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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
57351-57400 / 86044 show all | |||||||||||||||
| ltrigg-rtg1 | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | het | 98.7075 | 98.2437 | 99.1757 | 52.7025 | 2685 | 48 | 2647 | 22 | 8 | 36.3636 | |
| ltrigg-rtg2 | INDEL | D1_5 | HG002complexvar | homalt | 99.5212 | 99.0753 | 99.9711 | 52.6911 | 10500 | 98 | 10378 | 3 | 2 | 66.6667 | |
| hfeng-pmm2 | INDEL | I16_PLUS | HG002compoundhet | * | 94.8024 | 92.3472 | 97.3917 | 52.6892 | 1979 | 164 | 1979 | 53 | 52 | 98.1132 | |
| eyeh-varpipe | SNP | * | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 99.7522 | 99.8777 | 99.6270 | 52.6879 | 17156 | 21 | 16826 | 63 | 23 | 36.5079 | |
| anovak-vg | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 71.0827 | 79.4287 | 64.3238 | 52.6876 | 10927 | 2830 | 14341 | 7954 | 5860 | 73.6736 | |
| anovak-vg | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 71.0827 | 79.4287 | 64.3238 | 52.6876 | 10927 | 2830 | 14341 | 7954 | 5860 | 73.6736 | |
| ltrigg-rtg2 | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 91.7092 | 86.1153 | 98.0803 | 52.6837 | 1135 | 183 | 1124 | 22 | 22 | 100.0000 | |
| ndellapenna-hhga | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 85.0606 | 95.7652 | 76.5084 | 52.6827 | 13998 | 619 | 15343 | 4711 | 4543 | 96.4339 | |
| gduggal-bwafb | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 84.8799 | 77.9336 | 93.1858 | 52.6802 | 1056 | 299 | 2147 | 157 | 154 | 98.0892 | |
| cchapple-custom | INDEL | D6_15 | HG002complexvar | het | 97.1892 | 96.5064 | 97.8818 | 52.6751 | 3011 | 109 | 3974 | 86 | 77 | 89.5349 | |
| asubramanian-gatk | INDEL | * | HG002compoundhet | hetalt | 95.7396 | 92.5814 | 99.1208 | 52.6709 | 23312 | 1868 | 23449 | 208 | 188 | 90.3846 | |
| astatham-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 98.1969 | 98.0419 | 98.3525 | 52.6692 | 10865 | 217 | 10865 | 182 | 178 | 97.8022 | |
| astatham-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 97.3750 | 95.5710 | 99.2485 | 52.6679 | 6603 | 306 | 6603 | 50 | 45 | 90.0000 | |
| gduggal-snapvard | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 14.5215 | 7.8459 | 97.3510 | 52.6646 | 220 | 2584 | 147 | 4 | 4 | 100.0000 | |
| jlack-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 96.8636 | 96.4960 | 97.2340 | 52.6642 | 30871 | 1121 | 30794 | 876 | 794 | 90.6393 | |
| gduggal-bwavard | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | * | 60.8792 | 59.0648 | 62.8085 | 52.6630 | 21613 | 14979 | 21581 | 12779 | 12331 | 96.4942 | |
| egarrison-hhga | INDEL | I6_15 | * | het | 97.7387 | 97.1494 | 98.3352 | 52.6628 | 9747 | 286 | 9746 | 165 | 103 | 62.4242 | |
| hfeng-pmm1 | SNP | ti | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 99.4265 | 98.9020 | 99.9566 | 52.6521 | 27652 | 307 | 27651 | 12 | 3 | 25.0000 | |
| qzeng-custom | INDEL | D1_5 | HG002complexvar | homalt | 99.0114 | 98.8205 | 99.2030 | 52.6484 | 10473 | 125 | 10456 | 84 | 62 | 73.8095 | |
| egarrison-hhga | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 78.5618 | 72.3842 | 85.8922 | 52.6470 | 10702 | 4083 | 10825 | 1778 | 1586 | 89.2013 | |
| gduggal-bwafb | INDEL | I1_5 | * | homalt | 98.8253 | 98.7076 | 98.9433 | 52.6434 | 59647 | 781 | 59646 | 637 | 616 | 96.7033 | |
| rpoplin-dv42 | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 99.3679 | 99.4491 | 99.2868 | 52.6423 | 6679 | 37 | 6682 | 48 | 39 | 81.2500 | |
| ckim-dragen | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 96.8899 | 94.7026 | 99.1807 | 52.6407 | 6543 | 366 | 6537 | 54 | 52 | 96.2963 | |
| jmaeng-gatk | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 95.6672 | 92.3077 | 99.2806 | 52.6405 | 264 | 22 | 276 | 2 | 2 | 100.0000 | |
| dgrover-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | * | 97.5539 | 97.1103 | 98.0015 | 52.6392 | 1277 | 38 | 1275 | 26 | 18 | 69.2308 | |
| ndellapenna-hhga | SNP | * | map_siren | homalt | 99.8258 | 99.7135 | 99.9382 | 52.6378 | 54998 | 158 | 54999 | 34 | 30 | 88.2353 | |
| anovak-vg | INDEL | D16_PLUS | * | * | 64.9199 | 56.1321 | 76.9701 | 52.6377 | 3808 | 2976 | 3780 | 1131 | 815 | 72.0601 | |
| ltrigg-rtg2 | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 98.0306 | 96.7239 | 99.3730 | 52.6355 | 620 | 21 | 634 | 4 | 4 | 100.0000 | |
| ckim-vqsr | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 99.6469 | 99.8428 | 99.4518 | 52.6335 | 2540 | 4 | 2540 | 14 | 2 | 14.2857 | |
| qzeng-custom | INDEL | D16_PLUS | func_cds | homalt | 61.5385 | 100.0000 | 44.4444 | 52.6316 | 4 | 0 | 4 | 5 | 0 | 0.0000 | |
| jli-custom | INDEL | D6_15 | tech_badpromoters | het | 94.7368 | 90.0000 | 100.0000 | 52.6316 | 9 | 1 | 9 | 0 | 0 | ||
| jli-custom | INDEL | I16_PLUS | func_cds | het | 100.0000 | 100.0000 | 100.0000 | 52.6316 | 9 | 0 | 9 | 0 | 0 | ||
| gduggal-bwafb | INDEL | D6_15 | tech_badpromoters | het | 88.8889 | 80.0000 | 100.0000 | 52.6316 | 8 | 2 | 9 | 0 | 0 | ||
| mlin-fermikit | SNP | * | map_l100_m2_e1 | homalt | 74.4467 | 68.1285 | 82.0565 | 52.6294 | 18937 | 8859 | 18937 | 4141 | 3961 | 95.6532 | |
| ltrigg-rtg1 | SNP | * | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 99.8164 | 99.6914 | 99.9417 | 52.6220 | 17124 | 53 | 17138 | 10 | 7 | 70.0000 | |
| eyeh-varpipe | INDEL | D1_5 | HG002complexvar | * | 96.8177 | 96.1241 | 97.5214 | 52.6173 | 31447 | 1268 | 30808 | 783 | 734 | 93.7420 | |
| ckim-gatk | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 99.6078 | 99.8428 | 99.3740 | 52.6140 | 2540 | 4 | 2540 | 16 | 2 | 12.5000 | |
| gduggal-snapfb | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 87.5291 | 86.9258 | 88.1409 | 52.6080 | 19341 | 2909 | 20149 | 2711 | 1465 | 54.0391 | |
| hfeng-pmm1 | INDEL | I1_5 | * | homalt | 99.7725 | 99.7799 | 99.7651 | 52.5960 | 60295 | 133 | 60299 | 142 | 137 | 96.4789 | |
| raldana-dualsentieon | INDEL | I1_5 | HG002complexvar | homalt | 99.8477 | 99.8959 | 99.7995 | 52.5914 | 13434 | 14 | 13438 | 27 | 27 | 100.0000 | |
| hfeng-pmm2 | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 99.8225 | 99.7340 | 99.9112 | 52.5895 | 1125 | 3 | 1125 | 1 | 0 | 0.0000 | |
| qzeng-custom | INDEL | * | lowcmp_SimpleRepeat_homopolymer_6to10 | homalt | 99.2214 | 99.5485 | 98.8965 | 52.5869 | 11245 | 51 | 19268 | 215 | 45 | 20.9302 | |
| ckim-vqsr | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 99.2066 | 99.0169 | 99.3969 | 52.5864 | 1813 | 18 | 1813 | 11 | 2 | 18.1818 | |
| jli-custom | SNP | ti | map_siren | het | 99.5420 | 99.4806 | 99.6035 | 52.5864 | 62058 | 324 | 62054 | 247 | 50 | 20.2429 | |
| anovak-vg | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | * | 15.2866 | 9.6774 | 36.3636 | 52.5862 | 18 | 168 | 20 | 35 | 30 | 85.7143 | |
| gduggal-snapfb | SNP | ti | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 97.7559 | 98.8212 | 96.7133 | 52.5820 | 3940 | 47 | 3943 | 134 | 24 | 17.9104 | |
| ckim-dragen | INDEL | I16_PLUS | HG002compoundhet | * | 93.5490 | 91.3672 | 95.8374 | 52.5778 | 1958 | 185 | 1957 | 85 | 85 | 100.0000 | |
| asubramanian-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 94.8288 | 92.9433 | 96.7925 | 52.5751 | 3622 | 275 | 4617 | 153 | 140 | 91.5033 | |
| bgallagher-sentieon | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 97.8033 | 97.6268 | 97.9804 | 52.5687 | 10819 | 263 | 10819 | 223 | 219 | 98.2063 | |
| astatham-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | * | 97.7458 | 97.3384 | 98.1567 | 52.5683 | 1280 | 35 | 1278 | 24 | 17 | 70.8333 | |