title: WGS of Enterobacter 208 in fosfomycin
design: Mu208 was plated on agar containing 256 ug/mL fosfomycin. Resistant colonies were collected en mass, classified by size as medium (md), small (sm), or large (lg). DNA isolated subject to Illumina sequencing, quality control and adapter trimming was performed with bcl2fastq. Reads were mapped to their respective references via bwa mem. PCR and optical duplicates were marked and excluded from the analysis using PicardTools MarkDuplicates functionality. Aligned read counts were imported into Rs CNOGpro package. CNV events were called via CNOGpro using a bootstrapping method, which calculates an average gene number event giving a possible upper and lower bound.
library_name: 208_sm1