Description of Browser Tracks

The HGSV browser contains standard annotation tracks (genes, repeats, etc) generated by UCSC. Additionally, there are several tracks reporting data specific to the structural variation project.

UW Primate Clone End Tracks

These tracks report the individual ESP mappings for 9 fosmid libraries (the G248 library plus ABC7-ABC14). The correspondence between library name and samples is given below.

Library Name	Sample ID
G248	NA15510
ABC7	NA18517
ABC8	NA18507
ABC9	NA18956
ABC10	NA19240
ABC11	NA18555
ABC12	NA12878
ABC13	NA19129
ABC14	NA12156

Optimal ESP placements are determined using a 13-point scoring system which favors concordant placements and considers alignment length and sequence quality. All tracks report assignments based upon a 3 standard deviation cutoff employed for each library. Clones with a single best concordant placement (ends map on opposite strands pointing “inward” with an apparent clone size within 3 standard deviations of the library mean) are given in the concordant tracks. Clones with multiple, tied concordant placements are listed in the tie_concordant tracks. Similarly, clones with unique discordant placements are given in the discordant tracks and clones with multiple, tied discordant placements are given in the tie_discordant tracks. In order to improve visualization, discordant deletion clones that appear to be larger than 1 Mpb and inversion clones larger than 10 Mbp have been filtered from these discordant tracks. Such clones are available in the separate large_discordant track.

In addition, for the 8 libraries created from the HapMap samples (ABC7-ABC8) clones have been assigned to individual haplotypes based on phased HapMap SNP genotypes. These assignments are reported in the Hap_a and Hap_B tracks. A manuscript reporting the creation, analysis, and utility of these haplotype assignments is currently in preparation.

Selecting any individual clone will take you to a page reporting more details about that clone and its placement. Links to the ESP alignments and sequences are available. Additionally, by clicking on the “Select this Clone” link, the ID of the given clone will be added you own list of selected clones flagged for future reference. The list of clones selected in your current browser session is given by clicking on the “List Clones” link.

Fosmid ESP Analysis

This group of tracks summarizes sites of structural variation identified from the fosmid ESP map.

Predicted SVs: This track plots all sites predicted from the ESP map, regardless of validation status.
Validated SVs: This track reports individual, sample level validated sites of structural variation. For each site, the library name and validation method is given. The following validation types were used:

MCD	clone fingerprinting
Seq	clone sequencing
Nim	NimbleGen Array-CGH
Agi	Agilent Array-CGH
NIL	overlap with ‘novel’ insertion locus
FISH	inversion FISH assay

Note that the coordinates for these sites correspond to the variant region predicted by the ESPs, not to sequence derived breakpoints based on clone insert sequencing. A spreadsheet reporting this same information is available for download here.

Novel Insertion Loci: Coordinates for 525 regions of “novel”sequence insertion are given. More information on these sequences is available in the DATA DOWNLOAD section.
Sequenced Clones: This track depicts sequenced variants as described in Kidd et al (2008). Clicking on an individual track will display an annotated PDF image comparing the sequenced clones with the corresponding build35 sequence.

Fosmid Array CGH

These tracks display results from array CGH experiments targeted against a subset of variants predicted based on the ESP map. In each experiment sample NA15510 (G248) was used as the reference. For visualization bars beyond a 1.5 standard deviation threshold are colored.
Note: bar heights may be truncated by the browser. Complete array data is available at GEO under accessions GSE10037 and GSE10008.