Segmental 
Duplication DB

This page contains updated data regarding recent segmental duplications in the finishing human genome (build34; Jun 2003; hg16).   It focuses on genomic duplications>1 kb and >90% identity.

Additional Data Access

UCSC Genome Browser

This will allow you to browse the genome.

Statistics of Duplications

Based on whole genome assembly comparison (WGAC) (Joins analysis: after the generation of final global alignments, larger gaps (up to 20 kb insertion side; minimum side of gap �20 bp.) between two duplications were merged. See ref. 4). 

Histogram of aligned bases

Chromosomal distribution of inter and intrachromosomal duplication aligned bases (Joins analysis)

Histogram of non-redundant duplication

Proportion of non redundant duplication in each human chromosome (Joins analysis).

Histogram of length cuts

Analysis on various breakdowns of duplication lengths (Joins analysis). 

Histogram of percent identity cuts

Analysis on various breakdowns of duplication percent identity (Joins analysis). 

Chromosomal views of duplications with gaps

Views of duplications emphasizing gaps. Contig gaps <50kb are represented in dark green and contig gaps >50kb are represented in light green.  The WSSD duplication regions detected by whole-genome shotgun sequences (Excess depth of coverage) (top track) are black.  The whole genome assembly (WGAC) duplications (red and blue for inter and intrachromosomal, respectively) are broken into >98% similar (top) and <98% similar (bottom). 

Chromosomal views of duplications with whole genome shotgun sequence coverage

Views of duplications with whole genome shotgun sequence coverage. Contig gaps <50kb are represented in dark green and contig gaps >50kb are represented in light green.  The WSSD duplication regions detected by whole-genome shotgun sequences (Excess depth of coverage) (top track) are black.  The whole genome assembly (WGAC) duplications (red and blue for inter and intrachromosomal, respectively) are broken into >98% similar (top) and <98% similar (bottom).   The underlying gold bar shows whole genome shotgun sequence coverage. 

Chromosomal views showing inter & intrachromosomal duplication

Inter and intrachromosomal duplications from the perspective of individual chromosomes. The assembly (WGAC) duplications (red and blue for inter and intra chromosomal respectively) are shown at various percentage and length thresholds. 

Views of chromosomes emphasizing pericentromeric regions (2MB around centromeres)

Views of chromosomes emphasizing perientromeric regions (2MB) on each side with satellite repeats shown. The WSSD duplication regions (bottom track) are black.  The assembly (WGAC) duplications (red and blue for inter and intrachromosomal. Also satellite repeat locations have been added just above the chromosome sequence line.  Gaps are depicted as line discontinuities on the chromosomal sequence.

Segmental duplication coordinates

Excel format (10.7MB)    Unix gzip format (3.9MB)    Winzip format (3.9MB)