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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
40351-40400 / 86044 show all | |||||||||||||||
| ltrigg-rtg2 | SNP | * | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 100.0000 | 100.0000 | 100.0000 | 70.5882 | 5 | 0 | 5 | 0 | 0 | ||
| ltrigg-rtg1 | INDEL | I16_PLUS | lowcmp_SimpleRepeat_triTR_11to50 | * | 86.5672 | 78.3784 | 96.6667 | 70.5882 | 29 | 8 | 29 | 1 | 1 | 100.0000 | |
| jli-custom | SNP | ti | map_l100_m1_e0 | hetalt | 98.3051 | 100.0000 | 96.6667 | 70.5882 | 29 | 0 | 29 | 1 | 1 | 100.0000 | |
| ltrigg-rtg1 | SNP | * | map_l150_m2_e0 | hetalt | 100.0000 | 100.0000 | 100.0000 | 70.5882 | 20 | 0 | 20 | 0 | 0 | ||
| ltrigg-rtg1 | SNP | tv | map_l150_m2_e0 | hetalt | 100.0000 | 100.0000 | 100.0000 | 70.5882 | 20 | 0 | 20 | 0 | 0 | ||
| ltrigg-rtg2 | SNP | tv | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 100.0000 | 100.0000 | 100.0000 | 70.5882 | 5 | 0 | 5 | 0 | 0 | ||
| raldana-dualsentieon | SNP | ti | map_l150_m2_e0 | hetalt | 100.0000 | 100.0000 | 100.0000 | 70.5882 | 15 | 0 | 15 | 0 | 0 | ||
| ckim-dragen | INDEL | I16_PLUS | * | * | 97.2529 | 96.3306 | 98.1932 | 70.5888 | 6143 | 234 | 6141 | 113 | 94 | 83.1858 | |
| hfeng-pmm3 | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 98.9496 | 98.2541 | 99.6549 | 70.5915 | 92800 | 1649 | 92707 | 321 | 262 | 81.6199 | |
| jli-custom | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 99.0815 | 99.5612 | 98.6064 | 70.5927 | 28586 | 126 | 28586 | 404 | 25 | 6.1881 | |
| jli-custom | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 99.0815 | 99.5612 | 98.6064 | 70.5927 | 28586 | 126 | 28586 | 404 | 25 | 6.1881 | |
| ckim-vqsr | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.2908 | 99.7807 | 98.8056 | 70.5939 | 910 | 2 | 910 | 11 | 8 | 72.7273 | |
| ckim-gatk | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.2908 | 99.7807 | 98.8056 | 70.5939 | 910 | 2 | 910 | 11 | 8 | 72.7273 | |
| jlack-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 95.6615 | 97.9986 | 93.4332 | 70.5962 | 5729 | 117 | 5677 | 399 | 342 | 85.7143 | |
| jlack-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 95.6615 | 97.9986 | 93.4332 | 70.5962 | 5729 | 117 | 5677 | 399 | 342 | 85.7143 | |
| ckim-dragen | INDEL | I1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 99.5100 | 99.3604 | 99.6600 | 70.5987 | 2641 | 17 | 2638 | 9 | 2 | 22.2222 | |
| gduggal-bwafb | SNP | ti | map_l100_m2_e0 | het | 98.8152 | 98.9975 | 98.6336 | 70.5993 | 30315 | 307 | 30317 | 420 | 95 | 22.6190 | |
| ltrigg-rtg1 | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 98.0299 | 98.4252 | 97.6378 | 70.6019 | 125 | 2 | 124 | 3 | 0 | 0.0000 | |
| jlack-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 94.6398 | 99.5152 | 90.2198 | 70.6072 | 821 | 4 | 821 | 89 | 86 | 96.6292 | |
| jlack-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 94.6398 | 99.5152 | 90.2198 | 70.6072 | 821 | 4 | 821 | 89 | 86 | 96.6292 | |
| egarrison-hhga | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 93.6516 | 91.0112 | 96.4497 | 70.6087 | 162 | 16 | 163 | 6 | 5 | 83.3333 | |
| gduggal-bwafb | SNP | tv | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 99.0458 | 99.0458 | 99.0458 | 70.6113 | 519 | 5 | 519 | 5 | 4 | 80.0000 | |
| jlack-gatk | SNP | * | lowcmp_SimpleRepeat_diTR_11to50 | het | 99.4314 | 99.5510 | 99.3121 | 70.6126 | 6208 | 28 | 6208 | 43 | 21 | 48.8372 | |
| ndellapenna-hhga | INDEL | I1_5 | HG002complexvar | hetalt | 96.3808 | 94.4380 | 98.4052 | 70.6127 | 1630 | 96 | 1666 | 27 | 26 | 96.2963 | |
| jli-custom | SNP | tv | map_l125_m2_e0 | het | 98.9924 | 98.7933 | 99.1922 | 70.6143 | 10316 | 126 | 10315 | 84 | 21 | 25.0000 | |
| astatham-gatk | SNP | ti | map_l150_m2_e0 | homalt | 99.3599 | 98.8445 | 99.8806 | 70.6148 | 7528 | 88 | 7528 | 9 | 8 | 88.8889 | |
| rpoplin-dv42 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 97.4850 | 97.5225 | 97.4474 | 70.6155 | 1299 | 33 | 1298 | 34 | 32 | 94.1176 | |
| egarrison-hhga | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 85.5570 | 79.7101 | 92.3295 | 70.6177 | 330 | 84 | 325 | 27 | 17 | 62.9630 | |
| qzeng-custom | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 64.0961 | 94.0104 | 48.6239 | 70.6199 | 361 | 23 | 371 | 392 | 15 | 3.8265 | |
| egarrison-hhga | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 94.0522 | 92.1444 | 96.0407 | 70.6215 | 868 | 74 | 849 | 35 | 23 | 65.7143 | |
| jli-custom | SNP | ti | map_l125_m2_e1 | het | 99.1383 | 98.8526 | 99.4256 | 70.6228 | 18868 | 219 | 18866 | 109 | 33 | 30.2752 | |
| astatham-gatk | INDEL | I1_5 | HG002complexvar | hetalt | 98.0296 | 96.3499 | 99.7688 | 70.6232 | 1663 | 63 | 1726 | 4 | 4 | 100.0000 | |
| gduggal-bwafb | SNP | ti | map_l100_m2_e1 | het | 98.8201 | 99.0084 | 98.6326 | 70.6269 | 30653 | 307 | 30655 | 425 | 95 | 22.3529 | |
| gduggal-bwaplat | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 67.9939 | 52.5579 | 96.2669 | 70.6277 | 2065 | 1864 | 2063 | 80 | 56 | 70.0000 | |
| eyeh-varpipe | SNP | tv | map_l100_m2_e1 | hetalt | 99.4012 | 100.0000 | 98.8095 | 70.6294 | 43 | 0 | 166 | 2 | 1 | 50.0000 | |
| ckim-gatk | SNP | tv | map_l100_m2_e0 | homalt | 82.4340 | 70.1324 | 99.9691 | 70.6315 | 6462 | 2752 | 6462 | 2 | 0 | 0.0000 | |
| hfeng-pmm3 | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 98.2518 | 96.9828 | 99.5546 | 70.6344 | 450 | 14 | 447 | 2 | 0 | 0.0000 | |
| gduggal-bwaplat | INDEL | * | HG002compoundhet | * | 80.3779 | 69.5961 | 95.1127 | 70.6361 | 20851 | 9109 | 20843 | 1071 | 677 | 63.2120 | |
| ltrigg-rtg1 | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 97.3400 | 95.3206 | 99.4468 | 70.6377 | 8861 | 435 | 8988 | 50 | 50 | 100.0000 | |
| astatham-gatk | SNP | ti | map_l150_m2_e1 | homalt | 99.3663 | 98.8561 | 99.8818 | 70.6476 | 7605 | 88 | 7605 | 9 | 8 | 88.8889 | |
| cchapple-custom | SNP | ti | map_l100_m0_e0 | * | 96.8619 | 96.6377 | 97.0872 | 70.6515 | 21039 | 732 | 21032 | 631 | 173 | 27.4168 | |
| cchapple-custom | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 99.1034 | 98.6295 | 99.5819 | 70.6519 | 63548 | 883 | 64304 | 270 | 244 | 90.3704 | |
| jli-custom | SNP | * | map_l125_m2_e1 | het | 99.0901 | 98.8360 | 99.3454 | 70.6523 | 29295 | 345 | 29292 | 193 | 54 | 27.9793 | |
| hfeng-pmm1 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 99.2411 | 99.0960 | 99.3867 | 70.6527 | 3727 | 34 | 3727 | 23 | 22 | 95.6522 | |
| hfeng-pmm1 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 99.2411 | 99.0960 | 99.3867 | 70.6527 | 3727 | 34 | 3727 | 23 | 22 | 95.6522 | |
| rpoplin-dv42 | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | * | 91.5452 | 84.4086 | 100.0000 | 70.6542 | 157 | 29 | 157 | 0 | 0 | ||
| eyeh-varpipe | SNP | tv | map_l100_m2_e0 | * | 97.4043 | 99.7763 | 95.1424 | 70.6557 | 24977 | 56 | 24816 | 1267 | 21 | 1.6575 | |
| hfeng-pmm1 | SNP | * | map_l125_m2_e0 | * | 99.4680 | 99.2509 | 99.6861 | 70.6559 | 46373 | 350 | 46367 | 146 | 41 | 28.0822 | |
| asubramanian-gatk | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 98.7939 | 98.7939 | 98.7939 | 70.6564 | 901 | 11 | 901 | 11 | 9 | 81.8182 | |
| ciseli-custom | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 49.7009 | 35.0282 | 85.5263 | 70.6564 | 62 | 115 | 65 | 11 | 10 | 90.9091 | |