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This work presents experimental and molecular dynamics approaches towards deformation and phase transformation mechanisms of monocrystalline Si(100) subjected to nanoindentation. The nanoindentation experiment was conducted with a Berkovich indenter. Following the analysis using cross-sectional transmission electron microscopy with the samples prepared by focused ion beam milling, upon pressure release, metastable Si-III and Si-XII phases were identified inside the indentation-induced deformed region beneath the indent. We also demonstrated phase distributions during loading and unloading stages of spherical and Berkovich nanoindentations through molecular dynamics simulations. By searching the presence of the fifth neighboring atom within a non-bonding length, Si-III and Si-XII have been successfully distinguished from Si-I. Crystallinity of this mixed-phase was further identified by radial distribution functions.