This copy of the script with will have all lighting, sound, flying and scenery cues marked in, with indications of when they should be called, in order for cues and effects to happen at the correct time in the show. It may also include blocking, for use when actors forget or for understudy rehearsals, as well as backstage calls/any other information that it is useful for the Deputy Stage Manager to have to facilitate the running of the show.
The usual format is with a one-sided script mounted in a ring binder, with the cues written on the opposite, blank side of each page. Every Deputy Stage Manager or Stage Manager has their own style, but a prompt script should be easily readable and should be able to be picked up and used by another ember of stage management in the event that the Deputy Stage Manager can't call the show (due to illness, for example).
For musicals or operas, score should be integrated with script in order to call cues at the right point during music.