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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
70701-70750 / 86044 show all | |||||||||||||||
| mlin-fermikit | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 98.5545 | 99.7340 | 97.4026 | 53.7630 | 1125 | 3 | 1125 | 30 | 23 | 76.6667 | |
| ckim-dragen | INDEL | * | map_l100_m2_e1 | homalt | 98.5552 | 98.5948 | 98.5156 | 84.6468 | 1263 | 18 | 1261 | 19 | 10 | 52.6316 | |
| eyeh-varpipe | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 98.5555 | 98.1735 | 98.9404 | 72.7338 | 645 | 12 | 747 | 8 | 3 | 37.5000 | |
| hfeng-pmm1 | SNP | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 98.5556 | 97.3971 | 99.7420 | 65.4794 | 4640 | 124 | 4640 | 12 | 1 | 8.3333 | |
| ltrigg-rtg2 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 98.5556 | 97.4729 | 99.6627 | 53.9495 | 5747 | 149 | 5909 | 20 | 20 | 100.0000 | |
| ltrigg-rtg2 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 98.5556 | 97.4729 | 99.6627 | 53.9495 | 5747 | 149 | 5909 | 20 | 20 | 100.0000 | |
| asubramanian-gatk | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 98.5568 | 97.9679 | 99.1528 | 76.0152 | 5978 | 124 | 7490 | 64 | 52 | 81.2500 | |
| jlack-gatk | SNP | ti | lowcmp_SimpleRepeat_quadTR_11to50 | het | 98.5569 | 99.7479 | 97.3939 | 48.1612 | 6727 | 17 | 6727 | 180 | 3 | 1.6667 | |
| raldana-dualsentieon | INDEL | D1_5 | map_l100_m2_e0 | * | 98.5570 | 98.0157 | 99.1043 | 82.2749 | 1877 | 38 | 1881 | 17 | 5 | 29.4118 | |
| gduggal-bwavard | SNP | tv | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 98.5575 | 98.0766 | 99.0431 | 61.4154 | 6884 | 135 | 6831 | 66 | 45 | 68.1818 | |
| bgallagher-sentieon | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 98.5576 | 99.9158 | 97.2359 | 49.7376 | 4749 | 4 | 4749 | 135 | 134 | 99.2593 | |
| rpoplin-dv42 | SNP | ti | map_l250_m2_e0 | * | 98.5577 | 98.2428 | 98.8746 | 88.2672 | 4920 | 88 | 4920 | 56 | 37 | 66.0714 | |
| anovak-vg | SNP | * | func_cds | * | 98.5581 | 98.0331 | 99.0887 | 29.8522 | 17793 | 357 | 17724 | 163 | 111 | 68.0982 | |
| bgallagher-sentieon | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 98.5591 | 99.4186 | 97.7143 | 81.0401 | 171 | 1 | 171 | 4 | 1 | 25.0000 | |
| astatham-gatk | INDEL | I6_15 | segdup | * | 98.5591 | 97.7143 | 99.4186 | 92.8003 | 171 | 4 | 171 | 1 | 0 | 0.0000 | |
| ckim-vqsr | INDEL | I6_15 | segdup | * | 98.5591 | 97.7143 | 99.4186 | 93.9373 | 171 | 4 | 171 | 1 | 0 | 0.0000 | |
| dgrover-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 98.5591 | 99.4186 | 97.7143 | 81.1422 | 171 | 1 | 171 | 4 | 1 | 25.0000 | |
| ltrigg-rtg2 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 98.5596 | 97.4138 | 99.7327 | 50.5529 | 11187 | 297 | 11193 | 30 | 28 | 93.3333 | |
| rpoplin-dv42 | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | * | 98.5596 | 98.2560 | 98.8651 | 66.9902 | 3831 | 68 | 3833 | 44 | 35 | 79.5455 | |
| ndellapenna-hhga | SNP | * | map_l150_m0_e0 | * | 98.5596 | 97.5316 | 99.6095 | 77.4194 | 11735 | 297 | 11735 | 46 | 22 | 47.8261 | |
| hfeng-pmm3 | INDEL | D6_15 | map_siren | het | 98.5599 | 97.8571 | 99.2727 | 84.3483 | 274 | 6 | 273 | 2 | 0 | 0.0000 | |
| gduggal-bwaplat | SNP | tv | * | * | 98.5599 | 97.4574 | 99.6876 | 31.4101 | 945035 | 24655 | 945254 | 2962 | 440 | 14.8548 | |
| egarrison-hhga | INDEL | I1_5 | lowcmp_SimpleRepeat_triTR_11to50 | hetalt | 98.5600 | 98.4026 | 98.7179 | 33.7580 | 308 | 5 | 308 | 4 | 4 | 100.0000 | |
| dgrover-gatk | SNP | * | map_l250_m0_e0 | homalt | 98.5600 | 97.9332 | 99.1948 | 91.6845 | 616 | 13 | 616 | 5 | 3 | 60.0000 | |
| astatham-gatk | SNP | tv | map_l250_m2_e1 | homalt | 98.5600 | 97.6744 | 99.4618 | 86.4833 | 924 | 22 | 924 | 5 | 4 | 80.0000 | |
| hfeng-pmm1 | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 98.5604 | 97.4488 | 99.6975 | 72.9214 | 8900 | 233 | 8900 | 27 | 5 | 18.5185 | |
| hfeng-pmm1 | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 98.5604 | 97.4488 | 99.6975 | 72.9214 | 8900 | 233 | 8900 | 27 | 5 | 18.5185 | |
| jli-custom | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 98.5605 | 98.5736 | 98.5474 | 69.9656 | 1313 | 19 | 1289 | 19 | 14 | 73.6842 | |
| gduggal-snapplat | SNP | tv | HG002complexvar | homalt | 98.5607 | 97.4503 | 99.6966 | 24.7080 | 92686 | 2425 | 92657 | 282 | 135 | 47.8723 | |
| ltrigg-rtg1 | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 98.5609 | 99.3157 | 97.8175 | 79.7318 | 4209 | 29 | 4213 | 94 | 1 | 1.0638 | |
| jpowers-varprowl | SNP | * | map_l125_m0_e0 | homalt | 98.5610 | 97.4523 | 99.6952 | 74.0600 | 6541 | 171 | 6541 | 20 | 11 | 55.0000 | |
| hfeng-pmm1 | SNP | * | map_l250_m2_e1 | het | 98.5612 | 98.2523 | 98.8721 | 88.8393 | 5172 | 92 | 5172 | 59 | 11 | 18.6441 | |
| jli-custom | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 98.5612 | 98.0245 | 99.1037 | 50.2646 | 31360 | 632 | 31292 | 283 | 258 | 91.1661 | |
| ckim-vqsr | SNP | tv | segdup | homalt | 98.5612 | 97.3132 | 99.8416 | 90.0895 | 3151 | 87 | 3151 | 5 | 5 | 100.0000 | |
| ckim-dragen | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 98.5612 | 97.7676 | 99.3678 | 76.3607 | 1927 | 44 | 1886 | 12 | 6 | 50.0000 | |
| ckim-dragen | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 98.5612 | 97.7676 | 99.3678 | 76.3607 | 1927 | 44 | 1886 | 12 | 6 | 50.0000 | |
| hfeng-pmm1 | SNP | * | map_l250_m2_e0 | het | 98.5614 | 98.2672 | 98.8573 | 88.7531 | 5104 | 90 | 5104 | 59 | 11 | 18.6441 | |
| asubramanian-gatk | INDEL | I1_5 | lowcmp_SimpleRepeat_triTR_11to50 | het | 98.5619 | 97.6596 | 99.4810 | 64.5181 | 459 | 11 | 575 | 3 | 3 | 100.0000 | |
| ckim-dragen | SNP | ti | segdup | * | 98.5623 | 99.8106 | 97.3449 | 91.6401 | 19500 | 37 | 19505 | 532 | 9 | 1.6917 | |
| bgallagher-sentieon | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 98.5626 | 98.0720 | 99.0581 | 75.3578 | 1933 | 38 | 1893 | 18 | 10 | 55.5556 | |
| bgallagher-sentieon | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 98.5626 | 98.0720 | 99.0581 | 75.3578 | 1933 | 38 | 1893 | 18 | 10 | 55.5556 | |
| ndellapenna-hhga | SNP | tv | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 98.5635 | 98.2824 | 98.8462 | 65.4025 | 515 | 9 | 514 | 6 | 5 | 83.3333 | |
| hfeng-pmm2 | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 98.5639 | 99.8469 | 97.3134 | 72.4846 | 652 | 1 | 652 | 18 | 17 | 94.4444 | |
| rpoplin-dv42 | SNP | tv | map_l100_m0_e0 | het | 98.5640 | 98.8507 | 98.2789 | 68.7061 | 7139 | 83 | 7138 | 125 | 50 | 40.0000 | |
| mlin-fermikit | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | homalt | 98.5640 | 99.8834 | 97.2789 | 52.9349 | 857 | 1 | 858 | 24 | 21 | 87.5000 | |
| egarrison-hhga | INDEL | I1_5 | map_l100_m0_e0 | homalt | 98.5646 | 99.0385 | 98.0952 | 80.8743 | 206 | 2 | 206 | 4 | 2 | 50.0000 | |
| eyeh-varpipe | SNP | ti | map_l125_m0_e0 | het | 98.5647 | 99.5038 | 97.6432 | 79.9389 | 8222 | 41 | 8079 | 195 | 8 | 4.1026 | |
| jli-custom | INDEL | D1_5 | map_l125_m2_e0 | het | 98.5651 | 98.8220 | 98.3095 | 85.7566 | 755 | 9 | 756 | 13 | 3 | 23.0769 | |
| bgallagher-sentieon | INDEL | D1_5 | map_l100_m1_e0 | het | 98.5653 | 99.2556 | 97.8845 | 84.2173 | 1200 | 9 | 1203 | 26 | 4 | 15.3846 | |
| gduggal-bwafb | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_11to50 | het | 98.5655 | 97.5492 | 99.6032 | 43.6746 | 2229 | 56 | 2510 | 10 | 3 | 30.0000 | |