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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
64851-64900 / 86044 show all | |||||||||||||||
| jli-custom | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 97.6055 | 95.7176 | 99.5693 | 26.7854 | 7823 | 350 | 7860 | 34 | 32 | 94.1176 | |
| ltrigg-rtg2 | SNP | tv | func_cds | * | 99.5213 | 99.8856 | 99.1597 | 26.7631 | 4366 | 5 | 4366 | 37 | 0 | 0.0000 | |
| cchapple-custom | SNP | * | func_cds | * | 99.7855 | 99.9174 | 99.6539 | 26.7611 | 18135 | 15 | 18142 | 63 | 1 | 1.5873 | |
| eyeh-varpipe | SNP | ti | func_cds | het | 98.8564 | 99.9647 | 97.7724 | 26.7528 | 8501 | 3 | 8427 | 192 | 1 | 0.5208 | |
| ckim-vqsr | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 96.8082 | 94.2070 | 99.5571 | 26.7517 | 6700 | 412 | 6744 | 30 | 30 | 100.0000 | |
| ckim-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 96.8156 | 94.2210 | 99.5572 | 26.7488 | 6701 | 411 | 6745 | 30 | 30 | 100.0000 | |
| jmaeng-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 96.4855 | 93.5742 | 99.5838 | 26.7211 | 6655 | 457 | 6699 | 28 | 28 | 100.0000 | |
| ltrigg-rtg2 | INDEL | I1_5 | func_cds | * | 99.7230 | 100.0000 | 99.4475 | 26.7206 | 180 | 0 | 180 | 1 | 0 | 0.0000 | |
| ckim-gatk | INDEL | * | lowcmp_SimpleRepeat_triTR_11to50 | hetalt | 98.4617 | 97.0748 | 99.8889 | 26.7101 | 896 | 27 | 899 | 1 | 1 | 100.0000 | |
| ckim-vqsr | INDEL | * | lowcmp_SimpleRepeat_triTR_11to50 | hetalt | 98.4617 | 97.0748 | 99.8889 | 26.7101 | 896 | 27 | 899 | 1 | 1 | 100.0000 | |
| asubramanian-gatk | SNP | tv | * | het | 98.8211 | 97.8557 | 99.8057 | 26.7081 | 579008 | 12688 | 578944 | 1127 | 42 | 3.7267 | |
| qzeng-custom | SNP | ti | func_cds | * | 99.7894 | 99.8622 | 99.7168 | 26.7032 | 13768 | 19 | 13732 | 39 | 4 | 10.2564 | |
| gduggal-snapfb | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | het | 78.5748 | 67.1057 | 94.7725 | 26.6989 | 1834 | 899 | 5602 | 309 | 300 | 97.0874 | |
| mlin-fermikit | INDEL | I6_15 | lowcmp_SimpleRepeat_triTR_11to50 | hetalt | 86.3984 | 76.3713 | 99.4565 | 26.6932 | 181 | 56 | 183 | 1 | 1 | 100.0000 | |
| bgallagher-sentieon | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 96.3667 | 93.0278 | 99.9543 | 26.6834 | 4323 | 324 | 4375 | 2 | 2 | 100.0000 | |
| ckim-isaac | SNP | * | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 97.4799 | 95.1964 | 99.8756 | 26.6788 | 6421 | 324 | 6423 | 8 | 7 | 87.5000 | |
| ckim-dragen | SNP | tv | func_cds | homalt | 100.0000 | 100.0000 | 100.0000 | 26.6781 | 1704 | 0 | 1704 | 0 | 0 | ||
| ckim-gatk | SNP | ti | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 99.7545 | 99.6496 | 99.8596 | 26.6735 | 1422 | 5 | 1422 | 2 | 2 | 100.0000 | |
| ltrigg-rtg1 | INDEL | D16_PLUS | lowcmp_SimpleRepeat_triTR_51to200 | hetalt | 93.6170 | 88.0000 | 100.0000 | 26.6667 | 22 | 3 | 22 | 0 | 0 | ||
| ltrigg-rtg2 | INDEL | D16_PLUS | lowcmp_SimpleRepeat_triTR_51to200 | hetalt | 93.6170 | 88.0000 | 100.0000 | 26.6667 | 22 | 3 | 22 | 0 | 0 | ||
| eyeh-varpipe | INDEL | D1_5 | tech_badpromoters | homalt | 90.0000 | 100.0000 | 81.8182 | 26.6667 | 9 | 0 | 9 | 2 | 2 | 100.0000 | |
| rpoplin-dv42 | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_51to200 | hetalt | 64.6644 | 48.0447 | 98.8636 | 26.6667 | 86 | 93 | 87 | 1 | 1 | 100.0000 | |
| gduggal-bwaplat | SNP | * | * | * | 98.8646 | 98.0471 | 99.6958 | 26.6546 | 2994965 | 59654 | 2995523 | 9139 | 1314 | 14.3779 | |
| gduggal-snapfb | INDEL | D6_15 | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 88.9406 | 86.2302 | 91.8269 | 26.6314 | 382 | 61 | 382 | 34 | 33 | 97.0588 | |
| ckim-isaac | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 93.1476 | 88.3677 | 98.4741 | 26.6190 | 6085 | 801 | 6260 | 97 | 90 | 92.7835 | |
| gduggal-snapvard | INDEL | D6_15 | lowcmp_SimpleRepeat_triTR_51to200 | * | 40.1132 | 30.9859 | 56.8627 | 26.6187 | 44 | 98 | 58 | 44 | 40 | 90.9091 | |
| gduggal-snapvard | INDEL | D6_15 | lowcmp_SimpleRepeat_triTR_51to200 | het | 48.0929 | 41.6667 | 56.8627 | 26.6187 | 10 | 14 | 58 | 44 | 40 | 90.9091 | |
| asubramanian-gatk | INDEL | D16_PLUS | HG002compoundhet | hetalt | 95.9105 | 93.3091 | 98.6612 | 26.6062 | 1799 | 129 | 1916 | 26 | 22 | 84.6154 | |
| qzeng-custom | INDEL | I6_15 | lowcmp_SimpleRepeat_triTR_11to50 | hetalt | 97.4026 | 94.9367 | 100.0000 | 26.5823 | 225 | 12 | 290 | 0 | 0 | ||
| ndellapenna-hhga | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 96.6789 | 94.2328 | 99.2552 | 26.5783 | 4379 | 268 | 4398 | 33 | 30 | 90.9091 | |
| jpowers-varprowl | SNP | ti | func_cds | * | 99.5285 | 99.5285 | 99.5285 | 26.5751 | 13722 | 65 | 13722 | 65 | 9 | 13.8462 | |
| ndellapenna-hhga | SNP | tv | func_cds | homalt | 100.0000 | 100.0000 | 100.0000 | 26.5517 | 1704 | 0 | 1704 | 0 | 0 | ||
| ckim-dragen | INDEL | D16_PLUS | HG002compoundhet | hetalt | 96.4348 | 93.5685 | 99.4824 | 26.5399 | 1804 | 124 | 1922 | 10 | 10 | 100.0000 | |
| egarrison-hhga | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 96.9212 | 94.7708 | 99.1715 | 26.5340 | 4404 | 243 | 4429 | 37 | 35 | 94.5946 | |
| dgrover-gatk | INDEL | D16_PLUS | HG002compoundhet | hetalt | 97.0887 | 94.7095 | 99.5904 | 26.5237 | 1826 | 102 | 1945 | 8 | 8 | 100.0000 | |
| ckim-dragen | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 96.2607 | 92.7910 | 100.0000 | 26.5013 | 4312 | 335 | 4357 | 0 | 0 | ||
| ckim-dragen | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 97.3592 | 95.2372 | 99.5780 | 26.4946 | 5179 | 259 | 5191 | 22 | 22 | 100.0000 | |
| eyeh-varpipe | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_51to200 | * | 21.5835 | 18.1202 | 26.6833 | 26.4895 | 214 | 967 | 214 | 588 | 544 | 92.5170 | |
| hfeng-pmm2 | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 97.5229 | 95.1931 | 99.9696 | 26.4607 | 6555 | 331 | 6568 | 2 | 1 | 50.0000 | |
| jlack-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 96.2898 | 93.2880 | 99.4913 | 26.4604 | 5073 | 365 | 5085 | 26 | 21 | 80.7692 | |
| ckim-isaac | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 92.5840 | 86.9698 | 98.9730 | 26.4574 | 9658 | 1447 | 9926 | 103 | 93 | 90.2913 | |
| hfeng-pmm1 | INDEL | D16_PLUS | HG002compoundhet | hetalt | 96.7327 | 93.6722 | 100.0000 | 26.4571 | 1806 | 122 | 1918 | 0 | 0 | ||
| astatham-gatk | INDEL | D16_PLUS | HG002compoundhet | hetalt | 97.0065 | 94.5539 | 99.5897 | 26.4429 | 1823 | 105 | 1942 | 8 | 8 | 100.0000 | |
| qzeng-custom | SNP | tv | * | * | 99.4379 | 99.2180 | 99.6588 | 26.4392 | 962115 | 7583 | 958619 | 3282 | 549 | 16.7276 | |
| bgallagher-sentieon | INDEL | D16_PLUS | HG002compoundhet | hetalt | 96.6214 | 93.8278 | 99.5863 | 26.4359 | 1809 | 119 | 1926 | 8 | 8 | 100.0000 | |
| bgallagher-sentieon | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_51to200 | hetalt | 85.6059 | 75.0000 | 99.7054 | 26.4355 | 654 | 218 | 677 | 2 | 2 | 100.0000 | |
| eyeh-varpipe | SNP | * | func_cds | * | 98.2084 | 99.9669 | 96.5106 | 26.4105 | 18144 | 6 | 17950 | 649 | 1 | 0.1541 | |
| jli-custom | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 97.6090 | 95.7958 | 99.4921 | 26.3939 | 6813 | 299 | 6856 | 35 | 34 | 97.1429 | |
| cchapple-custom | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 99.1720 | 99.7378 | 98.6126 | 26.3903 | 7228 | 19 | 7179 | 101 | 98 | 97.0297 | |
| hfeng-pmm2 | INDEL | D16_PLUS | HG002compoundhet | hetalt | 96.7604 | 93.7241 | 100.0000 | 26.3804 | 1807 | 121 | 1920 | 0 | 0 | ||