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 K,Y,W,C,A caution ambiguous
neighbour_linked
narrow_src
. . . .
78 T K,Y,A,C,W,G caution ambiguous
neighbour_linked
narrow_src
. . . .
150 T C,Y mask homoplasic
single_src
neighbour_linked
. . . .
153 T Y,G mask homoplasic
single_src
neighbour_linked
. . . .
285 G K,T,A caution single_src
highly_ambiguous
gene-orf1ab 7 G X,V,D
320 C Y,S,T,A,G caution narrow_src
highly_ambiguous
gene-orf1ab 19 P X,X,S,T,A
538 A R,W,G caution ambiguous gene-orf1ab 91 E E,X,E
553 G T,K,C,A caution single_src
highly_ambiguous
gene-orf1ab 96 Q H,X,H,Q
558 G R,K,T caution single_src
highly_ambiguous
gene-orf1ab 98 G X,X,V
635 C T,Y mask highly_ambiguous
homoplasic
narrow_src
gene-orf1ab 124 R C,X
660 G K,S,A caution ambiguous gene-orf1ab 132 G X,X,D
663 G R,K,T,A caution single_src
highly_ambiguous
gene-orf1ab 133 G X,X,V,D
759 A D,T caution ambiguous
single_src
gene-orf1ab 165 H X,L
856 T C,A,Y caution single_src
highly_ambiguous
gene-orf1ab 197 P P,P,P
1001 G R,A caution ambiguous
amended
gene-orf1ab 246 E X,K
1406 G K,T,A,S caution single_src
highly_ambiguous
gene-orf1ab 381 E X,*,K,Z
1707 C T,A,Y mask highly_ambiguous
homoplasic
narrow_src
gene-orf1ab 481 S F,Y,X
1814 A . caution ambiguous
amended
gene-orf1ab 517 K .
1895 G K,T mask ambiguous gene-orf1ab 544 V X,L
1947 T C,Y,G caution ambiguous
narrow_src
gene-orf1ab 561 V A,X,G
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
2101 G K,T caution single_src
highly_ambiguous
gene-orf1ab 612 W X,C
2198 G R,T,A mask homoplasic
ambiguous
narrow_src
gene-orf1ab 645 G X,C,S
2247 G R,K,T,A caution single_src
highly_ambiguous
gene-orf1ab 661 G X,X,V,D
2381 G K,T caution single_src
highly_ambiguous
gene-orf1ab 706 G X,C
2604 G K,T mask homoplasic
ambiguous
single_src
gene-orf1ab 780 G X,V
3050 G K,T,A caution single_src
highly_ambiguous
gene-orf1ab 929 E X,*,K
3073 T C,W,Y caution single_src
highly_ambiguous
gene-orf1ab 936 C C,X,C
3145 G T mask homoplasic
single_src
gene-orf1ab 960 L F
3191 G T,K,C,A caution single_src
highly_ambiguous
gene-orf1ab 976 E *,X,Q,K
3480 C T,Y caution single_src
highly_ambiguous
gene-orf1ab 1072 A V,X
3504 A T,W,M,G caution single_src
highly_ambiguous
gene-orf1ab 1080 N I,X,X,S
3564 G K,T mask highly_ambiguous
highly_homoplasic
single_src
gene-orf1ab 1100 G X,V
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
3877 T K,C,A,G caution single_src
highly_ambiguous
gene-orf1ab 1204 A A,A,A,A
4050 A C mask homoplasic
single_src
amended
gene-orf1ab 1262 N T
4221 A D,T,W mask single_src
highly_homoplasic
gene-orf1ab 1319 K X,I,X
4463 T K,C,Y,G caution ambiguous
single_src
homoplasic
gene-orf1ab 1400 S X,P,X,A
4505 G R,K,T,A caution single_src
highly_ambiguous
gene-orf1ab 1414 G X,X,C,S
4692 C T,A caution single_src
highly_ambiguous
gene-orf1ab 1476 S F,Y
4854 G K,T,A caution single_src
highly_ambiguous
gene-orf1ab 1530 R X,I,K
4991 A T,C,M caution single_src
highly_ambiguous
gene-orf1ab 1576 N Y,H,X
5011 A C,M mask ambiguous
homoplasic
single_src
gene-orf1ab 1582 Q H,X
5130 C T,A,G caution single_src
highly_ambiguous
gene-orf1ab 1622 P L,H,R
5196 G T,K,C caution single_src
highly_ambiguous
gene-orf1ab 1644 G V,X,A
5233 G D,K,R,T,A caution single_src
highly_ambiguous
gene-orf1ab 1656 W X,X,X,C,*
5257 A M,W,G mask highly_ambiguous
single_src
gene-orf1ab 1664 L X,X,L
5322 T K,Y,W,A,G caution single_src
highly_ambiguous
gene-orf1ab 1686 I X,X,X,K,R
5375 G K,T,S caution single_src
highly_ambiguous
gene-orf1ab 1704 A X,S,X
5393 T C,Y caution ambiguous
amended
gene-orf1ab 1710 F L,X
5498 A R caution ambiguous
amended
gene-orf1ab 1745 K X
5657 G K,T,A,S caution ambiguous
single_src
gene-orf1ab 1798 V X,L,I,X
5736 C T,Y mask homoplasic
single_src
gene-orf1ab 1824 A V,X
5743 G T,S mask highly_ambiguous
neighbour_linked
narrow_src
gene-orf1ab 1826 E D,X
5744 T Y mask highly_ambiguous
neighbour_linked
narrow_src
gene-orf1ab 1827 Y X
5765 G R,K 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
5847 G T,K,C,A caution single_src
highly_ambiguous
gene-orf1ab 1861 G V,X,A,D
5880 G T,K,C,A caution single_src
highly_ambiguous
gene-orf1ab 1872 S I,X,T,N
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 K,R,T,C,A caution neighbour_linked gene-orf1ab 2015 S X,X,I,T,N
6310 C Y,M,T,A,G caution neighbour_linked gene-orf1ab 2015 S S,X,S,R,R
6312 C Y,M,T,A,G caution neighbour_linked gene-orf1ab 2016 T X,X,I,K,R
6483 G R,K,T caution single_src
highly_ambiguous
gene-orf1ab 2073 G X,X,V
6804 G T,K,C,A caution single_src
highly_ambiguous
gene-orf1ab 2180 C F,X,S,Y
6866 A T,W caution ambiguous gene-orf1ab 2201 N Y,X
6869 A T,W mask ambiguous
homoplasic
single_src
gene-orf1ab 2202 T S,X
6874 T C,Y,G mask single_src
highly_homoplasic
gene-orf1ab 2203 V V,V,V
6877 G K,T caution ambiguous
single_src
gene-orf1ab 2204 K X,N
6971 T C,W,Y caution neighbour_linked
single_src
gene-orf1ab 2236 L L,J,L
6975 G R,T caution neighbour_linked
single_src
gene-orf1ab 2237 S X,I
6977 G R,K,A caution neighbour_linked
single_src
gene-orf1ab 2238 V X,X,I
7017 G K,T,A,S caution single_src
highly_ambiguous
gene-orf1ab 2251 G X,V,D,X
7038 G R,K,T,A caution single_src
highly_ambiguous
gene-orf1ab 2258 G X,X,V,D
7090 T K,G caution ambiguous
single_src
gene-orf1ab 2275 N X,K
7118 T K,Y,C,A,G caution single_src
highly_ambiguous
gene-orf1ab 2285 S X,X,P,T,A
7214 G K,T,A caution single_src
highly_ambiguous
gene-orf1ab 2317 D X,Y,N
7246 G K,T caution single_src
highly_ambiguous
gene-orf1ab 2327 W X,C
7305 T K,A,Y caution ambiguous
single_src
gene-orf1ab 2347 M X,K,X
7396 T C,W,Y caution ambiguous gene-orf1ab 2377 I I,I,I
7805 G R,A caution single_src
highly_ambiguous
gene-orf1ab 2514 E X,K
8022 T K,C,G mask highly_ambiguous
highly_homoplasic
narrow_src
gene-orf1ab 2586 V X,A,G
8026 A T,W,G mask ambiguous
homoplasic
narrow_src
gene-orf1ab 2587 A A,A,A
8328 T G mask single_src
highly_homoplasic
gene-orf1ab 2688 L R
8459 G K,T caution single_src
highly_ambiguous
gene-orf1ab 2732 A X,S
8550 G K,T caution single_src
highly_ambiguous
gene-orf1ab 2762 G X,V
8658 A T,C,W,G caution single_src
highly_ambiguous
gene-orf1ab 2798 K I,T,X,R
8678 G R,T,A caution single_src
highly_ambiguous
gene-orf1ab 2805 E X,*,K
8688 G K,T,A,B caution single_src
highly_ambiguous
gene-orf1ab 2808 G X,V,E,X
8696 G K,R,B,T,A caution single_src
highly_ambiguous
gene-orf1ab 2811 A X,X,X,S,T
8790 G K,T mask highly_ambiguous
homoplasic
single_src
gene-orf1ab 2842 G X,V
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
8835 T C mask amplicon_drop_or_primer_artefact gene-orf1ab 2857 V A
8886 T A,C,W,Y mask single_src
highly_homoplasic
gene-orf1ab 2874 L *,S,X,X
8887 A R,C,G mask single_src
highly_homoplasic
gene-orf1ab 2874 L L,F,L
8943 G K,T,A caution single_src
highly_ambiguous
gene-orf1ab 2893 G X,V,D
8999 G K,T,A caution single_src
highly_ambiguous
gene-orf1ab 2912 A X,S,T
9039 C T,M,Y mask ambiguous
single_src
gene-orf1ab 2925 A V,X,X
9141 G K,R,T,C,A caution single_src
highly_ambiguous
gene-orf1ab 2959 G X,X,V,A,D
9249 G T,K,C caution single_src
highly_ambiguous
gene-orf1ab 2995 G V,X,A
9276 G T,K,C,A caution single_src
highly_ambiguous
gene-orf1ab 3004 W L,X,S,*
9471 G C,A,S caution ambiguous
single_src
gene-orf1ab 3069 R T,K,X
10046 G R,K,A caution single_src
highly_ambiguous
gene-orf1ab 3261 V X,X,I
10122 G K,T,S caution single_src
highly_ambiguous
gene-orf1ab 3286 G X,V,X
10129 T C,W,Y mask highly_ambiguous
homoplasic
single_src
gene-orf1ab 3288 T T,T,T
10157 G K,T,A caution single_src
highly_ambiguous
gene-orf1ab 3298 V X,L,I
10239 C M,A mask homoplasic
single_src
gene-orf1ab 3325 S X,Y
10266 G R,K,T,A caution single_src
highly_ambiguous
gene-orf1ab 3334 G X,X,V,D
10554 T D,A mask single_src
highly_homoplasic
gene-orf1ab 3430 L X,*
10716 A C,W,G mask single_src
highly_homoplasic
gene-orf1ab 3484 N T,X,S
10764 A T,C,G caution single_src
highly_ambiguous
gene-orf1ab 3500 Y F,S,C
10986 G D,K,C,S,T caution single_src
highly_ambiguous
gene-orf1ab 3574 R X,X,T,X,I
11048 G K,T caution single_src
highly_ambiguous
gene-orf1ab 3595 V X,F
11074 C T,Y mask highly_homoplasic gene-orf1ab 3603 F F,F
11083 G K,T,A mask highly_homoplasic gene-orf1ab 3606 L X,F,L
11392 G T,K,C caution single_src
highly_ambiguous
gene-orf1ab 3709 W C,X,C
11535 G K,T mask ambiguous
highly_homoplasic
single_src
gene-orf1ab 3757 G X,V
12041 G T,K,C,A caution single_src
highly_ambiguous
gene-orf1ab 3926 D Y,X,H,N
12164 G K,T,A caution single_src
highly_ambiguous
gene-orf1ab 3967 A X,S,T
12413 A R,T,C,G caution single_src
highly_ambiguous
gene-orf1ab 4050 N B,Y,H,D
12491 G T,K,C,A caution single_src
highly_ambiguous
gene-orf1ab 4076 D Y,X,H,N
12506 A R caution ambiguous
single_src
gene-orf1ab 4081 K X
12685 G K,T,A caution narrow_src
highly_ambiguous
gene-orf1ab 4140 Q X,H,Q
12698 A C,W,G caution single_src
highly_ambiguous
gene-orf1ab 4145 S R,X,G
12751 T A,W caution single_src
highly_ambiguous
gene-orf1ab 4162 A A,A
13117 A C,M,G mask single_src
highly_homoplasic
gene-orf1ab 4284 L L,L,L
13161 G K,T,A caution single_src
highly_ambiguous
gene-orf1ab 4299 C X,F,Y
13193 G K,T,A caution single_src
highly_ambiguous
gene-orf1ab 4310 V X,F,I
13239 C T,Y,G caution single_src
highly_ambiguous
gene-orf1ab 4325 S L,X,W
13402 T K,C,G 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,C,G caution neighbour_linked gene-orf1ab 4416 T L,P,R
13513 G K,T,A caution neighbour_linked gene-orf1ab 4416 T X,H,Q
13514 G T,C,A,S caution neighbour_linked gene-orf1ab 4417 G S,P,T,X
13571 G K,T mask highly_ambiguous
homoplasic
single_src
gene-orf1ab 4436 G X,F
13599 T C,Y mask single_src
highly_homoplasic
gene-orf1ab 4445 C A,X
13650 T K caution ambiguous
single_src
gene-orf1ab 4462 F X
13686 T C,A,Y caution neighbour_linked gene-orf1ab 4474 H T,K,X
13687 G T mask single_src
highly_homoplasic
neighbour_linked
gene-orf1ab 4474 H I
13693 A R,T,W caution neighbour_linked gene-orf1ab 4476 E K,N,X
14197 G K,T,A,S caution single_src
highly_ambiguous
gene-orf1ab 4644 T L,L,L,L
14222 T B,G mask single_src
highly_homoplasic
neighbour_linked
gene-orf1ab 4653 L X,E
14223 A C,G mask single_src
highly_homoplasic
neighbour_linked
gene-orf1ab 4653 L S,*
14225 C M,T,A,B mask single_src
highly_homoplasic
neighbour_linked
gene-orf1ab 4654 T X,*,K,X
14277 G K,T mask highly_ambiguous
homoplasic
single_src
gene-orf1ab 4671 R X,V
14488 G K,T,A caution single_src
highly_ambiguous
gene-orf1ab 4741 R X,D,E
14536 C T,Y caution single_src
highly_ambiguous
gene-orf1ab 4757 R D,D
14548 G D,R,K,A caution single_src
highly_ambiguous
gene-orf1ab 4761 K X,R,X,R
14553 A T,C,G caution single_src
highly_ambiguous
gene-orf1ab 4763 L F,S,C
14851 T C,A,G mask single_src
highly_homoplasic
gene-orf1ab 4862 L Y,,
14852 T C,Y,G mask single_src
highly_homoplasic
gene-orf1ab 4863 F L,L,V
15075 G K,T,A,S caution single_src
highly_ambiguous
gene-orf1ab 4937 K X,I,N,X
15103 C T caution single_src
highly_ambiguous
gene-orf1ab 4946 A L
15199 G K,T,A caution single_src
highly_ambiguous
gene-orf1ab 4978 T L,L,L
15230 G K,T,A caution single_src
highly_ambiguous
gene-orf1ab 4989 G X,F,I
15435 A R,G mask highly_ambiguous
homoplasic
single_src
gene-orf1ab 5057 E X,R
15513 T A,C,W caution single_src
ambiguous
gene-orf1ab 5083 N K,T,X
15521 T A mask amplicon_drop_or_primer_artefact gene-orf1ab 5086 F Y
15769 G R,K,T,A caution single_src
highly_ambiguous
gene-orf1ab 5168 V X,X,C,*
15771 T K,D,Y,H,W,A caution ambiguous
single_src
gene-orf1ab 5169 A X,X,X,X,X,Q
15922 T C,Y mask ambiguous
homoplasic
single_src
gene-orf1ab 5219 V C,C
16130 G T,A caution single_src
highly_ambiguous
gene-orf1ab 5289 G Y,N
16132 C T caution single_src
highly_ambiguous
gene-orf1ab 5289 G D
16188 G K,T caution single_src
highly_ambiguous
gene-orf1ab 5308 W X,V
16210 A R,D,W caution ambiguous
single_src
gene-orf1ab 5315 A L,L,L
16290 T K mask highly_ambiguous
single_src
gene-orf1ab 5342 A X
16537 G R,K,T,A caution ambiguous
single_src
gene-orf1ab 5424 S A,A,A,A
16738 G T,K,C caution single_src
highly_ambiguous
gene-orf1ab 5491 W G,G,G
16787 G K,T caution single_src
highly_ambiguous
gene-orf1ab 5508 G X,F
16887 C T,Y mask highly_homoplasic gene-orf1ab 5541 Y I,X
16988 G K,T,A caution single_src
highly_ambiguous
gene-orf1ab 5575 G X,S,T
17096 G K,T caution single_src
highly_ambiguous
gene-orf1ab 5611 G X,L
17178 T C,G mask single_src
highly_homoplasic
neighbour_linked
gene-orf1ab 5638 V S,W
17179 G T,S mask single_src
highly_homoplasic
neighbour_linked
gene-orf1ab 5638 V F,X
17182 G A mask single_src
highly_homoplasic
neighbour_linked
gene-orf1ab 5639 D I
17479 G K,T caution single_src
highly_ambiguous
gene-orf1ab 5738 K X,S
17567 G K,A mask single_src
highly_homoplasic
gene-orf1ab 5768 C X,I
17668 G R,K,T,S caution single_src
highly_ambiguous
gene-orf1ab 5801 K R,X,S,X
17675 T C,Y caution single_src
highly_ambiguous
gene-orf1ab 5804 I P,X
17716 G R,K,T,A caution single_src
highly_ambiguous
gene-orf1ab 5817 I ,X,Y,
17754 G K,T,S caution single_src
highly_ambiguous
gene-orf1ab 5830 W X,V,X
17848 G K,T,B caution single_src
highly_ambiguous
gene-orf1ab 5861 Q X,S,X
18297 G K,T,A caution single_src
highly_ambiguous
gene-orf1ab 6011 W X,V,E
18445 G K,T,A caution single_src
highly_ambiguous
gene-orf1ab 6060 R X,D,E
18465 T K,G caution single_src
highly_ambiguous
gene-orf1ab 6067 P X,R
18505 G R caution ambiguous
neighbour_linked
gene-orf1ab 6080 K K
18506 G K,S caution ambiguous
neighbour_linked
gene-orf1ab 6081 G X,X
18690 T K,C caution ambiguous
single_src
gene-orf1ab 6142 F X,S
18716 G K,T caution single_src
highly_ambiguous
gene-orf1ab 6151 C X,F
19250 G K,T,A caution single_src
highly_ambiguous
gene-orf1ab 6329 R X,*,K
19286 G R,T,C,A mask single_src
highly_homoplasic
gene-orf1ab 6341 G X,L,L,M
19298 A R,D,T,W 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,M,G caution highly_ambiguous
narrow_src
gene-orf1ab 6358 K X,X,R
19339 A R,M,W caution ambiguous
single_src
gene-orf1ab 6358 K K,X,X
19344 T K,C,A,Y caution ambiguous
amended
gene-orf1ab 6360 A X,P,H,X
19369 T Y,G caution ambiguous
amended
gene-orf1ab 6368 P H,Q
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 D,R,T,W,G mask ambiguous
single_src
gene-orf1ab 6428 S X,X,L,X,R
19732 G R,K,T,A caution homoplasic
narrow_src
gene-orf1ab 6489 G V,V,V,V
20056 G K,A mask ambiguous
homoplasic
single_src
gene-orf1ab 6597 E X,K
20123 T C,Y mask ambiguous
homoplasic
single_src
gene-orf1ab 6620 I L,L
20126 G R,K,S,A caution ambiguous
single_src
homoplasic
gene-orf1ab 6621 G X,X,Z,K
20128 G T,K,C,A caution single_src
highly_ambiguous
gene-orf1ab 6621 G D,X,D,E
20254 G K,T caution single_src
highly_ambiguous
gene-orf1ab 6663 I X,F
20465 A R,W,G mask highly_homoplasic
single_src
gene-orf1ab 6734 D X,X,V
20857 G T,K,C,A caution single_src
highly_ambiguous
gene-orf1ab 6864 R D,X,D,E
21149 G A mask single_src
highly_homoplasic
gene-orf1ab 6962 G K
21151 G D,T mask single_src
highly_homoplasic
gene-orf1ab 6962 G X,D
21209 T C,H mask single_src
highly_homoplasic
neighbour_linked
gene-orf1ab 6982 M R,X
21212 G A mask single_src
highly_homoplasic
neighbour_linked
gene-orf1ab 6983 G N
21281 G T,K,C,A caution single_src
highly_ambiguous
gene-orf1ab 7006 G Y,X,H,N
21302 C M,T,A,S caution neighbour_linked gene-orf1ab 7013 P X,Y,N,X
21304 C Y,S,M,T,A caution neighbour_linked gene-orf1ab 7013 P H,X,X,H,Q
21305 G R,K,T,A caution neighbour_linked gene-orf1ab 7014 R X,X,S,T
21379 T C,Y caution ambiguous
single_src
gene-orf1ab 7038 S L,L
21550 A C,M mask ambiguous
homoplasic
narrow_src
gene-orf1ab 7095 N T,T
21551 A R,T,W 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 Y,M,T,H,G caution ambiguous gene-S 32 F F,X,F,X,L
21968 T C,G mask single_src
highly_homoplasic
gene-S 136 C R,G
21987 G T,K,C,A mask amplicon_drop_or_primer_artefact
back_to_ref
gene-S 142 G V,X,A,D
22329 C V,T,M,Y caution ambiguous
single_src
gene-S 256 S X,L,X,X
22335 G K,T,A mask highly_ambiguous
amended
gene-S 258 W X,L,*
22389 T K,C,W,Y caution ambiguous
single_src
gene-S 276 L X,P,X,X
22393 A R,W,G caution ambiguous
amended
gene-S 277 L L,X,L
22410 G K,D,R,T,C,A caution narrow_src
highly_ambiguous
gene-S 283 G X,X,X,V,A,E
22416 T C,Y caution ambiguous
neighbour_linked
single_src
gene-S 285 I T,X
22420 A T,W caution ambiguous
neighbour_linked
single_src
gene-S 286 T T,T
22488 A R,C,M,T,W caution ambiguous
amended
gene-S 309 E X,A,X,V,X
22500 A R,M,W caution ambiguous
single_src
gene-S 313 Y X,X,X
22506 C T,Y,S caution single_src
highly_ambiguous
gene-S 315 T I,X,X
22515 T K,W,Y caution ambiguous
narrow_src
gene-S 318 F X,X,X
22516 T D,K,Y,C,W mask highly_ambiguous
single_src
gene-S 318 F X,X,F,F,X
22521 T K,Y mask highly_ambiguous gene-S 320 V X,X
22651 T C,A mask single_src
highly_homoplasic
gene-S 363 A A,A
22661 G T,A,S mask ambiguous
homoplasic
single_src
gene-S 367 V F,I,X
22797 C A,T,M,Y caution single_src
highly_ambiguous
homoplasic
gene-S 412 P Q,L,X,X
22802 C A,T,M,Y mask homoplasic
single_src
amended
interspecific_contamination
gene-S 414 Q K,*,X,X
22892 A T,C caution single_src
highly_ambiguous
gene-S 444 K *,Q
22904 A R,V,H,M,T,W,G caution single_src
highly_ambiguous
gene-S 448 N B,X,X,X,Y,X,D
23016 G T,K,C,A caution single_src
highly_ambiguous
gene-S 485 G V,X,A,D
23116 A T,W caution ambiguous
single_src
gene-S 518 L L,L
23122 A R,V,H,M,T,W,G caution single_src
highly_ambiguous
gene-S 520 A A,A,A,A,A,A,A
23144 A G caution ambiguous
amended
gene-S 528 K E
23162 G K,T,A caution single_src
highly_ambiguous
gene-S 534 V X,F,I
23288 G K,T,A caution single_src
highly_ambiguous
gene-S 576 V X,F,I
23291 C T,Y caution single_src
highly_ambiguous
gene-S 577 R C,X
23292 G R,K,T caution single_src
highly_ambiguous
gene-S 577 R X,X,L
23302 G K,T,A caution single_src
highly_ambiguous
gene-S 580 Q X,H,Q
23343 G R,K,T,A caution single_src
highly_ambiguous
gene-S 594 G X,X,V,D
23519 G K,T caution single_src
highly_ambiguous
gene-S 653 A X,S
23652 T C,A,Y caution single_src
highly_ambiguous
gene-S 697 M T,K,X
23738 A T,W,G caution single_src
highly_ambiguous
gene-S 726 I F,X,V
23745 C T,Y caution single_src
highly_ambiguous
gene-S 728 P L,X
23763 C S,T,Y,G caution single_src
highly_ambiguous
gene-S 734 T X,I,X,R
23766 C T,Y,S caution single_src
highly_ambiguous
gene-S 735 S L,X,X
23775 G K,T,S caution single_src
highly_ambiguous
gene-S 738 C X,F,X
23855 C T,A,Y caution single_src
highly_ambiguous
gene-S 765 R C,S,X
24389 A M,C,W mask highly_homoplasic
highly_ambiguous
narrow_src
nanopore_adapter
gene-S 943 S X,R,X
24390 G T,K,C,S mask highly_homoplasic
highly_ambiguous
narrow_src
nanopore_adapter
gene-S 943 S I,X,T,X
24410 G C,A mask amplicon_drop_or_primer_artefact
back_to_ref
gene-S 950 D H,N
24497 G T,K,C caution single_src
highly_ambiguous
gene-S 979 D Y,X,H
24557 G K,T,A caution single_src
highly_ambiguous
gene-S 999 G X,C,S
24622 T Y mask highly_ambiguous
single_src
gene-S 1020 A A
24673 A G caution ambiguous
amended
gene-S 1037 S S
24728 G K,T caution single_src
highly_ambiguous
gene-S 1056 A X,S
24933 G K,T mask highly_ambiguous
highly_homoplasic
narrow_src
gene-S 1124 G X,V
24942 A R,T,W caution ambiguous
single_src
gene-S 1127 D X,V,X
25202 T K mask highly_ambiguous gene-S 1214 W X
25381 A R,C,M mask homoplasic
single_src
gene-S 1273 T T,T,T
25382 T C mask single_src
highly_homoplasic
gene-S 1274 T Q
25446 T A,C,W,G caution single_src
highly_ambiguous
gene-ORF3a 18 G G,G,G,G
25798 A G caution ambiguous
amended
gene-ORF3a 136 K E
25902 T A,C,W,G caution single_src
highly_ambiguous
neighbour_linked
gene-ORF3a 170 T T,T,T,T
25908 T A,C,W caution single_src
highly_ambiguous
neighbour_linked
gene-ORF3a 172 G G,G,G
25961 C T,A,Y,S caution single_src
highly_ambiguous
gene-ORF3a 190 T I,N,X,X
26549 C T,Y mask homoplasic
single_src
gene-M 9 T T,T
26700 G K,T caution ambiguous
single_src
homoplasic
gene-M 60 V X,L
26709 G R,K,T,A caution ambiguous
amended
gene-M 63 A X,X,S,T
27033 G K,T,A,S caution single_src
highly_ambiguous
gene-M 171 A X,S,T,X
27534 T C,W,Y,G caution ambiguous
single_src
gene-ORF7a 47 H H,X,H,Q
27658 A D,T,W,G mask single_src
highly_homoplasic
neighbour_linked
gene-ORF7a 89 R X,*,X,G
27660 A T,C,V,G mask single_src
highly_homoplasic
neighbour_linked
gene-ORF7a 89 R S,S,X,R
27720 T K,C,W caution ambiguous
single_src
gene-ORF7a 109 F X,F,X
27760 T K,A,Y mask homoplasic
neighbour_linked
. . . .
27761 T C mask homoplasic
neighbour_linked
. . . .
27784 A T,W,G mask ambiguous
single_src
. . . .
27792 T K,W caution ambiguous
amended
. . . .
28004 T C,Y caution neighbour_linked
single_src
gene-ORF8 37 C C,C
28005 C T,Y,G caution neighbour_linked
single_src
gene-ORF8 38 P S,X,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
28184 T C,H mask single_src
highly_homoplasic
gene-ORF8 97 S S,X
28253 C Y,S,T,A,G mask highly_homoplasic gene-ORF8 120 F F,X,F,L,L
28517 G K,T,S caution ambiguous
single_src
gene-N 82 D X,Y,X
28559 G K,T caution single_src
highly_ambiguous
gene-N 96 G X,C
28676 A R,C,M,G caution ambiguous
single_src
gene-N 135 T X,P,X,A
28780 A R,D,W caution ambiguous
single_src
gene-N 169 K K,X,X
28881 G K,R,M,T,A caution neighbour_linked gene-N 203 R X,X,X,M,K
28882 G K,R,T,S,C,A caution neighbour_linked gene-N 203 R X,R,S,X,S,R
28883 G R,C,A,S caution neighbour_linked gene-N 204 G X,R,R,X
28886 A C,M,T,W,G caution single_src
highly_ambiguous
gene-N 205 T P,X,S,X,A
28985 G D,K,R,T,A mask highly_ambiguous
homoplasic
single_src
gene-N 238 G X,X,X,C,S
29037 C T,M,Y 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
29049 G R,T,A caution single_src
highly_ambiguous
gene-N 259 R X,L,Q
29058 G K,T,A mask single_src
highly_homoplasic
gene-N 262 R X,L,H
29378 A W caution ambiguous
amended
gene-N 369 K X
29425 G T,A,S mask ambiguous
homoplasic
single_src
gene-N 384 Q H,Q,X
29427 G K,R,T,S,C,A caution ambiguous
neighbour_linked
single_src
gene-N 385 R X,X,I,X,T,K
29428 A R,C,G caution ambiguous
neighbour_linked
single_src
gene-N 385 R R,S,R
29553 G T,A mask highly_homoplasic
single_src
. . . .
29594 A T,C mask single_src
highly_homoplasic
gene-ORF10 13 I L,L
29737 G K,R,T,S,C,A caution ambiguous
single_src
. . . .
29783 G T,K,C,A mask highly_homoplasic . . . .
29786 G K,C,S caution homoplasic
single_src
. . . .
29827 A T,G mask seq_end
highly_homoplasic
single_src
. . . .
29830 G T,C,A 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
amplicon_drop_or_primer_artefact Amplicon dropout and/or failed primer trimming
back_to_ref The alternate allele is sometimes not called for this position due to issues with amplicon dropout and/or primer trimming. For more details, see: https://github.com/W-L/ProblematicSites_SARS-CoV2/issues/7 and https://github.com/cov-lineages/pango-designation/issues/95

Suggestions, additions and issues are very gratefully received.