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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
17901-17950 / 86044 show all | |||||||||||||||
| cchapple-custom | SNP | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 98.8587 | 98.7069 | 99.0109 | 72.0332 | 2977 | 39 | 3003 | 30 | 3 | 10.0000 | |
| ckim-dragen | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 96.7471 | 99.7835 | 93.8900 | 68.9437 | 461 | 1 | 461 | 30 | 30 | 100.0000 | |
| ckim-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 99.8126 | 99.7437 | 99.8815 | 55.8039 | 25294 | 65 | 25297 | 30 | 17 | 56.6667 | |
| ckim-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 96.8156 | 94.2210 | 99.5572 | 26.7488 | 6701 | 411 | 6745 | 30 | 30 | 100.0000 | |
| ckim-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 96.8070 | 94.2013 | 99.5609 | 27.3655 | 6758 | 416 | 6802 | 30 | 30 | 100.0000 | |
| ckim-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 96.6289 | 93.8110 | 99.6213 | 24.3430 | 7594 | 501 | 7629 | 29 | 29 | 100.0000 | |
| ckim-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 96.6034 | 93.7599 | 99.6247 | 26.3649 | 7663 | 510 | 7699 | 29 | 29 | 100.0000 | |
| ckim-gatk | INDEL | I1_5 | map_l125_m2_e0 | * | 97.7534 | 98.8331 | 96.6970 | 90.4503 | 847 | 10 | 849 | 29 | 3 | 10.3448 | |
| ckim-gatk | INDEL | I1_5 | map_l125_m2_e1 | * | 97.7866 | 98.8506 | 96.7452 | 90.5203 | 860 | 10 | 862 | 29 | 3 | 10.3448 | |
| ckim-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 97.0062 | 95.1023 | 98.9878 | 50.0871 | 2835 | 146 | 2836 | 29 | 24 | 82.7586 | |
| ckim-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 95.5453 | 100.0000 | 91.4706 | 70.3833 | 311 | 0 | 311 | 29 | 28 | 96.5517 | |
| ckim-gatk | SNP | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 99.1690 | 98.9505 | 99.3886 | 67.1606 | 4714 | 50 | 4714 | 29 | 10 | 34.4828 | |
| ckim-isaac | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 84.8488 | 74.6492 | 98.2769 | 53.8272 | 1649 | 560 | 1654 | 29 | 24 | 82.7586 | |
| ckim-dragen | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 96.3255 | 93.2427 | 99.6191 | 24.9186 | 7548 | 547 | 7585 | 29 | 29 | 100.0000 | |
| ckim-dragen | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 96.3159 | 93.2216 | 99.6227 | 27.1443 | 7619 | 554 | 7658 | 29 | 29 | 100.0000 | |
| ckim-dragen | INDEL | D1_5 | map_l100_m0_e0 | het | 96.3955 | 97.6311 | 95.1907 | 86.7502 | 577 | 14 | 574 | 29 | 2 | 6.8966 | |
| ckim-dragen | INDEL | D1_5 | map_l150_m2_e1 | * | 96.8643 | 97.4293 | 96.3057 | 90.2509 | 758 | 20 | 756 | 29 | 4 | 13.7931 | |
| ckim-dragen | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_51to200 | het | 86.2391 | 93.9189 | 79.7203 | 77.1200 | 139 | 9 | 114 | 29 | 29 | 100.0000 | |
| ckim-dragen | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 94.1429 | 90.3366 | 98.2840 | 67.1270 | 1664 | 178 | 1661 | 29 | 28 | 96.5517 | |
| ckim-dragen | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 97.2521 | 95.5720 | 98.9924 | 51.2038 | 2849 | 132 | 2849 | 29 | 29 | 100.0000 | |
| cchapple-custom | INDEL | * | map_l250_m2_e0 | * | 93.5413 | 95.4683 | 91.6905 | 95.6635 | 316 | 15 | 320 | 29 | 3 | 10.3448 | |
| cchapple-custom | INDEL | * | map_l250_m2_e1 | * | 93.5790 | 95.4955 | 91.7379 | 95.7583 | 318 | 15 | 322 | 29 | 3 | 10.3448 | |
| cchapple-custom | INDEL | C1_5 | lowcmp_SimpleRepeat_diTR_11to50 | * | 0.0000 | 0.0000 | 84.7368 | 95.3466 | 0 | 0 | 161 | 29 | 2 | 6.8966 | |
| cchapple-custom | INDEL | C1_5 | lowcmp_SimpleRepeat_diTR_11to50 | het | 0.0000 | 0.0000 | 80.6667 | 95.5264 | 0 | 0 | 121 | 29 | 2 | 6.8966 | |
| cchapple-custom | INDEL | C6_15 | * | * | 95.9554 | 100.0000 | 92.2252 | 93.7957 | 7 | 0 | 344 | 29 | 11 | 37.9310 | |
| cchapple-custom | INDEL | D16_PLUS | * | homalt | 98.3125 | 98.3452 | 98.2800 | 59.3539 | 1664 | 28 | 1657 | 29 | 25 | 86.2069 | |
| cchapple-custom | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 97.8361 | 97.9984 | 97.6744 | 63.8236 | 1224 | 25 | 1218 | 29 | 25 | 86.2069 | |
| cchapple-custom | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 97.8361 | 97.9984 | 97.6744 | 63.8236 | 1224 | 25 | 1218 | 29 | 25 | 86.2069 | |
| cchapple-custom | INDEL | I16_PLUS | HG002compoundhet | het | 93.8692 | 89.3617 | 98.8556 | 50.9675 | 42 | 5 | 2505 | 29 | 26 | 89.6552 | |
| ckim-dragen | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 99.5015 | 99.5702 | 99.4329 | 75.1639 | 5097 | 22 | 5085 | 29 | 11 | 37.9310 | |
| ciseli-custom | INDEL | D1_5 | map_l125_m0_e0 | homalt | 78.7671 | 77.7027 | 79.8611 | 87.8069 | 115 | 33 | 115 | 29 | 24 | 82.7586 | |
| ciseli-custom | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 20.7836 | 13.0081 | 51.6667 | 91.2281 | 32 | 214 | 31 | 29 | 15 | 51.7241 | |
| cchapple-custom | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 98.4351 | 99.3209 | 97.5651 | 66.8707 | 1170 | 8 | 1162 | 29 | 29 | 100.0000 | |
| cchapple-custom | INDEL | I1_5 | map_l100_m1_e0 | het | 96.5366 | 96.6538 | 96.4198 | 83.9921 | 751 | 26 | 781 | 29 | 8 | 27.5862 | |
| cchapple-custom | INDEL | I1_5 | map_l100_m2_e0 | het | 96.5400 | 96.5952 | 96.4848 | 85.2941 | 766 | 27 | 796 | 29 | 8 | 27.5862 | |
| cchapple-custom | INDEL | I1_5 | map_l100_m2_e1 | het | 96.6133 | 96.6667 | 96.5599 | 85.3595 | 783 | 27 | 814 | 29 | 8 | 27.5862 | |
| cchapple-custom | SNP | ti | HG002complexvar | homalt | 99.8348 | 99.6852 | 99.9849 | 17.4009 | 192854 | 609 | 192184 | 29 | 25 | 86.2069 | |
| hfeng-pmm3 | INDEL | * | map_l100_m2_e0 | het | 98.4803 | 98.2228 | 98.7391 | 83.7628 | 2266 | 41 | 2271 | 29 | 5 | 17.2414 | |
| hfeng-pmm3 | INDEL | * | map_l100_m2_e1 | het | 98.5037 | 98.2501 | 98.7586 | 83.8596 | 2302 | 41 | 2307 | 29 | 5 | 17.2414 | |
| hfeng-pmm2 | INDEL | D1_5 | map_l100_m1_e0 | het | 98.4026 | 99.1729 | 97.6442 | 83.5954 | 1199 | 10 | 1202 | 29 | 2 | 6.8966 | |
| hfeng-pmm2 | INDEL | D1_5 | map_l100_m2_e0 | het | 98.4217 | 99.1242 | 97.7291 | 84.1426 | 1245 | 11 | 1248 | 29 | 2 | 6.8966 | |
| hfeng-pmm2 | INDEL | D1_5 | map_l100_m2_e1 | het | 98.4365 | 99.1325 | 97.7502 | 84.2651 | 1257 | 11 | 1260 | 29 | 2 | 6.8966 | |
| jlack-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 98.9955 | 99.0692 | 98.9219 | 52.5490 | 2661 | 25 | 2661 | 29 | 0 | 0.0000 | |
| jlack-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 98.6868 | 99.2734 | 98.1070 | 88.8808 | 1503 | 11 | 1503 | 29 | 14 | 48.2759 | |
| jli-custom | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 97.3931 | 96.1967 | 98.6197 | 73.1673 | 2074 | 82 | 2072 | 29 | 15 | 51.7241 | |
| hfeng-pmm2 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 96.8239 | 96.0191 | 97.6423 | 76.7662 | 1206 | 50 | 1201 | 29 | 6 | 20.6897 | |
| hfeng-pmm3 | SNP | tv | segdup | * | 99.7247 | 99.7890 | 99.6604 | 90.6553 | 8514 | 18 | 8510 | 29 | 5 | 17.2414 | |
| hfeng-pmm1 | INDEL | D6_15 | HG002complexvar | * | 97.1047 | 94.8887 | 99.4267 | 56.6618 | 5031 | 271 | 5029 | 29 | 25 | 86.2069 | |
| hfeng-pmm1 | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 95.2809 | 97.0252 | 93.5982 | 46.7059 | 424 | 13 | 424 | 29 | 29 | 100.0000 | |
| hfeng-pmm1 | INDEL | I16_PLUS | * | het | 98.4241 | 97.9397 | 98.9135 | 73.5192 | 2662 | 56 | 2640 | 29 | 4 | 13.7931 | |