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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
66951-67000 / 86044 show all | |||||||||||||||
| asubramanian-gatk | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 91.9411 | 87.7264 | 96.5812 | 72.9667 | 436 | 61 | 565 | 20 | 19 | 95.0000 | |
| asubramanian-gatk | INDEL | I6_15 | * | homalt | 97.0392 | 99.0223 | 95.1340 | 55.6784 | 6178 | 61 | 6178 | 316 | 307 | 97.1519 | |
| asubramanian-gatk | SNP | ti | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 98.7149 | 98.1219 | 99.3151 | 65.8879 | 3187 | 61 | 3190 | 22 | 6 | 27.2727 | |
| bgallagher-sentieon | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 97.1887 | 96.0131 | 98.3936 | 84.9441 | 1469 | 61 | 1470 | 24 | 17 | 70.8333 | |
| bgallagher-sentieon | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 97.1887 | 96.0131 | 98.3936 | 84.9441 | 1469 | 61 | 1470 | 24 | 17 | 70.8333 | |
| bgallagher-sentieon | SNP | ti | map_l100_m2_e0 | homalt | 99.7949 | 99.6668 | 99.9233 | 59.4718 | 18248 | 61 | 18248 | 14 | 12 | 85.7143 | |
| astatham-gatk | INDEL | * | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 99.7775 | 99.6287 | 99.9267 | 58.5881 | 16368 | 61 | 16366 | 12 | 1 | 8.3333 | |
| astatham-gatk | SNP | tv | lowcmp_SimpleRepeat_diTR_11to50 | het | 98.8731 | 98.0246 | 99.7364 | 69.1784 | 3027 | 61 | 3027 | 8 | 7 | 87.5000 | |
| cchapple-custom | INDEL | * | map_l100_m0_e0 | * | 95.2252 | 96.0972 | 94.3688 | 85.7659 | 1502 | 61 | 1525 | 91 | 22 | 24.1758 | |
| cchapple-custom | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 99.7222 | 99.4720 | 99.9738 | 61.6817 | 11491 | 61 | 11440 | 3 | 1 | 33.3333 | |
| cchapple-custom | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 99.7222 | 99.4720 | 99.9738 | 61.6817 | 11491 | 61 | 11440 | 3 | 1 | 33.3333 | |
| ckim-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 97.6681 | 97.1707 | 98.1707 | 76.7832 | 2095 | 61 | 2093 | 39 | 20 | 51.2821 | |
| ckim-gatk | INDEL | * | map_l100_m2_e1 | * | 97.0874 | 98.3759 | 95.8323 | 89.0990 | 3695 | 61 | 3702 | 161 | 20 | 12.4224 | |
| ciseli-custom | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | hetalt | 0.0000 | 11.5942 | 0.0000 | 0.0000 | 8 | 61 | 0 | 0 | 0 | ||
| ciseli-custom | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | hetalt | 0.0000 | 0.0000 | 0.0000 | 0 | 61 | 0 | 0 | 0 | |||
| ciseli-custom | SNP | tv | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 63.5187 | 93.8508 | 48.0041 | 71.9172 | 931 | 61 | 938 | 1016 | 8 | 0.7874 | |
| ckim-dragen | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | het | 99.5579 | 99.4508 | 99.6651 | 63.3945 | 11047 | 61 | 11012 | 37 | 16 | 43.2432 | |
| ckim-gatk | INDEL | I6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 93.8037 | 88.4906 | 99.7955 | 45.1178 | 469 | 61 | 488 | 1 | 1 | 100.0000 | |
| egarrison-hhga | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 96.3335 | 96.2182 | 96.4490 | 61.4990 | 1552 | 61 | 1521 | 56 | 30 | 53.5714 | |
| egarrison-hhga | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 98.2514 | 97.6938 | 98.8154 | 81.5275 | 2584 | 61 | 2586 | 31 | 13 | 41.9355 | |
| dgrover-gatk | INDEL | * | map_l100_m2_e1 | * | 98.3513 | 98.3759 | 98.3267 | 86.6891 | 3695 | 61 | 3702 | 63 | 16 | 25.3968 | |
| dgrover-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 94.9407 | 91.2482 | 98.9446 | 37.9197 | 636 | 61 | 750 | 8 | 8 | 100.0000 | |
| ckim-isaac | INDEL | I1_5 | map_l150_m0_e0 | * | 78.7671 | 65.3409 | 99.1379 | 93.2676 | 115 | 61 | 115 | 1 | 0 | 0.0000 | |
| dgrover-gatk | INDEL | I1_5 | HG002complexvar | het | 99.7798 | 99.6646 | 99.8952 | 58.2404 | 18128 | 61 | 18108 | 19 | 9 | 47.3684 | |
| dgrover-gatk | INDEL | I1_5 | HG002complexvar | hetalt | 98.0896 | 96.4658 | 99.7691 | 70.7729 | 1665 | 61 | 1728 | 4 | 4 | 100.0000 | |
| ckim-isaac | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 85.7762 | 80.3859 | 91.9414 | 59.8529 | 250 | 61 | 251 | 22 | 20 | 90.9091 | |
| ckim-isaac | SNP | ti | func_cds | homalt | 99.4184 | 98.8436 | 100.0000 | 17.1197 | 5214 | 61 | 5214 | 0 | 0 | ||
| ckim-vqsr | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | het | 99.5715 | 99.4508 | 99.6924 | 63.7612 | 11047 | 61 | 11021 | 34 | 16 | 47.0588 | |
| ckim-vqsr | INDEL | * | map_l150_m2_e1 | * | 96.1308 | 95.7609 | 96.5035 | 93.5147 | 1378 | 61 | 1380 | 50 | 7 | 14.0000 | |
| egarrison-hhga | INDEL | * | map_siren | hetalt | 84.9102 | 75.3036 | 97.3262 | 88.3489 | 186 | 61 | 182 | 5 | 4 | 80.0000 | |
| egarrison-hhga | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 79.5694 | 95.6738 | 68.1055 | 61.1370 | 1349 | 61 | 1420 | 665 | 621 | 93.3835 | |
| ckim-vqsr | INDEL | I6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 93.8037 | 88.4906 | 99.7955 | 45.1178 | 469 | 61 | 488 | 1 | 1 | 100.0000 | |
| hfeng-pmm3 | INDEL | I16_PLUS | * | het | 98.6061 | 97.7557 | 99.4715 | 72.8336 | 2657 | 61 | 2635 | 14 | 3 | 21.4286 | |
| hfeng-pmm3 | INDEL | * | lowcmp_SimpleRepeat_quadTR_51to200 | het | 95.4421 | 93.6983 | 97.2521 | 80.7365 | 907 | 61 | 814 | 23 | 16 | 69.5652 | |
| hfeng-pmm3 | INDEL | * | map_l100_m1_e0 | * | 98.6300 | 98.2989 | 98.9633 | 82.3910 | 3525 | 61 | 3532 | 37 | 9 | 24.3243 | |
| hfeng-pmm3 | SNP | tv | map_l150_m1_e0 | het | 99.2002 | 99.1218 | 99.2788 | 75.3081 | 6885 | 61 | 6883 | 50 | 5 | 10.0000 | |
| hfeng-pmm3 | SNP | tv | map_l150_m2_e0 | het | 99.2203 | 99.1589 | 99.2819 | 76.4022 | 7191 | 61 | 7189 | 52 | 5 | 9.6154 | |
| hfeng-pmm3 | SNP | tv | map_l150_m2_e1 | het | 99.2305 | 99.1698 | 99.2913 | 76.4144 | 7287 | 61 | 7285 | 52 | 5 | 9.6154 | |
| hfeng-pmm2 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 99.2445 | 98.8084 | 99.6845 | 73.8057 | 5058 | 61 | 5056 | 16 | 7 | 43.7500 | |
| hfeng-pmm1 | INDEL | D16_PLUS | HG002complexvar | het | 96.2431 | 94.4896 | 98.0630 | 66.6532 | 1046 | 61 | 810 | 16 | 6 | 37.5000 | |
| hfeng-pmm1 | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | * | 97.0579 | 95.3612 | 98.8161 | 48.1800 | 1254 | 61 | 1252 | 15 | 10 | 66.6667 | |
| jlack-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 97.6568 | 96.9051 | 98.4202 | 76.2358 | 1910 | 61 | 1869 | 30 | 19 | 63.3333 | |
| jlack-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 90.5668 | 83.1956 | 99.3711 | 46.1017 | 302 | 61 | 316 | 2 | 1 | 50.0000 | |
| jlack-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 97.6568 | 96.9051 | 98.4202 | 76.2358 | 1910 | 61 | 1869 | 30 | 19 | 63.3333 | |
| jlack-gatk | SNP | * | map_l250_m2_e0 | homalt | 98.6471 | 97.7290 | 99.5827 | 86.9731 | 2625 | 61 | 2625 | 11 | 8 | 72.7273 | |
| jlack-gatk | SNP | tv | map_l150_m1_e0 | homalt | 99.0943 | 98.4288 | 99.7688 | 70.0054 | 3884 | 62 | 3884 | 9 | 6 | 66.6667 | |
| jlack-gatk | INDEL | D16_PLUS | HG002complexvar | * | 96.5938 | 96.2264 | 96.9641 | 66.5839 | 1581 | 62 | 1565 | 49 | 36 | 73.4694 | |
| jlack-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | hetalt | 95.4996 | 92.1816 | 99.0654 | 24.7992 | 731 | 62 | 742 | 7 | 6 | 85.7143 | |
| hfeng-pmm3 | SNP | ti | map_l150_m0_e0 | * | 99.2301 | 99.2113 | 99.2490 | 79.5379 | 7799 | 62 | 7797 | 59 | 6 | 10.1695 | |
| hfeng-pmm2 | INDEL | D1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 99.7626 | 99.5802 | 99.9456 | 54.3815 | 14708 | 62 | 14709 | 8 | 4 | 50.0000 | |