SNP data for <em>Pterocarya macroptera</em>

Total_no_filter.vcf: Unfiltered SNP data for all samples of <em>Pterocarya macroptera</em> across in China, produced by Stacks. Total_Filter.vcf: SNP data was filtered: (1) markers with an observed heterozygosity &gt; 0.70 among individuals were removed to reduce the potential occurrence of paralogs, (2) minor allele frequency (MAF) &lt; 0.05, (3) only the first SNP locus of each read was retained by parameter write_single_snp to reduce physical linkage, and (4) a minimum of 70% of individuals within a population were required to process a locus. <br>

Total_no_filter.vcf：由Stacks软件生成的、采自中国境内所有大叶枫杨（Pterocarya macroptera）样本的未过滤单核苷酸多态性（Single Nucleotide Polymorphism，SNP）数据。Total_Filter.vcf：经过过滤处理的SNP数据，过滤规则如下：(1) 移除群体中观测杂合度大于0.70的标记，以降低旁系同源基因的潜在出现概率；(2) 过滤次要等位基因频率（minor allele frequency，MAF）小于0.05的标记；(3) 通过设置write_single_snp参数，仅保留每条测序读段的首个SNP位点，以减少物理连锁现象；(4) 要求群体内至少70%的个体可成功获取该位点的分型数据。

搜集汇总

背景与挑战

背景概述

该数据集提供了中国分布的Pterocarya macroptera（一种植物）的SNP数据，包含未过滤和过滤后的两个VCF文件，过滤过程包括去除高杂合度标记、设置最小等位基因频率阈值等步骤，适用于分子进化和生态适应研究。数据基于RAD-seq技术生成，发布于2023年，采用开放获取许可。