A subtweet is a way to make a point only to insiders -- those who know what you're talking about without you having to get all specific. Typically a subtweet has an air of mystery -- and allows the tweeter to get away with a jab or criticism without having to own it, since there is always ambiguity. (A Facebook equivalent is "vaguebooking" where you call out someone's behavior without mentioning them by name. ("Why do some people...")
Subtweets from famous people are often less difficult to figure out, because the context -- which is everything in decoding a subtweet -- is usually public knowledge. Looks like University of Michigan football coach Jim Harbaugh has just hit the subtweet circuit with his biblical-sounding, ominous tweet seemingly without a particular target: "You will reap what you sow." The tweet is without a target unless you know Harbaugh was fired from the 49ers before last season. And that the 49ers hired Jim Tomsula to replace him and fired Tomsula too, after he went 5-11. Sounds like Harbaugh is talking to the 49ers, but of course it's a subtweet -- so no one really knows.
Do not be deceived. You will reap what you sow.
— Coach Harbaugh (@CoachJim4UM) January 4, 2016
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