##variationPropertyDocumentationUrl=ftp://ftp.ncbi.nlm.nih.gov/snp/specs/dbSNP_BitField_latest.pdf ##dbSNP VCF file=ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606/VCF/v4.0/ByChromosomeNoGeno/00-All.vcf.gz Codes present in the dbSNP build 135 vcf file. Code Number Type Count % of SNPs Description Comment dbSNPBuildID 1 Integer First SNP Build for RS First dbSNP build in which the rs# appeared. Used to filtering by release. WGT 1 Integer Weight 00 - unmapped, 1 - weight 1 (mapped uniquely), 2 - weight 2 (twice on same scaffold), 3 - weight 3 or more (multiple hits) NS 1 Integer Number of Samples With Data AF 1 Float Allele Frequency GMAF 1 Float 15,708,397 30.94% Global Minor Allele Frequency Global Minor Allele Frequency [0, 0.5]; global population is 1000GenomesProject phase 1 genotype data from 629 individuals, released in the 08-04-2010 dataset VP 1 String Variation Property dbSNP bitfield. See propertery documentation for structure. Expanded into flags below. VC 1 String Variation Class Values are SNP, INDEL, MULTI-BASE, MIXED RSPOS 1 Integer Chr position reported in dbSNP May differ from column 2 especially for IN/DELs GENEINFO 1 String Pairs each of gene symbol:gene id. The gene symbol and id are delimited by a colon (:) and each pair is delimited by a vertical bar (|) Frequency Flags G5 0 Flag 8,664,535 17.06% >5% minor allele frequency in 1+ populations Variations common in at least one population G5A 0 Flag 6,134,618 12.08% >5% minor allele frequency in each and all populations Variations common in every typed population Discovery Flags KGPilot123 0 Flag 7,223,890 14.23% 1000 Genome discovery all pilots 2010(1,2,3) Submitted in project 2010 release (low coverage, trio and exome pilots) KGPhase1 0 Flag 37,957,067 74.75% 1000 Genome phase 1 (incl. June Interim phase 1) Submitted in project 2009 low coverage release KGPROD 0 Flag 39,470,805 77.74% Has 1000 Genome submission KGValidated 0 Flag - OTHERKG 0 Flag 23,073,440 45.44% non-1000 Genome submission Functional and Clinical Flags INT 0 Flag 18,778,915 36.98% In Intron FxnCode = 6 R5 0 Flag 705,643 1.39% In 5' gene region Within 2000 BPupstream of 5' end of gene feature. FxnCode = 15 REF 0 Flag 837,758 1.65% Has reference A coding region variation where one allele in the set is identical to the reference sequence. FxnCode = 8 U3 0 Flag 435,260 0.86% In 3' UTR Location is in an untranslated region (UTR). FxnCode = 53 NSM 0 Flag 495,804 0.98% Has non-synonymous missense A coding region variation where one allele in the set changes protein peptide. FxnClass = 42 R3 0 Flag 181,405 0.36% In 3' gene region Within 500 BP downstream of 3' end of gene feature. FxnCode = 13 SYN 0 Flag 306,011 0.60% Has synonymous A coding region variation where one allele in the set does not change the encoded amino acid. FxnCode = 3 S3D 0 Flag 269,455 0.53% Has 3D structure - SNP3D table U5 0 Flag 75,564 0.15% In 5' UTR Location is in an untranslated region (UTR). FxnCode = 55 NSF 0 Flag 25,881 0.05% Has non-synonymous frameshift A coding region variation where one allele in the set changes all downstream amino acids. FxnClass = 44 CLN 0 Flag 31,524 0.06% SNP is Clinical Includes LSDB,OMIM,TPA,Diagnostic LSD 0 Flag 29,910 0.06% Submitted from a locus-specific database OM 0 Flag 16,998 0.03% Has OMIM/OMIA NSN 0 Flag 14,144 0.03% Has non-synonymous nonsense A coding region variation where one allele in the set changes to STOP codon (TER). FxnClass = 41 DSS 0 Flag 4 0.00% In donor splice-site FxnCode = 75 ASS 0 Flag - In acceptor splice site FxnCode = 73 MUT 0 Flag - Is mutation (journal citation, explicit fact) a low frequency variation that is cited in journal and other reputable sources CDA 0 Flag - Variation is interrogated in a clinical diagnostic assay Validation Flags VLD 0 Flag 11,618,464 22.88% Is Validated. This bit is set if the snp has 2+ minor allele count based on frequency or genotype data. PM 0 Flag 91,348 0.18% SNP is Precious Preserved rs#'s (cannot cluster into lower rs#) Includes Clinical,Pubmed Cited WTD 0 Flag - Is Withdrawn by submitter If one member ss is withdrawn by submitter, then this bit is set. If all member ss' are withdrawn, then the rs is deleted to SNPHistory SSR 1 Integer 247,783 0.49% SNP Suspect Reason Code SNP Suspect Reason Code, 0 - unspecified, 1 - Paralog, 2 - byEST, 3 - Para_EST, 4 - oldAlign, 5 - other. Count in column D is non-zero Sequence Annotation Flags ASP 0 Flag 27,513,248 54.19% Is Assembly specific. True if the variation only maps to one assembly OTH 0 Flag 460,564 0.91% Has other snp with exactly the same set of mapped positions on NCBI refernce assembly. RV 0 Flag 1,631,182 3.21% RS orientation is reversed True if rs strand is reversed to reference assembly. CFL 0 Flag 1,022,762 2.01% Has Assembly conflict. True when weight 1 and 2 variations map to different chromosomes on different assemblies. NOC 0 Flag 598,455 1.18% Contig allele not present in SNP allele list. The reference sequence allele at the mapped position is not present in the SNP allele list, adjusted for orientation. Genotyping Flags GNO 0 Flag 14,214,758 27.99% Genotypes available. The snp has individual genotype (in SubInd table). HD 0 Flag 2,363,987 4.66% Marker is on high density genotyping kit (50K density or greater). The snp may have phenotype associations present in dbGaP. OMNI chip not included yet. GCF 0 Flag 484,745 0.95% Has Genotype Conflict Same (rs, ind), different genotype. N/N is not included. PH3 0 Flag 4,155,276 8.18% Phase 3 genotyped: filtered, non-redundant True if genotypes submitted in HapMap phase 3 Other Information SLO 0 Flag 10,624,194 20.92% Has SubmitterLinkOut - From SNP->SubSNP->Batch.link_out Submitter(s) have weblinks to this ID with more information about the variant. PMC 0 Flag 69,795 0.14% Links exist to PubMed Central article NOV 0 Flag 80,043 0.16% Rs cluster has non-overlapping allele sets. True when rs set has more than 2 alleles from different submissions and these sets share no alleles in common. TPA 0 Flag 13,700 0.03% Provisional Third Party Annotation(TPA) Currently rs from PHARMGKB who will give phenotype data MTP 0 Flag 9,250 0.02% Microattribution/third-party annotation(TPA:GWAS,PAGE) SAO 1 Integer 14,908 0.03% SNP Allele Origin SNP Allele Origin: 0 - unspecified, 1 - Germline, 2 - Somatic, 3 - Both. Count in column D is non-zero SCS 1 Integer 12,533 0.02% SNP Clinical Significance SNP Suspect Reason Code, 0 - unspecified, 1 - Paralog, 2 - byEST, 3 - Para_EST, 4 - oldAlign, 5 - other. Count in column D is non-zero 50,776,096 Total rows in VCF