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, starting with 00001 and increased when new keys are generated (renew CA with enabled option to renew keys).
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. For more information, see the Key Sequence section in CA Fields.
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 its keys.