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To assess the performance of an automatic chord estimation system, reference annotations are indispensable. However, owing to the complexity of music and the sometimes ambiguous harmonic structure of polyphonic music, chord annotations are inherently subjective, and as a result any derived accuracy estimates will be subjective as well. In this paper, we investigate the extent of the confounding effect of subjectivity in reference annotations. Our results show that this effect is important, and they affect different types of automatic chord estimation systems in different ways. Our results have implications for research on automatic chord estimation, but also on other fields that evaluate performance by comparing against human provided annotations that are confounded by subjectivity.