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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
35301-35350 / 86044 show all | |||||||||||||||
| jlack-gatk | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 95.8359 | 92.4591 | 99.4688 | 63.5748 | 8595 | 701 | 8613 | 46 | 42 | 91.3043 | |
| 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 | |
| jmaeng-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 98.9740 | 99.8086 | 98.1532 | 63.5791 | 8344 | 16 | 8344 | 157 | 156 | 99.3631 | |
| jmaeng-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 98.9740 | 99.8086 | 98.1532 | 63.5791 | 8344 | 16 | 8344 | 157 | 156 | 99.3631 | |
| rpoplin-dv42 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 94.9862 | 97.5782 | 92.5283 | 63.5798 | 14263 | 354 | 14130 | 1141 | 1110 | 97.2831 | |
| gduggal-snapfb | SNP | tv | map_siren | het | 97.7974 | 98.9374 | 96.6834 | 63.5849 | 28305 | 304 | 28306 | 971 | 266 | 27.3944 | |
| hfeng-pmm3 | INDEL | I1_5 | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 99.4393 | 99.6255 | 99.2537 | 63.5870 | 266 | 1 | 266 | 2 | 2 | 100.0000 | |
| qzeng-custom | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 91.8091 | 96.9639 | 87.1747 | 63.5912 | 511 | 16 | 1407 | 207 | 89 | 42.9952 | |
| ltrigg-rtg1 | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 94.0476 | 88.7640 | 100.0000 | 63.5922 | 79 | 10 | 75 | 0 | 0 | ||
| gduggal-snapvard | SNP | tv | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 96.3092 | 94.0011 | 98.7334 | 63.5924 | 1661 | 106 | 1637 | 21 | 7 | 33.3333 | |
| gduggal-bwafb | INDEL | I1_5 | HG002compoundhet | * | 88.8259 | 85.0923 | 92.9023 | 63.5931 | 10514 | 1842 | 11309 | 864 | 824 | 95.3704 | |
| ltrigg-rtg1 | SNP | * | map_l150_m1_e0 | het | 98.3972 | 97.0957 | 99.7341 | 63.5971 | 18755 | 561 | 18755 | 50 | 9 | 18.0000 | |
| jli-custom | SNP | * | map_l100_m0_e0 | * | 99.1662 | 98.8612 | 99.4730 | 63.5990 | 32467 | 374 | 32467 | 172 | 59 | 34.3023 | |
| gduggal-snapfb | SNP | * | tech_badpromoters | * | 93.1343 | 99.3631 | 87.6404 | 63.5992 | 156 | 1 | 156 | 22 | 1 | 4.5455 | |
| astatham-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 99.0563 | 99.8206 | 98.3037 | 63.5993 | 8345 | 15 | 8345 | 144 | 142 | 98.6111 | |
| astatham-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 99.0563 | 99.8206 | 98.3037 | 63.5993 | 8345 | 15 | 8345 | 144 | 142 | 98.6111 | |
| gduggal-snapvard | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 64.7166 | 48.4446 | 97.4485 | 63.6006 | 1822 | 1939 | 1986 | 52 | 43 | 82.6923 | |
| gduggal-snapvard | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 64.7166 | 48.4446 | 97.4485 | 63.6006 | 1822 | 1939 | 1986 | 52 | 43 | 82.6923 | |
| dgrover-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 99.6526 | 99.6524 | 99.6528 | 63.6057 | 860 | 3 | 861 | 3 | 2 | 66.6667 | |
| gduggal-bwafb | INDEL | I1_5 | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 95.9381 | 92.8839 | 99.2000 | 63.6099 | 248 | 19 | 248 | 2 | 2 | 100.0000 | |
| qzeng-custom | SNP | * | map_siren | * | 92.3867 | 86.6004 | 99.0016 | 63.6130 | 126634 | 19594 | 125047 | 1261 | 903 | 71.6098 | |
| raldana-dualsentieon | INDEL | D16_PLUS | lowcmp_SimpleRepeat_triTR_11to50 | * | 98.7179 | 98.0892 | 99.3548 | 63.6150 | 154 | 3 | 154 | 1 | 1 | 100.0000 | |
| gduggal-bwafb | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 91.6223 | 87.8582 | 95.7234 | 63.6163 | 7388 | 1021 | 5842 | 261 | 219 | 83.9080 | |
| bgallagher-sentieon | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 99.7244 | 99.8620 | 99.5872 | 63.6182 | 2171 | 3 | 2171 | 9 | 0 | 0.0000 | |
| qzeng-custom | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 64.5786 | 95.6522 | 48.7437 | 63.6197 | 22 | 1 | 97 | 102 | 88 | 86.2745 | |
| hfeng-pmm2 | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 99.6236 | 99.4987 | 99.7487 | 63.6197 | 397 | 2 | 397 | 1 | 1 | 100.0000 | |
| gduggal-bwafb | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 87.5847 | 96.7922 | 79.9769 | 63.6211 | 694 | 23 | 691 | 173 | 173 | 100.0000 | |
| ltrigg-rtg2 | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 99.3763 | 98.7603 | 100.0000 | 63.6228 | 239 | 3 | 243 | 0 | 0 | ||
| ckim-dragen | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 98.0612 | 98.8372 | 97.2973 | 63.6236 | 255 | 3 | 252 | 7 | 7 | 100.0000 | |
| mlin-fermikit | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 79.6367 | 72.0025 | 89.0817 | 63.6267 | 4552 | 1770 | 4569 | 560 | 555 | 99.1071 | |
| mlin-fermikit | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 79.6367 | 72.0025 | 89.0817 | 63.6267 | 4552 | 1770 | 4569 | 560 | 555 | 99.1071 | |
| ckim-isaac | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 95.3986 | 91.8696 | 99.2095 | 63.6282 | 28260 | 2501 | 28237 | 225 | 152 | 67.5556 | |
| hfeng-pmm2 | INDEL | D1_5 | * | hetalt | 97.1704 | 94.5242 | 99.9692 | 63.6326 | 9684 | 561 | 9726 | 3 | 1 | 33.3333 | |
| ckim-vqsr | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 99.4006 | 99.5116 | 99.2899 | 63.6333 | 35246 | 173 | 35235 | 252 | 21 | 8.3333 | |
| gduggal-snapplat | INDEL | D6_15 | * | homalt | 55.1666 | 41.1476 | 83.6743 | 63.6351 | 2603 | 3723 | 2168 | 423 | 248 | 58.6288 | |
| raldana-dualsentieon | SNP | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 98.5255 | 97.4811 | 99.5925 | 63.6357 | 4644 | 120 | 4644 | 19 | 2 | 10.5263 | |
| jmaeng-gatk | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | het | 99.4180 | 99.2798 | 99.5566 | 63.6361 | 11028 | 80 | 11002 | 49 | 18 | 36.7347 | |
| ltrigg-rtg1 | SNP | * | map_l100_m0_e0 | hetalt | 100.0000 | 100.0000 | 100.0000 | 63.6364 | 16 | 0 | 16 | 0 | 0 | ||
| ltrigg-rtg1 | SNP | ti | map_l125_m2_e0 | hetalt | 100.0000 | 100.0000 | 100.0000 | 63.6364 | 24 | 0 | 24 | 0 | 0 | ||
| ltrigg-rtg1 | SNP | ti | map_l125_m2_e1 | hetalt | 100.0000 | 100.0000 | 100.0000 | 63.6364 | 24 | 0 | 24 | 0 | 0 | ||
| ltrigg-rtg1 | SNP | tv | map_l100_m0_e0 | hetalt | 100.0000 | 100.0000 | 100.0000 | 63.6364 | 16 | 0 | 16 | 0 | 0 | ||
| qzeng-custom | INDEL | I6_15 | lowcmp_SimpleRepeat_triTR_51to200 | * | 62.6866 | 53.8462 | 75.0000 | 63.6364 | 7 | 6 | 12 | 4 | 4 | 100.0000 | |
| ndellapenna-hhga | INDEL | D6_15 | func_cds | homalt | 100.0000 | 100.0000 | 100.0000 | 63.6364 | 12 | 0 | 12 | 0 | 0 | ||
| gduggal-snapplat | INDEL | D6_15 | func_cds | * | 38.1503 | 25.5814 | 75.0000 | 63.6364 | 11 | 32 | 6 | 2 | 0 | 0.0000 | |
| gduggal-snapvard | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 0.0000 | 0.0000 | 37.5000 | 63.6364 | 0 | 106 | 18 | 30 | 11 | 36.6667 | |
| gduggal-snapplat | INDEL | I6_15 | tech_badpromoters | het | 36.3636 | 28.5714 | 50.0000 | 63.6364 | 2 | 5 | 2 | 2 | 0 | 0.0000 | |
| hfeng-pmm3 | INDEL | * | func_cds | hetalt | 88.8889 | 80.0000 | 100.0000 | 63.6364 | 4 | 1 | 4 | 0 | 0 | ||
| jlack-gatk | SNP | ti | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 99.7031 | 99.4668 | 99.9405 | 63.6364 | 1679 | 9 | 1679 | 1 | 1 | 100.0000 | |
| hfeng-pmm3 | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | hetalt | 96.8750 | 93.9394 | 100.0000 | 63.6364 | 31 | 2 | 32 | 0 | 0 | ||
| asubramanian-gatk | INDEL | * | func_cds | hetalt | 88.8889 | 80.0000 | 100.0000 | 63.6364 | 4 | 1 | 4 | 0 | 0 | ||