1.1 SNP tables
DoGSD database summarizes SNP number by chromosome of 127 samples (11 wolves and 116 dogs) and dbSNP(version 146) both on individual and nonredundant resolutions. Click the number, you will see the whole SNP list at a given chromosome.
1)Reference SNP list
The #Reference SNP would lead users to a reference SNP table which shows general SNP information of all samples. If this position hit in a gene, the gene id, consequence type and SNP effect will be shown. Click RSNP ID will go to the detail information page of this position, and click JBrowse link will open a JBrowse view panel.
In this page, users can use “Filter”, ”Edit Columns” and ”Choose Individual” function to do advance operations.
2) The reference SNP detail information
The detail information of reference SNP is used to exhibit the detail SNP information of a given SNP in DoGSD. The page mainly includes four parts that are general information, gene information, individual genotype and population analysis in this position.
General Information lists gene ID, version number, chromosome and position and SNP class of a given SNP. Furthermore, a link in RefSNP of version 1 will be given.
In gene information part, the gene model shows the gene list in which SNP located. The transcript and the protein part will show the transcript and protein related to the reference SNP. Click Gene ID will go to the detail information of gene in DoGSD, and click transcript or protein accession will go the Ensembl database.
In individual genotype part, the SNP of all samples at this position will be listed.
In population analysis part, the genotype frequencies and allele frequencies will be shown.
3) Individual SNP list
Click SNP ID will go to the detail information page of this SNP.
4) SNP detail information
The SNP detail information is used to view the SNP information of a specific individual at the given position. Users can see five parts of information.
The General Information part will show SNP ID, individual, SNP loaded time and NCBI rs id of a SNP.
The Allele Information part will show the individuals genotype information.
The Reference Map Information will show the position, derived and reference alleles.
The Gene Information will show the information about related gene, transcript and protein of a SNP.
The SNPs of other individuals in this position will show the genotype information in other individuals.
5) Gene detail information
The gene detail information shows SNPs located in the corresponding gene.
1.2 SNPs in Gene
SNP in Gene Statistics lists SNPs located in gene and coding regions. According to the protein sequence, we divided the SNP list into synonymous and non-synonymous ones. Click the number in the statistical column, you will see the whole SNP list.
1) All SNPs on Gene
The # All SNPs on Gene list is used to view SNP information located in different gene region. Click SNP ID will go to the detail information page of this SNP.
2) Coding SNP information
The #Coding Synonymous, #Coding NonSynonymous lists are used to view SNP annotated as synonymous and nonsynonymous, the residue change column gives residue change which derived by this SNP.
1.3 Browse on Chromosome
DoGSD database use JBrowse to visualize several data types, including the SNP, gene, transcript and the density information of SNP/300kb, allele frequency. At first, users need to choose the interested tracks in the Select Tracks page, and a region, then you can see what you choose in the JBrowse page.
DoGSD provides SNP search function, including search SNPs in single individual and comparison of SNPs in two or more individuals. Users can set several parameters to search through this database, including location in chromosome, SNP class (mainly SNP), SNP location in gene region and genotype. The search result page of single individual is a little different from compared individuals.
2.1 Single individual search
Use this search, user can view SNP data of each individual. To do this, uses must choose the "Show SNP information in individuals" in the search page. In single search result page, users can see the search condition set in the search page, and the total number of SNP is also returned. Below the search condition, uses can see the SNP list, the information including SNP ID, position, location (if SNP is located in gene, the gene name will be show) and flank sequence (upstream and downstream of 30bp at this position). Users also can click GBrowse link to see the SNP in GBrowse panel.And if you click the SNP ID link, a detail information will be showed.
2.2 Compared individuals search
Use this search,users can view SNP information of two or more individuals.To do this, users must choose "Show SNP information by individuals comparisons" in the search page.In compared individuals search result page, the SNP list shows SNP in selected individuals according to SNP location of referred individual. Therefore, the UniSNP ID referred to the reference SNP, and the order of individuals behind the Ref genotype column correspond to the order of selected individuals.
Users can download the SNP file and bam file and fastq file of specific samples in this database. The ftp site is ftp://download.big.ac.cn/pub/dogsd/