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If you subtract the highest federal tax due (including the 1099-MISC) $693 from the tax due without the 1099-MISC $376, you get a difference of $317. According to Turbotax the self employment tax for the amount she earned was $159. So I subtracted the $159 from $317 and get $158.

To my untrained eyes, it seems TurboTax is (virtually) doubling the self employed tax and adding that to our federal tax due.

What this tells me is you are in a 15% income bracket and your wife received somewhere around $1125 for her participation. On that she owes income tax as well as self employment tax. The self employment tax is just the social security and medicare portion.

Pay the whole thing today.
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