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Margin is profit as a percentage of the selling price. Markup is profit as a percentage of the cost price.
Run figures net of VAT for business-to-business work. If you price domestic jobs, show VAT as a separate line so the margin stays clear.
Use it to sanity check price structure. For tenders, use a QS prepared estimate with a BoQ plus prelims, overheads and profit, and risk allowances.
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