Good morning everyone,
I hope someone can help me with this issue. In my lab, we performed a targeted sequencing with Illumina MiSeq. We sequenced one single gene (whole gene, both introns and exons) in 96 samples, belonging to two different experimental groups. After the alignment and the duplicates removal, I decided to visualize my bam files using the Golden Helix Genome Browser. I noticed a reduction of the coverage for a 200bp region in the only coding exon of my sequenced gene. This reduction occurs in all my samples but it is more evident in one group than the other (statistically determined using read depth values).
How should I interpret these data?