Figure 5.

Minor iSNVs across the EV-D68 genome for three samples with putative dual infections. These three samples had more than twenty highly covered sites with minor variants in excess of 3 per cent frequency. On the left, iSNVs are colored by codon position or as non-coding, and given opacity depending on their frequency. The majority of these variants were at third positions and had similar frequencies across the amplicons, indicated by gray bars in the lower left panel. iSNVs in three amplicons (Amplicon 1 of sample SWE_046 and Amplicons 2 and 3 of sample SWE_007), however, were found at substantially lower frequency, possibly due to primer mismatches. The three panels on the right are indexed by iSNV order on the genome and show linkage disequilibrium between iSNVs (>1%) close enough to each other that they were covered at least 100-fold by the same sequencing read. Almost all of these variants at in complete linkage (dark red). A number of iSNVs just above 1 per cent in sample SWE_045 and SWE_046 are likely variants in the background of the dominant variant. Those are in complete ‘anti-linkage’ with neighboring iSNVs are ∼10 per cent (dark blue).