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The exhumation was carried out early on Monday morning after the graveyard area had been cordoned off by the police to ensure that the process is completed in a peaceful atmosphere.
A team of forensic experts from New Delhi, which arrived in Srinagar on Sunday, reached Shopian early morning and collected the samples from the bodies of the two victims.
The need for exhumation of the bodies arose to collect fresh samples for completion of the investigation of the crime, now being handled by the CBI.
The CBI took over the case after the Special Investigation Team of the state police failed to crack the case in three months time with mounting public pressure forcing the coalition government to handover the case to CBI for results.
The case took a new turn on Sunday, after the gynaecologist who was part of the team that conducted second autopsy on the bodies of 17-year Asiya Jan and her 22-year old sister-in-law Neelofar Jan is reported to have told the CBI investigators that vaginal swabs were never ever collected from the two victims.
A large number of locals had gathered at the graveyard periphery and watched the exhumation proceedings from a distance.
The town observed a complete shutdown today.