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According to Tando Jam police, the incident occurred near village Mureed Sipio's railway crossing.
The slain persons had been identified as Sachal Khaskheli, Aslam Chandio and Ameer Bux, resident of Benazirabad district who were travelling in the car.
The dead bodies were shifted to Liaquat University Hospital from where they would be handed over to the families.
The track was cleared after an hour after which the train, Peshawar to Karachi bound Rehman Baba Express, resumed the journey.