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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
31251-31300 / 86044 show all | |||||||||||||||
| ltrigg-rtg1 | INDEL | D16_PLUS | HG002complexvar | * | 95.0986 | 92.0876 | 98.3131 | 57.3034 | 1513 | 130 | 1457 | 25 | 19 | 76.0000 | |
| jli-custom | INDEL | * | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 99.7466 | 99.5860 | 99.9077 | 57.3042 | 28143 | 117 | 28146 | 26 | 19 | 73.0769 | |
| jlack-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | homalt | 99.9638 | 99.9277 | 100.0000 | 57.3061 | 1382 | 1 | 1382 | 0 | 0 | ||
| ndellapenna-hhga | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_51to200 | * | 65.0860 | 56.7347 | 76.3203 | 57.3091 | 417 | 318 | 448 | 139 | 119 | 85.6115 | |
| asubramanian-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 98.2431 | 99.2607 | 97.2461 | 57.3108 | 5639 | 42 | 5650 | 160 | 149 | 93.1250 | |
| ciseli-custom | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 45.1028 | 77.9188 | 31.7367 | 57.3110 | 921 | 261 | 921 | 1981 | 1814 | 91.5699 | |
| hfeng-pmm3 | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 99.8917 | 99.7835 | 100.0000 | 57.3148 | 461 | 1 | 461 | 0 | 0 | ||
| jmaeng-gatk | SNP | * | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 99.7960 | 99.6623 | 99.9299 | 57.3191 | 17119 | 58 | 17115 | 12 | 5 | 41.6667 | |
| jlack-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | homalt | 99.8544 | 100.0000 | 99.7093 | 57.3201 | 343 | 0 | 343 | 1 | 0 | 0.0000 | |
| egarrison-hhga | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 93.9523 | 95.2381 | 92.7007 | 57.3209 | 380 | 19 | 381 | 30 | 18 | 60.0000 | |
| egarrison-hhga | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 80.0812 | 74.2799 | 86.8654 | 57.3222 | 13126 | 4545 | 13260 | 2005 | 1766 | 88.0798 | |
| egarrison-hhga | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 80.0812 | 74.2799 | 86.8654 | 57.3222 | 13126 | 4545 | 13260 | 2005 | 1766 | 88.0798 | |
| egarrison-hhga | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 99.1405 | 99.2515 | 99.0299 | 57.3248 | 1326 | 10 | 1327 | 13 | 3 | 23.0769 | |
| hfeng-pmm3 | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 99.5772 | 99.1580 | 100.0000 | 57.3253 | 2473 | 21 | 2473 | 0 | 0 | ||
| hfeng-pmm3 | INDEL | * | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 99.7891 | 99.6426 | 99.9361 | 57.3259 | 28159 | 101 | 28161 | 18 | 11 | 61.1111 | |
| hfeng-pmm1 | INDEL | I6_15 | HG002complexvar | * | 98.2070 | 97.1411 | 99.2967 | 57.3261 | 4655 | 137 | 4659 | 33 | 33 | 100.0000 | |
| hfeng-pmm1 | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 99.7155 | 99.4327 | 100.0000 | 57.3263 | 3856 | 22 | 3856 | 0 | 0 | ||
| asubramanian-gatk | SNP | * | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 99.3297 | 98.9174 | 99.7455 | 57.3296 | 10964 | 120 | 10972 | 28 | 3 | 10.7143 | |
| hfeng-pmm1 | INDEL | I1_5 | * | * | 99.5147 | 99.2699 | 99.7606 | 57.3300 | 149564 | 1100 | 149609 | 359 | 252 | 70.1950 | |
| mlin-fermikit | SNP | ti | map_l125_m2_e0 | homalt | 66.8459 | 58.0120 | 78.8535 | 57.3303 | 6589 | 4769 | 6589 | 1767 | 1683 | 95.2462 | |
| anovak-vg | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | homalt | 27.6316 | 37.5000 | 21.8750 | 57.3333 | 6 | 10 | 7 | 25 | 17 | 68.0000 | |
| hfeng-pmm2 | INDEL | * | HG002complexvar | * | 99.1003 | 98.4520 | 99.7572 | 57.3339 | 75747 | 1191 | 75614 | 184 | 143 | 77.7174 | |
| dgrover-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 99.5813 | 99.8219 | 99.3418 | 57.3342 | 3924 | 7 | 3924 | 26 | 1 | 3.8462 | |
| ndellapenna-hhga | INDEL | * | HG002compoundhet | het | 62.3220 | 85.8085 | 48.9296 | 57.3342 | 3513 | 581 | 5051 | 5272 | 5065 | 96.0736 | |
| mlin-fermikit | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_51to200 | * | 69.4218 | 66.5306 | 72.5758 | 57.3368 | 489 | 246 | 479 | 181 | 180 | 99.4475 | |
| ckim-gatk | INDEL | * | HG002complexvar | homalt | 99.7525 | 99.8890 | 99.6164 | 57.3371 | 26997 | 30 | 27010 | 104 | 99 | 95.1923 | |
| jpowers-varprowl | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 31.1683 | 21.1733 | 59.0373 | 57.3384 | 1256 | 4676 | 1251 | 868 | 834 | 96.0829 | |
| ckim-dragen | INDEL | I6_15 | HG002complexvar | * | 98.1726 | 97.5167 | 98.8375 | 57.3399 | 4673 | 119 | 4676 | 55 | 54 | 98.1818 | |
| ckim-vqsr | SNP | * | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 99.5470 | 99.1558 | 99.9413 | 57.3410 | 17032 | 145 | 17028 | 10 | 8 | 80.0000 | |
| ckim-vqsr | INDEL | * | HG002complexvar | homalt | 99.7470 | 99.8705 | 99.6237 | 57.3434 | 26992 | 35 | 27005 | 102 | 98 | 96.0784 | |
| ltrigg-rtg2 | SNP | tv | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 99.8349 | 99.7617 | 99.9082 | 57.3447 | 10885 | 26 | 10888 | 10 | 6 | 60.0000 | |
| gduggal-bwavard | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 88.0582 | 79.0032 | 99.4576 | 57.3453 | 1490 | 396 | 1467 | 8 | 7 | 87.5000 | |
| hfeng-pmm1 | INDEL | * | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 99.7696 | 99.5895 | 99.9503 | 57.3476 | 28144 | 116 | 28146 | 14 | 7 | 50.0000 | |
| jli-custom | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 99.2109 | 98.7915 | 99.6339 | 57.3510 | 1635 | 20 | 1633 | 6 | 3 | 50.0000 | |
| gduggal-bwaplat | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 80.8933 | 68.5041 | 98.7531 | 57.3514 | 4039 | 1857 | 4039 | 51 | 49 | 96.0784 | |
| gduggal-bwaplat | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 80.8933 | 68.5041 | 98.7531 | 57.3514 | 4039 | 1857 | 4039 | 51 | 49 | 96.0784 | |
| jlack-gatk | INDEL | D6_15 | func_cds | het | 100.0000 | 100.0000 | 100.0000 | 57.3529 | 29 | 0 | 29 | 0 | 0 | ||
| jlack-gatk | INDEL | I16_PLUS | lowcmp_SimpleRepeat_homopolymer_6to10 | hetalt | 94.6684 | 92.8571 | 96.5517 | 57.3529 | 26 | 2 | 28 | 1 | 1 | 100.0000 | |
| ltrigg-rtg2 | INDEL | * | HG002compoundhet | hetalt | 97.1901 | 94.8491 | 99.6495 | 57.3566 | 23883 | 1297 | 23882 | 84 | 83 | 98.8095 | |
| jmaeng-gatk | INDEL | * | HG002complexvar | homalt | 99.7212 | 99.8779 | 99.5650 | 57.3567 | 26994 | 33 | 27007 | 118 | 111 | 94.0678 | |
| dgrover-gatk | INDEL | * | HG002complexvar | homalt | 99.7765 | 99.9223 | 99.6312 | 57.3581 | 27006 | 21 | 27016 | 100 | 96 | 96.0000 | |
| astatham-gatk | INDEL | * | HG002complexvar | homalt | 99.7747 | 99.9075 | 99.6422 | 57.3610 | 27002 | 25 | 27012 | 97 | 94 | 96.9072 | |
| ckim-gatk | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | * | 85.8873 | 84.9119 | 86.8852 | 57.3613 | 1784 | 317 | 1696 | 256 | 250 | 97.6562 | |
| hfeng-pmm1 | INDEL | * | * | * | 99.3397 | 99.0289 | 99.6526 | 57.3618 | 341196 | 3346 | 341057 | 1189 | 887 | 74.6005 | |
| asubramanian-gatk | INDEL | I1_5 | HG002complexvar | * | 99.2344 | 98.6572 | 99.8183 | 57.3625 | 32915 | 448 | 32967 | 60 | 50 | 83.3333 | |
| ltrigg-rtg1 | SNP | tv | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 99.8395 | 99.7434 | 99.9357 | 57.3637 | 10883 | 28 | 10887 | 7 | 4 | 57.1429 | |
| bgallagher-sentieon | INDEL | * | HG002complexvar | homalt | 99.7010 | 99.9186 | 99.4844 | 57.3638 | 27005 | 22 | 27015 | 140 | 135 | 96.4286 | |
| qzeng-custom | INDEL | D16_PLUS | lowcmp_SimpleRepeat_triTR_51to200 | * | 80.2168 | 80.4348 | 80.0000 | 57.3643 | 37 | 9 | 44 | 11 | 6 | 54.5455 | |
| cchapple-custom | SNP | * | map_l100_m0_e0 | homalt | 98.1150 | 96.3081 | 99.9911 | 57.3704 | 11191 | 429 | 11188 | 1 | 1 | 100.0000 | |
| ltrigg-rtg2 | SNP | tv | map_l125_m2_e1 | het | 98.4798 | 97.2993 | 99.6893 | 57.3735 | 10268 | 285 | 10267 | 32 | 2 | 6.2500 | |