3664 | 4 | 4 | 100.0000 | |
| ckim-vqsr | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | hetalt | 97.8966 | 96.4615 | 99.3750 | 22.2357 | 627 | 23 | 636 | 4 | 4 | 100.0000 | |
| ckim-vqsr | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_11to50 | * | 99.7790 | 99.6566 | 99.9017 | 44.3228 | 4063 | 14 | 4066 | 4 | 1 | 25.0000 | |
| ckim-vqsr | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 97.3494 | 96.6507 | 98.0583 | 77.4370 | 202 | 7 | 202 | 4 | 3 | 75.0000 | |
| ckim-vqsr | INDEL | D6_15 | map_l125_m1_e0 | * | 96.1373 | 95.7265 | 96.5517 | 92.8129 | 112 | 5 | 112 | 4 | 1 | 25.0000 | |
| ckim-vqsr | INDEL | D6_15 | map_l125_m1_e0 | het | 94.5736 | 95.3125 | 93.8462 | 94.4254 | 61 | 3 | 61 | 4 | 1 | 25.0000 | |
| ckim-vqsr | INDEL | D6_15 | map_l125_m2_e0 | * | 96.0000 | 95.2381 | 96.7742 | 93.0726 | 120 | 6 | 120 | 4 | 1 | 25.0000 | |
| ckim-vqsr | INDEL | D6_15 | map_l125_m2_e0 | het | 94.3662 | 94.3662 | 94.3662 | 94.5636 | 67 | 4 | 67 | 4 | 1 | 25.0000 | |
| ckim-vqsr | INDEL | D6_15 | map_l125_m2_e1 | * | 95.6522 | 94.5312 | 96.8000 | 93.1769 | 121 | 7 | 121 | 4 | 1 | 25.0000 | |
| ckim-vqsr | INDEL | D6_15 | map_l125_m2_e1 | het | 94.3662 | 94.3662 | 94.3662 | 94.6896 | 67 | 4 | 67 | 4 | 1 | 25.0000 | |
| ckim-vqsr | INDEL | D6_15 | segdup | homalt | 96.1538 | 100.0000 | 92.5926 | 92.3944 | 50 | 0 | 50 | 4 | 4 | 100.0000 | |
| ckim-vqsr | INDEL | I16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 93.9394 | 90.2913 | 97.8947 | 88.4988 | 186 | 20 | 186 | 4 | 2 | 50.0000 | |
| ckim-vqsr | INDEL | I1_5 | HG002complexvar | hetalt | 92.1493 | 85.6315 | 99.7409 | 68.7323 | 1478 | 248 | 1540 | 4 | 4 | 100.0000 | |
| ckim-vqsr | INDEL | I1_5 | HG002compoundhet | hetalt | 95.5975 | 91.5988 | 99.9612 | 55.8418 | 10238 | 939 | 10299 | 4 | 4 | 100.0000 | |
| ckim-vqsr | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 99.4113 | 99.1196 | 99.7048 | 77.3525 | 1351 | 12 | 1351 | 4 | 2 | 50.0000 | |
| ckim-vqsr | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_11to50 | het | 99.2975 | 98.8995 | 99.6988 | 78.3007 | 1348 | 15 | 1324 | 4 | 3 | 75.0000 | |
| ckim-vqsr | INDEL | I1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 99.1094 | 98.3822 | 99.8474 | 70.7576 | 2615 | 43 | 2617 | 4 | 3 | 75.0000 | |
| ckim-vqsr | INDEL | I1_5 | map_l100_m1_e0 | homalt | 99.5188 | 99.8069 | 99.2322 | 81.1709 | 517 | 1 | 517 | 4 | 3 | 75.0000 | |
| ckim-vqsr | INDEL | I1_5 | map_l100_m2_e0 | homalt | 99.5305 | 99.8117 | 99.2509 | 82.4688 | 530 | 1 | 530 | 4 | 3 | 75.0000 | |
| ckim-vqsr | INDEL | I1_5 | map_l100_m2_e1 | homalt | 99.5383 | 99.8148 | 99.2634 | 82.5064 | 539 | 1 | 539 | 4 | 3 | 75.0000 | |
| ckim-vqsr | INDEL | I1_5 | map_l250_m0_e0 | het | 81.2500 | 86.6667 | 76.4706 | 98.9875 | 13 | 2 | 13 | 4 | 0 | 0.0000 | |
| ckim-vqsr | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 96.6029 | 93.5337 | 99.8803 | 39.4384 | 3298 | 228 | 3339 | 4 | 4 | 100.0000 | |
| ckim-vqsr | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 96.3956 | 93.1863 | 99.8338 | 31.7550 | 2366 | 173 | 2403 | 4 | 4 | 100.0000 | |
| ckim-vqsr | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 96.3003 | 93.0030 | 99.8400 | 33.3511 | 2459 | 185 | 2496 | 4 | 4 | 100.0000 | |
| ckim-vqsr | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 96.6029 | 93.5337 | 99.8803 | 39.4384 | 3298 | 228 | 3339 | 4 | 4 | 100.0000 | |
| ckim-vqsr | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_11to50 | het | 98.5380 | 97.9508 | 99.1323 | 82.5906 | 478 | 10 | 457 | 4 | 0 | 0.0000 | |
| ckim-vqsr | SNP | * | lowcmp_SimpleRepeat_homopolymer_6to10 | homalt | 99.3474 | 98.7681 | 99.9335 | 54.7798 | 6013 | 75 | 6013 | 4 | 4 | 100.0000 | |
| ckim-vqsr | SNP | * | lowcmp_SimpleRepeat_quadTR_51to200 | * | 94.2446 | 91.6084 | 97.0370 | 92.7807 | 131 | 12 | 131 | 4 | 3 | 75.0000 | |
| ckim-vqsr | SNP | * | lowcmp_SimpleRepeat_quadTR_51to200 | het | 94.5274 | 93.1373 | 95.9596 | 92.6230 | 95 | 7 | 95 | 4 | 3 | 75.0000 | |
| ckim-vqsr | SNP | * | map_l100_m1_e0 | homalt | 59.0007 | 41.8509 | 99.9646 | 77.1745 | 11301 | 15702 | 11301 | 4 | 3 | 75.0000 | |
| ckim-vqsr | SNP | * | map_l100_m2_e0 | homalt | 59.7529 | 42.6116 | 99.9659 | 78.6625 | 11728 | 15795 | 11728 | 4 | 3 | 75.0000 | |
| ckim-vqsr | SNP | * | map_l100_m2_e1 | homalt | 59.9673 | 42.8299 | 99.9664 | 78.5551 | 11905 | 15891 | 11905 | 4 | 3 | 75.0000 | |
| ckim-vqsr | SNP | * | map_siren | homalt | 75.3334 | 60.4322 | 99.9880 | 62.9988 | 33332 | 21824 | 33323 | 4 | 4 | 100.0000 | |
| ckim-vqsr | SNP | ti | HG002compoundhet | homalt | 98.6436 | 97.3763 | 99.9445 | 31.0556 | 7200 | 194 | 7200 | 4 | 4 | 100.0000 | |
| ckim-vqsr | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 99.9181 | 100.0000 | 99.8363 | 52.3782 | 2439 | 0 | 2439 | 4 | 0 | 0.0000 | |
| ckim-vqsr | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 99.8736 | 100.0000 | 99.7475 | 55.0256 | 1580 | 0 | 1580 | 4 | 0 | 0.0000 | |
| egarrison-hhga | INDEL | C6_15 | * | * | 20.0000 | 14.2857 | 33.3333 | 95.4887 | 1 | 6 | 2 | 4 | 0 | 0.0000 | |
| egarrison-hhga | INDEL | C6_15 | * | het | 16.6667 | 14.2857 | 20.0000 | 78.2609 | 1 | 6 | 1 | 4 | 0 | 0.0000 | |
| egarrison-hhga | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 63.1989 | 46.4849 | 98.6799 | 45.9893 | 324 | 373 | 299 | 4 | 4 | 100.0000 | |
| egarrison-hhga | INDEL | D16_PLUS | lowcmp_SimpleRepeat_homopolymer_gt10 | homalt | 81.2500 | 86.6667 | 76.4706 | 96.2637 | 13 | 2 | 13 | 4 | 4 | 100.0000 | |
| egarrison-hhga | INDEL | D16_PLUS | map_l100_m0_e0 | het | 85.4749 | 89.4737 | 81.8182 | 90.4348 | 17 | 2 | 18 | 4 | 2 | 50.0000 | |
| egarrison-hhga | INDEL | D16_PLUS | segdup | * | 93.1619 | 93.1034 | 93.2203 | 92.7785 | 54 | 4 | 55 | 4 | 2 | 50.0000 | |
| egarrison-hhga | INDEL | D1_5 | map_l250_m1_e0 | * | 97.0588 | 96.4912 | 97.6331 | 95.1156 | 165 | 6 | 165 | 4 | 2 | 50.0000 | |
| egarrison-hhga | INDEL | D1_5 | map_l250_m1_e0 | het | 96.3964 | 96.3964 | 96.3964 | 95.2625 | 107 | 4 | 107 | 4 | 2 | 50.0000 | |
| egarrison-hhga | INDEL | D1_5 | map_l250_m2_e0 | * | 97.2678 | 96.7391 | 97.8022 | 95.3842 | 178 | 6 | 178 | 4 | 2 | 50.0000 | |
| egarrison-hhga | INDEL | D1_5 | map_l250_m2_e0 | het | 96.6942 | 96.6942 | 96.6942 | 95.4167 | 117 | 4 | 117 | 4 | 2 | 50.0000 | |
| egarrison-hhga | INDEL | D1_5 | map_l250_m2_e1 | * | 97.2826 | 96.7568 | 97.8142 | 95.4658 | 179 | 6 | 179 | 4 | 2 | 50.0000 | |