Compare alignment quality of multiple sequencing runs aligned against the same reference genome
Qualimap will do this for you. 


Go to qualimap.bioinfo.cipf.es
Run qualimap (default params are fine) on each BAM file
Open up the HTML output, and you can read off the %identity (they measure the opposite, i.e. mismatch rate, but 100% - mismatch rate is %identity of course), indel rate, etc.


One thing to watch out for (you don't mention it in your question, but just in case) is that you cannot directly compare Q scores - these are a bit of a mess and calculated very differently in each piece of software. 

Unsolicited suggestion: you might also try NGM-LR for mapping MinION data. We've found it beats the others for our data (though we map to a distant reference).