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Old 01-15-2016, 12:26 AM   #1
Junior Member
Location: Italy

Join Date: Jan 2016
Posts: 2
Default Difference between sequence coverage and physical coverage

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!
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Old 01-15-2016, 04:34 AM   #2
Devon Ryan
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480

The definition in this wikipedia article seems correct.
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coverage, physical coverage, sam, sam file, sequence coverage

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