Low coverage in specific exons of genes - sequencing errors?

Question

[amy__]

Hi all,

I have some WES from a range of companies. One set of samples has particularly low coverage in only some exons. All samples from all companies are plotted here, with the obviously low parts being from one company. (Sorry for the low quality image - it is better quality as pdf but I can't upload that).

Because my other samples from other sequencing companies are seemingly high coverage (e.g at the very top and bottom these are BGI and Novogene respectively), I suspect that it is not necessarily to do with the exons themselves.. any idea what may have gone wrong to make those ones low coverage?

Also, MUTYH is on the negative strand so its 5' - 3' the way that ensembl show the genomic loci eg. exon 1 is from chr5-45,339,970 to chr5-45,339,899 - hence why that one may look a bit funny.

Thanks!!

Amy

[GenoMax]

If the low coverage samples were limited to a specific batch done at a specific company (and there were no samples behaving normally in that batch) then it may come down to lot number of the Nextera exome kit somehow under performing in that region. Not sure what recourse you have but perhaps report this to the company/Illumina and see if they are willing to make some amends.

[amy__]

Thanks GenoMax, I have emailed Illumina so will see what they say! Thanks :)