I have aligned my sequences to a virus genome, I selected the sequence by IGV and BLAST it, obtaining a hit for Cytomegalovirus/HHV5:
Now, the genome of CMV is over 200 000 bp, whereas the hit is around 700 bp. What happened to the rest of the genome?
How shall I interpret the result? Could it be that there are few sequences of CMV in a vast majority of cellular DNA? (in that case, I would expect few reads but over the WHOLE CMV genome) Or is it simply a mapping error of the aligner? And how can I get a sure answer for the mapping then? The hit is present even with a mapping quality of 50, so it cannot be simply a spurious artefact.