You will get a 1099R for the money taken from the retirement plan. When you prepare your tax return, you will enter the information from the 1099R which will include the tax that was withheld. Just like tax withheld and shown on a W-2, when all of your income and all of the tax withheld from that income is entered, the software will reconcile your tax liability and determine if you should receive a refund or if you will owe more tax.
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