We present detailed Raman studies of graphene deposited on gallium nitride nanowires with different variations in height. Our results show that different density and height of nanowires being in contact with graphene impact graphene properties like roughness, strain and carrier concentration as well as density and type of induced defects. Detailed analysis of Raman spectra of graphene deposited on different nanowire substrates shows that bigger differences in nanowires height increase graphene strain, while higher number of nanowires in contact with graphene locally reduce the strain. Moreover, the value of graphene carrier concentration is found to be correlated with the density of nanowires in contact with graphene. Analysis of intensity ratios of Raman G, D and D bands enable to trace how nanowire substrate impacts the defect concentration and type. The lowest concentration of defects is observed for graphene deposited on nanowires of the lowest density. Contact between graphene and densely arranged nanowires leads to a large density of vacancies. On the other hand, grain boundaries are the main type of defects in graphene on rarely distributed nanowires. Our results also show modification of graphene carrier concentration and strain by different types of defects present in graphene.