Hi, my question is rather simple I think but I cannot find the answer in any of the documentation:

How does Bowtie2 treat a read pair where one mate aligns uniquely and one mate has multiple distinct alignments?

EX: mate1 of a pair aligns to chr3:3,000,000 while mate2 of a pair aligns to both chr3:3,000,400 and chr2:400,000 equally well.

Does bowtie2 know that the correct location of mate2 should be on chr3 or will it decide there is something wrong with the pair and attempt to align them unpaired? ie. mate1 will go to chr3 3,000,000 and mate2 will randomly be assigned to either chr3:3,000,400 or chr2:400,000? And finally, is there a way to alter whatever default behavior bowtie2 has in this regard?

Thanks!