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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
76701-76750 / 86044 show all | |||||||||||||||
| asubramanian-gatk | INDEL | * | HG002complexvar | homalt | 99.4823 | 99.5116 | 99.4530 | 57.3903 | 26895 | 132 | 26910 | 148 | 101 | 68.2432 | |
| eyeh-varpipe | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | homalt | 99.4824 | 99.4939 | 99.4709 | 56.5517 | 1376 | 7 | 1316 | 7 | 1 | 14.2857 | |
| astatham-gatk | INDEL | * | HG002complexvar | * | 99.4827 | 99.2916 | 99.6745 | 58.3541 | 76393 | 545 | 76257 | 249 | 212 | 85.1406 | |
| gduggal-bwafb | SNP | tv | map_l125_m2_e0 | homalt | 99.4828 | 99.1025 | 99.8660 | 70.9836 | 5963 | 54 | 5963 | 8 | 6 | 75.0000 | |
| raldana-dualsentieon | SNP | * | map_l250_m2_e1 | homalt | 99.4834 | 99.1906 | 99.7779 | 85.3835 | 2696 | 22 | 2696 | 6 | 3 | 50.0000 | |
| raldana-dualsentieon | SNP | ti | map_l250_m2_e0 | homalt | 99.4834 | 99.0852 | 99.8847 | 85.3537 | 1733 | 16 | 1733 | 2 | 1 | 50.0000 | |
| hfeng-pmm3 | INDEL | D6_15 | lowcmp_SimpleRepeat_triTR_11to50 | hetalt | 99.4836 | 98.9726 | 100.0000 | 18.6798 | 578 | 6 | 579 | 0 | 0 | ||
| hfeng-pmm1 | INDEL | D6_15 | lowcmp_SimpleRepeat_triTR_11to50 | hetalt | 99.4836 | 98.9726 | 100.0000 | 18.6798 | 578 | 6 | 579 | 0 | 0 | ||
| ltrigg-rtg1 | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 99.4840 | 98.9733 | 100.0000 | 60.3521 | 482 | 5 | 473 | 0 | 0 | ||
| ckim-dragen | SNP | * | map_l150_m1_e0 | homalt | 99.4842 | 99.2194 | 99.7504 | 65.7675 | 11185 | 88 | 11190 | 28 | 25 | 89.2857 | |
| hfeng-pmm1 | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 99.4843 | 99.6244 | 99.3446 | 67.0980 | 1061 | 4 | 1061 | 7 | 7 | 100.0000 | |
| ckim-gatk | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 99.4847 | 99.7826 | 99.1887 | 63.5467 | 35342 | 77 | 35331 | 289 | 22 | 7.6125 | |
| hfeng-pmm2 | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 99.4848 | 99.7183 | 99.2523 | 67.2382 | 1062 | 3 | 1062 | 8 | 8 | 100.0000 | |
| jli-custom | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 99.4849 | 99.1930 | 99.7786 | 75.9411 | 1352 | 11 | 1352 | 3 | 1 | 33.3333 | |
| hfeng-pmm3 | SNP | * | map_l100_m0_e0 | * | 99.4850 | 99.4123 | 99.5578 | 68.0774 | 32648 | 193 | 32644 | 145 | 21 | 14.4828 | |
| ndellapenna-hhga | SNP | ti | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 99.4850 | 99.2977 | 99.6730 | 35.9284 | 3959 | 28 | 3962 | 13 | 12 | 92.3077 | |
| raldana-dualsentieon | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 99.4851 | 99.1786 | 99.7934 | 64.4901 | 483 | 4 | 483 | 1 | 1 | 100.0000 | |
| hfeng-pmm3 | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 99.4851 | 99.1786 | 99.7934 | 64.5161 | 483 | 4 | 483 | 1 | 1 | 100.0000 | |
| hfeng-pmm1 | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 99.4851 | 99.1786 | 99.7934 | 64.4118 | 483 | 4 | 483 | 1 | 1 | 100.0000 | |
| asubramanian-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 99.4851 | 99.1786 | 99.7934 | 67.2973 | 483 | 4 | 483 | 1 | 1 | 100.0000 | |
| jlack-gatk | SNP | tv | lowcmp_SimpleRepeat_diTR_11to50 | * | 99.4853 | 99.5058 | 99.4648 | 66.6987 | 4832 | 24 | 4832 | 26 | 14 | 53.8462 | |
| rpoplin-dv42 | SNP | * | * | hetalt | 99.4854 | 99.8852 | 99.0888 | 49.8858 | 870 | 1 | 870 | 8 | 8 | 100.0000 | |
| rpoplin-dv42 | SNP | tv | * | hetalt | 99.4854 | 99.8852 | 99.0888 | 49.8858 | 870 | 1 | 870 | 8 | 8 | 100.0000 | |
| ckim-vqsr | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 99.4854 | 99.3353 | 99.6359 | 61.3327 | 1644 | 11 | 1642 | 6 | 3 | 50.0000 | |
| hfeng-pmm3 | SNP | * | map_l250_m2_e1 | homalt | 99.4855 | 99.5953 | 99.3759 | 87.8906 | 2707 | 11 | 2707 | 17 | 6 | 35.2941 | |
| hfeng-pmm1 | SNP | * | map_l250_m2_e1 | homalt | 99.4855 | 99.5953 | 99.3759 | 87.9341 | 2707 | 11 | 2707 | 17 | 6 | 35.2941 | |
| dgrover-gatk | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 99.4856 | 99.3676 | 99.6038 | 88.3504 | 1257 | 8 | 1257 | 5 | 5 | 100.0000 | |
| jli-custom | INDEL | * | lowcmp_SimpleRepeat_triTR_11to50 | * | 99.4857 | 99.1089 | 99.8653 | 46.8501 | 6673 | 60 | 6673 | 9 | 5 | 55.5556 | |
| astatham-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 99.4857 | 99.3958 | 99.5758 | 60.5358 | 1645 | 10 | 1643 | 7 | 4 | 57.1429 | |
| bgallagher-sentieon | SNP | tv | segdup | * | 99.4858 | 99.8125 | 99.1612 | 91.3387 | 8516 | 16 | 8512 | 72 | 6 | 8.3333 | |
| ltrigg-rtg1 | SNP | * | map_siren | * | 99.4858 | 99.2395 | 99.7333 | 50.0979 | 145115 | 1112 | 145108 | 388 | 49 | 12.6289 | |
| hfeng-pmm1 | INDEL | * | lowcmp_SimpleRepeat_triTR_11to50 | * | 99.4859 | 99.1534 | 99.8206 | 46.3856 | 6676 | 57 | 6678 | 12 | 5 | 41.6667 | |
| gduggal-bwafb | SNP | tv | map_l125_m1_e0 | homalt | 99.4861 | 99.1126 | 99.8624 | 68.8267 | 5808 | 52 | 5808 | 8 | 6 | 75.0000 | |
| hfeng-pmm3 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 99.4861 | 99.5813 | 99.3911 | 58.2577 | 8325 | 35 | 8325 | 51 | 50 | 98.0392 | |
| hfeng-pmm3 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 99.4861 | 99.5813 | 99.3911 | 58.2577 | 8325 | 35 | 8325 | 51 | 50 | 98.0392 | |
| ckim-vqsr | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 99.4862 | 100.0000 | 98.9777 | 68.5196 | 1065 | 0 | 1065 | 11 | 11 | 100.0000 | |
| ckim-vqsr | INDEL | D1_5 | map_siren | homalt | 99.4864 | 99.4007 | 99.5723 | 81.4444 | 1161 | 7 | 1164 | 5 | 4 | 80.0000 | |
| ckim-gatk | INDEL | D1_5 | map_siren | homalt | 99.4864 | 99.4007 | 99.5723 | 81.4444 | 1161 | 7 | 1164 | 5 | 4 | 80.0000 | |
| hfeng-pmm1 | SNP | tv | map_l125_m2_e0 | * | 99.4866 | 99.3147 | 99.6592 | 71.0071 | 16376 | 113 | 16374 | 56 | 16 | 28.5714 | |
| jmaeng-gatk | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.4869 | 99.9155 | 99.0621 | 74.5055 | 30735 | 26 | 30735 | 291 | 281 | 96.5636 | |
| bgallagher-sentieon | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 99.4872 | 99.3714 | 99.6033 | 48.0102 | 4268 | 27 | 4268 | 17 | 0 | 0.0000 | |
| astatham-gatk | SNP | ti | map_l125_m2_e0 | homalt | 99.4872 | 99.0755 | 99.9023 | 65.7910 | 11253 | 105 | 11253 | 11 | 10 | 90.9091 | |
| hfeng-pmm1 | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 99.4872 | 99.1352 | 99.8416 | 45.8405 | 2522 | 22 | 2522 | 4 | 0 | 0.0000 | |
| hfeng-pmm2 | SNP | tv | map_l100_m2_e0 | * | 99.4872 | 99.6005 | 99.3742 | 68.8945 | 24933 | 100 | 24929 | 157 | 17 | 10.8280 | |
| eyeh-varpipe | SNP | tv | map_l125_m1_e0 | hetalt | 99.4872 | 100.0000 | 98.9796 | 72.3944 | 30 | 0 | 97 | 1 | 0 | 0.0000 | |
| egarrison-hhga | INDEL | I1_5 | * | homalt | 99.4873 | 99.3910 | 99.5837 | 52.1988 | 60060 | 368 | 60044 | 251 | 188 | 74.9004 | |
| gduggal-bwafb | SNP | tv | map_l125_m2_e1 | homalt | 99.4877 | 99.1110 | 99.8673 | 71.0512 | 6020 | 54 | 6020 | 8 | 6 | 75.0000 | |
| rpoplin-dv42 | INDEL | D1_5 | map_siren | homalt | 99.4879 | 99.7432 | 99.2340 | 80.1520 | 1165 | 3 | 1166 | 9 | 7 | 77.7778 | |
| hfeng-pmm2 | INDEL | D6_15 | HG002complexvar | homalt | 99.4885 | 99.8289 | 99.1504 | 61.5359 | 1167 | 2 | 1167 | 10 | 9 | 90.0000 | |
| ltrigg-rtg2 | INDEL | I1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 99.4887 | 99.3450 | 99.6329 | 63.1294 | 1365 | 9 | 1357 | 5 | 1 | 20.0000 | |