Fig. 2.

Representation of variant allele frequency clade-defining mutations for 21J Delta and 21K Omicron along the SARS-CoV-2 genome. All 21J and 21K clade defining mutations along the genome are presented for P1-D1 (A) and P1-D7 (B), P5-D1 (C) and P5-D7 (D) and P6-D1 (E). Mutations are represented with the variant allele frequency on the first Y axis and the depth of each genomic position on the secondary Y axis. If the mutation was not present in the vcf file, the value was set at zero. The black arrows indicate clade defining mutations or deletions excluded for the proportion’s estimation of co-infection (no more than 13 per sample for the artic v4). P6-D1 recombination points were confirmed by Single Molecule Real Time sequencing.