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Ideal projective quantum measurement makes the system state collapse in one of the observable operator eigenstates $|ϕ_α\rangle$, making it a powerful tool for preparing the system in the desired pure state. Nevertheless, experimental realisations of projective measurement are not ideal. During the measurement time needed to overcome the classical noise of the apparatus, the system state is often (slightly) perturbed, which compromises the fidelity of initialisation. In this paper, we propose an analytical model to analyse the initialisation fidelity of the system performed by the single-shot readout. We derive a method to optimise parameters for the three most used cases of photon counting based readouts for NV colour centre in diamond, charge state, nuclear spin and low temperature electron spin readout. Our work is of relevance for the accurate description of initialisation fidelity of the quantum bit when the single-shot readout is used for initialisation via post-selection or real-time control.