For the analyzed DNA sequence data, read qualities having a Q30 value above 80% were selected according to recommendations by Illumina. After a quality check and data trimming, the sequence reads were assembled with Genomics Workbench 8.5.1 (CLC bio, Aarhus, Denmark). The read mapping module was termed as CLC Assembly Cell 4.0, which was based on an uncompressed Suffix-Array representing the entire reference genome in a single data structure (White paper on CLC read mapper; October 10, 2012). Sequence reads were mapped against the ATCC 26695 genome (NC_000915) as a reference, and single nucleotide variants (SNVs) were identified with Fixed Ploidy Variant Detection modules with default parameters and minor modifications to the mapping algorithm. Variant detection of the software was set to 1.
To exclude false-positive variants that resulted from sequencing errors, we selected variants that were present in >90.0% of mapped reads with a minimum coverage of 100. Insertions, deletions, and successive multi nucleotide variants were also excluded due to the previously reported complexity involved in detecting true variants [18 (link)].
To exclude false-positive variants that resulted from sequencing errors, we selected variants that were present in >90.0% of mapped reads with a minimum coverage of 100. Insertions, deletions, and successive multi nucleotide variants were also excluded due to the previously reported complexity involved in detecting true variants [18 (link)].