Per-Sample Processing/Pixel ownership test
Because the Default Framebuffer is owned by a resource external to OpenGL, it is possible that particular pixels of the default framebuffer are not owned by OpenGL. And therefore, OpenGL cannot write to those pixels. Fragments aimed at such pixels are therefore discarded at this stage of the pipeline.
Generally speaking, if the window you are rendering to is partially obscured by another window, the pixels covered by the other window are no longer owned by OpenGL and thus fail the ownership test. Any fragments that cover those pixels will be discarded. This also includes framebuffer clearing operations.
Note that this test only affects rendering to the default framebuffer. When rendering to a Framebuffer Object, all fragments pass this test.