I was looking at a bam file in the IGV viewer and saw:
What do the different read colors mean? Why is one read a light blue color, another green, another aquamarine (?), another purple and another two orange? What do these different read colors represent? The IGV docs have sections on interpreting color by insert size, pair orientation, bisulphide mode, splice junctions and sashimi plot, but none of them seems to be describing what I'm looking at there.
More generally, where are all these default behaviors documented? Are they somewhere in http://software.broadinstitute.org/software/igv/UserGuide and I'm missing them?