I am new to bioinformatics and I have a few questions regarding the analysis of my samples. In brief, I have 15 odd pairs of sequential bacterial clinical isolates collected from 15 humans. I have confirmed that the pairs are the same clinical isolate due to the low number of SNP in the core genome. However, I see a significant difference their phenotype. I would like to find the underlying genetic cause for this phenotype as I have the WGS data of these clinical isolates. I have looked at the presence and absence of genes and no significant difference was seen. What other ways is there to look at the these samples, could SNPs analysis explain this difference in phenotype? If so what kind of analysis would be needed? Any suggestions would be very helpful.