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To apply an alignment highlighting mode, select it in the Highlighting context menu:

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or on the Highlighting tab of the Options Panel. The :

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 The following modes are available:

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• Paired reads — highlights all paired reads in green. Note that the information about the pair is shown in the hint.

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• Agreements — .highlights symbols that coincide with the reference sequence. 

• Disagreements — highlights gaps and nucleotides that differ from the reference sequence.

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• Strand direction — highlights reads located on the direct strand in blue and reads on the complement strand in green.

• Gaps - highlights gaps.
• Transitions - highlights transitions.
• Transversions - highlights transversions.

To select a reference sequence use the Set this sequence as reference context menu or Reference sequence field in the Highlighting tab of the Options Panel.