Nextstrain Variants Track Settings
 
Nextstrain/GISAID Sample Variants from nextstrain.org/ncov   (All Variation and Repeats tracks)

Display mode:       Reset to defaults

Haplotype sorting display

When this display mode is enabled and genotypes are phased or homozygous, each genotype is split into two independent haplotypes. These local haplotypes are clustered by similarity around a central variant. Haplotypes are reordered for display using the clustering tree, which is drawn in the left label area. Local haplotype blocks can often be identified using this display.

Enable Haplotype sorting display
Haplotype sorting order:
using middle variant in viewing window as anchor.
To anchor the sorting to a particular variant, click on the variant in the genome browser, and then click on the 'Use this variant' button on the next page.
using the order in which samples appear in the underlying VCF file
using the tree specified in file associated with track
Haplotype coloring scheme:
reference alleles invisible, alternate alleles in black
reference alleles in blue, alternate alleles in red
first base of allele (A = red, C = blue, G = green, T = magenta)
Haplotype clustering tree leaf shape:
draw leaf clusters as <
draw leaf clusters as [
Haplotype sorting display height:

Filters

Exclude variants with Quality/confidence score (QUAL) score less than
Minimum minor allele frequency (if INFO column includes AF or AC+AN):

VCF configuration help

All subtracks:
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 All Variants  Variants in All Nextstrain/GISAID Samples from nextstrain.org/ncov   Schema 
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 A1a Variants  Variants in Clade A1a Nextstrain/GISAID Samples from nextstrain.org/ncov   Schema 
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 A2 Variants  Variants in Clade A2 Nextstrain/GISAID Samples from nextstrain.org/ncov   Schema 
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 A2a Variants  Variants in Clade A2a Nextstrain/GISAID Samples from nextstrain.org/ncov   Schema 
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 A3 Variants  Variants in Clade A3 Nextstrain/GISAID Samples from nextstrain.org/ncov   Schema 
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 A6 Variants  Variants in Clade A6 Nextstrain/GISAID Samples from nextstrain.org/ncov   Schema 
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 A7 Variants  Variants in Clade A7 Nextstrain/GISAID Samples from nextstrain.org/ncov   Schema 
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 B Variants  Variants in Clade B Nextstrain/GISAID Samples from nextstrain.org/ncov   Schema 
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 B1 Variants  Variants in Clade B1 Nextstrain/GISAID Samples from nextstrain.org/ncov   Schema 
pack
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 B2 Variants  Variants in Clade B2 Nextstrain/GISAID Samples from nextstrain.org/ncov   Schema 
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 B4 Variants  Variants in Clade B4 Nextstrain/GISAID Samples from nextstrain.org/ncov   Schema 
    

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 data into this track to display the variants of each sample that Nextstrain has obtained from GISAID.

Click on a variant to see more details including protein change (if applicable; protein changes use gene names in the Nextstrain Genes track) and the genotype for each GISAID sample.

Display Conventions

In "dense" mode, a vertical line is drawn at the position of each variant. In "pack" mode, the display shows a plot of all samples' variants, with samples ordered using Nextstrain's phylogenetic tree in order to highlight patterns of linkage.

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 variant is a vertical bar with white (invisible) representing the reference allele and black representing the non-reference allele(s). Tick marks are drawn at the top and bottom of each variant's vertical bar to make the bar more visible when most alleles are reference alleles.

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 thta UCSC downloads and extracts annotations for display.

Data Access

You can download the bigBed file underlying this track (nextstrainSamples*.vcf.gz) 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

This work is made possible by the open sharing of genetic data by research groups from all over the world. We gratefully acknowledge their contributions. Special 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.

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 nextstrain.org (see "DOWNLOAD DATA" link at bottom of page) - please contact the relevant authors where appropriate.

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

Sagulenko P, Puller V, Neher RA. TreeTime: Maximum-likelihood phylodynamic analysis. Virus Evol. 2018 Jan;4(1):vex042. PMID: 29340210; PMC: PMC5758920