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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
19701-19750 / 86044 show all | |||||||||||||||
| ltrigg-rtg2 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 99.1130 | 99.2516 | 98.9748 | 72.3987 | 2122 | 16 | 2124 | 22 | 4 | 18.1818 | |
| ltrigg-rtg2 | INDEL | C1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 0.0000 | 0.0000 | 92.2807 | 95.7828 | 0 | 1 | 263 | 22 | 4 | 18.1818 | |
| ltrigg-rtg2 | INDEL | C1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 0.0000 | 0.0000 | 92.2807 | 95.7828 | 0 | 1 | 263 | 22 | 4 | 18.1818 | |
| jli-custom | INDEL | I6_15 | HG002complexvar | homalt | 99.0196 | 99.8353 | 98.2172 | 53.8692 | 1212 | 2 | 1212 | 22 | 22 | 100.0000 | |
| jli-custom | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 98.2668 | 99.8469 | 96.7359 | 71.1719 | 652 | 1 | 652 | 22 | 22 | 100.0000 | |
| jli-custom | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 97.4424 | 96.0934 | 98.8298 | 71.9151 | 1894 | 77 | 1858 | 22 | 8 | 36.3636 | |
| jli-custom | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 97.4424 | 96.0934 | 98.8298 | 71.9151 | 1894 | 77 | 1858 | 22 | 8 | 36.3636 | |
| jli-custom | SNP | * | lowcmp_SimpleRepeat_triTR_11to50 | * | 99.7622 | 99.8232 | 99.7013 | 32.7459 | 7342 | 13 | 7343 | 22 | 3 | 13.6364 | |
| jli-custom | SNP | ti | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 99.1373 | 99.3577 | 98.9179 | 69.5704 | 2011 | 13 | 2011 | 22 | 5 | 22.7273 | |
| jli-custom | SNP | tv | map_l250_m1_e0 | het | 97.3617 | 96.0269 | 98.7342 | 85.3704 | 1716 | 71 | 1716 | 22 | 7 | 31.8182 | |
| jmaeng-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 97.5926 | 96.9745 | 98.2186 | 79.0180 | 1218 | 38 | 1213 | 22 | 9 | 40.9091 | |
| jmaeng-gatk | INDEL | * | map_siren | homalt | 99.1343 | 99.0960 | 99.1726 | 81.5411 | 2631 | 24 | 2637 | 22 | 15 | 68.1818 | |
| jpowers-varprowl | INDEL | D16_PLUS | map_l100_m1_e0 | * | 59.1682 | 52.8736 | 67.1642 | 96.2232 | 46 | 41 | 45 | 22 | 19 | 86.3636 | |
| jpowers-varprowl | INDEL | D16_PLUS | map_l100_m1_e0 | het | 70.4762 | 80.4348 | 62.7119 | 95.1199 | 37 | 9 | 37 | 22 | 19 | 86.3636 | |
| jpowers-varprowl | INDEL | D16_PLUS | map_l100_m2_e0 | * | 59.8250 | 53.3333 | 68.1159 | 96.2743 | 48 | 42 | 47 | 22 | 19 | 86.3636 | |
| jpowers-varprowl | INDEL | D16_PLUS | map_l100_m2_e0 | het | 70.3704 | 79.1667 | 63.3333 | 95.2978 | 38 | 10 | 38 | 22 | 19 | 86.3636 | |
| ltrigg-rtg1 | INDEL | D1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 99.6222 | 99.3336 | 99.9125 | 51.6616 | 25190 | 169 | 25113 | 22 | 14 | 63.6364 | |
| ltrigg-rtg1 | INDEL | D1_5 | map_siren | het | 97.9324 | 96.8819 | 99.0059 | 74.1048 | 2206 | 71 | 2191 | 22 | 1 | 4.5455 | |
| ltrigg-rtg1 | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | het | 98.7075 | 98.2437 | 99.1757 | 52.7025 | 2685 | 48 | 2647 | 22 | 8 | 36.3636 | |
| anovak-vg | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | homalt | 98.4133 | 98.4093 | 98.4173 | 55.0598 | 1361 | 22 | 1368 | 22 | 17 | 77.2727 | |
| bgallagher-sentieon | INDEL | I16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 96.7166 | 95.4426 | 98.0251 | 79.9026 | 1089 | 52 | 1092 | 22 | 18 | 81.8182 | |
| bgallagher-sentieon | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 95.3688 | 98.2332 | 92.6667 | 69.5122 | 278 | 5 | 278 | 22 | 22 | 100.0000 | |
| bgallagher-sentieon | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 97.8467 | 99.4746 | 96.2712 | 66.6478 | 568 | 3 | 568 | 22 | 22 | 100.0000 | |
| cchapple-custom | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 99.0919 | 98.8333 | 99.3518 | 73.8158 | 2965 | 35 | 3372 | 22 | 17 | 77.2727 | |
| astatham-gatk | SNP | tv | map_l150_m0_e0 | het | 91.2506 | 84.5586 | 99.0928 | 85.6322 | 2404 | 439 | 2403 | 22 | 3 | 13.6364 | |
| asubramanian-gatk | INDEL | C6_15 | HG002compoundhet | homalt | 0.0000 | 0.0000 | 42.1053 | 0 | 0 | 0 | 22 | 0 | 0.0000 | ||
| asubramanian-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 93.0029 | 89.2396 | 97.0976 | 37.9705 | 622 | 75 | 736 | 22 | 18 | 81.8182 | |
| asubramanian-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 99.5409 | 99.1719 | 99.9126 | 55.4663 | 25149 | 210 | 25156 | 22 | 13 | 59.0909 | |
| asubramanian-gatk | INDEL | D1_5 | map_l250_m1_e0 | het | 83.8428 | 86.4865 | 81.3559 | 96.8108 | 96 | 15 | 96 | 22 | 2 | 9.0909 | |
| asubramanian-gatk | INDEL | D1_5 | map_l250_m2_e0 | het | 84.6774 | 86.7769 | 82.6772 | 96.9287 | 105 | 16 | 105 | 22 | 2 | 9.0909 | |
| asubramanian-gatk | INDEL | D1_5 | map_l250_m2_e1 | het | 84.3373 | 86.0656 | 82.6772 | 96.9962 | 105 | 17 | 105 | 22 | 2 | 9.0909 | |
| asubramanian-gatk | INDEL | D6_15 | HG002complexvar | het | 98.2617 | 97.2756 | 99.2679 | 59.9547 | 3035 | 85 | 2983 | 22 | 18 | 81.8182 | |
| asubramanian-gatk | INDEL | I16_PLUS | * | het | 96.3656 | 93.7454 | 99.1366 | 77.2113 | 2548 | 170 | 2526 | 22 | 11 | 50.0000 | |
| asubramanian-gatk | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | * | 98.7291 | 97.9738 | 99.4961 | 65.8453 | 3820 | 79 | 4344 | 22 | 13 | 59.0909 | |
| asubramanian-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 98.8986 | 98.6225 | 99.1763 | 52.8592 | 2649 | 37 | 2649 | 22 | 1 | 4.5455 | |
| asubramanian-gatk | SNP | ti | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 98.7149 | 98.1219 | 99.3151 | 65.8879 | 3187 | 61 | 3190 | 22 | 6 | 27.2727 | |
| astatham-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_51to200 | het | 83.4086 | 85.9259 | 81.0345 | 77.5629 | 116 | 19 | 94 | 22 | 21 | 95.4545 | |
| astatham-gatk | INDEL | D1_5 | map_l150_m1_e0 | * | 96.6476 | 96.3738 | 96.9231 | 89.6121 | 691 | 26 | 693 | 22 | 4 | 18.1818 | |
| astatham-gatk | INDEL | D1_5 | map_l150_m2_e0 | * | 96.6463 | 96.1992 | 97.0976 | 90.1019 | 734 | 29 | 736 | 22 | 4 | 18.1818 | |
| astatham-gatk | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | * | 99.1904 | 98.9484 | 99.4336 | 67.7810 | 3858 | 41 | 3862 | 22 | 16 | 72.7273 | |
| asubramanian-gatk | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 98.1886 | 98.1028 | 98.2745 | 88.1406 | 1241 | 24 | 1253 | 22 | 8 | 36.3636 | |
| bgallagher-sentieon | INDEL | * | map_siren | homalt | 99.3618 | 99.5480 | 99.1763 | 81.3504 | 2643 | 12 | 2649 | 22 | 13 | 59.0909 | |
| bgallagher-sentieon | INDEL | * | segdup | het | 98.8787 | 99.2497 | 98.5105 | 95.1038 | 1455 | 11 | 1455 | 22 | 2 | 9.0909 | |
| bgallagher-sentieon | INDEL | D16_PLUS | HG002complexvar | het | 98.0634 | 98.6450 | 97.4886 | 68.5684 | 1092 | 15 | 854 | 22 | 12 | 54.5455 | |
| bgallagher-sentieon | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_51to200 | het | 83.0580 | 85.1852 | 81.0345 | 77.6062 | 115 | 20 | 94 | 22 | 21 | 95.4545 | |
| bgallagher-sentieon | INDEL | D1_5 | map_l100_m0_e0 | * | 98.2188 | 98.9571 | 97.4914 | 85.7120 | 854 | 9 | 855 | 22 | 4 | 18.1818 | |
| bgallagher-sentieon | INDEL | D1_5 | map_l125_m1_e0 | * | 98.5857 | 99.1728 | 98.0054 | 86.8862 | 1079 | 9 | 1081 | 22 | 5 | 22.7273 | |
| bgallagher-sentieon | INDEL | D1_5 | map_l125_m2_e0 | * | 98.6532 | 99.2126 | 98.1002 | 87.4743 | 1134 | 9 | 1136 | 22 | 5 | 22.7273 | |
| bgallagher-sentieon | INDEL | D1_5 | map_l125_m2_e1 | * | 98.6694 | 99.2221 | 98.1229 | 87.5306 | 1148 | 9 | 1150 | 22 | 5 | 22.7273 | |
| bgallagher-sentieon | INDEL | D6_15 | HG002complexvar | homalt | 99.0678 | 100.0000 | 98.1528 | 62.7696 | 1169 | 0 | 1169 | 22 | 21 | 95.4545 | |