This track displays a phylogenetic tree relating public SARS-CoV-2 genome sequences
NCBI Virus / GenBank,
COG-UK and the
China National Center for Bioinformation,
contributed by laboratories around the world,
and mutations found in those sequences. By default, only very common mutations (alternate allele found
in at least 1% of samples) are displayed, but other subtracks may be made visible in order to see
more rare mutations.
The phylogenetic tree is inferred by the
For display in the narrow space to the left of the main genome browser image, nodes in the tree
are collapsed unless a mutation is associated with a node; i.e. the only branching points displayed
are those at which mutations occurred.
The tree is colored by
lineage (Rambaut et al.).
The coloring scheme is adapted from Figure 1 of
(Alm et al.) which presents a unified view of a simplified
phylogenetic tree, Pangolin lineages,
Nextstrain clades and
|color||Pangolin lineage(s)||Nextstrain clade||GISAID clade|
||B.n (n > 1)
||n/a (color not used when coloring by lineage; overlaps on tree with B.4 - B.7)
||n/a (overlaps on tree with 19A)
||n/a (color not used when coloring by lineage; overlaps on tree with B.2)
||n/a (overlaps on tree with 19A)
||B.1.5, B.1.6, B.1.8, other B.1.n that overlap GISAID clade G
||B.1.9, B.1.13, B.1.22, B.1.22, B.1.36, B.1.37
||B.1.3, B.1.12, B.1.26, other B.1.n that overlap GISAID clade GH
In "dense" mode, a vertical line is drawn at each position where there is a mutation.
In "squish" and "pack" modes, the display shows a plot of all
samples' mutations, with samples ordered using the phylogenetic tree in order to highlight
patterns of linkage. "Full" display mode shows each mutation on its own row,
ordered by position instead of lineage.
Each sample is placed in a horizontal row of pixels; when the number of
samples exceeds the number of vertical pixels for the track, multiple
samples fall in the same pixel row and pixels are averaged across samples.
Each mutation is a vertical bar at its position in the SARS-CoV-2 genome
with white (invisible) representing the reference allele;
the non-reference allele is shown in red if it changes the protein sequence of a gene,
green if it falls within a gene but does not change the protein,
and black if it does not fall within a gene.
Tick marks are drawn at the top and bottom of each mutation's vertical bar
to make the bar more visible when most alleles are reference alleles.
Only single-nucleotide substitutions are displayed, not insertions or deletions.
The phylogenetic tree showing inferred relationships between the samples is depicted
in the left column of the display.
Mousing over this will show the sample identifiers.
At the default track height, about 100 samples are averaged into each row of pixels.
The track height can be adjusted in the track controls, which can be reached by
clicking on the gray button to the left of the tree or by right-clicking on the image.
Rob Lanfear regularly runs the
on all complete, high-coverage sequences available from
The pipeline aligns all sequences to the same reference genome used by the Genome Browser
(Katoh et al.).
It masks sites identified as problematic by the
(De Maio et al.),
as well as sites that are N's or gaps in >50% of samples.
(Price et al.)
is used to infer the phylogenetic tree;
sequences on very long branches are removed using
(Mai et al.).
The tree is re-rooted to hCoV-19/Wuhan/WH04/2020|EPI_ISL_406801|2020-01-05.
For full details, see the
UCSC makes a reduced version of the tree that contains only samples from fully public
databases (GenBank, COG-UK direct release, CNCB)
that do not prohibit UCSC from offering sequence mutations for download (see Data Access).
UCSC also makes several adjustments to the phylogenetic tree for compact display:
- We shorten "2019" and "2020" in dates to "19"
- We change the root of the tree to the reference genome used by the Genome Browser
- Nodes that do not have an associated mutation are collapsed using
(Turakhia et al.).
Files are available from our
The VCF data can be explored interactively with the
or the Data Integrator,
and accessed from scripts through our API.
repository includes all releases of the full phylogenetic tree.
This work is made possible by the open sharing of genetic data by research
groups from all over the world.
We gratefully acknowledge the authors and the originating laboratories where the clinical
specimen or virus isolate was first obtained and the submitting laboratories, where sequence
data have been generated and submitted to public databases,
on which this research is based.
Special thanks to
for developing, running and sharing the
Data usage policy
The data presented here is intended to rapidly disseminate analysis of
important pathogens. Unpublished data is included with permission of the data
generators, and does not impact their right to publish. Please contact the
if you intend to carry out further research using their data.
Authors and/or institutions that provided the sequences are listed in
A global phylogeny of SARS-CoV-2 sequences from GISAID.
Zenodo DOI: 10.5281/zenodo.3958883. 2020.
Rambaut A, Holmes EC, O'Toole Á, Hill V, McCrone JT, Ruis C, du Plessis L, Pybus OG.
A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology.
Nat Microbiol. 2020 Nov;5(11):1403-1407.
Alm E, Broberg EK, Connor T, Hodcroft EB, Komissarov AB, Maurer-Stroh S, Melidou A, Neher RA,
O'Toole Á, Pereyaslov D et al.
Geographical and temporal distribution of SARS-CoV-2 clades in the WHO European Region, January to
Euro Surveill. 2020 Aug;25(32).
PMID: 32794443; PMC: PMC7427299
Katoh K, Standley DM.
MAFFT multiple sequence alignment software version 7: improvements in performance and usability.
Mol Biol Evol. 2013 Apr;30(4):772-80.
PMID: 23329690; PMC: PMC3603318
De Maio N, Walker C, Borges R, Weilguny L, Slodkowicz G, Goldman N.
Masking strategies for SARS-CoV-2 alignments.
virological.org. 2020 May 13.
De Maio N, Gozashti L, Turakhia Y, Walker C, Lanfear R, Corbett-Detig R, Goldman N.
Updated analysis with data from 12th June 2020.
virological.org. 2020 July 14.
Turakhia Y, Thornlow B, Hinrichs AS, De Maio N, Gozashti L, Lanfear R, Haussler D, and Corbett-Detig R.
Ultrafast Sample Placement on Existing Trees (UShER) Empowers Real-Time Phylogenetics for the SARS-CoV-2 Pandemic.
bioRxiv. 2020 September 28.
Price MN, Dehal PS, Arkin AP.
FastTree 2--approximately maximum-likelihood trees for large alignments.
PLoS One. 2010 Mar 10;5(3):e9490.
PMID: 20224823; PMC: PMC2835736
Mai U, Mirarab S.
TreeShrink: fast and accurate detection of outlier long branches in collections of phylogenetic
BMC Genomics. 2018 May 8;19(Suppl 5):272.
PMID: 29745847; PMC: PMC5998883