Altitude is a more complex question than it seems. Your GPS measures position relative to satellite orbits. It doesn't know the altitude of the local terrain below you since it doesn't have a detailed world DEM (digital elevation model). Even "mean sea level" (often used as a reference on local maps) isn't a world constant since it varies between oceans. Instead GPS receivers have a rough model of the shape of the earth which they use as their reference "datum" (see http://en.wikipedia.org/wiki/Datum).

Different GPS receivers report the altitude in different ways, so they don't always agree with each other. Also nav software may correct the altitude reported by the GPS receiver to a different reference. You have to check the documentation for your particular GPS receiver and nav software to be sure.