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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
13451-13500 / 86044 show all | |||||||||||||||
| astatham-gatk | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 99.7617 | 99.9506 | 99.5734 | 57.9016 | 6069 | 3 | 6069 | 26 | 25 | 96.1538 | |
| asubramanian-gatk | INDEL | D16_PLUS | * | homalt | 98.2891 | 98.4634 | 98.1154 | 70.9396 | 1666 | 26 | 1666 | 32 | 25 | 78.1250 | |
| asubramanian-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 97.7654 | 98.0785 | 97.4543 | 75.1188 | 1225 | 24 | 1225 | 32 | 25 | 78.1250 | |
| asubramanian-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 97.7654 | 98.0785 | 97.4543 | 75.1188 | 1225 | 24 | 1225 | 32 | 25 | 78.1250 | |
| asubramanian-gatk | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | het | 96.0917 | 97.5369 | 94.6886 | 84.1739 | 594 | 15 | 517 | 29 | 25 | 86.2069 | |
| asubramanian-gatk | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 94.5966 | 91.5686 | 97.8316 | 84.9216 | 1401 | 129 | 1534 | 34 | 25 | 73.5294 | |
| asubramanian-gatk | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 94.5966 | 91.5686 | 97.8316 | 84.9216 | 1401 | 129 | 1534 | 34 | 25 | 73.5294 | |
| bgallagher-sentieon | SNP | * | HG002compoundhet | * | 99.8063 | 99.8025 | 99.8102 | 41.0420 | 25771 | 51 | 25764 | 49 | 25 | 51.0204 | |
| bgallagher-sentieon | SNP | * | map_l250_m2_e0 | het | 98.0598 | 98.7678 | 97.3619 | 90.6085 | 5130 | 64 | 5130 | 139 | 25 | 17.9856 | |
| bgallagher-sentieon | SNP | * | map_l250_m2_e1 | het | 98.0666 | 98.7652 | 97.3778 | 90.6744 | 5199 | 65 | 5199 | 140 | 25 | 17.8571 | |
| bgallagher-sentieon | SNP | * | map_siren | homalt | 99.8557 | 99.7643 | 99.9473 | 50.0857 | 55026 | 130 | 55017 | 29 | 25 | 86.2069 | |
| bgallagher-sentieon | SNP | ti | map_l125_m0_e0 | het | 98.6693 | 99.1771 | 98.1668 | 78.4213 | 8195 | 68 | 8193 | 153 | 25 | 16.3399 | |
| bgallagher-sentieon | SNP | tv | * | homalt | 99.9838 | 99.9759 | 99.9918 | 19.9074 | 377032 | 91 | 377017 | 31 | 25 | 80.6452 | |
| bgallagher-sentieon | SNP | tv | map_l100_m0_e0 | * | 98.9757 | 99.3865 | 98.5682 | 71.0162 | 11016 | 68 | 11015 | 160 | 25 | 15.6250 | |
| bgallagher-sentieon | SNP | tv | map_l100_m1_e0 | het | 99.1089 | 99.5719 | 98.6501 | 70.0769 | 15351 | 66 | 15347 | 210 | 25 | 11.9048 | |
| bgallagher-sentieon | SNP | tv | map_l100_m2_e0 | het | 99.1197 | 99.5817 | 98.6621 | 71.4019 | 15711 | 66 | 15707 | 213 | 25 | 11.7371 | |
| bgallagher-sentieon | SNP | tv | map_l100_m2_e1 | het | 99.1255 | 99.5859 | 98.6693 | 71.4407 | 15872 | 66 | 15868 | 214 | 25 | 11.6822 | |
| bgallagher-sentieon | SNP | tv | map_l150_m1_e0 | * | 98.9592 | 99.3402 | 98.5810 | 76.0604 | 10840 | 72 | 10838 | 156 | 25 | 16.0256 | |
| bgallagher-sentieon | SNP | tv | map_l150_m2_e0 | * | 98.9822 | 99.3659 | 98.6015 | 77.4624 | 11283 | 72 | 11281 | 160 | 25 | 15.6250 | |
| bgallagher-sentieon | SNP | tv | map_l150_m2_e1 | * | 98.9952 | 99.3740 | 98.6193 | 77.4754 | 11430 | 72 | 11428 | 160 | 25 | 15.6250 | |
| astatham-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 96.7778 | 99.6205 | 94.0928 | 82.7887 | 525 | 2 | 446 | 28 | 25 | 89.2857 | |
| astatham-gatk | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 98.0480 | 100.0000 | 96.1708 | 73.1621 | 653 | 0 | 653 | 26 | 25 | 96.1538 | |
| bgallagher-sentieon | INDEL | D16_PLUS | HG002compoundhet | homalt | 39.0244 | 100.0000 | 24.2424 | 67.9612 | 8 | 0 | 8 | 25 | 25 | 100.0000 | |
| jli-custom | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 99.0815 | 99.5612 | 98.6064 | 70.5927 | 28586 | 126 | 28586 | 404 | 25 | 6.1881 | |
| jli-custom | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 99.0815 | 99.5612 | 98.6064 | 70.5927 | 28586 | 126 | 28586 | 404 | 25 | 6.1881 | |
| jli-custom | SNP | ti | map_l125_m0_e0 | het | 98.6256 | 98.1363 | 99.1199 | 71.4709 | 8109 | 154 | 8109 | 72 | 25 | 34.7222 | |
| jli-custom | SNP | tv | map_l100_m0_e0 | * | 99.0774 | 98.8271 | 99.3290 | 64.5356 | 10954 | 130 | 10954 | 74 | 25 | 33.7838 | |
| jli-custom | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_51to200 | het | 79.3123 | 89.9408 | 70.9302 | 81.7410 | 152 | 17 | 61 | 25 | 25 | 100.0000 | |
| jli-custom | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 98.4486 | 97.4071 | 99.5127 | 25.8925 | 5297 | 141 | 5309 | 26 | 25 | 96.1538 | |
| jli-custom | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 97.5369 | 96.2764 | 98.8308 | 48.6037 | 2870 | 111 | 2874 | 34 | 25 | 73.5294 | |
| ltrigg-rtg1 | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 97.3694 | 95.3108 | 99.5190 | 31.4561 | 5183 | 255 | 5172 | 25 | 25 | 100.0000 | |
| ltrigg-rtg1 | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 97.0384 | 94.9067 | 99.2681 | 58.6918 | 6000 | 322 | 5968 | 44 | 25 | 56.8182 | |
| ltrigg-rtg1 | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 97.0384 | 94.9067 | 99.2681 | 58.6918 | 6000 | 322 | 5968 | 44 | 25 | 56.8182 | |
| ltrigg-rtg2 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 94.0313 | 89.5336 | 99.0048 | 44.4125 | 2438 | 285 | 2487 | 25 | 25 | 100.0000 | |
| ltrigg-rtg2 | INDEL | * | lowcmp_SimpleRepeat_quadTR_51to200 | * | 96.3833 | 94.7646 | 98.0583 | 61.6187 | 2516 | 139 | 2525 | 50 | 25 | 50.0000 | |
| jpowers-varprowl | SNP | tv | map_l125_m1_e0 | homalt | 98.9113 | 98.4471 | 99.3798 | 71.3800 | 5769 | 91 | 5769 | 36 | 25 | 69.4444 | |
| jpowers-varprowl | SNP | tv | map_l125_m2_e0 | homalt | 98.9229 | 98.4544 | 99.3960 | 73.5628 | 5924 | 93 | 5924 | 36 | 25 | 69.4444 | |
| jpowers-varprowl | SNP | tv | map_l125_m2_e1 | homalt | 98.9247 | 98.4524 | 99.4016 | 73.5688 | 5980 | 94 | 5980 | 36 | 25 | 69.4444 | |
| jmaeng-gatk | SNP | tv | map_siren | het | 94.8661 | 92.5932 | 97.2533 | 75.2567 | 26490 | 2119 | 26485 | 748 | 25 | 3.3423 | |
| jpowers-varprowl | INDEL | * | map_siren | homalt | 94.9463 | 91.6384 | 98.5020 | 74.3563 | 2433 | 222 | 2433 | 37 | 25 | 67.5676 | |
| jmaeng-gatk | INDEL | D6_15 | HG002complexvar | het | 98.8845 | 98.7179 | 99.0517 | 59.4483 | 3080 | 40 | 3029 | 29 | 25 | 86.2069 | |
| ckim-dragen | SNP | tv | map_l125_m1_e0 | het | 97.6861 | 98.8149 | 96.5827 | 77.3870 | 10006 | 120 | 10005 | 354 | 25 | 7.0622 | |
| cchapple-custom | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 97.5597 | 98.9214 | 96.2349 | 54.4582 | 642 | 7 | 639 | 25 | 25 | 100.0000 | |
| cchapple-custom | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_11to50 | * | 97.8094 | 96.1793 | 99.4957 | 50.2286 | 5513 | 219 | 5524 | 28 | 25 | 89.2857 | |
| cchapple-custom | INDEL | I6_15 | HG002complexvar | het | 98.1734 | 97.1975 | 99.1692 | 56.5725 | 2289 | 66 | 3581 | 30 | 25 | 83.3333 | |
| cchapple-custom | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 98.2572 | 99.6364 | 96.9158 | 68.2486 | 822 | 3 | 817 | 26 | 25 | 96.1538 | |
| cchapple-custom | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 98.2572 | 99.6364 | 96.9158 | 68.2486 | 822 | 3 | 817 | 26 | 25 | 96.1538 | |
| cchapple-custom | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 98.8536 | 98.8377 | 98.8695 | 82.8620 | 6803 | 80 | 6909 | 79 | 25 | 31.6456 | |
| cchapple-custom | SNP | * | lowcmp_SimpleRepeat_diTR_11to50 | het | 99.1314 | 98.9416 | 99.3219 | 67.8823 | 6170 | 66 | 6298 | 43 | 25 | 58.1395 | |
| cchapple-custom | SNP | * | segdup | * | 99.5856 | 99.8219 | 99.3504 | 91.8828 | 28017 | 50 | 27988 | 183 | 25 | 13.6612 | |