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)

Available databases

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