Fig. 4: The indels identified in the viral genomes sequenced in this study.

a The loci of the indels and their distribution in the sequenced genomes. The arrow chart on top represents the protein-coding genes of SARS-CoV-2, and the vertical lines below mark the loci of the indels. b–d The read coverage of the three long fragment deletions in ORF6, ORF7a, and ORF8, respectively. Arrow charts in the middle represent the protein-coding genes, and the curves of read coverage and split reads supporting the deletions are displayed above. Forward and reverse mapping reads are in blue and red, respectively. Sanger sequencing results of corresponding PCR fragments are displayed below; resulting protein mutations are shown at the bottom.