GACCCGGTGGGTTTTAC---ACTTAAAAACACAGTCTGTAC GACCCTGTGGGTTTTAC---ACTTAAAAACACAGTCTGTAC GTTTCAC---ACTTAAAAACACAGTCTGTAC GGTTTAC---ACTTAAAAGCACAGTCTGTAC CCACACTCTCCTAGCAC---ACTTAAAAACACAGTCTGTAC CCACACTCTCCTAGCACCATACTTAAAAACACAGTCTGTAC
It basically says there are reads that share part of a sequence and part of another one. The first 4 reads are the same sequence and it's a sequence that you can effectively find in the official SARS-CoV-2 assembly but the other two reads are a mix of this one with another sequence (and both are the same mix) but with only a small (3bps) indel of difference.
The sequence of the last two reads does not appear anywhere in the official SARS-CoV-2 sequence.
- What does it mean?
- Are these sequencing errors?
- If that is the case how is it that the same mistake is repeated with similar but not exactly the same data?
- If these are real RNA sequences present in the probe, why are these not used anywhere in the final assembly and how did they arrive there?
Is there any other option that I am missing?