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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
55051-55100 / 86044 show all | |||||||||||||||
| hfeng-pmm1 | SNP | ti | map_l250_m2_e0 | homalt | 99.5141 | 99.5426 | 99.4857 | 87.7793 | 1741 | 8 | 1741 | 9 | 2 | 22.2222 | |
| jli-custom | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 98.9880 | 99.0063 | 98.9698 | 87.7821 | 2690 | 27 | 2690 | 28 | 12 | 42.8571 | |
| bgallagher-sentieon | INDEL | * | map_l100_m0_e0 | het | 97.4344 | 98.4329 | 96.4559 | 87.7838 | 1005 | 16 | 1007 | 37 | 4 | 10.8108 | |
| ckim-dragen | INDEL | I6_15 | map_l100_m1_e0 | * | 96.9163 | 96.4912 | 97.3451 | 87.7838 | 110 | 4 | 110 | 3 | 0 | 0.0000 | |
| gduggal-bwavard | INDEL | I1_5 | map_l100_m0_e0 | * | 93.4216 | 94.4751 | 92.3913 | 87.7849 | 513 | 30 | 510 | 42 | 14 | 33.3333 | |
| ltrigg-rtg1 | INDEL | D16_PLUS | map_siren | het | 93.2340 | 88.4615 | 98.5507 | 87.7876 | 69 | 9 | 68 | 1 | 0 | 0.0000 | |
| hfeng-pmm2 | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 95.5559 | 93.0894 | 98.1567 | 87.7884 | 229 | 17 | 213 | 4 | 0 | 0.0000 | |
| gduggal-snapvard | INDEL | I6_15 | map_l150_m1_e0 | * | 60.8583 | 72.0000 | 52.7027 | 87.7888 | 18 | 7 | 39 | 35 | 27 | 77.1429 | |
| hfeng-pmm3 | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 96.1351 | 95.4545 | 96.8254 | 87.7907 | 63 | 3 | 61 | 2 | 0 | 0.0000 | |
| anovak-vg | INDEL | I16_PLUS | segdup | homalt | 60.0000 | 63.1579 | 57.1429 | 87.7907 | 12 | 7 | 12 | 9 | 5 | 55.5556 | |
| ciseli-custom | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 9.4488 | 5.6604 | 28.5714 | 87.7907 | 6 | 100 | 6 | 15 | 12 | 80.0000 | |
| ckim-gatk | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 94.4079 | 91.7293 | 97.2477 | 87.7940 | 122 | 11 | 106 | 3 | 3 | 100.0000 | |
| ckim-dragen | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 99.4458 | 99.2885 | 99.6035 | 87.7940 | 1256 | 9 | 1256 | 5 | 5 | 100.0000 | |
| ckim-vqsr | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 94.4079 | 91.7293 | 97.2477 | 87.7940 | 122 | 11 | 106 | 3 | 3 | 100.0000 | |
| astatham-gatk | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 94.4079 | 91.7293 | 97.2477 | 87.7940 | 122 | 11 | 106 | 3 | 3 | 100.0000 | |
| cchapple-custom | INDEL | I1_5 | map_l125_m2_e0 | het | 95.7357 | 95.5734 | 95.8984 | 87.7950 | 475 | 22 | 491 | 21 | 5 | 23.8095 | |
| dgrover-gatk | INDEL | I1_5 | map_l125_m2_e0 | * | 98.8330 | 98.7165 | 98.9498 | 87.7955 | 846 | 11 | 848 | 9 | 2 | 22.2222 | |
| dgrover-gatk | INDEL | * | map_l100_m0_e0 | * | 97.7081 | 98.0806 | 97.3384 | 87.7968 | 1533 | 30 | 1536 | 42 | 9 | 21.4286 | |
| bgallagher-sentieon | INDEL | D1_5 | map_l125_m2_e1 | het | 98.3302 | 99.2208 | 97.4555 | 87.7969 | 764 | 6 | 766 | 20 | 3 | 15.0000 | |
| rpoplin-dv42 | INDEL | D1_5 | map_l150_m1_e0 | homalt | 98.9107 | 99.5614 | 98.2684 | 87.7971 | 227 | 1 | 227 | 4 | 4 | 100.0000 | |
| asubramanian-gatk | INDEL | D16_PLUS | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 96.9697 | 100.0000 | 94.1176 | 87.7990 | 52 | 0 | 48 | 3 | 0 | 0.0000 | |
| asubramanian-gatk | INDEL | * | map_l125_m2_e1 | homalt | 96.1924 | 93.0233 | 99.5851 | 87.7995 | 720 | 54 | 720 | 3 | 1 | 33.3333 | |
| jlack-gatk | INDEL | I1_5 | map_l100_m2_e1 | * | 96.8991 | 98.3513 | 95.4892 | 87.8016 | 1372 | 23 | 1376 | 65 | 7 | 10.7692 | |
| egarrison-hhga | INDEL | I1_5 | map_l125_m2_e1 | het | 98.5192 | 98.2283 | 98.8119 | 87.8019 | 499 | 9 | 499 | 6 | 1 | 16.6667 | |
| qzeng-custom | INDEL | D1_5 | map_l150_m2_e0 | homalt | 85.4395 | 75.6198 | 98.1900 | 87.8035 | 183 | 59 | 217 | 4 | 4 | 100.0000 | |
| ckim-vqsr | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 99.4452 | 99.5833 | 99.3075 | 87.8041 | 717 | 3 | 717 | 5 | 4 | 80.0000 | |
| ckim-gatk | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 99.4452 | 99.5833 | 99.3075 | 87.8041 | 717 | 3 | 717 | 5 | 4 | 80.0000 | |
| ckim-dragen | INDEL | D6_15 | map_l125_m0_e0 | hetalt | 90.9091 | 83.3333 | 100.0000 | 87.8049 | 5 | 1 | 5 | 0 | 0 | ||
| ckim-dragen | SNP | ti | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 90.9091 | 83.3333 | 100.0000 | 87.8049 | 5 | 1 | 5 | 0 | 0 | ||
| qzeng-custom | INDEL | I6_15 | map_l100_m0_e0 | hetalt | 85.7143 | 75.0000 | 100.0000 | 87.8049 | 3 | 1 | 5 | 0 | 0 | ||
| mlin-fermikit | INDEL | I6_15 | map_l100_m0_e0 | * | 57.9710 | 45.4545 | 80.0000 | 87.8049 | 15 | 18 | 16 | 4 | 3 | 75.0000 | |
| raldana-dualsentieon | SNP | * | map_l250_m2_e0 | hetalt | 100.0000 | 100.0000 | 100.0000 | 87.8049 | 5 | 0 | 5 | 0 | 0 | ||
| raldana-dualsentieon | SNP | tv | map_l250_m2_e0 | hetalt | 100.0000 | 100.0000 | 100.0000 | 87.8049 | 5 | 0 | 5 | 0 | 0 | ||
| hfeng-pmm1 | SNP | ti | map_l250_m2_e1 | hetalt | 100.0000 | 100.0000 | 100.0000 | 87.8049 | 5 | 0 | 5 | 0 | 0 | ||
| eyeh-varpipe | INDEL | D16_PLUS | lowcmp_SimpleRepeat_homopolymer_gt10 | hetalt | 50.0000 | 33.3333 | 100.0000 | 87.8049 | 3 | 6 | 10 | 0 | 0 | ||
| astatham-gatk | SNP | ti | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 90.9091 | 83.3333 | 100.0000 | 87.8049 | 5 | 1 | 5 | 0 | 0 | ||
| bgallagher-sentieon | SNP | ti | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 90.9091 | 83.3333 | 100.0000 | 87.8049 | 5 | 1 | 5 | 0 | 0 | ||
| ciseli-custom | INDEL | D1_5 | map_l125_m0_e0 | homalt | 78.7671 | 77.7027 | 79.8611 | 87.8069 | 115 | 33 | 115 | 29 | 24 | 82.7586 | |
| ckim-dragen | INDEL | I1_5 | map_l125_m2_e0 | * | 96.7213 | 96.3827 | 97.0623 | 87.8080 | 826 | 31 | 826 | 25 | 6 | 24.0000 | |
| ckim-dragen | INDEL | I1_5 | HG002compoundhet | homalt | 62.2015 | 99.0881 | 45.3278 | 87.8082 | 326 | 3 | 325 | 392 | 391 | 99.7449 | |
| hfeng-pmm3 | SNP | tv | map_l250_m1_e0 | * | 98.7121 | 98.4511 | 98.9746 | 87.8091 | 2606 | 41 | 2606 | 27 | 4 | 14.8148 | |
| hfeng-pmm2 | SNP | ti | map_l250_m2_e1 | homalt | 99.5488 | 99.6050 | 99.4927 | 87.8092 | 1765 | 7 | 1765 | 9 | 2 | 22.2222 | |
| jmaeng-gatk | INDEL | D1_5 | map_l150_m1_e0 | homalt | 98.6726 | 97.8070 | 99.5536 | 87.8128 | 223 | 5 | 223 | 1 | 1 | 100.0000 | |
| asubramanian-gatk | INDEL | I1_5 | HG002compoundhet | homalt | 72.5446 | 98.7842 | 57.3192 | 87.8143 | 325 | 4 | 325 | 242 | 234 | 96.6942 | |
| asubramanian-gatk | SNP | tv | map_l100_m0_e0 | homalt | 37.6187 | 23.1669 | 100.0000 | 87.8146 | 891 | 2955 | 891 | 0 | 0 | ||
| hfeng-pmm1 | SNP | ti | map_l250_m2_e1 | homalt | 99.5205 | 99.5485 | 99.4924 | 87.8161 | 1764 | 8 | 1764 | 9 | 2 | 22.2222 | |
| asubramanian-gatk | INDEL | C16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 0.0000 | 0.0000 | 87.8165 | 0 | 0 | 0 | 77 | 0 | 0.0000 | ||
| asubramanian-gatk | INDEL | C16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 0.0000 | 0.0000 | 87.8165 | 0 | 0 | 0 | 77 | 0 | 0.0000 | ||
| gduggal-snapplat | INDEL | * | map_l100_m2_e0 | homalt | 84.9002 | 75.9715 | 96.2072 | 87.8170 | 958 | 303 | 1040 | 41 | 2 | 4.8781 | |
| jmaeng-gatk | SNP | ti | map_l100_m2_e1 | hetalt | 83.6364 | 74.1935 | 95.8333 | 87.8173 | 23 | 8 | 23 | 1 | 1 | 100.0000 | |