Can I filter issues that have been created from an incoming email message?

I have a number of mail handlers for creating new issues from email. I'd like to be able to select only issues created by email in a JQL statement for a webhook that I'm configuring. Is this possible? In other words: is there a JQL field that indicates if an issue has been created through a mail handler?

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It is not possible to get this data from a JQL. You could choose to create a separate user designated for issue creation through mail. If you configure this user to be the default reporter for your mail handlers, you can run a JQL on that reporter to get the information you are looking for.
Cheers

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