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problematic_sites_sarsCov2.vcf
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problematic_sites_sarsCov2.vcf
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##fileformat=VCFv4.3
##fileDate=2020-07-15-13:19
##source=http://virological.org/t/masking-strategies-for-sars-cov-2-alignments/480
##reference=MN908947.3
##contig=<ID=MN908947.3,length=29903>
##FILTER=<Description="Masking recommendation"
## caution = Sites that should be interpreted carefully, but not necessarily masked
## mask = Sites we recommend to always mask
##INFO=<Description="Initials of submitter"
## RCD = Russell Corbett-Detig
## MP = Matthew Parker
## NDM = Nicola De Maio
##EXC=<Description="List of reasons for suggested exclusion">
## 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
##SRC_COUNTRY=<Description="Source country/countries of samples with the variant">
##SRC_LAB=<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
## 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
## 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
## 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
## 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_COG_UK = Wellcome Sanger Institute, COG-UK Consortium
## Seattle_Flu_Study = Seattle Flu Study
## Sheffield = The Florey Institute, University of Sheffield Medical School
## TGEN = The Translational Genomics Research Institute
## University_of_Washington = University of Washington
## VIDRL = Victorian Infectious Diseases Reference Laboratory
##GENE=<Decription="Position falls into range of this gene">
##AAPOS=<Description="Position of amino acid residue within gene">
##REFAA=<Description="Reference amino acid residue">
##ALTAA=<Description="List of alternative amino acid residues (IUPAC ambiguity code)">
#CHROM POS ID REF ALT QUAL FILTER INFO EXC SRC_COUNTRY SRC_LAB GENE AAPOS REFAA ALTAA
MN908947.3 1 . A . . mask NDM seq_end . . . . . .
MN908947.3 2 . T . . mask NDM seq_end . . . . . .
MN908947.3 3 . T . . mask NDM seq_end . . . . . .
MN908947.3 4 . A . . mask NDM seq_end . . . . . .
MN908947.3 5 . A . . mask NDM seq_end . . . . . .
MN908947.3 6 . A . . mask NDM seq_end . . . . . .
MN908947.3 7 . G . . mask NDM seq_end . . . . . .
MN908947.3 8 . G . . mask NDM seq_end . . . . . .
MN908947.3 9 . T . . mask NDM seq_end . . . . . .
MN908947.3 10 . T . . mask NDM seq_end . . . . . .
MN908947.3 11 . T . . mask NDM seq_end . . . . . .
MN908947.3 12 . A . . mask NDM seq_end . . . . . .
MN908947.3 13 . T . . mask NDM seq_end . . . . . .
MN908947.3 14 . A . . mask NDM seq_end . . . . . .
MN908947.3 15 . C . . mask NDM seq_end . . . . . .
MN908947.3 16 . C . . mask NDM seq_end . . . . . .
MN908947.3 17 . T . . mask NDM seq_end . . . . . .
MN908947.3 18 . T . . mask NDM seq_end . . . . . .
MN908947.3 19 . C . . mask NDM seq_end . . . . . .
MN908947.3 20 . C . . mask NDM seq_end . . . . . .
MN908947.3 21 . C . . mask NDM seq_end . . . . . .
MN908947.3 22 . A . . mask NDM seq_end . . . . . .
MN908947.3 23 . G . . mask NDM seq_end . . . . . .
MN908947.3 24 . G . . mask NDM seq_end . . . . . .
MN908947.3 25 . T . . mask NDM seq_end . . . . . .
MN908947.3 26 . A . . mask NDM seq_end . . . . . .
MN908947.3 27 . A . . mask NDM seq_end . . . . . .
MN908947.3 28 . C . . mask NDM seq_end . . . . . .
MN908947.3 29 . A . . mask NDM seq_end . . . . . .
MN908947.3 30 . A . . mask NDM seq_end . . . . . .
MN908947.3 31 . A . . mask NDM seq_end . . . . . .
MN908947.3 32 . C . . mask NDM seq_end . . . . . .
MN908947.3 33 . C . . mask NDM seq_end . . . . . .
MN908947.3 34 . A . . mask NDM seq_end . . . . . .
MN908947.3 35 . A . . mask NDM seq_end . . . . . .
MN908947.3 36 . C . . mask NDM seq_end . . . . . .
MN908947.3 37 . C . . mask NDM seq_end . . . . . .
MN908947.3 38 . A . . mask NDM seq_end . . . . . .
MN908947.3 39 . A . . mask NDM seq_end . . . . . .
MN908947.3 40 . C . . mask NDM seq_end . . . . . .
MN908947.3 41 . T . . mask NDM seq_end . . . . . .
MN908947.3 42 . T . . mask NDM seq_end . . . . . .
MN908947.3 43 . T . . mask NDM seq_end . . . . . .
MN908947.3 44 . C . . mask NDM seq_end . . . . . .
MN908947.3 45 . G . . mask NDM seq_end . . . . . .
MN908947.3 46 . A . . mask NDM seq_end . . . . . .
MN908947.3 47 . T . . mask NDM seq_end . . . . . .
MN908947.3 48 . C . . mask NDM seq_end . . . . . .
MN908947.3 49 . T . . mask NDM seq_end . . . . . .
MN908947.3 50 . C . . mask NDM seq_end . . . . . .
MN908947.3 51 . T . . mask NDM seq_end . . . . . .
MN908947.3 52 . T . . mask NDM seq_end . . . . . .
MN908947.3 53 . G . . mask NDM seq_end . . . . . .
MN908947.3 54 . T . . mask NDM seq_end . . . . . .
MN908947.3 55 . A . . mask NDM seq_end . . . . . .
MN908947.3 76 . T W,A,C . caution NDM ambiguous;neighbour_linked;narrow_src Singapore;India NPHL;NCDC . . . .
MN908947.3 78 . T Y,K,W,A,G,C . caution NDM ambiguous;neighbour_linked;narrow_src Singapore;India NPHL;NCDC . . . .
MN908947.3 150 . T C,Y . mask RCD homoplasic;single_src;neighbour_linked USA University_of_Washington . . . .
MN908947.3 153 . T G,Y . mask RCD homoplasic;single_src;neighbour_linked USA University_of_Washington . . . .
MN908947.3 538 . A W . caution NDM;RCD ambiguous Italy IZSAM gene-orf1ab 91 E X
MN908947.3 635 . C Y,T . mask NDM;RCD highly_ambiguous;homoplasic;narrow_src Switzerland;Australia;UK ETH_Zurich;Doherty;COG_UK gene-orf1ab 124 R X,C
MN908947.3 660 . G K . caution NDM;RCD ambiguous Australia Doherty gene-orf1ab 132 G X
MN908947.3 1001 . G A . caution NDM ambiguous;amended UK Sanger_COG_UK gene-orf1ab 246 E K
MN908947.3 1814 . A . . caution NDM ambiguous;amended USA Minnesota gene-orf1ab 517 K .
MN908947.3 1895 . G T,K . mask NDM;RCD ambiguous UK Public_Health_England gene-orf1ab 544 V L,X
MN908947.3 2087 . T C,Y . caution NDM;RCD ambiguous India NCDC gene-orf1ab 608 L L,L
MN908947.3 2091 . C T,Y . mask NDM highly_ambiguous;homoplasic;narrow_src India;UK NCDC;NU-OMICS gene-orf1ab 609 T I,X
MN908947.3 2094 . C T,Y . mask NDM highly_ambiguous;narrow_src Belgium;India KU_Leuven;NCDC gene-orf1ab 610 S L,X
MN908947.3 2198 . G R,A . mask NDM;RCD homoplasic;ambiguous;narrow_src Netherlands Erasmus gene-orf1ab 645 G X,S
MN908947.3 2604 . G T,K . mask RCD homoplasic;ambiguous;single_src Australia Doherty gene-orf1ab 780 G V,X
MN908947.3 3145 . G T . mask NDM;RCD homoplasic;single_src Netherlands Erasmus gene-orf1ab 960 L F
MN908947.3 3564 . G K,T,Y,S,R . mask NDM;RCD highly_ambiguous;highly_homoplasic;single_src Australia VIDRL gene-orf1ab 1100 G X,V,X,X,X
MN908947.3 3639 . G R,A . mask RCD ambiguous;homoplasic;single_src UK Public_Health_Wales gene-orf1ab 1125 G X,D
MN908947.3 3778 . A G . mask RCD homoplasic;single_src Netherlands Erasmus gene-orf1ab 1171 T T
MN908947.3 4050 . A C . mask NDM;RCD homoplasic;single_src;amended Belgium KU_Leuven gene-orf1ab 1262 N T
MN908947.3 5011 . A M,C . mask RCD ambiguous;homoplasic;single_src USA Michigan_Health_Dept gene-orf1ab 1582 Q X,H
MN908947.3 5257 . A W,G . mask RCD highly_ambiguous;single_src Switzerland ETH_Zurich gene-orf1ab 1664 L X,L
MN908947.3 5393 . T Y . caution NDM ambiguous;amended USA;UK Houston;Sheffield gene-orf1ab 1710 F X
MN908947.3 5498 . A . . caution NDM ambiguous;amended USA;UK Houston;Sheffield gene-orf1ab 1745 K .
MN908947.3 5736 . C T,Y . mask NDM;RCD homoplasic;single_src Turkey Ministry_of_Health gene-orf1ab 1824 A V,X
MN908947.3 5743 . G S,T . mask RCD highly_ambiguous;neighbour_linked;narrow_src UK;Australia Public_Health_England;Doherty gene-orf1ab 1826 E X,D
MN908947.3 5744 . T Y . mask RCD highly_ambiguous;neighbour_linked;narrow_src UK;Australia Public_Health_England;Doherty gene-orf1ab 1827 Y X
MN908947.3 5765 . G A,K,R . caution RCD ambiguous;single_src;neighbour_linked Australia Doherty gene-orf1ab 1834 G S,X,X
MN908947.3 5766 . G C,S . caution RCD ambiguous;single_src;neighbour_linked Australia Doherty gene-orf1ab 1834 G A,X
MN908947.3 6167 . G R,S,K,C . mask RCD ambiguous;single_src Switzerland ETH_Zurich gene-orf1ab 1968 V X,X,X,L
MN908947.3 6255 . C T,Y . mask NDM;RCD highly_homoplasic;narrow_src Netherlands;South_Africa Erasmus;NHLS gene-orf1ab 1997 A V,X
MN908947.3 6309 . G T,A,R . caution NDM neighbour_linked . . gene-orf1ab 2015 S I,N,X
MN908947.3 6310 . C A,T,M . caution NDM neighbour_linked . . gene-orf1ab 2015 S R,S,X
MN908947.3 6312 . C A,Y,M,T,G . caution NDM neighbour_linked . . gene-orf1ab 2016 T K,X,X,I,R
MN908947.3 6866 . A W . caution NDM;RCD ambiguous Italy IZSAM gene-orf1ab 2201 N X
MN908947.3 6869 . A T,W,R . mask NDM;RCD ambiguous;homoplasic;single_src Italy IZSAM gene-orf1ab 2202 T S,X,X
MN908947.3 6971 . T C,K . caution NDM neighbour_linked;single_src Australia VIDRL gene-orf1ab 2236 L L,X
MN908947.3 6975 . G T . caution NDM neighbour_linked;single_src Australia VIDRL gene-orf1ab 2237 S I
MN908947.3 6977 . G A . caution NDM neighbour_linked;single_src Australia VIDRL gene-orf1ab 2238 V I
MN908947.3 7090 . T K . caution RCD ambiguous;single_src UK Public_Health_England gene-orf1ab 2275 N X
MN908947.3 7305 . T K . caution RCD ambiguous;single_src Switzerland ETH_Zurich gene-orf1ab 2347 M X
MN908947.3 7396 . T W . caution NDM;RCD ambiguous Italy IZSAM gene-orf1ab 2377 I I
MN908947.3 8022 . T K,G . mask NDM;RCD highly_ambiguous;highly_homoplasic;narrow_src India NCDC gene-orf1ab 2586 V X,G
MN908947.3 8026 . A W,T,G . mask RCD ambiguous;homoplasic;narrow_src South_Africa;India NHLS;NCDC gene-orf1ab 2587 A A,A,A
MN908947.3 8790 . G T,K . mask NDM;RCD highly_ambiguous;homoplasic;single_src Australia VIDRL gene-orf1ab 2842 G V,X
MN908947.3 8827 . T W,A . mask RCD ambiguous;neighbour_linked Italy IZSAM gene-orf1ab 2854 I I,I
MN908947.3 8828 . G K,T . mask RCD ambiguous;neighbour_linked Italy IZSAM gene-orf1ab 2855 A X,S
MN908947.3 9039 . C Y,M,T,A . mask NDM ambiguous;single_src India NCDC gene-orf1ab 2925 A X,X,V,D
MN908947.3 10129 . T Y,C,W . mask NDM;RCD highly_ambiguous;homoplasic;single_src USA Chan_Zuckerberg_Biohub gene-orf1ab 3288 T T,T,T
MN908947.3 10239 . C M,A . mask RCD homoplasic;single_src UK Sanger_COG_UK gene-orf1ab 3325 S X,Y
MN908947.3 11074 . C T,Y . mask NDM;RCD highly_homoplasic . . gene-orf1ab 3603 F F,F
MN908947.3 11083 . G T,K,A . mask NDM;RCD highly_homoplasic . . gene-orf1ab 3606 L F,X,L
MN908947.3 11535 . G T,K . mask NDM;RCD ambiguous;highly_homoplasic;single_src Australia VIDRL gene-orf1ab 3757 G V,X
MN908947.3 12506 . A R . caution RCD ambiguous;single_src Chile ISPC gene-orf1ab 4081 K X
MN908947.3 13402 . T K,G . mask NDM;RCD homoplasic;narrow_src;amended Belgium;India;Denmark KU_Leuven;NCDC;SSI gene-orf1ab 4379 Y X,*
MN908947.3 13408 . T K,C . mask NDM;RCD homoplasic;narrow_src;amended Belgium;India;South_Africa KU_Leuven;NCDC;SSI gene-orf1ab 4381 C X,C
MN908947.3 13476 . C T,Y . mask NDM highly_ambiguous;narrow_src Turkey Ministry_of_Health gene-orf1ab 4404 C V,X
MN908947.3 13512 . A T . caution NDM neighbour_linked . . gene-orf1ab 4416 T L
MN908947.3 13513 . G T,K . caution NDM neighbour_linked . . gene-orf1ab 4416 T H,X
MN908947.3 13514 . G A,K . caution NDM neighbour_linked . . gene-orf1ab 4417 G T,X
MN908947.3 13571 . G K,T . mask NDM;RCD highly_ambiguous;homoplasic;single_src Australia VIDRL gene-orf1ab 4436 G X,F
MN908947.3 13650 . T K . caution RCD ambiguous;single_src India CSIR gene-orf1ab 4462 F X
MN908947.3 13686 . T D,A,Y . caution NDM neighbour_linked . . gene-orf1ab 4474 H X,K,X
MN908947.3 13687 . G T . caution NDM neighbour_linked . . gene-orf1ab 4474 H I
MN908947.3 13693 . A T,G . caution NDM neighbour_linked . . gene-orf1ab 4476 E N,K
MN908947.3 14277 . G T,K . mask NDM;RCD highly_ambiguous;homoplasic;single_src Australia VIDRL gene-orf1ab 4671 R V,X
MN908947.3 15435 . A G,R . mask NDM;RCD highly_ambiguous;homoplasic;single_src India NCDC gene-orf1ab 5057 E R,X
MN908947.3 15771 . T Y,K,W,D,H . caution RCD ambiguous;single_src USA Chan_Zuckerberg_Biohub gene-orf1ab 5169 A X,X,X,X,X
MN908947.3 15922 . T Y,C . mask NDM;RCD ambiguous;homoplasic;single_src USA Chan_Zuckerberg_Biohub gene-orf1ab 5219 V C,C
MN908947.3 16210 . A W,D . caution RCD ambiguous;single_src Switzerland ETH_Zurich gene-orf1ab 5315 A L,L
MN908947.3 16290 . T K,Y . mask RCD highly_ambiguous;single_src UK Sanger_COG_UK gene-orf1ab 5342 A X,X
MN908947.3 16537 . G R . caution RCD ambiguous;single_src Qatar BRC gene-orf1ab 5424 S A
MN908947.3 16887 . C T,Y . mask NDM;RCD highly_homoplasic . . gene-orf1ab 5541 Y I,X
MN908947.3 18505 . G R . caution NDM;RCD ambiguous;neighbour_linked USA CDC_DVD gene-orf1ab 6080 K K
MN908947.3 18506 . G K . caution NDM;RCD ambiguous;neighbour_linked USA CDC_DVD gene-orf1ab 6081 G X
MN908947.3 18690 . T K . caution RCD ambiguous;single_src India NCDC gene-orf1ab 6142 F X
MN908947.3 19298 . A R,W,D,G . mask RCD highly_ambiguous;single_src Switzerland ETH_Zurich gene-orf1ab 6345 Y X,X,X,V
MN908947.3 19339 . A M,W,R . caution RCD ambiguous;single_src Switzerland ETH_Zurich gene-orf1ab 6358 K X,X,K
MN908947.3 19344 . T Y,C,K . caution NDM ambiguous;amended USA;UK Houston;Nottingham gene-orf1ab 6360 A X,P,X
MN908947.3 19369 . T C,Y . caution NDM ambiguous;amended USA;UK Houston;Nottingham gene-orf1ab 6368 P H,H
MN908947.3 19482 . T K . caution RCD ambiguous;single_src Switzerland ETH_Zurich gene-orf1ab 6406 G X
MN908947.3 19484 . C T,Y . mask NDM highly_ambiguous;amended UK COG_UK gene-orf1ab 6407 A L,L
MN908947.3 19548 . A R,W,G,T . mask RCD ambiguous;single_src Switzerland ETH_Zurich gene-orf1ab 6428 S X,X,R,L
MN908947.3 20056 . G K,T,A . mask RCD ambiguous;homoplasic;single_src UK Public_Health_England gene-orf1ab 6597 E X,N,K
MN908947.3 20123 . T Y,C,W . mask RCD ambiguous;homoplasic;single_src UK Public_Health_England gene-orf1ab 6620 I L,L,X
MN908947.3 21302 . C M,T,S . caution NDM neighbour_linked . . gene-orf1ab 7013 P X,Y,X
MN908947.3 21302 . C M,T,S . caution NDM neighbour_linked . . gene-orf1ab 7013 P X,Y,X
MN908947.3 21303 . A . . caution NDM neighbour_linked . . gene-orf1ab 7013 P .
MN908947.3 21304 . C A,M,T,Y . caution NDM neighbour_linked . . gene-orf1ab 7013 P Q,X,H,H
MN908947.3 21304 . C A,M,T,Y . caution NDM neighbour_linked . . gene-orf1ab 7013 P Q,X,H,H
MN908947.3 21305 . G A,S,R . caution NDM neighbour_linked . . gene-orf1ab 7014 R T,X,X
MN908947.3 21305 . G A,S,R . caution NDM neighbour_linked . . gene-orf1ab 7014 R T,X,X
MN908947.3 21379 . T Y,K . caution RCD ambiguous;single_src Switzerland ETH_Zurich gene-orf1ab 7038 S L,L
MN908947.3 21550 . A M,C . mask NDM;RCD ambiguous;homoplasic;narrow_src India CSIR gene-orf1ab 7095 N T,T
MN908947.3 21551 . A W,T,R . mask NDM;RCD ambiguous;homoplasic;narrow_src India CSIR gene-orf1ab 7096 N X,S,X
MN908947.3 21575 . C Y,T . mask NDM;RCD highly_homoplasic . . gene-S 5 L X,F
MN908947.3 21609 . T K,W . caution RCD ambiguous;single_src Switzerland ETH_Zurich gene-S 16 V X,X
MN908947.3 21658 . C M,Y,H,T,G . caution RCD ambiguous Switzerland ETH_Zurich gene-S 32 F X,F,X,F,L
MN908947.3 22335 . G T,K,A . mask NDM highly_ambiguous;amended UK COG_UK gene-S 258 W L,X,*
MN908947.3 22389 . T Y,C . caution RCD ambiguous;single_src UK Public_Health_England gene-S 276 L X,P
MN908947.3 22393 . A G . caution NDM ambiguous;amended UK;USA;UK Public_Health_England;Houston;Edinburgh gene-S 277 L L
MN908947.3 22416 . T Y,C . caution RCD ambiguous;neighbour_linked;single_src UK Public_Health_England gene-S 285 I X,T
MN908947.3 22420 . A W,T . caution RCD ambiguous;neighbour_linked;single_src UK Public_Health_England gene-S 286 T T,T
MN908947.3 22488 . A R,C . caution NDM ambiguous;amended UK;UK;USA;USA Edinburgh;Sheffield;Minnesota;Houston gene-S 309 E X,A
MN908947.3 22500 . A W . caution RCD ambiguous;single_src UK Public_Health_England gene-S 313 Y X
MN908947.3 22515 . T K,Y . caution NDM ambiguous;narrow_src India;Switzerland NCDC;. gene-S 318 F X,X
MN908947.3 22516 . T W,K,D,C,Y . mask RCD highly_ambiguous;single_src Switzerland ETH_Zurich gene-S 318 F X,X,X,F,F
MN908947.3 22521 . T K,G,Y . mask NDM;RCD highly_ambiguous Austria CeMM gene-S 320 V X,G,X
MN908947.3 22661 . G T,S,K,A . mask NDM;RCD ambiguous;homoplasic;single_src UK Public_Health_Scotland gene-S 367 V F,X,X,I
MN908947.3 22802 . C Y,M . mask NDM;RCD homoplasic;single_src;amended;interspecific_contamination USA TGEN gene-S 414 Q X,X
MN908947.3 23116 . A W,T . caution RCD ambiguous;single_src India NCDC gene-S 518 L L,L
MN908947.3 23144 . A . . caution NDM ambiguous;amended UK;USA;USA Sheffield;Houston;Minnesota gene-S 528 K .
MN908947.3 24389 . A W,M,C . mask MP;NDM;RCD highly_homoplasic;highly_ambiguous;narrow_src;nanopore_adapter Belgium;India;South_Africa;China KU_Leuven;NCDC;NHLS;Ditan gene-S 943 S X,X,R
MN908947.3 24390 . G S,T,C . mask MP;NDM;RCD highly_homoplasic;highly_ambiguous;narrow_src;nanopore_adapter Belgium;India;South_Africa;China KU_Leuven;NCDC;NHLS;Ditan gene-S 943 S X,I,T
MN908947.3 24622 . T Y . mask RCD highly_ambiguous;single_src India NCDC gene-S 1020 A A
MN908947.3 24673 . A . . caution NDM ambiguous;amended USA Minnesota gene-S 1037 S .
MN908947.3 24933 . G T,K . mask NDM;RCD highly_ambiguous;highly_homoplasic;narrow_src Australia VIDRL gene-S 1124 G V,X
MN908947.3 24942 . A W,G,R . caution NDM ambiguous;single_src Australia Doherty gene-S 1127 D X,G,X
MN908947.3 25202 . T K,Y . mask NDM;RCD highly_ambiguous UK Sanger_COG_UK gene-S 1214 W X,X
MN908947.3 25381 . A C,R,M . mask RCD homoplasic;single_src India ICMR gene-S 1273 T T,T,T
MN908947.3 25798 . A G,M . caution NDM ambiguous;amended UK Edinburgh gene-ORF3a 136 K E,X
MN908947.3 26549 . C T,Y . mask NDM;RCD homoplasic;single_src Turkey Ministry_of_Health gene-M 9 T T,T
MN908947.3 26709 . G T,R,A . caution NDM ambiguous;amended India NCDC gene-M 63 A S,X,T
MN908947.3 27534 . T W,Y . caution RCD ambiguous;single_src Switzerland ETH_Zurich gene-ORF7a 47 H X,H
MN908947.3 27720 . T K . caution RCD ambiguous;single_src Switzerland ETH_Zurich gene-ORF7a 109 F X
MN908947.3 27784 . A W,G . mask RCD ambiguous;single_src Switzerland ETH_Zurich . . . .
MN908947.3 27792 . T W,A,Y . caution NDM ambiguous;amended UK Edinburgh . . . .
MN908947.3 28004 . T C . caution NDM neighbour_linked;single_src Luxembourg LNS gene-ORF8 37 C C
MN908947.3 28005 . C T,G . caution NDM neighbour_linked;single_src Luxembourg LNS gene-ORF8 38 P S,A
MN908947.3 28006 . C T . caution NDM neighbour_linked;single_src Luxembourg LNS gene-ORF8 38 P L
MN908947.3 28008 . A G . caution NDM neighbour_linked;single_src Luxembourg LNS gene-ORF8 39 I V
MN908947.3 28253 . C Y,T,G,S,A . mask NDM;RCD highly_homoplasic . . gene-ORF8 120 F F,F,L,X,L
MN908947.3 28780 . A W,D,R . caution RCD ambiguous;single_src Switzerland ETH_Zurich gene-N 169 K X,X,K
MN908947.3 28881 . G A,R,T,K . caution NDM neighbour_linked . . gene-N 203 R K,X,M,X
MN908947.3 28882 . G A,R,T,K,S . caution NDM neighbour_linked . . gene-N 203 R R,R,S,X,X
MN908947.3 28883 . G C,S,R,A . caution NDM neighbour_linked . . gene-N 204 G R,X,X,R
MN908947.3 28985 . G R,S,D,T,K,A . mask NDM;RCD highly_ambiguous;homoplasic;single_src Switzerland ETH_Zurich gene-N 238 G X,X,X,C,X,S
MN908947.3 29037 . C Y,T,M . mask RCD homoplasic;ambiguous;single_src Australia VIDRL gene-N 255 S X,F,X
MN908947.3 29039 . A T,W . mask RCD homoplasic;ambiguous;single_src Australia;India VIDRL;ICMR gene-N 256 K *,X
MN908947.3 29378 . A W . caution NDM ambiguous;amended USA Minnesota gene-N 369 K X
MN908947.3 29425 . G T,S,A . mask NDM;RCD ambiguous;homoplasic;single_src Singapore NPHL gene-N 384 Q H,X,Q
MN908947.3 29427 . G S,R,T,K,C,A . caution RCD ambiguous;neighbour_linked;single_src Singapore NPHL gene-N 385 R X,X,I,X,T,K
MN908947.3 29428 . A G,R,C . caution RCD ambiguous;neighbour_linked;single_src Singapore NPHL gene-N 385 R R,R,S
MN908947.3 29553 . G A . mask NDM;RCD highly_homoplasic;single_src USA;USA University_of_Washington;Seattle_Flu_Study . . . .
MN908947.3 29737 . G K,A,T,S,C . caution RCD ambiguous;single_src UK Public_Health_Wales . . . .
MN908947.3 29804 . T . . mask NDM seq_end . . . . . .
MN908947.3 29805 . A . . mask NDM seq_end . . . . . .
MN908947.3 29806 . A . . mask NDM seq_end . . . . . .
MN908947.3 29807 . T . . mask NDM seq_end . . . . . .
MN908947.3 29808 . G . . mask NDM seq_end . . . . . .
MN908947.3 29809 . T . . mask NDM seq_end . . . . . .
MN908947.3 29810 . G . . mask NDM seq_end . . . . . .
MN908947.3 29811 . T . . mask NDM seq_end . . . . . .
MN908947.3 29812 . A . . mask NDM seq_end . . . . . .
MN908947.3 29813 . A . . mask NDM seq_end . . . . . .
MN908947.3 29814 . A . . mask NDM seq_end . . . . . .
MN908947.3 29815 . A . . mask NDM seq_end . . . . . .
MN908947.3 29816 . T . . mask NDM seq_end . . . . . .
MN908947.3 29817 . T . . mask NDM seq_end . . . . . .
MN908947.3 29818 . A . . mask NDM seq_end . . . . . .
MN908947.3 29819 . A . . mask NDM seq_end . . . . . .
MN908947.3 29820 . T . . mask NDM seq_end . . . . . .
MN908947.3 29821 . T . . mask NDM seq_end . . . . . .
MN908947.3 29822 . T . . mask NDM seq_end . . . . . .
MN908947.3 29823 . T . . mask NDM seq_end . . . . . .
MN908947.3 29824 . A . . mask NDM seq_end . . . . . .
MN908947.3 29825 . G . . mask NDM seq_end . . . . . .
MN908947.3 29826 . T . . mask NDM seq_end . . . . . .
MN908947.3 29827 . A C,G,T . mask NDM;RCD seq_end;highly_homoplasic;single_src India NIV . . . .
MN908947.3 29828 . G . . mask NDM seq_end . . . . . .
MN908947.3 29829 . T . . mask NDM seq_end . . . . . .
MN908947.3 29830 . G T,A,C,S . mask NDM;RCD seq_end;highly_homoplasic;single_src India NIV . . . .
MN908947.3 29831 . C . . mask NDM seq_end . . . . . .
MN908947.3 29832 . T . . mask NDM seq_end . . . . . .
MN908947.3 29833 . A . . mask NDM seq_end . . . . . .
MN908947.3 29834 . T . . mask NDM seq_end . . . . . .
MN908947.3 29835 . C . . mask NDM seq_end . . . . . .
MN908947.3 29836 . C . . mask NDM seq_end . . . . . .
MN908947.3 29837 . C . . mask NDM seq_end . . . . . .
MN908947.3 29838 . C . . mask NDM seq_end . . . . . .
MN908947.3 29839 . A . . mask NDM seq_end . . . . . .
MN908947.3 29840 . T . . mask NDM seq_end . . . . . .
MN908947.3 29841 . G . . mask NDM seq_end . . . . . .
MN908947.3 29842 . T . . mask NDM seq_end . . . . . .
MN908947.3 29843 . G . . mask NDM seq_end . . . . . .
MN908947.3 29844 . A . . mask NDM seq_end . . . . . .
MN908947.3 29845 . T . . mask NDM seq_end . . . . . .
MN908947.3 29846 . T . . mask NDM seq_end . . . . . .
MN908947.3 29847 . T . . mask NDM seq_end . . . . . .
MN908947.3 29848 . T . . mask NDM seq_end . . . . . .
MN908947.3 29849 . A . . mask NDM seq_end . . . . . .
MN908947.3 29850 . A . . mask NDM seq_end . . . . . .
MN908947.3 29851 . T . . mask NDM seq_end . . . . . .
MN908947.3 29852 . A . . mask NDM seq_end . . . . . .
MN908947.3 29853 . G . . mask NDM seq_end . . . . . .
MN908947.3 29854 . C . . mask NDM seq_end . . . . . .
MN908947.3 29855 . T . . mask NDM seq_end . . . . . .
MN908947.3 29856 . T . . mask NDM seq_end . . . . . .
MN908947.3 29857 . C . . mask NDM seq_end . . . . . .
MN908947.3 29858 . T . . mask NDM seq_end . . . . . .
MN908947.3 29859 . T . . mask NDM seq_end . . . . . .
MN908947.3 29860 . A . . mask NDM seq_end . . . . . .
MN908947.3 29861 . G . . mask NDM seq_end . . . . . .
MN908947.3 29862 . G . . mask NDM seq_end . . . . . .
MN908947.3 29863 . A . . mask NDM seq_end . . . . . .
MN908947.3 29864 . G . . mask NDM seq_end . . . . . .
MN908947.3 29865 . A . . mask NDM seq_end . . . . . .
MN908947.3 29866 . A . . mask NDM seq_end . . . . . .
MN908947.3 29867 . T . . mask NDM seq_end . . . . . .
MN908947.3 29868 . G . . mask NDM seq_end . . . . . .
MN908947.3 29869 . A . . mask NDM seq_end . . . . . .
MN908947.3 29870 . C . . mask NDM seq_end . . . . . .
MN908947.3 29871 . A . . mask NDM seq_end . . . . . .
MN908947.3 29872 . A . . mask NDM seq_end . . . . . .
MN908947.3 29873 . A . . mask NDM seq_end . . . . . .
MN908947.3 29874 . A . . mask NDM seq_end . . . . . .
MN908947.3 29875 . A . . mask NDM seq_end . . . . . .
MN908947.3 29876 . A . . mask NDM seq_end . . . . . .
MN908947.3 29877 . A . . mask NDM seq_end . . . . . .
MN908947.3 29878 . A . . mask NDM seq_end . . . . . .
MN908947.3 29879 . A . . mask NDM seq_end . . . . . .
MN908947.3 29880 . A . . mask NDM seq_end . . . . . .
MN908947.3 29881 . A . . mask NDM seq_end . . . . . .
MN908947.3 29882 . A . . mask NDM seq_end . . . . . .
MN908947.3 29883 . A . . mask NDM seq_end . . . . . .
MN908947.3 29884 . A . . mask NDM seq_end . . . . . .
MN908947.3 29885 . A . . mask NDM seq_end . . . . . .
MN908947.3 29886 . A . . mask NDM seq_end . . . . . .
MN908947.3 29887 . A . . mask NDM seq_end . . . . . .
MN908947.3 29888 . A . . mask NDM seq_end . . . . . .
MN908947.3 29889 . A . . mask NDM seq_end . . . . . .
MN908947.3 29890 . A . . mask NDM seq_end . . . . . .
MN908947.3 29891 . A . . mask NDM seq_end . . . . . .
MN908947.3 29892 . A . . mask NDM seq_end . . . . . .
MN908947.3 29893 . A . . mask NDM seq_end . . . . . .
MN908947.3 29894 . A . . mask NDM seq_end . . . . . .
MN908947.3 29895 . A . . mask NDM seq_end . . . . . .
MN908947.3 29896 . A . . mask NDM seq_end . . . . . .
MN908947.3 29897 . A . . mask NDM seq_end . . . . . .
MN908947.3 29898 . A . . mask NDM seq_end . . . . . .
MN908947.3 29899 . A . . mask NDM seq_end . . . . . .
MN908947.3 29900 . A . . mask NDM seq_end . . . . . .
MN908947.3 29901 . A . . mask NDM seq_end . . . . . .
MN908947.3 29902 . A . . mask NDM seq_end . . . . . .
MN908947.3 29903 . A . . mask NDM seq_end . . . . . .