Figure Legends
Figure 1. Phylogenetic analysis of SARS-CoV-2 from Yogyakarta and Central Java, Indonesia based on the Spike gene. A phylogenetic tree was constructed from the Spike gene of SARS-CoV-2 using the maximum likelihood statistical method, with 1,0000 bootstrap replications and the best substitution model for the dataset (GTR+Gamma).
Figure 2. Phylogenetic analysis of SARS-CoV-2 from Yogyakarta and Central Java, Indonesia based on the nsp12 (A),nsp3 (PLpro) (B), and nsp5 (3CLpro) (C)genes.
Figure 3. High frequency (hotspot) mutations (>10%) identified in the Spike (A),nsp12 (B), nsp3 (PLpro) (C), andnsp5 (3CLpro) (D) genes of Delta and Omicron variants.
Figure 4. Visualization of the 3D structure of the Spike(A), RdRp (B), nsp3 (PLpro) (C), and nsp5 (3CLpro) (D) containing identified mutations from the top and side view.
Table 1. Rates of nucleotide substitutions of the Spike, nsp12, nsp3, and nsp5 genes of SARS-CoV-2 Delta and Omicron variants found in this study.
Table 2. Selective pressure analysis on the Spike, nsp12, nsp3, and nsp5 genes of SARS-CoV-2 Delta and Omicron variants. Positively selected sites were shown.
Supplementary Table 1. The GISAID accession numbers of SARS-CoV-2 isolates identified in this study.
Supplementary Table 2.The GISAID accession numbers of the reference sequences of Alpha, Beta, Delta, Gamma, and Omicron variants.
Supplementary Table 3. The genome sequencing quality of all sequences identified in this study.
Supplementary Table 4. The genome position of the nsp3, nsp5, RdRp and Spike genes of SARS-CoV-2 based on the reference genome from Wuhan, China (hCoV-19/Wuhan/Hu-1/2019, GenBank accession number: NC_045512.2)
Supplementary Table 5. Synonymous and nonsynonymous mutations identified within the Spike, nsp12, nsp3, and nsp5 genes of SARS-CoV-2 Delta and Omicron variants.
Supplementary Table 6. Mutation effect analysis of the Spike(A) , and RdRp, nsp3, and nsp5 proteins (B) of SARS-CoV-2 Delta and Omicron variants.