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Three-dimensional composition maps of nominally pure Ge domes grown on Si(001) at were obtained from grazing incidence anomalous x-ray scattering data at the Ge edge. The data were analyzed in terms of a stack of layers with laterally varying concentration. The results demonstrated that the domes contained a Si-rich core covered by a Ge-rich shell and were independently supported by selective etch experiments. The composition profile resulted from substrate Si alloying into the Ge during growth to partially relax the stress in and under the domes.