jats:pUnderstanding the nature of the mid-gap defects in amorphous chalcogenide alloy-based phase change materials is crucial to guide the development of multi-level memories, selectors, and neuromorphic devices. Currently, however, the knowledge of the mid-gap defects is fragmented and the known structural and electrical characteristics of the defects cannot be unified in a single atomic model. In this work, a Ge–Ge chain defect model is built by artificial bond rearrangement in an amorphous GeTe network generated by atomic distortion, revealing a possible valence alternation mechanism in its formation. Atoms in the Ge–Ge chain are found to have a crystalline-like environment. The chain is found to have a negative-U property and to introduce mid-gap states. This model unifies the main known properties of the mid-gap defects in amorphous chalcogenide alloy-based phase change materials.</jats:p>