CoV-GLUE | Mutations | Mutation
Details of the codons used for the mutation across all lineages (CodonProp is the proportion each codon is used for this AA mutation):
ORF | CodonNum | Mut | ORF1abMut | MutType | RefCodon | MutCodon | AACount | CodonCount | CodonProp | Genome Position |
ORF1ab/nsp5A-B | 65 | N65N | N3328N | syn | aaT | aaC | 1222 | 1222 | 1 | 10247-10249 |
ORF1ab/nsp5A-B | 65 | N65S | N3328S | nonsyn | aAt | aGt | 365 | 365 | 1 | 10247-10249 |
ORF1ab/nsp5A-B | 65 | N65del | N3328del | del | AAT | --- | 33 | 33 | 1 | 10247-10249 |
ORF1ab/nsp5A-B | 65 | N65H | N3328H | nonsyn | Aat | Cat | 15 | 15 | 1 | 10247-10249 |
ORF1ab/nsp5A-B | 65 | N65Y | N3328Y | nonsyn | Aat | Tat | 11 | 10 | 0.909091 | 10247-10249 |
ORF1ab/nsp5A-B | 65 | N65Y | N3328Y | nonsyn | AaT | TaC | 11 | 1 | 0.0909091 | 10247-10249 |
ORF1ab/nsp5A-B | 65 | N65I | N3328I | nonsyn | aAt | aTt | 8 | 8 | 1 | 10247-10249 |
ORF1ab/nsp5A-B | 65 | N65K | N3328K | nonsyn | aaT | aaA | 7 | 5 | 0.714286 | 10247-10249 |
ORF1ab/nsp5A-B | 65 | N65K | N3328K | nonsyn | aaT | aaG | 7 | 2 | 0.285714 | 10247-10249 |
ORF1ab/nsp5A-B | 65 | N65del1 | N3328del1 | del | aaT | aa- | 6 | 3 | 0.5 | 10247-10249 |
ORF1ab/nsp5A-B | 65 | N65del1 | N3328del1 | del | Aat | -at | 6 | 2 | 0.333333 | 10247-10249 |
ORF1ab/nsp5A-B | 65 | N65del1 | N3328del1 | del | AaT | -aC | 6 | 1 | 0.166667 | 10247-10249 |
ORF1ab/nsp5A-B | 65 | N65D | N3328D | nonsyn | Aat | Gat | 2 | 2 | 1 | 10247-10249 |
ORF1ab/nsp5A-B | 65 | N65T | N3328T | nonsyn | aAt | aCt | 2 | 2 | 1 | 10247-10249 |
ORF1ab/nsp5A-B | 65 | N65V | N3328V | nonsyn | AAt | GTt | 2 | 2 | 1 | 10247-10249 |
ORF1ab/nsp5A-B | 65 | N65del2 | N3328del2 | del | AAT | --A | 1 | 1 | 1 | 10247-10249 |
Details of the mutation no within lineages (LineageCodonProp is the proportion the codon is observed at, at this particular site, on each lineage):
ORF | CodonNum | Mut | RefCodon | MutCodon | CodonCount | AACount | Lineage | LineageCodonProp |
ORF1ab/nsp5A-B | 65 | N65N | aaT | aaC | 1222 | 1222 | All | 0.000234 |
ORF1ab/nsp5A-B | 65 | N65N | aaT | aaC | 621 | 621 | B.1.362 | 0.956857 |
ORF1ab/nsp5A-B | 65 | N65S | aAt | aGt | 365 | 365 | All | 0.00007 |
ORF1ab/nsp5A-B | 65 | N65N | aaT | aaC | 212 | 212 | B.1.362.2 | 1 |
ORF1ab/nsp5A-B | 65 | N65S | aAt | aGt | 98 | 98 | B.1.617.2 | 0.000369 |
ORF1ab/nsp5A-B | 65 | N65N | aaT | aaC | 65 | 65 | AY.3 | 0.000647 |
ORF1ab/nsp5A-B | 65 | N65S | aAt | aGt | 64 | 64 | B.1.1.7 | 0.000057 |
ORF1ab/nsp5A-B | 65 | N65N | aaT | aaC | 58 | 58 | AY.47 | 0.001804 |
ORF1ab/nsp5A-B | 65 | N65N | aaT | aaC | 54 | 54 | B.1.177 | 0.000711 |
ORF1ab/nsp5A-B | 65 | N65S | aAt | aGt | 46 | 46 | AY.43 | 0.000204 |
ORF1ab/nsp5A-B | 65 | N65S | aAt | aGt | 45 | 45 | AY.4 | 0.00007 |
ORF1ab/nsp5A-B | 65 | N65N | aaT | aaC | 42 | 42 | B.1.177.63 | 0.113514 |
ORF1ab/nsp5A-B | 65 | N65del | AAT | --- | 33 | 33 | All | 0.000006 |
ORF1ab/nsp5A-B | 65 | N65N | aaT | aaC | 28 | 28 | AY.44 | 0.00017 |
ORF1ab/nsp5A-B | 65 | N65S | aAt | aGt | 24 | 24 | B.1.1.298 | 0.02069 |
ORF1ab/nsp5A-B | 65 | N65N | aaT | aaC | 20 | 20 | B.1.1.7 | 0.000018 |
ORF1ab/nsp5A-B | 65 | N65H | Aat | Cat | 15 | 15 | All | 0.000003 |
ORF1ab/nsp5A-B | 65 | N65N | aaT | aaC | 15 | 15 | B.1.362.1 | 1 |
ORF1ab/nsp5A-B | 65 | N65S | aAt | aGt | 13 | 13 | AY.103 | 0.000081 |
ORF1ab/nsp5A-B | 65 | N65N | aaT | aaC | 12 | 12 | AY.4 | 0.000019 |
ORF1ab/nsp5A-B | 65 | N65Y | Aat | Tat | 10 | 11 | All | 0.000002 |
ORF1ab/nsp5A-B | 65 | N65Y | AaT | TaC | 1 | 11 | All | 0 |
ORF1ab/nsp5A-B | 65 | N65del | AAT | --- | 11 | 11 | B.1.1.7 | 0.00001 |
ORF1ab/nsp5A-B | 65 | N65N | aaT | aaC | 10 | 10 | AY.114 | 0.002311 |
ORF1ab/nsp5A-B | 65 | N65N | aaT | aaC | 10 | 10 | B.1.1.50 | 0.006789 |
ORF1ab/nsp5A-B | 65 | N65N | aaT | aaC | 10 | 10 | B.1.617.2 | 0.000038 |
ORF1ab/nsp5A-B | 65 | N65I | aAt | aTt | 8 | 8 | All | 0.000002 |
ORF1ab/nsp5A-B | 65 | N65S | aAt | aGt | 8 | 8 | AY.102 | 0.000212 |
ORF1ab/nsp5A-B | 65 | N65K | aaT | aaA | 5 | 7 | All | 0.000001 |
ORF1ab/nsp5A-B | 65 | N65K | aaT | aaG | 2 | 7 | All | 0 |
ORF1ab/nsp5A-B | 65 | N65del1 | aaT | aa- | 3 | 6 | All | 0.000001 |
ORF1ab/nsp5A-B | 65 | N65del1 | Aat | -at | 2 | 6 | All | 0 |
ORF1ab/nsp5A-B | 65 | N65del1 | AaT | -aC | 1 | 6 | All | 0 |
ORF1ab/nsp5A-B | 65 | N65S | aAt | aGt | 6 | 6 | AY.3 | 0.00006 |
ORF1ab/nsp5A-B | 65 | N65H | Aat | Cat | 6 | 6 | B.1.525 | 0.000679 |
ORF1ab/nsp5A-B | 65 | N65N | aaT | aaC | 5 | 5 | AY.103 | 0.000031 |
ORF1ab/nsp5A-B | 65 | N65N | aaT | aaC | 5 | 5 | B.1 | 0.000046 |
ORF1ab/nsp5A-B | 65 | N65Y | Aat | Tat | 5 | 5 | B.1.1.7 | 0.000004 |
ORF1ab/nsp5A-B | 65 | N65N | aaT | aaC | 5 | 5 | B.1.2 | 0.000044 |
ORF1ab/nsp5A-B | 65 | N65S | aAt | aGt | 5 | 5 | B.1.36.29 | 0.002587 |
ORF1ab/nsp5A-B | 65 | N65del | AAT | --- | 4 | 4 | 0.222222 | |
ORF1ab/nsp5A-B | 65 | N65S | aAt | aGt | 4 | 4 | AY.105 | 0.002572 |
ORF1ab/nsp5A-B | 65 | N65S | aAt | aGt | 4 | 4 | AY.44 | 0.000024 |
ORF1ab/nsp5A-B | 65 | N65N | aaT | aaC | 4 | 4 | B.1.1 | 0.000073 |
ORF1ab/nsp5A-B | 65 | N65S | aAt | aGt | 4 | 4 | B.1.1.317 | 0.001647 |
ORF1ab/nsp5A-B | 65 | N65H | Aat | Cat | 4 | 4 | B.1.1.7 | 0.000004 |
ORF1ab/nsp5A-B | 65 | N65N | aaT | aaC | 3 | 3 | AY.43 | 0.000013 |
ORF1ab/nsp5A-B | 65 | N65S | aAt | aGt | 3 | 3 | AY.92 | 0.000862 |
ORF1ab/nsp5A-B | 65 | N65S | aAt | aGt | 3 | 3 | B.1.2 | 0.000026 |
ORF1ab/nsp5A-B | 65 | N65I | aAt | aTt | 2 | 2 | 0.111111 | |
ORF1ab/nsp5A-B | 65 | N65K | aaT | aaG | 2 | 2 | 0.111111 | |
ORF1ab/nsp5A-B | 65 | N65V | AAt | GTt | 2 | 2 | 0.111111 | |
ORF1ab/nsp5A-B | 65 | N65N | aaT | aaC | 2 | 2 | 0.111111 | |
ORF1ab/nsp5A-B | 65 | N65D | Aat | Gat | 2 | 2 | All | 0 |
ORF1ab/nsp5A-B | 65 | N65T | aAt | aCt | 2 | 2 | All | 0 |
ORF1ab/nsp5A-B | 65 | N65V | AAt | GTt | 2 | 2 | All | 0 |
ORF1ab/nsp5A-B | 65 | N65S | aAt | aGt | 2 | 2 | AY.101 | 0.000981 |
ORF1ab/nsp5A-B | 65 | N65N | aaT | aaC | 2 | 2 | AY.20 | 0.000078 |
ORF1ab/nsp5A-B | 65 | N65N | aaT | aaC | 2 | 2 | AY.25 | 0.000012 |
ORF1ab/nsp5A-B | 65 | N65del | AAT | --- | 2 | 2 | AY.4 | 0.000003 |
ORF1ab/nsp5A-B | 65 | N65del | AAT | --- | 2 | 2 | AY.4.5 | 0.000215 |
ORF1ab/nsp5A-B | 65 | N65N | aaT | aaC | 2 | 2 | AY.6 | 0.000082 |
ORF1ab/nsp5A-B | 65 | N65K | aaT | aaA | 2 | 2 | B.1 | 0.000018 |
ORF1ab/nsp5A-B | 65 | N65S | aAt | aGt | 2 | 2 | B.1 | 0.000018 |
ORF1ab/nsp5A-B | 65 | N65S | aAt | aGt | 2 | 2 | B.1.1 | 0.000036 |
ORF1ab/nsp5A-B | 65 | N65Y | Aat | Tat | 1 | 2 | B.1.1 | 0.000018 |
ORF1ab/nsp5A-B | 65 | N65Y | AaT | TaC | 1 | 2 | B.1.1 | 0.000018 |
ORF1ab/nsp5A-B | 65 | N65S | aAt | aGt | 2 | 2 | B.1.1.332 | 0.0625 |
ORF1ab/nsp5A-B | 65 | N65del | AAT | --- | 2 | 2 | B.1.177 | 0.000026 |
ORF1ab/nsp5A-B | 65 | N65S | aAt | aGt | 2 | 2 | B.1.177 | 0.000026 |
ORF1ab/nsp5A-B | 65 | N65S | aAt | aGt | 2 | 2 | B.1.214.2 | 0.001199 |
ORF1ab/nsp5A-B | 65 | N65S | aAt | aGt | 2 | 2 | B.1.36 | 0.000292 |
ORF1ab/nsp5A-B | 65 | N65N | aaT | aaC | 2 | 2 | B.1.36.19 | 0.018519 |
ORF1ab/nsp5A-B | 65 | N65N | aaT | aaC | 2 | 2 | B.1.427 | 0.000101 |
ORF1ab/nsp5A-B | 65 | N65Y | Aat | Tat | 2 | 2 | B.1.525 | 0.000226 |
ORF1ab/nsp5A-B | 65 | N65S | aAt | aGt | 2 | 2 | B.1.595 | 0.000522 |
ORF1ab/nsp5A-B | 65 | N65S | aAt | aGt | 2 | 2 | B.1.626 | 0.011429 |
ORF1ab/nsp5A-B | 65 | N65S | aAt | aGt | 2 | 2 | B.1.637 | 0.000146 |
ORF1ab/nsp5A-B | 65 | N65N | aaT | aaC | 2 | 2 | B.1.9.5 | 0.011364 |
ORF1ab/nsp5A-B | 65 | N65N | aaT | aaC | 2 | 2 | P.1 | 0.000032 |
ORF1ab/nsp5A-B | 65 | N65N | aaT | aaC | 2 | 2 | P.1.14 | 0.000096 |
ORF1ab/nsp5A-B | 65 | N65T | aAt | aCt | 1 | 1 | A.23.1 | 0.000704 |
ORF1ab/nsp5A-B | 65 | N65N | aaT | aaC | 1 | 1 | A.6 | 0.005128 |
ORF1ab/nsp5A-B | 65 | N65del2 | AAT | --A | 1 | 1 | All | 0 |
ORF1ab/nsp5A-B | 65 | N65S | aAt | aGt | 1 | 1 | AY.100 | 0.000046 |
ORF1ab/nsp5A-B | 65 | N65del | AAT | --- | 1 | 1 | AY.100 | 0.000046 |
ORF1ab/nsp5A-B | 65 | N65N | aaT | aaC | 1 | 1 | AY.100 | 0.000046 |
ORF1ab/nsp5A-B | 65 | N65N | aaT | aaC | 1 | 1 | AY.102 | 0.000027 |
ORF1ab/nsp5A-B | 65 | N65N | aaT | aaC | 1 | 1 | AY.105 | 0.000643 |
ORF1ab/nsp5A-B | 65 | N65N | aaT | aaC | 1 | 1 | AY.110 | 0.000113 |
ORF1ab/nsp5A-B | 65 | N65del | AAT | --- | 1 | 1 | AY.117 | 0.000085 |
ORF1ab/nsp5A-B | 65 | N65del1 | Aat | -at | 1 | 1 | AY.119 | 0.000035 |
ORF1ab/nsp5A-B | 65 | N65S | aAt | aGt | 1 | 1 | AY.119 | 0.000035 |
ORF1ab/nsp5A-B | 65 | N65N | aaT | aaC | 1 | 1 | AY.121 | 0.000135 |
ORF1ab/nsp5A-B | 65 | N65N | aaT | aaC | 1 | 1 | AY.23 | 0.00007 |
ORF1ab/nsp5A-B | 65 | N65I | aAt | aTt | 1 | 1 | AY.25 | 0.000006 |
ORF1ab/nsp5A-B | 65 | N65S | aAt | aGt | 1 | 1 | AY.25 | 0.000006 |
ORF1ab/nsp5A-B | 65 | N65S | aAt | aGt | 1 | 1 | AY.27 | 0.000065 |
ORF1ab/nsp5A-B | 65 | N65N | aaT | aaC | 1 | 1 | AY.29 | 0.000016 |
ORF1ab/nsp5A-B | 65 | N65H | Aat | Cat | 1 | 1 | AY.3 | 0.00001 |
ORF1ab/nsp5A-B | 65 | N65S | aAt | aGt | 1 | 1 | AY.39 | 0.000025 |
ORF1ab/nsp5A-B | 65 | N65del1 | aaT | aa- | 1 | 1 | AY.4 | 0.000002 |
ORF1ab/nsp5A-B | 65 | N65N | aaT | aaC | 1 | 1 | AY.4.2 | 0.000022 |
ORF1ab/nsp5A-B | 65 | N65del | AAT | --- | 1 | 1 | AY.43 | 0.000004 |
ORF1ab/nsp5A-B | 65 | N65del1 | AaT | -aC | 1 | 1 | AY.44 | 0.000006 |
ORF1ab/nsp5A-B | 65 | N65N | aaT | aaC | 1 | 1 | AY.46 | 0.000104 |
ORF1ab/nsp5A-B | 65 | N65I | aAt | aTt | 1 | 1 | AY.46.2 | 0.000635 |
ORF1ab/nsp5A-B | 65 | N65S | aAt | aGt | 1 | 1 | AY.47 | 0.000031 |
ORF1ab/nsp5A-B | 65 | N65N | aaT | aaC | 1 | 1 | AY.5 | 0.000021 |
ORF1ab/nsp5A-B | 65 | N65S | aAt | aGt | 1 | 1 | AY.5 | 0.000021 |
ORF1ab/nsp5A-B | 65 | N65S | aAt | aGt | 1 | 1 | AY.54 | 0.000095 |
ORF1ab/nsp5A-B | 65 | N65S | aAt | aGt | 1 | 1 | AY.58 | 0.000907 |
ORF1ab/nsp5A-B | 65 | N65S | aAt | aGt | 1 | 1 | AY.6 | 0.000041 |
ORF1ab/nsp5A-B | 65 | N65N | aaT | aaC | 1 | 1 | AY.7.1 | 0.000113 |
ORF1ab/nsp5A-B | 65 | N65S | aAt | aGt | 1 | 1 | AY.75 | 0.000056 |
ORF1ab/nsp5A-B | 65 | N65S | aAt | aGt | 1 | 1 | AY.8 | 0.000606 |
ORF1ab/nsp5A-B | 65 | N65I | aAt | aTt | 1 | 1 | AY.82 | 0.001357 |
ORF1ab/nsp5A-B | 65 | N65S | aAt | aGt | 1 | 1 | AY.84 | 0.000437 |
ORF1ab/nsp5A-B | 65 | N65H | Aat | Cat | 1 | 1 | AY.84 | 0.000437 |
ORF1ab/nsp5A-B | 65 | N65S | aAt | aGt | 1 | 1 | AY.9 | 0.000068 |
ORF1ab/nsp5A-B | 65 | N65H | Aat | Cat | 1 | 1 | B.1 | 0.000009 |
ORF1ab/nsp5A-B | 65 | N65del | AAT | --- | 1 | 1 | B.1 | 0.000009 |
ORF1ab/nsp5A-B | 65 | N65del1 | aaT | aa- | 1 | 1 | B.1 | 0.000009 |
ORF1ab/nsp5A-B | 65 | N65K | aaT | aaA | 1 | 1 | B.1.1 | 0.000018 |
ORF1ab/nsp5A-B | 65 | N65del1 | aaT | aa- | 1 | 1 | B.1.1 | 0.000018 |
ORF1ab/nsp5A-B | 65 | N65N | aaT | aaC | 1 | 1 | B.1.1.189 | 0.001513 |
ORF1ab/nsp5A-B | 65 | N65S | aAt | aGt | 1 | 1 | B.1.1.214 | 0.000055 |
ORF1ab/nsp5A-B | 65 | N65I | aAt | aTt | 1 | 1 | B.1.1.311 | 0.000358 |
ORF1ab/nsp5A-B | 65 | N65N | aaT | aaC | 1 | 1 | B.1.1.318 | 0.000302 |
ORF1ab/nsp5A-B | 65 | N65K | aaT | aaA | 1 | 1 | B.1.1.39 | 0.00051 |
ORF1ab/nsp5A-B | 65 | N65T | aAt | aCt | 1 | 1 | B.1.1.7 | 0.000001 |
ORF1ab/nsp5A-B | 65 | N65N | aaT | aaC | 1 | 1 | B.1.160 | 0.000031 |
ORF1ab/nsp5A-B | 65 | N65K | aaT | aaA | 1 | 1 | B.1.177 | 0.000013 |
ORF1ab/nsp5A-B | 65 | N65del | AAT | --- | 1 | 1 | B.1.177.4 | 0.000211 |
ORF1ab/nsp5A-B | 65 | N65del | AAT | --- | 1 | 1 | B.1.177.81 | 0.000189 |
ORF1ab/nsp5A-B | 65 | N65del | AAT | --- | 1 | 1 | B.1.179 | 0.003759 |
ORF1ab/nsp5A-B | 65 | N65N | aaT | aaC | 1 | 1 | B.1.182 | 0.007246 |
ORF1ab/nsp5A-B | 65 | N65del1 | Aat | -at | 1 | 1 | B.1.2 | 0.000009 |
ORF1ab/nsp5A-B | 65 | N65D | Aat | Gat | 1 | 1 | B.1.2 | 0.000009 |
ORF1ab/nsp5A-B | 65 | N65del2 | AAT | --A | 1 | 1 | B.1.2 | 0.000009 |
ORF1ab/nsp5A-B | 65 | N65D | Aat | Gat | 1 | 1 | B.1.221.2 | 0.004016 |
ORF1ab/nsp5A-B | 65 | N65N | aaT | aaC | 1 | 1 | B.1.258 | 0.000067 |
ORF1ab/nsp5A-B | 65 | N65S | aAt | aGt | 1 | 1 | B.1.258 | 0.000067 |
ORF1ab/nsp5A-B | 65 | N65Y | Aat | Tat | 1 | 1 | B.1.311 | 0.000275 |
ORF1ab/nsp5A-B | 65 | N65H | Aat | Cat | 1 | 1 | B.1.351 | 0.00003 |
ORF1ab/nsp5A-B | 65 | N65del | AAT | --- | 1 | 1 | B.1.36.18 | 0.00042 |
ORF1ab/nsp5A-B | 65 | N65N | aaT | aaC | 1 | 1 | B.1.366 | 0.004878 |
ORF1ab/nsp5A-B | 65 | N65N | aaT | aaC | 1 | 1 | B.1.367 | 0.000792 |
ORF1ab/nsp5A-B | 65 | N65N | aaT | aaC | 1 | 1 | B.1.526 | 0.000024 |
ORF1ab/nsp5A-B | 65 | N65del | AAT | --- | 1 | 1 | B.1.596 | 0.000087 |
ORF1ab/nsp5A-B | 65 | N65S | aAt | aGt | 1 | 1 | B.1.596 | 0.000087 |
ORF1ab/nsp5A-B | 65 | N65N | aaT | aaC | 1 | 1 | B.1.604 | 0.017241 |
ORF1ab/nsp5A-B | 65 | N65I | aAt | aTt | 1 | 1 | B.1.617.2 | 0.000004 |
ORF1ab/nsp5A-B | 65 | N65del | AAT | --- | 1 | 1 | B.1.621 | 0.000089 |
ORF1ab/nsp5A-B | 65 | N65S | aAt | aGt | 1 | 1 | B.1.633 | 0.041667 |
ORF1ab/nsp5A-B | 65 | N65Y | Aat | Tat | 1 | 1 | B.1.636 | 0.006711 |
ORF1ab/nsp5A-B | 65 | N65N | aaT | aaC | 1 | 1 | B.1.637 | 0.000073 |
ORF1ab/nsp5A-B | 65 | N65H | Aat | Cat | 1 | 1 | C.35 | 0.000774 |
ORF1ab/nsp5A-B | 65 | N65del | AAT | --- | 1 | 1 | C.35 | 0.000774 |
ORF1ab/nsp5A-B | 65 | N65N | aaT | aaC | 1 | 1 | C.37 | 0.000116 |
ORF1ab/nsp5A-B | 65 | N65N | aaT | aaC | 1 | 1 | D.2 | 0.000075 |
ORF1ab/nsp5A-B | 65 | N65I | aAt | aTt | 1 | 1 | D.2 | 0.000075 |
ORF1ab/nsp5A-B | 65 | N65del | AAT | --- | 1 | 1 | N.4 | 0.004255 |
ORF1ab/nsp5A-B | 65 | N65N | aaT | aaC | 1 | 1 | P.2 | 0.000187 |
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CoV-GLUE is still in development. CoV-GLUE was originally developed as part of COG-UK by Josh Singer using the GLUE framework at the MRC-University of Glasgow Centre for Virus Research (CVR). In 2021 it was redeveloped by Richard Orton to scale to the millions of genome sequences available. We acknowledge support from the MRC (MC_UU_12014/12), WT (220977/Z/20/Z) and UKRI G2P (MR/W005611/1). Please contact Richard Orton with any queries: Richard.Orton@glasgow.ac.uk
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