PrecisionFDA
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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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
43851-43900 / 86044 show all | |||||||||||||||
| gduggal-snapplat | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 87.6106 | 86.8839 | 88.3495 | 88.3802 | 17011 | 2568 | 17070 | 2251 | 184 | 8.1741 | |
| gduggal-bwafb | INDEL | I16_PLUS | HG002compoundhet | * | 58.0785 | 43.2571 | 88.3503 | 33.1438 | 927 | 1216 | 1039 | 137 | 136 | 99.2701 | |
| gduggal-bwavard | INDEL | * | map_l125_m2_e1 | * | 91.5391 | 94.9663 | 88.3507 | 90.2029 | 2113 | 112 | 2116 | 279 | 77 | 27.5986 | |
| qzeng-custom | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 91.6770 | 95.2628 | 88.3513 | 55.6869 | 1468 | 73 | 6227 | 821 | 401 | 48.8429 | |
| anovak-vg | INDEL | * | HG002complexvar | het | 72.0208 | 60.7851 | 88.3522 | 57.0408 | 28090 | 18122 | 30129 | 3972 | 2361 | 59.4411 | |
| ghariani-varprowl | INDEL | * | map_l100_m2_e0 | * | 90.4686 | 92.6889 | 88.3523 | 92.4226 | 3423 | 270 | 3421 | 451 | 206 | 45.6763 | |
| ciseli-custom | SNP | tv | map_l150_m2_e0 | homalt | 85.5692 | 82.9537 | 88.3551 | 74.3676 | 3387 | 696 | 3384 | 446 | 347 | 77.8027 | |
| ckim-isaac | INDEL | I16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | * | 66.5163 | 53.3333 | 88.3562 | 71.0030 | 256 | 224 | 258 | 34 | 20 | 58.8235 | |
| qzeng-custom | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 82.9227 | 78.1124 | 88.3643 | 60.1791 | 3112 | 872 | 3182 | 419 | 327 | 78.0430 | |
| ckim-isaac | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 60.8000 | 46.3415 | 88.3721 | 66.6667 | 38 | 44 | 38 | 5 | 5 | 100.0000 | |
| ckim-gatk | INDEL | D1_5 | map_l125_m0_e0 | het | 93.3136 | 98.8406 | 88.3721 | 92.6760 | 341 | 4 | 342 | 45 | 1 | 2.2222 | |
| gduggal-bwavard | INDEL | * | map_l125_m2_e0 | * | 91.5832 | 95.0364 | 88.3721 | 90.1236 | 2087 | 109 | 2090 | 275 | 74 | 26.9091 | |
| gduggal-snapvard | SNP | * | map_l150_m1_e0 | * | 92.1558 | 96.2756 | 88.3741 | 81.2786 | 29469 | 1140 | 29091 | 3827 | 280 | 7.3164 | |
| jlack-gatk | SNP | ti | map_l250_m0_e0 | * | 92.5591 | 97.1533 | 88.3798 | 95.5349 | 1331 | 39 | 1331 | 175 | 20 | 11.4286 | |
| mlin-fermikit | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 86.2115 | 84.1466 | 88.3803 | 58.2216 | 13503 | 2544 | 13516 | 1777 | 1745 | 98.1992 | |
| jlack-gatk | SNP | tv | map_l125_m0_e0 | * | 93.0649 | 98.2657 | 88.3869 | 84.2156 | 6516 | 115 | 6515 | 856 | 54 | 6.3084 | |
| rpoplin-dv42 | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 92.7175 | 97.4908 | 88.3898 | 77.5276 | 1321 | 34 | 1279 | 168 | 162 | 96.4286 | |
| mlin-fermikit | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 87.1515 | 85.9467 | 88.3906 | 61.9558 | 56167 | 9184 | 55976 | 7352 | 7082 | 96.3275 | |
| mlin-fermikit | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 87.1515 | 85.9467 | 88.3906 | 61.9558 | 56167 | 9184 | 55976 | 7352 | 7082 | 96.3275 | |
| eyeh-varpipe | SNP | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 93.2516 | 98.6776 | 88.3913 | 75.0612 | 4701 | 63 | 4500 | 591 | 44 | 7.4450 | |
| qzeng-custom | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 92.5975 | 97.2222 | 88.3929 | 44.7887 | 210 | 6 | 693 | 91 | 41 | 45.0549 | |
| ckim-vqsr | INDEL | * | map_l250_m2_e1 | het | 91.0345 | 93.8389 | 88.3929 | 97.8943 | 198 | 13 | 198 | 26 | 1 | 3.8462 | |
| ghariani-varprowl | SNP | tv | map_l250_m1_e0 | het | 92.9690 | 98.0414 | 88.3956 | 91.8864 | 1752 | 35 | 1752 | 230 | 31 | 13.4783 | |
| ckim-dragen | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 93.8462 | 100.0000 | 88.4058 | 90.3631 | 61 | 0 | 61 | 8 | 8 | 100.0000 | |
| cchapple-custom | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 93.8462 | 100.0000 | 88.4058 | 88.5000 | 61 | 0 | 61 | 8 | 7 | 87.5000 | |
| dgrover-gatk | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 93.8462 | 100.0000 | 88.4058 | 91.4604 | 61 | 0 | 61 | 8 | 7 | 87.5000 | |
| ciseli-custom | SNP | tv | map_l150_m2_e1 | homalt | 85.5896 | 82.9463 | 88.4069 | 74.3629 | 3429 | 705 | 3424 | 449 | 348 | 77.5056 | |
| egarrison-hhga | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | * | 87.8352 | 87.2704 | 88.4074 | 67.9175 | 31934 | 4658 | 32274 | 4232 | 3738 | 88.3270 | |
| qzeng-custom | INDEL | I16_PLUS | lowcmp_SimpleRepeat_quadTR_11to50 | het | 86.1163 | 83.9286 | 88.4211 | 59.0164 | 141 | 27 | 420 | 55 | 20 | 36.3636 | |
| asubramanian-gatk | INDEL | D16_PLUS | map_l100_m2_e1 | * | 87.5000 | 86.5979 | 88.4211 | 95.7342 | 84 | 13 | 84 | 11 | 3 | 27.2727 | |
| jpowers-varprowl | INDEL | D1_5 | func_cds | het | 93.3333 | 98.8235 | 88.4211 | 41.7178 | 84 | 1 | 84 | 11 | 10 | 90.9091 | |
| asubramanian-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 91.9391 | 95.7447 | 88.4244 | 72.2445 | 585 | 26 | 550 | 72 | 67 | 93.0556 | |
| gduggal-snapplat | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 61.5928 | 47.2536 | 88.4257 | 46.3421 | 1798 | 2007 | 1803 | 236 | 207 | 87.7119 | |
| ghariani-varprowl | INDEL | I1_5 | map_l250_m2_e1 | * | 91.0638 | 93.8596 | 88.4298 | 97.3206 | 107 | 7 | 107 | 14 | 4 | 28.5714 | |
| ghariani-varprowl | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 88.0745 | 87.7173 | 88.4346 | 62.4232 | 757 | 106 | 757 | 99 | 93 | 93.9394 | |
| gduggal-snapvard | INDEL | I1_5 | * | * | 88.2138 | 87.9937 | 88.4349 | 55.6066 | 132574 | 18089 | 133297 | 17432 | 13523 | 77.5757 | |
| gduggal-snapfb | SNP | * | lowcmp_SimpleRepeat_triTR_11to50 | het | 93.6725 | 99.5667 | 88.4372 | 45.0706 | 4596 | 20 | 4612 | 603 | 12 | 1.9901 | |
| ghariani-varprowl | INDEL | I1_5 | map_siren | het | 93.1801 | 98.4533 | 88.4430 | 87.0613 | 1655 | 26 | 1653 | 216 | 106 | 49.0741 | |
| mlin-fermikit | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 84.9953 | 81.8023 | 88.4476 | 37.9806 | 16848 | 3748 | 16836 | 2199 | 2149 | 97.7262 | |
| raldana-dualsentieon | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 93.2373 | 98.5618 | 88.4586 | 59.3016 | 1165 | 17 | 1165 | 152 | 150 | 98.6842 | |
| ghariani-varprowl | INDEL | * | segdup | * | 89.4068 | 90.3756 | 88.4586 | 97.2748 | 2310 | 246 | 2307 | 301 | 223 | 74.0864 | |
| gduggal-bwavard | SNP | ti | HG002compoundhet | * | 84.8363 | 81.4967 | 88.4613 | 41.1291 | 14244 | 3234 | 14298 | 1865 | 1554 | 83.3244 | |
| gduggal-snapfb | INDEL | * | map_l250_m0_e0 | het | 87.6190 | 86.7925 | 88.4615 | 96.4817 | 46 | 7 | 46 | 6 | 1 | 16.6667 | |
| gduggal-snapplat | INDEL | D1_5 | segdup | hetalt | 60.6593 | 46.1538 | 88.4615 | 98.5126 | 24 | 28 | 23 | 3 | 0 | 0.0000 | |
| bgallagher-sentieon | INDEL | D1_5 | map_l250_m0_e0 | * | 93.8776 | 100.0000 | 88.4615 | 97.3537 | 46 | 0 | 46 | 6 | 0 | 0.0000 | |
| qzeng-custom | INDEL | D6_15 | map_l150_m1_e0 | * | 85.9418 | 83.5616 | 88.4615 | 94.3723 | 61 | 12 | 69 | 9 | 3 | 33.3333 | |
| mlin-fermikit | INDEL | I6_15 | map_l100_m1_e0 | het | 81.9153 | 76.2712 | 88.4615 | 80.2281 | 45 | 14 | 46 | 6 | 5 | 83.3333 | |
| ckim-dragen | INDEL | I1_5 | map_l250_m0_e0 | * | 92.0000 | 95.8333 | 88.4615 | 97.8862 | 23 | 1 | 23 | 3 | 1 | 33.3333 | |
| ckim-dragen | INDEL | I6_15 | HG002compoundhet | het | 92.5867 | 97.1154 | 88.4615 | 85.5556 | 202 | 6 | 161 | 21 | 20 | 95.2381 | |
| jmaeng-gatk | INDEL | I6_15 | map_l150_m2_e1 | * | 86.7925 | 85.1852 | 88.4615 | 96.5517 | 23 | 4 | 23 | 3 | 1 | 33.3333 | |