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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
16651-16700 / 86044 show all | |||||||||||||||
| anovak-vg | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 37.4335 | 27.0492 | 60.7595 | 65.3509 | 33 | 89 | 48 | 31 | 14 | 45.1613 | |
| anovak-vg | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 26.2295 | 25.0000 | 27.5862 | 55.3846 | 6 | 18 | 8 | 21 | 14 | 66.6667 | |
| anovak-vg | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | homalt | 98.3912 | 98.6014 | 98.1818 | 44.9656 | 846 | 12 | 864 | 16 | 14 | 87.5000 | |
| anovak-vg | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 81.0909 | 85.5072 | 77.1084 | 86.6129 | 59 | 10 | 64 | 19 | 14 | 73.6842 | |
| anovak-vg | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 97.2183 | 97.1882 | 97.2484 | 66.9538 | 1348 | 39 | 1343 | 38 | 14 | 36.8421 | |
| hfeng-pmm2 | SNP | * | map_l125_m1_e0 | homalt | 99.8078 | 99.8107 | 99.8048 | 66.6048 | 16873 | 32 | 16873 | 33 | 14 | 42.4242 | |
| hfeng-pmm2 | SNP | * | map_l125_m2_e0 | homalt | 99.8130 | 99.8158 | 99.8101 | 69.0538 | 17343 | 32 | 17343 | 33 | 14 | 42.4242 | |
| hfeng-pmm2 | SNP | * | map_l125_m2_e1 | homalt | 99.8146 | 99.8175 | 99.8118 | 69.0869 | 17500 | 32 | 17500 | 33 | 14 | 42.4242 | |
| hfeng-pmm2 | SNP | ti | map_l100_m1_e0 | homalt | 99.8719 | 99.8775 | 99.8664 | 60.1447 | 17938 | 22 | 17938 | 24 | 14 | 58.3333 | |
| hfeng-pmm2 | SNP | ti | map_l100_m2_e0 | homalt | 99.8744 | 99.8798 | 99.8689 | 62.5825 | 18287 | 22 | 18287 | 24 | 14 | 58.3333 | |
| hfeng-pmm2 | SNP | ti | map_l100_m2_e1 | homalt | 99.8756 | 99.8810 | 99.8702 | 62.5670 | 18472 | 22 | 18472 | 24 | 14 | 58.3333 | |
| hfeng-pmm2 | SNP | ti | map_l125_m1_e0 | het | 99.1603 | 99.2500 | 99.0708 | 74.2780 | 18129 | 137 | 18125 | 170 | 14 | 8.2353 | |
| hfeng-pmm2 | SNP | ti | map_l125_m2_e0 | het | 99.1742 | 99.2636 | 99.0849 | 75.4183 | 18737 | 139 | 18733 | 173 | 14 | 8.0925 | |
| hfeng-pmm2 | SNP | ti | map_l125_m2_e1 | het | 99.1807 | 99.2718 | 99.0899 | 75.4485 | 18948 | 139 | 18944 | 174 | 14 | 8.0460 | |
| hfeng-pmm2 | SNP | tv | map_l150_m1_e0 | * | 99.1035 | 99.2944 | 98.9134 | 76.5808 | 10835 | 77 | 10833 | 119 | 14 | 11.7647 | |
| hfeng-pmm2 | SNP | tv | map_l150_m2_e0 | * | 99.1297 | 99.3219 | 98.9383 | 77.9235 | 11278 | 77 | 11276 | 121 | 14 | 11.5702 | |
| hfeng-pmm2 | SNP | tv | map_l150_m2_e1 | * | 99.1408 | 99.3306 | 98.9518 | 77.9286 | 11425 | 77 | 11423 | 121 | 14 | 11.5702 | |
| hfeng-pmm2 | SNP | tv | map_siren | het | 99.5196 | 99.5806 | 99.4588 | 60.5491 | 28489 | 120 | 28484 | 155 | 14 | 9.0323 | |
| hfeng-pmm3 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 96.4427 | 96.5699 | 96.3158 | 59.3148 | 366 | 13 | 366 | 14 | 14 | 100.0000 | |
| jlack-gatk | INDEL | * | lowcmp_SimpleRepeat_triTR_11to50 | * | 99.5542 | 99.4802 | 99.6283 | 49.3638 | 6698 | 35 | 6700 | 25 | 14 | 56.0000 | |
| jlack-gatk | INDEL | * | map_l125_m2_e1 | * | 94.6989 | 98.2022 | 91.4369 | 90.8050 | 2185 | 40 | 2189 | 205 | 14 | 6.8293 | |
| jlack-gatk | INDEL | * | map_siren | homalt | 99.0590 | 99.0207 | 99.0974 | 80.4586 | 2629 | 26 | 2635 | 24 | 14 | 58.3333 | |
| jlack-gatk | INDEL | D16_PLUS | HG002complexvar | hetalt | 92.3729 | 88.2591 | 96.8889 | 46.8085 | 218 | 29 | 436 | 14 | 14 | 100.0000 | |
| jlack-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 94.5501 | 90.3525 | 99.1566 | 32.4379 | 1461 | 156 | 1646 | 14 | 14 | 100.0000 | |
| jlack-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 94.4937 | 90.2365 | 99.1726 | 34.9981 | 1488 | 161 | 1678 | 14 | 14 | 100.0000 | |
| jlack-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 98.3938 | 98.5294 | 98.2585 | 65.1438 | 1072 | 16 | 1072 | 19 | 14 | 73.6842 | |
| jlack-gatk | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 94.0414 | 91.8486 | 96.3415 | 81.8634 | 631 | 56 | 632 | 24 | 14 | 58.3333 | |
| hfeng-pmm2 | INDEL | D1_5 | HG002complexvar | het | 98.9180 | 97.9581 | 99.8969 | 54.5187 | 20341 | 424 | 20346 | 21 | 14 | 66.6667 | |
| hfeng-pmm2 | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 96.5157 | 97.8799 | 95.1890 | 68.7433 | 277 | 6 | 277 | 14 | 14 | 100.0000 | |
| hfeng-pmm2 | SNP | * | HG002compoundhet | * | 97.7436 | 95.7052 | 99.8707 | 39.1925 | 24713 | 1109 | 24713 | 32 | 14 | 43.7500 | |
| hfeng-pmm1 | SNP | tv | map_l150_m1_e0 | * | 99.3066 | 99.0927 | 99.5213 | 73.8197 | 10813 | 99 | 10811 | 52 | 14 | 26.9231 | |
| hfeng-pmm1 | SNP | tv | map_l150_m2_e0 | * | 99.3292 | 99.1193 | 99.5400 | 75.2398 | 11255 | 100 | 11253 | 52 | 14 | 26.9231 | |
| hfeng-pmm1 | SNP | tv | map_l150_m2_e1 | * | 99.3334 | 99.1219 | 99.5459 | 75.2491 | 11401 | 101 | 11399 | 52 | 14 | 26.9231 | |
| hfeng-pmm1 | SNP | tv | map_siren | het | 99.6130 | 99.4093 | 99.8175 | 56.2607 | 28440 | 169 | 28435 | 52 | 14 | 26.9231 | |
| hfeng-pmm2 | INDEL | * | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 99.7892 | 99.6568 | 99.9219 | 57.6377 | 28163 | 97 | 28165 | 22 | 14 | 63.6364 | |
| jlack-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 98.6868 | 99.2734 | 98.1070 | 88.8808 | 1503 | 11 | 1503 | 29 | 14 | 48.2759 | |
| jlack-gatk | SNP | tv | HG002complexvar | homalt | 99.9385 | 99.8959 | 99.9811 | 22.6324 | 95012 | 99 | 94994 | 18 | 14 | 77.7778 | |
| jlack-gatk | SNP | tv | HG002compoundhet | het | 98.9462 | 99.4650 | 98.4329 | 56.5753 | 4648 | 25 | 4648 | 74 | 14 | 18.9189 | |
| jlack-gatk | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 98.4586 | 99.0170 | 97.9065 | 84.2545 | 2619 | 26 | 2619 | 56 | 14 | 25.0000 | |
| jlack-gatk | SNP | tv | lowcmp_SimpleRepeat_diTR_11to50 | * | 99.4853 | 99.5058 | 99.4648 | 66.6987 | 4832 | 24 | 4832 | 26 | 14 | 53.8462 | |
| jli-custom | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 94.2361 | 89.5703 | 99.4147 | 34.3662 | 2439 | 284 | 2548 | 15 | 14 | 93.3333 | |
| hfeng-pmm3 | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 98.8645 | 100.0000 | 97.7545 | 71.3796 | 653 | 0 | 653 | 15 | 14 | 93.3333 | |
| hfeng-pmm3 | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 99.1804 | 98.6259 | 99.7411 | 70.8758 | 45074 | 628 | 45075 | 117 | 14 | 11.9658 | |
| hfeng-pmm3 | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 99.1804 | 98.6259 | 99.7411 | 70.8758 | 45074 | 628 | 45075 | 117 | 14 | 11.9658 | |
| hfeng-pmm3 | SNP | * | map_l100_m1_e0 | het | 99.5486 | 99.4400 | 99.6575 | 64.8095 | 45105 | 254 | 45094 | 155 | 14 | 9.0323 | |
| hfeng-pmm3 | SNP | * | map_l100_m2_e0 | het | 99.5523 | 99.4461 | 99.6587 | 66.2016 | 46142 | 257 | 46131 | 158 | 14 | 8.8608 | |
| hfeng-pmm3 | SNP | * | map_l100_m2_e1 | het | 99.5538 | 99.4499 | 99.6580 | 66.2190 | 46640 | 258 | 46629 | 160 | 14 | 8.7500 | |
| hfeng-pmm3 | SNP | ti | map_l150_m1_e0 | * | 99.4898 | 99.4217 | 99.5579 | 74.0428 | 19598 | 114 | 19594 | 87 | 14 | 16.0920 | |
| hfeng-pmm3 | SNP | ti | map_l150_m2_e0 | * | 99.5024 | 99.4394 | 99.5655 | 75.5202 | 20397 | 115 | 20393 | 89 | 14 | 15.7303 | |
| hfeng-pmm3 | SNP | ti | map_l150_m2_e1 | * | 99.5026 | 99.4402 | 99.5651 | 75.5918 | 20607 | 116 | 20603 | 90 | 14 | 15.5556 | |