CGD has an instance of the JBrowse genome browser for viewing genome data.  A list of the genomes available in CGD can be accessed by clicking the JBrowse link in the Tools menu.  Please watch the JBrowse tutorial for more details about how to navigate and use JBrowse.

Figure 22.  JBrowse of C. clementina genome.

For the tracks of aligned reads (BAM files) in the C. clementina v1.0 genome, the table below describes what the read colors mean in JBrowse.

Aligned Read Color Meaning Color of Read
Forward Strand  
Reverse Strand  
Forward strand missing mate  
Reverse strand missing mate  
Forward strand not proper  
Reverse strand not proper  
Forward strand on different chromosome  
Reverse strand on different chromosome