• Human-friendly version of the vcf file
• Description of the columns in the vcf-version

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.