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 | 720 | I720V | nonsyn | Att | Gtt | 1138 | 1138 | 1 | 23720-23722 | |
S | 720 | I720del | del | ATT | --- | 40 | 40 | 1 | 23720-23722 | |
S | 720 | I720I | syn | atT | atC | 38 | 28 | 0.736842 | 23720-23722 | |
S | 720 | I720I | syn | atT | atA | 38 | 10 | 0.263158 | 23720-23722 | |
S | 720 | I720L | nonsyn | Att | Ctt | 15 | 15 | 1 | 23720-23722 | |
S | 720 | I720T | nonsyn | aTt | aCt | 11 | 10 | 0.909091 | 23720-23722 | |
S | 720 | I720T | nonsyn | aTT | aCA | 11 | 1 | 0.0909091 | 23720-23722 | |
S | 720 | I720del1 | del | aTt | a-t | 9 | 4 | 0.444444 | 23720-23722 | |
S | 720 | I720del1 | del | Att | -tt | 9 | 3 | 0.333333 | 23720-23722 | |
S | 720 | I720del1 | del | AtT | -tN | 9 | 1 | 0.111111 | 23720-23722 | |
S | 720 | I720del1 | del | atT | at- | 9 | 1 | 0.111111 | 23720-23722 | |
S | 720 | I720N | nonsyn | aTt | aAt | 4 | 4 | 1 | 23720-23722 | |
S | 720 | I720M | nonsyn | atT | atG | 3 | 3 | 1 | 23720-23722 | |
S | 720 | I720S | nonsyn | aTt | aGt | 2 | 2 | 1 | 23720-23722 | |
S | 720 | I720C | nonsyn | ATt | TGt | 2 | 2 | 1 | 23720-23722 | |
S | 720 | I720F | nonsyn | AtT | TtC | 2 | 1 | 0.5 | 23720-23722 | |
S | 720 | I720F | nonsyn | Att | Ttt | 2 | 1 | 0.5 | 23720-23722 | |
S | 720 | I720A | nonsyn | ATt | GCt | 1 | 1 | 1 | 23720-23722 | |
S | 720 | I720del2 | del | aTT | a-- | 1 | 1 | 1 | 23720-23722 |
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 | 720 | I720V | Att | Gtt | 1138 | 1138 | All | 0.000218 |
S | 720 | I720V | Att | Gtt | 798 | 798 | B.1.1.214 | 0.044255 |
S | 720 | I720V | Att | Gtt | 262 | 262 | P.4 | 0.996198 |
S | 720 | I720del | ATT | --- | 40 | 40 | All | 0.000008 |
S | 720 | I720I | atT | atC | 28 | 38 | All | 0.000005 |
S | 720 | I720I | atT | atA | 10 | 38 | All | 0.000002 |
S | 720 | I720V | Att | Gtt | 23 | 23 | AY.4 | 0.000036 |
S | 720 | I720L | Att | Ctt | 15 | 15 | All | 0.000003 |
S | 720 | I720L | Att | Ctt | 13 | 13 | AY.44 | 0.000079 |
S | 720 | I720T | aTt | aCt | 10 | 11 | All | 0.000002 |
S | 720 | I720T | aTT | aCA | 1 | 11 | All | 0 |
S | 720 | I720V | Att | Gtt | 10 | 10 | B.1.1.7 | 0.000009 |
S | 720 | I720I | atT | atC | 9 | 10 | B.1.1.7 | 0.000008 |
S | 720 | I720I | atT | atA | 1 | 10 | B.1.1.7 | 0.000001 |
S | 720 | I720del1 | aTt | a-t | 4 | 9 | All | 0.000001 |
S | 720 | I720del1 | Att | -tt | 3 | 9 | All | 0.000001 |
S | 720 | I720del1 | atT | at- | 1 | 9 | All | 0 |
S | 720 | I720del1 | AtT | -tN | 1 | 9 | All | 0 |
S | 720 | I720V | Att | Gtt | 8 | 8 | AY.43 | 0.000035 |
S | 720 | I720V | Att | Gtt | 8 | 8 | B.1.2 | 0.00007 |
S | 720 | I720I | atT | atC | 6 | 6 | AY.44 | 0.000037 |
S | 720 | I720I | atT | atA | 5 | 5 | AY.3 | 0.00005 |
S | 720 | I720del | ATT | --- | 5 | 5 | AY.43 | 0.000022 |
S | 720 | I720del | ATT | --- | 5 | 5 | B.1 | 0.000046 |
S | 720 | I720V | Att | Gtt | 5 | 5 | B.1.1.33 | 0.002104 |
S | 720 | I720N | aTt | aAt | 4 | 4 | All | 0.000001 |
S | 720 | I720V | Att | Gtt | 4 | 4 | AY.120 | 0.000149 |
S | 720 | I720V | Att | Gtt | 4 | 4 | AY.2 | 0.001425 |
S | 720 | I720del1 | aTt | a-t | 2 | 4 | AY.43 | 0.000009 |
S | 720 | I720del1 | Att | -tt | 1 | 4 | AY.43 | 0.000004 |
S | 720 | I720del1 | AtT | -tN | 1 | 4 | AY.43 | 0.000004 |
S | 720 | I720del | ATT | --- | 4 | 4 | P.1 | 0.000063 |
S | 720 | I720M | atT | atG | 3 | 3 | All | 0.000001 |
S | 720 | I720V | Att | Gtt | 3 | 3 | B.1 | 0.000027 |
S | 720 | I720del | ATT | --- | 3 | 3 | B.1.617.2 | 0.000011 |
S | 720 | I720M | atT | atG | 2 | 2 | 0.111111 | |
S | 720 | I720C | ATt | TGt | 2 | 2 | 0.111111 | |
S | 720 | I720S | aTt | aGt | 2 | 2 | All | 0 |
S | 720 | I720C | ATt | TGt | 2 | 2 | All | 0 |
S | 720 | I720F | AtT | TtC | 1 | 2 | All | 0 |
S | 720 | I720F | Att | Ttt | 1 | 2 | All | 0 |
S | 720 | I720del1 | atT | at- | 1 | 2 | AY.117 | 0.000085 |
S | 720 | I720del1 | aTt | a-t | 1 | 2 | AY.117 | 0.000085 |
S | 720 | I720T | aTt | aCt | 2 | 2 | AY.25 | 0.000012 |
S | 720 | I720del | ATT | --- | 2 | 2 | AY.25 | 0.000012 |
S | 720 | I720I | atT | atC | 1 | 2 | AY.4 | 0.000002 |
S | 720 | I720I | atT | atA | 1 | 2 | AY.4 | 0.000002 |
S | 720 | I720N | aTt | aAt | 2 | 2 | AY.43 | 0.000009 |
S | 720 | I720I | atT | atC | 2 | 2 | AY.47 | 0.000062 |
S | 720 | I720I | atT | atC | 1 | 2 | B.1 | 0.000009 |
S | 720 | I720I | atT | atA | 1 | 2 | B.1 | 0.000009 |
S | 720 | I720V | Att | Gtt | 2 | 2 | B.1.1 | 0.000036 |
S | 720 | I720V | Att | Gtt | 2 | 2 | B.1.1.222 | 0.000408 |
S | 720 | I720T | aTt | aCt | 2 | 2 | B.1.1.7 | 0.000002 |
S | 720 | I720V | Att | Gtt | 2 | 2 | B.1.177 | 0.000026 |
S | 720 | I720I | atT | atC | 2 | 2 | B.1.177 | 0.000026 |
S | 720 | I720del | ATT | --- | 2 | 2 | B.1.621 | 0.000177 |
S | 720 | I720T | aTt | aCt | 2 | 2 | D.2 | 0.00015 |
S | 720 | I720V | Att | Gtt | 2 | 2 | M.1 | 0.046512 |
S | 720 | I720del | ATT | --- | 2 | 2 | P.1.15 | 0.000465 |
S | 720 | I720A | ATt | GCt | 1 | 1 | All | 0 |
S | 720 | I720del2 | aTT | a-- | 1 | 1 | All | 0 |
S | 720 | I720del | ATT | --- | 1 | 1 | AY.100 | 0.000046 |
S | 720 | I720del | ATT | --- | 1 | 1 | AY.103 | 0.000006 |
S | 720 | I720del2 | aTT | a-- | 1 | 1 | AY.103 | 0.000006 |
S | 720 | I720I | atT | atC | 1 | 1 | AY.103 | 0.000006 |
S | 720 | I720V | Att | Gtt | 1 | 1 | AY.108 | 0.001103 |
S | 720 | I720I | atT | atA | 1 | 1 | AY.119 | 0.000035 |
S | 720 | I720del1 | Att | -tt | 1 | 1 | AY.25 | 0.000006 |
S | 720 | I720del | ATT | --- | 1 | 1 | AY.3 | 0.00001 |
S | 720 | I720T | aTt | aCt | 1 | 1 | AY.43 | 0.000004 |
S | 720 | I720L | Att | Ctt | 1 | 1 | AY.43 | 0.000004 |
S | 720 | I720del | ATT | --- | 1 | 1 | AY.44 | 0.000006 |
S | 720 | I720T | aTT | aCA | 1 | 1 | AY.44 | 0.000006 |
S | 720 | I720T | aTt | aCt | 1 | 1 | AY.53 | 0.000288 |
S | 720 | I720del | ATT | --- | 1 | 1 | AY.67 | 0.000464 |
S | 720 | I720I | atT | atC | 1 | 1 | AY.69 | 0.000187 |
S | 720 | I720del | ATT | --- | 1 | 1 | AY.84 | 0.000437 |
S | 720 | I720del | ATT | --- | 1 | 1 | AY.9.2 | 0.000037 |
S | 720 | I720del | ATT | --- | 1 | 1 | AY.95 | 0.000761 |
S | 720 | I720A | ATt | GCt | 1 | 1 | AY.99 | 0.001049 |
S | 720 | I720I | atT | atC | 1 | 1 | AY.99.2 | 0.000092 |
S | 720 | I720del1 | aTt | a-t | 1 | 1 | B.1 | 0.000009 |
S | 720 | I720T | aTt | aCt | 1 | 1 | B.1 | 0.000009 |
S | 720 | I720F | AtT | TtC | 1 | 1 | B.1.1 | 0.000018 |
S | 720 | I720V | Att | Gtt | 1 | 1 | B.1.1.101 | 0.01 |
S | 720 | I720I | atT | atC | 1 | 1 | B.1.1.217 | 0.003636 |
S | 720 | I720del | ATT | --- | 1 | 1 | B.1.1.372 | 0.000689 |
S | 720 | I720del | ATT | --- | 1 | 1 | B.1.1.409 | 0.002833 |
S | 720 | I720I | atT | atA | 1 | 1 | B.1.1.519 | 0.00004 |
S | 720 | I720del | ATT | --- | 1 | 1 | B.1.1.7 | 0.000001 |
S | 720 | I720F | Att | Ttt | 1 | 1 | B.1.1.7 | 0.000001 |
S | 720 | I720I | atT | atC | 1 | 1 | B.1.160 | 0.000031 |
S | 720 | I720I | atT | atC | 1 | 1 | B.1.177.54 | 0.000606 |
S | 720 | I720M | atT | atG | 1 | 1 | B.1.177.73 | 0.000566 |
S | 720 | I720T | aTt | aCt | 1 | 1 | B.1.177.86 | 0.000183 |
S | 720 | I720S | aTt | aGt | 1 | 1 | B.1.2 | 0.000009 |
S | 720 | I720N | aTt | aAt | 1 | 1 | B.1.2 | 0.000009 |
S | 720 | I720del1 | Att | -tt | 1 | 1 | B.1.2 | 0.000009 |
S | 720 | I720del | ATT | --- | 1 | 1 | B.1.2 | 0.000009 |
S | 720 | I720V | Att | Gtt | 1 | 1 | B.1.222 | 0.001692 |
S | 720 | I720V | Att | Gtt | 1 | 1 | B.1.36.29 | 0.000517 |
S | 720 | I720N | aTt | aAt | 1 | 1 | B.1.377 | 0.004566 |
S | 720 | I720L | Att | Ctt | 1 | 1 | B.1.438.1 | 0.000107 |
S | 720 | I720I | atT | atC | 1 | 1 | B.1.526 | 0.000024 |
S | 720 | I720S | aTt | aGt | 1 | 1 | B.1.617.2 | 0.000004 |
S | 720 | I720del | ATT | --- | 1 | 1 | B.1.620 | 0.000946 |
S | 720 | I720del | ATT | --- | 1 | 1 | B.1.627 | 0.00202 |
S | 720 | I720del | ATT | --- | 1 | 1 | B.1.638 | 0.052632 |
S | 720 | I720V | Att | Gtt | 1 | 1 | B.1.78 | 0.008547 |
S | 720 | I720del | ATT | --- | 1 | 1 | C.37 | 0.000116 |
S | 720 | I720del | ATT | --- | 1 | 1 | P.1.13 | 0.000898 |
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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