Variants view

The Variants view provides a table with a row for each variant position. This view is only available for reference-guided assemblies in .assembly format.

To access the Variant view, choose a contig from the Explorer panel. Then either choose View > Variants > (Contig Name) or Variants > Show Variant Table or right-click on the selected contig and choose Show Variant Table.

Each row in the table summarizes information for all of the variant bases in an aligned column. If you are viewing a SeqMan NGen assembly, only variants meeting the SNP filter stringency (High, Medium or Low) that you specified in the SeqMan NGen wizard are displayed.

For definitions of each data column, as well as instructions for showing, hiding, renaming or rearranging data columns, see Choosing and understanding Variants view columns.

The table below describes tasks related to the Variants view:

Task	How To
Open the Analysis view at the variant position	Double-click on any row in the table. This is especially useful in situations such as an amplicon assembled against a much longer reference. In this case, the Analysis view may appear virtually empty when viewed on its own. However, double-clicking on a row in this table will open the Alignment view at a populated position.
Show, hide, rename or rearrange data columns	For instructions, see Choosing and understanding Variants view columns.
Select a category of variants	Use the commands in the Variants menu or right-click menu options with the same names to select a large group of variants at once. Regardless of the current selection, you can select Variants > All or Variants > None. If you have already made a selection in the table, you can select everything that is not currently selected by using Variants > Invert Selection. Note that as of Lasergene 17.5, the option Select All of Type is not yet functional in GenVision Pro.
Change the status of selected variants	The leftmost column of the table (represented by a small triangle in the header) denotes the status of a variant. Initially, all variants are marked as putative. – Putative (the initial status for all variants in the table) – Confirmed – Rejected To change the status of variants, select one or more rows, then right-click on the leftmost column and choose Confirm (Reject, Question) Selected Variants. Alternatively, you can make the selection, then use the following menu commands: Variants > Confirm (Reject, Question) Selected Variants.
Hide/show multiple references bases	If there were multiple reference bases at the location of a variant, the leftmost column will feature a small triangle in that row. Click on the triangle to show the multiple reference bases. In .assembly projects, variants in adjacent columns are coalesced into a single insertion or deletion if they are of the same type, and if at least 80% of the reads with the called variant in one column have a variant in the adjacent column. Each coalesced multiple-base insertion or deletion can be opened to reveal individual variants by clicking the corresponding triangle to the left of the SNP column. After clicking a triangle, information on each position of the insertion/deletion is displayed in a separate row.
Choose which items should appear in the view	Press the Filter () tool in the top right of the view. See Filtering in the Variants view for detailed information.
Add, rearrange, rename, or remove table columns	Press the Change options in this view tool () in the top right of the view. For instructions and a description of each column type, see Filtering in the Variants view.
Show counts as a percent	Press the Show counts as percent tool ( ) in the top right of the view. This affects columns named Cnt.
Export data from the table	Press the Export data tool () in the top right of the view. This opens a save dialog in which you can save the tabular data in comma-separated (.csv) or tab-separated (.tab) format. See Export data to a file for details.
Toggle between showing/hiding the table header	Use the Show quick details tool () in the top right of the view.