CoV-GLUE-Viz: Lineages - Codon level mutations

CoV-GLUE is enabled by data from GISAID: https://www.gisaid.org

This tool is currently in the development phase (the Recent function is currently switched off).

Visualisation of codon level mutations: default display is All lineages combined (change via Select lineage), Spike protein (change via Select ORF, use 'SARS-CoV-2 Genome' to view the whole genome), non-synonymous mutations (change via Mutation Type), minimum mutation count of 5 (change via Min Count), logarithmic display on y-axis (change via Y-Axis Scale). Specific genomic regions (such as RBD or Furin cleavage site) can be highlighted (via Highlight Region), or genomic regions can be selected by entering their co-ordinates into Genome Start and Genome End. Deletions are represented as unlinked individual codon level deletions currently (e.g. the Spike 6 base deletion of codons 69-70 is presented via two separate and unlinked codon level deletions at 69 and 70). Currently all GISAID human SARS-CoV-2 sequences > 10,000 bases (minus duplicates) are included.

Filter the mutations by type (All, nonsyn, syn, del), time (ALL vs Recent), minimum count (>=), ORF, and/or enter genome coordinates.

Hover the mouse cursor over a point to view detailed information

Data table

The table displays information on all the codon level mutations currently displayed in the graph (after any filtering has been applied such as ORF, MinCount etc), ordered by descending frequency. The table can re-ordered using other by columns by clicking on the header - use Codon1 to sort by genome position.

All fields are simultaneously searched by entring criteria into searchbox e.g. search for specific mutations e.g. "E484K" (simply typing E484 will return all mutations at E484) or a genome position e.g. "28880". Stop codons are represented with an X in amino acids.

IMPORTANT: Searches are only performed on the current filtered dataset that is displayed in the graph - with any Time, ORF, MinCount, Genome Start/End filters already applied.