(1)A licensee of a bonded ware house, shall pay to the Government duty at the prescribed rates for the absence of the quantity of the spirit detected at the time when the spirit measured, gauged and proved for removal. The licensee shall pay the duty as aforesaid in lieu of the duty payable under Rule 491. Unless he is able to account for the absence in respect of spirits in bottles and also subject to the allowance of 0.50 percent (calculated at proof strength) in respect of spirits in any vessels.