PrecisionFDA
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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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
70701-70750 / 86044 show all | |||||||||||||||
| anovak-vg | INDEL | D6_15 | lowcmp_SimpleRepeat_triTR_51to200 | * | 22.4849 | 18.3099 | 29.1262 | 29.9320 | 26 | 116 | 30 | 73 | 61 | 83.5616 | |
| cchapple-custom | SNP | * | map_l250_m0_e0 | * | 95.4584 | 94.5667 | 96.3671 | 93.6675 | 2019 | 116 | 2016 | 76 | 21 | 27.6316 | |
| cchapple-custom | SNP | tv | map_l250_m1_e0 | * | 95.5601 | 95.6177 | 95.5026 | 89.6633 | 2531 | 116 | 2527 | 119 | 24 | 20.1681 | |
| ciseli-custom | INDEL | * | segdup | homalt | 85.4420 | 87.9167 | 83.1028 | 93.1884 | 844 | 116 | 841 | 171 | 150 | 87.7193 | |
| ckim-dragen | SNP | ti | map_l100_m2_e0 | homalt | 99.6194 | 99.3610 | 99.8792 | 57.3994 | 18192 | 117 | 18197 | 22 | 20 | 90.9091 | |
| ckim-isaac | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 90.9907 | 84.0382 | 99.1974 | 59.7025 | 616 | 117 | 618 | 5 | 2 | 40.0000 | |
| ckim-dragen | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 95.9473 | 92.9048 | 99.1959 | 36.3902 | 1532 | 117 | 1727 | 14 | 14 | 100.0000 | |
| cchapple-custom | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 98.3820 | 97.9096 | 98.8590 | 53.4408 | 5480 | 117 | 13083 | 151 | 132 | 87.4172 | |
| gduggal-bwafb | SNP | * | segdup | het | 98.4151 | 99.3244 | 97.5223 | 92.8812 | 17200 | 117 | 17200 | 437 | 12 | 2.7460 | |
| gduggal-bwaplat | INDEL | D1_5 | map_l100_m0_e0 | homalt | 70.5000 | 54.6512 | 99.2958 | 90.2204 | 141 | 117 | 141 | 1 | 0 | 0.0000 | |
| gduggal-bwaplat | INDEL | D1_5 | map_l150_m2_e1 | homalt | 69.1293 | 52.8226 | 100.0000 | 93.1414 | 131 | 117 | 131 | 0 | 0 | ||
| gduggal-bwaplat | INDEL | I1_5 | map_l150_m1_e0 | homalt | 58.0645 | 40.9091 | 100.0000 | 94.7641 | 81 | 117 | 81 | 0 | 0 | ||
| gduggal-bwavard | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 96.2853 | 97.2759 | 95.3147 | 68.9687 | 4178 | 117 | 4150 | 204 | 19 | 9.3137 | |
| ltrigg-rtg1 | INDEL | I1_5 | HG002complexvar | homalt | 99.5102 | 99.1299 | 99.8933 | 45.8849 | 13330 | 117 | 13110 | 14 | 9 | 64.2857 | |
| jmaeng-gatk | INDEL | * | map_siren | * | 97.8625 | 98.4211 | 97.3103 | 85.3526 | 7293 | 117 | 7308 | 202 | 30 | 14.8515 | |
| ltrigg-rtg1 | SNP | ti | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 99.5464 | 99.5815 | 99.5114 | 49.8381 | 27842 | 117 | 27901 | 137 | 8 | 5.8394 | |
| jpowers-varprowl | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_11to50 | het | 71.2396 | 76.0246 | 67.0213 | 78.1818 | 371 | 117 | 378 | 186 | 179 | 96.2366 | |
| jpowers-varprowl | SNP | tv | map_siren | homalt | 99.3790 | 99.3213 | 99.4367 | 59.4375 | 17123 | 117 | 17123 | 97 | 72 | 74.2268 | |
| jmaeng-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 98.6890 | 98.1776 | 99.2058 | 77.1478 | 6303 | 117 | 6246 | 50 | 22 | 44.0000 | |
| jmaeng-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 98.6890 | 98.1776 | 99.2058 | 77.1478 | 6303 | 117 | 6246 | 50 | 22 | 44.0000 | |
| ndellapenna-hhga | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 96.1666 | 95.2420 | 97.1093 | 71.1366 | 2342 | 117 | 2318 | 69 | 36 | 52.1739 | |
| qzeng-custom | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 94.3510 | 97.7144 | 91.2114 | 71.0965 | 5002 | 117 | 5376 | 518 | 61 | 11.7761 | |
| qzeng-custom | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 78.5615 | 65.6891 | 97.7083 | 41.1043 | 224 | 117 | 469 | 11 | 8 | 72.7273 | |
| mlin-fermikit | INDEL | D6_15 | map_siren | * | 81.1872 | 77.0138 | 85.8388 | 82.0071 | 392 | 117 | 394 | 65 | 53 | 81.5385 | |
| mlin-fermikit | SNP | ti | HG002compoundhet | homalt | 93.7665 | 98.4176 | 89.5352 | 35.5677 | 7277 | 117 | 7281 | 851 | 725 | 85.1939 | |
| hfeng-pmm1 | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 96.5561 | 93.3936 | 99.9404 | 41.4660 | 1654 | 117 | 1676 | 1 | 1 | 100.0000 | |
| hfeng-pmm1 | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 92.8280 | 87.1851 | 99.2519 | 87.9706 | 796 | 117 | 796 | 6 | 4 | 66.6667 | |
| jli-custom | INDEL | * | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 99.7466 | 99.5860 | 99.9077 | 57.3042 | 28143 | 117 | 28146 | 26 | 19 | 73.0769 | |
| jlack-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 95.6615 | 97.9986 | 93.4332 | 70.5962 | 5729 | 117 | 5677 | 399 | 342 | 85.7143 | |
| jlack-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 95.6615 | 97.9986 | 93.4332 | 70.5962 | 5729 | 117 | 5677 | 399 | 342 | 85.7143 | |
| hfeng-pmm3 | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 96.5561 | 93.3936 | 99.9404 | 41.2198 | 1654 | 117 | 1676 | 1 | 1 | 100.0000 | |
| hfeng-pmm3 | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 90.9506 | 83.7500 | 99.5058 | 87.7720 | 603 | 117 | 604 | 3 | 1 | 33.3333 | |
| hfeng-pmm2 | SNP | ti | map_l150_m1_e0 | * | 99.2981 | 99.4065 | 99.1899 | 76.2408 | 19595 | 117 | 19591 | 160 | 20 | 12.5000 | |
| gduggal-snapvard | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 74.2485 | 93.1298 | 61.7328 | 60.2144 | 1586 | 117 | 3299 | 2045 | 1364 | 66.6993 | |
| ghariani-varprowl | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 86.1643 | 84.6457 | 87.7384 | 69.2630 | 645 | 117 | 644 | 90 | 80 | 88.8889 | |
| gduggal-snapplat | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 85.3269 | 91.2425 | 80.1316 | 82.4013 | 1219 | 117 | 1218 | 302 | 5 | 1.6556 | |
| gduggal-snapvard | INDEL | * | lowcmp_SimpleRepeat_homopolymer_6to10 | hetalt | 0.0000 | 78.1308 | 0.0000 | 0.0000 | 418 | 117 | 0 | 0 | 0 | ||
| anovak-vg | INDEL | D1_5 | map_l150_m1_e0 | * | 81.6618 | 83.6820 | 79.7368 | 89.6132 | 600 | 117 | 606 | 154 | 60 | 38.9610 | |
| asubramanian-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 95.4167 | 92.9048 | 98.0682 | 36.5079 | 1532 | 117 | 1726 | 34 | 29 | 85.2941 | |
| anovak-vg | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 78.9511 | 85.2645 | 73.5081 | 83.3082 | 677 | 117 | 813 | 293 | 133 | 45.3925 | |
| astatham-gatk | INDEL | I1_5 | HG002complexvar | het | 99.6251 | 99.3568 | 99.8949 | 58.0548 | 18072 | 117 | 18051 | 19 | 9 | 47.3684 | |
| raldana-dualsentieon | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 96.1914 | 92.7644 | 99.8814 | 32.5739 | 1500 | 117 | 1685 | 2 | 2 | 100.0000 | |
| rpoplin-dv42 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 89.5684 | 81.4873 | 99.4286 | 37.8698 | 515 | 117 | 522 | 3 | 3 | 100.0000 | |
| raldana-dualsentieon | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 95.3947 | 91.7722 | 99.3151 | 87.7368 | 1305 | 117 | 1305 | 9 | 7 | 77.7778 | |
| raldana-dualsentieon | SNP | tv | lowcmp_SimpleRepeat_diTR_11to50 | * | 98.6778 | 97.5906 | 99.7894 | 64.3361 | 4739 | 117 | 4739 | 10 | 8 | 80.0000 | |
| raldana-dualsentieon | SNP | tv | map_l125_m2_e0 | * | 99.2122 | 99.2904 | 99.1340 | 71.8789 | 16372 | 117 | 16370 | 143 | 4 | 2.7972 | |
| raldana-dualsentieon | SNP | tv | map_l125_m2_e1 | * | 99.2171 | 99.2976 | 99.1368 | 71.9418 | 16540 | 117 | 16538 | 144 | 4 | 2.7778 | |
| rpoplin-dv42 | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | het | 98.8169 | 98.9467 | 98.6874 | 61.3838 | 10991 | 117 | 10977 | 146 | 120 | 82.1918 | |
| dgrover-gatk | SNP | ti | map_siren | homalt | 99.8204 | 99.6914 | 99.9498 | 49.0891 | 37799 | 117 | 37793 | 19 | 17 | 89.4737 | |
| egarrison-hhga | INDEL | * | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 99.5363 | 99.2878 | 99.7860 | 56.6980 | 16312 | 117 | 16318 | 35 | 21 | 60.0000 | |