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Japanese trains are great. They're always clean and on schedule. The longest wait I ever had for a train as far as I can recall is for five minutes which is good enough for me. There are some train stations where trains arrive every two or three minutes. This is because trains are using the same tracks but are going to different routes. The worst part of it that made it confusing is the fact some of them has skip trains. I think this is where your JR pass will come into use because there are times that I would be riding a skip train without me knowing it! So I'd have to ride the train going back. Some of their trains skip some stations as a means to give express travel to passengers in further areas. If you don't read the train station announcements very well, you can end up like me having to ride two or more trains just to get to the right station.