Graph-based Pangenome for Foxtail Millet (Setaria italica)

• 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.
• 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.
• 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.
• 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.
• pangenome.gfa: Graph-based pangenome of foxtail millet, integrating sequence diversity (e.g., presence-absence variations, structural variations) to reflect genome-wide complexity.

Upload test. Please use gfa file in V2.