d3954606ff07dd6169919e7059e53bc0d7e98b06 angie Fri Aug 28 08:27:34 2026 -0700 Now that XFJ.3.1 is excluded from masking of 21617 (in JN.1), we can include A21617G in descendants of XFJ.3.1. diff --git src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv index 6c6558ccb7f..c7ba8225d2a 100644 --- src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv +++ src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv @@ -4652,40 +4652,40 @@ XFG.39 XFG > C20178T > G29706N > C29614T > T27734C XFG.40 XFG > C20178T > C12473T,C25611T > G18803A,G22865T > G8056N,T12730N,C12973N,C13965N,C20451N,C26586N XFH JN.1.16.1 > G22132T > C5239T,C7869T,G12892A,T16600C,T21653C,A22107G, T28297C > C8818T > C21627A > C6310T > C3884T > C4993T > G4694A,C4891T,C9166T,T22566C,C23039G XFH.1 XFH > C29719A > A949G XFH.2 XFH > C16575T,G24697A XFJ B.1.1 > 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, 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 > G22599C > G22132T > C5239T, G12892A,T16600C,T21653C,A22107G, > C21627A > C22986T > T22896C > T22884G > C22792T,T22930A,A23933G,C25844T,G27414A,T28297C > T20799C XFJ.1 XFJ > G12769T XFJ.1.1 XFJ.1 > A15036G > C29200T > A12928G XFJ.1.2 XFJ.1 > A15036G > A22010G > C14913N,C25671N,C26110N XFJ.1.3 XFJ.1 > C2388T,A21875G,A22893G > T10717N XFJ.2 XFJ > G18903A XFJ.2.1 XFJ.2 > A22995T XFJ.2.2 XFJ.2 > C29386T > C7768T XFJ.3 XFJ > G25352T XFJ.3.1 XFJ.3 > C4893T -XFJ.3.1.1 XFJ.3.1 > G23599T +XFJ.3.1.1 XFJ.3.1 > A21617G > G23599T RA.1 XFJ.3.1.1 > C4021T > A22268T -XFJ.3.1.2 XFJ.3.1 > G28727T,A28959C > C9559N,C11962N +XFJ.3.1.2 XFJ.3.1 > A21617G > G28727T,A28959C > C9559N,C11962N RW.1 XFJ.3.1.2 > C9559T,C11962T > C2878T > A22995C > C29281N RW.1.1 RW.1 > G22865T RW.1.1.1 RW.1.1 > T7092G > C15450N RW.1.1.2 RW.1.1 > T8719C RW.1.1.3 RW.1.1 > C25413T -XFJ.3.1.3 XFJ.3.1 > C3587T > A6277N -XFJ.3.1.4 XFJ.3.1 > A19890G +XFJ.3.1.3 XFJ.3.1 > A21617G > C3587T > A6277N +XFJ.3.1.4 XFJ.3.1 > A21617G > A19890G XFJ.3.2 XFJ.3 > G14188A XFJ.4 XFJ > C18252T > A22012C, A22995C XFJ.4.1 XFJ.4 > A27300T > T1501C XFJ.5 XFJ > C7044T,G22346T > A2356N XFJ.6 XFJ > C7006T XFJ.7 XFJ > T27212C XFJ.8 XFJ > C1919T > C20470A XFJ.8.1 XFJ.8 > A1565G,G25352T > C24310N,G28079N XFJ.9 XFJ > T2308C,T10273C XFJ.10 XFJ > C21682T XFK XEC > C7113T > C12616T > A13121T > G15372T > C17502T,G21776A,G22203T,A25590G XFL XEC > T24376C > C593T,C3505T,G24193T > C5534T,A5535T,G28378T XFM B.1.1 > 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, 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 > G22599C > G22132T > C5239T, G12892A,T16600C,T21653C,A22107G, > C21627A > C22986T > T22896C > T22884G > C7869T,C8818T,T22930A,A23933G,C25844T,G27414A > G4504A,T4579A,T15207C,C21928T,A26555C XFN JN.1 > T23008N,T23010N > G24872T > T22928C > C23039G > G28884C > C25006T > C28291A > C21627A > G2060A > C10228T > G22865T,A27321G > C9365T,T16600C,T21653C,A22107G,G22132T,G22599C,G29543T XFN.1 XFN > T28600C