FastQC interpretation

[ifyouSEQelaine]

Hello,

I would love some advice on my linked image below. I was using FastQC to look at the data from a recent MiSeq run. All my isolates are flagged at the "Per base sequence content". I am to understand that a 'good' graph is expected to look like all the bases are of similar % throughout. The DNA sequenced is from Pseudomonas aeruginosa, and I am seeing a high GC content (as expected) and much lower AT content.

Any advice or explanation would be greatly helpful!

[GenoMax]

This type of pattern is observed in a couple of cases. One is random priming used in RNAseq libraries and other is where you are making libraries that include transposases. The bias at the beginning of the reads is likely due to the Nextera transposase sequence bias (similar to bias seen in "random priming") .