Genomes
SARS-CoV-2 genomes submitted from 2019-12-23 to 2020-08-29, including the reference genome NC_045512.2, were downloaded from NCBI Datasets (https://www.ncbi.nlm.nih.gov/sars-cov-2/) and 17,229 complete genomes (Supplementary S1) were retrieved for downstream analysis. All the other genomes (Supplementary S2) including 267 SARS, 59 MERS, 35 bat coronavirus and one pangolin coronavirus genomes (EPI_ISL_410539), were collected from GenBank or GISAID (https://www.gisaid.org/).