Tutorial

How to use ChickenSD database?

1.Browse

1.1 SNP tables

ChickenSD database summarizes SNP number by chromosome of 865 samples 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 VarID will go to the detail information page of this position.
In this page, users can use “Filter” 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 ChickenSD. The page mainly includes four parts that are general information, gene information, individual genotype and population analysis in this position.
General Information lists Reference SNP ID, chromosome and position, RefSNP allele and NCBI rsid of this SNP.
In gene information part, the SNP effect analyzed in VEP will be shown. Click Gene ID will go to the detail information of gene in ChickenSD.
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

ChickenSD houses all the individuals’ SNP information.
Users can view SNP list by chrom, and they can also filter the individuals by population.

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, organism and individual name 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 Browse on Chromosome

ChickenSD uses GBrowse to visualize several data types, including the SNP, gene, transcript and the density information of SNP/300kb. At first, users need to choose the interested tracks from the Select Tracks page, and a region, then you can see what you choose in the GBrowse page.

2. Search

ChickenSD provides SNP search function, including search SNPs in single individual and comparison of SNPs in two or more individuals.

2.1 Single individual search

Users can set several parameters to search through this database, including location in chromosome, SNP location in gene region, individuals, consequence type, and associated gene information.

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). 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 shown.

2.2 Compared individuals search

Use this search, users can view SNP information of two or more individuals. To do this, users must choose reference individual together with selected individuals from "Individual Information" in the search page. Consequence Type and associated gene parameters are also enable to be used.

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.

3. Download

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/chickensd/