Yeah, it'll definitely cause skew.  (Putting all the unmapped reads into bucket '0' is probably wrong, my thinking has been to modify this to put them into their own, separate bucket from all the other reads).  

The reason I don't think this is wrong is: my suspicion is that the genomic region partitioning is basically going to be used for computations that are "local," in the sense that they deal with all the reads (or data) within distinct genomic regions.  

In this context, I'm not sure I get why we'd want to scatter the unmapped reads across partitions -- logically, they'd go into a single (unmapped) partition, to be dealt with separately.  

Or maybe I'm misunderstanding the point of genomic region partitioning here?