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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
58901-58950 / 86044 show all | |||||||||||||||
| gduggal-bwavard | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 83.2462 | 89.4980 | 77.8108 | 88.9364 | 1355 | 159 | 1308 | 373 | 121 | 32.4397 | |
| ghariani-varprowl | INDEL | * | map_l125_m1_e0 | het | 91.1754 | 97.9026 | 85.3133 | 91.4837 | 1307 | 28 | 1307 | 225 | 73 | 32.4444 | |
| gduggal-snapplat | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_51to200 | het | 29.1667 | 53.8462 | 20.0000 | 79.3388 | 7 | 6 | 10 | 40 | 13 | 32.5000 | |
| ckim-isaac | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 96.6757 | 94.4354 | 99.0249 | 47.4574 | 4056 | 239 | 4062 | 40 | 13 | 32.5000 | |
| cchapple-custom | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 99.1305 | 99.0001 | 99.2612 | 79.9407 | 10693 | 108 | 10748 | 80 | 26 | 32.5000 | |
| gduggal-bwavard | SNP | tv | lowcmp_SimpleRepeat_triTR_11to50 | het | 97.5197 | 96.9598 | 98.0861 | 47.0350 | 2073 | 65 | 2050 | 40 | 13 | 32.5000 | |
| hfeng-pmm2 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 97.1661 | 96.2430 | 98.1070 | 74.8751 | 2075 | 81 | 2073 | 40 | 13 | 32.5000 | |
| egarrison-hhga | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 94.9937 | 96.5215 | 93.5135 | 55.4063 | 3635 | 131 | 3633 | 252 | 82 | 32.5397 | |
| egarrison-hhga | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 94.9937 | 96.5215 | 93.5135 | 55.4063 | 3635 | 131 | 3633 | 252 | 82 | 32.5397 | |
| anovak-vg | INDEL | * | map_l125_m0_e0 | het | 70.2289 | 68.8245 | 71.6918 | 91.8286 | 404 | 183 | 428 | 169 | 55 | 32.5444 | |
| ciseli-custom | INDEL | D1_5 | map_l250_m2_e1 | * | 66.7396 | 61.6216 | 72.7848 | 97.3275 | 114 | 71 | 115 | 43 | 14 | 32.5581 | |
| jpowers-varprowl | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 84.1610 | 92.6630 | 77.0880 | 87.8937 | 1023 | 81 | 1043 | 310 | 101 | 32.5806 | |
| egarrison-hhga | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 98.2341 | 97.7771 | 98.6954 | 80.9079 | 6730 | 153 | 6733 | 89 | 29 | 32.5843 | |
| jlack-gatk | SNP | ti | HG002complexvar | het | 99.8980 | 99.8818 | 99.9142 | 17.5660 | 314394 | 372 | 314340 | 270 | 88 | 32.5926 | |
| egarrison-hhga | SNP | tv | segdup | * | 99.5315 | 99.6015 | 99.4616 | 90.4428 | 8498 | 34 | 8498 | 46 | 15 | 32.6087 | |
| ckim-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 99.3536 | 99.3753 | 99.3320 | 81.7241 | 6840 | 43 | 6840 | 46 | 15 | 32.6087 | |
| ghariani-varprowl | INDEL | * | map_l125_m2_e1 | het | 91.2339 | 97.9403 | 85.3870 | 92.0826 | 1379 | 29 | 1379 | 236 | 77 | 32.6271 | |
| gduggal-snapfb | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 92.5170 | 90.9118 | 94.1799 | 42.0147 | 6072 | 607 | 10761 | 665 | 217 | 32.6316 | |
| gduggal-snapfb | SNP | tv | map_l100_m2_e1 | het | 97.1282 | 98.4628 | 95.8293 | 70.7561 | 15693 | 245 | 15693 | 683 | 223 | 32.6501 | |
| gduggal-bwaplat | SNP | * | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 93.5407 | 88.2533 | 99.5021 | 62.9815 | 9782 | 1302 | 9792 | 49 | 16 | 32.6531 | |
| gduggal-bwaplat | SNP | * | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 93.5398 | 88.1295 | 99.6579 | 61.6024 | 15138 | 2039 | 15150 | 52 | 17 | 32.6923 | |
| ndellapenna-hhga | SNP | tv | map_l100_m2_e0 | het | 99.0369 | 98.4154 | 99.6662 | 64.6823 | 15527 | 250 | 15527 | 52 | 17 | 32.6923 | |
| qzeng-custom | INDEL | * | map_l125_m2_e0 | het | 82.3208 | 74.2631 | 92.3398 | 93.0978 | 1033 | 358 | 1326 | 110 | 36 | 32.7273 | |
| ckim-vqsr | SNP | ti | HG002complexvar | het | 99.1493 | 98.3302 | 99.9822 | 17.7224 | 309510 | 5256 | 309462 | 55 | 18 | 32.7273 | |
| gduggal-snapfb | SNP | tv | map_l100_m2_e0 | het | 97.1053 | 98.4471 | 95.7997 | 70.6844 | 15532 | 245 | 15532 | 681 | 223 | 32.7460 | |
| ltrigg-rtg2 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 98.5354 | 97.7762 | 99.3066 | 59.4807 | 8222 | 187 | 8306 | 58 | 19 | 32.7586 | |
| ckim-dragen | INDEL | D16_PLUS | * | het | 97.5880 | 99.0820 | 96.1385 | 80.1270 | 3130 | 29 | 2888 | 116 | 38 | 32.7586 | |
| asubramanian-gatk | INDEL | * | lowcmp_SimpleRepeat_quadTR_51to200 | het | 94.5134 | 94.8347 | 94.1942 | 82.6140 | 918 | 50 | 941 | 58 | 19 | 32.7586 | |
| gduggal-snapfb | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 82.6900 | 88.2003 | 77.8277 | 75.2503 | 1039 | 139 | 1039 | 296 | 97 | 32.7703 | |
| jli-custom | SNP | * | map_l125_m0_e0 | het | 98.5516 | 98.0575 | 99.0508 | 71.6081 | 12418 | 246 | 12418 | 119 | 39 | 32.7731 | |
| gduggal-snapvard | INDEL | D1_5 | map_l125_m2_e1 | * | 88.0989 | 95.5920 | 81.6951 | 88.4146 | 1106 | 51 | 1388 | 311 | 102 | 32.7974 | |
| ghariani-varprowl | INDEL | * | map_l125_m2_e1 | * | 91.8033 | 94.3820 | 89.3617 | 94.1271 | 2100 | 125 | 2100 | 250 | 82 | 32.8000 | |
| jpowers-varprowl | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 97.8391 | 98.7777 | 96.9182 | 66.3842 | 54951 | 680 | 55130 | 1753 | 575 | 32.8009 | |
| egarrison-hhga | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 99.0424 | 98.7834 | 99.3028 | 71.2490 | 45146 | 556 | 45149 | 317 | 104 | 32.8076 | |
| egarrison-hhga | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 99.0424 | 98.7834 | 99.3028 | 71.2490 | 45146 | 556 | 45149 | 317 | 104 | 32.8076 | |
| anovak-vg | INDEL | I1_5 | segdup | het | 40.6839 | 28.2528 | 72.6496 | 97.2794 | 152 | 386 | 170 | 64 | 21 | 32.8125 | |
| hfeng-pmm2 | SNP | tv | HG002complexvar | * | 99.8387 | 99.7038 | 99.9739 | 21.6976 | 245423 | 729 | 245339 | 64 | 21 | 32.8125 | |
| ltrigg-rtg1 | SNP | * | map_l150_m2_e0 | * | 98.9313 | 98.0912 | 99.7860 | 68.8564 | 31244 | 608 | 31247 | 67 | 22 | 32.8358 | |
| gduggal-bwaplat | SNP | ti | map_l150_m2_e0 | het | 75.1762 | 60.5388 | 99.1490 | 91.7226 | 7798 | 5083 | 7806 | 67 | 22 | 32.8358 | |
| gduggal-bwaplat | SNP | ti | map_l150_m2_e1 | het | 75.2791 | 60.6685 | 99.1595 | 91.7406 | 7896 | 5119 | 7904 | 67 | 22 | 32.8358 | |
| ciseli-custom | INDEL | C1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 0.0000 | 0.0000 | 25.1366 | 95.2847 | 0 | 0 | 46 | 137 | 45 | 32.8467 | |
| ckim-dragen | SNP | ti | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 99.7964 | 99.8426 | 99.7503 | 54.7629 | 27915 | 44 | 27963 | 70 | 23 | 32.8571 | |
| asubramanian-gatk | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 98.9717 | 99.0613 | 98.8823 | 57.7880 | 6015 | 57 | 6193 | 70 | 23 | 32.8571 | |
| jpowers-varprowl | SNP | * | lowcmp_SimpleRepeat_diTR_11to50 | * | 95.1147 | 97.5960 | 92.7564 | 74.4795 | 9459 | 233 | 9540 | 745 | 245 | 32.8859 | |
| ghariani-varprowl | INDEL | * | map_siren | homalt | 94.2088 | 91.6008 | 96.9697 | 74.6820 | 2432 | 223 | 2432 | 76 | 25 | 32.8947 | |
| ciseli-custom | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | het | 79.6648 | 84.2067 | 75.5878 | 57.5613 | 9352 | 1754 | 9484 | 3063 | 1008 | 32.9089 | |
| anovak-vg | SNP | tv | * | het | 97.9352 | 98.2070 | 97.6649 | 27.4537 | 581095 | 10609 | 580225 | 13873 | 4566 | 32.9129 | |
| gduggal-bwaplat | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 83.9877 | 74.1728 | 96.7962 | 69.7744 | 4954 | 1725 | 4955 | 164 | 54 | 32.9268 | |
| ltrigg-rtg1 | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 98.8475 | 97.9811 | 99.7293 | 70.4300 | 32565 | 671 | 32421 | 88 | 29 | 32.9545 | |
| bgallagher-sentieon | SNP | ti | HG002complexvar | het | 99.9477 | 99.9234 | 99.9720 | 16.9632 | 314525 | 241 | 314471 | 88 | 29 | 32.9545 | |