Hello everyone, I have some new Illumina datasets that show non-uniform coverage (last image). My older datasets have uniform coverage across the whole genome (first image).
I don't know what library method was used for the first image, but for the second I am pretty sure it was the nextera kit. I extracted the gDNA with a phenol/chloroform procedure. I did not do the library prep but I will in the future.
What is the mostly likely reason for non-uniform coverage? How can I avoid this in the future?
Do you think the results warrant another sequencing run if I'm trying to identify mutations? A total of 3KB, in stretches of 10s to a few hundred bases, has zero coverage. The genome is AT-rich and about 4 Mb long. My guess is that this dataset if fine.
Images were generated with breseq.