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Old 07-21-2010, 03:15 AM   #1
christophpale
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Location: canada

Join Date: May 2010
Posts: 16
Default Interpretation of BWA mapping quality

Hi,
I understand that mapping quality of 0 means that reads align to multiple locations.

However,

1. what does mapping quality greater than 0 mean?

2. How does a read that mapped with mapping quality of 10 differ from the read that has a mapping quality of 20?

3. Is the BWA mappinq quality related to the distance to the next best match? If yes, what is the relationship between mapping quality and the distance to the next best match?
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