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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
73001-73050 / 86044 show all | |||||||||||||||
| rpoplin-dv42 | SNP | tv | map_l150_m2_e1 | * | 98.9641 | 98.8437 | 99.0847 | 74.8658 | 11369 | 133 | 11367 | 105 | 61 | 58.0952 | |
| jli-custom | SNP | * | map_l250_m0_e0 | homalt | 98.9641 | 98.7281 | 99.2013 | 90.2386 | 621 | 8 | 621 | 5 | 5 | 100.0000 | |
| ndellapenna-hhga | SNP | * | * | hetalt | 98.9643 | 98.7371 | 99.1926 | 47.1341 | 860 | 11 | 860 | 7 | 7 | 100.0000 | |
| ndellapenna-hhga | SNP | tv | * | hetalt | 98.9643 | 98.7371 | 99.1926 | 47.1341 | 860 | 11 | 860 | 7 | 7 | 100.0000 | |
| qzeng-custom | SNP | tv | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 98.9643 | 99.4833 | 98.4507 | 67.9503 | 27535 | 143 | 27515 | 433 | 39 | 9.0069 | |
| qzeng-custom | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 98.9647 | 99.8160 | 98.1279 | 69.9341 | 2170 | 4 | 2149 | 41 | 1 | 2.4390 | |
| hfeng-pmm3 | INDEL | D1_5 | map_l125_m2_e1 | * | 98.9647 | 99.0493 | 98.8803 | 84.7056 | 1146 | 11 | 1148 | 13 | 3 | 23.0769 | |
| ndellapenna-hhga | INDEL | D1_5 | map_l150_m2_e0 | homalt | 98.9648 | 98.7603 | 99.1701 | 87.9077 | 239 | 3 | 239 | 2 | 2 | 100.0000 | |
| egarrison-hhga | INDEL | D1_5 | map_l150_m2_e0 | homalt | 98.9648 | 98.7603 | 99.1701 | 88.7331 | 239 | 3 | 239 | 2 | 2 | 100.0000 | |
| qzeng-custom | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 98.9649 | 98.5390 | 99.3944 | 72.2038 | 16727 | 248 | 16577 | 101 | 58 | 57.4257 | |
| qzeng-custom | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 98.9649 | 98.5390 | 99.3944 | 72.2038 | 16727 | 248 | 16577 | 101 | 58 | 57.4257 | |
| raldana-dualsentieon | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 98.9650 | 99.5196 | 98.4165 | 72.8445 | 1243 | 6 | 1243 | 20 | 16 | 80.0000 | |
| raldana-dualsentieon | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 98.9650 | 99.5196 | 98.4165 | 72.8445 | 1243 | 6 | 1243 | 20 | 16 | 80.0000 | |
| ckim-dragen | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 98.9650 | 99.8245 | 98.1202 | 75.4285 | 30707 | 54 | 30692 | 588 | 582 | 98.9796 | |
| jli-custom | INDEL | I1_5 | map_l125_m1_e0 | het | 98.9652 | 98.3539 | 99.5842 | 84.9452 | 478 | 8 | 479 | 2 | 0 | 0.0000 | |
| hfeng-pmm2 | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 98.9653 | 98.6650 | 99.2674 | 69.4858 | 813 | 11 | 813 | 6 | 1 | 16.6667 | |
| astatham-gatk | INDEL | D16_PLUS | HG002complexvar | homalt | 98.9655 | 99.3080 | 98.6254 | 76.4372 | 287 | 2 | 287 | 4 | 3 | 75.0000 | |
| cchapple-custom | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | het | 98.9656 | 98.4786 | 99.4574 | 53.6403 | 10939 | 169 | 15763 | 86 | 67 | 77.9070 | |
| asubramanian-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 98.9657 | 98.3082 | 99.6321 | 61.0275 | 1627 | 28 | 1625 | 6 | 3 | 50.0000 | |
| jli-custom | SNP | tv | map_l125_m1_e0 | het | 98.9659 | 98.7656 | 99.1670 | 68.7560 | 10001 | 125 | 10000 | 84 | 21 | 25.0000 | |
| hfeng-pmm3 | SNP | * | map_l150_m0_e0 | het | 98.9660 | 98.8665 | 99.0658 | 81.0107 | 7850 | 90 | 7847 | 74 | 2 | 2.7027 | |
| bgallagher-sentieon | SNP | ti | map_l100_m0_e0 | het | 98.9661 | 99.2777 | 98.6565 | 72.6282 | 13882 | 101 | 13879 | 189 | 28 | 14.8148 | |
| ndellapenna-hhga | INDEL | * | map_l125_m2_e1 | homalt | 98.9664 | 98.9664 | 98.9664 | 85.9247 | 766 | 8 | 766 | 8 | 6 | 75.0000 | |
| bgallagher-sentieon | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 98.9665 | 98.7603 | 99.1736 | 69.4830 | 239 | 3 | 240 | 2 | 2 | 100.0000 | |
| mlin-fermikit | SNP | * | * | homalt | 98.9666 | 99.0041 | 98.9290 | 17.0911 | 1168409 | 11753 | 1168425 | 12649 | 12153 | 96.0787 | |
| raldana-dualsentieon | SNP | * | map_l150_m2_e1 | * | 98.9667 | 99.0283 | 98.9052 | 75.6537 | 31897 | 313 | 31891 | 353 | 12 | 3.3994 | |
| astatham-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 98.9667 | 98.0640 | 99.8862 | 50.8114 | 2634 | 52 | 2634 | 3 | 0 | 0.0000 | |
| ndellapenna-hhga | SNP | tv | map_l150_m2_e1 | * | 98.9668 | 98.2699 | 99.6737 | 73.4886 | 11303 | 199 | 11303 | 37 | 17 | 45.9459 | |
| jli-custom | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 98.9669 | 98.4733 | 99.4656 | 72.6845 | 1677 | 26 | 1675 | 9 | 2 | 22.2222 | |
| hfeng-pmm3 | INDEL | D1_5 | HG002complexvar | het | 98.9670 | 98.0448 | 99.9068 | 54.1875 | 20359 | 406 | 20363 | 19 | 11 | 57.8947 | |
| ltrigg-rtg2 | INDEL | * | map_l125_m1_e0 | homalt | 98.9671 | 98.2240 | 99.7214 | 80.0832 | 719 | 13 | 716 | 2 | 1 | 50.0000 | |
| asubramanian-gatk | SNP | tv | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 98.9673 | 98.9982 | 98.9364 | 66.6862 | 17392 | 176 | 17395 | 187 | 18 | 9.6257 | |
| raldana-dualsentieon | INDEL | * | map_l100_m2_e0 | homalt | 98.9674 | 98.8105 | 99.1249 | 82.9559 | 1246 | 15 | 1246 | 11 | 5 | 45.4545 | |
| ckim-vqsr | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 98.9677 | 97.9853 | 99.9699 | 67.4084 | 16633 | 342 | 16633 | 5 | 5 | 100.0000 | |
| ckim-vqsr | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 98.9677 | 97.9853 | 99.9699 | 67.4084 | 16633 | 342 | 16633 | 5 | 5 | 100.0000 | |
| jlack-gatk | SNP | ti | map_l100_m0_e0 | homalt | 98.9685 | 98.1219 | 99.8299 | 59.9927 | 7628 | 146 | 7628 | 13 | 11 | 84.6154 | |
| anovak-vg | SNP | tv | func_cds | homalt | 98.9685 | 98.7676 | 99.1701 | 25.0222 | 1683 | 21 | 1673 | 14 | 11 | 78.5714 | |
| hfeng-pmm3 | SNP | ti | map_l250_m2_e1 | het | 98.9688 | 98.9088 | 99.0288 | 89.4045 | 3263 | 36 | 3263 | 32 | 3 | 9.3750 | |
| dgrover-gatk | SNP | * | map_l150_m2_e0 | het | 98.9689 | 99.1805 | 98.7582 | 81.1353 | 19968 | 165 | 19962 | 251 | 50 | 19.9203 | |
| jli-custom | INDEL | I6_15 | lowcmp_SimpleRepeat_homopolymer_6to10 | homalt | 98.9691 | 97.9592 | 100.0000 | 80.9524 | 48 | 1 | 48 | 0 | 0 | ||
| cchapple-custom | INDEL | I16_PLUS | segdup | * | 98.9691 | 100.0000 | 97.9592 | 95.9098 | 47 | 0 | 48 | 1 | 0 | 0.0000 | |
| hfeng-pmm1 | INDEL | D16_PLUS | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 98.9691 | 100.0000 | 97.9592 | 83.6667 | 52 | 0 | 48 | 1 | 0 | 0.0000 | |
| raldana-dualsentieon | SNP | * | map_l150_m2_e0 | * | 98.9691 | 99.0236 | 98.9147 | 75.5843 | 31541 | 311 | 31535 | 346 | 12 | 3.4682 | |
| rpoplin-dv42 | INDEL | I6_15 | lowcmp_SimpleRepeat_homopolymer_6to10 | homalt | 98.9691 | 97.9592 | 100.0000 | 81.1024 | 48 | 1 | 48 | 0 | 0 | ||
| asubramanian-gatk | INDEL | I6_15 | lowcmp_SimpleRepeat_homopolymer_6to10 | homalt | 98.9691 | 97.9592 | 100.0000 | 81.8182 | 48 | 1 | 48 | 0 | 0 | ||
| jli-custom | SNP | ti | map_l125_m0_e0 | * | 98.9692 | 98.5504 | 99.3915 | 69.4510 | 12577 | 185 | 12577 | 77 | 30 | 38.9610 | |
| ltrigg-rtg1 | SNP | tv | segdup | * | 98.9694 | 99.5663 | 98.3796 | 89.2053 | 8495 | 37 | 8500 | 140 | 20 | 14.2857 | |
| ltrigg-rtg2 | SNP | ti | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 98.9695 | 98.0392 | 99.9176 | 57.2234 | 1200 | 24 | 1213 | 1 | 1 | 100.0000 | |
| egarrison-hhga | INDEL | * | * | homalt | 98.9696 | 99.0301 | 98.9091 | 55.3233 | 123958 | 1214 | 123939 | 1367 | 838 | 61.3021 | |
| ckim-gatk | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 98.9696 | 98.6829 | 99.2581 | 73.7654 | 93205 | 1244 | 93112 | 696 | 583 | 83.7644 | |