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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
5901-5950 / 86044 show all | |||||||||||||||
| ciseli-custom | INDEL | I1_5 | map_l100_m2_e1 | * | 63.6010 | 58.1362 | 70.1998 | 85.9497 | 811 | 584 | 808 | 343 | 294 | 85.7143 | |
| jlack-gatk | INDEL | * | map_siren | het | 95.6389 | 98.6025 | 92.8482 | 85.9136 | 4445 | 63 | 4453 | 343 | 22 | 6.4140 | |
| ghariani-varprowl | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 51.6840 | 41.4224 | 68.7044 | 73.6538 | 763 | 1079 | 753 | 343 | 297 | 86.5889 | |
| ghariani-varprowl | SNP | * | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 98.2430 | 99.5309 | 96.9881 | 59.7341 | 11032 | 52 | 11045 | 343 | 3 | 0.8746 | |
| gduggal-snapplat | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 50.1059 | 37.3855 | 75.9467 | 75.6447 | 1224 | 2050 | 1083 | 343 | 104 | 30.3207 | |
| gduggal-snapvard | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 4.7196 | 2.6063 | 24.9453 | 76.2474 | 106 | 3961 | 114 | 343 | 228 | 66.4723 | |
| gduggal-snapvard | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 9.3373 | 5.7895 | 24.1150 | 76.0466 | 77 | 1253 | 109 | 343 | 228 | 66.4723 | |
| gduggal-snapfb | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 72.4427 | 98.5075 | 57.2852 | 93.2156 | 462 | 7 | 460 | 343 | 27 | 7.8717 | |
| rpoplin-dv42 | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | het | 60.4235 | 77.7551 | 49.4100 | 70.5217 | 381 | 109 | 335 | 343 | 340 | 99.1254 | |
| anovak-vg | INDEL | I1_5 | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 67.8590 | 93.2584 | 53.3333 | 46.3895 | 249 | 18 | 392 | 343 | 331 | 96.5015 | |
| bgallagher-sentieon | SNP | * | map_l100_m0_e0 | het | 98.8545 | 99.3162 | 98.3971 | 73.2385 | 21060 | 145 | 21056 | 343 | 49 | 14.2857 | |
| bgallagher-sentieon | SNP | * | map_l150_m2_e1 | het | 98.8048 | 99.2830 | 98.3312 | 79.8100 | 20217 | 146 | 20211 | 343 | 50 | 14.5773 | |
| mlin-fermikit | SNP | * | map_l100_m1_e0 | het | 71.0748 | 55.5458 | 98.6565 | 54.0604 | 25195 | 20164 | 25187 | 343 | 11 | 3.2070 | |
| qzeng-custom | INDEL | I16_PLUS | HG002compoundhet | * | 72.9335 | 66.6356 | 80.5461 | 47.8493 | 1428 | 715 | 1416 | 342 | 260 | 76.0234 | |
| mlin-fermikit | INDEL | * | map_l100_m2_e0 | * | 75.2930 | 65.9626 | 87.6978 | 80.5947 | 2436 | 1257 | 2438 | 342 | 265 | 77.4854 | |
| qzeng-custom | INDEL | * | map_l100_m2_e0 | het | 83.5804 | 79.9740 | 87.5274 | 89.7430 | 1845 | 462 | 2400 | 342 | 54 | 15.7895 | |
| gduggal-snapvard | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 73.1549 | 89.1170 | 62.0422 | 57.0748 | 434 | 53 | 559 | 342 | 258 | 75.4386 | |
| cchapple-custom | INDEL | I6_15 | * | * | 97.7435 | 96.8215 | 98.6833 | 49.3635 | 24034 | 789 | 25632 | 342 | 305 | 89.1813 | |
| ckim-isaac | INDEL | * | * | hetalt | 87.6357 | 79.0308 | 98.3434 | 43.3219 | 19945 | 5292 | 20303 | 342 | 304 | 88.8889 | |
| gduggal-bwaplat | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 68.0328 | 54.2991 | 91.0658 | 88.7322 | 3486 | 2934 | 3486 | 342 | 80 | 23.3918 | |
| gduggal-bwaplat | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 68.0328 | 54.2991 | 91.0658 | 88.7322 | 3486 | 2934 | 3486 | 342 | 80 | 23.3918 | |
| gduggal-bwafb | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | * | 73.4367 | 65.0167 | 84.3621 | 45.9065 | 1366 | 735 | 1845 | 342 | 338 | 98.8304 | |
| cchapple-custom | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 92.8801 | 90.1364 | 95.7959 | 52.1555 | 5483 | 600 | 7793 | 342 | 302 | 88.3041 | |
| raldana-dualsentieon | SNP | * | map_l150_m2_e1 | het | 98.5420 | 98.7576 | 98.3273 | 78.0672 | 20110 | 253 | 20104 | 342 | 4 | 1.1696 | |
| rpoplin-dv42 | SNP | * | map_l100_m2_e1 | * | 99.4091 | 99.2775 | 99.5411 | 65.1919 | 74197 | 540 | 74186 | 342 | 199 | 58.1871 | |
| raldana-dualsentieon | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 96.6075 | 95.2464 | 98.0080 | 54.6884 | 16831 | 840 | 16827 | 342 | 333 | 97.3684 | |
| raldana-dualsentieon | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 96.6075 | 95.2464 | 98.0080 | 54.6884 | 16831 | 840 | 16827 | 342 | 333 | 97.3684 | |
| jmaeng-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 98.1915 | 97.4975 | 98.8955 | 61.4377 | 30622 | 786 | 30622 | 342 | 309 | 90.3509 | |
| jmaeng-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 98.1915 | 97.4975 | 98.8955 | 61.4377 | 30622 | 786 | 30622 | 342 | 309 | 90.3509 | |
| jmaeng-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 96.8830 | 96.2858 | 97.4877 | 51.4550 | 13273 | 512 | 13271 | 342 | 335 | 97.9532 | |
| jmaeng-gatk | SNP | * | map_l125_m0_e0 | * | 76.5092 | 63.0487 | 97.2773 | 89.3850 | 12222 | 7163 | 12219 | 342 | 29 | 8.4795 | |
| jpowers-varprowl | SNP | tv | map_l150_m1_e0 | * | 96.7188 | 96.5726 | 96.8655 | 80.4419 | 10538 | 374 | 10538 | 341 | 91 | 26.6862 | |
| jli-custom | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 99.4050 | 99.7685 | 99.0441 | 61.4043 | 35337 | 82 | 35333 | 341 | 20 | 5.8651 | |
| gduggal-snapplat | INDEL | * | map_l100_m2_e0 | * | 80.0736 | 72.4343 | 89.5141 | 91.6820 | 2675 | 1018 | 2911 | 341 | 39 | 11.4370 | |
| gduggal-snapplat | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 53.5363 | 39.1660 | 84.5632 | 59.4976 | 1869 | 2903 | 1868 | 341 | 287 | 84.1642 | |
| gduggal-snapvard | INDEL | C6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 0.0000 | 0.0000 | 30.5499 | 87.9361 | 0 | 0 | 150 | 341 | 58 | 17.0088 | |
| gduggal-snapvard | INDEL | C6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 0.0000 | 0.0000 | 30.5499 | 87.9361 | 0 | 0 | 150 | 341 | 58 | 17.0088 | |
| dgrover-gatk | SNP | * | map_l100_m2_e1 | het | 99.3747 | 99.4755 | 99.2742 | 71.6392 | 46652 | 246 | 46641 | 341 | 63 | 18.4751 | |
| egarrison-hhga | INDEL | * | lowcmp_SimpleRepeat_triTR_11to50 | * | 94.6258 | 94.3116 | 94.9422 | 66.8176 | 6350 | 383 | 6401 | 341 | 317 | 92.9619 | |
| qzeng-custom | SNP | ti | map_l125_m0_e0 | het | 76.7738 | 64.8796 | 94.0081 | 91.3630 | 5361 | 2902 | 5350 | 341 | 285 | 83.5777 | |
| ndellapenna-hhga | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_51to200 | * | 60.3133 | 55.2921 | 66.3376 | 42.9617 | 653 | 528 | 672 | 341 | 312 | 91.4956 | |
| hfeng-pmm2 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 97.6456 | 96.4829 | 98.8367 | 71.2472 | 29408 | 1072 | 28971 | 341 | 255 | 74.7801 | |
| hfeng-pmm2 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 97.6456 | 96.4829 | 98.8367 | 71.2472 | 29408 | 1072 | 28971 | 341 | 255 | 74.7801 | |
| bgallagher-sentieon | SNP | * | map_l150_m2_e0 | het | 98.7961 | 99.2748 | 98.3220 | 79.7541 | 19987 | 146 | 19981 | 341 | 50 | 14.6628 | |
| bgallagher-sentieon | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 97.6411 | 96.9703 | 98.3214 | 47.5930 | 19972 | 624 | 19973 | 341 | 336 | 98.5337 | |
| ndellapenna-hhga | INDEL | * | lowcmp_SimpleRepeat_triTR_11to50 | * | 94.6955 | 94.4156 | 94.9771 | 66.7371 | 6357 | 376 | 6429 | 340 | 300 | 88.2353 | |
| qzeng-custom | INDEL | I6_15 | HG002complexvar | * | 92.2263 | 91.5275 | 92.9358 | 54.4267 | 4386 | 406 | 4473 | 340 | 144 | 42.3529 | |
| gduggal-snapvard | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | * | 26.8403 | 19.6198 | 42.4704 | 32.3024 | 258 | 1057 | 251 | 340 | 290 | 85.2941 | |
| gduggal-snapvard | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | het | 35.5751 | 30.6061 | 42.4704 | 32.1470 | 101 | 229 | 251 | 340 | 290 | 85.2941 | |
| gduggal-snapvard | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 88.6006 | 96.8987 | 81.6117 | 67.2685 | 1531 | 49 | 1509 | 340 | 6 | 1.7647 | |