The EVS annotation source contains exome sequencing variants retrieved from the Exome Variant Server (EVS) for the NHLBI Exome Sequencing Project (ESP). The evs annotation data was generated from approximately 2500 exomes and evs_5400 from approximately 5400 exomes. (7500 exomes are the next milestone for this project in the next couple of months - see their website for project details: http://evs.gs.washington.edu/EVS/). Currently minor allele frequencies are given for European American and African American populations - see below for additional fields that you can use for variant selection and annotation.
The data in evs annotation source was retrieved from the project website on November 7, 2011, and evs_5400 was retrieved on December 15, 2011. If you find this data useful please cite their project:
Exome Variant Server, NHLBI Exome Sequencing Project (ESP), Seattle, WA (URL: http://evs.gs.washington.edu/EVS/) [December 15, 2011] (or [November 7, 2011] for the 2500 exome version)
You should run the following command to see the availability of most recent version of the evs database:
% vtools show annotations evs ESP
ESP-6500SI-V2-SSA137 NHLBI GO Exome Sequencing Project (Exome Variant
Server, NHLBI Exome Sequencing Project (ESP), Seattle,
WA (URL: http://evs.gs.washington.edu/EVS/) [6500
samples, February, 2013].)
ESP NHLBI GO Exome Sequencing Project (Exome Variant
Server, NHLBI Exome Sequencing Project (ESP), Seattle,
WA (URL: http://evs.gs.washington.edu/EVS/) [6500
samples, February, 2013].)
evs-6500 NHLBI GO Exome Sequencing Project (Exome Variant
Server, NHLBI Exome Sequencing Project (ESP), Seattle,
WA (URL: http://evs.gs.washington.edu/EVS/) [6500
samples, February, 2013].)
evs-hg19_20111107 NHLBI GO Exome Sequencing Project (Exome Variant
Server, NHLBI Exome Sequencing Project (ESP),
Seattle, WA (URL: http://evs.gs.washington.edu/EVS/)
[November, 2011].)
evs NHLBI GO Exome Sequencing Project (Exome Variant
Server, NHLBI Exome Sequencing Project (ESP), Seattle,
WA (URL: http://evs.gs.washington.edu/EVS/) [6500
samples, February, 2013].)
evs_5400 NHLBI GO Exome Sequencing Project (Exome Variant
Server, NHLBI Exome Sequencing Project (ESP),
Seattle, WA (URL: http://evs.gs.washington.edu/EVS/)
[5400 samples, December, 2011].)
% vtools show annotation ESP
Description: NHLBI GO Exome Sequencing Project (Exome Variant
Server, NHLBI Exome Sequencing Project (ESP), Seattle, WA (URL:
http://evs.gs.washington.edu/EVS/) [6500 samples, February, 2013].)
Database type: variant
Number of records: 1,998,204
Distinct variants: 1,998,173
Reference genome hg19: chr, pos, ref, alt
Field: chr
Type: string
Comment: Chromosome that the variant was found in.
Missing entries: 0
Unique Entries: 24
Field: pos
Type: integer
Comment: Location on the chromosome (NCBI 37 or hg19), 1-based.
Missing entries: 0
Unique Entries: 1,979,319
Range: 5994 - 249212579
Field: rs_id
Type: string
Comment: dbSNP reference SNP identifier (if available)
Missing entries: 1,068,352 (53.5% of 1,998,204 records)
Unique Entries: 921,262
Field: ref
Type: string
Comment: Variant alternate allele.
Missing entries: 0
Unique Entries: 8,026
Field: alt
Type: string
Comment: Reference allele.
Missing entries: 0
Unique Entries: 2,084
Field: dbSNPVersion
Type: string
Comment: dbSNP version which established the rs_id
Missing entries: 0
Unique Entries: 57
Field: EuropeanAmericanAltCount
Type: integer
Comment: The observed ref allele counts for the European
American population. Allele counts only include
genotypes with quality >= 30 and read depth >= 10.
Missing entries: 0
Unique Entries: 8,517
Range: 0 - 8600
Field: EuropeanAmericanRefCount
Type: integer
Comment: The observed ref allele counts for the European
American population. Allele counts only include
genotypes with quality >= 30 and read depth >= 10.
Missing entries: 0
Unique Entries: 8,599
Range: 0 - 8600
Field: AfricanAmericanAltCount
Type: integer
Comment: The observed alt allele counts for the African
American population. Allele counts only include
genotypes with quality >= 30 and read depth >= 10.
Missing entries: 0
Unique Entries: 4,406
Range: 0 - 4406
Field: AfricanAmericanRefCount
Type: integer
Comment: The observed ref allele counts for the African
American population. Allele counts only include
genotypes with quality >= 30 and read depth >= 10.
Missing entries: 0
Unique Entries: 4,407
Range: 0 - 4406
Field: AllAltCount
Type: integer
Comment: The observed alt allele counts for all populations.
Allele counts only include genotypes with quality >=
30 and read depth >= 10.
Missing entries: 0
Unique Entries: 12,543
Range: 0 - 13005
Field: AllRefCount
Type: integer
Comment: The observed ref allele counts for all populations.
Allele counts only include genotypes with quality >=
30 and read depth >= 10.
Missing entries: 0
Unique Entries: 12,971
Range: 0 - 13005
Field: EuropeanAmericanMaf
Type: float
Comment: The European American minor-allele frequency in
percent.
Missing entries: 0
Unique Entries: 67,810
Range: 0 - 0.650641
Field: AfricanAmericanMaf
Type: float
Comment: The African American minor-allele frequency in
percent.
Missing entries: 0
Unique Entries: 75,477
Range: 0 - 0.652047
Field: AllMaf
Type: float
Comment: The minor-allele frequency in percent for all
populations.
Missing entries: 0
Unique Entries: 85,231
Range: 7.7e-05 - 0.652174
Field: AvgSampleReadDepth
Type: integer
Comment: The average sample read depth.
Missing entries: 0
Unique Entries: 795
Range: 1 - 2855
Field: Genes
Type: string
Comment: One or more genes for which the SNP is in the coding
region (CCDS).
Missing entries: 0
Unique Entries: 19,395
Field: GeneAccession
Type: string
Comment: NCBI mRNA transcripts accession number.
Missing entries: 1,998,204 (100.0% of 1,998,204 records)
Field: FunctionGvs
Type: string
Comment: The GVS functions are calculated by the Exome Variant
Server; they are based on the alleles for all
populations and individuals; the bases in the coding
region are divided into codons (if a multiple of 3),
and the resulting amino acids are examined.
Missing entries: 0
Unique Entries: 157,919
Field: AminoAcidChange
Type: string
Comment: The corresponding amino acid change for a SNP.
Missing entries: 1,998,204 (100.0% of 1,998,204 records)
Field: ProteinPos
Type: string
Comment: The coresponding amino acid postion in a protein
relative to the whole protein length.
Missing entries: 1,998,204 (100.0% of 1,998,204 records)
Field: cDNAPos
Type: integer
Comment: The coresponding cDNA postion for a SNP.
Missing entries: 1,998,204 (100.0% of 1,998,204 records)
Field: ConservationScorePhastCons
Type: float
Comment: A number between 0 and 1 that describes the degree of
sequence conservation among 17 vertebrate species;
these numbers are downloaded from the UCSC Genome site
and are defined as the "posterior probability that the
corresponding alignment column was generated by the
conserved state of the phylo-HMM, given the model
parameters and the multiple alignment" (see UCSC
description).
Missing entries: 0
Unique Entries: 12
Range: 0 - .
Field: ConservationScoreGERP
Type: float
Comment: The rejected-substitution score from the program GERP,
a number between -11.6 and 5.82 that describes the
degree of sequence conservation among 34 mammalian
species, with 5.82 being the most conserved; these
scores were provided by Gregory M. Cooper of the
University of Washington Department of Genome Sciences
to the EVS project.
Missing entries: 0
Unique Entries: 187
Range: -12.3 - .
Field: GranthamScore
Type: integer
Comment: Grantham Scores categorize codon replacements into
classes of increasing chemical dissimilarity based on
the publication by Granthan R.in 1974, Amino acid
difference formula to help explain protein evolution.
Science 1974 185:862-864.
Missing entries: 0
Unique Entries: 9,363
Range: 5 - 99,99,99,99,99,99,99,99,99,99,99,99,99,99,99,99,99,99,99,99,99,99,99,99,99,99,99,99
Field: PolyPhenPrediction
Type: string
Comment: Prediction of possible impact of an amino acid
substitution on protein structure and function based
on Polymorphism Phenotyping (PolyPhen) program.
Missing entries: 0
Unique Entries: 23,374
Field: ChimpAllele
Type: string
Comment: Chimp alleles are acquired from UCSC human/chimp
alignment files. If the variation does not fall within
an alignment block, or if it is an indel, the chimp
allele is listed as "unknown". If the variation falls
within a gap in the alignment, it is listed as "-".
Missing entries: 0
Unique Entries: 6
Field: ClinicalLink
Type: string
Comment: The potential clinical implications associated with a
SNP (limited).
Missing entries: 0
Unique Entries: 5,918
Field: ExomeChip
Type: string
Comment: Whether a SNP is on the Illumina HumanExome Chip
Missing entries: 0
Unique Entries: 2
Field: FilterStatus
Type: string
Comment: A machine-learning technique called support vector
machine (SVM) classification was applied for variant
filtering. After the initial SNP calls were generated,
we re-examined the BAM files to collect additional
information about each variant site. Based on the
information, variants are initially filtered by
individual thresholds. For example, variants with
posterior probability <99% (glfMultiples SNP quality
<20), were <5bp away from an indel detected in the
1000 Genomes Pilot Project, had total depth across
samples of <5,379 or >5,379,000 reads (~1-1000 reads
per sample), having >65% of reads as heterozygotes
carrying the variant allele or where the absolute
squared correlation between allele (variant or
reference) and strand (forward or reverse) was >0.15
were marked as problematic SNPs. Sites failed 3 or
more criteria are used as negative examples to train
SVM classifier. HapMap3 and OMNI polymorphic sites
were used as positive examples. The SVM classifier
produces scores for each site, and we marked ~8.5% of
sites at threshold 0.3 as SVM filter-failed. The
unfiltered set had Ti/Tv = 2.63, and the filtered set
had Ti/Tv =2.78.
Missing entries: 0
Unique Entries: 1