Table 3 (Top) Densities of features in major cytogenetic bands by Giemsa staining. Pale-staining (R) and dark-staining (G) bands are compared, with alignment of cytogenetic bands to sequence as described in 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). (Bottom) Rank correlations of features, in 1 Mb intervals (p = 0.03, corrected for multiple comparisons).

Density of features per Mb in Giemsa-staining cytogenetic bands

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

Correlation of features in 1 Mbase 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