How can I see the reads supporting a variant?

In the Variant Table, there are two ways of viewing the reads that support a variant. After you have selected a specific variant, you can either click on the “Read Alignments” icon as shown below:

or click on the corresponding number of the Coverage column:


You will be directed to a JBrowse (  alignment viewer window, where you can have a graphical representation of the bam files containing the aligned reads (read more). 


Each of the "Reference sequence", "Coding sequences", "SNPs/Coverage" and "Sample name" tracks have more options regarding the display of information and you can change them by right-clicking on each track title.