To add bases to the variant reports and display them as variants in the Alignment and Strategy views, do the following:
1) In the Alignment View select the bases you want to add as variants.
2) In the menu, select:
Variant > Putative Variant to add the base as a putative variant.
Variant > Confirm Variant to add the base as a confirmed variant.
Variant > Reject Variant to add the base as a rejected variant.