How does Artemis calculate "coverage"?

[sshell]

Hello,

I would like to know what values are being plotted on the Y axis in Artemis when viewing sequence data with the "coverage" option. I am doing RNA-seq so I am interested in read depth at various positions along the genome. I can see that "coverage" is not the same as read depth, because the numbers on the Artemis Y axis don't match up to read depths that my colleague calculates directly from the BAM files. In the attached clip, for example, what does the number in the upper right corner represent?

Thanks for any help!

[aloliveira]

I don't know whats is going on, and I never used Artemis with coverage option. My guess: maybe the difference between the coverage is due to the way of the coverage was calculated. That way can be in KMER coverage or READ coverage.