PrecisionFDA
Truth Challenge
Engage and improve DNA test results with our community challenges
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
13701-13750 / 86044 show all | |||||||||||||||
| ckim-vqsr | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 93.3378 | 87.8389 | 99.5712 | 29.6743 | 1134 | 157 | 1161 | 5 | 5 | 100.0000 | |
| ckim-isaac | INDEL | D1_5 | map_l125_m2_e1 | homalt | 73.1293 | 57.7957 | 99.5370 | 81.0360 | 215 | 157 | 215 | 1 | 1 | 100.0000 | |
| hfeng-pmm3 | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 96.9781 | 94.7333 | 99.3319 | 50.0000 | 2824 | 157 | 2825 | 19 | 16 | 84.2105 | |
| hfeng-pmm3 | SNP | * | map_l100_m0_e0 | het | 99.3509 | 99.2596 | 99.4424 | 70.0348 | 21048 | 157 | 21044 | 118 | 11 | 9.3220 | |
| hfeng-pmm1 | SNP | ti | map_l100_m0_e0 | het | 99.2035 | 98.8772 | 99.5320 | 69.1542 | 13826 | 157 | 13823 | 65 | 16 | 24.6154 | |
| hfeng-pmm2 | SNP | ti | map_l125_m1_e0 | * | 99.4105 | 99.4648 | 99.3563 | 71.7136 | 29178 | 157 | 29174 | 189 | 23 | 12.1693 | |
| gduggal-bwaplat | INDEL | D16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 80.2442 | 67.8279 | 98.2249 | 72.7639 | 331 | 157 | 332 | 6 | 4 | 66.6667 | |
| gduggal-snapfb | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | homalt | 39.9604 | 56.2674 | 30.9816 | 39.7969 | 202 | 157 | 202 | 450 | 389 | 86.4444 | |
| gduggal-snapfb | INDEL | * | lowcmp_SimpleRepeat_triTR_11to50 | hetalt | 85.4625 | 82.9902 | 88.0866 | 50.9735 | 766 | 157 | 244 | 33 | 29 | 87.8788 | |
| eyeh-varpipe | SNP | ti | HG002complexvar | homalt | 99.9332 | 99.9188 | 99.9475 | 17.3280 | 193307 | 157 | 180798 | 95 | 69 | 72.6316 | |
| gduggal-bwafb | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 84.5240 | 82.7851 | 86.3375 | 67.9071 | 755 | 157 | 752 | 119 | 119 | 100.0000 | |
| gduggal-bwavard | INDEL | D16_PLUS | * | het | 72.3037 | 95.0301 | 58.3494 | 71.4553 | 3002 | 157 | 3026 | 2160 | 1899 | 87.9167 | |
| gduggal-bwafb | INDEL | D1_5 | HG002complexvar | homalt | 98.4856 | 98.5186 | 98.4525 | 57.9745 | 10441 | 157 | 10434 | 164 | 151 | 92.0732 | |
| anovak-vg | SNP | tv | segdup | het | 97.1722 | 97.0305 | 97.3143 | 94.5962 | 5130 | 157 | 5109 | 141 | 42 | 29.7872 | |
| asubramanian-gatk | INDEL | * | map_l150_m2_e0 | het | 87.3084 | 82.6711 | 92.4969 | 93.8067 | 749 | 157 | 752 | 61 | 6 | 9.8361 | |
| asubramanian-gatk | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_11to50 | * | 94.9172 | 93.4909 | 96.3878 | 56.5468 | 2255 | 157 | 3122 | 117 | 109 | 93.1624 | |
| anovak-vg | INDEL | * | map_l100_m1_e0 | homalt | 76.5861 | 87.2046 | 68.2728 | 79.5887 | 1070 | 157 | 1091 | 507 | 474 | 93.4911 | |
| anovak-vg | INDEL | D1_5 | map_l100_m2_e1 | het | 83.2523 | 87.6183 | 79.3007 | 85.1706 | 1111 | 157 | 1134 | 296 | 94 | 31.7568 | |
| bgallagher-sentieon | SNP | ti | map_l100_m1_e0 | het | 99.2799 | 99.4757 | 99.0849 | 68.0556 | 29785 | 157 | 29778 | 275 | 38 | 13.8182 | |
| jli-custom | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 95.2565 | 91.3831 | 99.4728 | 30.2126 | 1665 | 157 | 1698 | 9 | 8 | 88.8889 | |
| rpoplin-dv42 | SNP | * | map_l250_m2_e0 | * | 98.3456 | 98.0089 | 98.6847 | 88.0100 | 7728 | 157 | 7728 | 103 | 68 | 66.0194 | |
| hfeng-pmm2 | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 97.9622 | 96.2373 | 99.7500 | 82.0192 | 3990 | 156 | 3990 | 10 | 3 | 30.0000 | |
| jlack-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 94.5501 | 90.3525 | 99.1566 | 32.4379 | 1461 | 156 | 1646 | 14 | 14 | 100.0000 | |
| hfeng-pmm3 | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | het | 95.8650 | 94.2920 | 97.4914 | 60.1243 | 2577 | 156 | 2565 | 66 | 61 | 92.4242 | |
| gduggal-snapvard | SNP | * | map_l250_m1_e0 | homalt | 96.4845 | 93.6663 | 99.4776 | 87.2382 | 2307 | 156 | 2285 | 12 | 9 | 75.0000 | |
| gduggal-snapplat | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 37.5633 | 25.3589 | 72.4138 | 74.4493 | 53 | 156 | 42 | 16 | 3 | 18.7500 | |
| ckim-dragen | SNP | tv | map_l125_m2_e0 | * | 98.4063 | 99.0539 | 97.7671 | 75.5410 | 16333 | 156 | 16332 | 373 | 39 | 10.4558 | |
| ckim-dragen | SNP | * | map_l250_m2_e0 | het | 96.3481 | 96.9965 | 95.7083 | 91.3532 | 5038 | 156 | 5040 | 226 | 15 | 6.6372 | |
| ckim-dragen | SNP | ti | map_l125_m0_e0 | * | 98.1359 | 98.7776 | 97.5025 | 75.7277 | 12606 | 156 | 12610 | 323 | 39 | 12.0743 | |
| ciseli-custom | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | hetalt | 0.0000 | 6.5868 | 0.0000 | 0.0000 | 11 | 156 | 0 | 0 | 0 | ||
| ciseli-custom | INDEL | I1_5 | map_l125_m0_e0 | * | 56.0912 | 49.6774 | 64.4068 | 91.5984 | 154 | 156 | 152 | 84 | 66 | 78.5714 | |
| cchapple-custom | INDEL | D1_5 | HG002complexvar | hetalt | 0.0000 | 88.4615 | 0.0000 | 0.0000 | 1196 | 156 | 0 | 0 | 0 | ||
| cchapple-custom | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_51to200 | hetalt | 0.0000 | 68.2281 | 0.0000 | 0.0000 | 335 | 156 | 0 | 0 | 0 | ||
| qzeng-custom | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 92.3995 | 86.2069 | 99.5506 | 43.8131 | 975 | 156 | 443 | 2 | 2 | 100.0000 | |
| ltrigg-rtg1 | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 94.5208 | 90.5397 | 98.8682 | 37.7022 | 1493 | 156 | 1485 | 17 | 17 | 100.0000 | |
| ltrigg-rtg1 | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 97.2938 | 95.0000 | 99.7012 | 54.2527 | 2964 | 156 | 3003 | 9 | 8 | 88.8889 | |
| gduggal-bwafb | SNP | tv | map_l150_m2_e0 | * | 98.5004 | 98.6262 | 98.3749 | 78.4095 | 11199 | 156 | 11199 | 185 | 38 | 20.5405 | |
| gduggal-bwafb | SNP | tv | map_l150_m2_e1 | * | 98.5152 | 98.6437 | 98.3871 | 78.4497 | 11346 | 156 | 11346 | 186 | 38 | 20.4301 | |
| gduggal-bwaplat | INDEL | D1_5 | map_l125_m0_e0 | het | 70.5224 | 54.7826 | 98.9529 | 96.3515 | 189 | 156 | 189 | 2 | 0 | 0.0000 | |
| eyeh-varpipe | INDEL | I16_PLUS | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 19.3536 | 10.8571 | 89.0110 | 49.7238 | 19 | 156 | 81 | 10 | 10 | 100.0000 | |
| gduggal-bwavard | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_51to200 | homalt | 6.0241 | 3.1056 | 100.0000 | 68.7500 | 5 | 156 | 5 | 0 | 0 | ||
| bgallagher-sentieon | SNP | * | map_l125_m0_e0 | * | 98.8636 | 99.1953 | 98.5342 | 75.8607 | 19229 | 156 | 19226 | 286 | 50 | 17.4825 | |
| astatham-gatk | INDEL | * | map_l100_m1_e0 | het | 95.1305 | 93.0201 | 97.3389 | 86.8492 | 2079 | 156 | 2085 | 57 | 11 | 19.2982 | |
| astatham-gatk | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 94.6399 | 91.5309 | 97.9675 | 67.1249 | 1686 | 156 | 1687 | 35 | 30 | 85.7143 | |
| astatham-gatk | INDEL | I16_PLUS | HG002compoundhet | * | 94.5316 | 92.7671 | 96.3645 | 52.8349 | 1988 | 155 | 1988 | 75 | 75 | 100.0000 | |
| anovak-vg | INDEL | I6_15 | HG002compoundhet | het | 35.5369 | 25.4808 | 58.7053 | 30.0691 | 53 | 155 | 1723 | 1212 | 975 | 80.4455 | |
| anovak-vg | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 73.2802 | 81.7861 | 66.3768 | 81.5483 | 696 | 155 | 916 | 464 | 182 | 39.2241 | |
| anovak-vg | INDEL | D1_5 | map_l100_m2_e0 | het | 83.2747 | 87.6592 | 79.3079 | 85.1214 | 1101 | 155 | 1123 | 293 | 93 | 31.7406 | |
| asubramanian-gatk | INDEL | D1_5 | map_l100_m1_e0 | het | 90.9054 | 87.1795 | 94.9640 | 88.1323 | 1054 | 155 | 1056 | 56 | 6 | 10.7143 | |
| cchapple-custom | INDEL | I16_PLUS | * | hetalt | 0.0000 | 92.6120 | 0.0000 | 0.0000 | 1943 | 155 | 0 | 0 | 0 | ||