Low quality of reads in reverse files toward the last bases

Question

[deepti1rao]

I am intrigued by this trend of my illumina reads. The forward reads for every genomic DNA sample show a good per base sequence quality (mostly Q 25-30) even towards the last base (150 bp), while the file containing reverse reads shows a drop of upto Q 12. I see this trend in all my read files and am confused about what goes wrong when the sequencing guys perform the reverse read sequencing.

Answer 1

[Devon Ryan]

The quality for read #2 is typically worse than for read #1. Having said that, a drop of 12 is a bit much for 150 base reads, you typically only see large decreases with 250 base long rapid runs on HiSeq 2500s. It's possible that there was a technical issue late in the run, ask the people that run the machine. On the plus side, the quality still sounds OK for most uses.

[deepti1rao]

Can you elaborate on this: The quality for read #2 is typically worse than for read #1.????

[Devon Ryan]

There's no elaboration needed, that's generally the case for Illumina sequencers.