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 (How Mapq In Bwa Is Calculated?). 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.