I'm using Neo4j 3.4.9, and have been wondering why the reported disk space is correct (4.17GB) but the rest of the metrics don't add up. There are 2.3M nodes and 5.6M relationships. Most of the nodes are short texts (support ticket replies).
I've been using Kafka Streams to send data back and forward within the DB Engine and from/to outside, to other scripts etc.
The answer is as follows, the Total Store Size = the physical data store files (as in the table above) + the transaction log files size (neostore.transaction.db.). So if you doing a lot of write transactions in a short time the transaction log space can be big. Standard the transaction log files are kept for 7 days.