1099-s only shows the gross sales price. it excludes closing costs. your gain is the 1099-S less the cost of property including any improvements reduced by the higher of depreciation allowed or allowable (this means if you too much it's recapturable. if you took too little you need to adjust for the proper depreciation - too little means you would need to file form 3115 to adjust for the proper depreciation); less selling expenses/closing costs. These would nbe shown oin the closing statement. Not all closing costs are selling expenses. For example prorated real estate taxes, mortgage interest, utilities, HOA fees go on schedule E.
selling expenses might include these expenses imposed on the seller: transfer tax, home warranty fee, real estate sales commission, inspection fee, seller credits
Turbotax does make it a little difficult to handle the sale of rental property when there are multiple assets involved, since to get the correct results, sales proceeds and selling expenses must be allocated to each asset. Miss any and the net tax basis will not be included in computing gain or loss.
