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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
22401-22450 / 86044 show all | |||||||||||||||
| jlack-gatk | SNP | ti | HG002compoundhet | het | 99.4749 | 99.6739 | 99.2768 | 41.5881 | 9474 | 31 | 9472 | 69 | 16 | 23.1884 | |
| jlack-gatk | SNP | ti | lowcmp_SimpleRepeat_triTR_11to50 | het | 99.4965 | 99.7175 | 99.2765 | 38.0786 | 2471 | 7 | 2470 | 18 | 1 | 5.5556 | |
| ndellapenna-hhga | INDEL | I1_5 | HG002complexvar | homalt | 99.1510 | 99.0259 | 99.2764 | 48.8027 | 13317 | 131 | 13308 | 97 | 57 | 58.7629 | |
| rpoplin-dv42 | SNP | tv | map_l125_m2_e0 | * | 99.1468 | 99.0175 | 99.2763 | 70.8786 | 16327 | 162 | 16325 | 119 | 70 | 58.8235 | |
| ndellapenna-hhga | INDEL | I1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 98.7132 | 98.1565 | 99.2762 | 66.6200 | 2609 | 49 | 2606 | 19 | 10 | 52.6316 | |
| egarrison-hhga | INDEL | I1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 98.6941 | 98.1189 | 99.2762 | 66.9104 | 2608 | 50 | 2606 | 19 | 14 | 73.6842 | |
| hfeng-pmm1 | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 99.0369 | 98.7990 | 99.2759 | 70.2133 | 1234 | 15 | 1234 | 9 | 4 | 44.4444 | |
| hfeng-pmm1 | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 99.0369 | 98.7990 | 99.2759 | 70.2133 | 1234 | 15 | 1234 | 9 | 4 | 44.4444 | |
| eyeh-varpipe | SNP | * | * | hetalt | 99.5795 | 99.8852 | 99.2757 | 41.9596 | 870 | 1 | 7539 | 55 | 52 | 94.5455 | |
| ltrigg-rtg1 | INDEL | * | map_l100_m1_e0 | * | 97.3566 | 95.5103 | 99.2756 | 78.9689 | 3425 | 161 | 3426 | 25 | 7 | 28.0000 | |
| ltrigg-rtg1 | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 99.2905 | 99.3056 | 99.2754 | 83.8445 | 715 | 5 | 685 | 5 | 0 | 0.0000 | |
| ltrigg-rtg2 | INDEL | I1_5 | HG002complexvar | hetalt | 98.0883 | 96.9293 | 99.2754 | 77.2008 | 1673 | 53 | 1918 | 14 | 14 | 100.0000 | |
| gduggal-bwaplat | SNP | * | tech_badpromoters | * | 92.8814 | 87.2611 | 99.2754 | 66.7470 | 137 | 20 | 137 | 1 | 0 | 0.0000 | |
| hfeng-pmm3 | INDEL | I16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | het | 96.4336 | 93.7500 | 99.2754 | 88.7163 | 150 | 10 | 137 | 1 | 0 | 0.0000 | |
| hfeng-pmm3 | INDEL | I16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 96.1365 | 93.1900 | 99.2754 | 67.6056 | 260 | 19 | 274 | 2 | 2 | 100.0000 | |
| jli-custom | INDEL | D6_15 | lowcmp_SimpleRepeat_triTR_51to200 | * | 97.8571 | 96.4789 | 99.2754 | 41.7722 | 137 | 5 | 137 | 1 | 1 | 100.0000 | |
| astatham-gatk | INDEL | D1_5 | segdup | * | 99.2297 | 99.1840 | 99.2754 | 94.8823 | 1094 | 9 | 1096 | 8 | 2 | 25.0000 | |
| bgallagher-sentieon | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 95.0984 | 91.2587 | 99.2754 | 54.6053 | 261 | 25 | 274 | 2 | 2 | 100.0000 | |
| raldana-dualsentieon | INDEL | D6_15 | lowcmp_SimpleRepeat_triTR_51to200 | * | 97.8571 | 96.4789 | 99.2754 | 41.7722 | 137 | 5 | 137 | 1 | 1 | 100.0000 | |
| qzeng-custom | INDEL | I1_5 | lowcmp_SimpleRepeat_triTR_11to50 | hetalt | 95.3338 | 91.6933 | 99.2754 | 35.5140 | 287 | 26 | 137 | 1 | 1 | 100.0000 | |
| ckim-dragen | INDEL | D6_15 | lowcmp_SimpleRepeat_triTR_51to200 | * | 97.8571 | 96.4789 | 99.2754 | 43.2099 | 137 | 5 | 137 | 1 | 1 | 100.0000 | |
| dgrover-gatk | INDEL | * | * | homalt | 99.5819 | 99.8906 | 99.2752 | 59.0938 | 125035 | 137 | 125045 | 913 | 890 | 97.4808 | |
| ckim-isaac | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 94.3325 | 89.8592 | 99.2746 | 57.8234 | 957 | 108 | 958 | 7 | 4 | 57.1429 | |
| ltrigg-rtg2 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 98.4453 | 97.6298 | 99.2746 | 55.5967 | 8197 | 199 | 8211 | 60 | 20 | 33.3333 | |
| cchapple-custom | INDEL | * | segdup | homalt | 99.5843 | 99.8958 | 99.2746 | 93.0445 | 959 | 1 | 958 | 7 | 7 | 100.0000 | |
| rpoplin-dv42 | INDEL | I1_5 | HG002complexvar | hetalt | 96.6129 | 94.0904 | 99.2745 | 71.2548 | 1624 | 102 | 1642 | 12 | 11 | 91.6667 | |
| gduggal-bwaplat | INDEL | * | map_l125_m2_e0 | * | 76.5529 | 62.2951 | 99.2743 | 94.4882 | 1368 | 828 | 1368 | 10 | 2 | 20.0000 | |
| dgrover-gatk | SNP | * | map_l100_m2_e1 | het | 99.3747 | 99.4755 | 99.2742 | 71.6392 | 46652 | 246 | 46641 | 341 | 63 | 18.4751 | |
| ckim-dragen | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 99.1840 | 99.0942 | 99.2740 | 86.3749 | 1094 | 10 | 1094 | 8 | 8 | 100.0000 | |
| jli-custom | INDEL | * | segdup | homalt | 99.4802 | 99.6875 | 99.2739 | 93.3014 | 957 | 3 | 957 | 7 | 6 | 85.7143 | |
| hfeng-pmm3 | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 97.1733 | 95.1598 | 99.2739 | 61.8292 | 6016 | 306 | 6016 | 44 | 38 | 86.3636 | |
| hfeng-pmm3 | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 97.1733 | 95.1598 | 99.2739 | 61.8292 | 6016 | 306 | 6016 | 44 | 38 | 86.3636 | |
| ltrigg-rtg1 | INDEL | C1_5 | HG002complexvar | * | 91.9971 | 85.7143 | 99.2739 | 88.1471 | 6 | 1 | 957 | 7 | 2 | 28.5714 | |
| egarrison-hhga | SNP | * | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 98.9991 | 98.7265 | 99.2733 | 58.9450 | 3411 | 44 | 3415 | 25 | 14 | 56.0000 | |
| hfeng-pmm2 | SNP | * | map_l125_m1_e0 | * | 99.3629 | 99.4529 | 99.2732 | 71.9477 | 45079 | 248 | 45073 | 330 | 39 | 11.8182 | |
| ckim-gatk | INDEL | * | * | het | 99.4669 | 99.6616 | 99.2730 | 62.2737 | 193476 | 657 | 193095 | 1414 | 578 | 40.8769 | |
| hfeng-pmm3 | INDEL | D6_15 | map_siren | het | 98.5599 | 97.8571 | 99.2727 | 84.3483 | 274 | 6 | 273 | 2 | 0 | 0.0000 | |
| hfeng-pmm1 | INDEL | I16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 95.9441 | 92.8315 | 99.2727 | 67.4171 | 259 | 20 | 273 | 2 | 2 | 100.0000 | |
| gduggal-bwavard | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 93.1859 | 87.8023 | 99.2727 | 79.4623 | 835 | 116 | 819 | 6 | 5 | 83.3333 | |
| ltrigg-rtg2 | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 98.1891 | 97.1291 | 99.2726 | 27.7365 | 4635 | 137 | 4640 | 34 | 34 | 100.0000 | |
| gduggal-snapfb | SNP | * | map_l125_m0_e0 | homalt | 96.2940 | 93.4893 | 99.2723 | 82.1168 | 6275 | 437 | 6275 | 46 | 16 | 34.7826 | |
| ltrigg-rtg2 | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 98.8005 | 98.3333 | 99.2722 | 82.8678 | 708 | 12 | 682 | 5 | 0 | 0.0000 | |
| gduggal-bwafb | INDEL | D6_15 | lowcmp_SimpleRepeat_triTR_11to50 | * | 97.5847 | 95.9538 | 99.2721 | 31.4921 | 1660 | 70 | 1773 | 13 | 12 | 92.3077 | |
| ckim-dragen | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 98.0410 | 96.8402 | 99.2720 | 68.1668 | 15569 | 508 | 15546 | 114 | 94 | 82.4561 | |
| ckim-dragen | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 98.0410 | 96.8402 | 99.2720 | 68.1668 | 15569 | 508 | 15546 | 114 | 94 | 82.4561 | |
| gduggal-bwavard | SNP | ti | HG002complexvar | het | 98.2415 | 97.2329 | 99.2714 | 18.7202 | 306056 | 8710 | 302050 | 2217 | 1521 | 68.6062 | |
| cchapple-custom | INDEL | * | HG002complexvar | * | 98.8567 | 98.4455 | 99.2713 | 55.5354 | 75742 | 1196 | 78742 | 578 | 462 | 79.9308 | |
| ckim-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 96.8875 | 94.6157 | 99.2711 | 52.0847 | 6537 | 372 | 6537 | 48 | 43 | 89.5833 | |
| ckim-vqsr | INDEL | * | * | homalt | 99.5675 | 99.8658 | 99.2711 | 58.9429 | 125004 | 168 | 125017 | 918 | 901 | 98.1481 | |
| ltrigg-rtg1 | INDEL | I1_5 | map_l125_m2_e0 | * | 97.5042 | 95.7993 | 99.2710 | 82.8542 | 821 | 36 | 817 | 6 | 1 | 16.6667 | |