I am mapping some RNA-seq data with bwa and would like to do some analysis on where multi-mapped reads fall.
I know that I can extract multi-mapped reads by looking for mapq < 23 and/or the XA flag on the reads. However, I am wondering how bwa decides which location to report for a read that can be mapped to two different locations equally well. Does it choose a random one? Does it always report the first one? Something else?
Does anybody know what exactly bwa does here?