The mode of operation (i.e., the behavior of the Timer/Counter and the Output Compare pins) is defined by the combination of the Waveform Generation mode (WGM13:0) and Compare Output mode (COM1x1:0) bits. The Compare Output mode bits do not affect the counting sequence, while the Waveform Generation mode bits do. The COM1x1:0 bits control whether the PWM output generated should be inverted or not (inverted or non-inverted PWM). For non-PWM modes the COM1x1:0 bits control whether the output should be set, cleared or toggle at a Compare Match. See Compare Match Output Unit.
For detailed timing information refer to Timer/Counter Timing Diagrams.