f587c6cd4ffa90b371583bbbf80373172b9ca885 angie Mon Mar 28 16:22:32 2022 -0700 Added some more proposed recombinant lineages. diff --git src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv index 33e1576..b9469e0 100644 --- src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv +++ src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv @@ -337,20 +337,30 @@ B.1.640 C14408T > C241N > C3037T > A23403G > G25563T > C28005N,C28093N > C27925N > A23063T,C23604A > C10029N,C28887T > G23012N > A26492N > C1191T,C2416T,C2455T,C11956T,C16869T,C21588T,G21848C,G22132T,A22600C,A22743G,T22907A,C24138A,C25487T,T26767N,C27513T,C27807T,T29377C B.1.640.1 C14408T > C241N > C3037T > A23403G > G25563T > C28005T,C28093T > C27925A > A23063T,C23604A > C10029T,C28887T > A26492T > C1191T,C2416T,C2455T,C11956T,C16869T,C21588T,G21848C,G22132T,A22600C,A22743G,T22907A,C24138A,C25487T,T26767C,C27513T,C27807T,T29377C > C601T,A1620G,G6622T,G7328T,C9711T,G9756A,T11418C,C16575T,C20283T,T22191C,T23030C,G24368C,G29405C B.1.640.2 C14408T > C241N > C3037T > A23403G > G25563T > A23063T,C23604A > C28887T > G23012A > C1191T,C2416T,C2455T,C11956T,C16869T,C21588T,G21848C,G22132T,A22600C,A22743G,T22907A,C24138A,C25487T,C27513T,C27807T,T29377C > G9929A,T10561C,C11514T,C17004T,T17348C,A17916G,C18175T,C18804T,G19348T,T19680C,A21258G,G22205C,T23031C,G24977C,T26767G,T27833C,C27972T,T28002C,C28312T,G28337T,G29779N AA.1 C14408T > C241N > C3037T > A23403G > C6286T > C28932T > C22227T > G29645N > T445C > G21255C > C26801G > C5170T > G11132T > G22051T > C10078T > G11417T AV.1 C14408T > C241N > C3037T > A23403G > G28881A > G28883C > G28882A > C21846T > C23604A > G23012A > C9891T > C313T,T772C,G1820A,C2037T,C3743T,C5184T,A7479G,T11288A,G11291N,T11296N,T11503C,T14740G,C18395T,A21801G,T21992G,A21993T,C22687T,C22879G,A24950G,G24977C,T26159G,A26161T,G26709A,C26895N,C27297T,A28742G,C28744T A.23.1 T28144C > C8782T > G28878A > G29742N > G11230T > G28167A > G11266T,C22000T > C22033A,G23401T,T24097C > C4573T,C16575T,C23604G B.1.429 C14408T > C241N > C3037T > A23403G > G25563T > C1059T > C28887T > A28272T > C29362T > T22917G > C26681T > G17014T > G22018T > G21600T XC C14408T > C241N > C3037T > A23403G > G28881A > G28883C > G28882A > T22917G,C22995A > C7124T,G15451A,C16466T > C6402T > C21618G,C25469T > C23604G > C8986T,G9053T > C19220T,G28280C,A28281T,T28282A,C28977T > G4181T,C21846T,C27972T,G28048T,A28111G > G210N,C10029T,A11201G,A11332G,T26767C > C5239T,T5514C,G22081T,G27390T XD C14408T > C241N > C3037T > A23403G > C21846T > C10029T > C23854A,G23948T > C24130A,A28271T > C23525T,T23599G,C23604A > G22578A,T22673C,C22674T,T22679C,C22686T,A23040G,A23055G,A23063T,T23075C,A24424T,T24469A > G22992A,C22995A,A23013C,C25000T > T22882G > G22813T > G22898A > C23202A > C24503T > G23048A > G4181T > C19220T > C6402T,C7124T > C8986T,G9053T > G210N > A11201G,A11332G,G15451A,C16466T > C7851T > C21618G > A1321C,A8723G,C14407T,T15264C,G21641T,C25667T,G25855T,T26767C,T27638C,C27752T,C27874T,A28461G,G28881T,G28916T,G29402T,G29540A,G29645T XE C14408T > C241N > C3037T > A23403G > G28881A > G28883C > G28882A > C10029T > C23854A,G23948T,C27807T > A28271T > C10449A,C23525T,T23599G,C23604A,C26270T,C28311T > G22578A,C22674T,T22679C,C22686T,A23040G,A23055G,A23063T,T23075C,A24424T,T24469A,C25584T > G22992A,C22995A,A23013C,C25000T,A27259C > A18163G,T22882G,C26577G,G26709A > G22813T > T22200G > G22775A > C19955T > C15714T,C26060T > A20055G > C26858T > C12880T,C21618T > C17410T > G27382C,A27383T,T27384C > A22786C > A22688G > A29510C > A2832G > T5386G > G8393A > C3241T,G5924A > C14599T XF C14408T > C241N > C3037T > A23403G > G28881A > G28883C > G28882A > C21846T > C10029T > C15240T,C23854A,G23948T,C27807T > C21762T,C24130A,A28271T > C10449A,C23525T,T23599G,C23604A,C26270T,C28311T > G22578A,T22673C,C22674T,T22679C,C22686T,A23040G,A23055G,A23063T,T23075C,A24424T,T24469A,C25584T > G22992A,C22995A,A23013C,C25000T,A27259C > A18163G,T22882G,C26577G,G26709A > G22813T > G8393A,A11537G > T13195C > G22898A,A26530G > C23202A > C24503T > G23048A > G4181T > G210N > T1390C,A2255G,C29632T proposed422 C14408T > C241N > C3037T > A23403G > G28881A > G28883C > G28882A > C21846T > C10029T > C23854A,G23948T,C27807T > C21762T,C24130A,A28271T > C23525T,T23599G,C23604A,C26270T,C28311T > G22578A,T22673C,C22674T,T22679C,C22686T,A23040G,A23055G,A23063T,T23075C,A24424T,T24469A,C25584T > G22992A,C22995A,A23013C,C25000T,A27259C > T22882G,C26577G,G26709A > G22813T > G22898A,A26530G > C23202A > C24503T > G23048A > G4181T > C6402T,C7124T > C8986T,G9053T > G210N > A11201G,A11332G,G15451A,C16466T > C7851T > C4891T,C5310T,G12685T,C23664T proposed437 C14408T > C241N > C3037T > A23403G > G28881A > G28883C > G28882A > C21846T > C10029T > C23854A,G23948T,C27807T > C24130A,A28271T > C23525T,T23599G,C23604A,C26270T,C28311T > G22578A,T22673C,C22674T,T22679C,C22686T,A23040G,A23055G,A23063T,T23075C,A24424T,T24469A,C25584T > G22992A,C22995A,A23013C,C25000T,A27259C > T22882G,C26577G,G26709A > G22813T > G22898A,A26530G > C23202A > C24503T > G23048A > G4181T > C19220T > C6402T,C7124T > C8986T,G9053T > G210N > A11201G,A11332G,G15451A,C16466T > C21618G > C3486T,T6085C,C8917T,C8964T,A12524G,T19225G,C21597T,C25708T,A29301G > C7851N proposed439 C14408T > C241N > C3037T > A23403G > G28881A > G28883C > G28882A > C21846T > C10029T > C23854A,G23948T,C27807T > C21762T,C24130A,A28271T > C23525T,T23599G,C23604A,C26270T,C28311T > G22578A,T22673C,C22674T,T22679C,C22686T,A23040G,A23055G,A23063T,T23075C,A24424T,T24469A,C25584T > G22992A,C22995A,A23013C,C25000T,A27259C > T22882G,C26577G,G26709A > G22813T > G22898A,A26530G > C23202A > C24503T > G23048A > G22599A > G4181T > C19220T > C6402T,C7124T > C8986T,G9053T > G210N > A11201G,A11332G,G15451A,C16466T > C300T,C8829T,G12793T,A13428G,G19006T,T27768C proposed441 C14408T > C241N > C3037T > A23403G > G28881A > G28883C > G28882A > C21846T > C10029T > C23854A,G23948T,C27807T > C21762T,C24130A,A28271T > C23525T,T23599G,C23604A,C26270T,C28311T > G22578A,T22673C,C22674T,T22679C,C22686T,A23040G,A23055G,A23063T,T23075C,A24424T,T24469A,C25584T > G22992A,C22995A,A23013C,C25000T,A27259C > T22882G,C26577G,G26709A > G22813T > G22898A,A26530G > C23202A > C24503T > G23048A > G4181T > C19220T > C6402T,C7124T > C8986T,G9053T > G210N > A11201G,A11332G,G15451A,C16466T > C7851T > C21618G > C2842T,C6740T,A14457T,A14844G,C21292T,C26534T,C26873T +proposed446 C14408T > C241N > C3037T > A23403G > G28881A > G28883C > G28882A > C21846T > C10029T > C15240T,C23854A,G23948T,C27807T > C21762T,C24130A,A28271T > C10449A,C23525T,T23599G,C23604A,C26270T,C28311T > G22578A,T22673C,C22674T,T22679C,C22686T,A23040G,A23055G,A23063T,T23075C,A24424T,T24469A,C25584T > G22992A,C22995A,A23013C,C25000T,A27259C > A18163G,T22882G,C26577G,G26709A > G22813T > G8393A,A11537G > T13195C > G22898A,G23048A,C23202A,A26530G > C24503T > G22599A > C21595T > G4181T > G210T > C3505T,A4015G,A5584G proposed447 C14408T > C241N > C3037T > A23403G > G28881A > G28883C > G28882A > C10029T > C23854A,G23948T,C27807T > A28271T > C10449A,C23525T,T23599G,C23604A,C26270T,C28311T > G22578A,C22674T,T22679C,C22686T,A23040G,A23055G,A23063T,T23075C,A24424T,T24469A,C25584T > G22992A,C22995A,A23013C,C25000T,A27259C > A18163G,T22882G,C26577G,G26709A > G22813T > T22200G > G22775A > C19955T > G10447A,C15714T,C26060T > A20055G > C26858T > C9534T > C12880T,C21618T > C17410T > G27382C,A27383T,T27384C > C9344T,A9424G,C9866T > A22786C > A22688G > A29510C > C22792T > C10198T > A2832G > T5386G > G5924A > C5672T proposed448 C14408T > C241N > C3037T > A23403G > G28881A > G28883C > G28882A > C10029T > C23854A,G23948T,C27807T > A28271T > C10449A,C23525T,T23599G,C23604A,C26270T,C28311T > G22578A,C22674T,T22679C,C22686T,A23040G,A23055G,A23063T,T23075C,A24424T,T24469A,C25584T > G22992A,C22995A,A23013C,C25000T,A27259C > A18163G,T22882G,C26577G,G26709A > G22813T > T22200G > G22775A > C19955T > C15714T,C26060T > A20055G > C26858T > C12880T,C21618T > C17410T > G27382C,A27383T,T27384C > A22786C > A22688G > A29510C > C22792T > A2832G > T5386G > G8393A > C25624T > T902C,C904A,G1244A,C28435T +proposed449 C14408T > C241N > C3037T > A23403G > G28881A > G28883C > G28882A > C10029T,C23854A,G23948T,C27807T > A28271T > C10449A,C23525T,T23599G,C23604A,C26270T,C28311T > G22578A,C22674T,T22679C,C22686T,A23040G,A23055G,A23063T,T23075C,A24424T,T24469A,C25584T > G22992A,C22995A,A23013C,C25000T,A27259C > A18163G,T22882G,C26577G,G26709A > G22813T > T22200G > G22775A > C19955T > C15714T,C26060T > A20055G > C26858T > C21618T > C17410T > G27382C,A27383T,T27384C > A22786C > A22688G > A29510C > C22792T > A2832G > T5386G > G8393A > C3241T,G5924A > A11537G,T13195C > C27945T +proposed455 C14408T > C241N > C3037T > A23403G > G28881A > G28883C > G28882A > C21846T > C10029T > C15240T,C23854A,G23948T,C27807T > C21762T,C24130A,A28271T > C10449A,C23525T,T23599G,C23604A,C26270T,C28311T > G22578A,T22673C,C22674T,T22679C,C22686T,A23040G,A23055G,A23063T,T23075C,A24424T,T24469A,C25584T > G22992A,C22995A,A23013C,C25000T,A27259C > A18163G,T22882G,C26577G,G26709A > G22813T > G8393A,A11537G > T13195C > G22898A,G23048A,C23202A,A26530G > C24503T > T5386G > G4184A,C4321T > T670G > C832T,G7684A,C29167T +proposed460 C14408T > C241N > C3037T > A23403G > G28881A > G28883C > G28882A > C10029T > C15240T,C23854A,G23948T,C27807T > A28271T > C10449A,C23525T,T23599G,C23604A,C26270T,C28311T > G22578A,C22674T,T22679C,C22686T,A23040G,A23055G,A23063T,A24424T,T24469A,C25584T > G22992A,C22995A,A23013C,C25000T,A27259C > A18163G,T22882G,C26577G,G26709A > G22813T > G22775A > C19955T > C26060T > A20055G > C26858T > C21618T > G27382C,A27383T,T27384C > A22786C > A22688G > A29510C > C22792T > A2832G > T5386G > G8393A > A11537G,T13195C > C5147T,A16064G > A23767G +proposed463 C14408T > C241N > C3037T > A23403G > G28881A > G28883C > G28882A > C10029T > C23854A,G23948T,C27807T > A28271T > C10449A,C23525T,T23599G,C23604A,C26270T,C28311T > G22578A,C22674T,T22679C,C22686T,A23040G,A23055G,A23063T,T23075C,A24424T,T24469A,C25584T > G22992A,C22995A,A23013C,C25000T,A27259C > A18163G,T22882G,C26577G,G26709A > G22813T > T22200G > G22775A > C19955T > C15714T,C26060T > A20055G > C26858T > C21618T > C17410T > G27382C,A27383T,T27384C > A22786C > A22688G > A29510C > C22792T > A2832G > T5386G > G8393A > A11537G,T13195C > C3583T proposed464 C14408T > C241N > C3037T > A23403G > G28881A > G28883C > G28882A > C10029T > C23854A,G23948T,C27807T > A28271T > C10449A,C23525T,T23599G,C23604A,C26270T,C28311T > G22578A,C22674T,T22679C,C22686T,A23040G,A23055G,A23063T,T23075C,A24424T,T24469A,C25584T > G22992A,C22995A,A23013C,C25000T,A27259C > A18163G,T22882G,C26577G,G26709A > G22813T > T22200G > G22775A > C19955T > G10447A,C15714T,C26060T > A20055G > C26858T > C9534T > C12880T,C21618T > C17410T > G27382C,A27383T,T27384C > C9344T,A9424G,C9866T > A22786C > A22688G > A29510C > C10198T > A2832G > T5386G > G5924A > C875T,C3241T,G14229A +proposed467 C14408T > C241N > C3037T > A23403G > G28881A > G28883C > G28882A > C10029T > C15240T,C23854A,G23948T,C27807T > A28271T > C10449A,C23525T,T23599G,C23604A,C26270T,C28311T > G22578A,C22674T,T22679C,C22686T,A23040G,A23055G,A23063T,T23075C,A24424T,T24469A,C25584T > G22992A,C22995A,A23013C,C25000T,A27259C > A18163G,T22882G,C26577G,G26709A > G22813T > T22200G > G22775A > C19955T > C15714T,C26060T > A20055G > C26858T > C21618T > C17410T > G27382C,A27383T,T27384C > A22786C > A22688G > A29510C > A2832G > T5386G > G8393A > A11537G,T13195C > A5428G,C10376T,C12513T proposed468 C14408T > C241N > C3037T > A23403G > G28881A > G28883C > G28882A > C10029T > C23854A,G23948T,C27807T > A28271T > C10449A,C23525T,T23599G,C23604A,C26270T,C28311T > G22578A,C22674T,T22679C,C22686T,A23040G,A23055G,A23063T,T23075C,A24424T,T24469A,C25584T > G22992A,C22995A,A23013C,C25000T,A27259C > A18163G,T22882G,C26577G,G26709A > G22813T > T22200G > G22775A > C19955T > G10447A,C15714T,C26060T > A20055G,C26858T > C9534T > C12880T,C21618T > C17410T > G27382C,A27383T,T27384C > C9344T,A9424G,C9866T > A22786C > A22688G > A29510C > C10198T > A2832G > C2470T > A17615G proposed469 C14408T > C241N > C3037T > A23403G > G28881A > G28883C > G28882A > C10029T > C23854A,G23948T,C27807T > A28271T > C10449A,C23525T,T23599G,C23604A,C26270T,C28311T > G22578A,C22674T,T22679C,C22686T,A23040G,A23055G,A23063T,T23075C,A24424T,T24469A,C25584T > G22992A,C22995A,A23013C,C25000T,A27259C > A18163G,T22882G,C26577G,G26709A > G22813T > T22200G > G22775A > C19955T > G10447A,C15714T,C26060T > A20055G,C26858T > C9534T > C12880T,C21618T > C17410T > G27382C,A27383T,T27384C > C9344T,A9424G,C9866T > A22786C > A22688G > A29510C > C10198T > A2832G > C2470T > C4893T,G13295A,A25524G,C27131T +proposed471 C14408T > C241N > C3037T > A23403G > G28881A > G28883C > G28882A > C21846T > C10029T > C15240T,C23854A,G23948T,C27807T > C21762T,C24130A,A28271T > C10449A,C23525T,T23599G,C23604A,C26270T,C28311T > G22578A,T22673C,C22674T,T22679C,C22686T,A23040G,A23055G,A23063T,T23075C,A24424T,T24469A,C25584T > G22992A,C22995A,A23013C,C25000T,A27259C > A18163G,T22882G,C26577G,G26709A > G22813T > A11537G > T13195C > G22898A,G23048A,C23202A,A26530G > C24503T > C21595T > G4181T > C6402T,C7124T > C8986T,G9053T > G210T > G22599A > C5365T,C6196T +proposed478 C14408T > C241N > C3037T > A23403G > G28881A > G28883C > G28882A > C10029T > C23854A,G23948T,C27807T > A28271T > C10449A,C23525T,T23599G,C23604A,C26270T,C28311T > G22578A,C22674T,T22679C,C22686T,A23040G,A23055G,A23063T,T23075C,A24424T,T24469A,C25584T > G22992A,C22995A,A23013C,C25000T,A27259C > A18163G,T22882G,C26577G,G26709A > G22813T > T22200G > G22775A > C19955T > G10447A,C15714T,C26060T > A20055G > T670G,G4184A,C4321T > C9534T > C12880T,C21618T > C17410T > C9344T,A9424G > A22786C > A22688G > C2790T > C10198T > A26530G > C13994T,G21786T +proposed480 C14408T > C241N > C3037T > A23403G > G28881A > G28883C > G28882A > C10029T > C23854A,G23948T,C27807T > A28271T > C10449A,C23525T,T23599G,C23604A,C26270T,C28311T > G22578A,C22674T,T22679C,C22686T,A23040G,A23055G,A23063T,T23075C,A24424T,T24469A,C25584T > G22992A,C22995A,A23013C,C25000T,A27259C > A18163G,T22882G,C26577G,G26709A > G22813T > T22200G > G22775A > C19955T > G10447A,C15714T,C26060T > A20055G,C26858T > G4184A,C4321T > C9534T > C12880T,C21618T > C17410T > G27382C,A27383T,T27384C > C9344T,A9424G,C9866T > A22786C > A22688G > A29510C > C22792T > C10198T > A2832G > G10986A +proposed481 C14408T > C241N > C3037T > A23403G > G28881A > G28883C > G28882A > C21846T > C10029T > C15240T,C23854A,G23948T,C27807T > C21762T,C24130A,A28271T > C10449A,C23525T,T23599G,C23604A,C26270T,C28311T > G22578A,T22673C,C22674T,T22679C,C22686T,A23040G,A23055G,A23063T,T23075C,A24424T,T24469A,C25584T > G22992A,C22995A,A23013C,C25000T,A27259C > A18163G,T22882G,C26577G,G26709A > G22813T > G8393A,A11537G > T13195C > G22898A,G23048A,C23202A,A26530G > A2832G,C24503T > T5386G > G22599A > A28877T > G28878C > C2470T > A24190C,C26880A,A29510C