Chimpanzee and human segmental duplications

Publication

Result of this analysis is published here

Track Annotation

Four independent duplication analyses were performed and the duplication coordinates mapped back against human genome reference sequence for each chromosome.
These include:
human whole-genome assembly analysis of duplications (hWGAC, blue track),
human whole-genome shotgun sequence detection analysis of duplications (hWSSD, black track),
chimpanzee whole genome assembly analysis of duplication (cWGAC purple track),
chimpanzee whole-genome shotgun sequence detection analysis (cWSSD, light blue track) (see Reference)

Chimpanzee WGAC & WSSD

Chimpanzee tracks were mapped directly to the human genome (cWSSD) or mapped back by combined liftover and BLAST sequence similarity searches (cWGAC). In the case of the latter, if the chimpanzee sequence mapped to two or more regions with an equivalent score, both were flagged as duplicated. Whole genome assembly comparisons map all segmental duplications (>90% and >1 kb in length); while WSSD analyses target all regions (>94% identity and >10 kb in length). Previous studies have shown that duplications <96% are reliably predicted by WGAC within draft genome assemblies.

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Chromosomes are divided into 1 Mb sections with 100 Mb increments corresponding to genome coordinates (July 2003 Assembly). Gaps are represented as light green bars. Above and below the tracks, the average % sequence identity of cWSSD quality-corrected alignments and depth of coverage (5 kb windows) are depicted, respectively. The latter provides an approximation of copy-number for each region. 24 images are depicted corresponding to each human chromosome. In addition, we considered separately those regions of the chimpanzee genome that could not be mapped back to the human genome assembly and the finished chimpanzee chromosome 22 (corresponding to human chromosome 21). In these latter cases, coordinates are based on the chimpanzee genome assemblies.

UCSC Human Genome Browser Mirror

Sites of genome browser with human duplications and chimpanzee duplications, July 2003 assembly (build34)

Reference

Bailey, J. A., Yavor, A. M., Massa, H. F., Trask, B. J. & Eichler, E. E. Segmental duplications: organization and impact within the current human genome project assembly. Genome Res 11, 1005-17. (2001).
She, X. et al. Shotgun sequence assembly and recent segmental duplications within the human genome. Nature 431, 927-30 (2004).
Bailey, J. A. et al. Recent segmental duplications in the human genome. Science 297, 1003-7 (2002).