Insertions appear as a pair of red residues. The location of the insertion lies between these red residues. Details about the insertion can be found in the Selection Info tab or by hovering the mouse over the red residues to activate the tooltip. The image below shows a single residue insertion of 'C' that lies between the residues 'CT'.
Dash characters on a gray background represent deletions in the aligned sequence with respect to the genomic sequence. In other words, a dash character represents one or more contiguous bases that were present in the reference genomic sequence and absent from the aligned sequence.
Mismatches between the reads and the reference sequence are highlighted according to the mismatched base. In the image below, all five reads have a mismatch to A, indicating a single nucleotide polymorphism. One read has two mismatches to G, but these mismatches are not supported by any other reads.