I usually create .tdf files for .bam alignments, and I realize that the parameters used can have an effect on how coverage is visualized.
However, the middle panel of Figure 4C looks off to me (from Panneerdoss et al. 2018):
I don't remember encountering an issue when the scale is reported as 0-1, when there are clearly more than two levels of coverage (as in the middle panel of Figure 4C). Has anybody else seen a situation where the TDF normalization could explain this plot? I also know that you don't need a TDF file to see a scale of a zoomed-in view of read alignments, but somebody told me that this was because of the TDF normalization (and I don't want to say this is incorrect, without additional discussion).
NOTE: I also see the resolution in the above image isn't great. So, here is another view where you can see what I am describing (in the upper-left hand corner of each tract) a little better: http://advances.sciencemag.org/content/advances/4/10/eaar8263/F4.large.jpg?width=800&height=600&carousel=1