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Frequently an audit of this nature is triggered by a discrepancy between what you reported on your return and what third parties report on the 1099's sent to the IRS.
Sometimes this can be caused by duplicate reporting requirements, and other times it can be due to your accounting method. If the IRS receives 1099s totaling 1 million dollars paid to you and you report only 650,000 in gross sales, this would be a problem.
Certainly if you had 650K in payments reported to you from the credit card processor and you show on your return that you received only $500K in sales, this is a problem.
Be aware that once the IRS opens an audit case, almost every time they start probing into other areas of the tax return. They are not limited to auditing just the one item the letter mentions. For this reason, it is often wise to hire a representative who understands how to manage the examination.