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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
15101-15150 / 86044 show all | |||||||||||||||
| hfeng-pmm1 | SNP | ti | map_siren | homalt | 99.9011 | 99.8760 | 99.9261 | 52.1075 | 37869 | 47 | 37865 | 28 | 18 | 64.2857 | |
| hfeng-pmm2 | SNP | tv | * | het | 99.8886 | 99.8560 | 99.9212 | 22.0414 | 590844 | 852 | 590770 | 466 | 18 | 3.8627 | |
| hfeng-pmm3 | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | * | 97.6271 | 96.4286 | 98.8558 | 65.7524 | 1728 | 64 | 1728 | 20 | 18 | 90.0000 | |
| hfeng-pmm3 | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | het | 95.0004 | 93.9245 | 96.1014 | 81.4130 | 572 | 37 | 493 | 20 | 18 | 90.0000 | |
| jlack-gatk | INDEL | * | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 99.6624 | 99.7383 | 99.5867 | 60.0529 | 16386 | 43 | 16385 | 68 | 18 | 26.4706 | |
| jlack-gatk | INDEL | D16_PLUS | HG002complexvar | het | 97.0657 | 97.5610 | 96.5753 | 68.6359 | 1080 | 27 | 846 | 30 | 18 | 60.0000 | |
| jlack-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | * | 97.3321 | 96.2662 | 98.4219 | 60.3556 | 1186 | 46 | 1185 | 19 | 18 | 94.7368 | |
| jlack-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | het | 94.9497 | 96.6667 | 93.2927 | 74.5736 | 319 | 11 | 306 | 22 | 18 | 81.8182 | |
| hfeng-pmm2 | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 94.9772 | 98.5782 | 91.6300 | 69.1156 | 208 | 3 | 208 | 19 | 18 | 94.7368 | |
| hfeng-pmm2 | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 97.1586 | 95.2030 | 99.1964 | 50.6041 | 2838 | 143 | 2839 | 23 | 18 | 78.2609 | |
| hfeng-pmm1 | INDEL | D1_5 | HG002complexvar | * | 99.1888 | 98.4747 | 99.9133 | 56.8376 | 32216 | 499 | 32267 | 28 | 18 | 64.2857 | |
| hfeng-pmm1 | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.6018 | 99.6976 | 99.5062 | 56.7205 | 3627 | 11 | 3627 | 18 | 18 | 100.0000 | |
| gduggal-bwaplat | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 67.4944 | 52.3636 | 94.9227 | 82.7953 | 432 | 393 | 430 | 23 | 18 | 78.2609 | |
| gduggal-bwaplat | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 67.4944 | 52.3636 | 94.9227 | 82.7953 | 432 | 393 | 430 | 23 | 18 | 78.2609 | |
| gduggal-bwaplat | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 66.9905 | 53.7415 | 88.9096 | 95.4327 | 948 | 816 | 954 | 119 | 18 | 15.1261 | |
| gduggal-bwaplat | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 90.2910 | 84.7806 | 96.5674 | 90.4279 | 3593 | 645 | 3601 | 128 | 18 | 14.0625 | |
| gduggal-bwavard | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 46.9055 | 30.9190 | 97.1223 | 64.9698 | 683 | 1526 | 675 | 20 | 18 | 90.0000 | |
| gduggal-bwavard | INDEL | C6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 68.2353 | 100.0000 | 51.7857 | 95.9288 | 1 | 0 | 58 | 54 | 18 | 33.3333 | |
| gduggal-bwavard | INDEL | D1_5 | map_l100_m0_e0 | * | 91.4210 | 96.1761 | 87.1140 | 87.8478 | 830 | 33 | 818 | 121 | 18 | 14.8760 | |
| gduggal-bwavard | INDEL | D1_5 | map_l125_m2_e1 | het | 91.2581 | 98.8312 | 84.7630 | 90.8034 | 761 | 9 | 751 | 135 | 18 | 13.3333 | |
| gduggal-bwavard | SNP | * | map_l125_m1_e0 | homalt | 98.6701 | 97.5096 | 99.8585 | 66.2879 | 16484 | 421 | 16234 | 23 | 18 | 78.2609 | |
| gduggal-bwavard | SNP | * | map_l125_m2_e0 | homalt | 98.6652 | 97.4964 | 99.8623 | 68.6081 | 16940 | 435 | 16685 | 23 | 18 | 78.2609 | |
| gduggal-bwavard | SNP | * | map_l125_m2_e1 | homalt | 98.6568 | 97.4789 | 99.8635 | 68.6528 | 17090 | 442 | 16828 | 23 | 18 | 78.2609 | |
| gduggal-snapfb | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | hetalt | 52.7839 | 52.6946 | 52.8736 | 74.7093 | 88 | 79 | 46 | 41 | 18 | 43.9024 | |
| gduggal-bwafb | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 75.2156 | 61.3260 | 97.2393 | 52.0588 | 222 | 140 | 634 | 18 | 18 | 100.0000 | |
| gduggal-bwafb | INDEL | I16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | het | 41.7658 | 28.7500 | 76.3158 | 69.6000 | 46 | 114 | 58 | 18 | 18 | 100.0000 | |
| gduggal-bwafb | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 97.0511 | 96.3351 | 97.7778 | 77.6754 | 920 | 35 | 924 | 21 | 18 | 85.7143 | |
| gduggal-bwafb | INDEL | I1_5 | lowcmp_SimpleRepeat_triTR_11to50 | het | 96.7462 | 97.6596 | 95.8498 | 63.4393 | 459 | 11 | 485 | 21 | 18 | 85.7143 | |
| gduggal-bwafb | INDEL | I1_5 | map_siren | * | 97.6773 | 96.5391 | 98.8428 | 79.9276 | 2901 | 104 | 2904 | 34 | 18 | 52.9412 | |
| gduggal-bwafb | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 75.6619 | 66.8539 | 87.1429 | 65.7702 | 119 | 59 | 122 | 18 | 18 | 100.0000 | |
| gduggal-bwafb | SNP | * | segdup | homalt | 99.7625 | 99.6928 | 99.8322 | 89.4414 | 10710 | 33 | 10710 | 18 | 18 | 100.0000 | |
| eyeh-varpipe | SNP | ti | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 96.4666 | 99.0196 | 94.0419 | 60.5213 | 1212 | 12 | 1168 | 74 | 18 | 24.3243 | |
| eyeh-varpipe | SNP | tv | map_siren | het | 95.7583 | 99.7903 | 92.0396 | 63.5402 | 28549 | 60 | 28096 | 2430 | 18 | 0.7407 | |
| eyeh-varpipe | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 40.8000 | 26.0204 | 94.4444 | 60.8696 | 204 | 580 | 306 | 18 | 18 | 100.0000 | |
| eyeh-varpipe | INDEL | D16_PLUS | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 71.5596 | 75.0000 | 68.4211 | 65.4545 | 39 | 13 | 39 | 18 | 18 | 100.0000 | |
| eyeh-varpipe | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | homalt | 97.5728 | 98.9160 | 96.2656 | 77.1021 | 365 | 4 | 464 | 18 | 18 | 100.0000 | |
| eyeh-varpipe | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | homalt | 69.0901 | 55.6851 | 90.9953 | 55.8577 | 191 | 152 | 192 | 19 | 18 | 94.7368 | |
| eyeh-varpipe | INDEL | D6_15 | map_l125_m2_e0 | * | 86.1910 | 84.9206 | 87.5000 | 87.6423 | 107 | 19 | 133 | 19 | 18 | 94.7368 | |
| eyeh-varpipe | INDEL | D6_15 | map_l125_m2_e1 | * | 85.9091 | 84.3750 | 87.5000 | 87.8981 | 108 | 20 | 133 | 19 | 18 | 94.7368 | |
| eyeh-varpipe | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 44.1354 | 31.4607 | 73.9130 | 57.1429 | 28 | 61 | 51 | 18 | 18 | 100.0000 | |
| eyeh-varpipe | INDEL | I16_PLUS | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 63.6364 | 87.5000 | 50.0000 | 29.4118 | 7 | 1 | 18 | 18 | 18 | 100.0000 | |
| eyeh-varpipe | INDEL | I1_5 | segdup | homalt | 97.3667 | 98.3087 | 96.4427 | 92.5159 | 465 | 8 | 488 | 18 | 18 | 100.0000 | |
| gduggal-bwaplat | INDEL | * | lowcmp_SimpleRepeat_homopolymer_6to10 | homalt | 93.9544 | 88.7394 | 99.8206 | 58.1571 | 10024 | 1272 | 10013 | 18 | 18 | 100.0000 | |
| gduggal-bwaplat | INDEL | D16_PLUS | HG002compoundhet | het | 64.7528 | 50.1235 | 91.4414 | 72.1455 | 203 | 202 | 203 | 19 | 18 | 94.7368 | |
| gduggal-bwaplat | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 68.4640 | 56.8794 | 85.9743 | 82.6329 | 802 | 608 | 803 | 131 | 18 | 13.7405 | |
| gduggal-snapfb | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | hetalt | 60.0266 | 74.1071 | 50.4425 | 79.7491 | 83 | 29 | 57 | 56 | 18 | 32.1429 | |
| gduggal-snapfb | INDEL | I1_5 | segdup | * | 95.1081 | 96.7894 | 93.4842 | 94.5833 | 1025 | 34 | 1033 | 72 | 18 | 25.0000 | |
| ghariani-varprowl | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 30.4000 | 21.8391 | 50.0000 | 86.7133 | 19 | 68 | 19 | 19 | 18 | 94.7368 | |
| ghariani-varprowl | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 57.1429 | 66.6667 | 50.0000 | 84.9206 | 18 | 9 | 19 | 19 | 18 | 94.7368 | |
| ghariani-varprowl | INDEL | I16_PLUS | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 39.0244 | 34.0426 | 45.7143 | 78.5276 | 16 | 31 | 16 | 19 | 18 | 94.7368 | |