black dots under application icons on dock

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Close an app. When you click the red dot in the top-left corner of an open window, the window closes but the app stays open. Open apps have a black dot beneath them in the Dock. To close an app, choose “Quit app name” from the app menu (for example, in the Mail app, choose Quit Mail from the Mail menu). Or Control-click the app icon in the Dock and click Quit.