Ran it out off gas, refilled it now runs rough

Very likely that there was some trash in the bottom of your fuel tank and as it pulled the last bit of gas through it could have clogged the fuel filter, of the carburetor. Without knowing the make and model its possible there is no fuel filter some push mowers have a straight fuel line to the carb. If that is the case, on the bottom of the carb there is a bowl most mowers it has a bolt in the bottom middle of the bowl I would remove the bolt and drop the bowl, clean with a wire brush and carb cleaner and reinstall the bowl. I believe that will most likely solve your problem. If it doesn't or you have any questions please leave a comment I would like to help you resolve your problem!