Entering edit mode
9 months ago
amy__
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160
Hello,
I have a region which is low quality, but I was wondering how I can describe this region - it occurs next to a high coverage block of reads but I am not sure how to describe this.
Does anyone have any ideas? Thanks! Amy!
Low quality as in low coverage only? Or the PHRED scores are also low?
Interpretation needs to consider sequencing strategy. In pooled sequencing such a result could be a deletion in most chromosomes when compared to the reference, but a couple rare individuals carry copies of the reference haplotype.
If this is sequencing from an individual, such a result could also be due to amplification bias and heterozygous for the deletion, especially if the sample is polyploid.
Do you know how to find the phred scores using igv? I had previously checked phred scores before and after trimming with my WES sequences and all base phred scores were over 30 on average after trimming.
This region was seen in some other individuals from the same sequencing batch, and a nearby variant at position 151086831-C-CG was called as a duplication. Which I can't really see from the bams so it has me a little confused. They are diploid.
Thanks! Amy
It's been a while since I used IGV so I can't remember if quality scores are part of the output when you click on a read. But they do give the name of the read, which you can then look up in the fastq. But if you've quality trimmed the raw reads, you needn't worry about this.
I'm guessing you conflated low quality region with low coverage. Also, given the variants you are seeing appear fixed in your population you sampled, I suspect this extra section is not a sequencing artefact and is likely real. I am unfamiliar with how WES data is generated, but it could be something as simple as an exon with 2 different start sites, and one is just poorly expressed. You could translate the first part of the low coverage reads and see if you get any blastp hits.