Add a list of the chromosomes on the stats page, listing the count of guide on each chr. A visual representation (circos or karyotype), showing the position of the guides on the chromosomes provides a quick overview.
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Guides are still to small to be represented, and zooming too much makes movement so fast that it is very hard to have guides in view. (1)
Plus, there is spots where guides are really close to each other so they look like a single one. (2)
Several solutions (not exclusive) :
Thicken artificially the width of guides, will not fix (1)
On hover, reveal the number of guides which are actually in the "stack", and eventually add a tooltip with a list of the guides in the "stack"
Rename width & height of the chromosome in SVG manipulation (to something like length & thickness or so), to avoid confusion with DOM/SVG elements width & height