Note: Now updated daily
data about variants that have occurred in the current 2019/2020 outbreak of SARS-CoV-2.
Nextstrain has a powerful user interface for viewing the time stamped phylogenetic tree
that it infers from the patterns of variants in sequences worldwide.
Nextstrain maintains an ongoing pipeline that continuously obtains SARS-CoV-2 genome sequences
and metadata from GISAID,
aligns them against the reference genome
collects single-nucleotide variants (SNVs), and infers a phylogenetic tree.
This track shows the alternate allele frequency of each SNV reported by Nextstrain as a
bar graph with the height indicating the frequency.
(The Nextstrain Variants track offers a more detailed display of the variants,
breaking up the vertical bars according to the order of virus genome samples in the
Nextstrain downloads SARS-CoV-2 genomes from
as they are submitted by labs worldwide.
The sequences are processed by an
and annotations are written to a data file
that UCSC downloads and extracts annotations for display.
You can download the bigBed file underlying this track (nextstrainSamples*.bigWig) from our
Download Server. The data can be explored interactively with the
or the Data Integrator. The data can be
accessed from scripts through our API.
Command-line extraction can be accomplished using an example like the following command:
bigWigToWig -udcDir=. -chrom=NC_045512v2 -start=100 end=7875 http://hgdownload.soe.ucsc.edu/gbdb/wuhCor1/nextstrain/nextstrainSamples.bigWig myOutput.wig
Please refer to our mailing list archives for questions, or our
Data Access FAQ for more
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 Unpublished data is included with permission of the data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
respective authors (available via the
Nextstrain metadata.tsv file)
if you intend to carry out further research using their data.
Derived data, such as phylogenies, can be downloaded from
(see "DOWNLOAD DATA" link at bottom of page) -
please contact the relevant authors where appropriate.
sharing its analysis of genomes collected by
and to researchers worldwide for sharing their SARS-CoV-2 genome sequences.
Hadfield J, Megill C, Bell SM, Huddleston J, Potter B, Callender C, Sagulenko P, Bedford T, Neher
Nextstrain: real-time tracking of pathogen evolution.
Bioinformatics. 2018 Dec 1;34(23):4121-4123.
PMID: 29790939; PMC: PMC6247931
Sagulenko P, Puller V, Neher RA.
TreeTime: Maximum-likelihood phylodynamic analysis.
Virus Evol. 2018 Jan;4(1):vex042.
PMID: 29340210; PMC: PMC5758920