What does the read colors represent?

[Olivier]

Hi,

 

I am new to IGV and when i upload an alignment of my sequences with my references i have read with different colors: Gray, red and blue. it is the read itself which has a different color, it is not the mutations. Please see the picture attached. It must be really simple, but i did not find information on these colors

Thank you

Olivier 

[James Robinson]

If these are paired reads it means the template length (distance between the pairs) is out of expected bounds.  "Expected" is determined by applying statistics to the data itself and works in most cases.  If you have an unusual experiment, and yours looks unusual, this color coding is not useful and can be turned off.  To do so select right click and select "color alignments by > none".

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