69af6ad3c35e8e4e3c11cb8290d95a394908f407 angie Sat Dec 23 19:16:12 2023 -0800 Add 23G, 23H, 23I. Update labels for older clades to match current nextstrain.org labels. diff --git src/hg/utils/otto/sarscov2phylo/nextstrain.clade-mutations.tsv src/hg/utils/otto/sarscov2phylo/nextstrain.clade-mutations.tsv index d4e3a99..ef4e4dd 100644 --- src/hg/utils/otto/sarscov2phylo/nextstrain.clade-mutations.tsv +++ src/hg/utils/otto/sarscov2phylo/nextstrain.clade-mutations.tsv @@ -1,37 +1,40 @@ 19A 19B > T28144C > C8782T 20A > C14408T > C241T > C3037T > A23403G 20B > C14408T > C241T > C3037T > A23403G > G28881A > G28882A,G28883C 20C > C14408T > C241T > C3037T > A23403G > G25563T > C1059T 21E (Theta) > C14408T > C241T > C3037T > A23403G > G28881A > G28882A,G28883C > G25088T > A4926G,C7564A,C8139T,G9203A,T9867C,C11308A,C12049T,C12053T,C17074T,C17339T,A22356G,G23012A,A23063T,T23341C,C23604A,T24187A,G24836A,C24863T,A27897C,C29724T 21A (Delta) > C14408T > C241T > C3037T > A23403G > G29742T > T22917G > G210T,C21618G,T27638C,G28881T > C23604G,G29402T > C25469T > C22995A,G24410N 21B (Kappa) > C14408T > C241T > C3037T > A23403G > G29742T > T22917G > G210T,T27638C,G28881T > C23604G,G29402T > C25469T > C3457T,C4965T,A11201G,G17523T,A20396G,T21895C,G22022A,G23012C,A24775T,C26681T,T26767G 20D > C14408T > C241T > C3037T > A23403G > G28881A > G28882A,G28883C > G10097A > C23731T > C4002T > C13536T 20F > C14408T > C241T > C3037T > A23403G > G28881A > G28882A,G28883C > A1163T > T7540C,G16647T > G22992A,G23401A > C18555T -20E (EU1) > C14408T > C241T > C3037T > A23403G > C6286T > C28932T > C22227T > G29645T +20E > C14408T > C241T > C3037T > A23403G > C6286T > C28932T > C22227T > G29645T 21D (Eta) > C14408T > C241T > C3037T > A23403G > C28887T > C24748T,T26767C,A28699G > A21717G,G23012A,G23593C,T24224C,C26305T,C28308G > C1498T,A1807G,G2659A,C6285T,T8593C,C18171T,G29543T > C14407T,A20724G > C9565T 21G (Lambda) > C14408T > C241T > C3037T > A23403G > G28881A > G28882A,G28883C > G10097A > C23731T > C4002T > C13536T > T7424G,C9857T,T9867C,C10029T,A28271T,C28311T > G21786T,C21789T > C7124T,T22917A,T23031C 20G > C14408T > C241T > C3037T > A23403G > G25563T > C1059T > C27964T > C10319T > G25907T > C28869T > C28472T > A18424G > C21304T -20H (Beta,V2) > C14408T > C241T > C3037T > A23403G > G25563T > C1059T > C23664T > G5230T,A21801C,C25904T,C26456T > A10323G,G22813T > C28887T > G174T > A23063T > G23012A +20H (Beta) > C14408T > C241T > C3037T > A23403G > G25563T > C1059T > C23664T > G5230T,A21801C,C25904T,C26456T > A10323G,G22813T > C28887T > G174T > A23063T > G23012A 21H (Mu) > C14408T > C241T > C3037T > A23403G > G25563T > C18877T > A13057T,C23604A,C27925A,C28005T,C28093T > A23063T > C6037T,G23012A > C4878T,C10029T,A11451G,C17491T,C20148T,C21846T,G24410N,C28887T > T19035C,A21993C,T21995A,G22599A,A26492T 21C (Epsilon) > C14408T > C241T > C3037T > A23403G > G25563T > C1059T > C28887T > A28272T > C29362T > T22917G > C26681T > G17014T > G22018T > G21600T -20J (Gamma,V3) > C14408T > C241T > C3037T > A23403G > G28881A > G28882A,G28883C > G25088T > T26149C > A6613G,G17259T,C23525T > G21974T,G23012A,A23063T,C28512G,A28877T,G28878C > C12778T,C13860T > C3828T,A5648C,G28167A > C2749T > C24642T > T733C,A6319G +20J (Gamma) > C14408T > C241T > C3037T > A23403G > G28881A > G28882A,G28883C > G25088T > T26149C > A6613G,G17259T,C23525T > G21974T,G23012A,A23063T,C28512G,A28877T,G28878C > C12778T,C13860T > C3828T,A5648C,G28167A > C2749T > C24642T > T733C,A6319G 21F (Iota) > C14408T > C241T > C3037T > A23403G > G25563T > C1059T > C28869T > C23664T > C25517T,G28975A > A20262G > T9867C > A22320G > C21846T > A16500C -20I (Alpha,V1) > C14408T > C241T > C3037T > A23403G > G28881A > G28882A,G28883C > G28280C,A28281T,T28282A > A23063T > C15279T > C28977T > A28111G > C913T > C5986T,T6954C,C23604A,C23709T > C23271A > T16176C,T24506G,G24914C > C14676T,C27972T +20I (Alpha) > C14408T > C241T > C3037T > A23403G > G28881A > G28882A,G28883C > G28280C,A28281T,T28282A > A23063T > C15279T > C28977T > A28111G > C913T > C5986T,T6954C,C23604A,C23709T > C23271A > T16176C,T24506G,G24914C > C14676T,C27972T 21I (Delta) > C14408T > C241T > C3037T > A23403G > G29742T > T22917G > G210T,C21618G,T27638C,G28881T > C23604G,G29402T > C25469T > C22995A,G24410N > C27752T > A28461G > C16466T > T26767C > G15451A > T11418C > C9891T > C11514T > C5184T > A5584G > C13019T > C22227T 21J (Delta) > C14408T > C241T > C3037T > A23403G > G29742T > T22917G > G210T,C21618G,T27638C,G28881T > C23604G,G29402T > C25469T > C22995A,G24410N > C27752T > A28461G > C16466T > T26767C > G15451A > C10029T > C19220T > G28916T > G4181T > C27874T > C7124T > G9053T > C8986T > A11332G > A11201G 21K (BA.1) C14408T > C241N > C3037T > A23403G > G28881A > G28883C > G28882A > C21846T > C23604A > A23063T > T22882G,C22995A,A23013C,C23525T,C24130A > C10029T,G22578A,C22674T,T22679C,C22686T,G22813T,G22992A,A23040G,A23055G,T23075C,T23599G,A27259C,C27807T > C10449A,A18163G,C23854A,G23948T,A24424T,T24469A,C25000T,C25584T,C26270T,C26577G,G26709A,A28271T,C28311T > A2832G,G8393A,A11537G,T13195C,C15240T,C21762T,T22673C,G22898A,C23202A,A26530G 21L (BA.2) C14408T > C241N > C3037T > A23403G > G28881A > G28883C > G28882A > C23604A > A23063T > T22882G,C22995A,A23013C,C23525T > C10029T,G22578A,C22674T,T22679C,C22686T,G22813T,G22992A,A23040G,A23055G,T23075C,T23599G,A27259C,C27807T > C10449A,A18163G,C23854A,G23948T,A24424T,T24469A,C25000T,C25584T,C26270T,C26577G,G26709A,A28271T,C28311T > T670G, G4184A,C4321T,C9344T,A9424G,C9534T,C10198T,G10447A,C12880T,C15714T,C17410T,C19955T,A20055G,C21618T,T22200G,A22688G,G22775A,A22786C,C26060T,C26858T,G27382C,A27383T,T27384C,A29510C > C2790N,C9866N 21M (Omicron) C14408T > C241N > C3037T > A23403G > G28881A > G28883C > G28882A > C21846T > C10029T > T22679C,C25584T,C27807N > C22995A,A27259C,A28461N > C7124N,C21762T,G22578A,G22898N,G22992A,G23048N,C23604A > C23202N > G22813T,T22882G,A23013C,A23040G,A23055G,A23063T,T23075C,C23525T,T23599G > A11537N,C24130N,A26530N > T24469N,T13195N,C21595N,A24424N,G8393N,C15240N,T22673N,C22674N,C22686N,C26270N,A28271N,C28311N,C10449N,A18163N,C23854N,G23948N,C25000N,C26577N,G26709N 22A (BA.4) C14408T > C241N > C3037T > A23403G > G28881A > G28883C > G28882A > C10029T > C23854A,G23948T,C27807T > A28271T > C10449A,C23525T,T23599G,C23604A,C26270T,C28311T > C25000T > C22995A,A23055G,A23063T,T23075C,A24424T,T24469A,C25584T,A27259C > G22578A,C22674T,T22679C,C22686T > G22992A,A23013C > A18163G,T22882G,C26577G,G26709A > G22813T > T22200G > G22775A > C19955T > G10447A,C15714T,C26060T > A20055G > T670G,G4184A,C4321T,C26858T > C9534T > C12880T,C21618T > C17410T > G27382C,A27383T,T27384C > C9344T,A9424G > A22786C > A22688G > A29510C > C10198T > C2790T > C28724T > G12160A,G27788T > T22917N > T23018G 22B (BA.5) C14408T > C241N > C3037T > A23403G > G28881A > G28883C > G28882A > C10029T > C23854A,G23948T,C27807N > A28271T > C10449A,C23525N,T23599G,C23604A,C26270T,C28311T > C25000T > C22995A,A23055G,A23063T,T23075C,A24424T,T24469A,C25584T > G22578A,C22674T,T22679C,C22686T > G22992A,A23013C > A18163G,T22882G,C26577G,G26709A > G22813T > T22200G > G22775A > C19955T > G10447A,C15714T,C26060T > A20055G > T670G,G4184A,C4321T > C9534T > C12880T,C21618T > C17410T > A22786N > A22688G > A29510C > C10198T > C2790T > G12160A,T22917G,T23018G,G26529A > C9344T,A9424G,C27889N 22C (BA.2.12.1) C14408T > C241N > C3037T > A23403G > G28881A > G28883C > G28882A > C23604A > A23063T > T22882G,C22995A,A23013C,C23525T > C10029T,G22578A,C22674T,T22679C,C22686T,G22813T,G22992A,A23040G,A23055G,T23075C,T23599G,A27259C,C27807T > C10449A,A18163G,C23854A,G23948T,A24424T,T24469A,C25000T,C25584T,C26270T,C26577G,G26709A,A28271T,C28311T > A26530N > C2790N > T670G,G4184A,C4321T,C9344T,A9424G,C9534T,C9866N,C10198N,G10447A,C12880T,C15714T,C17410T,C19955T,A20055G,C21618T,T22200G,A22688G,G22775A,A22786C,C26060T,C26858T,G27382C,A27383T,T27384C,A29510C > C25416T > C23673T > C11674T > T22917A 22D (BA.2.75) C14408T > C241N > C3037T > A23403G > G28881A > G28883C > G28882A > C23604A > A23063T > T22882G,C22995A,A23013C,C23525T > C10029T,G22578A,C22674T,T22679C,C22686T,G22813T,G22992A,A23055G,T23075C,T23599G,A27259C,C27807T > C10449A,A18163G,C23854A,G23948T,A24424T,T24469A,C25000T,C25584T,C26270T,C26577G,G26709A,A28271T,C28311T > A26530N > C2790N > T670G,G4184A,C4321T,C9344T,A9424G,C9534T,C9866N,C10198N,G10447A,C12880T,C15714T,C17410T,C19955T,A20055G,C21618T,T22200G,A22688G,G22775A,A22786C,C26060T,C26858T,G27382C,A27383T,T27384C,A29510C > C25416T > A23040A > C22033A > C3796T,C3927T,C4586T,C5183T,A12444G,G15451A,A22190G,G22331A,G22577C,G22898A,T22942G,A26275G > A22001G,T22016C 22E (BQ.1) C14408T > C241N > C3037T > A23403G > G28881A > G28883C > G28882A > C10029T > C23854A,G23948T,C27807T > A28271T > C10449A,C23525T,T23599G,C23604A,C26270T,C28311T > C25000T > C22995A,A23055G,A23063T,T23075C,A24424T,T24469A,C25584T > G22578A,C22674T,T22679C,C22686T > G22992A,A23013C > A18163G,T22882G,C26577G,G26709A > G22813T > T22200G > G22775A > C19955T > G10447A,C15714T,C26060T > A20055G > T670G,G4184A,C4321T > C9534T > C12880T,C21618T > C17410T > A22786C > A22688G > A29510C > C10198T > C2790T > G12160A,T22917G,T23018G,G26529A > C9344T,A9424G > C27889T > C1931A > G28681T > G16935A > T2954C > C11750T > C28312T > A22893C > T14257C > T22942A 22F (XBB) C14408T > C241N > C3037T > A23403G > G28881A > G28883C > G28882A > C10029T,C23854A,G23948T,C27807T > A28271T > C10449A,C23525T,T23599G,C23604A,C26270T,C28311T > C25000T > A23055G,A23063T,T23075C,A27259C > G22578A,C22674T,T22679C,C22686T,A24424T,C25584T T24469A > G22992A,C22995A,A23013C > A18163G,C26577G > G26709A > T22882G > G22813T > G22775A > C19955T > C15714T > G10447A,C26060T > A20055G > T670G,G4184A,C4321T,C26858T > C9534T > C12880T,C21618T > C17410T > G27382C,A27383T,T27384C > C9344T,A9424G,C9866T > A22786C > A22688G > A29510C > C10198T > C2790T > T16342C > C15738T > G15451A,T15939C,T21810C,C22000A > A405G > T17859C > C22109G,T22200A > G22577C,G22898A,T22942G,T23019C,C25416T,A26275G > A19326G > G22599C,C22664A,G22895C,T22896C,T23031C > G510N 23A (XBB.1.5) C14408T > C241N > C3037T > A23403G > G28881A > G28883C > G28882A > C10029T,C23854A,G23948T,C27807T > A28271T > C10449A,C23525T,T23599G,C23604A,C26270T,C28311T > C25000T > A23055G,A23063T,T23075C,A27259C > G22578A,C22674T,T22679C,C22686T,A24424T,C25584T T24469A > G22992A,C22995A,A23013C > A18163G,C26577G > G26709A > T22882G > G22813T > G22775A > C19955T > C15714T > G10447A,C26060T > A20055G > T670G,G4184A,C4321T,C26858T > C9534T > C12880T,C21618T > C17410T > G27382C,A27383T,T27384C > C9344T,A9424G,C9866T > A22786C > A22688G > A29510C > C10198T > C2790T > T16342C > C15738T > G15451A,T15939C,T21810C,C22000A > A405G > T17859C > C22109G,T22200A > G22577C,G22898A,T22942G,T23019C,C25416T,A26275G > A19326G > G22599C,C22664A,G22895C,T22896C,T23031C > G510G > G22317T > G27915T > T23018C > T17124N 23B (XBB.1.16) C14408T > C241N > C3037T > A23403G > G28881A > G28883C > G28882A > C10029T,C23854A,G23948T,C27807T > A28271T > C10449A,C23525T,T23599G,C23604A,C26270T,C28311T > C25000T > A23055G,A23063T,T23075C,A27259C > G22578A,C22674T,T22679C,C22686T,A24424T,C25584T T24469A > G22992A, A23013C > A18163G,C26577G > G26709A > T22882G > G22813T > G22775A > C19955T > C15714T > G10447A,C26060T > A20055G > T670G,G4184A,C4321T,C26858T > C9534T > C12880T,C21618T > C17410T > G27382C,A27383T,T27384C > C9344T,A9424G,C9866T > A22786C > A22688G > A29510C > C10198T > C2790T > T16342C > C15738T > G15451A,T15939C,T21810C,C22000A > A405G > T17859C > C22109G,T22200A > G22577C,G22898A,T22942G,T23019C,C25416T,A26275G > A19326G > G22599C,C22664A,G22895C,T22896C,T23031C > G510G > G22317T > G27915T > C11956T > T12730A > C11750T,A14856G,G18703T,T23018C,A28447G > C22995G > A22101T > T28297N,C29386N 23C (CH.1.1) C14408T > C241N > C3037T > A23403G > G28881A > G28883C > G28882A > C23604A > A23063T > T22882G,C22995A,A23013C,C23525T > C10029T,G22578A,C22674T,T22679C,C22686T,G22813T,G22992A,A23055G,T23075C,T23599G,A27259C,C27807T > C10449A,A18163G,C23854A,G23948T,A24424T,T24469A,C25000T,C25584T,C26270T,C26577G,G26709A,A28271T,C28311T > C2790T > T670G,G4184A,C4321T,C9344T,A9424G,C9534T,C9866T,C10198T,G10447A,C12880T,C15714T,C17410T,C19955T,A20055G,C21618T,T22200G,A22688G,G22775A,A22786C,C26060T,C26858T,G27382C,A27383T,T27384C,A29510C > C25416T > A23040A > C22033A > C3796T,C3927T,C4586T,C5183T,A12444G,G15451A,A22190G,G22331A,G22577C,G22898A,T22942G,A26275G > A22001G,T22016C > G18583A > C3857A > T23019C > G22599C > A20741G > A22893C > T22917G 23D (XBB.1.9) C14408T > C241N > C3037T > A23403G > G28881A > G28883C > G28882A > C10029T,C23854A,G23948T,C27807T > A28271T > C10449A,C23525T,T23599G,C23604A,C26270T,C28311T > C25000T > A23055G,A23063T,T23075C,A27259C > G22578A,C22674T,T22679C,C22686T,A24424T,C25584T T24469A > G22992A,C22995A,A23013C > A18163G,C26577G > G26709A > T22882G > G22813T > G22775A > C19955T > C15714T > G10447A,C26060T > A20055G > T670G,G4184A,C4321T,C26858T > C9534T > C12880T,C21618T > C17410T > G27382C,A27383T,T27384C > C9344T,A9424G,C9866T > A22786C > A22688G > A29510C > C10198T > C2790T > T16342C > C15738T > G15451A,T15939C,T21810C,C22000A > A405G > T17859C > C22109G,T22200A > G22577C,G22898A,T22942G,T23019C,C25416T,A26275G > A19326G > G22599C,C22664A,G22895C,T22896C,T23031C > G510G > G22317T > G27915T > T28297C > C12789T > G5720A 23E (XBB.2.3) C14408T > C241N > C3037T > A23403G > G28881A > G28883C > G28882A > C10029T,C23854A,G23948T,C27807T > A28271T > C10449A,C23525T,T23599G,C23604A,C26270T,C28311T > C25000T > A23055G,A23063T,T23075C,A27259C > G22578A,C22674T,T22679C,C22686T,A24424T,C25584T T24469A > G22992A,C22995A,A23013C > A18163G,C26577G > G26709A > T22882G > G22813T > G22775A > C19955T > C15714T > G10447A,C26060T > A20055G > T670G,G4184A,C4321T,C26858T > C9534T > C12880T,C21618T > C17410T > G27382C,A27383T,T27384C > C9344T,A9424G,C9866T > A22786C > A22688G > A29510C > C10198T > C2790T > > C15738T > G15451A,T15939C,T21810C,C22000A > A405G > T17859C > C22109G,T22200A > G22577C,G22898A,T22942G,T23019C,C25416T,A26275G > A19326G > G22599C,C22664A,G22895C,T22896C,T23031C > G510G > A22320G > C27431T > C23123T > T16342T > T23018C 23F (EG.5.1) C14408T > C241N > C3037T > A23403G > G28881A > G28883C > G28882A > C10029T,C23854A,G23948T,C27807T > A28271T > C10449A,C23525T,T23599G,C23604A,C26270T,C28311T > C25000T > A23055G,A23063T,T23075C,A27259C > G22578A,C22674T,T22679C,C22686T,A24424T,C25584T T24469A > G22992A,C22995A,A23013C > A18163G,C26577G > G26709A > T22882G > G22813T > G22775A > C19955T > C15714T > G10447A,C26060T > A20055G > T670G,G4184A,C4321T,C26858T > C9534T > C12880T,C21618T > C17410T > G27382C,A27383T,T27384C > C9344T,A9424G,C9866T > A22786C > A22688G > A29510C > C10198T > C2790T > T16342C > C15738T > G15451A,T15939C,T21810C,C22000A > A405G > T17859C > C22109G,T22200A > G22577C,G22898A,T22942G,T23019C,C25416T,A26275G > A19326G > G22599C,C22664A,G22895C,T22896C,T23031C > G510G > G22317T > G27915T > T28297C > C12789T > G5720A > T23018C > A27507C > A16878T > T22930A > C2334T,C9693T > C22480T > C29625T > A18492G,G21718T +23G (XBB.1.5.70) C14408T > C241N > C3037T > A23403G > G28881A > G28883C > G28882A > C10029T,C23854A,G23948T,C27807T > A28271T > C10449A,C23525T,T23599G,C23604A,C26270T,C28311T > C25000T > A23055G,A23063T,T23075C,A27259C > G22578A,C22674T,T22679C,C22686T,A24424T,C25584T T24469A > G22992A,C22995A,A23013C > A18163G,C26577G > G26709A > T22882G > G22813T > G22775A > C19955T > C15714T > G10447A,C26060T > A20055G > T670G,G4184A,C4321T,C26858T > C9534T > C12880T,C21618T > C17410T > G27382C,A27383T,T27384C > C9344T,A9424G,C9866T > A22786C > A22688G > A29510C > C10198T > C2790T > T16342C > C15738T > G15451A,T15939C,T21810C,C22000A > A405G > T17859C > C22109G,T22200A > G22577C,G22898A,T22942G,T23019C,C25416T,A26275G > A19326G > G22599C,C22664A,G22895C,T22896C,T23031C > G510G > G22317T > G27915T > T23018C > T17124C > C27059T > C28005T > C1973T,T8737C,C22624T,G22927T,T22928C,A25045G > C7564T,G12467T +23H (HK.3) C14408T > C241N > C3037T > A23403G > G28881A > G28883C > G28882A > C10029T,C23854A,G23948T,C27807T > A28271T > C10449A,C23525T,T23599G,C23604A,C26270T,C28311T > C25000T > A23055G,A23063T,T23075C,A27259C > G22578A,C22674T,T22679C,C22686T,A24424T,C25584T T24469A > G22992A,C22995A,A23013C > A18163G,C26577G > G26709A > T22882G > G22813T > G22775A > C19955T > C15714T > G10447A,C26060T > A20055G > T670G,G4184A,C4321T,C26858T > C9534T > C12880T,C21618T > C17410T > G27382C,A27383T,T27384C > C9344T,A9424G,C9866T > A22786C > A22688G > A29510C > C10198T > C2790T > T16342C > C15738T > G15451A,T15939C,T21810C,C22000A > A405G > T17859C > C22109G,T22200A > G22577C,G22898A,T22942G,T23019C,C25416T,A26275G > A19326G > G22599C,C22664A,G22895C,T22896C,T23031C > G510G > G22317T > G27915T > T28297C > C12789T > G5720A > T23018C > A27507C > A16878T > T22930A > C2334T,C9693T > C22480T > C29625T > A18492G,G21718T > G13627A,C25572T > C6541T > G22927T +23I (BA.2.86) C14408T > C241N > C3037T > A23403G > G28881A > G28883C > G28882A > A23063T > T22882G,C22995A, C23525T > C10029T,G22578A,C22674T,T22679C,C22686T,G22813T,G22992A, A23055G,T23075C,T23599G,A27259C,C27807T > C10449A,A18163G,C23854A,G23948T,A24424T,T24469A,C25000T,C25584T,C26270T,C26577G,G26709A,A28271T,C28311T > T670G,C2790T,G4184A,C4321T,C9344T,A9424G,C9534T, C10198T,G10447A,C12880T,C15714T,C17410T,C19955T,A20055G,C21618T,T22200G,A22688G,G22775A,A22786C,C26060T,C26858T,G27382C,A27383T,T27384C,A29510C > A23040A > T22917G > C22295A > A22556G,A22629C > C897A,G3431T,A7842G,C8293T,G8393A,G11042T,C12789T,T13339C,T15756A,A18492G, C21711T,G21941T,T22032C,C22033A,A22034G,C22208T,C22353A,G22577C,G22770A, T23018C,T23019C, C23271T,C23423T,C23604G,C24378T,C24990T,C25207T,G26529C,A26610G,C26833T,C28958A > C21622N,G21624N,G22895N,T22896N,G22898N,A22910N,C22916N,T22942N,T23005N,G23012N,C23013N,G23222N,C26681N