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The service operates with a single rake comprising seven chair cars and one executive chair car.
The Railway Ministry has also sanctioned a 16-car Vande Bharat sleeper.
At present, passengers boarding from Ernakulam often struggle to secure tickets, while travellers from Coimbatore receive a larger share.
The eight-coach train has seven chair cars, one executive chair car and a total of 600 seats.
The controversy erupted on Saturday after Southern Railway posted a video of the performance on its official X handle.
Television visuals showed students singing the song which is associated with the Rashtriya Swayamsevak Sangh (RSS), during the train journey.
The train's fare is also likely to be on a par with Jan Satabdi fares, sources say.
According to reports, the train's first service might be an inaugural special run.
The fare details for the new Vande Bharat have yet to be announced, but commuters hope it won't be too different from last year's fares.
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