Fig. 1

Comparison of SNP calls calculated from alignments of Illumina reads to a nearly identical reference. Genomic DNA from the Listeriosis Reference Service for Canada’s (LRS) Listeria monocytogenes strain HPB5622 culture was indexed and sequenced eight times. The resulting reads were aligned with the Burrows-Wheeler Aligner using an L. monocytogenes strain 08-5578 chromosome sequence obtained from the National Center for Biotechnology Information (NCBI) archive as a reference. The 08-5578 chromosome sequence differs from the HPB5622 chromosome at three nucleotide positions. Four SNP-callers (BCFtools [BCF], FreeBayes, UnifiedGenotyper [UGT], and VarScan) were used to identify nucleotide differences. The numbers of true positive (a), false positive (b), and the proportions of calls made that correctly identified true positive sites (c) relative to the calculated coverages of assemblies are shown