I have just calculated gene coding desnsity across some bacterial genomes. It is coming out quite high at ~87%, I think it is usually around 80%. I simply counted the ATGC's in my .ffn file and subtracted that from the total nucleotide count.
When calculating coding density should I include ribosomal DNA sequences? I also counted the entire gene region, not just the coding domain. Maybe this is why it is coming out higher?