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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
1901-1950 / 86044 show all | |||||||||||||||
| gduggal-snapvard | SNP | ti | map_siren | homalt | 97.9831 | 96.2100 | 99.8227 | 51.8924 | 36479 | 1437 | 36035 | 64 | 54 | 84.3750 | |
| ltrigg-rtg2 | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | * | 98.5306 | 97.6388 | 99.4388 | 47.4185 | 35728 | 864 | 35971 | 203 | 125 | 61.5764 | |
| dgrover-gatk | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | * | 98.5918 | 98.4368 | 98.7473 | 52.7193 | 36020 | 572 | 35944 | 456 | 425 | 93.2018 | |
| raldana-dualsentieon | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 96.5692 | 95.2826 | 97.8910 | 53.1171 | 36114 | 1788 | 35925 | 774 | 749 | 96.7700 | |
| astatham-gatk | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | * | 98.5463 | 98.3740 | 98.7193 | 52.5147 | 35997 | 595 | 35921 | 466 | 435 | 93.3476 | |
| jlack-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 95.7595 | 95.2166 | 96.3087 | 53.9807 | 36089 | 1813 | 35901 | 1376 | 1269 | 92.2238 | |
| ciseli-custom | SNP | * | map_l125_m2_e0 | * | 81.1188 | 76.8380 | 85.9047 | 77.6345 | 35901 | 10822 | 35830 | 5879 | 1516 | 25.7867 | |
| gduggal-bwaplat | SNP | ti | map_l100_m2_e1 | * | 83.7577 | 72.3674 | 99.4034 | 80.9971 | 35811 | 13674 | 35822 | 215 | 67 | 31.1628 | |
| bgallagher-sentieon | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | * | 98.2571 | 98.0815 | 98.4334 | 52.3164 | 35890 | 702 | 35814 | 570 | 538 | 94.3860 | |
| jli-custom | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | * | 98.6166 | 98.0433 | 99.1967 | 49.3156 | 35876 | 716 | 35813 | 290 | 255 | 87.9310 | |
| ciseli-custom | SNP | * | map_l100_m2_e0 | het | 81.8850 | 77.2883 | 87.0629 | 75.7023 | 35861 | 10538 | 35782 | 5317 | 161 | 3.0280 | |
| ckim-dragen | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | * | 98.1771 | 97.9914 | 98.3635 | 52.4340 | 35857 | 735 | 35764 | 595 | 553 | 92.9412 | |
| qzeng-custom | SNP | * | map_l100_m1_e0 | het | 87.7038 | 79.5123 | 97.7769 | 80.6669 | 36066 | 9293 | 35714 | 812 | 655 | 80.6650 | |
| astatham-gatk | SNP | * | map_l100_m2_e0 | het | 86.8923 | 76.9650 | 99.7597 | 75.4072 | 35711 | 10688 | 35700 | 86 | 33 | 38.3721 | |
| ckim-gatk | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | * | 98.2317 | 97.7700 | 98.6978 | 52.2722 | 35776 | 816 | 35699 | 471 | 434 | 92.1444 | |
| gduggal-snapvard | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | het | 73.0691 | 85.1079 | 64.0141 | 42.9883 | 13413 | 2347 | 35693 | 20065 | 18085 | 90.1321 | |
| ckim-vqsr | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | * | 98.2046 | 97.6826 | 98.7322 | 52.3033 | 35744 | 848 | 35667 | 458 | 432 | 94.3231 | |
| gduggal-bwaplat | SNP | * | map_l100_m2_e0 | het | 86.5211 | 76.7517 | 99.1404 | 84.8771 | 35612 | 10787 | 35636 | 309 | 82 | 26.5372 | |
| jmaeng-gatk | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | * | 98.0855 | 97.5186 | 98.6590 | 52.4830 | 35684 | 908 | 35608 | 484 | 451 | 93.1818 | |
| eyeh-varpipe | INDEL | * | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 99.3072 | 99.0383 | 99.5775 | 51.0793 | 16271 | 158 | 35588 | 151 | 137 | 90.7285 | |
| ciseli-custom | SNP | ti | map_siren | homalt | 93.8892 | 94.2504 | 93.5307 | 51.3255 | 35736 | 2180 | 35566 | 2460 | 1879 | 76.3821 | |
| gduggal-bwaplat | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 83.8912 | 73.6757 | 97.3956 | 82.4238 | 35564 | 12707 | 35564 | 951 | 276 | 29.0221 | |
| ltrigg-rtg1 | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | * | 97.9756 | 96.4774 | 99.5211 | 49.0897 | 35303 | 1289 | 35537 | 171 | 109 | 63.7427 | |
| rpoplin-dv42 | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | * | 97.3954 | 97.0977 | 97.6949 | 62.0775 | 35530 | 1062 | 35516 | 838 | 810 | 96.6587 | |
| cchapple-custom | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 99.2564 | 99.6414 | 98.8744 | 60.9154 | 35292 | 127 | 35487 | 404 | 50 | 12.3762 | |
| hfeng-pmm1 | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | * | 98.2538 | 97.1415 | 99.3919 | 50.2946 | 35546 | 1046 | 35469 | 217 | 179 | 82.4885 | |
| hfeng-pmm2 | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | * | 98.2164 | 97.1032 | 99.3555 | 50.5488 | 35532 | 1060 | 35455 | 230 | 205 | 89.1304 | |
| ckim-dragen | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 99.7746 | 99.8617 | 99.6878 | 62.5042 | 35370 | 49 | 35441 | 111 | 28 | 25.2252 | |
| gduggal-snapvard | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 65.9821 | 77.5633 | 57.4100 | 52.3175 | 13821 | 3998 | 35430 | 26284 | 22200 | 84.4620 | |
| jpowers-varprowl | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 56.7953 | 54.2639 | 59.5745 | 64.3309 | 35462 | 29889 | 35420 | 24035 | 23631 | 98.3191 | |
| jpowers-varprowl | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 56.7953 | 54.2639 | 59.5745 | 64.3309 | 35462 | 29889 | 35420 | 24035 | 23631 | 98.3191 | |
| hfeng-pmm3 | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | * | 98.1954 | 96.9884 | 99.4328 | 50.3319 | 35490 | 1102 | 35413 | 202 | 180 | 89.1089 | |
| gduggal-snapfb | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 84.6436 | 98.9102 | 73.9737 | 69.3624 | 35033 | 386 | 35409 | 12458 | 341 | 2.7372 | |
| jlack-gatk | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | * | 97.2911 | 96.9146 | 97.6705 | 52.3019 | 35463 | 1129 | 35387 | 844 | 761 | 90.1659 | |
| bgallagher-sentieon | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 99.4306 | 99.8701 | 98.9950 | 61.8984 | 35373 | 46 | 35362 | 359 | 20 | 5.5710 | |
| dgrover-gatk | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 99.5314 | 99.8673 | 99.1977 | 62.4958 | 35372 | 47 | 35361 | 286 | 20 | 6.9930 | |
| rpoplin-dv42 | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 99.8560 | 99.8560 | 99.8559 | 61.0125 | 35368 | 51 | 35352 | 51 | 31 | 60.7843 | |
| gduggal-bwaplat | SNP | ti | map_l100_m2_e0 | * | 83.6206 | 72.1656 | 99.3982 | 81.0322 | 35333 | 13628 | 35344 | 214 | 67 | 31.3084 | |
| ltrigg-rtg1 | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 99.4242 | 99.5483 | 99.3004 | 56.7770 | 35259 | 160 | 35343 | 249 | 16 | 6.4257 | |
| ltrigg-rtg2 | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 99.3249 | 99.5483 | 99.1025 | 56.2469 | 35259 | 160 | 35334 | 320 | 23 | 7.1875 | |
| jli-custom | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 99.4050 | 99.7685 | 99.0441 | 61.4043 | 35337 | 82 | 35333 | 341 | 20 | 5.8651 | |
| ckim-gatk | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 99.4847 | 99.7826 | 99.1887 | 63.5467 | 35342 | 77 | 35331 | 289 | 22 | 7.6125 | |
| jlack-gatk | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 98.7961 | 99.7741 | 97.8371 | 63.8462 | 35339 | 80 | 35328 | 781 | 32 | 4.0973 | |
| jmaeng-gatk | SNP | * | map_l125_m2_e1 | * | 84.7588 | 74.8379 | 97.7121 | 85.2730 | 35325 | 11877 | 35319 | 827 | 55 | 6.6505 | |
| jmaeng-gatk | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 99.5601 | 99.6979 | 99.4226 | 63.8015 | 35312 | 107 | 35301 | 205 | 16 | 7.8049 | |
| ckim-gatk | SNP | * | map_l125_m2_e1 | * | 84.7700 | 74.7850 | 97.8324 | 85.1204 | 35300 | 11902 | 35294 | 782 | 60 | 7.6726 | |
| gduggal-bwafb | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 98.1407 | 99.3309 | 96.9788 | 67.1842 | 35182 | 237 | 35277 | 1099 | 205 | 18.6533 | |
| qzeng-custom | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 98.7057 | 99.2433 | 98.1739 | 67.8653 | 35151 | 268 | 35268 | 656 | 60 | 9.1463 | |
| raldana-dualsentieon | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | * | 97.6279 | 96.5566 | 98.7231 | 49.8328 | 35332 | 1260 | 35256 | 456 | 427 | 93.6404 | |
| ckim-vqsr | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 99.4006 | 99.5116 | 99.2899 | 63.6333 | 35246 | 173 | 35235 | 252 | 21 | 8.3333 | |