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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
67801-67850 / 86044 show all | |||||||||||||||
| qzeng-custom | INDEL | * | map_l125_m2_e0 | het | 82.3208 | 74.2631 | 92.3398 | 93.0978 | 1033 | 358 | 1326 | 110 | 36 | 32.7273 | |
| ckim-dragen | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 99.9248 | 99.8496 | 100.0000 | 41.9185 | 1328 | 2 | 1326 | 0 | 0 | ||
| ckim-dragen | SNP | ti | map_l250_m0_e0 | * | 96.5066 | 96.7883 | 96.2264 | 93.0796 | 1326 | 44 | 1326 | 52 | 4 | 7.6923 | |
| ckim-gatk | INDEL | I1_5 | map_l100_m1_e0 | * | 97.9664 | 98.7304 | 97.2141 | 87.0980 | 1322 | 17 | 1326 | 38 | 5 | 13.1579 | |
| ckim-gatk | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 99.4749 | 99.2515 | 99.6992 | 51.2106 | 1326 | 10 | 1326 | 4 | 0 | 0.0000 | |
| bgallagher-sentieon | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 99.5122 | 99.2515 | 99.7743 | 48.6278 | 1326 | 10 | 1326 | 3 | 0 | 0.0000 | |
| astatham-gatk | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_11to50 | het | 99.2975 | 98.9729 | 99.6243 | 77.9307 | 1349 | 14 | 1326 | 5 | 3 | 60.0000 | |
| ghariani-varprowl | SNP | ti | map_l250_m0_e0 | * | 94.5118 | 96.7883 | 92.3398 | 94.5924 | 1326 | 44 | 1326 | 110 | 17 | 15.4545 | |
| ghariani-varprowl | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 95.7049 | 99.1018 | 92.5331 | 67.6378 | 1324 | 12 | 1326 | 107 | 8 | 7.4766 | |
| hfeng-pmm3 | INDEL | I1_5 | map_l100_m1_e0 | * | 98.9903 | 98.7304 | 99.2515 | 81.3277 | 1322 | 17 | 1326 | 10 | 3 | 30.0000 | |
| egarrison-hhga | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | homalt | 98.5141 | 98.0044 | 99.0291 | 71.8816 | 1326 | 27 | 1326 | 13 | 8 | 61.5385 | |
| ckim-vqsr | INDEL | I1_5 | map_l100_m2_e0 | * | 97.7479 | 96.7105 | 98.8077 | 88.3990 | 1323 | 45 | 1326 | 16 | 4 | 25.0000 | |
| egarrison-hhga | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 99.1405 | 99.2515 | 99.0299 | 57.3248 | 1326 | 10 | 1327 | 13 | 3 | 23.0769 | |
| dgrover-gatk | INDEL | I1_5 | map_l100_m1_e0 | * | 98.9542 | 98.8051 | 99.1038 | 84.0367 | 1323 | 16 | 1327 | 12 | 4 | 33.3333 | |
| dgrover-gatk | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 99.5499 | 99.3263 | 99.7744 | 49.3526 | 1327 | 9 | 1327 | 3 | 0 | 0.0000 | |
| jli-custom | INDEL | I1_5 | map_l100_m1_e0 | * | 99.2513 | 98.9544 | 99.5499 | 81.4397 | 1325 | 14 | 1327 | 6 | 3 | 50.0000 | |
| hfeng-pmm2 | INDEL | I1_5 | map_l100_m1_e0 | * | 98.8805 | 98.8051 | 98.9560 | 83.1786 | 1323 | 16 | 1327 | 14 | 4 | 28.5714 | |
| dgrover-gatk | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_11to50 | het | 99.3716 | 99.1196 | 99.6249 | 78.0612 | 1351 | 12 | 1328 | 5 | 3 | 60.0000 | |
| ckim-gatk | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_11to50 | het | 99.4085 | 99.1930 | 99.6249 | 78.2367 | 1352 | 11 | 1328 | 5 | 3 | 60.0000 | |
| gduggal-snapfb | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 59.4713 | 60.2535 | 58.7091 | 58.8203 | 1331 | 878 | 1328 | 934 | 788 | 84.3683 | |
| gduggal-snapfb | INDEL | * | map_l125_m2_e1 | het | 93.4708 | 92.8977 | 94.0510 | 85.3951 | 1308 | 100 | 1328 | 84 | 14 | 16.6667 | |
| gduggal-bwafb | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 97.0762 | 99.4760 | 94.7894 | 67.5394 | 1329 | 7 | 1328 | 73 | 4 | 5.4795 | |
| rpoplin-dv42 | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 91.6966 | 94.8227 | 88.7701 | 73.3903 | 1337 | 73 | 1328 | 168 | 145 | 86.3095 | |
| rpoplin-dv42 | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 99.9248 | 99.8496 | 100.0000 | 40.4484 | 1328 | 2 | 1328 | 0 | 0 | ||
| rpoplin-dv42 | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_11to50 | het | 97.4301 | 97.2854 | 97.5753 | 76.8498 | 1326 | 37 | 1328 | 33 | 32 | 96.9697 | |
| bgallagher-sentieon | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_11to50 | het | 99.3716 | 99.1196 | 99.6249 | 77.6829 | 1351 | 12 | 1328 | 5 | 3 | 60.0000 | |
| bgallagher-sentieon | INDEL | I1_5 | map_l100_m1_e0 | * | 98.9183 | 98.8798 | 98.9568 | 83.1237 | 1324 | 15 | 1328 | 14 | 4 | 28.5714 | |
| gduggal-snapplat | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 57.4030 | 44.5498 | 80.6804 | 63.6484 | 1410 | 1755 | 1328 | 318 | 230 | 72.3270 | |
| ghariani-varprowl | INDEL | * | map_l150_m2_e0 | * | 91.0274 | 94.3892 | 87.8968 | 95.3487 | 1329 | 79 | 1329 | 183 | 52 | 28.4153 | |
| gduggal-bwavard | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | homalt | 99.0508 | 98.2646 | 99.8497 | 54.9729 | 1359 | 24 | 1329 | 2 | 0 | 0.0000 | |
| mlin-fermikit | INDEL | D1_5 | map_l100_m2_e1 | * | 77.5709 | 68.5921 | 89.2545 | 77.9440 | 1330 | 609 | 1329 | 160 | 138 | 86.2500 | |
| asubramanian-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 99.9248 | 99.8496 | 100.0000 | 41.6849 | 1328 | 2 | 1329 | 0 | 0 | ||
| astatham-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 100.0000 | 100.0000 | 100.0000 | 41.6667 | 1330 | 0 | 1330 | 0 | 0 | ||
| bgallagher-sentieon | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 100.0000 | 100.0000 | 100.0000 | 41.8452 | 1330 | 0 | 1330 | 0 | 0 | ||
| gduggal-bwavard | INDEL | I1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 94.6355 | 97.3799 | 92.0415 | 69.2422 | 1338 | 36 | 1330 | 115 | 100 | 86.9565 | |
| gduggal-bwafb | SNP | ti | map_l250_m0_e0 | * | 97.5073 | 97.0803 | 97.9381 | 93.5330 | 1330 | 40 | 1330 | 28 | 9 | 32.1429 | |
| ckim-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 100.0000 | 100.0000 | 100.0000 | 41.6411 | 1330 | 0 | 1330 | 0 | 0 | ||
| cchapple-custom | INDEL | I16_PLUS | HG002complexvar | * | 97.1576 | 96.1803 | 98.1550 | 66.7729 | 1259 | 50 | 1330 | 25 | 18 | 72.0000 | |
| hfeng-pmm2 | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 100.0000 | 100.0000 | 100.0000 | 38.6814 | 1330 | 0 | 1330 | 0 | 0 | ||
| hfeng-pmm1 | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 100.0000 | 100.0000 | 100.0000 | 38.3689 | 1330 | 0 | 1330 | 0 | 0 | ||
| jlack-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 100.0000 | 100.0000 | 100.0000 | 41.0461 | 1330 | 0 | 1330 | 0 | 0 | ||
| hfeng-pmm3 | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 100.0000 | 100.0000 | 100.0000 | 38.4829 | 1330 | 0 | 1330 | 0 | 0 | ||
| ckim-vqsr | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 100.0000 | 100.0000 | 100.0000 | 41.6411 | 1330 | 0 | 1330 | 0 | 0 | ||
| dgrover-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 100.0000 | 100.0000 | 100.0000 | 41.8452 | 1330 | 0 | 1330 | 0 | 0 | ||
| egarrison-hhga | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 98.3381 | 97.7256 | 98.9583 | 75.2486 | 1332 | 31 | 1330 | 14 | 5 | 35.7143 | |
| mlin-fermikit | INDEL | I1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 98.2337 | 97.2344 | 99.2537 | 66.3739 | 1336 | 38 | 1330 | 10 | 9 | 90.0000 | |
| qzeng-custom | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | het | 90.2766 | 96.5517 | 84.7674 | 66.2145 | 588 | 21 | 1330 | 239 | 80 | 33.4728 | |
| jli-custom | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 100.0000 | 100.0000 | 100.0000 | 40.8100 | 1330 | 0 | 1330 | 0 | 0 | ||
| jli-custom | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_11to50 | het | 98.9286 | 99.0462 | 98.8113 | 76.1938 | 1350 | 13 | 1330 | 16 | 10 | 62.5000 | |
| jmaeng-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 100.0000 | 100.0000 | 100.0000 | 41.6155 | 1330 | 0 | 1330 | 0 | 0 | ||