PrecisionFDA
Truth Challenge
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Explore HG002 comparison results
Use this interactive explorer to filter all results across submission entries and multiple dimensions.
| Entry | Type | Subtype | Subset | Genotype | F-score | Recall | Precision | Frac_NA | Truth TP | Truth FN | Query TP | Query FP | FP gt | % FP ma | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
15001-15050 / 86044 show all | |||||||||||||||
| ckim-isaac | SNP | * | map_l150_m0_e0 | homalt | 62.3254 | 45.2922 | 99.8921 | 68.1060 | 1852 | 2237 | 1852 | 2 | 2 | 100.0000 | |
| gduggal-bwavard | SNP | ti | map_l100_m2_e0 | homalt | 98.5295 | 97.2036 | 99.8921 | 62.3227 | 17797 | 512 | 17597 | 19 | 15 | 78.9474 | |
| gduggal-snapplat | SNP | * | map_l100_m0_e0 | homalt | 93.3571 | 87.6248 | 99.8920 | 65.0376 | 10182 | 1438 | 10176 | 11 | 11 | 100.0000 | |
| gduggal-bwaplat | SNP | tv | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 82.6476 | 70.4805 | 99.8919 | 47.7991 | 924 | 387 | 924 | 1 | 1 | 100.0000 | |
| bgallagher-sentieon | SNP | * | * | * | 99.9296 | 99.9673 | 99.8919 | 18.9151 | 3053620 | 999 | 3053471 | 3303 | 195 | 5.9037 | |
| bgallagher-sentieon | SNP | ti | HG002compoundhet | homalt | 99.9053 | 99.9189 | 99.8918 | 30.4822 | 7388 | 6 | 7388 | 8 | 8 | 100.0000 | |
| astatham-gatk | SNP | tv | map_l100_m2_e1 | homalt | 99.5848 | 99.2797 | 99.8918 | 61.7406 | 9235 | 67 | 9235 | 10 | 6 | 60.0000 | |
| jli-custom | SNP | ti | HG002compoundhet | homalt | 99.9121 | 99.9324 | 99.8918 | 30.7138 | 7389 | 5 | 7389 | 8 | 8 | 100.0000 | |
| hfeng-pmm3 | SNP | tv | lowcmp_SimpleRepeat_quadTR_11to50 | * | 99.4812 | 99.0741 | 99.8917 | 37.3686 | 7383 | 69 | 7380 | 8 | 2 | 25.0000 | |
| astatham-gatk | INDEL | * | lowcmp_SimpleRepeat_triTR_11to50 | hetalt | 99.6744 | 99.4583 | 99.8915 | 29.8859 | 918 | 5 | 921 | 1 | 1 | 100.0000 | |
| dgrover-gatk | INDEL | * | lowcmp_SimpleRepeat_triTR_11to50 | hetalt | 99.6744 | 99.4583 | 99.8915 | 30.2044 | 918 | 5 | 921 | 1 | 1 | 100.0000 | |
| bgallagher-sentieon | INDEL | * | lowcmp_SimpleRepeat_triTR_11to50 | hetalt | 99.5654 | 99.2416 | 99.8913 | 28.9575 | 916 | 7 | 919 | 1 | 1 | 100.0000 | |
| gduggal-bwaplat | SNP | ti | map_l150_m0_e0 | homalt | 49.9321 | 33.2850 | 99.8913 | 89.4326 | 919 | 1842 | 919 | 1 | 1 | 100.0000 | |
| gduggal-bwavard | SNP | ti | map_l125_m2_e1 | homalt | 98.6250 | 97.3905 | 99.8913 | 68.5234 | 11159 | 299 | 11030 | 12 | 9 | 75.0000 | |
| jli-custom | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 99.9319 | 99.9727 | 99.8911 | 50.1493 | 3665 | 1 | 3668 | 4 | 4 | 100.0000 | |
| ltrigg-rtg2 | SNP | ti | map_l150_m1_e0 | * | 98.7324 | 97.6004 | 99.8910 | 62.9401 | 19239 | 473 | 19242 | 21 | 7 | 33.3333 | |
| ltrigg-rtg1 | SNP | ti | map_l125_m1_e0 | homalt | 99.7461 | 99.6016 | 99.8910 | 65.4505 | 11001 | 44 | 11001 | 12 | 12 | 100.0000 | |
| ckim-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 99.9318 | 99.9727 | 99.8910 | 51.2943 | 3665 | 1 | 3665 | 4 | 4 | 100.0000 | |
| hfeng-pmm1 | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_11to50 | * | 97.8185 | 95.8304 | 99.8909 | 57.5027 | 5493 | 239 | 5494 | 6 | 4 | 66.6667 | |
| hfeng-pmm1 | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 99.8909 | 99.8909 | 99.8909 | 48.7917 | 3662 | 4 | 3662 | 4 | 4 | 100.0000 | |
| ckim-vqsr | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 99.9182 | 99.9454 | 99.8909 | 51.3011 | 3664 | 2 | 3664 | 4 | 4 | 100.0000 | |
| hfeng-pmm3 | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 99.8636 | 99.8363 | 99.8908 | 48.6619 | 3660 | 6 | 3660 | 4 | 4 | 100.0000 | |
| ltrigg-rtg2 | INDEL | D1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 99.7421 | 99.5938 | 99.8908 | 50.6550 | 14710 | 60 | 14636 | 16 | 7 | 43.7500 | |
| astatham-gatk | SNP | tv | map_l100_m2_e0 | homalt | 99.5809 | 99.2728 | 99.8908 | 61.7518 | 9147 | 67 | 9147 | 10 | 6 | 60.0000 | |
| hfeng-pmm1 | SNP | * | lowcmp_SimpleRepeat_triTR_11to50 | het | 99.4888 | 99.0901 | 99.8907 | 31.1720 | 4574 | 42 | 4570 | 5 | 0 | 0.0000 | |
| hfeng-pmm2 | SNP | * | lowcmp_SimpleRepeat_triTR_11to50 | * | 99.6319 | 99.3746 | 99.8906 | 32.4559 | 7309 | 46 | 7305 | 8 | 1 | 12.5000 | |
| hfeng-pmm3 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 99.3457 | 98.8069 | 99.8904 | 75.6735 | 911 | 11 | 911 | 1 | 0 | 0.0000 | |
| gduggal-bwavard | SNP | ti | map_l125_m2_e0 | homalt | 98.6173 | 97.3763 | 99.8904 | 68.4929 | 11060 | 298 | 10932 | 12 | 9 | 75.0000 | |
| hfeng-pmm1 | SNP | tv | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 99.1947 | 98.5087 | 99.8903 | 63.5767 | 17306 | 262 | 17297 | 19 | 5 | 26.3158 | |
| cchapple-custom | SNP | ti | HG002complexvar | het | 99.7945 | 99.6988 | 99.8903 | 17.3501 | 313818 | 948 | 313318 | 344 | 249 | 72.3837 | |
| asubramanian-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 99.6034 | 99.3181 | 99.8903 | 51.3153 | 3641 | 25 | 3642 | 4 | 4 | 100.0000 | |
| asubramanian-gatk | SNP | ti | map_siren | * | 78.3158 | 64.4054 | 99.8903 | 68.2204 | 64634 | 35721 | 64622 | 71 | 23 | 32.3944 | |
| gduggal-bwafb | SNP | * | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 99.7989 | 99.7078 | 99.8902 | 34.3036 | 2730 | 8 | 2728 | 3 | 1 | 33.3333 | |
| dgrover-gatk | INDEL | * | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 99.8478 | 99.8054 | 99.8902 | 58.2232 | 28205 | 55 | 28208 | 31 | 20 | 64.5161 | |
| egarrison-hhga | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 99.6711 | 99.4530 | 99.8901 | 68.0141 | 909 | 5 | 909 | 1 | 0 | 0.0000 | |
| dgrover-gatk | SNP | ti | map_l150_m1_e0 | homalt | 99.5618 | 99.2357 | 99.8901 | 68.6615 | 7271 | 56 | 7271 | 8 | 6 | 75.0000 | |
| gduggal-bwafb | SNP | ti | map_l150_m0_e0 | homalt | 99.2528 | 98.6237 | 99.8899 | 77.4057 | 2723 | 38 | 2723 | 3 | 2 | 66.6667 | |
| astatham-gatk | SNP | ti | HG002compoundhet | * | 99.2746 | 98.6669 | 99.8899 | 35.7263 | 17245 | 233 | 17243 | 19 | 18 | 94.7368 | |
| ltrigg-rtg1 | SNP | * | map_l150_m2_e1 | homalt | 99.7587 | 99.6280 | 99.8898 | 72.7027 | 11783 | 44 | 11789 | 13 | 13 | 100.0000 | |
| jlack-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 95.3273 | 91.1635 | 99.8897 | 40.2875 | 5375 | 521 | 5435 | 6 | 5 | 83.3333 | |
| jlack-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 95.3273 | 91.1635 | 99.8897 | 40.2875 | 5375 | 521 | 5435 | 6 | 5 | 83.3333 | |
| bgallagher-sentieon | INDEL | I1_5 | HG002complexvar | het | 99.7743 | 99.6591 | 99.8897 | 57.8575 | 18127 | 62 | 18108 | 20 | 10 | 50.0000 | |
| eyeh-varpipe | SNP | * | map_l125_m1_e0 | homalt | 99.8501 | 99.8107 | 99.8895 | 68.7779 | 16873 | 32 | 16269 | 18 | 10 | 55.5556 | |
| jmaeng-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 99.7868 | 99.6845 | 99.8894 | 55.8752 | 25279 | 80 | 25282 | 28 | 15 | 53.5714 | |
| ckim-vqsr | SNP | * | * | het | 99.4736 | 99.0611 | 99.8894 | 26.9578 | 1855996 | 17591 | 1855876 | 2054 | 101 | 4.9172 | |
| cchapple-custom | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 98.7220 | 97.5815 | 99.8894 | 72.8284 | 928 | 23 | 903 | 1 | 1 | 100.0000 | |
| gduggal-bwafb | SNP | tv | map_siren | homalt | 99.6686 | 99.4490 | 99.8893 | 56.7363 | 17145 | 95 | 17145 | 19 | 11 | 57.8947 | |
| hfeng-pmm2 | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 99.2845 | 98.6871 | 99.8893 | 67.1756 | 902 | 12 | 902 | 1 | 0 | 0.0000 | |
| hfeng-pmm3 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 99.7097 | 99.5308 | 99.8892 | 74.1552 | 3606 | 17 | 3606 | 4 | 1 | 25.0000 | |
| jli-custom | INDEL | * | lowcmp_SimpleRepeat_triTR_11to50 | hetalt | 98.5175 | 97.1831 | 99.8891 | 27.3167 | 897 | 26 | 901 | 1 | 1 | 100.0000 | |