CpG Analysis of Intergenic Regions in BetaCoV/Wuhan/IVDC-HB-01/2019 (SARS-CoV-2)

This project analyzes the distribution of CpG sites in the intergenic regions of the BetaCoV/Wuhan/IVDC-HB-01/2019 (SARS-CoV-2) genome. The analysis provides insights into the genomic characteristics of this virus, highlighting regions with potential functional significance.Key findings include:- One dominant region (`Intergenic_Region_1`) exhibits a significantly high CpG count (110 CpG sites), suggesting a potential functional or structural role.- Most other intergenic regions show low or negligible CpG content, consistent with CpG depletion commonly observed in coronaviruses.- Observed/expected (O/E) ratios reveal both enrichment and depletion patterns, reflecting evolutionary pressures such as host immune evasion and mutational biases.The dataset includes:- A tab-delimited file (`BetaCoV_IVDC_HB_01_cpg_analysis.txt`) containing CpG counts and O/E ratios for each intergenic region.- Visualizations: - Bar chart showing CpG counts across regions. - Line plot illustrating O/E ratios.- Python scripts used for extracting intergenic regions, calculating CpG metrics, and generating plots.This work contributes to understanding the genomic architecture of BetaCoV/Wuhan/IVDC-HB-01/2019 and its evolutionary strategies. The analysis was performed using Biopython, Pandas, and Matplotlib.Published at:10.6084/m9.figshare.28705184