Mishra has been replaced by A M Jain, who was posted in police recruitment board as DIG, official sources said.
Mishra has been attached to the DGP office, they said.
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Violence-hit Muzaffarnagar lies in Saharanpur range.
ADG Bhavesh Kumar Singh has also been sent to Saharanpur to assist ADG (Law and Order) Arun Kumar in controlling the situation.
Violence in Muzaffarnagar has claimed 26 lives.
Tension has been running high in the district since three persons were killed in Kawal village on August 27 over an eveteasing incident.