Reference-based Stacks.vcf

Genotype-by-Sequencing (GBS) DNA reads were produced from European C. sativa accessions. GBS reads were aligned to the <i>C. sativa</i> genome using Burrows-Wheeler Aligner (BWA)-MEM. Single nucleotide polymorphisms were called using Stacks. Only SNPs with a minor allele frequency greater than 0.05 and a missingness less than 20% were kept; only the first SNP in each locus was kept as well. <br>本数据集的DNA读段通过基因型测序（Genotype-by-Sequencing, GBS）技术，从欧洲大麻（C. sativa）种质资源中生成。使用Burrows-Wheeler比对器（Burrows-Wheeler Aligner, BWA）的MEM算法，将所得GBS读段比对至大麻（C. sativa）参考基因组。采用Stacks软件完成单核苷酸多态性（Single Nucleotide Polymorphism, SNP）的变异检测。仅保留次要等位基因频率大于0.05、缺失率低于20%的SNP位点，且每个基因座仅保留首个检测到的SNP位点。