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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
74551-74600 / 86044 show all | |||||||||||||||
| ckim-dragen | INDEL | I16_PLUS | * | * | 97.2529 | 96.3306 | 98.1932 | 70.5888 | 6143 | 234 | 6141 | 113 | 94 | 83.1858 | |
| ciseli-custom | INDEL | D1_5 | map_l100_m0_e0 | * | 77.3981 | 72.8853 | 82.5065 | 89.4982 | 629 | 234 | 632 | 134 | 63 | 47.0149 | |
| ciseli-custom | INDEL | I6_15 | lowcmp_SimpleRepeat_triTR_11to50 | hetalt | 0.0000 | 1.2658 | 0.0000 | 0.0000 | 3 | 234 | 0 | 0 | 0 | ||
| hfeng-pmm1 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 97.8735 | 96.4965 | 99.2905 | 49.4936 | 6445 | 234 | 6437 | 46 | 35 | 76.0870 | |
| hfeng-pmm3 | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 96.5539 | 93.3636 | 99.9700 | 43.1520 | 3292 | 234 | 3332 | 1 | 1 | 100.0000 | |
| hfeng-pmm3 | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 96.5539 | 93.3636 | 99.9700 | 43.1520 | 3292 | 234 | 3332 | 1 | 1 | 100.0000 | |
| hfeng-pmm3 | SNP | * | map_l125_m1_e0 | * | 99.5551 | 99.4838 | 99.6266 | 69.4654 | 45093 | 234 | 45087 | 169 | 26 | 15.3846 | |
| hfeng-pmm2 | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 93.1378 | 87.1570 | 100.0000 | 32.6259 | 1588 | 234 | 1619 | 0 | 0 | ||
| asubramanian-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 93.0557 | 90.2945 | 95.9912 | 59.3990 | 2177 | 234 | 2179 | 91 | 83 | 91.2088 | |
| gduggal-bwavard | SNP | ti | map_l100_m0_e0 | homalt | 98.3810 | 96.9900 | 99.8126 | 63.0879 | 7540 | 234 | 7457 | 14 | 11 | 78.5714 | |
| gduggal-bwaplat | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 80.3149 | 68.8830 | 96.2963 | 71.1384 | 518 | 234 | 520 | 20 | 19 | 95.0000 | |
| ckim-isaac | SNP | * | lowcmp_SimpleRepeat_homopolymer_6to10 | homalt | 98.0159 | 96.1564 | 99.9488 | 52.1398 | 5854 | 234 | 5857 | 3 | 3 | 100.0000 | |
| eyeh-varpipe | INDEL | * | map_l100_m2_e0 | * | 94.5816 | 93.6637 | 95.5178 | 92.5332 | 3459 | 234 | 4944 | 232 | 182 | 78.4483 | |
| raldana-dualsentieon | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 97.4660 | 96.4965 | 98.4552 | 52.4855 | 6445 | 234 | 6437 | 101 | 99 | 98.0198 | |
| gduggal-snapfb | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | het | 43.0800 | 29.0909 | 82.9861 | 28.5360 | 96 | 234 | 239 | 49 | 49 | 100.0000 | |
| gduggal-snapvard | SNP | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 82.6781 | 95.0672 | 73.1457 | 83.0764 | 4529 | 235 | 4497 | 1651 | 43 | 2.6045 | |
| asubramanian-gatk | INDEL | * | map_l125_m2_e0 | het | 88.2149 | 83.1057 | 93.9935 | 92.2139 | 1156 | 235 | 1158 | 74 | 7 | 9.4595 | |
| ciseli-custom | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 46.1817 | 33.6158 | 73.7500 | 67.0103 | 119 | 235 | 118 | 42 | 40 | 95.2381 | |
| ckim-dragen | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 96.9960 | 94.1673 | 100.0000 | 24.9114 | 3794 | 235 | 3813 | 0 | 0 | ||
| ndellapenna-hhga | SNP | tv | map_l125_m1_e0 | * | 99.1238 | 98.5327 | 99.7220 | 67.2834 | 15781 | 235 | 15781 | 44 | 22 | 50.0000 | |
| hfeng-pmm3 | INDEL | I1_5 | HG002complexvar | * | 99.5912 | 99.2956 | 99.8886 | 56.4158 | 33128 | 235 | 33172 | 37 | 24 | 64.8649 | |
| hfeng-pmm1 | INDEL | I1_5 | HG002complexvar | * | 99.5778 | 99.2956 | 99.8615 | 56.6148 | 33128 | 235 | 33171 | 46 | 29 | 63.0435 | |
| raldana-dualsentieon | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 98.2933 | 97.4269 | 99.1752 | 74.7089 | 8898 | 235 | 8898 | 74 | 10 | 13.5135 | |
| raldana-dualsentieon | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 98.2933 | 97.4269 | 99.1752 | 74.7089 | 8898 | 235 | 8898 | 74 | 10 | 13.5135 | |
| rpoplin-dv42 | SNP | * | map_l150_m2_e0 | het | 98.9235 | 98.8328 | 99.0144 | 75.6918 | 19898 | 235 | 19892 | 198 | 117 | 59.0909 | |
| gduggal-bwavard | INDEL | I6_15 | lowcmp_SimpleRepeat_triTR_11to50 | hetalt | 0.0000 | 0.8439 | 0.0000 | 0.0000 | 2 | 235 | 0 | 0 | 0 | ||
| gduggal-bwavard | SNP | * | segdup | homalt | 98.6646 | 97.8125 | 99.5315 | 88.9251 | 10508 | 235 | 10411 | 49 | 47 | 95.9184 | |
| gduggal-bwafb | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | het | 95.0403 | 91.4014 | 98.9810 | 39.0442 | 2498 | 235 | 6994 | 72 | 57 | 79.1667 | |
| eyeh-varpipe | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 97.4514 | 96.5009 | 98.4209 | 44.2767 | 6481 | 235 | 7230 | 116 | 68 | 58.6207 | |
| egarrison-hhga | SNP | ti | map_l125_m2_e0 | het | 99.2599 | 98.7550 | 99.7699 | 71.8619 | 18641 | 235 | 18641 | 43 | 16 | 37.2093 | |
| ckim-isaac | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 70.1745 | 56.1567 | 93.5185 | 58.4615 | 301 | 235 | 303 | 21 | 15 | 71.4286 | |
| egarrison-hhga | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | * | 82.0091 | 80.8442 | 83.2080 | 53.2969 | 996 | 236 | 996 | 201 | 178 | 88.5572 | |
| ndellapenna-hhga | SNP | tv | map_l125_m2_e0 | * | 99.1430 | 98.5687 | 99.7239 | 69.3029 | 16253 | 236 | 16253 | 45 | 22 | 48.8889 | |
| mlin-fermikit | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 89.1561 | 84.4122 | 94.4649 | 85.8278 | 1278 | 236 | 1280 | 75 | 7 | 9.3333 | |
| bgallagher-sentieon | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 97.1938 | 95.0545 | 99.4316 | 25.2614 | 4536 | 236 | 4548 | 26 | 26 | 100.0000 | |
| gduggal-snapplat | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 34.7356 | 24.1158 | 62.0690 | 73.8149 | 75 | 236 | 72 | 44 | 25 | 56.8182 | |
| gduggal-snapplat | INDEL | * | map_l150_m2_e1 | het | 79.5622 | 74.4589 | 85.4167 | 95.3345 | 688 | 236 | 738 | 126 | 19 | 15.0794 | |
| gduggal-snapfb | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 92.8220 | 96.7435 | 89.2061 | 36.1513 | 7011 | 236 | 7000 | 847 | 807 | 95.2774 | |
| ghariani-varprowl | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | * | 19.9827 | 12.2677 | 53.8462 | 92.1805 | 33 | 236 | 28 | 24 | 13 | 54.1667 | |
| ckim-isaac | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 92.8267 | 87.4867 | 98.8609 | 64.0750 | 1650 | 236 | 1649 | 19 | 5 | 26.3158 | |
| gduggal-bwaplat | SNP | * | segdup | homalt | 98.8522 | 97.8032 | 99.9239 | 88.9336 | 10507 | 236 | 10502 | 8 | 8 | 100.0000 | |
| hfeng-pmm3 | SNP | * | map_l125_m2_e0 | * | 99.5641 | 99.4949 | 99.6335 | 71.1339 | 46487 | 236 | 46481 | 171 | 26 | 15.2047 | |
| hfeng-pmm3 | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 99.0431 | 98.3803 | 99.7148 | 74.9713 | 14335 | 236 | 14335 | 41 | 7 | 17.0732 | |
| hfeng-pmm3 | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 99.0431 | 98.3803 | 99.7148 | 74.9713 | 14335 | 236 | 14335 | 41 | 7 | 17.0732 | |
| hfeng-pmm3 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 96.9697 | 94.1176 | 100.0000 | 25.6765 | 3792 | 237 | 3818 | 0 | 0 | ||
| hfeng-pmm3 | SNP | * | map_l125_m2_e1 | * | 99.5664 | 99.4979 | 99.6351 | 71.1769 | 46965 | 237 | 46959 | 172 | 26 | 15.1163 | |
| jlack-gatk | INDEL | D16_PLUS | * | * | 96.2606 | 96.5065 | 96.0159 | 70.3319 | 6547 | 237 | 6531 | 271 | 163 | 60.1476 | |
| hfeng-pmm1 | SNP | ti | map_l125_m2_e0 | * | 99.4583 | 99.2167 | 99.7011 | 70.4657 | 30021 | 237 | 30017 | 90 | 25 | 27.7778 | |
| hfeng-pmm1 | SNP | ti | map_l125_m2_e1 | * | 99.4622 | 99.2247 | 99.7008 | 70.5014 | 30332 | 237 | 30328 | 91 | 25 | 27.4725 | |
| hfeng-pmm2 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 97.8606 | 96.0047 | 99.7897 | 49.8726 | 5695 | 237 | 5695 | 12 | 11 | 91.6667 | |