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2025
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| Online Access: | https://doi.org/10.5281/zenodo.17337658 |
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| _version_ | 1866902258086576128 |
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| author | Wu, Tianhao |
| author_facet | Wu, Tianhao |
| contents | <div>This dataset encompasses key genomic resources for foxtail millet (<em>Setaria italica</em>), including a graph-based pangenome and variant call format (VCF) files with filtered genetic variations.</div> <ul> <li>4.filter_maf0.05_miss0.1.vcf.gz: VCF file containing single-nucleotide polymorphisms (SNPs) and small insertions/deletions (indels), derived from filtering of 3.final.vcf.gz, with filtering criteria of minor allele frequency (MAF) ≥ 0.05 and missing data rate ≤ 0.1.</li> <li>4.filter_maf0.05_miss0.1.sv50.vcf.gz: VCF file of structural variations (SVs) (with length ≥ 50 bp), derived from filtering of 3.final.vcf.gz, with filtering criteria of minor allele frequency (MAF) ≥ 0.05 and missing data rate ≤ 0.1.</li> <li>4.filter_maf0.01_miss0.1.vcf.gz: VCF file containing single-nucleotide polymorphisms (SNPs) and small insertions/deletions (indels), derived from filtering of 3.final.vcf.gz, with filtering criteria of minor allele frequency (MAF) ≥ 0.01 and missing data rate ≤ 0.1.</li> <li>3.final.vcf.gz: VCF file obtained directly by calling structural variations (SVs) from assembled genomes via the Syri pipeline, without sequencing depth information, resulting in a relatively high false positive rate for variants.</li> <li>pangenome.gfa: Graph-based pangenome of foxtail millet, integrating sequence diversity (e.g., presence-absence variations, structural variations) to reflect genome-wide complexity.</li> </ul> <p>Upload test. Please use gfa file in V2.</p> |
| format | Recurso digital |
| id | zenodo_https___doi_org_10_5281_zenodo_17337658 |
| institution | Zenodo |
| language | |
| publishDate | 2025 |
| publisher | Zenodo |
| record_format | zenodo |
| spellingShingle | Graph-based Pangenome for Foxtail Millet (Setaria italica) Wu, Tianhao <div>This dataset encompasses key genomic resources for foxtail millet (<em>Setaria italica</em>), including a graph-based pangenome and variant call format (VCF) files with filtered genetic variations.</div> <ul> <li>4.filter_maf0.05_miss0.1.vcf.gz: VCF file containing single-nucleotide polymorphisms (SNPs) and small insertions/deletions (indels), derived from filtering of 3.final.vcf.gz, with filtering criteria of minor allele frequency (MAF) ≥ 0.05 and missing data rate ≤ 0.1.</li> <li>4.filter_maf0.05_miss0.1.sv50.vcf.gz: VCF file of structural variations (SVs) (with length ≥ 50 bp), derived from filtering of 3.final.vcf.gz, with filtering criteria of minor allele frequency (MAF) ≥ 0.05 and missing data rate ≤ 0.1.</li> <li>4.filter_maf0.01_miss0.1.vcf.gz: VCF file containing single-nucleotide polymorphisms (SNPs) and small insertions/deletions (indels), derived from filtering of 3.final.vcf.gz, with filtering criteria of minor allele frequency (MAF) ≥ 0.01 and missing data rate ≤ 0.1.</li> <li>3.final.vcf.gz: VCF file obtained directly by calling structural variations (SVs) from assembled genomes via the Syri pipeline, without sequencing depth information, resulting in a relatively high false positive rate for variants.</li> <li>pangenome.gfa: Graph-based pangenome of foxtail millet, integrating sequence diversity (e.g., presence-absence variations, structural variations) to reflect genome-wide complexity.</li> </ul> <p>Upload test. Please use gfa file in V2.</p> |
| title | Graph-based Pangenome for Foxtail Millet (Setaria italica) |
| url | https://doi.org/10.5281/zenodo.17337658 |