10670fc04382aaae97374b9a9a4b88c718a3d94f
angie
Tue Dec 7 18:36:52 2021 -0800
Broaden B.1.1.529 and add new sublineages BA.1 (Omicron) and BA.2 ("outlier"/"stealth"/"Decepticron") - pango-designation v1.2.106
diff --git src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv
index 90f3360..ec1784c 100644
--- src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv
+++ src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv
@@ -218,21 +218,23 @@
P.1.17 C14408T > C241N > C3037T > A23403G > G28881A > G28883C > G28882A > C23525T > G23012A > A6613G,G25088T > A22812C,A23063T,T26149C > G21974T,A28877T,G28878C > C28512G > C13860T,G17259T > C12778T > A5648C > C3828T,G28167A > C24642T > T733C,C2749T > A6319G > G22132T > C21614T > C21621A > C21638T > T11296G > C28603T > C346T
P.1.17.1 C14408T > C241N > C3037T > A23403G > G28881A > G28883C > G28882A > C23525T > G23012A > A6613G,G25088T > A22812C,A23063T,T26149C > G21974T,A28877T,G28878C > C28512G > C13860T,G17259T > C12778T > A5648C > C3828T,G28167A > C24642T > T733C,C2749T > A6319G > G22132T > C21614T > C21621A > C21638T > T11296G > C28603T > C346T > T11288A,G11291A > A6704G > G19999T > C21707T
P.2 C14408T > C241N > C3037T > A23403G > G28881A > G28883C > G28882A > G25088T > C12053T > C29754N > G23012A > C100N > G28975T > T10667G > C11824T > G28628T
P.3 C14408T > C241N > C3037T > A23403G > G28881A > G28883C > G28882A > G25088T > A22356N,C29724N > C23604A > T9867C > A4926G,C7564A,C11308A,T24187A,A27897C > T23341C > C12049T,C12053T,G23012A,A23063T > G24836A,C24863T > C17339T > C17074T
P.4 C14408T > C241N > C3037T > A23403G > G28881A > G28883C > G28882A > G25088T > G1811A > C3177T,C11450A,C12880T > A136N,C9693T,T9867C,C12008T,A15932G,G18756T,T20745C,G21987N,T22917G,A23720G,G25540A,C25708T,A28271C,C28932T
P.5 C14408T > C241N > C3037T > A23403G > G28881A > G28883C > G28882A > G25088T > C24904T > G25906T > G5180A,G9929A,C21846T > G23012C,A23064C,C27807T,A28271T,C28311T
P.6 C14408T > C241N > C3037T > A23403G > G28881A > G28883C > G28882A > G25088T > C12053T > G21305A > G2534T > C1077T,C3736T,C7043T,C10029T,A14113G,C24382T > G23587C,C25665T > C8980T,G23593T
P.7 C14408T > C241N > C3037T > A23403G > G28881A > G28883C > G28882A > G25088T > C12053T > C17676T > C17172T,C25844T,C28311T
C.37 C14408T > C241N > C3037T > A23403G > G28881A > G28883C > G28882A > G10097A > C23731T > C4002T > C13536T > T7424G,T9867C,A28271T > C9857T > C10029T,C28311T > G21786T,C21789T > C7124T > T22917A,T23031C > C24138A > G28913T
C.37.1 C14408T > C241N > C3037T > A23403G > G28881A > G28883C > G28882A > G10097A > C23731T > C4002T > C13536T > T7424G,T9867C,A28271T > C9857T > C10029T,C28311T > G21786T,C21789T > C7124T > T22917A,T23031C > C24138A > G28913T > C29311T > C26894T > T11296G > A28877T > G28878C > C20806T
B.1.621 C14408T > C241N > C3037T > A23403G > G25563T > C18877T > C28005T,C28093T > C27925A > A13057T,C23604A > A23063T > C6037T,G23012A > C10029T,A11451G,C20148T > C17491T,C21846T,C28887T > C4878T > A21993C,T21995A > T19035C,G22599A,A26492T > A3428G,A28272T
B.1.621.1 C14408T > C241N > C3037T > A23403G > G25563T > C18877T > C28005T,C28093T > C27925A > A13057T,C23604A > A23063T > C6037T,G23012A > C10029T,A11451G,C20148T > C17491T,C21846T,C28887T > C4878T > A21993C,T21995A > T19035C,G22599A,A26492T > A3428G,A28272T > C17707T > C5192T > A6704G,T22384A > C9120T > C20402T > T29748N > C28657T > G26167T
B.1.160 C14408T > C241N > C3037T > A23403G > G25563T > C26735T > C18877T > G28975C > T26876C > G29399A > C25710T > G9526T,G22992A > G5629T > C11497T
B.1.1.315 C14408T > C241N > C3037T > A23403G > G28881A > G28883C > G28882A > C29466T > C22388T,C26060T,A29771N > T3256C,C19718T > A1163T,G19542T
B.1.1.232 C14408T > C241N > C3037T > A23403G > G28881A > G28883C > G28882A > C6573T > G12191T > T16479C > T2537G
-B.1.1.529 C14408T > C241N > C3037T > A23403G > G28881A > G28883C > G28882A > C21846T > C23604A > G23012N > A23063T > T22882G,C22995A,A23013C,C23525T,C24130A > A2832N,T5386N,G8393N,C10029T,C10449A,A11537N,T13195N,C15240N,A18163G,C21762N,G22578A,T22673N,C22674T,T22679C,C22686N,G22813T,G22898N,G22992A,A23040G,G23048N,A23055G,T23075N,C23202N,T23599G,C23854N,G23948T,A24424N,T24469N,C24503N,C25000T,C25584T,C26270T,A26530N,C26577G,G26709A,A27259C,C27807T,A28271N,C28311N
+B.1.1.529 C14408T > C241N > C3037T > A23403G > G28881A > G28883C > G28882A > C21846N > C23604A > G23012N > A23063T > T22882G,C22995A,A23013C,C23525T > C10029T,C21762N,G22578A,T22673N,C22674T,T22679C,C22686T,G22813T,G22898N,G22992A,A23040G,G23048N,A23055G,T23075C,C23202N,T23599G,A27259C,C27807T > C10449A,A18163G,C25000T,C25584T,C26270T,C26577G,G26709A
+BA.1 C14408T > C241N > C3037T > A23403G > G28881A > G28883C > G28882A > C21846T > C23604A > A23063T > T22882G,C22995A,A23013C,C23525T > C10029T,C21762T,G22578A,T22673C,C22674T,T22679C,C22686T,G22813T,G22898A,G22992A,A23040G,G23048A,A23055G,T23075N,C23202A,T23599G,A27259C,C27807T > C10449A,A18163G,C25000T,C25584T,C26270T,C26577G,G26709A > T5386G,G8393A,A11537G,T13195C,C15240T > A2832G,A26530G,A28271T,C28311T > G23948T,C24130A,A24424T > C23854A,T24469A,C24503T
+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,C25000T,C25584T,C26270T,C26577G,G26709A > T670G,C2790T,G4184A,C4321T,C9344T,A9424G,C9534T,C10198T,G10447A,C12880T,C15714T,C17410T,C19955T,A20055G,C21618T,T22200G,A22688G,G22775A,A22786C,C23854A,G23948T,A24424T,T24469A,C26060T,C26858T,G27382C,A27383T,T27384C,A29510C
B.1.637 C14408T > C241N > C3037T > A23403G > G25563T > C1059T > G28975A > C25517T > A20262G > T9867C > C27925T > C9891T > A9749G > T22917G > A21801G,T22032C > C28887T > G11804A
B.1.639 C14408T > C241N > C3037T > A23403G > G23012A > A28271G > T22020C,C22995A,C24138A,G24368T,T27919C,A28742G
B.1.640 C14408T > C241N > C3037T > A23403G > G25563T > C28005N,C28093N > C27925N > A23063T,C23604A > C10029T,C28887T > A26492T > C601T,C1191T,A1620G,C2416T,C2455T,G6622T,G7328T,C9711T,G9756A,T11418C,C11956T,C16575T,C16869T,C20283T,C21588T,G21848C,G22132T,T22191C,A22600C,A22743G,T22907A,T23030C,T23031N,C24138A,G24368C,C25487T,T26767C,C27513T,C27807T,T29377C,G29405C,G29465N
AA.1 C14408T > C241N > C3037T > A23403G > C6286T > C28932T > C22227T > G29645N > T445C > G21255C > C26801G > C5170T > G11132T > G22051T > C10078T > G11417T
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