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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
77101-77150 / 86044 show all | |||||||||||||||
| jlack-gatk | INDEL | I16_PLUS | HG002compoundhet | * | 89.6882 | 87.2608 | 92.2546 | 52.5070 | 1870 | 273 | 1870 | 157 | 144 | 91.7197 | |
| jli-custom | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.6951 | 99.8992 | 99.4918 | 73.2959 | 30730 | 31 | 30737 | 157 | 151 | 96.1783 | |
| hfeng-pmm2 | SNP | tv | map_l100_m2_e0 | * | 99.4872 | 99.6005 | 99.3742 | 68.8945 | 24933 | 100 | 24929 | 157 | 17 | 10.8280 | |
| jmaeng-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 98.9740 | 99.8086 | 98.1532 | 63.5791 | 8344 | 16 | 8344 | 157 | 156 | 99.3631 | |
| jmaeng-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 98.9740 | 99.8086 | 98.1532 | 63.5791 | 8344 | 16 | 8344 | 157 | 156 | 99.3631 | |
| jli-custom | SNP | ti | map_l100_m1_e0 | * | 99.4974 | 99.3240 | 99.6713 | 60.4603 | 47607 | 324 | 47605 | 157 | 50 | 31.8471 | |
| jli-custom | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 98.4961 | 97.7763 | 99.2266 | 43.2593 | 20138 | 458 | 20142 | 157 | 149 | 94.9045 | |
| ckim-isaac | INDEL | * | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 98.6542 | 98.2774 | 99.0338 | 56.4448 | 16146 | 283 | 16093 | 157 | 70 | 44.5860 | |
| gduggal-bwavard | INDEL | * | lowcmp_SimpleRepeat_triTR_51to200 | het | 29.7953 | 74.0000 | 18.6528 | 60.2062 | 37 | 13 | 36 | 157 | 149 | 94.9045 | |
| eyeh-varpipe | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 94.2388 | 99.8503 | 89.2244 | 68.0061 | 1334 | 2 | 1300 | 157 | 4 | 2.5478 | |
| gduggal-bwafb | INDEL | * | HG002compoundhet | hetalt | 88.3144 | 80.5679 | 97.7090 | 73.4740 | 20287 | 4893 | 6696 | 157 | 155 | 98.7261 | |
| 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 | |
| gduggal-bwaplat | INDEL | I1_5 | * | hetalt | 82.6726 | 71.4515 | 98.0748 | 76.8337 | 7999 | 3196 | 7998 | 157 | 152 | 96.8153 | |
| mlin-fermikit | INDEL | D1_5 | map_l100_m2_e0 | * | 77.4662 | 68.4073 | 89.2906 | 77.7912 | 1310 | 605 | 1309 | 157 | 136 | 86.6242 | |
| ndellapenna-hhga | SNP | tv | * | homalt | 99.9152 | 99.8722 | 99.9583 | 20.9089 | 376641 | 482 | 376648 | 157 | 123 | 78.3439 | |
| mlin-fermikit | SNP | * | map_l150_m2_e1 | het | 55.7873 | 38.9825 | 98.0593 | 70.1751 | 7938 | 12425 | 7933 | 157 | 5 | 3.1847 | |
| anovak-vg | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 94.8058 | 95.8213 | 93.8116 | 73.3592 | 2316 | 101 | 2380 | 157 | 134 | 85.3503 | |
| bgallagher-sentieon | SNP | * | HG002complexvar | het | 99.9449 | 99.9235 | 99.9662 | 18.4844 | 465141 | 356 | 465011 | 157 | 50 | 31.8471 | |
| bgallagher-sentieon | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | homalt | 81.2428 | 98.3287 | 69.2157 | 47.0954 | 353 | 6 | 353 | 157 | 156 | 99.3631 | |
| raldana-dualsentieon | SNP | ti | map_l125_m0_e0 | * | 98.7816 | 98.7933 | 98.7699 | 72.8522 | 12608 | 154 | 12606 | 157 | 6 | 3.8217 | |
| gduggal-bwafb | SNP | tv | segdup | het | 98.1577 | 99.2623 | 97.0773 | 93.8623 | 5248 | 39 | 5248 | 158 | 6 | 3.7975 | |
| gduggal-bwavard | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 90.2617 | 90.9209 | 89.6121 | 75.0082 | 1402 | 140 | 1363 | 158 | 97 | 61.3924 | |
| jpowers-varprowl | INDEL | D1_5 | map_siren | * | 94.5668 | 93.7093 | 95.4401 | 81.4755 | 3307 | 222 | 3307 | 158 | 114 | 72.1519 | |
| gduggal-snapfb | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_51to200 | homalt | 44.7458 | 92.9577 | 29.4643 | 46.0241 | 66 | 5 | 66 | 158 | 142 | 89.8734 | |
| gduggal-snapplat | SNP | tv | HG002compoundhet | homalt | 93.1015 | 91.1747 | 95.1114 | 51.4204 | 3089 | 299 | 3074 | 158 | 115 | 72.7848 | |
| gduggal-snapvard | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 29.6245 | 17.6158 | 93.0702 | 66.7638 | 2023 | 9461 | 2122 | 158 | 138 | 87.3418 | |
| ghariani-varprowl | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 86.5974 | 85.2531 | 87.9848 | 76.9339 | 1162 | 201 | 1157 | 158 | 144 | 91.1392 | |
| hfeng-pmm2 | SNP | tv | map_l100_m2_e1 | * | 99.4903 | 99.6045 | 99.3764 | 68.9155 | 25183 | 100 | 25179 | 158 | 17 | 10.7595 | |
| jlack-gatk | INDEL | D1_5 | map_l100_m2_e0 | het | 93.5776 | 98.9650 | 88.7464 | 88.5144 | 1243 | 13 | 1246 | 158 | 10 | 6.3291 | |
| hfeng-pmm1 | SNP | * | map_siren | het | 99.5907 | 99.3571 | 99.8255 | 53.5727 | 90406 | 585 | 90392 | 158 | 38 | 24.0506 | |
| hfeng-pmm3 | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 96.9360 | 95.1324 | 98.8093 | 46.5673 | 13114 | 671 | 13112 | 158 | 151 | 95.5696 | |
| hfeng-pmm3 | INDEL | I1_5 | HG002compoundhet | * | 96.3303 | 94.1081 | 98.6599 | 63.2057 | 11628 | 728 | 11632 | 158 | 151 | 95.5696 | |
| hfeng-pmm3 | SNP | * | map_l100_m2_e0 | het | 99.5523 | 99.4461 | 99.6587 | 66.2016 | 46142 | 257 | 46131 | 158 | 14 | 8.8608 | |
| cchapple-custom | INDEL | * | map_l100_m2_e0 | het | 95.1944 | 96.5756 | 93.8521 | 85.6721 | 2228 | 79 | 2412 | 158 | 40 | 25.3165 | |
| ckim-dragen | SNP | tv | HG002complexvar | * | 99.9267 | 99.9175 | 99.9359 | 22.5633 | 245949 | 203 | 246200 | 158 | 80 | 50.6329 | |
| ckim-gatk | INDEL | * | map_l100_m1_e0 | * | 97.0622 | 98.4384 | 95.7240 | 88.3725 | 3530 | 56 | 3537 | 158 | 20 | 12.6582 | |
| anovak-vg | INDEL | D1_5 | map_l100_m0_e0 | * | 82.9849 | 83.7775 | 82.2072 | 86.7066 | 723 | 140 | 730 | 158 | 62 | 39.2405 | |
| anovak-vg | INDEL | I16_PLUS | HG002compoundhet | homalt | 35.7724 | 100.0000 | 21.7822 | 38.4146 | 3 | 0 | 44 | 158 | 97 | 61.3924 | |
| mlin-fermikit | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 82.3039 | 88.8889 | 76.6272 | 63.8696 | 536 | 67 | 518 | 158 | 158 | 100.0000 | |
| mlin-fermikit | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 94.8031 | 99.5995 | 90.4474 | 84.6880 | 1492 | 6 | 1496 | 158 | 129 | 81.6456 | |
| ndellapenna-hhga | INDEL | I1_5 | HG002compoundhet | homalt | 80.1968 | 99.0881 | 67.3554 | 78.4506 | 326 | 3 | 326 | 158 | 149 | 94.3038 | |
| ltrigg-rtg2 | SNP | ti | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 99.3250 | 99.5294 | 99.1213 | 51.0494 | 17767 | 84 | 17824 | 158 | 11 | 6.9620 | |
| ltrigg-rtg2 | SNP | tv | HG002complexvar | het | 99.8062 | 99.7174 | 99.8951 | 21.1944 | 150308 | 426 | 150523 | 158 | 48 | 30.3797 | |
| dgrover-gatk | SNP | tv | lowcmp_SimpleRepeat_quadTR_11to50 | het | 98.2887 | 99.8934 | 96.7349 | 41.2956 | 4684 | 5 | 4681 | 158 | 1 | 0.6329 | |
| dgrover-gatk | SNP | ti | map_l125_m1_e0 | het | 99.2150 | 99.2992 | 99.1308 | 75.9575 | 18138 | 128 | 18134 | 159 | 33 | 20.7547 | |
| jlack-gatk | INDEL | D1_5 | map_l100_m2_e0 | * | 95.2850 | 98.5379 | 92.2401 | 87.2851 | 1887 | 28 | 1890 | 159 | 11 | 6.9182 | |
| jlack-gatk | INDEL | D1_5 | map_l100_m2_e1 | het | 93.6001 | 98.9748 | 88.7791 | 88.5873 | 1255 | 13 | 1258 | 159 | 10 | 6.2893 | |
| hfeng-pmm3 | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 94.1239 | 92.6980 | 95.5943 | 77.1597 | 3745 | 295 | 3450 | 159 | 125 | 78.6164 | |
| jli-custom | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | * | 88.6545 | 85.9115 | 91.5784 | 51.4278 | 1805 | 296 | 1729 | 159 | 156 | 98.1132 | |
| ltrigg-rtg1 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 97.1389 | 95.5295 | 98.8034 | 63.4805 | 13142 | 615 | 13129 | 159 | 34 | 21.3836 | |