• Global Batch CNV graph – The Global Batch CNV graph displays the global coverage for all the loaded sequence alignment projects. Each report column represents a different project, and each report row represents a different region in the BED file. The default range for the average normalized coverage is 0.8 to 1.2, but you can modify this value as appropriate. The closer that the average normalized coverage is to one for a given project/region combination, the greater the likelihood that the region does not contain a CNV relative to all the other projects that were loaded. The region names are taken from the 4th column of the BED file that used to define the regions for the projects. Any region that has an average normalized coverage value that falls outside the default range is highlighted, where red indicates an average normalized coverage that falls below the minimum coverage threshold (default value = 0.8) and therefore, a possible deletion, and green indicates an average normalized coverage that exceeds the maximum coverage threshold (default value = 1.2), and therefore, a possible duplication.

• Sample-Specific Batch CNV graph – The Sample-Specific Batch CNV graph displays expands the display that is shown in the Global Batch CNV graph to show the average normalized coverage across all the regions just for the selected sample. Because this graph is simply an expanded view of the coverage for a project (a row) in the Global Batch CNV report, there is direct correlation in the display of the coverage levels - the same regions that were highlighted in red in the Global Batch CNV graph are highlighted in red in the Sample-Specific Batch CNV graph, and the same regions that were highlighted in green in the Global Batch CNV graph are highlighted in green in the Sample-Specific Batch CNV graph.

• Region-Specific Batch CNV graph – The Region-Specific Batch CNV graph expands the display that is shown in both the Global Batch CNV graph and the Sample-Specific Batch CNV graph to show the normalized coverage for every nucleotide within the selected region.

• You can hold your mouse pointer over any position in the Global Batch CNV graph to open a tooltip that displays the following information about the position: the Project/Sample ID, the locus, and the average normalized coverage for the position.

• You click on any point in the Global Batch CNV graph to dynamically update the Sample-Specific CNV graph.

• You can click on any point (a region) in the Global Batch CNV graph or the Sample-Specific Batch CNV graph to dynamically update the Region-Specific Batch CNV graph.

• You can adjust the range for the Shading to exclude noise, for example, 25-75% and ensure better reliability of the calls. If a call falls outside the Shading range after you adjust it, then the call is a reliable call. If the call remains within the Shading range after you adjust it, then the call is more than likely a false positive or noise.