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the reference voltage is the the voltage that the ADC will convert the analog signal with respect it. suppose for example, in your application you have an input analog signal with maximum peak-to-peak is 1 V. then you should make the reference voltage of the ADC equal to 1 V. Assume that you are using 8 bits ADC, when the input of 1 V is applied the converter will make this comparision: 1V/1V*8=8 = FF. if an input of 0,5 is applied the result is (0.5/1)*8=4=0F.
in simple way, the reference voltage of the ADC should be equal to the maximum expected input analog signal