The 1099 doesn’t show the amount of money that you deposited or withdrew, it shows the gross proceeds for any positions that were closed during the tax year.
For example, let's use an account that had a $100 deposit:
The customer purchased ABC shares for $100
The customer sells ABC shares for a gain of $10 (making their proceeds $110 on that trade)
The customer purchased XYZ shares for $50
The customer sells XYZ shares for a gain of $10 (making their proceeds $60 on that trade)
In this example, the customer’s gross proceeds were $110 + $60 = $170. The customer’s gross proceeds of $170 will be reported in the 1099, even though the customer only deposited $100.