When you only have single reads data, coverage is one of the main resources for interpretation.

To assist in this interpretation, CLC Genomics Workbench displays a coverage graph along the contig by clicking the checkbox in the Side Panel.

In addition to the graphical analysis, CLC Genomics Workbench provides these options:

• By placing the mouse cursor on the graph, you see the exact coverage at a certain position.
• When you zoom out on a large contig, it may be difficult to discern smaller regions of low coverage. In this case, click the Find Low Coverage button at the top of the Side Panel. Clicking once will select the first part of the contig with coverage at or below the number specified above the button (Low coverage threshold). Click again to find the next part with low coverage.

In reference assembly, a region of no coverage indicates genome-scale mutations. If the sequencing data contains e.g. a deletion, this will appear as a region of no coverage in the reference assembly.

Adjusting for sequencing errors

Problems during the sequencing process prior to the assembly will also result in low coverage regions.

In this case, you may wish to re-sequence these parts of the contig, e.g. using traditional "Sanger"-sequencing techniques. Due to the integrated nature of the CLC Genomics Workbench you can easily go to the primer designer and design PCR and sequencing primers to cover the low-coverage region.