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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
39801-39850 / 86044 show all | |||||||||||||||
| ciseli-custom | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 48.8684 | 40.9881 | 60.5000 | 69.8341 | 755 | 1087 | 726 | 474 | 272 | 57.3840 | |
| gduggal-snapfb | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 71.8249 | 74.6024 | 69.2468 | 69.8343 | 1595 | 543 | 1664 | 739 | 192 | 25.9811 | |
| dgrover-gatk | INDEL | I1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 99.6608 | 99.4733 | 99.8491 | 69.8452 | 2644 | 14 | 2646 | 4 | 3 | 75.0000 | |
| mlin-fermikit | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 95.9297 | 98.8747 | 93.1551 | 69.8469 | 11422 | 130 | 11432 | 840 | 741 | 88.2143 | |
| mlin-fermikit | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 95.9297 | 98.8747 | 93.1551 | 69.8469 | 11422 | 130 | 11432 | 840 | 741 | 88.2143 | |
| ckim-vqsr | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 95.8621 | 98.2332 | 93.6027 | 69.8477 | 278 | 5 | 278 | 19 | 19 | 100.0000 | |
| jmaeng-gatk | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 95.5172 | 97.8799 | 93.2660 | 69.8477 | 277 | 6 | 277 | 20 | 20 | 100.0000 | |
| jpowers-varprowl | INDEL | D1_5 | HG002compoundhet | * | 18.0756 | 14.9571 | 22.8370 | 69.8480 | 1830 | 10405 | 1816 | 6136 | 5980 | 97.4576 | |
| ltrigg-rtg1 | SNP | * | map_l150_m0_e0 | * | 98.1003 | 96.5675 | 99.6825 | 69.8517 | 11619 | 413 | 11615 | 37 | 15 | 40.5405 | |
| jpowers-varprowl | INDEL | I1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 95.4096 | 96.1426 | 94.6877 | 69.8615 | 1321 | 53 | 1319 | 74 | 68 | 91.8919 | |
| ckim-isaac | INDEL | I6_15 | HG002compoundhet | homalt | 15.7021 | 38.7097 | 9.8485 | 69.8630 | 12 | 19 | 13 | 119 | 118 | 99.1597 | |
| gduggal-bwafb | INDEL | I16_PLUS | map_siren | het | 46.8750 | 30.6122 | 100.0000 | 69.8630 | 15 | 34 | 22 | 0 | 0 | ||
| gduggal-snapplat | SNP | * | map_l125_m2_e0 | homalt | 94.2904 | 89.2489 | 99.9355 | 69.8671 | 15507 | 1868 | 15497 | 10 | 9 | 90.0000 | |
| hfeng-pmm2 | SNP | tv | map_l125_m2_e0 | homalt | 99.7840 | 99.8006 | 99.7674 | 69.8673 | 6005 | 12 | 6005 | 14 | 5 | 35.7143 | |
| jmaeng-gatk | SNP | tv | map_l100_m2_e0 | homalt | 82.5067 | 70.2301 | 99.9845 | 69.8682 | 6471 | 2743 | 6471 | 1 | 1 | 100.0000 | |
| gduggal-snapfb | SNP | tv | map_l100_m1_e0 | * | 97.5300 | 97.9838 | 97.0805 | 69.8683 | 24007 | 494 | 24008 | 722 | 232 | 32.1330 | |
| jli-custom | SNP | ti | map_l150_m2_e0 | homalt | 99.7105 | 99.5011 | 99.9209 | 69.8737 | 7578 | 38 | 7578 | 6 | 6 | 100.0000 | |
| hfeng-pmm3 | SNP | ti | map_l125_m0_e0 | homalt | 99.6659 | 99.6437 | 99.6881 | 69.8765 | 4475 | 16 | 4475 | 14 | 5 | 35.7143 | |
| ckim-gatk | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | * | 96.9529 | 94.0860 | 100.0000 | 69.8795 | 175 | 11 | 175 | 0 | 0 | ||
| ckim-vqsr | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | * | 96.9529 | 94.0860 | 100.0000 | 69.8795 | 175 | 11 | 175 | 0 | 0 | ||
| eyeh-varpipe | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 97.6390 | 97.8308 | 97.4480 | 69.8833 | 902 | 20 | 1031 | 27 | 12 | 44.4444 | |
| jli-custom | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 98.1373 | 96.5517 | 99.7758 | 69.8852 | 448 | 16 | 445 | 1 | 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 | |
| gduggal-snapfb | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 70.7005 | 95.7309 | 56.0463 | 69.8866 | 740 | 33 | 774 | 607 | 47 | 7.7430 | |
| gduggal-snapplat | SNP | * | map_l125_m2_e1 | homalt | 94.3221 | 89.3053 | 99.9361 | 69.8871 | 15657 | 1875 | 15646 | 10 | 9 | 90.0000 | |
| ghariani-varprowl | INDEL | D16_PLUS | lowcmp_SimpleRepeat_triTR_11to50 | * | 50.5051 | 47.7707 | 53.5714 | 69.8925 | 75 | 82 | 75 | 65 | 61 | 93.8462 | |
| ltrigg-rtg2 | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 97.5532 | 95.7934 | 99.3789 | 69.8925 | 1298 | 57 | 1280 | 8 | 3 | 37.5000 | |
| ckim-gatk | SNP | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 98.8872 | 98.7069 | 99.0682 | 69.8958 | 2977 | 39 | 2977 | 28 | 9 | 32.1429 | |
| mlin-fermikit | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | * | 87.3444 | 86.0491 | 88.6792 | 69.8967 | 1542 | 250 | 1551 | 198 | 185 | 93.4343 | |
| raldana-dualsentieon | SNP | * | map_l150_m2_e1 | homalt | 99.7077 | 99.5096 | 99.9066 | 69.9014 | 11769 | 58 | 11769 | 11 | 8 | 72.7273 | |
| anovak-vg | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | homalt | 81.0388 | 91.2786 | 72.8646 | 69.9021 | 1235 | 118 | 1254 | 467 | 416 | 89.0792 | |
| astatham-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 99.4595 | 100.0000 | 98.9247 | 69.9029 | 92 | 0 | 92 | 1 | 1 | 100.0000 | |
| hfeng-pmm2 | INDEL | I16_PLUS | HG002complexvar | hetalt | 96.6649 | 94.3284 | 99.1202 | 69.9029 | 316 | 19 | 338 | 3 | 3 | 100.0000 | |
| dgrover-gatk | SNP | ti | map_l100_m2_e1 | hetalt | 100.0000 | 100.0000 | 100.0000 | 69.9029 | 31 | 0 | 31 | 0 | 0 | ||
| dgrover-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 99.4595 | 100.0000 | 98.9247 | 69.9029 | 92 | 0 | 92 | 1 | 1 | 100.0000 | |
| jli-custom | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 99.2174 | 99.3885 | 99.0469 | 69.9044 | 3738 | 23 | 3741 | 36 | 34 | 94.4444 | |
| jli-custom | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 99.2174 | 99.3885 | 99.0469 | 69.9044 | 3738 | 23 | 3741 | 36 | 34 | 94.4444 | |
| ghariani-varprowl | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 29.6692 | 20.3322 | 54.8638 | 69.9063 | 710 | 2782 | 705 | 580 | 561 | 96.7241 | |
| gduggal-snapvard | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 60.8637 | 44.5230 | 96.1538 | 69.9074 | 126 | 157 | 125 | 5 | 4 | 80.0000 | |
| mlin-fermikit | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | homalt | 95.4998 | 94.1176 | 96.9231 | 69.9074 | 64 | 4 | 63 | 2 | 2 | 100.0000 | |
| jlack-gatk | INDEL | I16_PLUS | HG002complexvar | homalt | 96.5625 | 100.0000 | 93.3535 | 69.9091 | 309 | 0 | 309 | 22 | 21 | 95.4545 | |
| jli-custom | SNP | ti | map_l150_m2_e1 | homalt | 99.7134 | 99.5060 | 99.9217 | 69.9097 | 7655 | 38 | 7655 | 6 | 6 | 100.0000 | |
| hfeng-pmm2 | SNP | tv | map_l125_m2_e1 | homalt | 99.7860 | 99.8024 | 99.7696 | 69.9104 | 6062 | 12 | 6062 | 14 | 5 | 35.7143 | |
| anovak-vg | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | homalt | 34.1463 | 100.0000 | 20.5882 | 69.9115 | 1 | 0 | 7 | 27 | 22 | 81.4815 | |
| gduggal-snapplat | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 35.8000 | 22.6696 | 85.0767 | 69.9119 | 608 | 2074 | 610 | 107 | 84 | 78.5047 | |
| mlin-fermikit | SNP | ti | lowcmp_SimpleRepeat_diTR_11to50 | * | 95.5288 | 96.1960 | 94.8708 | 69.9124 | 4653 | 184 | 4661 | 252 | 157 | 62.3016 | |
| hfeng-pmm3 | INDEL | I16_PLUS | HG002complexvar | homalt | 99.0385 | 100.0000 | 98.0952 | 69.9140 | 309 | 0 | 309 | 6 | 5 | 83.3333 | |
| astatham-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 97.1652 | 97.0740 | 97.2565 | 69.9160 | 3948 | 119 | 3935 | 111 | 98 | 88.2883 | |
| mlin-fermikit | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 74.5853 | 86.8721 | 65.3433 | 69.9161 | 761 | 115 | 609 | 323 | 321 | 99.3808 | |
| jmaeng-gatk | SNP | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 98.9505 | 98.4748 | 99.4309 | 69.9164 | 2970 | 46 | 2970 | 17 | 4 | 23.5294 | |