Figure 2. . A) Sequence differences among EMC/2012, England/Qatar/2012 and England1. The sequences of the 3 genomes were aligned, and differences between the sequence of England/Qatar/2012 and England1 (upper row) or EMC/2012 and England1 (lower row) were tabulated. The colored vertical ticks indicate nucleotide differences (change to A: red, change to T: dark red, change to G: indigo, change to C: medium blue, gap: gray). B) Non-consensus variants detected in the virus sample. The Illumina readset (Illumina, San Diego, CA, USA) for England/Qatar/2012 was mapped to the England/Qatar/2012 genome. Nucleotide positions showing nucleotides that differed from the consensus were tabulated. Colored dots indicate nucleotide positions with >1%–5% (gray), >5%–10% (orange), and >10% (red) nonconsensus variants. Positions with >5% variation and observed nucleotides are as follows: 14311: T, 92.07; G, 7.81; C, 0.12. 18460: C, 94.03; T, 5.97. 18692: G, 85.35; T, 14.65. 22385: G, 83.59; A, 16.41; C, 0.01. 26554: A, 90.85; G, 9.00; T, 0.15. C) Open reading frame (ORF) analysis of England/Qatar/2012. The positions of stop codons in each of the 3 forward ORFs are indicated by vertical black lines; the presence of ORFs of >75 aa are indicated by a closed box. ORF nomenclature is from Van Boheemen et al. (3).