To see the Variants view, you must first perform a multiple alignment. When the alignment is complete, the Variants view opens showing a Compute Variants button. Click the button to calculate the variants.

If you have specified a reference sequence, variants are calculated against the reference. If no reference sequence was specified prior to alignment, variants are calculated against the consensus sequence. Pressing the button results in a table of variants being displayed in the view.

Once the Variants view has been enabled, you can access it by clicking the Variants tab or by choosing View > Variants > Show.


The rows in the table represent the variants in each aligned sequence. The table columns are described below:

Column Name Description
Codons When a translated feature is present on the reference sequence at the position of a variant, a codon change is displayed in this column.
Cons Pos The nucleotide position where the variant occurs, as measured from the 5’ end of the consensus sequence.
Feature Distance The distance from the nearest known feature, if any.
Feature Name Name of the feature (if any) that contains the variant.
Impact The impact of the variant or indel on the genome, displayed as one of the following values:

  • Synonymous – No amino acid changes.

  • Non Synonymous – Amino acid substitution only.

  • Nonsense – Amino acid to translational stop.

  • Frameshift – An indel within a coding region and which is not a multiple of 3, thereby changing the reading frame.

  • No Start – A change that disrupts the start codon.

  • No Stop – A change that converts a stop codon to an amino acid, and thereby extends the reading frame.

  • Inframe Insertion – An insertion within a coding region whose length is divisible by 3. The type is followed by the word Conservative if the insertion occurs between two codons, and Disruptive if it occurs with a codon.

  • Inframe Deletion – A deletion within a coding region whose length is divisible by 3. The type is followed by the word Conservative if the insertion occurs between two codons, and Disruptive if it occurs within two codons.

    If sorting by the Impact column, the column is ordered by severity. For example, a Frameshift is more severe than a Nonsense change.
Length The total length of the variant, whether it consists of a 1-base SNP or a multi-base insertion or deletion.
Ref Bases The base(s) found at that position in the reference sequence.
Ref Codons The codon found at that position in the reference sequence.
Ref Pos The nucleotide position where the variant occurs, as measured from the 5’ end of the reference sequence.
Ref Translation The translation of the codon found at that position in the reference sequence.
Sequence The name of the sequence that contains the variant, when compared to the designated reference sequence.
Strand The strand where the variant is located. A right-facing arrow (>) denotes the forward strand, while a left-facing arrow (<) denotes a reverse-oriented strand.
Type Specifies the variation type: SNP for nucleotide sequences, Sub (stitution) for proteins, Del (etion) or Ins (ertion) for either. A deletion or insertion is followed by the length of the deletion/insertion.
Var Bases The base(s) found at that position in a non-reference sequence.
Var Codons The codon found at that position in a non-reference sequence.
Var Pos The nucleotide position where the variant occurs, as measured from the 5’ end of the sequence containing the variant.
Var Translation The translation of the codon found at that position in a non-reference sequence.


Tasks pertaining to the Variants view:

Task How to…
Select or deselect all variant rows in the table Select all variants using Variants > Select > Select All. Remove the selection using Variants > Select > Select None. Selection is often following by using a copy command.
Select individual variant rows Use the mouse or use Shift+click or Cmd/Ctrl+click. Selection is often following by using a copy command.
Select all rows except for the currently-selected rows After first selecting one or more rows (see above), choose Variants > Select > Invert Selection. Selection is often following by using a copy command.
Sort variants Click on a column header to sort variants by the values in that column. Some columns are sorted alphabetically, some numerically, and some with custom orders. Click again to reverse the order. You can sort by multiple columns by pressing the Alt key (Windows) or the ??? key (Mac) while clicking additional column headers.

Note: In Lasergene 17.4 (the first version featuring this view), sorting by sequence name may be slow.
Navigate to a variant Click the variant in the table. The Sequences view and Overview will navigate to that variant.
Navigate to a variant and show the Sequences view Double-click the variant in the table. The Sequences view will appear. The Sequences view and Overview will navigate to that variant.
Choose columns that should appear in the view and their order Press the Choose or rearrange columns () tool in the top right of the view. Items in the list on the right are the columns currently being displayed and the order in which they appear. Make selections and use the up/down and right/left arrows to add, subtract, and reorganize these columns as desired.
Export data from the view Click the Export Data tool (), a shortcut to the File > Export Data subcommands. See Export data to a file.

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