What is the "ls" directory in my home directory?
That ls/ directory is not standard on Mac, so its something you or another user on the Mac have created (either directly, or indirectly by being created by some third party program).
It hasn't got anything to do with the ls command. However, it could reasonably have been made by someone in the middle of a mkdir command thinking that they should just list the directory first - and then erraneously running mkdir ls.
By the way - the directory /Users/xxxx is not called the root directory, but rather the user's home directory.