The outermost circle (orange to blue) shows the relative magnitude of DNA curvature, smoothed over a large window. Note that in the
E. coli K-12 genome, there are several dark blue regions, indicating areas which are much more curved than the average (grey), and that there are relatively few regions which are LESS curved than average (e.g., dark orange). Also note that in general the region around the replication terminus is more curved (bluish) than the region around the origin (greyish).
The second circle is the stacking energy, in kcal/mol. Less stacking energy (e.g., a smaller number) means that the helix will melt more readily, and is shaded red. This is correlated with (but not quite the same as) the AT content. Note that there are several regions which are dark red, indicating they will melt quite readily. For example, see the region around the
rfaJ gene, near the replication origin. Again, note that there are more red regions (e.g., regions which would melt more easily) than there are green regions (which are more difficult to melt). The distribution for stacking energy is also skewed.
The third circle is ``position preference'', which is related to the flexibility of the DNA. The scale is such that green regions are MORE FLEXIBLE, whilst violet regions are more rigid. There seems to be a fairly good correlation between flexible (``green'') regions and clusters of highly expressed genes.
All of this is described in more detail
elsewhere, as well as in our "DNA Structural Atlas" paper (see the paper by
Pedersen et al.in the references below).
Genome Organisation in Escherichia coli 
Usually, the GenBank files for sequenced genomes will contain locations of predicted genes. The genes going in the ``forward'' (clockwise) direction are blue, whilst genes on the other strand are red. Also, rRNA and tRNA genes are shown, although for most bacterial chromosomes, the tRNA genes are too small. Notice that in the E. coli K-12 genome, the seven rRNA genes light up with distinctive structural features - they are generally more GC-rich, more flexible (and of course more highly expressed) and are repeated throughout the chromosome. 
There are many different ways of calculating repeats. For the Genome Atlas plots, "Global Direct Repeats" are obtained from a 
The inverted repeats is calculated in the same way, but only the hits on the opposite strand are taken into consideration. Note that there are far fewer significant hits on the other strand. This is true for many bacterial genomes, although in eukaryotic chromosomes, the global inverted repeats is often equal to the global direct repeats.
The inner-most two circles contain information about the base-composition of the genome, smoothed over a large window. The ``GC-skew'' is simply the number of G's minus the number of C's, over a 10,000 bp window. Thus, if there are more G's than C's, a positive number results (turquoise), whilst more C's than G's, will result in a negative number (violet). This can be useful in visualising the replication origin and terminus. 
The inner-most circle is the percent AT. In the case of E. coli, which is nearly 50% AT content, on average, the scale goes from 45% (turquoise) to 55% (red). 
Most (>90%)
of the proteins are present in very low amounts (less than 100 copies per cell).
