[steven]

Thanks! Very useful paper for my purpose. It looks like if the run is RNA-Seq (or miRNA-seq etc...), the % coverage should be really low (the paper said that > 93% of uniquely mapped reads fell into exon regions). In this case, our numbers are funny . Oh well, dont know what is happening here.

It also depends on what kind of RNA you are working with (total RNA, polyA+ selected, cytoplasmic, nuclear, ribo-minus, etc). Plus this number of 93% is not a golden standard..
You may be interested in these previous threads: here and there