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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
25551-25600 / 86044 show all | |||||||||||||||
| jli-custom | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_51to200 | homalt | 94.9807 | 96.8504 | 93.1818 | 46.5587 | 123 | 4 | 123 | 9 | 8 | 88.8889 | |
| jli-custom | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_51to200 | * | 96.8585 | 95.2922 | 98.4772 | 64.0511 | 587 | 29 | 582 | 9 | 9 | 100.0000 | |
| jli-custom | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 95.2565 | 91.3831 | 99.4728 | 30.2126 | 1665 | 157 | 1698 | 9 | 8 | 88.8889 | |
| jli-custom | INDEL | D1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 99.8713 | 99.8037 | 99.9390 | 54.3200 | 14741 | 29 | 14742 | 9 | 4 | 44.4444 | |
| jli-custom | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 95.8637 | 96.0976 | 95.6311 | 88.8829 | 197 | 8 | 197 | 9 | 5 | 55.5556 | |
| jli-custom | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 95.8637 | 96.0976 | 95.6311 | 88.8829 | 197 | 8 | 197 | 9 | 5 | 55.5556 | |
| jli-custom | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 92.4901 | 95.1220 | 90.0000 | 74.9304 | 78 | 4 | 81 | 9 | 9 | 100.0000 | |
| jli-custom | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 98.9669 | 98.4733 | 99.4656 | 72.6845 | 1677 | 26 | 1675 | 9 | 2 | 22.2222 | |
| jpowers-varprowl | INDEL | I1_5 | map_l125_m0_e0 | * | 94.3709 | 91.9355 | 96.9388 | 89.0052 | 285 | 25 | 285 | 9 | 6 | 66.6667 | |
| jpowers-varprowl | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | * | 17.7156 | 10.2151 | 66.6667 | 89.1129 | 19 | 167 | 18 | 9 | 9 | 100.0000 | |
| jpowers-varprowl | SNP | * | lowcmp_SimpleRepeat_diTR_51to200 | het | 77.9661 | 85.1852 | 71.8750 | 97.8261 | 23 | 4 | 23 | 9 | 0 | 0.0000 | |
| jpowers-varprowl | SNP | * | map_l250_m1_e0 | homalt | 98.0829 | 96.5895 | 99.6231 | 89.3663 | 2379 | 84 | 2379 | 9 | 5 | 55.5556 | |
| jpowers-varprowl | SNP | * | map_l250_m2_e0 | homalt | 98.1866 | 96.7610 | 99.6549 | 90.0329 | 2599 | 87 | 2599 | 9 | 5 | 55.5556 | |
| jpowers-varprowl | SNP | * | map_l250_m2_e1 | homalt | 98.1703 | 96.7255 | 99.6588 | 90.0637 | 2629 | 89 | 2629 | 9 | 5 | 55.5556 | |
| jpowers-varprowl | SNP | ti | lowcmp_SimpleRepeat_diTR_51to200 | * | 78.0488 | 100.0000 | 64.0000 | 97.3461 | 16 | 0 | 16 | 9 | 0 | 0.0000 | |
| jpowers-varprowl | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | homalt | 99.0596 | 99.8095 | 98.3209 | 76.9759 | 524 | 1 | 527 | 9 | 6 | 66.6667 | |
| jpowers-varprowl | INDEL | D16_PLUS | segdup | * | 80.4978 | 77.5862 | 83.6364 | 94.2827 | 45 | 13 | 46 | 9 | 8 | 88.8889 | |
| jpowers-varprowl | INDEL | D16_PLUS | segdup | het | 86.6873 | 94.5946 | 80.0000 | 94.4030 | 35 | 2 | 36 | 9 | 8 | 88.8889 | |
| jpowers-varprowl | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | homalt | 4.7393 | 2.5381 | 35.7143 | 92.6316 | 5 | 192 | 5 | 9 | 7 | 77.7778 | |
| jpowers-varprowl | INDEL | D1_5 | map_l250_m1_e0 | * | 92.5373 | 90.6433 | 94.5122 | 95.5544 | 155 | 16 | 155 | 9 | 4 | 44.4444 | |
| jpowers-varprowl | INDEL | D1_5 | map_l250_m2_e0 | * | 93.0748 | 91.3043 | 94.9153 | 95.7686 | 168 | 16 | 168 | 9 | 4 | 44.4444 | |
| jpowers-varprowl | INDEL | D1_5 | map_l250_m2_e1 | * | 93.1129 | 91.3514 | 94.9438 | 95.8431 | 169 | 16 | 169 | 9 | 4 | 44.4444 | |
| ltrigg-rtg1 | INDEL | * | map_l125_m0_e0 | * | 95.9750 | 93.1973 | 98.9234 | 83.1757 | 822 | 60 | 827 | 9 | 2 | 22.2222 | |
| ltrigg-rtg1 | INDEL | D16_PLUS | HG002complexvar | het | 95.7312 | 92.5926 | 99.0900 | 55.4905 | 1025 | 82 | 980 | 9 | 3 | 33.3333 | |
| ltrigg-rtg1 | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 97.4377 | 95.6458 | 99.2980 | 71.4667 | 1296 | 59 | 1273 | 9 | 4 | 44.4444 | |
| ltrigg-rtg1 | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 95.1377 | 91.6667 | 98.8820 | 71.9708 | 803 | 73 | 796 | 9 | 9 | 100.0000 | |
| ltrigg-rtg1 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 97.2816 | 94.8346 | 99.8583 | 45.6289 | 6334 | 345 | 6341 | 9 | 7 | 77.7778 | |
| ltrigg-rtg1 | INDEL | D6_15 | HG002compoundhet | homalt | 80.0000 | 91.6667 | 70.9677 | 60.7595 | 22 | 2 | 22 | 9 | 8 | 88.8889 | |
| ltrigg-rtg1 | INDEL | I16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | * | 87.0717 | 78.5417 | 97.6804 | 73.6054 | 377 | 103 | 379 | 9 | 9 | 100.0000 | |
| ltrigg-rtg1 | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.4898 | 99.2366 | 99.7443 | 67.0997 | 3510 | 27 | 3511 | 9 | 6 | 66.6667 | |
| ltrigg-rtg1 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 97.7454 | 95.7670 | 99.8073 | 46.5308 | 4570 | 202 | 4661 | 9 | 9 | 100.0000 | |
| jli-custom | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 97.6684 | 97.6684 | 97.6684 | 90.9048 | 377 | 9 | 377 | 9 | 4 | 44.4444 | |
| jli-custom | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 97.4820 | 98.1884 | 96.7857 | 90.8765 | 271 | 5 | 271 | 9 | 4 | 44.4444 | |
| jli-custom | SNP | * | map_l125_m0_e0 | homalt | 99.5817 | 99.2998 | 99.8651 | 65.5375 | 6665 | 47 | 6665 | 9 | 9 | 100.0000 | |
| jli-custom | SNP | ti | map_l250_m0_e0 | * | 97.5483 | 95.8394 | 99.3192 | 90.4686 | 1313 | 57 | 1313 | 9 | 7 | 77.7778 | |
| jli-custom | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 99.5146 | 99.6528 | 99.3767 | 68.2498 | 1435 | 5 | 1435 | 9 | 0 | 0.0000 | |
| jli-custom | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 99.2358 | 99.4530 | 99.0196 | 68.7861 | 909 | 5 | 909 | 9 | 0 | 0.0000 | |
| jli-custom | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 99.1690 | 99.0514 | 99.2868 | 87.9764 | 1253 | 12 | 1253 | 9 | 4 | 44.4444 | |
| jli-custom | SNP | tv | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 99.8303 | 99.7434 | 99.9174 | 59.7828 | 10883 | 28 | 10881 | 9 | 5 | 55.5556 | |
| jli-custom | SNP | tv | map_siren | homalt | 99.8403 | 99.7332 | 99.9477 | 52.3546 | 17194 | 46 | 17191 | 9 | 9 | 100.0000 | |
| jmaeng-gatk | INDEL | D16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 94.0868 | 89.5385 | 99.1220 | 39.9179 | 873 | 102 | 1016 | 9 | 9 | 100.0000 | |
| jmaeng-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 97.3890 | 97.1354 | 97.6440 | 85.9662 | 373 | 11 | 373 | 9 | 2 | 22.2222 | |
| jmaeng-gatk | INDEL | D16_PLUS | map_l100_m1_e0 | het | 88.7014 | 95.6522 | 82.6923 | 96.1223 | 44 | 2 | 43 | 9 | 4 | 44.4444 | |
| jmaeng-gatk | INDEL | D16_PLUS | map_l100_m2_e0 | het | 88.9670 | 95.8333 | 83.0189 | 96.5762 | 46 | 2 | 44 | 9 | 4 | 44.4444 | |
| jmaeng-gatk | INDEL | D16_PLUS | map_l100_m2_e1 | het | 89.5935 | 96.0784 | 83.9286 | 96.4602 | 49 | 2 | 47 | 9 | 4 | 44.4444 | |
| jmaeng-gatk | INDEL | D16_PLUS | map_siren | het | 92.3788 | 96.1538 | 88.8889 | 96.1410 | 75 | 3 | 72 | 9 | 2 | 22.2222 | |
| jmaeng-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 97.8808 | 96.9816 | 98.7968 | 67.2217 | 739 | 23 | 739 | 9 | 5 | 55.5556 | |
| jmaeng-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | het | 97.2306 | 96.8831 | 97.5806 | 79.1129 | 373 | 12 | 363 | 9 | 8 | 88.8889 | |
| jmaeng-gatk | INDEL | D1_5 | map_l250_m0_e0 | * | 90.0000 | 97.8261 | 83.3333 | 98.2813 | 45 | 1 | 45 | 9 | 0 | 0.0000 | |
| jmaeng-gatk | INDEL | D1_5 | map_l250_m0_e0 | het | 86.4865 | 96.9697 | 78.0488 | 98.4139 | 32 | 1 | 32 | 9 | 0 | 0.0000 | |