How to find SNP information from SorGSD

We try to provide an easy to use web interface to browse, search and compare SNPs in SorGSD.

If you are not familiar with these functionalities, please go through the following examples step by step,

to get some feelings how to use this database.

Example 1: How to find non-synonymous SNPs in chromosome 1 of sweet sorghum E-Tian?

E-Tian is a sweet sorghum introduced to China from Russia in the early 1970s. We may easily find all non-synonymous SNPs and their coding amino acid residues to further study if they are related to potential functional changes.

  • Move over your mouse to the Browse button in the top of the main page to show a pull-down menu.
  • Move down your mouse to the non-synonymous SNPs, and click this sub-menu to show a table of Distribution of Nonsynonymous SNPs on each chromosome.
  • Move down you mouse to the last line of the Improved varieties section to find the E-tian accession.
  • Move your mouse to the first column (chr1) and click the number 1995 to bring up a table of Coding NonSynonymous SNP Information in E-Tian on chrom 1 You will find the first SNP snp_sb047064858514 at position chr1:1010740.
    • The reference genome BTx623 has a T while E-Tian has a C at this position.
    • The transcript of this allele change from Atc to Gtc
    • The amino acid residue encoded by this codon changes from Isoleucine to Valine.
  • Click the SorGSD accession snp_sb047064858514, you will see the details of this SNP including upstream and downstream sequences, codon and SNPs in other accessions (Ji_2371 and SS79) at this position.
  • Click the Gene ID Sobic.001G011700 in the Gene information table to show the page GenGene Detail For Sobic.001G011700 for this special gene.
  • Click the Gene ID Sobic.001G011700 to display the annotations for this gene in Phytozome.

Example 2: How to find all stop codon lost variants in grain sorghum Ji_2731?

Stop codons (TAG, TAA, TGA) are terminators of protein translation. If one nucleotide in the triplet changes to another one, then this codon may lost the function as a terminator, and encode an abnormal protein. We may find this type of SNP in Ji_2731 for experimental validation.

  • Click the Search button in the top of the main page to bring up the Search page.
  • Click the Chromosome selection option "Chr1" and change to All, to select all chromosomes.
  • In the Individual window, select Ji_2731.
  • In the SNP type window, tick off the Missense Variant check box, and tick on the Stop Lost check box.
  • Click the Search button at the bottom of the page to show search results.
  • You may find 6 SNPs as the search results. The first 4 with a light green background were identified by both pipelines.
  • Click the SNP ID snp_sb045063965161 to show you the detail information for this SNP in chromosome 1, position 13355486.
  • You will find that the A to G substitution causes the loss of the TAA stop codon.
  • You may also find that dozens of other accessions have the same A to G substitution at this position.

Example 3: How to compare SNPs among three sorghum lines?

SorGSD can be used to find and compare SNPs among several sorghum lines. You may find all missense (non-synonymous) SNPs in the first 50kb of chromosome 1, in two sweet sorghum Keller and E-Tian, and a grain sorghum Ji_2731.

  • Click the Compare button to bring up the Comparison page.
  • Click the Chromosome check radio, type in 1 in the start and 500000 in the end input box.
  • Select Keller in the sorghum accession selection window, then click the double arrow to move this accession into the Selected Individuals window.
  • Select E-Tian in the sorghum accession selection window, then click the double arrow to move this accession into the Selected Individuals window.
  • Select Ji_2731 in the sorghum accession selection window, then click the double arrow to move this accession into the Selected Individuals window.
  • Check the SNP Type window to see if you selected the Missense Variant.
  • Click the Compare button, you will see the search results. A table lists the 10 SNPs found in this region. Comparing with the reference genome BT-623, you may find that Ji_2731 has 9, E-Tian has 2 and Keller has 1 missense SNPs in this region.
  • Click the UniSNP ID to show the detail information about this SNP.

Example 4: How to find SNPs in Ji_2731 for the gene Sobic.006G057900?

The gene locus Sobic.006G057900 is located in chromosome 6. It was reported that this gene controls sorghum flowing time (Murphy et al.) recently. We may find if there is any SNPs in the Ji_2371 sorghum line.

  • Click the Search button.
  • Select Gene Name and type in your gene Sobic.006G057900.
  • Select an Accession Ji_2731.
  • Select All SNP type.
  • Select All Genotype.
  • Click the Search button. You will get the search result with a table of 13 SNPs.
  • Click on the first SNP ID snp_sb045064281254, you will see the detail annotation for this SNP.