It's a process id. You can see it in the output of SHOW PROCESSLIST.
So, each Id represents a thread, and each thread represents a connection? So an entry like this in the query log:
031029 9:56:43 6 Quit
:: would represent a connection returned to the pool through an explicit close or timeout? (in this case "pool" being a DataSource managed by Tomcat)
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dream. code.
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