I just want to make sure my interpretation is correct: a MAPQ value of 255 indicates that the mapping quality is "not available" because it's a unique alignment, and a unique alignment means that it has a 0 probability of mapping to the wrong place, therefore: -10*log10(0 probability of error) = inf (ie. "not available") 



tldr: MAPQ of 255 has little actual meaning.

Whether 255 actually means that an alignment is unique or "I don't want to bother returning a meaningful value" is aligner dependent. In practice, tools that produce MAPQ of 255 are doing so because they aren't calculating a real MAPQ and are just indicating, "this is a more likely alignment than anything else I could find". How much more likely this particular alignment is is purely a matter of the settings you use, which are pretty arbitrary. As a rule of thumb, assume that MAPQ values from splice-aware aligners lack any standard phred-scale interpretation.