I am analysing yeast strains NGS results containing amplicons for fragments of genes. I've mapped reads to whole genome S288C and EC1118. I compared the results. One amplicon were mapped to fragment of gene A in S288C reference. This amplicon matches in reference coordinates for gene A. The lenght of amplicon is 600bp.
I've done the same thing to EC1118 reference and I've discovered that this amplicon were mapped to about 75% of the same fragment of gene A. The mapping results showed that reads were shifted about 150bp. (and cover intron sequence).
Gene A has different coordinates in references and I took this into analysis.
Why do I have displacement in results?
Could it be caused by some kind of rearrangements?
I would really appreciate for help. Best, Agata