We have obtained high-resolution spectra of Jupiters Great Red Spot (GRS) between 4.6 and 5.4 microns using telescopes on Mauna Kea in order to derive gas abundances and to constrain its cloud structure between 0.5 and 5~bars. We used line profiles of deuterated methane CH3D at 4.66 microns to infer the presence of an opaque cloud at 5+/-1 bar. From thermochemical models this is almost certainly a water cloud. We also used the strength of Fraunhofer lines in the GRS to obtain the ratio of reflected sunlight to thermal emission. The level of the reflecting layer was constrained to be at 570+/-30 mbar based on fitting strong ammonia lines at 5.32 microns. We identify this layer as an ammonia cloud based on the temperature where gaseous ammonia condenses. We found evidence for a strongly absorbing, but not totally opaque, cloud layer at pressures deeper than 1.3 bar by combining Cassini/CIRS spectra of the GRS at 7.18 microns with ground-based spectra at 5 microns. This is consistent with the predicted level of an NH4SH cloud. We also constrained the vertical profile of water and ammonia. The GRS spectrum is matched by a saturated water profile above an opaque water cloud at 5~bars. The pressure of the water cloud constrains Jupiters O/H ratio to be at least 1.1 times solar. The ammonia mole fraction is 200+/-50ppm for pressures between 0.7 and 5 bar. Its abundance is 40 ppm at the estimated pressure of the reflecting layer. We obtained 0.8+/-0.2 ppm for PH3, a factor of 2 higher than in the warm collar surrounding the GRS. We detected all 5 naturally occurring isotopes of germanium in GeH4 in the Great Red Spot. We obtained an average value of 0.35+/-0.05 ppb for GeH4. Finally, we measured 0.8+/-0.2 ppb for CO in the deep atmosphere.
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