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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
74301-74350 / 86044 show all | |||||||||||||||
| hfeng-pmm2 | INDEL | I16_PLUS | * | * | 97.5355 | 96.5031 | 98.5902 | 69.5601 | 6154 | 223 | 6154 | 88 | 61 | 69.3182 | |
| ndellapenna-hhga | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_11to50 | * | 93.4664 | 90.7546 | 96.3452 | 62.2067 | 2189 | 223 | 2188 | 83 | 56 | 67.4699 | |
| qzeng-custom | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | * | 96.0217 | 94.2549 | 97.8560 | 49.0716 | 3675 | 224 | 8535 | 187 | 123 | 65.7754 | |
| ndellapenna-hhga | INDEL | * | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 99.4308 | 99.2074 | 99.6552 | 61.9169 | 28036 | 224 | 28038 | 97 | 74 | 76.2887 | |
| ndellapenna-hhga | INDEL | D6_15 | HG002complexvar | het | 92.6198 | 92.8205 | 92.4200 | 56.3998 | 2896 | 224 | 2975 | 244 | 197 | 80.7377 | |
| ltrigg-rtg2 | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 95.2032 | 91.8723 | 98.7848 | 43.0326 | 2532 | 224 | 2520 | 31 | 30 | 96.7742 | |
| jpowers-varprowl | INDEL | I1_5 | HG002compoundhet | het | 20.5402 | 73.6471 | 11.9344 | 70.4320 | 626 | 224 | 691 | 5099 | 5074 | 99.5097 | |
| jpowers-varprowl | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 64.0490 | 51.5152 | 84.6429 | 72.1393 | 238 | 224 | 237 | 43 | 41 | 95.3488 | |
| jli-custom | SNP | ti | map_l150_m1_e0 | * | 99.2008 | 98.8636 | 99.5403 | 71.1664 | 19488 | 224 | 19486 | 90 | 35 | 38.8889 | |
| jli-custom | INDEL | I16_PLUS | * | het | 95.1311 | 91.7586 | 98.7610 | 68.1314 | 2494 | 224 | 2471 | 31 | 8 | 25.8065 | |
| ciseli-custom | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 93.5617 | 98.6804 | 88.9479 | 75.7364 | 16751 | 224 | 16756 | 2082 | 698 | 33.5255 | |
| ciseli-custom | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 93.5617 | 98.6804 | 88.9479 | 75.7364 | 16751 | 224 | 16756 | 2082 | 698 | 33.5255 | |
| ciseli-custom | INDEL | D1_5 | map_l150_m1_e0 | * | 74.0933 | 68.7587 | 80.3252 | 92.6268 | 493 | 224 | 494 | 121 | 55 | 45.4545 | |
| ciseli-custom | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 81.0114 | 86.8467 | 75.9109 | 68.6846 | 1479 | 224 | 1500 | 476 | 205 | 43.0672 | |
| ckim-dragen | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_51to200 | hetalt | 85.2090 | 74.3119 | 99.8512 | 25.9912 | 648 | 224 | 671 | 1 | 1 | 100.0000 | |
| ckim-dragen | SNP | ti | map_l150_m1_e0 | * | 98.2015 | 98.8636 | 97.5482 | 76.3868 | 19488 | 224 | 19495 | 490 | 66 | 13.4694 | |
| ckim-gatk | INDEL | D1_5 | HG002complexvar | * | 99.5163 | 99.3153 | 99.7181 | 58.5688 | 32491 | 224 | 32545 | 92 | 72 | 78.2609 | |
| gduggal-bwaplat | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 86.6815 | 77.7114 | 97.9925 | 71.6067 | 781 | 224 | 781 | 16 | 10 | 62.5000 | |
| gduggal-bwavard | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 88.2006 | 78.9671 | 99.8794 | 42.7486 | 841 | 224 | 828 | 1 | 1 | 100.0000 | |
| gduggal-bwaplat | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | hetalt | 78.6704 | 65.5385 | 98.3834 | 40.9277 | 426 | 224 | 426 | 7 | 7 | 100.0000 | |
| rpoplin-dv42 | SNP | ti | map_l150_m2_e1 | * | 99.1367 | 98.9191 | 99.3552 | 75.1649 | 20499 | 224 | 20495 | 133 | 93 | 69.9248 | |
| rpoplin-dv42 | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 94.3322 | 93.7096 | 94.9630 | 67.1681 | 3337 | 224 | 3337 | 177 | 170 | 96.0452 | |
| hfeng-pmm2 | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 94.8673 | 90.5405 | 99.6283 | 86.5685 | 2144 | 224 | 2144 | 8 | 3 | 37.5000 | |
| hfeng-pmm1 | INDEL | D6_15 | HG002complexvar | het | 95.9519 | 92.8205 | 99.3019 | 57.0271 | 2896 | 224 | 2845 | 20 | 17 | 85.0000 | |
| hfeng-pmm1 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 97.1407 | 94.4403 | 100.0000 | 26.2560 | 3805 | 224 | 3831 | 0 | 0 | ||
| hfeng-pmm3 | INDEL | I16_PLUS | * | * | 97.6899 | 96.4874 | 98.9228 | 68.1825 | 6153 | 224 | 6153 | 67 | 53 | 79.1045 | |
| ckim-isaac | INDEL | I16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | * | 66.5163 | 53.3333 | 88.3562 | 71.0030 | 256 | 224 | 258 | 34 | 20 | 58.8235 | |
| gduggal-snapfb | SNP | * | map_l250_m2_e0 | het | 94.2359 | 95.6873 | 92.8278 | 87.5230 | 4970 | 224 | 4970 | 384 | 172 | 44.7917 | |
| gduggal-snapfb | SNP | * | map_l250_m2_e1 | het | 94.2221 | 95.7257 | 92.7651 | 87.6052 | 5039 | 225 | 5039 | 393 | 175 | 44.5293 | |
| gduggal-snapplat | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 69.2765 | 58.7912 | 84.3137 | 82.8571 | 321 | 225 | 430 | 80 | 10 | 12.5000 | |
| gduggal-snapplat | INDEL | D1_5 | map_l125_m2_e1 | * | 85.6170 | 80.5532 | 91.3601 | 93.0292 | 932 | 225 | 1068 | 101 | 21 | 20.7921 | |
| ghariani-varprowl | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | hetalt | 0.0000 | 3.4335 | 0.0000 | 0.0000 | 8 | 225 | 0 | 0 | 0 | ||
| ghariani-varprowl | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 83.8511 | 96.7311 | 73.9980 | 86.2278 | 6658 | 225 | 6739 | 2368 | 15 | 0.6334 | |
| gduggal-snapplat | SNP | ti | segdup | * | 99.0792 | 98.8483 | 99.3111 | 92.8755 | 19312 | 225 | 19317 | 134 | 17 | 12.6866 | |
| gduggal-bwafb | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 91.3518 | 88.3601 | 94.5531 | 56.1456 | 1708 | 225 | 1788 | 103 | 103 | 100.0000 | |
| gduggal-bwafb | INDEL | * | map_l100_m2_e1 | * | 96.0874 | 94.0096 | 98.2592 | 84.3618 | 3531 | 225 | 3556 | 63 | 22 | 34.9206 | |
| jmaeng-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 97.3148 | 95.2850 | 99.4329 | 24.6012 | 4547 | 225 | 4559 | 26 | 26 | 100.0000 | |
| astatham-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 97.7240 | 96.4410 | 99.0416 | 63.3898 | 6097 | 225 | 6097 | 59 | 50 | 84.7458 | |
| astatham-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 97.7240 | 96.4410 | 99.0416 | 63.3898 | 6097 | 225 | 6097 | 59 | 50 | 84.7458 | |
| qzeng-custom | INDEL | I1_5 | map_l100_m2_e1 | het | 81.0781 | 72.2222 | 92.4092 | 89.7647 | 585 | 225 | 840 | 69 | 13 | 18.8406 | |
| qzeng-custom | SNP | * | segdup | het | 98.3153 | 98.7007 | 97.9329 | 93.6755 | 17092 | 225 | 16961 | 358 | 11 | 3.0726 | |
| ndellapenna-hhga | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 98.7167 | 98.4558 | 98.9789 | 74.5335 | 14346 | 225 | 14346 | 148 | 46 | 31.0811 | |
| ndellapenna-hhga | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 98.7167 | 98.4558 | 98.9789 | 74.5335 | 14346 | 225 | 14346 | 148 | 46 | 31.0811 | |
| ckim-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 93.1008 | 91.8360 | 94.4009 | 50.5628 | 2531 | 225 | 2529 | 150 | 146 | 97.3333 | |
| cchapple-custom | SNP | * | map_l250_m2_e1 | het | 95.2117 | 95.7257 | 94.7032 | 91.6862 | 5039 | 225 | 5042 | 282 | 65 | 23.0496 | |
| ciseli-custom | INDEL | * | map_l150_m2_e1 | homalt | 63.5484 | 54.2683 | 76.6571 | 91.7065 | 267 | 225 | 266 | 81 | 59 | 72.8395 | |
| ckim-isaac | INDEL | * | HG002compoundhet | homalt | 60.3591 | 67.2012 | 54.7816 | 76.0328 | 461 | 225 | 464 | 383 | 372 | 97.1279 | |
| ckim-dragen | SNP | ti | map_l100_m1_e0 | het | 98.1230 | 99.2485 | 97.0227 | 71.3768 | 29717 | 225 | 29720 | 912 | 87 | 9.5395 | |
| egarrison-hhga | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_11to50 | * | 84.0543 | 76.5381 | 93.2075 | 68.0466 | 734 | 225 | 741 | 54 | 46 | 85.1852 | |
| hfeng-pmm3 | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 96.9533 | 94.0867 | 100.0000 | 30.1357 | 3580 | 225 | 3605 | 0 | 0 | ||