Answers.Body: <p>Could it be that these are reads with their mates found on other chromosomes? That's <a href="https://igv.org/doc/desktop/#UserGuide/tracks/alignments/paired_end_alignments/#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.sstatic.net/l8dSy.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/l8dSy.png" alt="color codes from IGV docs" /></a></p>
  <p>Pairs aligned to different chromosomes: Each read is colored by the chromosome of its mate</p>
  </blockquote>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-07-08T19:18:18.620Z
Answers.LastActivityDate: 2024-06-21T00:30:24.587Z
Answers.LastEditDate: 2024-06-21T00:30:24.587Z
Answers.UserDisplayName: Ram RS
Body: <p>I was looking at a bam file in the IGV viewer and saw:</p>
  
  <p><a href="https://i.sstatic.net/7JGv1.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/7JGv1.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>
  
Tags: <phylogenetics><visualization><igv>
Title: What do the read colors in IGV mean?
ThreadText: # What do the read colors in IGV mean?
  
  (Asked by: username_0 on 2019-07-08)
  
  I was looking at a bam file in the IGV viewer and saw:
  
  [![IGV screenshot](https://i.sstatic.net/7JGv1.png)](https://i.sstatic.net/7JGv1.png)
  
  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](http://software.broadinstitute.org/software/igv/UserGuide) have sections on interpreting color [by insert size](http://software.broadinstitute.org/software/igv/interpreting_insert_size), p[air orientation](http://software.broadinstitute.org/software/igv/interpreting_pair_orientations), [bisulphide mode](http://software.broadinstitute.org/software/igv/interpreting_bisulfite_mode), [splice junctions](http://software.broadinstitute.org/software/igv/splice_junctions) and [sashimi plot](http://software.broadinstitute.org/software/igv/Sashimi), 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?
  
  **Tags:** phylogenetics, visualization, igv
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2019-07-08. Score: 5 | Accepted answer
  
  Could it be that these are reads with their mates found on other chromosomes? That's [the part of the IGV documentation](https://igv.org/doc/desktop/#UserGuide/tracks/alignments/paired_end_alignments/#insert-size) which seems to make sense in this context:
  
  > [![color codes from IGV docs](https://i.sstatic.net/l8dSy.png)](https://i.sstatic.net/l8dSy.png)
  >
  > Pairs aligned to different chromosomes: Each read is colored by the chromosome of its mate
  
  
  ---
  
  