Fig. 5

Single nucleotide polymorphisms on the Chlamydia trachomatis genome associated with (a) ocular localization and (b) disease severity at genome-wide significance. a Ocular localization-associated SNPs across the C. trachomatis genome. There were 1007 SNPs identified in coding and non-coding regions and included in permutation-based linear regression models in the Ct genome-wide association analysis. The threshold for genome-wide significance is indicated by the dashed line (p* < 0.05). The y-axis shows the –log10 p value. A –log10 p value of 1.3 is equivalent to a permuted p value of 0.05 (p* < 0.05). Synonymous (black) and non-synonymous SNPs (red) are indicated. Regions informative for ocular localization and genes of interest are labelled in blue. b Disease severity-associated SNPs across the Ct genome. From 129 SNPs identified in coding and non-coding regions, SNPs associated with the disease severity phenotype at genome-wide significance are identified using permutation-based ordinal logistic regression models adjusting for age in the Ct genome-wide association analysis. The threshold for genome-wide significance is indicated by the dashed line (p* < 0.05). The y-axis shows the –log10 p value. A log10 p value of 1.3 is equivalent to a permuted p value of 0.05 (p* < 0.05). Genes significantly associated with disease severity are labelled in blue