Schema for Nextstrain Genes - Genes annotated by nextstrain.org/ncov
  Database: wuhCor1    Primary Table: nextstrainGene Data last updated: 2020-11-23
Big Bed File: /gbdb/wuhCor1/nextstrain/nextstrainGene.bb
Item Count: 14
Format description: Browser Extensible Data
fieldexampledescription
chromNC_045512v2Reference sequence chromosome or scaffold
chromStart13467Start position in chromosome
chromEnd21555End position in chromosome
nameORF1bName of item.

Sample Rows
 
chromchromStartchromEndname
NC_045512v21346721555ORF1b
NC_045512v22156225384S
NC_045512v22539226220ORF3a
NC_045512v22624426472E
NC_045512v22652227191M
NC_045512v22720127387ORF6
NC_045512v22739327759ORF7a
NC_045512v22775527887ORF7b
NC_045512v22789328259ORF8
NC_045512v22827329533N

Nextstrain Genes (nextstrainGene) Track Description
 

Description

Nextstrain.org displays data about variants 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 variants in sequences worldwide, but does not offer a detailed plot of variants along the genome, so we have processed their genome annotations into genome browser tracks.

Use this track in conjunction with the track Nextstrain Variants (protein-coding variants 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