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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
27351-27400 / 86044 show all | |||||||||||||||
| ckim-vqsr | INDEL | I1_5 | map_l100_m0_e0 | het | 95.9671 | 94.7853 | 97.1787 | 91.9444 | 309 | 17 | 310 | 9 | 0 | 0.0000 | |
| ckim-vqsr | SNP | ti | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 99.3658 | 98.8087 | 99.9291 | 26.8533 | 1410 | 17 | 1410 | 1 | 1 | 100.0000 | |
| dgrover-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 98.0674 | 97.7089 | 98.4286 | 73.8024 | 725 | 17 | 689 | 11 | 5 | 45.4545 | |
| dgrover-gatk | SNP | * | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 99.9214 | 99.9010 | 99.9417 | 55.7201 | 17160 | 17 | 17156 | 10 | 8 | 80.0000 | |
| dgrover-gatk | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 99.2822 | 99.3573 | 99.2072 | 83.9930 | 2628 | 17 | 2628 | 21 | 7 | 33.3333 | |
| egarrison-hhga | INDEL | D16_PLUS | lowcmp_SimpleRepeat_homopolymer_gt10 | * | 82.2581 | 75.0000 | 91.0714 | 96.6981 | 51 | 17 | 51 | 5 | 4 | 80.0000 | |
| egarrison-hhga | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 98.2552 | 98.0301 | 98.4813 | 60.8417 | 846 | 17 | 843 | 13 | 10 | 76.9231 | |
| egarrison-hhga | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_51to200 | het | 55.0999 | 88.5135 | 40.0000 | 49.5006 | 131 | 17 | 182 | 273 | 271 | 99.2674 | |
| egarrison-hhga | INDEL | D6_15 | lowcmp_SimpleRepeat_homopolymer_6to10 | hetalt | 67.6759 | 54.0541 | 90.4762 | 58.8235 | 20 | 17 | 19 | 2 | 2 | 100.0000 | |
| egarrison-hhga | INDEL | I16_PLUS | map_siren | * | 83.2113 | 80.2326 | 86.4198 | 84.0551 | 69 | 17 | 70 | 11 | 7 | 63.6364 | |
| egarrison-hhga | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | hetalt | 95.4743 | 92.1659 | 99.0291 | 42.7778 | 200 | 17 | 204 | 2 | 2 | 100.0000 | |
| egarrison-hhga | INDEL | I1_5 | map_l100_m1_e0 | * | 98.8042 | 98.7304 | 98.8781 | 83.3892 | 1322 | 17 | 1322 | 15 | 3 | 20.0000 | |
| egarrison-hhga | INDEL | I1_5 | map_l100_m2_e0 | * | 98.7934 | 98.7573 | 98.8296 | 84.6491 | 1351 | 17 | 1351 | 16 | 3 | 18.7500 | |
| egarrison-hhga | SNP | * | lowcmp_SimpleRepeat_homopolymer_6to10 | homalt | 99.7945 | 99.7208 | 99.8684 | 54.9696 | 6071 | 17 | 6072 | 8 | 7 | 87.5000 | |
| egarrison-hhga | SNP | tv | map_l100_m0_e0 | homalt | 99.7265 | 99.5580 | 99.8956 | 63.0055 | 3829 | 17 | 3829 | 4 | 3 | 75.0000 | |
| eyeh-varpipe | INDEL | * | map_l125_m2_e0 | hetalt | 73.6278 | 59.5238 | 96.4912 | 93.6947 | 25 | 17 | 55 | 2 | 1 | 50.0000 | |
| ckim-isaac | INDEL | D16_PLUS | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 85.9341 | 80.4598 | 92.2078 | 71.1610 | 70 | 17 | 71 | 6 | 5 | 83.3333 | |
| ckim-isaac | INDEL | D16_PLUS | lowcmp_SimpleRepeat_triTR_51to200 | * | 75.3247 | 63.0435 | 93.5484 | 55.0725 | 29 | 17 | 29 | 2 | 2 | 100.0000 | |
| ckim-isaac | INDEL | D16_PLUS | map_l100_m0_e0 | het | 16.6667 | 10.5263 | 40.0000 | 95.2381 | 2 | 17 | 2 | 3 | 1 | 33.3333 | |
| ckim-isaac | INDEL | D1_5 | map_l100_m2_e1 | hetalt | 77.1930 | 66.6667 | 91.6667 | 89.2216 | 34 | 17 | 33 | 3 | 3 | 100.0000 | |
| ckim-isaac | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | hetalt | 78.7936 | 69.0909 | 91.6667 | 70.8738 | 38 | 17 | 55 | 5 | 4 | 80.0000 | |
| ckim-isaac | INDEL | D6_15 | lowcmp_SimpleRepeat_homopolymer_gt10 | * | 70.5404 | 70.1754 | 70.9091 | 97.0238 | 40 | 17 | 39 | 16 | 5 | 31.2500 | |
| ckim-isaac | INDEL | D6_15 | map_l150_m0_e0 | het | 25.0000 | 15.0000 | 75.0000 | 97.9695 | 3 | 17 | 3 | 1 | 1 | 100.0000 | |
| ckim-isaac | INDEL | D6_15 | map_l150_m2_e1 | homalt | 58.5366 | 41.3793 | 100.0000 | 80.0000 | 12 | 17 | 12 | 0 | 0 | ||
| ckim-isaac | INDEL | I16_PLUS | lowcmp_SimpleRepeat_quadTR_51to200 | * | 51.4286 | 34.6154 | 100.0000 | 86.1538 | 9 | 17 | 9 | 0 | 0 | ||
| ckim-isaac | INDEL | I1_5 | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 96.1516 | 93.6330 | 98.8095 | 54.5946 | 250 | 17 | 249 | 3 | 1 | 33.3333 | |
| ndellapenna-hhga | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 93.0752 | 90.4494 | 95.8580 | 71.6918 | 161 | 17 | 162 | 7 | 6 | 85.7143 | |
| ndellapenna-hhga | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 91.7051 | 92.1296 | 91.2844 | 63.1134 | 199 | 17 | 199 | 19 | 15 | 78.9474 | |
| ndellapenna-hhga | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 95.1002 | 96.1712 | 94.0529 | 81.2552 | 427 | 17 | 427 | 27 | 22 | 81.4815 | |
| ndellapenna-hhga | SNP | ti | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 99.8164 | 99.7288 | 99.9041 | 43.6419 | 6251 | 17 | 6252 | 6 | 5 | 83.3333 | |
| ndellapenna-hhga | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 90.6780 | 86.2903 | 95.5357 | 87.6243 | 107 | 17 | 107 | 5 | 3 | 60.0000 | |
| ndellapenna-hhga | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 96.7880 | 96.3753 | 97.2043 | 81.1588 | 452 | 17 | 452 | 13 | 13 | 100.0000 | |
| mlin-fermikit | INDEL | D6_15 | lowcmp_SimpleRepeat_homopolymer_6to10 | hetalt | 70.1754 | 54.0541 | 100.0000 | 66.6667 | 20 | 17 | 20 | 0 | 0 | ||
| mlin-fermikit | INDEL | D6_15 | lowcmp_SimpleRepeat_homopolymer_gt10 | het | 70.7177 | 59.5238 | 87.0968 | 98.6964 | 25 | 17 | 27 | 4 | 3 | 75.0000 | |
| mlin-fermikit | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | homalt | 84.7458 | 91.1458 | 79.1855 | 59.0741 | 175 | 17 | 175 | 46 | 43 | 93.4783 | |
| mlin-fermikit | INDEL | D6_15 | map_l125_m0_e0 | het | 49.6025 | 41.3793 | 61.9048 | 83.7209 | 12 | 17 | 13 | 8 | 4 | 50.0000 | |
| mlin-fermikit | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 87.8850 | 84.2593 | 91.8367 | 77.9775 | 91 | 17 | 90 | 8 | 8 | 100.0000 | |
| mlin-fermikit | INDEL | I16_PLUS | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 72.7674 | 63.8298 | 84.6154 | 79.0323 | 30 | 17 | 33 | 6 | 6 | 100.0000 | |
| mlin-fermikit | INDEL | I1_5 | lowcmp_SimpleRepeat_triTR_51to200 | * | 39.0244 | 32.0000 | 50.0000 | 68.0000 | 8 | 17 | 8 | 8 | 7 | 87.5000 | |
| mlin-fermikit | INDEL | I1_5 | map_l250_m0_e0 | * | 42.4242 | 29.1667 | 77.7778 | 95.4315 | 7 | 17 | 7 | 2 | 1 | 50.0000 | |
| mlin-fermikit | INDEL | I6_15 | lowcmp_SimpleRepeat_homopolymer_6to10 | hetalt | 76.0563 | 61.3636 | 100.0000 | 74.2857 | 27 | 17 | 27 | 0 | 0 | ||
| ltrigg-rtg2 | INDEL | D16_PLUS | map_l100_m1_e0 | * | 88.0008 | 80.4598 | 97.1014 | 83.0882 | 70 | 17 | 67 | 2 | 1 | 50.0000 | |
| ltrigg-rtg2 | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 81.6591 | 71.1864 | 95.7447 | 71.8563 | 42 | 17 | 45 | 2 | 2 | 100.0000 | |
| ltrigg-rtg2 | INDEL | I1_5 | map_l150_m1_e0 | het | 96.5664 | 94.3144 | 98.9286 | 82.5218 | 282 | 17 | 277 | 3 | 0 | 0.0000 | |
| ltrigg-rtg2 | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 98.6723 | 99.5675 | 97.7930 | 57.7847 | 3914 | 17 | 3988 | 90 | 2 | 2.2222 | |
| ndellapenna-hhga | INDEL | D16_PLUS | HG002complexvar | homalt | 84.2511 | 94.1176 | 76.2570 | 66.9437 | 272 | 17 | 273 | 85 | 60 | 70.5882 | |
| ndellapenna-hhga | INDEL | D16_PLUS | map_l100_m2_e0 | * | 83.1183 | 81.1111 | 85.2273 | 88.2353 | 73 | 17 | 75 | 13 | 6 | 46.1538 | |
| ndellapenna-hhga | INDEL | D1_5 | map_l100_m0_e0 | het | 97.2058 | 97.1235 | 97.2881 | 83.7734 | 574 | 17 | 574 | 16 | 4 | 25.0000 | |
| ndellapenna-hhga | INDEL | D1_5 | map_l100_m2_e0 | hetalt | 75.5177 | 64.5833 | 90.9091 | 92.6829 | 31 | 17 | 30 | 3 | 2 | 66.6667 | |
| ndellapenna-hhga | INDEL | D1_5 | map_l100_m2_e1 | hetalt | 77.1930 | 66.6667 | 91.6667 | 92.2414 | 34 | 17 | 33 | 3 | 2 | 66.6667 | |