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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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66851-66900 / 86044 show all | |||||||||||||||
| hfeng-pmm2 | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 93.7500 | 98.3607 | 89.5522 | 91.1842 | 60 | 1 | 60 | 7 | 5 | 71.4286 | |
| hfeng-pmm2 | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 99.1736 | 98.3607 | 100.0000 | 70.2970 | 120 | 2 | 120 | 0 | 0 | ||
| hfeng-pmm2 | INDEL | I6_15 | lowcmp_SimpleRepeat_triTR_11to50 | het | 99.1736 | 98.3607 | 100.0000 | 59.3857 | 120 | 2 | 119 | 0 | 0 | ||
| hfeng-pmm1 | INDEL | I6_15 | lowcmp_SimpleRepeat_triTR_11to50 | het | 99.1736 | 98.3607 | 100.0000 | 59.1065 | 120 | 2 | 119 | 0 | 0 | ||
| hfeng-pmm3 | INDEL | I6_15 | lowcmp_SimpleRepeat_triTR_11to50 | het | 99.1736 | 98.3607 | 100.0000 | 58.6806 | 120 | 2 | 119 | 0 | 0 | ||
| hfeng-pmm3 | SNP | * | map_l250_m0_e0 | * | 98.2916 | 98.3607 | 98.2226 | 92.8676 | 2100 | 35 | 2100 | 38 | 6 | 15.7895 | |
| jlack-gatk | INDEL | D16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 97.5610 | 98.3607 | 96.7742 | 71.5106 | 480 | 8 | 480 | 16 | 12 | 75.0000 | |
| jlack-gatk | INDEL | D16_PLUS | lowcmp_SimpleRepeat_triTR_11to50 | het | 98.3182 | 98.3607 | 98.2759 | 81.7035 | 60 | 1 | 57 | 1 | 0 | 0.0000 | |
| jlack-gatk | INDEL | D1_5 | map_l250_m2_e1 | het | 86.3309 | 98.3607 | 76.9231 | 97.0115 | 120 | 2 | 120 | 36 | 1 | 2.7778 | |
| gduggal-bwavard | INDEL | D1_5 | map_l250_m2_e1 | het | 79.4702 | 98.3607 | 66.6667 | 96.2081 | 120 | 2 | 120 | 60 | 4 | 6.6667 | |
| gduggal-bwavard | INDEL | I6_15 | lowcmp_SimpleRepeat_triTR_11to50 | het | 79.0807 | 98.3607 | 66.1202 | 63.2530 | 120 | 2 | 121 | 62 | 56 | 90.3226 | |
| raldana-dualsentieon | INDEL | * | map_l125_m1_e0 | homalt | 98.6977 | 98.3607 | 99.0371 | 84.0640 | 720 | 12 | 720 | 7 | 3 | 42.8571 | |
| raldana-dualsentieon | INDEL | D16_PLUS | lowcmp_SimpleRepeat_triTR_11to50 | het | 98.3329 | 98.3607 | 98.3051 | 75.0000 | 60 | 1 | 58 | 1 | 1 | 100.0000 | |
| raldana-dualsentieon | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 99.1736 | 98.3607 | 100.0000 | 68.7500 | 120 | 2 | 120 | 0 | 0 | ||
| jmaeng-gatk | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_11to50 | het | 98.3238 | 98.3607 | 98.2869 | 82.7101 | 480 | 8 | 459 | 8 | 2 | 25.0000 | |
| jmaeng-gatk | INDEL | I6_15 | lowcmp_SimpleRepeat_triTR_11to50 | het | 99.1736 | 98.3607 | 100.0000 | 62.9283 | 120 | 2 | 119 | 0 | 0 | ||
| ltrigg-rtg2 | INDEL | D16_PLUS | lowcmp_SimpleRepeat_triTR_11to50 | het | 99.1736 | 98.3607 | 100.0000 | 67.0588 | 60 | 1 | 56 | 0 | 0 | ||
| ltrigg-rtg1 | INDEL | D16_PLUS | lowcmp_SimpleRepeat_triTR_11to50 | het | 99.1736 | 98.3607 | 100.0000 | 66.4671 | 60 | 1 | 56 | 0 | 0 | ||
| ltrigg-rtg1 | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 99.1736 | 98.3607 | 100.0000 | 64.1566 | 120 | 2 | 119 | 0 | 0 | ||
| ltrigg-rtg2 | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 99.1736 | 98.3607 | 100.0000 | 64.2643 | 120 | 2 | 119 | 0 | 0 | ||
| jmaeng-gatk | INDEL | D16_PLUS | lowcmp_SimpleRepeat_triTR_11to50 | het | 98.3329 | 98.3607 | 98.3051 | 81.7901 | 60 | 1 | 58 | 1 | 1 | 100.0000 | |
| cchapple-custom | INDEL | D16_PLUS | lowcmp_SimpleRepeat_triTR_11to50 | het | 97.8383 | 98.3607 | 97.3214 | 62.5418 | 60 | 1 | 109 | 3 | 3 | 100.0000 | |
| ckim-gatk | INDEL | I1_5 | map_l100_m2_e0 | het | 97.1459 | 98.3607 | 95.9608 | 90.0195 | 780 | 13 | 784 | 33 | 1 | 3.0303 | |
| cchapple-custom | INDEL | I6_15 | lowcmp_SimpleRepeat_triTR_11to50 | het | 99.1736 | 98.3607 | 100.0000 | 47.7208 | 120 | 2 | 367 | 0 | 0 | ||
| ckim-gatk | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_11to50 | het | 98.7468 | 98.3607 | 99.1361 | 82.5283 | 480 | 8 | 459 | 4 | 0 | 0.0000 | |
| ckim-gatk | INDEL | I6_15 | lowcmp_SimpleRepeat_triTR_11to50 | het | 99.1736 | 98.3607 | 100.0000 | 63.0435 | 120 | 2 | 119 | 0 | 0 | ||
| ghariani-varprowl | INDEL | I1_5 | map_l100_m2_e0 | het | 94.1968 | 98.3607 | 90.3712 | 90.4265 | 780 | 13 | 779 | 83 | 29 | 34.9398 | |
| dgrover-gatk | SNP | * | map_l250_m2_e0 | homalt | 99.0440 | 98.3619 | 99.7357 | 86.6145 | 2642 | 44 | 2642 | 7 | 5 | 71.4286 | |
| 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 | |
| gduggal-bwavard | SNP | tv | map_l125_m2_e0 | het | 93.1678 | 98.3624 | 88.4944 | 83.4152 | 10271 | 171 | 10245 | 1332 | 64 | 4.8048 | |
| bgallagher-sentieon | INDEL | * | map_l150_m1_e0 | het | 97.5150 | 98.3626 | 96.6819 | 90.6743 | 841 | 14 | 845 | 29 | 4 | 13.7931 | |
| hfeng-pmm2 | INDEL | * | map_l150_m1_e0 | het | 97.3465 | 98.3626 | 96.3512 | 90.4715 | 841 | 14 | 845 | 32 | 3 | 9.3750 | |
| astatham-gatk | SNP | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 99.0488 | 98.3627 | 99.7446 | 66.6690 | 4686 | 78 | 4686 | 12 | 7 | 58.3333 | |
| ckim-dragen | SNP | * | map_l150_m0_e0 | * | 97.7617 | 98.3627 | 97.1680 | 81.2391 | 11835 | 197 | 11837 | 345 | 42 | 12.1739 | |
| gduggal-bwafb | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 88.3710 | 98.3627 | 80.2220 | 89.1848 | 781 | 13 | 795 | 196 | 29 | 14.7959 | |
| jpowers-varprowl | SNP | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 96.6892 | 98.3627 | 95.0717 | 77.9691 | 4686 | 78 | 4707 | 244 | 55 | 22.5410 | |
| ghariani-varprowl | INDEL | * | segdup | het | 90.4926 | 98.3629 | 83.7885 | 96.1254 | 1442 | 24 | 1442 | 279 | 206 | 73.8351 | |
| ghariani-varprowl | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 90.4279 | 98.3630 | 83.6775 | 77.1548 | 2103 | 35 | 2107 | 411 | 380 | 92.4574 | |
| jlack-gatk | SNP | ti | map_l250_m2_e1 | het | 92.2399 | 98.3631 | 86.8344 | 94.0808 | 3245 | 54 | 3245 | 492 | 42 | 8.5366 | |
| rpoplin-dv42 | SNP | ti | map_l250_m2_e1 | homalt | 98.9217 | 98.3634 | 99.4863 | 87.6793 | 1743 | 29 | 1743 | 9 | 9 | 100.0000 | |
| raldana-dualsentieon | SNP | tv | map_l125_m0_e0 | het | 98.3750 | 98.3640 | 98.3860 | 76.8948 | 4329 | 72 | 4328 | 71 | 1 | 1.4085 | |
| ckim-gatk | INDEL | D6_15 | HG002compoundhet | het | 90.0227 | 98.3645 | 82.9851 | 68.6916 | 842 | 14 | 834 | 171 | 169 | 98.8304 | |
| jlack-gatk | SNP | * | map_l125_m0_e0 | * | 94.5944 | 98.3647 | 91.1024 | 82.9942 | 19068 | 317 | 19065 | 1862 | 148 | 7.9484 | |
| ckim-vqsr | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 98.9263 | 98.3656 | 99.4933 | 72.9052 | 30634 | 509 | 30634 | 156 | 20 | 12.8205 | |
| ckim-vqsr | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 98.9263 | 98.3656 | 99.4933 | 72.9052 | 30634 | 509 | 30634 | 156 | 20 | 12.8205 | |
| jlack-gatk | INDEL | I1_5 | map_l125_m2_e0 | * | 96.2945 | 98.3664 | 94.3080 | 90.1657 | 843 | 14 | 845 | 51 | 5 | 9.8039 | |
| gduggal-bwavard | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | homalt | 99.1183 | 98.3683 | 99.8798 | 44.5703 | 844 | 14 | 831 | 1 | 0 | 0.0000 | |
| ndellapenna-hhga | SNP | ti | map_l150_m2_e1 | * | 99.0741 | 98.3690 | 99.7895 | 74.1500 | 20385 | 338 | 20385 | 43 | 23 | 53.4884 | |
| astatham-gatk | INDEL | D1_5 | map_l250_m2_e0 | * | 96.2766 | 98.3696 | 94.2708 | 95.7248 | 181 | 3 | 181 | 11 | 1 | 9.0909 | |
| jlack-gatk | INDEL | D1_5 | map_l250_m2_e0 | * | 90.2743 | 98.3696 | 83.4101 | 96.5457 | 181 | 3 | 181 | 36 | 1 | 2.7778 | |