693b252e4597e0d97badea0f19b9836ded21ddae angie Wed May 24 11:02:16 2023 -0700 Added 23A, 23B. diff --git src/hg/utils/otto/sarscov2phylo/nextstrain.clade-mutations.tsv src/hg/utils/otto/sarscov2phylo/nextstrain.clade-mutations.tsv index a096a23..ffc1725 100644 --- src/hg/utils/otto/sarscov2phylo/nextstrain.clade-mutations.tsv +++ src/hg/utils/otto/sarscov2phylo/nextstrain.clade-mutations.tsv @@ -17,15 +17,17 @@ 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 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 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 (Omicron) 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 (Omicron) 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 (Omicron) 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 (Omicron) 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 (Omicron) 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 (Omicron) 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 (Omicron) 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 (Omicron) 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 (Omicron) 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 (Omicron) 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