The Notts boss was incensed with McDermid's imcompetent performance, following the sending off of Matt Somner and, after originally giving a penalty, going back on a decision that would have given Notts a chance to take the lead.
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Following the match, Thompson told BBC Radio Nottinghams Colin Slater:
"If the referee was on fire, I'd dial 998!"
Thompson has until the 19th December to respond to the charge, which was today confirmed by the FA.
It is thought that he will take any punishment, after recently confessing his guilt.
NCM were first to tell of the story, with an exclusive on September 6th.