Graph-based Pangenome for Foxtail Millet (Setaria italica)

This dataset encompasses key genomic resources for foxtail millet (Setaria italica), including a graph-based pangenome and variant call format (VCF) files with filtered genetic variations. 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.本数据集涵盖谷子（Setaria italica）的关键基因组学资源，包括基于图形的泛基因组（graph-based pangenome）以及带有筛选后遗传变异的变异调用格式（Variant Call Format, VCF）文件。 4.filter_maf0.05_miss0.1.vcf.gz：该VCF文件包含单核苷酸多态性（single-nucleotide polymorphisms, SNPs）与小型插入缺失（small insertions/deletions, indels），由3.final.vcf.gz筛选得到，筛选标准为次要等位基因频率（minor allele frequency, MAF）≥0.05且缺失数据率≤0.1。 4.filter_maf0.05_miss0.1.sv50.vcf.gz：该VCF文件包含长度≥50 bp的结构变异（structural variations, SVs），由3.final.vcf.gz筛选得到，筛选标准为次要等位基因频率（MAF）≥0.05且缺失数据率≤0.1。 4.filter_maf0.01_miss0.1.vcf.gz：该VCF文件包含单核苷酸多态性（SNPs）与小型插入缺失（indels），由3.final.vcf.gz筛选得到，筛选标准为次要等位基因频率（MAF）≥0.01且缺失数据率≤0.1。 3.final.vcf.gz：该VCF文件是通过Syri流程对组装基因组进行结构变异（SVs）调用后直接得到的，未包含测序深度信息，因此变异的假阳性率相对较高。 pangenome.gfa：谷子的基于图形的泛基因组（graph-based pangenome），整合了序列多样性（如有无变异、结构变异）以反映全基因组的复杂性。 上传测试，请使用V2版本的GFA文件。