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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
53751-53800 / 86044 show all | |||||||||||||||
| mlin-fermikit | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 88.0705 | 92.7235 | 83.8622 | 38.1946 | 6193 | 486 | 6184 | 1190 | 1162 | 97.6471 | |
| hfeng-pmm3 | INDEL | D6_15 | HG002complexvar | het | 95.8678 | 92.7244 | 99.2318 | 57.2218 | 2893 | 227 | 2842 | 22 | 17 | 77.2727 | |
| hfeng-pmm2 | INDEL | D6_15 | HG002compoundhet | * | 95.3103 | 92.7251 | 98.0438 | 33.3983 | 8374 | 657 | 8370 | 167 | 162 | 97.0060 | |
| gduggal-snapvard | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | het | 78.0403 | 92.7260 | 67.3704 | 39.0451 | 9650 | 757 | 18923 | 9165 | 8275 | 90.2891 | |
| gduggal-snapfb | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 38.9269 | 92.7273 | 24.6341 | 91.7522 | 102 | 8 | 101 | 309 | 13 | 4.2071 | |
| raldana-dualsentieon | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | het | 95.0404 | 92.7273 | 97.4719 | 75.5662 | 357 | 28 | 347 | 9 | 8 | 88.8889 | |
| mlin-fermikit | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 74.3472 | 92.7273 | 62.0482 | 92.1103 | 102 | 8 | 103 | 63 | 45 | 71.4286 | |
| ckim-vqsr | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | hetalt | 95.3442 | 92.7273 | 98.1132 | 61.5942 | 51 | 4 | 52 | 1 | 1 | 100.0000 | |
| asubramanian-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | hetalt | 94.4781 | 92.7273 | 96.2963 | 63.5135 | 51 | 4 | 52 | 2 | 2 | 100.0000 | |
| hfeng-pmm2 | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | hetalt | 96.2264 | 92.7273 | 100.0000 | 63.8889 | 51 | 4 | 52 | 0 | 0 | ||
| jlack-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 96.2264 | 92.7273 | 100.0000 | 91.0132 | 102 | 8 | 102 | 0 | 0 | ||
| hfeng-pmm3 | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 96.2264 | 92.7273 | 100.0000 | 91.5980 | 102 | 8 | 102 | 0 | 0 | ||
| ckim-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | hetalt | 95.3442 | 92.7273 | 98.1132 | 61.5942 | 51 | 4 | 52 | 1 | 1 | 100.0000 | |
| ckim-isaac | INDEL | D1_5 | HG002complexvar | het | 94.5641 | 92.7330 | 96.4689 | 45.1790 | 19256 | 1509 | 18687 | 684 | 323 | 47.2222 | |
| rpoplin-dv42 | INDEL | * | HG002compoundhet | * | 93.3591 | 92.7336 | 93.9930 | 68.4001 | 27783 | 2177 | 27758 | 1774 | 1747 | 98.4780 | |
| ckim-vqsr | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 93.6836 | 92.7338 | 94.6530 | 63.9970 | 5641 | 442 | 5523 | 312 | 296 | 94.8718 | |
| ghariani-varprowl | INDEL | D1_5 | map_l100_m1_e0 | homalt | 95.1473 | 92.7365 | 97.6868 | 77.2562 | 549 | 43 | 549 | 13 | 2 | 15.3846 | |
| jpowers-varprowl | INDEL | D1_5 | map_l100_m1_e0 | homalt | 95.8115 | 92.7365 | 99.0975 | 76.8491 | 549 | 43 | 549 | 5 | 2 | 40.0000 | |
| ckim-isaac | SNP | ti | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 94.1838 | 92.7372 | 95.6762 | 65.3122 | 1877 | 147 | 1903 | 86 | 6 | 6.9767 | |
| astatham-gatk | INDEL | * | map_l125_m2_e0 | het | 94.9267 | 92.7390 | 97.2201 | 89.8845 | 1290 | 101 | 1294 | 37 | 5 | 13.5135 | |
| rpoplin-dv42 | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 95.9446 | 92.7410 | 99.3774 | 27.6985 | 7474 | 585 | 7502 | 47 | 46 | 97.8723 | |
| rpoplin-dv42 | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 95.9446 | 92.7410 | 99.3774 | 27.6985 | 7474 | 585 | 7502 | 47 | 46 | 97.8723 | |
| asubramanian-gatk | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 95.0515 | 92.7419 | 97.4790 | 91.0526 | 115 | 9 | 116 | 3 | 2 | 66.6667 | |
| ckim-dragen | INDEL | * | lowcmp_SimpleRepeat_homopolymer_gt10 | * | 94.2454 | 92.7419 | 95.7983 | 99.9211 | 115 | 9 | 114 | 5 | 3 | 60.0000 | |
| gduggal-bwafb | INDEL | I1_5 | map_l150_m2_e1 | het | 95.3061 | 92.7445 | 98.0132 | 89.7349 | 294 | 23 | 296 | 6 | 1 | 16.6667 | |
| ckim-vqsr | INDEL | I1_5 | map_l150_m2_e1 | het | 94.6912 | 92.7445 | 96.7213 | 94.6529 | 294 | 23 | 295 | 10 | 1 | 10.0000 | |
| ltrigg-rtg1 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 95.9739 | 92.7447 | 99.4362 | 52.4133 | 15493 | 1212 | 15872 | 90 | 88 | 97.7778 | |
| ltrigg-rtg1 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 95.9739 | 92.7447 | 99.4362 | 52.4133 | 15493 | 1212 | 15872 | 90 | 88 | 97.7778 | |
| ckim-isaac | SNP | ti | HG002compoundhet | hetalt | 96.2366 | 92.7461 | 100.0000 | 18.6364 | 537 | 42 | 537 | 0 | 0 | ||
| gduggal-bwavard | INDEL | * | map_l100_m1_e0 | homalt | 95.9129 | 92.7465 | 99.3031 | 75.5380 | 1138 | 89 | 1140 | 8 | 5 | 62.5000 | |
| mlin-fermikit | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | het | 89.4933 | 92.7475 | 86.4597 | 53.2254 | 14617 | 1143 | 14482 | 2268 | 2204 | 97.1781 | |
| ckim-dragen | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 96.2383 | 92.7494 | 100.0000 | 30.4125 | 4426 | 346 | 4471 | 0 | 0 | ||
| hfeng-pmm3 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 96.2383 | 92.7494 | 100.0000 | 31.0430 | 4426 | 346 | 4476 | 0 | 0 | ||
| ckim-vqsr | INDEL | * | HG002compoundhet | * | 93.9622 | 92.7503 | 95.2061 | 62.6940 | 27788 | 2172 | 27665 | 1393 | 1381 | 99.1385 | |
| asubramanian-gatk | INDEL | D1_5 | HG002complexvar | hetalt | 94.5568 | 92.7515 | 96.4339 | 73.6698 | 1254 | 98 | 1298 | 48 | 47 | 97.9167 | |
| bgallagher-sentieon | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 96.1822 | 92.7531 | 99.8747 | 34.7506 | 2355 | 184 | 2391 | 3 | 3 | 100.0000 | |
| astatham-gatk | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 95.0556 | 92.7536 | 97.4747 | 74.1176 | 384 | 30 | 386 | 10 | 10 | 100.0000 | |
| asubramanian-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 88.1816 | 92.7536 | 84.0391 | 90.9546 | 256 | 20 | 258 | 49 | 3 | 6.1225 | |
| ckim-vqsr | SNP | ti | HG002complexvar | hetalt | 96.2406 | 92.7536 | 100.0000 | 40.3727 | 192 | 15 | 192 | 0 | 0 | ||
| egarrison-hhga | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 94.3344 | 92.7536 | 95.9700 | 83.7025 | 1024 | 80 | 1024 | 43 | 20 | 46.5116 | |
| qzeng-custom | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 85.6095 | 92.7536 | 79.4872 | 92.6630 | 256 | 20 | 279 | 72 | 9 | 12.5000 | |
| mlin-fermikit | SNP | ti | HG002complexvar | hetalt | 96.0000 | 92.7536 | 99.4819 | 33.9041 | 192 | 15 | 192 | 1 | 1 | 100.0000 | |
| ndellapenna-hhga | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 92.8054 | 92.7536 | 92.8571 | 88.0342 | 64 | 5 | 65 | 5 | 5 | 100.0000 | |
| gduggal-snapfb | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 49.0421 | 92.7536 | 33.3333 | 92.3171 | 64 | 5 | 63 | 126 | 5 | 3.9683 | |
| ckim-dragen | INDEL | * | HG002complexvar | hetalt | 95.4523 | 92.7548 | 98.3114 | 67.8279 | 3431 | 268 | 3668 | 63 | 63 | 100.0000 | |
| ckim-isaac | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | het | 88.0210 | 92.7552 | 83.7467 | 49.6639 | 2535 | 198 | 2195 | 426 | 362 | 84.9765 | |
| ndellapenna-hhga | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 93.2288 | 92.7559 | 93.7066 | 80.9569 | 87607 | 6842 | 88251 | 5927 | 5106 | 86.1481 | |
| dgrover-gatk | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 95.1520 | 92.7565 | 97.6744 | 76.4794 | 461 | 36 | 462 | 11 | 11 | 100.0000 | |
| gduggal-bwaplat | INDEL | D1_5 | segdup | homalt | 96.2428 | 92.7577 | 100.0000 | 94.6099 | 333 | 26 | 333 | 0 | 0 | ||
| jlack-gatk | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | homalt | 77.9859 | 92.7577 | 67.2727 | 45.6641 | 333 | 26 | 333 | 162 | 160 | 98.7654 | |