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| Format: | Recurso digital |
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Zenodo
2025
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| Online Access: | https://doi.org/10.5281/zenodo.17337658 |
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Table of 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>