Smelly loo

My parents have a six year old, four- bed house with three toilets. One, on the first floor is hardly ever used. There has been a musky, but not unpleasant smell in the well- ventilated toilet room for a while and on examination I've found the level of water in the toilet bowl to be very low. Is this due to evaporation and perhaps allowing a smell to come up the pipes into the room (the toilet is not leaking)? Or....does an unflushed loo give off a smell if the water is in the holding chamber of the toilet for too long....eg going stagnant?

Yes, almost certainly evaporation