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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
58301-58350 / 86044 show all | |||||||||||||||
| hfeng-pmm1 | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 98.0769 | 100.0000 | 96.2264 | 77.0893 | 153 | 0 | 153 | 6 | 5 | 83.3333 | |
| hfeng-pmm1 | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.9381 | 99.9059 | 99.9703 | 56.7400 | 20180 | 19 | 20180 | 6 | 6 | 100.0000 | |
| hfeng-pmm1 | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 99.3683 | 98.8824 | 99.8589 | 49.4773 | 4247 | 48 | 4247 | 6 | 0 | 0.0000 | |
| hfeng-pmm1 | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 99.0815 | 98.3991 | 99.7735 | 47.4300 | 2643 | 43 | 2643 | 6 | 0 | 0.0000 | |
| hfeng-pmm1 | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 95.0022 | 90.7095 | 99.7214 | 86.4766 | 2148 | 220 | 2148 | 6 | 4 | 66.6667 | |
| hfeng-pmm1 | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 92.2750 | 85.9974 | 99.5413 | 87.6183 | 1302 | 212 | 1302 | 6 | 4 | 66.6667 | |
| hfeng-pmm1 | SNP | * | lowcmp_SimpleRepeat_diTR_11to50 | het | 97.7476 | 95.6863 | 99.8995 | 66.9763 | 5967 | 269 | 5967 | 6 | 5 | 83.3333 | |
| hfeng-pmm1 | SNP | * | lowcmp_SimpleRepeat_triTR_11to50 | * | 99.6524 | 99.3882 | 99.9179 | 31.7465 | 7310 | 45 | 7306 | 6 | 1 | 16.6667 | |
| hfeng-pmm1 | SNP | ti | HG002compoundhet | het | 96.8662 | 93.9821 | 99.9329 | 37.3774 | 8933 | 572 | 8934 | 6 | 2 | 33.3333 | |
| hfeng-pmm1 | SNP | ti | HG002compoundhet | homalt | 99.9392 | 99.9594 | 99.9189 | 30.5967 | 7391 | 3 | 7391 | 6 | 6 | 100.0000 | |
| hfeng-pmm1 | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 99.3551 | 98.9186 | 99.7954 | 49.2385 | 2927 | 32 | 2927 | 6 | 0 | 0.0000 | |
| hfeng-pmm1 | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 99.0937 | 98.5254 | 99.6685 | 47.3225 | 1804 | 27 | 1804 | 6 | 0 | 0.0000 | |
| hfeng-pmm1 | SNP | ti | lowcmp_SimpleRepeat_quadTR_11to50 | het | 99.3889 | 98.8731 | 99.9101 | 37.5970 | 6668 | 76 | 6668 | 6 | 0 | 0.0000 | |
| hfeng-pmm1 | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 95.1927 | 91.2096 | 99.5395 | 87.2592 | 1297 | 125 | 1297 | 6 | 4 | 66.6667 | |
| hfeng-pmm1 | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 92.8280 | 87.1851 | 99.2519 | 87.9706 | 796 | 117 | 796 | 6 | 4 | 66.6667 | |
| hfeng-pmm1 | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 98.0979 | 96.4062 | 99.8501 | 81.6005 | 3997 | 149 | 3997 | 6 | 4 | 66.6667 | |
| hfeng-pmm1 | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 97.1484 | 94.6692 | 99.7610 | 81.1745 | 2504 | 141 | 2504 | 6 | 4 | 66.6667 | |
| hfeng-pmm1 | SNP | tv | lowcmp_SimpleRepeat_diTR_11to50 | het | 97.9888 | 96.2435 | 99.7985 | 65.0879 | 2972 | 116 | 2972 | 6 | 5 | 83.3333 | |
| hfeng-pmm1 | SNP | tv | segdup | homalt | 99.8765 | 99.9382 | 99.8149 | 90.2264 | 3236 | 2 | 3236 | 6 | 6 | 100.0000 | |
| hfeng-pmm2 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 99.5711 | 99.3100 | 99.8335 | 74.5893 | 3598 | 25 | 3598 | 6 | 2 | 33.3333 | |
| hfeng-pmm2 | INDEL | * | lowcmp_SimpleRepeat_homopolymer_gt10 | * | 84.9320 | 77.4194 | 94.0594 | 99.9207 | 96 | 28 | 95 | 6 | 0 | 0.0000 | |
| hfeng-pmm2 | INDEL | * | map_l125_m1_e0 | homalt | 99.3179 | 99.4536 | 99.1826 | 84.3929 | 728 | 4 | 728 | 6 | 4 | 66.6667 | |
| hfeng-pmm2 | INDEL | * | map_l150_m2_e1 | homalt | 98.9858 | 99.1870 | 98.7854 | 88.2938 | 488 | 4 | 488 | 6 | 4 | 66.6667 | |
| hfeng-pmm3 | INDEL | D1_5 | map_l150_m0_e0 | het | 98.0464 | 99.0099 | 97.1014 | 89.8080 | 200 | 2 | 201 | 6 | 0 | 0.0000 | |
| hfeng-pmm3 | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | * | 98.9050 | 97.9929 | 99.8342 | 48.4986 | 3613 | 74 | 3613 | 6 | 3 | 50.0000 | |
| hfeng-pmm3 | INDEL | I16_PLUS | HG002complexvar | homalt | 99.0385 | 100.0000 | 98.0952 | 69.9140 | 309 | 0 | 309 | 6 | 5 | 83.3333 | |
| hfeng-pmm3 | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 97.0766 | 95.1952 | 99.0338 | 86.4144 | 634 | 32 | 615 | 6 | 0 | 0.0000 | |
| hfeng-pmm3 | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 97.0766 | 95.1952 | 99.0338 | 86.4144 | 634 | 32 | 615 | 6 | 0 | 0.0000 | |
| hfeng-pmm3 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 98.9492 | 98.9492 | 98.9492 | 64.2902 | 565 | 6 | 565 | 6 | 6 | 100.0000 | |
| hfeng-pmm3 | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 99.1143 | 98.5907 | 99.6435 | 73.6743 | 1679 | 24 | 1677 | 6 | 0 | 0.0000 | |
| hfeng-pmm3 | INDEL | I6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 93.4426 | 96.6102 | 90.4762 | 76.4045 | 57 | 2 | 57 | 6 | 6 | 100.0000 | |
| hfeng-pmm3 | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 97.7137 | 96.5174 | 98.9399 | 71.3273 | 582 | 21 | 560 | 6 | 4 | 66.6667 | |
| hfeng-pmm3 | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 98.0769 | 100.0000 | 96.2264 | 77.1879 | 153 | 0 | 153 | 6 | 5 | 83.3333 | |
| hfeng-pmm3 | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 99.8555 | 99.7467 | 99.9646 | 71.3411 | 16932 | 43 | 16932 | 6 | 3 | 50.0000 | |
| hfeng-pmm3 | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 90.8078 | 84.4560 | 98.1928 | 91.2540 | 326 | 60 | 326 | 6 | 0 | 0.0000 | |
| hfeng-pmm3 | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 88.5375 | 81.1594 | 97.3913 | 91.0784 | 224 | 52 | 224 | 6 | 0 | 0.0000 | |
| hfeng-pmm3 | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 99.8555 | 99.7467 | 99.9646 | 71.3411 | 16932 | 43 | 16932 | 6 | 3 | 50.0000 | |
| hfeng-pmm3 | SNP | * | lowcmp_SimpleRepeat_quadTR_51to200 | * | 84.0467 | 75.5245 | 94.7368 | 93.3255 | 108 | 35 | 108 | 6 | 1 | 16.6667 | |
| hfeng-pmm3 | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 93.8877 | 88.8889 | 99.4823 | 87.1394 | 1152 | 144 | 1153 | 6 | 1 | 16.6667 | |
| hfeng-pmm3 | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 90.9674 | 84.0188 | 99.1690 | 88.3848 | 715 | 136 | 716 | 6 | 1 | 16.6667 | |
| hfeng-pmm3 | SNP | tv | lowcmp_SimpleRepeat_quadTR_11to50 | het | 99.2056 | 98.5498 | 99.8702 | 37.4713 | 4621 | 68 | 4618 | 6 | 0 | 0.0000 | |
| jlack-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | homalt | 99.7418 | 99.9261 | 99.5582 | 73.6157 | 1352 | 1 | 1352 | 6 | 3 | 50.0000 | |
| jlack-gatk | INDEL | * | lowcmp_SimpleRepeat_homopolymer_6to10 | hetalt | 97.2503 | 95.7009 | 98.8506 | 74.0943 | 512 | 23 | 516 | 6 | 6 | 100.0000 | |
| jlack-gatk | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 98.0087 | 96.3087 | 99.7699 | 41.5864 | 2583 | 99 | 2601 | 6 | 6 | 100.0000 | |
| jlack-gatk | INDEL | * | map_l125_m0_e0 | homalt | 98.2456 | 98.5915 | 97.9021 | 87.7673 | 280 | 4 | 280 | 6 | 4 | 66.6667 | |
| jlack-gatk | INDEL | * | map_l150_m1_e0 | homalt | 98.5915 | 98.4848 | 98.6985 | 88.1613 | 455 | 7 | 455 | 6 | 3 | 50.0000 | |
| jlack-gatk | INDEL | * | map_l150_m2_e0 | homalt | 98.6472 | 98.5447 | 98.7500 | 89.0884 | 474 | 7 | 474 | 6 | 3 | 50.0000 | |
| jlack-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 98.5212 | 99.2593 | 97.7941 | 64.3045 | 268 | 2 | 266 | 6 | 3 | 50.0000 | |
| jlack-gatk | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_51to200 | homalt | 94.8617 | 94.4882 | 95.2381 | 52.2727 | 120 | 7 | 120 | 6 | 5 | 83.3333 | |
| jlack-gatk | INDEL | D16_PLUS | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 96.0894 | 98.8506 | 93.4783 | 84.2466 | 86 | 1 | 86 | 6 | 0 | 0.0000 | |