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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
5951-6000 / 86044 show all | |||||||||||||||
| astatham-gatk | INDEL | D1_5 | HG002compoundhet | * | 96.5582 | 95.6110 | 97.5244 | 66.3015 | 11698 | 537 | 11700 | 297 | 294 | 98.9899 | |
| astatham-gatk | SNP | * | map_l150_m2_e1 | homalt | 99.3541 | 98.8501 | 99.8633 | 70.8527 | 11691 | 136 | 11691 | 16 | 13 | 81.2500 | |
| anovak-vg | SNP | ti | map_l150_m2_e1 | het | 76.0299 | 89.7810 | 65.9316 | 81.6800 | 11685 | 1330 | 11600 | 5994 | 1333 | 22.2389 | |
| cchapple-custom | INDEL | I1_5 | HG002compoundhet | * | 96.1801 | 94.5694 | 97.8466 | 66.9542 | 11685 | 671 | 13268 | 292 | 281 | 96.2329 | |
| ndellapenna-hhga | INDEL | I1_5 | HG002compoundhet | * | 95.9469 | 94.5452 | 97.3908 | 62.1995 | 11682 | 674 | 11683 | 313 | 258 | 82.4281 | |
| mlin-fermikit | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 81.8009 | 78.9787 | 84.8322 | 50.9671 | 11677 | 3108 | 11678 | 2088 | 2070 | 99.1379 | |
| eyeh-varpipe | SNP | * | map_l150_m2_e0 | homalt | 99.8398 | 99.7949 | 99.8849 | 75.5076 | 11675 | 24 | 11277 | 13 | 8 | 61.5385 | |
| hfeng-pmm2 | SNP | * | map_l150_m2_e0 | homalt | 99.7735 | 99.7863 | 99.7607 | 73.5081 | 11674 | 25 | 11674 | 28 | 11 | 39.2857 | |
| asubramanian-gatk | SNP | ti | segdup | het | 98.1746 | 97.0158 | 99.3614 | 92.7228 | 11671 | 359 | 11669 | 75 | 4 | 5.3333 | |
| ckim-isaac | SNP | ti | segdup | het | 98.4687 | 97.0158 | 99.9657 | 87.9143 | 11671 | 359 | 11671 | 4 | 0 | 0.0000 | |
| hfeng-pmm1 | SNP | * | map_l150_m2_e0 | homalt | 99.7606 | 99.7521 | 99.7692 | 73.4870 | 11670 | 29 | 11670 | 27 | 10 | 37.0370 | |
| hfeng-pmm3 | SNP | * | map_l150_m2_e0 | homalt | 99.7521 | 99.7350 | 99.7691 | 73.4090 | 11668 | 31 | 11668 | 27 | 10 | 37.0370 | |
| gduggal-snapfb | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 80.3731 | 72.7114 | 89.8397 | 50.0523 | 11668 | 4379 | 12441 | 1407 | 1388 | 98.6496 | |
| gduggal-bwaplat | SNP | ti | map_l100_m2_e1 | homalt | 77.3423 | 63.0691 | 99.9657 | 71.0565 | 11664 | 6830 | 11653 | 4 | 4 | 100.0000 | |
| egarrison-hhga | SNP | * | map_l150_m2_e0 | homalt | 99.7775 | 99.6410 | 99.9143 | 73.3265 | 11657 | 42 | 11657 | 10 | 10 | 100.0000 | |
| ltrigg-rtg1 | SNP | * | map_l150_m2_e0 | homalt | 99.7604 | 99.6324 | 99.8886 | 72.6706 | 11656 | 43 | 11658 | 13 | 13 | 100.0000 | |
| hfeng-pmm2 | INDEL | I1_5 | HG002compoundhet | * | 96.1838 | 94.3347 | 98.1069 | 65.2150 | 11656 | 700 | 11660 | 225 | 222 | 98.6667 | |
| eyeh-varpipe | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 83.1973 | 74.7833 | 93.7446 | 68.3849 | 11649 | 3928 | 61758 | 4121 | 4009 | 97.2822 | |
| ltrigg-rtg2 | SNP | * | map_l150_m2_e0 | homalt | 99.7345 | 99.5384 | 99.9314 | 70.4233 | 11645 | 54 | 11647 | 8 | 7 | 87.5000 | |
| mlin-fermikit | SNP | ti | segdup | het | 97.7090 | 96.7914 | 98.6442 | 84.9489 | 11644 | 386 | 11641 | 160 | 0 | 0.0000 | |
| raldana-dualsentieon | SNP | * | map_l150_m2_e0 | homalt | 99.7131 | 99.5213 | 99.9056 | 69.8863 | 11643 | 56 | 11643 | 11 | 8 | 72.7273 | |
| bgallagher-sentieon | SNP | * | map_l150_m2_e0 | homalt | 99.6746 | 99.4871 | 99.8627 | 70.7014 | 11639 | 60 | 11639 | 16 | 12 | 75.0000 | |
| jli-custom | SNP | * | map_l150_m2_e0 | homalt | 99.7002 | 99.4871 | 99.9142 | 70.0015 | 11639 | 60 | 11639 | 10 | 10 | 100.0000 | |
| ndellapenna-hhga | SNP | * | map_l150_m2_e0 | homalt | 99.6916 | 99.4786 | 99.9056 | 72.3853 | 11638 | 61 | 11638 | 11 | 10 | 90.9091 | |
| jli-custom | INDEL | I1_5 | HG002compoundhet | * | 96.2734 | 94.1810 | 98.4609 | 66.0757 | 11637 | 719 | 11643 | 182 | 172 | 94.5055 | |
| gduggal-snapvard | INDEL | I1_5 | HG002complexvar | homalt | 92.5606 | 86.5333 | 99.4905 | 33.4524 | 11637 | 1811 | 10935 | 56 | 51 | 91.0714 | |
| hfeng-pmm1 | INDEL | I1_5 | HG002compoundhet | * | 96.2606 | 94.1648 | 98.4519 | 64.4321 | 11635 | 721 | 11638 | 183 | 176 | 96.1749 | |
| jlack-gatk | SNP | * | map_l150_m2_e1 | homalt | 99.0927 | 98.3512 | 99.8455 | 71.6669 | 11632 | 195 | 11632 | 18 | 13 | 72.2222 | |
| gduggal-bwaplat | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 77.1235 | 65.2618 | 94.2549 | 80.4969 | 11629 | 6190 | 11632 | 709 | 196 | 27.6446 | |
| hfeng-pmm3 | INDEL | I1_5 | HG002compoundhet | * | 96.3303 | 94.1081 | 98.6599 | 63.2057 | 11628 | 728 | 11632 | 158 | 151 | 95.5696 | |
| ltrigg-rtg1 | INDEL | I1_5 | HG002compoundhet | * | 96.6675 | 94.0758 | 99.4060 | 64.7187 | 11624 | 732 | 11547 | 69 | 52 | 75.3623 | |
| ltrigg-rtg1 | SNP | * | map_l150_m0_e0 | * | 98.1003 | 96.5675 | 99.6825 | 69.8517 | 11619 | 413 | 11615 | 37 | 15 | 40.5405 | |
| jpowers-varprowl | SNP | * | map_l150_m2_e1 | homalt | 98.9483 | 98.2413 | 99.6655 | 76.3898 | 11619 | 208 | 11619 | 39 | 26 | 66.6667 | |
| ckim-vqsr | SNP | tv | map_l100_m2_e0 | het | 84.3040 | 73.6198 | 98.6157 | 86.5798 | 11615 | 4162 | 11612 | 163 | 1 | 0.6135 | |
| ghariani-varprowl | SNP | * | map_l150_m2_e1 | homalt | 98.9183 | 98.1990 | 99.6482 | 74.5368 | 11614 | 213 | 11614 | 41 | 25 | 60.9756 | |
| gduggal-bwaplat | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 81.0947 | 69.5121 | 97.3091 | 55.1710 | 11612 | 5093 | 11608 | 321 | 314 | 97.8193 | |
| gduggal-bwaplat | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 81.0947 | 69.5121 | 97.3091 | 55.1710 | 11612 | 5093 | 11608 | 321 | 314 | 97.8193 | |
| ckim-dragen | SNP | * | map_l150_m2_e0 | homalt | 99.4944 | 99.2307 | 99.7595 | 68.4345 | 11609 | 90 | 11614 | 28 | 25 | 89.2857 | |
| gduggal-snapplat | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 44.0360 | 38.0774 | 52.2053 | 83.4017 | 11606 | 18874 | 14180 | 12982 | 2052 | 15.8065 | |
| gduggal-snapplat | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 44.0360 | 38.0774 | 52.2053 | 83.4017 | 11606 | 18874 | 14180 | 12982 | 2052 | 15.8065 | |
| qzeng-custom | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | * | 98.2242 | 97.7347 | 98.7186 | 47.5188 | 11606 | 269 | 11787 | 153 | 107 | 69.9346 | |
| cchapple-custom | INDEL | D1_5 | HG002compoundhet | * | 96.3466 | 94.8427 | 97.8989 | 66.1292 | 11604 | 631 | 12627 | 271 | 261 | 96.3100 | |
| ckim-dragen | INDEL | D1_5 | HG002compoundhet | * | 95.8880 | 94.8263 | 96.9738 | 65.9095 | 11602 | 633 | 11600 | 362 | 359 | 99.1713 | |
| ckim-isaac | SNP | ti | map_l150_m2_e0 | * | 72.1859 | 56.5571 | 99.7506 | 77.5984 | 11601 | 8911 | 11601 | 29 | 5 | 17.2414 | |
| dgrover-gatk | SNP | * | map_l150_m2_e0 | homalt | 99.5153 | 99.1538 | 99.8795 | 71.2083 | 11600 | 99 | 11600 | 14 | 10 | 71.4286 | |
| rpoplin-dv42 | INDEL | D1_5 | HG002compoundhet | * | 95.7563 | 94.7855 | 96.7473 | 62.2778 | 11597 | 638 | 11600 | 390 | 380 | 97.4359 | |
| bgallagher-sentieon | INDEL | D1_5 | HG002compoundhet | * | 95.8155 | 94.7855 | 96.8682 | 66.0428 | 11597 | 638 | 11599 | 375 | 373 | 99.4667 | |
| eyeh-varpipe | SNP | * | map_l100_m0_e0 | homalt | 99.8121 | 99.7935 | 99.8307 | 65.9910 | 11596 | 24 | 11205 | 19 | 8 | 42.1053 | |
| ltrigg-rtg1 | INDEL | D1_5 | HG002compoundhet | * | 96.8842 | 94.7609 | 99.1047 | 63.0486 | 11594 | 641 | 11623 | 105 | 78 | 74.2857 | |
| hfeng-pmm2 | SNP | * | map_l100_m0_e0 | homalt | 99.7504 | 99.7418 | 99.7590 | 63.9103 | 11590 | 30 | 11590 | 28 | 11 | 39.2857 | |