title: WGS analysis of rifampicin-resistant M. smegmatis
design: Mapping high-quality reads to the reference genome with BWA-MEM (v0.7.17-r1188). Calling variants with FreeBayes (v1.3.6). Filtering variants with BCFtools (v1.18), and IV. Annotating variant effects with SnpEff (v5.0e).  Given the stringent criteria of the Snippy pipeline in variant calling, we manually inspected the mapped bases at each position using SAMtools (v1.18) mpileup on the BAM files generated by BWA-MEM.
identifiers.namespace: SUB15374514
identifiers.id: R9-F