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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
1001-1050 / 86044 show all | |||||||||||||||
| gduggal-bwavard | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 85.7527 | 75.1764 | 99.7922 | 61.3457 | 23125 | 7636 | 23046 | 48 | 38 | 79.1667 | |
| ckim-gatk | SNP | * | map_l100_m2_e1 | homalt | 84.0675 | 72.5428 | 99.9455 | 68.3772 | 20164 | 7632 | 20164 | 11 | 7 | 63.6364 | |
| ckim-gatk | SNP | * | map_l100_m2_e0 | homalt | 83.9525 | 72.3722 | 99.9448 | 68.4557 | 19919 | 7604 | 19919 | 11 | 7 | 63.6364 | |
| ciseli-custom | SNP | * | map_l100_m0_e0 | * | 81.1632 | 76.8673 | 85.9677 | 74.4366 | 25244 | 7597 | 25198 | 4113 | 1141 | 27.7413 | |
| ckim-vqsr | SNP | tv | map_l125_m2_e0 | * | 69.7523 | 53.9693 | 98.5819 | 89.6043 | 8899 | 7590 | 8898 | 128 | 1 | 0.7813 | |
| anovak-vg | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 0.0000 | 27.5800 | 0.0000 | 0.0000 | 2889 | 7586 | 0 | 0 | 0 | ||
| qzeng-custom | SNP | tv | * | * | 99.4379 | 99.2180 | 99.6588 | 26.4392 | 962115 | 7583 | 958619 | 3282 | 549 | 16.7276 | |
| ckim-gatk | SNP | * | map_l100_m1_e0 | homalt | 83.6574 | 71.9327 | 99.9485 | 66.2938 | 19424 | 7579 | 19424 | 10 | 7 | 70.0000 | |
| jmaeng-gatk | SNP | * | map_l100_m2_e1 | homalt | 84.2134 | 72.7551 | 99.9555 | 67.5514 | 20223 | 7573 | 20223 | 9 | 8 | 88.8889 | |
| ckim-gatk | SNP | ti | map_l125_m2_e1 | * | 85.1950 | 75.2331 | 98.1978 | 84.5085 | 22998 | 7571 | 22994 | 422 | 45 | 10.6635 | |
| jmaeng-gatk | SNP | ti | map_l125_m2_e1 | * | 85.1656 | 75.2364 | 98.1141 | 84.6685 | 22999 | 7570 | 22995 | 442 | 41 | 9.2760 | |
| qzeng-custom | SNP | * | map_l125_m2_e1 | het | 84.1292 | 74.4636 | 96.6784 | 86.6172 | 22071 | 7569 | 21888 | 752 | 615 | 81.7819 | |
| mlin-fermikit | SNP | ti | * | homalt | 99.0118 | 99.0588 | 98.9648 | 15.5441 | 795481 | 7558 | 795502 | 8321 | 8052 | 96.7672 | |
| ckim-gatk | SNP | ti | map_l125_m2_e0 | * | 85.0542 | 75.0248 | 98.1789 | 84.5122 | 22701 | 7557 | 22697 | 421 | 45 | 10.6888 | |
| jmaeng-gatk | SNP | ti | map_l125_m2_e0 | * | 85.0261 | 75.0281 | 98.0984 | 84.6739 | 22702 | 7556 | 22698 | 440 | 41 | 9.3182 | |
| jmaeng-gatk | SNP | * | map_l100_m2_e0 | homalt | 84.0977 | 72.5829 | 99.9550 | 67.6272 | 19977 | 7546 | 19977 | 9 | 8 | 88.8889 | |
| ckim-isaac | SNP | tv | map_siren | het | 84.7375 | 73.6377 | 99.7775 | 56.9492 | 21067 | 7542 | 21072 | 47 | 12 | 25.5319 | |
| qzeng-custom | SNP | * | map_l125_m2_e0 | het | 84.0186 | 74.3127 | 96.6407 | 86.6277 | 21787 | 7531 | 21605 | 751 | 614 | 81.7577 | |
| jmaeng-gatk | SNP | * | map_l100_m1_e0 | homalt | 83.8037 | 72.1438 | 99.9590 | 65.3578 | 19481 | 7522 | 19481 | 8 | 8 | 100.0000 | |
| jmaeng-gatk | SNP | ti | map_l125_m1_e0 | * | 84.6118 | 74.3855 | 98.0980 | 83.7120 | 21821 | 7514 | 21817 | 423 | 41 | 9.6927 | |
| ckim-gatk | SNP | ti | map_l125_m1_e0 | * | 84.6397 | 74.3855 | 98.1731 | 83.5274 | 21821 | 7514 | 21817 | 406 | 44 | 10.8374 | |
| gduggal-snapplat | SNP | ti | * | homalt | 99.4971 | 99.0644 | 99.9337 | 17.3977 | 795526 | 7513 | 795327 | 528 | 217 | 41.0985 | |
| jpowers-varprowl | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 35.3007 | 32.2054 | 39.0543 | 51.0895 | 3569 | 7513 | 3568 | 5568 | 5531 | 99.3355 | |
| mlin-fermikit | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 92.8446 | 92.0624 | 93.6403 | 70.3210 | 86952 | 7497 | 86813 | 5896 | 5729 | 97.1676 | |
| ckim-vqsr | SNP | tv | map_l125_m1_e0 | * | 69.0966 | 53.2030 | 98.5313 | 88.9389 | 8521 | 7495 | 8520 | 127 | 1 | 0.7874 | |
| ckim-isaac | SNP | tv | map_l125_m2_e1 | * | 70.9236 | 55.0459 | 99.6739 | 73.8556 | 9169 | 7488 | 9171 | 30 | 9 | 30.0000 | |
| ckim-vqsr | SNP | ti | map_l100_m2_e1 | het | 85.9506 | 75.8301 | 99.1886 | 83.8404 | 23477 | 7483 | 23472 | 192 | 12 | 6.2500 | |
| gduggal-snapplat | INDEL | I6_15 | * | het | 35.6936 | 25.4959 | 59.4871 | 60.4118 | 2558 | 7475 | 2505 | 1706 | 46 | 2.6964 | |
| astatham-gatk | SNP | * | map_l125_m2_e1 | * | 91.3125 | 84.1829 | 99.7615 | 76.3148 | 39736 | 7466 | 39730 | 95 | 43 | 45.2632 | |
| ciseli-custom | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 62.2772 | 53.6141 | 74.2796 | 69.6025 | 8619 | 7457 | 8378 | 2901 | 2024 | 69.7690 | |
| ciseli-custom | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 62.2772 | 53.6141 | 74.2796 | 69.6025 | 8619 | 7457 | 8378 | 2901 | 2024 | 69.7690 | |
| qzeng-custom | SNP | * | map_l125_m1_e0 | het | 83.6399 | 73.7567 | 96.5816 | 86.1149 | 20941 | 7451 | 20766 | 735 | 611 | 83.1293 | |
| gduggal-bwavard | SNP | ti | * | homalt | 99.5201 | 99.0724 | 99.9718 | 15.7269 | 795590 | 7449 | 791466 | 223 | 186 | 83.4081 | |
| gduggal-snapvard | INDEL | D1_5 | * | homalt | 90.7791 | 84.7811 | 97.6903 | 44.1687 | 41480 | 7446 | 44115 | 1043 | 1010 | 96.8360 | |
| ckim-vqsr | SNP | ti | map_l100_m2_e0 | het | 85.8634 | 75.7005 | 99.1784 | 83.8574 | 23181 | 7441 | 23176 | 192 | 12 | 6.2500 | |
| ckim-isaac | SNP | tv | map_l125_m2_e0 | * | 70.8343 | 54.9397 | 99.6700 | 73.8494 | 9059 | 7430 | 9061 | 30 | 9 | 30.0000 | |
| ckim-isaac | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 94.4269 | 92.1672 | 96.8002 | 61.2699 | 87051 | 7398 | 86368 | 2855 | 2059 | 72.1191 | |
| anovak-vg | INDEL | I6_15 | * | het | 35.7228 | 26.3530 | 55.4313 | 44.2246 | 2644 | 7389 | 4312 | 3467 | 1789 | 51.6008 | |
| astatham-gatk | SNP | * | map_l125_m2_e0 | * | 91.3143 | 84.1877 | 99.7590 | 76.2743 | 39335 | 7388 | 39329 | 95 | 43 | 45.2632 | |
| ckim-vqsr | SNP | ti | map_l100_m1_e0 | het | 85.6453 | 75.3523 | 99.1953 | 82.9534 | 22562 | 7380 | 22557 | 183 | 10 | 5.4645 | |
| eyeh-varpipe | INDEL | D6_15 | * | * | 75.4633 | 71.7500 | 79.5820 | 47.2482 | 18721 | 7371 | 18658 | 4787 | 4643 | 96.9919 | |
| gduggal-snapvard | INDEL | I6_15 | HG002compoundhet | * | 20.6071 | 16.5147 | 27.3957 | 31.7261 | 1449 | 7325 | 1478 | 3917 | 3324 | 84.8609 | |
| gduggal-snapvard | INDEL | I1_5 | HG002compoundhet | * | 44.4193 | 40.7689 | 48.7878 | 63.5182 | 5037 | 7318 | 5393 | 5661 | 4783 | 84.4904 | |
| gduggal-snapvard | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 59.1721 | 54.4401 | 64.8052 | 53.7673 | 8736 | 7311 | 8947 | 4859 | 4228 | 87.0138 | |
| mlin-fermikit | SNP | * | map_l125_m2_e1 | homalt | 66.2819 | 58.2991 | 76.7977 | 57.4167 | 10221 | 7311 | 10221 | 3088 | 2926 | 94.7539 | |
| ckim-isaac | SNP | tv | map_l125_m1_e0 | * | 70.3696 | 54.3831 | 99.6682 | 71.7978 | 8710 | 7306 | 8712 | 29 | 9 | 31.0345 | |
| astatham-gatk | SNP | * | map_l125_m2_e1 | het | 85.8279 | 75.3644 | 99.6653 | 80.7852 | 22338 | 7302 | 22332 | 75 | 27 | 36.0000 | |
| ckim-isaac | SNP | ti | map_l100_m2_e1 | homalt | 75.4653 | 60.6143 | 99.9554 | 56.7172 | 11210 | 7284 | 11210 | 5 | 5 | 100.0000 | |
| mlin-fermikit | SNP | * | map_l125_m2_e0 | homalt | 66.1120 | 58.0777 | 76.7260 | 57.2932 | 10091 | 7284 | 10091 | 3061 | 2900 | 94.7403 | |
| ghariani-varprowl | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 63.8421 | 54.7304 | 76.5939 | 75.6642 | 8799 | 7278 | 8770 | 2680 | 2299 | 85.7836 | |