Both plasmid at different position is it due to repitation or already found 2 plasmid?
There are a couple of possibilities:
• Assembly artifacts / duplications: During genome assembly, especially with short-read data, repeats and plasmids sometimes get assembled more than once in slightly different contexts (different contig positions or orientations). This can make it look like there are two plasmids when in fact there’s only one.
• Plasmid integration / partial copies: Sometimes a plasmid (or parts of it) can integrate into the chromosome or into another plasmid, so you see the same sequence at two different positions.
• Genuine multiple plasmids: Some bacteria can harbor multiple plasmids, even very similar or identical ones, if they have different replication origins (replicons) that allow them to coexist. But if the plasmid sequence is exactly the same, it’s less likely to be two independent plasmids, unless the isolate really carries two copies.
In most cases, what you’re seeing is due to assembly repetition, not two separate plasmids; unless you have experimental confirmation showing multiple plasmids of the same size.
Check the origin of replication of the plasmids. In principle, E. coli should retain only one plasmid with the same origin of replication.
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