omicron_ba2_mutations_full.yaml

variant:
  short: 'om2'
  nextstrain: '21L'
  pangolin: 'BA.2'
source:
- https://github.com/cov-lineages/pango-designation/issues/361
- https://github.com/hodcroftlab/covariants/blob/master/defining_mutations/21L.Omicron.tsv
mut:
  670: 'T>G' # ORF1a:S135R 
  2790: 'C>T' # ORF1a:T842I 
  4184: 'G>A' # ORF1a:G1307S 
  4321: 'C>T' #  
  9424: 'A>G' #  
  9344: 'C>T' # ORF1a:L3027F 
  9534: 'C>T' # ORF1a:T3090I 
  10198: 'C>T' #  
  10447: 'G>A' #  
  11288: '-----'  # see below:
  #actually, due to repeated 'T's flanking the region, can be any of these:
  #11284: '---------' # SGF3675del
  #11288: '---------' # SGF3675del
  12880: 'C>T' #  
  15714: 'C>T' #  
  17410: 'C>T' # ORF1b:R1315C 
  19955: 'C>T' # ORF1b:T2163I 
  20055: 'A>G' #  
  21618: 'C>T' # S:T19I 
  21633: '---------' # S:d24-27
  #21987: '---------' # VYY143del -- there is an outlier which has instead 21987:'G>A' # S:G142D ...
  21987: 'G>A' # S:G142D ...but that outlier seems more frequent outisde of S Africa 
  22200: 'T>G' # S:V213G 
  22674: 'C>T' # S:S371F 
  22688: 'A>G' # S:T376A 
  22775: 'G>A' # S:D405N 
  22786: 'A>C' # S:R408S - covariants and cov-spectrum
  #22786: 'A>T' # R408S - table in issue 361
  26060: 'C>T' # ORF3a:T223I 
  26858: 'C>T' #  
  27382: 'GAT>CTC' # ORF6:D61L 
  29510: 'A>C' # N:S413R
shared:
  241: 'C>T' #  
  3037: 'C>T' #  
  9866: 'C>T' # ORF1a:L3201L   Outside of S Africa, (C9866T - ORF1a:L3201F) is common, but within S Africa it is not (Not in CERI-KRISP-K032307)
  10029: 'C>T' # ORF1a:T3255I 
  10449: 'C>A' # ORF1a:P3395H 
  #13195: 'T>C' # syn nsp10
  14408: 'C>T' # ORF1b:P314L 
  18163: 'A>G' # ORF1b:I1566V 
  22578: 'G>A' # S:G339D 
  22679: 'T>C' # S:S373P 
  22686: 'C>T' # S:S375F 
  22813: 'G>T' # S:K417N 
  22882: 'T>G' # S:N440K 
  22992: 'G>A' # S:S477N 
  22995: 'C>A' # S:T478K 
  23013: 'A>C' # S:E484A 
  23040: 'A>G' # S:Q493R 
  23055: 'A>G' # S:Q498R 
  23063: 'A>T' # S:N501Y 
  23075: 'T>C' # S:Y505H 
  23403: 'A>G' # S:D614G 
  23525: 'C>T' # S:H655Y 
  23599: 'T>G' # S:N679K 
  23604: 'C>A' # S:P681H 
  23854: 'C>A' # S:N764K 
  23948: 'G>T' # S:D796Y 
  24424: 'A>T' # S:Q954H 
  24469: 'T>A' # S:N969K 
  25000: 'C>T' #  
  25584: 'C>T' #  
  26270: 'C>T' # E:T9I 
  26577: 'C>G' # M:Q19E 
  26709: 'G>A' # M:A63T 
  27259: 'A>C' #  
  27807: 'C>T' #  
  28271: 'A>T' #  
  28311: 'C>T' # N:P13L ORF9b:P10S
  28362: '---------' # N:d31-33 ORF9b:d27-29
  28881: 'GGG>AAC' # N:RG203KR