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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
27551-27600 / 86044 show all | |||||||||||||||
| ndellapenna-hhga | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 79.7416 | 66.9975 | 98.4728 | 66.8746 | 10329 | 5088 | 9672 | 150 | 125 | 83.3333 | |
| ckim-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 98.0533 | 97.6374 | 98.4728 | 67.8136 | 63807 | 1544 | 63576 | 986 | 844 | 85.5984 | |
| ckim-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 98.0533 | 97.6374 | 98.4728 | 67.8136 | 63807 | 1544 | 63576 | 986 | 844 | 85.5984 | |
| bgallagher-sentieon | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 98.9281 | 99.3885 | 98.4721 | 71.1857 | 3738 | 23 | 3738 | 58 | 56 | 96.5517 | |
| bgallagher-sentieon | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 98.9281 | 99.3885 | 98.4721 | 71.1857 | 3738 | 23 | 3738 | 58 | 56 | 96.5517 | |
| egarrison-hhga | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 97.6760 | 96.8929 | 98.4720 | 68.6413 | 15093 | 484 | 15080 | 234 | 134 | 57.2650 | |
| egarrison-hhga | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 98.5257 | 98.5798 | 98.4716 | 73.3734 | 21588 | 311 | 21584 | 335 | 163 | 48.6567 | |
| jli-custom | INDEL | D1_5 | HG002compoundhet | * | 97.1251 | 95.8153 | 98.4712 | 65.0788 | 11723 | 512 | 11723 | 182 | 174 | 95.6044 | |
| ckim-isaac | INDEL | * | map_l125_m2_e1 | het | 80.8213 | 68.5369 | 98.4709 | 89.9312 | 965 | 443 | 966 | 15 | 5 | 33.3333 | |
| jmaeng-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 97.9638 | 97.4619 | 98.4709 | 54.8834 | 31180 | 812 | 31104 | 483 | 468 | 96.8944 | |
| ltrigg-rtg2 | INDEL | * | map_l100_m0_e0 | het | 96.5544 | 94.7111 | 98.4709 | 76.6706 | 967 | 54 | 966 | 15 | 0 | 0.0000 | |
| rpoplin-dv42 | INDEL | * | map_l125_m1_e0 | * | 98.0229 | 97.5795 | 98.4704 | 98.6389 | 2056 | 51 | 2060 | 32 | 13 | 40.6250 | |
| rpoplin-dv42 | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 95.1465 | 92.0399 | 98.4702 | 62.7698 | 4891 | 423 | 4892 | 76 | 70 | 92.1053 | |
| ltrigg-rtg1 | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 98.7849 | 99.1019 | 98.4699 | 79.4919 | 10704 | 97 | 10747 | 167 | 2 | 1.1976 | |
| egarrison-hhga | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 81.6150 | 69.6868 | 98.4699 | 49.2653 | 1869 | 813 | 1802 | 28 | 24 | 85.7143 | |
| qzeng-custom | INDEL | I1_5 | map_siren | homalt | 90.0289 | 82.9208 | 98.4698 | 74.4832 | 1005 | 207 | 1094 | 17 | 4 | 23.5294 | |
| gduggal-bwaplat | INDEL | * | HG002complexvar | * | 90.8863 | 84.3874 | 98.4697 | 61.0933 | 64926 | 12012 | 64799 | 1007 | 684 | 67.9245 | |
| jlack-gatk | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 98.3660 | 98.2626 | 98.4696 | 72.6251 | 92808 | 1641 | 92717 | 1441 | 1058 | 73.4212 | |
| jmaeng-gatk | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 98.1176 | 97.7691 | 98.4687 | 60.2554 | 15689 | 358 | 15690 | 244 | 227 | 93.0328 | |
| hfeng-pmm3 | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 95.8936 | 93.4498 | 98.4686 | 80.8504 | 642 | 45 | 643 | 10 | 6 | 60.0000 | |
| ckim-isaac | INDEL | D1_5 | map_l150_m1_e0 | * | 76.6610 | 62.7615 | 98.4683 | 90.0131 | 450 | 267 | 450 | 7 | 3 | 42.8571 | |
| hfeng-pmm2 | SNP | tv | map_l150_m1_e0 | het | 98.7581 | 99.0498 | 98.4681 | 78.5736 | 6880 | 66 | 6878 | 107 | 10 | 9.3458 | |
| gduggal-bwafb | INDEL | D1_5 | map_siren | homalt | 98.8048 | 99.1438 | 98.4681 | 82.4522 | 1158 | 10 | 1157 | 18 | 12 | 66.6667 | |
| egarrison-hhga | INDEL | D6_15 | lowcmp_SimpleRepeat_triTR_11to50 | hetalt | 68.1056 | 52.0548 | 98.4674 | 26.8908 | 304 | 280 | 257 | 4 | 4 | 100.0000 | |
| rpoplin-dv42 | INDEL | D1_5 | map_l100_m0_e0 | homalt | 99.0366 | 99.6124 | 98.4674 | 83.9975 | 257 | 1 | 257 | 4 | 4 | 100.0000 | |
| ckim-gatk | INDEL | D6_15 | * | * | 98.2230 | 97.9802 | 98.4670 | 55.8597 | 25565 | 527 | 25564 | 398 | 344 | 86.4322 | |
| dgrover-gatk | SNP | tv | map_l150_m2_e0 | het | 98.8320 | 99.2002 | 98.4666 | 81.2986 | 7194 | 58 | 7192 | 112 | 20 | 17.8571 | |
| gduggal-bwaplat | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 90.9395 | 84.4821 | 98.4657 | 87.4931 | 38610 | 7092 | 38635 | 602 | 167 | 27.7409 | |
| gduggal-bwaplat | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 90.9395 | 84.4821 | 98.4657 | 87.4931 | 38610 | 7092 | 38635 | 602 | 167 | 27.7409 | |
| ltrigg-rtg2 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 98.0316 | 97.6012 | 98.4657 | 62.5780 | 13427 | 330 | 13413 | 209 | 47 | 22.4880 | |
| ltrigg-rtg2 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 98.0316 | 97.6012 | 98.4657 | 62.5780 | 13427 | 330 | 13413 | 209 | 47 | 22.4880 | |
| ckim-vqsr | INDEL | I1_5 | map_l100_m2_e1 | het | 96.5415 | 94.6914 | 98.4655 | 90.6122 | 767 | 43 | 770 | 12 | 1 | 8.3333 | |
| raldana-dualsentieon | INDEL | D16_PLUS | HG002complexvar | * | 96.5485 | 94.7048 | 98.4655 | 65.1748 | 1556 | 87 | 1540 | 24 | 18 | 75.0000 | |
| ckim-isaac | INDEL | I1_5 | * | * | 96.6542 | 94.9085 | 98.4652 | 49.5628 | 142993 | 7671 | 142942 | 2228 | 1638 | 73.5189 | |
| cchapple-custom | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 97.7635 | 97.0721 | 98.4649 | 72.6946 | 431 | 13 | 449 | 7 | 7 | 100.0000 | |
| gduggal-bwafb | SNP | * | map_l150_m0_e0 | * | 98.2636 | 98.0635 | 98.4645 | 81.5621 | 11799 | 233 | 11799 | 184 | 58 | 31.5217 | |
| ltrigg-rtg2 | INDEL | * | lowcmp_SimpleRepeat_homopolymer_6to10 | hetalt | 97.5413 | 96.6355 | 98.4642 | 83.8745 | 517 | 18 | 577 | 9 | 9 | 100.0000 | |
| jmaeng-gatk | SNP | ti | map_siren | het | 96.0962 | 93.8396 | 98.4641 | 69.3151 | 58539 | 3843 | 58530 | 913 | 76 | 8.3242 | |
| jlack-gatk | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 98.6913 | 98.9198 | 98.4639 | 87.5787 | 1282 | 14 | 1282 | 20 | 9 | 45.0000 | |
| ckim-isaac | INDEL | D1_5 | map_l125_m2_e1 | * | 79.3602 | 66.4650 | 98.4635 | 87.9214 | 769 | 388 | 769 | 12 | 6 | 50.0000 | |
| ndellapenna-hhga | INDEL | D6_15 | * | hetalt | 65.7378 | 49.3394 | 98.4629 | 43.6387 | 4033 | 4141 | 3459 | 54 | 41 | 75.9259 | |
| ckim-vqsr | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 97.8744 | 97.2930 | 98.4628 | 79.3759 | 1222 | 34 | 1217 | 19 | 7 | 36.8421 | |
| ckim-isaac | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 91.7019 | 85.8108 | 98.4615 | 77.2063 | 381 | 63 | 384 | 6 | 5 | 83.3333 | |
| jmaeng-gatk | INDEL | D6_15 | map_l100_m2_e1 | homalt | 96.9697 | 95.5224 | 98.4615 | 87.2798 | 64 | 3 | 64 | 1 | 1 | 100.0000 | |
| ltrigg-rtg2 | INDEL | C1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 0.0000 | 0.0000 | 98.4615 | 95.8586 | 0 | 0 | 128 | 2 | 0 | 0.0000 | |
| jpowers-varprowl | INDEL | I1_5 | map_l150_m0_e0 | homalt | 96.9697 | 95.5224 | 98.4615 | 84.3373 | 64 | 3 | 64 | 1 | 1 | 100.0000 | |
| bgallagher-sentieon | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_51to200 | * | 75.8244 | 61.6505 | 98.4615 | 58.8608 | 127 | 79 | 128 | 2 | 1 | 50.0000 | |
| astatham-gatk | INDEL | I6_15 | map_siren | het | 93.7729 | 89.5105 | 98.4615 | 87.4396 | 128 | 15 | 128 | 2 | 1 | 50.0000 | |
| gduggal-snapplat | INDEL | D1_5 | map_l150_m1_e0 | homalt | 83.1300 | 71.9298 | 98.4615 | 91.6560 | 164 | 64 | 192 | 3 | 0 | 0.0000 | |
| ghariani-varprowl | INDEL | D1_5 | func_cds | homalt | 92.0863 | 86.4865 | 98.4615 | 24.4186 | 64 | 10 | 64 | 1 | 0 | 0.0000 | |