This is the IGV view from reads illumina mapped to a reference bacterial genome. The window shows a specific bacterial gene.
Each sample is a gut profile from a donnor. (WGS illumina).
In the upper sample i see red, blue and green vertical lines in some of the reads for a particular position whereas in the botton sample almost all reads contain the red , green and blue at that position when compared to the reference.
Do you think is it possible that the upper sample can contain two different strains or could there be another explanation. How would you interpret the image.