Fig. 2

Results of NGS study. a Positions of variants (SNVs and inserts) and read coverage along the genome of the wildtype virus (WT) and its synthetic constructs (assembly and in-cellulo). Genomic coordinates and annotations are specified in the “genome” panel. Positions of variants are marked by vertical bars (blue and red) in the “variants” panel; summary of variants for all samples (first row in the “variants” panel), and sample-specific variants (three different rows for in-cellulo, assembly, and WT) are shown. Eight Positions (1 indel and 7 SNVs) with VAF at least 0.15 that also passed Position Bias and Strand Bias filters were marked by red bars; 6 of them are found in the WT strain only. b Analysis of 32 CDS SNVs. The nucleotide variability at SNV positions is based on a set of 618 aligned DENV2 genomes, represented by the corresponding sequence logo in the “variability” panel. The coordinates of SNVs are specified in the x-axis; corresponding genes are specified in the bottom row. The variability at each position is represented by a stack of letters. The relative sizes of the letters indicate their frequency in the alignment at specific position, where the total height of the letters depicts the information content of the position in bits. The SNVs at each position are depicted in the “SNVs” panel in the following format: reference codon (reference AA) → variant codon (variant AA). The altered nucleotides are marked in red. The variant allele frequencies (VAF) at each position were specified in the “VAF” panel. Non-synonymous SNVs (18%) were marked by “N”. Positions that overlap with regions that undergo a conserved selection for strong or weak mRNA folding (based on [16]) were marked by “s” or “w” respectively. Seven CDS SNVs with VAF of at least 0.15 that also passed Position Bias and Strand Bias filters were marked by red asterisks