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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
14601-14650 / 86044 show all | |||||||||||||||
| astatham-gatk | INDEL | * | tech_badpromoters | het | 98.7013 | 97.4359 | 100.0000 | 53.6585 | 38 | 1 | 38 | 0 | 0 | ||
| astatham-gatk | SNP | * | HG002complexvar | het | 98.7010 | 97.4496 | 99.9850 | 18.8713 | 453625 | 11872 | 453498 | 68 | 28 | 41.1765 | |
| ltrigg-rtg2 | SNP | * | map_l150_m1_e0 | * | 98.7010 | 97.5595 | 99.8696 | 62.6893 | 29862 | 747 | 29864 | 39 | 9 | 23.0769 | |
| ckim-vqsr | SNP | tv | HG002compoundhet | homalt | 98.7009 | 97.5502 | 99.8791 | 43.2979 | 3305 | 83 | 3304 | 4 | 3 | 75.0000 | |
| ltrigg-rtg1 | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 98.7006 | 97.8372 | 99.5793 | 71.1392 | 47227 | 1044 | 47105 | 199 | 54 | 27.1357 | |
| bgallagher-sentieon | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 98.7006 | 97.6510 | 99.7730 | 41.9121 | 2619 | 63 | 2637 | 6 | 6 | 100.0000 | |
| ckim-dragen | INDEL | D1_5 | map_l125_m1_e0 | homalt | 98.7005 | 97.9943 | 99.4169 | 85.1515 | 342 | 7 | 341 | 2 | 2 | 100.0000 | |
| ckim-vqsr | INDEL | I1_5 | segdup | het | 98.7001 | 98.6989 | 98.7013 | 96.8242 | 531 | 7 | 532 | 7 | 0 | 0.0000 | |
| eyeh-varpipe | SNP | tv | map_siren | hetalt | 98.7001 | 98.7654 | 98.6348 | 72.7948 | 80 | 1 | 289 | 4 | 4 | 100.0000 | |
| eyeh-varpipe | SNP | tv | map_l250_m1_e0 | * | 98.7000 | 99.5089 | 97.9042 | 90.2532 | 2634 | 13 | 2616 | 56 | 6 | 10.7143 | |
| raldana-dualsentieon | INDEL | * | map_siren | * | 98.6998 | 98.2726 | 99.1307 | 80.1633 | 7282 | 128 | 7298 | 64 | 16 | 25.0000 | |
| rpoplin-dv42 | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 98.6996 | 97.7430 | 99.6751 | 54.6036 | 3681 | 85 | 3681 | 12 | 7 | 58.3333 | |
| rpoplin-dv42 | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 98.6996 | 97.7430 | 99.6751 | 54.6036 | 3681 | 85 | 3681 | 12 | 7 | 58.3333 | |
| astatham-gatk | SNP | * | map_l250_m2_e1 | homalt | 98.6994 | 97.7189 | 99.6997 | 86.4012 | 2656 | 62 | 2656 | 8 | 7 | 87.5000 | |
| ckim-vqsr | SNP | tv | lowcmp_SimpleRepeat_quadTR_11to50 | * | 98.6992 | 99.3022 | 98.1034 | 41.3093 | 7400 | 52 | 7397 | 143 | 1 | 0.6993 | |
| hfeng-pmm1 | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 98.6991 | 97.6504 | 99.7706 | 72.0664 | 15211 | 366 | 15219 | 35 | 25 | 71.4286 | |
| gduggal-bwavard | SNP | tv | map_l100_m0_e0 | homalt | 98.6984 | 97.6079 | 99.8135 | 64.7875 | 3754 | 92 | 3747 | 7 | 5 | 71.4286 | |
| jlack-gatk | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 98.6982 | 98.8933 | 98.5039 | 87.7567 | 1251 | 14 | 1251 | 19 | 13 | 68.4211 | |
| hfeng-pmm3 | INDEL | D1_5 | map_l125_m1_e0 | het | 98.6982 | 99.0358 | 98.3629 | 83.8617 | 719 | 7 | 721 | 12 | 2 | 16.6667 | |
| astatham-gatk | SNP | * | HG002compoundhet | het | 98.6981 | 97.5878 | 99.8340 | 46.2177 | 13836 | 342 | 13834 | 23 | 22 | 95.6522 | |
| gduggal-snapvard | SNP | tv | * | het | 98.6977 | 99.0250 | 98.3726 | 31.6253 | 585935 | 5769 | 583366 | 9651 | 1423 | 14.7446 | |
| raldana-dualsentieon | INDEL | * | map_l125_m1_e0 | homalt | 98.6977 | 98.3607 | 99.0371 | 84.0640 | 720 | 12 | 720 | 7 | 3 | 42.8571 | |
| jpowers-varprowl | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 98.6974 | 98.6597 | 98.7351 | 66.8148 | 2650 | 36 | 2654 | 34 | 0 | 0.0000 | |
| ltrigg-rtg2 | INDEL | D1_5 | map_l125_m1_e0 | homalt | 98.6971 | 97.7077 | 99.7067 | 78.8724 | 341 | 8 | 340 | 1 | 1 | 100.0000 | |
| gduggal-bwafb | SNP | * | map_l100_m2_e0 | het | 98.6971 | 99.0172 | 98.3791 | 71.2956 | 45943 | 456 | 45945 | 757 | 143 | 18.8904 | |
| hfeng-pmm3 | INDEL | I6_15 | HG002complexvar | homalt | 98.6971 | 99.8353 | 97.5845 | 54.9183 | 1212 | 2 | 1212 | 30 | 30 | 100.0000 | |
| ltrigg-rtg2 | INDEL | * | segdup | het | 98.6970 | 98.5675 | 98.8268 | 93.0098 | 1445 | 21 | 1432 | 17 | 2 | 11.7647 | |
| gduggal-bwavard | SNP | tv | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 98.6965 | 98.0478 | 99.3539 | 59.8156 | 10698 | 213 | 10610 | 69 | 47 | 68.1159 | |
| qzeng-custom | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 98.6961 | 99.6184 | 97.7906 | 64.7616 | 3916 | 15 | 3895 | 88 | 3 | 3.4091 | |
| asubramanian-gatk | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 98.6957 | 98.6957 | 98.6957 | 72.7488 | 227 | 3 | 227 | 3 | 2 | 66.6667 | |
| cchapple-custom | INDEL | D1_5 | map_l100_m2_e1 | homalt | 98.6957 | 97.7419 | 99.6683 | 80.5358 | 606 | 14 | 601 | 2 | 2 | 100.0000 | |
| jli-custom | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 98.6957 | 98.3216 | 99.0726 | 47.6211 | 10896 | 186 | 10896 | 102 | 98 | 96.0784 | |
| hfeng-pmm1 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | hetalt | 98.6957 | 97.4249 | 100.0000 | 76.3562 | 227 | 6 | 231 | 0 | 0 | ||
| eyeh-varpipe | SNP | * | map_l100_m2_e1 | * | 98.6948 | 99.7404 | 97.6710 | 69.5344 | 74543 | 194 | 72256 | 1723 | 51 | 2.9600 | |
| astatham-gatk | SNP | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 98.6948 | 97.7785 | 99.6284 | 69.3550 | 2949 | 67 | 2949 | 11 | 6 | 54.5455 | |
| egarrison-hhga | INDEL | I1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 98.6941 | 98.1189 | 99.2762 | 66.9104 | 2608 | 50 | 2606 | 19 | 14 | 73.6842 | |
| ghariani-varprowl | SNP | tv | map_l150_m2_e0 | homalt | 98.6939 | 98.0896 | 99.3057 | 75.8431 | 4005 | 78 | 4005 | 28 | 15 | 53.5714 | |
| bgallagher-sentieon | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 98.6936 | 99.8565 | 97.5576 | 63.3125 | 8348 | 12 | 8348 | 209 | 208 | 99.5215 | |
| bgallagher-sentieon | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 98.6936 | 99.8565 | 97.5576 | 63.3125 | 8348 | 12 | 8348 | 209 | 208 | 99.5215 | |
| hfeng-pmm3 | SNP | * | map_l250_m1_e0 | het | 98.6931 | 98.4648 | 98.9225 | 88.7103 | 4682 | 73 | 4682 | 51 | 3 | 5.8824 | |
| hfeng-pmm3 | INDEL | D1_5 | map_l150_m2_e0 | * | 98.6930 | 98.8204 | 98.5658 | 87.1803 | 754 | 9 | 756 | 11 | 3 | 27.2727 | |
| hfeng-pmm3 | INDEL | I6_15 | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 98.6928 | 97.4194 | 100.0000 | 81.9477 | 151 | 4 | 152 | 0 | 0 | ||
| hfeng-pmm2 | INDEL | D6_15 | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 98.6928 | 97.4194 | 100.0000 | 83.3333 | 151 | 4 | 151 | 0 | 0 | ||
| ckim-vqsr | INDEL | I6_15 | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 98.6928 | 97.4194 | 100.0000 | 82.8829 | 151 | 4 | 152 | 0 | 0 | ||
| ckim-gatk | INDEL | I6_15 | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 98.6928 | 97.4194 | 100.0000 | 82.8829 | 151 | 4 | 152 | 0 | 0 | ||
| bgallagher-sentieon | INDEL | I6_15 | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 98.6928 | 97.4194 | 100.0000 | 82.4480 | 151 | 4 | 152 | 0 | 0 | ||
| ndellapenna-hhga | SNP | ti | map_l100_m0_e0 | het | 98.6920 | 97.6686 | 99.7371 | 67.9732 | 13657 | 326 | 13658 | 36 | 19 | 52.7778 | |
| ltrigg-rtg2 | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 98.6920 | 97.4178 | 100.0000 | 77.5262 | 830 | 22 | 794 | 0 | 0 | ||
| ltrigg-rtg2 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | hetalt | 98.6916 | 98.2143 | 99.1736 | 83.4247 | 110 | 2 | 120 | 1 | 1 | 100.0000 | |
| ndellapenna-hhga | SNP | tv | map_l125_m0_e0 | * | 98.6916 | 97.8284 | 99.5702 | 72.2163 | 6487 | 144 | 6487 | 28 | 13 | 46.4286 | |