That really depends on what you use to make the game, but in general it refers to the programming instructions contained in the files of your project. For Unity you would likely have some .cs files with C# code in them. For a Phaser game such as I'm working on it will be spread around some .js and .html files. There are countless kinds.
What you would need to put on GitHub is not just the source code but all the files your game needs such as code, images, sounds, fonts, w/e.