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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
79901-79950 / 86044 show all | |||||||||||||||
| ckim-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 98.7377 | 99.8240 | 97.6748 | 57.4932 | 5671 | 10 | 5671 | 135 | 133 | 98.5185 | |
| ckim-gatk | SNP | ti | * | het | 99.7182 | 99.6780 | 99.7585 | 24.7182 | 1277763 | 4128 | 1277713 | 3093 | 133 | 4.3000 | |
| ndellapenna-hhga | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 88.0130 | 91.8782 | 84.4600 | 56.4024 | 1086 | 96 | 1087 | 200 | 133 | 66.5000 | |
| ndellapenna-hhga | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 96.1705 | 96.3571 | 95.9846 | 35.8391 | 6983 | 264 | 6980 | 292 | 133 | 45.5479 | |
| ndellapenna-hhga | INDEL | I16_PLUS | HG002compoundhet | * | 86.2940 | 82.1745 | 90.8483 | 50.5089 | 1761 | 382 | 1767 | 178 | 133 | 74.7191 | |
| qzeng-custom | SNP | * | map_l100_m2_e0 | homalt | 87.8998 | 78.8141 | 99.3533 | 60.6693 | 21692 | 5831 | 21356 | 139 | 133 | 95.6835 | |
| mlin-fermikit | INDEL | * | lowcmp_SimpleRepeat_homopolymer_6to10 | homalt | 98.7368 | 98.6632 | 98.8105 | 55.8582 | 11145 | 151 | 11131 | 134 | 133 | 99.2537 | |
| mlin-fermikit | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 82.2770 | 90.3226 | 75.5474 | 70.8511 | 476 | 51 | 414 | 134 | 133 | 99.2537 | |
| ckim-vqsr | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 98.6293 | 99.8437 | 97.4442 | 51.1779 | 5109 | 8 | 5109 | 134 | 133 | 99.2537 | |
| ckim-vqsr | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 98.7289 | 99.8064 | 97.6744 | 57.4974 | 5670 | 11 | 5670 | 135 | 133 | 98.5185 | |
| ghariani-varprowl | SNP | ti | map_l150_m1_e0 | * | 97.8236 | 98.3918 | 97.2619 | 78.7439 | 19395 | 317 | 19395 | 546 | 133 | 24.3590 | |
| ghariani-varprowl | SNP | ti | map_l150_m2_e0 | * | 97.8795 | 98.4497 | 97.3158 | 80.1688 | 20194 | 318 | 20194 | 557 | 133 | 23.8779 | |
| gduggal-snapplat | INDEL | D1_5 | HG002complexvar | hetalt | 53.4943 | 40.5325 | 78.6432 | 87.0210 | 548 | 804 | 626 | 170 | 133 | 78.2353 | |
| gduggal-snapfb | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 72.0906 | 64.0796 | 82.3907 | 55.6695 | 644 | 361 | 641 | 137 | 133 | 97.0803 | |
| gduggal-snapfb | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 70.8362 | 61.8574 | 82.8641 | 49.8157 | 373 | 230 | 677 | 140 | 133 | 95.0000 | |
| raldana-dualsentieon | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.6721 | 99.9543 | 99.3915 | 75.2467 | 21889 | 10 | 21889 | 134 | 133 | 99.2537 | |
| rpoplin-dv42 | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 97.9893 | 96.9635 | 99.0370 | 71.9042 | 15104 | 473 | 15118 | 147 | 133 | 90.4762 | |
| rpoplin-dv42 | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 93.9710 | 90.6042 | 97.5975 | 61.3424 | 5728 | 594 | 5728 | 141 | 133 | 94.3262 | |
| rpoplin-dv42 | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 93.9710 | 90.6042 | 97.5975 | 61.3424 | 5728 | 594 | 5728 | 141 | 133 | 94.3262 | |
| rpoplin-dv42 | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | * | 91.6503 | 90.9598 | 92.3513 | 65.0841 | 1630 | 162 | 1630 | 135 | 133 | 98.5185 | |
| jlack-gatk | INDEL | D16_PLUS | * | het | 95.4976 | 98.6705 | 92.5225 | 78.1303 | 3117 | 42 | 2883 | 233 | 133 | 57.0815 | |
| jlack-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 93.3647 | 97.9109 | 89.2219 | 85.2038 | 1781 | 38 | 1548 | 187 | 133 | 71.1230 | |
| jlack-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 93.3647 | 97.9109 | 89.2219 | 85.2038 | 1781 | 38 | 1548 | 187 | 133 | 71.1230 | |
| jlack-gatk | INDEL | I1_5 | HG002compoundhet | het | 90.5365 | 97.8824 | 84.2162 | 85.4468 | 832 | 18 | 779 | 146 | 134 | 91.7808 | |
| jlack-gatk | SNP | * | map_l125_m0_e0 | het | 92.5432 | 98.6576 | 87.1425 | 85.9677 | 12494 | 170 | 12491 | 1843 | 134 | 7.2708 | |
| hfeng-pmm3 | INDEL | I1_5 | * | homalt | 99.7866 | 99.8014 | 99.7717 | 52.1729 | 60308 | 120 | 60313 | 138 | 134 | 97.1014 | |
| ndellapenna-hhga | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 99.3149 | 99.0149 | 99.6167 | 57.6636 | 55083 | 548 | 55098 | 212 | 134 | 63.2075 | |
| mlin-fermikit | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 95.0821 | 95.4655 | 94.7017 | 82.7295 | 3958 | 188 | 3968 | 222 | 134 | 60.3604 | |
| qzeng-custom | SNP | * | map_l100_m2_e1 | homalt | 87.9899 | 78.9574 | 99.3560 | 60.6459 | 21947 | 5849 | 21600 | 140 | 134 | 95.7143 | |
| bgallagher-sentieon | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 98.5576 | 99.9158 | 97.2359 | 49.7376 | 4749 | 4 | 4749 | 135 | 134 | 99.2593 | |
| anovak-vg | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 94.8058 | 95.8213 | 93.8116 | 73.3592 | 2316 | 101 | 2380 | 157 | 134 | 85.3503 | |
| astatham-gatk | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | het | 77.5406 | 92.6531 | 66.6667 | 80.5140 | 454 | 36 | 278 | 139 | 134 | 96.4029 | |
| eyeh-varpipe | INDEL | I16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | het | 32.5233 | 24.3750 | 48.8550 | 47.4950 | 39 | 121 | 128 | 134 | 134 | 100.0000 | |
| gduggal-bwavard | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 92.9844 | 91.6684 | 94.3387 | 81.8623 | 13357 | 1214 | 13181 | 791 | 134 | 16.9406 | |
| gduggal-bwavard | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 92.9844 | 91.6684 | 94.3387 | 81.8623 | 13357 | 1214 | 13181 | 791 | 134 | 16.9406 | |
| gduggal-bwafb | INDEL | I1_5 | HG002complexvar | homalt | 98.3809 | 97.8212 | 98.9471 | 49.0711 | 13155 | 293 | 13156 | 140 | 134 | 95.7143 | |
| gduggal-bwafb | SNP | * | map_l125_m1_e0 | * | 98.8277 | 98.8550 | 98.8005 | 72.4101 | 44808 | 519 | 44808 | 544 | 134 | 24.6324 | |
| eyeh-varpipe | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 91.3695 | 99.3801 | 84.5540 | 81.4321 | 28534 | 178 | 27026 | 4937 | 134 | 2.7142 | |
| eyeh-varpipe | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 91.3695 | 99.3801 | 84.5540 | 81.4321 | 28534 | 178 | 27026 | 4937 | 134 | 2.7142 | |
| eyeh-varpipe | SNP | ti | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 97.8170 | 99.3884 | 96.2946 | 56.5927 | 27788 | 171 | 27079 | 1042 | 134 | 12.8599 | |
| cchapple-custom | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 95.4372 | 94.3693 | 96.5296 | 62.7138 | 3838 | 229 | 4061 | 146 | 134 | 91.7808 | |
| cchapple-custom | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 92.3529 | 89.7315 | 95.1320 | 41.7997 | 2473 | 283 | 2775 | 142 | 134 | 94.3662 | |
| ciseli-custom | SNP | * | map_l125_m2_e0 | het | 76.6942 | 71.0212 | 83.3520 | 81.2570 | 20822 | 8496 | 20798 | 4154 | 134 | 3.2258 | |
| ciseli-custom | SNP | tv | map_l250_m2_e0 | * | 66.4506 | 60.8258 | 73.2218 | 92.3535 | 1753 | 1129 | 1750 | 640 | 134 | 20.9375 | |
| ciseli-custom | SNP | tv | map_l250_m2_e1 | * | 66.5781 | 60.9396 | 73.3664 | 92.3960 | 1777 | 1139 | 1774 | 644 | 134 | 20.8075 | |
| ckim-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_51to200 | * | 85.4055 | 83.0652 | 87.8815 | 45.0961 | 981 | 200 | 979 | 135 | 134 | 99.2593 | |
| cchapple-custom | SNP | tv | map_l100_m2_e1 | * | 97.2075 | 97.9156 | 96.5096 | 71.7543 | 24756 | 527 | 24747 | 895 | 134 | 14.9721 | |
| cchapple-custom | SNP | tv | map_l100_m2_e1 | het | 96.3138 | 98.0926 | 94.5983 | 75.6213 | 15634 | 304 | 15674 | 895 | 134 | 14.9721 | |
| ckim-dragen | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_51to200 | homalt | 70.6140 | 100.0000 | 54.5763 | 33.4086 | 161 | 0 | 161 | 134 | 134 | 100.0000 | |
| egarrison-hhga | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 97.6760 | 96.8929 | 98.4720 | 68.6413 | 15093 | 484 | 15080 | 234 | 134 | 57.2650 | |