Table 2 A distance matrix of number of nucleotide differences between lineages (DONANA05 is the lineage name of the reference genome; GRW11 is the lineage of sample cc82; GRW4 is the lineage of sample 51242; SGS1-A is lineage SGS1 represented by sample 1309; SGS1-B is lineage SGS1 represented by sample 735) computed from the concatenated alignment of 25 genes (Additional file 6: Table S3)