I assume that when an IRS computer analyzes a filing generated by TurboTax, it checks your input data against fiducial sources such as 1099s filed by the organizations that generated the income, and makes other sanity and consistency checks.
Then if all the input data passes those validations, it uses its own algorithms to determine how much tax is due and whether you have overpaid or underpaid.
In other words, if TurboTax has made an inaccurate intermediate calculation, the IRS computer is oblivious to it. I think that the IRS computers extract only a few items from the filed form, and draw conclusions from those.
Any disagreements?
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No disagreements, for the most part. Here's a breakdown of how the IRS reviews a tax return:
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