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Table 1 Summary of the genotypic variables

From: Comparative genomics of 274 Vibrio cholerae genomes reveals mobile functions structuring three niche dimensions

Attribute Explanation Before After Annotated
Protein families CD-HIT clusters [22] 21,146 17,560 9,819
Functions Level-3 subsystems [20] 4,260 3,105 1,828
SNPs Marker SNPs [3] 7,880 2,545 659
Subsystems Level-3 subsystems [20] 706 444 398
Phages Phages [21] 6 4 4
Clusters Remove redundancy [6] 0 1,647 0
Total   33,998 25,305 12,708
  1. Number of variables is shown before and after the clustering procedure to remove redundancy [6], as well as the number of variables annotated with level-1 subsystems [9]. The full matrix of 25,305 variables used in the manuscript is provided in Additional file 3 and Additional file 4. See text for details.