Graphite crystals used to prepare graphene-based heterostructures are generally assumed to be defect free. We report here scanning tunneling microscopy results that show graphite commonly used to prepare graphene devices can contain a significant amount of native defects. Extensive scanning of the surface allows us to determine the concentration of native defects to be 6.610 cm. We further study the effects of these native defects on the electronic properties of Bernal-stacked bilayer graphene. We observe gate-dependent intravalley scattering and successfully compare our experimental results to T-matrix-based calculations, revealing a clear carrier density dependence in the distribution of the scattering vectors. We also present a technique for evaluating the spatial distribution of short-scale scattering. A theoretical analysis based on the Boltzmann transport equation predicts that the dilute native defects identified here are an important extrinsic source of scattering, ultimately setting the mobility at low temperatures.

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