This is nothing to be concerned about. The only reason that this is shown as anything is because it assumes that since you have a ~/.mysql_history, you probably have mysql installed, which means you're probably using it. If you were using it as root, then all the commands you would have entered inside of mysql would be recorded in this file. This just means that you may have never used it while logged in as root.
Glad to help. chrootkit is only an indicator of current problems, and if it's a good hack, chrootkit is worthless. Look into using something such as tripwire to protect files that should not change (i.e. /bin, /sbin, /usr/bin, /usr/sbin, some stuff in /lib) to give you a better idea of what's going on.
chkrootkit is a good tool, but it also throws many false positives. Don't trust it as your only tool in the detection of intrusion.