How does Tophat rank alignment?

[hyj004]

Hello

I am wondering how Tophat ranks alignment from bowtie.

For example,
'A' read is mapped to 10 locations by bowtie.
Mapping quality of these 10 locations is set to 255 because bowtie reports 255 if a read aligns to genome.
In the end, Tophat outputs only two locations out of 10 after ranking the alignment result.

Does anyone know how Tophat ranks alignemts?Does Tophat use mismatch information for this?

I would appreciate if somebody could answer this question.
Thanks!!