Can a read be aligned more than once?

Question

[guntul]

In linear reference(sam,bam) or in pangenomic alignment(gam,gaf), is it possible to a read that is aligned twice or more? Can we observe that a read appear more than one line in alignment files?

[GenoMax]

Yes a read can be aligned more than once (I don't specifically know about gam/gaf). It would be called a "multi-mapping" read. You could imagine reads aligning to multiple places because there are multiple copies of a gene (e.g. rRNA) or there can be common domains in multiple genes.