PrecisionFDA
Truth Challenge
Engage and improve DNA test results with our community challenges
Explore HG002 comparison results
Use this interactive explorer to filter all results across submission entries and multiple dimensions.
| Entry | Type | Subtype | Subset | Genotype | F-score | Recall | Precision | Frac_NA | Truth TP | Truth FN | Query TP | Query FP | FP gt | % FP ma | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
82801-82850 / 86044 show all | |||||||||||||||
| jmaeng-gatk | SNP | * | map_l250_m2_e0 | het | 73.7629 | 59.8383 | 96.1336 | 96.8561 | 3108 | 2086 | 3108 | 125 | 9 | 7.2000 | |
| jpowers-varprowl | INDEL | I16_PLUS | HG002compoundhet | hetalt | 0.0000 | 0.3344 | 0.0000 | 0.0000 | 7 | 2086 | 0 | 0 | 0 | ||
| ckim-gatk | INDEL | * | HG002compoundhet | hetalt | 95.5666 | 91.7156 | 99.7551 | 50.3022 | 23094 | 2086 | 23217 | 57 | 57 | 100.0000 | |
| gduggal-snapvard | INDEL | D16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 3.5385 | 1.9267 | 21.6495 | 84.1374 | 41 | 2087 | 42 | 152 | 95 | 62.5000 | |
| ghariani-varprowl | INDEL | I16_PLUS | * | hetalt | 0.0000 | 0.4766 | 0.0000 | 0.0000 | 10 | 2088 | 0 | 0 | 0 | ||
| gduggal-snapplat | INDEL | * | map_siren | * | 79.6077 | 71.8219 | 89.2868 | 89.6136 | 5322 | 2088 | 5709 | 685 | 78 | 11.3869 | |
| gduggal-bwaplat | INDEL | I6_15 | * | hetalt | 85.2525 | 75.5818 | 97.7610 | 47.7759 | 6463 | 2088 | 6462 | 148 | 138 | 93.2432 | |
| ckim-isaac | SNP | ti | map_l150_m0_e0 | het | 74.1407 | 59.0347 | 99.6358 | 83.5333 | 3009 | 2088 | 3009 | 11 | 1 | 9.0909 | |
| gduggal-snapvard | INDEL | I16_PLUS | * | hetalt | 0.0000 | 0.4290 | 0.0000 | 0.0000 | 9 | 2089 | 0 | 0 | 0 | ||
| ckim-gatk | SNP | ti | map_l250_m1_e0 | * | 69.7981 | 54.3568 | 97.4931 | 96.0316 | 2489 | 2090 | 2489 | 64 | 8 | 12.5000 | |
| gduggal-bwavard | INDEL | I16_PLUS | * | hetalt | 0.0000 | 0.3813 | 0.0000 | 0.0000 | 8 | 2090 | 0 | 0 | 0 | ||
| jpowers-varprowl | INDEL | I16_PLUS | * | hetalt | 0.0000 | 0.3337 | 0.0000 | 0.0000 | 7 | 2091 | 0 | 0 | 0 | ||
| gduggal-snapplat | INDEL | I16_PLUS | HG002compoundhet | hetalt | 0.0000 | 0.0478 | 0.0000 | 0.0000 | 1 | 2092 | 0 | 0 | 0 | ||
| ciseli-custom | INDEL | I16_PLUS | HG002compoundhet | hetalt | 0.0000 | 0.0478 | 0.0000 | 0.0000 | 1 | 2092 | 0 | 0 | 0 | ||
| ckim-gatk | SNP | * | map_l250_m2_e1 | het | 74.0542 | 60.2394 | 96.0909 | 96.7655 | 3171 | 2093 | 3171 | 129 | 10 | 7.7519 | |
| asubramanian-gatk | INDEL | I1_5 | * | * | 99.0996 | 98.6108 | 99.5933 | 59.2515 | 148571 | 2093 | 148648 | 607 | 454 | 74.7941 | |
| gduggal-snapfb | INDEL | I16_PLUS | HG002compoundhet | hetalt | 0.0000 | 0.0000 | 0.0000 | 0 | 2093 | 0 | 0 | 0 | |||
| jmaeng-gatk | SNP | ti | map_l250_m1_e0 | * | 69.7263 | 54.2477 | 97.5648 | 96.1076 | 2484 | 2095 | 2484 | 62 | 7 | 11.2903 | |
| anovak-vg | SNP | * | HG002compoundhet | homalt | 80.7165 | 80.5695 | 80.8640 | 38.2684 | 8687 | 2095 | 7974 | 1887 | 1143 | 60.5723 | |
| ghariani-varprowl | INDEL | D1_5 | HG002complexvar | * | 93.6809 | 93.5932 | 93.7688 | 56.5500 | 30619 | 2096 | 30473 | 2025 | 1375 | 67.9012 | |
| gduggal-snapplat | INDEL | I16_PLUS | * | hetalt | 0.0000 | 0.0477 | 0.0000 | 0.0000 | 1 | 2097 | 0 | 0 | 0 | ||
| ciseli-custom | INDEL | I16_PLUS | * | hetalt | 0.0000 | 0.0477 | 0.0000 | 0.0000 | 1 | 2097 | 0 | 0 | 0 | ||
| ckim-isaac | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 96.5751 | 94.0794 | 99.2069 | 56.5853 | 33322 | 2097 | 33647 | 269 | 28 | 10.4089 | |
| ckim-vqsr | INDEL | * | HG002compoundhet | hetalt | 95.5428 | 91.6720 | 99.7550 | 50.3140 | 23083 | 2097 | 23206 | 57 | 57 | 100.0000 | |
| gduggal-snapfb | INDEL | I16_PLUS | * | hetalt | 0.0000 | 0.0000 | 0.0000 | 0 | 2098 | 0 | 0 | 0 | |||
| jmaeng-gatk | SNP | * | map_l150_m0_e0 | homalt | 65.4719 | 48.6916 | 99.8996 | 84.7432 | 1991 | 2098 | 1991 | 2 | 2 | 100.0000 | |
| cchapple-custom | INDEL | * | * | het | 99.2026 | 98.9188 | 99.4881 | 58.0034 | 192034 | 2099 | 238847 | 1229 | 782 | 63.6290 | |
| ghariani-varprowl | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 56.5337 | 42.2760 | 85.3023 | 63.5610 | 1538 | 2100 | 1538 | 265 | 235 | 88.6792 | |
| jmaeng-gatk | SNP | * | map_l250_m2_e1 | het | 73.9537 | 60.0874 | 96.1398 | 96.8694 | 3163 | 2101 | 3163 | 127 | 9 | 7.0866 | |
| jpowers-varprowl | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 56.6114 | 42.2485 | 85.7701 | 63.4733 | 1537 | 2101 | 1537 | 255 | 235 | 92.1569 | |
| ckim-gatk | INDEL | * | * | hetalt | 95.5159 | 91.6749 | 99.6928 | 55.9040 | 23136 | 2101 | 23365 | 72 | 70 | 97.2222 | |
| ciseli-custom | INDEL | D6_15 | HG002complexvar | * | 60.6154 | 60.3471 | 60.8861 | 55.7398 | 3199 | 2102 | 3202 | 2057 | 1257 | 61.1084 | |
| gduggal-bwavard | INDEL | I16_PLUS | HG002compoundhet | * | 2.2297 | 1.8199 | 2.8777 | 49.0469 | 39 | 2104 | 40 | 1350 | 1263 | 93.5556 | |
| gduggal-snapvard | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 0.0000 | 54.7020 | 0.0000 | 0.0000 | 2542 | 2105 | 0 | 0 | 0 | ||
| ckim-gatk | SNP | * | map_l150_m0_e0 | homalt | 65.2389 | 48.4226 | 99.9495 | 85.6968 | 1980 | 2109 | 1980 | 1 | 1 | 100.0000 | |
| ndellapenna-hhga | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 80.6222 | 79.0628 | 82.2442 | 83.6336 | 7964 | 2109 | 8143 | 1758 | 1536 | 87.3720 | |
| gduggal-bwaplat | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 76.5888 | 63.9069 | 95.5499 | 83.7077 | 3736 | 2110 | 3736 | 174 | 72 | 41.3793 | |
| gduggal-bwaplat | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 76.5888 | 63.9069 | 95.5499 | 83.7077 | 3736 | 2110 | 3736 | 174 | 72 | 41.3793 | |
| ckim-vqsr | INDEL | * | * | hetalt | 95.4941 | 91.6313 | 99.6969 | 55.9167 | 23125 | 2112 | 23354 | 71 | 70 | 98.5915 | |
| ciseli-custom | SNP | tv | * | homalt | 98.4608 | 99.4400 | 97.5007 | 22.4395 | 375011 | 2112 | 373610 | 9577 | 3591 | 37.4961 | |
| ckim-isaac | SNP | tv | map_l150_m0_e0 | * | 66.0468 | 49.3531 | 99.8062 | 82.1762 | 2060 | 2114 | 2060 | 4 | 1 | 25.0000 | |
| ghariani-varprowl | INDEL | I16_PLUS | HG002compoundhet | * | 1.7907 | 1.3532 | 2.6460 | 56.7653 | 29 | 2114 | 29 | 1067 | 1059 | 99.2502 | |
| hfeng-pmm1 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 97.9439 | 96.7636 | 99.1534 | 64.2879 | 63236 | 2115 | 63011 | 538 | 416 | 77.3234 | |
| hfeng-pmm1 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 97.9439 | 96.7636 | 99.1534 | 64.2879 | 63236 | 2115 | 63011 | 538 | 416 | 77.3234 | |
| ltrigg-rtg2 | SNP | ti | * | * | 99.8963 | 99.8985 | 99.8940 | 15.8136 | 2083396 | 2116 | 2083301 | 2210 | 180 | 8.1448 | |
| ckim-gatk | SNP | tv | map_siren | het | 95.0179 | 92.6002 | 97.5652 | 74.8662 | 26492 | 2117 | 26487 | 661 | 26 | 3.9334 | |
| ciseli-custom | INDEL | * | map_siren | * | 74.2881 | 71.4035 | 77.4156 | 83.7506 | 5291 | 2119 | 5296 | 1545 | 1017 | 65.8252 | |
| eyeh-varpipe | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 18.7138 | 10.4396 | 90.2235 | 66.4165 | 247 | 2119 | 323 | 35 | 30 | 85.7143 | |
| jmaeng-gatk | SNP | tv | map_siren | het | 94.8661 | 92.5932 | 97.2533 | 75.2567 | 26490 | 2119 | 26485 | 748 | 25 | 3.3423 | |
| anovak-vg | INDEL | D6_15 | * | het | 76.4820 | 81.7202 | 71.8750 | 45.3746 | 9473 | 2119 | 11523 | 4509 | 3518 | 78.0217 | |