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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
15501-15550 / 86044 show all | |||||||||||||||
| hfeng-pmm3 | SNP | * | map_l100_m2_e1 | homalt | 99.8561 | 99.8381 | 99.8740 | 63.2761 | 27751 | 45 | 27751 | 35 | 17 | 48.5714 | |
| hfeng-pmm2 | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | * | 97.4316 | 96.3170 | 98.5722 | 66.0922 | 1726 | 66 | 1726 | 25 | 17 | 68.0000 | |
| hfeng-pmm2 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 92.2579 | 87.4251 | 97.6562 | 63.9582 | 876 | 126 | 875 | 21 | 17 | 80.9524 | |
| hfeng-pmm2 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 98.0092 | 98.6133 | 97.4125 | 67.2319 | 640 | 9 | 640 | 17 | 17 | 100.0000 | |
| hfeng-pmm2 | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 98.5639 | 99.8469 | 97.3134 | 72.4846 | 652 | 1 | 652 | 18 | 17 | 94.4444 | |
| hfeng-pmm2 | SNP | ti | map_l125_m0_e0 | * | 99.1282 | 99.3496 | 98.9077 | 76.2142 | 12679 | 83 | 12677 | 140 | 17 | 12.1429 | |
| hfeng-pmm2 | SNP | tv | map_l100_m1_e0 | * | 99.4801 | 99.5919 | 99.3687 | 67.2876 | 24401 | 100 | 24397 | 155 | 17 | 10.9677 | |
| hfeng-pmm2 | SNP | tv | map_l100_m2_e0 | * | 99.4872 | 99.6005 | 99.3742 | 68.8945 | 24933 | 100 | 24929 | 157 | 17 | 10.8280 | |
| hfeng-pmm2 | SNP | tv | map_l100_m2_e1 | * | 99.4903 | 99.6045 | 99.3764 | 68.9155 | 25183 | 100 | 25179 | 158 | 17 | 10.7595 | |
| jlack-gatk | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 89.0056 | 80.5701 | 99.4139 | 40.3057 | 3081 | 743 | 3223 | 19 | 17 | 89.4737 | |
| jlack-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 96.9617 | 96.7357 | 97.1888 | 78.6888 | 1215 | 41 | 1210 | 35 | 17 | 48.5714 | |
| jlack-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 99.7395 | 99.7766 | 99.7024 | 56.2348 | 14737 | 33 | 14739 | 44 | 17 | 38.6364 | |
| jlack-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | homalt | 95.5224 | 100.0000 | 91.4286 | 46.0154 | 192 | 0 | 192 | 18 | 17 | 94.4444 | |
| jlack-gatk | INDEL | I16_PLUS | HG002compoundhet | het | 61.9313 | 91.4894 | 46.8085 | 90.8382 | 43 | 4 | 22 | 25 | 17 | 68.0000 | |
| ckim-isaac | INDEL | D16_PLUS | HG002compoundhet | hetalt | 86.1574 | 76.3485 | 98.8582 | 24.5694 | 1472 | 456 | 1645 | 19 | 17 | 89.4737 | |
| ckim-isaac | INDEL | D1_5 | HG002complexvar | homalt | 94.8892 | 91.0360 | 99.0830 | 48.9641 | 9648 | 950 | 9617 | 89 | 17 | 19.1011 | |
| ckim-isaac | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 67.8674 | 53.7223 | 92.1233 | 62.9442 | 267 | 230 | 269 | 23 | 17 | 73.9130 | |
| ckim-isaac | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 90.8242 | 84.7922 | 97.7800 | 34.6306 | 959 | 172 | 969 | 22 | 17 | 77.2727 | |
| dgrover-gatk | SNP | ti | map_siren | homalt | 99.8204 | 99.6914 | 99.9498 | 49.0891 | 37799 | 117 | 37793 | 19 | 17 | 89.4737 | |
| ckim-isaac | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 96.6052 | 94.2754 | 99.0530 | 53.1678 | 3656 | 222 | 3661 | 35 | 17 | 48.5714 | |
| ckim-isaac | SNP | * | map_l125_m2_e1 | * | 73.7959 | 58.5590 | 99.7510 | 72.8548 | 27641 | 19561 | 27643 | 69 | 17 | 24.6377 | |
| ckim-isaac | SNP | tv | HG002complexvar | het | 95.8287 | 92.0463 | 99.9352 | 18.9218 | 138745 | 11989 | 138887 | 90 | 17 | 18.8889 | |
| ckim-isaac | SNP | tv | HG002compoundhet | het | 84.5719 | 74.3206 | 98.1038 | 53.1755 | 3473 | 1200 | 3725 | 72 | 17 | 23.6111 | |
| ckim-vqsr | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 93.2704 | 87.7615 | 99.5173 | 36.9269 | 3356 | 468 | 3505 | 17 | 17 | 100.0000 | |
| ckim-vqsr | INDEL | * | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 99.6915 | 99.4869 | 99.8970 | 58.9754 | 28115 | 145 | 28118 | 29 | 17 | 58.6207 | |
| dgrover-gatk | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 94.0819 | 89.2259 | 99.4969 | 40.1872 | 3412 | 412 | 3560 | 18 | 17 | 94.4444 | |
| dgrover-gatk | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | het | 99.5450 | 99.5769 | 99.5131 | 63.1488 | 11061 | 47 | 11036 | 54 | 17 | 31.4815 | |
| egarrison-hhga | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 97.3469 | 96.9970 | 97.6994 | 59.7282 | 1292 | 40 | 1274 | 30 | 17 | 56.6667 | |
| egarrison-hhga | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 91.6667 | 93.6170 | 89.7959 | 66.0312 | 176 | 12 | 176 | 20 | 17 | 85.0000 | |
| egarrison-hhga | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 95.2221 | 93.4610 | 97.0508 | 84.9985 | 1415 | 99 | 1415 | 43 | 17 | 39.5349 | |
| egarrison-hhga | SNP | * | lowcmp_SimpleRepeat_quadTR_11to50 | het | 99.3197 | 98.9592 | 99.6829 | 37.2866 | 11314 | 119 | 11317 | 36 | 17 | 47.2222 | |
| egarrison-hhga | SNP | * | map_l100_m1_e0 | homalt | 99.8480 | 99.7630 | 99.9332 | 60.8894 | 26939 | 64 | 26939 | 18 | 17 | 94.4444 | |
| egarrison-hhga | SNP | * | map_l125_m0_e0 | het | 98.9341 | 98.2154 | 99.6635 | 75.5931 | 12438 | 226 | 12438 | 42 | 17 | 40.4762 | |
| egarrison-hhga | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 98.9430 | 98.7588 | 99.1279 | 78.7129 | 2387 | 30 | 2387 | 21 | 17 | 80.9524 | |
| egarrison-hhga | SNP | tv | map_l125_m1_e0 | * | 99.3983 | 99.0135 | 99.7861 | 68.1855 | 15858 | 158 | 15858 | 34 | 17 | 50.0000 | |
| egarrison-hhga | SNP | tv | map_l125_m2_e0 | * | 99.4065 | 99.0357 | 99.7800 | 70.1050 | 16330 | 159 | 16330 | 36 | 17 | 47.2222 | |
| egarrison-hhga | SNP | tv | map_l125_m2_e1 | * | 99.4064 | 99.0334 | 99.7822 | 70.1626 | 16496 | 161 | 16496 | 36 | 17 | 47.2222 | |
| egarrison-hhga | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 95.9717 | 97.4713 | 94.5175 | 69.3960 | 424 | 11 | 431 | 25 | 17 | 68.0000 | |
| egarrison-hhga | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 85.5570 | 79.7101 | 92.3295 | 70.6177 | 330 | 84 | 325 | 27 | 17 | 62.9630 | |
| ckim-vqsr | INDEL | I16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 96.2919 | 94.3909 | 98.2712 | 79.8126 | 1077 | 64 | 1080 | 19 | 17 | 89.4737 | |
| ckim-vqsr | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 99.4808 | 99.3427 | 99.6193 | 80.0419 | 10730 | 71 | 10730 | 41 | 17 | 41.4634 | |
| ckim-vqsr | SNP | ti | HG002compoundhet | * | 98.9109 | 97.9517 | 99.8891 | 36.4634 | 17120 | 358 | 17120 | 19 | 17 | 89.4737 | |
| gduggal-snapplat | SNP | * | segdup | het | 98.6817 | 98.5044 | 98.8598 | 94.8279 | 17058 | 259 | 17080 | 197 | 17 | 8.6294 | |
| gduggal-snapplat | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 89.5432 | 89.7781 | 89.3096 | 71.8319 | 3601 | 410 | 3609 | 432 | 17 | 3.9352 | |
| gduggal-snapplat | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 69.4882 | 58.7467 | 85.0365 | 91.8258 | 225 | 158 | 233 | 41 | 17 | 41.4634 | |
| gduggal-snapplat | SNP | ti | segdup | * | 99.0792 | 98.8483 | 99.3111 | 92.8755 | 19312 | 225 | 19317 | 134 | 17 | 12.6866 | |
| gduggal-snapvard | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_51to200 | * | 1.8576 | 0.9740 | 20.0000 | 60.0000 | 6 | 610 | 6 | 24 | 17 | 70.8333 | |
| gduggal-snapvard | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_51to200 | het | 3.3520 | 1.8293 | 20.0000 | 59.4595 | 3 | 161 | 6 | 24 | 17 | 70.8333 | |
| gduggal-snapfb | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 75.3468 | 98.8372 | 60.8781 | 62.7229 | 2465 | 29 | 2482 | 1595 | 17 | 1.0658 | |
| gduggal-snapfb | SNP | * | segdup | homalt | 99.6002 | 99.7114 | 99.4891 | 90.4625 | 10712 | 31 | 10711 | 55 | 17 | 30.9091 | |