This powerful tool allows you to explore genetic variant distributions across different populations for a specific genomic region. Here’s how to use the various features:

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1. Dashboard Overview

At the top of the page, you’ll see the genomic coordinates you’re exploring.

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2. Control Panel

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Minimum Allele Frequency Slider

  • Adjust this slider to filter variants based on their allele frequency.
  • The current minimum allele frequency is displayed below the slider.

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Statistics Card

  • Shows the total number of variants that meet your current filtering criteria.

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Bin Settings

  • Choose between fixed bins (0-1, step 0.1) or computed bins for the histograms.
  • Fixed bins are uniform across all populations, while computed bins adjust to each population’s data distribution.

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3. Population Distribution Chart

This bar chart shows the number of variants present in each population above your chosen minimum allele frequency.

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4. Population-Specific Histograms

For each population, you’ll see a histogram showing the distribution of allele frequencies:

  • AFR (African/African American)
  • AMI (Amish)
  • AMR (Admixed American)
  • ASJ (Ashkenazi Jewish)
  • EAS (East Asian)
  • FIN (Finnish)
  • NFE (Non-Finnish European)
  • SAS (South Asian)

These histograms help you visualize how common or rare variants are within each population.

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5. Geographic Distribution Heatmap

At the bottom of the dashboard, you’ll find a heatmap representing the geographic distribution of variants:

  • Each row represents a variant.
  • Each column represents a population.
  • Blue cells indicate rare variants (allele frequency < 5%).
  • Dark blue cells indicate common variants (allele frequency ≥ 5%).

This heatmap allows you to quickly identify patterns in variant distribution across populations.

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Tips for Using the Dashboard

  1. Start by setting your desired minimum allele frequency using the slider.
  2. Observe how this affects the total number of variants in the Statistics card.
  3. Look at the Population Distribution chart to see which populations have the most variants above your threshold.
  4. Explore individual population histograms to understand the frequency distribution within each group.
  5. Use the Geographic Distribution Heatmap to identify patterns across all populations simultaneously.
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