Fig. 5
From: StrainGE: a toolkit to track and characterize low-abundance strains in complex microbial communities
StrainGE detected a long-term, persistent strain of E. coli in a woman with rUTI. a Relative abundances predicted by StrainGE are shown for all E. coli strains detected. b For all sample pairs containing a strain matching to E. coli 1190, plot shows pairwise ACNI and gap similarity scores. Size of the circle indicates the percentage of the common callable genome. c Zoom in on a region of the chromosome of E. coli 1190. Gray shaded areas indicate “callable” regions, where StrainGR had enough read data to make a strong allele call. Predicted gaps are shaded black. The blue line represents the number of SNVs per 1,000 bp, observed in at least 3 samples. d Further zoom-in representing a region where StrainGR identified a nonsynonymous SNV that was consistently detected across all 1190-like strains