I am looking at the output from BWA mem 0.7.17. The XA tag are alternative alignments. I am having a question: how does BWA decide to list the actual alignments of these XA alignments? I saw sometimes, the Alternative Alignments are listed sometimes not. In most cases, there was no alignments in the result file corresponds to the XA tag-mentioned alignments. Does this mean that all the XA-tag listed alignments are SUB-OPTIMAL compared to the the ONE alignment that listed these SA alignments?