A whole sequence

You have the depth of your reads in windows along a whole chromosome, as bedGraph, for one sample or several.

karyon NC_000962.3 sampleA.bedgraph sampleB.bedgraph -o genome.svg

The place is the whole sequence, by its name, and each file is a row. The first sample drops to nothing where it has lost a stretch and doubles where it carries one twice. A bedGraph does not say how long the sequence is, so karyon draws as far as the files reach and says so; write the span, as NC_000962.3:1-4,411,532, to set it yourself.

Change it

To	Write
Zoom into the stretch with no reads	NC_000962.3:1,400,000-1,560,000 in place of NC_000962.3
A log scale for the depth	sampleA.bedgraph --log
Make depth windows from a BAM	mosdepth --by 10000 sample reads.bam, then draw sample.regions.bed.gz

The example files: sampleA.bedgraph and sampleB.bedgraph. Every option: karyon help coverage, or the command line reference.