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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
18151-18200 / 86044 show all | |||||||||||||||
| astatham-gatk | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 98.2387 | 96.8364 | 99.6823 | 87.5285 | 1255 | 41 | 1255 | 4 | 4 | 100.0000 | |
| gduggal-snapvard | SNP | tv | map_l150_m0_e0 | homalt | 96.9441 | 94.3524 | 99.6823 | 78.3751 | 1253 | 75 | 1255 | 4 | 3 | 75.0000 | |
| jli-custom | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 99.7085 | 99.7349 | 99.6820 | 71.4048 | 1881 | 5 | 1881 | 6 | 3 | 50.0000 | |
| ltrigg-rtg2 | INDEL | * | map_l100_m2_e1 | homalt | 98.6597 | 97.6581 | 99.6820 | 78.7966 | 1251 | 30 | 1254 | 4 | 2 | 50.0000 | |
| raldana-dualsentieon | SNP | tv | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 97.1576 | 94.7581 | 99.6819 | 66.9239 | 940 | 52 | 940 | 3 | 1 | 33.3333 | |
| qzeng-custom | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 87.0799 | 77.3066 | 99.6819 | 40.4484 | 4558 | 1338 | 1880 | 6 | 5 | 83.3333 | |
| qzeng-custom | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 87.0799 | 77.3066 | 99.6819 | 40.4484 | 4558 | 1338 | 1880 | 6 | 5 | 83.3333 | |
| hfeng-pmm2 | SNP | * | map_siren | * | 99.6789 | 99.6758 | 99.6819 | 56.1450 | 145754 | 474 | 145731 | 465 | 62 | 13.3333 | |
| hfeng-pmm3 | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 97.5896 | 95.5833 | 99.6819 | 79.9854 | 6579 | 304 | 6580 | 21 | 4 | 19.0476 | |
| ltrigg-rtg2 | SNP | ti | HG002compoundhet | het | 99.3400 | 99.0005 | 99.6817 | 37.0509 | 9410 | 95 | 9396 | 30 | 8 | 26.6667 | |
| egarrison-hhga | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 99.3357 | 98.9921 | 99.6817 | 59.1116 | 35062 | 357 | 35070 | 112 | 48 | 42.8571 | |
| jlack-gatk | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 95.5817 | 91.8058 | 99.6815 | 70.4887 | 605 | 54 | 626 | 2 | 1 | 50.0000 | |
| jlack-gatk | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 95.5817 | 91.8058 | 99.6815 | 70.4887 | 605 | 54 | 626 | 2 | 1 | 50.0000 | |
| astatham-gatk | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 98.8939 | 98.1187 | 99.6815 | 82.4367 | 4068 | 78 | 4068 | 13 | 7 | 53.8462 | |
| egarrison-hhga | SNP | ti | lowcmp_SimpleRepeat_quadTR_11to50 | * | 99.3832 | 99.0868 | 99.6813 | 36.6712 | 10634 | 98 | 10635 | 34 | 19 | 55.8824 | |
| eyeh-varpipe | SNP | tv | HG002complexvar | * | 99.7847 | 99.8883 | 99.6813 | 20.5762 | 245880 | 275 | 235205 | 752 | 120 | 15.9574 | |
| qzeng-custom | SNP | tv | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.7317 | 99.7821 | 99.6812 | 62.4851 | 10075 | 22 | 10007 | 32 | 21 | 65.6250 | |
| ltrigg-rtg1 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 97.4336 | 95.2855 | 99.6808 | 39.8879 | 19625 | 971 | 19673 | 63 | 52 | 82.5397 | |
| ltrigg-rtg2 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 98.7995 | 97.9339 | 99.6807 | 49.2515 | 31331 | 661 | 31528 | 101 | 86 | 85.1485 | |
| ltrigg-rtg1 | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 97.2881 | 95.0078 | 99.6805 | 52.4677 | 609 | 32 | 624 | 2 | 2 | 100.0000 | |
| dgrover-gatk | SNP | * | map_siren | * | 99.6607 | 99.6410 | 99.6805 | 56.6949 | 145703 | 525 | 145680 | 467 | 103 | 22.0557 | |
| egarrison-hhga | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 57.0126 | 39.9235 | 99.6805 | 45.7539 | 313 | 471 | 312 | 1 | 1 | 100.0000 | |
| hfeng-pmm1 | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_11to50 | * | 98.6301 | 97.6017 | 99.6805 | 67.8645 | 936 | 23 | 936 | 3 | 3 | 100.0000 | |
| hfeng-pmm3 | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_11to50 | * | 98.6301 | 97.6017 | 99.6805 | 67.8425 | 936 | 23 | 936 | 3 | 3 | 100.0000 | |
| jmaeng-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 99.7998 | 99.9198 | 99.6800 | 62.5636 | 2492 | 2 | 2492 | 8 | 0 | 0.0000 | |
| gduggal-bwafb | SNP | * | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 99.6944 | 99.7089 | 99.6800 | 57.2704 | 17127 | 50 | 17130 | 55 | 30 | 54.5455 | |
| astatham-gatk | SNP | * | map_l150_m1_e0 | * | 91.4460 | 84.4686 | 99.6799 | 78.7872 | 25855 | 4754 | 25849 | 83 | 39 | 46.9880 | |
| jpowers-varprowl | SNP | * | map_l125_m2_e0 | homalt | 99.1290 | 98.5842 | 99.6799 | 71.9156 | 17129 | 246 | 17129 | 55 | 40 | 72.7273 | |
| ghariani-varprowl | SNP | * | map_l125_m0_e0 | homalt | 98.5153 | 97.3778 | 99.6797 | 71.5507 | 6536 | 176 | 6536 | 21 | 10 | 47.6190 | |
| gduggal-bwaplat | INDEL | I1_5 | map_l100_m2_e0 | homalt | 73.7841 | 58.5687 | 99.6795 | 89.4166 | 311 | 220 | 311 | 1 | 1 | 100.0000 | |
| jlack-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 98.8871 | 98.1073 | 99.6795 | 84.5007 | 933 | 18 | 933 | 3 | 3 | 100.0000 | |
| cchapple-custom | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 99.4050 | 99.1319 | 99.6795 | 63.7841 | 571 | 5 | 622 | 2 | 2 | 100.0000 | |
| ltrigg-rtg1 | INDEL | * | lowcmp_SimpleRepeat_triTR_11to50 | hetalt | 98.9130 | 98.1582 | 99.6795 | 48.5714 | 906 | 17 | 933 | 3 | 3 | 100.0000 | |
| ltrigg-rtg1 | SNP | * | lowcmp_SimpleRepeat_diTR_11to50 | * | 99.4158 | 99.1539 | 99.6791 | 63.8395 | 9610 | 82 | 9630 | 31 | 5 | 16.1290 | |
| hfeng-pmm2 | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_11to50 | * | 98.4161 | 97.1846 | 99.6791 | 68.7813 | 932 | 27 | 932 | 3 | 3 | 100.0000 | |
| hfeng-pmm1 | SNP | * | map_l125_m1_e0 | * | 99.4583 | 99.2389 | 99.6786 | 68.9911 | 44982 | 345 | 44976 | 145 | 41 | 28.2759 | |
| ckim-gatk | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 99.7702 | 99.8620 | 99.6786 | 64.4814 | 2171 | 3 | 2171 | 7 | 0 | 0.0000 | |
| ckim-vqsr | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 99.7241 | 99.7700 | 99.6783 | 64.5024 | 2169 | 5 | 2169 | 7 | 0 | 0.0000 | |
| ckim-dragen | SNP | tv | * | * | 99.8136 | 99.9495 | 99.6782 | 25.0811 | 969200 | 490 | 969499 | 3130 | 164 | 5.2396 | |
| gduggal-bwafb | SNP | tv | map_l250_m2_e1 | homalt | 98.9350 | 98.2030 | 99.6781 | 89.3193 | 929 | 17 | 929 | 3 | 3 | 100.0000 | |
| ltrigg-rtg1 | INDEL | D1_5 | map_l100_m2_e1 | homalt | 99.5161 | 99.3548 | 99.6779 | 80.8747 | 616 | 4 | 619 | 2 | 2 | 100.0000 | |
| asubramanian-gatk | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 99.6549 | 99.6320 | 99.6779 | 64.1892 | 2166 | 8 | 2166 | 7 | 0 | 0.0000 | |
| rpoplin-dv42 | SNP | tv | HG002compoundhet | het | 99.5284 | 99.3794 | 99.6779 | 54.5836 | 4644 | 29 | 4642 | 15 | 10 | 66.6667 | |
| asubramanian-gatk | SNP | * | map_l125_m2_e1 | het | 51.2109 | 34.4568 | 99.6778 | 92.5521 | 10213 | 19427 | 10210 | 33 | 8 | 24.2424 | |
| bgallagher-sentieon | SNP | ti | lowcmp_SimpleRepeat_triTR_11to50 | het | 99.7984 | 99.9193 | 99.6778 | 30.7392 | 2476 | 2 | 2475 | 8 | 0 | 0.0000 | |
| egarrison-hhga | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 99.5857 | 99.4940 | 99.6776 | 63.2345 | 2163 | 11 | 2164 | 7 | 2 | 28.5714 | |
| raldana-dualsentieon | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 99.4171 | 99.1580 | 99.6775 | 58.2394 | 2473 | 21 | 2473 | 8 | 0 | 0.0000 | |
| ltrigg-rtg2 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 98.4672 | 97.2859 | 99.6775 | 38.9821 | 20037 | 559 | 20088 | 65 | 55 | 84.6154 | |
| asubramanian-gatk | INDEL | I1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | hetalt | 98.0728 | 96.5190 | 99.6774 | 73.3677 | 305 | 11 | 309 | 1 | 1 | 100.0000 | |
| ckim-isaac | SNP | tv | map_l100_m2_e1 | het | 79.3382 | 65.8928 | 99.6774 | 69.5352 | 10502 | 5436 | 10505 | 34 | 8 | 23.5294 | |