Example charts generated by the coverageAnalysis plugin
The charts that are generated by the coverageAnalysis plugin include Plot, Overlay,
or Display menus that allow you to customize the data that is displayed in each chart.
Click (Search) (in the top right corner of a chart) to open the chart Viewing
Options panel, where you can further customize a chart. Click (Help) to open a
description of the chart.
Figure 1
Representative Depth of Coverage Chart
The Depth of Coverage Chart shows the distribution of targeted base coverage. The X
‑
axis
represents the base read depth. The left Y-axis represents the number of reads at a given base
read depth or a range (bin) of base read depths, as a percentage of the total number of base
reads. The right Y-axis represents the cumulative count of the number of reads at a given read
depth or greater, as a percentage of the total number of reads. The individual orange bars
represent the percentage of reads in the specific range of base read depths. The blue curve
measures the cumulative reads at a given base read depth or greater. If your analysis includes a
regions of interest file, this chart reflects only target regions (reads that fall within a region of
interest). Use the Plot dropdown list to switch between Maximum Read Depth, 99.9% of All
Reads, and Normalized Coverage plots.
Figure 2
Representation Plots
Use the Display dropdown list to switch between Pass/Fail vs. Target G/C Content, Pass/Fail vs.
Target Length, Representation vs. Target G/C Content, and Representation vs. Target Length
plots. This figure shows an example Pass/Fail vs. Target G/C Content plot.
Appendix D
coverageAnalysis plugin in Genexus
™
Software
Example charts generated by the coverageAnalysis plugin
D
Genexus
™
Integrated Sequencer User Guide
147
