Schema for 1000G Ph3 Vars - 1000 Genomes Phase 3 Integrated Variant Calls from IGSR: SNVs and Indels
  Database: hg38    Primary Table: tgpPhase3
VCF File: /gbdb/hg38/1000Genomes/ALL.chr1.shapeit2_integrated_snvindels_v2a_27022019.GRCh38.phased.vcf.gz
Format description: The fields of a Variant Call Format data line
See the Variant Call Format specification for more details
fielddescription
chromAn identifier from the reference genome
posThe reference position, with the 1st base having position 1
idSemi-colon separated list of unique identifiers where available
refReference base(s)
altComma separated list of alternate non-reference alleles called on at least one of the samples
qualPhred-scaled quality score for the assertion made in ALT. i.e. give -10log_10 prob(call in ALT is wrong)
filterPASS if this position has passed all filters. Otherwise, a semicolon-separated list of codes for filters that fail
infoAdditional information encoded as a semicolon-separated series of short keys with optional comma-separated values
formatIf genotype columns are specified in header, a semicolon-separated list of of short keys starting with GT
genotypesIf genotype columns are specified in header, a tab-separated set of genotype column values; each value is a colon-separated list of values corresponding to keys in the format column

Sample Rows
 
chromposidrefaltqualfilterinfoformatgenotypes
110416.CCCTAAC.PASSAC=240;AN=5096;DP=365460;AF=0.05;EAS_AF=0.06;EUR_AF=0.07;AFR_AF=0.01;AMR_AF=0.06;SAS_AF=0.05;VT=INDEL;NS=2548GT0|00|00|00|00|00|00|00|00|00|0...
116103.TG.PASSAC=118;AN=5096;DP=29994;AF=0.02;EAS_AF=0;EUR_AF=0.04;AFR_AF=0.03;AMR_AF=0.03;SAS_AF=0.01;VT=SNP;NS=2548GT0|00|00|00|00|00|00|00|00|00|0...
117496.ACA.PASSAC=25;AN=5096;DP=189765;AF=0;EAS_AF=0;EUR_AF=0;AFR_AF=0.02;AMR_AF=0;SAS_AF=0;VT=INDEL;NS=2548GT0|00|00|00|00|00|00|00|00|00|0...
151479.TA.PASSAC=531;AN=5096;DP=17461;AF=0.1;EAS_AF=0;EUR_AF=0.19;AFR_AF=0.02;AMR_AF=0.11;SAS_AF=0.23;VT=SNP;NS=2548GT0|10|00|00|00|00|00|10|11|00|0...
151898.CA.PASSAC=426;AN=5096;DP=15331;AF=0.08;EAS_AF=0.05;EUR_AF=0.14;AFR_AF=0.06;AMR_AF=0.06;SAS_AF=0.11;VT=SNP;NS=2548GT1|00|00|01|00|11|10|00|00|01|0...
151928.GA.PASSAC=367;AN=5096;DP=17022;AF=0.07;EAS_AF=0.01;EUR_AF=0.14;AFR_AF=0.05;AMR_AF=0.06;SAS_AF=0.09;VT=SNP;NS=2548GT1|00|00|01|00|11|10|00|00|01|0...
151954.GC.PASSAC=1;AN=5096;DP=18469;AF=0;EAS_AF=0;EUR_AF=0;AFR_AF=0;AMR_AF=0;SAS_AF=0;VT=SNP;NS=2548GT0|00|00|00|00|00|00|00|00|00|0...
154490.GA.PASSAC=494;AN=5096;DP=24006;AF=0.1;EAS_AF=0;EUR_AF=0.18;AFR_AF=0.02;AMR_AF=0.1;SAS_AF=0.21;VT=SNP;NS=2548GT0|10|00|00|00|00|00|10|11|00|0...
154669.CT.PASSAC=1;AN=5096;DP=23532;AF=0;EAS_AF=0;EUR_AF=0;AFR_AF=0;AMR_AF=0;SAS_AF=0;VT=SNP;NS=2548GT0|00|00|00|00|00|00|00|00|00|0...
154708.GC.PASSAC=1198;AN=5096;DP=23694;AF=0.24;EAS_AF=0.07;EUR_AF=0.39;AFR_AF=0.19;AMR_AF=0.27;SAS_AF=0.29;VT=SNP;NS=2548GT1|01|10|11|00|11|10|01|01|01|0...

1000G Ph3 Vars (tgpPhase3) Track Description
 

Description

This track shows approximately 73 million single nucleotide variants (SNVs) and 5 million short insertions/deletions (indels) produced by the International Genome Sample Resource (IGSR) from sequence data generated by the 1000 Genomes Project in its Phase 3 sequencing of 2,504 genomes from 16 populations worldwide.

Variants were called on the autosomes (chromosomes 1 through 22) and on the Pseudo-Autosomal Regions (PARs) of chromosome X. Therefore this track has no annotations on alternate haplotype sequences, fix patches, chromosome Y, or the non-PAR portion (the majority) of chromosome X.

The variant genotypes have been phased (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

The genomes of 2,504 individuals were sequenced using both whole-genome sequencing (mean depth = 7.4x) and targeted exome sequencing (mean depth = 65.7x). Sequence reads were aligned to the reference genome using alt-aware BWA-MEM (Zheng-Bradley et al.). Variant discovery and quality control were performed as described in (Lowy-Gallego et al.). See also:

Data Access

VCF files were downloaded from EBI and are also available for download from UCSC.

Credits

Thanks to the International Genome Sample Resource (IGSR) for making these variant calls freely available.

References

Zheng-Bradley X, Streeter I, Fairley S, Richardson D, Clarke L, Flicek P, 1000 Genomes Project Consortium. Alignment of 1000 Genomes Project reads to reference assembly GRCh38. Gigascience. 2017 Jul 1;6(7):1-8. PMID: 28531267; PMC: PMC5522380

Fairley S, Lowy-Gallego E, Perry E, Flicek P. The International Genome Sample Resource (IGSR) collection of open human genomic variation resources. Nucleic Acids Res. 2019 Oct 4. PMID: 31584097

Lowy-Gallego E, Fairley S, Zheng-Bradley X, Ruffier M, Clarke L, Flicek P, 1000 Genomes Project Consortium. Variant calling on the GRCh38 assembly with the data from phase three of the 1000 Genomes Project [version 1; peer review: 2 not approved]. Wellcome Open Research. 2019 Mar. 11.

1000 Genomes Project Consortium, Auton A, Brooks LD, Durbin RM, Garrison EP, Kang HM, Korbel JO, Marchini JL, McCarthy S, McVean GA et al. A global reference for human genetic variation. Nature. 2015 Oct 1;526(7571):68-74. PMID: 26432245