Hi, everyone,

Bowtie has an XA tag (XA:i:<n>), and its definition is as follows according to the manual.

For a read with no reported alignments, <N> is 0 if the read had no alignments. If [-m] was specified and the read's alignments were supressed because the [-m] ceiling was exceeded, <N> equals the [-m] ceiling + 1, to indicate that there were at least that many valid alignments (but all were suppressed). In [-M] mode, if the alignment was randomly selected because the [-M] ceiling was exceeded, <N> equals the [-M] ceiling + 1, to indicate that there were at least that many valid alignments (of which one was reported at random).

Does XA:i:0 mean unique mapping, and XA:i:1 mean two alignments?

Thanks a lot!