Bowtie: Reporting one of multiple valid mapping locations

Question

[Sander]

Dear Biostars,

I'm slightly confused by the way Bowtie reports reads that align to multiple locations. If I understand correctly from the manual, by default only 1 alignment is returned (-k 1). But this may not necessarily be the best alignment, because then --best must be specified as well. So is this a random or just a 'good' alignment? And what is the difference with -M 1? According to the manual this gives 1 random alignment from the best alignments, but is this not the same as -k 1?

Kinds regards,
Sander

Answer 1

[GouthamAtla]

-k is not related to 'best' alignment. -k is related to multimapped reads. A read may map at various places with v.high quality/best mapping, but only one position is reported by default.

[Sander]

So with -k 1, in the case that a read maps to various places, which position is reported?