Figure 4

Using BRIG to map unassembled sequence reads against a complete genome reference. BRIG images showing genomic regions shared by E. coli O157:H7 str. Sakai and related bacteria. The reference sequence is E. coli O157:H7 str. Sakai [GenBank: BA000007] with individual rings representing 10 genomes (Table 3). A. Rings show depth of coverage from unassembled, simulated 100 base-pair Illumina reads mapped onto the E. coli O157:H7 str. Sakai genome using the BWA [24] read-mapping application. Graph height in each ring is proportional to the number of reads mapping at each nucleotide position in the reference genome from 0 to 30× coverage. Regions with a genome coverage greater than 30× are shown as solid blue bands. B. For comparison, rings show BLASTn comparisons between the same genome sequences used in panel A (Table 3) against the E. coli O157:H7 str. Sakai genome. Long tick marks on the outer and inner circumference of the ring indicate increments of 500 kilobase-pairs and short tick marks indicate 100 kilobase-pairs. E. coli O157:H7 str. Sakai prophage and prophage-like (Sp & SpLE) regions are annotated in black and blue, respectively, using co-ordinates taken from Hayashi et al. [20].