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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
73351-73400 / 86044 show all | |||||||||||||||
| mlin-fermikit | INDEL | * | lowcmp_SimpleRepeat_triTR_11to50 | het | 94.9292 | 96.3368 | 93.5621 | 42.6632 | 3524 | 134 | 3517 | 242 | 235 | 97.1074 | |
| jlack-gatk | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 95.6728 | 91.8003 | 99.8864 | 30.0913 | 3493 | 312 | 3518 | 4 | 3 | 75.0000 | |
| bgallagher-sentieon | INDEL | D1_5 | map_siren | * | 99.2660 | 99.4899 | 99.0431 | 81.6382 | 3511 | 18 | 3519 | 34 | 6 | 17.6471 | |
| hfeng-pmm2 | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 93.2754 | 89.6920 | 97.1571 | 51.8026 | 3524 | 405 | 3520 | 103 | 96 | 93.2039 | |
| egarrison-hhga | INDEL | D6_15 | * | hetalt | 65.0139 | 48.4952 | 98.5994 | 42.7885 | 3964 | 4210 | 3520 | 50 | 43 | 86.0000 | |
| jlack-gatk | INDEL | * | map_l100_m1_e0 | * | 95.3278 | 97.9922 | 92.8044 | 87.6441 | 3514 | 72 | 3521 | 273 | 26 | 9.5238 | |
| astatham-gatk | INDEL | * | map_l100_m2_e0 | * | 96.5801 | 95.1530 | 98.0507 | 86.7138 | 3514 | 179 | 3521 | 70 | 18 | 25.7143 | |
| hfeng-pmm1 | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 93.4040 | 89.7684 | 97.3466 | 51.5533 | 3527 | 402 | 3522 | 96 | 90 | 93.7500 | |
| jmaeng-gatk | INDEL | * | map_l100_m1_e0 | * | 96.9028 | 98.0201 | 95.8107 | 88.4970 | 3515 | 71 | 3522 | 154 | 21 | 13.6364 | |
| hfeng-pmm1 | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.5198 | 99.6042 | 99.4355 | 71.4918 | 3523 | 14 | 3523 | 20 | 20 | 100.0000 | |
| hfeng-pmm3 | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.5480 | 99.6325 | 99.4637 | 71.3697 | 3524 | 13 | 3524 | 19 | 19 | 100.0000 | |
| jli-custom | INDEL | * | map_l100_m1_e0 | * | 98.4897 | 98.1595 | 98.8222 | 83.0077 | 3520 | 66 | 3524 | 42 | 15 | 35.7143 | |
| ltrigg-rtg1 | INDEL | * | map_l100_m2_e0 | * | 97.3361 | 95.4779 | 99.2680 | 80.2721 | 3526 | 167 | 3526 | 26 | 7 | 26.9231 | |
| jlack-gatk | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 98.9618 | 99.7173 | 98.2178 | 72.3769 | 3527 | 10 | 3527 | 64 | 63 | 98.4375 | |
| hfeng-pmm2 | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.5485 | 99.7455 | 99.3523 | 71.7771 | 3528 | 9 | 3528 | 23 | 22 | 95.6522 | |
| gduggal-snapfb | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 70.1273 | 67.6890 | 72.7479 | 71.4311 | 3465 | 1654 | 3529 | 1322 | 311 | 23.5250 | |
| asubramanian-gatk | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 92.1790 | 86.6893 | 98.4109 | 40.6421 | 3315 | 509 | 3530 | 57 | 49 | 85.9649 | |
| gduggal-bwaplat | INDEL | * | map_siren | het | 87.4010 | 78.3274 | 98.8522 | 90.8215 | 3531 | 977 | 3531 | 41 | 15 | 36.5854 | |
| jmaeng-gatk | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.4228 | 99.8304 | 99.0185 | 72.8574 | 3531 | 6 | 3531 | 35 | 34 | 97.1429 | |
| raldana-dualsentieon | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.3948 | 99.8304 | 98.9630 | 72.1359 | 3531 | 6 | 3531 | 37 | 37 | 100.0000 | |
| ckim-vqsr | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.5070 | 99.8586 | 99.1578 | 72.7530 | 3532 | 5 | 3532 | 30 | 30 | 100.0000 | |
| astatham-gatk | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.4789 | 99.8586 | 99.1021 | 72.7252 | 3532 | 5 | 3532 | 32 | 32 | 100.0000 | |
| hfeng-pmm3 | INDEL | * | map_l100_m1_e0 | * | 98.6300 | 98.2989 | 98.9633 | 82.3910 | 3525 | 61 | 3532 | 37 | 9 | 24.3243 | |
| ckim-dragen | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.2414 | 99.9435 | 98.5491 | 72.6182 | 3535 | 2 | 3532 | 52 | 52 | 100.0000 | |
| ckim-gatk | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.5071 | 99.8869 | 99.1302 | 72.7419 | 3533 | 4 | 3533 | 31 | 31 | 100.0000 | |
| dgrover-gatk | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.5071 | 99.8869 | 99.1302 | 72.8167 | 3533 | 4 | 3533 | 31 | 31 | 100.0000 | |
| bgallagher-sentieon | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.2834 | 99.8869 | 98.6872 | 72.6216 | 3533 | 4 | 3533 | 47 | 47 | 100.0000 | |
| asubramanian-gatk | SNP | tv | map_l125_m2_e1 | het | 50.1525 | 33.4976 | 99.7460 | 93.1412 | 3535 | 7018 | 3534 | 9 | 2 | 22.2222 | |
| jli-custom | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.5913 | 99.8586 | 99.3255 | 71.8824 | 3532 | 5 | 3534 | 24 | 24 | 100.0000 | |
| cchapple-custom | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 97.6012 | 95.7537 | 99.5214 | 52.8600 | 902 | 40 | 3535 | 17 | 15 | 88.2353 | |
| gduggal-snapplat | SNP | tv | map_l150_m2_e1 | homalt | 92.2034 | 85.5346 | 100.0000 | 76.0404 | 3536 | 598 | 3535 | 0 | 0 | ||
| mlin-fermikit | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 91.3183 | 97.0313 | 86.2405 | 69.6055 | 3530 | 108 | 3535 | 564 | 553 | 98.0496 | |
| dgrover-gatk | INDEL | * | map_l100_m1_e0 | * | 98.3431 | 98.3826 | 98.3037 | 85.8553 | 3528 | 58 | 3535 | 61 | 16 | 26.2295 | |
| egarrison-hhga | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 95.5535 | 97.1688 | 93.9910 | 58.3407 | 3535 | 103 | 3535 | 226 | 68 | 30.0885 | |
| mlin-fermikit | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 96.5901 | 96.7267 | 96.4539 | 49.3016 | 3546 | 120 | 3536 | 130 | 124 | 95.3846 | |
| ndellapenna-hhga | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 94.3311 | 97.1963 | 91.6300 | 59.5874 | 3536 | 102 | 3536 | 323 | 127 | 39.3189 | |
| ckim-gatk | INDEL | * | map_l100_m1_e0 | * | 97.0622 | 98.4384 | 95.7240 | 88.3725 | 3530 | 56 | 3537 | 158 | 20 | 12.6582 | |
| hfeng-pmm2 | INDEL | * | map_l100_m1_e0 | * | 98.3031 | 98.4384 | 98.1682 | 84.3925 | 3530 | 56 | 3537 | 66 | 13 | 19.6970 | |
| ndellapenna-hhga | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 98.1272 | 97.5987 | 98.6615 | 84.6994 | 3536 | 87 | 3538 | 48 | 30 | 62.5000 | |
| cchapple-custom | INDEL | * | map_l100_m1_e0 | * | 95.9601 | 96.4584 | 95.4668 | 83.7178 | 3459 | 127 | 3538 | 168 | 48 | 28.5714 | |
| cchapple-custom | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 96.8519 | 95.9843 | 97.7354 | 64.7626 | 3418 | 143 | 3539 | 82 | 70 | 85.3659 | |
| jli-custom | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 95.3300 | 94.5545 | 96.1183 | 76.3193 | 3820 | 220 | 3541 | 143 | 117 | 81.8182 | |
| ckim-isaac | SNP | ti | map_l150_m1_e0 | homalt | 65.1458 | 48.3281 | 99.9153 | 66.1412 | 3541 | 3786 | 3541 | 3 | 3 | 100.0000 | |
| jmaeng-gatk | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 96.0820 | 92.4836 | 99.9718 | 25.6399 | 3519 | 286 | 3543 | 1 | 1 | 100.0000 | |
| ndellapenna-hhga | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 93.7883 | 91.0957 | 96.6448 | 54.7687 | 3550 | 347 | 3543 | 123 | 90 | 73.1707 | |
| mlin-fermikit | SNP | tv | map_l125_m2_e1 | homalt | 64.9030 | 58.3635 | 73.0928 | 57.1933 | 3545 | 2529 | 3545 | 1305 | 1228 | 94.0996 | |
| eyeh-varpipe | SNP | tv | HG002complexvar | hetalt | 99.6700 | 99.6774 | 99.6626 | 29.8422 | 309 | 1 | 3545 | 12 | 11 | 91.6667 | |
| bgallagher-sentieon | INDEL | * | map_l100_m1_e0 | * | 98.3343 | 98.6615 | 98.0094 | 85.1549 | 3538 | 48 | 3545 | 72 | 17 | 23.6111 | |
| ckim-vqsr | SNP | tv | map_l100_m2_e0 | homalt | 55.5756 | 38.4849 | 99.9718 | 81.4225 | 3546 | 5668 | 3546 | 1 | 0 | 0.0000 | |
| egarrison-hhga | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 98.2951 | 97.8471 | 98.7472 | 84.7253 | 3545 | 78 | 3547 | 45 | 27 | 60.0000 | |