Sequence Alignment Project Mutation Report

NextGENe Online Help : NextGENe Viewer Reports and Tools : Sequence Alignment Project Mutation Report

When you complete a sequence alignment project, (either single end sequence data, paired- reads/mate-paired data, or transcriptome data), the Sequence Alignment project Mutation report, or simply, the Mutation report, is automatically generated for the project, but it is not automatically displayed. You must 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.

The Mutation report lists each variant in order of their sequence position. Purple text indicates reported variants. Blue text indicates novel variants. Gray text indicates variants that were automatically or manually deleted. By default, the Mutation report always displays certain information for the variants that are included in the report, but you can always modify the information that is displayed. See Sequence Alignment Project Mutation Report Settings.

The report is interactive.

• Double-click an entry in the report to move the Alignment viewer to the corresponding location where you can view the reads for the position.

• Double-click a variant call in the Alignment viewer to move the report to the corresponding location. The entire row for the variant is highlighted in yellow in the report.

• Right-click a variant call in the report to open a context menu that provides various options for working with the selected variant. You can also click Search in this context menu to open a Search dialog box in which you can enter options for searching for specific information in the report, and if you have a subscription to Pathway Studio, an option is available for viewing the biological pathway information for the gene where the variant is located in Pathway Studio.

Option	Comment
Search	Opens a Search dialog box with the field to search determined by the column from which you selected the option. For example, if you opened the search from the Gene column, then the Search Gene dialog box opens. If you open the search from the Chr (chromosome) column, then the Search Chr dialog box opens. Regardless of the dialog box that opens, the search criteria (Options, Direction, and Scope) are always the same. You use the options on this dialog box to search the Mutation report for the first occurrence of the search string that meets all the search criteria. You use the Next button to move through all the search results.
Delete	Click this option to remove a variant call for a position. Although the position is no longer called a variant, the sequence of the reads is not changed. Note: To view a deleted variant in the Mutation report, you must select “Deleted” on the Filters tab on the Mutation Report Settings dialog box. The deleted variants are highlighted in gray and the Comments column displays “Deleted” for each variant. See Filter tab, Annotation sub-tab.
Undo Deletion	Undoes a selected manual deletion. The position is again called a variant.
Confirm	Click this option to select variants in which you have a high degree of confidence. Note: To view a confirmed variant in the Mutation report, you must select “Confirmed” on the Filters tab on the Mutation Report Settings dialog box. The confirmed variants are displayed in black text in the Mutation report and the Comments column displays “Checked” for each variant. See Filter tab, Annotation sub-tab.
Undo Confirmation	Undoes the manual confirmation of a selected variant.
Undo	Undo the last edit action that was carried out for the variant.
View Edit History	Available only if User Management is turned (see Configuring User Management) and only after at least one edit action (for example, Deletion) has been carried out for the variant call. Opens the Edit History dialog box, which displays all the edit operations that have been carried by all users for the selected variant. See To view the Edit history for a variant.
Copy	Copies the selected text in the cell to your clipboard. To copy text in a range of cells, click and hold the left mouse button and drag the mouse to select the region that you are copying. Use standard keyboard commands or menu commands to paste the copied text into a third-party application. Note: You can also copy the Mutation report as an image. Press and hold the [Shift] key and the [Ctrl] key and then click and hold the left mouse button and draw a box around the region of the image that you want to copy. The selected region is filled with black. Right-click and Copy as Picture to copy the selected region as an image to your clipboard. Use standard keyboard commands or menu commands to paste the copied image into a third-party application.
View in Pathway Studio	If you have a subscription to Pathway Studio, then select this option to import the gene where the variant is located into Pathway Studio and visualize the biological pathway information for the gene. Note: Before you can use the Mutation report in conjunction with Pathway Studio, your Pathway Studio access option must be set for the NextGENe Viewer. See Process menu in NextGENe Viewer main menu.

• To save the Mutation report as a tab-delimited text (*.txt) file, on the NextGENe Viewer main menu, click Reports > Mutation Report > Save Mutation Report. By default, the report is named <project>_name_Mutation _Report and it is saved in the project output folder, but you can change one or both of these values.

After you save the Mutation report, the date and time that the report was saved as well as 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