Need to change coverage QC to include parts of the UTRs

[niemasd]

I believe our current QC including the coverage QC ignore the UTRs entirely. However, Joel Wertheim pointed out to me that there are important mutations of interest that occur in the UTRs, e.g. C241T. Instead of ignoring both UTRs entirely, I propose we just ignore the first 100 and last 50 bases of the reference genome, which is what NextStrain does