The extra tax mentioned by the program is the early withdrawal penalty of 10% of the amount withdrawn, when the withdrawal is made before age 59 1/2 and the withdrawal does not qualify as one of the exceptions to the penalty.
TurboTax will calculate the amount of the penalty and include in the final calculation of tax due (or refund). You do not need to pay it separately or receive a separate tax bill.
The penalty is transferred to line 59 of your form 1040.
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