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All pins on the 3rd header of the Mega2560 only involve the ATmega2560 mcu chip or the ground GND, +5V, +3V3, and VIN nets:
Some pins of interest:
:NCjust means "no connection" and does nothing.
:IOREFpin is in fact just connected to the
:RESETpin does eventually make it to the corresponding ATmega2560 pin, but it is part of a wider net involving also reset of the ATmega16u2, so it is mapped only to a
- Four of the digital I/O pins also act as JTAG test pins: TDI (Test Data In); TDO (Test Data Out); TCK (Test Clock); 4. TMS (Test Mode Select).