There are two parts to this equation.
First: Depreciation issue - You have what you paid minus all the depreciation allowed or allowable equals your basis. Second: Unused expenses carry over
You have the sales proceeds. The sale minus the basis PLUS unallowed (carried over) losses over the years equals your gain. Check your old Sch E forms to see if you had carryover losses. If you changed software to do your taxes, you may have forgotten to add it in and it got lost along the way.
Make sure that years with losses are being accounted for and added in to reduce your gain.
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