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Charge transport in solids at low temperature reveals a material’s mesoscopic properties and structure. Under a magnetic field, Shubnikov–de Haas (SdH) oscillations inform complex quantum transport phenomena that are not limited by the ground state characteristics and have facilitated extensive explorations of quantum and topological interest in two- and three-dimensional materials. Here, in elemental metal Cr with two incommensurately superposed lattices of ions and a spin-density-wave ground state, we reveal that the phases of several low-frequency SdH oscillations in ${\sigma }_{\mathit{xx}} \left({\rho }_{\mathit{xx}}\right)$and ${\sigma }_{\mathit{yy}} \left({\rho }_{\mathit{yy}}\right)$are no longer identical but opposite. These relationships contrast with the SdH oscillations from normal cyclotron orbits that maintain identical phases between ${\sigma }_{\mathit{xx}} \left({\rho }_{\mathit{xx}}\right)$and ${\sigma }_{\mathit{yy}} \left({\rho }_{\mathit{yy}}\right)$ . We trace the origin of the low-frequency SdH oscillations to quantum interference effects arising from the incommensurate orbits of Cr’s superposed reciprocal lattices and explain the observed $\pi$-phase shift by the reconnection of anisotropic joint open and closed orbits.