Rice Diversity: GWAS Viewer

© 2013-2015 Rice Diversity Project | Developed by Darcy Branchini, Genevieve DeClerck, Francisco Agosto-Perez using Highcharts JS by Highsoft Solutions AS.

To begin, add a chart by selecting an experiment, trait and germplasm (sub-population) using the side-bar on the left.

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  • The GWAS Viewer is optimized to work in Google Chrome or Firefox.
  • Add/remove charts - To add a chart, select an experiment first. A trait, sub-population, and germplasm can be selected based on the experiment. Once you've selected the appropriate parameters, then click "Add Plot." To remove a chart, simply select the chart you'd like to remove, then click "Remove Plot".
  • Zoom in/out - To zoom in, select area by clicking and dragging the mouse over an area on a plot or select a chromosome under zoom/print section. To zoom out, click "Reset Zoom". Note that a synchronized zoom (across all charts on the screen) is available with limitation - if using the synchronized zoom, you can only add up to 6 plots at one time. Otherwise, there is no limit to the number of charts. This feature can be toggled on/off by checking the box labeled "Synchronized Zoom".
  • The "ruler" is synchronized across all charts to see how a data point aligns in relation to a data point on another plot. It's activated by hovering or moving your mouse over any plot.
  • Add candidate genes by uploading a file - or - by entering a comma-separated list of LOC_IDs. The file must be tab-delimited with columns identical to the template provided.
  • If you are zoomed in to a very small area, genome annotation data will automatically appear.
  • Additional information is available by clicking on a data point - trait p-value (expressed as -log10(P)) or gene, plus a click through to the genome browser that takes you to the location of the SNP in the MSU7 genome annotation, zoomed out with 5000 bp on either side of the SNP so that you can view its genomic context.
  • Print all charts on display as a PDF by clicking "Print All" - or - print/export one chart as a JPEG, PNG, SVG (vector image) or PDF by clicking the "bars" button (top-right of each plot).

Synchronized Zoom

Synchronized Zoom only works with 6 or less charts and there are more than 6 charts on the page. Please remove the extra charts and try again.