Fig. 5

a Schematic alignment of SRR833154 reads to the reference R, H37Rv, with subsequent variant calling detecting five high-quality SNPs in this particular region. b These and all other SNPs across the genome are integrated with the reference into graph G, followed by the alignment of the same reads. c Reads that previously did not align to R, now align onto a haplotype of the graph G. Formation of a pileup allows for the detection of four new variants in this region