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We have simulated the variance in the diffracted electron intensity as a function of scattering vector in fluctuation electron microscopy for a range of fully amorphous and nanocrystal-containing metallic glass models. Variance peaks are obvious for glasses that contain well-developed short-to-medium range order but absent for their parent liquids. The variance peaks are very sensitive to the presence and especially the size of the nanocrystal embryos or nuclei embedded in the glass matrix but much less so to the variations in the type or degree of the cluster ordering developed in fully amorphous materials.