07cbdefa64e387ad41f07f6c900a058cfbbe118c angie Tue Nov 2 12:50:50 2021 -0700 Adding mutation sets for Nextstrain Clades and selected Pango lineages (mostly VoCs) for use with matUtils annotate --clade-mutations. These are based on paths in the current tree, but with forward & back-mutations removed or changed to N. AY.* path ends checked vs. table in https://www.pango.network/summary-of-designated-ay-lineages/ . diff --git src/hg/utils/otto/sarscov2phylo/nextstrain.clade-mutations.tsv src/hg/utils/otto/sarscov2phylo/nextstrain.clade-mutations.tsv new file mode 100644 index 0000000..e1274db --- /dev/null +++ src/hg/utils/otto/sarscov2phylo/nextstrain.clade-mutations.tsv @@ -0,0 +1,20 @@ +19A +19B > T28144C > C8782T +20A > C14408T > C241T > C3037T > A23403G +20B > C14408T > C241T > C3037T > A23403G > G28881A > G28882A,G28883C +20C > C14408T > C241T > C3037T > A23403G > G25563T > C1059T +21E(Theta) > C14408T > C241T > C3037T > A23403G > G28881A > G28882A,G28883C > G25088T > A4926G,C7564A,C8139T,G9203A,T9867C,C11308A,C12049T,C12053T,C17074T,C17339T,A22356G,G23012A,A23063T,T23341C,C23604A,T24187A,G24836A,C24863T,A27897C,C29724T +21A(Delta) > C14408T > C241T > C3037T > A23403G > G29742T > T22917G > G210T,C21618G,T27638C,G28881T > C23604G,G29402T > C25469T > C22995A,G24410A,A28461G +21B(Kappa) > C14408T > C241T > C3037T > A23403G > G29742T > T22917G > G210T,T27638C,G28881T > C23604G,G29402T > C25469T > C3457T,C4965T,A11201G,G17523T,A20396G,T21895C,G22022A,G23012C,A24775T,C26681T,T26767G +20D > C14408T > C241T > C3037T > A23403G > G28881A > G28882A,G28883C > G10097A > C23731T > C4002T > C13536T +20F > C14408T > C241T > C3037T > A23403G > G28881A > G28882A,G28883C > A1163T > T7540C,G16647T > G22992A,G23401A > C18555T +20E(EU1) > C14408T > C241T > C3037T > A23403G > C6286T > C28932T > C22227T > G29645T +21D(Eta) > C14408T > C241T > C3037T > A23403G > C28887T > C24748T,T26767C,A28699G > A21717G,G23012A,G23593C,T24224C,C26305T,C28308G > C1498T,A1807G,G2659A,C6285T,T8593C,C18171T,G29543T > C14407T,A20724G > C9565T +21G(Lambda) > C14408T > C241T > C3037T > A23403G > G28881A > G28882A,G28883C > G10097A > C23731T > C4002T > C13536T > T7424G,C9857T,T9867C,C10029T,A28271T,C28311T > G21786T,C21789T > C7124T,T22917A,T23031C +20G > C14408T > C241T > C3037T > A23403G > G25563T > C1059T > C27964T > C10319T > G25907T > C28869T > C28472T > A18424G > C21304T +20H(Beta,V2) > C14408T > C241T > C3037T > A23403G > G25563T > C1059T > C23664T > G5230T,A21801C,C25904T,C26456T > A10323G,G22813T > C28887T > G174T > A23063T > G23012A +21H(Mu) > C14408T > C241T > C3037T > A23403G > G25563T > C18877T > A13057T,C23604A,C27925A,C28005T,C28093T > A23063T > C6037T,G23012A > C4878T,C10029T,A11451G,C17491T,C20148T,C21846T,G24410A,C28887T > T19035C,A21993C,T21995A,G22599A,A26492T +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