what is the seat fee?

Hi Again,

Yes the JR Pass covers all fares and fees, so this is something you don't have to worry about as a JR Pass user.
Things change if you are buying tickets the normal way. Than you pay the full fare with consists of 3 parts.

1.) Is the fare or the price for the distance traveled. You always pay this fare for both local trains and special express trains.

2.) The 2nd is the seat fee, you can see this as the extra charge for special express trains such as the Shinkansen. Local trains do not require this.

3.) The last is the seat reservation fee, this is generally around 200-500 yen depending on the train and season and has to be paid if you decide to reserve a seat number up front. The guarantees seating as supposed to a non-reserved seat. The JR Pass also covers this!

When looking up ticket prices, always look at the total amount displayed in Hyperdia.

I hope this clears things up.