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the IV and scale question

I've learned that the I, IV, and V chord are the most used chords in any key. However, I'm not sure why the major pentatonic removes the IV (4) from its scale. You would think the bassist would be playing root A whenever the A chord is being played by the guitarist

example: the song "Lady Picture Show" by Stone Temple Pilots starts off with E, B, and A repeat for intro and verse. When creating my bass line I can't hit the root note of "A" bc its not in the E major pent scale. This seems off to me...

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E minor pentatonic is your friend in most cases.

1 b3 4 5 b7

E G A B D