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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
74001-74050 / 86044 show all | |||||||||||||||
| raldana-dualsentieon | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 95.0639 | 91.0895 | 99.4009 | 86.9340 | 2157 | 211 | 2157 | 13 | 10 | 76.9231 | |
| jmaeng-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 96.2878 | 93.9576 | 98.7365 | 52.3236 | 3281 | 211 | 3282 | 42 | 37 | 88.0952 | |
| gduggal-snapfb | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | homalt | 0.0000 | 0.0000 | 0.0000 | 0 | 211 | 0 | 0 | 0 | |||
| ghariani-varprowl | SNP | * | map_l150_m1_e0 | homalt | 98.8738 | 98.1283 | 99.6307 | 72.3027 | 11062 | 211 | 11062 | 41 | 25 | 60.9756 | |
| ghariani-varprowl | SNP | ti | map_siren | homalt | 99.5932 | 99.4435 | 99.7434 | 52.5183 | 37705 | 211 | 37706 | 97 | 56 | 57.7320 | |
| gduggal-snapplat | SNP | tv | map_l250_m2_e0 | homalt | 87.3121 | 77.4813 | 100.0000 | 90.2170 | 726 | 211 | 726 | 0 | 0 | ||
| gduggal-snapplat | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | homalt | 0.0000 | 0.0000 | 0.0000 | 0 | 211 | 0 | 0 | 0 | |||
| gduggal-snapplat | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 40.8570 | 44.3272 | 37.8906 | 67.8795 | 168 | 211 | 291 | 477 | 388 | 81.3417 | |
| gduggal-snapplat | INDEL | I6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 21.3305 | 14.5749 | 39.7590 | 79.5062 | 36 | 211 | 33 | 50 | 0 | 0.0000 | |
| gduggal-snapvard | SNP | * | lowcmp_SimpleRepeat_triTR_11to50 | * | 96.3550 | 97.1312 | 95.5910 | 44.3893 | 7144 | 211 | 7068 | 326 | 14 | 4.2945 | |
| gduggal-snapvard | SNP | tv | lowcmp_SimpleRepeat_quadTR_11to50 | * | 93.8195 | 97.1685 | 90.6935 | 51.4915 | 7241 | 211 | 7153 | 734 | 47 | 6.4033 | |
| mlin-fermikit | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_51to200 | hetalt | 68.3658 | 51.9362 | 100.0000 | 43.6433 | 228 | 211 | 297 | 0 | 0 | ||
| qzeng-custom | INDEL | I6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 75.1472 | 60.1887 | 100.0000 | 53.6122 | 319 | 211 | 122 | 0 | 0 | ||
| gduggal-bwavard | INDEL | D6_15 | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 68.5368 | 52.3702 | 99.1416 | 33.0460 | 232 | 211 | 231 | 2 | 1 | 50.0000 | |
| gduggal-bwavard | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 66.8599 | 89.2948 | 53.4347 | 70.0637 | 1760 | 211 | 1758 | 1532 | 1441 | 94.0601 | |
| gduggal-bwavard | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 66.8599 | 89.2948 | 53.4347 | 70.0637 | 1760 | 211 | 1758 | 1532 | 1441 | 94.0601 | |
| gduggal-bwafb | INDEL | * | map_l100_m2_e0 | * | 96.2600 | 94.2865 | 98.3179 | 84.2676 | 3482 | 211 | 3507 | 60 | 20 | 33.3333 | |
| ciseli-custom | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 51.0479 | 89.1961 | 35.7556 | 37.7138 | 1742 | 211 | 1732 | 3112 | 2889 | 92.8342 | |
| anovak-vg | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_11to50 | het | 83.8258 | 90.7659 | 77.8716 | 35.7639 | 2074 | 211 | 2305 | 655 | 476 | 72.6718 | |
| asubramanian-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 96.1487 | 95.7792 | 96.5210 | 75.6177 | 4788 | 211 | 4772 | 172 | 130 | 75.5814 | |
| asubramanian-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 96.1487 | 95.7792 | 96.5210 | 75.6177 | 4788 | 211 | 4772 | 172 | 130 | 75.5814 | |
| jli-custom | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | hetalt | 90.6149 | 83.1470 | 99.5567 | 28.0153 | 1041 | 211 | 1123 | 5 | 5 | 100.0000 | |
| ckim-vqsr | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 97.8202 | 96.1199 | 99.5818 | 26.2339 | 5227 | 211 | 5239 | 22 | 22 | 100.0000 | |
| ckim-vqsr | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 97.4580 | 95.5784 | 99.4130 | 24.4663 | 4561 | 211 | 4573 | 27 | 27 | 100.0000 | |
| egarrison-hhga | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 95.7416 | 95.5607 | 95.9231 | 39.1360 | 4542 | 211 | 4541 | 193 | 74 | 38.3420 | |
| ckim-isaac | INDEL | D1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 98.9925 | 98.5647 | 99.4241 | 53.5139 | 14558 | 212 | 14501 | 84 | 48 | 57.1429 | |
| dgrover-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 98.2421 | 98.0870 | 98.3978 | 52.9535 | 10870 | 212 | 10870 | 177 | 173 | 97.7401 | |
| gduggal-bwaplat | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 73.3411 | 59.7723 | 94.8795 | 89.6250 | 315 | 212 | 315 | 17 | 16 | 94.1176 | |
| gduggal-bwaplat | INDEL | I1_5 | map_l100_m1_e0 | het | 83.8279 | 72.7156 | 98.9492 | 92.4321 | 565 | 212 | 565 | 6 | 1 | 16.6667 | |
| gduggal-bwafb | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_51to200 | hetalt | 72.2230 | 56.8228 | 99.0741 | 25.0000 | 279 | 212 | 107 | 1 | 1 | 100.0000 | |
| ghariani-varprowl | INDEL | I16_PLUS | lowcmp_SimpleRepeat_quadTR_11to50 | * | 55.0492 | 45.3608 | 70.0000 | 75.3208 | 176 | 212 | 175 | 75 | 71 | 94.6667 | |
| ghariani-varprowl | SNP | * | map_l150_m2_e0 | homalt | 98.9108 | 98.1879 | 99.6443 | 74.5311 | 11487 | 212 | 11487 | 41 | 25 | 60.9756 | |
| ghariani-varprowl | SNP | tv | map_l125_m2_e0 | * | 97.4321 | 98.7143 | 96.1827 | 78.0708 | 16277 | 212 | 16277 | 646 | 117 | 18.1115 | |
| gduggal-snapfb | SNP | * | map_l250_m2_e1 | homalt | 95.5941 | 92.2001 | 99.2475 | 92.8509 | 2506 | 212 | 2506 | 19 | 10 | 52.6316 | |
| raldana-dualsentieon | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_51to200 | * | 78.0920 | 69.5839 | 88.9706 | 48.6792 | 485 | 212 | 484 | 60 | 59 | 98.3333 | |
| ltrigg-rtg1 | INDEL | * | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 99.5721 | 99.2498 | 99.8965 | 56.0085 | 28048 | 212 | 27998 | 29 | 16 | 55.1724 | |
| ltrigg-rtg1 | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | het | 98.7118 | 98.0915 | 99.3400 | 56.1553 | 10896 | 212 | 10837 | 72 | 12 | 16.6667 | |
| jpowers-varprowl | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | het | 25.7159 | 56.7347 | 16.6259 | 49.0343 | 278 | 212 | 272 | 1364 | 1359 | 99.6334 | |
| ltrigg-rtg1 | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 93.4727 | 88.3644 | 99.2078 | 40.1968 | 1610 | 212 | 1628 | 13 | 12 | 92.3077 | |
| qzeng-custom | INDEL | I16_PLUS | HG002complexvar | * | 86.4583 | 83.8044 | 89.2857 | 60.9632 | 1097 | 212 | 1100 | 132 | 51 | 38.6364 | |
| qzeng-custom | SNP | ti | map_l250_m0_e0 | homalt | 67.7742 | 51.3761 | 99.5475 | 94.9738 | 224 | 212 | 220 | 1 | 1 | 100.0000 | |
| mlin-fermikit | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 87.1157 | 91.3786 | 83.2329 | 63.6787 | 2247 | 212 | 2209 | 445 | 437 | 98.2022 | |
| mlin-fermikit | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_11to50 | * | 95.7607 | 94.8001 | 96.7410 | 36.3288 | 3865 | 212 | 3859 | 130 | 125 | 96.1538 | |
| ltrigg-rtg2 | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 94.9326 | 91.0397 | 99.1732 | 34.1898 | 2154 | 212 | 2159 | 18 | 18 | 100.0000 | |
| ltrigg-rtg2 | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | * | 98.5119 | 97.7585 | 99.2769 | 36.5690 | 9246 | 212 | 9199 | 67 | 51 | 76.1194 | |
| jlack-gatk | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 92.7461 | 88.4908 | 97.4313 | 66.6799 | 1630 | 212 | 1631 | 43 | 33 | 76.7442 | |
| hfeng-pmm1 | INDEL | D16_PLUS | * | * | 97.5778 | 96.8750 | 98.2909 | 66.6166 | 6572 | 212 | 6556 | 114 | 68 | 59.6491 | |
| hfeng-pmm1 | INDEL | I16_PLUS | * | * | 97.6402 | 96.6756 | 98.6242 | 68.7700 | 6165 | 212 | 6165 | 86 | 59 | 68.6047 | |
| hfeng-pmm1 | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 92.2750 | 85.9974 | 99.5413 | 87.6183 | 1302 | 212 | 1302 | 6 | 4 | 66.6667 | |
| ciseli-custom | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 60.2448 | 65.3028 | 55.9140 | 55.1447 | 399 | 212 | 468 | 369 | 297 | 80.4878 | |