We use a science-grade skipper charge-coupled device (skipper CCD) operating in a low-radiation background environment to develop a semiempirical model that characterizes the origin of single-electron events in CCDs. We identify, separate, and quantify three independent contributions to the single-electron events, which were previously bundled together and classified as "dark counts": dark current, amplifier light, and spurious charge. We measure a dark current, which depends on exposure, of (5.89±0.77)×10-4e-/pix/day, and an unprecedentedly low spurious charge contribution of (1.52±0.07)×10-4e-/pix, which is exposure independent. In addition, we provide a technique to study events produced by light emitted from the amplifier, which allows the detector's operation to be optimized to minimize this effect to a level below the dark-current contribution. Our accurate characterization of the single-electron events allows one to greatly extend the sensitivity of experiments searching for dark matter or coherent neutrino scattering. Moreover, an accurate understanding of the origin of single-electron events is critical to further progress in ongoing research and development efforts of skipper and conventional CCDs.