The mysql-cis.audit file inside your Nmap data directory contains configuration checks described in the CIS MySQL v1.0.2 benchmark. It is used by the mysql-audit script to perform configuration checks by carrying out a series of tests. A test looks like this:

-- Logging
test { id="3.1", desc="Skip symbolic links", sql="SHOW variables WHERE Variable_name = 'log_error' AND Value IS NOT NULL", check=function(rowstab) 
  return { status = not(isEmpty(rowstab[1])) }
end
}

You may set the mysql-audit script argument to select an alternate database:

$nmap -sV --script mysql-audit --script-args mysql-audit.filename=/pentest/mysql.audit <target>