ProblematicSites_SARS-CoV2
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.