Menu Command

Description

Variant Report

To display a report of all variants in a contig. This command is accessible from the Alignment View, Strategy View or after selecting a contig, scaffold or group of Unlocated contigs in the Project Summary window. If a scaffold or group of Unlocated contigs is selected, SeqMan Pro scans all the contigs included in the selection.

Update Variant Report

To update the data in a Variant Report (Variant > Variant Report). This command is disabled unless an .sqd file is open and is normally hidden from view in the Variant menu. To reveal the command, hold down the Alt (Win) or Option (Mac) key while clicking on the Variant menu.

Show/Hide Variants

To toggle between showing/hiding variants in the Alignment and Strategy views.

Sort by Variant

To sort sequences in the Alignment View so that sample sequences with variant bases in the aligned column are sorted to the top and samples with non-variant bases are sorted to the bottom.

Confirm Variant

To confirm that a selected residue is an actual variant.

Reject Variant

To reject that a selected residue is an actual variant.

Putative Variant

To indicate that a selected residue is a putative variant.

Select all of type

With the Variant Report open and a row selected, adds a confirmation checkmark to the SNP column for all variants that match the Type of the selection.

Show VCF Variants

To view an existing VCF Variant Table.

Append Checked Variants to VCF

To create a new VCF Variant Table, or to append to an existing one. Only confirmed (checked) variants from the Variant Report are added to the table. VCF Variant tables have the file extension .vcf.

Open dbSNP

To open the page in the dbSNP database corresponding to a selected variant in the Variants Summary report. The assembly must contain dbSNP rs IDs. To use the command, click on a contig, choose Variant > Variant Reports and locate a variant with an ID in the dbSNP column. Select the variant and choose Variant > Open DB SNP.