SupplementaryTables.zip

Supplementary Table 1. Genomic, population genetic parameters, and phylogenetic, phenotypic, and ecological data of 15,235 prokaryotic species based on NCBI taxonomy. The table contains two sub-tables: one with the parameter values and the other providing descriptions of these parameters. The table is in Excel format.

Supplementary Table 2. The correlation coefficient matrix of all parameters (NCBI taxonomy). The table is in Excel format.

Supplementary Table 3. Genomic, population genetic parameters, and phylogenetic, phenotypic, and ecological data of 42,470 prokaryotic species based on GTDB taxonomy. The table is in Excel format.

Supplementary Table 4. The correlation coefficient matrix of all parameters (GTDB taxonomy). The table is in Excel format.

MAP_rawdata.tar.gz

Whole Genome Alignments

This folder contains two subfolders: "Representative Dataset" and "Clonal Group Dataset". "Representative Dataset": Contains whole genome alignments for representative genomes of species with ≥10 representative strains. The files are named as “Species_taxid.whole_genome_aln.fasta”. "Clonal Group Dataset": Contains whole genome alignments for clonal groups with ≥10 strains. The files are named as “Species_taxid.CGid.whole_genome_aln.fasta”. Each genome is named by its "biosample-accession". Data in both datasets are compressed in 7z format. 

SNP Matrix

This folder also contains two subfolders: "Representative Dataset" and "Clonal Group Dataset". These subfolders include core-genome SNP matrix files corresponding to the whole genome alignments in the datasets mentioned above. The files are named as “Species_taxid.snp.matrix” (Representative Dataset) or “Species_taxid.CGid.snp.matrix” (Clonal Group Dataset). In each SNP matrix, rows represent SNP positions in the reference genome, and columns represent the strains. Data are compressed in 7z format.

Pangenome

This folder contains the presence/absence matrix of pan-genes (generated by Panaroo analysis) for species with ≥10 representative strains. In each matrix, rows represent pan-genes, and columns represent the representative strains. Gene presence is indicated by “1”, and gene absence by “0”. The files are named as “Species_taxid.gene_presence_absence.Rtab”. Data are compressed in gzip format.