text: user298: 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?
  
  user650: Could it be that these are reads with their mates found on other chromosomes? That's the part of the IGV documentation which seems to make sense in this context:
  
  
  for paired end reads that are coded by the chromosome on which their mates can be found
  
  
original_text: 298: <p>I was looking at a bam file in the IGV viewer and saw:</p>
  
  <p><a href="https://i.imgur.com/SFmHJVV.png" rel="nofollow noreferrer"><img src="https://i.imgur.com/SFmHJVV.png" alt="IGV screenshot"></a></p>
  
  <p>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 <a href="http://software.broadinstitute.org/software/igv/UserGuide" rel="nofollow noreferrer">IGV docs</a> have sections on interpreting color <a href="http://software.broadinstitute.org/software/igv/interpreting_insert_size" rel="nofollow noreferrer">by insert size</a>, p<a href="http://software.broadinstitute.org/software/igv/interpreting_pair_orientations" rel="nofollow noreferrer">air orientation</a>, <a href="http://software.broadinstitute.org/software/igv/interpreting_bisulfite_mode" rel="nofollow noreferrer">bisulphide mode</a>, <a href="http://software.broadinstitute.org/software/igv/splice_junctions" rel="nofollow noreferrer">splice junctions</a> and <a href="http://software.broadinstitute.org/software/igv/Sashimi" rel="nofollow noreferrer">sashimi plot</a>, but none of them seems to be describing what I'm looking at there. </p>
  
  <p>More generally, where are all these default behaviors documented? Are they somewhere in <a href="http://software.broadinstitute.org/software/igv/UserGuide" rel="nofollow noreferrer">http://software.broadinstitute.org/software/igv/UserGuide</a> and I'm missing them?</p>
   650: <p>Could it be that these are reads with their mates found on other chromosomes? That's <a href="http://software.broadinstitute.org/software/igv/interpreting_insert_size" rel="nofollow noreferrer">the part of the IGV documentation</a> which seems to make sense in this context:</p>
  <blockquote>
  <p><a href="https://i.stack.imgur.com/l8dSy.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/l8dSy.png" alt="color codes from IGV docs" /></a></p>
  <p>for paired end reads that are coded by the chromosome on which their mates can be found</p>
  </blockquote>
  