In paired end mode chimeric pairs are labeled as discordant and thrown out. How does Bowtie2 handle chimeric singletons? Lets say you map only R1 reads and some of the reads map to different chromosomes, depending on the side of the singleton. Does this R1 singleton get a low mapping score or does bowtie2 label it as a chimera somehow?
It appears BWA-mem labels these as "SA:" in a sam file. Anything similar happening in Bowtie2?