It sounds like you may have answered the questions about annualizing your income under the federal return, but not the state return. Since you have filed this return already, the letter is the important part now.
Because you have received a letter from your state Department of Revenue, you can use the Audit Support Center to look into this issue for you. Follow this link for more.
You can also file an Accuracy claim and have the return examined that way. Follow this link for more about that.
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