IGB displays insertions, deletions and mismatches as follows:

• Insertions - Residues flanking insertion site are shown in black with a white background by default (purple on white here); triangular shapes between them point to the location of the inserted base(s) present in the aligned sequence but not in the reference. Select an insertion to display the sequence of inserted bases

• Deletions - Residues deleted in the aligned sequenced relative to the reference appear as horizontal lines that are of the same color and connect flanking residues.
• Mismatches - Residues in the aligned sequence that do not match the corresponding base in the reference appear as highlighted bases. To highlight mismatches, click Load Sequence

Use the zoom stripe (shown in gray) as a guide to compare mismatches, deletions, and insertions between different read alignments and the reference.

Insertions, Deletions, and Mismatches in IGB

To re-create this scene in IGB:

• Open tomato genome S_lycopersicum_Feb_2014 (ITAG2.4)
• Select Current Genome > chrC-NC_007898.3 (tomato chloroplast genome)
• Click Load Sequence to load chloroplast genome sequence
• Zoom to chrC-NC_007898.3:72,724-102,016 (enter in Quick Search box, top left)
• Select Data Access > Available Data > Plastid Resquencing > Baxter's Early Bush_a
• Click Load Data to load alignments for Baxter's Early Bush tomato cultivar
• Expand stack height to 150 reads per track (right-click track and select Set Stack Height)
• Use vertical zoomer to stretch read alignments vertically
• Enter chrC-NC_007898.3:84,675-84,721 in Quick Search box to zoom to region
• Scroll down until the reference sequence comes into view