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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
46851-46900 / 86044 show all | |||||||||||||||
| ndellapenna-hhga | SNP | ti | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 97.9401 | 97.5296 | 98.3541 | 69.0300 | 1974 | 50 | 1972 | 33 | 5 | 15.1515 | |
| jmaeng-gatk | INDEL | I1_5 | HG002complexvar | hetalt | 91.9469 | 85.2839 | 99.7392 | 69.0289 | 1472 | 254 | 1530 | 4 | 4 | 100.0000 | |
| ltrigg-rtg2 | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 97.8464 | 98.6772 | 97.0296 | 69.0281 | 19320 | 259 | 19501 | 597 | 25 | 4.1876 | |
| ltrigg-rtg2 | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 97.8464 | 98.6772 | 97.0296 | 69.0281 | 19320 | 259 | 19501 | 597 | 25 | 4.1876 | |
| mlin-fermikit | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 91.9790 | 96.8591 | 87.5672 | 69.0278 | 1141 | 37 | 1141 | 162 | 155 | 95.6790 | |
| astatham-gatk | SNP | * | map_l100_m1_e0 | * | 91.9136 | 85.1664 | 99.8219 | 69.0267 | 61663 | 10740 | 61652 | 110 | 52 | 47.2727 | |
| ckim-dragen | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 94.1784 | 93.5471 | 94.8182 | 69.0265 | 9423 | 650 | 9259 | 506 | 472 | 93.2806 | |
| hfeng-pmm1 | SNP | * | map_l125_m2_e0 | homalt | 99.8100 | 99.7928 | 99.8273 | 69.0265 | 17339 | 36 | 17339 | 30 | 12 | 40.0000 | |
| gduggal-snapplat | SNP | tv | HG002compoundhet | het | 71.6435 | 82.9018 | 63.0774 | 69.0248 | 3874 | 799 | 3919 | 2294 | 156 | 6.8004 | |
| gduggal-snapfb | SNP | * | map_l100_m2_e0 | het | 97.2954 | 98.1875 | 96.4194 | 69.0247 | 45558 | 841 | 45562 | 1692 | 659 | 38.9480 | |
| astatham-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 99.6522 | 99.4792 | 99.8258 | 69.0232 | 573 | 3 | 573 | 1 | 1 | 100.0000 | |
| ckim-vqsr | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 94.7235 | 93.8350 | 95.6289 | 69.0222 | 9452 | 621 | 9298 | 425 | 390 | 91.7647 | |
| bgallagher-sentieon | SNP | ti | map_l100_m0_e0 | * | 99.2132 | 99.3340 | 99.0926 | 69.0197 | 21626 | 145 | 21623 | 198 | 35 | 17.6768 | |
| ltrigg-rtg1 | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 98.6415 | 98.1210 | 99.1677 | 69.0182 | 1671 | 32 | 1668 | 14 | 0 | 0.0000 | |
| jmaeng-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 97.3197 | 98.8079 | 95.8756 | 69.0152 | 4393 | 53 | 4347 | 187 | 182 | 97.3262 | |
| gduggal-snapfb | SNP | ti | map_l100_m2_e0 | homalt | 98.4558 | 97.1544 | 99.7924 | 69.0150 | 17788 | 521 | 17789 | 37 | 21 | 56.7568 | |
| ckim-dragen | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 99.8269 | 99.8611 | 99.7927 | 69.0150 | 1438 | 2 | 1444 | 3 | 2 | 66.6667 | |
| dgrover-gatk | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 99.6537 | 99.9306 | 99.3785 | 69.0135 | 1439 | 1 | 1439 | 9 | 0 | 0.0000 | |
| jlack-gatk | INDEL | D16_PLUS | * | homalt | 98.8194 | 98.9362 | 98.7028 | 69.0115 | 1674 | 18 | 1674 | 22 | 15 | 68.1818 | |
| cchapple-custom | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 98.8427 | 98.3427 | 99.3479 | 69.0114 | 47471 | 800 | 76325 | 501 | 389 | 77.6447 | |
| eyeh-varpipe | INDEL | * | HG002compoundhet | het | 65.1467 | 80.9233 | 54.5181 | 69.0092 | 3313 | 781 | 1267 | 1057 | 968 | 91.5799 | |
| ckim-dragen | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 98.2507 | 97.3988 | 99.1176 | 69.0064 | 337 | 9 | 337 | 3 | 2 | 66.6667 | |
| ltrigg-rtg1 | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 85.8671 | 76.8612 | 97.2637 | 69.0054 | 382 | 115 | 391 | 11 | 10 | 90.9091 | |
| eyeh-varpipe | SNP | ti | map_l100_m2_e1 | * | 99.3531 | 99.7211 | 98.9878 | 69.0049 | 49347 | 138 | 48410 | 495 | 32 | 6.4647 | |
| eyeh-varpipe | SNP | tv | map_l100_m1_e0 | * | 97.3811 | 99.7714 | 95.1026 | 69.0013 | 24445 | 56 | 24274 | 1250 | 21 | 1.6800 | |
| ckim-vqsr | INDEL | D16_PLUS | HG002complexvar | het | 98.3872 | 98.7353 | 98.0415 | 69.0000 | 1093 | 14 | 851 | 17 | 10 | 58.8235 | |
| egarrison-hhga | SNP | * | map_l125_m2_e1 | homalt | 99.8144 | 99.7034 | 99.9257 | 69.0000 | 17480 | 52 | 17480 | 13 | 13 | 100.0000 | |
| astatham-gatk | SNP | ti | map_l100_m2_e1 | hetalt | 100.0000 | 100.0000 | 100.0000 | 69.0000 | 31 | 0 | 31 | 0 | 0 | ||
| ndellapenna-hhga | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | homalt | 93.8462 | 89.7059 | 98.3871 | 69.0000 | 61 | 7 | 61 | 1 | 0 | 0.0000 | |
| jlack-gatk | SNP | ti | map_l150_m1_e0 | homalt | 99.0574 | 98.2530 | 99.8751 | 68.9978 | 7199 | 128 | 7199 | 9 | 7 | 77.7778 | |
| qzeng-custom | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 97.9190 | 99.2554 | 96.6182 | 68.9966 | 2666 | 20 | 2657 | 93 | 4 | 4.3011 | |
| qzeng-custom | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 82.7253 | 89.2979 | 77.0540 | 68.9962 | 4464 | 535 | 4755 | 1416 | 413 | 29.1667 | |
| qzeng-custom | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 82.7253 | 89.2979 | 77.0540 | 68.9962 | 4464 | 535 | 4755 | 1416 | 413 | 29.1667 | |
| rpoplin-dv42 | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 99.8360 | 99.8906 | 99.7814 | 68.9936 | 913 | 1 | 913 | 2 | 1 | 50.0000 | |
| jpowers-varprowl | INDEL | I1_5 | HG002compoundhet | * | 10.3239 | 8.1742 | 14.0078 | 68.9924 | 1010 | 11346 | 1001 | 6145 | 6014 | 97.8682 | |
| egarrison-hhga | SNP | ti | map_l125_m1_e0 | * | 99.4628 | 99.0932 | 99.8351 | 68.9921 | 29069 | 266 | 29069 | 48 | 24 | 50.0000 | |
| eyeh-varpipe | SNP | ti | map_l100_m2_e0 | * | 99.3504 | 99.7181 | 98.9854 | 68.9913 | 48823 | 138 | 47903 | 491 | 32 | 6.5173 | |
| hfeng-pmm1 | SNP | * | map_l125_m1_e0 | * | 99.4583 | 99.2389 | 99.6786 | 68.9911 | 44982 | 345 | 44976 | 145 | 41 | 28.2759 | |
| ltrigg-rtg2 | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 98.0423 | 99.2126 | 96.8992 | 68.9904 | 126 | 1 | 125 | 4 | 0 | 0.0000 | |
| gduggal-snapfb | SNP | ti | map_l100_m2_e1 | homalt | 98.4714 | 97.1829 | 99.7946 | 68.9893 | 17973 | 521 | 17974 | 37 | 21 | 56.7568 | |
| ghariani-varprowl | SNP | ti | map_l100_m1_e0 | * | 98.6066 | 98.9944 | 98.2219 | 68.9891 | 47449 | 482 | 47451 | 859 | 183 | 21.3038 | |
| mlin-fermikit | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 95.2598 | 94.5285 | 96.0025 | 68.9889 | 29439 | 1704 | 29443 | 1226 | 756 | 61.6639 | |
| mlin-fermikit | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 95.2598 | 94.5285 | 96.0025 | 68.9889 | 29439 | 1704 | 29443 | 1226 | 756 | 61.6639 | |
| eyeh-varpipe | INDEL | * | lowcmp_SimpleRepeat_quadTR_51to200 | het | 66.0791 | 54.5455 | 83.7981 | 68.9868 | 528 | 440 | 631 | 122 | 64 | 52.4590 | |
| cchapple-custom | SNP | ti | map_l100_m2_e1 | * | 97.7339 | 97.6781 | 97.7898 | 68.9863 | 48336 | 1149 | 48316 | 1092 | 276 | 25.2747 | |
| bgallagher-sentieon | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 99.7394 | 99.6528 | 99.8261 | 68.9860 | 574 | 2 | 574 | 1 | 1 | 100.0000 | |
| mlin-fermikit | SNP | ti | map_l150_m2_e0 | het | 55.8942 | 39.0731 | 98.1471 | 68.9855 | 5033 | 7848 | 5032 | 95 | 5 | 5.2632 | |
| gduggal-bwavard | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 46.3415 | 30.3191 | 98.2759 | 68.9840 | 57 | 131 | 57 | 1 | 1 | 100.0000 | |
| ckim-dragen | SNP | ti | map_l100_m2_e1 | * | 98.6777 | 99.2968 | 98.0664 | 68.9837 | 49137 | 348 | 49145 | 969 | 108 | 11.1455 | |
| ckim-vqsr | SNP | ti | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 98.9599 | 98.7154 | 99.2056 | 68.9820 | 1998 | 26 | 1998 | 16 | 7 | 43.7500 | |