You are probably in bad need of a good carb cleaning or rebuild. That cylinder is more than likely starving for fuel and getting enough every once in a while to cause a backfire. The backfire is probably a result in getting just enough fuel in that particular cylinder to cause it to pop on the downstroke. In such a case you probably are not even aware that the cylinder is not firing until you hear the pop. Very common after a bike sits for a long period or when the tank gets garbage in it which goes through the carbs.