Skip to main content
Fig. 2 | Genome Medicine

Fig. 2

From: Population-based analysis of ocular Chlamydia trachomatis in trachoma-endemic West African communities identifies genomic markers of disease severity

Fig. 2

Whole genome sequencing (WGS) quality filtering processes and threshold criteria for inclusion in analyses. Ct DNA detected using droplet digital PCR [45]. WGS data were obtained using SureSelect target enrichment [31] (or chlamydial cell culture) and Illumina paired-end sequencing. FastQC [53] was used to assess basic WGS quality. SNP alleles were called against reference strain Ct A/HAR-13 using an alternative coverage-based approach where a missing call was assigned to a site if the total coverage was less than 20× depth or where one of the four nucleotides accounted for at least 80% total coverage [60]. There was a clear relationship between the mean depth of coverage and genome-wide proportion of missing calls; therefore, only sequences with greater than 10× mean depth of coverage over the whole genome were retained using the GATK Best Practices threshold [56, 57]. Heterozygous calls were removed and SNPs with a minor allele frequency (MAF) of less than 25% were removed. Samples with greater than 25% genome-wide missing data and 30% missing data per SNP were excluded from the analysis. WGS sequence quality is shown in detail in Additional file 12: Figure S12. *n = 157 including the 71 Bijagós sequences in addition to 48 Rombo District sequences and 38 reference sequences

Back to article page