Gap4 provides views of the data for an assembly project at 3 levels of resolution: the whole project can be seen from the Contig Selector (see section Contig Selector), the most detail from the Contig Editor (see section Editing in gap4), and the Contig Overview Displays, described in this section, provide an intermediate level of information and data manipulation. They are available from the main gap4 View menu.
These middle level resolution displays provide graphical overviews of individual contigs or sets of contigs. The possible information shown includes readings, templates, tags, restriction enzyme sites, stop codons, plots of the consensus quality, read coverage, read-pair coverage, strand coverage and consensus confidence. The displays of readings, templates, tags, restriction enzyme sites and plots of the consensus quality can be shown in a single window called the Template Display (see section Template Display). The plots of reading coverage, read-pair coverage, strand coverage and consensus confidence can be shown in a single display called the Consistency Display (see section Consistency Display), or as separate plots. The Stop Codon Plot (see section Plotting Stop Codons) and a more informative version of the Restriction Enzyme Plot (see section Plotting Restriction Enzymes) can be shown in separate windows.