Additional file 1.
List of CDSs which occur once in the genome of one safe strain but more than once in genomes of other safe strains. A list of CDSs which have only one copy in one safe strain, but have more than one ortholog in one or more other safe strains. For example, hokE occurs once in the K-12 genome but multiple times in the W genome. The CDS count of each strain does not reconcile unless these one-to-many and many-to-many relationships are considered. Detailed CDS counts are provided within the file. The counts explain the CDS skew which occurs when counting the number of CDSs in Figure 2 for K-12, B, or ATCC 8739. For example, in ATCC 8739 one copy of EcolC_3064 is present, while two are present in W as ECW_m0635 and ECW_m0636. When shared orthologs are counted the number in the ATCC 8739-W region can be one or two, depending on whether the number of orthologs is taken from W or ATCC 8739s context. We have thus detailed all orthologous CDSs which are found in different copy numbers in the other safe strains genomes.
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Archer et al. BMC Genomics 2011 12:9 doi:10.1186/1471-2164-12-9