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In some comments I see a number, like "1" or "4" or "5", but in other comments there is no number. What is the significance of this number?

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What does the number mean?

Comments can be upvoted by any user who has more than 15 reputation points:

Image from above meta post showing comment with vote and flag icon

Also users with more than 15 reputation can flag comments1 for being inappropriate or noisy. If enough flags are cast, the comment is automatically deleted.

Why should comments be upvoted?

If you think a comment contains a useful addition to a post or is contributing to the current meta-discussion (on Meta only, of course): Upvote it.

What gives?

  • When there are many comments on a post, some comments are hidden when the page loads, and there is a button to “show N more comments”. The comments with the fewest upvotes are hidden first. The threshold depends on the number of comments on the post and whether the site is a main or meta site.
  • When the question reaches a certain threshold of answers (30 on most sites), all comments with zero votes on both the question and all answers will be collapsed.
  • No reputation of any kind is earned or lost from comment votes, though the Commentator badge is awarded for leaving 10 comments, and the Pundit badge is awarded to those who left 10 comments, each with a score of 5 or more.

[...]

  • If a comment with zero votes and no trigger keywords (see below) is flagged by three users, it will be automatically deleted. There is no penalty for this. Flagged comments will be surfaced to moderators, so if you have a problem with a comment, flag it.
  • Comments with upvotes require more flags to be deleted without moderator intervention: 1 more flag per 3 votes above 3 (i.e. number of flags = 3 + score/3).

(How does comment voting and flagging work?)

1 - Oh and all users can flag comments on their own posts regardless of reputation.

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