The number shown under one's name during chat, is the total rep (global) combined from all of StackExcahnge sites the user is a member of.
Here is the link to MSO that confirms this for sure. MSO is the mother of all metas and lets us know what is going on stack wide. If it's something stack-wide (like chat) this is the definitive source. Something specific to a particular site gets more attention on the individual site meta.
