The value of the input is whatever what was typed-in (or pasted) if a choice was not selected.
That is assuming you are talking about jQuery UI Autocomplete, and not some other autocomplete widget.
Again, we are not mind-readers.
Make a demo (use jsFiddle) or at least show a picture.
See the demo:
Type in "rub". You will see one choice, "ruby". Don't chose it.
$('#autocomplete').val() will yield "rub".
If you want something else, you need to explain it so that we can understand. We can't guess what you are thinking.