PrecisionFDA
Truth Challenge
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Explore HG002 comparison results
Use this interactive explorer to filter all results across submission entries and multiple dimensions.
| Entry | Type | Subtype | Subset | Genotype | F-score | Recall | Precision | Frac_NA | Truth TP | Truth FN | Query TP | Query FP | FP gt | % FP ma | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
69601-69650 / 86044 show all | |||||||||||||||
| ckim-isaac | SNP | tv | map_l100_m2_e0 | * | 75.7866 | 61.1033 | 99.7587 | 67.3111 | 15296 | 9737 | 15299 | 37 | 12 | 32.4324 | |
| ckim-vqsr | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | * | 97.9637 | 97.9911 | 97.9364 | 69.6975 | 1756 | 36 | 1756 | 37 | 31 | 83.7838 | |
| ckim-vqsr | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 96.6665 | 93.9188 | 99.5798 | 30.8815 | 8726 | 565 | 8768 | 37 | 37 | 100.0000 | |
| ckim-vqsr | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 96.6665 | 93.9188 | 99.5798 | 30.8815 | 8726 | 565 | 8768 | 37 | 37 | 100.0000 | |
| ckim-vqsr | INDEL | D6_15 | HG002complexvar | hetalt | 93.7593 | 91.3129 | 96.3403 | 47.3985 | 925 | 88 | 974 | 37 | 37 | 100.0000 | |
| egarrison-hhga | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 85.8513 | 89.0547 | 82.8704 | 80.0000 | 179 | 22 | 179 | 37 | 34 | 91.8919 | |
| egarrison-hhga | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 63.3593 | 46.6406 | 98.7609 | 37.5052 | 3346 | 3828 | 2949 | 37 | 33 | 89.1892 | |
| hfeng-pmm3 | SNP | tv | map_l150_m0_e0 | * | 99.0651 | 99.0177 | 99.1125 | 80.0536 | 4133 | 41 | 4132 | 37 | 3 | 8.1081 | |
| jlack-gatk | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 96.2201 | 93.2179 | 99.4222 | 33.5409 | 6350 | 462 | 6367 | 37 | 31 | 83.7838 | |
| hfeng-pmm1 | SNP | tv | map_l100_m0_e0 | het | 99.2295 | 98.9754 | 99.4850 | 70.4702 | 7148 | 74 | 7147 | 37 | 11 | 29.7297 | |
| hfeng-pmm2 | INDEL | * | map_l100_m0_e0 | het | 97.3349 | 98.2370 | 96.4491 | 87.4337 | 1003 | 18 | 1005 | 37 | 3 | 8.1081 | |
| hfeng-pmm2 | INDEL | * | map_l150_m1_e0 | * | 97.9254 | 98.5800 | 97.2794 | 89.7079 | 1319 | 19 | 1323 | 37 | 6 | 16.2162 | |
| hfeng-pmm3 | INDEL | I1_5 | HG002complexvar | * | 99.5912 | 99.2956 | 99.8886 | 56.4158 | 33128 | 235 | 33172 | 37 | 24 | 64.8649 | |
| hfeng-pmm3 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 97.2193 | 95.0054 | 99.5389 | 60.9375 | 7989 | 420 | 7988 | 37 | 23 | 62.1622 | |
| hfeng-pmm2 | SNP | tv | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 99.0538 | 98.3322 | 99.7862 | 63.3791 | 17275 | 293 | 17266 | 37 | 4 | 10.8108 | |
| hfeng-pmm3 | INDEL | * | map_l100_m1_e0 | * | 98.6300 | 98.2989 | 98.9633 | 82.3910 | 3525 | 61 | 3532 | 37 | 9 | 24.3243 | |
| hfeng-pmm3 | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 94.4481 | 90.3112 | 98.9821 | 58.9266 | 3598 | 386 | 3598 | 37 | 30 | 81.0811 | |
| hfeng-pmm2 | INDEL | D1_5 | map_siren | * | 99.1528 | 99.3483 | 98.9580 | 80.2591 | 3506 | 23 | 3514 | 37 | 6 | 16.2162 | |
| jlack-gatk | INDEL | I1_5 | map_l150_m1_e0 | * | 95.4901 | 98.0237 | 93.0841 | 91.9135 | 496 | 10 | 498 | 37 | 4 | 10.8108 | |
| jlack-gatk | INDEL | I1_5 | map_l150_m2_e1 | het | 93.2461 | 97.4763 | 89.3678 | 93.8559 | 309 | 8 | 311 | 37 | 2 | 5.4054 | |
| jlack-gatk | SNP | * | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 99.8341 | 99.8836 | 99.7848 | 57.0872 | 17157 | 20 | 17153 | 37 | 8 | 21.6216 | |
| jlack-gatk | INDEL | I1_5 | map_l100_m0_e0 | * | 95.9835 | 98.7109 | 93.4028 | 88.9103 | 536 | 7 | 538 | 38 | 3 | 7.8947 | |
| hfeng-pmm3 | SNP | * | map_l250_m0_e0 | * | 98.2916 | 98.3607 | 98.2226 | 92.8676 | 2100 | 35 | 2100 | 38 | 6 | 15.7895 | |
| hfeng-pmm3 | SNP | ti | * | homalt | 99.9929 | 99.9905 | 99.9953 | 16.6242 | 802962 | 76 | 802953 | 38 | 27 | 71.0526 | |
| hfeng-pmm3 | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 98.5901 | 97.6240 | 99.5756 | 74.7725 | 8916 | 217 | 8916 | 38 | 5 | 13.1579 | |
| hfeng-pmm3 | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 98.5901 | 97.6240 | 99.5756 | 74.7725 | 8916 | 217 | 8916 | 38 | 5 | 13.1579 | |
| jlack-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 99.2477 | 99.2381 | 99.2572 | 75.1119 | 5080 | 39 | 5078 | 38 | 20 | 52.6316 | |
| jlack-gatk | INDEL | * | lowcmp_SimpleRepeat_quadTR_51to200 | het | 96.0781 | 96.4876 | 95.6720 | 82.3695 | 934 | 34 | 840 | 38 | 30 | 78.9474 | |
| jlack-gatk | INDEL | I16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 95.1113 | 93.6897 | 96.5766 | 79.4254 | 1069 | 72 | 1072 | 38 | 21 | 55.2632 | |
| hfeng-pmm2 | INDEL | * | map_l125_m1_e0 | het | 97.7323 | 98.2772 | 97.1935 | 88.0494 | 1312 | 23 | 1316 | 38 | 3 | 7.8947 | |
| hfeng-pmm2 | INDEL | * | map_l125_m2_e0 | het | 97.7864 | 98.2746 | 97.3031 | 88.7801 | 1367 | 24 | 1371 | 38 | 3 | 7.8947 | |
| hfeng-pmm2 | INDEL | * | map_l125_m2_e1 | het | 97.8130 | 98.2955 | 97.3352 | 88.8707 | 1384 | 24 | 1388 | 38 | 3 | 7.8947 | |
| hfeng-pmm2 | INDEL | * | map_l150_m2_e0 | * | 97.9932 | 98.6506 | 97.3445 | 90.3934 | 1389 | 19 | 1393 | 38 | 6 | 15.7895 | |
| hfeng-pmm2 | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 99.5103 | 99.5446 | 99.4760 | 35.3827 | 7214 | 33 | 7214 | 38 | 38 | 100.0000 | |
| hfeng-pmm2 | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 98.7125 | 97.6953 | 99.7510 | 72.1894 | 15218 | 359 | 15225 | 38 | 29 | 76.3158 | |
| hfeng-pmm2 | INDEL | I6_15 | HG002complexvar | * | 98.1553 | 97.1411 | 99.1910 | 57.4123 | 4655 | 137 | 4659 | 38 | 37 | 97.3684 | |
| hfeng-pmm2 | SNP | * | map_l100_m1_e0 | homalt | 99.8648 | 99.8704 | 99.8593 | 60.9853 | 26968 | 35 | 26968 | 38 | 19 | 50.0000 | |
| hfeng-pmm2 | SNP | * | map_l100_m2_e0 | homalt | 99.8674 | 99.8728 | 99.8619 | 63.3992 | 27488 | 35 | 27488 | 38 | 19 | 50.0000 | |
| hfeng-pmm2 | SNP | * | map_l100_m2_e1 | homalt | 99.8687 | 99.8741 | 99.8633 | 63.3911 | 27761 | 35 | 27761 | 38 | 19 | 50.0000 | |
| hfeng-pmm3 | INDEL | * | map_siren | het | 98.9897 | 98.8243 | 99.1556 | 80.3605 | 4455 | 53 | 4462 | 38 | 4 | 10.5263 | |
| qzeng-custom | SNP | ti | map_l150_m2_e1 | homalt | 80.1365 | 67.1910 | 99.2610 | 72.9055 | 5169 | 2524 | 5104 | 38 | 38 | 100.0000 | |
| qzeng-custom | INDEL | D16_PLUS | map_l125_m1_e0 | het | 54.1353 | 90.0000 | 38.7097 | 94.2056 | 18 | 2 | 24 | 38 | 0 | 0.0000 | |
| qzeng-custom | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 96.8040 | 97.3134 | 96.2999 | 62.2704 | 978 | 27 | 989 | 38 | 13 | 34.2105 | |
| qzeng-custom | INDEL | D6_15 | lowcmp_SimpleRepeat_triTR_51to200 | * | 79.6385 | 80.2817 | 79.0055 | 39.4649 | 114 | 28 | 143 | 38 | 18 | 47.3684 | |
| mlin-fermikit | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 73.7321 | 76.6917 | 70.9924 | 82.6490 | 102 | 31 | 93 | 38 | 38 | 100.0000 | |
| mlin-fermikit | INDEL | I1_5 | HG002compoundhet | hetalt | 79.4743 | 66.1627 | 99.4916 | 57.4825 | 7395 | 3782 | 7437 | 38 | 38 | 100.0000 | |
| mlin-fermikit | INDEL | I1_5 | map_l100_m0_e0 | homalt | 67.7419 | 60.5769 | 76.8293 | 73.2463 | 126 | 82 | 126 | 38 | 36 | 94.7368 | |
| mlin-fermikit | SNP | ti | lowcmp_SimpleRepeat_homopolymer_6to10 | homalt | 98.8267 | 99.3639 | 98.2952 | 44.3446 | 2187 | 14 | 2191 | 38 | 38 | 100.0000 | |
| mlin-fermikit | SNP | ti | lowcmp_SimpleRepeat_quadTR_11to50 | het | 98.3589 | 97.3161 | 99.4242 | 37.2504 | 6563 | 181 | 6562 | 38 | 5 | 13.1579 | |
| mlin-fermikit | SNP | ti | map_l125_m0_e0 | het | 49.2645 | 32.8331 | 98.6182 | 61.3058 | 2713 | 5550 | 2712 | 38 | 3 | 7.8947 | |