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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
22751-22800 / 86044 show all | |||||||||||||||
| jli-custom | SNP | * | map_l100_m0_e0 | het | 98.8927 | 98.5522 | 99.2355 | 65.8743 | 20898 | 307 | 20898 | 161 | 48 | 29.8137 | |
| ckim-vqsr | SNP | * | map_l100_m1_e0 | * | 76.6064 | 62.3814 | 99.2353 | 82.7403 | 45166 | 27237 | 45158 | 348 | 14 | 4.0230 | |
| ltrigg-rtg2 | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 98.0137 | 96.8220 | 99.2350 | 34.3144 | 914 | 30 | 908 | 7 | 7 | 100.0000 | |
| egarrison-hhga | SNP | * | lowcmp_SimpleRepeat_diTR_11to50 | het | 98.4322 | 97.6427 | 99.2345 | 66.5194 | 6089 | 147 | 6093 | 47 | 18 | 38.2979 | |
| ckim-vqsr | SNP | * | map_l100_m2_e0 | * | 77.0107 | 62.9198 | 99.2344 | 83.7056 | 46538 | 27426 | 46530 | 359 | 16 | 4.4568 | |
| ltrigg-rtg1 | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | * | 97.2339 | 95.3125 | 99.2344 | 58.7664 | 1708 | 84 | 1685 | 13 | 10 | 76.9231 | |
| hfeng-pmm2 | SNP | ti | map_l100_m0_e0 | * | 99.3277 | 99.4212 | 99.2343 | 69.9178 | 21645 | 126 | 21642 | 167 | 19 | 11.3772 | |
| bgallagher-sentieon | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 99.2885 | 99.3428 | 99.2341 | 89.3299 | 907 | 6 | 907 | 7 | 6 | 85.7143 | |
| rpoplin-dv42 | INDEL | D1_5 | map_siren | homalt | 99.4879 | 99.7432 | 99.2340 | 80.1520 | 1165 | 3 | 1166 | 9 | 7 | 77.7778 | |
| jli-custom | INDEL | I1_5 | map_l100_m1_e0 | homalt | 99.6154 | 100.0000 | 99.2337 | 79.2939 | 518 | 0 | 518 | 4 | 3 | 75.0000 | |
| jmaeng-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 95.8238 | 92.6407 | 99.2335 | 33.1757 | 1498 | 119 | 1683 | 13 | 13 | 100.0000 | |
| raldana-dualsentieon | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 97.9951 | 96.7873 | 99.2334 | 74.5777 | 2380 | 79 | 2330 | 18 | 13 | 72.2222 | |
| egarrison-hhga | SNP | * | map_l250_m0_e0 | * | 98.0810 | 96.9555 | 99.2330 | 92.5099 | 2070 | 65 | 2070 | 16 | 6 | 37.5000 | |
| hfeng-pmm1 | SNP | * | map_l150_m0_e0 | * | 99.0843 | 98.9362 | 99.2329 | 79.6567 | 11904 | 128 | 11901 | 92 | 18 | 19.5652 | |
| jlack-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 99.2829 | 99.3333 | 99.2326 | 76.5804 | 2980 | 20 | 2974 | 23 | 8 | 34.7826 | |
| ghariani-varprowl | SNP | ti | segdup | homalt | 99.5818 | 99.9334 | 99.2326 | 88.7647 | 7500 | 5 | 7500 | 58 | 36 | 62.0690 | |
| mlin-fermikit | SNP | tv | HG002complexvar | * | 98.1368 | 97.0653 | 99.2323 | 22.0366 | 238931 | 7224 | 238861 | 1848 | 1739 | 94.1017 | |
| mlin-fermikit | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 77.7997 | 63.9808 | 99.2322 | 42.2569 | 10688 | 6017 | 10856 | 84 | 82 | 97.6190 | |
| mlin-fermikit | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 77.7997 | 63.9808 | 99.2322 | 42.2569 | 10688 | 6017 | 10856 | 84 | 82 | 97.6190 | |
| ckim-vqsr | INDEL | I1_5 | map_l100_m1_e0 | homalt | 99.5188 | 99.8069 | 99.2322 | 81.1709 | 517 | 1 | 517 | 4 | 3 | 75.0000 | |
| jli-custom | SNP | ti | lowcmp_SimpleRepeat_quadTR_11to50 | * | 99.5868 | 99.9441 | 99.2321 | 39.7088 | 10726 | 6 | 10726 | 83 | 1 | 1.2048 | |
| gduggal-bwaplat | INDEL | * | map_l125_m1_e0 | * | 75.7994 | 61.3194 | 99.2320 | 94.1880 | 1292 | 815 | 1292 | 10 | 2 | 20.0000 | |
| hfeng-pmm3 | INDEL | D6_15 | HG002complexvar | het | 95.8678 | 92.7244 | 99.2318 | 57.2218 | 2893 | 227 | 2842 | 22 | 17 | 77.2727 | |
| asubramanian-gatk | SNP | * | segdup | het | 98.0720 | 96.9394 | 99.2313 | 93.3046 | 16787 | 530 | 16781 | 130 | 4 | 3.0769 | |
| bgallagher-sentieon | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | hetalt | 97.6981 | 96.2121 | 99.2308 | 79.2000 | 127 | 5 | 129 | 1 | 1 | 100.0000 | |
| astatham-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | hetalt | 97.7006 | 96.2169 | 99.2308 | 24.4186 | 763 | 30 | 774 | 6 | 6 | 100.0000 | |
| ltrigg-rtg2 | INDEL | D6_15 | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 99.2394 | 99.2481 | 99.2308 | 79.1667 | 264 | 2 | 258 | 2 | 1 | 50.0000 | |
| qzeng-custom | SNP | ti | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 99.2303 | 99.2299 | 99.2308 | 68.4878 | 1675 | 13 | 1677 | 13 | 7 | 53.8462 | |
| qzeng-custom | SNP | tv | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 99.3290 | 99.4275 | 99.2308 | 69.0660 | 521 | 3 | 516 | 4 | 4 | 100.0000 | |
| rpoplin-dv42 | INDEL | I1_5 | map_l100_m1_e0 | homalt | 99.4220 | 99.6139 | 99.2308 | 80.6620 | 516 | 2 | 516 | 4 | 2 | 50.0000 | |
| eyeh-varpipe | SNP | * | map_l150_m2_e1 | hetalt | 99.6139 | 100.0000 | 99.2308 | 75.0480 | 20 | 0 | 129 | 1 | 0 | 0.0000 | |
| ckim-isaac | INDEL | I1_5 | map_l100_m2_e0 | het | 89.3971 | 81.3367 | 99.2308 | 86.3273 | 645 | 148 | 645 | 5 | 1 | 20.0000 | |
| ckim-dragen | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 97.5748 | 95.9732 | 99.2308 | 77.4697 | 143 | 6 | 129 | 1 | 1 | 100.0000 | |
| ckim-gatk | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 99.4089 | 99.5877 | 99.2308 | 76.0442 | 48072 | 199 | 47859 | 371 | 265 | 71.4286 | |
| gduggal-snapplat | SNP | * | segdup | * | 98.9750 | 98.7209 | 99.2304 | 93.4858 | 27708 | 359 | 27723 | 215 | 30 | 13.9535 | |
| ndellapenna-hhga | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 96.6252 | 94.1534 | 99.2303 | 30.5059 | 4493 | 279 | 4512 | 35 | 32 | 91.4286 | |
| jmaeng-gatk | INDEL | * | * | homalt | 99.5485 | 99.8690 | 99.2301 | 59.0290 | 125008 | 164 | 125021 | 970 | 941 | 97.0103 | |
| jmaeng-gatk | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 98.8577 | 98.4881 | 99.2301 | 73.8561 | 93021 | 1428 | 92930 | 721 | 622 | 86.2691 | |
| ckim-isaac | SNP | tv | map_l250_m2_e0 | het | 63.3205 | 46.4948 | 99.2299 | 92.2101 | 902 | 1038 | 902 | 7 | 1 | 14.2857 | |
| qzeng-custom | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 99.3593 | 99.4891 | 99.2298 | 79.0524 | 3895 | 20 | 3865 | 30 | 20 | 66.6667 | |
| hfeng-pmm3 | SNP | tv | map_l125_m0_e0 | * | 99.1700 | 99.1102 | 99.2298 | 75.2152 | 6572 | 59 | 6571 | 51 | 7 | 13.7255 | |
| bgallagher-sentieon | SNP | ti | map_l125_m2_e1 | * | 99.3333 | 99.4373 | 99.2295 | 72.6907 | 30397 | 172 | 30393 | 236 | 42 | 17.7966 | |
| anovak-vg | SNP | * | map_l150_m2_e0 | homalt | 88.0238 | 79.0922 | 99.2294 | 72.9596 | 9253 | 2446 | 9143 | 71 | 59 | 83.0986 | |
| bgallagher-sentieon | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | * | 99.0886 | 98.9484 | 99.2292 | 67.4228 | 3858 | 41 | 3862 | 30 | 18 | 60.0000 | |
| bgallagher-sentieon | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.5837 | 99.9406 | 99.2292 | 75.9456 | 21886 | 13 | 21886 | 170 | 169 | 99.4118 | |
| jlack-gatk | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.0110 | 98.7939 | 99.2291 | 68.2739 | 901 | 11 | 901 | 7 | 5 | 71.4286 | |
| raldana-dualsentieon | INDEL | D6_15 | HG002complexvar | * | 96.9018 | 94.6813 | 99.2289 | 57.2443 | 5020 | 282 | 5019 | 39 | 37 | 94.8718 | |
| ndellapenna-hhga | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 97.1729 | 95.2004 | 99.2289 | 61.5550 | 5653 | 285 | 5662 | 44 | 38 | 86.3636 | |
| egarrison-hhga | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 98.8850 | 98.5441 | 99.2284 | 79.4839 | 3858 | 57 | 3858 | 30 | 23 | 76.6667 | |
| egarrison-hhga | SNP | ti | map_l250_m0_e0 | het | 97.7729 | 96.3597 | 99.2282 | 93.4065 | 900 | 34 | 900 | 7 | 1 | 14.2857 | |