To display variants in the Strategy View, select Variant > Show Variants.
The Strategy View changes as follows:
•Locations of bases in the contig that correspond to variant base locations in the aligned sample sequences are indicated with black hash marks on the contig goalpost.
•If the reference sequence is from a GenBank file, locations of bases annotated as features of type “variation” are indicated with colored hash marks on the reference sequence arrow. The default color is green.
•Locations of variant bases in sample sequences are indicated with colored hash marks on the sequence arrows. These colors can be changed to suit your preferences from the Variant Discovery parameters. Default colors are:
o Blue for putative variants
o Green for confirmed variants
o Red for rejected variants
•To hide variants in the Strategy View, select Variant > Hide Variants to return to the normal display.