Mycobacterium tuberculosis single nucleotide polymorphisms: endemic and epidemic isolates from RFLP types 0.0142 and 0.0728 in Alberta, Canada

Whole genome sequencing was performed on the Illumina HiSeq 2500. Paired-end reads were trimmed to remove adaptors and low-quality bases using Trim Galore v 0.2.6. We mapped reads to H37Rv (NC_000962.3) using BWA-MEM v 0.7.7. We used GATK v 2.8.1 for indel realignment and variant calling. We created SNP alignments from variant calls produced by reference guided assembly. SNPs falling in repetitive regions of the MTB genome (i.e. PE/PPE genes) and SNPs that corresponded to a gap or ambiguous call in other isolates were removed.