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/nsp3 | 1607 | T1607T | T2425T | syn | acT | acC | 13368 | 13362 | 0.999551 | 7538-7540 |
ORF1ab/nsp3 | 1607 | T1607T | T2425T | syn | acT | acG | 13368 | 3 | 0.000224417 | 7538-7540 |
ORF1ab/nsp3 | 1607 | T1607T | T2425T | syn | acT | acA | 13368 | 3 | 0.000224417 | 7538-7540 |
ORF1ab/nsp3 | 1607 | T1607del | T2425del | del | ACT | --- | 86 | 86 | 1 | 7538-7540 |
ORF1ab/nsp3 | 1607 | T1607I | T2425I | nonsyn | aCt | aTt | 20 | 17 | 0.85 | 7538-7540 |
ORF1ab/nsp3 | 1607 | T1607I | T2425I | nonsyn | aCT | aTC | 20 | 3 | 0.15 | 7538-7540 |
ORF1ab/nsp3 | 1607 | T1607N | T2425N | nonsyn | aCt | aAt | 4 | 4 | 1 | 7538-7540 |
ORF1ab/nsp3 | 1607 | T1607del1 | T2425del1 | del | acT | ac- | 2 | 2 | 1 | 7538-7540 |
ORF1ab/nsp3 | 1607 | T1607F | T2425F | nonsyn | ACt | TTt | 1 | 1 | 1 | 7538-7540 |
ORF1ab/nsp3 | 1607 | T1607A | T2425A | nonsyn | Act | Gct | 1 | 1 | 1 | 7538-7540 |
ORF1ab/nsp3 | 1607 | T1607P | T2425P | nonsyn | Act | Cct | 1 | 1 | 1 | 7538-7540 |
ORF1ab/nsp3 | 1607 | T1607S | T2425S | nonsyn | Act | Tct | 1 | 1 | 1 | 7538-7540 |
ORF1ab/nsp3 | 1607 | T1607D | T2425D | nonsyn | ACt | GAt | 1 | 1 | 1 | 7538-7540 |
ORF1ab/nsp3 | 1607 | T1607del2 | T2425del2 | del | aCT | a-- | 1 | 1 | 1 | 7538-7540 |
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/nsp3 | 1607 | T1607T | acT | acC | 13362 | 13368 | All | 0.002556 |
ORF1ab/nsp3 | 1607 | T1607T | acT | acA | 3 | 13368 | All | 0.000001 |
ORF1ab/nsp3 | 1607 | T1607T | acT | acG | 3 | 13368 | All | 0.000001 |
ORF1ab/nsp3 | 1607 | T1607T | acT | acC | 13168 | 13168 | D.2 | 0.988143 |
ORF1ab/nsp3 | 1607 | T1607del | ACT | --- | 86 | 86 | All | 0.000016 |
ORF1ab/nsp3 | 1607 | T1607T | acT | acC | 51 | 51 | B.1 | 0.000467 |
ORF1ab/nsp3 | 1607 | T1607T | acT | acC | 41 | 41 | B.1.1 | 0.000744 |
ORF1ab/nsp3 | 1607 | T1607del | ACT | --- | 36 | 36 | B.1.1.7 | 0.000032 |
ORF1ab/nsp3 | 1607 | T1607T | acT | acC | 26 | 26 | B.1.1.25 | 0.014781 |
ORF1ab/nsp3 | 1607 | T1607I | aCt | aTt | 17 | 20 | All | 0.000003 |
ORF1ab/nsp3 | 1607 | T1607I | aCT | aTC | 3 | 20 | All | 0.000001 |
ORF1ab/nsp3 | 1607 | T1607T | acT | acC | 10 | 10 | B.1.1.7 | 0.000009 |
ORF1ab/nsp3 | 1607 | T1607T | acT | acC | 8 | 8 | AY.4 | 0.000012 |
ORF1ab/nsp3 | 1607 | T1607del | ACT | --- | 8 | 8 | B.1.177 | 0.000105 |
ORF1ab/nsp3 | 1607 | T1607T | acT | acC | 7 | 7 | AY.44 | 0.000043 |
ORF1ab/nsp3 | 1607 | T1607T | acT | acC | 6 | 6 | AY.26 | 0.00017 |
ORF1ab/nsp3 | 1607 | T1607del | ACT | --- | 5 | 5 | AY.4 | 0.000008 |
ORF1ab/nsp3 | 1607 | T1607T | acT | acC | 5 | 5 | B.1.177.7 | 0.000824 |
ORF1ab/nsp3 | 1607 | T1607T | acT | acC | 5 | 5 | B.1.2 | 0.000044 |
ORF1ab/nsp3 | 1607 | T1607N | aCt | aAt | 4 | 4 | All | 0.000001 |
ORF1ab/nsp3 | 1607 | T1607T | acT | acC | 4 | 4 | B.1.1.161 | 0.014134 |
ORF1ab/nsp3 | 1607 | T1607T | acT | acC | 3 | 3 | AY.114 | 0.000693 |
ORF1ab/nsp3 | 1607 | T1607T | acT | acC | 3 | 3 | AY.43 | 0.000013 |
ORF1ab/nsp3 | 1607 | T1607del | ACT | --- | 3 | 3 | B.1 | 0.000027 |
ORF1ab/nsp3 | 1607 | T1607del | ACT | --- | 3 | 3 | B.1.1 | 0.000054 |
ORF1ab/nsp3 | 1607 | T1607I | aCt | aTt | 2 | 2 | 0.111111 | |
ORF1ab/nsp3 | 1607 | T1607N | aCt | aAt | 2 | 2 | 0.111111 | |
ORF1ab/nsp3 | 1607 | T1607T | acT | acA | 1 | 2 | 0.055556 | |
ORF1ab/nsp3 | 1607 | T1607T | acT | acG | 1 | 2 | 0.055556 | |
ORF1ab/nsp3 | 1607 | T1607del1 | acT | ac- | 2 | 2 | All | 0 |
ORF1ab/nsp3 | 1607 | T1607del | ACT | --- | 2 | 2 | AY.25 | 0.000012 |
ORF1ab/nsp3 | 1607 | T1607T | acT | acC | 2 | 2 | AY.25 | 0.000012 |
ORF1ab/nsp3 | 1607 | T1607T | acT | acC | 2 | 2 | AY.3 | 0.00002 |
ORF1ab/nsp3 | 1607 | T1607del | ACT | --- | 2 | 2 | AY.43 | 0.000009 |
ORF1ab/nsp3 | 1607 | T1607T | acT | acC | 2 | 2 | AY.92 | 0.000575 |
ORF1ab/nsp3 | 1607 | T1607I | aCt | aTt | 2 | 2 | B.1.1.7 | 0.000002 |
ORF1ab/nsp3 | 1607 | T1607del | ACT | --- | 2 | 2 | B.1.177.16 | 0.001329 |
ORF1ab/nsp3 | 1607 | T1607del | ACT | --- | 2 | 2 | B.1.177.54 | 0.001213 |
ORF1ab/nsp3 | 1607 | T1607del | ACT | --- | 1 | 1 | A | 0.000387 |
ORF1ab/nsp3 | 1607 | T1607A | Act | Gct | 1 | 1 | All | 0 |
ORF1ab/nsp3 | 1607 | T1607P | Act | Cct | 1 | 1 | All | 0 |
ORF1ab/nsp3 | 1607 | T1607del2 | aCT | a-- | 1 | 1 | All | 0 |
ORF1ab/nsp3 | 1607 | T1607F | ACt | TTt | 1 | 1 | All | 0 |
ORF1ab/nsp3 | 1607 | T1607D | ACt | GAt | 1 | 1 | All | 0 |
ORF1ab/nsp3 | 1607 | T1607S | Act | Tct | 1 | 1 | All | 0 |
ORF1ab/nsp3 | 1607 | T1607T | acT | acC | 1 | 1 | AS.1 | 0.009524 |
ORF1ab/nsp3 | 1607 | T1607N | aCt | aAt | 1 | 1 | AY.100 | 0.000046 |
ORF1ab/nsp3 | 1607 | T1607T | acT | acC | 1 | 1 | AY.100 | 0.000046 |
ORF1ab/nsp3 | 1607 | T1607T | acT | acC | 1 | 1 | AY.103 | 0.000006 |
ORF1ab/nsp3 | 1607 | T1607T | acT | acC | 1 | 1 | AY.119 | 0.000035 |
ORF1ab/nsp3 | 1607 | T1607T | acT | acC | 1 | 1 | AY.12 | 0.000316 |
ORF1ab/nsp3 | 1607 | T1607D | ACt | GAt | 1 | 1 | AY.120 | 0.000037 |
ORF1ab/nsp3 | 1607 | T1607del | ACT | --- | 1 | 1 | AY.24 | 0.000431 |
ORF1ab/nsp3 | 1607 | T1607I | aCt | aTt | 1 | 1 | AY.25 | 0.000006 |
ORF1ab/nsp3 | 1607 | T1607I | aCt | aTt | 1 | 1 | AY.3 | 0.00001 |
ORF1ab/nsp3 | 1607 | T1607T | acT | acC | 1 | 1 | AY.39 | 0.000025 |
ORF1ab/nsp3 | 1607 | T1607del1 | acT | ac- | 1 | 1 | AY.39.1 | 0.00004 |
ORF1ab/nsp3 | 1607 | T1607I | aCt | aTt | 1 | 1 | AY.4 | 0.000002 |
ORF1ab/nsp3 | 1607 | T1607S | Act | Tct | 1 | 1 | AY.4 | 0.000002 |
ORF1ab/nsp3 | 1607 | T1607del | ACT | --- | 1 | 1 | AY.4.5 | 0.000107 |
ORF1ab/nsp3 | 1607 | T1607I | aCt | aTt | 1 | 1 | AY.43 | 0.000004 |
ORF1ab/nsp3 | 1607 | T1607T | acT | acC | 1 | 1 | AY.46 | 0.000104 |
ORF1ab/nsp3 | 1607 | T1607del | ACT | --- | 1 | 1 | AY.46.2 | 0.000635 |
ORF1ab/nsp3 | 1607 | T1607I | aCT | aTC | 1 | 1 | AY.46.2 | 0.000635 |
ORF1ab/nsp3 | 1607 | T1607T | acT | acC | 1 | 1 | AY.47 | 0.000031 |
ORF1ab/nsp3 | 1607 | T1607T | acT | acC | 1 | 1 | AY.5 | 0.000021 |
ORF1ab/nsp3 | 1607 | T1607del | ACT | --- | 1 | 1 | AY.6 | 0.000041 |
ORF1ab/nsp3 | 1607 | T1607del | ACT | --- | 1 | 1 | AY.66 | 0.00107 |
ORF1ab/nsp3 | 1607 | T1607T | acT | acG | 1 | 1 | AY.67 | 0.000464 |
ORF1ab/nsp3 | 1607 | T1607T | acT | acC | 1 | 1 | AY.75 | 0.000056 |
ORF1ab/nsp3 | 1607 | T1607T | acT | acG | 1 | 1 | AY.9 | 0.000068 |
ORF1ab/nsp3 | 1607 | T1607I | aCt | aTt | 1 | 1 | AY.9.2 | 0.000037 |
ORF1ab/nsp3 | 1607 | T1607T | acT | acC | 1 | 1 | AZ.2 | 0.000821 |
ORF1ab/nsp3 | 1607 | T1607A | Act | Gct | 1 | 1 | B.1 | 0.000009 |
ORF1ab/nsp3 | 1607 | T1607N | aCt | aAt | 1 | 1 | B.1 | 0.000009 |
ORF1ab/nsp3 | 1607 | T1607I | aCt | aTt | 1 | 1 | B.1 | 0.000009 |
ORF1ab/nsp3 | 1607 | T1607del | ACT | --- | 1 | 1 | B.1.1.159 | 0.004673 |
ORF1ab/nsp3 | 1607 | T1607T | acT | acC | 1 | 1 | B.1.1.214 | 0.000055 |
ORF1ab/nsp3 | 1607 | T1607del | ACT | --- | 1 | 1 | B.1.1.232 | 0.001815 |
ORF1ab/nsp3 | 1607 | T1607del | ACT | --- | 1 | 1 | B.1.1.236 | 0.006897 |
ORF1ab/nsp3 | 1607 | T1607del | ACT | --- | 1 | 1 | B.1.1.306 | 0.000438 |
ORF1ab/nsp3 | 1607 | T1607del | ACT | --- | 1 | 1 | B.1.1.311 | 0.000358 |
ORF1ab/nsp3 | 1607 | T1607del | ACT | --- | 1 | 1 | B.1.1.315 | 0.008475 |
ORF1ab/nsp3 | 1607 | T1607del | ACT | --- | 1 | 1 | B.1.1.46 | 0.004367 |
ORF1ab/nsp3 | 1607 | T1607P | Act | Cct | 1 | 1 | B.1.1.7 | 0.000001 |
ORF1ab/nsp3 | 1607 | T1607del2 | aCT | a-- | 1 | 1 | B.1.1.7 | 0.000001 |
ORF1ab/nsp3 | 1607 | T1607del | ACT | --- | 1 | 1 | B.1.161 | 0.017241 |
ORF1ab/nsp3 | 1607 | T1607I | aCt | aTt | 1 | 1 | B.1.177 | 0.000013 |
ORF1ab/nsp3 | 1607 | T1607T | acT | acC | 1 | 1 | B.1.177 | 0.000013 |
ORF1ab/nsp3 | 1607 | T1607del | ACT | --- | 1 | 1 | B.1.177.19 | 0.001431 |
ORF1ab/nsp3 | 1607 | T1607del | ACT | --- | 1 | 1 | B.1.177.21 | 0.000076 |
ORF1ab/nsp3 | 1607 | T1607del | ACT | --- | 1 | 1 | B.1.177.51 | 0.004566 |
ORF1ab/nsp3 | 1607 | T1607del | ACT | --- | 1 | 1 | B.1.177.57 | 0.000281 |
ORF1ab/nsp3 | 1607 | T1607del | ACT | --- | 1 | 1 | B.1.177.81 | 0.000189 |
ORF1ab/nsp3 | 1607 | T1607T | acT | acA | 1 | 1 | B.1.177.81 | 0.000189 |
ORF1ab/nsp3 | 1607 | T1607del1 | acT | ac- | 1 | 1 | B.1.2 | 0.000009 |
ORF1ab/nsp3 | 1607 | T1607I | aCT | aTC | 1 | 1 | B.1.2 | 0.000009 |
ORF1ab/nsp3 | 1607 | T1607I | aCt | aTt | 1 | 1 | B.1.206 | 0.000816 |
ORF1ab/nsp3 | 1607 | T1607T | acT | acC | 1 | 1 | B.1.210 | 0.002132 |
ORF1ab/nsp3 | 1607 | T1607del | ACT | --- | 1 | 1 | B.1.258 | 0.000067 |
ORF1ab/nsp3 | 1607 | T1607T | acT | acC | 1 | 1 | B.1.258 | 0.000067 |
ORF1ab/nsp3 | 1607 | T1607I | aCt | aTt | 1 | 1 | B.1.335 | 0.010309 |
ORF1ab/nsp3 | 1607 | T1607F | ACt | TTt | 1 | 1 | B.1.36.16 | 0.001425 |
ORF1ab/nsp3 | 1607 | T1607I | aCt | aTt | 1 | 1 | B.1.404 | 0.001302 |
ORF1ab/nsp3 | 1607 | T1607I | aCt | aTt | 1 | 1 | B.1.416 | 0.001269 |
ORF1ab/nsp3 | 1607 | T1607I | aCt | aTt | 1 | 1 | B.1.429 | 0.000024 |
ORF1ab/nsp3 | 1607 | T1607I | aCt | aTt | 1 | 1 | B.1.44 | 0.008333 |
ORF1ab/nsp3 | 1607 | T1607T | acT | acC | 1 | 1 | B.1.526 | 0.000024 |
ORF1ab/nsp3 | 1607 | T1607T | acT | acA | 1 | 1 | B.1.561 | 0.000397 |
ORF1ab/nsp3 | 1607 | T1607T | acT | acC | 1 | 1 | B.1.596 | 0.000087 |
ORF1ab/nsp3 | 1607 | T1607I | aCT | aTC | 1 | 1 | B.1.617.2 | 0.000004 |
ORF1ab/nsp3 | 1607 | T1607del | ACT | --- | 1 | 1 | B.1.621 | 0.000089 |
ORF1ab/nsp3 | 1607 | T1607T | acT | acC | 1 | 1 | B.1.628 | 0.000352 |
ORF1ab/nsp3 | 1607 | T1607T | acT | acC | 1 | 1 | P.2 | 0.000187 |
ORF1ab/nsp3 | 1607 | T1607del | ACT | --- | 1 | 1 | Q.1 | 0.000126 |
ORF1ab/nsp3 | 1607 | T1607del | ACT | --- | 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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