PrecisionFDA
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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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
74901-74950 / 86044 show all | |||||||||||||||
| ckim-isaac | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 93.8528 | 88.9193 | 99.3658 | 31.1088 | 4550 | 567 | 4544 | 29 | 25 | 86.2069 | |
| eyeh-varpipe | SNP | ti | map_l250_m1_e0 | * | 98.9581 | 99.3885 | 98.5313 | 90.1600 | 4551 | 28 | 4495 | 67 | 6 | 8.9552 | |
| mlin-fermikit | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 79.6367 | 72.0025 | 89.0817 | 63.6267 | 4552 | 1770 | 4569 | 560 | 555 | 99.1071 | |
| mlin-fermikit | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 79.6367 | 72.0025 | 89.0817 | 63.6267 | 4552 | 1770 | 4569 | 560 | 555 | 99.1071 | |
| qzeng-custom | SNP | tv | HG002compoundhet | het | 97.5388 | 97.4321 | 97.6458 | 58.3399 | 4553 | 120 | 5641 | 136 | 28 | 20.5882 | |
| ndellapenna-hhga | INDEL | I6_15 | HG002complexvar | * | 96.1681 | 95.0125 | 97.3521 | 56.1640 | 4553 | 239 | 4559 | 124 | 74 | 59.6774 | |
| astatham-gatk | SNP | tv | HG002compoundhet | het | 98.5818 | 97.4321 | 99.7590 | 55.5988 | 4553 | 120 | 4553 | 11 | 11 | 100.0000 | |
| anovak-vg | SNP | * | map_l250_m2_e1 | het | 71.9604 | 86.4932 | 61.6087 | 92.1600 | 4553 | 711 | 4519 | 2816 | 645 | 22.9048 | |
| qzeng-custom | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 87.0799 | 77.3066 | 99.6819 | 40.4484 | 4558 | 1338 | 1880 | 6 | 5 | 83.3333 | |
| qzeng-custom | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 87.0799 | 77.3066 | 99.6819 | 40.4484 | 4558 | 1338 | 1880 | 6 | 5 | 83.3333 | |
| ndellapenna-hhga | INDEL | D6_15 | HG002complexvar | * | 88.9462 | 85.9864 | 92.1169 | 57.7872 | 4559 | 743 | 4569 | 391 | 292 | 74.6803 | |
| rpoplin-dv42 | INDEL | I6_15 | HG002complexvar | * | 96.7965 | 95.1586 | 98.4917 | 56.6586 | 4560 | 232 | 4571 | 70 | 64 | 91.4286 | |
| ciseli-custom | SNP | ti | lowcmp_SimpleRepeat_diTR_11to50 | * | 76.6099 | 94.2733 | 64.5210 | 69.8327 | 4560 | 277 | 4701 | 2585 | 206 | 7.9691 | |
| ckim-vqsr | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 97.4580 | 95.5784 | 99.4130 | 24.4663 | 4561 | 211 | 4573 | 27 | 27 | 100.0000 | |
| ckim-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 97.4690 | 95.5993 | 99.4132 | 24.4623 | 4562 | 210 | 4574 | 27 | 27 | 100.0000 | |
| mlin-fermikit | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 77.6790 | 63.6186 | 99.7178 | 29.4964 | 4564 | 2610 | 4593 | 13 | 13 | 100.0000 | |
| asubramanian-gatk | SNP | * | lowcmp_SimpleRepeat_triTR_11to50 | het | 99.0021 | 98.8951 | 99.1093 | 37.8896 | 4565 | 51 | 4562 | 41 | 2 | 4.8781 | |
| hfeng-pmm3 | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 97.7726 | 95.6622 | 99.9782 | 25.5368 | 4565 | 207 | 4577 | 1 | 0 | 0.0000 | |
| jmaeng-gatk | SNP | ti | map_l150_m0_e0 | * | 72.7820 | 58.0842 | 97.4381 | 92.2027 | 4566 | 3295 | 4564 | 120 | 17 | 14.1667 | |
| cchapple-custom | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 0.0000 | 95.7041 | 0.0000 | 0.0000 | 4567 | 205 | 0 | 0 | 0 | ||
| gduggal-bwavard | SNP | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 93.9826 | 95.8648 | 92.1728 | 78.1956 | 4567 | 197 | 4522 | 384 | 48 | 12.5000 | |
| anovak-vg | SNP | ti | lowcmp_SimpleRepeat_diTR_11to50 | * | 90.7748 | 94.4594 | 87.3670 | 66.7807 | 4569 | 268 | 5007 | 724 | 345 | 47.6519 | |
| ltrigg-rtg1 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 97.7454 | 95.7670 | 99.8073 | 46.5308 | 4570 | 202 | 4661 | 9 | 9 | 100.0000 | |
| ghariani-varprowl | SNP | * | lowcmp_SimpleRepeat_triTR_11to50 | het | 97.4281 | 99.0035 | 95.9022 | 49.9948 | 4570 | 46 | 4587 | 196 | 1 | 0.5102 | |
| raldana-dualsentieon | SNP | * | lowcmp_SimpleRepeat_triTR_11to50 | het | 99.3909 | 99.0035 | 99.7815 | 31.9351 | 4570 | 46 | 4566 | 10 | 2 | 20.0000 | |
| hfeng-pmm2 | SNP | * | lowcmp_SimpleRepeat_triTR_11to50 | het | 99.4561 | 99.0468 | 99.8688 | 31.9345 | 4572 | 44 | 4568 | 6 | 0 | 0.0000 | |
| ckim-gatk | SNP | ti | map_l150_m0_e0 | * | 72.8820 | 58.1733 | 97.5459 | 92.0553 | 4573 | 3288 | 4571 | 115 | 19 | 16.5217 | |
| qzeng-custom | SNP | * | lowcmp_SimpleRepeat_triTR_11to50 | het | 99.2828 | 99.0685 | 99.4980 | 45.3418 | 4573 | 43 | 4559 | 23 | 2 | 8.6957 | |
| gduggal-snapvard | SNP | tv | lowcmp_SimpleRepeat_quadTR_11to50 | het | 91.5334 | 97.5261 | 86.2345 | 56.9835 | 4573 | 116 | 4523 | 722 | 38 | 5.2632 | |
| hfeng-pmm1 | SNP | * | lowcmp_SimpleRepeat_triTR_11to50 | het | 99.4888 | 99.0901 | 99.8907 | 31.1720 | 4574 | 42 | 4570 | 5 | 0 | 0.0000 | |
| rpoplin-dv42 | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 92.5656 | 91.5183 | 93.6371 | 69.0667 | 4575 | 424 | 4562 | 310 | 290 | 93.5484 | |
| rpoplin-dv42 | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 92.5656 | 91.5183 | 93.6371 | 69.0667 | 4575 | 424 | 4562 | 310 | 290 | 93.5484 | |
| hfeng-pmm3 | SNP | * | lowcmp_SimpleRepeat_triTR_11to50 | het | 99.5648 | 99.1334 | 100.0000 | 32.4169 | 4576 | 40 | 4572 | 0 | 0 | ||
| mlin-fermikit | SNP | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 95.9832 | 96.0537 | 95.9128 | 70.7498 | 4576 | 188 | 4576 | 195 | 106 | 54.3590 | |
| gduggal-snapvard | SNP | * | map_l250_m1_e0 | het | 81.0291 | 96.2566 | 69.9614 | 91.9347 | 4577 | 178 | 4530 | 1945 | 87 | 4.4730 | |
| jli-custom | SNP | * | map_l250_m1_e0 | het | 97.5495 | 96.2776 | 98.8555 | 86.3033 | 4578 | 177 | 4578 | 53 | 23 | 43.3962 | |
| ndellapenna-hhga | SNP | * | lowcmp_SimpleRepeat_triTR_11to50 | het | 99.5327 | 99.1984 | 99.8692 | 31.8675 | 4579 | 37 | 4580 | 6 | 1 | 16.6667 | |
| gduggal-snapplat | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 56.3704 | 41.2427 | 89.0242 | 57.5472 | 4580 | 6525 | 4607 | 568 | 500 | 88.0282 | |
| hfeng-pmm2 | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 97.9370 | 95.9975 | 99.9565 | 25.8751 | 4581 | 191 | 4593 | 2 | 1 | 50.0000 | |
| ltrigg-rtg1 | SNP | tv | HG002compoundhet | het | 98.8241 | 98.0526 | 99.6078 | 50.3515 | 4582 | 91 | 4572 | 18 | 4 | 22.2222 | |
| astatham-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 97.6772 | 96.0184 | 99.3942 | 25.6555 | 4582 | 190 | 4594 | 28 | 27 | 96.4286 | |
| ciseli-custom | SNP | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 76.2286 | 96.1797 | 63.1327 | 74.0117 | 4582 | 182 | 4615 | 2695 | 108 | 4.0074 | |
| qzeng-custom | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 87.8199 | 86.2627 | 89.4344 | 51.7765 | 4584 | 730 | 11495 | 1358 | 772 | 56.8483 | |
| egarrison-hhga | INDEL | D6_15 | HG002complexvar | * | 89.5440 | 86.4579 | 92.8586 | 57.3769 | 4584 | 718 | 4590 | 353 | 276 | 78.1870 | |
| gduggal-bwafb | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 82.2424 | 75.3576 | 90.5117 | 53.1553 | 4584 | 1499 | 5590 | 586 | 545 | 93.0034 | |
| egarrison-hhga | SNP | * | lowcmp_SimpleRepeat_triTR_11to50 | het | 99.6200 | 99.3718 | 99.8694 | 32.0414 | 4587 | 29 | 4588 | 6 | 2 | 33.3333 | |
| dgrover-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 97.7426 | 96.1442 | 99.3950 | 25.7739 | 4588 | 184 | 4600 | 28 | 27 | 96.4286 | |
| ckim-vqsr | SNP | * | lowcmp_SimpleRepeat_triTR_11to50 | het | 99.6636 | 99.5017 | 99.8260 | 39.5847 | 4593 | 23 | 4589 | 8 | 3 | 37.5000 | |
| gduggal-bwavard | SNP | tv | lowcmp_SimpleRepeat_quadTR_11to50 | het | 97.4259 | 97.9953 | 96.8630 | 51.4454 | 4595 | 94 | 4539 | 147 | 42 | 28.5714 | |
| gduggal-bwavard | SNP | ti | lowcmp_SimpleRepeat_diTR_11to50 | * | 94.8869 | 95.0176 | 94.7566 | 72.8903 | 4596 | 241 | 4554 | 252 | 104 | 41.2698 | |