As machine gun fire crackled around the besieged Islamist encampment in eastern Cairo today, a 12-year-old boy called Omar was sat on a mattress drinking from his carton of orange juice. Just a few yards away, the bodies of 31 protesters lay on the grubby, blood-caked floor.

Many had been shot through the head and chest with high velocity bullets; some bore gnarled lips betraying the agonising throes of death.

When asked how he felt to witness such scenes, the young boy - wearing Puma flip-flops and blue jeans - remained silent and appeared confused for a few moments. Then, with childlike fragility, he said very simply: “It's not very nice”.

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Whatever else the Egyptian state was hoping to achieve by launching its long-awaited crackdown, the hundreds of young children who were cowering inside the besieged sit-in will not likely forget the ferocity of a government which has now declared war on the country's Islamists.

Egypt's leaders have unleashed a chain of unforeseeable consequences. Deadly clashes were reported in provinces around the country, as police stations, government institutions and Coptic churches were attacked in apparent revenge attacks.

Scores were killed, hundreds more injured.

In a sign of how deeply the crackdown will affect Egypt's ongoing political transition, Mohamed el-Baradei, the vice President and Nobel laureate, resigned in protest over the crackdown. Meanwhile Egypt's interim government has imposed a month-long state of emergency and night time curfew.

Inside the Rabaa al-Adawiya Mosque, the building which lies at the heart of the east Cairo encampment, crying babies clung to their mothers as gunfire raged around them following the start of the operation.

In the centre of the prayer hall, laid out on the carpet among hundreds of women and toddlers in the stifling heat, ten bodies had been placed side by side inside a cordon.

A little girl of about seven or eight, wearing pink trousers and a T-shirt, made her way from one side of the mosque to the other by tottering between the heads of the corpses.

“The police and the army don't understand any language except force,” said Khalid Mohsen, a 50-year-old engineer who was trapped inside the siege. “They want to kill anybody who has an opposing view.”

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Given the sheer level of firepower unleashed on protesters, it is a view which many Islamists may find hard to argue with.

According to witnesses the gunfire began early in the morning at around six o'clock, as security forces who had surrounded the site launched their ferocious assault. At a separate encampment in the west of the city, a similar operation was also ordered.

By late afternoon the shooting was still continuing. Heavy semi-automatic bursts of gunfire echoed around the nearby suburbs throughout the day. If there was any let up, it was brief. For about 10 hours, the supporters of Mohamed Morsi were subjected to a near-continuous barrage of live fire.

Single sniper shots shrieked down Nasr Road, the main thoroughfare leading through the camp; sustained bursts of machine gun fire clattered into nearby buildings; wayward rounds shredded through the labyrinthine networks of tents and tarpaulin shacks.

At the nearby hospital, staff draped the windows with blinds as a precaution against sniper rounds.

One doctor at the hospital, who gave his name only as Ahmed, said that even the Israeli invasion of Gaza in 2008 had not been as bad.

“I was working there as a medic during that battle,” he told The Independent. “The Jews were much more humane that what is happening today. Even in war, the rules are more respectable than this.

"In 12 days of fighting in Gaza, there were less dead than in six hours here."

Amid the dizzying chaos of the massacre - the third which has been perpetrated against Egypt's Islamists in a little over a month - reliable casualty figures were difficult to come by.

According to Egypt's Health Ministry, 149 people were confirmed dead. Yet the true figure is likely to be much higher. Dr Hisham Ibrahim, the head of the Rabaa al-Adawiya field clinic, told The Independent that several hundred people had been killed.

Whatever the final tally, the constant stream of bullet-riddled, disfigured protesters meant it was impossible to store the corpses properly. Inside a room which during the previous two massacres has been used as a morgue, 42 bodies were crammed up against each other on the floor.

As the carnage unfolded and more protesters were killed, other areas were appropriated to house the dead.

Behind the stage which has been used by Islamist leaders to rally pro-Morsi supporters for the past six weeks, 25 bodies were laid out wrapped in white shawls, unrefrigerated in the sweltering August sun.

Next to the Rabaa al-Adawiya Mosque - where flies were soon gathering on the ten corpses laid out in the prayer hall - another room being used as a makeshift morgue.

A total of 31 bodies had been placed here. Volunteers had no time for sentimentality; the same hall was being used to treat wounded protesters, many of whom were lying moaning in agony just yards from the nearby cadavers.

"It's a genocide," said Dr Yehia Makkayah, a medic at the Rabaa hospital. "They want us to disappear from the country. I could never imagine that Egyptians would shoot Egyptians using these weapons."

Such was the chaos inside the hospital, a reception area on the second floor had been utilised as yet another morgue to store a further 26 bodies. One floor up in a tiny storeroom, two more corpses were lying in gleaming pools of fresh blood.

Corridors barely two yards wide were lined with dozens upon dozens of wounded. Luckier patients received drip feeds from a friend or relative; those who were luckier still had the luxury of a hospital bed. The floors were sticky with blood and vomit.

The sheer volume of the dead and the dying meant it was often impossible to move up and down the main staircase. Injured protesters, most of them felled by live fire, were stretchered up to the operating rooms, blood trickling from their wounds as they went. The dead were stretchered in the other direction, down to the lower level morgues.

"The army are the dogs of the Israelis," said Mohamed Mostafa, a vet who was keeping vigil at the bedside of his brother-in-law, a 36-year-old whose spine had been shattered by a bullet. "They are not Egyptians."

At the main morgue beside the field clinic, the mother of one victim, 16-year-old Malik Safwat, struggled to reach him through the tightly-packed rows of corpses.

"Don’t move that body," said one of the morgue attendants to a volunteer trying to clear a path. "Move a lighter one." She eventually found him, tearfully shaking his left knee from side to side as if to try and wake him up. His sister had also arrived. "My darling," she said in a trembling voice. “Why my darling?”

By around 5pm, the security services had gained access to the hospital and were clearing everybody out into the surrounding streets. Thousands of people began filing out of the camp, as police bulldozers moved in to destroy the remaining tents.

Condemnation as death toll nears 300 mark

Amid the dizzying chaos of the massacre – the third which has been perpetrated against Egypt’s Islamists in a little over a month – reliable casualty figures were difficult to come by.

Egyptian state news agency said 235 were killed across the country today and 2,001 were injured. Yet the true figure is likely to be much higher. The Associated Press news agency reported 278 deaths. And at least 250 have died since the army seized power last month.

Western powers condemned the bloodshed with US Secretary of State John Kerry and David Cameron both denouncing the violence. Mr Kerry said that the “path toward violence leads only to greater instability, economic disaster and suffering”.

Alex Delmar-Morgan

LIVE: Latest updates on Cairo bloodshed

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