Description

Nextstrain.org displays data about mutations that occur in the current 2019/2020 outbreak. Nextstrain has a powerful user interface for viewing the evolutionary tree that it infers from the patterns of mutations in sequences worldwide, but does not offer a detailed plot of mutations along the genome, so we have processed their genome annotations into genome browser tracks.

Use this track in conjunction with the track Nextstrain Mutations (protein-coding mutations use gene names from this track).

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 (nextstrainGene) 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.

Credits

Thanks to nextstrain.org for sharing its analysis of genomes collected by GISAID, and to researchers worldwide for sharing their SARS-CoV-2 genome sequences.

References

Hadfield J, Megill C, Bell SM, Huddleston J, Potter B, Callender C, Sagulenko P, Bedford T, Neher RA. Nextstrain: real-time tracking of pathogen evolution. Bioinformatics. 2018 Dec 1;34(23):4121-4123. PMID: 29790939; PMC: PMC6247931