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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
20651-20700 / 86044 show all | |||||||||||||||
| jpowers-varprowl | SNP | ti | map_l150_m2_e0 | * | 97.3631 | 96.6654 | 98.0710 | 80.0739 | 19828 | 684 | 19828 | 390 | 140 | 35.8974 | |
| ltrigg-rtg2 | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 97.3628 | 96.0366 | 98.7261 | 44.4248 | 315 | 13 | 310 | 4 | 4 | 100.0000 | |
| cchapple-custom | INDEL | I1_5 | map_l100_m2_e1 | * | 97.3625 | 97.0609 | 97.6659 | 83.8268 | 1354 | 41 | 1339 | 32 | 10 | 31.2500 | |
| ltrigg-rtg2 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 97.3624 | 95.4205 | 99.3850 | 51.9079 | 15940 | 765 | 16321 | 101 | 99 | 98.0198 | |
| ltrigg-rtg2 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 97.3624 | 95.4205 | 99.3850 | 51.9079 | 15940 | 765 | 16321 | 101 | 99 | 98.0198 | |
| hfeng-pmm1 | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 97.3621 | 99.0244 | 95.7547 | 90.6402 | 203 | 2 | 203 | 9 | 7 | 77.7778 | |
| hfeng-pmm1 | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 97.3621 | 99.0244 | 95.7547 | 90.6402 | 203 | 2 | 203 | 9 | 7 | 77.7778 | |
| ltrigg-rtg1 | INDEL | D1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | hetalt | 97.3617 | 96.3504 | 98.3945 | 78.0353 | 396 | 15 | 429 | 7 | 7 | 100.0000 | |
| jli-custom | SNP | tv | map_l250_m1_e0 | het | 97.3617 | 96.0269 | 98.7342 | 85.3704 | 1716 | 71 | 1716 | 22 | 7 | 31.8182 | |
| astatham-gatk | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_11to50 | * | 97.3614 | 95.6053 | 99.1831 | 62.6285 | 2306 | 106 | 2307 | 19 | 14 | 73.6842 | |
| hfeng-pmm2 | INDEL | D1_5 | map_l150_m1_e0 | het | 97.3614 | 99.1701 | 95.6175 | 89.2020 | 478 | 4 | 480 | 22 | 2 | 9.0909 | |
| ckim-gatk | INDEL | I16_PLUS | * | * | 97.3609 | 96.6128 | 98.1207 | 70.7109 | 6161 | 216 | 6161 | 118 | 83 | 70.3390 | |
| ckim-dragen | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 97.3608 | 96.0725 | 98.6842 | 78.4703 | 636 | 26 | 600 | 8 | 7 | 87.5000 | |
| jli-custom | INDEL | I16_PLUS | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 97.3607 | 94.8571 | 100.0000 | 64.1026 | 166 | 9 | 168 | 0 | 0 | ||
| ckim-vqsr | INDEL | I16_PLUS | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 97.3607 | 94.8571 | 100.0000 | 65.1452 | 166 | 9 | 168 | 0 | 0 | ||
| gduggal-snapvard | SNP | ti | map_l100_m0_e0 | homalt | 97.3605 | 95.2148 | 99.6052 | 63.3538 | 7402 | 372 | 7316 | 29 | 23 | 79.3103 | |
| asubramanian-gatk | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 97.3602 | 96.1713 | 98.5789 | 73.8003 | 1482 | 59 | 1873 | 27 | 17 | 62.9630 | |
| ltrigg-rtg1 | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 97.3600 | 95.2580 | 99.5569 | 48.5171 | 683 | 34 | 674 | 3 | 3 | 100.0000 | |
| ckim-dragen | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 97.3592 | 95.2372 | 99.5780 | 26.4946 | 5179 | 259 | 5191 | 22 | 22 | 100.0000 | |
| anovak-vg | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 97.3590 | 97.3698 | 97.3483 | 58.9147 | 3776 | 102 | 3818 | 104 | 49 | 47.1154 | |
| ckim-dragen | INDEL | * | map_l125_m0_e0 | homalt | 97.3588 | 97.5352 | 97.1831 | 87.5874 | 277 | 7 | 276 | 8 | 5 | 62.5000 | |
| ltrigg-rtg1 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 97.3588 | 95.3386 | 99.4664 | 56.7621 | 41315 | 2020 | 41569 | 223 | 143 | 64.1256 | |
| jli-custom | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 97.3586 | 95.0374 | 99.7961 | 32.0399 | 2413 | 126 | 2447 | 5 | 5 | 100.0000 | |
| dgrover-gatk | INDEL | D1_5 | HG002compoundhet | hetalt | 97.3579 | 95.2232 | 99.5905 | 58.8743 | 9728 | 488 | 9729 | 40 | 39 | 97.5000 | |
| jmaeng-gatk | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 97.3579 | 94.8518 | 100.0000 | 40.3320 | 608 | 33 | 611 | 0 | 0 | ||
| ckim-vqsr | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | het | 97.3574 | 99.5074 | 95.2984 | 84.1819 | 606 | 3 | 527 | 26 | 22 | 84.6154 | |
| anovak-vg | SNP | * | HG002complexvar | het | 97.3572 | 96.6062 | 98.1199 | 19.3647 | 449702 | 15798 | 439022 | 8412 | 6308 | 74.9881 | |
| ckim-dragen | SNP | * | map_l125_m0_e0 | het | 97.3570 | 98.4523 | 96.2857 | 80.0772 | 12468 | 196 | 12469 | 481 | 37 | 7.6923 | |
| ltrigg-rtg1 | INDEL | * | map_l100_m1_e0 | * | 97.3566 | 95.5103 | 99.2756 | 78.9689 | 3425 | 161 | 3426 | 25 | 7 | 28.0000 | |
| dgrover-gatk | INDEL | I6_15 | HG002complexvar | hetalt | 97.3563 | 94.8487 | 100.0000 | 56.1679 | 1160 | 63 | 1201 | 0 | 0 | ||
| gduggal-bwafb | SNP | tv | map_l150_m0_e0 | het | 97.3551 | 97.7489 | 96.9644 | 82.8486 | 2779 | 64 | 2779 | 87 | 20 | 22.9885 | |
| ckim-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 97.3551 | 95.7767 | 98.9864 | 63.1106 | 6055 | 267 | 6055 | 62 | 49 | 79.0323 | |
| ckim-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 97.3551 | 95.7767 | 98.9864 | 63.1106 | 6055 | 267 | 6055 | 62 | 49 | 79.0323 | |
| hfeng-pmm1 | INDEL | D1_5 | map_l125_m0_e0 | het | 97.3547 | 95.9420 | 98.8095 | 83.7916 | 331 | 14 | 332 | 4 | 0 | 0.0000 | |
| hfeng-pmm2 | INDEL | D6_15 | lowcmp_SimpleRepeat_triTR_51to200 | hetalt | 97.3545 | 94.8454 | 100.0000 | 23.3333 | 92 | 5 | 92 | 0 | 0 | ||
| hfeng-pmm3 | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 97.3545 | 94.8591 | 99.9847 | 25.8525 | 6532 | 354 | 6544 | 1 | 0 | 0.0000 | |
| asubramanian-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_triTR_51to200 | hetalt | 97.3545 | 94.8454 | 100.0000 | 23.3333 | 92 | 5 | 92 | 0 | 0 | ||
| jli-custom | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | het | 97.3541 | 96.3636 | 98.3651 | 75.9186 | 371 | 14 | 361 | 6 | 5 | 83.3333 | |
| jmaeng-gatk | INDEL | * | map_siren | het | 97.3536 | 98.6247 | 96.1148 | 86.8437 | 4446 | 62 | 4453 | 180 | 15 | 8.3333 | |
| ghariani-varprowl | SNP | * | map_l125_m2_e1 | het | 97.3535 | 98.9777 | 95.7818 | 79.7151 | 29337 | 303 | 29337 | 1292 | 237 | 18.3437 | |
| ndellapenna-hhga | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 97.3535 | 95.3835 | 99.4066 | 24.9710 | 3843 | 186 | 3853 | 23 | 21 | 91.3043 | |
| eyeh-varpipe | INDEL | I1_5 | map_l100_m1_e0 | homalt | 97.3535 | 98.2625 | 96.4612 | 82.0271 | 509 | 9 | 845 | 31 | 28 | 90.3226 | |
| egarrison-hhga | INDEL | I1_5 | HG002compoundhet | hetalt | 97.3530 | 95.2492 | 99.5519 | 56.2316 | 10646 | 531 | 10663 | 48 | 44 | 91.6667 | |
| asubramanian-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 97.3524 | 99.2470 | 95.5288 | 54.1878 | 8303 | 63 | 8888 | 416 | 317 | 76.2019 | |
| gduggal-snapfb | SNP | ti | map_l100_m1_e0 | het | 97.3515 | 98.0162 | 96.6958 | 65.8783 | 29348 | 594 | 29352 | 1003 | 436 | 43.4696 | |
| qzeng-custom | SNP | tv | HG002complexvar | hetalt | 97.3511 | 95.1613 | 99.6441 | 38.9130 | 295 | 15 | 280 | 1 | 1 | 100.0000 | |
| qzeng-custom | SNP | * | HG002complexvar | hetalt | 97.3511 | 95.1613 | 99.6441 | 38.9130 | 295 | 15 | 280 | 1 | 1 | 100.0000 | |
| raldana-dualsentieon | INDEL | * | map_l100_m0_e0 | het | 97.3501 | 97.0617 | 97.6401 | 84.2716 | 991 | 30 | 993 | 24 | 1 | 4.1667 | |
| hfeng-pmm1 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 97.3498 | 96.6561 | 98.0535 | 76.7797 | 1214 | 42 | 1209 | 24 | 3 | 12.5000 | |
| astatham-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 97.3494 | 96.6507 | 98.0583 | 76.5909 | 202 | 7 | 202 | 4 | 3 | 75.0000 | |