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Database: hg18 Primary Table: snp130 Row Count: 18,833,531 Data last updated: 2009-08-18
Format description: Polymorphism data from dbSnp database or genotyping arrays
On download server: MariaDB table dump directory
| field | example | SQL type | description |
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| bin | 585 | smallint(5) unsigned | Indexing field to speed chromosome range queries. |
| chrom | chr1 | varchar(31) | Reference sequence chromosome or scaffold |
| chromStart | 259 | int(10) unsigned | Start position in chrom |
| chromEnd | 260 | int(10) unsigned | End position in chrom |
| name | rs72477211 | varchar(15) | dbSNP Reference SNP identifier |
| score | 0 | smallint(5) unsigned | Not used |
| strand | + | enum('+', '-') | Which DNA strand contains the observed alleles |
| refNCBI | C | blob | Reference genomic sequence from dbSNP |
| refUCSC | C | blob | Reference genomic sequence from UCSC lookup of chrom,chromStart,chromEnd |
| observed | A/G | varchar(255) | The sequences of the observed alleles from rs-fasta files |
| molType | genomic | enum('unknown', 'genomic', 'cDNA') | Sample type from exemplar submitted sequence (ss) |
| class | single | enum('unknown', 'single', 'in-del', 'het', 'microsatellite', 'named', 'mixed', 'mnp', 'insertion', 'deletion') | Class of variant (single, in-del, named, mixed, etc.) |
| valid | unknown | set('unknown', 'by-cluster', 'by-frequency', 'by-submitter', 'by-2hit-2allele', 'by-hapmap', 'by-1000genomes') | Validation status of the SNP |
| avHet | 0 | float | Average heterozygosity from all observations |
| avHetSE | 0 | float | Standard Error for the average heterozygosity |
| func | unknown | set('unknown', 'coding-synon', 'intron', 'near-gene-3', 'near-gene-5', 'nonsense', 'missense', 'frameshift', 'untranslated-3', 'untranslated-5') | Functional category of the SNP (coding-synon, coding-nonsynon, intron, etc.) |
| locType | exact | enum('range', 'exact', 'between', 'rangeInsertion', 'rangeSubstitution', 'rangeDeletion') | Type of mapping inferred from size on reference; may not agree with class |
| weight | 3 | int(10) unsigned | The quality of the alignment: 1 = unique mapping, 2 = non-unique, 3 = many matches |
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