When there is more than one possible mapping place for a read, being both places of equal score,
Where 'bwa mem' mapper finally maps it?
What about the mapping quality scores for the read?
When there is more than one possible mapping place for a read, being both places of equal score,
Where 'bwa mem' mapper finally maps it?
What about the mapping quality scores for the read?
It depends on your settings, but I think the default is multimapping the reads. So the same read will be present in multiple locations. Mapping quality will be 0 (meaning the read maps equally well in multiple places).
Are you certain about multi-mapping? bwa mem manual entry does not say anything specific but the older sampe/samse explicitly say that
Repetitive read pairs will be placed randomly.
Repetitive hits will be randomly chosen.