Welcome @anushree
The outputs you describe seem a bit odd to have been produced by Galaxy. Would you like to compare to this simple run I just created?
Other than that, in order for IGV to have base-level resolution for any input, any format, the database key needs to be set in IGV and your file from Galaxy needs to have that same database key assigned. This prior topic explains, and you can ask questions if this is your issue.
The example in my shared history above will link to IGV anywhere since the database key was hg19 and this is already known by IGV. If you need a custom key instead, this isn’t overly complicated, we can explain how, and you only need to do this set-up once per-custom genome, then you can assign the key to more data later on to visualize it in that same browser.
We can follow up more. Maybe share your history along with some screenshots for what you are seeing in IGV. With both of those we should be able to pin-point exactly what is going on. 