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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
14901-14950 / 86044 show all | |||||||||||||||
| jli-custom | INDEL | * | map_l100_m2_e1 | het | 98.3311 | 98.0367 | 98.6272 | 84.1536 | 2297 | 46 | 2299 | 32 | 9 | 28.1250 | |
| egarrison-hhga | INDEL | * | map_l100_m2_e1 | het | 97.4787 | 97.9513 | 97.0105 | 84.5478 | 2295 | 48 | 2304 | 71 | 31 | 43.6620 | |
| mlin-fermikit | SNP | * | map_l250_m1_e0 | * | 45.7291 | 31.7641 | 81.6080 | 76.7628 | 2294 | 4928 | 2294 | 517 | 446 | 86.2669 | |
| ltrigg-rtg2 | INDEL | I6_15 | HG002complexvar | het | 98.2137 | 97.4098 | 99.0310 | 49.5355 | 2294 | 61 | 2044 | 20 | 9 | 45.0000 | |
| qzeng-custom | INDEL | * | map_siren | homalt | 90.9652 | 86.4030 | 96.0361 | 77.3592 | 2294 | 361 | 2447 | 101 | 23 | 22.7723 | |
| gduggal-snapplat | INDEL | I1_5 | map_siren | * | 81.2847 | 76.3062 | 86.9582 | 90.3597 | 2293 | 712 | 2307 | 346 | 22 | 6.3584 | |
| ckim-isaac | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 84.1772 | 73.3974 | 98.6684 | 34.6801 | 2290 | 830 | 2297 | 31 | 21 | 67.7419 | |
| cchapple-custom | INDEL | I6_15 | HG002complexvar | het | 98.1734 | 97.1975 | 99.1692 | 56.5725 | 2289 | 66 | 3581 | 30 | 25 | 83.3333 | |
| jli-custom | INDEL | I6_15 | HG002complexvar | het | 98.4497 | 97.1975 | 99.7346 | 57.2913 | 2289 | 66 | 2255 | 6 | 1 | 16.6667 | |
| gduggal-snapvard | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 96.3822 | 94.6628 | 98.1651 | 78.9575 | 2288 | 129 | 2247 | 42 | 19 | 45.2381 | |
| hfeng-pmm2 | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_11to50 | * | 97.0727 | 94.8590 | 99.3921 | 62.0781 | 2288 | 124 | 2289 | 14 | 8 | 57.1429 | |
| hfeng-pmm1 | INDEL | I6_15 | HG002complexvar | het | 98.5354 | 97.1550 | 99.9556 | 58.9168 | 2288 | 67 | 2252 | 1 | 1 | 100.0000 | |
| astatham-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 98.1132 | 96.6216 | 99.6516 | 87.6280 | 2288 | 80 | 2288 | 8 | 8 | 100.0000 | |
| bgallagher-sentieon | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_11to50 | * | 96.9904 | 94.8590 | 99.2198 | 62.4389 | 2288 | 124 | 2289 | 18 | 13 | 72.2222 | |
| ltrigg-rtg1 | INDEL | I6_15 | HG002complexvar | het | 98.2042 | 97.1125 | 99.3207 | 49.9393 | 2287 | 68 | 2047 | 14 | 8 | 57.1429 | |
| gduggal-bwaplat | INDEL | * | segdup | * | 94.1537 | 89.4757 | 99.3478 | 96.2604 | 2287 | 269 | 2285 | 15 | 9 | 60.0000 | |
| jmaeng-gatk | SNP | tv | map_l150_m2_e0 | homalt | 71.7739 | 55.9882 | 99.9563 | 81.6747 | 2286 | 1797 | 2286 | 1 | 1 | 100.0000 | |
| hfeng-pmm3 | INDEL | I6_15 | HG002complexvar | het | 98.4917 | 97.0701 | 99.9556 | 58.8257 | 2286 | 69 | 2250 | 1 | 1 | 100.0000 | |
| ndellapenna-hhga | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 94.1550 | 90.0354 | 98.6695 | 35.2238 | 2286 | 253 | 2299 | 31 | 28 | 90.3226 | |
| ckim-isaac | SNP | ti | map_l250_m1_e0 | * | 66.4534 | 49.9017 | 99.4343 | 90.2759 | 2285 | 2294 | 2285 | 13 | 2 | 15.3846 | |
| hfeng-pmm2 | INDEL | I6_15 | HG002complexvar | het | 98.4267 | 97.0276 | 99.8668 | 58.9949 | 2285 | 70 | 2249 | 3 | 2 | 66.6667 | |
| gduggal-bwaplat | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 77.7513 | 65.3494 | 95.9630 | 64.1921 | 2282 | 1210 | 2282 | 96 | 29 | 30.2083 | |
| ckim-gatk | SNP | tv | map_l150_m2_e0 | homalt | 71.6934 | 55.8903 | 99.9562 | 82.4006 | 2282 | 1801 | 2282 | 1 | 0 | 0.0000 | |
| qzeng-custom | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 94.4513 | 96.2447 | 92.7236 | 43.0556 | 2281 | 89 | 2281 | 179 | 171 | 95.5307 | |
| ndellapenna-hhga | INDEL | * | map_l100_m2_e1 | het | 97.2372 | 97.3111 | 97.1634 | 84.0911 | 2280 | 63 | 2295 | 67 | 27 | 40.2985 | |
| ckim-dragen | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_11to50 | het | 99.7593 | 99.7812 | 99.7374 | 46.7118 | 2280 | 5 | 2279 | 6 | 2 | 33.3333 | |
| ckim-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_11to50 | het | 99.8250 | 99.7812 | 99.8688 | 48.0455 | 2280 | 5 | 2283 | 3 | 0 | 0.0000 | |
| bgallagher-sentieon | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_11to50 | het | 99.8468 | 99.7812 | 99.9125 | 46.5872 | 2280 | 5 | 2283 | 2 | 0 | 0.0000 | |
| jmaeng-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_11to50 | het | 99.8250 | 99.7812 | 99.8688 | 48.1162 | 2280 | 5 | 2283 | 3 | 0 | 0.0000 | |
| dgrover-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_11to50 | het | 99.8468 | 99.7812 | 99.9125 | 47.3260 | 2280 | 5 | 2283 | 2 | 0 | 0.0000 | |
| jlack-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_11to50 | het | 99.7594 | 99.7374 | 99.7814 | 47.4494 | 2279 | 6 | 2282 | 5 | 0 | 0.0000 | |
| astatham-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_11to50 | het | 99.8248 | 99.7374 | 99.9124 | 46.8961 | 2279 | 6 | 2282 | 2 | 0 | 0.0000 | |
| ckim-isaac | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 85.3274 | 76.4173 | 96.5895 | 46.1939 | 2278 | 703 | 2294 | 81 | 62 | 76.5432 | |
| gduggal-snapplat | SNP | ti | map_l150_m0_e0 | homalt | 90.3251 | 82.5063 | 99.7809 | 77.2958 | 2278 | 483 | 2277 | 5 | 5 | 100.0000 | |
| gduggal-snapplat | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 29.4305 | 22.6149 | 42.1263 | 81.2487 | 2278 | 7795 | 2734 | 3756 | 1082 | 28.8072 | |
| rpoplin-dv42 | INDEL | * | map_l100_m2_e1 | het | 97.6450 | 97.2258 | 98.0678 | 84.3523 | 2278 | 65 | 2284 | 45 | 20 | 44.4444 | |
| ckim-dragen | INDEL | * | map_l100_m2_e1 | het | 96.3159 | 97.1831 | 95.4641 | 88.2397 | 2277 | 66 | 2273 | 108 | 10 | 9.2593 | |
| raldana-dualsentieon | INDEL | * | map_l100_m2_e1 | het | 97.6853 | 97.1831 | 98.1928 | 83.5574 | 2277 | 66 | 2282 | 42 | 8 | 19.0476 | |
| cchapple-custom | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_11to50 | het | 99.6929 | 99.6061 | 99.7799 | 36.0694 | 2276 | 9 | 2720 | 6 | 4 | 66.6667 | |
| ckim-vqsr | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_11to50 | het | 99.7372 | 99.6061 | 99.8685 | 48.0892 | 2276 | 9 | 2279 | 3 | 0 | 0.0000 | |
| asubramanian-gatk | INDEL | I6_15 | HG002complexvar | het | 98.1220 | 96.6454 | 99.6443 | 60.1594 | 2276 | 79 | 2241 | 8 | 3 | 37.5000 | |
| rpoplin-dv42 | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_11to50 | het | 99.6717 | 99.6061 | 99.7373 | 45.9408 | 2276 | 9 | 2278 | 6 | 3 | 50.0000 | |
| bgallagher-sentieon | INDEL | * | map_l100_m2_e0 | het | 98.0419 | 98.6129 | 97.4776 | 86.6167 | 2275 | 32 | 2280 | 59 | 11 | 18.6441 | |
| raldana-dualsentieon | INDEL | I6_15 | HG002complexvar | het | 98.1424 | 96.5605 | 99.7771 | 58.4090 | 2274 | 81 | 2238 | 5 | 4 | 80.0000 | |
| ckim-gatk | INDEL | * | map_l100_m2_e0 | het | 96.1386 | 98.5696 | 93.8246 | 90.4219 | 2274 | 33 | 2279 | 150 | 14 | 9.3333 | |
| jlack-gatk | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_11to50 | * | 96.4993 | 94.2786 | 98.8271 | 62.5995 | 2274 | 138 | 2275 | 27 | 22 | 81.4815 | |
| hfeng-pmm1 | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_11to50 | * | 96.7867 | 94.2786 | 99.4318 | 62.0564 | 2274 | 138 | 2275 | 13 | 7 | 53.8462 | |
| gduggal-bwaplat | INDEL | * | HG002compoundhet | het | 66.0619 | 55.5447 | 81.4921 | 84.3450 | 2274 | 1820 | 2272 | 516 | 182 | 35.2713 | |
| gduggal-bwafb | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 89.0456 | 96.0304 | 83.0080 | 88.0462 | 2274 | 94 | 2296 | 470 | 74 | 15.7447 | |
| jli-custom | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_11to50 | het | 99.6931 | 99.5186 | 99.8683 | 44.6416 | 2274 | 11 | 2275 | 3 | 0 | 0.0000 | |