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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
33651-33700 / 86044 show all | |||||||||||||||
| ciseli-custom | INDEL | D1_5 | map_l250_m0_e0 | het | 62.0843 | 60.6061 | 63.6364 | 98.5739 | 20 | 13 | 21 | 12 | 1 | 8.3333 | |
| ciseli-custom | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 65.0000 | 86.6667 | 52.0000 | 85.0299 | 13 | 2 | 13 | 12 | 1 | 8.3333 | |
| ciseli-custom | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 65.0000 | 86.6667 | 52.0000 | 85.0299 | 13 | 2 | 13 | 12 | 1 | 8.3333 | |
| gduggal-snapplat | INDEL | I1_5 | map_l100_m0_e0 | homalt | 86.6295 | 80.7692 | 93.4066 | 89.1538 | 168 | 40 | 170 | 12 | 1 | 8.3333 | |
| gduggal-snapplat | INDEL | I6_15 | segdup | het | 37.0075 | 26.5060 | 61.2903 | 95.4210 | 22 | 61 | 19 | 12 | 1 | 8.3333 | |
| gduggal-snapplat | SNP | * | lowcmp_SimpleRepeat_triTR_11to50 | het | 86.1010 | 77.3614 | 97.0668 | 59.1479 | 3571 | 1045 | 3574 | 108 | 9 | 8.3333 | |
| gduggal-snapplat | SNP | ti | func_cds | het | 99.3942 | 99.3532 | 99.4351 | 33.3621 | 8449 | 55 | 8449 | 48 | 4 | 8.3333 | |
| gduggal-snapplat | SNP | tv | segdup | het | 98.3319 | 98.0329 | 98.6327 | 95.7233 | 5183 | 104 | 5194 | 72 | 6 | 8.3333 | |
| gduggal-snapfb | INDEL | D1_5 | map_l250_m2_e0 | * | 95.1872 | 96.7391 | 93.6842 | 95.1568 | 178 | 6 | 178 | 12 | 1 | 8.3333 | |
| gduggal-snapfb | INDEL | D1_5 | map_l250_m2_e0 | het | 93.6000 | 96.6942 | 90.6977 | 93.6233 | 117 | 4 | 117 | 12 | 1 | 8.3333 | |
| gduggal-snapfb | INDEL | D1_5 | map_l250_m2_e1 | * | 95.2128 | 96.7568 | 93.7173 | 95.2381 | 179 | 6 | 179 | 12 | 1 | 8.3333 | |
| gduggal-snapfb | INDEL | D1_5 | map_l250_m2_e1 | het | 93.6508 | 96.7213 | 90.7692 | 93.7137 | 118 | 4 | 118 | 12 | 1 | 8.3333 | |
| gduggal-snapfb | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 73.8072 | 96.5392 | 59.7403 | 70.7317 | 530 | 19 | 552 | 372 | 31 | 8.3333 | |
| gduggal-snapplat | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | homalt | 65.1353 | 53.6585 | 82.8571 | 85.6026 | 198 | 171 | 290 | 60 | 5 | 8.3333 | |
| bgallagher-sentieon | SNP | tv | segdup | * | 99.4858 | 99.8125 | 99.1612 | 91.3387 | 8516 | 16 | 8512 | 72 | 6 | 8.3333 | |
| astatham-gatk | INDEL | * | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 99.7775 | 99.6287 | 99.9267 | 58.5881 | 16368 | 61 | 16366 | 12 | 1 | 8.3333 | |
| asubramanian-gatk | INDEL | D1_5 | map_l125_m1_e0 | het | 89.7485 | 86.7769 | 92.9308 | 90.5838 | 630 | 96 | 631 | 48 | 4 | 8.3333 | |
| asubramanian-gatk | INDEL | D1_5 | map_l125_m2_e0 | het | 89.8280 | 86.6492 | 93.2489 | 90.9553 | 662 | 102 | 663 | 48 | 4 | 8.3333 | |
| asubramanian-gatk | INDEL | D1_5 | map_l125_m2_e1 | het | 89.9101 | 86.7532 | 93.3054 | 91.0049 | 668 | 102 | 669 | 48 | 4 | 8.3333 | |
| asubramanian-gatk | INDEL | I1_5 | map_l100_m0_e0 | * | 91.0720 | 85.4512 | 97.4843 | 89.1665 | 464 | 79 | 465 | 12 | 1 | 8.3333 | |
| asubramanian-gatk | INDEL | I1_5 | map_l150_m1_e0 | * | 89.6780 | 83.2016 | 97.2477 | 92.2073 | 421 | 85 | 424 | 12 | 1 | 8.3333 | |
| asubramanian-gatk | INDEL | I1_5 | map_l150_m1_e0 | het | 83.9718 | 75.2508 | 94.9791 | 93.8067 | 225 | 74 | 227 | 12 | 1 | 8.3333 | |
| jmaeng-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 99.4749 | 99.2317 | 99.7192 | 49.7413 | 4262 | 33 | 4262 | 12 | 1 | 8.3333 | |
| jmaeng-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 99.2155 | 98.8831 | 99.5502 | 52.7537 | 2656 | 30 | 2656 | 12 | 1 | 8.3333 | |
| jmaeng-gatk | INDEL | * | map_siren | het | 97.3536 | 98.6247 | 96.1148 | 86.8437 | 4446 | 62 | 4453 | 180 | 15 | 8.3333 | |
| jmaeng-gatk | INDEL | D1_5 | map_l100_m0_e0 | * | 95.5921 | 97.9143 | 93.3775 | 89.4196 | 845 | 18 | 846 | 60 | 5 | 8.3333 | |
| ltrigg-rtg1 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 98.4853 | 98.2646 | 98.7069 | 72.8496 | 906 | 16 | 916 | 12 | 1 | 8.3333 | |
| ltrigg-rtg1 | SNP | * | map_l100_m2_e1 | het | 99.0006 | 98.3219 | 99.6887 | 57.1362 | 46111 | 787 | 46109 | 144 | 12 | 8.3333 | |
| hfeng-pmm2 | SNP | * | map_l125_m2_e0 | het | 99.1177 | 99.2564 | 98.9794 | 75.5476 | 29100 | 218 | 29094 | 300 | 25 | 8.3333 | |
| hfeng-pmm2 | SNP | * | map_l250_m0_e0 | het | 97.4257 | 98.0080 | 96.8504 | 93.8031 | 1476 | 30 | 1476 | 48 | 4 | 8.3333 | |
| hfeng-pmm2 | SNP | ti | HG002compoundhet | het | 96.7284 | 93.7822 | 99.8656 | 37.2373 | 8914 | 591 | 8916 | 12 | 1 | 8.3333 | |
| hfeng-pmm2 | SNP | tv | map_l100_m2_e1 | het | 99.2765 | 99.4541 | 99.0995 | 70.8119 | 15851 | 87 | 15847 | 144 | 12 | 8.3333 | |
| jlack-gatk | INDEL | D6_15 | map_l125_m1_e0 | * | 92.9461 | 95.7265 | 90.3226 | 91.9897 | 112 | 5 | 112 | 12 | 1 | 8.3333 | |
| jlack-gatk | INDEL | D6_15 | map_l125_m2_e0 | het | 89.3333 | 94.3662 | 84.8101 | 93.8807 | 67 | 4 | 67 | 12 | 1 | 8.3333 | |
| jlack-gatk | INDEL | D6_15 | map_l125_m2_e1 | het | 89.3333 | 94.3662 | 84.8101 | 94.0197 | 67 | 4 | 67 | 12 | 1 | 8.3333 | |
| jlack-gatk | INDEL | D6_15 | map_siren | het | 92.5170 | 97.1429 | 88.3117 | 88.1992 | 272 | 8 | 272 | 36 | 3 | 8.3333 | |
| jlack-gatk | INDEL | I6_15 | map_siren | het | 91.9861 | 92.3077 | 91.6667 | 87.8583 | 132 | 11 | 132 | 12 | 1 | 8.3333 | |
| hfeng-pmm1 | SNP | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 98.5556 | 97.3971 | 99.7420 | 65.4794 | 4640 | 124 | 4640 | 12 | 1 | 8.3333 | |
| hfeng-pmm3 | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 98.5241 | 97.2660 | 99.8150 | 78.5959 | 6475 | 182 | 6476 | 12 | 1 | 8.3333 | |
| jlack-gatk | INDEL | * | map_l100_m2_e0 | het | 93.6860 | 98.1795 | 89.5858 | 89.8045 | 2265 | 42 | 2271 | 264 | 22 | 8.3333 | |
| ckim-vqsr | INDEL | I1_5 | map_l100_m1_e0 | het | 96.5955 | 94.8520 | 98.4043 | 89.8378 | 737 | 40 | 740 | 12 | 1 | 8.3333 | |
| ckim-vqsr | INDEL | I1_5 | map_l100_m2_e0 | het | 96.5990 | 94.8298 | 98.4355 | 90.5728 | 752 | 41 | 755 | 12 | 1 | 8.3333 | |
| ckim-vqsr | INDEL | I1_5 | map_l100_m2_e1 | het | 96.5415 | 94.6914 | 98.4655 | 90.6122 | 767 | 43 | 770 | 12 | 1 | 8.3333 | |
| ckim-vqsr | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 99.4006 | 99.5116 | 99.2899 | 63.6333 | 35246 | 173 | 35235 | 252 | 21 | 8.3333 | |
| ckim-isaac | SNP | ti | map_l250_m2_e0 | het | 69.1244 | 53.0117 | 99.3092 | 92.1654 | 1725 | 1529 | 1725 | 12 | 1 | 8.3333 | |
| ckim-isaac | SNP | ti | map_l250_m2_e1 | het | 69.1304 | 53.0161 | 99.3186 | 92.2279 | 1749 | 1550 | 1749 | 12 | 1 | 8.3333 | |
| ckim-isaac | SNP | ti | map_siren | het | 88.1134 | 78.8433 | 99.8538 | 52.2793 | 49184 | 13198 | 49191 | 72 | 6 | 8.3333 | |
| ckim-vqsr | INDEL | * | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 99.7592 | 99.5922 | 99.9267 | 60.1242 | 16362 | 67 | 16361 | 12 | 1 | 8.3333 | |
| qzeng-custom | SNP | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 96.3797 | 98.5411 | 94.3110 | 80.2460 | 2972 | 44 | 2984 | 180 | 15 | 8.3333 | |
| qzeng-custom | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 98.3268 | 99.3263 | 97.3471 | 64.9445 | 1327 | 9 | 1321 | 36 | 3 | 8.3333 | |