Your mortgage itself is not accounted for when taking depreciation. Yes, you would depreciate the amount you paid, but sometimes a mortgage has other expenses such as consolidating other bills if you did a refinance. So you do not use your mortgage to determine your depreciation deduction. You use your purchase price.
Other than the interest you pay on the mortgage, your actual mortgage is not relevant to your taxes and deductions. You would deduct the mortgage interest in the same way you would on any other rental property in the interest section.
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