title: WGS of MTB BDQ R mutant
design: WGS was carried out on the Illumina MiSeq platform (Illumina, San Diego, CA, USA) using the Nextera XT DNA library kit. Resequencing analysis was performed on Qiagen CLC Genomics Workbench version 10 (Qiagen, The Netherlands) using the H37Rv Sanger reference genome (Genbank NC000962.3) for variant detection. Identification of mutations within rv0678, atpE, rv1979c and rv2535c was then carried out. In order to identify single nucleotide polymorphisms (SNPs) or insertions/deletions (indels): minimum paired coverage depth of 5, frequency of >30% [20], length and similarity fractions of 0.8 each; forward-reverse balance of 0.05 and a Phred score of Q20 (99% accuracy) at both variant positions and nucleotides within a radius of 5bp.