FIG. 6.

Screenshot of JCVI's Advanced Reference Viewer (http://gos.jcvi.org/openAccess/advancedReferenceviewer.html). A reference contig or genome, in this case, Prochlorococcus marinus strain AS9601, shown on the x axis, against which metagenomic reads, in this case, from the Global Ocean Survey (115), is aligned and arrayed by similarity to the reference sequence on the y axis. Reads have been color coded according to sampling site to highlight site-to-site variations in Prochlorococcus populations but can be color coded by any type of metadata or other features such as the consistency of read mate pairs. Genomic islands peculiar to strain AS9601 are easily identified as gaps in the read coverage (between 60 and 70 kb). This viewer also allows users to zoom into regions of interest for higher resolution. (Image courtesy of Doug Rusch.)