The main interface of SVA

The main user interface of SVA is divided into several panels, as illustrated in the figure below:

• A: The project panel summarizes the current SVA project, including the information on the subjects and the annotation databases, etc.
• B. The pie chart panel provides a brief summay on the functional composition of the SNVs and INDELs identified.
• C. The log panel keeps a track of the tasks performed, and sometimes is used to briefly output analytical results.
• D. The SVA tables separately list annotated single nucleotide variants (SNVs), INDELs, and structural variants (SVs). These tables also respond to different filters that the users may apply.
• E. The SVA genome browser graphically displays genomic features and identified variants, and allows the user to interact with these data for more details or navigating to external resources.
• F. A variant density overview across the genome.
• G. Status bars display the current status of the program and the currently active SVA table.