Inheritance patterns of the unitigs

This analysis investigates the hits from the GWAS analysis:

• The inheritance patterns of the unitigs on the core genome phylogeny - Uptake of unitigs and association with MIC.

  • How changes uptake of the unitigs correlate with changes in PBP types

• Mappings of the unitigs to known gene regions, and the average effect size of unitigs in basepair positions within those regions.

Subtree at node 13193

• Removed descendant from node 157 in that subtree because the downstream branches don’t aquire the unitigs.

Effect size distribution along basepair positions

• We blasted some of the high effect size unitigs in the region.
• We found that a single reference genome contained nearly 380 out of the 394 unitigs.
• Calculated the average effecet size for each base pair position.

A total of 306 out of the 394 unitigs map to the iga_2, pabB, lytB_2 region. The following shows an excerpt from the plot above focusing on that region.

#> [1] 306