I played a bit around with visualizing the RNA reads from the sequencing of the bacterial transcriptome and see that a lot of reads align to the regions in the genome that are not annotated as genes.
Of course, the explanation could be contamination with the bacterial DNA during sequencing, but since the samples were subjected to DNase treatment this is a less likely explanation. Another possibility is that those non-annotated regions are actual genes, but this is even less likely.
I'm wondering whether the real reason is actually that the RNA polymerase during the transcription doesn't stop immediately at the end of the protein encoded by the gene, but continues until it falls off the strand in either rho-dependent or independent way.
What do you think?
