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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
54001-54050 / 86044 show all | |||||||||||||||
| mlin-fermikit | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 84.6414 | 86.8827 | 82.5129 | 86.9736 | 1126 | 170 | 1123 | 238 | 154 | 64.7059 | |
| ckim-gatk | INDEL | D6_15 | map_l100_m1_e0 | homalt | 98.4127 | 96.8750 | 100.0000 | 86.9748 | 62 | 2 | 62 | 0 | 0 | ||
| ckim-vqsr | INDEL | D6_15 | map_l100_m1_e0 | homalt | 98.4127 | 96.8750 | 100.0000 | 86.9748 | 62 | 2 | 62 | 0 | 0 | ||
| egarrison-hhga | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | hetalt | 92.7536 | 86.4865 | 100.0000 | 86.9748 | 32 | 5 | 31 | 0 | 0 | ||
| gduggal-snapfb | INDEL | D1_5 | map_l125_m2_e1 | * | 96.0083 | 96.7156 | 95.3112 | 86.9753 | 1119 | 38 | 1118 | 55 | 9 | 16.3636 | |
| asubramanian-gatk | INDEL | I16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 91.1519 | 95.1220 | 87.5000 | 86.9767 | 39 | 2 | 49 | 7 | 6 | 85.7143 | |
| jmaeng-gatk | INDEL | I16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 95.3125 | 100.0000 | 91.0448 | 86.9776 | 122 | 0 | 122 | 12 | 11 | 91.6667 | |
| raldana-dualsentieon | INDEL | D1_5 | map_l150_m2_e0 | homalt | 98.5386 | 97.5207 | 99.5781 | 86.9780 | 236 | 6 | 236 | 1 | 1 | 100.0000 | |
| egarrison-hhga | INDEL | I16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | het | 86.2319 | 85.0000 | 87.5000 | 86.9801 | 136 | 24 | 126 | 18 | 8 | 44.4444 | |
| jlack-gatk | INDEL | * | map_siren | hetalt | 95.3604 | 91.4980 | 99.5633 | 86.9812 | 226 | 21 | 228 | 1 | 0 | 0.0000 | |
| jmaeng-gatk | SNP | ti | map_l125_m2_e1 | het | 88.9909 | 82.0139 | 97.2654 | 86.9813 | 15654 | 3433 | 15650 | 440 | 39 | 8.8636 | |
| jmaeng-gatk | INDEL | D16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 92.6206 | 97.5940 | 88.1295 | 86.9820 | 649 | 16 | 490 | 66 | 61 | 92.4242 | |
| jmaeng-gatk | SNP | ti | map_l125_m2_e0 | het | 88.8720 | 81.8288 | 97.2418 | 86.9822 | 15446 | 3430 | 15442 | 438 | 39 | 8.9041 | |
| jmaeng-gatk | INDEL | * | map_l125_m2_e0 | homalt | 98.8838 | 98.6894 | 99.0789 | 86.9841 | 753 | 10 | 753 | 7 | 4 | 57.1429 | |
| astatham-gatk | INDEL | * | map_siren | hetalt | 96.8685 | 93.9271 | 100.0000 | 86.9855 | 232 | 15 | 234 | 0 | 0 | ||
| qzeng-custom | SNP | * | map_l100_m0_e0 | het | 82.7631 | 72.8602 | 95.7815 | 86.9859 | 15450 | 5755 | 15326 | 675 | 562 | 83.2593 | |
| rpoplin-dv42 | INDEL | I1_5 | map_l125_m2_e1 | het | 98.1069 | 96.8504 | 99.3964 | 86.9861 | 492 | 16 | 494 | 3 | 2 | 66.6667 | |
| ltrigg-rtg2 | INDEL | C1_5 | HG002complexvar | het | 91.6047 | 85.7143 | 98.3645 | 86.9869 | 6 | 1 | 421 | 7 | 2 | 28.5714 | |
| gduggal-bwaplat | SNP | ti | map_l125_m2_e1 | * | 76.0359 | 61.5656 | 99.3981 | 86.9873 | 18820 | 11749 | 18827 | 114 | 34 | 29.8246 | |
| jli-custom | INDEL | * | map_l125_m2_e1 | het | 98.3616 | 98.0114 | 98.7143 | 86.9876 | 1380 | 28 | 1382 | 18 | 4 | 22.2222 | |
| ckim-vqsr | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 93.9997 | 91.5094 | 96.6292 | 86.9883 | 97 | 9 | 86 | 3 | 3 | 100.0000 | |
| ckim-gatk | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 93.9997 | 91.5094 | 96.6292 | 86.9883 | 97 | 9 | 86 | 3 | 3 | 100.0000 | |
| anovak-vg | INDEL | * | map_l150_m1_e0 | homalt | 76.1726 | 83.7662 | 69.8413 | 86.9894 | 387 | 75 | 396 | 171 | 153 | 89.4737 | |
| gduggal-bwafb | INDEL | I6_15 | map_l125_m2_e0 | homalt | 96.7742 | 100.0000 | 93.7500 | 86.9919 | 15 | 0 | 15 | 1 | 1 | 100.0000 | |
| ckim-dragen | INDEL | I16_PLUS | map_siren | hetalt | 96.7742 | 93.7500 | 100.0000 | 86.9919 | 15 | 1 | 16 | 0 | 0 | ||
| jlack-gatk | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 91.9540 | 90.2256 | 93.7500 | 86.9919 | 120 | 13 | 105 | 7 | 0 | 0.0000 | |
| hfeng-pmm2 | INDEL | I6_15 | map_l100_m1_e0 | homalt | 98.4615 | 96.9697 | 100.0000 | 86.9919 | 32 | 1 | 32 | 0 | 0 | ||
| eyeh-varpipe | INDEL | D1_5 | map_l150_m1_e0 | het | 97.9475 | 98.5477 | 97.3545 | 86.9924 | 475 | 7 | 552 | 15 | 5 | 33.3333 | |
| anovak-vg | INDEL | I1_5 | map_l100_m0_e0 | * | 58.1032 | 59.3002 | 56.9536 | 86.9940 | 322 | 221 | 344 | 260 | 177 | 68.0769 | |
| hfeng-pmm1 | SNP | * | map_l250_m1_e0 | homalt | 99.4527 | 99.5940 | 99.3117 | 86.9979 | 2453 | 10 | 2453 | 17 | 6 | 35.2941 | |
| gduggal-bwafb | INDEL | I6_15 | map_l100_m0_e0 | * | 84.7458 | 75.7576 | 96.1538 | 87.0000 | 25 | 8 | 25 | 1 | 1 | 100.0000 | |
| hfeng-pmm2 | INDEL | D1_5 | map_l125_m2_e1 | * | 98.4147 | 99.1357 | 97.7041 | 87.0012 | 1147 | 10 | 1149 | 27 | 4 | 14.8148 | |
| jlack-gatk | INDEL | I6_15 | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 99.1870 | 98.3871 | 100.0000 | 87.0021 | 61 | 1 | 62 | 0 | 0 | ||
| asubramanian-gatk | INDEL | D1_5 | map_l125_m2_e1 | homalt | 95.8217 | 92.4731 | 99.4220 | 87.0023 | 344 | 28 | 344 | 2 | 1 | 50.0000 | |
| ndellapenna-hhga | SNP | tv | map_l250_m2_e1 | * | 97.9485 | 96.6049 | 99.3300 | 87.0027 | 2817 | 99 | 2817 | 19 | 10 | 52.6316 | |
| asubramanian-gatk | SNP | * | map_l100_m2_e1 | het | 64.0057 | 47.1171 | 99.7652 | 87.0062 | 22097 | 24801 | 22091 | 52 | 14 | 26.9231 | |
| asubramanian-gatk | INDEL | D1_5 | map_l125_m2_e0 | homalt | 95.8748 | 92.5824 | 99.4100 | 87.0065 | 337 | 27 | 337 | 2 | 1 | 50.0000 | |
| jpowers-varprowl | SNP | tv | map_l150_m0_e0 | het | 93.9990 | 95.0405 | 92.9800 | 87.0071 | 2702 | 141 | 2702 | 204 | 53 | 25.9804 | |
| gduggal-bwaplat | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | homalt | 74.4454 | 59.6206 | 99.0826 | 87.0083 | 220 | 149 | 216 | 2 | 1 | 50.0000 | |
| cchapple-custom | INDEL | D6_15 | map_l100_m0_e0 | het | 93.5871 | 96.6667 | 90.6977 | 87.0091 | 58 | 2 | 78 | 8 | 3 | 37.5000 | |
| hfeng-pmm3 | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 95.5521 | 92.6829 | 98.6047 | 87.0091 | 228 | 18 | 212 | 3 | 0 | 0.0000 | |
| jpowers-varprowl | INDEL | D6_15 | map_l100_m2_e1 | het | 73.3945 | 88.8889 | 62.5000 | 87.0095 | 120 | 15 | 120 | 72 | 69 | 95.8333 | |
| gduggal-bwaplat | SNP | ti | map_l125_m2_e0 | * | 75.8315 | 61.2995 | 99.3947 | 87.0105 | 18548 | 11710 | 18555 | 113 | 34 | 30.0885 | |
| bgallagher-sentieon | INDEL | D6_15 | map_l100_m1_e0 | * | 96.3250 | 96.5116 | 96.1390 | 87.0110 | 249 | 9 | 249 | 10 | 2 | 20.0000 | |
| bgallagher-sentieon | INDEL | I1_5 | map_l125_m2_e0 | * | 98.7770 | 98.8331 | 98.7209 | 87.0110 | 847 | 10 | 849 | 11 | 2 | 18.1818 | |
| ltrigg-rtg1 | INDEL | * | map_l150_m0_e0 | * | 95.2820 | 92.2179 | 98.5567 | 87.0112 | 474 | 40 | 478 | 7 | 2 | 28.5714 | |
| qzeng-custom | SNP | * | map_l150_m2_e0 | * | 81.2952 | 70.0678 | 96.8072 | 87.0114 | 22318 | 9534 | 22073 | 728 | 620 | 85.1648 | |
| ndellapenna-hhga | INDEL | I6_15 | map_l100_m2_e0 | homalt | 95.2381 | 90.9091 | 100.0000 | 87.0130 | 30 | 3 | 30 | 0 | 0 | ||
| ckim-dragen | INDEL | I16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 87.9121 | 97.5610 | 80.0000 | 87.0130 | 40 | 1 | 40 | 10 | 9 | 90.0000 | |
| hfeng-pmm2 | SNP | * | map_l250_m1_e0 | homalt | 99.4730 | 99.6346 | 99.3120 | 87.0152 | 2454 | 9 | 2454 | 17 | 6 | 35.2941 | |