Comparison of cytogenetic bands
We next examined the overall correspondence between cytobands and exonic density and other genomic features. Table 4 gives the average densities of features in the R bands versus G bands based on the assembly-corrected alignment. Genomic intervals residing in R bands were significantly richer in exons, CpG islands, GC content, Alu repeats and minisatellites than those in G bands. The reverse is true for LINE1 elements. These observations accord with predictions based on a variety of indirect methods [52], or a selected set of genes [53], but only now can be investigated directly using the sequence of the entire genome. The increased exonic density in R bands was fairly modest (approximately 30%), and may reflect attenuation due to alignment error. In addition, the analysis did not account for variation in staining intensity in G bands [41]. The results across the chromosomes were fairly consistent, however, and the R/G exonic density ratio exceeded 2.0 on two chromosomes (13 and 21) and was below 1.0 on only one chromosome (Y). The increased density of CpG islands in R bands was more striking (59%), whereas GC content was only a few percent higher (42.2 versus 39.8% in G bands), again consistent with previous observations [54]. The results for the cytobands are also reflected in pairwise correlations of the genomic features across 1 Mb intervals. These correlations do not depend on the cytoband alignment, and most features were positively correlated. LINE1 elements again differed from other features, showing a negative correlation with exons, CpG islands, GC content and Alu repeats.
Table 4  (a) Density of features per megabase in Giemsa-staining cytogenetic bands
R   G  R/G ratio
Exons   0.0415   0.0319  1.30
CpG islands   0.0119   0.0075  1.59
GC content   42.23%   39.76%  1.06
LINE1 repeats   0.1435   0.1602  0.90
Alu repeats   0.1204   0.0937  1.28
Minisatellites   0.0090   0.0078  1.15
(b) Correlation of features in 1Mb intervals
Exon  CpG  GC  LINE1   Alu  Minisatellite
Exon  1.00  0.65  0.64  -0.26  0.73  0.19
CpG   1.00  0.73  -0.42  0.58  0.16
GC    1.00  -0.54  0.61  0.13
LINE1     1.00  -0.20  0.28
Alu      1.00  0.23
Minisatellite       1.00
(a) Pale-staining (R) and dark-staining (G) bands are compared, with alignment of cytogenetic bands to sequence as described in the text. All of the features except LINE1 elements are denser in the R bands. The true differences are likely to be larger, as errors in cytoband alignment will tend to understate the differences in the band types. The differences in the bands are highly significant at p < 0.001 for all features except for minisatellites (p = 0.006). (b) Rank correlations of features, in 1Mb intervals (p = 0.03, corrected for multiple comparisons).