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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
18651-18700 / 86044 show all | |||||||||||||||
| gduggal-snapvard | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 89.9292 | 85.2071 | 95.2055 | 89.4101 | 432 | 75 | 417 | 21 | 10 | 47.6190 | |
| gduggal-snapvard | SNP | tv | map_l100_m1_e0 | homalt | 98.2646 | 96.7599 | 99.8168 | 61.4274 | 8750 | 293 | 8718 | 16 | 10 | 62.5000 | |
| ghariani-varprowl | INDEL | * | map_l250_m1_e0 | het | 85.3147 | 96.3158 | 76.5690 | 97.3834 | 183 | 7 | 183 | 56 | 10 | 17.8571 | |
| ghariani-varprowl | INDEL | * | map_l250_m2_e0 | het | 86.0169 | 96.6667 | 77.4809 | 97.4752 | 203 | 7 | 203 | 59 | 10 | 16.9492 | |
| ghariani-varprowl | INDEL | * | map_l250_m2_e1 | het | 86.0759 | 96.6825 | 77.5665 | 97.5340 | 204 | 7 | 204 | 59 | 10 | 16.9492 | |
| ghariani-varprowl | INDEL | D1_5 | func_cds | * | 91.6923 | 93.7107 | 89.7590 | 41.3428 | 149 | 10 | 149 | 17 | 10 | 58.8235 | |
| ghariani-varprowl | INDEL | D1_5 | func_cds | het | 91.3978 | 100.0000 | 84.1584 | 48.7310 | 85 | 0 | 85 | 16 | 10 | 62.5000 | |
| ghariani-varprowl | INDEL | D1_5 | map_l125_m0_e0 | * | 90.8918 | 96.5726 | 85.8423 | 90.8419 | 479 | 17 | 479 | 79 | 10 | 12.6582 | |
| hfeng-pmm2 | INDEL | D16_PLUS | HG002compoundhet | homalt | 61.5385 | 100.0000 | 44.4444 | 70.4918 | 8 | 0 | 8 | 10 | 10 | 100.0000 | |
| hfeng-pmm2 | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 96.7495 | 97.6834 | 95.8333 | 57.2816 | 253 | 6 | 253 | 11 | 10 | 90.9091 | |
| hfeng-pmm2 | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 98.8186 | 99.1632 | 98.4765 | 57.3034 | 711 | 6 | 711 | 11 | 10 | 90.9091 | |
| hfeng-pmm2 | INDEL | D1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 99.8164 | 99.6885 | 99.9447 | 54.6733 | 25280 | 79 | 25281 | 14 | 10 | 71.4286 | |
| hfeng-pmm2 | INDEL | I16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 96.0630 | 100.0000 | 92.4242 | 86.0759 | 122 | 0 | 122 | 10 | 10 | 100.0000 | |
| hfeng-pmm2 | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 96.9762 | 95.3595 | 98.6486 | 84.3187 | 1459 | 71 | 1460 | 20 | 10 | 50.0000 | |
| hfeng-pmm2 | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 96.9762 | 95.3595 | 98.6486 | 84.3187 | 1459 | 71 | 1460 | 20 | 10 | 50.0000 | |
| hfeng-pmm2 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 91.1243 | 93.9024 | 88.5057 | 75.9669 | 77 | 5 | 77 | 10 | 10 | 100.0000 | |
| hfeng-pmm2 | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | * | 99.1370 | 98.6663 | 99.6121 | 66.8126 | 3847 | 52 | 3852 | 15 | 10 | 66.6667 | |
| hfeng-pmm2 | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 99.3785 | 98.8765 | 99.8856 | 58.5898 | 55006 | 625 | 54996 | 63 | 10 | 15.8730 | |
| hfeng-pmm2 | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 99.0097 | 98.4465 | 99.5795 | 70.5535 | 44992 | 710 | 44993 | 190 | 10 | 5.2632 | |
| hfeng-pmm2 | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 99.0097 | 98.4465 | 99.5795 | 70.5535 | 44992 | 710 | 44993 | 190 | 10 | 5.2632 | |
| hfeng-pmm1 | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 99.1653 | 98.5252 | 99.8138 | 69.6830 | 45028 | 674 | 45028 | 84 | 10 | 11.9048 | |
| hfeng-pmm1 | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 99.1653 | 98.5252 | 99.8138 | 69.6830 | 45028 | 674 | 45028 | 84 | 10 | 11.9048 | |
| hfeng-pmm1 | SNP | * | map_l100_m0_e0 | homalt | 99.7374 | 99.7074 | 99.7675 | 63.8562 | 11586 | 34 | 11586 | 27 | 10 | 37.0370 | |
| hfeng-pmm1 | SNP | * | map_l150_m1_e0 | homalt | 99.7516 | 99.7427 | 99.7604 | 71.3075 | 11244 | 29 | 11244 | 27 | 10 | 37.0370 | |
| hfeng-pmm1 | SNP | * | map_l150_m2_e0 | homalt | 99.7606 | 99.7521 | 99.7692 | 73.4870 | 11670 | 29 | 11670 | 27 | 10 | 37.0370 | |
| hfeng-pmm1 | SNP | * | map_l150_m2_e1 | homalt | 99.7632 | 99.7548 | 99.7717 | 73.5145 | 11798 | 29 | 11798 | 27 | 10 | 37.0370 | |
| hfeng-pmm1 | SNP | * | map_l250_m1_e0 | het | 98.4804 | 98.1283 | 98.8350 | 88.4918 | 4666 | 89 | 4666 | 55 | 10 | 18.1818 | |
| hfeng-pmm1 | SNP | ti | HG002complexvar | het | 99.8377 | 99.6899 | 99.9860 | 16.6225 | 313790 | 976 | 313739 | 44 | 10 | 22.7273 | |
| hfeng-pmm1 | SNP | ti | map_l250_m1_e0 | * | 98.9508 | 98.8644 | 99.0374 | 88.1947 | 4527 | 52 | 4527 | 44 | 10 | 22.7273 | |
| hfeng-pmm1 | SNP | ti | map_l250_m2_e0 | * | 99.0408 | 98.9617 | 99.1200 | 88.5996 | 4956 | 52 | 4956 | 44 | 10 | 22.7273 | |
| hfeng-pmm1 | SNP | ti | map_l250_m2_e1 | * | 99.0337 | 98.9362 | 99.1315 | 88.6771 | 5022 | 54 | 5022 | 44 | 10 | 22.7273 | |
| hfeng-pmm1 | SNP | tv | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 99.4519 | 98.9956 | 99.9125 | 62.9106 | 27400 | 278 | 27391 | 24 | 10 | 41.6667 | |
| hfeng-pmm1 | SNP | tv | map_l150_m1_e0 | het | 99.0753 | 98.7331 | 99.4200 | 74.8128 | 6858 | 88 | 6856 | 40 | 10 | 25.0000 | |
| hfeng-pmm1 | SNP | tv | map_l150_m2_e0 | het | 99.1075 | 98.7728 | 99.4445 | 75.8631 | 7163 | 89 | 7161 | 40 | 10 | 25.0000 | |
| hfeng-pmm1 | SNP | tv | map_l150_m2_e1 | het | 99.1123 | 98.7752 | 99.4518 | 75.8770 | 7258 | 90 | 7256 | 40 | 10 | 25.0000 | |
| hfeng-pmm2 | INDEL | * | lowcmp_SimpleRepeat_homopolymer_6to10 | homalt | 99.9159 | 99.9292 | 99.9026 | 55.9613 | 11288 | 8 | 11288 | 11 | 10 | 90.9091 | |
| hfeng-pmm2 | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | het | 98.9153 | 98.1365 | 99.7066 | 60.6969 | 10901 | 207 | 10875 | 32 | 10 | 31.2500 | |
| jlack-gatk | INDEL | I16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | * | 93.2955 | 91.2500 | 95.4348 | 82.0942 | 438 | 42 | 439 | 21 | 10 | 47.6190 | |
| jlack-gatk | INDEL | I1_5 | map_siren | * | 97.8278 | 98.7022 | 96.9687 | 83.0880 | 2966 | 39 | 2975 | 93 | 10 | 10.7527 | |
| jlack-gatk | SNP | * | map_l150_m0_e0 | homalt | 98.5532 | 97.4566 | 99.6748 | 74.6529 | 3985 | 104 | 3985 | 13 | 10 | 76.9231 | |
| jlack-gatk | SNP | * | segdup | homalt | 99.8743 | 99.8418 | 99.9069 | 88.3916 | 10726 | 17 | 10726 | 10 | 10 | 100.0000 | |
| jlack-gatk | SNP | ti | * | hetalt | 98.8034 | 99.3127 | 98.2993 | 52.8846 | 578 | 4 | 578 | 10 | 10 | 100.0000 | |
| jlack-gatk | SNP | ti | lowcmp_SimpleRepeat_diTR_11to50 | * | 99.5658 | 99.5452 | 99.5863 | 69.3755 | 4815 | 22 | 4815 | 20 | 10 | 50.0000 | |
| jlack-gatk | SNP | ti | segdup | * | 98.4574 | 99.8106 | 97.1403 | 92.8551 | 19500 | 37 | 19498 | 574 | 10 | 1.7422 | |
| jlack-gatk | SNP | tv | map_siren | homalt | 99.5956 | 99.2807 | 99.9124 | 53.4780 | 17116 | 124 | 17113 | 15 | 10 | 66.6667 | |
| jli-custom | INDEL | * | map_l100_m0_e0 | * | 97.9520 | 97.8887 | 98.0154 | 84.8379 | 1530 | 33 | 1531 | 31 | 10 | 32.2581 | |
| hfeng-pmm3 | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 96.8310 | 97.1731 | 96.4912 | 69.5187 | 275 | 8 | 275 | 10 | 10 | 100.0000 | |
| hfeng-pmm3 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 98.6389 | 97.8193 | 99.4723 | 75.3576 | 6280 | 140 | 6221 | 33 | 10 | 30.3030 | |
| hfeng-pmm3 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 98.6389 | 97.8193 | 99.4723 | 75.3576 | 6280 | 140 | 6221 | 33 | 10 | 30.3030 | |
| hfeng-pmm3 | SNP | * | HG002compoundhet | homalt | 99.8980 | 99.8887 | 99.9072 | 34.7339 | 10770 | 12 | 10770 | 10 | 10 | 100.0000 | |