Q: When the journal gives a reference number to the manuscript, what does it mean?
The reference number that a journal assigns to a manuscript is popularly known as the manuscript ID. It is a unique number that is assigned by a journal to every manuscript that is submitted to the journal. The purpose behind assigning such a reference number is to facilitate ease of communication, particularly since a lot of functions/processes at the backend of the journal are managed through online submission systems. The manuscript id is a unique reference point that the journal uses to help the submission system identify and track the manuscript.
Once you have received a manuscript ID, you can be sure that your submission process is complete. It is a kind of documentation of the fact that the journal has received your manuscript. As the author, you are required to quote this number each time you communicate with the journal as the journal identifies the manuscript with this number and not by the author name or manuscript title. All email inquiries, revisions, etc. would need this number to be quoted.