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The substrate DOES EFFECT MOSFET operation. There is a shift in threshold voltage when substrate is connected at any other voltage different from source. In mosfet there exists two pn junction diodes. Consider an example of nMOS. There is a diode from n+ source to p substrate and other from n+ drain to p substrate. When substrate is connected to source, this is like you have shorted the two terminals of diode. So you this diode does not matters in this case. But there is still a drain to substrate diode. In CMOS IC design, this diode, if get forward biased, could results in large current leakage. So, there is always a reverse biased current leakage in the drain - substrate diode. You can also think as a parasitic npn bipolar transistor, with drain and source being n side and substrate p as a base.
There is shift in Vth ( threshold voltage) of MOSFET, if source and substrate are not connected to same terminal. For mosfet structure |dw:1360603792348:dw| The M1 has more threshold voltage than M2. So if both the gate are tied to same potential, the current from drain of M1 to ground will be less than the current in same condition except, M1 source and substrate are also connected together. Sometimes in a design it becomes very difficult to tolerate this Vth shift. So source- substrate are connected together, but it causes some area penalty, you have to change substrate to connect it at different potential from ground ( in case of NMOS for PMOS it is high supply ( vdd)). [ there are many ways in IC designing to isolate one substrate from another].
SO YOU CAN SEE HOW SUBSTRATE EFFECT THE OPERATION OF MOSFET.