We consider a disordered quantum metamaterial formed by an array of superconducting flux qubits coupled to microwave photons in a cavity. We map the system on the Tavis-Cummings model accounting for the disorder in frequencies of the qubits. The complex transmittance is calculated with the parameters taken from state-of-the-art experiments. We demonstrate that photon phase shift measurements allow to distinguish individual resonances in the metamaterial with up to 100 qubits, in spite of the decoherence spectral width being remarkably larger than the effective coupling constant. Our simulations are in agreement with the results of the recently reported experiment.
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