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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
32101-32150 / 86044 show all | |||||||||||||||
| hfeng-pmm3 | INDEL | I1_5 | map_l150_m2_e1 | het | 97.7828 | 97.1609 | 98.4127 | 89.5937 | 308 | 9 | 310 | 5 | 0 | 0.0000 | |
| hfeng-pmm3 | INDEL | I1_5 | segdup | * | 99.4321 | 99.1501 | 99.7156 | 94.0254 | 1050 | 9 | 1052 | 3 | 2 | 66.6667 | |
| hfeng-pmm3 | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 99.4690 | 98.9437 | 100.0000 | 83.2738 | 843 | 9 | 843 | 0 | 0 | ||
| hfeng-pmm3 | SNP | ti | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 99.5902 | 99.2647 | 99.9178 | 64.5481 | 1215 | 9 | 1215 | 1 | 0 | 0.0000 | |
| hfeng-pmm3 | SNP | ti | map_l150_m0_e0 | homalt | 99.6199 | 99.6740 | 99.5658 | 75.7331 | 2752 | 9 | 2752 | 12 | 4 | 33.3333 | |
| hfeng-pmm3 | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 99.1045 | 98.2249 | 100.0000 | 84.7380 | 498 | 9 | 498 | 0 | 0 | ||
| hfeng-pmm3 | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 99.6987 | 99.3992 | 100.0000 | 81.4570 | 1489 | 9 | 1489 | 0 | 0 | ||
| hfeng-pmm2 | SNP | * | map_l250_m1_e0 | homalt | 99.4730 | 99.6346 | 99.3120 | 87.0152 | 2454 | 9 | 2454 | 17 | 6 | 35.2941 | |
| hfeng-pmm2 | SNP | ti | map_l150_m0_e0 | homalt | 99.6019 | 99.6740 | 99.5298 | 75.8368 | 2752 | 9 | 2752 | 13 | 5 | 38.4615 | |
| hfeng-pmm2 | SNP | tv | lowcmp_SimpleRepeat_diTR_51to200 | * | 77.2727 | 65.3846 | 94.4444 | 96.9072 | 17 | 9 | 17 | 1 | 0 | 0.0000 | |
| hfeng-pmm3 | INDEL | * | lowcmp_SimpleRepeat_triTR_11to50 | hetalt | 99.5101 | 99.0249 | 100.0000 | 30.0763 | 914 | 9 | 916 | 0 | 0 | ||
| hfeng-pmm3 | INDEL | * | lowcmp_SimpleRepeat_triTR_51to200 | hetalt | 96.2656 | 92.8000 | 100.0000 | 29.5181 | 116 | 9 | 117 | 0 | 0 | ||
| hfeng-pmm3 | INDEL | * | map_l100_m1_e0 | homalt | 99.2665 | 99.2665 | 99.2665 | 80.9205 | 1218 | 9 | 1218 | 9 | 4 | 44.4444 | |
| hfeng-pmm3 | INDEL | * | map_l100_m2_e0 | homalt | 99.2469 | 99.2863 | 99.2076 | 82.1525 | 1252 | 9 | 1252 | 10 | 4 | 40.0000 | |
| hfeng-pmm3 | INDEL | * | map_l100_m2_e1 | homalt | 99.2587 | 99.2974 | 99.2200 | 82.2364 | 1272 | 9 | 1272 | 10 | 4 | 40.0000 | |
| hfeng-pmm1 | INDEL | * | segdup | hetalt | 96.4143 | 93.0769 | 100.0000 | 94.8341 | 121 | 9 | 123 | 0 | 0 | ||
| hfeng-pmm1 | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_51to200 | het | 76.6255 | 94.6746 | 64.3564 | 81.0507 | 160 | 9 | 65 | 36 | 36 | 100.0000 | |
| hfeng-pmm1 | INDEL | D16_PLUS | map_siren | * | 92.3827 | 93.7063 | 91.0959 | 92.6633 | 134 | 9 | 133 | 13 | 1 | 7.6923 | |
| hfeng-pmm1 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 99.5749 | 99.1533 | 100.0000 | 79.4702 | 1054 | 9 | 1054 | 0 | 0 | ||
| hfeng-pmm1 | INDEL | D1_5 | map_l150_m0_e0 | * | 97.7337 | 96.8858 | 98.5965 | 88.2183 | 280 | 9 | 281 | 4 | 1 | 25.0000 | |
| hfeng-pmm1 | INDEL | D1_5 | map_l250_m1_e0 | * | 97.0060 | 94.7368 | 99.3865 | 93.6477 | 162 | 9 | 162 | 1 | 0 | 0.0000 | |
| hfeng-pmm1 | INDEL | D1_5 | map_l250_m2_e0 | * | 97.2222 | 95.1087 | 99.4318 | 94.0999 | 175 | 9 | 175 | 1 | 0 | 0.0000 | |
| hfeng-pmm1 | INDEL | D1_5 | map_l250_m2_e1 | * | 97.2376 | 95.1351 | 99.4350 | 94.2157 | 176 | 9 | 176 | 1 | 0 | 0.0000 | |
| hfeng-pmm1 | INDEL | I16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 94.4785 | 89.5349 | 100.0000 | 77.9841 | 77 | 9 | 83 | 0 | 0 | ||
| hfeng-pmm1 | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 91.7431 | 84.7458 | 100.0000 | 74.1463 | 50 | 9 | 53 | 0 | 0 | ||
| hfeng-pmm1 | INDEL | I16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | het | 96.4276 | 94.3750 | 98.5714 | 88.7910 | 151 | 9 | 138 | 2 | 0 | 0.0000 | |
| jlack-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 95.8084 | 98.6133 | 93.1587 | 67.2857 | 640 | 9 | 640 | 47 | 47 | 100.0000 | |
| jlack-gatk | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_11to50 | het | 98.4292 | 98.1557 | 98.7041 | 82.3820 | 479 | 9 | 457 | 6 | 2 | 33.3333 | |
| jlack-gatk | SNP | * | lowcmp_SimpleRepeat_triTR_11to50 | het | 99.2883 | 99.8050 | 98.7768 | 40.6294 | 4607 | 9 | 4603 | 57 | 3 | 5.2632 | |
| jlack-gatk | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 96.3636 | 95.9276 | 96.8037 | 90.7789 | 212 | 9 | 212 | 7 | 5 | 71.4286 | |
| jlack-gatk | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 98.8636 | 97.9730 | 99.7706 | 84.0117 | 435 | 9 | 435 | 1 | 1 | 100.0000 | |
| jlack-gatk | SNP | ti | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 99.7031 | 99.4668 | 99.9405 | 63.6364 | 1679 | 9 | 1679 | 1 | 1 | 100.0000 | |
| jlack-gatk | SNP | ti | lowcmp_SimpleRepeat_triTR_11to50 | * | 99.6292 | 99.7696 | 99.4893 | 34.4273 | 3897 | 9 | 3896 | 20 | 3 | 15.0000 | |
| jlack-gatk | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 98.9076 | 98.2249 | 99.6000 | 84.9034 | 498 | 9 | 498 | 2 | 2 | 100.0000 | |
| jlack-gatk | SNP | tv | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 99.6881 | 99.4907 | 99.8864 | 60.3693 | 1758 | 9 | 1758 | 2 | 2 | 100.0000 | |
| jlack-gatk | INDEL | I1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 99.4903 | 99.4178 | 99.5630 | 74.2111 | 1366 | 8 | 1367 | 6 | 0 | 0.0000 | |
| jlack-gatk | INDEL | I1_5 | map_l150_m1_e0 | het | 93.4527 | 97.3244 | 89.8773 | 93.2797 | 291 | 8 | 293 | 33 | 2 | 6.0606 | |
| jlack-gatk | INDEL | I1_5 | map_l150_m2_e0 | het | 93.2231 | 97.4110 | 89.3805 | 93.8420 | 301 | 8 | 303 | 36 | 2 | 5.5556 | |
| jlack-gatk | INDEL | I1_5 | map_l150_m2_e1 | het | 93.2461 | 97.4763 | 89.3678 | 93.8559 | 309 | 8 | 311 | 37 | 2 | 5.4054 | |
| jlack-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 99.5086 | 99.8706 | 99.1491 | 56.7671 | 6176 | 8 | 6176 | 53 | 2 | 3.7736 | |
| jlack-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 96.2264 | 92.7273 | 100.0000 | 91.0132 | 102 | 8 | 102 | 0 | 0 | ||
| jlack-gatk | SNP | * | lowcmp_SimpleRepeat_quadTR_51to200 | het | 94.4724 | 92.1569 | 96.9072 | 92.3682 | 94 | 8 | 94 | 3 | 3 | 100.0000 | |
| jlack-gatk | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 95.4733 | 93.5484 | 97.4790 | 90.8672 | 116 | 8 | 116 | 3 | 2 | 66.6667 | |
| jlack-gatk | SNP | tv | lowcmp_SimpleRepeat_quadTR_11to50 | het | 95.6256 | 99.8294 | 91.7615 | 43.4184 | 4681 | 8 | 4678 | 420 | 1 | 0.2381 | |
| jli-custom | INDEL | * | lowcmp_SimpleRepeat_triTR_51to200 | hetalt | 96.6942 | 93.6000 | 100.0000 | 26.0870 | 117 | 8 | 119 | 0 | 0 | ||
| jli-custom | INDEL | * | segdup | hetalt | 96.8254 | 93.8462 | 100.0000 | 94.4815 | 122 | 8 | 124 | 0 | 0 | ||
| hfeng-pmm2 | INDEL | D16_PLUS | map_l100_m2_e1 | * | 88.5572 | 91.7526 | 85.5769 | 93.7799 | 89 | 8 | 89 | 15 | 3 | 20.0000 | |
| hfeng-pmm2 | INDEL | D1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | homalt | 99.9312 | 99.9214 | 99.9410 | 54.0442 | 10170 | 8 | 10170 | 6 | 6 | 100.0000 | |
| hfeng-pmm2 | INDEL | D1_5 | map_l150_m2_e1 | * | 97.9683 | 98.9717 | 96.9849 | 89.2621 | 770 | 8 | 772 | 24 | 4 | 16.6667 | |
| hfeng-pmm2 | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 99.3610 | 99.0730 | 99.6508 | 61.9238 | 855 | 8 | 856 | 3 | 2 | 66.6667 | |