A committee substitute is a revised version of legislation proposed for consideration and adoption by a committee. The committee substitute replaces, in whole, the original bill that was referred to a committee, including conference committees.
It is quite common for the language of a committee substitute to be entirely different from previous versions of a bill, especially in the House of Representatives when a bill is introduced as a shell bill. The House and Senate each have rules specifying when and how a committee substitute may be introduced.