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problematic_sites_sarsCov2_22_12_2020.vcf
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##fileformat=VCFv4.3
##fileDate=2020-12-22-11:15
##source=http://virological.org/t/masking-strategies-for-sars-cov-2-alignments/480
##reference=MN908947.3
##contig=<ID=MN908947.3,length=29903>
##FILTER=<ID=caution,Description="Sites that should be interpreted carefully, but not necessarily masked">
##FILTER=<ID=mask,Description="Sites we recommend to always mask">
##INFO=<ID=SUB,Number=.,Type=String,Description="Initials of submitter">
## LG = Landen Gozashti
## RCD = Russell Corbett-Detig
## MP = Matthew Parker
## NDM = Nicola De Maio
##INFO=<ID=EXC,Number=.,Type=String,Description="List of reasons for mask/caution">
## 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
## 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=<ID=SRC_COUNTRY,Number=.,Type=String,Description="Source country/countries of samples with the variant">
##INFO=<ID=SRC_LAB,Number=.,Type=String,Description="Source laboratory/laboratories of samples with the variant (ordered to match the respective values in SRC_COUNTRY)">
## 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
## KU_Leuven = KU Leuven
## LNS = Laboratoire National de Santé
## 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
##INFO=<ID=GENE,Number=1,Type=String,Description="Position falls into range of this gene">
##INFO=<ID=AA_POS,Number=1,Type=Integer,Description="Position of amino acid residue within gene">
##INFO=<ID=AA_REF,Number=1,Type=String,Description="Reference amino acid residue">
##INFO=<ID=AA_ALT,Number=.,Type=String,Description="List of alternative amino acid residues (IUPAC ambiguity code)">
#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 W,K,A,C,Y . 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,W,G,Y,A,C . 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 G,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=.
MN908947.3 285 . G A,K,T . 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=D,X,V
MN908947.3 538 . A W,G,R . caution SUB=NDM,RCD;EXC=ambiguous;SRC_COUNTRY=Italy;SRC_LAB=IZSAM;GENE=gene-orf1ab;AA_POS=91;AA_REF=E;AA_ALT=X,E,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 K,T,R . 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,V,X
MN908947.3 635 . C Y,T . 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=X,C
MN908947.3 660 . G K,A,S . caution SUB=NDM,RCD;EXC=ambiguous;SRC_COUNTRY=Australia;SRC_LAB=Doherty;GENE=gene-orf1ab;AA_POS=132;AA_REF=G;AA_ALT=X,D,X
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 Y,A,C . 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 A,R . 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=K,X
MN908947.3 1707 . C Y,T,A . 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=X,F,Y
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 T,K . 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=L,X
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 2381 . G T,K . 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=C,X
MN908947.3 2604 . G T,K . 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=V,X
MN908947.3 3073 . T Y,C,W . 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,C,X
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 3564 . G T,K . 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=V,X
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 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 T,D,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=I,X,X
MN908947.3 4463 . T G,C,Y,K . 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=A,P,X,X
MN908947.3 5011 . A M,C . 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=X,H
MN908947.3 5257 . A W,G,M . 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,L,X
MN908947.3 5393 . T Y,C . 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=X,L
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,S,A . 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,X,I
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 S,T . 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=X,D
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 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 A,T,C,K,R . caution SUB=NDM;EXC=neighbour_linked;SRC_COUNTRY=.;SRC_LAB=.;GENE=gene-orf1ab;AA_POS=2015;AA_REF=S;AA_ALT=N,I,T,X,X
MN908947.3 6310 . C A,T,M,Y,G . caution SUB=NDM;EXC=neighbour_linked;SRC_COUNTRY=.;SRC_LAB=.;GENE=gene-orf1ab;AA_POS=2015;AA_REF=S;AA_ALT=R,S,X,S,R
MN908947.3 6312 . C A,G,T,M,Y . caution SUB=NDM;EXC=neighbour_linked;SRC_COUNTRY=.;SRC_LAB=.;GENE=gene-orf1ab;AA_POS=2016;AA_REF=T;AA_ALT=K,R,I,X,X
MN908947.3 6483 . G K,T,R . 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,V,X
MN908947.3 6866 . A W,T . caution SUB=NDM,RCD;EXC=ambiguous;SRC_COUNTRY=Italy;SRC_LAB=IZSAM;GENE=gene-orf1ab;AA_POS=2201;AA_REF=N;AA_ALT=X,Y
MN908947.3 6869 . A W,T . 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=X,S
MN908947.3 6874 . T G,Y,C . 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 T,R . 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=I,X
MN908947.3 6977 . G K,A,R . 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,I,X
MN908947.3 7017 . G K,T,S,A . 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,X,D
MN908947.3 7038 . G A,K,T,R . 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=D,X,V,X
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 7214 . G K,A,T . 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,N,Y
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 W,C,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 8022 . T K,G,C . 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,G,A
MN908947.3 8026 . A W,G,T . 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 8696 . G A,R,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=2811;AA_REF=A;AA_ALT=T,X,X,S,X
MN908947.3 8790 . G T,K . 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=V,X
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 8886 . T A,Y,C,W . 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=*,X,S,X
MN908947.3 8887 . A C,G,R . 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=F,L,L
MN908947.3 9039 . C Y,M,T . mask SUB=NDM;EXC=ambiguous,single_src;SRC_COUNTRY=India;SRC_LAB=NCDC;GENE=gene-orf1ab;AA_POS=2925;AA_REF=A;AA_ALT=X,X,V
MN908947.3 9471 . G A,S,C . caution SUB=RCD;EXC=ambiguous,single_src;SRC_COUNTRY=India;SRC_LAB=NCDC;GENE=gene-orf1ab;AA_POS=3069;AA_REF=R;AA_ALT=K,X,T
MN908947.3 10046 . G R,A,K . 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,I,X
MN908947.3 10122 . G S,K,T . 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,X,V
MN908947.3 10129 . T Y,C,W . 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,A,T . 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,I,L
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 10986 . G K,D,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 T,K,A . mask SUB=NDM,RCD;EXC=highly_homoplasic;SRC_COUNTRY=.;SRC_LAB=.;GENE=gene-orf1ab;AA_POS=3606;AA_REF=L;AA_ALT=F,X,L
MN908947.3 11535 . G T,K . 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=V,X
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 T,K,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=H,X,Q
MN908947.3 12751 . T W,A . 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 13402 . T G,K,C . 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,G,C . caution SUB=NDM;EXC=neighbour_linked;SRC_COUNTRY=.;SRC_LAB=.;GENE=gene-orf1ab;AA_POS=4416;AA_REF=T;AA_ALT=L,R,P
MN908947.3 13513 . G T,K,A . caution SUB=NDM;EXC=neighbour_linked;SRC_COUNTRY=.;SRC_LAB=.;GENE=gene-orf1ab;AA_POS=4416;AA_REF=T;AA_ALT=H,X,Q
MN908947.3 13514 . G A,T,S,C . caution SUB=NDM;EXC=neighbour_linked;SRC_COUNTRY=.;SRC_LAB=.;GENE=gene-orf1ab;AA_POS=4417;AA_REF=G;AA_ALT=T,S,X,P
MN908947.3 13571 . G T,K . 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=F,X
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 A,C,Y . caution SUB=NDM;EXC=neighbour_linked;SRC_COUNTRY=.;SRC_LAB=.;GENE=gene-orf1ab;AA_POS=4474;AA_REF=H;AA_ALT=K,T,X
MN908947.3 13687 . G T . caution SUB=NDM;EXC=neighbour_linked;SRC_COUNTRY=.;SRC_LAB=.;GENE=gene-orf1ab;AA_POS=4474;AA_REF=H;AA_ALT=I
MN908947.3 13687 . G T . mask SUB=LG;EXC=single_src,highly_homoplasic;SRC_COUNTRY=USA;SRC_LAB=University_of_Washington;GENE=gene-orf1ab;AA_POS=4474;AA_REF=H;AA_ALT=I
MN908947.3 13693 . A T,R,W . caution SUB=NDM;EXC=neighbour_linked;SRC_COUNTRY=.;SRC_LAB=.;GENE=gene-orf1ab;AA_POS=4476;AA_REF=E;AA_ALT=N,K,X
MN908947.3 14197 . G K,S,A,T . 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 G,B . 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=E,X
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 T,A,B,M . 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=*,K,X,X
MN908947.3 14277 . G T,K . 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=V,X
MN908947.3 14548 . G R,D,A,K . 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=R,X,R,X
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 15769 . G K,T,A,R . 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,C,*,X
MN908947.3 15771 . T A,Y,W,D,K,H . 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=Q,X,X,X,X,X
MN908947.3 15922 . T Y,C . 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 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 W,D,R . 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 T,A,K,R . 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 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 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 T,K . 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=S,X
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,B,T . 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,X,S
MN908947.3 18445 . G A,K,T . 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=E,X,D
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 19298 . A D,W,T,R . 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 Y,C,K,A . 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,X,H
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 W,K . 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 R,W,G,T,D . 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,R,L,X
MN908947.3 19732 . G T,K,A,R . 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 Y,C . 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 A,K,R,S . 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=K,X,X,Z
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 G,R,W . 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=V,X,X
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 T,D . 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=D,X
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 21302 . C T,S,A,M . caution SUB=NDM;EXC=neighbour_linked;SRC_COUNTRY=.;SRC_LAB=.;GENE=gene-orf1ab;AA_POS=7013;AA_REF=P;AA_ALT=Y,X,N,X
MN908947.3 21304 . C T,A,M,S,Y . caution SUB=NDM;EXC=neighbour_linked;SRC_COUNTRY=.;SRC_LAB=.;GENE=gene-orf1ab;AA_POS=7013;AA_REF=P;AA_ALT=H,Q,X,X,H
MN908947.3 21305 . G A,R,T,K . caution SUB=NDM;EXC=neighbour_linked;SRC_COUNTRY=.;SRC_LAB=.;GENE=gene-orf1ab;AA_POS=7014;AA_REF=R;AA_ALT=T,X,S,X
MN908947.3 21379 . T Y,C . 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 M,C . 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 W,T,R . 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 T,M,Y,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 22329 . C T,Y,M,V . 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=L,X,X,X
MN908947.3 22335 . G T,K,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=L,X,*
MN908947.3 22389 . T Y,W,C,K . 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,X,P,X
MN908947.3 22393 . A W,R,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=X,L,L
MN908947.3 22416 . T Y,C . 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=X,T
MN908947.3 22420 . A W,T . 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,T,M,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,V,X,X
MN908947.3 22500 . A W,R,M . 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 S,Y,T . 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=X,X,I
MN908947.3 22515 . T Y,W,K . 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 W,D,K,C,Y . 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,X,F,F
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 22661 . G T,S,A . 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,X,I
MN908947.3 22802 . C M,A,T,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=X,K,*,X
MN908947.3 23116 . A W,T . 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 M,W,G,R,V,T,H . 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 A,K,T . 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=I,X,F
MN908947.3 23291 . C Y,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,C
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 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 23745 . C Y,T . 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=X,L
MN908947.3 23766 . C Y,T,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=X,L,X
MN908947.3 23855 . C T,Y,A . 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,X,S
MN908947.3 24389 . A W,M,C . 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,X,R
MN908947.3 24390 . G T,S,K,C . 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,X,T
MN908947.3 24497 . G K,C,T . 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=X,H,Y
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 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 T,W,R . caution SUB=NDM;EXC=ambiguous,single_src;SRC_COUNTRY=Australia;SRC_LAB=Doherty;GENE=gene-S;AA_POS=1127;AA_REF=D;AA_ALT=V,X,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 C,R,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 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 25961 . C T,Y,A,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,X,N,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 T,K . 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=L,X
MN908947.3 26709 . G R,A,T,K . caution SUB=NDM;EXC=ambiguous,amended;SRC_COUNTRY=India;SRC_LAB=NCDC;GENE=gene-M;AA_POS=63;AA_REF=A;AA_ALT=X,T,S,X
MN908947.3 27534 . T W,Y,G,C . 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=X,H,Q,H
MN908947.3 27658 . A T,W,D,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 G,V,C,T . 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=R,X,S,S
MN908947.3 27720 . T K,W,C . 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,X,F
MN908947.3 27760 . T K,Y,A . 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 W,G,T . 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 Y,C . 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,G,Y . 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,A,X
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,T,G,A,S . mask SUB=NDM,RCD;EXC=highly_homoplasic;SRC_COUNTRY=.;SRC_LAB=.;GENE=gene-ORF8;AA_POS=120;AA_REF=F;AA_ALT=F,F,L,L,X
MN908947.3 28517 . G K,S,T . 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,X,Y
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 G,M,C,R . 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=A,X,P,X
MN908947.3 28780 . A W,D,R . 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=X,X,K
MN908947.3 28881 . G A,R,T,K,M . caution SUB=NDM;EXC=neighbour_linked;SRC_COUNTRY=.;SRC_LAB=.;GENE=gene-N;AA_POS=203;AA_REF=R;AA_ALT=K,X,M,X,X
MN908947.3 28882 . G A,R,T,S,K,C . caution SUB=NDM;EXC=neighbour_linked;SRC_COUNTRY=.;SRC_LAB=.;GENE=gene-N;AA_POS=203;AA_REF=R;AA_ALT=R,R,S,X,X,S
MN908947.3 28883 . G C,A,S,R . caution SUB=NDM;EXC=neighbour_linked;SRC_COUNTRY=.;SRC_LAB=.;GENE=gene-N;AA_POS=204;AA_REF=G;AA_ALT=R,R,X,X
MN908947.3 28985 . G R,D,T,K,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,C,X,S
MN908947.3 29037 . C T,Y,M . 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 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,S,A . 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,X,Q
MN908947.3 29427 . G A,K,R,T,C,S . 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=K,X,X,I,T,X
MN908947.3 29428 . A R,G,C . 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,R,S
MN908947.3 29553 . G A,T . 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 T,K,A,S,C,R . caution SUB=RCD;EXC=ambiguous,single_src;SRC_COUNTRY=UK;SRC_LAB=Public_Health_Wales;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 G,T . 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,A,C . 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