View Variant Data in JBrowse2

• Start a new session
• Select Linear Genome view and launch.
• At Select the assembly (variant data must exist for this genome).
  • Ardu.gnm1. Then, the feature (Chromosome, Aradu.A01). Open.
  • A featureless viewer appears and tracks need to be selected.
• At viewer.
  • Open track selecter(☰).
  • In the “Available tracks panel” (right), choose ‘Arachis duranensis V14167 Annotations’
  • In the “Available tracks panel” (right) under diversity, choose “aradu1_araip1.gnm1.div.Otyama_Kulkarni_2020.main.vcf”.
• Go to your favorite genic region (example: aradu.V14167.gnm1.Aradu.A01:300,002..528,417)
  • In the “Available tracks panel” (right) under diversity, choose “aradu1_araip1.gnm1.div.Otyama_Kulkarni_2020.main.vcf”.
  • If needed zoom to a level where the features are available (may need to try a few zoom levels).
  • Now one can visualize if region of interest has features in the proximity from the variant viewer.