Gene-resolved CpG and UpA dinucleotide indices across 4.9 million SARS-CoV-2 genomes

This dataset contains gene-specific CpG and UpA dinucleotide indices calculated across 4,914,000 SARS-CoV-2 genomes. Indices are provided for 13 open reading frames: ORF1a, ORF1b, S, E, M, N, ORF3a, ORF6, ORF7a, ORF7b, ORF8, ORF9b, and ORF10. For each gene, the dataset includes: Mean, median, standard deviation, min/max, and quartiles for CpG and UpA indicesWilcoxon signed-rank test results comparing CpG vs UpA within each gene (sample size = 100,000)Data is provided in machine-readable CSV format and individual gene reports in .txt Note: Indices for short genes (e.g., E, ORF10) may exceed 1.0 due to normalization methods and should be interpreted with caution. ======================================================================SARS-CoV-2 GENE-RESOLVED CpG AND UpA INDICES - SUMMARYDataset: 4,914,000 genomesGenes: ORF1a, ORF1b, S, E, M, N, ORF3a, ORF6, ORF7a, ORF7b, ORF8, ORF9b, ORF10Method: Wilcoxon signed-rank test (sample n=100,000 per gene)====================================================================== Gene CpG_mean UpG_mean Δ(UpG-CpG) Wilcoxon_p Sig----------------------------------------------------------------------ORF1a 0.3433 0.8485 0.5052 <1e-100 YESORF1b 0.4161 0.8904 0.4743 <1e-100 YESS 0.2333 0.7117 0.4784 <1e-100 YESE 1.3435 1.0813 -0.2622 <1e-100 YESM 0.6568 0.8491 0.1923 <1e-100 YESN 0.5664 0.5128 -0.0537 <1e-100 YESORF3a 0.5334 0.7215 0.1881 <1e-100 YESORF6 0.3785 0.8346 0.4561 <1e-100 YESORF7a 0.5192 0.6428 0.1236 <1e-100 YESORF7b 0.3296 0.6989 0.3693 <1e-100 YESORF8 0.6957 0.8972 0.2015 <1e-100 YESORF9b 0.8740 0.6780 -0.1961 <1e-100 YESORF10 1.4480 1.2525 -0.1955 <1e-100 YES Note: Indices for short genes (E, ORF10) >1.0 may reflect normalization artifacts.Data format: CSV + individual gene reports (.txt). Calculated in Python (Pandas/SciPy). GVAtlas.Org