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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
13451-13500 / 86044 show all | |||||||||||||||
| astatham-gatk | INDEL | D6_15 | * | homalt | 98.8889 | 99.8893 | 97.9083 | 55.4989 | 6319 | 7 | 6319 | 135 | 133 | 98.5185 | |
| ckim-vqsr | INDEL | D6_15 | * | homalt | 98.8887 | 99.8735 | 97.9231 | 55.6564 | 6318 | 8 | 6318 | 134 | 131 | 97.7612 | |
| rpoplin-dv42 | SNP | * | map_l150_m1_e0 | het | 98.8884 | 98.7989 | 98.9780 | 74.2870 | 19084 | 232 | 19078 | 197 | 116 | 58.8832 | |
| ckim-gatk | SNP | * | segdup | * | 98.8880 | 99.3409 | 98.4392 | 93.5811 | 27882 | 185 | 27876 | 442 | 14 | 3.1674 | |
| ckim-dragen | INDEL | I1_5 | map_l100_m2_e1 | homalt | 98.8879 | 98.8889 | 98.8868 | 81.3172 | 534 | 6 | 533 | 6 | 5 | 83.3333 | |
| ckim-dragen | SNP | ti | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 98.8879 | 97.9575 | 99.8361 | 58.2906 | 1199 | 25 | 1218 | 2 | 2 | 100.0000 | |
| jlack-gatk | SNP | * | func_cds | het | 98.8875 | 99.9731 | 97.8251 | 36.6500 | 11158 | 3 | 11155 | 248 | 1 | 0.4032 | |
| ckim-gatk | SNP | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 98.8872 | 98.7069 | 99.0682 | 69.8958 | 2977 | 39 | 2977 | 28 | 9 | 32.1429 | |
| astatham-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 98.8871 | 99.2258 | 98.5507 | 63.9239 | 8331 | 65 | 8296 | 122 | 109 | 89.3443 | |
| jlack-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 98.8871 | 98.1073 | 99.6795 | 84.5007 | 933 | 18 | 933 | 3 | 3 | 100.0000 | |
| jlack-gatk | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 98.8869 | 98.7135 | 99.0610 | 53.7961 | 844 | 11 | 844 | 8 | 0 | 0.0000 | |
| cchapple-custom | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 98.8869 | 99.6041 | 98.1799 | 38.4191 | 10316 | 41 | 10303 | 191 | 187 | 97.9058 | |
| qzeng-custom | SNP | * | HG002compoundhet | homalt | 98.8868 | 98.8963 | 98.8772 | 42.3069 | 10663 | 119 | 8190 | 93 | 74 | 79.5699 | |
| dgrover-gatk | INDEL | * | map_l125_m2_e0 | homalt | 98.8867 | 98.9515 | 98.8220 | 87.0968 | 755 | 8 | 755 | 9 | 4 | 44.4444 | |
| gduggal-bwafb | SNP | tv | map_l100_m2_e0 | * | 98.8866 | 99.1651 | 98.6097 | 70.4745 | 24824 | 209 | 24824 | 350 | 55 | 15.7143 | |
| ckim-dragen | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 98.8861 | 98.5202 | 99.2547 | 76.5663 | 6325 | 95 | 6259 | 47 | 29 | 61.7021 | |
| ckim-dragen | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 98.8861 | 98.5202 | 99.2547 | 76.5663 | 6325 | 95 | 6259 | 47 | 29 | 61.7021 | |
| jli-custom | INDEL | I1_5 | map_l125_m2_e0 | het | 98.8859 | 98.1891 | 99.5927 | 86.2696 | 488 | 9 | 489 | 2 | 0 | 0.0000 | |
| asubramanian-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 98.8858 | 98.0576 | 99.7281 | 33.7984 | 1464 | 29 | 1467 | 4 | 3 | 75.0000 | |
| asubramanian-gatk | SNP | * | * | homalt | 98.8858 | 97.8294 | 99.9654 | 17.5292 | 1154544 | 25617 | 1154521 | 400 | 39 | 9.7500 | |
| dgrover-gatk | INDEL | D16_PLUS | * | homalt | 98.8856 | 99.6454 | 98.1374 | 70.5317 | 1686 | 6 | 1686 | 32 | 23 | 71.8750 | |
| dgrover-gatk | INDEL | D6_15 | * | het | 98.8856 | 99.4565 | 98.3212 | 62.9800 | 11529 | 63 | 11479 | 196 | 167 | 85.2041 | |
| ckim-gatk | SNP | * | HG002compoundhet | hetalt | 98.8856 | 97.7958 | 100.0000 | 22.8728 | 843 | 19 | 843 | 0 | 0 | ||
| ckim-gatk | SNP | tv | HG002compoundhet | hetalt | 98.8856 | 97.7958 | 100.0000 | 22.8728 | 843 | 19 | 843 | 0 | 0 | ||
| bgallagher-sentieon | INDEL | * | map_l150_m2_e1 | homalt | 98.8855 | 99.1870 | 98.5859 | 89.3019 | 488 | 4 | 488 | 7 | 4 | 57.1429 | |
| egarrison-hhga | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 98.8850 | 98.5441 | 99.2284 | 79.4839 | 3858 | 57 | 3858 | 30 | 23 | 76.6667 | |
| egarrison-hhga | SNP | * | HG002compoundhet | * | 98.8848 | 98.3812 | 99.3937 | 39.7483 | 25404 | 418 | 25408 | 155 | 114 | 73.5484 | |
| ltrigg-rtg1 | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 98.8848 | 99.7965 | 97.9897 | 57.5988 | 3923 | 8 | 3997 | 82 | 1 | 1.2195 | |
| ltrigg-rtg1 | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 98.8845 | 99.1738 | 98.5968 | 78.6472 | 6602 | 55 | 6605 | 94 | 1 | 1.0638 | |
| jmaeng-gatk | INDEL | D6_15 | HG002complexvar | het | 98.8845 | 98.7179 | 99.0517 | 59.4483 | 3080 | 40 | 3029 | 29 | 25 | 86.2069 | |
| hfeng-pmm2 | SNP | tv | lowcmp_SimpleRepeat_quadTR_11to50 | het | 98.8844 | 98.3152 | 99.4603 | 36.9967 | 4610 | 79 | 4607 | 25 | 0 | 0.0000 | |
| egarrison-hhga | INDEL | * | map_l125_m2_e0 | homalt | 98.8838 | 98.6894 | 99.0789 | 86.4407 | 753 | 10 | 753 | 7 | 4 | 57.1429 | |
| jmaeng-gatk | INDEL | * | map_l125_m2_e0 | homalt | 98.8838 | 98.6894 | 99.0789 | 86.9841 | 753 | 10 | 753 | 7 | 4 | 57.1429 | |
| jlack-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 98.8835 | 99.1132 | 98.6549 | 87.3860 | 2347 | 21 | 2347 | 32 | 17 | 53.1250 | |
| ghariani-varprowl | SNP | tv | map_l125_m2_e1 | homalt | 98.8833 | 98.4030 | 99.3682 | 71.6795 | 5977 | 97 | 5977 | 38 | 24 | 63.1579 | |
| hfeng-pmm1 | INDEL | * | lowcmp_SimpleRepeat_quadTR_51to200 | homalt | 98.8832 | 98.9837 | 98.7830 | 57.5731 | 487 | 5 | 487 | 6 | 5 | 83.3333 | |
| hfeng-pmm1 | INDEL | * | map_l150_m2_e1 | homalt | 98.8832 | 98.9837 | 98.7830 | 88.0630 | 487 | 5 | 487 | 6 | 3 | 50.0000 | |
| jli-custom | INDEL | * | map_l150_m2_e1 | homalt | 98.8832 | 98.9837 | 98.7830 | 88.3699 | 487 | 5 | 487 | 6 | 4 | 66.6667 | |
| hfeng-pmm3 | INDEL | * | lowcmp_SimpleRepeat_quadTR_51to200 | homalt | 98.8832 | 98.9837 | 98.7830 | 57.7187 | 487 | 5 | 487 | 6 | 5 | 83.3333 | |
| hfeng-pmm3 | INDEL | * | map_l150_m2_e1 | homalt | 98.8832 | 98.9837 | 98.7830 | 87.5316 | 487 | 5 | 487 | 6 | 3 | 50.0000 | |
| dgrover-gatk | SNP | tv | map_l250_m1_e0 | homalt | 98.8830 | 98.2477 | 99.5266 | 85.6901 | 841 | 15 | 841 | 4 | 3 | 75.0000 | |
| ndellapenna-hhga | SNP | * | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 98.8830 | 98.6107 | 99.1567 | 58.6659 | 3407 | 48 | 3410 | 29 | 25 | 86.2069 | |
| ckim-dragen | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 98.8829 | 98.3619 | 99.4094 | 51.8057 | 2642 | 44 | 2693 | 16 | 3 | 18.7500 | |
| jli-custom | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 98.8825 | 98.9969 | 98.7683 | 87.0977 | 1283 | 13 | 1283 | 16 | 6 | 37.5000 | |
| ndellapenna-hhga | SNP | ti | map_l125_m2_e1 | het | 98.8822 | 98.0248 | 99.7547 | 70.7116 | 18710 | 377 | 18710 | 46 | 20 | 43.4783 | |
| egarrison-hhga | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 98.8822 | 98.9362 | 98.8283 | 47.8545 | 3627 | 39 | 3627 | 43 | 30 | 69.7674 | |
| gduggal-bwaplat | SNP | ti | segdup | homalt | 98.8821 | 97.8281 | 99.9591 | 88.2036 | 7342 | 163 | 7338 | 3 | 3 | 100.0000 | |
| gduggal-bwafb | SNP | tv | map_l250_m1_e0 | homalt | 98.8817 | 98.1308 | 99.6441 | 88.5431 | 840 | 16 | 840 | 3 | 3 | 100.0000 | |
| asubramanian-gatk | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 98.8815 | 98.4877 | 99.2784 | 83.9265 | 2605 | 40 | 2614 | 19 | 9 | 47.3684 | |
| ghariani-varprowl | SNP | tv | map_l125_m2_e0 | homalt | 98.8811 | 98.4045 | 99.3623 | 71.6697 | 5921 | 96 | 5921 | 38 | 24 | 63.1579 | |