Commercial jet aircraft fly in the lower stratosphere to avoid the turbulence which is common in the troposphere below. The stratosphere is very dry; air there contains little water vapor. Because of this, few clouds are found in this layer; almost all clouds occur in the lower, more humid troposphere.
It is also the layer that contains all of our weather. To avoid turbulence and bad weather, larger planes will sometimes fly in the upper boundary of the Troposphere, called the Tropopause, or even into the lower boundary of the next layer, called the Stratosphere.Jul 1, 2015