Schema for snp150Mult
  Database: hg38    Primary Table: snp150Mult    Row Count: 14   Data last updated: 2017-04-18
Format description: Polymorphism data from dbSNP
fieldexampleSQL type info description
bin 683smallint(5) unsigned range Indexing field to speed chromosome range queries.
chrom chr1varchar(31) values Reference sequence chromosome or scaffold
chromStart 12888224int(10) unsigned range Start position in chrom
chromEnd 12888225int(10) unsigned range End position in chrom
name rs75414784varchar(15) values dbSNP Reference SNP (rs) identifier
score 0smallint(5) unsigned range Not used
strand +enum('+', '-') values Which DNA strand contains the observed alleles
refNCBI Cblob values Reference genomic sequence from dbSNP
refUCSC Cblob values Reference genomic sequence from UCSC lookup of chrom,chromStart,chromEnd
observed (401 BP INDEL)/-varchar(255) values The sequences of the observed alleles from rs-fasta files
molType genomicenum('unknown', 'genomic', 'cDNA', 'mito') values Sample type from exemplar submitted SNPs (ss)
class namedenum('single', 'in-del', 'microsatellite', 'named', 'mnp', 'insertion', 'deletion') values Class of variant (single, in-del, named, mixed, etc.)
valid unknownset('unknown', 'by-cluster', 'by-frequency', 'by-submitter', 'by-2hit-2allele', 'by-hapmap', 'by-1000genomes') values Validation status of the SNP
avHet 0float range Average heterozygosity from all observations. Note: may be computed on small number of samples.
avHetSE 0float range Standard Error for the average heterozygosity
func unknownset('unknown', 'coding-synon', 'intron', 'near-gene-3', 'near-gene-5', 'ncRNA', 'nonsense', 'missense', 'stop-loss', 'frameshift', 'cds-indel', 'untranslated-3', 'untranslated-5', 'splice-3', 'splice-5') values Functional category of the SNP (coding-synon, coding-nonsynon, intron, etc.)
locType exactenum('range', 'exact', 'between', 'rangeInsertion', 'rangeSubstitution', 'rangeDeletion', 'fuzzy') values Type of mapping inferred from size on reference; may not agree with class
weight 1int(10) unsigned range The quality of the alignment: 1 = unique mapping, 2 = non-unique, 3 = many matches
exceptions MultipleAlignmentsset('RefAlleleMismatch', 'DuplicateObserved', 'MixedObserved', 'FlankMismatchGenomeLonger', 'FlankMismatchGenomeEqual', 'FlankMismatchGenomeShorter', 'NamedDeletionZeroSpan', 'NamedInsertionNonzeroSpan', 'SingleClassLongerSpan', 'SingleClassZeroSpan', 'SingleClassTriAllelic', 'SingleClassQuadAllelic', 'ObservedWrongFormat', 'ObservedTooLong', 'ObservedContainsIupac', 'ObservedMismatch', 'MultipleAlignments', 'NonIntegerChromCount', 'AlleleFreqSumNot1', 'SingleAlleleFreq', 'InconsistentAlleles') values Unusual conditions noted by UCSC that may indicate a problem with the data
submitterCount 1smallint(5) unsigned range Number of distinct submitter handles for submitted SNPs for this ref SNP
submitters BCMHGSC_JDW,longblob   List of submitter handles
alleleFreqCount 0smallint(5) unsigned range Number of observed alleles with frequency data
alleles  longblob   Observed alleles for which frequency data are available
alleleNs  longblob   Count of chromosomes (2N) on which each allele was observed. Note: this is extrapolated by dbSNP from submitted frequencies and total sample 2N, and is not always an integer.
alleleFreqs  longblob   Allele frequencies
bitfields observed-mismatchset('unknown', 'clinically-assoc', 'maf-5-some-pop', 'maf-5-all-pops', 'has-omim-omia', 'microattr-tpa', 'submitted-by-lsdb', 'genotype-conflict', 'rs-cluster-nonoverlapping-alleles', 'observed-mismatch') values SNP attributes extracted from dbSNP's SNP_bitfield table

Connected Tables and Joining Fields
        hg38.snp150.exceptions (via snp150Mult.exceptions)
      hg38.snp150Common.exceptions (via snp150Mult.exceptions)
      hg38.snp150ExceptionDesc.exception (via snp150Mult.exceptions)
      hg38.snp150Flagged.exceptions (via snp150Mult.exceptions)
      hg38.snp150.name (via snp150Mult.name)
      hg38.snp150CodingDbSnp.name (via snp150Mult.name)
      hg38.snp150Common.name (via snp150Mult.name)
      hg38.snp150Flagged.name (via snp150Mult.name)
      hg38.snp150OrthoPt5Pa2Rm8.name (via snp150Mult.name)
      hg38.snp150Seq.acc (via snp150Mult.name)

Sample Rows
 
binchromchromStartchromEndnamescorestrandrefNCBIrefUCSCobservedmolTypeclassvalidavHetavHetSEfunclocTypeweightexceptionssubmitterCountsubmittersalleleFreqCountallelesalleleNsalleleFreqsbitfields
683chr11288822412888225rs754147840+CC(401 BP INDEL)/-genomicnamedunknown00unknownexact1MultipleAlignments1BCMHGSC_JDW,0observed-mismatch
1391chr14105714741105714743rs711085150+TTTT(363 BP DELETION)/-genomicnamedunknown00unknownrangeSubstitution1FlankMismatchGenomeEqual,MultipleAlignments,SingleAlleleFreq1HUMANGENOME_JCVI,1-,2.000000,1.000000,observed-mismatch
585chr14_KI270846v1_alt6206862069rs711085150+CC(363 BP DELETION)/-genomicnamedunknown00unknownrangeDeletion1FlankMismatchGenomeShorter,MultipleAlignments,SingleAlleleFreq1HUMANGENOME_JCVI,1-,2.000000,1.000000,observed-mismatch
586chr14_KI270846v1_alt182510182512rs711085150+TTTT(363 BP DELETION)/-genomicnamedunknown00unknownrangeSubstitution1FlankMismatchGenomeEqual,MultipleAlignments,SingleAlleleFreq1HUMANGENOME_JCVI,1-,2.000000,1.000000,observed-mismatch
937chr174614654046146541rs789485920+CC(315 BP INDEL)/-genomicnamedunknown00unknownexact1MultipleAlignments1BCMHGSC_JDW,0observed-mismatch
589chr17_GL000258v2_alt640129640130rs789485920-GG(315 BP INDEL)/-genomicnamedunknown00unknownexact1MultipleAlignments1BCMHGSC_JDW,0observed-mismatch
595chr17_GL000258v2_alt14225671422568rs789485920-GG(315 BP INDEL)/-genomicnamedunknown00unknownexact1MultipleAlignments1BCMHGSC_JDW,0observed-mismatch
591chr17_KI270908v1_alt848646848647rs789485920+CC(315 BP INDEL)/-genomicnamedunknown00unknownexact1MultipleAlignments1BCMHGSC_JDW,0observed-mismatch
585chr1_KI270766v1_alt114292114293rs754147840-GG(401 BP INDEL)/-genomicnamedunknown00unknownexact1MultipleAlignments1BCMHGSC_JDW,0observed-mismatch
586chr1_KI270766v1_alt195657195658rs754147840-GG(401 BP INDEL)/-genomicnamedunknown00unknownexact1MultipleAlignments1BCMHGSC_JDW,0observed-mismatch

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.