tableName	shortLabel	type	longLabel	visibility	priority	colorR	colorG	colorB	altColorR	altColorG	altColorB	useScore	private	restrictCount	restrictList	url	html	grp	canPack	settings
spikeMuts	Spike Mutations	bigBed 9 +	Spike protein mutations from community annotation (Jan 2021)	0	100	0	0	0	127	127	127	0	0	0			<h2>Description</h2> \n<p>\nThe SARS-CoV-2 spike protein, which binds the virus to host cells, is a key target of vaccine development to\ncombat COVID-19, and mutations in this protein have potential to change infectivity and response to disease treatments\nas well as vaccine efficacy.\nAs of January 2021 more than a dozen mutations in this protein have been detected via sequencing worldwide, and\none particular mutation, <em>N501</em>, has been designated a 'Variant of Concern', as epidemiological markers\nsuggest viruses carrying this mutation are significantly more transmissible.</p>\n<p>\nThis track presents amino acid mutations identified in the SARS-CoV2 Spike protein, based on the\n<a target="_blank" \nhref="https://github.com/hodcroftlab/covariants#covariants-sars-cov-2-mutations-and-variants-of-interest">\nCoVariants: SARS-CoV-2 Mutations and Variants of Interest</a>\ncommunity annotation at \n<a target="_blank" href="https://covariants.org">CoVariants.org</a>,\nsupplemented by the\n<a target="_blank" href="https://en.wikipedia.org/wiki/Variants_of_SARS-CoV-2">\nVariants of SARS-CoV-2</a> Wikipedia page.</p>\n\n<p>\nMutations in this track: H69-, D80Y, S98F, A222V, N439K, Y453F, S477N, E484, N501, D614G, A626S, P681H, A701B, V1122</p>\n<p>\nInformation provided for each mutation, if available, includes:\n<ul>\n<li>Date first sequenced</li>\n<li>Notes of clinical significance</li>\n<li>Notes regarding geographic incidence</li>\n<li>Link to charts and tables presenting geographic distribution</li>\n<li>Link to Nextstrain build</li>\n<li>Links to relevant publications</li>\n</ul>\n</p>\n\n<h2>Display Conventions</h2>\n<p>\nThe track items are colored based on the date when the mutation was first identified:\n\n<table cellpadding="2">\n<tr><td>Red</td><td style='background-color:#FF0000; padding-left: 20px;'></td><td>Most recent (Fall/Winter 2020-2021)</td></tr>\n<tr><td>Purple</td><td style='background-color:#800080; padding-left: 20px;'></td><td>Summer 2020</td></tr>\n<tr><td>Blue</td><td style='background-color:#0000FF; padding-left: 20px;'></td><td>Oldest (Winter/Spring 2020)</td></tr>\n</table>\n<p>\nThe mutation name, e.g. N501 as well as alternative identifiers (e.g. N501Y, 501Y) can be typed in to the browser position box to navigate the browser to the mutation position and highlight the mutation in the browser window.</p>\n\n<h2>Credits</h2>\n<p>\nThanks to <a target="_blank" href="https://neherlab.org/emma-hodcroft.html">Emma B. Hodcroft</a>, Institute of Social and Preventive Medicine, University of Bern, Switzerland\nfor leading and maintaining the community annotation resource on which this track is largely based.<p>\n\n<h2>References</h2>\n<p>\n<a target="_blank" href="https://github.com/hodcroftlab/covariants#covariants-sars-cov-2-mutations-and-variants-of-interest">CoVariants: SARS-CoV-2 Mutations and Variants of Interest</a>\nEmma B. Hodcroft, Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland\n</p>\n<p>\n<a target="_blank" href="https://en.wikipedia.org/wiki/Variants_of_SARS-CoV-2">Variants of SARS-CoV-2</a>, Wikipedia\n</p>\n\n\n\n<!-- Redmine Track #26782 -->\n	varRep	1	bedNameLabel Mutation\nbigDataUrl /gbdb/wuhCor1/spikeMuts/spikeMuts.bb\ngroup varRep\nitemRgb on\nlongLabel Spike protein mutations from community annotation (Jan 2021)\nmouseOver $name $clinicalNotes\nnoScoreFilter on\nsearchIndex name\nsearchTrix /gbdb/wuhCor1/spikeMuts/spikeMutsSearch.ix\nshortLabel Spike Mutations\ntrack spikeMuts\ntype bigBed 9 +\nurls geographyChartsUrl="$$" nextstrainBuildUrl="$$"\n