IGV coverage bar has color, but no mutation?

I attached a screenshot of an IGV output, what could be the reason(s) for the coverage bar to havea color but no mutation was detected? (4 total all G)

enter image description here

mutation igv

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written 3.5 years ago by chrisgr •

I guess G is not the reference allele on the genome

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written 3.5 years ago by Nicolas Rosewick

Thanks for your response! Sorry I messed up, you're right. I wanted to post a very simple example of what I was struggling with. Let me try again with a new one. Why does the G mutation have a color in the coverage bar and the T at the left does not? or what could be potential reasons for it?

enter image description here

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written 3.5 years ago by chrisgr •

2 answers

From IGV doc :

If a nucleotide differs from the reference sequence in greater than 20% of quality weighted reads, IGV colors the bar in proportion to the read count of each base (A, C, G, T).

https://software.broadinstitute.org/software/igv/AlignmentData

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written 3.5 years ago by Nicolas Rosewick

Yes that's it thanks so much!

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written 3.5 years ago by chrisgr •

This is possibly due to the threshold in the IGV preferences pop-up menu --> Alignments tab --> scroll down to 'Coverage Track Options' --> in there 'Coverage allele fraction threshold'. I think, by default its set at 0.2. So if variant allele fraction is <20%, the coverage track wouldn't show colour difference. If you expect (or think relevant), put it to something lower, like 0.05

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written 3.5 years ago by Amitm

Yes 20% seems so high, I received VCF files from Novogene, and the VCFs also have this 20% threshold (only contain mutations with 20%+ alt). I can't do a somatic analysis myself based on those VCf files because I can't see if the mutation is there in the control VCF (even though it's 1 or 2%). I don't see why they would do that.

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written 3.5 years ago by chrisgr •