Reference-based Stacks.vcf

Genotype-by-Sequencing (GBS) DNA reads were produced from European C. sativa accessions. GBS reads were aligned to the C. sativa 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.

本数据集的DNA测序读段通过基因型测序（Genotype-by-Sequencing, GBS）技术，从欧洲C. sativa种质材料中获得。随后，使用Burrows-Wheeler比对工具（Burrows-Wheeler Aligner, BWA）的MEM算法，将所有GBS测序读段比对至C. sativa参考基因组。接着，采用生物信息学工具Stacks完成单核苷酸多态性（Single Nucleotide Polymorphisms, SNPs）的分型调用。最终筛选条件如下：仅保留次要等位基因频率大于0.05、缺失率低于20%的SNPs，同时仅保留每个基因座上的首个SNP。