To declare that a pair aligns discordantly, Bowtie 2 requires that both mates align uniquely. This is a conservative threshold, but this is often desirable when seeking structural variants.By default, Bowtie 2 searches for both concordant and discordant alignments, though searching for discordant ...
Suppress discordant alignments for paired reads: By default, bowtie2 looks for discordant alignments if it cannot find any concordant alignments. A discordant alignment is an alignment where both mates align uniquely, but that does not satisfy the paired-end constraints . This option disables that ...