The tool is equipped with several interactive features to enhance user experience and make data visualization seamless:

1. Zoom Option:

   • Use the mouse scroll button to zoom in and out of the synteny plot
   • Alternatively, click the zoom icon located at the upper-right corner of the image for precise control

2. Adjust Image with Arrows:

   • Utilize the arrows at the left corner of the page to reposition the image and adjust its alignment as needed

3. Scrolling Bar:

   • A scrolling bar is available below the synteny plot to view the complete image from end to end

4. Background Color Mode:

   • Switch between black and white background modes for optimal visualization
   • The option is accessible via the navigation bar or the upper-right corner of the page

5. Chord Map Settings:

   • For a customized view of the chord map, a settings option is provided just above the map

6. Navigation Bar: The movable navigation bar includes:
   • Go Back Button: Return to the previous step
   • Upload Option: Upload data files directly
   • Example Data: Load example datasets
   • Filter Button: Filter required synteny blocks
   • Hide Button: Toggle synteny block details
   • View Button: Access uploaded data
   • Background Color Option: Switch between black and white modes
   • Orientation Option: Adjust navigation bar position

Annotations and Chromosomal Breakpoint Visualization

To visualize chromosomal breakpoints in the reference genome, users can explore the example dataset labeled "Annotated Genome". This dataset includes additional information, such as annotations and chromosomal breakpoints, alongside synteny block data.

Key visualization features:

• Chromosomal breakpoints in the reference genome are shown as red arrows in the synteny plot
• Breakpoints are highlighted in the chord map as red lines on the reference genome chord
• These features enable precise identification of structural changes and their genomic locations

Color tagging Mutation types

CHITRA provides a color-coding to distinguish between different types of mutations and synteny relationships for the selected ribbons:

1. Color Tags Feature:

   • Located in the top navigation bar
   • Allows users to visually categorize and highlight different mutation types

2. Available Mutation Types:

   • SYN (Green): Syntenic regions
   • INV (Red): Inversions
   • TRANS (Blue): Translocations
   • INVTR (Purple): Inverted translocations
   • DUP (Yellow): Duplications

3. How to Use:

   • Click on the "Color Tags" button in the top toolbar
   • Select the mutation types you want to highlight
   • The corresponding regions in the synteny plot will be colored according to their mutation type
   • Multiple mutation types can be selected simultaneously for comparative analysis

4. Visual Integration:

   • Colors are consistently applied across both the synteny plot and chord map
   • Helps in quick identification and analysis of different genomic rearrangements
   • Enhances the understanding of complex genomic relationships