I withdrew my 401k account early ( $12,000-ish) and was under the impression that I would also have to pay a 10% penalty, only owed $299. Can someone clarify this for me?

I thought that I would be taxed a total of 10% come income tax time, making that around $1200 give or take, however ended only owing $299. I'm kind of confused on whether or not I'm still going to owe on this on top of the $299. Did my annual withholding factor in on that 10% penalty as well?