We have a reference sequence with 40Ns located in the middle of it. After aligning the reads to the reference with the 40Ns, what is the best way to view the contigs that over lap the 40Ns region? Where can I get information on how many reads and contigs are covering that region using a bam file? I have sorted and indexed the bam file, but I'm not sure where to go from here. If anybody has done something like this, your help would be appreciated.