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The 24-year-old is three races away from claiming a fourth Olympic gold medal, 48 hours after she became the  first British woman to win three.
Trott finished second in the scratch race, won the individual pursuit and then easily won the elimination race.
She holds an eight-point advantage over Jolien D'Hoore of Belgium, with American Sarah Hammer in third place.
Trott won three of the six events to take the title in 2012 and, if anything, looks even stronger four years on.
Tatsiana Sharakova of Belarus comfortably won the opening scratch race of the competition, with Trott holding off RideLondon Classique winner Kirsten Wild of the Netherlands to finish second.
In the individual pursuit, Trott took nearly five seconds off of her time from London 2012 to leave her rivals trailing.
She clocked three minutes 25.054 seconds to thrash Sharakova by more than 12 seconds - lapping her with 1km to go - and beat pursuit specialist Hammer, who was the silver medallist in London, by more than a second.
In the elimination race - where one rider is lost every two laps - Trott looked serene, never in danger while Hammer struggled to live with the pace.
Hammer was eventually third, leaving Trott to blow D'Hoore away on the final sprint, even having time to wave to the crowd on the home straight.
The Briton. who is engaged to five-time gold medallist Jason Kenny, will return to the velodrome on Tuesday for the time trial, flying lap and points race.
Earlier, fellow Briton Mark Cavendish took silver in the men's omnium.
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Both Team GB entrants in the women's sprint reached the quarter-finals as Becky James and Katy Marchant won their respective heats.
James, 24, edged Virginie Cueff of France on the home straight before Marchant, 23, overcame German Miriam Welte.
On Tuesday (14:00 BST), James, who has already won silver in the women's keirin, will face China's Zhong Tianshi.
Marchant faces Lithuanian Simona Krupeckaite for a place in the semi-finals.
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Defending champion Laura Trott leads the Olympic women's omnium at halfway after a masterful display on Monday.