Table 2. List of SNP input files ("input_files_list.csv") to be compared by SNPer.

sp1	sp2	sp3
AF1_HA.csv	AF2_HA.csv	AF6_HA.csv
AF1_M.csv	AF2_M.csv	AF6_M.csv
AF1_NA.csv	AF2_NA.csv	AF6_NA.csv
AF1_NEP.csv	AF2_NEP.csv	AF6_NEP.csv
AF1_NP.csv	AF2_NP.csv	AF6_NP.csv
AF1_PA.csv	AF2_PA.csv	AF6_PA.csv
AF1_PB1.csv	AF2_PB1.csv	AF6_PB1.csv
AF1_PB2.csv	AF2_PB2.csv	AF6_PB2.csv

SNPs from eight fragments of sp1, sp 2 and sp3 were compared by SNPer. Each computational SNPs comparison among three viral subpopulations was conducted according to the name of the files listed in each row. For instance, for row #1, SNPer compared the SNPs data in file “AF1_HA.csv” of population 1 (sp1), “AF2_HA.csv” file from population 2 (sp2) and “AF6_HA.csv” file from population 3 (sp3).