IGV alignment explanation

Question

[David]

Hello,

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.

Answer 1

[h.mon]

Yes, it is possible the upper sample contains two strains - that would be my first guess. However, your data seems unusually good: in general, one also sees a lot of low frequency SNPs, due to sequencing errors. Is this simulated data?

[David]

Thanks @h.mon . The reference genome is a hybrid assembly (illumina + nanopore) which is probably why it looks so good. short reads were mapped back to the assembly.

Indeed i think i have two strains mapping to the reference genome which could explain the phenotype i observe in the individuals gut.

Thanks !!!!