quick & dirty comparison of MBTA commuter rail fare zones with JR East fares from Shinjukupic.twitter.com/54bAY8l3nz
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the steep jump in MBCR from 1A to 1 is clearly visible when applied to a smoother fare gradient like you find in Tokyo--you can also clearly see that the jump from 1 to 2 is pretty slight, and the same is true for 3 thru 10, which is why I ignored them
of course, this ONLY shows JR East fares--it costs 920 yen to go from Shinjuku to Machida by JR, because it's an indirect route with a transfer in Yokohama...but you could also take Odakyu, which goes direct and only costs 300~500ish yen (I forget)
Every station (and every company within a given station) has its own fare map--Japan doesn't use a zone-based system, but instead uses a strictly distance-based one. This obviates the need for transfers, whether free or charged; you just pay for each segment seperately
Although there's a different fare map for every station/company, one thing that's pretty consistent is the intervals. For example, if this map were showing JR prices from Yokohama instead of Shinjuku, the closest stops would still be 140 yen, then 160, etc etc
This isn't limited to trains, either--most bus routes also have a distance-based fare (you grab a ticket while boarding, then pay when you leave, based on what the on-board electronic fare chart says you owe). Some bus routes apply a flat fare, though.
Oh, one last note: JR Fares are a bit more expensive, mile for mile, than private railway (eg Odakyu, Tokyu, etc) fares. They are still cheaper, mile for mile, than subway fares.
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