1000G Ph1 Vars Track Settings
 
1000 Genomes Phase 1 Integrated Variant Calls: SNVs, Indels, SVs   (All Variation tracks)

Display mode:   

Haplotype sorting display

Enable Haplotype sorting display
Haplotype sorting order:
using middle variant in viewing window as anchor.
If this mode is selected and genotypes are phased or homozygous, then each genotype is split into two independent haplotypes. These local haplotypes are clustered by similarity around a central variant. Haplotypes are reordered for display using the clustering tree, which is drawn in the left label area. Local haplotype blocks can often be identified using this display.
To anchor the sorting to a particular variant, click on the variant in the genome browser, and then click on the 'Use this variant' button on the next page.
using the order in which samples appear in the underlying VCF file
Haplotype clustering tree leaf shape:
draw branches whose samples are all identical as <
draw branches whose samples are all identical as [
Allele coloring scheme:
reference alleles invisible, alternate alleles in black
reference alleles in blue, alternate alleles in red
first base of allele (A = red, C = blue, G = green, T = magenta)
Haplotype sorting display height:

Filters

Exclude variants with Quality/confidence score (QUAL) score less than
Minimum minor allele frequency (if INFO column includes AF or AC+AN):

VCF configuration help

View table schema
Data last updated: 2012-10-10

Description

This track shows ~38,200,000 single nucleotide variants (SNVs), ~3,900,000 short insertion/deletion variants (indels), and ~14,000 large deletions (also called structural variants, or SVs) discovered by the 1000 Genomes Project through its Phase 1 sequencing of 1,092 genomes from 14 populations in Africa, Europe, East Asia and the Americas.

The variant genotypes have been phased by the 1000 Genomes Project (i.e., the two alleles of each diploid genotype have been assigned to two haplotypes, one inherited from each parent). This extra information enables a clustering of independent haplotypes by local similarity for display.

Display Conventions

In "dense" mode, a vertical line is drawn at the position of each variant. In "pack" mode, since these variants have been phased, the display shows a clustering of haplotypes in the viewed range, sorted by similarity of alleles weighted by proximity to a central variant. The clustering view can highlight local patterns of linkage.

In the clustering display, each sample's phased diploid genotype is split into two independent haplotypes. Each haplotype is placed in a horizontal row of pixels; when the number of haplotypes exceeds the number of vertical pixels for the track, multiple haplotypes fall in the same pixel row and pixels are averaged across haplotypes.

Each variant is a vertical bar with white (invisible) representing the reference allele and black representing the non-reference allele(s). Tick marks are drawn at the top and bottom of each variant's vertical bar to make the bar more visible when most alleles are reference alleles. The vertical bar for the central variant used in clustering is outlined in purple. In order to avoid long compute times, the range of alleles used in clustering may be limited; alleles used in clustering have purple tick marks at the top and bottom.

The clustering tree is displayed to the left of the main image. It does not represent relatedness of individuals; it simply shows the arrangement of local haplotypes by similarity. When a rightmost branch is purple, it means that all haplotypes in that branch are identical, at least within the range of variants used in clustering.

Methods

Single-nucleotide variants, short insertions/deletions, and larger deletions were called from alignments of 1,092 individuals' low-coverage genomes and high-coverage exomes. For each type of variant, the results of multiple variant-calling methods were merged and filtered in order to provide high-confidence variant calls. For more details, see:

Credits

Thanks to the 1000 Genomes Project for making these data available in advance of publication.

References

1000 Genomes Pilot Project:
1000 Genomes Project Consortium. A map of human genome variation from population-scale sequencing. Nature. 2010 Oct 28;467(7319):1061-73.

Phase 1 of the 1000 Genomes Project:
1000 Genomes Project Consortium, Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, Handsaker RE, Kang HM, Marth GT, McVean GA. An integrated map of genetic variation from 1,092 human genomes. Nature. 2012 Nov 1;491(7422):56-65.

1000 Genomes Frequently Asked Questions (FAQ)