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When you transfer stock from an SEP to a ROTH IRA you are performing a CONVERSION.
A conversion to a Roth IRA results in taxation of any untaxed amounts. You will be taxed on the value of the stocks when they move to the ROTH.
The taxable amount that is converted is added to your income taxes and your regular income rate is applied to your total income.
The SEP is tax deferred so when you move money or assets to the ROTH you will be taxed.