I am analyzing the reads for the SARS-CoV-2 assembly with id SRR11140748. Apparently these reads were obtained with parallel sequencing by Illumina and Oxford Nanopore Technologies.
I have found these reads
As you can see, the second one has an exact copy at the tail of its beginning:
I have found other issues apparently caused by rearrangements of the virus genome, but this case seems to be different. It seems unlikely that the virus mutated in such a way and then a read was cut exactly this way. What is the most likely explanation for this read?
It's not the only one displaying the same or similar behavior. for example this other one has a copy at the tail but from bps not exactly at the beginning (CACCGGAAGCCAATATGGATC):