List of Supplementary files:
Supplementary file 1: List of GISAID IDs with metadata of SARS-CoV-2 sequences of isolates sampled from various States/Union Territories of India (Dataset_1: 42,989 entries; as of Aug 15, 2021)
Supplementary file 2: Python script for generating States/UT wise plots of WHO designated VoC and VoI.
Supplementary file 3: Curated GISAID and GenBank IDs and associated metadata of SARS-CoV-2 genome sequences from India (Dataset_2: 11,864 entries; as of May 26, 2021)
Supplementary file 4: List of GISAID and GenBank IDs for non-redundant SARS-CoV-2 genomes from India used for evolutionary analysis (Dataset_3: 6859 entries)
Supplementary file 5: List of GISAID and GenBank IDs corresponding to Spike gene data (Dataset_5: 9538) 
Supplementary file 6: Regression plot for Root-to-tip distances vs time of isolation of SARS-CoV-2 isolates from India.
Supplementary file 7: Bar plot of fine level population structure of SARS-CoV-2 isolates from India. 
Supplementary file 8: Sites under positive selection in spike gene sequences belonging to SARS-CoV-2 isolates from India 
Supplementary file 9: Functional annotations for Sites under positive selection in spike gene sequences belonging to SARS-CoV-2 isolates from India
Supplementary file 10: Functional annotations of significantly variable sites in spike protein sequences belonging to SARS-CoV-2 isolates from India 
