GC content RNA-seq

Question

[UserA]

Hello, For one project, we sent a large number of samples, each containing 2 or 3 bacterial strains, to the illumina NovaSeq 6000 paired-end sequencer. For some samples, I observe on the GCcontent graph as 2 peaks close together. Could this be due to the fact that my strains do not have the same GC%? In this case why don't I observe it on the other samples?

[GenoMax]

that my strains do not have the same GC%?

That is one possibility.

In this case why don't I observe it on the other samples?

It is possible that you have varying amounts of rRNA and that may be resulting in the doublets.