Ah, the humble recon photo, the unsung hero of many a caper.
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Waypoints (also occasionally called god-rods) are sub-job beacons that appear in missions. They point the current character in the direction of important job specific items, such as locations, keys, levers or other significant details. You access them by clicking so they show up temporarily. To see them permanently, click to open the Binocucom. They will automatically tower over rooftops. Depending on which character is being used at the moment, the waypoint will have their signature color and a small circle at the top with an even smaller circle in the middle. There is another waypoint variation where it shows where a job is and it shows the character's logo at the top along with their color and the job name.