Summary Report
The Summary report displays the Run Statistics for a sequence alignment project and up to five project reports—Mutation report, Expression report, Coverage Curve report, Structural Variation report, and Distribution report—in a single view. After you select Reports > Summary Report, the Summary Report Settings dialog box opens.
If you have already selected post-processing report options for the project, then these report options are displayed on the dialog box; otherwise, it is blank. You can select additional reports to be included in the Summary report and you must also select a Settings file for each report. If applicable, you can edit a report or reports, or you can remove reports, and then click OK to generate the Summary report.
 | For information about adding reports to the Summary report, selecting the Settings file for a report and/or selecting a different reports, see To modify the Summary report view. |
By default, when the Summary report first opens, it is displayed on the right side of the opened NextGENe viewer. You can click the Switch Report Layout icon on the NextGENe Viewer toolbar to select the location for showing the report (to the right or at the bottom of the NextGENe Viewer), or to elect to show only the report (the Alignment viewer is hidden), or to hide the report. When a project is opened in the default alignment view, you can click the Report Selection icon on the NextGENe Viewer toolbar to toggle between the Summary report and the Mutation report.
From top to bottom, the default Summary report view displays the following:
• A Report toolbar that contains options for showing/hiding the various Summary report sections (such as showing/hiding the Header pane, showing/hiding the Run Statistics pane and so on), an option for saving the report as a PDF, and an option for modifying the Summary report settings.
Icon | Function |
|---|---|
 | Show/Hide Summary Report Header icon - Show/hide the Header (top) pane. |
 | Show/Hide Statistics Info icon - Show/hide the Run Statistics (second) pane. |
 | Show/Hide Mutation Report1 icon - Show/hide the Mutation report pane. One icon is displayed for each Mutation report that is generated for the Summary report. |
 | Show/Hide Coverage Curve Report1 icon - Show/hide the Coverage Curve report pane.One icon is displayed for each Coverage Curve report that is generated for the Summary report. |
 | Show/Hide Expression Report1 icon - Show/hide the Expression report pane.One icon is displayed for each Expression report that is generated for the Summary report. |
 | Show/Hide Structural Variation Report1 icon - Show/hide the Structural Variation report pane. One icon is displayed for each Structural Variation report that is generated for the Summary report. |
 | Show/Hide Distribution Report1 icon - Show/hide the Distribution report pane.One icon is displayed for each Distribution report that is generated for the Summary report. |
 | Save as PDF icon - Save the Summary report that is currently displayed in the NextGENe viewer as a PDF. After you save the Summary report, the date and time that the report was saved and your username are added to the audit trail for the project in the ReportEditHistory.log file. This log file is saved in an AuditTrail folder in the <Project Name>.files folder for the appropriate project; for example: Illumina\Haloplex\Alignment\2.4.0.1\D_Output\D_Output.files\AuditTrail |
 | Settings icon - Opens the Summary Report Settings dialog box. You use the options on this dialog box to change the report view to better suit your working needs. See To modify the Summary report view. |
 | Refresh icon - Refreshes the Summary report display after you have changed the Summary report settings, for example, you have added another report to the display. |
• A Header toolbar that contains options for customizing the information that is displayed in the Header (top) pane of the Summary report as well as options for showing/hiding the Custom header or the Default Header.
Icon | Description |
|---|---|
 | Show/Hide Custom Header icon - A toggle that shows or hides the Custom header in the Header pane of the report. When you first open the Summary report for a sequence alignment project, by default, the Custom header is displayed in the Header pane. Note: The Custom header displays the default information that is defined in the DefaultHeader.ini file or custom information that you specify using the Edit Header function. |
 | Show/Hide Default Header icon - A toggle that shows or hides the Default header in the Header pane of the report, which includes the following information about the project: Project Name, Date Created, Date Modified, the NextGENe version that was used to run the analysis, and the NextGENe Viewer version that was used to review the analysis. |
 | Edit Header icon - Click this icon to open the Header Editor dialog box and customize the information that is displayed in the Summary report header. See To customize the Summary report header. |
• The Run Statistics pane, which displays the _StatInfo.txt file for the sequence alignment project in its entirety. Use the pane’s scroll bar to view all the information that is displayed in the pane. (See _StatInfo.txt.)
• The report panes, such as the Mutation report pane, which displays the corresponding report in its entirety for the sequence alignment project. The possible report panes are the Mutation report pane, the Coverage Curve report pane, the Expression report pane, the Structural Variation report pane, and the Distribution report pane. Use the pane’s scroll bar to view all of the report in the pane. Use the Show/Hide icons at the top of the report pane to show/hide various sections of the report, or the report itself.
The order in which the report panes are displayed in the Summary report when the report first opens is determined by the order in which you selected the reports on the Summary Report Settings dialog box. Use the scroll bar on the viewer to scroll through the reports.
| | You can rearrange the order in which the reports are displayed in the Summary report. See To modify the Summary report view. |