How to use SorGSD database?

1.Browse

1.1 SNP tables

SorGSD database summarizes SNP number by chromosome of 48 sorghum lines both on individual and nonredundant resolutions. Click the number, you will see the whole SNP list at a given chromosome.

 

Chrom: the chromosome of sorghum.
#Reference SNP: refers to the unique SNP number in this database.
From the third to the tenth columns refers to the Individual SNP lists of all our samples.

 

1.1.1)Reference SNP list

The "#Reference SNP" would lead users to a reference SNP table which shows general SNP information of all samples. In this page, users will see the colored genotype of all samples at a given position which identified by sample¡¯s name. If this position hits in a gene, the gene name and the located region will be shown. Click "RSNP ID" will go to the detail information page of this position, and click "GBrowse" link will open a GBrowse view panel.

1.1.2)The reference SNP detail information

The detail information of reference SNP is used to exhibit the detail SNP information of a given SNP in SorGSD. The page mainly includes three parts which are "general information", "gene information" and "SNPs of other individuals in this position". "General Information" lists gene ID, version number, chromosome and position and SNP class of a given SNP. In "gene information" part, the gene model shows the gene list in which SNP located. The transcript and the protein part show the transcript and protein related to the reference SNP. Click "Gene ID" will go to the detail information of gene in SorGSD, and click "transcript" or "protein" accession will go the Ensembl database. In "SNPs of other individuals part",the SNP of all samples at this position will be listed.

1.1.3)Individual SNP list

The "#sample_id" list represents individual SNP list which shows general information about SNPs of the sample. Click "SNP ID" will go to the detail information page of this SNP.

1.1.4)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 6 parts of information.

The "General Information" part will show SNP ID, individual, and SNP loaded time of a SNP.

The "Allele Information" part will show the individual¡¯s genotype information, 30bp of 3 flank and 5 flank sequence.

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.

The "Fasta information" will show 50 bps sequence of upstream and downstream of this SNP.

1.1.5)Gene detail information

The gene detail information shows SNPs located in the corresponding gene.

1.2 SNPs in Gene

"SNPs in Gene" 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.

1.2.1)SNP hit in gene

The "#SNP Hit in Gene" list is used to view SNP information located in different gene region, that is 3¡¯ UTR, 5¡¯ UTR, intron, CDS,splice_site,NON_CDS. Click "SNP ID" will go to the detail information page of this SNP.

1.2.2)Coding SNP information

The "#SNP coding", "#Coding Synonymous", "#Coding NonSynonymous" lists are used to view SNP located in gene CDS region, annotated as synonymous and nonsynonymous, the residue change column gives residue change which derived by this SNP.

1.3 Browse on Chromosome

SorGSD database use GBrowse to visualize several data types, including the indel, 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 "GBrowse" page.

2 Search

SorGSD 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, user 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

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 also can download the search result. To download the result, first choose the SNP, and then click the "download" button. Two download models are supported. The "Text" model will list the selected items in a web page, and the "File" model will save the selected items in a file.