4b526917c44114d3d9fa18e6dd31bee769b5a24f angie Mon Apr 4 09:44:28 2022 -0700 Added proposed482. G210T in XS and proposed446 needs to be masked for pangolin. XD samples should have 29742; some do, some don't, so mask that in (HT Cornelius Roemer). Added miscRecombOrContam to prevent non-XM descendants of XM branch from being labeled XM (HT Cornelius Roemer). diff --git src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv index e164ccd..1ccd29a 100644 --- src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv +++ src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv @@ -344,38 +344,40 @@ BA.2.9 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 > C22792T > C25624T BA.2.10 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 > T16342C BA.3 C14408T > C241N > C3037T > A23403G > G28881A > G28883C > G28882A > C21846T > 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,C26270T,C26577G,G26709A,A28271T,C28311T > C21762T,G22898A > T670G,G4184A,C4321T,C9534T,G10447A,C12880T,C15714T,G22775A,C26060T,C26858T,A29510C > C832T,C11235T B.1.637 C14408T > C241N > C3037T > A23403G > G25563T > C1059T > G28975A > C25517T > A20262G > T9867C > C27925T > C9891T > A9749G > T22917G > A21801G,T22032C > C28887T > G11804A B.1.637.1 C14408T > C241N > C3037T > A23403G > G25563T > C1059T > G28975A > C25517T > A20262N > T9867C > C27925T > C9891T > A9749G > T22917G > A21801G,T22032C > C28887T > G11804A > C25413T,C25703T > G28044T > C24138A > C5581T > T7249C,C16575T > T6345C > C556T,G25437C > G370T,T606C,C4449T,C10029T,A13535G,C22353T,G22898C,C22995G,C23604G,C25904T,T26767C,C28311T 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 > 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 B.1.641 C14408T > C241N > C3037T > A23403G > G25563T > C1059T > C16329T > C12756T,C12786T,G13459A,T23020G,A23064C,T26047G,C27131T > G6894T,C9430T,C9711T,A10323G,C12073T,C12076T,C12213T,C12596T,A17199G,T26160C,G27996T,G28209T,T28889C > C7267T,C9724T,A16266G,C21846T > C1282T,C1513T,C2388T,T2489C,C4113T,C4206T,C4540T,C5284T,C7029T,C7093T,C7764T,C9073T,C9532T,C9598T,C9611T,C9679T,C9712T,C9745T,C10183T,C10279T,T10423C,A14041G,C14322T,G14557T,C15738T,G15921T,G17278T,G18546T,C18646T,G19891T,C20283T,A21203G,C21707T,C21727T,T23398C,T24028C,C26313T,C26455T,C26464T,C26894T,C27297T,T27384C,C28775T,C29445T,C29578T,C29666T 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 +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 > G29742N 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 +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 > G210N > C3505T,A4015G,A5584G XG 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 XH 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 XJ 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 XK 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 XL 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 XQ 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 XR 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 -XS 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 +XS 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 > G210N > G22599A > C5365T,C6196T XM 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,A27259C > G22992A,C22995A,A23013C,C25000T > A18163G,T22882G,C26577G,G26709A > G22813T > T22200G > G22775A > C19955T > C26060T > A20055G > C26858T > C21618T > G27382C,A27383T,T27384C > A22786C > A22688G > A29510C > A2832G > T5386G > G8393A > A11537G,T13195C > C2470T +miscRecombOrContam 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,A27259C > G22992A,C22995A,A23013C,C25000T > A18163G,T22882G,C26577G,G26709A > G22813T > T22200G > G22775A > C19955T > C26060T > A20055G > C26858T > C21618T > G27382C,A27383T,T27384C > A22786C > A22688G > A29510C > A2832G > T5386G > G8393A > A11537G,T13195C > C22792T 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 XN 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 XP 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 > A28877N > G28878N > C2470T > A24190C,C26880A,A29510C +proposed482 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,A27259C > G22578A,C22674T,T22679C,C22686T,A23040G > G22992A,A23013C > A18163G,T22882G,C26577G,G26709A > G22813T > T22200G > G22775A > C19955T > G10447A,C15714T,C26060T > A20055G > T670G,G4184A,C4321T > C9534T > C12880T,C21618T > C17410T > C9344T,A9424G,C9866T > A22786C > A22688G > C10198T > C2790T > A26530G > G14653T,C25844T