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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
19501-19550 / 86044 show all | |||||||||||||||
| egarrison-hhga | INDEL | * | map_l150_m2_e1 | het | 97.5133 | 97.4026 | 97.6242 | 89.7600 | 900 | 24 | 904 | 22 | 6 | 27.2727 | |
| ckim-isaac | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 85.7762 | 80.3859 | 91.9414 | 59.8529 | 250 | 61 | 251 | 22 | 20 | 90.9091 | |
| ckim-isaac | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 75.1358 | 70.1613 | 80.8696 | 87.6477 | 87 | 37 | 93 | 22 | 0 | 0.0000 | |
| ckim-isaac | SNP | tv | map_l150_m2_e0 | * | 67.6247 | 51.1845 | 99.6230 | 78.7586 | 5812 | 5543 | 5813 | 22 | 7 | 31.8182 | |
| ckim-isaac | SNP | tv | map_l150_m2_e1 | * | 67.7075 | 51.2780 | 99.6284 | 78.7389 | 5898 | 5604 | 5899 | 22 | 7 | 31.8182 | |
| ckim-vqsr | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 96.2746 | 95.6815 | 96.8750 | 75.2809 | 709 | 32 | 682 | 22 | 19 | 86.3636 | |
| ckim-vqsr | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_51to200 | het | 83.4086 | 85.9259 | 81.0345 | 77.7778 | 116 | 19 | 94 | 22 | 21 | 95.4545 | |
| ckim-vqsr | INDEL | D1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 99.7571 | 99.6017 | 99.9130 | 55.8468 | 25258 | 101 | 25261 | 22 | 14 | 63.6364 | |
| ckim-vqsr | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | * | 99.6415 | 99.4695 | 99.8142 | 51.5034 | 11812 | 63 | 11817 | 22 | 15 | 68.1818 | |
| ckim-vqsr | INDEL | D1_5 | map_l125_m0_e0 | het | 95.4416 | 97.1014 | 93.8375 | 93.2052 | 335 | 10 | 335 | 22 | 1 | 4.5455 | |
| ckim-vqsr | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 97.8202 | 96.1199 | 99.5818 | 26.2339 | 5227 | 211 | 5239 | 22 | 22 | 100.0000 | |
| ckim-vqsr | INDEL | I1_5 | HG002complexvar | het | 99.6583 | 99.4392 | 99.8784 | 58.1585 | 18087 | 102 | 18064 | 22 | 13 | 59.0909 | |
| ckim-vqsr | SNP | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 98.9186 | 98.5743 | 99.2654 | 69.9659 | 2973 | 43 | 2973 | 22 | 9 | 40.9091 | |
| ckim-vqsr | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 99.4334 | 99.3865 | 99.4804 | 79.7057 | 4212 | 26 | 4212 | 22 | 8 | 36.3636 | |
| egarrison-hhga | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 94.1071 | 92.2942 | 95.9927 | 56.4631 | 527 | 44 | 527 | 22 | 15 | 68.1818 | |
| egarrison-hhga | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 97.5105 | 95.6899 | 99.4017 | 30.5702 | 3641 | 164 | 3655 | 22 | 22 | 100.0000 | |
| egarrison-hhga | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 94.2276 | 93.3190 | 95.1542 | 68.0956 | 433 | 31 | 432 | 22 | 16 | 72.7273 | |
| egarrison-hhga | SNP | ti | map_l150_m0_e0 | * | 99.1041 | 98.4989 | 99.7167 | 79.0350 | 7743 | 118 | 7743 | 22 | 10 | 45.4545 | |
| egarrison-hhga | SNP | tv | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 98.2141 | 97.8892 | 98.5411 | 67.8190 | 1484 | 32 | 1486 | 22 | 10 | 45.4545 | |
| egarrison-hhga | SNP | tv | lowcmp_SimpleRepeat_diTR_11to50 | het | 98.7140 | 98.1541 | 99.2803 | 63.6850 | 3031 | 57 | 3035 | 22 | 10 | 45.4545 | |
| eyeh-varpipe | INDEL | C1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 0.0000 | 0.0000 | 21.4286 | 90.0000 | 0 | 0 | 6 | 22 | 5 | 22.7273 | |
| eyeh-varpipe | INDEL | C1_5 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 0.0000 | 0.0000 | 71.4286 | 95.0323 | 0 | 0 | 55 | 22 | 16 | 72.7273 | |
| ckim-isaac | INDEL | D16_PLUS | * | homalt | 88.9191 | 81.0875 | 98.4252 | 54.0612 | 1372 | 320 | 1375 | 22 | 6 | 27.2727 | |
| ckim-isaac | INDEL | D1_5 | map_l100_m1_e0 | * | 83.8870 | 73.1061 | 98.3977 | 82.4582 | 1351 | 497 | 1351 | 22 | 10 | 45.4545 | |
| ckim-isaac | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 82.4180 | 70.7101 | 98.7723 | 34.9310 | 1673 | 693 | 1770 | 22 | 18 | 81.8182 | |
| ckim-isaac | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 90.8242 | 84.7922 | 97.7800 | 34.6306 | 959 | 172 | 969 | 22 | 17 | 77.2727 | |
| dgrover-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 99.5603 | 99.5507 | 99.5700 | 75.2360 | 5096 | 23 | 5094 | 22 | 10 | 45.4545 | |
| dgrover-gatk | INDEL | * | map_l150_m1_e0 | het | 97.6722 | 97.8947 | 97.4508 | 91.3510 | 837 | 18 | 841 | 22 | 3 | 13.6364 | |
| dgrover-gatk | INDEL | * | map_l150_m2_e0 | het | 97.8027 | 98.0132 | 97.5930 | 91.8342 | 888 | 18 | 892 | 22 | 3 | 13.6364 | |
| dgrover-gatk | INDEL | * | map_l150_m2_e1 | het | 97.7901 | 97.9437 | 97.6369 | 91.8626 | 905 | 19 | 909 | 22 | 3 | 13.6364 | |
| dgrover-gatk | INDEL | D16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 97.3843 | 99.1803 | 95.6522 | 71.9357 | 484 | 4 | 484 | 22 | 18 | 81.8182 | |
| dgrover-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 96.3472 | 95.8165 | 96.8839 | 75.3835 | 710 | 31 | 684 | 22 | 19 | 86.3636 | |
| dgrover-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_51to200 | het | 83.0580 | 85.1852 | 81.0345 | 77.8626 | 115 | 20 | 94 | 22 | 21 | 95.4545 | |
| dgrover-gatk | INDEL | D1_5 | map_l100_m1_e0 | * | 98.8105 | 98.8095 | 98.8115 | 84.8192 | 1826 | 22 | 1829 | 22 | 5 | 22.7273 | |
| dgrover-gatk | INDEL | D1_5 | map_l100_m2_e0 | * | 98.8260 | 98.7990 | 98.8530 | 85.3498 | 1892 | 23 | 1896 | 22 | 5 | 22.7273 | |
| dgrover-gatk | INDEL | D1_5 | map_l100_m2_e1 | * | 98.8405 | 98.8138 | 98.8671 | 85.4314 | 1916 | 23 | 1920 | 22 | 5 | 22.7273 | |
| gduggal-snapvard | SNP | tv | map_siren | homalt | 98.2279 | 96.6415 | 99.8673 | 55.2791 | 16661 | 579 | 16552 | 22 | 13 | 59.0909 | |
| gduggal-snapvard | SNP | tv | segdup | homalt | 98.3768 | 97.4676 | 99.3031 | 90.1749 | 3156 | 82 | 3135 | 22 | 21 | 95.4545 | |
| ghariani-varprowl | INDEL | * | segdup | homalt | 93.7217 | 90.2083 | 97.5197 | 91.8211 | 866 | 94 | 865 | 22 | 17 | 77.2727 | |
| ghariani-varprowl | INDEL | D16_PLUS | lowcmp_SimpleRepeat_homopolymer_gt10 | het | 68.0000 | 77.2727 | 60.7143 | 97.3585 | 34 | 10 | 34 | 22 | 12 | 54.5455 | |
| ghariani-varprowl | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 18.9387 | 11.0818 | 65.0794 | 81.9484 | 42 | 337 | 41 | 22 | 12 | 54.5455 | |
| gduggal-snapfb | INDEL | I6_15 | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 75.4062 | 69.0323 | 83.0769 | 78.2609 | 107 | 48 | 108 | 22 | 21 | 95.4545 | |
| gduggal-snapfb | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | hetalt | 8.3333 | 100.0000 | 4.3478 | 75.7895 | 1 | 0 | 1 | 22 | 0 | 0.0000 | |
| gduggal-snapfb | SNP | * | tech_badpromoters | * | 93.1343 | 99.3631 | 87.6404 | 63.5992 | 156 | 1 | 156 | 22 | 1 | 4.5455 | |
| gduggal-snapfb | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | hetalt | 8.3333 | 100.0000 | 4.3478 | 75.7895 | 1 | 0 | 1 | 22 | 0 | 0.0000 | |
| gduggal-snapplat | INDEL | D1_5 | map_l250_m2_e0 | * | 81.1136 | 75.5435 | 87.5706 | 97.8091 | 139 | 45 | 155 | 22 | 5 | 22.7273 | |
| gduggal-snapplat | INDEL | D1_5 | map_l250_m2_e0 | het | 81.0385 | 79.3388 | 82.8125 | 97.9338 | 96 | 25 | 106 | 22 | 5 | 22.7273 | |
| gduggal-snapplat | INDEL | D1_5 | map_l250_m2_e1 | * | 81.2198 | 75.6757 | 87.6404 | 97.8476 | 140 | 45 | 156 | 22 | 5 | 22.7273 | |
| gduggal-snapplat | INDEL | D1_5 | map_l250_m2_e1 | het | 81.1906 | 79.5082 | 82.9457 | 97.9666 | 97 | 25 | 107 | 22 | 5 | 22.7273 | |
| gduggal-snapplat | INDEL | D1_5 | segdup | homalt | 91.2889 | 88.3008 | 94.4862 | 94.9101 | 317 | 42 | 377 | 22 | 10 | 45.4545 | |