A hybrid Bacon-Shor surface code is implemented using a fault tolerant quantum computer comprising hybrid acoustic-electric qubits. A control circuit includes an asymmetrically threaded superconducting quantum interference devices (ATS) that excites phonons in a mechanical resonator by driving a storage mode of the mechanical resonator and dissipates phonons from the mechanical resonator via an open transmission line coupled to the control circuit. The hybrid Bacon-Shor surface code only couples four phononic modes per given ATS, reducing cross-talk as compared to other systems that couple more phononic modes per ATS. Also, measurements are performed such that three parity measurements are taken between a phononic readout mode and a transmon qubit in a given syndrome measurement cycle.