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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
86001-86044 / 86044 show all | |||||||||||||||
| gduggal-bwaplat | SNP | ti | * | * | 99.0047 | 98.3196 | 99.6994 | 24.2468 | 2050467 | 35044 | 2050804 | 6183 | 880 | 14.2326 | |
| asubramanian-gatk | SNP | * | * | het | 98.9725 | 98.1066 | 99.8538 | 23.0377 | 1838113 | 35474 | 1837999 | 2691 | 109 | 4.0505 | |
| anovak-vg | SNP | ti | * | * | 98.4812 | 98.2960 | 98.6672 | 19.8346 | 2049980 | 35538 | 2043729 | 27607 | 12786 | 46.3143 | |
| ciseli-custom | SNP | * | * | * | 97.7648 | 98.8356 | 96.7169 | 21.5138 | 3019065 | 35569 | 3006072 | 102041 | 11838 | 11.6012 | |
| anovak-vg | SNP | * | * | het | 98.0636 | 98.0936 | 98.0337 | 24.0083 | 1837883 | 35718 | 1828909 | 36684 | 13178 | 35.9230 | |
| asubramanian-gatk | SNP | ti | map_siren | * | 78.3158 | 64.4054 | 99.8903 | 68.2204 | 64634 | 35721 | 64622 | 71 | 23 | 32.3944 | |
| mlin-fermikit | SNP | ti | * | * | 98.9073 | 98.2768 | 99.5460 | 14.9446 | 2049581 | 35937 | 2049572 | 9348 | 8085 | 86.4891 | |
| ckim-isaac | SNP | ti | HG002complexvar | * | 96.1858 | 92.7592 | 99.8753 | 15.7158 | 471622 | 36815 | 471809 | 589 | 446 | 75.7216 | |
| mlin-fermikit | SNP | * | map_siren | * | 83.3638 | 74.6157 | 94.4357 | 47.0930 | 109109 | 37119 | 109094 | 6428 | 5503 | 85.6098 | |
| ckim-isaac | SNP | * | * | homalt | 98.3805 | 96.8182 | 99.9940 | 14.4545 | 1142612 | 37550 | 1142668 | 69 | 50 | 72.4638 | |
| ckim-vqsr | SNP | * | map_siren | * | 85.1088 | 74.3093 | 99.5811 | 71.1680 | 108661 | 37567 | 108641 | 457 | 31 | 6.7834 | |
| ckim-isaac | SNP | * | map_siren | * | 84.8645 | 73.7800 | 99.8686 | 51.5315 | 107887 | 38341 | 107900 | 142 | 41 | 28.8732 | |
| asubramanian-gatk | SNP | ti | * | * | 99.0306 | 98.1234 | 99.9548 | 19.2315 | 2046375 | 39136 | 2046316 | 926 | 90 | 9.7192 | |
| gduggal-snapplat | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 67.1528 | 57.9879 | 79.7584 | 80.2389 | 54769 | 39680 | 61674 | 15652 | 4576 | 29.2359 | |
| gduggal-snapplat | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 48.6764 | 39.2603 | 64.0343 | 80.0683 | 25657 | 39694 | 30253 | 16992 | 4936 | 29.0490 | |
| gduggal-snapplat | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 48.6764 | 39.2603 | 64.0343 | 80.0683 | 25657 | 39694 | 30253 | 16992 | 4936 | 29.0490 | |
| gduggal-snapplat | SNP | * | * | * | 99.0030 | 98.6815 | 99.3266 | 26.8746 | 3014360 | 40274 | 3015151 | 20442 | 2819 | 13.7902 | |
| asubramanian-gatk | SNP | * | map_l100_m1_e0 | * | 60.2018 | 43.0908 | 99.8527 | 84.6729 | 31199 | 41204 | 31193 | 46 | 12 | 26.0870 | |
| ckim-vqsr | SNP | * | * | * | 99.2866 | 98.6511 | 99.9303 | 23.6837 | 3013415 | 41204 | 3013272 | 2101 | 144 | 6.8539 | |
| asubramanian-gatk | SNP | * | map_l100_m2_e0 | * | 60.9821 | 43.8984 | 99.8339 | 85.3165 | 32469 | 41495 | 32463 | 54 | 14 | 25.9259 | |
| asubramanian-gatk | SNP | * | map_l100_m2_e1 | * | 61.2013 | 44.1254 | 99.8365 | 85.2564 | 32978 | 41759 | 32972 | 54 | 14 | 25.9259 | |
| mlin-fermikit | SNP | * | * | het | 98.7978 | 97.7460 | 99.8724 | 15.9070 | 1831370 | 42231 | 1831279 | 2340 | 46 | 1.9658 | |
| gduggal-snapplat | INDEL | I1_5 | * | * | 77.0401 | 71.8692 | 83.0128 | 69.8058 | 108281 | 42383 | 109381 | 22383 | 1242 | 5.5489 | |
| ghariani-varprowl | INDEL | * | * | * | 87.2025 | 87.3272 | 87.0781 | 72.0067 | 300877 | 43663 | 300632 | 44612 | 40345 | 90.4353 | |
| gduggal-bwavard | INDEL | * | * | * | 87.3464 | 87.1769 | 87.5166 | 58.1126 | 300361 | 44181 | 299341 | 42698 | 38856 | 91.0019 | |
| gduggal-bwaplat | INDEL | * | * | * | 92.6621 | 87.0843 | 99.0034 | 65.2816 | 300042 | 44500 | 299917 | 3019 | 1851 | 61.3117 | |
| ckim-isaac | SNP | * | * | het | 98.6547 | 97.3796 | 99.9637 | 16.8583 | 1824505 | 49096 | 1825101 | 663 | 63 | 9.5023 | |
| jpowers-varprowl | INDEL | * | * | * | 86.4885 | 85.2886 | 87.7226 | 56.7888 | 293855 | 50687 | 293627 | 41095 | 40121 | 97.6299 | |
| anovak-vg | SNP | * | * | * | 98.4545 | 98.3357 | 98.5736 | 21.3437 | 3003796 | 50838 | 2987348 | 43227 | 18700 | 43.2600 | |
| mlin-fermikit | SNP | * | * | * | 98.8629 | 98.2311 | 99.5029 | 16.3803 | 3000602 | 54032 | 3000527 | 14990 | 12200 | 81.3876 | |
| asubramanian-gatk | SNP | * | map_siren | * | 76.4845 | 61.9738 | 99.8677 | 70.7590 | 90623 | 55605 | 90605 | 120 | 35 | 29.1667 | |
| ckim-isaac | SNP | ti | * | * | 98.6272 | 97.3318 | 99.9576 | 14.8667 | 2029873 | 55645 | 2030218 | 862 | 462 | 53.5963 | |
| gduggal-snapvard | INDEL | * | * | * | 83.0264 | 83.4429 | 82.6139 | 57.1178 | 287491 | 57045 | 327755 | 68976 | 51941 | 75.3030 | |
| gduggal-snapplat | INDEL | * | * | het | 75.6756 | 70.3729 | 81.8427 | 68.5533 | 136617 | 57516 | 150007 | 33280 | 2606 | 7.8305 | |
| ckim-isaac | SNP | * | HG002complexvar | * | 95.9550 | 92.3552 | 99.8467 | 16.9098 | 696714 | 57671 | 697067 | 1070 | 847 | 79.1589 | |
| anovak-vg | INDEL | I1_5 | * | het | 38.2803 | 26.6836 | 67.7044 | 67.2836 | 21091 | 57950 | 25553 | 12189 | 4021 | 32.9888 | |
| gduggal-bwaplat | SNP | * | * | * | 98.8646 | 98.0471 | 99.6958 | 26.6546 | 2994965 | 59654 | 2995523 | 9139 | 1314 | 14.3779 | |
| ciseli-custom | INDEL | * | * | * | 83.5453 | 82.5314 | 84.5844 | 60.0787 | 284352 | 60186 | 284718 | 51890 | 36584 | 70.5030 | |
| asubramanian-gatk | SNP | * | * | * | 98.9379 | 97.9985 | 99.8954 | 21.0150 | 2993480 | 61139 | 2993343 | 3133 | 150 | 4.7877 | |
| anovak-vg | INDEL | I1_5 | * | * | 54.8287 | 54.8578 | 54.7996 | 53.4671 | 82651 | 68013 | 84844 | 69982 | 59671 | 85.2662 | |
| anovak-vg | INDEL | * | * | het | 69.4961 | 61.0200 | 80.7068 | 58.0873 | 118460 | 75673 | 131172 | 31357 | 16629 | 53.0312 | |
| ckim-isaac | SNP | * | * | * | 98.5357 | 97.1616 | 99.9494 | 15.9907 | 2967930 | 86704 | 2968584 | 1504 | 880 | 58.5106 | |
| anovak-vg | INDEL | * | * | * | 70.4960 | 69.7491 | 71.2591 | 54.1876 | 240315 | 104227 | 248606 | 100270 | 81436 | 81.2167 | |
| gduggal-snapplat | INDEL | * | * | * | 76.4210 | 69.0418 | 85.5664 | 67.7420 | 237878 | 106664 | 258555 | 43614 | 6600 | 15.1328 | |