Abstract

Clean reads were firstly mapped to transcripts using Bowtie2, then SNPs were called SNPs using SAMtools. Raw SNPs with a minimum depth of 4 and minimum quality of 20 were filtered out using Vcftools (Danecek et al., 2011), and SNPs clustered within 50 bp were also filtered out. SNPs were annotated using snpEFF(http://snpeff.sourceforge.net/

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