If the method and years are correct, the difference has to be with either date placed in service or basis. Basis is often adjusted when moving by accident. If you know the depreciation should be $1,000 then you can adjust the basis until you get the correct amount.
For example: You have a basis of $100,000 and are getting $995 depreciation, you can adjust the basis up to give you the depreciation you should be taking. Continue adjusting the basis until you get the correct depreciation amount.
The lower of FMV or cost basis is used for the original depreciation and someone may have used the higher by accident or someone could have made a typo years ago. The program has you split out land, (since it doesn't depreciate) whereas maybe someone in the past included it. There are too many what ifs, all you can do is follow suit for what has been done at this point. Get the right method, the right years, the right in service date and adjust the basis until you get the right depreciation.
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