SARS-CoV-2 S, E, M, N CpG/UpA Analysis Across n = 9,356,279 Unique Genomes from 2020 till early 2025

RIGOROUS QC REPORT: CpG/UpA ANALYSIS================================================== Input File: D:\thb\cpg_upa_analysis_full.csvGenerated: 2025-09-24 12:19:57 BASIC METRICS--------------------Total rows in CSV: 9,356,279Unique headers: 9,356,279Duplicate headers: 0Duplicate rate: 0.00% COMPLETENESS & DATA QUALITY------------------------------S_CpG: Missing/invalid: 0 (0.00%) Zero values: 2,228 (0.02%) Note: Spike CpG = 0 may indicate poor quality S_UpA: Missing/invalid: 0 (0.00%) Zero values: 216 (0.00%) E_CpG: Missing/invalid: 0 (0.00%) Zero values: 18,190 (0.19%) E_UpA: Missing/invalid: 0 (0.00%) Zero values: 16,604 (0.18%) M_CpG: Missing/invalid: 0 (0.00%) Zero values: 22,735 (0.24%) M_UpA: Missing/invalid: 0 (0.00%) Zero values: 2,517 (0.03%) N_CpG: Missing/invalid: 0 (0.00%) Zero values: 1,742 (0.02%) N_UpA: Missing/invalid: 0 (0.00%) Zero values: 1,521 (0.02%) DESCRIPTIVE STATISTICS------------------------- count mean std min 25% 50% 75% maxS_CpG 9356279.0 30.021791 2.513833 0.0 29.0 31.0 31.0 52.0S_UpA 9356279.0 259.627123 19.025273 0.0 262.0 266.0 269.0 277.0E_CpG 9356279.0 10.873067 0.905457 0.0 11.0 11.0 11.0 14.0E_UpA 9356279.0 21.247357 1.713963 0.0 21.0 21.0 22.0 27.0M_CpG 9356279.0 19.227216 2.592106 0.0 20.0 20.0 20.0 27.0M_UpA 9356279.0 44.805629 4.805670 0.0 46.0 46.0 46.0 54.0N_CpG 9356279.0 38.808457 2.054732 0.0 38.0 39.0 40.0 43.0N_UpA 9356279.0 43.144844 2.204255 0.0 43.0 43.0 44.0 54.0 --------------------• No duplicates / data integrity confirmed.• All gene regions successfully extracted.