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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
22801-22850 / 86044 show all | |||||||||||||||
| jmaeng-gatk | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 98.9011 | 98.5761 | 99.2282 | 89.6010 | 900 | 13 | 900 | 7 | 6 | 85.7143 | |
| ghariani-varprowl | SNP | ti | HG002complexvar | het | 99.4535 | 99.6801 | 99.2280 | 19.8744 | 313754 | 1007 | 313878 | 2442 | 84 | 3.4398 | |
| hfeng-pmm3 | INDEL | D6_15 | * | homalt | 99.3845 | 99.5416 | 99.2279 | 50.7795 | 6297 | 29 | 6297 | 49 | 45 | 91.8367 | |
| hfeng-pmm2 | INDEL | D1_5 | map_l100_m0_e0 | homalt | 99.4197 | 99.6124 | 99.2278 | 81.9638 | 257 | 1 | 257 | 2 | 2 | 100.0000 | |
| bgallagher-sentieon | INDEL | D1_5 | map_l100_m0_e0 | homalt | 99.4197 | 99.6124 | 99.2278 | 83.8529 | 257 | 1 | 257 | 2 | 2 | 100.0000 | |
| gduggal-bwaplat | SNP | tv | HG002complexvar | hetalt | 90.9054 | 83.8710 | 99.2278 | 44.0605 | 260 | 50 | 257 | 2 | 2 | 100.0000 | |
| gduggal-bwaplat | SNP | * | HG002complexvar | hetalt | 90.9054 | 83.8710 | 99.2278 | 44.0605 | 260 | 50 | 257 | 2 | 2 | 100.0000 | |
| gduggal-bwafb | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | het | 97.6431 | 96.1084 | 99.2277 | 42.1750 | 10002 | 405 | 15032 | 117 | 72 | 61.5385 | |
| egarrison-hhga | INDEL | * | HG002compoundhet | hetalt | 84.8570 | 74.1223 | 99.2275 | 55.5672 | 18664 | 6516 | 18112 | 141 | 123 | 87.2340 | |
| ckim-isaac | INDEL | D1_5 | HG002compoundhet | hetalt | 92.5735 | 86.7561 | 99.2273 | 35.2319 | 8863 | 1353 | 9117 | 71 | 65 | 91.5493 | |
| hfeng-pmm3 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 97.9085 | 96.6244 | 99.2272 | 64.2470 | 63145 | 2206 | 62918 | 490 | 402 | 82.0408 | |
| hfeng-pmm3 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 97.9085 | 96.6244 | 99.2272 | 64.2470 | 63145 | 2206 | 62918 | 490 | 402 | 82.0408 | |
| bgallagher-sentieon | INDEL | I1_5 | map_siren | het | 99.0779 | 98.9292 | 99.2271 | 81.4696 | 1663 | 18 | 1669 | 13 | 1 | 7.6923 | |
| asubramanian-gatk | INDEL | * | lowcmp_SimpleRepeat_triTR_11to50 | * | 99.0488 | 98.8712 | 99.2269 | 57.4163 | 6657 | 76 | 6931 | 54 | 10 | 18.5185 | |
| jli-custom | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 98.4961 | 97.7763 | 99.2266 | 43.2593 | 20138 | 458 | 20142 | 157 | 149 | 94.9045 | |
| ltrigg-rtg1 | INDEL | I1_5 | map_l100_m1_e0 | homalt | 99.3235 | 99.4208 | 99.2263 | 79.9379 | 515 | 3 | 513 | 4 | 2 | 50.0000 | |
| ndellapenna-hhga | INDEL | I1_5 | map_l100_m1_e0 | homalt | 99.1304 | 99.0347 | 99.2263 | 80.8802 | 513 | 5 | 513 | 4 | 2 | 50.0000 | |
| mlin-fermikit | INDEL | D1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 98.6655 | 98.1110 | 99.2262 | 52.5551 | 14491 | 279 | 14491 | 113 | 109 | 96.4602 | |
| ndellapenna-hhga | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 99.4268 | 99.6283 | 99.2261 | 57.2682 | 2948 | 11 | 2949 | 23 | 1 | 4.3478 | |
| jlack-gatk | INDEL | * | lowcmp_SimpleRepeat_quadTR_51to200 | hetalt | 95.9073 | 92.8033 | 99.2261 | 33.2760 | 1109 | 86 | 1154 | 9 | 8 | 88.8889 | |
| hfeng-pmm1 | INDEL | * | map_l125_m2_e1 | homalt | 99.2899 | 99.3540 | 99.2258 | 85.3746 | 769 | 5 | 769 | 6 | 3 | 50.0000 | |
| cchapple-custom | INDEL | I6_15 | HG002compoundhet | het | 96.1554 | 93.2692 | 99.2258 | 33.4003 | 194 | 14 | 9869 | 77 | 72 | 93.5065 | |
| qzeng-custom | INDEL | I1_5 | * | homalt | 99.1725 | 99.1196 | 99.2255 | 48.3268 | 59896 | 532 | 59833 | 467 | 326 | 69.8073 | |
| jlack-gatk | SNP | tv | lowcmp_SimpleRepeat_diTR_11to50 | het | 99.3694 | 99.5142 | 99.2251 | 69.4063 | 3073 | 15 | 3073 | 24 | 12 | 50.0000 | |
| ltrigg-rtg1 | INDEL | * | map_l100_m2_e1 | * | 97.3272 | 95.5005 | 99.2250 | 80.3823 | 3587 | 169 | 3585 | 28 | 7 | 25.0000 | |
| hfeng-pmm1 | INDEL | * | map_siren | * | 98.7669 | 98.3131 | 99.2250 | 80.4107 | 7285 | 125 | 7298 | 57 | 12 | 21.0526 | |
| bgallagher-sentieon | SNP | ti | map_l125_m2_e0 | * | 99.3281 | 99.4316 | 99.2249 | 72.6504 | 30086 | 172 | 30082 | 235 | 42 | 17.8723 | |
| ckim-dragen | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | hetalt | 97.3061 | 95.4603 | 99.2248 | 24.1920 | 757 | 36 | 768 | 6 | 6 | 100.0000 | |
| ckim-vqsr | INDEL | * | map_l125_m2_e1 | homalt | 99.2248 | 99.2248 | 99.2248 | 87.3859 | 768 | 6 | 768 | 6 | 3 | 50.0000 | |
| raldana-dualsentieon | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 99.2248 | 99.2248 | 99.2248 | 62.6628 | 256 | 2 | 256 | 2 | 2 | 100.0000 | |
| jmaeng-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 99.2248 | 99.2248 | 99.2248 | 63.9161 | 256 | 2 | 256 | 2 | 2 | 100.0000 | |
| gduggal-bwavard | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 59.7005 | 42.6942 | 99.2246 | 54.0503 | 4903 | 6581 | 4863 | 38 | 33 | 86.8421 | |
| bgallagher-sentieon | SNP | ti | map_l125_m1_e0 | * | 99.3257 | 99.4273 | 99.2243 | 71.0550 | 29167 | 168 | 29163 | 228 | 42 | 18.4211 | |
| jli-custom | SNP | tv | map_l125_m0_e0 | * | 98.7959 | 98.3713 | 99.2242 | 70.3527 | 6523 | 108 | 6523 | 51 | 18 | 35.2941 | |
| anovak-vg | SNP | * | map_siren | homalt | 93.9262 | 89.1653 | 99.2241 | 49.9600 | 49180 | 5976 | 48469 | 379 | 316 | 83.3773 | |
| jlack-gatk | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 99.3078 | 99.3917 | 99.2240 | 48.4791 | 2941 | 18 | 2941 | 23 | 2 | 8.6957 | |
| ckim-isaac | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | hetalt | 78.3824 | 64.7764 | 99.2239 | 34.3044 | 811 | 441 | 895 | 7 | 4 | 57.1429 | |
| ckim-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | hetalt | 97.2401 | 95.3342 | 99.2238 | 23.4653 | 756 | 37 | 767 | 6 | 6 | 100.0000 | |
| jli-custom | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | hetalt | 97.2401 | 95.3342 | 99.2238 | 23.4653 | 756 | 37 | 767 | 6 | 5 | 83.3333 | |
| ckim-vqsr | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | hetalt | 97.2401 | 95.3342 | 99.2238 | 23.4653 | 756 | 37 | 767 | 6 | 6 | 100.0000 | |
| gduggal-bwavard | INDEL | I1_5 | map_l100_m2_e1 | homalt | 97.2587 | 95.3704 | 99.2233 | 74.6305 | 515 | 25 | 511 | 4 | 2 | 50.0000 | |
| jli-custom | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 99.4393 | 99.6564 | 99.2231 | 66.7595 | 31036 | 107 | 31036 | 243 | 19 | 7.8189 | |
| jli-custom | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 99.4393 | 99.6564 | 99.2231 | 66.7595 | 31036 | 107 | 31036 | 243 | 19 | 7.8189 | |
| ltrigg-rtg1 | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 97.1871 | 95.2331 | 99.2231 | 35.3659 | 899 | 45 | 894 | 7 | 7 | 100.0000 | |
| gduggal-bwaplat | SNP | ti | map_l125_m0_e0 | * | 63.7993 | 47.0146 | 99.2230 | 91.1459 | 6000 | 6762 | 6002 | 47 | 16 | 34.0426 | |
| hfeng-pmm1 | SNP | tv | map_l125_m0_e0 | het | 98.9058 | 98.5912 | 99.2223 | 76.3803 | 4339 | 62 | 4338 | 34 | 9 | 26.4706 | |
| rpoplin-dv42 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 99.2545 | 99.2866 | 99.2223 | 77.4843 | 1531 | 11 | 1531 | 12 | 9 | 75.0000 | |
| gduggal-bwafb | SNP | ti | map_siren | * | 99.3101 | 99.3981 | 99.2222 | 57.2359 | 99751 | 604 | 99755 | 782 | 145 | 18.5422 | |
| dgrover-gatk | INDEL | D1_5 | map_l100_m0_e0 | homalt | 99.0291 | 98.8372 | 99.2218 | 84.4337 | 255 | 3 | 255 | 2 | 2 | 100.0000 | |
| ckim-gatk | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | * | 98.5939 | 97.9738 | 99.2218 | 68.0216 | 3820 | 79 | 3825 | 30 | 15 | 50.0000 | |