April to May Japan trip 2020

Hello,

I am travelling to Japan for the very first time in April 2020. I arrive in Tokyo and head down the same day to Hiroshima. I will spend a couple of days in Hiroshima, then head to Osaka for just under a week, then onto Kyoto for a couple of days and up to Tokyo for a few more days before leaving japan.

So my question. I am quite confident on getting from city to city with a JR pass. However I am getting a little stuck on knowing what lines are covered by the JR pass whilst traveling around cities such as Osaka, Kyoto and Tokyo. I have looked at subway maps etc but still am very confused.

What train lines and subway lines are covered by the JR pass whilst in Osaka, Kyoto and Tokyo?

Many thanks. :)