The atmosphere of Jupiter is the largest planetary atmosphere in the Solar System. It is mostly made of molecular hydrogen and helium in roughly solar proportions; other chemical compounds are present only in small amounts and include methane, ammonia, hydrogen sulfide and water. Although water is thought to reside deep in the atmosphere, its directly measured concentration is very low. The nitrogen, sulfur, and noble gas abundances in Jupiter's atmosphere exceed solar values by a factor of about three.
The atmosphere of Jupiter lacks a clear lower boundary and gradually transitions into the liquid interior of the planet. From lowest to highest, the atmospheric layers are the troposphere, stratosphere, thermosphere and exosphere. Each layer has characteristic temperature gradients. The lowest layer, the troposphere, has a complicated system of clouds and hazes, comprising layers of ammonia, ammonium hydrosulfide and water. The upper ammonia clouds visible at Jupiter's surface are organized in a dozen zonal bands parallel to the equator and are bounded by powerful zonal atmospheric flows (winds) known as jets. The bands alternate in color: the dark bands are called belts, while light ones are called zones. Zones, which are colder than belts, correspond to upwellings, while belts mark descending air. The zones' lighter color is believed to result from ammonia ice; what gives the belts their darker colors is not known with certainty. The origins of the banded structure and jets are not well understood, though two models exist. The shallow model holds that they are surface phenomena overlaying a stable interior. In the deep model, the bands and jets are just surface manifestations of deep circulation in Jupiter's mantle of molecular hydrogen, which is organized into cylinders.
The Jovian atmosphere shows a wide range of active phenomena, including band instabilities, vortices (cyclones and anticyclones), storms and lightning. The vortices reveal themselves as large red, white or brown spots (ovals). The largest two spots are the Great Red Spot (GRS) and Oval BA, which is also red. These two and most of the other large spots are anticyclonic. Smaller anticyclones tend to be white. Vortices are thought to be relatively shallow structures with depths not exceeding several hundred kilometers. Located in the southern hemisphere, the GRS is the largest known vortex in the Solar System. It could engulf two or three Earths and has existed for at least three hundred years. Oval BA, south of GRS, is a red spot a third the size of GRS that formed in 2000 from the merging of three white ovals.
Jupiter has powerful storms, often accompanied by lightning strikes. The storms are a result of moist convection in the atmosphere connected to the evaporation and condensation of water. They are sites of strong upward motion of the air, which leads to the formation of bright and dense clouds. The storms form mainly in belt regions. The lightning strikes on Jupiter are hundreds of times more powerful than those seen on Earth. However, there are so few, that the amount of lightning activity is comparable to Earth.
Image Credit: NASA/JPL-Caltech/SwRI/MSSS/Eric Jorgensen
Explanation from: https://www.nasa.gov/image-feature/jpl/pia21377/jupiter-pearl-and-swirling-cloud-tops