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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
63651-63700 / 86044 show all | |||||||||||||||
| hfeng-pmm2 | INDEL | * | map_l100_m0_e0 | homalt | 98.6328 | 99.2141 | 98.0583 | 83.0759 | 505 | 4 | 505 | 10 | 5 | 50.0000 | |
| hfeng-pmm2 | INDEL | * | map_siren | het | 98.6272 | 98.7134 | 98.5411 | 82.4078 | 4450 | 58 | 4458 | 66 | 5 | 7.5758 | |
| hfeng-pmm2 | INDEL | D16_PLUS | HG002complexvar | homalt | 98.1002 | 98.2699 | 97.9310 | 75.1286 | 284 | 5 | 284 | 6 | 5 | 83.3333 | |
| hfeng-pmm2 | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_51to200 | het | 95.7107 | 95.7317 | 95.6897 | 85.9903 | 157 | 7 | 111 | 5 | 5 | 100.0000 | |
| hfeng-pmm2 | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | * | 97.4314 | 95.4545 | 99.4920 | 57.5943 | 1176 | 56 | 1175 | 6 | 5 | 83.3333 | |
| hfeng-pmm2 | INDEL | I16_PLUS | HG002complexvar | homalt | 99.0385 | 100.0000 | 98.0952 | 70.2550 | 309 | 0 | 309 | 6 | 5 | 83.3333 | |
| hfeng-pmm2 | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 88.4615 | 100.0000 | 79.3103 | 87.8661 | 23 | 0 | 23 | 6 | 5 | 83.3333 | |
| hfeng-pmm2 | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 95.3941 | 92.5121 | 98.4615 | 73.8956 | 383 | 31 | 384 | 6 | 5 | 83.3333 | |
| 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 | I16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 94.2529 | 100.0000 | 89.1304 | 87.6011 | 41 | 0 | 41 | 5 | 5 | 100.0000 | |
| hfeng-pmm2 | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 86.2745 | 91.6667 | 81.4815 | 79.3893 | 22 | 2 | 22 | 5 | 5 | 100.0000 | |
| hfeng-pmm2 | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 99.0524 | 98.2806 | 99.8365 | 59.1178 | 34810 | 609 | 34800 | 57 | 5 | 8.7719 | |
| hfeng-pmm2 | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.9480 | 99.9257 | 99.9703 | 57.5983 | 20184 | 15 | 20184 | 6 | 5 | 83.3333 | |
| hfeng-pmm2 | SNP | * | lowcmp_SimpleRepeat_diTR_11to50 | * | 98.3601 | 96.8531 | 99.9148 | 65.6503 | 9387 | 305 | 9387 | 8 | 5 | 62.5000 | |
| hfeng-pmm3 | SNP | tv | map_l125_m1_e0 | het | 99.3576 | 99.2988 | 99.4165 | 70.9308 | 10055 | 71 | 10053 | 59 | 5 | 8.4746 | |
| hfeng-pmm3 | SNP | tv | map_l125_m1_e0 | homalt | 99.7525 | 99.7270 | 99.7780 | 67.2958 | 5844 | 16 | 5844 | 13 | 5 | 38.4615 | |
| hfeng-pmm3 | SNP | tv | map_l125_m2_e0 | het | 99.3771 | 99.3201 | 99.4342 | 72.2814 | 10371 | 71 | 10369 | 59 | 5 | 8.4746 | |
| hfeng-pmm3 | SNP | tv | map_l125_m2_e0 | homalt | 99.7590 | 99.7341 | 99.7838 | 69.7058 | 6001 | 16 | 6001 | 13 | 5 | 38.4615 | |
| hfeng-pmm3 | SNP | tv | map_l125_m2_e1 | het | 99.3837 | 99.3272 | 99.4402 | 72.3386 | 10482 | 71 | 10480 | 59 | 5 | 8.4746 | |
| hfeng-pmm3 | SNP | tv | map_l125_m2_e1 | homalt | 99.7612 | 99.7366 | 99.7859 | 69.7479 | 6058 | 16 | 6058 | 13 | 5 | 38.4615 | |
| hfeng-pmm3 | SNP | tv | map_l150_m1_e0 | het | 99.2002 | 99.1218 | 99.2788 | 75.3081 | 6885 | 61 | 6883 | 50 | 5 | 10.0000 | |
| hfeng-pmm3 | SNP | tv | map_l150_m2_e0 | het | 99.2203 | 99.1589 | 99.2819 | 76.4022 | 7191 | 61 | 7189 | 52 | 5 | 9.6154 | |
| hfeng-pmm3 | SNP | tv | map_l150_m2_e1 | het | 99.2305 | 99.1698 | 99.2913 | 76.4144 | 7287 | 61 | 7285 | 52 | 5 | 9.6154 | |
| hfeng-pmm3 | SNP | tv | segdup | * | 99.7247 | 99.7890 | 99.6604 | 90.6553 | 8514 | 18 | 8510 | 29 | 5 | 17.2414 | |
| hfeng-pmm3 | SNP | tv | segdup | homalt | 99.8920 | 99.9382 | 99.8457 | 90.1933 | 3236 | 2 | 3236 | 5 | 5 | 100.0000 | |
| jlack-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 99.5795 | 99.7661 | 99.3937 | 76.6906 | 2133 | 5 | 2131 | 13 | 5 | 38.4615 | |
| jlack-gatk | INDEL | * | lowcmp_SimpleRepeat_homopolymer_gt10 | * | 52.6631 | 81.4516 | 38.9105 | 99.8116 | 101 | 23 | 100 | 157 | 5 | 3.1847 | |
| jlack-gatk | INDEL | * | lowcmp_SimpleRepeat_triTR_11to50 | het | 99.5350 | 99.4806 | 99.5894 | 54.0098 | 3639 | 19 | 3638 | 15 | 5 | 33.3333 | |
| jlack-gatk | INDEL | * | map_l125_m2_e1 | homalt | 98.7734 | 98.8372 | 98.7097 | 86.3987 | 765 | 9 | 765 | 10 | 5 | 50.0000 | |
| jlack-gatk | INDEL | * | map_l150_m2_e1 | homalt | 98.4772 | 98.5772 | 98.3773 | 89.0274 | 485 | 7 | 485 | 8 | 5 | 62.5000 | |
| jlack-gatk | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.0110 | 98.7939 | 99.2291 | 68.2739 | 901 | 11 | 901 | 7 | 5 | 71.4286 | |
| jlack-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 96.8132 | 94.2797 | 99.4867 | 30.0790 | 890 | 54 | 969 | 5 | 5 | 100.0000 | |
| jlack-gatk | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_51to200 | homalt | 94.8617 | 94.4882 | 95.2381 | 52.2727 | 120 | 7 | 120 | 6 | 5 | 83.3333 | |
| jlack-gatk | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_11to50 | het | 97.5761 | 98.2544 | 96.9072 | 81.0824 | 394 | 7 | 376 | 12 | 5 | 41.6667 | |
| jlack-gatk | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_51to200 | hetalt | 96.0080 | 93.7143 | 98.4169 | 35.2137 | 328 | 22 | 373 | 6 | 5 | 83.3333 | |
| jlack-gatk | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_51to200 | homalt | 97.1429 | 100.0000 | 94.4444 | 62.8866 | 102 | 0 | 102 | 6 | 5 | 83.3333 | |
| jlack-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 97.9263 | 97.7011 | 98.1524 | 69.9306 | 425 | 10 | 425 | 8 | 5 | 62.5000 | |
| jlack-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 99.3837 | 99.3515 | 99.4160 | 78.0297 | 1532 | 10 | 1532 | 9 | 5 | 55.5556 | |
| jlack-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 87.6621 | 78.3888 | 99.4236 | 31.5582 | 1012 | 279 | 1035 | 6 | 5 | 83.3333 | |
| jlack-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | hetalt | 97.5385 | 96.3504 | 98.7562 | 71.8093 | 396 | 15 | 397 | 5 | 5 | 100.0000 | |
| jlack-gatk | INDEL | D1_5 | map_l100_m0_e0 | het | 91.3204 | 98.6464 | 85.0073 | 89.4535 | 583 | 8 | 584 | 103 | 5 | 4.8544 | |
| jlack-gatk | INDEL | D1_5 | map_l125_m1_e0 | het | 91.7875 | 99.0358 | 85.5279 | 90.3635 | 719 | 7 | 721 | 122 | 5 | 4.0984 | |
| jlack-gatk | INDEL | D1_5 | map_l125_m2_e0 | het | 92.0548 | 99.0838 | 85.9570 | 90.8790 | 757 | 7 | 759 | 124 | 5 | 4.0323 | |
| jlack-gatk | INDEL | D1_5 | map_l125_m2_e1 | het | 92.0567 | 99.0909 | 85.9551 | 90.9534 | 763 | 7 | 765 | 125 | 5 | 4.0000 | |
| jlack-gatk | INDEL | D1_5 | map_l150_m2_e1 | * | 92.9289 | 98.5861 | 87.8857 | 91.6492 | 767 | 11 | 769 | 106 | 5 | 4.7170 | |
| jlack-gatk | INDEL | D1_5 | segdup | * | 95.5828 | 98.9121 | 92.4704 | 95.7903 | 1091 | 12 | 1093 | 89 | 5 | 5.6180 | |
| jlack-gatk | INDEL | D6_15 | map_l100_m2_e1 | * | 92.3351 | 94.1818 | 90.5594 | 88.7090 | 259 | 16 | 259 | 27 | 5 | 18.5185 | |
| jlack-gatk | INDEL | D6_15 | map_siren | * | 94.4231 | 96.4637 | 92.4670 | 85.5628 | 491 | 18 | 491 | 40 | 5 | 12.5000 | |
| jlack-gatk | INDEL | D6_15 | segdup | * | 92.8571 | 95.2880 | 90.5473 | 94.7561 | 182 | 9 | 182 | 19 | 5 | 26.3158 | |
| jlack-gatk | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 95.4677 | 94.4444 | 96.5135 | 88.1879 | 629 | 37 | 609 | 22 | 5 | 22.7273 | |