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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
57351-57400 / 86044 show all | |||||||||||||||
| jlack-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 97.5769 | 96.6102 | 98.5632 | 70.4835 | 342 | 12 | 343 | 5 | 5 | 100.0000 | |
| jlack-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 95.7955 | 92.0590 | 99.8481 | 42.7080 | 3246 | 280 | 3287 | 5 | 4 | 80.0000 | |
| jlack-gatk | INDEL | I6_15 | map_siren | homalt | 96.7391 | 98.8889 | 94.6809 | 84.1484 | 89 | 1 | 89 | 5 | 3 | 60.0000 | |
| jlack-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 99.6416 | 99.4125 | 99.8717 | 75.1815 | 3892 | 23 | 3892 | 5 | 5 | 100.0000 | |
| jlack-gatk | SNP | * | lowcmp_SimpleRepeat_homopolymer_6to10 | homalt | 99.9343 | 99.9507 | 99.9179 | 54.3410 | 6085 | 3 | 6085 | 5 | 5 | 100.0000 | |
| jlack-gatk | SNP | * | map_siren | hetalt | 95.1220 | 96.2963 | 93.9759 | 79.4045 | 78 | 3 | 78 | 5 | 4 | 80.0000 | |
| jlack-gatk | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 99.7223 | 99.4893 | 99.9565 | 63.3985 | 11493 | 59 | 11493 | 5 | 5 | 100.0000 | |
| jlack-gatk | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 99.7223 | 99.4893 | 99.9565 | 63.3985 | 11493 | 59 | 11493 | 5 | 5 | 100.0000 | |
| jlack-gatk | SNP | tv | map_l250_m0_e0 | homalt | 97.1429 | 96.8912 | 97.3958 | 93.0207 | 187 | 6 | 187 | 5 | 3 | 60.0000 | |
| jlack-gatk | SNP | tv | map_siren | hetalt | 95.1220 | 96.2963 | 93.9759 | 79.4045 | 78 | 3 | 78 | 5 | 4 | 80.0000 | |
| jli-custom | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | hetalt | 90.6149 | 83.1470 | 99.5567 | 28.0153 | 1041 | 211 | 1123 | 5 | 5 | 100.0000 | |
| jli-custom | INDEL | * | lowcmp_SimpleRepeat_triTR_11to50 | het | 99.4647 | 99.0705 | 99.8621 | 50.6131 | 3624 | 34 | 3620 | 5 | 1 | 20.0000 | |
| jli-custom | INDEL | * | map_l125_m0_e0 | homalt | 98.5965 | 98.9437 | 98.2517 | 86.9644 | 281 | 3 | 281 | 5 | 4 | 80.0000 | |
| jli-custom | INDEL | * | map_l150_m1_e0 | homalt | 98.9177 | 98.9177 | 98.9177 | 87.2411 | 457 | 5 | 457 | 5 | 3 | 60.0000 | |
| jli-custom | INDEL | * | map_l150_m2_e0 | homalt | 98.9605 | 98.9605 | 98.9605 | 88.3873 | 476 | 5 | 476 | 5 | 3 | 60.0000 | |
| hfeng-pmm3 | INDEL | D1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | homalt | 99.9263 | 99.9017 | 99.9509 | 53.9245 | 10168 | 10 | 10168 | 5 | 5 | 100.0000 | |
| hfeng-pmm3 | INDEL | D1_5 | map_l250_m1_e0 | * | 97.9710 | 98.8304 | 97.1264 | 94.1037 | 169 | 2 | 169 | 5 | 1 | 20.0000 | |
| hfeng-pmm3 | INDEL | D1_5 | map_l250_m1_e0 | het | 97.3451 | 99.0991 | 95.6522 | 94.4923 | 110 | 1 | 110 | 5 | 1 | 20.0000 | |
| hfeng-pmm3 | INDEL | D1_5 | map_l250_m2_e0 | * | 98.1132 | 98.9130 | 97.3262 | 94.4329 | 182 | 2 | 182 | 5 | 1 | 20.0000 | |
| hfeng-pmm3 | INDEL | D1_5 | map_l250_m2_e0 | het | 97.5610 | 99.1736 | 96.0000 | 94.6831 | 120 | 1 | 120 | 5 | 1 | 20.0000 | |
| hfeng-pmm3 | INDEL | D1_5 | map_l250_m2_e1 | * | 98.1233 | 98.9189 | 97.3404 | 94.5285 | 183 | 2 | 183 | 5 | 1 | 20.0000 | |
| hfeng-pmm3 | INDEL | D1_5 | map_l250_m2_e1 | het | 97.5806 | 99.1803 | 96.0317 | 94.7522 | 121 | 1 | 121 | 5 | 1 | 20.0000 | |
| hfeng-pmm3 | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 98.3153 | 96.9789 | 99.6891 | 57.4040 | 1605 | 50 | 1603 | 5 | 2 | 40.0000 | |
| hfeng-pmm3 | INDEL | I16_PLUS | * | hetalt | 96.0725 | 92.6597 | 99.7463 | 58.0281 | 1944 | 154 | 1966 | 5 | 5 | 100.0000 | |
| hfeng-pmm3 | INDEL | I16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 94.2356 | 91.2621 | 97.4093 | 87.4594 | 188 | 18 | 188 | 5 | 2 | 40.0000 | |
| hfeng-pmm3 | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 90.1961 | 100.0000 | 82.1429 | 87.8261 | 23 | 0 | 23 | 5 | 4 | 80.0000 | |
| hfeng-pmm3 | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 95.9022 | 93.2367 | 98.7245 | 72.6257 | 386 | 28 | 387 | 5 | 4 | 80.0000 | |
| hfeng-pmm3 | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 96.0630 | 100.0000 | 92.4242 | 90.7950 | 61 | 0 | 61 | 5 | 4 | 80.0000 | |
| hfeng-pmm3 | INDEL | I16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 94.2529 | 100.0000 | 89.1304 | 87.2928 | 41 | 0 | 41 | 5 | 5 | 100.0000 | |
| hfeng-pmm3 | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_11to50 | * | 97.6815 | 95.5513 | 99.9088 | 57.5685 | 5477 | 255 | 5478 | 5 | 3 | 60.0000 | |
| hfeng-pmm3 | INDEL | I1_5 | map_l100_m0_e0 | homalt | 98.8124 | 100.0000 | 97.6526 | 78.1089 | 208 | 0 | 208 | 5 | 3 | 60.0000 | |
| hfeng-pmm3 | INDEL | I1_5 | map_l100_m1_e0 | het | 98.7719 | 98.1982 | 99.3523 | 82.2488 | 763 | 14 | 767 | 5 | 0 | 0.0000 | |
| hfeng-pmm3 | INDEL | I1_5 | map_l100_m1_e0 | homalt | 99.5197 | 100.0000 | 99.0440 | 78.7398 | 518 | 0 | 518 | 5 | 3 | 60.0000 | |
| hfeng-pmm3 | INDEL | I1_5 | map_l100_m2_e0 | het | 98.7326 | 98.1084 | 99.3647 | 83.4872 | 778 | 15 | 782 | 5 | 0 | 0.0000 | |
| hfeng-pmm3 | INDEL | I1_5 | map_l100_m2_e0 | homalt | 99.5314 | 100.0000 | 99.0672 | 80.3663 | 531 | 0 | 531 | 5 | 3 | 60.0000 | |
| hfeng-pmm3 | INDEL | I1_5 | map_l100_m2_e1 | het | 98.7593 | 98.1481 | 99.3781 | 83.5851 | 795 | 15 | 799 | 5 | 0 | 0.0000 | |
| hfeng-pmm3 | INDEL | I1_5 | map_l100_m2_e1 | homalt | 99.5392 | 100.0000 | 99.0826 | 80.4869 | 540 | 0 | 540 | 5 | 3 | 60.0000 | |
| hfeng-pmm3 | INDEL | I1_5 | map_l125_m0_e0 | * | 98.5533 | 98.7097 | 98.3974 | 87.4598 | 306 | 4 | 307 | 5 | 2 | 40.0000 | |
| hfeng-pmm3 | INDEL | I1_5 | map_l125_m1_e0 | het | 98.4509 | 97.9424 | 98.9648 | 85.0418 | 476 | 10 | 478 | 5 | 0 | 0.0000 | |
| hfeng-pmm3 | INDEL | I1_5 | map_l125_m2_e0 | het | 98.3826 | 97.7867 | 98.9858 | 86.3018 | 486 | 11 | 488 | 5 | 0 | 0.0000 | |
| hfeng-pmm3 | INDEL | I1_5 | map_l125_m2_e1 | het | 98.4178 | 97.8346 | 99.0079 | 86.3821 | 497 | 11 | 499 | 5 | 0 | 0.0000 | |
| hfeng-pmm3 | INDEL | I1_5 | map_l150_m1_e0 | het | 97.8207 | 97.3244 | 98.3221 | 88.5998 | 291 | 8 | 293 | 5 | 0 | 0.0000 | |
| hfeng-pmm3 | INDEL | I1_5 | map_l150_m2_e0 | het | 97.7251 | 97.0874 | 98.3713 | 89.5400 | 300 | 9 | 302 | 5 | 0 | 0.0000 | |
| 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 | map_siren | homalt | 99.7534 | 99.9175 | 99.5898 | 76.7011 | 1211 | 1 | 1214 | 5 | 3 | 60.0000 | |
| hfeng-pmm3 | INDEL | I6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 95.1339 | 92.7126 | 97.6852 | 79.5455 | 229 | 18 | 211 | 5 | 3 | 60.0000 | |
| hfeng-pmm3 | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 94.3525 | 92.6174 | 96.1538 | 75.7009 | 138 | 11 | 125 | 5 | 3 | 60.0000 | |
| hfeng-pmm3 | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 99.5327 | 99.1851 | 99.8828 | 53.0235 | 4260 | 35 | 4260 | 5 | 0 | 0.0000 | |
| hfeng-pmm3 | SNP | * | lowcmp_SimpleRepeat_quadTR_51to200 | het | 80.4469 | 70.5882 | 93.5065 | 93.3102 | 72 | 30 | 72 | 5 | 0 | 0.0000 | |
| hfeng-pmm3 | SNP | ti | HG002compoundhet | homalt | 99.9256 | 99.9189 | 99.9324 | 30.4123 | 7388 | 6 | 7388 | 5 | 5 | 100.0000 | |