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Does The Mapping Of A Read'S Pair Affect Its Own Mapping Score In Bwa?

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I would like to know more about how BWA treats the mapping score of paired end reads.

I am familiar with the process used to assign mapping scores by BWA (thanks to this post). I see that the mapping score is affected by the correct mapping of a read's pair. But to what extent?

For instance, if one read in a pair is mapped and the other is not, does the mapped read receive a reduction in its own mapping score.

Further, does anyone know the file and location of the BWA which assigns mapping score?

Thanks in advance.


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