Multi Mapping Loci Meaning

[mattg478]

Hi Thanks for this super useful software!

I have some Parse Bioscience snRNA data that I have been trying to map.
I get lots of multimapping reads (>70%) and have been trying to work out what the issue is.

Would you be able to clarify what exactly counts as a loci for multi mapping?
Do reads mapping to two different exons across a splice site count as multiple loci?
Do reads mapping across an exon/intron boundary count multiple loci?
If there are two genomic features overlapping (eg a non-coding gene in the intron of another gene) would a read mapping here count multiple loci?

Thank you,
Matt