9ea690d413932da6911d75a073d3a5d95673d7d4 angie Wed Aug 14 13:08:23 2024 -0700 Added 24C (KP.3) diff --git src/hg/utils/otto/sarscov2phylo/nextstrain.clade-mutations.tsv src/hg/utils/otto/sarscov2phylo/nextstrain.clade-mutations.tsv index dd6dbb1..3093d5e 100644 --- src/hg/utils/otto/sarscov2phylo/nextstrain.clade-mutations.tsv +++ src/hg/utils/otto/sarscov2phylo/nextstrain.clade-mutations.tsv @@ -28,15 +28,16 @@ 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 24A (JN.1) 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,A23013A > T22917G > C22295A > A22556G,A22629C > C897A,G3431T,A7842G,C8293T,G8393A,G11042T,C12789T,T13339C,T15756A,A18492G,C21622T,G21624C,C21711T,G21941T,T22032C,C22033A,A22034G,C22208T,C22353A,G22577C,G22770A,G22895C,T22896A,G22898A,A22910G,C22916T,T22942A,T23005A,G23012A,T23018C,T23019C,G23222A,C23271T,C23423T,C23604G,C24378T,C24990T,C25207T,G26529C,A26610G,C26681T,C26833T,C28958A > A6183G,C12815T > G21770N > T3565C,G11727A,C18894T,T22926C > T27810C 24B (JN.1.11.1) 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,A23013A > T22917G > C22295A > A22556G,A22629C > C897A,G3431T,A7842G,C8293T,G8393A,G11042T,C12789T,T13339C,T15756A,A18492G,C21622T,G21624C,C21711T,G21941T,T22032C,C22033A,A22034G,C22208T,C22353A,G22577C,G22770A,G22895C,T22896A,G22898A,A22910G,C22916T,T22942A,T23005A,G23012A,T23018C,T23019C,G23222A,C23271T,C23423T,C23604G,C24378T,C24990T,C25207T,G26529C,A26610G,C26681T,C26833T,C28958A > A6183G,C12815T > G21770N > T3565C,G11727A,C18894T,T22926C > T27810C > T23008N,T23010N > G17334T,G24872T > C7113T > T22928C +24C (KP.3) 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,A23013A > T22917G > C22295A > A22556G,A22629C > C897A,G3431T,A7842G,C8293T,G8393A,G11042T,C12789T,T13339C,T15756A,A18492G,C21622T,G21624C,C21711T,G21941T,T22032C,C22033A,A22034G,C22208T,C22353A,G22577C,G22770A,G22895C,T22896A,G22898A,A22910G,C22916T,T22942A,T23005A,G23012A,T23018C,T23019C,G23222A,C23271T,C23423T,C23604G,C24378T,C24990T,C25207T,G26529C,A26610G,C26681T,C26833T,C28958A > A6183G,C12815T > G21770N > T3565C,G11727A,C18894T,T22926C > T27810C > T23008N,T23010N > G17334T,G24872T > C7113T > T22928C > C23039G