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BWA mapping quality scores?
Does anyone know if BWA gives ambiguous reads a mapping quality score of 0? I believe I have read somewhere that it does, but I can't find this anywhere... -
In SAM, how can I know a read is mapped ambiguously?
In .sam file, how can I know if an alignment is ambiguous. (A read is mapped to multiple places)?
Forgive me if this can be found in SAM's Spec....
