I filed a 1099-MISC, it was for $3000. The taxes taken out on the federal level should have been 15.3% or $459 but turbo tax took $635 off of my federal return. Why?

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The 15.3% you are referring to is for self-employment taxes. You will owe these taxes on your net self-employment income but you will also owe regular income taxes on this income. This income gets added to all of your other income to determine your total tax liability. Also, the additional income may have lessened the amount of credits that you were eligible for such as the EIC, which could also decrease your refund.