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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
49001-49050 / 86044 show all | |||||||||||||||
| jli-custom | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_51to200 | het | 79.3123 | 89.9408 | 70.9302 | 81.7410 | 152 | 17 | 61 | 25 | 25 | 100.0000 | |
| cchapple-custom | INDEL | I1_5 | map_l125_m1_e0 | homalt | 98.6094 | 97.8593 | 99.3711 | 81.7451 | 320 | 7 | 316 | 2 | 1 | 50.0000 | |
| ckim-gatk | INDEL | I16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | * | 94.7735 | 92.5000 | 97.1616 | 81.7457 | 444 | 36 | 445 | 13 | 12 | 92.3077 | |
| jmaeng-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 99.3451 | 99.1719 | 99.5189 | 81.7458 | 6826 | 57 | 6826 | 33 | 11 | 33.3333 | |
| hfeng-pmm3 | INDEL | I16_PLUS | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 98.9011 | 100.0000 | 97.8261 | 81.7460 | 45 | 0 | 45 | 1 | 1 | 100.0000 | |
| raldana-dualsentieon | INDEL | I16_PLUS | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 98.9011 | 100.0000 | 97.8261 | 81.7460 | 45 | 0 | 45 | 1 | 1 | 100.0000 | |
| cchapple-custom | INDEL | D1_5 | map_l100_m1_e0 | * | 96.7211 | 97.3485 | 96.1018 | 81.7490 | 1799 | 49 | 1775 | 72 | 9 | 12.5000 | |
| ciseli-custom | SNP | tv | map_l125_m2_e0 | het | 74.6164 | 68.4639 | 81.9839 | 81.7497 | 7149 | 3293 | 7149 | 1571 | 62 | 3.9465 | |
| ciseli-custom | SNP | tv | map_l125_m2_e1 | het | 74.7394 | 68.6345 | 82.0365 | 81.7503 | 7243 | 3310 | 7243 | 1586 | 64 | 4.0353 | |
| ckim-vqsr | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 99.3603 | 99.2881 | 99.4326 | 81.7523 | 6834 | 49 | 6834 | 39 | 15 | 38.4615 | |
| jpowers-varprowl | INDEL | * | map_l100_m0_e0 | homalt | 95.3441 | 92.5344 | 98.3299 | 81.7524 | 471 | 38 | 471 | 8 | 5 | 62.5000 | |
| hfeng-pmm2 | INDEL | D1_5 | map_l100_m2_e0 | homalt | 99.5905 | 99.5090 | 99.6721 | 81.7529 | 608 | 3 | 608 | 2 | 2 | 100.0000 | |
| qzeng-custom | INDEL | I16_PLUS | map_siren | * | 65.7764 | 70.9302 | 61.3208 | 81.7556 | 61 | 25 | 65 | 41 | 5 | 12.1951 | |
| jpowers-varprowl | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 94.4831 | 99.6276 | 89.8438 | 81.7577 | 2408 | 9 | 2415 | 273 | 131 | 47.9853 | |
| gduggal-bwaplat | SNP | tv | map_l125_m2_e0 | homalt | 64.4820 | 47.5819 | 100.0000 | 81.7585 | 2863 | 3154 | 2863 | 0 | 0 | ||
| ckim-dragen | SNP | * | map_l150_m2_e0 | het | 97.5195 | 98.7086 | 96.3588 | 81.7586 | 19873 | 260 | 19874 | 751 | 69 | 9.1878 | |
| rpoplin-dv42 | INDEL | I6_15 | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 96.3740 | 94.1935 | 98.6577 | 81.7625 | 146 | 9 | 147 | 2 | 1 | 50.0000 | |
| gduggal-bwafb | INDEL | I6_15 | map_l100_m1_e0 | homalt | 93.7500 | 90.9091 | 96.7742 | 81.7647 | 30 | 3 | 30 | 1 | 1 | 100.0000 | |
| jlack-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 98.8719 | 99.3172 | 98.4305 | 81.7659 | 6836 | 47 | 6836 | 109 | 22 | 20.1835 | |
| gduggal-snapplat | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_51to200 | het | 19.2870 | 17.7778 | 21.0762 | 81.7661 | 24 | 111 | 47 | 176 | 45 | 25.5682 | |
| jmaeng-gatk | SNP | tv | map_l100_m2_e1 | * | 88.4662 | 80.9714 | 97.4899 | 81.7669 | 20472 | 4811 | 20468 | 527 | 16 | 3.0361 | |
| hfeng-pmm2 | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 95.5238 | 93.1587 | 98.0122 | 81.7675 | 640 | 47 | 641 | 13 | 7 | 53.8462 | |
| ndellapenna-hhga | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 91.1765 | 88.5714 | 93.9394 | 81.7680 | 31 | 4 | 31 | 2 | 1 | 50.0000 | |
| ndellapenna-hhga | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 95.7480 | 95.8991 | 95.5975 | 81.7695 | 912 | 39 | 912 | 42 | 37 | 88.0952 | |
| gduggal-snapplat | SNP | ti | map_l100_m2_e0 | hetalt | 86.1538 | 93.3333 | 80.0000 | 81.7708 | 28 | 2 | 28 | 7 | 7 | 100.0000 | |
| ghariani-varprowl | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 87.7018 | 87.7726 | 87.6311 | 81.7733 | 3180 | 443 | 3174 | 448 | 412 | 91.9643 | |
| gduggal-snapplat | INDEL | * | * | hetalt | 51.2002 | 36.0859 | 88.1005 | 81.7746 | 9107 | 16130 | 9151 | 1236 | 915 | 74.0291 | |
| bgallagher-sentieon | INDEL | I1_5 | map_l100_m2_e0 | homalt | 99.5314 | 100.0000 | 99.0672 | 81.7749 | 531 | 0 | 531 | 5 | 4 | 80.0000 | |
| jpowers-varprowl | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 94.0567 | 97.5229 | 90.8285 | 81.7751 | 19094 | 485 | 19163 | 1935 | 59 | 3.0491 | |
| jpowers-varprowl | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 94.0567 | 97.5229 | 90.8285 | 81.7751 | 19094 | 485 | 19163 | 1935 | 59 | 3.0491 | |
| qzeng-custom | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 99.4970 | 99.5995 | 99.3948 | 81.7770 | 1492 | 6 | 1478 | 9 | 8 | 88.8889 | |
| gduggal-bwavard | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 24.8564 | 19.5402 | 34.1463 | 81.7778 | 17 | 70 | 14 | 27 | 16 | 59.2593 | |
| hfeng-pmm2 | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_11to50 | het | 97.0547 | 95.4918 | 98.6696 | 81.7778 | 466 | 22 | 445 | 6 | 1 | 16.6667 | |
| jli-custom | INDEL | I1_5 | map_l125_m1_e0 | homalt | 99.5434 | 100.0000 | 99.0909 | 81.7780 | 327 | 0 | 327 | 3 | 2 | 66.6667 | |
| jmaeng-gatk | SNP | tv | map_l100_m2_e0 | * | 88.3689 | 80.8253 | 97.4657 | 81.7790 | 20233 | 4800 | 20229 | 526 | 16 | 3.0418 | |
| ghariani-varprowl | SNP | ti | map_l125_m0_e0 | het | 96.8041 | 98.4267 | 95.2342 | 81.7798 | 8133 | 130 | 8133 | 407 | 98 | 24.0786 | |
| raldana-dualsentieon | INDEL | D6_15 | map_siren | homalt | 98.8506 | 99.2308 | 98.4733 | 81.7803 | 129 | 1 | 129 | 2 | 1 | 50.0000 | |
| qzeng-custom | INDEL | * | map_l100_m2_e1 | homalt | 85.5777 | 78.8447 | 93.5680 | 81.7812 | 1010 | 271 | 1382 | 95 | 15 | 15.7895 | |
| gduggal-snapplat | SNP | tv | map_l150_m0_e0 | homalt | 88.6840 | 79.6687 | 100.0000 | 81.7822 | 1058 | 270 | 1059 | 0 | 0 | ||
| rpoplin-dv42 | INDEL | I6_15 | map_siren | * | 93.6968 | 90.1639 | 97.5177 | 81.7829 | 275 | 30 | 275 | 7 | 6 | 85.7143 | |
| gduggal-snapplat | SNP | tv | map_l100_m1_e0 | het | 94.6299 | 94.5320 | 94.7279 | 81.7875 | 14574 | 843 | 14572 | 811 | 394 | 48.5820 | |
| jmaeng-gatk | INDEL | D16_PLUS | lowcmp_SimpleRepeat_triTR_11to50 | het | 98.3329 | 98.3607 | 98.3051 | 81.7901 | 60 | 1 | 58 | 1 | 1 | 100.0000 | |
| gduggal-snapfb | INDEL | D6_15 | map_l100_m2_e1 | * | 75.6012 | 62.9091 | 94.7090 | 81.7919 | 173 | 102 | 179 | 10 | 9 | 90.0000 | |
| gduggal-bwavard | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 55.3143 | 76.7267 | 43.2455 | 81.7971 | 511 | 155 | 509 | 668 | 383 | 57.3353 | |
| gduggal-bwavard | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 55.3143 | 76.7267 | 43.2455 | 81.7971 | 511 | 155 | 509 | 668 | 383 | 57.3353 | |
| jlack-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 92.1621 | 97.7230 | 87.2000 | 81.7983 | 515 | 12 | 436 | 64 | 51 | 79.6875 | |
| hfeng-pmm2 | INDEL | * | map_l100_m1_e0 | homalt | 99.1863 | 99.3480 | 99.0252 | 81.8088 | 1219 | 8 | 1219 | 12 | 6 | 50.0000 | |
| astatham-gatk | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_11to50 | het | 99.1121 | 98.7531 | 99.4737 | 81.8095 | 396 | 5 | 378 | 2 | 1 | 50.0000 | |
| gduggal-snapplat | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 37.9771 | 33.2554 | 44.2615 | 81.8105 | 711 | 1427 | 860 | 1083 | 11 | 1.0157 | |
| egarrison-hhga | INDEL | I1_5 | HG002compoundhet | homalt | 78.9281 | 98.4802 | 65.8537 | 81.8115 | 324 | 5 | 324 | 168 | 152 | 90.4762 | |