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The first Indian to compete in the 100m hurdles in the Olympics, the debutant produced another below-par show as she clocked 13.17s in her repechage heat to finish 16th overall out of 40 total runners.
Jyothi has now broken the 60-meter hurdles national record six times.
The officials eventually disqualified the Chinese runner Yanni Wu and upgraded Jyothi's medal to silver.
Quartermiler Aishwarya Mishra (53.07 seconds) and Tajaswin Shankar were the other medal winning Indians on the day, with a bronze in women's 400m final and gruelling men's decathlon.
Results 1-4