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The peak position of Raman spectra of epitaxial graphene is an excellent indicator of film quality and reveals irregularities, such as graphene thickness inhomogeneity and SiC substrate defects. A comparison of microscopic Raman maps and scanning probe microscopy images of the same position of the sample revealed that wave numbers of Raman peaks (G and 2D band peaks) were strongly correlated with the strain in the graphene film. The increase in number of graphene layers (2 to 3–4 layers) induced phonon softening (~6 cm-1) and broadening (~6 cm-1) of the 2D band peak. Significant phonon softening and abnormal broadening of the Raman peaks were observed at residual scratches on the SiC substrate. The quantitative layer number distribution of graphene on SiC is successfully estimated from the wave number distribution of the 2D band peak. 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