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To investigate the formation of gross well width fluctuations in InGaN quantum wells subjected to a growth interruption or temperature ramp, the impact of substrate miscut on the morphology of thin InGaN epitaxial layers grown on GaN pseudo-substrates has been studied. Following a growth interruption, the InGaN layer morphology consists of interlinking strips of InGaN separated by elongated troughs. The troughs tend to align along the same direction as the step edges in the underlying GaN pseudo-substrate and the spacing of the troughs varies in direct proportion to the step edge spacing. However, the troughs are on average more widely spaced than the terrace edges, and analysis of the distribution of trough spacings and step edge spacings suggests that it may be double-monolayer steps which most influence the trough formation. A mechanism for trough formation is proposed in which indium is preferentially incorporated at double-monolayer step edges and that the resulting indium-rich regions decompose during the growth interruption, forming a trough.