Selecting Save image from the right-click pop-up menu save the lower display panel containing the Sequence track as an image. Specify the image file format by setting the filename extension in the file save dialog to. Right-click on Sequence track to select Show translation from the pop-up menu and to select a Translation Table. The translation is shown for the strand indicated. 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. This strand will show the complement nucleotides and reverse complement translations. An arrow pointing left indicates that the negative strand is showing. The direction of the arrow indicates which strand is currently displayed. Note that the sequence and the arrow are only displayed when zoomed in to a sufficiently small region.Īlternatively, right-click on Sequence track to select Flip strand from the pop-up menu. You can change the strand that is displayed by clicking on the arrow in the title to the left of the track. A useful discussion about this can found on Bioinformatics StackExchange (see for example response #11 on this thread). However, the convention for the use of case and N, is not completely standardised, and depends on the creator of the genome sequence. Lower case letters often mark repeated regions, and N/n may represent ambigous nucleotides. In addtion to the upper case letters A, C, G, and T, you may see lower case letters for these bases, and also N / n.
IGV displays the sequence of bases as they appear in the FASTA file for the reference genome. To change this default nucleotide coloring scheme see the Modify the prefs.properties file page. 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). 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).
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