thousandGenomes

The samples for the 1000 Genomes Project mostly are anonymous and have no associated medical or phenotype data. Variants in this annotation database are sometimes considered to be 'neutral' and could be removed if the goal of a study is to look for variants with high penetrance that dispose to rare Mendelian diseases. This database contains all of the variants supplied by the 1000 Genomes Project. The original vcf file can be obtained from here:

ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20110521/ALL.wgs.phase1_release_v3.20101123.snps_indels_sv.sites.vcf.gz

All of the annotation data supplied through the INFO fields in the VCF file can be used to annotate, filter or select project variants. A description of the fields available in the database are listed below.

% vtools show annotation thousandGenomes -v2
Annotation database thousandGenomes (version hg19_v3_20101123)
Description:            1000 Genomes VCF file analyzed in March 2012 from data
  generated from phase 1 of the project (available from: ftp://ftp.1000genomes
  .ebi.ac.uk/vol1/ftp/release/20110521/ALL.wgs.phase1_release_v3.20101123.snps
  _indels_sv.sites.vcf.gz).
Database type:          variant
Number of records:      39,701,227
Distinct variants:      39,701,227
Reference genome hg19:  chr, pos, ref, alt

Field:                  chr
Type:                   string
Missing entries:        0
Unique Entries:         23

Field:                  pos
Type:                   integer
Missing entries:        0
Unique Entries:         35,755,441
Range:                  56 - 249239465

Field:                  dbsnp_id
Type:                   string
Comment:                DB SNP ID
Missing entries:        0
Unique Entries:         39,628,006

Field:                  ref
Type:                   string
Comment:                Reference allele (as on the + strand)
Missing entries:        0
Unique Entries:         50,996

Field:                  alt
Type:                   string
Comment:                Alternative allele (as on the + strand)
Missing entries:        0
Unique Entries:         19,919

Field:                  LDAF_INFO
Type:                   float
Comment:                MLE Allele Frequency Accounting for LD
Missing entries:        0
Unique Entries:         10,001
Range:                  0 - 1

Field:                  AVGPOST_INFO
Type:                   float
Comment:                Average posterior probability from MaCH/Thunder
Missing entries:        0
Unique Entries:         4,365
Range:                  0.5242 - 1

Field:                  RSQ_INFO
Type:                   float
Comment:                Genotype imputation quality from MaCH/Thunder
Missing entries:        0
Unique Entries:         9,500
Range:                  0 - 1

Field:                  ERATE_INFO
Type:                   float
Comment:                Per-marker Mutation rate from MaCH/Thunder
Missing entries:        0
Unique Entries:         1,395
Range:                  0.0001 - 0.2051

Field:                  THETA_INFO
Type:                   float
Comment:                Per-marker Transition rate from MaCH/Thunder
Missing entries:        0
Unique Entries:         828
Range:                  0 - 0.1493

Field:                  CIEND_INFO
Type:                   string
Comment:                Confidence interval around END for imprecise variants
Missing entries:        39,692,293 (100.0% of 39,701,227 records)
Unique Entries:         1,097

Field:                  CIPOS_INFO
Type:                   string
Comment:                Confidence interval around POS for imprecise variants
Missing entries:        39,692,293 (100.0% of 39,701,227 records)
Unique Entries:         984

Field:                  END_INFO
Type:                   integer
Comment:                End position of the variant described in this record
Missing entries:        39,692,293 (100.0% of 39,701,227 records)
Unique Entries:         1,097
Range:                  -10,145 - 0,0

Field:                  HOMLEN_INFO
Type:                   integer
Comment:                Length of base pair identical micro-homology at event
                        breakpoints
Missing entries:        39,692,371 (100.0% of 39,701,227 records)
Unique Entries:         162
Range:                  0 - 415

Field:                  HOMSEQ_INFO
Type:                   string
Comment:                Sequence of base pair identical micro-homology at
                        event breakpoints
Missing entries:        39,694,177 (100.0% of 39,701,227 records)
Unique Entries:         2,465

Field:                  SVLEN_INFO
Type:                   integer
Comment:                Difference in length between REF and ALT alleles
Missing entries:        39,692,293 (100.0% of 39,701,227 records)
Unique Entries:         5,540
Range:                  -964078 - 190

Field:                  SVTYPE_INFO
Type:                   string
Comment:                Type of structural variant
Missing entries:        39,692,293 (100.0% of 39,701,227 records)
Unique Entries:         1

Field:                  AC_INFO
Type:                   integer
Comment:                Alternate allele count
Missing entries:        0
Unique Entries:         2,185
Range:                  0 - 2184

Field:                  AN_INFO
Type:                   integer
Comment:                Total allele count
Missing entries:        0
Unique Entries:         2
Range:                  1659 - 2184

Field:                  AA_INFO
Type:                   string
Comment:                Ancestral Allele, ftp://ftp.1000genomes.ebi.ac.uk/vol1
                        /ftp/pilot_data/technical/reference/ancestral_alignmen
                        ts/README
Missing entries:        8,934 (0.0% of 39,701,227 records)
Unique Entries:         37,047

Field:                  AF_INFO
Type:                   float
Comment:                Global allele frequency based on AC/AN
Missing entries:        0
Unique Entries:         10,001
Range:                  0 - 1

Field:                  AMR_AF_INFO
Type:                   float
Comment:                Allele frequency for samples from AMR based on AC/AN
Missing entries:        19,038,919 (48.0% of 39,701,227 records)
Unique Entries:         102
Range:                  0.0028 - 1

Field:                  ASN_AF_INFO
Type:                   float
Comment:                Allele frequency for samples from ASN based on AC/AN
Missing entries:        24,655,050 (62.1% of 39,701,227 records)
Unique Entries:         104
Range:                  0.0017 - 1

Field:                  AFR_AF_INFO
Type:                   float
Comment:                Allele frequency for samples from AFR based on AC/AN
Missing entries:        12,995,707 (32.7% of 39,701,227 records)
Unique Entries:         103
Range:                  0.002 - 1

Field:                  EUR_AF_INFO
Type:                   float
Comment:                Allele frequency for samples from EUR based on AC/AN
Missing entries:        22,081,461 (55.6% of 39,701,227 records)
Unique Entries:         105
Range:                  0.0013 - 1

Field:                  VT_INFO
Type:                   string
Comment:                Variant type
Missing entries:        0
Unique Entries:         3

Field:                  SNPSOURCE_INFO
Type:                   string
Comment:                indicates if a snp was called when analyzing the low
                        coverage or exome alignment data
Missing entries:        1,452,448 (3.7% of 39,701,227 records)
Unique Entries:         3