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Data-sets relating to these meta-analyses have been included as separate supplementary files (as Microsoft Excel or comma separated text) that accompany this manuscript.
A detailed guide of the figures and table is provided in a separate supplementary file.
You also may submit separate, supplementary statements to highlight any particular topics that you wish to bring to our attention.
Alternatively, you may upload your manuscript as one file that contains all of the textual material plus separate figure files (one for each figure) and separate Supplementary Material files.
In a separate supplementary spread-sheet file, we also provide the raw data.
A separate Supplementary Table S2 summarizes assemblies where every library is normalized to the library with least number of reads.
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The concatenated sequences of the 86 nonvertical genes showed strong phylogenetic incongruence (P < 0.001, AU test) with either figure 1 A or B, as the two ST60 strains were well separated (supplementary fig. S3 B, Supplementary Material online).
Interestingly, these genomes harbor homologs that form a separate group (Supplementary Material 1, Supplementary Material online).
However, the trees constructed for TraD and TraC, like the tree of TraG, indicate that these proteins from pTiC58 are most closely related to the orthologous proteins of pAtK84b, whereas those of pTi-SAKURA are on a separate branch (supplementary fig. S2 B and C, Supplementary Material online, and fig. 4 B).
As precipitation during the growing season includes precipitation in May, they were used in separate models (Supplementary Dataset S4).
The majority of mutations with NC above 0.1 were found within all six libraries from the same DNA sample prepared on four separate occasions (Supplementary Figs. 4 7).
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