Your question is rather vague.
But it seems that you have to:
Perform FFT on both audio files
Searching the net should provide you with example code and libraries for various programming languages and how to apply FFTs to WAV files.
Scale the results
Because you want the percentage ratio you have to scale both FFTs to the same level.
Caluclate the percentage ratio for each frequency
The simplest part:
ratio[freq] = 100 * scaled_fft1[freq] / scaled_fft2[freq]
Display the result
A simpley x-y diagram where x is the frequency and y is the above calculated ratio.