Difference between sequence coverage and physical coverage

[sircamp]

Hi to everyone,

I'm looking to understand the difference between these two kinds of coverage:

Sequence Coverage and Physical coverage.
I searched on web and I saw that there are different definitions of these.

Does Anyone know the right defenition? How can I extract them from a SAM file?

Which part of SAM file must be considered to calculate these two coverage values?

Thanks in advance to everyone!

[dpryan]

The definition in this wikipedia article seems correct.