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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
27001-27050 / 86044 show all | |||||||||||||||
| gduggal-snapvard | INDEL | I6_15 | HG002complexvar | het | 67.8635 | 76.9851 | 60.6744 | 48.9450 | 1813 | 542 | 2393 | 1551 | 1213 | 78.2076 | |
| hfeng-pmm2 | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | hetalt | 95.8621 | 92.0530 | 100.0000 | 48.9510 | 139 | 12 | 146 | 0 | 0 | ||
| jmaeng-gatk | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 99.4582 | 99.2565 | 99.6607 | 48.9520 | 2937 | 22 | 2937 | 10 | 1 | 10.0000 | |
| ckim-isaac | INDEL | D1_5 | HG002complexvar | homalt | 94.8892 | 91.0360 | 99.0830 | 48.9641 | 9648 | 950 | 9617 | 89 | 17 | 19.1011 | |
| gduggal-bwavard | INDEL | * | lowcmp_SimpleRepeat_triTR_11to50 | * | 77.5159 | 76.4592 | 78.6021 | 48.9675 | 5148 | 1585 | 5128 | 1396 | 1280 | 91.6905 | |
| ltrigg-rtg1 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 96.8306 | 94.1224 | 99.6991 | 48.9729 | 6950 | 434 | 6959 | 21 | 10 | 47.6190 | |
| jmaeng-gatk | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | homalt | 84.4765 | 97.7716 | 74.3644 | 48.9730 | 351 | 8 | 351 | 121 | 119 | 98.3471 | |
| rpoplin-dv42 | INDEL | I1_5 | lowcmp_SimpleRepeat_triTR_51to200 | * | 96.0000 | 96.0000 | 96.0000 | 48.9796 | 24 | 1 | 24 | 1 | 0 | 0.0000 | |
| ckim-dragen | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 98.9486 | 98.3236 | 99.5816 | 48.9801 | 4223 | 72 | 4284 | 18 | 5 | 27.7778 | |
| jli-custom | SNP | tv | HG002compoundhet | * | 99.6414 | 99.6526 | 99.6301 | 48.9851 | 8892 | 31 | 8889 | 33 | 14 | 42.4242 | |
| ltrigg-rtg1 | INDEL | * | lowcmp_SimpleRepeat_quadTR_51to200 | hetalt | 95.4707 | 92.3849 | 98.7698 | 48.9915 | 1104 | 91 | 1124 | 14 | 13 | 92.8571 | |
| hfeng-pmm1 | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_51to200 | homalt | 97.6378 | 97.6378 | 97.6378 | 48.9960 | 124 | 3 | 124 | 3 | 2 | 66.6667 | |
| hfeng-pmm1 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 97.7028 | 95.7181 | 99.7716 | 48.9962 | 5678 | 254 | 5678 | 13 | 10 | 76.9231 | |
| rpoplin-dv42 | INDEL | I16_PLUS | * | hetalt | 91.5838 | 84.7950 | 99.5541 | 49.0051 | 1779 | 319 | 1786 | 8 | 7 | 87.5000 | |
| mlin-fermikit | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 83.3295 | 82.0722 | 84.6259 | 49.0103 | 31107 | 6795 | 30957 | 5624 | 5549 | 98.6664 | |
| egarrison-hhga | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 94.2348 | 96.1840 | 92.3630 | 49.0134 | 2697 | 107 | 2697 | 223 | 68 | 30.4933 | |
| gduggal-snapfb | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 63.0372 | 53.0172 | 77.7273 | 49.0151 | 246 | 218 | 342 | 98 | 96 | 97.9592 | |
| jli-custom | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | * | 99.6118 | 99.3853 | 99.8394 | 49.0173 | 11802 | 73 | 11810 | 19 | 12 | 63.1579 | |
| ckim-vqsr | SNP | * | tech_badpromoters | * | 98.4026 | 98.0892 | 98.7179 | 49.0196 | 154 | 3 | 154 | 2 | 2 | 100.0000 | |
| rpoplin-dv42 | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 88.5924 | 80.0699 | 99.1453 | 49.0196 | 229 | 57 | 232 | 2 | 2 | 100.0000 | |
| ckim-gatk | SNP | * | tech_badpromoters | * | 98.4026 | 98.0892 | 98.7179 | 49.0196 | 154 | 3 | 154 | 2 | 2 | 100.0000 | |
| ckim-isaac | INDEL | D6_15 | HG002complexvar | het | 83.3579 | 80.6410 | 86.2642 | 49.0301 | 2516 | 604 | 1972 | 314 | 100 | 31.8471 | |
| hfeng-pmm2 | SNP | * | * | hetalt | 99.8851 | 99.7704 | 100.0000 | 49.0323 | 869 | 2 | 869 | 0 | 0 | ||
| hfeng-pmm2 | SNP | tv | * | hetalt | 99.8851 | 99.7704 | 100.0000 | 49.0323 | 869 | 2 | 869 | 0 | 0 | ||
| jpowers-varprowl | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | het | 25.7159 | 56.7347 | 16.6259 | 49.0343 | 278 | 212 | 272 | 1364 | 1359 | 99.6334 | |
| hfeng-pmm2 | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_51to200 | homalt | 95.7529 | 97.6378 | 93.9394 | 49.0347 | 124 | 3 | 124 | 8 | 7 | 87.5000 | |
| jpowers-varprowl | INDEL | I6_15 | * | het | 67.8850 | 81.9496 | 57.9408 | 49.0356 | 8222 | 1811 | 8267 | 6001 | 5983 | 99.7000 | |
| egarrison-hhga | INDEL | I1_5 | HG002complexvar | homalt | 99.1848 | 99.1225 | 99.2472 | 49.0370 | 13330 | 118 | 13315 | 101 | 64 | 63.3663 | |
| ckim-isaac | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 96.6131 | 94.3079 | 99.0337 | 49.0411 | 5832 | 352 | 5842 | 57 | 26 | 45.6140 | |
| gduggal-bwavard | INDEL | I16_PLUS | HG002compoundhet | * | 2.2297 | 1.8199 | 2.8777 | 49.0469 | 39 | 2104 | 40 | 1350 | 1263 | 93.5556 | |
| ltrigg-rtg2 | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 99.2263 | 99.6260 | 98.8298 | 49.0498 | 3996 | 15 | 4054 | 48 | 0 | 0.0000 | |
| dgrover-gatk | SNP | tv | HG002compoundhet | * | 99.7478 | 99.7647 | 99.7310 | 49.0520 | 8902 | 21 | 8897 | 24 | 15 | 62.5000 | |
| cchapple-custom | INDEL | D16_PLUS | HG002compoundhet | homalt | 29.7030 | 75.0000 | 18.5185 | 49.0566 | 6 | 2 | 5 | 22 | 22 | 100.0000 | |
| raldana-dualsentieon | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 96.2310 | 94.8350 | 97.6687 | 49.0598 | 13073 | 712 | 13071 | 312 | 308 | 98.7179 | |
| jlack-gatk | SNP | ti | map_siren | homalt | 99.6031 | 99.2879 | 99.9204 | 49.0602 | 37646 | 270 | 37640 | 30 | 20 | 66.6667 | |
| hfeng-pmm2 | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_51to200 | * | 81.2500 | 70.8752 | 95.1830 | 49.0677 | 494 | 203 | 494 | 25 | 23 | 92.0000 | |
| egarrison-hhga | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 99.5478 | 99.4890 | 99.6066 | 49.0683 | 2531 | 13 | 2532 | 10 | 2 | 20.0000 | |
| rpoplin-dv42 | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 99.8769 | 99.7950 | 99.9589 | 49.0692 | 2434 | 5 | 2434 | 1 | 0 | 0.0000 | |
| eyeh-varpipe | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 93.8809 | 89.9476 | 98.1740 | 49.0700 | 7552 | 844 | 7527 | 140 | 92 | 65.7143 | |
| gduggal-bwafb | INDEL | I1_5 | HG002complexvar | homalt | 98.3809 | 97.8212 | 98.9471 | 49.0711 | 13155 | 293 | 13156 | 140 | 134 | 95.7143 | |
| qzeng-custom | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | * | 96.0217 | 94.2549 | 97.8560 | 49.0716 | 3675 | 224 | 8535 | 187 | 123 | 65.7754 | |
| cchapple-custom | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 97.8248 | 96.2264 | 99.4772 | 49.0761 | 714 | 28 | 3235 | 17 | 15 | 88.2353 | |
| mlin-fermikit | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 58.6637 | 41.7103 | 98.8365 | 49.0818 | 1595 | 2229 | 1699 | 20 | 18 | 90.0000 | |
| ciseli-custom | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 82.4109 | 89.4163 | 76.4235 | 49.0835 | 3278 | 388 | 3248 | 1002 | 864 | 86.2275 | |
| astatham-gatk | SNP | tv | HG002compoundhet | * | 99.1767 | 98.5543 | 99.8069 | 49.0836 | 8794 | 129 | 8789 | 17 | 16 | 94.1176 | |
| egarrison-hhga | SNP | ti | * | hetalt | 98.9708 | 99.1409 | 98.8014 | 49.0846 | 577 | 5 | 577 | 7 | 7 | 100.0000 | |
| mlin-fermikit | INDEL | D16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 68.6099 | 52.3077 | 99.6743 | 49.0879 | 510 | 465 | 612 | 2 | 1 | 50.0000 | |
| anovak-vg | INDEL | D16_PLUS | * | het | 72.6101 | 70.2754 | 75.1054 | 49.0881 | 2220 | 939 | 2495 | 827 | 601 | 72.6723 | |
| dgrover-gatk | SNP | ti | map_siren | homalt | 99.8204 | 99.6914 | 99.9498 | 49.0891 | 37799 | 117 | 37793 | 19 | 17 | 89.4737 | |
| ltrigg-rtg1 | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | * | 97.9756 | 96.4774 | 99.5211 | 49.0897 | 35303 | 1289 | 35537 | 171 | 109 | 63.7427 | |