The picture is a view of an rna-seq bam file from tophat alignment.
On the left side, in red, are some alignments shifted away from the leftmost exon.
These "shifted-exons" are sometimes 1 base long, a base that can be found in many other locations including the real exon.
Why would the aligner pick that specific shifted location?
Image at: https://ibb.co/gxv9Cv