Originally referred to hiding footprints; now means hiding any evidence. After the party, they covered their tracks by cleaning up before the parents arrived.
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Metaphorical Use
Often used metaphorically for hiding digital or indirect evidence. She covered her tracks by deleting her emails and internet history.
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Negative Connotation
Usually implies wrongdoing or guilt; not often used for innocent situations. To avoid suspicion, the corrupt official covered his tracks with fake documents.