NV frequency in vaccinated cases and pairwise cross-correlation analysis. (a) Frequency of S protein amino acid alterations present in >3 % of completely (top, calculated for a total of 152 samples) and partially (bottom, total of 137 samples) vaccinated cases. (b) Odds ratio indicating the extent of association of specific variants with vaccination breakthrough cases. (c) Pairwise cross-correlation plot between all non-synonymous missense NVs present in >3 % of all the SARS-CoV-2 samples identified from Telangana, India, during April 2020 to October, 2021; the size of all coloured ‘squares’ is inversely proportional to the corresponding P-value of the correlation. Positions with P>0.05 appear as blank (or white). The colour key for positive (blue) and negative (red) correlation is given below the plot.