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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
2251-2300 / 86044 show all | |||||||||||||||
| hfeng-pmm3 | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.7158 | 99.7919 | 99.6397 | 70.7329 | 30697 | 64 | 30697 | 111 | 106 | 95.4955 | |
| jli-custom | SNP | ti | map_l100_m2_e1 | het | 99.3237 | 99.1505 | 99.4976 | 64.3340 | 30697 | 263 | 30695 | 155 | 38 | 24.5161 | |
| ndellapenna-hhga | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 98.8647 | 98.5647 | 99.1665 | 69.0402 | 30696 | 447 | 30695 | 258 | 94 | 36.4341 | |
| ndellapenna-hhga | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 98.8647 | 98.5647 | 99.1665 | 69.0402 | 30696 | 447 | 30695 | 258 | 94 | 36.4341 | |
| hfeng-pmm2 | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.6591 | 99.7822 | 99.5363 | 71.5494 | 30694 | 67 | 30694 | 143 | 139 | 97.2028 | |
| raldana-dualsentieon | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 99.0544 | 98.5583 | 99.5556 | 65.3417 | 30694 | 449 | 30694 | 137 | 9 | 6.5693 | |
| raldana-dualsentieon | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 99.0544 | 98.5583 | 99.5556 | 65.3417 | 30694 | 449 | 30694 | 137 | 9 | 6.5693 | |
| ckim-dragen | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 98.9650 | 99.8245 | 98.1202 | 75.4285 | 30707 | 54 | 30692 | 588 | 582 | 98.9796 | |
| raldana-dualsentieon | SNP | ti | map_l100_m2_e1 | het | 99.0592 | 99.1473 | 98.9712 | 67.5574 | 30696 | 264 | 30689 | 319 | 6 | 1.8809 | |
| rpoplin-dv42 | SNP | ti | map_l100_m2_e1 | het | 99.3494 | 99.1473 | 99.5523 | 65.6527 | 30696 | 264 | 30688 | 138 | 83 | 60.1449 | |
| hfeng-pmm1 | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.6995 | 99.7594 | 99.6396 | 71.1645 | 30687 | 74 | 30687 | 111 | 109 | 98.1982 | |
| bgallagher-sentieon | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 98.2203 | 97.7012 | 98.7450 | 60.3971 | 30686 | 722 | 30686 | 390 | 372 | 95.3846 | |
| bgallagher-sentieon | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 98.2203 | 97.7012 | 98.7450 | 60.3971 | 30686 | 722 | 30686 | 390 | 372 | 95.3846 | |
| jlack-gatk | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.1165 | 99.7497 | 98.4914 | 72.1867 | 30684 | 77 | 30684 | 470 | 460 | 97.8723 | |
| ndellapenna-hhga | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 89.7592 | 95.7940 | 84.4397 | 65.4433 | 29198 | 1282 | 30682 | 5654 | 5190 | 91.7934 | |
| ndellapenna-hhga | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 89.7592 | 95.7940 | 84.4397 | 65.4433 | 29198 | 1282 | 30682 | 5654 | 5190 | 91.7934 | |
| ghariani-varprowl | SNP | ti | map_l100_m2_e1 | het | 98.1632 | 99.0762 | 97.2668 | 74.0488 | 30674 | 286 | 30676 | 862 | 158 | 18.3295 | |
| jpowers-varprowl | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 95.2602 | 98.2179 | 92.4754 | 79.7293 | 30588 | 555 | 30675 | 2496 | 323 | 12.9407 | |
| jpowers-varprowl | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 95.2602 | 98.2179 | 92.4754 | 79.7293 | 30588 | 555 | 30675 | 2496 | 323 | 12.9407 | |
| hfeng-pmm1 | SNP | ti | map_l100_m2_e1 | het | 99.4037 | 99.0762 | 99.7333 | 64.8020 | 30674 | 286 | 30667 | 82 | 20 | 24.3902 | |
| gduggal-snapfb | SNP | * | map_l150_m2_e0 | * | 96.3250 | 96.2326 | 96.4176 | 78.3427 | 30652 | 1200 | 30655 | 1139 | 529 | 46.4442 | |
| gduggal-bwafb | SNP | ti | map_l100_m2_e1 | het | 98.8201 | 99.0084 | 98.6326 | 70.6269 | 30653 | 307 | 30655 | 425 | 95 | 22.3529 | |
| ghariani-varprowl | INDEL | I1_5 | HG002complexvar | * | 92.9673 | 92.2577 | 93.6879 | 54.6199 | 30779 | 2583 | 30650 | 2065 | 1585 | 76.7554 | |
| egarrison-hhga | SNP | ti | map_l100_m2_e1 | het | 99.3984 | 98.9890 | 99.8111 | 65.4651 | 30647 | 313 | 30648 | 58 | 18 | 31.0345 | |
| ckim-vqsr | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 98.9263 | 98.3656 | 99.4933 | 72.9052 | 30634 | 509 | 30634 | 156 | 20 | 12.8205 | |
| ckim-vqsr | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 98.9263 | 98.3656 | 99.4933 | 72.9052 | 30634 | 509 | 30634 | 156 | 20 | 12.8205 | |
| ckim-dragen | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 98.1519 | 97.5866 | 98.7237 | 61.6188 | 30650 | 758 | 30631 | 396 | 367 | 92.6768 | |
| ckim-dragen | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 98.1519 | 97.5866 | 98.7237 | 61.6188 | 30650 | 758 | 30631 | 396 | 367 | 92.6768 | |
| gduggal-snapvard | SNP | * | map_l150_m2_e1 | * | 92.4051 | 96.3396 | 88.7794 | 82.5294 | 31031 | 1179 | 30628 | 3871 | 287 | 7.4141 | |
| ltrigg-rtg2 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 98.2142 | 97.3128 | 99.1325 | 55.0694 | 30564 | 844 | 30624 | 268 | 105 | 39.1791 | |
| ltrigg-rtg2 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 98.2142 | 97.3128 | 99.1325 | 55.0694 | 30564 | 844 | 30624 | 268 | 105 | 39.1791 | |
| jmaeng-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 98.1915 | 97.4975 | 98.8955 | 61.4377 | 30622 | 786 | 30622 | 342 | 309 | 90.3509 | |
| jmaeng-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 98.1915 | 97.4975 | 98.8955 | 61.4377 | 30622 | 786 | 30622 | 342 | 309 | 90.3509 | |
| cchapple-custom | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.3690 | 99.6782 | 99.0618 | 71.6714 | 30662 | 99 | 30621 | 290 | 283 | 97.5862 | |
| qzeng-custom | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 97.8254 | 98.0798 | 97.5723 | 79.1147 | 30545 | 598 | 30586 | 761 | 104 | 13.6662 | |
| qzeng-custom | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 97.8254 | 98.0798 | 97.5723 | 79.1147 | 30545 | 598 | 30586 | 761 | 104 | 13.6662 | |
| rpoplin-dv42 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 97.7633 | 97.2714 | 98.2602 | 58.6360 | 30551 | 857 | 30554 | 541 | 494 | 91.3124 | |
| rpoplin-dv42 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 97.7633 | 97.2714 | 98.2602 | 58.6360 | 30551 | 857 | 30554 | 541 | 494 | 91.3124 | |
| astatham-gatk | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 98.9634 | 98.0991 | 99.8431 | 67.2451 | 30551 | 592 | 30551 | 48 | 17 | 35.4167 | |
| astatham-gatk | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 98.9634 | 98.0991 | 99.8431 | 67.2451 | 30551 | 592 | 30551 | 48 | 17 | 35.4167 | |
| gduggal-bwafb | INDEL | * | HG002compoundhet | het | 91.2904 | 85.5154 | 97.9020 | 36.8528 | 3501 | 593 | 30518 | 654 | 528 | 80.7339 | |
| mlin-fermikit | SNP | ti | map_l100_m2_e1 | * | 73.7873 | 61.6490 | 91.8775 | 54.5530 | 30507 | 18978 | 30507 | 2697 | 2372 | 87.9496 | |
| ndellapenna-hhga | SNP | ti | map_l100_m2_e1 | het | 99.1089 | 98.4335 | 99.7937 | 64.2644 | 30475 | 485 | 30477 | 63 | 24 | 38.0952 | |
| ghariani-varprowl | INDEL | D1_5 | HG002complexvar | * | 93.6809 | 93.5932 | 93.7688 | 56.5500 | 30619 | 2096 | 30473 | 2025 | 1375 | 67.9012 | |
| rpoplin-dv42 | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.3981 | 99.0572 | 99.7414 | 71.0854 | 30471 | 290 | 30469 | 79 | 73 | 92.4051 | |
| ckim-vqsr | SNP | ti | map_l100_m1_e0 | * | 77.5493 | 63.5768 | 99.3932 | 81.5266 | 30473 | 17458 | 30468 | 186 | 13 | 6.9893 | |
| asubramanian-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 97.7710 | 96.8925 | 98.6656 | 61.3340 | 30432 | 976 | 30464 | 412 | 353 | 85.6796 | |
| asubramanian-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 97.7710 | 96.8925 | 98.6656 | 61.3340 | 30432 | 976 | 30464 | 412 | 353 | 85.6796 | |
| ltrigg-rtg1 | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.5400 | 99.2100 | 99.8721 | 70.2148 | 30518 | 243 | 30461 | 39 | 32 | 82.0513 | |
| gduggal-bwaplat | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 81.2482 | 70.2896 | 96.2549 | 70.8872 | 30460 | 12875 | 30456 | 1185 | 636 | 53.6709 | |