Currently, variation data in iDog including genomic variants, ancient imputed SNPs, breed-specific SNPs, variants mapped to conseved region, and disease/traits associated variants.

For ancient imputed variants, iDog constructs a pipeline to process data.

1.1 Search results

The #Reference SNP will redirect users to a reference SNP table that shows the general SNP information of all samples. If one SNP locates in a gene, the gene id, consequence type and SNP effect will be displayed. Clicking the RSNP ID will redirect to the detail information page of this position, and clicking the JBrowse link will open the JBrowse view panel.

1.2 The reference SNP detail information

The reference SNP is non-redundant SNP collection by combining all the individuals in the whole genome scale, the detailed information is used to display the whole information of a given SNP site, which mainly contains general information, gene information, individual genotype and population analysis.

General Information will list the gene ID, version number, chromosome and position, and SNP class of a given SNP. A link in RefSNP of version 1 will also be given.

In gene information, the gene model table shows the gene list where SNP are located. The transcript and protein table will show the transcript and protein related to the reference SNP. Clicking on a Gene ID will redirect to the detail information of that gene in DoGSD, and clicking on the transcript or protein accession will redirect to the Ensembl database.

In individual genotype, the SNP of all samples at this position will be listed.

In population analysis, the genotype frequencies and allele frequencies will be displayed.

1.3 Browse on Chromosome

DoGSD database uses JBrowse to visualize several data types, including the SNP ,Indels, gene. Users would need to choose interested tracks in the Select Tracks menu, and a region of interest.