Graphene Mobile has its own option for adding Google Analytics code. Go to WP Admin > Appearance > Graphene Mobile > Google Analytics Options.
You can also use the “Copy relevant Graphene settings” preset to quickly copy the Graphene settings that are similar to the Graphene Mobile settings. Saves going back and forth between the two, but make sure you check how the mobile theme looks, as some items suited for desktop may not be suitable for mobile, e.g. big social sharing buttons.