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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
25151-25200 / 86044 show all | |||||||||||||||
| egarrison-hhga | SNP | * | HG002compoundhet | het | 98.5499 | 97.5455 | 99.5752 | 43.4625 | 13830 | 348 | 13830 | 59 | 31 | 52.5424 | |
| mlin-fermikit | SNP | ti | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 99.1067 | 98.2534 | 99.9750 | 43.4659 | 3994 | 71 | 3992 | 1 | 0 | 0.0000 | |
| gduggal-bwafb | INDEL | * | func_cds | het | 94.3524 | 92.9907 | 95.7547 | 43.4667 | 199 | 15 | 203 | 9 | 7 | 77.7778 | |
| hfeng-pmm3 | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_11to50 | het | 99.4287 | 98.9934 | 99.8677 | 43.4696 | 2262 | 23 | 2265 | 3 | 0 | 0.0000 | |
| qzeng-custom | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 92.7237 | 93.5806 | 91.8824 | 43.4731 | 2624 | 180 | 2626 | 232 | 212 | 91.3793 | |
| ndellapenna-hhga | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_51to200 | homalt | 100.0000 | 100.0000 | 100.0000 | 43.4783 | 13 | 0 | 13 | 0 | 0 | ||
| ckim-isaac | INDEL | D6_15 | lowcmp_SimpleRepeat_triTR_51to200 | het | 71.6186 | 79.1667 | 65.3846 | 43.4783 | 19 | 5 | 17 | 9 | 9 | 100.0000 | |
| ltrigg-rtg1 | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_51to200 | homalt | 100.0000 | 100.0000 | 100.0000 | 43.4783 | 13 | 0 | 13 | 0 | 0 | ||
| jli-custom | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | hetalt | 95.6522 | 91.6667 | 100.0000 | 43.4783 | 11 | 1 | 13 | 0 | 0 | ||
| anovak-vg | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 49.4570 | 43.9271 | 56.5797 | 43.4855 | 4868 | 6214 | 5009 | 3844 | 2967 | 77.1852 | |
| ckim-vqsr | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 99.6885 | 99.4406 | 99.9375 | 43.4875 | 1600 | 9 | 1600 | 1 | 1 | 100.0000 | |
| jpowers-varprowl | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 45.4140 | 30.7174 | 87.0736 | 43.4900 | 1460 | 3293 | 1455 | 216 | 197 | 91.2037 | |
| hfeng-pmm2 | SNP | tv | HG002compoundhet | homalt | 99.7933 | 99.7639 | 99.8228 | 43.5008 | 3380 | 8 | 3380 | 6 | 5 | 83.3333 | |
| hfeng-pmm1 | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 96.5842 | 93.4203 | 99.9700 | 43.5033 | 3294 | 232 | 3334 | 1 | 1 | 100.0000 | |
| hfeng-pmm1 | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 96.5842 | 93.4203 | 99.9700 | 43.5033 | 3294 | 232 | 3334 | 1 | 1 | 100.0000 | |
| gduggal-snapvard | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 72.8639 | 81.3378 | 65.9890 | 43.5053 | 2663 | 611 | 5875 | 3028 | 2874 | 94.9141 | |
| ckim-isaac | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 91.8499 | 88.8266 | 95.0863 | 43.5099 | 14254 | 1793 | 14165 | 732 | 583 | 79.6448 | |
| cchapple-custom | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_51to200 | het | 89.4961 | 81.4815 | 99.2593 | 43.5146 | 22 | 5 | 134 | 1 | 1 | 100.0000 | |
| eyeh-varpipe | SNP | ti | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 99.7046 | 99.9754 | 99.4352 | 43.5229 | 4064 | 1 | 4049 | 23 | 5 | 21.7391 | |
| ckim-isaac | INDEL | D1_5 | HG002compoundhet | * | 88.8135 | 85.9501 | 91.8743 | 43.5269 | 10516 | 1719 | 10436 | 923 | 829 | 89.8158 | |
| ckim-isaac | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 91.1346 | 84.9322 | 98.3142 | 43.5277 | 13094 | 2323 | 13472 | 231 | 203 | 87.8788 | |
| cchapple-custom | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 99.8668 | 99.7340 | 100.0000 | 43.5354 | 1125 | 3 | 1118 | 0 | 0 | ||
| ckim-isaac | SNP | ti | tech_badpromoters | het | 88.6076 | 79.5455 | 100.0000 | 43.5484 | 35 | 9 | 35 | 0 | 0 | ||
| ndellapenna-hhga | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_51to200 | homalt | 80.8511 | 80.2817 | 81.4286 | 43.5484 | 57 | 14 | 57 | 13 | 11 | 84.6154 | |
| gduggal-snapfb | INDEL | D6_15 | func_cds | * | 82.0513 | 74.4186 | 91.4286 | 43.5484 | 32 | 11 | 32 | 3 | 3 | 100.0000 | |
| gduggal-bwaplat | INDEL | I6_15 | func_cds | * | 87.1795 | 79.0698 | 97.1429 | 43.5484 | 34 | 9 | 34 | 1 | 1 | 100.0000 | |
| ltrigg-rtg2 | INDEL | I6_15 | HG002complexvar | homalt | 98.9542 | 98.5173 | 99.3950 | 43.5610 | 1196 | 18 | 1150 | 7 | 4 | 57.1429 | |
| ckim-dragen | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_11to50 | * | 99.7914 | 99.7547 | 99.8281 | 43.5620 | 4067 | 10 | 4065 | 7 | 3 | 42.8571 | |
| gduggal-bwaplat | SNP | ti | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 92.5642 | 86.3306 | 99.7681 | 43.5629 | 3442 | 545 | 3442 | 8 | 8 | 100.0000 | |
| gduggal-bwaplat | INDEL | I16_PLUS | HG002compoundhet | hetalt | 78.6021 | 65.0263 | 99.3421 | 43.5644 | 1361 | 732 | 1359 | 9 | 8 | 88.8889 | |
| astatham-gatk | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 98.6561 | 97.3479 | 100.0000 | 43.5644 | 624 | 17 | 627 | 0 | 0 | ||
| jli-custom | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 94.9543 | 90.6336 | 99.7076 | 43.5644 | 329 | 34 | 341 | 1 | 1 | 100.0000 | |
| jmaeng-gatk | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 99.9659 | 99.9318 | 100.0000 | 43.5670 | 1465 | 1 | 1465 | 0 | 0 | ||
| gduggal-snapfb | INDEL | * | func_cds | het | 88.4234 | 85.0467 | 92.0792 | 43.5754 | 182 | 32 | 186 | 16 | 10 | 62.5000 | |
| qzeng-custom | INDEL | I1_5 | lowcmp_SimpleRepeat_triTR_11to50 | het | 98.3975 | 98.7234 | 98.0737 | 43.5889 | 464 | 6 | 1782 | 35 | 13 | 37.1429 | |
| mlin-fermikit | INDEL | I1_5 | tech_badpromoters | * | 100.0000 | 100.0000 | 100.0000 | 43.5897 | 22 | 0 | 22 | 0 | 0 | ||
| jlack-gatk | INDEL | D16_PLUS | lowcmp_SimpleRepeat_triTR_51to200 | hetalt | 88.8889 | 80.0000 | 100.0000 | 43.5897 | 20 | 5 | 22 | 0 | 0 | ||
| gduggal-snapplat | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 63.9702 | 49.9564 | 88.9115 | 43.5949 | 3440 | 3446 | 3496 | 436 | 391 | 89.6789 | |
| gduggal-snapfb | SNP | * | lowcmp_SimpleRepeat_triTR_11to50 | * | 95.5647 | 99.6601 | 91.7926 | 43.5950 | 7330 | 25 | 7348 | 657 | 15 | 2.2831 | |
| ltrigg-rtg1 | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 97.3346 | 95.0228 | 99.7616 | 43.5987 | 2081 | 109 | 2092 | 5 | 4 | 80.0000 | |
| rpoplin-dv42 | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_51to200 | * | 80.9237 | 76.2066 | 86.2632 | 43.6078 | 900 | 281 | 898 | 143 | 143 | 100.0000 | |
| ndellapenna-hhga | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 62.1033 | 45.2072 | 99.1667 | 43.6090 | 731 | 886 | 595 | 5 | 4 | 80.0000 | |
| cchapple-custom | SNP | tv | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 99.7161 | 99.4907 | 99.9426 | 43.6105 | 1758 | 9 | 1742 | 1 | 1 | 100.0000 | |
| mlin-fermikit | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | hetalt | 47.0332 | 30.8307 | 99.1285 | 43.6118 | 386 | 866 | 455 | 4 | 3 | 75.0000 | |
| asubramanian-gatk | INDEL | I6_15 | lowcmp_SimpleRepeat_triTR_11to50 | * | 98.8452 | 98.0861 | 99.6161 | 43.6147 | 410 | 8 | 519 | 2 | 1 | 50.0000 | |
| eyeh-varpipe | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 70.2794 | 91.7657 | 56.9459 | 43.6183 | 1081 | 97 | 3718 | 2811 | 2776 | 98.7549 | |
| ckim-dragen | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 97.4894 | 95.1923 | 99.9000 | 43.6220 | 2970 | 150 | 2998 | 3 | 3 | 100.0000 | |
| gduggal-snapvard | INDEL | * | func_cds | * | 83.0794 | 82.2472 | 83.9286 | 43.6242 | 366 | 79 | 423 | 81 | 65 | 80.2469 | |
| dgrover-gatk | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 98.7362 | 97.5039 | 100.0000 | 43.6266 | 625 | 16 | 628 | 0 | 0 | ||
| gduggal-snapvard | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 57.8592 | 55.4482 | 60.4894 | 43.6279 | 17739 | 14253 | 30010 | 19602 | 17898 | 91.3070 | |