If you file a qui tam action, the government will know your identity, and your name will likely be disclosed to the defendant at some point: the question is how long that process will take. Under the law, the defendant is not supposed to learn that you have filed the lawsuit during the initial period when the complaint is under seal. However, in practice, defendants sometimes figure out that an FCA case has been filed, as well as the identity of the relator. When the government announces its decision regarding intervention and the complaint is served on the defendant, the seal period is officially over and your identity will be revealed.
There are circumstances in which you may be able to file a qui tam action and then voluntarily dismiss it during the period under seal without having your identity ever revealed to the defendant, but there is no guarantee of anonymity. If you are seriously concerned about the disclosure of your identity, your attorney may be able to help you minimize that risk and prepare for the eventual disclosure.