Tutorial: TB Diversity - how do I find Polymorphisms?

Overview
Searching for SNPs
Browsing SNPs
Explore SNPs by Gene

Overview

You can now search and compare 30+ sequenced strains selected to represent the phylogenetic diversity of TB. The Diversity Sequencing start page gives you an overview of the evolutionary relationships and geographic origins of the strains — in the main menu, select "Genomic Data" > "Diversity Sequencing":

From here you have a number of ways to explore polymorphisms:

Searching for SNPs

A. by Strain
Go to Search by Strain in the Diversity Sequencing menu - here you can select one or more strains to include (on the left) by checking off a group in the top list, then selecting individual strains below. Next, select one or more groups and strains to exclude shared mutations.

Click the "Compare Strains" button, and you will see a table of results:

The results are grouped in tabs according to their nature. For coding SNPs, each row shows the mutation's location in the genome, the gene that is affected, the nucleotide mutation, and (if applicable) the resulting amino acid mutation, and drug resistance. Click on the "View" link to see the SNP in an alignment with all other strains:

You can navigate through the alignment using the overview area at the top, where the current view is outlined in red, or use the scroll bars.

B. Search by Location

If you are interested in polymorphisms in all strains, but want to limit your search to a specific region of the TB genome, click on Search by Location in the Diversity Sequencing menu:



Besides entering the name of a gene you have the option to search genome-wide; in either case you can limit the range by entering start and stop coordinates, either in nucleotide or amino acid coordinates.

Browsing SNPs

The first view we offer is a page with a comparison of mutation counts.
The shaded fields show the total number of mutations in a strain compared to the reference H37Rv. All other cells in any row indicate the number of mutations not shared with another strain (column).

If you click on any cell, you will see a list of mutations:

Click on a mutation to ope the Polymorphism Feature Detail page:

When you click on one of the highlighted strain names, GenomeView will open and display the aligned reads for that particular strain and mutation:

(Java is required to launch this application; select "Open with Java Webstart", then click "Allow" to permit access to your computer.)

Explore SNPs by Gene

Each gene detail page displays polymorphisms in two ways:
1. The gene overview graph shows SNPs as green lines overlaid on the gene transcript. When hovering over a SNP, a tooltip lists the reference allele and the polymorphic strains, indicating the resulting amino acid mutation. Clicking on a SNP will bring you to the Polymorphism Feature Detail page

2. The diversity graph shows mutations color-coded by category, with the height of the bars indicating the number of polymorphic strains in each region. Clicking on a bar will open a list of SNPs in that portion of the gene.