##fileformat=VCFv4.3 ##fileDate=2021-10-27-18:39 ##source=http://virological.org/t/masking-strategies-for-sars-cov-2-alignments/480 ##reference=MN908947.3 ##contig= ##FILTER= ##FILTER= ##INFO= ## CF = Charles Foster ## LG = Landen Gozashti ## RCD = Russell Corbett-Detig ## SN = Son Nguyen ## TS = Theo Sanderson ## MP = Matthew Parker ## NDM = Nicola De Maio ##INFO= ## seq_end = Alignment ends are affected by low coverage and high error rates(masking recommended, but might be more stringent than necessary) ## ambiguous = Sites which show an excess of ambiguous basecalls relative to the number of alternative alleles, often emerging from a single country or sequencing laboratory ## amended = Previous sequencing errors which now appear to have been fixed in the latest versions of the GISAID sequences, at least in sequences from some of the sequencing laboratories ## amplicon_drop_or_primer_artefact = Amplicon dropout and/or failed primer trimming ## back_to_ref = The alternate allele is not called for this position due to issues with amplicon dropout and primer trimming. For more details, see: https://github.com/W-L/ProblematicSites_SARS-CoV2/issues/7 and https://github.com/cov-lineages/pango-designation/issues/95 ## highly_ambiguous = Sites with a very high proportion of ambiguous characters, relative to the number of alternative alleles ## highly_homoplasic = Positions which are extremely homoplasic - it is sometimes not necessarily clear if these are hypermutable sites or sequencing artefacts ## homoplasic = Homoplasic sites, with many mutation events needed to explain a relatively small alternative allele count ## interspecific_contamination = Cases (so far only one instance) in which the known sequencing issue is due to contamination from genetic material that does not have SARS-CoV-2 origin ## nanopore_adapter = Cases in which the known sequencing issue is due to the adapter sequences in nanopore reads ## narrow_src = Variants which are found in sequences from only a few sequencing labs (usually two or three), possibly as a consequence of the same artefact reproduced independently ## neighbour_linked = Proximal variants displaying near perfect linkage ## single_src = Only observed in samples from a single laboratory ##INFO= ##INFO= ## APL = Alberta Precision Labs ## Aalborg_University = Aalborg University ## BRC = Biomedical Research Center ## CDC_DVD = Centers for Disease Control and Prevention, Division of Viral Diseases ## COG_UK = COVID-19 Genomics UK (COG-UK) Consortium ## CSIR = The Council of Scientific and Industrial Research ## CUB = Charité-Universitätsmedizin Berlin ## CeMM = The CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences ## Chan_Zuckerberg_Biohub = Chan Zuckerberg Biohub ## Ditan = Beijing Ditan Hospital ## Doherty = The Peter Doherty Institute for Infection and Immunity ## ETH_Zurich = Department of Biosystems Science and Engineering, ETH Zürich ## Edinburgh = Virology Department, Royal Infirmary of Edinburgh ## Erasmus = Erasmus Medical Center ## FIOCRUZ = Oswaldo Cruz Foundation ## Houston = Houston Methodist Hospital ## ICMR = Indian Council of Medical Research ## ISPC = Instituto de Salud Publica de Chile ## IZSAM = Istituto zooprofilattico sperimentale dell'Abruzzo e del Molise ## India = Multiple sources in India ## KDCPA = Korea Disease Control and Prevention Agency ## KU_Leuven = KU Leuven ## LACPHL = Los Angeles County Public Health Laboratory ## LNS = Laboratoire National de Santé ## MGSC = Microbial Genome Sequencing Center ## Michigan_Health_Dept = Michigan Department of Health and Human Services ## Ministry_of_Health = Ministry of Health ## Minnesota = Minnesota Department of Health, Public Health Laboratory ## NCDC = National Centre for Disease Control ## NHLS = National Health Laboratory Service ## NICDNHLS = National Institute for Communicable Diseases of the National Health Laboratory Service ## NIV = National Institute of Virology ## NPHL = National Public Health Laboratory ## NU-OMICS = NU-OMICS, Northumbria University ## Nottingham = Queens Medical Centre, COG-UK Consortium ## Public_Health_England = Public Health England ## Public_Health_Scotland = Public Health Scotland ## Public_Health_Wales = Public Health Wales ## SSI = Statens Serum Institut ## Sanger = Wellcome Sanger Institute ## Sanger_COG_UK = Wellcome Sanger Institute, COG-UK Consortium ## Seattle_Flu_Study = Seattle Flu Study ## Sheffield = The Florey Institute, University of Sheffield Medical School ## Sichuan_University = State Key Laboratory of Biotherapy of Sichuan University ## TGEN = The Translational Genomics Research Institute ## UNMHSC = Center for Global Health, University of New Mexico Health Sciences Center ## UW_CFAR = University of Washington, Center for AIDS Research ## UW_Virology = University of Washington, Department of Virology ## University_of_Melbourne = University of Melbourne, Microbiological Diagnostic Unit Public Health Laboratory ## University_of_Washington = University of Washington ## VIDRL = Victorian Infectious Diseases Reference Laboratory ## WHO_Russia = WHO National Influenza Centre Russian Federation ## WPHL = Wyoming Public Health Laboratory ##INFO= ##INFO= ##INFO= ##INFO= #CHROM POS ID REF ALT QUAL FILTER INFO MN908947.3 1 . A . . mask SUB=NDM;EXC=seq_end MN908947.3 2 . T . . mask SUB=NDM;EXC=seq_end MN908947.3 3 . T . . mask SUB=NDM;EXC=seq_end MN908947.3 4 . A . . mask SUB=NDM;EXC=seq_end MN908947.3 5 . A . . mask SUB=NDM;EXC=seq_end MN908947.3 6 . A . . mask SUB=NDM;EXC=seq_end MN908947.3 7 . G . . mask SUB=NDM;EXC=seq_end MN908947.3 8 . G . . mask SUB=NDM;EXC=seq_end MN908947.3 9 . T . . mask SUB=NDM;EXC=seq_end MN908947.3 10 . T . . mask SUB=NDM;EXC=seq_end MN908947.3 11 . T . . mask SUB=NDM;EXC=seq_end MN908947.3 12 . A . . mask SUB=NDM;EXC=seq_end MN908947.3 13 . T . . mask SUB=NDM;EXC=seq_end MN908947.3 14 . A . . mask SUB=NDM;EXC=seq_end MN908947.3 15 . C . . mask SUB=NDM;EXC=seq_end MN908947.3 16 . C . . mask SUB=NDM;EXC=seq_end MN908947.3 17 . T . . mask SUB=NDM;EXC=seq_end MN908947.3 18 . T . . mask SUB=NDM;EXC=seq_end MN908947.3 19 . C . . mask SUB=NDM;EXC=seq_end MN908947.3 20 . C . . mask SUB=NDM;EXC=seq_end MN908947.3 21 . C . . mask SUB=NDM;EXC=seq_end MN908947.3 22 . A . . mask SUB=NDM;EXC=seq_end MN908947.3 23 . G . . mask SUB=NDM;EXC=seq_end MN908947.3 24 . G . . mask SUB=NDM;EXC=seq_end MN908947.3 25 . T . . mask SUB=NDM;EXC=seq_end MN908947.3 26 . A . . mask SUB=NDM;EXC=seq_end MN908947.3 27 . A . . mask SUB=NDM;EXC=seq_end MN908947.3 28 . C . . mask SUB=NDM;EXC=seq_end MN908947.3 29 . A . . mask SUB=NDM;EXC=seq_end MN908947.3 30 . A . . mask SUB=NDM;EXC=seq_end MN908947.3 31 . A . . mask SUB=NDM;EXC=seq_end MN908947.3 32 . C . . mask SUB=NDM;EXC=seq_end MN908947.3 33 . C . . mask SUB=NDM;EXC=seq_end MN908947.3 34 . A . . mask SUB=NDM;EXC=seq_end MN908947.3 35 . A . . mask SUB=NDM;EXC=seq_end MN908947.3 36 . C . . mask SUB=NDM;EXC=seq_end MN908947.3 37 . C . . mask SUB=NDM;EXC=seq_end MN908947.3 38 . A . . mask SUB=NDM;EXC=seq_end MN908947.3 39 . A . . mask SUB=NDM;EXC=seq_end MN908947.3 40 . C . . mask SUB=NDM;EXC=seq_end MN908947.3 41 . T . . mask SUB=NDM;EXC=seq_end MN908947.3 42 . T . . mask SUB=NDM;EXC=seq_end MN908947.3 43 . T . . mask SUB=NDM;EXC=seq_end MN908947.3 44 . C . . mask SUB=NDM;EXC=seq_end MN908947.3 45 . G . . mask SUB=NDM;EXC=seq_end MN908947.3 46 . A . . mask SUB=NDM;EXC=seq_end MN908947.3 47 . T . . mask SUB=NDM;EXC=seq_end MN908947.3 48 . C . . mask SUB=NDM;EXC=seq_end MN908947.3 49 . T . . mask SUB=NDM;EXC=seq_end MN908947.3 50 . C . . mask SUB=NDM;EXC=seq_end MN908947.3 51 . T . . mask SUB=NDM;EXC=seq_end MN908947.3 52 . T . . mask SUB=NDM;EXC=seq_end MN908947.3 53 . G . . mask SUB=NDM;EXC=seq_end MN908947.3 54 . T . . mask SUB=NDM;EXC=seq_end MN908947.3 55 . A . . mask SUB=NDM;EXC=seq_end MN908947.3 76 . T K,Y,W,C,A . caution SUB=NDM;EXC=ambiguous,neighbour_linked,narrow_src;SRC_COUNTRY=Singapore,India;SRC_LAB=NPHL,NCDC;GENE=.;AA_POS=.;AA_REF=.;AA_ALT=. MN908947.3 78 . T K,Y,A,C,W,G . caution SUB=NDM;EXC=ambiguous,neighbour_linked,narrow_src;SRC_COUNTRY=Singapore,India;SRC_LAB=NPHL,NCDC;GENE=.;AA_POS=.;AA_REF=.;AA_ALT=. MN908947.3 150 . T C,Y . mask SUB=RCD;EXC=homoplasic,single_src,neighbour_linked;SRC_COUNTRY=USA;SRC_LAB=University_of_Washington;GENE=.;AA_POS=.;AA_REF=.;AA_ALT=. MN908947.3 153 . T Y,G . mask SUB=RCD;EXC=homoplasic,single_src,neighbour_linked;SRC_COUNTRY=USA;SRC_LAB=University_of_Washington;GENE=.;AA_POS=.;AA_REF=.;AA_ALT=. MN908947.3 285 . G K,T,A . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=Australia;SRC_LAB=VIDRL,University_of_Melbourne;GENE=gene-orf1ab;AA_POS=7;AA_REF=G;AA_ALT=X,V,D MN908947.3 320 . C Y,S,T,A,G . caution SUB=LG;EXC=narrow_src,highly_ambiguous;SRC_COUNTRY=USA;SRC_LAB=.;GENE=gene-orf1ab;AA_POS=19;AA_REF=P;AA_ALT=X,X,S,T,A MN908947.3 538 . A R,W,G . caution SUB=NDM,RCD;EXC=ambiguous;SRC_COUNTRY=Italy;SRC_LAB=IZSAM;GENE=gene-orf1ab;AA_POS=91;AA_REF=E;AA_ALT=E,X,E MN908947.3 553 . G T,K,C,A . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=Australia;SRC_LAB=VIDRL,University_of_Melbourne;GENE=gene-orf1ab;AA_POS=96;AA_REF=Q;AA_ALT=H,X,H,Q MN908947.3 558 . G R,K,T . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=Australia;SRC_LAB=VIDRL,University_of_Melbourne;GENE=gene-orf1ab;AA_POS=98;AA_REF=G;AA_ALT=X,X,V MN908947.3 635 . C T,Y . mask SUB=NDM,RCD;EXC=highly_ambiguous,homoplasic,narrow_src;SRC_COUNTRY=Switzerland,Australia,UK;SRC_LAB=ETH_Zurich,Doherty,COG_UK;GENE=gene-orf1ab;AA_POS=124;AA_REF=R;AA_ALT=C,X MN908947.3 660 . G K,S,A . caution SUB=NDM,RCD;EXC=ambiguous;SRC_COUNTRY=Australia;SRC_LAB=Doherty;GENE=gene-orf1ab;AA_POS=132;AA_REF=G;AA_ALT=X,X,D MN908947.3 663 . G R,K,T,A . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=Australia;SRC_LAB=VIDRL;GENE=gene-orf1ab;AA_POS=133;AA_REF=G;AA_ALT=X,X,V,D MN908947.3 759 . A D,T . caution SUB=RCD;EXC=ambiguous,single_src;SRC_COUNTRY=USA;SRC_LAB=UW_Virology;GENE=gene-orf1ab;AA_POS=165;AA_REF=H;AA_ALT=X,L MN908947.3 856 . T C,A,Y . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=Switzerland;SRC_LAB=ETH_Zurich;GENE=gene-orf1ab;AA_POS=197;AA_REF=P;AA_ALT=P,P,P MN908947.3 1001 . G R,A . caution SUB=NDM;EXC=ambiguous,amended;SRC_COUNTRY=UK;SRC_LAB=Sanger_COG_UK;GENE=gene-orf1ab;AA_POS=246;AA_REF=E;AA_ALT=X,K MN908947.3 1406 . G K,T,A,S . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=Australia;SRC_LAB=VIDRL;GENE=gene-orf1ab;AA_POS=381;AA_REF=E;AA_ALT=X,*,K,Z MN908947.3 1707 . C T,A,Y . mask SUB=RCD;EXC=highly_ambiguous,homoplasic,narrow_src;SRC_COUNTRY=India;SRC_LAB=NCDC;GENE=gene-orf1ab;AA_POS=481;AA_REF=S;AA_ALT=F,Y,X MN908947.3 1814 . A . . caution SUB=NDM;EXC=ambiguous,amended;SRC_COUNTRY=USA;SRC_LAB=Minnesota;GENE=gene-orf1ab;AA_POS=517;AA_REF=K;AA_ALT=. MN908947.3 1895 . G K,T . mask SUB=NDM,RCD;EXC=ambiguous;SRC_COUNTRY=UK;SRC_LAB=Public_Health_England;GENE=gene-orf1ab;AA_POS=544;AA_REF=V;AA_ALT=X,L MN908947.3 1947 . T C,Y,G . caution SUB=RCD;EXC=ambiguous,narrow_src;SRC_COUNTRY=India;SRC_LAB=NCDC;GENE=gene-orf1ab;AA_POS=561;AA_REF=V;AA_ALT=A,X,G MN908947.3 2087 . T Y . caution SUB=NDM,RCD;EXC=ambiguous;SRC_COUNTRY=India;SRC_LAB=NCDC;GENE=gene-orf1ab;AA_POS=608;AA_REF=L;AA_ALT=L MN908947.3 2091 . C T,Y . mask SUB=NDM;EXC=highly_ambiguous,homoplasic,narrow_src;SRC_COUNTRY=India,UK;SRC_LAB=NCDC,NU-OMICS;GENE=gene-orf1ab;AA_POS=609;AA_REF=T;AA_ALT=I,X MN908947.3 2094 . C T,Y . mask SUB=NDM;EXC=highly_ambiguous,narrow_src;SRC_COUNTRY=Belgium,India;SRC_LAB=KU_Leuven,NCDC;GENE=gene-orf1ab;AA_POS=610;AA_REF=S;AA_ALT=L,X MN908947.3 2101 . G K,T . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=Australia;SRC_LAB=VIDRL,University_of_Melbourne;GENE=gene-orf1ab;AA_POS=612;AA_REF=W;AA_ALT=X,C MN908947.3 2198 . G R,T,A . mask SUB=NDM,RCD;EXC=homoplasic,ambiguous,narrow_src;SRC_COUNTRY=Netherlands;SRC_LAB=Erasmus;GENE=gene-orf1ab;AA_POS=645;AA_REF=G;AA_ALT=X,C,S MN908947.3 2247 . G R,K,T,A . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=Australia;SRC_LAB=VIDRL;GENE=gene-orf1ab;AA_POS=661;AA_REF=G;AA_ALT=X,X,V,D MN908947.3 2381 . G K,T . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=Australia;SRC_LAB=VIDRL,University_of_Melbourne;GENE=gene-orf1ab;AA_POS=706;AA_REF=G;AA_ALT=X,C MN908947.3 2604 . G K,T . mask SUB=RCD;EXC=homoplasic,ambiguous,single_src;SRC_COUNTRY=Australia;SRC_LAB=Doherty;GENE=gene-orf1ab;AA_POS=780;AA_REF=G;AA_ALT=X,V MN908947.3 3050 . G K,T,A . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=Australia;SRC_LAB=VIDRL;GENE=gene-orf1ab;AA_POS=929;AA_REF=E;AA_ALT=X,*,K MN908947.3 3073 . T C,W,Y . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=Switzerland;SRC_LAB=ETH_Zurich;GENE=gene-orf1ab;AA_POS=936;AA_REF=C;AA_ALT=C,X,C MN908947.3 3145 . G T . mask SUB=NDM,RCD;EXC=homoplasic,single_src;SRC_COUNTRY=Netherlands;SRC_LAB=Erasmus;GENE=gene-orf1ab;AA_POS=960;AA_REF=L;AA_ALT=F MN908947.3 3191 . G T,K,C,A . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=Australia;SRC_LAB=VIDRL;GENE=gene-orf1ab;AA_POS=976;AA_REF=E;AA_ALT=*,X,Q,K MN908947.3 3480 . C T,Y . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=Australia;SRC_LAB=VIDRL;GENE=gene-orf1ab;AA_POS=1072;AA_REF=A;AA_ALT=V,X MN908947.3 3504 . A T,W,M,G . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=Australia;SRC_LAB=VIDRL;GENE=gene-orf1ab;AA_POS=1080;AA_REF=N;AA_ALT=I,X,X,S MN908947.3 3564 . G K,T . mask SUB=NDM,RCD;EXC=highly_ambiguous,highly_homoplasic,single_src;SRC_COUNTRY=Australia;SRC_LAB=VIDRL;GENE=gene-orf1ab;AA_POS=1100;AA_REF=G;AA_ALT=X,V MN908947.3 3639 . G R,A . mask SUB=RCD;EXC=ambiguous,homoplasic,single_src;SRC_COUNTRY=UK;SRC_LAB=Public_Health_Wales;GENE=gene-orf1ab;AA_POS=1125;AA_REF=G;AA_ALT=X,D MN908947.3 3778 . A G . mask SUB=RCD;EXC=homoplasic,single_src;SRC_COUNTRY=Netherlands;SRC_LAB=Erasmus;GENE=gene-orf1ab;AA_POS=1171;AA_REF=T;AA_ALT=T MN908947.3 3877 . T K,C,A,G . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=UK;SRC_LAB=Sanger;GENE=gene-orf1ab;AA_POS=1204;AA_REF=A;AA_ALT=A,A,A,A MN908947.3 4050 . A C . mask SUB=NDM,RCD;EXC=homoplasic,single_src,amended;SRC_COUNTRY=Belgium;SRC_LAB=KU_Leuven;GENE=gene-orf1ab;AA_POS=1262;AA_REF=N;AA_ALT=T MN908947.3 4221 . A D,T,W . mask SUB=LG;EXC=single_src,highly_homoplasic;SRC_COUNTRY=USA;SRC_LAB=University_of_Washington;GENE=gene-orf1ab;AA_POS=1319;AA_REF=K;AA_ALT=X,I,X MN908947.3 4463 . T K,C,Y,G . caution SUB=RCD;EXC=ambiguous,single_src,homoplasic;SRC_COUNTRY=Benin;SRC_LAB=CUB;GENE=gene-orf1ab;AA_POS=1400;AA_REF=S;AA_ALT=X,P,X,A MN908947.3 4505 . G R,K,T,A . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=Australia;SRC_LAB=VIDRL;GENE=gene-orf1ab;AA_POS=1414;AA_REF=G;AA_ALT=X,X,C,S MN908947.3 4692 . C T,A . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=Switzerland;SRC_LAB=ETH_Zurich;GENE=gene-orf1ab;AA_POS=1476;AA_REF=S;AA_ALT=F,Y MN908947.3 4854 . G K,T,A . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=Australia;SRC_LAB=VIDRL;GENE=gene-orf1ab;AA_POS=1530;AA_REF=R;AA_ALT=X,I,K MN908947.3 4991 . A T,C,M . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=UK;SRC_LAB=Sanger;GENE=gene-orf1ab;AA_POS=1576;AA_REF=N;AA_ALT=Y,H,X MN908947.3 5011 . A C,M . mask SUB=RCD;EXC=ambiguous,homoplasic,single_src;SRC_COUNTRY=USA;SRC_LAB=Michigan_Health_Dept;GENE=gene-orf1ab;AA_POS=1582;AA_REF=Q;AA_ALT=H,X MN908947.3 5130 . C T,A,G . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=Switzerland;SRC_LAB=VIDRL;GENE=gene-orf1ab;AA_POS=1622;AA_REF=P;AA_ALT=L,H,R MN908947.3 5196 . G T,K,C . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=Australia;SRC_LAB=VIDRL;GENE=gene-orf1ab;AA_POS=1644;AA_REF=G;AA_ALT=V,X,A MN908947.3 5233 . G D,K,R,T,A . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=Australia;SRC_LAB=VIDRL;GENE=gene-orf1ab;AA_POS=1656;AA_REF=W;AA_ALT=X,X,X,C,* MN908947.3 5257 . A M,W,G . mask SUB=RCD;EXC=highly_ambiguous,single_src;SRC_COUNTRY=Switzerland;SRC_LAB=ETH_Zurich;GENE=gene-orf1ab;AA_POS=1664;AA_REF=L;AA_ALT=X,X,L MN908947.3 5322 . T K,Y,W,A,G . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=Switzerland;SRC_LAB=ETH_Zurich;GENE=gene-orf1ab;AA_POS=1686;AA_REF=I;AA_ALT=X,X,X,K,R MN908947.3 5375 . G K,T,S . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=Australia;SRC_LAB=VIDRL;GENE=gene-orf1ab;AA_POS=1704;AA_REF=A;AA_ALT=X,S,X MN908947.3 5393 . T C,Y . caution SUB=NDM;EXC=ambiguous,amended;SRC_COUNTRY=USA,UK;SRC_LAB=Houston,Sheffield;GENE=gene-orf1ab;AA_POS=1710;AA_REF=F;AA_ALT=L,X MN908947.3 5498 . A R . caution SUB=NDM;EXC=ambiguous,amended;SRC_COUNTRY=USA,UK;SRC_LAB=Houston,Sheffield;GENE=gene-orf1ab;AA_POS=1745;AA_REF=K;AA_ALT=X MN908947.3 5657 . G K,T,A,S . caution SUB=RCD;EXC=ambiguous,single_src;SRC_COUNTRY=India;SRC_LAB=NCDC;GENE=gene-orf1ab;AA_POS=1798;AA_REF=V;AA_ALT=X,L,I,X MN908947.3 5736 . C T,Y . mask SUB=NDM,RCD;EXC=homoplasic,single_src;SRC_COUNTRY=Turkey;SRC_LAB=Ministry_of_Health;GENE=gene-orf1ab;AA_POS=1824;AA_REF=A;AA_ALT=V,X MN908947.3 5743 . G T,S . mask SUB=RCD;EXC=highly_ambiguous,neighbour_linked,narrow_src;SRC_COUNTRY=UK,Australia;SRC_LAB=Public_Health_England,Doherty;GENE=gene-orf1ab;AA_POS=1826;AA_REF=E;AA_ALT=D,X MN908947.3 5744 . T Y . mask SUB=RCD;EXC=highly_ambiguous,neighbour_linked,narrow_src;SRC_COUNTRY=UK,Australia;SRC_LAB=Public_Health_England,Doherty;GENE=gene-orf1ab;AA_POS=1827;AA_REF=Y;AA_ALT=X MN908947.3 5765 . G R,K . caution SUB=RCD;EXC=ambiguous,single_src,neighbour_linked;SRC_COUNTRY=Australia;SRC_LAB=Doherty;GENE=gene-orf1ab;AA_POS=1834;AA_REF=G;AA_ALT=X,X MN908947.3 5766 . G S . caution SUB=RCD;EXC=ambiguous,single_src,neighbour_linked;SRC_COUNTRY=Australia;SRC_LAB=Doherty;GENE=gene-orf1ab;AA_POS=1834;AA_REF=G;AA_ALT=X MN908947.3 5847 . G T,K,C,A . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=Australia;SRC_LAB=VIDRL;GENE=gene-orf1ab;AA_POS=1861;AA_REF=G;AA_ALT=V,X,A,D MN908947.3 5880 . G T,K,C,A . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=Australia;SRC_LAB=VIDRL;GENE=gene-orf1ab;AA_POS=1872;AA_REF=S;AA_ALT=I,X,T,N MN908947.3 6167 . G R,K . mask SUB=RCD;EXC=ambiguous,single_src;SRC_COUNTRY=Switzerland;SRC_LAB=ETH_Zurich;GENE=gene-orf1ab;AA_POS=1968;AA_REF=V;AA_ALT=X,X MN908947.3 6255 . C T . mask SUB=NDM,RCD;EXC=highly_homoplasic,narrow_src;SRC_COUNTRY=Netherlands,South_Africa;SRC_LAB=Erasmus,NHLS;GENE=gene-orf1ab;AA_POS=1997;AA_REF=A;AA_ALT=V MN908947.3 6309 . G K,R,T,C,A . caution SUB=NDM;EXC=neighbour_linked;SRC_COUNTRY=.;SRC_LAB=.;GENE=gene-orf1ab;AA_POS=2015;AA_REF=S;AA_ALT=X,X,I,T,N MN908947.3 6310 . C Y,M,T,A,G . caution SUB=NDM;EXC=neighbour_linked;SRC_COUNTRY=.;SRC_LAB=.;GENE=gene-orf1ab;AA_POS=2015;AA_REF=S;AA_ALT=S,X,S,R,R MN908947.3 6312 . C Y,M,T,A,G . caution SUB=NDM;EXC=neighbour_linked;SRC_COUNTRY=.;SRC_LAB=.;GENE=gene-orf1ab;AA_POS=2016;AA_REF=T;AA_ALT=X,X,I,K,R MN908947.3 6483 . G R,K,T . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=Australia;SRC_LAB=VIDRL,University_of_Melbourne;GENE=gene-orf1ab;AA_POS=2073;AA_REF=G;AA_ALT=X,X,V MN908947.3 6804 . G T,K,C,A . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=Australia;SRC_LAB=VIDRL;GENE=gene-orf1ab;AA_POS=2180;AA_REF=C;AA_ALT=F,X,S,Y MN908947.3 6866 . A T,W . caution SUB=NDM,RCD;EXC=ambiguous;SRC_COUNTRY=Italy;SRC_LAB=IZSAM;GENE=gene-orf1ab;AA_POS=2201;AA_REF=N;AA_ALT=Y,X MN908947.3 6869 . A T,W . mask SUB=NDM,RCD;EXC=ambiguous,homoplasic,single_src;SRC_COUNTRY=Italy;SRC_LAB=IZSAM;GENE=gene-orf1ab;AA_POS=2202;AA_REF=T;AA_ALT=S,X MN908947.3 6874 . T C,Y,G . mask SUB=LG;EXC=single_src,highly_homoplasic;SRC_COUNTRY=Russia;SRC_LAB=WHO_Russia;GENE=gene-orf1ab;AA_POS=2203;AA_REF=V;AA_ALT=V,V,V MN908947.3 6877 . G K,T . caution SUB=RCD;EXC=ambiguous,single_src;SRC_COUNTRY=Swiss;SRC_LAB=ETH_Zurich;GENE=gene-orf1ab;AA_POS=2204;AA_REF=K;AA_ALT=X,N MN908947.3 6971 . T C,W,Y . caution SUB=NDM;EXC=neighbour_linked,single_src;SRC_COUNTRY=Australia;SRC_LAB=VIDRL;GENE=gene-orf1ab;AA_POS=2236;AA_REF=L;AA_ALT=L,J,L MN908947.3 6975 . G R,T . caution SUB=NDM;EXC=neighbour_linked,single_src;SRC_COUNTRY=Australia;SRC_LAB=VIDRL;GENE=gene-orf1ab;AA_POS=2237;AA_REF=S;AA_ALT=X,I MN908947.3 6977 . G R,K,A . caution SUB=NDM;EXC=neighbour_linked,single_src;SRC_COUNTRY=Australia;SRC_LAB=VIDRL;GENE=gene-orf1ab;AA_POS=2238;AA_REF=V;AA_ALT=X,X,I MN908947.3 7017 . G K,T,A,S . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=Australia;SRC_LAB=VIDRL,University_of_Melbourne;GENE=gene-orf1ab;AA_POS=2251;AA_REF=G;AA_ALT=X,V,D,X MN908947.3 7038 . G R,K,T,A . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=Australia;SRC_LAB=VIDRL,University_of_Melbourne;GENE=gene-orf1ab;AA_POS=2258;AA_REF=G;AA_ALT=X,X,V,D MN908947.3 7090 . T K,G . caution SUB=RCD;EXC=ambiguous,single_src;SRC_COUNTRY=UK;SRC_LAB=Public_Health_England;GENE=gene-orf1ab;AA_POS=2275;AA_REF=N;AA_ALT=X,K MN908947.3 7118 . T K,Y,C,A,G . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=Switzerland;SRC_LAB=ETH_Zurich;GENE=gene-orf1ab;AA_POS=2285;AA_REF=S;AA_ALT=X,X,P,T,A MN908947.3 7214 . G K,T,A . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=Australia;SRC_LAB=VIDRL,University_of_Melbourne;GENE=gene-orf1ab;AA_POS=2317;AA_REF=D;AA_ALT=X,Y,N MN908947.3 7246 . G K,T . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=Australia;SRC_LAB=VIDRL,University_of_Melbourne;GENE=gene-orf1ab;AA_POS=2327;AA_REF=W;AA_ALT=X,C MN908947.3 7305 . T K,A,Y . caution SUB=RCD;EXC=ambiguous,single_src;SRC_COUNTRY=Switzerland;SRC_LAB=ETH_Zurich;GENE=gene-orf1ab;AA_POS=2347;AA_REF=M;AA_ALT=X,K,X MN908947.3 7396 . T C,W,Y . caution SUB=NDM,RCD;EXC=ambiguous;SRC_COUNTRY=Italy;SRC_LAB=IZSAM;GENE=gene-orf1ab;AA_POS=2377;AA_REF=I;AA_ALT=I,I,I MN908947.3 7805 . G R,A . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=Australia;SRC_LAB=VIDRL;GENE=gene-orf1ab;AA_POS=2514;AA_REF=E;AA_ALT=X,K MN908947.3 8022 . T K,C,G . mask SUB=NDM,RCD;EXC=highly_ambiguous,highly_homoplasic,narrow_src;SRC_COUNTRY=India;SRC_LAB=NCDC;GENE=gene-orf1ab;AA_POS=2586;AA_REF=V;AA_ALT=X,A,G MN908947.3 8026 . A T,W,G . mask SUB=RCD;EXC=ambiguous,homoplasic,narrow_src;SRC_COUNTRY=South_Africa,India;SRC_LAB=NHLS,NCDC;GENE=gene-orf1ab;AA_POS=2587;AA_REF=A;AA_ALT=A,A,A MN908947.3 8328 . T G . mask SUB=LG;EXC=single_src,highly_homoplasic;SRC_COUNTRY=South_Africa;SRC_LAB=NICDNHLS;GENE=gene-orf1ab;AA_POS=2688;AA_REF=L;AA_ALT=R MN908947.3 8459 . G K,T . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=Australia;SRC_LAB=VIDRL,University_of_Melbourne;GENE=gene-orf1ab;AA_POS=2732;AA_REF=A;AA_ALT=X,S MN908947.3 8550 . G K,T . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=Australia;SRC_LAB=VIDRL;GENE=gene-orf1ab;AA_POS=2762;AA_REF=G;AA_ALT=X,V MN908947.3 8658 . A T,C,W,G . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=USA;SRC_LAB=Houston;GENE=gene-orf1ab;AA_POS=2798;AA_REF=K;AA_ALT=I,T,X,R MN908947.3 8678 . G R,T,A . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=Australia;SRC_LAB=VIDRL;GENE=gene-orf1ab;AA_POS=2805;AA_REF=E;AA_ALT=X,*,K MN908947.3 8688 . G K,T,A,B . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=Australia;SRC_LAB=VIDRL;GENE=gene-orf1ab;AA_POS=2808;AA_REF=G;AA_ALT=X,V,E,X MN908947.3 8696 . G K,R,B,T,A . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=Australia;SRC_LAB=VIDRL,University_of_Melbourne;GENE=gene-orf1ab;AA_POS=2811;AA_REF=A;AA_ALT=X,X,X,S,T MN908947.3 8790 . G K,T . mask SUB=NDM,RCD;EXC=highly_ambiguous,homoplasic,single_src;SRC_COUNTRY=Australia;SRC_LAB=VIDRL;GENE=gene-orf1ab;AA_POS=2842;AA_REF=G;AA_ALT=X,V MN908947.3 8827 . T W . mask SUB=RCD;EXC=ambiguous,neighbour_linked;SRC_COUNTRY=Italy;SRC_LAB=IZSAM;GENE=gene-orf1ab;AA_POS=2854;AA_REF=I;AA_ALT=I MN908947.3 8828 . G K,A . mask SUB=RCD;EXC=ambiguous,neighbour_linked;SRC_COUNTRY=Italy;SRC_LAB=IZSAM;GENE=gene-orf1ab;AA_POS=2855;AA_REF=A;AA_ALT=X,T MN908947.3 8835 . T C . mask SUB=TS;EXC=amplicon_drop_or_primer_artefact;SRC_COUNTRY=.;SRC_LAB=.;GENE=gene-orf1ab;AA_POS=2857;AA_REF=V;AA_ALT=A MN908947.3 8886 . T A,C,W,Y . mask SUB=LG;EXC=single_src,highly_homoplasic;SRC_COUNTRY=USA;SRC_LAB=University_of_Washington;GENE=gene-orf1ab;AA_POS=2874;AA_REF=L;AA_ALT=*,S,X,X MN908947.3 8887 . A R,C,G . mask SUB=LG;EXC=single_src,highly_homoplasic;SRC_COUNTRY=Russia;SRC_LAB=WHO_Russia;GENE=gene-orf1ab;AA_POS=2874;AA_REF=L;AA_ALT=L,F,L MN908947.3 8943 . G K,T,A . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=Australia;SRC_LAB=VIDRL;GENE=gene-orf1ab;AA_POS=2893;AA_REF=G;AA_ALT=X,V,D MN908947.3 8999 . G K,T,A . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=Australia;SRC_LAB=VIDRL;GENE=gene-orf1ab;AA_POS=2912;AA_REF=A;AA_ALT=X,S,T MN908947.3 9039 . C T,M,Y . mask SUB=NDM;EXC=ambiguous,single_src;SRC_COUNTRY=India;SRC_LAB=NCDC;GENE=gene-orf1ab;AA_POS=2925;AA_REF=A;AA_ALT=V,X,X MN908947.3 9141 . G K,R,T,C,A . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=Australia;SRC_LAB=VIDRL;GENE=gene-orf1ab;AA_POS=2959;AA_REF=G;AA_ALT=X,X,V,A,D MN908947.3 9249 . G T,K,C . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=Australia;SRC_LAB=VIDRL;GENE=gene-orf1ab;AA_POS=2995;AA_REF=G;AA_ALT=V,X,A MN908947.3 9276 . G T,K,C,A . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=Switzerland;SRC_LAB=ETH_Zurich;GENE=gene-orf1ab;AA_POS=3004;AA_REF=W;AA_ALT=L,X,S,* MN908947.3 9471 . G C,A,S . caution SUB=RCD;EXC=ambiguous,single_src;SRC_COUNTRY=India;SRC_LAB=NCDC;GENE=gene-orf1ab;AA_POS=3069;AA_REF=R;AA_ALT=T,K,X MN908947.3 10046 . G R,K,A . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=UK;SRC_LAB=Sanger;GENE=gene-orf1ab;AA_POS=3261;AA_REF=V;AA_ALT=X,X,I MN908947.3 10122 . G K,T,S . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=Australia;SRC_LAB=VIDRL,University_of_Melbourne;GENE=gene-orf1ab;AA_POS=3286;AA_REF=G;AA_ALT=X,V,X MN908947.3 10129 . T C,W,Y . mask SUB=NDM,RCD;EXC=highly_ambiguous,homoplasic,single_src;SRC_COUNTRY=USA;SRC_LAB=Chan_Zuckerberg_Biohub;GENE=gene-orf1ab;AA_POS=3288;AA_REF=T;AA_ALT=T,T,T MN908947.3 10157 . G K,T,A . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=Australia;SRC_LAB=VIDRL,University_of_Melbourne;GENE=gene-orf1ab;AA_POS=3298;AA_REF=V;AA_ALT=X,L,I MN908947.3 10239 . C M,A . mask SUB=RCD;EXC=homoplasic,single_src;SRC_COUNTRY=UK;SRC_LAB=Sanger_COG_UK;GENE=gene-orf1ab;AA_POS=3325;AA_REF=S;AA_ALT=X,Y MN908947.3 10266 . G R,K,T,A . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=Australia;SRC_LAB=VIDRL,University_of_Melbourne;GENE=gene-orf1ab;AA_POS=3334;AA_REF=G;AA_ALT=X,X,V,D MN908947.3 10554 . T D,A . mask SUB=LG;EXC=single_src,highly_homoplasic;SRC_COUNTRY=USA;SRC_LAB=University_of_Washington;GENE=gene-orf1ab;AA_POS=3430;AA_REF=L;AA_ALT=X,* MN908947.3 10716 . A C,W,G . mask SUB=LG;EXC=single_src,highly_homoplasic;SRC_COUNTRY=Denmark;SRC_LAB=Aalborg_University;GENE=gene-orf1ab;AA_POS=3484;AA_REF=N;AA_ALT=T,X,S MN908947.3 10764 . A T,C,G . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=Canada;SRC_LAB=APL;GENE=gene-orf1ab;AA_POS=3500;AA_REF=Y;AA_ALT=F,S,C MN908947.3 10986 . G D,K,C,S,T . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=Australia;SRC_LAB=VIDRL,University_of_Melbourne;GENE=gene-orf1ab;AA_POS=3574;AA_REF=R;AA_ALT=X,X,T,X,I MN908947.3 11048 . G K,T . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=Australia;SRC_LAB=VIDRL,University_of_Melbourne;GENE=gene-orf1ab;AA_POS=3595;AA_REF=V;AA_ALT=X,F MN908947.3 11074 . C T,Y . mask SUB=NDM,RCD;EXC=highly_homoplasic;SRC_COUNTRY=.;SRC_LAB=.;GENE=gene-orf1ab;AA_POS=3603;AA_REF=F;AA_ALT=F,F MN908947.3 11083 . G K,T,A . mask SUB=NDM,RCD;EXC=highly_homoplasic;SRC_COUNTRY=.;SRC_LAB=.;GENE=gene-orf1ab;AA_POS=3606;AA_REF=L;AA_ALT=X,F,L MN908947.3 11392 . G T,K,C . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=Australia;SRC_LAB=VIDRL;GENE=gene-orf1ab;AA_POS=3709;AA_REF=W;AA_ALT=C,X,C MN908947.3 11535 . G K,T . mask SUB=NDM,RCD;EXC=ambiguous,highly_homoplasic,single_src;SRC_COUNTRY=Australia;SRC_LAB=VIDRL;GENE=gene-orf1ab;AA_POS=3757;AA_REF=G;AA_ALT=X,V MN908947.3 12041 . G T,K,C,A . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=Australia;SRC_LAB=VIDRL;GENE=gene-orf1ab;AA_POS=3926;AA_REF=D;AA_ALT=Y,X,H,N MN908947.3 12164 . G K,T,A . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=Australia;SRC_LAB=VIDRL;GENE=gene-orf1ab;AA_POS=3967;AA_REF=A;AA_ALT=X,S,T MN908947.3 12413 . A R,T,C,G . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=USA;SRC_LAB=MGSC;GENE=gene-orf1ab;AA_POS=4050;AA_REF=N;AA_ALT=B,Y,H,D MN908947.3 12491 . G T,K,C,A . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=Australia;SRC_LAB=VIDRL;GENE=gene-orf1ab;AA_POS=4076;AA_REF=D;AA_ALT=Y,X,H,N MN908947.3 12506 . A R . caution SUB=RCD;EXC=ambiguous,single_src;SRC_COUNTRY=Chile;SRC_LAB=ISPC;GENE=gene-orf1ab;AA_POS=4081;AA_REF=K;AA_ALT=X MN908947.3 12685 . G K,T,A . caution SUB=LG;EXC=narrow_src,highly_ambiguous;SRC_COUNTRY=India;SRC_LAB=India;GENE=gene-orf1ab;AA_POS=4140;AA_REF=Q;AA_ALT=X,H,Q MN908947.3 12698 . A C,W,G . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=USA;SRC_LAB=Houston;GENE=gene-orf1ab;AA_POS=4145;AA_REF=S;AA_ALT=R,X,G MN908947.3 12751 . T A,W . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=Switzerland;SRC_LAB=ETH_Zurich;GENE=gene-orf1ab;AA_POS=4162;AA_REF=A;AA_ALT=A,A MN908947.3 13117 . A C,M,G . mask SUB=LG;EXC=single_src,highly_homoplasic;SRC_COUNTRY=Denmark;SRC_LAB=Aalborg_University;GENE=gene-orf1ab;AA_POS=4284;AA_REF=L;AA_ALT=L,L,L MN908947.3 13161 . G K,T,A . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=Australia;SRC_LAB=VIDRL;GENE=gene-orf1ab;AA_POS=4299;AA_REF=C;AA_ALT=X,F,Y MN908947.3 13193 . G K,T,A . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=Australia;SRC_LAB=VIDRL;GENE=gene-orf1ab;AA_POS=4310;AA_REF=V;AA_ALT=X,F,I MN908947.3 13239 . C T,Y,G . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=Australia;SRC_LAB=VIDRL;GENE=gene-orf1ab;AA_POS=4325;AA_REF=S;AA_ALT=L,X,W MN908947.3 13402 . T K,C,G . mask SUB=NDM,RCD;EXC=homoplasic,narrow_src,amended;SRC_COUNTRY=Belgium,India,Denmark;SRC_LAB=KU_Leuven,NCDC,SSI;GENE=gene-orf1ab;AA_POS=4379;AA_REF=Y;AA_ALT=X,Y,* MN908947.3 13408 . T K . mask SUB=NDM,RCD;EXC=homoplasic,narrow_src,amended;SRC_COUNTRY=Belgium,India,South_Africa;SRC_LAB=KU_Leuven,NCDC,SSI;GENE=gene-orf1ab;AA_POS=4381;AA_REF=C;AA_ALT=X MN908947.3 13476 . C T,Y . mask SUB=NDM;EXC=highly_ambiguous,narrow_src;SRC_COUNTRY=Turkey;SRC_LAB=Ministry_of_Health;GENE=gene-orf1ab;AA_POS=4404;AA_REF=C;AA_ALT=V,X MN908947.3 13512 . A T,C,G . caution SUB=NDM;EXC=neighbour_linked;SRC_COUNTRY=.;SRC_LAB=.;GENE=gene-orf1ab;AA_POS=4416;AA_REF=T;AA_ALT=L,P,R MN908947.3 13513 . G K,T,A . caution SUB=NDM;EXC=neighbour_linked;SRC_COUNTRY=.;SRC_LAB=.;GENE=gene-orf1ab;AA_POS=4416;AA_REF=T;AA_ALT=X,H,Q MN908947.3 13514 . G T,C,A,S . caution SUB=NDM;EXC=neighbour_linked;SRC_COUNTRY=.;SRC_LAB=.;GENE=gene-orf1ab;AA_POS=4417;AA_REF=G;AA_ALT=S,P,T,X MN908947.3 13571 . G K,T . mask SUB=NDM,RCD;EXC=highly_ambiguous,homoplasic,single_src;SRC_COUNTRY=Australia;SRC_LAB=VIDRL;GENE=gene-orf1ab;AA_POS=4436;AA_REF=G;AA_ALT=X,F MN908947.3 13599 . T C,Y . mask SUB=LG;EXC=single_src,highly_homoplasic;SRC_COUNTRY=Russia;SRC_LAB=WHO_Russia;GENE=gene-orf1ab;AA_POS=4445;AA_REF=C;AA_ALT=A,X MN908947.3 13650 . T K . caution SUB=RCD;EXC=ambiguous,single_src;SRC_COUNTRY=India;SRC_LAB=CSIR;GENE=gene-orf1ab;AA_POS=4462;AA_REF=F;AA_ALT=X MN908947.3 13686 . T C,A,Y . caution SUB=NDM;EXC=neighbour_linked;SRC_COUNTRY=.;SRC_LAB=.;GENE=gene-orf1ab;AA_POS=4474;AA_REF=H;AA_ALT=T,K,X MN908947.3 13687 . G T . mask SUB=LG;EXC=single_src,highly_homoplasic,neighbour_linked;SRC_COUNTRY=USA;SRC_LAB=University_of_Washington;GENE=gene-orf1ab;AA_POS=4474;AA_REF=H;AA_ALT=I MN908947.3 13693 . A R,T,W . caution SUB=NDM;EXC=neighbour_linked;SRC_COUNTRY=.;SRC_LAB=.;GENE=gene-orf1ab;AA_POS=4476;AA_REF=E;AA_ALT=K,N,X MN908947.3 14197 . G K,T,A,S . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=Australia;SRC_LAB=VIDRL,University_of_Melbourne;GENE=gene-orf1ab;AA_POS=4644;AA_REF=T;AA_ALT=L,L,L,L MN908947.3 14222 . T B,G . mask SUB=LG;EXC=single_src,highly_homoplasic,neighbour_linked;SRC_COUNTRY=USA;SRC_LAB=University_of_Washington;GENE=gene-orf1ab;AA_POS=4653;AA_REF=L;AA_ALT=X,E MN908947.3 14223 . A C,G . mask SUB=LG;EXC=single_src,highly_homoplasic,neighbour_linked;SRC_COUNTRY=USA;SRC_LAB=University_of_Washington;GENE=gene-orf1ab;AA_POS=4653;AA_REF=L;AA_ALT=S,* MN908947.3 14225 . C M,T,A,B . mask SUB=LG;EXC=single_src,highly_homoplasic,neighbour_linked;SRC_COUNTRY=USA;SRC_LAB=University_of_Washington;GENE=gene-orf1ab;AA_POS=4654;AA_REF=T;AA_ALT=X,*,K,X MN908947.3 14277 . G K,T . mask SUB=NDM,RCD;EXC=highly_ambiguous,homoplasic,single_src;SRC_COUNTRY=Australia;SRC_LAB=VIDRL;GENE=gene-orf1ab;AA_POS=4671;AA_REF=R;AA_ALT=X,V MN908947.3 14488 . G K,T,A . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=Australia;SRC_LAB=VIDRL;GENE=gene-orf1ab;AA_POS=4741;AA_REF=R;AA_ALT=X,D,E MN908947.3 14536 . C T,Y . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=Australia;SRC_LAB=VIDRL;GENE=gene-orf1ab;AA_POS=4757;AA_REF=R;AA_ALT=D,D MN908947.3 14548 . G D,R,K,A . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=Australia;SRC_LAB=VIDRL,University_of_Melbourne;GENE=gene-orf1ab;AA_POS=4761;AA_REF=K;AA_ALT=X,R,X,R MN908947.3 14553 . A T,C,G . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=USA;SRC_LAB=ETH_Zurich;GENE=gene-orf1ab;AA_POS=4763;AA_REF=L;AA_ALT=F,S,C MN908947.3 14851 . T C,A,G . mask SUB=LG;EXC=single_src,highly_homoplasic;SRC_COUNTRY=Switzerland;SRC_LAB=ETH_Zurich;GENE=gene-orf1ab;AA_POS=4862;AA_REF=L;AA_ALT=Y,*,* MN908947.3 14852 . T C,Y,G . mask SUB=LG;EXC=single_src,highly_homoplasic;SRC_COUNTRY=Switzerland;SRC_LAB=ETH_Zurich;GENE=gene-orf1ab;AA_POS=4863;AA_REF=F;AA_ALT=L,L,V MN908947.3 15075 . G K,T,A,S . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=Australia;SRC_LAB=VIDRL;GENE=gene-orf1ab;AA_POS=4937;AA_REF=K;AA_ALT=X,I,N,X MN908947.3 15103 . C T . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=USA;SRC_LAB=Houston;GENE=gene-orf1ab;AA_POS=4946;AA_REF=A;AA_ALT=L MN908947.3 15199 . G K,T,A . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=Australia;SRC_LAB=VIDRL;GENE=gene-orf1ab;AA_POS=4978;AA_REF=T;AA_ALT=L,L,L MN908947.3 15230 . G K,T,A . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=Australia;SRC_LAB=VIDRL;GENE=gene-orf1ab;AA_POS=4989;AA_REF=G;AA_ALT=X,F,I MN908947.3 15435 . A R,G . mask SUB=NDM,RCD;EXC=highly_ambiguous,homoplasic,single_src;SRC_COUNTRY=India;SRC_LAB=NCDC;GENE=gene-orf1ab;AA_POS=5057;AA_REF=E;AA_ALT=X,R MN908947.3 15513 . T A,C,W . caution SUB=LG;EXC=single_src,ambiguous;SRC_COUNTRY=India;SRC_LAB=NCDC;GENE=gene-orf1ab;AA_POS=5083;AA_REF=N;AA_ALT=K,T,X MN908947.3 15521 . T A . mask SUB=TS;EXC=amplicon_drop_or_primer_artefact;SRC_COUNTRY=.;SRC_LAB=.;GENE=gene-orf1ab;AA_POS=5086;AA_REF=F;AA_ALT=I MN908947.3 15769 . G R,K,T,A . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=Australia;SRC_LAB=VIDRL,University_of_Melbourne;GENE=gene-orf1ab;AA_POS=5168;AA_REF=V;AA_ALT=X,X,C,* MN908947.3 15771 . T K,D,Y,H,W,A . caution SUB=RCD;EXC=ambiguous,single_src;SRC_COUNTRY=USA;SRC_LAB=Chan_Zuckerberg_Biohub;GENE=gene-orf1ab;AA_POS=5169;AA_REF=A;AA_ALT=X,X,X,X,X,Q MN908947.3 15922 . T C,Y . mask SUB=NDM,RCD;EXC=ambiguous,homoplasic,single_src;SRC_COUNTRY=USA;SRC_LAB=Chan_Zuckerberg_Biohub;GENE=gene-orf1ab;AA_POS=5219;AA_REF=V;AA_ALT=C,C MN908947.3 16130 . G T,A . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=USA;SRC_LAB=Houston;GENE=gene-orf1ab;AA_POS=5289;AA_REF=G;AA_ALT=Y,N MN908947.3 16132 . C T . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=USA;SRC_LAB=Houston;GENE=gene-orf1ab;AA_POS=5289;AA_REF=G;AA_ALT=D MN908947.3 16188 . G K,T . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=Australia;SRC_LAB=VIDRL,University_of_Melbourne;GENE=gene-orf1ab;AA_POS=5308;AA_REF=W;AA_ALT=X,V MN908947.3 16210 . A R,D,W . caution SUB=RCD;EXC=ambiguous,single_src;SRC_COUNTRY=Switzerland;SRC_LAB=ETH_Zurich;GENE=gene-orf1ab;AA_POS=5315;AA_REF=A;AA_ALT=L,L,L MN908947.3 16290 . T K . mask SUB=RCD;EXC=highly_ambiguous,single_src;SRC_COUNTRY=UK;SRC_LAB=Sanger_COG_UK;GENE=gene-orf1ab;AA_POS=5342;AA_REF=A;AA_ALT=X MN908947.3 16537 . G R,K,T,A . caution SUB=RCD;EXC=ambiguous,single_src;SRC_COUNTRY=Qatar;SRC_LAB=BRC;GENE=gene-orf1ab;AA_POS=5424;AA_REF=S;AA_ALT=A,A,A,A MN908947.3 16738 . G T,K,C . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=Australia;SRC_LAB=VIDRL;GENE=gene-orf1ab;AA_POS=5491;AA_REF=W;AA_ALT=G,G,G MN908947.3 16787 . G K,T . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=Australia;SRC_LAB=VIDRL,University_of_Melbourne;GENE=gene-orf1ab;AA_POS=5508;AA_REF=G;AA_ALT=X,F MN908947.3 16887 . C T,Y . mask SUB=NDM,RCD;EXC=highly_homoplasic;SRC_COUNTRY=.;SRC_LAB=.;GENE=gene-orf1ab;AA_POS=5541;AA_REF=Y;AA_ALT=I,X MN908947.3 16988 . G K,T,A . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=Australia;SRC_LAB=VIDRL;GENE=gene-orf1ab;AA_POS=5575;AA_REF=G;AA_ALT=X,S,T MN908947.3 17096 . G K,T . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=Australia;SRC_LAB=VIDRL,University_of_Melbourne;GENE=gene-orf1ab;AA_POS=5611;AA_REF=G;AA_ALT=X,L MN908947.3 17178 . T C,G . mask SUB=LG;EXC=single_src,highly_homoplasic,neighbour_linked;SRC_COUNTRY=USA;SRC_LAB=University_of_Washington;GENE=gene-orf1ab;AA_POS=5638;AA_REF=V;AA_ALT=S,W MN908947.3 17179 . G T,S . mask SUB=LG;EXC=single_src,highly_homoplasic,neighbour_linked;SRC_COUNTRY=USA;SRC_LAB=University_of_Washington;GENE=gene-orf1ab;AA_POS=5638;AA_REF=V;AA_ALT=F,X MN908947.3 17182 . G A . mask SUB=LG;EXC=single_src,highly_homoplasic,neighbour_linked;SRC_COUNTRY=USA;SRC_LAB=University_of_Washington;GENE=gene-orf1ab;AA_POS=5639;AA_REF=D;AA_ALT=I MN908947.3 17479 . G K,T . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=Australia;SRC_LAB=VIDRL,University_of_Melbourne;GENE=gene-orf1ab;AA_POS=5738;AA_REF=K;AA_ALT=X,S MN908947.3 17567 . G K,A . mask SUB=LG;EXC=single_src,highly_homoplasic;SRC_COUNTRY=USA;SRC_LAB=WPHL;GENE=gene-orf1ab;AA_POS=5768;AA_REF=C;AA_ALT=X,I MN908947.3 17668 . G R,K,T,S . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=Australia;SRC_LAB=VIDRL;GENE=gene-orf1ab;AA_POS=5801;AA_REF=K;AA_ALT=R,X,S,X MN908947.3 17675 . T C,Y . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=Switzerland;SRC_LAB=ETH_Zurich;GENE=gene-orf1ab;AA_POS=5804;AA_REF=I;AA_ALT=P,X MN908947.3 17716 . G R,K,T,A . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=Australia;SRC_LAB=VIDRL;GENE=gene-orf1ab;AA_POS=5817;AA_REF=I;AA_ALT=*,X,Y,* MN908947.3 17754 . G K,T,S . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=Australia;SRC_LAB=VIDRL,University_of_Melbourne;GENE=gene-orf1ab;AA_POS=5830;AA_REF=W;AA_ALT=X,V,X MN908947.3 17848 . G K,T,B . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=Australia;SRC_LAB=VIDRL,University_of_Melbourne;GENE=gene-orf1ab;AA_POS=5861;AA_REF=Q;AA_ALT=X,S,X MN908947.3 18297 . G K,T,A . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=Australia;SRC_LAB=VIDRL;GENE=gene-orf1ab;AA_POS=6011;AA_REF=W;AA_ALT=X,V,E MN908947.3 18445 . G K,T,A . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=Australia;SRC_LAB=VIDRL,University_of_Melbourne;GENE=gene-orf1ab;AA_POS=6060;AA_REF=R;AA_ALT=X,D,E MN908947.3 18465 . T K,G . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=UK;SRC_LAB=Sanger;GENE=gene-orf1ab;AA_POS=6067;AA_REF=P;AA_ALT=X,R MN908947.3 18505 . G R . caution SUB=NDM,RCD;EXC=ambiguous,neighbour_linked;SRC_COUNTRY=USA;SRC_LAB=CDC_DVD;GENE=gene-orf1ab;AA_POS=6080;AA_REF=K;AA_ALT=K MN908947.3 18506 . G K,S . caution SUB=NDM,RCD;EXC=ambiguous,neighbour_linked;SRC_COUNTRY=USA;SRC_LAB=CDC_DVD;GENE=gene-orf1ab;AA_POS=6081;AA_REF=G;AA_ALT=X,X MN908947.3 18690 . T K,C . caution SUB=RCD;EXC=ambiguous,single_src;SRC_COUNTRY=India;SRC_LAB=NCDC;GENE=gene-orf1ab;AA_POS=6142;AA_REF=F;AA_ALT=X,S MN908947.3 18716 . G K,T . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=Australia;SRC_LAB=VIDRL;GENE=gene-orf1ab;AA_POS=6151;AA_REF=C;AA_ALT=X,F MN908947.3 19250 . G K,T,A . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=Australia;SRC_LAB=VIDRL;GENE=gene-orf1ab;AA_POS=6329;AA_REF=R;AA_ALT=X,*,K MN908947.3 19286 . G R,T,C,A . mask SUB=LG;EXC=single_src,highly_homoplasic;SRC_COUNTRY=South_Korea;SRC_LAB=KDCPA;GENE=gene-orf1ab;AA_POS=6341;AA_REF=G;AA_ALT=X,L,L,M MN908947.3 19298 . A R,D,T,W . mask SUB=RCD;EXC=highly_ambiguous,single_src;SRC_COUNTRY=Switzerland;SRC_LAB=ETH_Zurich;GENE=gene-orf1ab;AA_POS=6345;AA_REF=Y;AA_ALT=X,X,L,X MN908947.3 19299 . T Y,G . mask SUB=RCD;EXC=homoplasic,ambiguous,narrow_src;SRC_COUNTRY=China;SRC_LAB=Ditan;GENE=gene-orf1ab;AA_POS=6345;AA_REF=Y;AA_ALT=X,R MN908947.3 19338 . A R,M,G . caution SUB=RCD;EXC=highly_ambiguous,narrow_src;SRC_COUNTRY=UK;SRC_LAB=Public_Health_England,Public_Health_Wales;GENE=gene-orf1ab;AA_POS=6358;AA_REF=K;AA_ALT=X,X,R MN908947.3 19339 . A R,M,W . caution SUB=RCD;EXC=ambiguous,single_src;SRC_COUNTRY=Switzerland;SRC_LAB=ETH_Zurich;GENE=gene-orf1ab;AA_POS=6358;AA_REF=K;AA_ALT=K,X,X MN908947.3 19344 . T K,C,A,Y . caution SUB=NDM;EXC=ambiguous,amended;SRC_COUNTRY=USA,UK;SRC_LAB=Houston,Nottingham;GENE=gene-orf1ab;AA_POS=6360;AA_REF=A;AA_ALT=X,P,H,X MN908947.3 19369 . T Y,G . caution SUB=NDM;EXC=ambiguous,amended;SRC_COUNTRY=USA,UK;SRC_LAB=Houston,Nottingham;GENE=gene-orf1ab;AA_POS=6368;AA_REF=P;AA_ALT=H,Q MN908947.3 19406 . G R,K,A . caution SUB=RCD;EXC=highly_ambiguous,single_src;SRC_COUNTRY=Switzerland;SRC_LAB=ETH_Zurich;GENE=gene-orf1ab;AA_POS=6381;AA_REF=G;AA_ALT=X,X,K MN908947.3 19482 . T K,W . caution SUB=RCD;EXC=ambiguous,single_src;SRC_COUNTRY=Switzerland;SRC_LAB=ETH_Zurich;GENE=gene-orf1ab;AA_POS=6406;AA_REF=G;AA_ALT=X,X MN908947.3 19484 . C T,Y . mask SUB=NDM;EXC=highly_ambiguous,amended;SRC_COUNTRY=UK;SRC_LAB=COG_UK;GENE=gene-orf1ab;AA_POS=6407;AA_REF=A;AA_ALT=L,L MN908947.3 19548 . A D,R,T,W,G . mask SUB=RCD;EXC=ambiguous,single_src;SRC_COUNTRY=Switzerland;SRC_LAB=ETH_Zurich;GENE=gene-orf1ab;AA_POS=6428;AA_REF=S;AA_ALT=X,X,L,X,R MN908947.3 19732 . G R,K,T,A . caution SUB=RCD;EXC=homoplasic,narrow_src;SRC_COUNTRY=Switzerland;SRC_LAB=ETH_Zurich;GENE=gene-orf1ab;AA_POS=6489;AA_REF=G;AA_ALT=V,V,V,V MN908947.3 20056 . G K,A . mask SUB=RCD;EXC=ambiguous,homoplasic,single_src;SRC_COUNTRY=UK;SRC_LAB=Public_Health_England;GENE=gene-orf1ab;AA_POS=6597;AA_REF=E;AA_ALT=X,K MN908947.3 20123 . T C,Y . mask SUB=RCD;EXC=ambiguous,homoplasic,single_src;SRC_COUNTRY=UK;SRC_LAB=Public_Health_England;GENE=gene-orf1ab;AA_POS=6620;AA_REF=I;AA_ALT=L,L MN908947.3 20126 . G R,K,S,A . caution SUB=RCD;EXC=ambiguous,single_src,homoplasic;SRC_COUNTRY=UK;SRC_LAB=Public_Health_England;GENE=gene-orf1ab;AA_POS=6621;AA_REF=G;AA_ALT=X,X,Z,K MN908947.3 20128 . G T,K,C,A . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=Australia;SRC_LAB=VIDRL;GENE=gene-orf1ab;AA_POS=6621;AA_REF=G;AA_ALT=D,X,D,E MN908947.3 20254 . G K,T . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=Australia;SRC_LAB=VIDRL,University_of_Melbourne;GENE=gene-orf1ab;AA_POS=6663;AA_REF=I;AA_ALT=X,F MN908947.3 20465 . A R,W,G . mask SUB=RCD;EXC=highly_homoplasic,single_src;SRC_COUNTRY=USA;SRC_LAB=UNMHSC;GENE=gene-orf1ab;AA_POS=6734;AA_REF=D;AA_ALT=X,X,V MN908947.3 20857 . G T,K,C,A . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=Switzerland;SRC_LAB=ETH_Zurich;GENE=gene-orf1ab;AA_POS=6864;AA_REF=R;AA_ALT=D,X,D,E MN908947.3 21149 . G A . mask SUB=LG;EXC=single_src,highly_homoplasic;SRC_COUNTRY=USA;SRC_LAB=University_of_Washington;GENE=gene-orf1ab;AA_POS=6962;AA_REF=G;AA_ALT=K MN908947.3 21151 . G D,T . mask SUB=LG;EXC=single_src,highly_homoplasic;SRC_COUNTRY=USA;SRC_LAB=University_of_Washington;GENE=gene-orf1ab;AA_POS=6962;AA_REF=G;AA_ALT=X,D MN908947.3 21209 . T C,H . mask SUB=LG;EXC=single_src,highly_homoplasic,neighbour_linked;SRC_COUNTRY=USA;SRC_LAB=University_of_Washington;GENE=gene-orf1ab;AA_POS=6982;AA_REF=M;AA_ALT=R,X MN908947.3 21212 . G A . mask SUB=LG;EXC=single_src,highly_homoplasic,neighbour_linked;SRC_COUNTRY=USA;SRC_LAB=University_of_Washington;GENE=gene-orf1ab;AA_POS=6983;AA_REF=G;AA_ALT=N MN908947.3 21281 . G T,K,C,A . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=Australia;SRC_LAB=VIDRL;GENE=gene-orf1ab;AA_POS=7006;AA_REF=G;AA_ALT=Y,X,H,N MN908947.3 21302 . C M,T,A,S . caution SUB=NDM;EXC=neighbour_linked;SRC_COUNTRY=.;SRC_LAB=.;GENE=gene-orf1ab;AA_POS=7013;AA_REF=P;AA_ALT=X,Y,N,X MN908947.3 21304 . C Y,S,M,T,A . caution SUB=NDM;EXC=neighbour_linked;SRC_COUNTRY=.;SRC_LAB=.;GENE=gene-orf1ab;AA_POS=7013;AA_REF=P;AA_ALT=H,X,X,H,Q MN908947.3 21305 . G R,K,T,A . caution SUB=NDM;EXC=neighbour_linked;SRC_COUNTRY=.;SRC_LAB=.;GENE=gene-orf1ab;AA_POS=7014;AA_REF=R;AA_ALT=X,X,S,T MN908947.3 21379 . T C,Y . caution SUB=RCD;EXC=ambiguous,single_src;SRC_COUNTRY=Switzerland;SRC_LAB=ETH_Zurich;GENE=gene-orf1ab;AA_POS=7038;AA_REF=S;AA_ALT=L,L MN908947.3 21550 . A C,M . mask SUB=NDM,RCD;EXC=ambiguous,homoplasic,narrow_src;SRC_COUNTRY=India;SRC_LAB=CSIR;GENE=gene-orf1ab;AA_POS=7095;AA_REF=N;AA_ALT=T,T MN908947.3 21551 . A R,T,W . mask SUB=NDM,RCD;EXC=ambiguous,homoplasic,narrow_src;SRC_COUNTRY=India;SRC_LAB=CSIR;GENE=gene-orf1ab;AA_POS=7096;AA_REF=N;AA_ALT=X,S,X MN908947.3 21575 . C T,Y . mask SUB=NDM,RCD;EXC=highly_homoplasic;SRC_COUNTRY=.;SRC_LAB=.;GENE=gene-S;AA_POS=5;AA_REF=L;AA_ALT=F,X MN908947.3 21609 . T K,W . caution SUB=RCD;EXC=ambiguous,single_src;SRC_COUNTRY=Switzerland;SRC_LAB=ETH_Zurich;GENE=gene-S;AA_POS=16;AA_REF=V;AA_ALT=X,X MN908947.3 21658 . C Y,M,T,H,G . caution SUB=RCD;EXC=ambiguous;SRC_COUNTRY=Switzerland;SRC_LAB=ETH_Zurich;GENE=gene-S;AA_POS=32;AA_REF=F;AA_ALT=F,X,F,X,L MN908947.3 21968 . T C,G . mask SUB=LG;EXC=single_src,highly_homoplasic;SRC_COUNTRY=USA;SRC_LAB=LACPHL;GENE=gene-S;AA_POS=136;AA_REF=C;AA_ALT=R,G MN908947.3 21987 . G T,K,C,A . mask SUB=SN,CF;EXC=amplicon_drop_or_primer_artefact,back_to_ref;SRC_COUNTRY=.;SRC_LAB=.;GENE=gene-S;AA_POS=142;AA_REF=G;AA_ALT=V,X,A,D MN908947.3 22329 . C V,T,M,Y . caution SUB=RCD;EXC=ambiguous,single_src;SRC_COUNTRY=USA;SRC_LAB=UW_CFAR;GENE=gene-S;AA_POS=256;AA_REF=S;AA_ALT=X,L,X,X MN908947.3 22335 . G K,T,A . mask SUB=NDM;EXC=highly_ambiguous,amended;SRC_COUNTRY=UK;SRC_LAB=COG_UK;GENE=gene-S;AA_POS=258;AA_REF=W;AA_ALT=X,L,* MN908947.3 22389 . T K,C,W,Y . caution SUB=RCD;EXC=ambiguous,single_src;SRC_COUNTRY=UK;SRC_LAB=Public_Health_England;GENE=gene-S;AA_POS=276;AA_REF=L;AA_ALT=X,P,X,X MN908947.3 22393 . A R,W,G . caution SUB=NDM;EXC=ambiguous,amended;SRC_COUNTRY=UK,USA,UK;SRC_LAB=Public_Health_England,Houston,Edinburgh;GENE=gene-S;AA_POS=277;AA_REF=L;AA_ALT=L,X,L MN908947.3 22410 . G K,D,R,T,C,A . caution SUB=LG;EXC=narrow_src,highly_ambiguous;SRC_COUNTRY=Australia;SRC_LAB=.;GENE=gene-S;AA_POS=283;AA_REF=G;AA_ALT=X,X,X,V,A,E MN908947.3 22416 . T C,Y . caution SUB=RCD;EXC=ambiguous,neighbour_linked,single_src;SRC_COUNTRY=UK;SRC_LAB=Public_Health_England;GENE=gene-S;AA_POS=285;AA_REF=I;AA_ALT=T,X MN908947.3 22420 . A T,W . caution SUB=RCD;EXC=ambiguous,neighbour_linked,single_src;SRC_COUNTRY=UK;SRC_LAB=Public_Health_England;GENE=gene-S;AA_POS=286;AA_REF=T;AA_ALT=T,T MN908947.3 22488 . A R,C,M,T,W . caution SUB=NDM;EXC=ambiguous,amended;SRC_COUNTRY=UK,UK,USA,USA;SRC_LAB=Edinburgh,Sheffield,Minnesota,Houston;GENE=gene-S;AA_POS=309;AA_REF=E;AA_ALT=X,A,X,V,X MN908947.3 22500 . A R,M,W . caution SUB=RCD;EXC=ambiguous,single_src;SRC_COUNTRY=UK;SRC_LAB=Public_Health_England;GENE=gene-S;AA_POS=313;AA_REF=Y;AA_ALT=X,X,X MN908947.3 22506 . C T,Y,S . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=Australia;SRC_LAB=VIDRL,University_of_Melbourne;GENE=gene-S;AA_POS=315;AA_REF=T;AA_ALT=I,X,X MN908947.3 22515 . T K,W,Y . caution SUB=NDM;EXC=ambiguous,narrow_src;SRC_COUNTRY=India,Switzerland;SRC_LAB=NCDC,.;GENE=gene-S;AA_POS=318;AA_REF=F;AA_ALT=X,X,X MN908947.3 22516 . T D,K,Y,C,W . mask SUB=RCD;EXC=highly_ambiguous,single_src;SRC_COUNTRY=Switzerland;SRC_LAB=ETH_Zurich;GENE=gene-S;AA_POS=318;AA_REF=F;AA_ALT=X,X,F,F,X MN908947.3 22521 . T K,Y . mask SUB=NDM,RCD;EXC=highly_ambiguous;SRC_COUNTRY=Austria;SRC_LAB=CeMM;GENE=gene-S;AA_POS=320;AA_REF=V;AA_ALT=X,X MN908947.3 22651 . T C,A . mask SUB=LG;EXC=single_src,highly_homoplasic;SRC_COUNTRY=Switzerland;SRC_LAB=ETH_Zurich;GENE=gene-S;AA_POS=363;AA_REF=A;AA_ALT=A,A MN908947.3 22661 . G T,A,S . mask SUB=NDM,RCD;EXC=ambiguous,homoplasic,single_src;SRC_COUNTRY=UK;SRC_LAB=Public_Health_Scotland;GENE=gene-S;AA_POS=367;AA_REF=V;AA_ALT=F,I,X MN908947.3 22797 . C A,T,M,Y . caution SUB=LG;EXC=single_src,highly_ambiguous,homoplasic;SRC_COUNTRY=Switzerland;SRC_LAB=ETH_Zurich;GENE=gene-S;AA_POS=412;AA_REF=P;AA_ALT=Q,L,X,X MN908947.3 22802 . C A,T,M,Y . mask SUB=NDM,RCD;EXC=homoplasic,single_src,amended,interspecific_contamination;SRC_COUNTRY=USA;SRC_LAB=TGEN;GENE=gene-S;AA_POS=414;AA_REF=Q;AA_ALT=K,*,X,X MN908947.3 22892 . A T,C . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=USA;SRC_LAB=Houston;GENE=gene-S;AA_POS=444;AA_REF=K;AA_ALT=*,Q MN908947.3 22904 . A R,V,H,M,T,W,G . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=Canada;SRC_LAB=APL;GENE=gene-S;AA_POS=448;AA_REF=N;AA_ALT=B,X,X,X,Y,X,D MN908947.3 23016 . G T,K,C,A . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=Australia;SRC_LAB=VIDRL;GENE=gene-S;AA_POS=485;AA_REF=G;AA_ALT=V,X,A,D MN908947.3 23116 . A T,W . caution SUB=RCD;EXC=ambiguous,single_src;SRC_COUNTRY=India;SRC_LAB=NCDC;GENE=gene-S;AA_POS=518;AA_REF=L;AA_ALT=L,L MN908947.3 23122 . A R,V,H,M,T,W,G . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=USA;SRC_LAB=Chan_Zuckerberg_Biohub;GENE=gene-S;AA_POS=520;AA_REF=A;AA_ALT=A,A,A,A,A,A,A MN908947.3 23144 . A G . caution SUB=NDM;EXC=ambiguous,amended;SRC_COUNTRY=UK,USA,USA;SRC_LAB=Sheffield,Houston,Minnesota;GENE=gene-S;AA_POS=528;AA_REF=K;AA_ALT=E MN908947.3 23162 . G K,T,A . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=Australia;SRC_LAB=VIDRL,University_of_Melbourne;GENE=gene-S;AA_POS=534;AA_REF=V;AA_ALT=X,F,I MN908947.3 23288 . G K,T,A . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=Australia;SRC_LAB=VIDRL;GENE=gene-S;AA_POS=576;AA_REF=V;AA_ALT=X,F,I MN908947.3 23291 . C T,Y . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=Australia;SRC_LAB=VIDRL,University_of_Melbourne;GENE=gene-S;AA_POS=577;AA_REF=R;AA_ALT=C,X MN908947.3 23292 . G R,K,T . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=Australia;SRC_LAB=VIDRL,University_of_Melbourne;GENE=gene-S;AA_POS=577;AA_REF=R;AA_ALT=X,X,L MN908947.3 23302 . G K,T,A . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=Australia;SRC_LAB=VIDRL,University_of_Melbourne;GENE=gene-S;AA_POS=580;AA_REF=Q;AA_ALT=X,H,Q MN908947.3 23343 . G R,K,T,A . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=Australia;SRC_LAB=VIDRL;GENE=gene-S;AA_POS=594;AA_REF=G;AA_ALT=X,X,V,D MN908947.3 23519 . G K,T . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=Australia;SRC_LAB=VIDRL,University_of_Melbourne;GENE=gene-S;AA_POS=653;AA_REF=A;AA_ALT=X,S MN908947.3 23652 . T C,A,Y . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=USA;SRC_LAB=MGSC;GENE=gene-S;AA_POS=697;AA_REF=M;AA_ALT=T,K,X MN908947.3 23738 . A T,W,G . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=Australia;SRC_LAB=VIDRL;GENE=gene-S;AA_POS=726;AA_REF=I;AA_ALT=F,X,V MN908947.3 23745 . C T,Y . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=Australia;SRC_LAB=VIDRL,University_of_Melbourne;GENE=gene-S;AA_POS=728;AA_REF=P;AA_ALT=L,X MN908947.3 23763 . C S,T,Y,G . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=Australia;SRC_LAB=VIDRL;GENE=gene-S;AA_POS=734;AA_REF=T;AA_ALT=X,I,X,R MN908947.3 23766 . C T,Y,S . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=Australia;SRC_LAB=VIDRL,University_of_Melbourne;GENE=gene-S;AA_POS=735;AA_REF=S;AA_ALT=L,X,X MN908947.3 23775 . G K,T,S . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=Australia;SRC_LAB=VIDRL;GENE=gene-S;AA_POS=738;AA_REF=C;AA_ALT=X,F,X MN908947.3 23855 . C T,A,Y . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=Australia;SRC_LAB=VIDRL,University_of_Melbourne;GENE=gene-S;AA_POS=765;AA_REF=R;AA_ALT=C,S,X MN908947.3 24389 . A M,C,W . mask SUB=MP,NDM,RCD;EXC=highly_homoplasic,highly_ambiguous,narrow_src,nanopore_adapter;SRC_COUNTRY=Belgium,India,South_Africa,China;SRC_LAB=KU_Leuven,NCDC,NHLS,Ditan;GENE=gene-S;AA_POS=943;AA_REF=S;AA_ALT=X,R,X MN908947.3 24390 . G T,K,C,S . mask SUB=MP,NDM,RCD;EXC=highly_homoplasic,highly_ambiguous,narrow_src,nanopore_adapter;SRC_COUNTRY=Belgium,India,South_Africa,China;SRC_LAB=KU_Leuven,NCDC,NHLS,Ditan;GENE=gene-S;AA_POS=943;AA_REF=S;AA_ALT=I,X,T,X MN908947.3 24410 . G C,A . mask SUB=TS;EXC=amplicon_drop_or_primer_artefact,back_to_ref;SRC_COUNTRY=.;SRC_LAB=.;GENE=gene-S;AA_POS=950;AA_REF=D;AA_ALT=H,N MN908947.3 24497 . G T,K,C . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=Australia;SRC_LAB=VIDRL,University_of_Melbourne;GENE=gene-S;AA_POS=979;AA_REF=D;AA_ALT=Y,X,H MN908947.3 24557 . G K,T,A . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=Australia;SRC_LAB=VIDRL;GENE=gene-S;AA_POS=999;AA_REF=G;AA_ALT=X,C,S MN908947.3 24622 . T Y . mask SUB=RCD;EXC=highly_ambiguous,single_src;SRC_COUNTRY=India;SRC_LAB=NCDC;GENE=gene-S;AA_POS=1020;AA_REF=A;AA_ALT=A MN908947.3 24673 . A G . caution SUB=NDM;EXC=ambiguous,amended;SRC_COUNTRY=USA;SRC_LAB=Minnesota;GENE=gene-S;AA_POS=1037;AA_REF=S;AA_ALT=S MN908947.3 24728 . G K,T . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=Australia;SRC_LAB=VIDRL;GENE=gene-S;AA_POS=1056;AA_REF=A;AA_ALT=X,S MN908947.3 24933 . G K,T . mask SUB=NDM,RCD;EXC=highly_ambiguous,highly_homoplasic,narrow_src;SRC_COUNTRY=Australia;SRC_LAB=VIDRL;GENE=gene-S;AA_POS=1124;AA_REF=G;AA_ALT=X,V MN908947.3 24942 . A R,T,W . caution SUB=NDM;EXC=ambiguous,single_src;SRC_COUNTRY=Australia;SRC_LAB=Doherty;GENE=gene-S;AA_POS=1127;AA_REF=D;AA_ALT=X,V,X MN908947.3 25202 . T K . mask SUB=NDM,RCD;EXC=highly_ambiguous;SRC_COUNTRY=UK;SRC_LAB=Sanger_COG_UK;GENE=gene-S;AA_POS=1214;AA_REF=W;AA_ALT=X MN908947.3 25381 . A R,C,M . mask SUB=RCD;EXC=homoplasic,single_src;SRC_COUNTRY=India;SRC_LAB=ICMR;GENE=gene-S;AA_POS=1273;AA_REF=T;AA_ALT=T,T,T MN908947.3 25382 . T C . mask SUB=LG;EXC=single_src,highly_homoplasic;SRC_COUNTRY=China;SRC_LAB=Sichuan_University;GENE=gene-S;AA_POS=1274;AA_REF=T;AA_ALT=Q MN908947.3 25446 . T A,C,W,G . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=Switzerland;SRC_LAB=ETH_Zurich;GENE=gene-ORF3a;AA_POS=18;AA_REF=G;AA_ALT=G,G,G,G MN908947.3 25798 . A G . caution SUB=NDM;EXC=ambiguous,amended;SRC_COUNTRY=UK;SRC_LAB=Edinburgh;GENE=gene-ORF3a;AA_POS=136;AA_REF=K;AA_ALT=E MN908947.3 25902 . T A,C,W,G . caution SUB=LG;EXC=single_src,highly_ambiguous,neighbour_linked;SRC_COUNTRY=USA;SRC_LAB=Chan_Zuckerberg_Biohub;GENE=gene-ORF3a;AA_POS=170;AA_REF=T;AA_ALT=T,T,T,T MN908947.3 25908 . T A,C,W . caution SUB=LG;EXC=single_src,highly_ambiguous,neighbour_linked;SRC_COUNTRY=USA;SRC_LAB=Chan_Zuckerberg_Biohub;GENE=gene-ORF3a;AA_POS=172;AA_REF=G;AA_ALT=G,G,G MN908947.3 25961 . C T,A,Y,S . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=Australia;SRC_LAB=VIDRL,University_of_Melbourne;GENE=gene-ORF3a;AA_POS=190;AA_REF=T;AA_ALT=I,N,X,X MN908947.3 26549 . C T,Y . mask SUB=NDM,RCD;EXC=homoplasic,single_src;SRC_COUNTRY=Turkey;SRC_LAB=Ministry_of_Health;GENE=gene-M;AA_POS=9;AA_REF=T;AA_ALT=T,T MN908947.3 26700 . G K,T . caution SUB=RCD;EXC=ambiguous,single_src,homoplasic;SRC_COUNTRY=Switzerland;SRC_LAB=ETH_Zurich;GENE=gene-M;AA_POS=60;AA_REF=V;AA_ALT=X,L MN908947.3 26709 . G R,K,T,A . caution SUB=NDM;EXC=ambiguous,amended;SRC_COUNTRY=India;SRC_LAB=NCDC;GENE=gene-M;AA_POS=63;AA_REF=A;AA_ALT=X,X,S,T MN908947.3 27033 . G K,T,A,S . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=Australia;SRC_LAB=VIDRL;GENE=gene-M;AA_POS=171;AA_REF=A;AA_ALT=X,S,T,X MN908947.3 27534 . T C,W,Y,G . caution SUB=RCD;EXC=ambiguous,single_src;SRC_COUNTRY=Switzerland;SRC_LAB=ETH_Zurich;GENE=gene-ORF7a;AA_POS=47;AA_REF=H;AA_ALT=H,X,H,Q MN908947.3 27658 . A D,T,W,G . mask SUB=LG;EXC=single_src,highly_homoplasic,neighbour_linked;SRC_COUNTRY=USA;SRC_LAB=University_of_Washington;GENE=gene-ORF7a;AA_POS=89;AA_REF=R;AA_ALT=X,*,X,G MN908947.3 27660 . A T,C,V,G . mask SUB=LG;EXC=single_src,highly_homoplasic,neighbour_linked;SRC_COUNTRY=USA;SRC_LAB=University_of_Washington;GENE=gene-ORF7a;AA_POS=89;AA_REF=R;AA_ALT=S,S,X,R MN908947.3 27720 . T K,C,W . caution SUB=RCD;EXC=ambiguous,single_src;SRC_COUNTRY=Switzerland;SRC_LAB=ETH_Zurich;GENE=gene-ORF7a;AA_POS=109;AA_REF=F;AA_ALT=X,F,X MN908947.3 27760 . T K,A,Y . mask SUB=RCD;EXC=homoplasic,neighbour_linked;SRC_COUNTRY=.;SRC_LAB=.;GENE=.;AA_POS=.;AA_REF=.;AA_ALT=. MN908947.3 27761 . T C . mask SUB=RCD;EXC=homoplasic,neighbour_linked;SRC_COUNTRY=.;SRC_LAB=.;GENE=.;AA_POS=.;AA_REF=.;AA_ALT=. MN908947.3 27784 . A T,W,G . mask SUB=RCD;EXC=ambiguous,single_src;SRC_COUNTRY=Switzerland;SRC_LAB=ETH_Zurich;GENE=.;AA_POS=.;AA_REF=.;AA_ALT=. MN908947.3 27792 . T K,W . caution SUB=NDM;EXC=ambiguous,amended;SRC_COUNTRY=UK;SRC_LAB=Edinburgh;GENE=.;AA_POS=.;AA_REF=.;AA_ALT=. MN908947.3 28004 . T C,Y . caution SUB=NDM;EXC=neighbour_linked,single_src;SRC_COUNTRY=Luxembourg;SRC_LAB=LNS;GENE=gene-ORF8;AA_POS=37;AA_REF=C;AA_ALT=C,C MN908947.3 28005 . C T,Y,G . caution SUB=NDM;EXC=neighbour_linked,single_src;SRC_COUNTRY=Luxembourg;SRC_LAB=LNS;GENE=gene-ORF8;AA_POS=38;AA_REF=P;AA_ALT=S,X,A MN908947.3 28006 . C T . caution SUB=NDM;EXC=neighbour_linked,single_src;SRC_COUNTRY=Luxembourg;SRC_LAB=LNS;GENE=gene-ORF8;AA_POS=38;AA_REF=P;AA_ALT=L MN908947.3 28008 . A G . caution SUB=NDM;EXC=neighbour_linked,single_src;SRC_COUNTRY=Luxembourg;SRC_LAB=LNS;GENE=gene-ORF8;AA_POS=39;AA_REF=I;AA_ALT=V MN908947.3 28184 . T C,H . mask SUB=LG;EXC=single_src,highly_homoplasic;SRC_COUNTRY=USA;SRC_LAB=University_of_Washington;GENE=gene-ORF8;AA_POS=97;AA_REF=S;AA_ALT=S,X MN908947.3 28253 . C Y,S,T,A,G . mask SUB=NDM,RCD;EXC=highly_homoplasic;SRC_COUNTRY=.;SRC_LAB=.;GENE=gene-ORF8;AA_POS=120;AA_REF=F;AA_ALT=F,X,F,L,L MN908947.3 28517 . G K,T,S . caution SUB=RCD;EXC=ambiguous,single_src;SRC_COUNTRY=Australia;SRC_LAB=Doherty;GENE=gene-N;AA_POS=82;AA_REF=D;AA_ALT=X,Y,X MN908947.3 28559 . G K,T . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=Australia;SRC_LAB=VIDRL,University_of_Melbourne;GENE=gene-N;AA_POS=96;AA_REF=G;AA_ALT=X,C MN908947.3 28676 . A R,C,M,G . caution SUB=RCD;EXC=ambiguous,single_src;SRC_COUNTRY=India;SRC_LAB=NCDC/CSIR;GENE=gene-N;AA_POS=135;AA_REF=T;AA_ALT=X,P,X,A MN908947.3 28780 . A R,D,W . caution SUB=RCD;EXC=ambiguous,single_src;SRC_COUNTRY=Switzerland;SRC_LAB=ETH_Zurich;GENE=gene-N;AA_POS=169;AA_REF=K;AA_ALT=K,X,X MN908947.3 28881 . G K,R,M,T,A . caution SUB=NDM;EXC=neighbour_linked;SRC_COUNTRY=.;SRC_LAB=.;GENE=gene-N;AA_POS=203;AA_REF=R;AA_ALT=X,X,X,M,K MN908947.3 28882 . G K,R,T,S,C,A . caution SUB=NDM;EXC=neighbour_linked;SRC_COUNTRY=.;SRC_LAB=.;GENE=gene-N;AA_POS=203;AA_REF=R;AA_ALT=X,R,S,X,S,R MN908947.3 28883 . G R,C,A,S . caution SUB=NDM;EXC=neighbour_linked;SRC_COUNTRY=.;SRC_LAB=.;GENE=gene-N;AA_POS=204;AA_REF=G;AA_ALT=X,R,R,X MN908947.3 28886 . A C,M,T,W,G . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=Switzerland;SRC_LAB=ETH_Zurich;GENE=gene-N;AA_POS=205;AA_REF=T;AA_ALT=P,X,S,X,A MN908947.3 28985 . G D,K,R,T,A . mask SUB=NDM,RCD;EXC=highly_ambiguous,homoplasic,single_src;SRC_COUNTRY=Switzerland;SRC_LAB=ETH_Zurich;GENE=gene-N;AA_POS=238;AA_REF=G;AA_ALT=X,X,X,C,S MN908947.3 29037 . C T,M,Y . mask SUB=RCD;EXC=homoplasic,ambiguous,single_src;SRC_COUNTRY=Australia;SRC_LAB=VIDRL;GENE=gene-N;AA_POS=255;AA_REF=S;AA_ALT=F,X,X MN908947.3 29039 . A T,W . mask SUB=RCD;EXC=homoplasic,ambiguous,single_src;SRC_COUNTRY=Australia,India;SRC_LAB=VIDRL,ICMR;GENE=gene-N;AA_POS=256;AA_REF=K;AA_ALT=*,X MN908947.3 29049 . G R,T,A . caution SUB=LG;EXC=single_src,highly_ambiguous;SRC_COUNTRY=USA;SRC_LAB=MGSC;GENE=gene-N;AA_POS=259;AA_REF=R;AA_ALT=X,L,Q MN908947.3 29058 . G K,T,A . mask SUB=LG;EXC=single_src,highly_homoplasic;SRC_COUNTRY=USA;SRC_LAB=WPHL;GENE=gene-N;AA_POS=262;AA_REF=R;AA_ALT=X,L,H MN908947.3 29378 . A W . caution SUB=NDM;EXC=ambiguous,amended;SRC_COUNTRY=USA;SRC_LAB=Minnesota;GENE=gene-N;AA_POS=369;AA_REF=K;AA_ALT=X MN908947.3 29425 . G T,A,S . mask SUB=NDM,RCD;EXC=ambiguous,homoplasic,single_src;SRC_COUNTRY=Singapore;SRC_LAB=NPHL;GENE=gene-N;AA_POS=384;AA_REF=Q;AA_ALT=H,Q,X MN908947.3 29427 . G K,R,T,S,C,A . caution SUB=RCD;EXC=ambiguous,neighbour_linked,single_src;SRC_COUNTRY=Singapore;SRC_LAB=NPHL;GENE=gene-N;AA_POS=385;AA_REF=R;AA_ALT=X,X,I,X,T,K MN908947.3 29428 . A R,C,G . caution SUB=RCD;EXC=ambiguous,neighbour_linked,single_src;SRC_COUNTRY=Singapore;SRC_LAB=NPHL;GENE=gene-N;AA_POS=385;AA_REF=R;AA_ALT=R,S,R MN908947.3 29553 . G T,A . mask SUB=NDM,RCD;EXC=highly_homoplasic,single_src;SRC_COUNTRY=USA,USA;SRC_LAB=University_of_Washington,Seattle_Flu_Study;GENE=.;AA_POS=.;AA_REF=.;AA_ALT=. MN908947.3 29594 . A T,C . mask SUB=LG;EXC=single_src,highly_homoplasic;SRC_COUNTRY=USA;SRC_LAB=University_of_Washington;GENE=gene-ORF10;AA_POS=13;AA_REF=I;AA_ALT=L,L MN908947.3 29737 . G K,R,T,S,C,A . caution SUB=RCD;EXC=ambiguous,single_src;SRC_COUNTRY=UK;SRC_LAB=Public_Health_Wales;GENE=.;AA_POS=.;AA_REF=.;AA_ALT=. MN908947.3 29783 . G T,K,C,A . mask SUB=LG;EXC=highly_homoplasic;SRC_COUNTRY=USA;SRC_LAB=.;GENE=.;AA_POS=.;AA_REF=.;AA_ALT=. MN908947.3 29786 . G K,C,S . caution SUB=RCD;EXC=homoplasic,single_src;SRC_COUNTRY=Brazil;SRC_LAB=FIOCRUZ;GENE=.;AA_POS=.;AA_REF=.;AA_ALT=. MN908947.3 29804 . T . . mask SUB=NDM;EXC=seq_end MN908947.3 29805 . A . . mask SUB=NDM;EXC=seq_end MN908947.3 29806 . A . . mask SUB=NDM;EXC=seq_end MN908947.3 29807 . T . . mask SUB=NDM;EXC=seq_end MN908947.3 29808 . G . . mask SUB=NDM;EXC=seq_end MN908947.3 29809 . T . . mask SUB=NDM;EXC=seq_end MN908947.3 29810 . G . . mask SUB=NDM;EXC=seq_end MN908947.3 29811 . T . . mask SUB=NDM;EXC=seq_end MN908947.3 29812 . A . . mask SUB=NDM;EXC=seq_end MN908947.3 29813 . A . . mask SUB=NDM;EXC=seq_end MN908947.3 29814 . A . . mask SUB=NDM;EXC=seq_end MN908947.3 29815 . A . . mask SUB=NDM;EXC=seq_end MN908947.3 29816 . T . . mask SUB=NDM;EXC=seq_end MN908947.3 29817 . T . . mask SUB=NDM;EXC=seq_end MN908947.3 29818 . A . . mask SUB=NDM;EXC=seq_end MN908947.3 29819 . A . . mask SUB=NDM;EXC=seq_end MN908947.3 29820 . T . . mask SUB=NDM;EXC=seq_end MN908947.3 29821 . T . . mask SUB=NDM;EXC=seq_end MN908947.3 29822 . T . . mask SUB=NDM;EXC=seq_end MN908947.3 29823 . T . . mask SUB=NDM;EXC=seq_end MN908947.3 29824 . A . . mask SUB=NDM;EXC=seq_end MN908947.3 29825 . G . . mask SUB=NDM;EXC=seq_end MN908947.3 29826 . T . . mask SUB=NDM;EXC=seq_end MN908947.3 29827 . A T,G . mask SUB=NDM,RCD;EXC=seq_end,highly_homoplasic,single_src;SRC_COUNTRY=India;SRC_LAB=NIV;GENE=.;AA_POS=.;AA_REF=.;AA_ALT=. MN908947.3 29828 . G . . mask SUB=NDM;EXC=seq_end MN908947.3 29829 . T . . mask SUB=NDM;EXC=seq_end MN908947.3 29830 . G T,C,A . mask SUB=NDM,RCD;EXC=seq_end,highly_homoplasic,single_src;SRC_COUNTRY=India;SRC_LAB=NIV;GENE=.;AA_POS=.;AA_REF=.;AA_ALT=. MN908947.3 29831 . C . . mask SUB=NDM;EXC=seq_end MN908947.3 29832 . T . . mask SUB=NDM;EXC=seq_end MN908947.3 29833 . A . . mask SUB=NDM;EXC=seq_end MN908947.3 29834 . T . . mask SUB=NDM;EXC=seq_end MN908947.3 29835 . C . . mask SUB=NDM;EXC=seq_end MN908947.3 29836 . C . . mask SUB=NDM;EXC=seq_end MN908947.3 29837 . C . . mask SUB=NDM;EXC=seq_end MN908947.3 29838 . C . . mask SUB=NDM;EXC=seq_end MN908947.3 29839 . A . . mask SUB=NDM;EXC=seq_end MN908947.3 29840 . T . . mask SUB=NDM;EXC=seq_end MN908947.3 29841 . G . . mask SUB=NDM;EXC=seq_end MN908947.3 29842 . T . . mask SUB=NDM;EXC=seq_end MN908947.3 29843 . G . . mask SUB=NDM;EXC=seq_end MN908947.3 29844 . A . . mask SUB=NDM;EXC=seq_end MN908947.3 29845 . T . . mask SUB=NDM;EXC=seq_end MN908947.3 29846 . T . . mask SUB=NDM;EXC=seq_end MN908947.3 29847 . T . . mask SUB=NDM;EXC=seq_end MN908947.3 29848 . T . . mask SUB=NDM;EXC=seq_end MN908947.3 29849 . A . . mask SUB=NDM;EXC=seq_end MN908947.3 29850 . A . . mask SUB=NDM;EXC=seq_end MN908947.3 29851 . T . . mask SUB=NDM;EXC=seq_end MN908947.3 29852 . A . . mask SUB=NDM;EXC=seq_end MN908947.3 29853 . G . . mask SUB=NDM;EXC=seq_end MN908947.3 29854 . C . . mask SUB=NDM;EXC=seq_end MN908947.3 29855 . T . . mask SUB=NDM;EXC=seq_end MN908947.3 29856 . T . . mask SUB=NDM;EXC=seq_end MN908947.3 29857 . C . . mask SUB=NDM;EXC=seq_end MN908947.3 29858 . T . . mask SUB=NDM;EXC=seq_end MN908947.3 29859 . T . . mask SUB=NDM;EXC=seq_end MN908947.3 29860 . A . . mask SUB=NDM;EXC=seq_end MN908947.3 29861 . G . . mask SUB=NDM;EXC=seq_end MN908947.3 29862 . G . . mask SUB=NDM;EXC=seq_end MN908947.3 29863 . A . . mask SUB=NDM;EXC=seq_end MN908947.3 29864 . G . . mask SUB=NDM;EXC=seq_end MN908947.3 29865 . A . . mask SUB=NDM;EXC=seq_end MN908947.3 29866 . A . . mask SUB=NDM;EXC=seq_end MN908947.3 29867 . T . . mask SUB=NDM;EXC=seq_end MN908947.3 29868 . G . . mask SUB=NDM;EXC=seq_end MN908947.3 29869 . A . . mask SUB=NDM;EXC=seq_end MN908947.3 29870 . C . . mask SUB=NDM;EXC=seq_end MN908947.3 29871 . A . . mask SUB=NDM;EXC=seq_end MN908947.3 29872 . A . . mask SUB=NDM;EXC=seq_end MN908947.3 29873 . A . . mask SUB=NDM;EXC=seq_end MN908947.3 29874 . A . . mask SUB=NDM;EXC=seq_end MN908947.3 29875 . A . . mask SUB=NDM;EXC=seq_end MN908947.3 29876 . A . . mask SUB=NDM;EXC=seq_end MN908947.3 29877 . A . . mask SUB=NDM;EXC=seq_end MN908947.3 29878 . A . . mask SUB=NDM;EXC=seq_end MN908947.3 29879 . A . . mask SUB=NDM;EXC=seq_end MN908947.3 29880 . A . . mask SUB=NDM;EXC=seq_end MN908947.3 29881 . A . . mask SUB=NDM;EXC=seq_end MN908947.3 29882 . A . . mask SUB=NDM;EXC=seq_end MN908947.3 29883 . A . . mask SUB=NDM;EXC=seq_end MN908947.3 29884 . A . . mask SUB=NDM;EXC=seq_end MN908947.3 29885 . A . . mask SUB=NDM;EXC=seq_end MN908947.3 29886 . A . . mask SUB=NDM;EXC=seq_end MN908947.3 29887 . A . . mask SUB=NDM;EXC=seq_end MN908947.3 29888 . A . . mask SUB=NDM;EXC=seq_end MN908947.3 29889 . A . . mask SUB=NDM;EXC=seq_end MN908947.3 29890 . A . . mask SUB=NDM;EXC=seq_end MN908947.3 29891 . A . . mask SUB=NDM;EXC=seq_end MN908947.3 29892 . A . . mask SUB=NDM;EXC=seq_end MN908947.3 29893 . A . . mask SUB=NDM;EXC=seq_end MN908947.3 29894 . A . . mask SUB=NDM;EXC=seq_end MN908947.3 29895 . A . . mask SUB=NDM;EXC=seq_end MN908947.3 29896 . A . . mask SUB=NDM;EXC=seq_end MN908947.3 29897 . A . . mask SUB=NDM;EXC=seq_end MN908947.3 29898 . A . . mask SUB=NDM;EXC=seq_end MN908947.3 29899 . A . . mask SUB=NDM;EXC=seq_end MN908947.3 29900 . A . . mask SUB=NDM;EXC=seq_end MN908947.3 29901 . A . . mask SUB=NDM;EXC=seq_end MN908947.3 29902 . A . . mask SUB=NDM;EXC=seq_end MN908947.3 29903 . A . . mask SUB=NDM;EXC=seq_end