PCL1606 WT strain
Sequencing libraries were prepared using the PCRfree TrueSeq Kit from Illumina. 250 bp paired-end reads were sequenced using an Illumina MiSeq platform. Illumina raw reads, in fastq format, were trimmed using SeqtrimNext v2.1.3 in order to remove low quality and low complexity sequences, adapters, polyA tails and several contaminant sequences. Useful reads were then mapped against their respective genome references (Bamy Genbank: NC_009725; Pcl Genbank: CP011110) to prepare data for subsequent variant calling by using BWA that was configured with options B 20 A 30 O 30 E 3 to ensure high quality alignments and accurate mapping scoring in order to prevent the calling of false variants. In the next step, a pileup file from each mapped sample was created using Samtools mpileup with the following options, BQ 26 q 30 d 10000000, as the Samtools official documentation recommends to obtain accurate results. Finally, mutations and InDels were independently called with VarScan2 using the pileup of bam files.