This is common on so many toilets who have been exposed to chemicals, coming from the ground into your potable water, but it will not hurt you. Yet, it makes toilets, showers and other things 'green'
Go to:
www.pollyproducts.biz
That website has a cleaner is guaranteed to remove your stains.
Spray Pollys on to stain. Wait for about 1 minute. Flush. Finished.