Q: What does it mean if one of my rejected articles appears online?

Firstly, sorry to hear that your article was rejected.

Now, when we look at the site where you said the article has appeared, we see that it is on Research Square, which is a well-known site for sharing preprints. A preprint is a submission-ready, non-peer reviewed paper shared on a designated site. It is typically submitted to the preprint site just before submitting to a journal. It is done for several reasons, such as establishing the primacy of the research, allowing other researchers to gain from it even while the evaluation by the journal is ongoing, and gaining from feedback by other researchers. You may learn more about preprints here: The role of preprints in research dissemination

Coming to your query, it is unlikely that the journal rejected the article but put it up on the preprint site. As mentioned above, preprints are typically uploaded before or at the same time as submitting to a journal. If the journal indeed did so, it may have happened through a technical glitch or a human error. If that is the case, you may consider checking this with the journal.

However, it is more likely that one of the coauthors shared this paper. We see that the paper has five coauthors (including you). Also, the date on the site (provided toward the top right) shows that it was uploaded on February 26, which is over a month ago, perhaps the time around which you all submitted to the site. So, it may be that one of the other authors uploaded this on Research Square, either without informing you (or the others) or may have informed you but you or all may have missed this communication. It would be better to check this with the other authors. Although their action in either case is not unethical, it is a bit surprising. However, given the rationale for preprints, their action was probably a wise one. Although the article has neither received any comments nor been downloaded, it has been viewed a few times already.

Finally, as you may know, you can always submit the article to another journal, making any fixes as necessary based on any comments from BMC Genomics.

To know more about preprints, you may go through these resources:

• How researchers and journals can use preprints to make research freely accessible
• "Preprints have enormous potential to revolutionize peer review and science"
• Does a manuscript rejection imply rejection of the preprint as well?