Schema for snp142CodingDbSnp
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Database: mm10 Primary Table: snp142CodingDbSnp Row Count: 1,951,211   Data last updated: 2015-11-21
Format description: Annotations of the effects of SNPs on translated protein sequence. On download server: MariaDB table dump directory
field | example | SQL type | description |
bin | 609 | smallint(6) | Indexing field to speed chromosome range queries. |
chrom | chr1 | varchar(255) | Reference sequence chromosome or scaffold |
chromStart | 3216135 | int(10) unsigned | Start position in chromosome |
chromEnd | 3216136 | int(10) unsigned | End position in chromosome |
name | rs222134274 | varchar(255) | Reference SNP identifier |
transcript | NM_001011874 | varchar(255) | Accession of the transcript modified by SNP |
frame | 3 | enum('1', '2', '3', 'n/a') | Frame of transcript's codon modified by SNP |
alleleCount | 2 | int(11) | Number of annotated alleles for SNP |
funcCodes | 8,3, | longblob | dbSNP function codes (e.g. 42=missense) |
alleles | T,C, | longblob | Observed nucleotide alleles corresponding to funcCodes |
codons | GAT,GAC, | longblob | Codons corresponding to funcCodes |
peptides | D,D, | longblob | Amino acid sequence corresponding to funcCodes |
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Connected Tables and Joining Fields
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mm10.snp142.name (via snp142CodingDbSnp.name)
mm10.snp142Common.name (via snp142CodingDbSnp.name)
mm10.snp142Mult.name (via snp142CodingDbSnp.name)
mm10.snp142Seq.acc (via snp142CodingDbSnp.name)
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Sample Rows
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bin | chrom | chromStart | chromEnd | name | transcript | frame | alleleCount | funcCodes | alleles | codons | peptides |
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609 | chr1 | 3216135 | 3216136 | rs222134274 | NM_001011874 | 3 | 2 | 8,3, | T,C, | GAT,GAC, | D,D, |
609 | chr1 | 3216135 | 3216136 | rs222134274 | XM_006495550 | 3 | 2 | 8,3, | T,C, | GAT,GAC, | D,D, |
609 | chr1 | 3216381 | 3216382 | rs243921731 | NM_001011874 | 3 | 2 | 8,3, | A,T, | CCA,CCT, | P,P, |
609 | chr1 | 3216381 | 3216382 | rs243921731 | XM_006495550 | 3 | 2 | 8,3, | A,T, | CCA,CCT, | P,P, |
609 | chr1 | 3216423 | 3216424 | rs264606683 | NM_001011874 | 3 | 2 | 8,3, | G,C, | GGG,GGC, | G,G, |
609 | chr1 | 3216423 | 3216424 | rs264606683 | XM_006495550 | 3 | 2 | 8,3, | G,C, | GGG,GGC, | G,G, |
609 | chr1 | 3216435 | 3216436 | rs51278881 | NM_001011874 | 3 | 2 | 8,3, | T,C, | TTT,TTC, | F,F, |
609 | chr1 | 3216435 | 3216436 | rs51278881 | XM_006495550 | 3 | 2 | 8,3, | T,C, | TTT,TTC, | F,F, |
609 | chr1 | 3216741 | 3216742 | rs31156237 | NM_001011874 | 3 | 2 | 8,3, | C,A, | ATC,ATA, | I,I, |
609 | chr1 | 3216741 | 3216742 | rs31156237 | XM_006495550 | 3 | 2 | 8,3, | C,A, | ATC,ATA, | I,I, |
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Note: all start coordinates in our database are 0-based, not
1-based. See explanation
here.
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