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We model the impact of non-uniform cloud cover on transit transmissionspectra. Patchy clouds exist in nearly every solar system atmosphere, browndwarfs, and transiting exoplanets. Our major findings suggest that fractionalcloud coverage can exactly mimic high mean molecular weight atmospheres andvice-versa over certain wavelength regions, in particular, over the HubbleSpace Telescope (HST) Wide Field Camera 3 (WFC3) bandpass (1.1-1.7 $\mu$m). Wealso find that patchy cloud coverage exhibits a signature that is differentfrom uniform global clouds. Furthermore, we explain analytically why the"patchy cloud-high mean molecular weight" degeneracy exists. We also explorethe degeneracy of non-uniform cloud coverage in atmospheric retrievals on bothsynthetic and real planets. We find from retrievals on a synthetic solarcomposition hot Jupiter with patchy clouds and a cloud free high mean molecularweight warm Neptune, that both cloud free high mean molecular weightatmospheres and partially cloudy atmospheres can explain the data equally well.Another key find is that the HST WFC3 transit transmission spectra of two wellobserved objects, the hot Jupiter HD189733b and the warm Neptune HAT-P-11b, canbe explained well by solar composition atmospheres with patchy clouds withoutthe need to invoke high mean molecular weight or global clouds. The degeneracybetween high molecular weight and solar composition partially cloudyatmospheres can be broken by observing the molecular Rayleigh scatteringdifferences between the two. Furthermore, the signature of partially cloudylimbs also appears as a $\sim$100 ppm residual in the ingress and egress of thetransit light curves, provided the transit timing is known to seconds.

The Influence of Non-Uniform Cloud Cover on Transit Transmission Spectra