Supplemental wage withholding
The IRS lets employers withhold a flat percentage on separately paid bonuses, commissions, and similar supplemental wages (up to a high-dollar threshold that uses a different method). That flat rate is often higher than your average tax rate, which is why the deposit looks small.
When you file, the bonus is just more ordinary income in your bracket. Withholding is not the tax. A large bonus can still increase your total tax; it does not stay taxed at the flat supplemental rate forever.