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Fig. 3 | Genome Medicine

Fig. 3

From: Illuminating uveitis: metagenomic deep sequencing identifies common and rare pathogens

Fig. 3

Identification of rubella virus (RV) by metagenomic deep sequencing (MDS). a Illustrates how the 9688 nucleotide paired-end sequence reads obtained from sequencing the RNA extracted from subject 6’s aqueous fluid aligned to the most closely matched RV genome (GenBank DQ388280.1): 99.3 % of the total RV genome is represented. Positions of synonymous (black vertical lines) and non-synonymous (red vertical lines) variants are shown. Of the 149 substitutions, 107 were synonymous and 42 were non-synonymous. Of the 42 non-synonymous mutations, 25 occurred within the coding region for the E1 and E2 glycoproteins. Per unit length, the number of non-synonymous mutations in the E1 and E2 proteins was 6.3-fold higher than in the non-structural proteins. The cyan marker above the E1 gene represents the 739-nucleotide sequence window recommended by the World Health Organization (WHO) for RV genotyping. b Phylogenetic analysis of subject 6’s RV strain obtained from MDS with 32 WHO reference strains, GUZ_GER92 (Stuttgart strain), and the RV27/3 vaccine strain, demonstrating that the subject’s RV sequence was most closely related to the genotype 1G viruses and not the vaccine strain

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