Schema for snp150Flagged
  Database: hg38    Primary Table: snp150Flagged    Row Count: 203,915   Data last updated: 2020-06-15
fieldexampleSQL type info
bin 592smallint(5) unsigned range
chrom chr1varchar(31) values
chromStart 948135int(10) unsigned range
chromEnd 948136int(10) unsigned range
name rs267598747varchar(15) values
score 0smallint(5) unsigned range
strand +enum('+', '-') values
refNCBI Gblob values
refUCSC Gblob values
observed A/Gvarchar(255) values
molType genomicenum('unknown', 'genomic', 'cDNA', 'mito') values
class singleenum('single', 'in-del', 'microsatellite', 'named', 'mnp', 'insertion', 'deletion') values
valid by-clusterset('unknown', 'by-cluster', 'by-frequency', 'by-submitter', 'by-2hit-2allele', 'by-hapmap', 'by-1000genomes') values
avHet 0float range
avHetSE 0float range
func coding-synonset('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
locType exactenum('range', 'exact', 'between', 'rangeInsertion', 'rangeSubstitution', 'rangeDeletion', 'fuzzy') values
weight 1int(10) unsigned range
exceptions  set('RefAlleleMismatch', 'DuplicateObserved', 'MixedObserved', 'FlankMismatchGenomeLonger', 'FlankMismatchGenomeEqual', 'FlankMismatchGenomeShorter', 'NamedDeletionZeroSpan', 'NamedInsertionNonzeroSpan', 'SingleClassLongerSpan', 'SingleClassZeroSpan', 'SingleClassTriAllelic', 'SingleClassQuadAllelic', 'ObservedWrongFormat', 'ObservedTooLong', 'ObservedContainsIupac', 'ObservedMismatch', 'MultipleAlignments', 'NonIntegerChromCount', 'AlleleFreqSumNot1', 'SingleAlleleFreq', 'InconsistentAlleles') values
submitterCount 1smallint(5) unsigned range
submitters YSAMUELS,longblob  
alleleFreqCount 0smallint(5) unsigned range
alleles  longblob  
alleleNs  longblob  
alleleFreqs  longblob  
bitfields clinically-assoc,submitted-...set('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

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

Sample Rows
 
binchromchromStartchromEndnamescorestrandrefNCBIrefUCSCobservedmolTypeclassvalidavHetavHetSEfunclocTypeweightexceptionssubmitterCountsubmittersalleleFreqCountallelesalleleNsalleleFreqsbitfields
592chr1948135948136rs2675987470+GGA/Ggenomicsingleby-cluster00coding-synonexact11YSAMUELS,0clinically-assoc,submitted-by-lsdb
592chr1955963955964rs2675987480+GGA/C/Ggenomicsingleby-cluster,by-frequency0.0000330.004069coding-synonexact1SingleClassTriAllelic,InconsistentAlleles2EVA_EXAC,YSAMUELS,2C,G,2.000000,120776.000000,0.000017,0.999983,clinically-assoc,submitted-by-lsdb
592chr1970787970788rs2675987590+GGA/Ggenomicsingleby-cluster00intron,ncRNA,missenseexact11YSAMUELS,0clinically-assoc,submitted-by-lsdb
592chr110141421014143rs7862010050+CCC/Tgenomicsingleunknown00nonsenseexact11CLINVAR,0clinically-assoc,has-omim-omia,submitted-by-lsdb
592chr110143191014319rs6726013450+---/Ggenomicinsertionunknown00frameshiftbetween11CLINVAR,0clinically-assoc,has-omim-omia,submitted-by-lsdb
592chr110143581014359rs6726013120+GGG/Tgenomicsingleby-cluster0.0000170.002892nonsenseexact12CLINVAR,EVA_EXAC,2G,T,119543.000000,1.000000,0.999992,0.000008,clinically-assoc,has-omim-omia,submitted-by-lsdb
592chr110223121022313rs8792537870+AAA/Tgenomicsingleunknown00ncRNA,missenseexact11CLINVAR,0clinically-assoc,submitted-by-lsdb
592chr110415811041582rs5877772990+CCC/Tgenomicsingleby-cluster00ncRNA,nonsenseexact12ILLUMINA,OMIM-CURATED-RECORDS,0clinically-assoc,has-omim-omia,submitted-by-lsdb
592chr110415821041583rs1503597240+AAA/Ggenomicsingleby-cluster,by-frequency,by-1000genomes0.0091830.067134ncRNA,missenseexact1111000GENOMES,CLINVAR,EVA-GONL,EVA_DECODE,EVA_EXAC,EXOME_CHIP,ILLUMINA,JJLAB,NHLBI-ESP,TOPMED,WEILL_CORNELL_DGM,2A,G,111119.000000,555.000000,0.995030,0.004970,clinically-assoc,submitted-by-lsdb
592chr110421401042140rs8792537880+---/Cgenomicinsertionunknown00ncRNA,frameshiftbetween1MixedObserved1CLINVAR,0clinically-assoc,submitted-by-lsdb

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