What does 在 mean in "你在吗"?
在 in 你在吗? means 'is present'
大考时你在这里吗? = Were you here during the final exam?
大考时你在那里吗? = Were you there during the final exam?
大考时你在(学校)吗? = Were you at the school during the final exam?
大考时你在吗? = Were you present during the final exam? (It doesn't mention where the final exam took place, so you can use 'were present' or 'were there')
Similarly:
他犯案时你在現場吗? = Were you at the scene when he committed the crime?
他犯案时你在吗? = Were you present/ there when he committed the crime?