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Interactive deletion frequency graphs

This file contains interactive versions of all deletion graphs of Funk et al 2024. This file requires a working internet connection to load since jQuery and plotly.js code is not embedded to reduce file size.

The "Go To..." menu at the top left allows to quickly navigate to a specific graph via a sidebar table of content. Checkboxes next to each graph allow to show or hide the graph and the buttons at the top allow to hide or show all graphs at once. Clicking on the name of a hidden graph will set it to be shown and move the view over to the graph. Clicking on the name of a subcategory will cause all associated graphs to be shown and move the view to the first graph of that subcategory. To close the sidebar, simply click anywhere outside it.

To zoom into a particular part of the figure, click-and-drag your mouse across is. To reset the zoom, double-click in an empty area of the graph. To see the entire graph, double-click in an empty area while at the default zoom level. Zoom levels can also be controlled via the menu in the upper-right corner of the graph.

At the bottom of the graph, the cursor changes into a horizontal double arrow, clicking and dragging allows to move the displayed region left or right.

The graphs default to showing the HA cleavage site and extend on either side until coverage drops to less than 1% of the respective maximum for all replicates and samples of the graph. While there are some deletions with high apparent frequencies in the flanking regions, these frequencies are likely to be inflated due to the low coverage in these regions, since insertion frequency is calculated with regards to the actual coverage at the same position.

0 10 20 30 40 cRNA vRNA −50k 0 50k 100k deletions per 1000 consensus reads coverage A A A G A A A A A A A A replicate 2, size 4 nts 0.11/1000 consensus reads ccucaAAGAaaaaa: ambiguous ccuca----aaaaa 0.07‰ aagaaAAAAaagag: ambiguous aagaa----aagag 0.03‰ Deletion frequencies in RdRp-containing samples are plotted as positive Legend contains only deletion sizes observed for this template Click on a legend item to toggle display of corresponding data Double-click on a shown legend item to show only corresponding data, double-click on a hidden legend item to show all data Replicate 1 Replicate 2 Coverage RdRp-containing samples is plotted as positive Coverage background/input samples is plotted as negative Deletion frequencies in background samples are plotted as negative RNA sequence with substitutions compared to LPAIV highlighted Predicted RdRp-trapping RNA structure heatmap Deletion infobox appears when hovering over a bar Structure infobox appears when hovering over heatmap Legend on the right might be scrollable if too long Total frequency of deletions of this size at this position Stability of RNA structure (lower is more stable) {} () <> . G-C base pair A-U base pair G-U base pair unpaired nucleotide Strength of base pair RdRp footprint Reference Deleted sequence Deletion type Nucleotide in RdRp active site Frequency of this deletion Breakdown of all insertions of this size at this position, with one alignment per insertion deletion size 1 nts deletions 2 nts deletions 3 nts deletions 4 nts deletions 5 nts deletions 6 nts deletions 9 nts deletions 11 nts deletions 12 nts deletions coverage replicate 1 coverage replicate 2 cRNA position 1046 dG= -7.90 kcal mol -1 AUGUCCCUCAAAGAAAAAAAAGAGGACUAUUUGGGGCUAU ..{<{{{...[---AAAAAAAGAG-----]..}}}>}... Amino acid sequence Q R K

RNA structure predictions were made using ViennaRNA following the same method as the Python script available at https://github.com/dr-funk/trapped-RdRp/tree/v1.0/slidingfold, with an RdRp footprint of 20 nucleotides with the active site in position 5, and a window size of 10 nucleotides on each side of the RdRp.