It depends which arrangement you are on.
Under CIS, the deduction applies to the labour element of your invoice. Materials, plant hire, VAT and certain other costs are excluded. The rate HMRC returns when we verify you depends on whether you are registered for CIS, unregistered, or hold gross payment status.
Under PAYE umbrella, income tax and employee National Insurance are deducted through PAYE. Student loan repayments and pension contributions come off where they apply. Employment costs and our charge are also accounted for. Every line appears on your payslip.