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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
27001-27050 / 86044 show all | |||||||||||||||
| anovak-vg | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 0.0000 | 0.0000 | 66.6667 | 0 | 1 | 0 | 3 | 1 | 33.3333 | ||
| bgallagher-sentieon | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 99.1340 | 98.9224 | 99.3464 | 71.8750 | 459 | 5 | 456 | 3 | 1 | 33.3333 | |
| bgallagher-sentieon | SNP | ti | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 99.9139 | 99.9016 | 99.9262 | 45.6684 | 4061 | 4 | 4061 | 3 | 1 | 33.3333 | |
| bgallagher-sentieon | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 97.5610 | 96.9697 | 98.1595 | 91.0734 | 160 | 5 | 160 | 3 | 1 | 33.3333 | |
| bgallagher-sentieon | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 97.1660 | 96.7742 | 97.5610 | 90.7865 | 120 | 4 | 120 | 3 | 1 | 33.3333 | |
| cchapple-custom | INDEL | * | func_cds | het | 98.6264 | 98.5981 | 98.6547 | 47.0309 | 211 | 3 | 220 | 3 | 1 | 33.3333 | |
| anovak-vg | INDEL | I6_15 | map_l250_m1_e0 | * | 48.9796 | 42.8571 | 57.1429 | 96.3918 | 3 | 4 | 4 | 3 | 1 | 33.3333 | |
| anovak-vg | INDEL | I6_15 | map_l250_m1_e0 | het | 30.7692 | 25.0000 | 40.0000 | 96.1538 | 1 | 3 | 2 | 3 | 1 | 33.3333 | |
| anovak-vg | INDEL | I6_15 | map_l250_m2_e0 | * | 53.3333 | 50.0000 | 57.1429 | 96.6825 | 4 | 4 | 4 | 3 | 1 | 33.3333 | |
| anovak-vg | INDEL | I6_15 | map_l250_m2_e0 | het | 40.0000 | 40.0000 | 40.0000 | 96.4286 | 2 | 3 | 2 | 3 | 1 | 33.3333 | |
| anovak-vg | INDEL | I6_15 | map_l250_m2_e1 | * | 53.3333 | 50.0000 | 57.1429 | 96.8037 | 4 | 4 | 4 | 3 | 1 | 33.3333 | |
| anovak-vg | INDEL | I6_15 | map_l250_m2_e1 | het | 40.0000 | 40.0000 | 40.0000 | 96.5517 | 2 | 3 | 2 | 3 | 1 | 33.3333 | |
| anovak-vg | SNP | * | lowcmp_SimpleRepeat_quadTR_51to200 | het | 58.1498 | 70.5882 | 49.4382 | 90.1657 | 72 | 30 | 88 | 90 | 30 | 33.3333 | |
| astatham-gatk | INDEL | * | func_cds | * | 99.5531 | 99.7753 | 99.3318 | 44.9080 | 444 | 1 | 446 | 3 | 1 | 33.3333 | |
| astatham-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 99.5829 | 99.5667 | 99.5991 | 76.3025 | 2987 | 13 | 2981 | 12 | 4 | 33.3333 | |
| astatham-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | homalt | 99.8893 | 100.0000 | 99.7788 | 74.1369 | 1353 | 0 | 1353 | 3 | 1 | 33.3333 | |
| astatham-gatk | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 99.3031 | 98.7158 | 99.8974 | 47.9345 | 2921 | 38 | 2921 | 3 | 1 | 33.3333 | |
| astatham-gatk | SNP | ti | map_l250_m1_e0 | het | 89.5242 | 81.7722 | 98.8998 | 92.0567 | 2427 | 541 | 2427 | 27 | 9 | 33.3333 | |
| astatham-gatk | SNP | ti | map_l250_m2_e0 | het | 89.3237 | 81.3768 | 98.9907 | 92.3822 | 2648 | 606 | 2648 | 27 | 9 | 33.3333 | |
| astatham-gatk | SNP | ti | map_l250_m2_e1 | het | 89.3914 | 81.4792 | 99.0055 | 92.4310 | 2688 | 611 | 2688 | 27 | 9 | 33.3333 | |
| astatham-gatk | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 97.5610 | 96.9697 | 98.1595 | 91.0341 | 160 | 5 | 160 | 3 | 1 | 33.3333 | |
| astatham-gatk | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 97.1660 | 96.7742 | 97.5610 | 90.7029 | 120 | 4 | 120 | 3 | 1 | 33.3333 | |
| astatham-gatk | SNP | tv | map_l100_m2_e1 | * | 91.8357 | 85.0651 | 99.7773 | 71.9862 | 21507 | 3776 | 21503 | 48 | 16 | 33.3333 | |
| astatham-gatk | SNP | tv | map_l125_m1_e0 | * | 91.3826 | 84.3531 | 99.6900 | 75.2873 | 13510 | 2506 | 13508 | 42 | 14 | 33.3333 | |
| astatham-gatk | SNP | tv | map_l125_m2_e0 | * | 91.4434 | 84.4502 | 99.6992 | 76.7428 | 13925 | 2564 | 13923 | 42 | 14 | 33.3333 | |
| astatham-gatk | SNP | tv | map_l125_m2_e1 | * | 91.4416 | 84.4450 | 99.7023 | 76.7879 | 14066 | 2591 | 14064 | 42 | 14 | 33.3333 | |
| astatham-gatk | SNP | tv | map_l250_m0_e0 | * | 93.9497 | 90.3268 | 97.8754 | 93.7472 | 691 | 74 | 691 | 15 | 5 | 33.3333 | |
| asubramanian-gatk | INDEL | * | func_cds | * | 98.8729 | 98.4270 | 99.3228 | 86.9360 | 438 | 7 | 440 | 3 | 1 | 33.3333 | |
| asubramanian-gatk | INDEL | * | map_l125_m1_e0 | homalt | 96.1134 | 92.8962 | 99.5614 | 86.8865 | 680 | 52 | 681 | 3 | 1 | 33.3333 | |
| asubramanian-gatk | INDEL | * | map_l125_m2_e0 | homalt | 96.2060 | 93.0537 | 99.5792 | 87.7027 | 710 | 53 | 710 | 3 | 1 | 33.3333 | |
| asubramanian-gatk | INDEL | * | map_l125_m2_e1 | homalt | 96.1924 | 93.0233 | 99.5851 | 87.7995 | 720 | 54 | 720 | 3 | 1 | 33.3333 | |
| asubramanian-gatk | INDEL | * | map_l150_m1_e0 | homalt | 95.2710 | 91.5584 | 99.2974 | 89.4045 | 423 | 39 | 424 | 3 | 1 | 33.3333 | |
| asubramanian-gatk | INDEL | * | map_l150_m2_e0 | homalt | 95.2388 | 91.4761 | 99.3243 | 90.2332 | 440 | 41 | 441 | 3 | 1 | 33.3333 | |
| asubramanian-gatk | INDEL | * | map_l150_m2_e1 | homalt | 95.3495 | 91.6667 | 99.3407 | 90.2129 | 451 | 41 | 452 | 3 | 1 | 33.3333 | |
| asubramanian-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 96.8750 | 96.8750 | 96.8750 | 86.3636 | 372 | 12 | 372 | 12 | 4 | 33.3333 | |
| asubramanian-gatk | INDEL | D1_5 | map_l100_m0_e0 | homalt | 95.1807 | 91.8605 | 98.7500 | 85.1943 | 237 | 21 | 237 | 3 | 1 | 33.3333 | |
| asubramanian-gatk | INDEL | D1_5 | map_l100_m1_e0 | homalt | 96.6121 | 93.9189 | 99.4643 | 83.9725 | 556 | 36 | 557 | 3 | 1 | 33.3333 | |
| asubramanian-gatk | INDEL | D1_5 | map_l100_m2_e0 | homalt | 96.7204 | 94.1080 | 99.4819 | 84.5641 | 575 | 36 | 576 | 3 | 1 | 33.3333 | |
| asubramanian-gatk | INDEL | D1_5 | map_l100_m2_e1 | homalt | 96.6837 | 94.0323 | 99.4889 | 84.6255 | 583 | 37 | 584 | 3 | 1 | 33.3333 | |
| asubramanian-gatk | INDEL | D6_15 | map_l100_m1_e0 | * | 93.4132 | 90.6977 | 96.2963 | 88.8224 | 234 | 24 | 234 | 9 | 3 | 33.3333 | |
| asubramanian-gatk | INDEL | D6_15 | map_l100_m2_e0 | * | 93.3594 | 90.5303 | 96.3710 | 89.2314 | 239 | 25 | 239 | 9 | 3 | 33.3333 | |
| asubramanian-gatk | INDEL | D6_15 | map_l100_m2_e1 | * | 93.4397 | 90.5455 | 96.5251 | 89.0301 | 249 | 26 | 250 | 9 | 3 | 33.3333 | |
| asubramanian-gatk | INDEL | D6_15 | map_l125_m1_e0 | * | 94.7368 | 92.3077 | 97.2973 | 92.3183 | 108 | 9 | 108 | 3 | 1 | 33.3333 | |
| asubramanian-gatk | INDEL | D6_15 | map_l125_m1_e0 | het | 94.4882 | 93.7500 | 95.2381 | 93.7808 | 60 | 4 | 60 | 3 | 1 | 33.3333 | |
| asubramanian-gatk | INDEL | D6_15 | map_l125_m2_e0 | * | 94.2623 | 91.2698 | 97.4576 | 92.5174 | 115 | 11 | 115 | 3 | 1 | 33.3333 | |
| asubramanian-gatk | INDEL | D6_15 | map_l125_m2_e0 | het | 94.2857 | 92.9577 | 95.6522 | 93.7838 | 66 | 5 | 66 | 3 | 1 | 33.3333 | |
| asubramanian-gatk | INDEL | D6_15 | map_l125_m2_e1 | * | 93.9271 | 90.6250 | 97.4790 | 92.6407 | 116 | 12 | 116 | 3 | 1 | 33.3333 | |
| asubramanian-gatk | INDEL | D6_15 | map_l125_m2_e1 | het | 94.2857 | 92.9577 | 95.6522 | 93.9314 | 66 | 5 | 66 | 3 | 1 | 33.3333 | |
| asubramanian-gatk | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 94.1176 | 100.0000 | 88.8889 | 91.3462 | 24 | 0 | 24 | 3 | 1 | 33.3333 | |
| asubramanian-gatk | SNP | * | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 76.9231 | 100.0000 | 62.5000 | 69.2308 | 5 | 0 | 5 | 3 | 1 | 33.3333 | |