How would you interpret these base-distribution-by-cycle results?

Question

[jsuzuki]

I have RNAseq results from Illumina sequencing of in vitro transcribed mRNA. The coding sequence has been GC optimized. I got the following graph of base distributions for two different replicates and I'm confused about this weirdness at 150. Can anyone provide some interpretation? What is happening in either graph A or B below? The base quality takes a hit around 150 as well dipping from 35 to 30.

Thank you!

Answer 1

[GenoMax]

In Graph 1: 150 cycles is where read 1 ended and the sequencing flipped over to the second end for Read 2. This is how that plot looks when viewed zoomed out. If these are tagmentation/random primer based libraries then there is a pattern (these are not fully random) that shows up in initial 10-15 bases for each read.