Lets say we have two reads A and B that are paired. Suppose A is uniquely mappable, but B is not uniquely mappable. B maps in two spots. One close to A (say 400 bp) and one far away (100000 bp). Does BWA use that information about proximity to uniquely map B? So mapq > 0 for B in this case.
So, I guess what I'm asking is: are there situations where A and B would have mapq=0 if they were treated as single-end reads, but they have mapq >0 when treated as paired-end, assuming all other things are equal?
The reason I am asking this question is I computed mappability for single-end reads and I noticed that some of my paired-end fragments end in places that shouldn't be uniquely mappable. I used the samtools option to remove reads that have mapq=0, so I think I should only have uniquely mapped reads.