Jones opened the game with a 91-yard return and made the score 14-7 later in the first quarter with an 87-yarder, tying an FBS record held by many.
Chunn ran in from 8 yards out to give the Trojans a 28-10 halftime lead. Chunn passed Danny Grant, who played for Troy in the 1960s when it was an NAIA school, for most touchdowns scored, all of Chunn's coming on the ground.
Blace Brown made two interceptions, his third career two-pick game for Troy (5-1, 8-2 Sun Belt), which has won four straight.
The Chanticleers (0-6, 1-10) have lost eight straight.
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