spliced alignment algorithm
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
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Your picture is not working. I suggest you try https://imgbb.com/
Perhaps someone can comment on this possible explanation: Might this be a result of a 2-pass alignment.The first pass determined a "shifted exon" based on one read that was mapped unambiguously with 5-6 bases to that region. The second pass then mapped ambiguous 1-base exons to that location. .
That sounds plausible to me yes.