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 |
N | 76 | T76I | nonsyn | aCc | aTc | 292 | 292 | 1 | 28499-28501 | |
N | 76 | T76T | syn | acC | acT | 58 | 49 | 0.844828 | 28499-28501 | |
N | 76 | T76T | syn | acC | acA | 58 | 8 | 0.137931 | 28499-28501 | |
N | 76 | T76T | syn | acC | acG | 58 | 1 | 0.0172414 | 28499-28501 | |
N | 76 | T76A | nonsyn | Acc | Gcc | 24 | 24 | 1 | 28499-28501 | |
N | 76 | T76del | del | ACC | --- | 17 | 17 | 1 | 28499-28501 | |
N | 76 | T76S | nonsyn | Acc | Tcc | 16 | 13 | 0.8125 | 28499-28501 | |
N | 76 | T76S | nonsyn | aCc | aGc | 16 | 2 | 0.125 | 28499-28501 | |
N | 76 | T76S | nonsyn | AcC | TcG | 16 | 1 | 0.0625 | 28499-28501 | |
N | 76 | T76N | nonsyn | aCc | aAc | 8 | 8 | 1 | 28499-28501 | |
N | 76 | T76L | nonsyn | ACC | CTT | 7 | 6 | 0.857143 | 28499-28501 | |
N | 76 | T76L | nonsyn | ACc | CTc | 7 | 1 | 0.142857 | 28499-28501 | |
N | 76 | T76P | nonsyn | Acc | Ccc | 1 | 1 | 1 | 28499-28501 | |
N | 76 | T76F | nonsyn | ACc | TTc | 1 | 1 | 1 | 28499-28501 | |
N | 76 | T76del2 | del | aCC | a-- | 1 | 1 | 1 | 28499-28501 |
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 |
N | 76 | T76I | aCc | aTc | 292 | 292 | All | 0.000056 |
N | 76 | T76I | aCc | aTc | 129 | 129 | B.1.1.218 | 0.992308 |
N | 76 | T76T | acC | acT | 49 | 58 | All | 0.000009 |
N | 76 | T76T | acC | acA | 8 | 58 | All | 0.000002 |
N | 76 | T76T | acC | acG | 1 | 58 | All | 0 |
N | 76 | T76I | aCc | aTc | 33 | 33 | B.1.1.7 | 0.00003 |
N | 76 | T76A | Acc | Gcc | 24 | 24 | All | 0.000005 |
N | 76 | T76I | aCc | aTc | 22 | 22 | B.1 | 0.000202 |
N | 76 | T76del | ACC | --- | 17 | 17 | All | 0.000003 |
N | 76 | T76S | Acc | Tcc | 13 | 16 | All | 0.000002 |
N | 76 | T76S | aCc | aGc | 2 | 16 | All | 0 |
N | 76 | T76S | AcC | TcG | 1 | 16 | All | 0 |
N | 76 | T76I | aCc | aTc | 16 | 16 | B.1.1.519 | 0.000635 |
N | 76 | T76I | aCc | aTc | 11 | 11 | P.1 | 0.000173 |
N | 76 | T76A | Acc | Gcc | 10 | 10 | AY.4 | 0.000016 |
N | 76 | T76N | aCc | aAc | 8 | 8 | All | 0.000002 |
N | 76 | T76L | ACC | CTT | 6 | 7 | All | 0.000001 |
N | 76 | T76L | ACc | CTc | 1 | 7 | All | 0 |
N | 76 | T76S | Acc | Tcc | 7 | 7 | AY.103 | 0.000043 |
N | 76 | T76T | acC | acT | 7 | 7 | B.1.637 | 0.000512 |
N | 76 | T76I | aCc | aTc | 6 | 6 | AY.4 | 0.000009 |
N | 76 | T76T | acC | acT | 6 | 6 | B.1.1.214 | 0.000333 |
N | 76 | T76T | acC | acT | 6 | 6 | B.1.1.7 | 0.000005 |
N | 76 | T76I | aCc | aTc | 5 | 5 | AY.25 | 0.00003 |
N | 76 | T76I | aCc | aTc | 5 | 5 | B.1.596 | 0.000436 |
N | 76 | T76L | ACC | CTT | 4 | 4 | 0.222222 | |
N | 76 | T76I | aCc | aTc | 4 | 4 | AY.44 | 0.000024 |
N | 76 | T76I | aCc | aTc | 4 | 4 | B.1.1.464 | 0.005891 |
N | 76 | T76T | acC | acT | 4 | 4 | B.1.243 | 0.000278 |
N | 76 | T76I | aCc | aTc | 3 | 3 | AY.30 | 0.001187 |
N | 76 | T76T | acC | acT | 3 | 3 | AY.4 | 0.000005 |
N | 76 | T76T | acC | acA | 2 | 3 | B.1 | 0.000018 |
N | 76 | T76T | acC | acG | 1 | 3 | B.1 | 0.000009 |
N | 76 | T76T | acC | acT | 3 | 3 | B.1.1.291 | 0.002227 |
N | 76 | T76N | aCc | aAc | 3 | 3 | B.1.1.7 | 0.000003 |
N | 76 | T76I | aCc | aTc | 3 | 3 | B.1.2 | 0.000026 |
N | 76 | T76T | acC | acT | 3 | 3 | B.1.2 | 0.000026 |
N | 76 | T76I | aCc | aTc | 3 | 3 | B.1.427 | 0.000151 |
N | 76 | T76I | aCc | aTc | 3 | 3 | B.1.429 | 0.000071 |
N | 76 | T76T | acC | acT | 3 | 3 | B.1.526 | 0.000071 |
N | 76 | T76A | Acc | Gcc | 3 | 3 | B.1.617.2 | 0.000011 |
N | 76 | T76del | ACC | --- | 2 | 2 | 0.111111 | |
N | 76 | T76S | Acc | Tcc | 2 | 2 | AY.43 | 0.000009 |
N | 76 | T76T | acC | acA | 2 | 2 | AY.43 | 0.000009 |
N | 76 | T76I | aCc | aTc | 2 | 2 | B.1.1.284 | 0.000215 |
N | 76 | T76I | aCc | aTc | 2 | 2 | B.1.1.337 | 0.007194 |
N | 76 | T76A | Acc | Gcc | 2 | 2 | B.1.177.54 | 0.001213 |
N | 76 | T76T | acC | acT | 2 | 2 | B.1.429 | 0.000047 |
N | 76 | T76I | aCc | aTc | 2 | 2 | P.2 | 0.000373 |
N | 76 | T76I | aCc | aTc | 2 | 2 | P.3 | 0.00319 |
N | 76 | T76F | ACc | TTc | 1 | 1 | All | 0 |
N | 76 | T76del2 | aCC | a-- | 1 | 1 | All | 0 |
N | 76 | T76P | Acc | Ccc | 1 | 1 | All | 0 |
N | 76 | T76T | acC | acA | 1 | 1 | AY.102 | 0.000027 |
N | 76 | T76I | aCc | aTc | 1 | 1 | AY.103 | 0.000006 |
N | 76 | T76A | Acc | Gcc | 1 | 1 | AY.103 | 0.000006 |
N | 76 | T76I | aCc | aTc | 1 | 1 | AY.16.1 | 0.00047 |
N | 76 | T76I | aCc | aTc | 1 | 1 | AY.18 | 0.010101 |
N | 76 | T76T | acC | acT | 1 | 1 | AY.23 | 0.00007 |
N | 76 | T76N | aCc | aAc | 1 | 1 | AY.25 | 0.000006 |
N | 76 | T76S | Acc | Tcc | 1 | 1 | AY.25 | 0.000006 |
N | 76 | T76del | ACC | --- | 1 | 1 | AY.3 | 0.00001 |
N | 76 | T76I | aCc | aTc | 1 | 1 | AY.3 | 0.00001 |
N | 76 | T76I | aCc | aTc | 1 | 1 | AY.34 | 0.000097 |
N | 76 | T76N | aCc | aAc | 1 | 1 | AY.4 | 0.000002 |
N | 76 | T76P | Acc | Ccc | 1 | 1 | AY.44 | 0.000006 |
N | 76 | T76N | aCc | aAc | 1 | 1 | AY.44 | 0.000006 |
N | 76 | T76A | Acc | Gcc | 1 | 1 | AY.46.4 | 0.000165 |
N | 76 | T76A | Acc | Gcc | 1 | 1 | AY.47 | 0.000031 |
N | 76 | T76I | aCc | aTc | 1 | 1 | AY.53 | 0.000288 |
N | 76 | T76I | aCc | aTc | 1 | 1 | AY.67 | 0.000464 |
N | 76 | T76T | acC | acA | 1 | 1 | AY.69 | 0.000187 |
N | 76 | T76T | acC | acT | 1 | 1 | AY.9 | 0.000068 |
N | 76 | T76del | ACC | --- | 1 | 1 | AY.9.2 | 0.000037 |
N | 76 | T76T | acC | acT | 1 | 1 | AY.9.2 | 0.000037 |
N | 76 | T76del | ACC | --- | 1 | 1 | AZ.2 | 0.000821 |
N | 76 | T76S | aCc | aGc | 1 | 1 | B.1 | 0.000009 |
N | 76 | T76del | ACC | --- | 1 | 1 | B.1 | 0.000009 |
N | 76 | T76L | ACC | CTT | 1 | 1 | B.1.1 | 0.000018 |
N | 76 | T76A | Acc | Gcc | 1 | 1 | B.1.1 | 0.000018 |
N | 76 | T76del | ACC | --- | 1 | 1 | B.1.1 | 0.000018 |
N | 76 | T76I | aCc | aTc | 1 | 1 | B.1.1.139 | 0.022727 |
N | 76 | T76del | ACC | --- | 1 | 1 | B.1.1.139 | 0.022727 |
N | 76 | T76del | ACC | --- | 1 | 1 | B.1.1.216 | 0.00089 |
N | 76 | T76N | aCc | aAc | 1 | 1 | B.1.1.218 | 0.007692 |
N | 76 | T76I | aCc | aTc | 1 | 1 | B.1.1.220 | 0.001859 |
N | 76 | T76I | aCc | aTc | 1 | 1 | B.1.1.28 | 0.000311 |
N | 76 | T76I | aCc | aTc | 1 | 1 | B.1.1.291 | 0.000742 |
N | 76 | T76S | Acc | Tcc | 1 | 1 | B.1.1.356 | 0.008547 |
N | 76 | T76A | Acc | Gcc | 1 | 1 | B.1.1.37 | 0.000193 |
N | 76 | T76I | aCc | aTc | 1 | 1 | B.1.1.372 | 0.000689 |
N | 76 | T76S | aCc | aGc | 1 | 1 | B.1.1.39 | 0.00051 |
N | 76 | T76I | aCc | aTc | 1 | 1 | B.1.1.406 | 0.006494 |
N | 76 | T76T | acC | acT | 1 | 1 | B.1.1.519 | 0.00004 |
N | 76 | T76del | ACC | --- | 1 | 1 | B.1.1.63 | 0.000386 |
N | 76 | T76del | ACC | --- | 1 | 1 | B.1.1.7 | 0.000001 |
N | 76 | T76A | Acc | Gcc | 1 | 1 | B.1.1.7 | 0.000001 |
N | 76 | T76L | ACC | CTT | 1 | 1 | B.1.1.7 | 0.000001 |
N | 76 | T76I | aCc | aTc | 1 | 1 | B.1.139 | 0.000733 |
N | 76 | T76I | aCc | aTc | 1 | 1 | B.1.146 | 0.004237 |
N | 76 | T76I | aCc | aTc | 1 | 1 | B.1.160 | 0.000031 |
N | 76 | T76T | acC | acT | 1 | 1 | B.1.160 | 0.000031 |
N | 76 | T76I | aCc | aTc | 1 | 1 | B.1.160.16 | 0.000929 |
N | 76 | T76T | acC | acT | 1 | 1 | B.1.177 | 0.000013 |
N | 76 | T76I | aCc | aTc | 1 | 1 | B.1.177 | 0.000013 |
N | 76 | T76A | Acc | Gcc | 1 | 1 | B.1.177.21 | 0.000076 |
N | 76 | T76I | aCc | aTc | 1 | 1 | B.1.177.31 | 0.011494 |
N | 76 | T76del | ACC | --- | 1 | 1 | B.1.177.63 | 0.002703 |
N | 76 | T76I | aCc | aTc | 1 | 1 | B.1.177.7 | 0.000165 |
N | 76 | T76del2 | aCC | a-- | 1 | 1 | B.1.2 | 0.000009 |
N | 76 | T76T | acC | acT | 1 | 1 | B.1.240 | 0.000216 |
N | 76 | T76I | aCc | aTc | 1 | 1 | B.1.240 | 0.000216 |
N | 76 | T76A | Acc | Gcc | 1 | 1 | B.1.243 | 0.00007 |
N | 76 | T76T | acC | acT | 1 | 1 | B.1.311 | 0.000275 |
N | 76 | T76S | Acc | Tcc | 1 | 1 | B.1.325 | 0.006897 |
N | 76 | T76I | aCc | aTc | 1 | 1 | B.1.329 | 0.000608 |
N | 76 | T76T | acC | acA | 1 | 1 | B.1.351.5 | 0.0006 |
N | 76 | T76I | aCc | aTc | 1 | 1 | B.1.36.26 | 0.002857 |
N | 76 | T76I | aCc | aTc | 1 | 1 | B.1.409 | 0.000781 |
N | 76 | T76del | ACC | --- | 1 | 1 | B.1.415 | 0.014286 |
N | 76 | T76del | ACC | --- | 1 | 1 | B.1.427 | 0.00005 |
N | 76 | T76S | Acc | Tcc | 1 | 1 | B.1.438.1 | 0.000107 |
N | 76 | T76del | ACC | --- | 1 | 1 | B.1.439 | 0.005917 |
N | 76 | T76T | acC | acT | 1 | 1 | B.1.453 | 0.003236 |
N | 76 | T76T | acC | acA | 1 | 1 | B.1.497 | 0.000315 |
N | 76 | T76I | aCc | aTc | 1 | 1 | B.1.526 | 0.000024 |
N | 76 | T76A | Acc | Gcc | 1 | 1 | B.1.526 | 0.000024 |
N | 76 | T76I | aCc | aTc | 1 | 1 | B.1.582 | 0.000491 |
N | 76 | T76I | aCc | aTc | 1 | 1 | B.1.595 | 0.000261 |
N | 76 | T76N | aCc | aAc | 1 | 1 | B.1.617.2 | 0.000004 |
N | 76 | T76L | ACc | CTc | 1 | 1 | B.1.617.2 | 0.000004 |
N | 76 | T76I | aCc | aTc | 1 | 1 | B.1.617.2 | 0.000004 |
N | 76 | T76F | ACc | TTc | 1 | 1 | B.1.617.3 | 0.002985 |
N | 76 | T76I | aCc | aTc | 1 | 1 | B.1.621 | 0.000089 |
N | 76 | T76S | AcC | TcG | 1 | 1 | B.1.621 | 0.000089 |
N | 76 | T76I | aCc | aTc | 1 | 1 | B.39 | 0.002331 |
N | 76 | T76I | aCc | aTc | 1 | 1 | C.37 | 0.000116 |
N | 76 | T76T | acC | acT | 1 | 1 | C.37 | 0.000116 |
N | 76 | T76T | acC | acT | 1 | 1 | D.2 | 0.000075 |
N | 76 | T76I | aCc | aTc | 1 | 1 | D.2 | 0.000075 |
N | 76 | T76del | ACC | --- | 1 | 1 | P.1 | 0.000016 |
N | 76 | T76T | acC | acT | 1 | 1 | P.1 | 0.000016 |
N | 76 | T76I | aCc | aTc | 1 | 1 | P.1.1 | 0.000318 |
N | 76 | T76I | aCc | aTc | 1 | 1 | P.1.14 | 0.000048 |
N | 76 | T76I | aCc | aTc | 1 | 1 | P.1.15 | 0.000232 |
N | 76 | T76del | ACC | --- | 1 | 1 | Q.2 | 0.000613 |
N | 76 | T76I | aCc | aTc | 1 | 1 | Q.8 | 0.000165 |
N | 76 | T76I | aCc | aTc | 1 | 1 | R.1 | 0.00009 |
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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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