PrecisionFDA
Truth Challenge
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Explore HG002 comparison results
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| Entry | Type | Subtype | Subset | Genotype | F-score | Recall | Precision | Frac_NA | Truth TP | Truth FN | Query TP | Query FP | FP gt | % FP ma | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
52451-52500 / 86044 show all | |||||||||||||||
| gduggal-bwafb | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 41.8118 | 28.3019 | 80.0000 | 60.9375 | 15 | 38 | 20 | 5 | 5 | 100.0000 | |
| dgrover-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 94.3538 | 99.2084 | 89.9522 | 60.9346 | 376 | 3 | 376 | 42 | 42 | 100.0000 | |
| jli-custom | INDEL | I16_PLUS | HG002complexvar | het | 94.3784 | 89.7744 | 99.4801 | 60.9343 | 597 | 68 | 574 | 3 | 0 | 0.0000 | |
| raldana-dualsentieon | SNP | tv | map_l100_m2_e0 | homalt | 99.8479 | 99.7612 | 99.9348 | 60.9327 | 9192 | 22 | 9192 | 6 | 3 | 50.0000 | |
| ckim-gatk | SNP | tv | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 99.7448 | 99.5473 | 99.9432 | 60.9323 | 1759 | 8 | 1759 | 1 | 1 | 100.0000 | |
| anovak-vg | SNP | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 95.6272 | 95.0801 | 96.1806 | 60.9315 | 1662 | 86 | 1662 | 66 | 49 | 74.2424 | |
| hfeng-pmm2 | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | * | 98.5441 | 97.3505 | 99.7673 | 60.9276 | 1286 | 35 | 1286 | 3 | 1 | 33.3333 | |
| anovak-vg | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 86.4894 | 84.3750 | 88.7125 | 60.9235 | 486 | 90 | 503 | 64 | 41 | 64.0625 | |
| ciseli-custom | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 71.6876 | 76.6436 | 67.3336 | 60.9234 | 11203 | 3414 | 12081 | 5861 | 3450 | 58.8637 | |
| ckim-isaac | SNP | tv | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 96.3802 | 93.5166 | 99.4246 | 60.9201 | 16429 | 1139 | 16588 | 96 | 15 | 15.6250 | |
| jmaeng-gatk | INDEL | * | * | * | 99.1098 | 99.0216 | 99.1981 | 60.9184 | 341171 | 3371 | 341038 | 2757 | 1621 | 58.7958 | |
| ciseli-custom | INDEL | I6_15 | HG002complexvar | het | 39.0345 | 26.1146 | 77.2559 | 60.9179 | 615 | 1740 | 625 | 184 | 138 | 75.0000 | |
| anovak-vg | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 26.5613 | 34.4262 | 21.6216 | 60.9155 | 21 | 40 | 24 | 87 | 40 | 45.9770 | |
| cchapple-custom | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 99.2564 | 99.6414 | 98.8744 | 60.9154 | 35292 | 127 | 35487 | 404 | 50 | 12.3762 | |
| gduggal-snapplat | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 56.1615 | 41.5637 | 86.5642 | 60.9124 | 3397 | 4776 | 3434 | 533 | 458 | 85.9287 | |
| raldana-dualsentieon | SNP | tv | map_l100_m2_e1 | homalt | 99.8494 | 99.7635 | 99.9354 | 60.9109 | 9280 | 22 | 9280 | 6 | 3 | 50.0000 | |
| jlack-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 98.6126 | 98.8520 | 98.3745 | 60.9084 | 1636 | 19 | 1634 | 27 | 12 | 44.4444 | |
| ciseli-custom | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 85.0321 | 87.0220 | 83.1312 | 60.9052 | 751 | 112 | 754 | 153 | 72 | 47.0588 | |
| ghariani-varprowl | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 82.6345 | 81.9473 | 83.3333 | 60.9010 | 404 | 89 | 405 | 81 | 78 | 96.2963 | |
| asubramanian-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 96.8292 | 99.0334 | 94.7210 | 60.8998 | 11373 | 111 | 11986 | 668 | 500 | 74.8503 | |
| mlin-fermikit | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 95.8242 | 95.3125 | 96.3415 | 60.8992 | 549 | 27 | 553 | 21 | 19 | 90.4762 | |
| ghariani-varprowl | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 45.3446 | 44.0478 | 46.7201 | 60.8982 | 16695 | 21207 | 16673 | 19014 | 18688 | 98.2855 | |
| jpowers-varprowl | INDEL | * | * | het | 88.4014 | 94.9432 | 82.7031 | 60.8976 | 184316 | 9817 | 184394 | 38565 | 37886 | 98.2393 | |
| anovak-vg | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 37.5202 | 27.1605 | 60.6557 | 60.8974 | 22 | 59 | 37 | 24 | 17 | 70.8333 | |
| gduggal-bwafb | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 33.0430 | 20.5706 | 83.9344 | 60.8974 | 137 | 529 | 256 | 49 | 49 | 100.0000 | |
| gduggal-bwafb | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 33.0430 | 20.5706 | 83.9344 | 60.8974 | 137 | 529 | 256 | 49 | 49 | 100.0000 | |
| qzeng-custom | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 88.7617 | 87.5000 | 90.0602 | 60.8952 | 252 | 36 | 598 | 66 | 60 | 90.9091 | |
| jmaeng-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 99.8583 | 99.9226 | 99.7940 | 60.8923 | 3875 | 3 | 3875 | 8 | 0 | 0.0000 | |
| hfeng-pmm2 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 97.4023 | 95.4216 | 99.4669 | 60.8921 | 8024 | 385 | 8023 | 43 | 32 | 74.4186 | |
| cchapple-custom | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 98.6906 | 99.4825 | 97.9112 | 60.8903 | 18072 | 94 | 18047 | 385 | 366 | 95.0649 | |
| cchapple-custom | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 98.6906 | 99.4825 | 97.9112 | 60.8903 | 18072 | 94 | 18047 | 385 | 366 | 95.0649 | |
| egarrison-hhga | SNP | * | map_l100_m1_e0 | homalt | 99.8480 | 99.7630 | 99.9332 | 60.8894 | 26939 | 64 | 26939 | 18 | 17 | 94.4444 | |
| rpoplin-dv42 | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 99.7230 | 99.7230 | 99.7230 | 60.8884 | 360 | 1 | 360 | 1 | 0 | 0.0000 | |
| ckim-isaac | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 94.4491 | 90.7138 | 98.5051 | 60.8883 | 28251 | 2892 | 28401 | 431 | 172 | 39.9072 | |
| ckim-isaac | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 94.4491 | 90.7138 | 98.5051 | 60.8883 | 28251 | 2892 | 28401 | 431 | 172 | 39.9072 | |
| gduggal-snapplat | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 56.3564 | 39.9149 | 95.8304 | 60.8880 | 2719 | 4093 | 2735 | 119 | 102 | 85.7143 | |
| ltrigg-rtg2 | INDEL | I1_5 | lowcmp_SimpleRepeat_triTR_11to50 | het | 99.2454 | 98.9362 | 99.5565 | 60.8846 | 465 | 5 | 449 | 2 | 0 | 0.0000 | |
| ltrigg-rtg2 | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 99.4816 | 99.3427 | 99.6209 | 60.8825 | 1058 | 7 | 1051 | 4 | 2 | 50.0000 | |
| gduggal-bwafb | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 91.1270 | 87.3774 | 95.2128 | 60.8815 | 57102 | 8249 | 63963 | 3216 | 2822 | 87.7488 | |
| gduggal-bwafb | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 91.1270 | 87.3774 | 95.2128 | 60.8815 | 57102 | 8249 | 63963 | 3216 | 2822 | 87.7488 | |
| gduggal-snapfb | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 86.7363 | 86.3984 | 87.0769 | 60.8804 | 27136 | 4272 | 28091 | 4169 | 1922 | 46.1022 | |
| gduggal-snapfb | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 86.7363 | 86.3984 | 87.0769 | 60.8804 | 27136 | 4272 | 28091 | 4169 | 1922 | 46.1022 | |
| ndellapenna-hhga | INDEL | D1_5 | HG002compoundhet | * | 69.2944 | 67.8709 | 70.7788 | 60.8775 | 8304 | 3931 | 8388 | 3463 | 3380 | 97.6032 | |
| hfeng-pmm1 | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 99.2565 | 99.2593 | 99.2537 | 60.8759 | 268 | 2 | 266 | 2 | 0 | 0.0000 | |
| jlack-gatk | SNP | tv | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.8910 | 99.8415 | 99.9405 | 60.8743 | 10081 | 16 | 10081 | 6 | 6 | 100.0000 | |
| mlin-fermikit | SNP | * | map_l125_m1_e0 | het | 60.7541 | 43.9737 | 98.2445 | 60.8741 | 12485 | 15907 | 12480 | 223 | 8 | 3.5874 | |
| qzeng-custom | SNP | tv | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 99.6831 | 99.5234 | 99.8433 | 60.8736 | 10859 | 52 | 10830 | 17 | 7 | 41.1765 | |
| ckim-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_homopolymer_6to10 | hetalt | 95.8904 | 94.5946 | 97.2222 | 60.8696 | 35 | 2 | 35 | 1 | 1 | 100.0000 | |
| hfeng-pmm2 | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_51to200 | homalt | 96.5174 | 95.0980 | 97.9798 | 60.8696 | 97 | 5 | 97 | 2 | 2 | 100.0000 | |
| eyeh-varpipe | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 40.8000 | 26.0204 | 94.4444 | 60.8696 | 204 | 580 | 306 | 18 | 18 | 100.0000 | |