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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
13151-13200 / 86044 show all | |||||||||||||||
| ltrigg-rtg1 | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 97.4824 | 95.5531 | 99.4912 | 43.7067 | 13172 | 613 | 13100 | 67 | 62 | 92.5373 | |
| jmaeng-gatk | INDEL | D1_5 | map_l125_m1_e0 | het | 94.9786 | 98.7603 | 91.4758 | 91.3901 | 717 | 9 | 719 | 67 | 4 | 5.9702 | |
| jli-custom | SNP | tv | map_l150_m1_e0 | het | 98.7145 | 98.4020 | 99.0291 | 72.7212 | 6835 | 111 | 6834 | 67 | 19 | 28.3582 | |
| jmaeng-gatk | INDEL | * | * | hetalt | 95.2835 | 91.2311 | 99.7126 | 56.1602 | 23024 | 2213 | 23247 | 67 | 66 | 98.5075 | |
| gduggal-snapfb | SNP | ti | map_l250_m0_e0 | het | 92.8266 | 92.8266 | 92.8266 | 90.7653 | 867 | 67 | 867 | 67 | 29 | 43.2836 | |
| gduggal-snapfb | INDEL | C1_5 | * | * | 35.4772 | 90.0000 | 22.0930 | 85.2234 | 9 | 1 | 19 | 67 | 6 | 8.9552 | |
| gduggal-snapfb | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 88.8749 | 91.2134 | 86.6534 | 76.1180 | 436 | 42 | 435 | 67 | 12 | 17.9104 | |
| hfeng-pmm1 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 99.4096 | 99.6175 | 99.2025 | 47.1436 | 8334 | 32 | 8334 | 67 | 66 | 98.5075 | |
| gduggal-snapvard | SNP | * | lowcmp_SimpleRepeat_diTR_51to200 | het | 20.9524 | 40.7407 | 14.1026 | 96.9614 | 11 | 16 | 11 | 67 | 1 | 1.4925 | |
| gduggal-snapplat | SNP | ti | lowcmp_SimpleRepeat_quadTR_51to200 | het | 17.8082 | 19.6970 | 16.2500 | 98.7063 | 13 | 53 | 13 | 67 | 2 | 2.9851 | |
| gduggal-snapplat | INDEL | D6_15 | HG002compoundhet | hetalt | 51.7417 | 35.1859 | 97.7226 | 44.3646 | 2868 | 5283 | 2875 | 67 | 52 | 77.6119 | |
| gduggal-snapplat | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_51to200 | homalt | 35.0186 | 30.4348 | 41.2281 | 58.5455 | 49 | 112 | 47 | 67 | 58 | 86.5672 | |
| rpoplin-dv42 | INDEL | * | HG002compoundhet | hetalt | 95.8717 | 92.3153 | 99.7130 | 50.6553 | 23245 | 1935 | 23276 | 67 | 66 | 98.5075 | |
| rpoplin-dv42 | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 99.8633 | 99.8472 | 99.8795 | 59.6020 | 55546 | 85 | 55530 | 67 | 38 | 56.7164 | |
| rpoplin-dv42 | SNP | * | map_siren | homalt | 99.7831 | 99.6882 | 99.8783 | 53.6066 | 54984 | 172 | 54983 | 67 | 63 | 94.0299 | |
| ckim-dragen | INDEL | D16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 92.8571 | 98.5656 | 87.7737 | 71.4137 | 481 | 7 | 481 | 67 | 61 | 91.0448 | |
| ckim-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_51to200 | * | 82.1817 | 76.4706 | 88.8147 | 52.8718 | 533 | 164 | 532 | 67 | 66 | 98.5075 | |
| ckim-gatk | INDEL | D1_5 | map_l150_m2_e0 | * | 95.0802 | 98.5583 | 91.8392 | 92.3713 | 752 | 11 | 754 | 67 | 5 | 7.4627 | |
| ciseli-custom | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 81.7400 | 74.7573 | 90.1615 | 62.2924 | 616 | 208 | 614 | 67 | 57 | 85.0746 | |
| ciseli-custom | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 82.6277 | 88.7597 | 77.2881 | 67.7243 | 229 | 29 | 228 | 67 | 46 | 68.6567 | |
| cchapple-custom | INDEL | C1_5 | HG002complexvar | het | 90.6065 | 85.7143 | 96.0910 | 77.9776 | 6 | 1 | 1647 | 67 | 24 | 35.8209 | |
| cchapple-custom | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_51to200 | * | 89.1338 | 86.8027 | 91.5935 | 49.4610 | 638 | 97 | 730 | 67 | 66 | 98.5075 | |
| cchapple-custom | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 98.0973 | 99.5904 | 96.6483 | 30.9022 | 1945 | 8 | 1932 | 67 | 67 | 100.0000 | |
| ckim-dragen | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 97.4560 | 96.0456 | 98.9084 | 63.8644 | 6072 | 250 | 6071 | 67 | 60 | 89.5522 | |
| ckim-dragen | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 97.4560 | 96.0456 | 98.9084 | 63.8644 | 6072 | 250 | 6071 | 67 | 60 | 89.5522 | |
| egarrison-hhga | SNP | * | map_l150_m1_e0 | * | 99.3388 | 98.9023 | 99.7792 | 73.2772 | 30273 | 336 | 30273 | 67 | 32 | 47.7612 | |
| egarrison-hhga | SNP | ti | map_l100_m1_e0 | * | 99.5648 | 99.2719 | 99.8594 | 62.6430 | 47582 | 349 | 47583 | 67 | 31 | 46.2687 | |
| eyeh-varpipe | INDEL | C1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 0.0000 | 0.0000 | 62.7778 | 95.6793 | 0 | 0 | 113 | 67 | 49 | 73.1343 | |
| ckim-vqsr | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_51to200 | * | 82.1817 | 76.4706 | 88.8147 | 52.8718 | 533 | 164 | 532 | 67 | 66 | 98.5075 | |
| dgrover-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_51to200 | * | 82.5440 | 77.0445 | 88.8889 | 53.2920 | 537 | 160 | 536 | 67 | 66 | 98.5075 | |
| ckim-isaac | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 91.9132 | 85.7987 | 98.9660 | 29.1571 | 6102 | 1010 | 6413 | 67 | 58 | 86.5672 | |
| ckim-isaac | INDEL | I16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 71.1731 | 58.4575 | 90.9582 | 67.0080 | 667 | 474 | 674 | 67 | 37 | 55.2239 | |
| ckim-isaac | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 71.5265 | 61.2613 | 85.9244 | 78.5005 | 408 | 258 | 409 | 67 | 27 | 40.2985 | |
| ckim-isaac | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 71.5265 | 61.2613 | 85.9244 | 78.5005 | 408 | 258 | 409 | 67 | 27 | 40.2985 | |
| ckim-isaac | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 84.5242 | 79.9191 | 89.6923 | 68.2772 | 593 | 149 | 583 | 67 | 46 | 68.6567 | |
| dgrover-gatk | INDEL | I1_5 | HG002compoundhet | het | 95.2481 | 98.5882 | 92.1269 | 86.8653 | 838 | 12 | 784 | 67 | 66 | 98.5075 | |
| mlin-fermikit | SNP | * | func_cds | * | 99.4453 | 99.2617 | 99.6295 | 19.0809 | 18016 | 134 | 18016 | 67 | 48 | 71.6418 | |
| qzeng-custom | INDEL | D1_5 | map_siren | * | 93.2868 | 89.0337 | 97.9666 | 83.5685 | 3142 | 387 | 3228 | 67 | 43 | 64.1791 | |
| qzeng-custom | INDEL | I16_PLUS | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 49.7946 | 72.3404 | 37.9630 | 69.8324 | 34 | 13 | 41 | 67 | 1 | 1.4925 | |
| qzeng-custom | INDEL | I1_5 | map_l100_m2_e0 | het | 80.9908 | 72.0050 | 92.5390 | 89.7242 | 571 | 222 | 831 | 67 | 13 | 19.4030 | |
| ndellapenna-hhga | INDEL | * | map_l100_m2_e1 | het | 97.2372 | 97.3111 | 97.1634 | 84.0911 | 2280 | 63 | 2295 | 67 | 27 | 40.2985 | |
| qzeng-custom | INDEL | * | lowcmp_SimpleRepeat_quadTR_51to200 | homalt | 88.9612 | 90.4472 | 87.5233 | 61.4224 | 445 | 47 | 470 | 67 | 49 | 73.1343 | |
| ltrigg-rtg2 | INDEL | D6_15 | HG002complexvar | * | 97.7900 | 96.9257 | 98.6698 | 51.5393 | 5139 | 163 | 4970 | 67 | 50 | 74.6269 | |
| ltrigg-rtg2 | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | * | 98.5119 | 97.7585 | 99.2769 | 36.5690 | 9246 | 212 | 9199 | 67 | 51 | 76.1194 | |
| ltrigg-rtg2 | SNP | * | map_l125_m2_e1 | het | 98.5451 | 97.3516 | 99.7684 | 58.0187 | 28855 | 785 | 28856 | 67 | 6 | 8.9552 | |
| ltrigg-rtg2 | INDEL | D1_5 | * | hetalt | 97.9310 | 96.5544 | 99.3475 | 70.1886 | 9892 | 353 | 10049 | 66 | 65 | 98.4848 | |
| qzeng-custom | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 88.7617 | 87.5000 | 90.0602 | 60.8952 | 252 | 36 | 598 | 66 | 60 | 90.9091 | |
| qzeng-custom | INDEL | I1_5 | map_l100_m1_e0 | het | 80.8356 | 71.8147 | 92.4485 | 89.2761 | 558 | 219 | 808 | 66 | 13 | 19.6970 | |
| mlin-fermikit | INDEL | I16_PLUS | HG002compoundhet | homalt | 8.3333 | 100.0000 | 4.3478 | 68.0556 | 3 | 0 | 3 | 66 | 66 | 100.0000 | |
| mlin-fermikit | SNP | * | map_l125_m0_e0 | het | 49.1614 | 32.7622 | 98.4323 | 62.8190 | 4149 | 8515 | 4144 | 66 | 3 | 4.5455 | |