There are two coverage graphics in the Strategy View: Coverage Threshold at the top of the view, and the Depth of Coverage shown beneath the Conflicts bar.
The graph labeled Coverage Threshold represents the coverage within the assembly as it compares to the threshold parameters defined under Strategy viewing parameters. The Coverage Threshold graph is summarized by a line that varies in thickness and color. It is divided into four categories, based on the settings you selected in the Strategy Viewing parameters.
•A thin red line represents a region sequenced only once.
•A medium blue line is for a region sequenced on one strand only, even if the coverage in that region meets the Coverage Threshold value.
•A medium green line indicates a region sequenced on both strands but failing the Minimum Number on Each Strand parameter.
•A thick green line represents a region sequenced on both strands and that matches or exceeds the Coverage Threshold and Minimum Number on Each Strand values.
•A thick red line represents a region that exceeds the Maximum Expected Coverage parameter.
The graph labeled Depth of Coverage represents the depth of sequences throughout the assembly. The numbers to the left of the graph indicate the actual number of sequences represented.
Depending on the volume of sequences in your assembly, you may need to expand the top portion of the Strategy View in order to display the entire Depth of Coverage graph. You can expand this area by clicking and dragging down the bar located between the graph area and the list of constituent sequences. Also note that it may be helpful to zoom in slightly in order to view more gradual changes in coverage along the length of your contig.
The various colors shown in the Depth of Coverage graph represent the same regions as defined by the colors shown in the Coverage Threshold graph (see above).
Note: Certain actions may affect the current classification (coloring) of the sequences in the Strategy Views. For example, deleting a contig (Contig > Delete Contig) or scaffold (Contig > Delete Scaffold) may remove one of a paired end pair. The coloring of its pair sequence would then be updated to black. Other actions that affect coloring include: adding or deleting sequences from your project, adjusting the Pair Specifier parameters, and complementing (Contig > Complement Contig), aligning, force joining, splitting, or ordering contigs.