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 |
ORF3a | 162 | S162S | syn | agT | agC | 1833 | 1833 | 1 | 25876-25878 | |
ORF3a | 162 | S162G | nonsyn | Agt | Ggt | 651 | 651 | 1 | 25876-25878 | |
ORF3a | 162 | S162I | nonsyn | aGt | aTt | 85 | 85 | 1 | 25876-25878 | |
ORF3a | 162 | S162del | del | AGT | --- | 68 | 68 | 1 | 25876-25878 | |
ORF3a | 162 | S162T | nonsyn | aGt | aCt | 62 | 62 | 1 | 25876-25878 | |
ORF3a | 162 | S162N | nonsyn | aGt | aAt | 42 | 42 | 1 | 25876-25878 | |
ORF3a | 162 | S162R | nonsyn | Agt | Cgt | 23 | 12 | 0.521739 | 25876-25878 | |
ORF3a | 162 | S162R | nonsyn | agT | agA | 23 | 9 | 0.391304 | 25876-25878 | |
ORF3a | 162 | S162R | nonsyn | agT | agG | 23 | 2 | 0.0869565 | 25876-25878 | |
ORF3a | 162 | S162C | nonsyn | Agt | Tgt | 7 | 7 | 1 | 25876-25878 | |
ORF3a | 162 | S162del1 | del | agT | ag- | 1 | 1 | 1 | 25876-25878 | |
ORF3a | 162 | S162V | nonsyn | AGt | GTt | 1 | 1 | 1 | 25876-25878 | |
ORF3a | 162 | S162del2 | del | aGT | a-- | 1 | 1 | 1 | 25876-25878 |
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 |
ORF3a | 162 | S162S | agT | agC | 1833 | 1833 | All | 0.000351 |
ORF3a | 162 | S162S | agT | agC | 1629 | 1629 | B.1.177.54 | 0.987871 |
ORF3a | 162 | S162G | Agt | Ggt | 651 | 651 | All | 0.000125 |
ORF3a | 162 | S162I | aGt | aTt | 85 | 85 | All | 0.000016 |
ORF3a | 162 | S162G | Agt | Ggt | 79 | 79 | AY.9.2 | 0.002902 |
ORF3a | 162 | S162G | Agt | Ggt | 73 | 73 | B.1.324 | 0.117175 |
ORF3a | 162 | S162del | AGT | --- | 68 | 68 | All | 0.000013 |
ORF3a | 162 | S162T | aGt | aCt | 62 | 62 | All | 0.000012 |
ORF3a | 162 | S162T | aGt | aCt | 58 | 58 | B.1.1.7 | 0.000052 |
ORF3a | 162 | S162G | Agt | Ggt | 56 | 56 | AY.44 | 0.000341 |
ORF3a | 162 | S162G | Agt | Ggt | 56 | 56 | B.1.517 | 0.023911 |
ORF3a | 162 | S162G | Agt | Ggt | 53 | 53 | B.1.1.7 | 0.000047 |
ORF3a | 162 | S162S | agT | agC | 43 | 43 | V.1 | 0.977273 |
ORF3a | 162 | S162N | aGt | aAt | 42 | 42 | All | 0.000008 |
ORF3a | 162 | S162G | Agt | Ggt | 36 | 36 | AY.103 | 0.000224 |
ORF3a | 162 | S162G | Agt | Ggt | 36 | 36 | AY.25 | 0.000217 |
ORF3a | 162 | S162G | Agt | Ggt | 33 | 33 | B.1.2 | 0.000291 |
ORF3a | 162 | S162S | agT | agC | 31 | 31 | V.2 | 1 |
ORF3a | 162 | S162I | aGt | aTt | 29 | 29 | B.1.1.7 | 0.000026 |
ORF3a | 162 | S162G | Agt | Ggt | 28 | 28 | R.1 | 0.00252 |
ORF3a | 162 | S162S | agT | agC | 27 | 27 | AY.3 | 0.000269 |
ORF3a | 162 | S162R | Agt | Cgt | 12 | 23 | All | 0.000002 |
ORF3a | 162 | S162R | agT | agA | 9 | 23 | All | 0.000002 |
ORF3a | 162 | S162R | agT | agG | 2 | 23 | All | 0 |
ORF3a | 162 | S162S | agT | agC | 23 | 23 | B.1.2 | 0.000203 |
ORF3a | 162 | S162G | Agt | Ggt | 23 | 23 | B.1.620 | 0.02176 |
ORF3a | 162 | S162G | Agt | Ggt | 20 | 20 | AY.4 | 0.000031 |
ORF3a | 162 | S162del | AGT | --- | 19 | 19 | B.1.1.7 | 0.000017 |
ORF3a | 162 | S162G | Agt | Ggt | 19 | 19 | B.1.177 | 0.00025 |
ORF3a | 162 | S162G | Agt | Ggt | 19 | 19 | B.1.36.22 | 0.022947 |
ORF3a | 162 | S162S | agT | agC | 17 | 17 | B.1 | 0.000156 |
ORF3a | 162 | S162G | Agt | Ggt | 16 | 16 | AY.36 | 0.002371 |
ORF3a | 162 | S162I | aGt | aTt | 14 | 14 | AY.4 | 0.000022 |
ORF3a | 162 | S162S | agT | agC | 14 | 14 | P.1.4 | 0.013672 |
ORF3a | 162 | S162S | agT | agC | 11 | 11 | P.1 | 0.000173 |
ORF3a | 162 | S162G | Agt | Ggt | 11 | 11 | P.1 | 0.000173 |
ORF3a | 162 | S162G | Agt | Ggt | 10 | 10 | AY.119 | 0.000353 |
ORF3a | 162 | S162S | agT | agC | 10 | 10 | B.1.177 | 0.000132 |
ORF3a | 162 | S162G | Agt | Ggt | 8 | 8 | B.1.617.2 | 0.00003 |
ORF3a | 162 | S162C | Agt | Tgt | 7 | 7 | All | 0.000001 |
ORF3a | 162 | S162N | aGt | aAt | 7 | 7 | AY.103 | 0.000043 |
ORF3a | 162 | S162G | Agt | Ggt | 7 | 7 | AY.4.2 | 0.000152 |
ORF3a | 162 | S162N | aGt | aAt | 7 | 7 | B.1.1.7 | 0.000006 |
ORF3a | 162 | S162R | Agt | Cgt | 7 | 7 | B.1.617.2 | 0.000026 |
ORF3a | 162 | S162G | Agt | Ggt | 6 | 6 | AY.16 | 0.002278 |
ORF3a | 162 | S162I | aGt | aTt | 6 | 6 | AY.44 | 0.000037 |
ORF3a | 162 | S162del | AGT | --- | 6 | 6 | B.1 | 0.000055 |
ORF3a | 162 | S162G | Agt | Ggt | 5 | 5 | AY.43 | 0.000022 |
ORF3a | 162 | S162del | AGT | --- | 5 | 5 | AY.43 | 0.000022 |
ORF3a | 162 | S162G | Agt | Ggt | 5 | 5 | B.1 | 0.000046 |
ORF3a | 162 | S162G | Agt | Ggt | 5 | 5 | B.1.346 | 0.006553 |
ORF3a | 162 | S162G | Agt | Ggt | 4 | 4 | AY.102 | 0.000106 |
ORF3a | 162 | S162I | aGt | aTt | 4 | 4 | AY.119 | 0.000141 |
ORF3a | 162 | S162G | Agt | Ggt | 4 | 4 | AY.78 | 0.006163 |
ORF3a | 162 | S162G | Agt | Ggt | 4 | 4 | B.1.596 | 0.000349 |
ORF3a | 162 | S162N | aGt | aAt | 4 | 4 | B.1.617.2 | 0.000015 |
ORF3a | 162 | S162I | aGt | aTt | 3 | 3 | AY.25 | 0.000018 |
ORF3a | 162 | S162G | Agt | Ggt | 3 | 3 | AY.29 | 0.000047 |
ORF3a | 162 | S162N | aGt | aAt | 3 | 3 | AY.4 | 0.000005 |
ORF3a | 162 | S162R | agT | agA | 2 | 3 | AY.4 | 0.000003 |
ORF3a | 162 | S162R | agT | agG | 1 | 3 | AY.4 | 0.000002 |
ORF3a | 162 | S162N | aGt | aAt | 3 | 3 | AY.43 | 0.000013 |
ORF3a | 162 | S162I | aGt | aTt | 3 | 3 | AY.74 | 0.000347 |
ORF3a | 162 | S162R | agT | agA | 2 | 3 | B.1 | 0.000018 |
ORF3a | 162 | S162R | agT | agG | 1 | 3 | B.1 | 0.000009 |
ORF3a | 162 | S162N | aGt | aAt | 3 | 3 | B.1.1.519 | 0.000119 |
ORF3a | 162 | S162S | agT | agC | 3 | 3 | B.1.1.7 | 0.000003 |
ORF3a | 162 | S162S | agT | agC | 3 | 3 | B.1.177.4 | 0.000633 |
ORF3a | 162 | S162I | aGt | aTt | 3 | 3 | P.1.10 | 0.000808 |
ORF3a | 162 | S162G | Agt | Ggt | 2 | 2 | 0.111111 | |
ORF3a | 162 | S162del | AGT | --- | 2 | 2 | 0.111111 | |
ORF3a | 162 | S162I | aGt | aTt | 2 | 2 | AD.2 | 0.000438 |
ORF3a | 162 | S162G | Agt | Ggt | 2 | 2 | AY.20 | 0.000078 |
ORF3a | 162 | S162G | Agt | Ggt | 2 | 2 | AY.37 | 0.000632 |
ORF3a | 162 | S162S | agT | agC | 2 | 2 | AY.4 | 0.000003 |
ORF3a | 162 | S162G | Agt | Ggt | 2 | 2 | AY.5 | 0.000041 |
ORF3a | 162 | S162G | Agt | Ggt | 2 | 2 | AY.61 | 0.00021 |
ORF3a | 162 | S162T | aGt | aCt | 2 | 2 | B.1 | 0.000018 |
ORF3a | 162 | S162I | aGt | aTt | 2 | 2 | B.1.1 | 0.000036 |
ORF3a | 162 | S162S | agT | agC | 2 | 2 | B.1.1 | 0.000036 |
ORF3a | 162 | S162R | agT | agA | 1 | 2 | B.1.1 | 0.000018 |
ORF3a | 162 | S162R | Agt | Cgt | 1 | 2 | B.1.1 | 0.000018 |
ORF3a | 162 | S162G | Agt | Ggt | 2 | 2 | B.1.1.28 | 0.000622 |
ORF3a | 162 | S162del | AGT | --- | 2 | 2 | B.1.1.315 | 0.016949 |
ORF3a | 162 | S162G | Agt | Ggt | 2 | 2 | B.1.1.434 | 0.000697 |
ORF3a | 162 | S162C | Agt | Tgt | 2 | 2 | B.1.1.7 | 0.000002 |
ORF3a | 162 | S162del | AGT | --- | 2 | 2 | B.1.177 | 0.000026 |
ORF3a | 162 | S162S | agT | agC | 2 | 2 | B.1.177.56 | 0.001335 |
ORF3a | 162 | S162G | Agt | Ggt | 2 | 2 | B.1.214.3 | 0.014286 |
ORF3a | 162 | S162N | aGt | aAt | 2 | 2 | B.1.351 | 0.000059 |
ORF3a | 162 | S162R | Agt | Cgt | 2 | 2 | B.1.526 | 0.000047 |
ORF3a | 162 | S162N | aGt | aAt | 2 | 2 | B.1.617.1 | 0.000258 |
ORF3a | 162 | S162del | AGT | --- | 2 | 2 | B.1.617.2 | 0.000008 |
ORF3a | 162 | S162I | aGt | aTt | 2 | 2 | B.1.617.2 | 0.000008 |
ORF3a | 162 | S162del | AGT | --- | 2 | 2 | B.1.621 | 0.000177 |
ORF3a | 162 | S162S | agT | agC | 2 | 2 | D.2 | 0.00015 |
ORF3a | 162 | S162N | aGt | aAt | 2 | 2 | D.2 | 0.00015 |
ORF3a | 162 | S162del | AGT | --- | 2 | 2 | P.1 | 0.000032 |
ORF3a | 162 | S162del | AGT | --- | 2 | 2 | P.1.15 | 0.000465 |
ORF3a | 162 | S162del | AGT | --- | 1 | 1 | A | 0.000387 |
ORF3a | 162 | S162R | Agt | Cgt | 1 | 1 | A.23.1 | 0.000704 |
ORF3a | 162 | S162del | AGT | --- | 1 | 1 | AD.2 | 0.000219 |
ORF3a | 162 | S162del2 | aGT | a-- | 1 | 1 | All | 0 |
ORF3a | 162 | S162V | AGt | GTt | 1 | 1 | All | 0 |
ORF3a | 162 | S162del1 | agT | ag- | 1 | 1 | All | 0 |
ORF3a | 162 | S162I | aGt | aTt | 1 | 1 | AY.103 | 0.000006 |
ORF3a | 162 | S162C | Agt | Tgt | 1 | 1 | AY.103 | 0.000006 |
ORF3a | 162 | S162G | Agt | Ggt | 1 | 1 | AY.110 | 0.000113 |
ORF3a | 162 | S162S | agT | agC | 1 | 1 | AY.113 | 0.000142 |
ORF3a | 162 | S162del | AGT | --- | 1 | 1 | AY.120 | 0.000037 |
ORF3a | 162 | S162I | aGt | aTt | 1 | 1 | AY.120.2.1 | 0.000498 |
ORF3a | 162 | S162N | aGt | aAt | 1 | 1 | AY.20 | 0.000039 |
ORF3a | 162 | S162N | aGt | aAt | 1 | 1 | AY.23 | 0.00007 |
ORF3a | 162 | S162del | AGT | --- | 1 | 1 | AY.25 | 0.000006 |
ORF3a | 162 | S162T | aGt | aCt | 1 | 1 | AY.25 | 0.000006 |
ORF3a | 162 | S162del | AGT | --- | 1 | 1 | AY.29 | 0.000016 |
ORF3a | 162 | S162I | aGt | aTt | 1 | 1 | AY.3.1 | 0.000085 |
ORF3a | 162 | S162G | Agt | Ggt | 1 | 1 | AY.30 | 0.000396 |
ORF3a | 162 | S162G | Agt | Ggt | 1 | 1 | AY.32 | 0.000532 |
ORF3a | 162 | S162G | Agt | Ggt | 1 | 1 | AY.33 | 0.000067 |
ORF3a | 162 | S162N | aGt | aAt | 1 | 1 | AY.39 | 0.000025 |
ORF3a | 162 | S162I | aGt | aTt | 1 | 1 | AY.39.1 | 0.00004 |
ORF3a | 162 | S162del | AGT | --- | 1 | 1 | AY.4 | 0.000002 |
ORF3a | 162 | S162C | Agt | Tgt | 1 | 1 | AY.4 | 0.000002 |
ORF3a | 162 | S162C | Agt | Tgt | 1 | 1 | AY.4.2 | 0.000022 |
ORF3a | 162 | S162I | aGt | aTt | 1 | 1 | AY.4.3 | 0.000842 |
ORF3a | 162 | S162del | AGT | --- | 1 | 1 | AY.4.5 | 0.000107 |
ORF3a | 162 | S162S | agT | agC | 1 | 1 | AY.43 | 0.000004 |
ORF3a | 162 | S162I | aGt | aTt | 1 | 1 | AY.43 | 0.000004 |
ORF3a | 162 | S162S | agT | agC | 1 | 1 | AY.44 | 0.000006 |
ORF3a | 162 | S162I | aGt | aTt | 1 | 1 | AY.46 | 0.000104 |
ORF3a | 162 | S162G | Agt | Ggt | 1 | 1 | AY.46.6 | 0.000072 |
ORF3a | 162 | S162I | aGt | aTt | 1 | 1 | AY.47 | 0.000031 |
ORF3a | 162 | S162S | agT | agC | 1 | 1 | AY.5 | 0.000021 |
ORF3a | 162 | S162V | AGt | GTt | 1 | 1 | AY.5 | 0.000021 |
ORF3a | 162 | S162G | Agt | Ggt | 1 | 1 | AY.54 | 0.000095 |
ORF3a | 162 | S162del | AGT | --- | 1 | 1 | AY.68 | 0.000274 |
ORF3a | 162 | S162S | agT | agC | 1 | 1 | AY.7.1 | 0.000113 |
ORF3a | 162 | S162R | agT | agA | 1 | 1 | AY.7.2 | 0.000559 |
ORF3a | 162 | S162S | agT | agC | 1 | 1 | AY.71 | 0.000475 |
ORF3a | 162 | S162R | agT | agA | 1 | 1 | AY.9 | 0.000068 |
ORF3a | 162 | S162S | agT | agC | 1 | 1 | AY.9 | 0.000068 |
ORF3a | 162 | S162S | agT | agC | 1 | 1 | AY.9.2 | 0.000037 |
ORF3a | 162 | S162I | aGt | aTt | 1 | 1 | AY.9.2 | 0.000037 |
ORF3a | 162 | S162N | aGt | aAt | 1 | 1 | AY.90 | 0.000684 |
ORF3a | 162 | S162I | aGt | aTt | 1 | 1 | AY.96 | 0.002075 |
ORF3a | 162 | S162S | agT | agC | 1 | 1 | AY.98 | 0.000079 |
ORF3a | 162 | S162G | Agt | Ggt | 1 | 1 | AY.98.1 | 0.000048 |
ORF3a | 162 | S162del | AGT | --- | 1 | 1 | B | 0.000128 |
ORF3a | 162 | S162G | Agt | Ggt | 1 | 1 | B.1.1 | 0.000018 |
ORF3a | 162 | S162del | AGT | --- | 1 | 1 | B.1.1.214 | 0.000055 |
ORF3a | 162 | S162del1 | agT | ag- | 1 | 1 | B.1.1.216 | 0.00089 |
ORF3a | 162 | S162S | agT | agC | 1 | 1 | B.1.1.28 | 0.000311 |
ORF3a | 162 | S162del | AGT | --- | 1 | 1 | B.1.1.409 | 0.002833 |
ORF3a | 162 | S162S | agT | agC | 1 | 1 | B.1.1.50 | 0.000679 |
ORF3a | 162 | S162del2 | aGT | a-- | 1 | 1 | B.1.1.7 | 0.000001 |
ORF3a | 162 | S162R | agT | agA | 1 | 1 | B.1.1.7 | 0.000001 |
ORF3a | 162 | S162I | aGt | aTt | 1 | 1 | B.1.128 | 0.000635 |
ORF3a | 162 | S162N | aGt | aAt | 1 | 1 | B.1.143 | 0.021277 |
ORF3a | 162 | S162N | aGt | aAt | 1 | 1 | B.1.160 | 0.000031 |
ORF3a | 162 | S162del | AGT | --- | 1 | 1 | B.1.160 | 0.000031 |
ORF3a | 162 | S162del | AGT | --- | 1 | 1 | B.1.160.23 | 0.004831 |
ORF3a | 162 | S162R | agT | agA | 1 | 1 | B.1.177.18 | 0.00116 |
ORF3a | 162 | S162N | aGt | aAt | 1 | 1 | B.1.177.33 | 0.001645 |
ORF3a | 162 | S162del | AGT | --- | 1 | 1 | B.1.177.4 | 0.000211 |
ORF3a | 162 | S162del | AGT | --- | 1 | 1 | B.1.177.51 | 0.004566 |
ORF3a | 162 | S162G | Agt | Ggt | 1 | 1 | B.1.177.56 | 0.000668 |
ORF3a | 162 | S162del | AGT | --- | 1 | 1 | B.1.177.62 | 0.001192 |
ORF3a | 162 | S162G | Agt | Ggt | 1 | 1 | B.1.177.72 | 0.00339 |
ORF3a | 162 | S162S | agT | agC | 1 | 1 | B.1.177.81 | 0.000189 |
ORF3a | 162 | S162I | aGt | aTt | 1 | 1 | B.1.2 | 0.000009 |
ORF3a | 162 | S162C | Agt | Tgt | 1 | 1 | B.1.2 | 0.000009 |
ORF3a | 162 | S162del | AGT | --- | 1 | 1 | B.1.221 | 0.000071 |
ORF3a | 162 | S162C | Agt | Tgt | 1 | 1 | B.1.221 | 0.000071 |
ORF3a | 162 | S162R | Agt | Cgt | 1 | 1 | B.1.243 | 0.00007 |
ORF3a | 162 | S162del | AGT | --- | 1 | 1 | B.1.258.16 | 0.001637 |
ORF3a | 162 | S162I | aGt | aTt | 1 | 1 | B.1.333 | 0.010526 |
ORF3a | 162 | S162N | aGt | aAt | 1 | 1 | B.1.36 | 0.000146 |
ORF3a | 162 | S162T | aGt | aCt | 1 | 1 | B.1.36 | 0.000146 |
ORF3a | 162 | S162del | AGT | --- | 1 | 1 | B.1.416.1 | 0.001563 |
ORF3a | 162 | S162del | AGT | --- | 1 | 1 | B.1.427 | 0.00005 |
ORF3a | 162 | S162N | aGt | aAt | 1 | 1 | B.1.438.1 | 0.000107 |
ORF3a | 162 | S162del | AGT | --- | 1 | 1 | B.1.525 | 0.000113 |
ORF3a | 162 | S162S | agT | agC | 1 | 1 | B.1.525 | 0.000113 |
ORF3a | 162 | S162I | aGt | aTt | 1 | 1 | B.1.525 | 0.000113 |
ORF3a | 162 | S162G | Agt | Ggt | 1 | 1 | B.1.526 | 0.000024 |
ORF3a | 162 | S162G | Agt | Ggt | 1 | 1 | B.1.527 | 0.003704 |
ORF3a | 162 | S162G | Agt | Ggt | 1 | 1 | B.1.551 | 0.00129 |
ORF3a | 162 | S162del | AGT | --- | 1 | 1 | B.1.596 | 0.000087 |
ORF3a | 162 | S162I | aGt | aTt | 1 | 1 | B.1.615 | 0.04 |
ORF3a | 162 | S162del | AGT | --- | 1 | 1 | B.1.617.1 | 0.000129 |
ORF3a | 162 | S162I | aGt | aTt | 1 | 1 | B.1.637 | 0.000073 |
ORF3a | 162 | S162del | AGT | --- | 1 | 1 | B.1.638 | 0.052632 |
ORF3a | 162 | S162G | Agt | Ggt | 1 | 1 | C.37 | 0.000116 |
ORF3a | 162 | S162I | aGt | aTt | 1 | 1 | D.2 | 0.000075 |
ORF3a | 162 | S162G | Agt | Ggt | 1 | 1 | D.2 | 0.000075 |
ORF3a | 162 | S162G | Agt | Ggt | 1 | 1 | P.1.17 | 0.000162 |
ORF3a | 162 | S162S | agT | agC | 1 | 1 | U.3 | 0.003861 |
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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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