Date Range
Use this slider to filter the data based on the sample date. This may include inferred dates for ancestral nodes in the tree, and thus the date range here can be wider than the sample collection range.
2019-12-13
2023-03-25
Color By
Change the metadata field which the visualisation is coloured by.
The phylogeny, map and frequencies panel (if available) will all be coloured in a consistent fashion.
The phylogeny, map and frequencies panel (if available) will all be coloured in a consistent fashion.
Country
Filter Data
Use this box to filter the displayed data based upon filtering criteria.
For instance, start typing a country's name to filter the data accordingly.
Data is filtered by forming a union of selected values within each category, and then taking the intersection between categories (if more than one category is selected).
Scroll to the bottom of the main page (under the data visualisation) to see an expanded display of filters and available values.
Filter options prefixed with "(M)" are filters specific to the Measurements panel. They will have no effect on the phylogeny tree or other panels.
Data is filtered by forming a union of selected values within each category, and then taking the intersection between categories (if more than one category is selected).
Scroll to the bottom of the main page (under the data visualisation) to see an expanded display of filters and available values.
Filter options prefixed with "(M)" are filters specific to the Measurements panel. They will have no effect on the phylogeny tree or other panels.
Type filter query here...
Tree
This panel displays the evolutionary relationships among samples, illustrating their genetic relatedness and inferred ancestry.
The exact options available depend on the dataset and specific analysis performed.
If Branch Length is available, you can choose to display the tree branches in terms of (nucleotide) divergence or (inferred) time. It is often helpful to toggle on confidence intervals to gauge the uncertainty in the reconstruction of internal node dates.
The exact options available depend on the dataset and specific analysis performed.
If Branch Length is available, you can choose to display the tree branches in terms of (nucleotide) divergence or (inferred) time. It is often helpful to toggle on confidence intervals to gauge the uncertainty in the reconstruction of internal node dates.
clade
Sample Name
Select...
Map
This panel displays the geographical distribution of samples.
The geographic resolution chooses the metadata values which define where samples are placed on the map. This can be the same as the selected color-by but is often not!
The geographic resolution chooses the metadata values which define where samples are placed on the map. This can be the same as the selected color-by but is often not!
division
Entropy
This panel displays the observed diversity across the current genome or a selected CDS. All options are in the panel itself.
Frequency
This panel displays the prevalence of a characteristic over time, determined by the color-by.
Normalize frequencies controls whether the vertical axis represents the entire dataset or only the samples currently visible (e.g. due to filtering). This option is not available when data is limited to prevent numerical issues.
Normalize frequencies controls whether the vertical axis represents the entire dataset or only the samples currently visible (e.g. due to filtering). This option is not available when data is limited to prevent numerical issues.
Animation Options
Change various options relating to how the animation proceeds.
Display
Control whether to show the tree and the map side-by-side (grid) or expanded (full).
Language
English
Phylogenetic analysis of SARS-CoV-2 diversity in Japan
Built with kkosaki/ncov. Maintained by Center for Medical Genetics, Keio University School of Medicine. Data updated 2023-03-30. Enabled by data from 
.Showing 8530 of 8530 genomes sampled between Dec 2019 and Mar 2023.
Phylogeny
Geography
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