The sequence in the holder reference of EAC CVC certificates should identify a public key. For CAs created and managed by EJBCA this sequence is normally an automatic property in the CA token. It starts with 00001 and is increased when new keys are generated (renew CA with checkbox to renew keys checked).
You can also set a specific value for the initial sequence, which will then be increased when renewing keys, or you can change the sequence at any time. See section about Key sequence in User guide for more information.
For entity (IS, DV, AT and ST) requests that are received, the sequence in the issued certificates are taken from the request. The entity knows best how to index it's keys.