Table S9 NCBI SARS-CoV-2 samples SNVs called during the first and second waves

The table contains immunological, genomic and sequencing features of single nucleotide variants (SNVs) from 38,685 whole genome sequences from the NCBI sequence read archive. The SARS-CoV-2 samples from the first pandemic wave (defined as January 1 to July 31, 2020) and the second wave (defined as August 1 to December 31 2020) were sequenced using Illumina paired-end amplicons with a minimum average depth of coverage of 200 x and fewer than 10,000 sites with a depth of coverage lower than 100x. Additionally, we selected SNVs present in both minus and plus strands at a minimum frequency of 2%, occurring at sites with a minimum depth of 100x, having a minimum within-sample frequency of 5% and located between sites 101 and 29778 of the genome to exclude sites at the extremities that are prone to sequencing errors and have been frequently masked.