Genomic region with much higher coverage than the rest of the genome

[Eddif]

Hello everybody,
My question is regarding strange phenomenon I observed in a recently assembled microbial genome. My genome was sequenced using PacBio library, which generated two contigs, one for the genome and the other for the plasmid.
Then I used previously sequenced Illumina library for verification and error correction of the PacBio assembly, and the results revealed a 60 kbp region with almost doubled coverage (see attached).
I tried to look for SNPs, to check whether these are two regions that were collapsed during the assembly, but there are none of them.
I also checked the pairing of the reads, and I found reads that are overlapping on both edges of the region from normal to high coverage. There are no paired reads on the edges that their pair was mapped to any other region of the genome.

Does any one experienced such coverage issue and knows what is it or how to deal with it?

Thank you,
Eddie

[hkg]

I know this is a very late reply, but I just came across your message in a search.

Do you have any idea what this region might be? Could it be some sort of genomic island? I guess if it was a repeated region, then you would have seen some SNPs, which you didn't.

Do post if you found out what was going on

[shimbalama]

Looks real

That looks like a pretty clear cut case of a repeated region