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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
11301-11350 / 86044 show all | |||||||||||||||
| gduggal-bwafb | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 90.9106 | 86.5682 | 95.7115 | 51.1635 | 5981 | 928 | 4419 | 198 | 174 | 87.8788 | |
| astatham-gatk | SNP | ti | map_l125_m0_e0 | homalt | 99.0916 | 98.3745 | 99.8192 | 66.7668 | 4418 | 73 | 4418 | 8 | 7 | 87.5000 | |
| ckim-vqsr | SNP | tv | map_l150_m1_e0 | het | 77.1500 | 63.6050 | 98.0249 | 91.7841 | 4418 | 2528 | 4417 | 89 | 0 | 0.0000 | |
| ckim-dragen | INDEL | * | map_siren | het | 97.4637 | 98.1145 | 96.8216 | 84.6377 | 4423 | 85 | 4417 | 145 | 14 | 9.6552 | |
| ndellapenna-hhga | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 84.4065 | 96.1747 | 75.2044 | 56.2444 | 3721 | 148 | 4416 | 1456 | 1419 | 97.4588 | |
| ghariani-varprowl | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 73.4052 | 61.1563 | 91.7896 | 37.5114 | 4432 | 2815 | 4416 | 395 | 339 | 85.8228 | |
| gduggal-snapvard | INDEL | * | map_l100_m1_e0 | * | 85.9341 | 89.2080 | 82.8920 | 85.9643 | 3199 | 387 | 4414 | 911 | 427 | 46.8716 | |
| jpowers-varprowl | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 73.4486 | 61.1425 | 91.9567 | 37.2269 | 4431 | 2816 | 4413 | 386 | 340 | 88.0829 | |
| rpoplin-dv42 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 95.7653 | 92.1626 | 99.6610 | 30.6426 | 4398 | 374 | 4410 | 15 | 15 | 100.0000 | |
| gduggal-bwavard | INDEL | * | map_siren | het | 90.9729 | 98.0035 | 84.8835 | 87.6032 | 4418 | 90 | 4408 | 785 | 417 | 53.1210 | |
| gduggal-bwaplat | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 76.5373 | 63.7864 | 95.6597 | 61.8480 | 4407 | 2502 | 4408 | 200 | 55 | 27.5000 | |
| gduggal-bwavard | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 85.1692 | 86.5403 | 83.8409 | 73.2417 | 4430 | 689 | 4405 | 849 | 604 | 71.1425 | |
| gduggal-snapplat | INDEL | D1_5 | * | hetalt | 56.5026 | 42.2548 | 85.2469 | 84.6995 | 4329 | 5916 | 4403 | 762 | 572 | 75.0656 | |
| mlin-fermikit | SNP | tv | map_l125_m1_e0 | het | 60.2787 | 43.5216 | 98.0187 | 62.6103 | 4407 | 5719 | 4403 | 89 | 1 | 1.1236 | |
| jmaeng-gatk | SNP | ti | map_l150_m2_e0 | homalt | 73.2296 | 57.7731 | 99.9773 | 80.4374 | 4400 | 3216 | 4400 | 1 | 1 | 100.0000 | |
| ndellapenna-hhga | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 96.6789 | 94.2328 | 99.2552 | 26.5783 | 4379 | 268 | 4398 | 33 | 30 | 90.9091 | |
| hfeng-pmm2 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 96.6759 | 93.5657 | 100.0000 | 27.8543 | 4348 | 299 | 4398 | 0 | 0 | ||
| anovak-vg | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 51.1017 | 43.2290 | 62.4805 | 48.0708 | 1063 | 1396 | 4398 | 2641 | 1993 | 75.4638 | |
| mlin-fermikit | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 81.7362 | 74.1234 | 91.0918 | 40.7803 | 4397 | 1535 | 4397 | 430 | 427 | 99.3023 | |
| gduggal-bwavard | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 69.3783 | 53.2297 | 99.5922 | 52.1673 | 4450 | 3910 | 4396 | 18 | 16 | 88.8889 | |
| gduggal-bwavard | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 69.3783 | 53.2297 | 99.5922 | 52.1673 | 4450 | 3910 | 4396 | 18 | 16 | 88.8889 | |
| ckim-isaac | SNP | * | lowcmp_SimpleRepeat_triTR_11to50 | het | 97.1923 | 94.8440 | 99.6599 | 28.7215 | 4378 | 238 | 4395 | 15 | 0 | 0.0000 | |
| gduggal-bwaplat | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 86.3639 | 77.4336 | 97.6228 | 60.1470 | 4399 | 1282 | 4394 | 107 | 91 | 85.0467 | |
| eyeh-varpipe | SNP | tv | lowcmp_SimpleRepeat_quadTR_11to50 | het | 95.1371 | 99.6801 | 90.9901 | 43.0795 | 4674 | 15 | 4393 | 435 | 14 | 3.2184 | |
| jlack-gatk | SNP | ti | map_l125_m0_e0 | homalt | 98.7968 | 97.8179 | 99.7955 | 67.3853 | 4393 | 98 | 4393 | 9 | 7 | 77.7778 | |
| gduggal-snapplat | SNP | * | map_l250_m2_e0 | het | 87.7154 | 84.4628 | 91.2284 | 94.8727 | 4387 | 807 | 4389 | 422 | 202 | 47.8673 | |
| eyeh-varpipe | SNP | * | lowcmp_SimpleRepeat_triTR_11to50 | het | 98.5435 | 99.8700 | 97.2518 | 40.3648 | 4610 | 6 | 4388 | 124 | 9 | 7.2581 | |
| cchapple-custom | SNP | ti | map_l250_m1_e0 | * | 96.3982 | 95.8943 | 96.9074 | 89.5799 | 4391 | 188 | 4387 | 140 | 38 | 27.1429 | |
| jpowers-varprowl | SNP | ti | map_l125_m0_e0 | homalt | 98.7168 | 97.6397 | 99.8179 | 72.4456 | 4385 | 106 | 4385 | 8 | 6 | 75.0000 | |
| ltrigg-rtg1 | SNP | ti | map_l250_m1_e0 | * | 97.6589 | 95.6541 | 99.7497 | 82.8747 | 4380 | 199 | 4383 | 11 | 6 | 54.5455 | |
| gduggal-snapplat | INDEL | D1_5 | HG002compoundhet | hetalt | 57.5062 | 42.2964 | 89.7972 | 79.0515 | 4321 | 5895 | 4383 | 498 | 424 | 85.1406 | |
| ghariani-varprowl | SNP | ti | map_l125_m0_e0 | homalt | 98.6718 | 97.5952 | 99.7724 | 69.9542 | 4383 | 108 | 4383 | 10 | 6 | 60.0000 | |
| ckim-gatk | SNP | ti | map_l150_m2_e0 | homalt | 73.0167 | 57.5236 | 99.9316 | 81.2297 | 4381 | 3235 | 4381 | 3 | 2 | 66.6667 | |
| qzeng-custom | SNP | tv | map_l125_m2_e0 | homalt | 84.1423 | 73.1594 | 99.0054 | 69.1320 | 4402 | 1615 | 4380 | 44 | 44 | 100.0000 | |
| eyeh-varpipe | SNP | ti | map_l125_m0_e0 | homalt | 99.8314 | 99.7996 | 99.8632 | 71.9880 | 4482 | 9 | 4379 | 6 | 3 | 50.0000 | |
| ndellapenna-hhga | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 74.0374 | 59.1106 | 99.0498 | 29.9414 | 4785 | 3310 | 4378 | 42 | 35 | 83.3333 | |
| gduggal-snapplat | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 88.2507 | 80.5274 | 97.6127 | 83.3538 | 4367 | 1056 | 4375 | 107 | 45 | 42.0561 | |
| gduggal-snapplat | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 88.2507 | 80.5274 | 97.6127 | 83.3538 | 4367 | 1056 | 4375 | 107 | 45 | 42.0561 | |
| bgallagher-sentieon | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 96.3667 | 93.0278 | 99.9543 | 26.6834 | 4323 | 324 | 4375 | 2 | 2 | 100.0000 | |
| ckim-gatk | SNP | * | map_l250_m2_e0 | * | 70.6281 | 55.4724 | 97.1784 | 96.2246 | 4374 | 3511 | 4374 | 127 | 10 | 7.8740 | |
| hfeng-pmm1 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 96.3880 | 93.0278 | 100.0000 | 27.8191 | 4323 | 324 | 4372 | 0 | 0 | ||
| egarrison-hhga | SNP | tv | func_cds | * | 99.9543 | 100.0000 | 99.9086 | 28.4546 | 4371 | 0 | 4371 | 4 | 0 | 0.0000 | |
| bgallagher-sentieon | SNP | tv | func_cds | * | 99.8287 | 100.0000 | 99.6579 | 29.0453 | 4371 | 0 | 4370 | 15 | 0 | 0.0000 | |
| eyeh-varpipe | SNP | ti | lowcmp_SimpleRepeat_diTR_11to50 | * | 95.6571 | 97.7672 | 93.6362 | 64.2950 | 4729 | 108 | 4370 | 297 | 64 | 21.5488 | |
| eyeh-varpipe | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 47.7195 | 36.5649 | 68.6675 | 29.6562 | 1090 | 1891 | 4370 | 1994 | 1989 | 99.7492 | |
| ndellapenna-hhga | SNP | tv | func_cds | * | 99.9314 | 99.9771 | 99.8857 | 28.0901 | 4370 | 1 | 4370 | 5 | 0 | 0.0000 | |
| hfeng-pmm2 | SNP | tv | func_cds | * | 99.9200 | 100.0000 | 99.8401 | 29.0024 | 4371 | 0 | 4370 | 7 | 0 | 0.0000 | |
| ckim-dragen | SNP | tv | func_cds | * | 99.3521 | 99.9771 | 98.7347 | 37.1039 | 4370 | 1 | 4370 | 56 | 0 | 0.0000 | |
| jli-custom | SNP | tv | func_cds | * | 99.8629 | 99.9771 | 99.7489 | 28.1332 | 4370 | 1 | 4370 | 11 | 0 | 0.0000 | |
| gduggal-bwafb | SNP | tv | func_cds | * | 99.4763 | 99.9542 | 99.0029 | 37.0021 | 4369 | 2 | 4369 | 44 | 0 | 0.0000 | |