This section shows how to open and optimize SeqMan Pro’s Variant Report.

  1. If you came to this topic directly from Part A, the file Templated assembly.assembly will already be open. Otherwise, launch SeqMan Pro and use File > Open to open it.
  1. Because this was a reference-guided bacterial assembly, the Project Summary window contains a single contig containing the bacterial chromosome. Click once on the contig’s name to select it.

  1. Open the Variant Report using the Variant > Variant Report menu command.

  1. Maximize the Variants Summary report window.

Imagine that you wish to identify those variants which are most likely to alter function of genes in E. coli. You will therefore want to focus on variations predicted to have a non-synonymous impact on the E. coli genome. In the next step, you will filter out some of the variants and only leave those predicted to cause a coding change.

  1. To show only variants that cause coding changes, click the Filter button.

In the Variant Filter Criteria dialog, remove the checkmarks next to Non-coding and Synonymous, then close the dialog using the ‘x’ or button in the top corner.

All remaining variants consist of those with a non-synonymous impact.

  1. Use the scrollbar on the bottom of the report to scroll right, and observe the many data columns available in this report. While each column is useful in certain circumstances, many will not be needed for this tutorial workflow.
  1. To remove unneeded columns from the report, right-click anywhere in the report and select Show/Hide Column. Check or uncheck boxes until the Show Column dialog matches the one below:

  1. Close the Show Columns dialog by clicking the ‘x’ in the top corner.

Proceed to 2. Evaluating variants in the Alignment and Strategy views.

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