Description

This track displays variant base calls from the publicly released genome sequences of several individuals:

• 5 Sub-Saharan African genomes sequenced by Penn State University:

• !Gubi (KB1),
• G/aq'o (NB1),
• !Ai (MD8),
• D#kgao (TK1),
• Archbishop Desmond Tutu (ABTutu),

• 6 individuals from the 1000 Genome Project high-coverage pilot:

• a CEU daughter and parents (NA12878, NA12891, NA12892)
• a YRI daughter and parents (NA19240, NA19238, NA19239)

• and independently published genomes:

• Craig Venter,
• James Watson,
• Anonymous Yoruba individual NA18507,
• Anonymous Han Chinese individual (YH, YanHuang Project),
• Seong-Jim Kim (SJK),
• Anonymous Korean individual (AK1),
• Anonymous Irish male,
• Gregory Lucier,
• Stephen Quake,
• Extinct Palaeo-Eskimo Saqqaq individual

Note: The Khoisan languages are characterized by clicks, denoting additional consonants. The ! is a palatal click, / is a dental click, and # is an alveolar click (Le Roux and White, 2004).

Display Conventions and Configuration

Substitutions and indels are displayed as boxes. When read frequency data are available, they are displayed in the mouseover text (e.g. "T:8 G:3" means that 8 reads contained a T and 3 reads contained a G at that base position), and box colors are used to show the proportion of alleles. In the genome browser, when viewing the forward strand of the reference genome (the normal case), the displayed alleles are relative to the forward strand. When viewing the reverse strand of the reference genome ("reverse" button), the displayed alleles are reverse-complemented to match the reverse strand.

On the details page for each variant, the alleles are given for the forward strand of the reference genome. Frequency and phenotype data are shown when available.

Sources

KB1, NB1, MD8, TK1, ABTutu (Penn State) (Schuster et al.)
SNPs are from the allSNPs.txt file which can be downloaded from Galaxy. The indels are also available for download from Galaxy.

CEU trio NA12878, NA12891, NA12892; YRI trio NA19240, NA19238, NA19239 (1000 Genomes Project) (1000 Genomes)
The variants shown are from the 1000 Genomes Project's March 2010 release. The CEU variant calls were based on sequence data from the Wellcome Trust Sanger Insititute and the Broad Institute, using the Illumina/Solexa platform. The YRI variant calls were based on sequence data from the Baylor College of Medicine Human Genome Sequencing Center and Applied Biosystems, using the SOLiD platform. For more information on the mapping, variant calling, filtering and validation, see the pilot 2 README file. The variant calls are available from the March 2010 release subdirectory at EBI and at NCBI.

Craig Venter (JCVI) (Levy et al.)
An overview is given here. This subtrack contains Venter's single-base and multi-base variants and small (< 100 bp) insertions/deletions from the file HuRef.InternalHuRef-NCBI.gff, filtered to include only Method 1 variants (where each variant was kept in its original form and not post-processed), and to exclude any variants that had N as an allele. JCVI hosts a genome browser.

James Watson (CSHL) (Wheeler et al.)
These single-base variants came from the file watson_snp.gff.gz. CSHL hosts a genome browser.

Yoruba NA18507 (Illumina Cambridge/Solexa) (Bentley et al.)
Illumina released the read sequences to the NCBI Short Read Archive. Aakrosh Ratan in the Miller Lab at Penn State University (PSU) mapped the sequence reads to the reference genome and called single-base variants and small insertions/deletions (< 20 bp) using MAQ.

YH (YanHuang Project) (Wang et al.)
The YanHuang Project released these single-base variants from the genome of a Han Chinese individual. The data are available from the YH database in the file yhsnp_add.gff. The YanHuang Project hosts a genome browser.

SJK (GUMS/KOBIC) (Ahn et al.)
Researchers at Gachon University of Medicine and Science (GUMS) and the Korean Bioinformation Center (KOBIC) released these single-base variants from the genome of Seong-Jin Kim. The data are available from KOBIC in the file KOREF-solexa-snp-X30_Q40d4D100.gff.

AK1 (Genomic Medicine Institute) (Kim et al.)
The variants shown are from the AK1_SNP.tar.gz download.

Stephen Quake (Stanford) (Pushkarev et al.)
The variants shown are from the Trait-o-matic download.

Anonymous Irish male (Tong et al.)
The SNPs shown are from the Galaxy library, Irish whole genome.

Gregory Lucier (Life Technologies)
The SNPs shown are from Nimbus Informatics. Sequencing was done using the Life SOLiD platform.

Palaeo-Eskimo Saqqaq individual (Saqqaq Genome Project) (Rasmussen et al.)
The variants shown are all the SNPs found by the SNPest program, and in a second track the high confidence SNPs from the first set. The allele counts are not available for these tracks but read depth is available. The read depth was put in place of the allele counts to give a measure of the reliability of the call.

References

KB1, NB1, MD8, TK1, ABTutu (Penn State)
Schuster SC, Miller W, Ratan A, Tomsho LP, Giardine B, Kasson LR, Harris RS, Petersen DC, Zhao F, Qi J, et al. Complete Khoisan and Bantu genomes from southern Africa. Nature. 2010 Feb 18;463(7283):943-7.

Le Roux, W., and White, A. The voices of the San living in Southern Africa today. Cape Town: Kwla books (2004)

CEU trio NA12878, NA12891, NA12892; YRI trio NA19240, NA19238, NA19239 (1000 Genomes)
1000 Genomes Project Consortium, Durbin RM, Abecasis GR, Altshuler DL, Auton A, Brooks LD, Durbin RM, Gibbs RA, Hurles ME, McVean GA. A map of human genome variation from population-scale sequencing. Nature. 2010 Oct 28;467(7319):1061-73.

Craig Venter (JCVI)
Levy S, Sutton G, Ng PC, Feuk L, Halpern AL, Walenz BP, Axelrod N, Huang J, Kirkness EF, Denisov G, et al. The diploid genome sequence of an individual human. PLoS Biol. 2007 Sep 4;5(10):e254.

James Watson (CSHL)
Wheeler DA, Srinivasan M, Egholm M, Shen Y, Chen L, McGuire A, He W, Chen YJ, Makhijani V, Roth GT, et al. The complete genome of an individual by massively parallel DNA sequencing. Nature. 2008 Apr 17;452(7189):872-6.

Yoruba NA18507 (Illumina Cambridge/Solexa)
Bentley DR, Balasubramanian S, Swerdlow HP, Smith GP, Milton J, Brown CG, Hall KP, Evers DJ, Barnes CL, Bignell HR, et al. Accurate whole human genome sequencing using reversible terminator chemistry. Nature. 2008 Nov 6;456(7218):53-9.

YH (YanHuang Project)
Wang J, Wang W, Li R, Li Y, Tian G, Goodman L, Fan W, Zhang J, Li J, Zhang J, et al. The diploid genome sequence of an Asian individual. Nature. 2008 Nov 6;456(7218):60-5.

SJK (GUMS/KOBIC)
Ahn SM, Kim TH, Lee S, Kim D, Ghang H, Kim DS, Kim BC, Kim SY, Kim WY, Kim C, et al. The first Korean genome sequence and analysis: full genome sequencing for a socio-ethnic group. Genome Res. 2009 Sep;19(9):1622-9.

AK1 (Genomic Medicine Institute)
Jong-Il Kim, Young Seok Ju, Hansoo Park, Sheehyun Kim, Seonwook Lee, Jae-Hyuk Yi, Joann Mudge, Neil A. Miller, Dongwan Hong, Callum J. Bell, et al. A highly annotated whole-genome sequence of a Korean individual. Nature 460, 1011-1015 (20 August 2009).

Stephen Quake
Pushkarev D, Neff NF, Quake SR "Single-molecule Sequencing of an Individual Human Genome" Nature Biotech 27, 847-850 (10 August 2009) doi:10.1038 PDF

Anonymous Irish Male
Tong P, Prendergast JG, Lohan AJ, Farrington SM, Cronin S, Friel N, Bradley DG, Hardiman O, Evans A, Wilson JF, Loftus B. Sequencing and analysis of an Irish human genome. Genome Biol. 2010;11(9):R91.

Gregory Lucier
Not published, data provided by Life Technologies and Nimbus Informatics.

Palaeo-Eskimo Saqqaq individual
Rasmussen M, Li Y, Lindgreen S, Pedersen JS, Albrechtsen A, Moltke I, Metspalu M, Metspalu E, Kivisild T, Gupta R, et al. Ancient Human Genome Sequence of an Extinct Palaeo-Eskimo. Nature 463, 757-762 (11 February 2010).