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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
67501-67550 / 86044 show all | |||||||||||||||
| jli-custom | INDEL | I1_5 | map_l100_m2_e1 | het | 99.1307 | 98.5185 | 99.7506 | 83.4469 | 798 | 12 | 800 | 2 | 0 | 0.0000 | |
| ckim-dragen | INDEL | D16_PLUS | HG002compoundhet | het | 93.6315 | 98.5185 | 89.2063 | 59.4595 | 399 | 6 | 281 | 34 | 31 | 91.1765 | |
| cchapple-custom | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 98.7173 | 98.5185 | 98.9170 | 61.7931 | 266 | 4 | 274 | 3 | 3 | 100.0000 | |
| gduggal-bwafb | INDEL | D1_5 | HG002complexvar | homalt | 98.4856 | 98.5186 | 98.4525 | 57.9745 | 10441 | 157 | 10434 | 164 | 151 | 92.0732 | |
| raldana-dualsentieon | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 99.0441 | 98.5197 | 99.5742 | 73.0561 | 32744 | 492 | 32737 | 140 | 116 | 82.8571 | |
| raldana-dualsentieon | SNP | tv | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 98.9932 | 98.5200 | 99.4710 | 64.4487 | 17308 | 260 | 17299 | 92 | 10 | 10.8696 | |
| ckim-dragen | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 98.8861 | 98.5202 | 99.2547 | 76.5663 | 6325 | 95 | 6259 | 47 | 29 | 61.7021 | |
| ckim-dragen | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 98.8861 | 98.5202 | 99.2547 | 76.5663 | 6325 | 95 | 6259 | 47 | 29 | 61.7021 | |
| ghariani-varprowl | SNP | tv | map_l100_m0_e0 | * | 97.0755 | 98.5204 | 95.6724 | 76.1776 | 10920 | 164 | 10921 | 494 | 87 | 17.6113 | |
| egarrison-hhga | SNP | tv | map_l125_m0_e0 | * | 99.1050 | 98.5221 | 99.6948 | 73.4104 | 6533 | 98 | 6533 | 20 | 9 | 45.0000 | |
| gduggal-snapfb | SNP | ti | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 66.7373 | 98.5222 | 50.4586 | 77.9321 | 3200 | 48 | 3246 | 3187 | 55 | 1.7258 | |
| ltrigg-rtg2 | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | het | 98.7792 | 98.5236 | 99.0362 | 55.6925 | 10944 | 164 | 10892 | 106 | 23 | 21.6981 | |
| ltrigg-rtg1 | INDEL | * | lowcmp_SimpleRepeat_triTR_11to50 | het | 99.1048 | 98.5238 | 99.6927 | 45.3838 | 3604 | 54 | 3568 | 11 | 2 | 18.1818 | |
| egarrison-hhga | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 98.8292 | 98.5239 | 99.1363 | 69.4693 | 19290 | 289 | 19284 | 168 | 37 | 22.0238 | |
| egarrison-hhga | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 98.8292 | 98.5239 | 99.1363 | 69.4693 | 19290 | 289 | 19284 | 168 | 37 | 22.0238 | |
| ciseli-custom | SNP | * | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 89.3094 | 98.5239 | 81.6710 | 71.7637 | 3404 | 51 | 3431 | 770 | 248 | 32.2078 | |
| jpowers-varprowl | INDEL | D1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 98.0893 | 98.5240 | 97.6583 | 55.6495 | 14552 | 218 | 14555 | 349 | 337 | 96.5616 | |
| eyeh-varpipe | SNP | * | lowcmp_SimpleRepeat_diTR_11to50 | het | 95.7234 | 98.5247 | 93.0769 | 67.4612 | 6144 | 92 | 5324 | 396 | 73 | 18.4343 | |
| hfeng-pmm1 | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 99.1653 | 98.5252 | 99.8138 | 69.6830 | 45028 | 674 | 45028 | 84 | 10 | 11.9048 | |
| hfeng-pmm1 | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 99.1653 | 98.5252 | 99.8138 | 69.6830 | 45028 | 674 | 45028 | 84 | 10 | 11.9048 | |
| 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 | |
| ckim-gatk | INDEL | * | map_l125_m0_e0 | * | 95.2938 | 98.5261 | 92.2669 | 92.7054 | 869 | 13 | 871 | 73 | 6 | 8.2192 | |
| astatham-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 99.1576 | 98.5265 | 99.7969 | 32.7413 | 1471 | 22 | 1474 | 3 | 3 | 100.0000 | |
| hfeng-pmm3 | INDEL | D1_5 | HG002complexvar | * | 99.2121 | 98.5267 | 99.9072 | 56.6840 | 32233 | 482 | 32285 | 30 | 19 | 63.3333 | |
| jli-custom | SNP | * | map_l150_m2_e1 | het | 98.8617 | 98.5267 | 99.1989 | 74.7124 | 20063 | 300 | 20060 | 162 | 49 | 30.2469 | |
| ndellapenna-hhga | INDEL | I1_5 | map_l100_m0_e0 | * | 98.6175 | 98.5267 | 98.7085 | 84.4298 | 535 | 8 | 535 | 7 | 2 | 28.5714 | |
| astatham-gatk | SNP | * | lowcmp_SimpleRepeat_triTR_11to50 | het | 99.2363 | 98.5269 | 99.9560 | 35.0014 | 4548 | 68 | 4544 | 2 | 1 | 50.0000 | |
| eyeh-varpipe | INDEL | D1_5 | map_l100_m2_e0 | homalt | 97.3783 | 98.5270 | 96.2560 | 85.4148 | 602 | 9 | 797 | 31 | 25 | 80.6452 | |
| jlack-gatk | INDEL | D1_5 | map_l100_m2_e0 | homalt | 99.1763 | 98.5270 | 99.8342 | 82.2959 | 602 | 9 | 602 | 1 | 1 | 100.0000 | |
| ghariani-varprowl | SNP | * | map_l125_m1_e0 | homalt | 99.0868 | 98.5271 | 99.6530 | 67.5166 | 16656 | 249 | 16656 | 58 | 39 | 67.2414 | |
| jlack-gatk | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | het | 97.7311 | 98.5279 | 96.9471 | 62.1515 | 15528 | 232 | 15370 | 484 | 412 | 85.1240 | |
| gduggal-bwafb | SNP | tv | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 99.1176 | 98.5286 | 99.7136 | 61.8611 | 1741 | 26 | 1741 | 5 | 5 | 100.0000 | |
| ckim-gatk | INDEL | * | map_l125_m1_e0 | * | 96.6080 | 98.5287 | 94.7608 | 90.7066 | 2076 | 31 | 2080 | 115 | 11 | 9.5652 | |
| hfeng-pmm3 | INDEL | * | map_l125_m1_e0 | * | 98.6235 | 98.5287 | 98.7186 | 85.1274 | 2076 | 31 | 2080 | 27 | 6 | 22.2222 | |
| ltrigg-rtg1 | SNP | tv | map_l125_m2_e1 | * | 99.1333 | 98.5291 | 99.7448 | 64.3814 | 16412 | 245 | 16417 | 42 | 9 | 21.4286 | |
| gduggal-snapfb | INDEL | I1_5 | map_l150_m2_e1 | homalt | 98.0428 | 98.5294 | 97.5610 | 92.5617 | 201 | 3 | 200 | 5 | 3 | 60.0000 | |
| gduggal-snapfb | SNP | ti | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 92.4085 | 98.5294 | 87.0036 | 79.8311 | 1206 | 18 | 1205 | 180 | 12 | 6.6667 | |
| jlack-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 98.3938 | 98.5294 | 98.2585 | 65.1438 | 1072 | 16 | 1072 | 19 | 14 | 73.6842 | |
| jli-custom | INDEL | D1_5 | map_l125_m1_e0 | * | 98.5753 | 98.5294 | 98.6213 | 85.3547 | 1072 | 16 | 1073 | 15 | 5 | 33.3333 | |
| ckim-dragen | INDEL | I1_5 | map_l150_m2_e1 | homalt | 98.2837 | 98.5294 | 98.0392 | 87.7182 | 201 | 3 | 200 | 4 | 3 | 75.0000 | |
| ndellapenna-hhga | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 98.8172 | 98.5296 | 99.1064 | 71.0184 | 45030 | 672 | 45029 | 406 | 140 | 34.4828 | |
| ndellapenna-hhga | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 98.8172 | 98.5296 | 99.1064 | 71.0184 | 45030 | 672 | 45029 | 406 | 140 | 34.4828 | |
| gduggal-bwafb | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 93.9516 | 98.5298 | 89.7799 | 55.6361 | 8243 | 123 | 8240 | 938 | 934 | 99.5736 | |
| egarrison-hhga | SNP | * | map_l150_m2_e0 | het | 99.1156 | 98.5298 | 99.7085 | 75.6800 | 19837 | 296 | 19837 | 58 | 22 | 37.9310 | |
| cchapple-custom | INDEL | * | HG002complexvar | het | 98.8709 | 98.5307 | 99.2135 | 57.1695 | 45533 | 679 | 52101 | 413 | 306 | 74.0920 | |
| ckim-gatk | INDEL | * | map_l100_m0_e0 | het | 94.5578 | 98.5309 | 90.8927 | 91.4725 | 1006 | 15 | 1008 | 101 | 5 | 4.9505 | |
| astatham-gatk | SNP | tv | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 99.2005 | 98.5314 | 99.8788 | 66.3539 | 17310 | 258 | 17301 | 21 | 11 | 52.3810 | |
| ndellapenna-hhga | SNP | tv | map_l125_m1_e0 | * | 99.1238 | 98.5327 | 99.7220 | 67.2834 | 15781 | 235 | 15781 | 44 | 22 | 50.0000 | |
| jli-custom | SNP | ti | map_l150_m2_e0 | het | 98.9128 | 98.5327 | 99.2958 | 74.7496 | 12692 | 189 | 12690 | 90 | 30 | 33.3333 | |
| ckim-dragen | INDEL | * | map_l100_m1_e0 | homalt | 98.5318 | 98.5330 | 98.5306 | 83.5835 | 1209 | 18 | 1207 | 18 | 10 | 55.5556 | |