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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
20151-20200 / 86044 show all | |||||||||||||||
| ndellapenna-hhga | SNP | tv | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 99.4006 | 99.1437 | 99.6587 | 62.2119 | 27441 | 237 | 27449 | 94 | 60 | 63.8298 | |
| ckim-gatk | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 97.9160 | 99.5572 | 96.3281 | 83.1889 | 1349 | 6 | 1233 | 47 | 30 | 63.8298 | |
| asubramanian-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 92.1502 | 94.7199 | 89.7161 | 77.6402 | 2063 | 115 | 1928 | 221 | 141 | 63.8009 | |
| gduggal-bwaplat | INDEL | I1_5 | * | * | 93.7478 | 88.8514 | 99.2155 | 64.5183 | 133867 | 16797 | 133798 | 1058 | 675 | 63.7996 | |
| rpoplin-dv42 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 96.7592 | 96.2430 | 97.2808 | 87.7639 | 2075 | 81 | 2075 | 58 | 37 | 63.7931 | |
| gduggal-snapplat | INDEL | D1_5 | HG002compoundhet | * | 46.3272 | 44.0131 | 48.8981 | 72.6225 | 5385 | 6850 | 5880 | 6145 | 3920 | 63.7917 | |
| gduggal-snapfb | INDEL | * | HG002complexvar | homalt | 93.4910 | 91.9932 | 95.0384 | 54.0929 | 24863 | 2164 | 24901 | 1300 | 829 | 63.7692 | |
| mlin-fermikit | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 86.9863 | 88.6640 | 85.3710 | 87.2287 | 2409 | 308 | 2416 | 414 | 264 | 63.7681 | |
| ckim-isaac | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 82.0986 | 72.9041 | 93.9468 | 53.8786 | 4609 | 1713 | 4625 | 298 | 190 | 63.7584 | |
| ckim-isaac | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 82.0986 | 72.9041 | 93.9468 | 53.8786 | 4609 | 1713 | 4625 | 298 | 190 | 63.7584 | |
| jpowers-varprowl | INDEL | * | map_l150_m2_e1 | het | 92.1590 | 92.8571 | 91.4712 | 91.9353 | 858 | 66 | 858 | 80 | 51 | 63.7500 | |
| ltrigg-rtg1 | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | * | 97.9756 | 96.4774 | 99.5211 | 49.0897 | 35303 | 1289 | 35537 | 171 | 109 | 63.7427 | |
| ckim-isaac | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 83.1246 | 82.0664 | 84.2105 | 65.4096 | 1112 | 243 | 896 | 168 | 107 | 63.6905 | |
| jli-custom | INDEL | * | * | het | 99.5119 | 99.3015 | 99.7232 | 58.0133 | 192777 | 1356 | 192389 | 534 | 340 | 63.6704 | |
| jlack-gatk | SNP | tv | map_l100_m1_e0 | homalt | 99.3888 | 98.9052 | 99.8772 | 60.2177 | 8944 | 99 | 8944 | 11 | 7 | 63.6364 | |
| jlack-gatk | SNP | tv | map_l100_m2_e0 | homalt | 99.4002 | 98.9255 | 99.8795 | 62.7206 | 9115 | 99 | 9115 | 11 | 7 | 63.6364 | |
| jlack-gatk | SNP | tv | map_l100_m2_e1 | homalt | 99.4059 | 98.9357 | 99.8806 | 62.6933 | 9203 | 99 | 9203 | 11 | 7 | 63.6364 | |
| jlack-gatk | SNP | tv | map_l125_m1_e0 | homalt | 99.1843 | 98.5666 | 99.8099 | 65.3618 | 5776 | 84 | 5776 | 11 | 7 | 63.6364 | |
| jlack-gatk | SNP | tv | map_l125_m2_e0 | homalt | 99.1889 | 98.5707 | 99.8149 | 67.8533 | 5931 | 86 | 5931 | 11 | 7 | 63.6364 | |
| jlack-gatk | SNP | tv | map_l125_m2_e1 | homalt | 99.1882 | 98.5677 | 99.8166 | 67.8547 | 5987 | 87 | 5987 | 11 | 7 | 63.6364 | |
| jlack-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 97.4121 | 96.3255 | 98.5235 | 67.0062 | 734 | 28 | 734 | 11 | 7 | 63.6364 | |
| jlack-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | * | 98.6004 | 98.3998 | 98.8017 | 51.3514 | 3628 | 59 | 3628 | 44 | 28 | 63.6364 | |
| hfeng-pmm3 | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 97.1636 | 95.9569 | 98.4012 | 71.9413 | 712 | 30 | 677 | 11 | 7 | 63.6364 | |
| hfeng-pmm3 | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 97.2828 | 95.8599 | 98.7486 | 72.8116 | 903 | 39 | 868 | 11 | 7 | 63.6364 | |
| hfeng-pmm3 | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_11to50 | * | 96.8059 | 94.2371 | 99.5186 | 62.0495 | 2273 | 139 | 2274 | 11 | 7 | 63.6364 | |
| hfeng-pmm2 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 98.6376 | 98.7722 | 98.5034 | 72.1591 | 724 | 9 | 724 | 11 | 7 | 63.6364 | |
| hfeng-pmm2 | INDEL | * | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 99.7892 | 99.6568 | 99.9219 | 57.6377 | 28163 | 97 | 28165 | 22 | 14 | 63.6364 | |
| hfeng-pmm2 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 93.2118 | 90.9722 | 95.5645 | 79.3505 | 262 | 26 | 237 | 11 | 7 | 63.6364 | |
| ckim-isaac | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 70.1319 | 59.4340 | 85.5263 | 73.7024 | 63 | 43 | 65 | 11 | 7 | 63.6364 | |
| ckim-isaac | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 82.4178 | 78.4483 | 86.8106 | 63.9896 | 364 | 100 | 362 | 55 | 35 | 63.6364 | |
| ckim-vqsr | INDEL | D1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 99.7571 | 99.6017 | 99.9130 | 55.8468 | 25258 | 101 | 25261 | 22 | 14 | 63.6364 | |
| ckim-vqsr | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 97.0443 | 95.9215 | 98.1938 | 78.8174 | 635 | 27 | 598 | 11 | 7 | 63.6364 | |
| egarrison-hhga | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 98.5283 | 98.3529 | 98.7044 | 50.2636 | 836 | 14 | 838 | 11 | 7 | 63.6364 | |
| egarrison-hhga | INDEL | I16_PLUS | map_siren | * | 83.2113 | 80.2326 | 86.4198 | 84.0551 | 69 | 17 | 70 | 11 | 7 | 63.6364 | |
| jli-custom | INDEL | I16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | * | 95.5344 | 93.5417 | 97.6139 | 77.7831 | 449 | 31 | 450 | 11 | 7 | 63.6364 | |
| jli-custom | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.9133 | 99.8812 | 99.9455 | 56.3725 | 20175 | 24 | 20175 | 11 | 7 | 63.6364 | |
| ltrigg-rtg2 | INDEL | D16_PLUS | * | * | 96.9914 | 94.9292 | 99.1450 | 56.0917 | 6440 | 344 | 6378 | 55 | 35 | 63.6364 | |
| ltrigg-rtg1 | INDEL | D1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 99.6222 | 99.3336 | 99.9125 | 51.6616 | 25190 | 169 | 25113 | 22 | 14 | 63.6364 | |
| ltrigg-rtg1 | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 99.2002 | 98.7477 | 99.6569 | 58.1790 | 3233 | 41 | 3195 | 11 | 7 | 63.6364 | |
| mlin-fermikit | SNP | * | lowcmp_SimpleRepeat_diTR_51to200 | homalt | 59.4595 | 73.3333 | 50.0000 | 96.4630 | 11 | 4 | 11 | 11 | 7 | 63.6364 | |
| rpoplin-dv42 | SNP | ti | lowcmp_SimpleRepeat_diTR_11to50 | * | 99.7622 | 99.7519 | 99.7725 | 68.8442 | 4825 | 12 | 4825 | 11 | 7 | 63.6364 | |
| rpoplin-dv42 | SNP | tv | map_l250_m2_e1 | het | 97.8128 | 97.8626 | 97.7631 | 87.3293 | 1923 | 42 | 1923 | 44 | 28 | 63.6364 | |
| rpoplin-dv42 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 99.1930 | 99.1930 | 99.1930 | 76.9218 | 1352 | 11 | 1352 | 11 | 7 | 63.6364 | |
| mlin-fermikit | INDEL | D6_15 | map_l100_m0_e0 | * | 67.1440 | 61.1650 | 74.4186 | 83.6190 | 63 | 40 | 64 | 22 | 14 | 63.6364 | |
| raldana-dualsentieon | INDEL | * | lowcmp_SimpleRepeat_triTR_11to50 | * | 99.4334 | 99.0346 | 99.8354 | 46.3028 | 6668 | 65 | 6670 | 11 | 7 | 63.6364 | |
| rpoplin-dv42 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 96.3619 | 97.0541 | 95.6795 | 75.5568 | 1219 | 37 | 1218 | 55 | 35 | 63.6364 | |
| ndellapenna-hhga | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 94.2193 | 94.2819 | 94.1567 | 58.3748 | 709 | 43 | 709 | 44 | 28 | 63.6364 | |
| ndellapenna-hhga | INDEL | I16_PLUS | lowcmp_SimpleRepeat_quadTR_11to50 | * | 87.2160 | 81.7010 | 93.5294 | 74.9816 | 317 | 71 | 318 | 22 | 14 | 63.6364 | |
| ndellapenna-hhga | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_11to50 | * | 97.1160 | 95.4815 | 98.8074 | 51.9618 | 5473 | 259 | 5468 | 66 | 42 | 63.6364 | |
| ndellapenna-hhga | INDEL | I1_5 | segdup | * | 98.8658 | 98.7724 | 98.9593 | 94.1605 | 1046 | 13 | 1046 | 11 | 7 | 63.6364 | |