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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
69351-69400 / 86044 show all | |||||||||||||||
| astatham-gatk | SNP | ti | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 99.7327 | 99.4668 | 100.0000 | 64.1699 | 1679 | 9 | 1679 | 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 | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 99.1143 | 98.5907 | 99.6435 | 73.6743 | 1679 | 24 | 1677 | 6 | 0 | 0.0000 | |
| ltrigg-rtg2 | INDEL | D1_5 | HG002compoundhet | het | 97.0089 | 97.1644 | 96.8539 | 67.7653 | 1679 | 49 | 1724 | 56 | 27 | 48.2143 | |
| dgrover-gatk | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 97.2777 | 94.8052 | 99.8826 | 40.8681 | 1679 | 92 | 1701 | 2 | 2 | 100.0000 | |
| gduggal-snapvard | SNP | tv | func_cds | homalt | 99.2613 | 98.5915 | 99.9402 | 26.1484 | 1680 | 24 | 1671 | 1 | 1 | 100.0000 | |
| ghariani-varprowl | SNP | ti | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 93.8322 | 99.5261 | 88.7546 | 70.2144 | 1680 | 8 | 1689 | 214 | 129 | 60.2804 | |
| jli-custom | INDEL | D16_PLUS | * | homalt | 99.0858 | 99.2908 | 98.8817 | 67.1754 | 1680 | 12 | 1680 | 19 | 13 | 68.4211 | |
| ltrigg-rtg2 | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | * | 87.9863 | 79.9619 | 97.8009 | 49.2660 | 1680 | 421 | 1690 | 38 | 36 | 94.7368 | |
| jpowers-varprowl | SNP | ti | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 92.9799 | 99.5261 | 87.2417 | 71.6212 | 1680 | 8 | 1689 | 247 | 126 | 51.0121 | |
| hfeng-pmm2 | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 99.1148 | 98.6494 | 99.5846 | 73.9124 | 1680 | 23 | 1678 | 7 | 2 | 28.5714 | |
| hfeng-pmm1 | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 99.1148 | 98.6494 | 99.5846 | 74.0889 | 1680 | 23 | 1678 | 7 | 1 | 14.2857 | |
| ghariani-varprowl | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 78.6349 | 78.0148 | 79.2648 | 83.6794 | 1682 | 474 | 1682 | 440 | 405 | 92.0455 | |
| ckim-vqsr | SNP | ti | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 99.8220 | 99.6445 | 100.0000 | 64.1135 | 1682 | 6 | 1682 | 0 | 0 | ||
| gduggal-bwavard | SNP | tv | func_cds | homalt | 99.3503 | 98.7089 | 100.0000 | 25.9620 | 1682 | 22 | 1674 | 0 | 0 | ||
| cchapple-custom | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 0.0000 | 94.9746 | 0.0000 | 0.0000 | 1682 | 89 | 0 | 0 | 0 | ||
| rpoplin-dv42 | SNP | ti | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 99.7923 | 99.6445 | 99.9406 | 65.1625 | 1682 | 6 | 1682 | 1 | 1 | 100.0000 | |
| ckim-dragen | INDEL | D16_PLUS | * | homalt | 97.0588 | 99.4681 | 94.7635 | 72.2066 | 1683 | 9 | 1683 | 93 | 84 | 90.3226 | |
| anovak-vg | SNP | tv | func_cds | homalt | 98.9685 | 98.7676 | 99.1701 | 25.0222 | 1683 | 21 | 1673 | 14 | 11 | 78.5714 | |
| bgallagher-sentieon | SNP | ti | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 99.8222 | 99.7630 | 99.8814 | 64.1429 | 1684 | 4 | 1684 | 2 | 2 | 100.0000 | |
| dgrover-gatk | SNP | ti | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 99.8814 | 99.7630 | 100.0000 | 64.2235 | 1684 | 4 | 1684 | 0 | 0 | ||
| jlack-gatk | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 98.9127 | 98.8843 | 98.9412 | 74.7999 | 1684 | 19 | 1682 | 18 | 4 | 22.2222 | |
| ckim-gatk | SNP | ti | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 99.8814 | 99.7630 | 100.0000 | 64.0862 | 1684 | 4 | 1684 | 0 | 0 | ||
| jmaeng-gatk | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 99.2044 | 98.8843 | 99.5266 | 75.4930 | 1684 | 19 | 1682 | 8 | 1 | 12.5000 | |
| ltrigg-rtg1 | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 97.3152 | 95.0875 | 99.6497 | 51.5280 | 1684 | 87 | 1707 | 6 | 5 | 83.3333 | |
| mlin-fermikit | SNP | ti | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 94.2645 | 99.7630 | 89.3404 | 69.5631 | 1684 | 4 | 1693 | 202 | 155 | 76.7327 | |
| rpoplin-dv42 | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 98.4511 | 98.9430 | 97.9639 | 73.8833 | 1685 | 18 | 1684 | 35 | 28 | 80.0000 | |
| gduggal-bwafb | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 83.1128 | 95.5215 | 73.5573 | 89.2251 | 1685 | 79 | 1708 | 614 | 76 | 12.3779 | |
| gduggal-bwaplat | SNP | tv | func_cds | homalt | 99.4394 | 98.8850 | 100.0000 | 27.0563 | 1685 | 19 | 1685 | 0 | 0 | ||
| jmaeng-gatk | SNP | ti | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 99.9111 | 99.8223 | 100.0000 | 64.1566 | 1685 | 3 | 1685 | 0 | 0 | ||
| jli-custom | SNP | ti | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 99.8814 | 99.8223 | 99.9407 | 64.3853 | 1685 | 3 | 1685 | 1 | 0 | 0.0000 | |
| jmaeng-gatk | INDEL | D16_PLUS | * | homalt | 99.0018 | 99.6454 | 98.3664 | 70.1757 | 1686 | 6 | 1686 | 28 | 20 | 71.4286 | |
| raldana-dualsentieon | SNP | ti | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 99.9111 | 99.8815 | 99.9407 | 63.6892 | 1686 | 2 | 1686 | 1 | 1 | 100.0000 | |
| raldana-dualsentieon | INDEL | D16_PLUS | * | homalt | 99.2348 | 99.6454 | 98.8277 | 68.4541 | 1686 | 6 | 1686 | 20 | 16 | 80.0000 | |
| eyeh-varpipe | INDEL | * | HG002complexvar | hetalt | 61.1209 | 45.5799 | 92.7426 | 76.1697 | 1686 | 2013 | 3642 | 285 | 277 | 97.1930 | |
| dgrover-gatk | INDEL | D16_PLUS | * | homalt | 98.8856 | 99.6454 | 98.1374 | 70.5317 | 1686 | 6 | 1686 | 32 | 23 | 71.8750 | |
| bgallagher-sentieon | INDEL | D16_PLUS | * | homalt | 98.7698 | 99.6454 | 97.9094 | 70.3716 | 1686 | 6 | 1686 | 36 | 27 | 75.0000 | |
| astatham-gatk | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 94.6399 | 91.5309 | 97.9675 | 67.1249 | 1686 | 156 | 1687 | 35 | 30 | 85.7143 | |
| hfeng-pmm3 | SNP | ti | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 99.9407 | 99.8815 | 100.0000 | 64.4454 | 1686 | 2 | 1686 | 0 | 0 | ||
| hfeng-pmm1 | SNP | ti | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 99.9407 | 99.8815 | 100.0000 | 65.2514 | 1686 | 2 | 1686 | 0 | 0 | ||
| hfeng-pmm2 | SNP | ti | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 99.9407 | 99.8815 | 100.0000 | 65.8566 | 1686 | 2 | 1686 | 0 | 0 | ||
| ckim-vqsr | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 99.2934 | 99.0605 | 99.5275 | 75.3924 | 1687 | 16 | 1685 | 8 | 3 | 37.5000 | |
| ckim-vqsr | INDEL | D16_PLUS | * | homalt | 99.0314 | 99.7045 | 98.3673 | 70.9863 | 1687 | 5 | 1687 | 28 | 22 | 78.5714 | |
| gduggal-snapvard | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 62.3368 | 46.0175 | 96.5915 | 42.2906 | 1687 | 1979 | 1757 | 62 | 55 | 88.7097 | |
| astatham-gatk | INDEL | D16_PLUS | * | homalt | 99.1187 | 99.7045 | 98.5397 | 70.8497 | 1687 | 5 | 1687 | 25 | 20 | 80.0000 | |
| cchapple-custom | SNP | ti | map_l250_m2_e0 | homalt | 98.1670 | 96.4551 | 99.9407 | 84.8332 | 1687 | 62 | 1686 | 1 | 1 | 100.0000 | |
| ckim-gatk | INDEL | D16_PLUS | * | homalt | 99.0314 | 99.7045 | 98.3673 | 70.9863 | 1687 | 5 | 1687 | 28 | 22 | 78.5714 | |
| ciseli-custom | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 47.6114 | 41.5540 | 55.7361 | 61.7356 | 1690 | 2377 | 1681 | 1335 | 1256 | 94.0824 | |
| dgrover-gatk | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 94.7315 | 91.7481 | 97.9155 | 67.3720 | 1690 | 152 | 1691 | 36 | 30 | 83.3333 | |
| jlack-gatk | INDEL | D1_5 | HG002compoundhet | het | 92.3786 | 97.8009 | 87.5259 | 78.5190 | 1690 | 38 | 1691 | 241 | 200 | 82.9876 | |