Fig. 6

Genome visualisation of the NS5A viral protein within a subtype 3a query sequence via the HCV-GLUE web report. The submitted query sequence in green is contrasted with a user-selected reference sequence in blue. Differences between the query and reference are highlighted in inverted grey. In a the 93H RAS is highlighted by a red annotation bar and is shown to have arisen from a single nucleotide change relative to the subtype 3a reference (NC_009824) in the first nucleotide position within the codon. In b the query sequence contains amino-acid differences relative to the subtype 3a reference sequence at positions 231, 239 and 240. There are nucleotide differences within codons 234 and 235 but these are synonymous. The amino acid differences at 231 and 239 are atypical for subtype 3a as indicated by the yellow annotation bars, whereas the Arginine (R) at position 240 is typical for the subtype. In c the subtype 3a query sequence is shown alongside the HCV master reference (NC_004102); an insertion of 5 amino acids in the query sequence between codon locations 407 and 408 is shown; the consecutive nucleotide positions 7478 and 7479 in the master reference are also given to clarify the insertion