I have found the following ways to determine if a tag can be mapped to more than one place using a SAM file produced by bwa produced from single-read sequencing data:
the presence of the characters "XT:A:R"
the presence of the characters "XA:Z:"
mapping quality (MAPQ) of 0.
For my data, I find these definitions all give close, but not identical counts. Why is that and which is the right definition?
MAPQ==0 means a multiple hit
Thanks. It has been corrected in my question.