a, Frequency calibration of the ESR frequencies is implemented by interleaving calibration sequences with the randomized benchmarking experiment. After acquisition of three random sequences (one sequence is repeated 125 times), we check if the ESR frequency is still on-resonance by applying a low-power (26 dB lower than the typical operating power) π-rotation. If the spin-up probability is above the threshold of 50% of the readout visibility, the experiment will continue. If the spin-up probability is below the threshold, the resonance frequency will be recalibrated until all ESR frequencies pass the check, and the measurement will continue. More sophisticated frequency tracking schemes could also contribute to higher gate fidelities37,38,39. b, c, Resonance frequency fluctuations \({\rm{\Delta }}f={f}_{1\downarrow }-{f}_{{\rm{avg}}}\) of f 1↓ (b) and \({\rm{\Delta }}f={f}_{2\downarrow }-{f}_{{\rm{avg}}}\) of f 2↓ (c) during the measurement period. We subtracted the average values of the respective frequencies f avg for better visibility. Over 13 h of data acquisition, Q1 experiences multiple jumps of about 600 kHz, while the fluctuations of Q2 remain within about 300 kHz. Since the resonance frequency fluctuations of Q1 and Q2 are uncorrelated, we exclude fluctuations of B 0 or the microwave reference clock as the cause of the frequency changes. d, Variation of exchange coupling \({\rm{\Delta }}J=J-{J}_{{\rm{avg}}}\) during the measurement period. We subtracted the average value J avg for better visibility. The exchange coupling is relatively stable during the experiment. If the frequency fluctuations in b and c were to originate from charge noise, it is unlikely that J would remain unaffected. Furthermore, since the Stark shift of Q1 and Q2 is approximately 30 MHz V−1, a 600-kHz jump would require a change of the bias voltage applied to the D1 and D2 gates of about 20 mV. Such a change in the electrostatic environment would deteriorate qubit readout via the single-electron transistor charge sensor, but we noticed no substantial change of the readout level during the experiment. On this basis, we further exclude charge noise from being the cause of the frequency changes. We conclude that the frequency jumps are most probably caused by spin flips of residual 29Si nuclei that locally couple to the quantum dots. Source data