This track shows data from the Human Genome Structural Variation Project.
Clone ends from nine individuals from Kidd, et al.
were mapped to the reference Human genome. This track
shows clones whose end mappings were discordant with the reference
genome in one of the following ways:
- deletion: Clone mapping too large
relative to reference
- insertion: Clone mapping too small
relative to reference
- inversion: In appropriate orientation,
clone mapping spans potential inversion breakpoint
- OEA: One End Anchored clones (only one
end could be mapped to reference)
- transchrm: Clone ends map to different chromosomes
(name indicates identity of other chromosome after the underscore).
Each individual's discordant clone end mappings are in a different
subtrack. The nine individuals' labels used in Kidd, et al.,
populations of origin, and
Coriell Cell Repository catalog IDs are shown here:
Excerpted from Kidd, et al.:
We selected eight individuals as part of the first phase of the Human
Genome Structural Variation Project. This included four individuals of
Yoruba Nigerian ethnicity and four individuals of non-African
ethnicity. For each individual we constructed a whole genomic library
of about 1 million clones, using a fosmid subcloning strategy.
Each library was arrayed and both ends of each clone insert were
sequenced to generate a pair of high-quality end sequences (termed an
end-sequence pair (ESP)).
The overall approach generated a physical clone map for each
individual human genome, flagging regions discrepant by size or
orientation on the basis of the placement of end sequences against the
Across all eight libraries, we mapped 6.1 million clones to distinct
locations against the reference sequence
Of these, 76,767 were discordant by length and/or orientation,
indicating potential sites of structural variation. About 0.4%
(23,742) of the ESPs mapped with only one end to the reference
assembly despite the presence of high-quality sequence at the other
end (termed one-end anchored (OEA) clones).
Note: This track contains many more than the 76,767 + 23,742 items
mentioned above because it also includes clones whose ends map to
different chromosomes (transchrm).
Kidd JM, Cooper GM, Donahue WF, Hayden HS, Sampas N, Graves T, Hansen N,
Teague B, Alkan C, Antonacci F, et al.
Mapping and sequencing of structural variation from eight
Nature. 2008 May 1;453(7191):56-64.