The ammonia fraction is a measure of the preservation of the silage and represents the difference between crude protein total and crude protein as a percentage.
A high NH3 percentage indicates poor preservation and high protein loss. Silage with high NH3 can also be a sign of clostridia ("harmful microbes"). These also convert protein into NH3. Incidentally, the protein converted into NH3 is still usable, but not as high quality as the crude protein variant.