Fig. 2: Manhattan plot for pan-genome-wide associations for invasive vs. non-invasive UPEC. | Nature Communications

Fig. 2: Manhattan plot for pan-genome-wide associations for invasive vs. non-invasive UPEC.

From: Horizontally acquired papGII-containing pathogenicity islands underlie the emergence of invasive uropathogenic Escherichia coli lineages

Fig. 2

Data are based on 30,705 clusters of orthologous genes (COGs) identified in 722 UPEC isolates. Fecal isolates were not considered in this analysis because they present no urinary phenotype. The plot shows genes assigned to 4764 unique COGs identified in the genome of reference strain UMN026 (CC69). Each dot represents one COG. The vertical axis denotes raw P values of Fisher’s exact statistics. To account for the effects of sample size and population structure, the genome-wide significance threshold (dotted line, P = 1.42 × 10−18) was inferred from a simulated dataset using treeWAS. The horizontal axis gives the nucleotide position in the chromosome. COGs part of pathogenicity islands (PAIs), prophage regions, or the two plasmids of UMN026 are color-labeled, including the High Pathogenicity Island (HPI) and PAIUMN026-pheV, a papGII-containing PAI. The remaining 25,941 COGs of the pan-genome that did not map to UMN026 were not pan-genome-wide significant (Supplementary Fig. 21).

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