Track Descriptions & Citations

Tracks Built into this Server

Ideogram

Cytogenetic chromosome bands. Annotations from the UCSC Genome Browser Database (cytoBand.txt.gz).

Entrez genes

mRNA sequences from NCBI RefSeq resource. Annotations from the UCSC Genome Browser Database (refGene.txt.gz, refLink.txt.gz, refSeqSummary.txt.gz). Both RefSeq short descriptions and longer summaries (for annotated genes) are searchable, but only short descriptions are displayed alongside features.

CNVs

CNV calls from Li et al. (2008). Blue bars indicate deletions, red indicated duplications.

Genotyped SNPs

SNPs genotyped on the Illumina 650K platform and passing quality control. SNPs are colored according to their annotation in dbSNP build 128. Nonsynonymous SNPs are red, synonymous SNPs are green, SNPs that fall in UTRs are orange, and any SNP that falls within 2kb of a gene is blue. SNPs without annotations are white, and all other SNPs are black. Triangles oriented in an east-west fashion denote SNPs that fall in the 5% tail of the worldwide FST distribution.Clicking on the SNP generates a pie chart of the worldwide allele frequencies.

HapMap SNPs

SNPs in the phase 2 HapMap. Colors are as for Illumina SNPs.

Fst

The position of a SNP in the worldwide FST distribution. Values are -log(10) of the fraction of SNPs with a more extreme value than the SNP in question.

Continent Heterozygosity

Smoothed heterozygosity in a 3 SNP window.

iHS Continent

iHS, as calculated in Voight et al. (2006). Presented is the -log10 of the empirical p-value for a window of 30 SNPs.

XP-EHH Continent

XP-EHH, calculated as in Sabeti et al. (2007)

3-frame translation (forward)

This track shows the position of stop codons at low magnifications, and the 3-frame translation at high magnifications. Only the forward strand is shown.

DNA/GC Content

No additional information available.

3-frame translation (reverse)

This track shows the position of stop codons at low magnifications, and the 3-frame translation at high magnifications. Only the reverse strand is shown.

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Generic genome browser version 1.68