In BWA SAM option field, there is a user reserved tag:
XT
Type: Unique/Repeat/N/Mate-sw
which annotated as follow:
XT:A:U unique read. XT:A:R multiple mappings for that read. XT:A:M (one-mate recovered) , one of the pairs is uniquely mapped and the other isn't. XT:A:U flag alone and discarded any others tag values.
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