Genome sequence accession numbers The genome sequences of the parental strains used to generate recombinant sequences and the previously sequenced C. trachomatis strains used in the whole genome alignment studies are in the DDBJ/EMBL/GenBank database under the following accession numbers: D/UW3Cx, AE001273; L2-434Bu, AM884176; L2/UCH1, AM884177; L1/440/LN, HE601950; L3/404/LN, HE601955; D(s)/2923, ACFJ01000001; E/11023, CP001890; E/150, CP001886; G/9768, CP001887; G/11074, CP001889; G/11222, CP001888; F/70, ABYF01000001; F(s)/70, ABYG01000001; J/6276, ABYD01000001; J(s)/6276, ABYE01000001. The C. trachomatis Salubrinal manufacturer genome accession numbers of the

recombinants used in this study have been deposited in the DDBJ/EMBL/GenBank database under the following accession numbers: RC-F/69,

CP002671; RC-L2(s)/46, CP002672; RC-F(s)/852, PRN1371 CP002673; RC-J/943, CP002674; RC-J/953, CP002675; RC-L2(s)/3, CP002676; RC-F(s)/342, CP002677; RC-J(s)/122, CP002678; RC-J/966, CP002679; J/6276tet1, CP002680; RC-L2/971, CP002681; RC-L2/55, CP002682. Acknowledgements We would like to thank Sara Weeks and Robert Heinzen for critical review of the manuscript. Chris Sullivan from the Center for Genome Research and Biocomputing at Oregon State University is acknowledged for his help with genome sequence analysis. Brian Knaus in the Department of Forestry at Oregon State University is acknowledged for his advice with developing the genome wide association methods. This research was supported by grants AI088540-02 and AI086469-01 from the National Institutes of Health. Electronic supplementary material Additional file 1: Figure S1: Genome-wide association analysis of the attachment efficiency phenotype. Genome-wide p-values from Fisher’s exact test are given on the Y-axis. The check details results were collected from an alignment of the twelve recombinants and the three parents used for creating the recombinants. Genome position is indicated along X-axis, beginning with

CT001 as defined for the DUW/3 genome [31]. The brackets and ORF numbers indicate the genes present in the genomic regions showing the highest MTMR9 inverse p-values in these analyses. (PDF 475 KB) Additional file 2: Table S1: Gene products associated with attachment efficiency phenotype. D/UW3 and L2-434 gene designations, and putative membrane localization are given for gene products with amino acid changes that are associated with attachment efficiency. NS AA changes indicate the number of non-synonymous amino acid changes that are associated with attachment efficiency. Indel status indicates whether an in-frame insertion or deletion within a protein is associated with attachment efficiency. Elongation/truncation status indicated whether a protein has either an N or C-terminal truncation/elongation that is associated with attachment efficiency. (PDF 95 KB) Additional file 3: Table S2: Polymorphic membrane protein charge analysis.