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 |
S | 1158 | N1158N | syn | aaT | aaC | 591 | 591 | 1 | 25034-25036 | |
S | 1158 | N1158del | del | AAT | --- | 107 | 107 | 1 | 25034-25036 | |
S | 1158 | N1158D | nonsyn | Aat | Gat | 59 | 58 | 0.983051 | 25034-25036 | |
S | 1158 | N1158D | nonsyn | AaT | GaC | 59 | 1 | 0.0169492 | 25034-25036 | |
S | 1158 | N1158S | nonsyn | aAt | aGt | 42 | 41 | 0.97619 | 25034-25036 | |
S | 1158 | N1158S | nonsyn | aAT | aGC | 42 | 1 | 0.0238095 | 25034-25036 | |
S | 1158 | N1158K | nonsyn | aaT | aaG | 13 | 7 | 0.538462 | 25034-25036 | |
S | 1158 | N1158K | nonsyn | aaT | aaA | 13 | 6 | 0.461538 | 25034-25036 | |
S | 1158 | N1158H | nonsyn | Aat | Cat | 12 | 12 | 1 | 25034-25036 | |
S | 1158 | N1158T | nonsyn | aAt | aCt | 12 | 12 | 1 | 25034-25036 | |
S | 1158 | N1158Y | nonsyn | Aat | Tat | 11 | 11 | 1 | 25034-25036 | |
S | 1158 | N1158I | nonsyn | aAt | aTt | 5 | 5 | 1 | 25034-25036 | |
S | 1158 | N1158G | nonsyn | AAT | GGC | 2 | 1 | 0.5 | 25034-25036 | |
S | 1158 | N1158G | nonsyn | AAt | GGt | 2 | 1 | 0.5 | 25034-25036 | |
S | 1158 | N1158del2 | del | aAT | a-- | 1 | 1 | 1 | 25034-25036 | |
S | 1158 | N1158E | nonsyn | AaT | GaG | 1 | 1 | 1 | 25034-25036 | |
S | 1158 | N1158del1 | del | Aat | -at | 1 | 1 | 1 | 25034-25036 |
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 |
S | 1158 | N1158N | aaT | aaC | 591 | 591 | All | 0.000113 |
S | 1158 | N1158N | aaT | aaC | 145 | 145 | B.1.1.7 | 0.00013 |
S | 1158 | N1158del | AAT | --- | 107 | 107 | All | 0.00002 |
S | 1158 | N1158N | aaT | aaC | 83 | 83 | AY.4 | 0.000129 |
S | 1158 | N1158N | aaT | aaC | 82 | 82 | AY.103 | 0.000509 |
S | 1158 | N1158N | aaT | aaC | 77 | 77 | B.1.518 | 0.905882 |
S | 1158 | N1158D | Aat | Gat | 58 | 59 | All | 0.000011 |
S | 1158 | N1158D | AaT | GaC | 1 | 59 | All | 0 |
S | 1158 | N1158del | AAT | --- | 50 | 50 | B.1.1.7 | 0.000045 |
S | 1158 | N1158S | aAt | aGt | 41 | 42 | All | 0.000008 |
S | 1158 | N1158S | aAT | aGC | 1 | 42 | All | 0 |
S | 1158 | N1158N | aaT | aaC | 26 | 26 | AY.3 | 0.000259 |
S | 1158 | N1158D | Aat | Gat | 21 | 21 | AY.44 | 0.000128 |
S | 1158 | N1158N | aaT | aaC | 15 | 15 | B.1.617.2 | 0.000056 |
S | 1158 | N1158K | aaT | aaG | 7 | 13 | All | 0.000001 |
S | 1158 | N1158K | aaT | aaA | 6 | 13 | All | 0.000001 |
S | 1158 | N1158T | aAt | aCt | 12 | 12 | All | 0.000002 |
S | 1158 | N1158H | Aat | Cat | 12 | 12 | All | 0.000002 |
S | 1158 | N1158N | aaT | aaC | 12 | 12 | P.1 | 0.000189 |
S | 1158 | N1158Y | Aat | Tat | 11 | 11 | All | 0.000002 |
S | 1158 | N1158N | aaT | aaC | 11 | 11 | AY.26 | 0.000311 |
S | 1158 | N1158S | aAt | aGt | 10 | 10 | B.1.1.7 | 0.000009 |
S | 1158 | N1158N | aaT | aaC | 9 | 9 | AY.116 | 0.002581 |
S | 1158 | N1158D | Aat | Gat | 9 | 9 | AY.121 | 0.001218 |
S | 1158 | N1158N | aaT | aaC | 8 | 8 | AY.46.4 | 0.001316 |
S | 1158 | N1158del | AAT | --- | 8 | 8 | B.1.177 | 0.000105 |
S | 1158 | N1158N | aaT | aaC | 7 | 7 | AY.102 | 0.000186 |
S | 1158 | N1158N | aaT | aaC | 7 | 7 | AY.25 | 0.000042 |
S | 1158 | N1158del | AAT | --- | 7 | 7 | AY.4 | 0.000011 |
S | 1158 | N1158S | aAt | aGt | 6 | 6 | AY.4 | 0.000009 |
S | 1158 | N1158I | aAt | aTt | 5 | 5 | All | 0.000001 |
S | 1158 | N1158N | aaT | aaC | 5 | 5 | AY.39 | 0.000124 |
S | 1158 | N1158N | aaT | aaC | 5 | 5 | AY.4.2 | 0.000108 |
S | 1158 | N1158del | AAT | --- | 5 | 5 | AY.4.5 | 0.000537 |
S | 1158 | N1158K | aaT | aaA | 5 | 5 | AY.99.2 | 0.000461 |
S | 1158 | N1158N | aaT | aaC | 5 | 5 | B.1.177 | 0.000066 |
S | 1158 | N1158N | aaT | aaC | 5 | 5 | B.1.408 | 0.01845 |
S | 1158 | N1158N | aaT | aaC | 4 | 4 | AY.22 | 0.008368 |
S | 1158 | N1158S | aAt | aGt | 4 | 4 | AY.43 | 0.000018 |
S | 1158 | N1158N | aaT | aaC | 4 | 4 | AY.44 | 0.000024 |
S | 1158 | N1158N | aaT | aaC | 4 | 4 | B.1.1 | 0.000073 |
S | 1158 | N1158N | aaT | aaC | 4 | 4 | B.1.2 | 0.000035 |
S | 1158 | N1158N | aaT | aaC | 4 | 4 | B.1.596 | 0.000349 |
S | 1158 | N1158N | aaT | aaC | 4 | 4 | Q.3 | 0.00058 |
S | 1158 | N1158N | aaT | aaC | 3 | 3 | AE.8 | 0.001467 |
S | 1158 | N1158T | aAt | aCt | 3 | 3 | AY.4 | 0.000005 |
S | 1158 | N1158H | Aat | Cat | 3 | 3 | AY.44 | 0.000018 |
S | 1158 | N1158N | aaT | aaC | 3 | 3 | B.1 | 0.000027 |
S | 1158 | N1158D | Aat | Gat | 3 | 3 | B.1.1.7 | 0.000003 |
S | 1158 | N1158D | Aat | Gat | 3 | 3 | B.1.177 | 0.00004 |
S | 1158 | N1158S | aAt | aGt | 3 | 3 | B.1.2 | 0.000026 |
S | 1158 | N1158N | aaT | aaC | 3 | 3 | B.1.258 | 0.0002 |
S | 1158 | N1158N | aaT | aaC | 3 | 3 | C.37 | 0.000348 |
S | 1158 | N1158N | aaT | aaC | 3 | 3 | D.2 | 0.000225 |
S | 1158 | N1158N | aaT | aaC | 3 | 3 | P.3 | 0.004785 |
S | 1158 | N1158S | aAT | aGC | 1 | 2 | 0.055556 | |
S | 1158 | N1158D | AaT | GaC | 1 | 2 | 0.055556 | |
S | 1158 | N1158G | AAt | GGt | 1 | 2 | 0.055556 | |
S | 1158 | N1158D | Aat | Gat | 1 | 2 | 0.055556 | |
S | 1158 | N1158G | AAT | GGC | 1 | 2 | 0.055556 | |
S | 1158 | N1158S | aAt | aGt | 1 | 2 | 0.055556 | |
S | 1158 | N1158G | AAt | GGt | 1 | 2 | All | 0 |
S | 1158 | N1158G | AAT | GGC | 1 | 2 | All | 0 |
S | 1158 | N1158D | Aat | Gat | 2 | 2 | AY.103 | 0.000012 |
S | 1158 | N1158N | aaT | aaC | 2 | 2 | AY.110 | 0.000225 |
S | 1158 | N1158del | AAT | --- | 2 | 2 | AY.111 | 0.000366 |
S | 1158 | N1158N | aaT | aaC | 2 | 2 | AY.114 | 0.000462 |
S | 1158 | N1158del | AAT | --- | 2 | 2 | AY.120 | 0.000074 |
S | 1158 | N1158del | AAT | --- | 2 | 2 | AY.19 | 0.002281 |
S | 1158 | N1158D | Aat | Gat | 2 | 2 | AY.3 | 0.00002 |
S | 1158 | N1158N | aaT | aaC | 2 | 2 | AY.3.1 | 0.000171 |
S | 1158 | N1158D | Aat | Gat | 2 | 2 | AY.4 | 0.000003 |
S | 1158 | N1158del | AAT | --- | 2 | 2 | AY.43 | 0.000009 |
S | 1158 | N1158N | aaT | aaC | 2 | 2 | AY.43 | 0.000009 |
S | 1158 | N1158N | aaT | aaC | 2 | 2 | AY.5 | 0.000041 |
S | 1158 | N1158K | aaT | aaG | 2 | 2 | AY.5 | 0.000041 |
S | 1158 | N1158D | Aat | Gat | 2 | 2 | AY.9 | 0.000135 |
S | 1158 | N1158Y | Aat | Tat | 2 | 2 | B.1.1 | 0.000036 |
S | 1158 | N1158H | Aat | Cat | 2 | 2 | B.1.1.232 | 0.00363 |
S | 1158 | N1158H | Aat | Cat | 2 | 2 | B.1.1.7 | 0.000002 |
S | 1158 | N1158T | aAt | aCt | 2 | 2 | B.1.1.7 | 0.000002 |
S | 1158 | N1158S | aAt | aGt | 2 | 2 | B.1.160 | 0.000062 |
S | 1158 | N1158T | aAt | aCt | 2 | 2 | B.1.2 | 0.000018 |
S | 1158 | N1158N | aaT | aaC | 2 | 2 | B.1.241 | 0.001623 |
S | 1158 | N1158N | aaT | aaC | 2 | 2 | B.1.243 | 0.000139 |
S | 1158 | N1158N | aaT | aaC | 2 | 2 | B.1.429 | 0.000047 |
S | 1158 | N1158N | aaT | aaC | 2 | 2 | B.1.526 | 0.000047 |
S | 1158 | N1158D | Aat | Gat | 2 | 2 | B.1.617.2 | 0.000008 |
S | 1158 | N1158N | aaT | aaC | 2 | 2 | B.1.621 | 0.000177 |
S | 1158 | N1158N | aaT | aaC | 1 | 1 | 0.055556 | |
S | 1158 | N1158N | aaT | aaC | 1 | 1 | A.28 | 0.002646 |
S | 1158 | N1158S | aAt | aGt | 1 | 1 | AE.6 | 0.038462 |
S | 1158 | N1158E | AaT | GaG | 1 | 1 | All | 0 |
S | 1158 | N1158del1 | Aat | -at | 1 | 1 | All | 0 |
S | 1158 | N1158del2 | aAT | a-- | 1 | 1 | All | 0 |
S | 1158 | N1158S | aAt | aGt | 1 | 1 | AY.103 | 0.000006 |
S | 1158 | N1158K | aaT | aaA | 1 | 1 | AY.103 | 0.000006 |
S | 1158 | N1158N | aaT | aaC | 1 | 1 | AY.105 | 0.000643 |
S | 1158 | N1158D | Aat | Gat | 1 | 1 | AY.116 | 0.000287 |
S | 1158 | N1158D | Aat | Gat | 1 | 1 | AY.117 | 0.000085 |
S | 1158 | N1158del | AAT | --- | 1 | 1 | AY.118 | 0.000063 |
S | 1158 | N1158T | aAt | aCt | 1 | 1 | AY.119 | 0.000035 |
S | 1158 | N1158S | aAt | aGt | 1 | 1 | AY.120 | 0.000037 |
S | 1158 | N1158I | aAt | aTt | 1 | 1 | AY.14 | 0.000088 |
S | 1158 | N1158N | aaT | aaC | 1 | 1 | AY.14 | 0.000088 |
S | 1158 | N1158N | aaT | aaC | 1 | 1 | AY.20 | 0.000039 |
S | 1158 | N1158D | Aat | Gat | 1 | 1 | AY.26 | 0.000028 |
S | 1158 | N1158K | aaT | aaG | 1 | 1 | AY.27 | 0.000065 |
S | 1158 | N1158S | aAt | aGt | 1 | 1 | AY.29 | 0.000016 |
S | 1158 | N1158N | aaT | aaC | 1 | 1 | AY.29 | 0.000016 |
S | 1158 | N1158T | aAt | aCt | 1 | 1 | AY.29 | 0.000016 |
S | 1158 | N1158Y | Aat | Tat | 1 | 1 | AY.3 | 0.00001 |
S | 1158 | N1158T | aAt | aCt | 1 | 1 | AY.3 | 0.00001 |
S | 1158 | N1158del | AAT | --- | 1 | 1 | AY.30 | 0.000396 |
S | 1158 | N1158E | AaT | GaG | 1 | 1 | AY.32 | 0.000532 |
S | 1158 | N1158I | aAt | aTt | 1 | 1 | AY.34 | 0.000097 |
S | 1158 | N1158S | aAt | aGt | 1 | 1 | AY.34 | 0.000097 |
S | 1158 | N1158S | aAt | aGt | 1 | 1 | AY.34.1 | 0.00051 |
S | 1158 | N1158S | aAt | aGt | 1 | 1 | AY.39 | 0.000025 |
S | 1158 | N1158S | aAt | aGt | 1 | 1 | AY.39.1 | 0.00004 |
S | 1158 | N1158N | aaT | aaC | 1 | 1 | AY.39.1 | 0.00004 |
S | 1158 | N1158Y | Aat | Tat | 1 | 1 | AY.4 | 0.000002 |
S | 1158 | N1158I | aAt | aTt | 1 | 1 | AY.4 | 0.000002 |
S | 1158 | N1158H | Aat | Cat | 1 | 1 | AY.4 | 0.000002 |
S | 1158 | N1158del2 | aAT | a-- | 1 | 1 | AY.4 | 0.000002 |
S | 1158 | N1158D | Aat | Gat | 1 | 1 | AY.43 | 0.000004 |
S | 1158 | N1158H | Aat | Cat | 1 | 1 | AY.43 | 0.000004 |
S | 1158 | N1158Y | Aat | Tat | 1 | 1 | AY.44 | 0.000006 |
S | 1158 | N1158D | Aat | Gat | 1 | 1 | AY.45 | 0.000122 |
S | 1158 | N1158N | aaT | aaC | 1 | 1 | AY.46 | 0.000104 |
S | 1158 | N1158D | Aat | Gat | 1 | 1 | AY.46 | 0.000104 |
S | 1158 | N1158D | Aat | Gat | 1 | 1 | AY.5 | 0.000021 |
S | 1158 | N1158del | AAT | --- | 1 | 1 | AY.5 | 0.000021 |
S | 1158 | N1158N | aaT | aaC | 1 | 1 | AY.51 | 0.000909 |
S | 1158 | N1158S | aAt | aGt | 1 | 1 | AY.54 | 0.000095 |
S | 1158 | N1158Y | Aat | Tat | 1 | 1 | AY.55 | 0.000917 |
S | 1158 | N1158N | aaT | aaC | 1 | 1 | AY.59 | 0.00053 |
S | 1158 | N1158K | aaT | aaG | 1 | 1 | AY.59 | 0.00053 |
S | 1158 | N1158del | AAT | --- | 1 | 1 | AY.6 | 0.000041 |
S | 1158 | N1158del | AAT | --- | 1 | 1 | AY.60 | 0.000938 |
S | 1158 | N1158D | Aat | Gat | 1 | 1 | AY.67 | 0.000464 |
S | 1158 | N1158del | AAT | --- | 1 | 1 | AY.7 | 0.000196 |
S | 1158 | N1158Y | Aat | Tat | 1 | 1 | AY.74 | 0.000116 |
S | 1158 | N1158I | aAt | aTt | 1 | 1 | AY.75 | 0.000056 |
S | 1158 | N1158N | aaT | aaC | 1 | 1 | AY.75.1 | 0.00018 |
S | 1158 | N1158del | AAT | --- | 1 | 1 | AY.81 | 0.001992 |
S | 1158 | N1158del | AAT | --- | 1 | 1 | AY.85 | 0.000427 |
S | 1158 | N1158H | Aat | Cat | 1 | 1 | AY.9 | 0.000068 |
S | 1158 | N1158del | AAT | --- | 1 | 1 | AY.9 | 0.000068 |
S | 1158 | N1158del | AAT | --- | 1 | 1 | AY.9.2 | 0.000037 |
S | 1158 | N1158N | aaT | aaC | 1 | 1 | AY.98 | 0.000079 |
S | 1158 | N1158S | aAt | aGt | 1 | 1 | AY.98.1 | 0.000048 |
S | 1158 | N1158Y | Aat | Tat | 1 | 1 | AY.99.2 | 0.000092 |
S | 1158 | N1158K | aaT | aaG | 1 | 1 | B.1 | 0.000009 |
S | 1158 | N1158del1 | Aat | -at | 1 | 1 | B.1 | 0.000009 |
S | 1158 | N1158S | aAt | aGt | 1 | 1 | B.1 | 0.000009 |
S | 1158 | N1158Y | Aat | Tat | 1 | 1 | B.1 | 0.000009 |
S | 1158 | N1158del | AAT | --- | 1 | 1 | B.1 | 0.000009 |
S | 1158 | N1158del | AAT | --- | 1 | 1 | B.1.1.159 | 0.004673 |
S | 1158 | N1158Y | Aat | Tat | 1 | 1 | B.1.1.187 | 0.00885 |
S | 1158 | N1158N | aaT | aaC | 1 | 1 | B.1.1.214 | 0.000055 |
S | 1158 | N1158del | AAT | --- | 1 | 1 | B.1.1.236 | 0.006897 |
S | 1158 | N1158N | aaT | aaC | 1 | 1 | B.1.1.277 | 0.000759 |
S | 1158 | N1158N | aaT | aaC | 1 | 1 | B.1.1.284 | 0.000107 |
S | 1158 | N1158N | aaT | aaC | 1 | 1 | B.1.1.37 | 0.000193 |
S | 1158 | N1158I | aAt | aTt | 1 | 1 | B.1.1.519 | 0.00004 |
S | 1158 | N1158del | AAT | --- | 1 | 1 | B.1.160.23 | 0.004831 |
S | 1158 | N1158T | aAt | aCt | 1 | 1 | B.1.177 | 0.000013 |
S | 1158 | N1158del | AAT | --- | 1 | 1 | B.1.177.17 | 0.000821 |
S | 1158 | N1158del | AAT | --- | 1 | 1 | B.1.177.21 | 0.000076 |
S | 1158 | N1158N | aaT | aaC | 1 | 1 | B.1.177.38 | 0.010417 |
S | 1158 | N1158S | aAt | aGt | 1 | 1 | B.1.177.4 | 0.000211 |
S | 1158 | N1158del | AAT | --- | 1 | 1 | B.1.177.4 | 0.000211 |
S | 1158 | N1158del | AAT | --- | 1 | 1 | B.1.177.48 | 0.003125 |
S | 1158 | N1158del | AAT | --- | 1 | 1 | B.1.177.54 | 0.000606 |
S | 1158 | N1158del | AAT | --- | 1 | 1 | B.1.177.60 | 0.000218 |
S | 1158 | N1158del | AAT | --- | 1 | 1 | B.1.177.69 | 0.001484 |
S | 1158 | N1158S | aAt | aGt | 1 | 1 | B.1.177.80 | 0.001912 |
S | 1158 | N1158del | AAT | --- | 1 | 1 | B.1.177.9 | 0.001332 |
S | 1158 | N1158D | Aat | Gat | 1 | 1 | B.1.2 | 0.000009 |
S | 1158 | N1158H | Aat | Cat | 1 | 1 | B.1.2 | 0.000009 |
S | 1158 | N1158N | aaT | aaC | 1 | 1 | B.1.212 | 0.016667 |
S | 1158 | N1158del | AAT | --- | 1 | 1 | B.1.221.1 | 0.002907 |
S | 1158 | N1158K | aaT | aaG | 1 | 1 | B.1.222 | 0.001692 |
S | 1158 | N1158T | aAt | aCt | 1 | 1 | B.1.243 | 0.00007 |
S | 1158 | N1158H | Aat | Cat | 1 | 1 | B.1.258.7 | 0.001912 |
S | 1158 | N1158N | aaT | aaC | 1 | 1 | B.1.351 | 0.00003 |
S | 1158 | N1158D | Aat | Gat | 1 | 1 | B.1.351 | 0.00003 |
S | 1158 | N1158S | aAt | aGt | 1 | 1 | B.1.36 | 0.000146 |
S | 1158 | N1158N | aaT | aaC | 1 | 1 | B.1.369 | 0.000285 |
S | 1158 | N1158N | aaT | aaC | 1 | 1 | B.1.409 | 0.000781 |
S | 1158 | N1158N | aaT | aaC | 1 | 1 | B.1.527 | 0.003704 |
S | 1158 | N1158D | Aat | Gat | 1 | 1 | B.1.558 | 0.004566 |
S | 1158 | N1158del | AAT | --- | 1 | 1 | B.1.617.2 | 0.000004 |
S | 1158 | N1158Y | Aat | Tat | 1 | 1 | B.1.617.2 | 0.000004 |
S | 1158 | N1158N | aaT | aaC | 1 | 1 | B.1.618 | 0.004032 |
S | 1158 | N1158N | aaT | aaC | 1 | 1 | B.29 | 0.003509 |
S | 1158 | N1158N | aaT | aaC | 1 | 1 | B.3 | 0.000831 |
S | 1158 | N1158del | AAT | --- | 1 | 1 | C.17 | 0.055556 |
S | 1158 | N1158del | AAT | --- | 1 | 1 | C.37 | 0.000116 |
S | 1158 | N1158del | AAT | --- | 1 | 1 | P.1 | 0.000016 |
S | 1158 | N1158S | aAt | aGt | 1 | 1 | P.1 | 0.000016 |
S | 1158 | N1158N | aaT | aaC | 1 | 1 | P.1.10 | 0.000269 |
S | 1158 | N1158K | aaT | aaG | 1 | 1 | P.1.12 | 0.000484 |
S | 1158 | N1158del | AAT | --- | 1 | 1 | P.1.15 | 0.000232 |
S | 1158 | N1158N | aaT | aaC | 1 | 1 | P.1.2 | 0.001156 |
S | 1158 | N1158del | AAT | --- | 1 | 1 | U.3 | 0.003861 |
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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