Sequence Track Options
When zoomed in sufficiently, the reference genome Sequence track appears at the top of the lower panel above the Genes track, if any, in the IGV display as shown in the Screenshot (2015.04.01). The sequence is represented by colored bars or colored letters, depending on zoom level, with adenine in green, cytosine in blue, guanine in yellow, and thymine in red (A, C, G, T).
Flipping the Strand
You can change the strand that is displayed by clicking on the arrow in the title to the left of the track. Note that the sequence and the arrow are only displayed when zoomed in to a sufficiently small region.
The direction of the arrow indicates which strand is currently displayed. An arrow pointing left indicates that the negative strand is showing. This strand will show the complement nucleotides and reverse complement translations.
With the reference genome sequence track, you can optionally display a 3-band track that shows a 3-frame translation of the amino acid sequence for the corresponding nucleotide sequence. The translation is shown for the strand indicated.
Amino acids are displayed as blocks colored in alternating shades of gray. Methionines are colored green, and all stop codons are colored red. When you zoom all the way in, the amino acid symbols will appear.
You can toggle the display of this translation track by clicking once, anywhere in the sequence or translation track, or by toggling Show Translation in the track popup menu.