Clinical data associated with the manuscript, "Low Prevalence of Conjunctival Infection with Chlamydia trachomatis in a Treatment-Naïve Trachoma-Endemic Region of the Solomon Islands". Sequence data used in phylogenetic analysis are available from GenBank. All chromosome sequences were mapped to the C. trachomatis A/HAR/13 reference sequence (GenBank accession number: CP000051.1) and plasmid sequences mapped to B/Jali/20 reference sequence (GenBank accession number: FM865436.1).