The Queen is apparently concerned that she might be the monarch presiding over the breaking up of the Union and be the last Queen of Scotland.
A source quoted in The Mirror said: "The Queen is a unionist, there is now a great deal of concern.
“If there is a Yes vote that puts us into uncharted territory constitutionally . Nothing is certain and her being Queen of Scotland is not a given.”
Maintaining the Union is believed to have been the main topic of conversation between the Queen and David Cameron as the Prime Minister visited Balmoral over the weekend.
Palace aides have stressed that the Queen remains neutral on the issue as with all political debates.
The Queen has attended a service of commemoration for WW1 soldiers in Aberdeenshire's Crathie Kirk Church.
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The Queen and Duke of Edinburgh received a warm welcome at the Athletes' Village in Dalmarnock today, where one Games delegate said he could "die happy" after meeting Her Majesty.
Solomon Islands chef de mission Ronald Bei Talasasa, who was too small to catch a glimpse of the royal couple when they visited his country in 1974, said: "I love the Queen, I love England. It was a great honour. For me to meet her was a dream. I can now die happy."
The Queen, who was accompanied by Prince Philip, was introduced to athletes and Games volunteers on her visit to the Commonwealth Games Village.
Australian 100m hurdles champion and London 2012 gold medallist, Sally Pearson, spoke of her conversation with the Queen: "She said 'I think you've brought the weather with you' and I told her that I think it's all due to change next week."
The Queen has revealed what the secret message says she put in the Games' baton, as she officially opened the Commonwealth Games.
The baton has travelled more than 100,000 miles around the world visiting 71 nations before arriving back in Glasgow.
Reading it out as she formally declared the Games open, she said: "The baton relay represents a calling together of people from every part of the Commonwealth and serves as a reminder of our shared ideals and ambitions as a diverse, resourceful and cohesive family."
Wishing her best wishes to the competing athletes, the Queen added: "Your accomplishments over the coming days will encourage us all to strengthen the bonds that unite us.
"You remind us that young people, those under 25 years of age, make up half of our Commonwealth citizens; and it is to you that we entrust our values and our future.
"It now gives me the greatest pleasure to declare the 20th Commonwealth Games open."
Estimate, the racehorse which has tested positive for a banned substance, helped make sporting history for the Queen as she became the first reigning monarch to win Royal Ascot's Gold Cup.
The Queen was pictured beaming as Estimate crossed the line in first place during the dramatic race last year.
Prime Minister David Cameron congratulated the Queen in a tweet saying: ''Huge congratulations to Her Majesty for Estimate's victory at Royal Ascot - first time ever a reigning monarch's horse has won the Gold Cup.''
Her Majesty won £155,960 in prize money after Estimate's victory.
The Queen has been informed of her racehorse's failed drugs test, her majesty's racing advisor said.
Estimate, which won the Gold Cup at Royal Ascot in 2013, tested positive for morphine - a prohibited substance.
Sir Michael Stoute, the racehorse's trainer, is offering his "full co-operation" to the investigation, John Warren, from the Queen's bloodstock and racing advisor, said.
"Sir Michael is working closely with the feed company involved to discover how the product may have become contaminated prior to delivery to his stables,
"As the BHA investigates this matter, including potential links between the different cases, Sir Michael continues to offer his full co-operation.
"Her Majesty has been informed of the situation."
Estimate, a racehorse owned by the Queen and trained by Sir Michael Stoute, has tested positive for morphine, a prohibited substance, Buckingham Palace announced.
Initial indications are that the positive test resulted from the consumption of a contaminated feed product, the palace said.
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The Queen has arrived at Rosyth Dockyard in Scotland to formally name the largest ship ever built for the Royal Navy.
The ceremony marks the completion of the 65,000 tonne aircraft carrier after five years of construction work which took place at six different shipyards across the UK.
To honour the warship's birthplace in Scotland Her Majesty will smash a bottle of Islay whisky, from the first distillery she visited, against the bow.