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Search for SNP in Cape Buffalo

The Cape Buffalo SNP that are accessible from this page are described in Novel SNP Discovery in African Buffalo, Syncerus caffer, Using High-Throughput Sequencing. PLoS ONE 7(11): e48792. doi:10.1371/journal.pone.0048792

50bp short read SOLiD sequences from two pools of 4 and 5 Cape buffalo (Syncerus caffer) respectively were mapped to the cow genome sequence (UMD3). SNP were called using the GATK pipeline and only SNP that were called as "PASS" and that were represented by both reference and alternate alleles are presented here. SNP for which only alternate alleles were detected are excluded from the database since they may be fixed and therefore uninformative in Cape buffalo. DNA was provided by the Van Helden group at Stellenbosch University, Cape Town, SA. Short reads are available from the sequence read archive at NCBI (accession number SRA051668.1)

SNP loci are annotated with restriction enzymes that cut at the site with either the reference or the alternate allele. Sets of SNP that are cut by a specific enzyme can be selected to create a panel of SNP for low cost RFLP assays. All gene names (Gene Name, Ensembl Gene ID and Gene description) map to whole gene regions defined as from 1000bp upstream to 1000 downstream and including introns. Exon Ids map to coding sequences only.

If the number of SNP returned is less than 1,000 then you will be able to design primers against each of them

The data table is available as a gzipped tab delimited flatfile (4.2M). The complete set of all ~12million SNP (184M) is available as a vcf file. This includes all Low Quality SNP as well as PASS SNP as there was no difference in validation rate between these two classes.

Gene NameEnsembl Gene IDGene description
eg: ARBK2_BOVINENSBTAG00000000005Beta-adrenergic receptor
Exon ID
Use % sign as wildcard eg 'ENSBTAG%' will find all SNP within gene regions and 'ENSBTAE%' will find all SNP with Exons
Co-ordinates of region of interest in UMD3 Bovine Genome
Chromosome (integer)StartEnd
Eg; 180000000100000000
Only positions cut by this restriction enzyme
Only Loci with this consequnece
Minimum interval between adjacent SNP

SNP for
ConsequenceCount
Count 271,981

SNP were selected with:

Health Warning

All SNP are relative to Bos taurus UMD3.1 Hereford reference genome.Mapping to another genus will inevitably cause some errors. 83% of SNP loci amplified in our tests and both alleles were detected for 67% of loci.