<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>

CC BY-SA 4.0
2019-07-08T19:18:18.620Z
2024-06-21T00:30:24.587Z
2024-06-21T00:30:24.587Z
Ram RS
<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>

<phylogenetics><visualization><igv>
What do the read colors in IGV mean?
# 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

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## 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


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