Request for Omicron (B.1.1.529) Lineage VCF

[m-crown]

Request for Omicron (B.1.1.529) Lineage VCF

This lineage is described at outbreak.info and Pango-Designation.

[m-crown]

Omicron (B.1.1.529)

Omicron (and BA.1 and BA.2) VCF files are primarily built from Andrew Rambaut's list of shared and exclusive mutations between B.1.1.529, BA.1 and BA.2

Most resources no longer list a specific Omicron mutation list, but instead focus on BA.1 and BA.2. Where resources provide support for the mutations listed in Pango-Designation issue 361 these are linked in the table.

NOTE: Pango-Designation issue 361 notes for 11288_11296del seen in Omicron, BA.1 (and BA.1.1) and BA.2 that:

The exact position of this deletion is ambiguous in nucelotide coordinates.

Omicron VCF contains the deletion as described in Pango-Designation issue 361

nt	product	AA	source
C3037T	NSP3	F106F	Pango-Designation
C10029T	NSP4	T492I	Pango-Designation
C10449A	NSP5	P132H	Pango-Designation
11288-11296del	NSP6	S106del, G107del, F108del	Pango-Designation
C14408T	NSP12	P323L	Pango-Designation
A18163G	NSP14	I42V	Pango-Designation
21987-21995del	Surface Glycoprotein	G142D, V143del, Y144del, Y145del	outbreak.info, Pango-Designation
G22578A	Surface Glycoprotein	G339D	outbreak.info, Pango-Designation
T22679C	Surface Glycoprotein	S373P	outbreak.info, Pango-Designation
C22686T	Surface Glycoprotein	S375F	outbreak.info, Pango-Designation
G22813T	Surface Glycoprotein	K417N	Pango-Designation
T22882G	Surface Glycoprotein	N440K	Pango-Designation
G22992A	Surface Glycoprotein	S477N	outbreak.info, Pango-Designation
C22995A	Surface Glycoprotein	T478K	outbreak.info, Pango-Designation
A23013C	Surface Glycoprotein	E484A	outbreak.info, Pango-Designation
A23040G	Surface Glycoprotein	Q493R	outbreak.info, Pango-Designation
A23055G	Surface Glycoprotein	Q498R	outbreak.info, Pango-Designation
A23063T	Surface Glycoprotein	N501Y	outbreak.info, Pango-Designation
T23075C	Surface Glycoprotein	Y505H	outbreak.info, Pango-Designation
A23403G	Surface Glycoprotein	D614G	outbreak.info, Pango-Designation
C23525T	Surface Glycoprotein	H655Y	outbreak.info, Pango-Designation
T23599G	Surface Glycoprotein	N679K	outbreak.info, Pango-Designation
C23604A	Surface Glycoprotein	P681H	outbreak.info, Pango-Designation
C23854A	Surface Glycoprotein	N764K	outbreak.info, Pango-Designation
G23948T	Surface Glycoprotein	D796Y	outbreak.info, Pango-Designation
A24424T	Surface Glycoprotein	Q954H	outbreak.info, Pango-Designation
T24469A	Surface Glycoprotein	N969K	outbreak.info, Pango-Designation
C25000T	Surface Glycoprotein	D1146D	Pango-Designation
C25584T	ORF3a	T64T	Pango-Designation
C26270T	E	T9I	outbreak.info, Pango-Designation
C26577G	M	Q19E	outbreak.info, Pango-Designation
G26709A	M	A63T	outbreak.info, Pango-Designation
A27259C	ORF6	R20R	Pango-Designation
C27807T	ORF7b	L18L	Pango-Designation
A28271T	Intergenic		Pango-Designation
C28311T	N	P13L	outbreak.info, Pango-Designation
28362_28370del	N	E31del, R32del, S33del	outbreak.info, Pango-Designation
G28881A, G28882A, G28883C	N	R203K, G204R	outbreak.info, Pango-Designation

[m-crown]

Omicron (B.1.1.529) VCF added in e689b2d, closing issue, VCF can be found here