As you saw in Part B, step 1, short indels were included in the Variants Report. However, any indels long enough to inhibit assembly are instead gathered in another report called the Structural Variation Report.
- Return to the Project Summary window (with “Templated assembly.assembly” in the header) and again select the sole contig listed.
- Choose Contig > Structural Variation Report.
- To investigate a putative deletion, double-click on Ref Pos 1339324 to open it in the Alignment View.
- The Alignment View opens to the left side of the deletion.
- Determine the range of the deletion by looking in the top left corner.
- Navigate to the right edge of the deletion by selecting Edit > Go To Position, typing in the number on the right (e.g., 1340091 in the image above), selecting Position Skips Consensus Gaps, and then clicking OK.
- Select Contig > Strategy View to launch the Strategy View.
- Click and hold the Show All Reads icon (), then slide the cursor to the right and click on the key icon:
- In the ensuing Show dialog, choose Split Sequence. All other options will be deselected automatically. Close the Show dialog by clicking the ‘x’ or button in its top corner.
- Again go to the same position. Repeatedly click the Zoom In tool () until any pink arrows appear approximately the size of the ones below.
The pink “split sequence pair” arrows graphically represent a read that has been split to match sequence before and after the deletion. Scroll down and note pink arrows on either side of the line showing the split. This pattern offers visual confirmation of the deletion relative to the reference sequence.
- Close SeqMan Pro using File > Exit (Win) or SeqMan Pro > Quit SeqMan Pro (Mac).
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