Emulator Layers

These layers are toggled by hotkeys. They default to the number keys.
Graphics Layers 1-4 default to 1-4. These manage most of the screen.
The Sprites Layer defaults to 5. This manages Link and most other moving objects.
Clipping Windows default to 8. This manages the light cone provided by the Lamp.
Transparency defaults to 9. This manages many effects.
Consider disabling them via the Input Menu option "Customize Hotkeys."

Zone Graphics Layer 1 Graphics Layer 2 Graphics Layer 3 Graphics Layer 4 Transparency
Link's House    
Outside Link's House    
Hyrule Castle