I found that sometimes y-axis is shown perpendicular with x-axis at counterclockwise direction but sometimes y-axis is shown perpendicular with x-axis at clockwise rotation. What is the difference between them ?
What comes in my mind is that for a counterclockwise rotation of a system they put y-axis perpendicular in counter clockwise direction w.r.t x-axis to define any function related to that system
&
for a clockwise rotation of a system they put y-axis perpendicular in clockwise direction w.r.t x-axis to define any function related to that system.

For 2D coordinate systems there is not substantial difference with the two systems it is purely a matter of convention.
For 3D coordinate systems we can distinguish between Right Hand System and Left Hand System.
Refer also to this MSE OP for more details.