Figure 1

Overview map of features on the entire human genome, based on the working draft assembly (15 June 2000 release) and finished sequences for chromosomes 21 and 22. Ideograms are oriented with the p-arm at the top, and are assembly-corrected to form an approximate cytogenetic alignment with the features of the draft assembly depicted to the right of each ideogram. Sequencing gaps at the centromeres and contiguous heterochromatic regions are represented by horizontal lines. Chromosome 19 is an exception, for which evidence suggests that both heterochromatic regions are at least partially sequenced. Genomic features are presented as densities (that is, proportion of base pairs occupied by each feature) in nonoverlapping 1Mb intervals. The densities are corrected for sequencing gaps, indicated in the draft assembly as 50-200 kb segments of Ns (unsequenced nucleotides), but (with the exception of GC content) are not corrected for sporadic Ns of lower-quality base calls, because these would not interfere with assignment of the feature to the assembly. Exon density (red) is based on high-scoring pairs from Table 1, not necessarily in ORFs. CpG island density (blue) is based on standard definitions [45] of a run of at least 200 bases with GC content >50% and observed over expected CpG >0.6, and implemented using the program cpg [90]. GC content (green) is the number of G or C bases divided by the number of non-N bases in the 1Mb interval. LINE1 (blue) and Alu (black) repeat elements were determined using RepeatMasker [91] and minisatellites of repeat size 20-50bp by the etandem program of the EMBOSS suite [84]. Density ranges were selected to illuminate features across the genome while preserving a common scale to facilitate comparison. A number of values exceed the range for the feature and are truncated, with a small dot of the corresponding color placed under the ordinate. The data points for the figure are available in the additional data file.