Hi

I am plotted a karyoplot for genecoverage data and (screenshot has attached below) this is how the plot looks like.

How come we see coverage across centromeric regions?

Doesn't that mean centromeres have genes located over them?

can one comment on the colored regions as well. I am only sure of red to be the centromeric regions. What does black, gray and blue regions mean? NOT as per G banding, but in general, what do they infer?

To interpret my results better, I would need the answers to above questions. Any comments are appreciated. Thanks.