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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
35251-35300 / 86044 show all | |||||||||||||||
| ltrigg-rtg1 | INDEL | I6_15 | map_l125_m1_e0 | het | 89.2193 | 83.3333 | 96.0000 | 82.0144 | 25 | 5 | 24 | 1 | 0 | 0.0000 | |
| ltrigg-rtg1 | INDEL | I6_15 | map_l125_m2_e0 | * | 94.0775 | 90.5660 | 97.8723 | 87.6640 | 48 | 5 | 46 | 1 | 0 | 0.0000 | |
| ltrigg-rtg1 | INDEL | I6_15 | map_l125_m2_e0 | het | 89.2193 | 83.3333 | 96.0000 | 84.4720 | 25 | 5 | 24 | 1 | 0 | 0.0000 | |
| ltrigg-rtg1 | INDEL | I6_15 | map_l125_m2_e1 | * | 94.0775 | 90.5660 | 97.8723 | 87.9487 | 48 | 5 | 46 | 1 | 0 | 0.0000 | |
| ltrigg-rtg1 | INDEL | I6_15 | map_l125_m2_e1 | het | 89.2193 | 83.3333 | 96.0000 | 84.6626 | 25 | 5 | 24 | 1 | 0 | 0.0000 | |
| ltrigg-rtg1 | INDEL | I6_15 | segdup | * | 98.2573 | 97.1429 | 99.3976 | 90.0360 | 170 | 5 | 165 | 1 | 1 | 100.0000 | |
| ltrigg-rtg1 | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 99.7779 | 99.5567 | 100.0000 | 51.3978 | 1123 | 5 | 1130 | 0 | 0 | ||
| ltrigg-rtg1 | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 99.2905 | 99.3056 | 99.2754 | 83.8445 | 715 | 5 | 685 | 5 | 0 | 0.0000 | |
| ltrigg-rtg1 | SNP | ti | segdup | homalt | 99.7604 | 99.9334 | 99.5880 | 88.0751 | 7500 | 5 | 7494 | 31 | 31 | 100.0000 | |
| ltrigg-rtg1 | SNP | tv | func_cds | * | 99.4080 | 99.8856 | 98.9350 | 27.2263 | 4366 | 5 | 4366 | 47 | 0 | 0.0000 | |
| ltrigg-rtg1 | SNP | tv | func_cds | het | 99.0291 | 99.8118 | 98.2586 | 27.7763 | 2652 | 5 | 2652 | 47 | 0 | 0.0000 | |
| ltrigg-rtg1 | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 96.9927 | 99.4152 | 94.6855 | 62.3980 | 850 | 5 | 873 | 49 | 1 | 2.0408 | |
| ltrigg-rtg1 | SNP | tv | lowcmp_SimpleRepeat_diTR_51to200 | het | 76.9679 | 70.5882 | 84.6154 | 95.8861 | 12 | 5 | 11 | 2 | 1 | 50.0000 | |
| ltrigg-rtg1 | SNP | tv | lowcmp_SimpleRepeat_quadTR_51to200 | * | 92.3981 | 88.0952 | 97.1429 | 87.9310 | 37 | 5 | 34 | 1 | 0 | 0.0000 | |
| ltrigg-rtg1 | SNP | tv | lowcmp_SimpleRepeat_quadTR_51to200 | het | 91.0841 | 86.1111 | 96.6667 | 86.3014 | 31 | 5 | 29 | 1 | 0 | 0.0000 | |
| ltrigg-rtg1 | SNP | tv | map_l250_m1_e0 | homalt | 99.6487 | 99.4159 | 99.8826 | 86.0259 | 851 | 5 | 851 | 1 | 1 | 100.0000 | |
| ltrigg-rtg1 | SNP | tv | map_l250_m2_e0 | homalt | 99.6791 | 99.4664 | 99.8928 | 87.0650 | 932 | 5 | 932 | 1 | 1 | 100.0000 | |
| ltrigg-rtg1 | SNP | tv | map_l250_m2_e1 | homalt | 99.6822 | 99.4715 | 99.8938 | 87.1662 | 941 | 5 | 941 | 1 | 1 | 100.0000 | |
| ltrigg-rtg2 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | hetalt | 97.7541 | 96.2121 | 99.3464 | 87.0886 | 127 | 5 | 152 | 1 | 1 | 100.0000 | |
| ltrigg-rtg2 | INDEL | * | map_l100_m0_e0 | hetalt | 91.8033 | 84.8485 | 100.0000 | 94.2857 | 28 | 5 | 30 | 0 | 0 | ||
| ltrigg-rtg2 | INDEL | * | map_l125_m2_e0 | hetalt | 93.6709 | 88.0952 | 100.0000 | 95.5429 | 37 | 5 | 39 | 0 | 0 | ||
| ltrigg-rtg2 | INDEL | * | map_l150_m0_e0 | homalt | 98.1481 | 96.9512 | 99.3750 | 85.5856 | 159 | 5 | 159 | 1 | 1 | 100.0000 | |
| ltrigg-rtg2 | INDEL | * | segdup | hetalt | 98.0392 | 96.1538 | 100.0000 | 95.7193 | 125 | 5 | 133 | 0 | 0 | ||
| ltrigg-rtg2 | INDEL | * | segdup | homalt | 99.5827 | 99.4792 | 99.6865 | 92.2340 | 955 | 5 | 954 | 3 | 3 | 100.0000 | |
| jli-custom | INDEL | I6_15 | segdup | * | 98.5507 | 97.1429 | 100.0000 | 91.7715 | 170 | 5 | 170 | 0 | 0 | ||
| jli-custom | SNP | * | func_cds | het | 99.8568 | 99.9552 | 99.7586 | 24.6835 | 11156 | 5 | 11156 | 27 | 0 | 0.0000 | |
| 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 | * | lowcmp_SimpleRepeat_homopolymer_6to10 | homalt | 99.9097 | 99.9179 | 99.9015 | 54.3245 | 6083 | 5 | 6083 | 6 | 4 | 66.6667 | |
| jli-custom | SNP | * | lowcmp_SimpleRepeat_quadTR_51to200 | homalt | 93.5065 | 87.8049 | 100.0000 | 92.9961 | 36 | 5 | 36 | 0 | 0 | ||
| jli-custom | SNP | ti | HG002compoundhet | homalt | 99.9121 | 99.9324 | 99.8918 | 30.7138 | 7389 | 5 | 7389 | 8 | 8 | 100.0000 | |
| jli-custom | SNP | ti | lowcmp_SimpleRepeat_quadTR_51to200 | homalt | 92.3077 | 85.7143 | 100.0000 | 92.8741 | 30 | 5 | 30 | 0 | 0 | ||
| jli-custom | SNP | ti | map_l250_m0_e0 | homalt | 99.1945 | 98.8532 | 99.5381 | 89.7296 | 431 | 5 | 431 | 2 | 2 | 100.0000 | |
| 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_lt101bp_gt95identity_merged | homalt | 99.4059 | 99.0138 | 99.8012 | 86.4311 | 502 | 5 | 502 | 1 | 0 | 0.0000 | |
| jli-custom | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 99.7995 | 99.6662 | 99.9331 | 80.2093 | 1493 | 5 | 1493 | 1 | 0 | 0.0000 | |
| jmaeng-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 98.6450 | 99.3179 | 97.9812 | 73.0406 | 728 | 5 | 728 | 15 | 10 | 66.6667 | |
| jmaeng-gatk | INDEL | * | lowcmp_SimpleRepeat_homopolymer_6to10 | homalt | 99.9204 | 99.9557 | 99.8850 | 56.3788 | 11291 | 5 | 11291 | 13 | 12 | 92.3077 | |
| jmaeng-gatk | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 99.6714 | 99.9177 | 99.4264 | 57.8940 | 6067 | 5 | 6067 | 35 | 34 | 97.1429 | |
| jmaeng-gatk | INDEL | * | lowcmp_SimpleRepeat_triTR_51to200 | het | 90.6475 | 90.0000 | 91.3043 | 86.0606 | 45 | 5 | 42 | 4 | 2 | 50.0000 | |
| jmaeng-gatk | INDEL | * | map_l100_m0_e0 | hetalt | 91.8033 | 84.8485 | 100.0000 | 91.6427 | 28 | 5 | 29 | 0 | 0 | ||
| jmaeng-gatk | INDEL | * | map_l125_m1_e0 | hetalt | 93.3333 | 87.5000 | 100.0000 | 93.2692 | 35 | 5 | 35 | 0 | 0 | ||
| jmaeng-gatk | INDEL | * | map_l125_m2_e0 | hetalt | 93.6709 | 88.0952 | 100.0000 | 93.7710 | 37 | 5 | 37 | 0 | 0 | ||
| jmaeng-gatk | INDEL | * | map_l250_m0_e0 | * | 87.9518 | 93.5897 | 82.9545 | 98.5586 | 73 | 5 | 73 | 15 | 2 | 13.3333 | |
| jmaeng-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 99.2070 | 98.8739 | 99.5423 | 76.1072 | 439 | 5 | 435 | 2 | 0 | 0.0000 | |
| jmaeng-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 95.8781 | 99.0512 | 92.9019 | 82.4220 | 522 | 5 | 445 | 34 | 34 | 100.0000 | |
| jmaeng-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 98.6339 | 99.5404 | 97.7437 | 66.8858 | 1083 | 5 | 1083 | 25 | 19 | 76.0000 | |
| jmaeng-gatk | INDEL | D16_PLUS | lowcmp_SimpleRepeat_homopolymer_gt10 | * | 96.1832 | 92.6471 | 100.0000 | 97.0071 | 63 | 5 | 63 | 0 | 0 | ||
| jmaeng-gatk | INDEL | D16_PLUS | lowcmp_SimpleRepeat_homopolymer_gt10 | het | 93.9759 | 88.6364 | 100.0000 | 97.0787 | 39 | 5 | 39 | 0 | 0 | ||
| jmaeng-gatk | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 99.4059 | 99.0138 | 99.8012 | 86.4347 | 502 | 5 | 502 | 1 | 1 | 100.0000 | |