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What does it mean when one says "you are breathing down my throat"? Would it mean you are making them uncomfortable by the way you are questioning them? Or not giving them enough room?
The correct phrase is "breathing down one's neck." It means that someone is standing too close to you for comfort. Often it implies that they are watching you closely to see that you are doing something correctly.
"I hate trying to cook when my mother-in-law is visiting. She's always right there in the kitchen with me, breathing down my neck."
"breath down ones throat" 
Re: "breath down ones throat" 
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