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.