Bimodal %GC plot of fastqc output in RNASeq

Question

[devbt15]

Dear all,

Recently I performed RNASeq 150 bp paired-ends reads in rice (Illumina). I performed fastqc on the fastq files and obtained %GC plots (in the link below):

As shown in the plot, a second bump is observed at 70%. However, fastqc does not suggest any overrepresented sequences or adaptor contamination.

Any suggestions on what these could be?

Regards.

[GenoMax]

Please use instructions here to add images : How to add images to a Biostars post

Have you checked to make sure that there is no rRNA contamination in your data. Has the data been trimmed?

Answer 1

[shelkmike]

The genome of rice indeed has a bimodal GC content distribution https://pubmed.ncbi.nlm.nih.gov/25527839/ . This unusual property is characteristic of genomes of some monocots.