From that study, you will see that you are asked to measure the in vitro methylation
level over the 35S rDNA gene bodies. The longest of this is the RDN37-1 gene which
runs in the figure from approximately 454000 to 458500. The actual gene is 
longer than these coordinates but we stick to these coordinates as it corresponds
to the view on Fig. 6A. Your task is to extract windowed data from these coordinates
using a command like `nanalogue window-dens`, then you can count how many windowed
values fall in the range 0-0.5 and 0.5-1.0.

Alternate solutions
===================

There are several ways to answer this question. For example,
you can visualize the mod BAM file in IGV at the locus in question and
perform a rough count as to how many reads are heavily modified and
how many are unmodified.