Segmental Duplication DB

This page contains updated data regarding recent segmental duplications in the finishing human genome (build36; March 2006; hg18).   It focuses on genomic duplications >1 kb and >90% identity.

Additional Data Access

UCSC Genome Browser

This browser will allow you to explore sequences of the genome.

Statistics of Duplications

Based on whole genome assembly comparison (WGAC) (Joins analysis: after the generation of final globalalignments, larger gaps (up to 20 kb insertion side; minimum size 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 (simple) of duplications

Chromosomal views of segmental duplications in chromosomes. Gaps are depicted as line discontinuities on the chromosomal sequence. The WSSD Duplication regions (top track) detected by whole-genome shotgun sequences (Excess depth of coverage) are black. The whole genome assembly (WGAC) duplications are shown in red and blue for inter and intra chromosomal, respectively.  

Chromosomal views (scale) of duplications

Chromosomal views of segmental duplications with % identities in chromosomes. Gaps are depicted as line discontinuities on the chromosomal sequence. The WSSD Duplication regions (top track) detected by whole-genome shotgun sequences (Excess depth of coverage with % identity of alignment) are black. The whole genome assembly (WGAC) duplications are shown in red and blue for inter and intra chromosomal, respectively.

Chromosomal views showing Inter & Intrachromosomal duplication (blowups)

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

Segmental duplication coordinates

Excel format (35MB)    Tab delimited (10Mb)   UCSC Genome Browser file (10Mb)