Tip #5. Web Application permissions override Site level ones

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Be careful when assing permissions for the Web Application level, because your can break the Site level permissions you set up previously.

Web Application settings supersede what located below, so, all permissions which are set at Web Application level, “Central Administration > Application Management > User Permissions for Web Application” will override the Site level permissions.

For example, your user with “Contributor” rights on the site level can’t delete anything, if you deny "delete" permission at Web App level.

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