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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
11501-11550 / 86044 show all | |||||||||||||||
| gduggal-bwafb | SNP | ti | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.1862 | 98.9111 | 99.4628 | 53.1375 | 9992 | 110 | 9998 | 54 | 37 | 68.5185 | |
| gduggal-bwafb | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 81.4625 | 93.8889 | 71.9409 | 88.0905 | 676 | 44 | 682 | 266 | 37 | 13.9098 | |
| gduggal-bwaplat | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 85.2150 | 75.8321 | 97.2477 | 53.3761 | 1481 | 472 | 1484 | 42 | 37 | 88.0952 | |
| ndellapenna-hhga | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 95.7480 | 95.8991 | 95.5975 | 81.7695 | 912 | 39 | 912 | 42 | 37 | 88.0952 | |
| ndellapenna-hhga | INDEL | * | segdup | * | 97.8664 | 97.7308 | 98.0024 | 98.7178 | 2498 | 58 | 2502 | 51 | 37 | 72.5490 | |
| ndellapenna-hhga | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 74.1810 | 59.3050 | 99.0185 | 33.0396 | 4847 | 3326 | 4439 | 44 | 37 | 84.0909 | |
| qzeng-custom | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 98.2222 | 98.4038 | 98.0413 | 45.0797 | 1048 | 17 | 2703 | 54 | 37 | 68.5185 | |
| ltrigg-rtg2 | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 97.6510 | 98.5407 | 96.7772 | 70.9827 | 28293 | 419 | 28618 | 953 | 37 | 3.8825 | |
| ltrigg-rtg2 | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 97.6510 | 98.5407 | 96.7772 | 70.9827 | 28293 | 419 | 28618 | 953 | 37 | 3.8825 | |
| qzeng-custom | SNP | ti | map_l150_m2_e0 | homalt | 79.9782 | 66.9643 | 99.2706 | 72.9194 | 5100 | 2516 | 5036 | 37 | 37 | 100.0000 | |
| mlin-fermikit | INDEL | * | map_l150_m0_e0 | homalt | 61.1296 | 56.0976 | 67.1533 | 85.8617 | 92 | 72 | 92 | 45 | 37 | 82.2222 | |
| mlin-fermikit | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | homalt | 86.8106 | 91.8782 | 82.2727 | 58.6466 | 181 | 16 | 181 | 39 | 37 | 94.8718 | |
| mlin-fermikit | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 97.9145 | 97.8347 | 97.9944 | 55.0665 | 4202 | 93 | 4202 | 86 | 37 | 43.0233 | |
| gduggal-snapfb | INDEL | I6_15 | lowcmp_SimpleRepeat_triTR_11to50 | het | 65.4311 | 59.8361 | 72.1805 | 46.5863 | 73 | 49 | 96 | 37 | 37 | 100.0000 | |
| gduggal-snapfb | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 33.9862 | 95.3401 | 20.6789 | 83.3507 | 757 | 37 | 792 | 3038 | 37 | 1.2179 | |
| gduggal-snapvard | INDEL | D6_15 | map_l125_m2_e0 | * | 71.5037 | 71.4286 | 71.5789 | 85.3395 | 90 | 36 | 136 | 54 | 37 | 68.5185 | |
| gduggal-snapvard | INDEL | D6_15 | map_l125_m2_e1 | * | 70.7555 | 70.3125 | 71.2042 | 85.5303 | 90 | 38 | 136 | 55 | 37 | 67.2727 | |
| gduggal-snapvard | INDEL | D6_15 | segdup | het | 71.7253 | 78.2609 | 66.1972 | 93.2445 | 72 | 20 | 94 | 48 | 37 | 77.0833 | |
| gduggal-snapvard | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 54.2716 | 87.3611 | 39.3624 | 86.5975 | 629 | 91 | 605 | 932 | 37 | 3.9700 | |
| gduggal-snapfb | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 83.8207 | 76.4233 | 92.8036 | 43.9496 | 1141 | 352 | 619 | 48 | 37 | 77.0833 | |
| ghariani-varprowl | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 67.2129 | 61.2360 | 74.4828 | 76.8000 | 109 | 69 | 108 | 37 | 37 | 100.0000 | |
| ghariani-varprowl | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 83.2117 | 93.4426 | 75.0000 | 70.8955 | 114 | 8 | 117 | 39 | 37 | 94.8718 | |
| ghariani-varprowl | INDEL | I6_15 | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 74.0111 | 93.5484 | 61.2245 | 84.4444 | 58 | 4 | 60 | 38 | 37 | 97.3684 | |
| ghariani-varprowl | INDEL | D6_15 | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 87.8646 | 98.7097 | 79.1667 | 84.0000 | 153 | 2 | 152 | 40 | 37 | 92.5000 | |
| raldana-dualsentieon | INDEL | D6_15 | HG002complexvar | * | 96.9018 | 94.6813 | 99.2289 | 57.2443 | 5020 | 282 | 5019 | 39 | 37 | 94.8718 | |
| raldana-dualsentieon | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.3948 | 99.8304 | 98.9630 | 72.1359 | 3531 | 6 | 3531 | 37 | 37 | 100.0000 | |
| rpoplin-dv42 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 96.7592 | 96.2430 | 97.2808 | 87.7639 | 2075 | 81 | 2075 | 58 | 37 | 63.7931 | |
| rpoplin-dv42 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 98.8158 | 98.6325 | 98.9998 | 83.5908 | 5049 | 70 | 5048 | 51 | 37 | 72.5490 | |
| rpoplin-dv42 | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 99.0139 | 98.4069 | 99.6285 | 44.6543 | 10192 | 165 | 10191 | 38 | 37 | 97.3684 | |
| rpoplin-dv42 | INDEL | * | map_siren | het | 98.2013 | 98.0257 | 98.3774 | 81.3714 | 4419 | 89 | 4426 | 73 | 37 | 50.6849 | |
| rpoplin-dv42 | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.6271 | 99.4292 | 99.8258 | 72.6049 | 21774 | 125 | 21771 | 38 | 37 | 97.3684 | |
| rpoplin-dv42 | SNP | * | map_l125_m1_e0 | homalt | 99.4988 | 99.2251 | 99.7740 | 66.6415 | 16774 | 131 | 16774 | 38 | 37 | 97.3684 | |
| rpoplin-dv42 | SNP | ti | map_l250_m2_e0 | * | 98.5577 | 98.2428 | 98.8746 | 88.2672 | 4920 | 88 | 4920 | 56 | 37 | 66.0714 | |
| rpoplin-dv42 | SNP | tv | HG002complexvar | homalt | 99.9385 | 99.9201 | 99.9569 | 22.8530 | 95035 | 76 | 95011 | 41 | 37 | 90.2439 | |
| egarrison-hhga | INDEL | I6_15 | HG002compoundhet | hetalt | 95.3278 | 91.5310 | 99.4533 | 27.1869 | 7814 | 723 | 7823 | 43 | 37 | 86.0465 | |
| 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 | |
| eyeh-varpipe | INDEL | * | map_l150_m1_e0 | * | 96.5735 | 96.1136 | 97.0378 | 95.4187 | 1286 | 52 | 1769 | 54 | 37 | 68.5185 | |
| egarrison-hhga | INDEL | * | lowcmp_SimpleRepeat_homopolymer_6to10 | homalt | 99.6460 | 99.6990 | 99.5931 | 55.9882 | 11262 | 34 | 11258 | 46 | 37 | 80.4348 | |
| ckim-vqsr | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 91.4428 | 98.3425 | 85.4478 | 84.5800 | 356 | 6 | 229 | 39 | 37 | 94.8718 | |
| ckim-vqsr | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_51to200 | het | 79.1209 | 100.0000 | 65.4545 | 84.4193 | 169 | 0 | 72 | 38 | 37 | 97.3684 | |
| ckim-vqsr | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 96.6665 | 93.9188 | 99.5798 | 30.8815 | 8726 | 565 | 8768 | 37 | 37 | 100.0000 | |
| ckim-vqsr | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 96.6665 | 93.9188 | 99.5798 | 30.8815 | 8726 | 565 | 8768 | 37 | 37 | 100.0000 | |
| ckim-vqsr | INDEL | D6_15 | HG002complexvar | hetalt | 93.7593 | 91.3129 | 96.3403 | 47.3985 | 925 | 88 | 974 | 37 | 37 | 100.0000 | |
| ckim-vqsr | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 96.6703 | 94.6112 | 98.8210 | 55.5926 | 3687 | 210 | 3688 | 44 | 37 | 84.0909 | |
| ckim-isaac | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 85.6169 | 76.2817 | 97.5556 | 48.0669 | 1473 | 458 | 1756 | 44 | 37 | 84.0909 | |
| ckim-isaac | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 85.6169 | 76.2817 | 97.5556 | 48.0669 | 1473 | 458 | 1756 | 44 | 37 | 84.0909 | |
| ckim-isaac | INDEL | I16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 71.1731 | 58.4575 | 90.9582 | 67.0080 | 667 | 474 | 674 | 67 | 37 | 55.2239 | |
| ckim-isaac | INDEL | I6_15 | HG002complexvar | homalt | 79.2387 | 69.4399 | 92.2574 | 47.0554 | 843 | 371 | 846 | 71 | 37 | 52.1127 | |
| dgrover-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 97.6358 | 95.7046 | 99.6464 | 30.5076 | 10628 | 477 | 10709 | 38 | 37 | 97.3684 | |