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-   -   Interpretation of BWA mapping quality (http://seqanswers.com/forums/showthread.php?t=6065)

christophpale 07-21-2010 03:15 AM

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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