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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
10001-10050 / 86044 show all | |||||||||||||||
| gduggal-snapfb | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 88.5630 | 82.2103 | 95.9796 | 32.1478 | 5661 | 1225 | 1886 | 79 | 51 | 64.5570 | |
| gduggal-snapfb | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | het | 57.4519 | 55.8442 | 59.1549 | 62.6561 | 215 | 170 | 336 | 232 | 51 | 21.9828 | |
| gduggal-snapplat | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 28.9593 | 17.5631 | 82.4742 | 66.3778 | 320 | 1502 | 320 | 68 | 51 | 75.0000 | |
| ghariani-varprowl | SNP | ti | map_l250_m2_e1 | het | 95.1903 | 97.7872 | 92.7278 | 92.3245 | 3226 | 73 | 3226 | 253 | 51 | 20.1581 | |
| gduggal-snapplat | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 55.7555 | 54.6245 | 56.9343 | 95.0071 | 691 | 574 | 702 | 531 | 51 | 9.6045 | |
| gduggal-snapvard | INDEL | * | map_l150_m0_e0 | * | 82.1730 | 92.2179 | 74.1015 | 92.7012 | 474 | 40 | 701 | 245 | 50 | 20.4082 | |
| gduggal-snapfb | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 72.1995 | 97.7700 | 57.2314 | 91.8059 | 833 | 19 | 831 | 621 | 50 | 8.0515 | |
| gduggal-snapfb | SNP | tv | map_l250_m2_e0 | het | 94.4093 | 96.1856 | 92.6975 | 87.4548 | 1866 | 74 | 1866 | 147 | 50 | 34.0136 | |
| gduggal-snapfb | SNP | tv | map_l250_m2_e1 | het | 94.3848 | 96.2341 | 92.6053 | 87.5145 | 1891 | 74 | 1891 | 151 | 50 | 33.1126 | |
| gduggal-snapvard | INDEL | D1_5 | map_l150_m1_e0 | het | 83.7248 | 98.3402 | 72.8916 | 90.7572 | 474 | 8 | 605 | 225 | 50 | 22.2222 | |
| gduggal-snapvard | INDEL | I6_15 | map_l125_m1_e0 | * | 59.6747 | 64.1509 | 55.7823 | 82.2678 | 34 | 19 | 82 | 65 | 50 | 76.9231 | |
| gduggal-snapvard | INDEL | I6_15 | map_l125_m1_e0 | het | 65.6975 | 86.6667 | 52.8986 | 82.1244 | 26 | 4 | 73 | 65 | 50 | 76.9231 | |
| gduggal-snapvard | INDEL | I6_15 | segdup | * | 60.2107 | 55.4286 | 65.8960 | 90.9708 | 97 | 78 | 114 | 59 | 50 | 84.7458 | |
| gduggal-snapvard | INDEL | I6_15 | segdup | het | 71.6829 | 85.5422 | 61.6883 | 91.3966 | 71 | 12 | 95 | 59 | 50 | 84.7458 | |
| gduggal-snapvard | SNP | * | segdup | homalt | 98.5503 | 97.6171 | 99.5016 | 88.8814 | 10487 | 256 | 10381 | 52 | 50 | 96.1538 | |
| ghariani-varprowl | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 70.4495 | 67.4641 | 73.7113 | 75.8706 | 141 | 68 | 143 | 51 | 50 | 98.0392 | |
| ghariani-varprowl | INDEL | I16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 47.1513 | 38.8350 | 60.0000 | 86.3874 | 80 | 126 | 78 | 52 | 50 | 96.1538 | |
| gduggal-snapfb | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 77.8072 | 93.6126 | 66.5680 | 74.1046 | 894 | 61 | 900 | 452 | 50 | 11.0619 | |
| gduggal-snapfb | INDEL | I6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 47.8883 | 35.6275 | 73.0159 | 53.4483 | 88 | 159 | 138 | 51 | 50 | 98.0392 | |
| gduggal-snapfb | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 70.1721 | 68.3616 | 72.0812 | 51.2376 | 121 | 56 | 142 | 55 | 50 | 90.9091 | |
| rpoplin-dv42 | SNP | tv | map_l100_m0_e0 | het | 98.5640 | 98.8507 | 98.2789 | 68.7061 | 7139 | 83 | 7138 | 125 | 50 | 40.0000 | |
| mlin-fermikit | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 90.3030 | 95.8199 | 85.3868 | 72.4980 | 298 | 13 | 298 | 51 | 50 | 98.0392 | |
| mlin-fermikit | SNP | tv | segdup | * | 97.8523 | 97.1988 | 98.5147 | 87.3016 | 8293 | 239 | 8291 | 125 | 50 | 40.0000 | |
| qzeng-custom | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_51to200 | het | 83.1167 | 92.6829 | 75.3404 | 62.6343 | 152 | 12 | 498 | 163 | 50 | 30.6748 | |
| ltrigg-rtg2 | INDEL | D6_15 | * | hetalt | 97.5461 | 95.7915 | 99.3661 | 40.2288 | 7830 | 344 | 7838 | 50 | 50 | 100.0000 | |
| ltrigg-rtg2 | INDEL | D6_15 | HG002complexvar | * | 97.7900 | 96.9257 | 98.6698 | 51.5393 | 5139 | 163 | 4970 | 67 | 50 | 74.6269 | |
| ltrigg-rtg2 | SNP | * | segdup | homalt | 99.7490 | 99.9628 | 99.5362 | 88.2598 | 10739 | 4 | 10731 | 50 | 50 | 100.0000 | |
| ndellapenna-hhga | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 99.2273 | 98.7916 | 99.6668 | 58.8530 | 34991 | 428 | 34997 | 117 | 50 | 42.7350 | |
| qzeng-custom | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 85.0650 | 84.5638 | 85.5721 | 60.8569 | 126 | 23 | 344 | 58 | 50 | 86.2069 | |
| qzeng-custom | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 95.6210 | 97.3818 | 93.9229 | 89.2161 | 2306 | 62 | 2411 | 156 | 50 | 32.0513 | |
| qzeng-custom | SNP | ti | map_l125_m1_e0 | homalt | 82.9138 | 71.1453 | 99.3472 | 63.5077 | 7858 | 3187 | 7762 | 51 | 50 | 98.0392 | |
| ndellapenna-hhga | INDEL | * | map_siren | het | 97.8580 | 98.1145 | 97.6028 | 80.6313 | 4423 | 85 | 4438 | 109 | 50 | 45.8716 | |
| ndellapenna-hhga | INDEL | D1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 99.5852 | 99.4085 | 99.7626 | 54.0647 | 25209 | 150 | 25209 | 60 | 50 | 83.3333 | |
| dgrover-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 96.9211 | 94.3694 | 99.6146 | 31.5700 | 12989 | 775 | 13182 | 51 | 50 | 98.0392 | |
| dgrover-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 96.8950 | 94.3201 | 99.6144 | 34.3188 | 13235 | 797 | 13433 | 52 | 50 | 96.1538 | |
| ckim-isaac | SNP | * | * | homalt | 98.3805 | 96.8182 | 99.9940 | 14.4545 | 1142612 | 37550 | 1142668 | 69 | 50 | 72.4638 | |
| ckim-vqsr | INDEL | D16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 93.5214 | 97.8947 | 89.5221 | 87.3282 | 651 | 14 | 487 | 57 | 50 | 87.7193 | |
| egarrison-hhga | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 96.7392 | 94.5387 | 99.0446 | 39.1669 | 5574 | 322 | 5598 | 54 | 50 | 92.5926 | |
| egarrison-hhga | SNP | * | map_l100_m2_e0 | * | 99.5430 | 99.2483 | 99.8395 | 64.7214 | 73408 | 556 | 73409 | 118 | 50 | 42.3729 | |
| egarrison-hhga | SNP | * | map_l100_m2_e1 | * | 99.5464 | 99.2547 | 99.8398 | 64.7282 | 74180 | 557 | 74181 | 119 | 50 | 42.0168 | |
| ckim-isaac | INDEL | D6_15 | HG002compoundhet | hetalt | 90.9387 | 83.9774 | 99.1585 | 17.7185 | 6845 | 1306 | 7188 | 61 | 50 | 81.9672 | |
| dgrover-gatk | SNP | * | map_l150_m2_e0 | het | 98.9689 | 99.1805 | 98.7582 | 81.1353 | 19968 | 165 | 19962 | 251 | 50 | 19.9203 | |
| dgrover-gatk | SNP | * | map_l150_m2_e1 | het | 98.9757 | 99.1897 | 98.7625 | 81.1801 | 20198 | 165 | 20192 | 253 | 50 | 19.7628 | |
| dgrover-gatk | SNP | ti | map_l100_m2_e0 | * | 99.5249 | 99.4730 | 99.5767 | 67.5957 | 48703 | 258 | 48696 | 207 | 50 | 24.1546 | |
| dgrover-gatk | SNP | ti | map_l100_m2_e1 | * | 99.5279 | 99.4766 | 99.5792 | 67.5880 | 49226 | 259 | 49219 | 208 | 50 | 24.0385 | |
| egarrison-hhga | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 93.3178 | 93.0147 | 93.6229 | 58.8750 | 1012 | 76 | 1013 | 69 | 50 | 72.4638 | |
| egarrison-hhga | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 96.7392 | 94.5387 | 99.0446 | 39.1669 | 5574 | 322 | 5598 | 54 | 50 | 92.5926 | |
| ckim-vqsr | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_51to200 | * | 92.6522 | 92.5170 | 92.7878 | 58.2513 | 680 | 55 | 669 | 52 | 50 | 96.1538 | |
| gduggal-bwaplat | INDEL | I1_5 | HG002complexvar | homalt | 95.0189 | 90.9429 | 99.4774 | 52.2999 | 12230 | 1218 | 12183 | 64 | 50 | 78.1250 | |
| gduggal-bwaplat | INDEL | I6_15 | HG002complexvar | * | 86.2963 | 77.2538 | 97.7362 | 64.0519 | 3702 | 1090 | 3713 | 86 | 50 | 58.1395 | |