/ProblematicSites_SARS-CoV2

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Human-friendly version of the vcf file

POS REF ALT FILTER EXC GENE AA_POS AA_REF AA_ALT
1-55 . . mask seq_end . . . .
76 T W,A,C caution ambiguous
neighbour_linked
narrow_src		 . . . .
78 T Y,K,W,A,G caution ambiguous
neighbour_linked
narrow_src		 . . . .
150 T C,Y mask homoplasic
single_src
neighbour_linked		 . . . .
153 T G,Y mask homoplasic
single_src
neighbour_linked		 . . . .
538 A W caution ambiguous gene-orf1ab 91 E X
635 C Y,T mask highly_ambiguous
homoplasic
narrow_src		 gene-orf1ab 124 R X,C
660 G K,A caution ambiguous gene-orf1ab 132 G X,D
759 A D,T caution ambiguous
single_src		 gene-orf1ab 165 H X,L
1001 G A caution ambiguous
amended		 gene-orf1ab 246 E K
1707 C Y,T,A mask highly_ambiguous
homoplasic
narrow_src		 gene-orf1ab 481 S X,F,Y
1814 A . caution ambiguous
amended		 gene-orf1ab 517 K .
1895 G T,K mask ambiguous gene-orf1ab 544 V L,X
1947 T C,Y caution ambiguous
narrow_src		 gene-orf1ab 561 V A,X
2087 T Y caution ambiguous gene-orf1ab 608 L L
2091 C T,Y mask highly_ambiguous
homoplasic
narrow_src		 gene-orf1ab 609 T I,X
2094 C T,Y mask highly_ambiguous
narrow_src		 gene-orf1ab 610 S L,X
2198 G R,T,A mask homoplasic
ambiguous
narrow_src		 gene-orf1ab 645 G X,C,S
2604 G T,K mask homoplasic
ambiguous
single_src		 gene-orf1ab 780 G V,X
3145 G T mask homoplasic
single_src		 gene-orf1ab 960 L F
3564 G T,K mask highly_ambiguous
highly_homoplasic
single_src		 gene-orf1ab 1100 G V,X
3639 G R,A mask ambiguous
homoplasic
single_src		 gene-orf1ab 1125 G X,D
3778 A G mask homoplasic
single_src		 gene-orf1ab 1171 T T
4050 A C mask homoplasic
single_src
amended		 gene-orf1ab 1262 N T
4463 T C,Y caution ambiguous
single_src
homoplasic		 gene-orf1ab 1400 S P,X
5011 A M,C mask ambiguous
homoplasic
single_src		 gene-orf1ab 1582 Q X,H
5257 A W,G,M mask highly_ambiguous
single_src		 gene-orf1ab 1664 L X,L,X
5393 T Y caution ambiguous
amended		 gene-orf1ab 1710 F X
5498 A . caution ambiguous
amended		 gene-orf1ab 1745 K .
5657 G S,K,T,A caution ambiguous
single_src		 gene-orf1ab 1798 V X,X,L,I
5736 C T,Y mask homoplasic
single_src		 gene-orf1ab 1824 A V,X
5743 G S,T mask highly_ambiguous
neighbour_linked
narrow_src		 gene-orf1ab 1826 E X,D
5744 T Y mask highly_ambiguous
neighbour_linked
narrow_src		 gene-orf1ab 1827 Y X
5765 G K,R caution ambiguous
single_src
neighbour_linked		 gene-orf1ab 1834 G X,X
5766 G S caution ambiguous
single_src
neighbour_linked		 gene-orf1ab 1834 G X
6167 G R,K mask ambiguous
single_src		 gene-orf1ab 1968 V X,X
6255 C T mask highly_homoplasic
narrow_src		 gene-orf1ab 1997 A V
6309 G T,R,A caution neighbour_linked gene-orf1ab 2015 S I,X,N
6310 C A,T,M caution neighbour_linked gene-orf1ab 2015 S R,S,X
6312 C A,M,T,G caution neighbour_linked gene-orf1ab 2016 T K,X,I,R
6866 A W,T caution ambiguous gene-orf1ab 2201 N X,Y
6869 A W,T mask ambiguous
homoplasic
single_src		 gene-orf1ab 2202 T X,S
6877 G K,T caution ambiguous
single_src		 gene-orf1ab 2204 K X,N
6971 T C,W caution neighbour_linked
single_src		 gene-orf1ab 2236 L L,J
6975 G T caution neighbour_linked
single_src		 gene-orf1ab 2237 S I
6977 G A caution neighbour_linked
single_src		 gene-orf1ab 2238 V I
7090 T K caution ambiguous
single_src		 gene-orf1ab 2275 N X
7305 T K caution ambiguous
single_src		 gene-orf1ab 2347 M X
7396 T W,Y caution ambiguous gene-orf1ab 2377 I I,I
8022 T K,G,C mask highly_ambiguous
highly_homoplasic
narrow_src		 gene-orf1ab 2586 V X,G,A
8026 A W,G,T mask ambiguous
homoplasic
narrow_src		 gene-orf1ab 2587 A A,A,A
8790 G T,K mask highly_ambiguous
homoplasic
single_src		 gene-orf1ab 2842 G V,X
8827 T W mask ambiguous
neighbour_linked		 gene-orf1ab 2854 I I
8828 G K,A mask ambiguous
neighbour_linked		 gene-orf1ab 2855 A X,T
9039 C Y,M,T mask ambiguous
single_src		 gene-orf1ab 2925 A X,X,V
9471 G S,C caution ambiguous
single_src		 gene-orf1ab 3069 R X,T
10129 T Y,C,W mask highly_ambiguous
homoplasic
single_src		 gene-orf1ab 3288 T T,T,T
10239 C M,A mask homoplasic
single_src		 gene-orf1ab 3325 S X,Y
11074 C T,Y mask highly_homoplasic gene-orf1ab 3603 F F,F
11083 G T,K,A mask highly_homoplasic gene-orf1ab 3606 L F,X,L
11535 G T,K mask ambiguous
highly_homoplasic
single_src		 gene-orf1ab 3757 G V,X
12506 A R caution ambiguous
single_src		 gene-orf1ab 4081 K X
13402 T G,K,C mask homoplasic
narrow_src
amended		 gene-orf1ab 4379 Y *,X,Y
13408 T K mask homoplasic
narrow_src
amended		 gene-orf1ab 4381 C X
13476 C T,Y mask highly_ambiguous
narrow_src		 gene-orf1ab 4404 C V,X
13512 A T,G caution neighbour_linked gene-orf1ab 4416 T L,R
13513 G T,K caution neighbour_linked gene-orf1ab 4416 T H,X
13514 G A,S caution neighbour_linked gene-orf1ab 4417 G T,X
13571 G T,K mask highly_ambiguous
homoplasic
single_src		 gene-orf1ab 4436 G F,X
13650 T K caution ambiguous
single_src		 gene-orf1ab 4462 F X
13686 T A,Y caution neighbour_linked gene-orf1ab 4474 H K,X
13687 G T caution neighbour_linked gene-orf1ab 4474 H I
13693 A W,T caution neighbour_linked gene-orf1ab 4476 E X,N
14277 G T,K mask highly_ambiguous
homoplasic
single_src		 gene-orf1ab 4671 R V,X
15435 A R,G mask highly_ambiguous
homoplasic
single_src		 gene-orf1ab 5057 E X,R
15771 T Y,W,K,D,H caution ambiguous
single_src		 gene-orf1ab 5169 A X,X,X,X,X
15922 T Y,C mask ambiguous
homoplasic
single_src		 gene-orf1ab 5219 V C,C
16210 A W,D caution ambiguous
single_src		 gene-orf1ab 5315 A L,L
16290 T K mask highly_ambiguous
single_src		 gene-orf1ab 5342 A X
16537 G K,T,R caution ambiguous
single_src		 gene-orf1ab 5424 S A,A,A
16887 C T,Y mask highly_homoplasic gene-orf1ab 5541 Y I,X
18505 G R caution ambiguous
neighbour_linked		 gene-orf1ab 6080 K K
18506 G K caution ambiguous
neighbour_linked		 gene-orf1ab 6081 G X
18690 T K,C caution ambiguous
single_src		 gene-orf1ab 6142 F X,S
19298 A D,W,T,R mask highly_ambiguous
single_src		 gene-orf1ab 6345 Y X,X,L,X
19299 T Y,G mask homoplasic
ambiguous
narrow_src		 gene-orf1ab 6345 Y X,R
19338 A R,G,M caution highly_ambiguous
narrow_src		 gene-orf1ab 6358 K X,R,X
19339 A M,W,R caution ambiguous
single_src		 gene-orf1ab 6358 K X,X,K
19344 T Y,K,C caution ambiguous
amended		 gene-orf1ab 6360 A X,X,P
19369 T Y caution ambiguous
amended		 gene-orf1ab 6368 P H
19406 G R,K,A caution highly_ambiguous
single_src		 gene-orf1ab 6381 G X,X,K
19482 T K,W caution ambiguous
single_src		 gene-orf1ab 6406 G X,X
19484 C T,Y mask highly_ambiguous
amended		 gene-orf1ab 6407 A L,L
19548 A R,W,G,T,D mask ambiguous
single_src		 gene-orf1ab 6428 S X,X,R,L,X
19732 G K,T,R caution homoplasic
narrow_src		 gene-orf1ab 6489 G V,V,V
20056 G K,A mask ambiguous
homoplasic
single_src		 gene-orf1ab 6597 E X,K
20123 T Y,C mask ambiguous
homoplasic
single_src		 gene-orf1ab 6620 I L,L
20126 G K,A,S,R caution ambiguous
single_src
homoplasic		 gene-orf1ab 6621 G X,K,Z,X
20465 A G,R,W mask highly_homoplasic
single_src		 gene-orf1ab 6734 D V,X,X
21302 C T,A,S caution neighbour_linked gene-orf1ab 7013 P Y,N,X
21304 C A,T,Y caution neighbour_linked gene-orf1ab 7013 P Q,H,H
21305 G A,R caution neighbour_linked gene-orf1ab 7014 R T,X
21379 T Y caution ambiguous
single_src		 gene-orf1ab 7038 S L
21550 A M,C mask ambiguous
homoplasic
narrow_src		 gene-orf1ab 7095 N T,T
21551 A W,T,R mask ambiguous
homoplasic
narrow_src		 gene-orf1ab 7096 N X,S,X
21575 C T,Y mask highly_homoplasic gene-S 5 L F,X
21609 T K,W caution ambiguous
single_src		 gene-S 16 V X,X
21658 C M,Y,H,T,G caution ambiguous gene-S 32 F X,F,X,F,L
22329 C Y,T caution ambiguous
single_src		 gene-S 256 S X,L
22335 G T,K,A mask highly_ambiguous
amended		 gene-S 258 W L,X,*
22389 T Y,C caution ambiguous
single_src		 gene-S 276 L X,P
22393 A G caution ambiguous
amended		 gene-S 277 L L
22416 T Y,C caution ambiguous
neighbour_linked
single_src		 gene-S 285 I X,T
22420 A W,T caution ambiguous
neighbour_linked
single_src		 gene-S 286 T T,T
22488 A R,M,C caution ambiguous
amended		 gene-S 309 E X,X,A
22500 A W,M caution ambiguous
single_src		 gene-S 313 Y X,X
22515 T K,Y caution ambiguous
narrow_src		 gene-S 318 F X,X
22516 T W,D,K,C,Y mask highly_ambiguous
single_src		 gene-S 318 F X,X,X,F,F
22521 T K,Y mask highly_ambiguous gene-S 320 V X,X
22661 G T,S,A mask ambiguous
homoplasic
single_src		 gene-S 367 V F,X,I
22802 C M,A,T,Y mask homoplasic
single_src
amended
interspecific_contamination		 gene-S 414 Q X,K,*,X
23116 A W,T caution ambiguous
single_src		 gene-S 518 L L,L
23144 A . caution ambiguous
amended		 gene-S 528 K .
24389 A W,M,C mask highly_homoplasic
highly_ambiguous
narrow_src
nanopore_adapter		 gene-S 943 S X,X,R
24390 G T,S,K,C mask highly_homoplasic
highly_ambiguous
narrow_src
nanopore_adapter		 gene-S 943 S I,X,X,T
24622 T Y mask highly_ambiguous
single_src		 gene-S 1020 A A
24673 A . caution ambiguous
amended		 gene-S 1037 S .
24933 G K,T mask highly_ambiguous
highly_homoplasic
narrow_src		 gene-S 1124 G X,V
24942 A W,G,R caution ambiguous
single_src		 gene-S 1127 D X,G,X
25202 T K mask highly_ambiguous gene-S 1214 W X
25381 A C,R,M mask homoplasic
single_src		 gene-S 1273 T T,T,T
25798 A G caution ambiguous
amended		 gene-ORF3a 136 K E
26549 C T,Y mask homoplasic
single_src		 gene-M 9 T T,T
26700 G T,K caution ambiguous
single_src
homoplasic		 gene-M 60 V L,X
26709 G A,T,R caution ambiguous
amended		 gene-M 63 A T,S,X
27534 T W,C,Y caution ambiguous
single_src		 gene-ORF7a 47 H X,H,H
27720 T K caution ambiguous
single_src		 gene-ORF7a 109 F X
27760 T K,Y,A mask homoplasic
neighbour_linked		 . . . .
27761 T C mask homoplasic
neighbour_linked		 . . . .
27784 A W,G,T mask ambiguous
single_src		 . . . .
27792 T W caution ambiguous
amended		 . . . .
28004 T C,Y caution neighbour_linked
single_src		 gene-ORF8 37 C C,C
28005 C T,G caution neighbour_linked
single_src		 gene-ORF8 38 P S,A
28006 C T caution neighbour_linked
single_src		 gene-ORF8 38 P L
28008 A G caution neighbour_linked
single_src		 gene-ORF8 39 I V
28253 C Y,T,G,A,S mask highly_homoplasic gene-ORF8 120 F F,F,L,L,X
28517 G S,K,T caution ambiguous
single_src		 gene-N 82 D X,X,Y
28676 A M,C caution ambiguous
single_src		 gene-N 135 T X,P
28780 A D,W,R caution ambiguous
single_src		 gene-N 169 K X,X,K
28881 G A,R,T,K caution neighbour_linked gene-N 203 R K,X,M,X
28882 G A,R,T,K,S caution neighbour_linked gene-N 203 R R,R,S,X,X
28883 G C,S,A caution neighbour_linked gene-N 204 G R,X,R
28985 G R,D,T,K,A mask highly_ambiguous
homoplasic
single_src		 gene-N 238 G X,X,C,X,S
29037 C T,Y,M mask homoplasic
ambiguous
single_src		 gene-N 255 S F,X,X
29039 A T,W mask homoplasic
ambiguous
single_src		 gene-N 256 K *,X
29378 A W caution ambiguous
amended		 gene-N 369 K X
29425 G T,S,A mask ambiguous
homoplasic
single_src		 gene-N 384 Q H,X,Q
29427 G S,K,A,T,R,C caution ambiguous
neighbour_linked
single_src		 gene-N 385 R X,X,K,I,X,T
29428 A R caution ambiguous
neighbour_linked
single_src		 gene-N 385 R R
29553 G A,T mask highly_homoplasic
single_src		 . . . .
29737 G K,A,T,S,C caution ambiguous
single_src		 . . . .
29786 G K,C caution homoplasic
single_src		 . . . .
29827 A G,T mask seq_end
highly_homoplasic
single_src		 . . . .
29830 G T,A,C mask seq_end
highly_homoplasic
single_src		 . . . .
29804-29903 . . mask seq_end . . . .

Description of the columns in the vcf-version

The information presented in the table above is also available as a .vcf formatted file.

The VCF files have the 8 mandatory columns outlined in the VCF v4.3 specification, some of which contain non-standard content:

Header Description
CHROM Name of the reference sequence
POS 1-based position of the variation on the reference
ID NA
REF Reference base
ALT List of alternative alleles at the position (IUPAC ambiguity code)
QUAL NA
FILTER Masking recommendation (mask or interpret with caution)
INFO Key=value metadata pairs

Metadata in the INFO column current includes the following:

INFO keys Description
SUB Initials of submitter
EXC List of reasons for suggested exclusion (tags described in separate table)
SRC_COUNTRY Source country/countries of samples with the variant (excluded from the human-friendly VCF)
SRC_LAB Source laboratory/laboratories of samples with the variant, ordered to match the respective values in SRC_COUNTRY (excluded from the human-friendly VCF)
GENE Position falls into range of this gene
AAPOS Position of amino acid residue within gene
REFAA Reference amino acid residue
ALTAA List of alternative amino acid residues (IUPAC ambiguity code)

Descriptions of reasons for mask/caution (values for EXC in the INFO column) are as follows:

Tag Description
seq_end Alignment ends are affected by low coverage and high error rates
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

Suggestions, additions and issues are very gratefully received.