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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
34951-35000 / 86044 show all | |||||||||||||||
| ckim-isaac | INDEL | * | lowcmp_AllRepeats_gt200bp_gt95identity_merged | * | 82.3529 | 70.0000 | 100.0000 | 99.4125 | 14 | 6 | 14 | 0 | 0 | ||
| ckim-isaac | INDEL | * | tech_badpromoters | homalt | 90.0000 | 81.8182 | 100.0000 | 50.9091 | 27 | 6 | 27 | 0 | 0 | ||
| ckim-gatk | INDEL | D6_15 | map_siren | het | 96.8229 | 98.2143 | 95.4704 | 89.1534 | 275 | 5 | 274 | 13 | 2 | 15.3846 | |
| ckim-gatk | INDEL | D6_15 | segdup | hetalt | 94.6237 | 89.7959 | 100.0000 | 90.4968 | 44 | 5 | 44 | 0 | 0 | ||
| ckim-gatk | INDEL | I16_PLUS | * | homalt | 97.7080 | 99.6797 | 95.8128 | 71.8495 | 1556 | 5 | 1556 | 68 | 67 | 98.5294 | |
| ckim-gatk | INDEL | I16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 96.1564 | 94.7368 | 97.6190 | 90.9968 | 90 | 5 | 82 | 2 | 0 | 0.0000 | |
| ckim-gatk | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 95.6971 | 98.2332 | 93.2886 | 69.7769 | 278 | 5 | 278 | 20 | 20 | 100.0000 | |
| ckim-gatk | INDEL | I1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 99.6000 | 99.6361 | 99.5640 | 74.0720 | 1369 | 5 | 1370 | 6 | 0 | 0.0000 | |
| ckim-gatk | INDEL | I1_5 | map_l100_m0_e0 | * | 97.3834 | 99.0792 | 95.7447 | 89.2325 | 538 | 5 | 540 | 24 | 3 | 12.5000 | |
| ckim-gatk | INDEL | I1_5 | map_l100_m0_e0 | het | 96.2697 | 98.4663 | 94.1691 | 91.3906 | 321 | 5 | 323 | 20 | 0 | 0.0000 | |
| ckim-gatk | INDEL | I6_15 | HG002compoundhet | het | 86.2400 | 97.5962 | 77.2512 | 84.6657 | 203 | 5 | 163 | 48 | 47 | 97.9167 | |
| ckim-gatk | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 99.2418 | 98.9224 | 99.5633 | 72.5090 | 459 | 5 | 456 | 2 | 0 | 0.0000 | |
| ckim-gatk | INDEL | I6_15 | map_l100_m1_e0 | * | 96.4602 | 95.6140 | 97.3214 | 89.5814 | 109 | 5 | 109 | 3 | 1 | 33.3333 | |
| ckim-gatk | INDEL | I6_15 | map_l100_m2_e0 | * | 96.5217 | 95.6897 | 97.3684 | 90.3635 | 111 | 5 | 111 | 3 | 1 | 33.3333 | |
| ckim-gatk | INDEL | I6_15 | map_l100_m2_e1 | * | 96.5217 | 95.6897 | 97.3684 | 90.5863 | 111 | 5 | 111 | 3 | 1 | 33.3333 | |
| ckim-gatk | SNP | * | lowcmp_SimpleRepeat_quadTR_51to200 | homalt | 93.5065 | 87.8049 | 100.0000 | 93.1818 | 36 | 5 | 36 | 0 | 0 | ||
| ckim-gatk | SNP | ti | func_cds | het | 99.5548 | 99.9412 | 99.1713 | 33.6071 | 8499 | 5 | 8497 | 71 | 1 | 1.4085 | |
| ckim-gatk | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 99.2958 | 99.4125 | 99.1794 | 88.4605 | 846 | 5 | 846 | 7 | 6 | 85.7143 | |
| ckim-gatk | SNP | ti | lowcmp_SimpleRepeat_quadTR_51to200 | homalt | 92.3077 | 85.7143 | 100.0000 | 93.1350 | 30 | 5 | 30 | 0 | 0 | ||
| ckim-gatk | SNP | ti | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 99.7545 | 99.6496 | 99.8596 | 26.6735 | 1422 | 5 | 1422 | 2 | 2 | 100.0000 | |
| ckim-gatk | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 96.3563 | 95.9677 | 96.7480 | 90.6535 | 119 | 5 | 119 | 4 | 2 | 50.0000 | |
| ckim-gatk | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 99.4059 | 99.0138 | 99.8012 | 86.2267 | 502 | 5 | 502 | 1 | 1 | 100.0000 | |
| ckim-gatk | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 99.3703 | 99.3703 | 99.3703 | 89.2862 | 789 | 5 | 789 | 5 | 5 | 100.0000 | |
| cchapple-custom | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 98.7421 | 98.7469 | 98.7374 | 50.0631 | 394 | 5 | 391 | 5 | 5 | 100.0000 | |
| cchapple-custom | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 98.4644 | 97.8261 | 99.1111 | 60.3873 | 225 | 5 | 223 | 2 | 2 | 100.0000 | |
| cchapple-custom | INDEL | D16_PLUS | lowcmp_SimpleRepeat_triTR_11to50 | * | 97.4481 | 96.8153 | 98.0892 | 60.3535 | 152 | 5 | 154 | 3 | 3 | 100.0000 | |
| cchapple-custom | INDEL | D16_PLUS | map_l100_m0_e0 | * | 77.9661 | 82.1429 | 74.1935 | 94.2056 | 23 | 5 | 23 | 8 | 1 | 12.5000 | |
| cchapple-custom | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | homalt | 99.3179 | 98.6450 | 100.0000 | 77.5032 | 364 | 5 | 355 | 0 | 0 | ||
| cchapple-custom | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 99.8117 | 99.6241 | 100.0000 | 33.6853 | 1325 | 5 | 1319 | 0 | 0 | ||
| cchapple-custom | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_51to200 | hetalt | 0.0000 | 89.7959 | 0.0000 | 0.0000 | 44 | 5 | 0 | 0 | 0 | ||
| cchapple-custom | INDEL | D1_5 | map_l150_m0_e0 | homalt | 96.3707 | 94.1176 | 98.7342 | 89.6053 | 80 | 5 | 78 | 1 | 1 | 100.0000 | |
| cchapple-custom | INDEL | D1_5 | map_l250_m1_e0 | * | 94.8142 | 97.0760 | 92.6554 | 94.4234 | 166 | 5 | 164 | 13 | 1 | 7.6923 | |
| cchapple-custom | INDEL | D1_5 | map_l250_m2_e0 | * | 94.6665 | 97.2826 | 92.1875 | 94.6711 | 179 | 5 | 177 | 15 | 1 | 6.6667 | |
| cchapple-custom | INDEL | D1_5 | map_l250_m2_e1 | * | 94.6948 | 97.2973 | 92.2280 | 94.7767 | 180 | 5 | 178 | 15 | 1 | 6.6667 | |
| cchapple-custom | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | hetalt | 0.0000 | 87.1795 | 0.0000 | 0.0000 | 34 | 5 | 0 | 0 | 0 | ||
| cchapple-custom | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 99.4050 | 99.1319 | 99.6795 | 63.7841 | 571 | 5 | 622 | 2 | 2 | 100.0000 | |
| cchapple-custom | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_51to200 | homalt | 84.9390 | 96.8944 | 75.6098 | 24.9084 | 156 | 5 | 155 | 50 | 50 | 100.0000 | |
| cchapple-custom | INDEL | D6_15 | lowcmp_SimpleRepeat_triTR_51to200 | hetalt | 0.0000 | 94.8454 | 0.0000 | 0.0000 | 92 | 5 | 0 | 0 | 0 | ||
| cchapple-custom | INDEL | D6_15 | map_l150_m2_e1 | * | 94.2808 | 94.1176 | 94.4444 | 90.3330 | 80 | 5 | 85 | 5 | 3 | 60.0000 | |
| cchapple-custom | INDEL | D6_15 | map_siren | homalt | 96.5251 | 96.1538 | 96.8992 | 78.3557 | 125 | 5 | 125 | 4 | 2 | 50.0000 | |
| cchapple-custom | INDEL | D6_15 | segdup | hetalt | 0.0000 | 89.7959 | 0.0000 | 0.0000 | 44 | 5 | 0 | 0 | 0 | ||
| cchapple-custom | INDEL | I16_PLUS | HG002compoundhet | het | 93.8692 | 89.3617 | 98.8556 | 50.9675 | 42 | 5 | 2505 | 29 | 26 | 89.6552 | |
| cchapple-custom | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 99.4518 | 99.3532 | 99.5506 | 74.6799 | 768 | 5 | 886 | 4 | 2 | 50.0000 | |
| cchapple-custom | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_51to200 | het | 89.4961 | 81.4815 | 99.2593 | 43.5146 | 22 | 5 | 134 | 1 | 1 | 100.0000 | |
| cchapple-custom | INDEL | I1_5 | lowcmp_SimpleRepeat_triTR_11to50 | het | 99.2714 | 98.9362 | 99.6089 | 56.7644 | 465 | 5 | 764 | 3 | 2 | 66.6667 | |
| cchapple-custom | INDEL | I6_15 | map_l100_m0_e0 | * | 88.7845 | 84.8485 | 93.1034 | 92.0330 | 28 | 5 | 27 | 2 | 1 | 50.0000 | |
| cchapple-custom | INDEL | I6_15 | map_l125_m1_e0 | het | 88.3191 | 83.3333 | 93.9394 | 91.8919 | 25 | 5 | 31 | 2 | 0 | 0.0000 | |
| cchapple-custom | INDEL | I6_15 | map_l125_m2_e0 | het | 88.3191 | 83.3333 | 93.9394 | 92.8726 | 25 | 5 | 31 | 2 | 0 | 0.0000 | |
| cchapple-custom | INDEL | I6_15 | map_l125_m2_e1 | het | 88.3191 | 83.3333 | 93.9394 | 93.0672 | 25 | 5 | 31 | 2 | 0 | 0.0000 | |
| cchapple-custom | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 97.6744 | 95.4545 | 100.0000 | 84.6970 | 105 | 5 | 101 | 0 | 0 | ||