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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
29151-29200 / 86044 show all | |||||||||||||||
| gduggal-snapfb | INDEL | * | map_l250_m2_e1 | het | 90.1679 | 89.0995 | 91.2621 | 94.7636 | 188 | 23 | 188 | 18 | 3 | 16.6667 | |
| gduggal-bwaplat | INDEL | D6_15 | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 82.1997 | 70.3008 | 98.9474 | 87.7261 | 187 | 79 | 188 | 2 | 1 | 50.0000 | |
| gduggal-bwaplat | INDEL | I16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 79.8194 | 68.1004 | 96.4103 | 67.2819 | 190 | 89 | 188 | 7 | 7 | 100.0000 | |
| gduggal-bwafb | SNP | tv | map_l250_m0_e0 | homalt | 98.4293 | 97.4093 | 99.4709 | 94.3430 | 188 | 5 | 188 | 1 | 1 | 100.0000 | |
| jli-custom | INDEL | I1_5 | map_l125_m0_e0 | het | 98.4293 | 97.9167 | 98.9474 | 87.9975 | 188 | 4 | 188 | 2 | 0 | 0.0000 | |
| jmaeng-gatk | INDEL | I1_5 | map_l125_m0_e0 | het | 95.4250 | 97.3958 | 93.5323 | 94.0708 | 187 | 5 | 188 | 13 | 0 | 0.0000 | |
| jmaeng-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 94.4724 | 100.0000 | 89.5238 | 67.9878 | 188 | 0 | 188 | 22 | 21 | 95.4545 | |
| ltrigg-rtg1 | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | homalt | 98.4293 | 97.9167 | 98.9474 | 40.2516 | 188 | 4 | 188 | 2 | 0 | 0.0000 | |
| bgallagher-sentieon | INDEL | I1_5 | map_l125_m0_e0 | het | 97.4026 | 97.3958 | 97.4093 | 89.8634 | 187 | 5 | 188 | 5 | 0 | 0.0000 | |
| bgallagher-sentieon | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 94.2356 | 100.0000 | 89.0995 | 67.4383 | 188 | 0 | 188 | 23 | 22 | 95.6522 | |
| asubramanian-gatk | SNP | ti | map_l250_m0_e0 | het | 33.4817 | 20.1285 | 99.4709 | 99.1011 | 188 | 746 | 188 | 1 | 1 | 100.0000 | |
| asubramanian-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | homalt | 96.4103 | 97.9167 | 94.9495 | 46.7742 | 188 | 4 | 188 | 10 | 9 | 90.0000 | |
| asubramanian-gatk | INDEL | I1_5 | map_l150_m1_e0 | homalt | 97.1429 | 94.4444 | 100.0000 | 87.6802 | 187 | 11 | 188 | 0 | 0 | ||
| asubramanian-gatk | SNP | ti | HG002complexvar | hetalt | 94.4724 | 90.8213 | 98.4293 | 40.4984 | 188 | 19 | 188 | 3 | 0 | 0.0000 | |
| astatham-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 95.1899 | 100.0000 | 90.8213 | 67.6056 | 188 | 0 | 188 | 19 | 18 | 94.7368 | |
| ckim-vqsr | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 94.9495 | 100.0000 | 90.3846 | 67.5000 | 188 | 0 | 188 | 20 | 19 | 95.0000 | |
| dgrover-gatk | INDEL | I1_5 | map_l125_m0_e0 | het | 97.9098 | 97.3958 | 98.4293 | 90.7996 | 187 | 5 | 188 | 3 | 0 | 0.0000 | |
| dgrover-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 95.1899 | 100.0000 | 90.8213 | 67.7067 | 188 | 0 | 188 | 19 | 18 | 94.7368 | |
| hfeng-pmm3 | INDEL | I16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 94.2356 | 91.2621 | 97.4093 | 87.4594 | 188 | 18 | 188 | 5 | 2 | 40.0000 | |
| hfeng-pmm3 | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 96.9072 | 100.0000 | 94.0000 | 65.5766 | 188 | 0 | 188 | 12 | 11 | 91.6667 | |
| hfeng-pmm2 | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 93.5323 | 89.9522 | 97.4093 | 74.9025 | 188 | 21 | 188 | 5 | 4 | 80.0000 | |
| hfeng-pmm2 | INDEL | I16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 93.7656 | 91.2621 | 96.4103 | 87.8429 | 188 | 18 | 188 | 7 | 2 | 28.5714 | |
| jlack-gatk | INDEL | I1_5 | map_l125_m0_e0 | het | 92.8334 | 97.3958 | 88.6792 | 93.3977 | 187 | 5 | 188 | 24 | 0 | 0.0000 | |
| jlack-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 89.3112 | 100.0000 | 80.6867 | 66.4748 | 188 | 0 | 188 | 45 | 44 | 97.7778 | |
| qzeng-custom | INDEL | * | map_l250_m2_e1 | het | 76.6254 | 69.1943 | 85.8447 | 98.2768 | 146 | 65 | 188 | 31 | 16 | 51.6129 | |
| ltrigg-rtg2 | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 95.6898 | 94.0299 | 97.4093 | 80.1031 | 189 | 12 | 188 | 5 | 0 | 0.0000 | |
| mlin-fermikit | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 80.4826 | 84.6154 | 76.7347 | 91.5952 | 187 | 34 | 188 | 57 | 31 | 54.3860 | |
| ndellapenna-hhga | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | homalt | 96.1637 | 95.4315 | 96.9072 | 51.1335 | 188 | 9 | 188 | 6 | 6 | 100.0000 | |
| cchapple-custom | INDEL | * | map_l250_m1_e0 | het | 90.8928 | 93.6842 | 88.2629 | 95.8219 | 178 | 12 | 188 | 25 | 2 | 8.0000 | |
| ckim-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 94.9495 | 100.0000 | 90.3846 | 67.5000 | 188 | 0 | 188 | 20 | 19 | 95.0000 | |
| gduggal-snapvard | INDEL | C1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 0.0000 | 0.0000 | 36.8627 | 88.3108 | 0 | 0 | 188 | 322 | 39 | 12.1118 | |
| egarrison-hhga | INDEL | I1_5 | map_l125_m0_e0 | het | 97.6501 | 97.3958 | 97.9058 | 89.8727 | 187 | 5 | 187 | 4 | 1 | 25.0000 | |
| rpoplin-dv42 | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 93.9862 | 93.5323 | 94.4444 | 85.3550 | 188 | 13 | 187 | 11 | 5 | 45.4545 | |
| gduggal-bwaplat | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | het | 61.6145 | 48.5714 | 84.2342 | 85.1703 | 187 | 198 | 187 | 35 | 5 | 14.2857 | |
| eyeh-varpipe | INDEL | I1_5 | map_l250_m2_e1 | * | 97.1292 | 97.3684 | 96.8912 | 95.0078 | 111 | 3 | 187 | 6 | 5 | 83.3333 | |
| gduggal-bwavard | INDEL | I1_5 | map_l150_m1_e0 | homalt | 96.9151 | 95.4545 | 98.4211 | 81.2808 | 189 | 9 | 187 | 3 | 1 | 33.3333 | |
| gduggal-snapfb | INDEL | * | map_l250_m2_e0 | het | 90.1205 | 89.0476 | 91.2195 | 94.6489 | 187 | 23 | 187 | 18 | 3 | 16.6667 | |
| astatham-gatk | SNP | tv | map_l250_m0_e0 | homalt | 97.3958 | 96.8912 | 97.9058 | 92.3692 | 187 | 6 | 187 | 4 | 3 | 75.0000 | |
| ciseli-custom | INDEL | D1_5 | map_l150_m2_e0 | homalt | 78.2427 | 77.2727 | 79.2373 | 89.5806 | 187 | 55 | 187 | 49 | 40 | 81.6327 | |
| ckim-dragen | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 93.7343 | 99.4681 | 88.6256 | 69.5087 | 187 | 1 | 187 | 24 | 24 | 100.0000 | |
| jlack-gatk | SNP | tv | map_l250_m0_e0 | homalt | 97.1429 | 96.8912 | 97.3958 | 93.0207 | 187 | 6 | 187 | 5 | 3 | 60.0000 | |
| hfeng-pmm2 | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 96.1440 | 99.4681 | 93.0348 | 67.3701 | 187 | 1 | 187 | 14 | 13 | 92.8571 | |
| ndellapenna-hhga | INDEL | I1_5 | map_l125_m0_e0 | het | 98.1627 | 97.3958 | 98.9418 | 89.2062 | 187 | 5 | 187 | 2 | 0 | 0.0000 | |
| qzeng-custom | INDEL | * | map_l250_m2_e0 | het | 76.6664 | 69.0476 | 86.1751 | 98.2597 | 145 | 65 | 187 | 30 | 16 | 53.3333 | |
| ltrigg-rtg2 | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | homalt | 98.1627 | 97.3958 | 98.9418 | 36.7893 | 187 | 5 | 187 | 2 | 0 | 0.0000 | |
| qzeng-custom | INDEL | D6_15 | map_l100_m1_e0 | het | 78.1102 | 88.8889 | 69.6629 | 87.0262 | 112 | 14 | 186 | 81 | 8 | 9.8765 | |
| mlin-fermikit | INDEL | D1_5 | map_l100_m0_e0 | homalt | 70.9924 | 72.0930 | 69.9248 | 75.4613 | 186 | 72 | 186 | 80 | 74 | 92.5000 | |
| mlin-fermikit | INDEL | D6_15 | map_l100_m2_e0 | * | 75.2386 | 70.0758 | 81.2227 | 82.7430 | 185 | 79 | 186 | 43 | 33 | 76.7442 | |
| mlin-fermikit | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 79.4110 | 79.6748 | 79.1489 | 83.7595 | 196 | 50 | 186 | 49 | 46 | 93.8776 | |
| mlin-fermikit | INDEL | I6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 48.6822 | 32.4528 | 97.3822 | 61.4141 | 172 | 358 | 186 | 5 | 5 | 100.0000 | |