Nextstrain.org displays
data about mutations 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 mutations 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
(NC_045512.2),
and infers a phylogenetic tree.
This track shows the alternate allele frequency of each mutation reported by Nextstrain as a
bar graph with the height indicating the frequency.
(The Nextstrain Mutations track offers a more detailed display of the mutations,
breaking up the vertical bars according to the order of virus genome samples in the
phylogenetic tree.)
Methods
Nextstrain downloads SARS-CoV-2 genomes from
GISAID
as they are submitted by labs worldwide.
The sequences are processed by an
automated pipeline
and annotations are written to a data file
that UCSC downloads and extracts annotations for display.
Data Access
You can download the bigBed file underlying this track (nextstrainSamples*.bigWig) from our
Download Server. The data can be explored interactively with the
Table Browser
or the Data Integrator. The data can be
accessed from scripts through our API.
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 Unpublished data is included with permission of the data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
nextstrain.org
(see "DOWNLOAD DATA" link at bottom of page) -
please contact the relevant authors where appropriate.
Credits
Thanks to
nextstrain.org for
sharing its analysis of genomes collected by
GISAID EpiCoV TM,
and to researchers worldwide for sharing their SARS-CoV-2 genome sequences.
US Server