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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
59151-59200 / 86044 show all | |||||||||||||||
| dgrover-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 98.1224 | 97.5578 | 98.6935 | 48.6222 | 20093 | 503 | 20094 | 266 | 260 | 97.7444 | |
| gduggal-bwavard | SNP | ti | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 99.0866 | 98.7946 | 99.3804 | 48.6184 | 4016 | 49 | 4010 | 25 | 11 | 44.0000 | |
| cchapple-custom | INDEL | D6_15 | * | het | 98.5018 | 98.2488 | 98.7561 | 48.6146 | 11389 | 203 | 20403 | 257 | 215 | 83.6576 | |
| ckim-isaac | INDEL | * | * | homalt | 96.2069 | 93.1918 | 99.4236 | 48.6128 | 116650 | 8522 | 116601 | 676 | 381 | 56.3609 | |
| ckim-isaac | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 85.3420 | 79.4704 | 92.1504 | 48.6116 | 2551 | 659 | 2524 | 215 | 182 | 84.6512 | |
| gduggal-bwafb | INDEL | * | tech_badpromoters | * | 95.9637 | 93.4211 | 98.6486 | 48.6111 | 71 | 5 | 73 | 1 | 1 | 100.0000 | |
| jlack-gatk | SNP | ti | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.8960 | 99.8713 | 99.9208 | 48.6105 | 10089 | 13 | 10089 | 8 | 7 | 87.5000 | |
| ckim-vqsr | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 92.7350 | 99.3135 | 86.9739 | 48.6097 | 434 | 3 | 434 | 65 | 65 | 100.0000 | |
| jpowers-varprowl | SNP | ti | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 99.3721 | 99.2620 | 99.4824 | 48.6065 | 4035 | 30 | 4036 | 21 | 4 | 19.0476 | |
| jli-custom | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 97.5369 | 96.2764 | 98.8308 | 48.6037 | 2870 | 111 | 2874 | 34 | 25 | 73.5294 | |
| ckim-isaac | INDEL | I1_5 | * | homalt | 96.6849 | 93.9498 | 99.5841 | 48.5995 | 56772 | 3656 | 56743 | 237 | 135 | 56.9620 | |
| gduggal-snapfb | SNP | * | HG002compoundhet | * | 83.3987 | 98.0094 | 72.5790 | 48.5976 | 25308 | 514 | 25579 | 9664 | 581 | 6.0120 | |
| cchapple-custom | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_11to50 | het | 98.4844 | 97.4321 | 99.5596 | 48.5952 | 1328 | 35 | 4973 | 22 | 19 | 86.3636 | |
| ndellapenna-hhga | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 99.4691 | 99.4104 | 99.5279 | 48.5945 | 2529 | 15 | 2530 | 12 | 1 | 8.3333 | |
| hfeng-pmm1 | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | hetalt | 95.8621 | 92.0530 | 100.0000 | 48.5915 | 139 | 12 | 146 | 0 | 0 | ||
| hfeng-pmm2 | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | homalt | 99.8249 | 99.6503 | 100.0000 | 48.5869 | 855 | 3 | 855 | 0 | 0 | ||
| hfeng-pmm2 | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 99.7647 | 99.7647 | 99.7647 | 48.5783 | 848 | 2 | 848 | 2 | 2 | 100.0000 | |
| ckim-vqsr | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | homalt | 85.5072 | 98.6072 | 75.4797 | 48.5746 | 354 | 5 | 354 | 115 | 114 | 99.1304 | |
| ckim-vqsr | INDEL | D1_5 | tech_badpromoters | * | 97.2973 | 94.7368 | 100.0000 | 48.5714 | 18 | 1 | 18 | 0 | 0 | ||
| dgrover-gatk | INDEL | D1_5 | tech_badpromoters | * | 97.2973 | 94.7368 | 100.0000 | 48.5714 | 18 | 1 | 18 | 0 | 0 | ||
| ckim-gatk | INDEL | D1_5 | tech_badpromoters | * | 97.2973 | 94.7368 | 100.0000 | 48.5714 | 18 | 1 | 18 | 0 | 0 | ||
| gduggal-bwaplat | INDEL | I6_15 | func_cds | het | 85.7143 | 75.0000 | 100.0000 | 48.5714 | 18 | 6 | 18 | 0 | 0 | ||
| eyeh-varpipe | INDEL | I6_15 | * | hetalt | 42.6506 | 27.4354 | 95.7540 | 48.5714 | 2346 | 6205 | 2413 | 107 | 106 | 99.0654 | |
| gduggal-snapfb | INDEL | I1_5 | tech_badpromoters | het | 61.5385 | 100.0000 | 44.4444 | 48.5714 | 8 | 0 | 8 | 10 | 0 | 0.0000 | |
| hfeng-pmm2 | INDEL | D1_5 | tech_badpromoters | * | 97.2973 | 94.7368 | 100.0000 | 48.5714 | 18 | 1 | 18 | 0 | 0 | ||
| jli-custom | INDEL | D1_5 | tech_badpromoters | * | 97.2973 | 94.7368 | 100.0000 | 48.5714 | 18 | 1 | 18 | 0 | 0 | ||
| ltrigg-rtg1 | INDEL | * | lowcmp_SimpleRepeat_triTR_11to50 | hetalt | 98.9130 | 98.1582 | 99.6795 | 48.5714 | 906 | 17 | 933 | 3 | 3 | 100.0000 | |
| jmaeng-gatk | INDEL | D1_5 | tech_badpromoters | * | 97.2973 | 94.7368 | 100.0000 | 48.5714 | 18 | 1 | 18 | 0 | 0 | ||
| astatham-gatk | INDEL | D1_5 | tech_badpromoters | * | 97.2973 | 94.7368 | 100.0000 | 48.5714 | 18 | 1 | 18 | 0 | 0 | ||
| bgallagher-sentieon | INDEL | D1_5 | tech_badpromoters | * | 97.2973 | 94.7368 | 100.0000 | 48.5714 | 18 | 1 | 18 | 0 | 0 | ||
| asubramanian-gatk | INDEL | D1_5 | tech_badpromoters | * | 97.2973 | 94.7368 | 100.0000 | 48.5714 | 18 | 1 | 18 | 0 | 0 | ||
| ltrigg-rtg2 | SNP | ti | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 99.4714 | 99.5136 | 99.4293 | 48.5634 | 27823 | 136 | 27875 | 160 | 12 | 7.5000 | |
| raldana-dualsentieon | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 99.6302 | 99.4260 | 99.8353 | 48.5599 | 2425 | 14 | 2425 | 4 | 0 | 0.0000 | |
| ckim-isaac | INDEL | * | HG002complexvar | * | 91.9300 | 88.4153 | 95.7357 | 48.5598 | 68025 | 8913 | 67037 | 2986 | 1352 | 45.2780 | |
| ckim-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 92.6361 | 99.3135 | 86.8000 | 48.5597 | 434 | 3 | 434 | 66 | 66 | 100.0000 | |
| raldana-dualsentieon | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | * | 99.3872 | 99.0063 | 99.7710 | 48.5556 | 11757 | 118 | 11762 | 27 | 17 | 62.9630 | |
| hfeng-pmm2 | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | * | 99.3527 | 98.8800 | 99.8300 | 48.5551 | 11742 | 133 | 11747 | 20 | 11 | 55.0000 | |
| ckim-isaac | INDEL | I1_5 | HG002complexvar | * | 93.9569 | 91.3347 | 96.7341 | 48.5479 | 30472 | 2891 | 30419 | 1027 | 555 | 54.0409 | |
| asubramanian-gatk | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 99.1337 | 98.6144 | 99.6585 | 48.5413 | 2918 | 41 | 2918 | 10 | 2 | 20.0000 | |
| ckim-isaac | INDEL | * | * | het | 96.5214 | 95.9358 | 97.1142 | 48.5384 | 186243 | 7890 | 184953 | 5496 | 3918 | 71.2882 | |
| hfeng-pmm1 | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 97.2519 | 95.6239 | 98.9362 | 48.5377 | 14138 | 647 | 14136 | 152 | 147 | 96.7105 | |
| hfeng-pmm1 | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | * | 98.9744 | 98.1557 | 99.8069 | 48.5309 | 3619 | 68 | 3619 | 7 | 4 | 57.1429 | |
| jpowers-varprowl | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 34.5038 | 68.9034 | 23.0141 | 48.5298 | 421 | 190 | 423 | 1415 | 1414 | 99.9293 | |
| ckim-gatk | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | homalt | 85.4041 | 98.6072 | 75.3191 | 48.5214 | 354 | 5 | 354 | 116 | 115 | 99.1379 | |
| astatham-gatk | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | homalt | 85.5072 | 98.6072 | 75.4797 | 48.5181 | 354 | 5 | 354 | 115 | 114 | 99.1304 | |
| ltrigg-rtg1 | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 97.3600 | 95.2580 | 99.5569 | 48.5171 | 683 | 34 | 674 | 3 | 3 | 100.0000 | |
| rpoplin-dv42 | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 95.9540 | 95.2267 | 96.6924 | 48.5132 | 13127 | 658 | 13126 | 449 | 442 | 98.4410 | |
| hfeng-pmm3 | INDEL | I6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 91.7263 | 84.7170 | 100.0000 | 48.5116 | 449 | 81 | 467 | 0 | 0 | ||
| jpowers-varprowl | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | * | 57.8545 | 55.6351 | 60.2584 | 48.5091 | 20358 | 16234 | 20333 | 13410 | 13207 | 98.4862 | |
| cchapple-custom | INDEL | I6_15 | HG002complexvar | homalt | 98.1176 | 99.2586 | 97.0025 | 48.4991 | 1205 | 9 | 1165 | 36 | 35 | 97.2222 | |