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Good morning, everyone, please take a seat on the bus where I'll brief you on today's training.

Q1) What does "where" refer to in this sentence? I think "where" refers to "the bus".

Q2) If "where" refers to "the bus", can I use "in which" instead of "where"? as in

Good morning, everyone, please take a seat on the bus in which I'll brief you on today's training.

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No, you need to use "where."

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fire1please take a seat on the bus, in which I'll brief you on today's training.

You need a comma whether you say 'where' or 'in which'. 'where' is a much better choice. If I were you, I'd forget about the other choice.

CJ