##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