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/nsp12 | 788 | Y788Y | Y5180Y | syn | taT | taC | 575 | 575 | 1 | 15802-15804 |
ORF1ab/nsp12 | 788 | Y788del | Y5180del | del | TAT | --- | 9 | 9 | 1 | 15802-15804 |
ORF1ab/nsp12 | 788 | Y788C | Y5180C | nonsyn | tAT | tGC | 7 | 6 | 0.857143 | 15802-15804 |
ORF1ab/nsp12 | 788 | Y788C | Y5180C | nonsyn | tAt | tGt | 7 | 1 | 0.142857 | 15802-15804 |
ORF1ab/nsp12 | 788 | Y788del1 | Y5180del1 | del | taT | ta- | 5 | 4 | 0.8 | 15802-15804 |
ORF1ab/nsp12 | 788 | Y788del1 | Y5180del1 | del | tAt | t-t | 5 | 1 | 0.2 | 15802-15804 |
ORF1ab/nsp12 | 788 | Y788X | Y5180X | nonsyn | taT | taA | 4 | 4 | 1 | 15802-15804 |
ORF1ab/nsp12 | 788 | Y788H | Y5180H | nonsyn | Tat | Cat | 4 | 4 | 1 | 15802-15804 |
ORF1ab/nsp12 | 788 | Y788F | Y5180F | nonsyn | tAt | tTt | 4 | 4 | 1 | 15802-15804 |
ORF1ab/nsp12 | 788 | Y788S | Y5180S | nonsyn | tAt | tCt | 3 | 2 | 0.666667 | 15802-15804 |
ORF1ab/nsp12 | 788 | Y788S | Y5180S | nonsyn | TAt | AGt | 3 | 1 | 0.333333 | 15802-15804 |
ORF1ab/nsp12 | 788 | Y788L | Y5180L | nonsyn | tAT | tTA | 2 | 2 | 1 | 15802-15804 |
ORF1ab/nsp12 | 788 | Y788D | Y5180D | nonsyn | Tat | Gat | 2 | 2 | 1 | 15802-15804 |
ORF1ab/nsp12 | 788 | Y788N | Y5180N | nonsyn | Tat | Aat | 1 | 1 | 1 | 15802-15804 |
ORF1ab/nsp12 | 788 | Y788R | Y5180R | nonsyn | TAt | CGt | 1 | 1 | 1 | 15802-15804 |
ORF1ab/nsp12 | 788 | Y788G | Y5180G | nonsyn | TAT | GGG | 1 | 1 | 1 | 15802-15804 |
ORF1ab/nsp12 | 788 | Y788E | Y5180E | nonsyn | TaT | GaA | 1 | 1 | 1 | 15802-15804 |
ORF1ab/nsp12 | 788 | Y788K | Y5180K | nonsyn | TaT | AaG | 1 | 1 | 1 | 15802-15804 |
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/nsp12 | 788 | Y788Y | taT | taC | 575 | 575 | All | 0.00011 |
ORF1ab/nsp12 | 788 | Y788Y | taT | taC | 110 | 110 | B.1.1.7 | 0.000098 |
ORF1ab/nsp12 | 788 | Y788Y | taT | taC | 59 | 59 | A.15 | 0.936508 |
ORF1ab/nsp12 | 788 | Y788Y | taT | taC | 49 | 49 | AY.4 | 0.000076 |
ORF1ab/nsp12 | 788 | Y788Y | taT | taC | 44 | 44 | B.1.177.4 | 0.009287 |
ORF1ab/nsp12 | 788 | Y788Y | taT | taC | 36 | 36 | AY.43 | 0.000159 |
ORF1ab/nsp12 | 788 | Y788Y | taT | taC | 24 | 24 | B.1.1.144 | 0.685714 |
ORF1ab/nsp12 | 788 | Y788Y | taT | taC | 18 | 18 | B.1.617.2 | 0.000068 |
ORF1ab/nsp12 | 788 | Y788Y | taT | taC | 16 | 16 | AY.25 | 0.000096 |
ORF1ab/nsp12 | 788 | Y788Y | taT | taC | 14 | 14 | AY.44 | 0.000085 |
ORF1ab/nsp12 | 788 | Y788Y | taT | taC | 14 | 14 | AY.56 | 0.022472 |
ORF1ab/nsp12 | 788 | Y788Y | taT | taC | 13 | 13 | AY.103 | 0.000081 |
ORF1ab/nsp12 | 788 | Y788Y | taT | taC | 13 | 13 | AY.5 | 0.000268 |
ORF1ab/nsp12 | 788 | Y788Y | taT | taC | 13 | 13 | P.1 | 0.000205 |
ORF1ab/nsp12 | 788 | Y788Y | taT | taC | 10 | 10 | AY.119 | 0.000353 |
ORF1ab/nsp12 | 788 | Y788Y | taT | taC | 10 | 10 | B.1.2 | 0.000088 |
ORF1ab/nsp12 | 788 | Y788del | TAT | --- | 9 | 9 | All | 0.000002 |
ORF1ab/nsp12 | 788 | Y788Y | taT | taC | 8 | 8 | AY.29 | 0.000126 |
ORF1ab/nsp12 | 788 | Y788C | tAT | tGC | 6 | 7 | 0.333333 | |
ORF1ab/nsp12 | 788 | Y788C | tAt | tGt | 1 | 7 | 0.055556 | |
ORF1ab/nsp12 | 788 | Y788C | tAT | tGC | 6 | 7 | All | 0.000001 |
ORF1ab/nsp12 | 788 | Y788C | tAt | tGt | 1 | 7 | All | 0 |
ORF1ab/nsp12 | 788 | Y788Y | taT | taC | 7 | 7 | AY.26 | 0.000198 |
ORF1ab/nsp12 | 788 | Y788Y | taT | taC | 7 | 7 | B.1.351 | 0.000208 |
ORF1ab/nsp12 | 788 | Y788Y | taT | taC | 6 | 6 | B.1.258 | 0.000399 |
ORF1ab/nsp12 | 788 | Y788del1 | taT | ta- | 4 | 5 | All | 0.000001 |
ORF1ab/nsp12 | 788 | Y788del1 | tAt | t-t | 1 | 5 | All | 0 |
ORF1ab/nsp12 | 788 | Y788Y | taT | taC | 5 | 5 | AY.102 | 0.000133 |
ORF1ab/nsp12 | 788 | Y788Y | taT | taC | 5 | 5 | B.1.110.3 | 0.003592 |
ORF1ab/nsp12 | 788 | Y788Y | taT | taC | 5 | 5 | B.1.177 | 0.000066 |
ORF1ab/nsp12 | 788 | Y788F | tAt | tTt | 4 | 4 | 0.222222 | |
ORF1ab/nsp12 | 788 | Y788H | Tat | Cat | 4 | 4 | All | 0.000001 |
ORF1ab/nsp12 | 788 | Y788X | taT | taA | 4 | 4 | All | 0.000001 |
ORF1ab/nsp12 | 788 | Y788F | tAt | tTt | 4 | 4 | All | 0.000001 |
ORF1ab/nsp12 | 788 | Y788Y | taT | taC | 4 | 4 | AY.3 | 0.00004 |
ORF1ab/nsp12 | 788 | Y788Y | taT | taC | 4 | 4 | AY.37 | 0.001264 |
ORF1ab/nsp12 | 788 | Y788Y | taT | taC | 4 | 4 | AY.39 | 0.000099 |
ORF1ab/nsp12 | 788 | Y788Y | taT | taC | 4 | 4 | AY.98.1 | 0.000194 |
ORF1ab/nsp12 | 788 | Y788Y | taT | taC | 4 | 4 | B.1 | 0.000037 |
ORF1ab/nsp12 | 788 | Y788Y | taT | taC | 4 | 4 | B.1.36 | 0.000584 |
ORF1ab/nsp12 | 788 | Y788Y | taT | taC | 4 | 4 | B.1.526 | 0.000094 |
ORF1ab/nsp12 | 788 | Y788Y | taT | taC | 4 | 4 | B.1.621 | 0.000354 |
ORF1ab/nsp12 | 788 | Y788X | taT | taA | 3 | 3 | 0.166667 | |
ORF1ab/nsp12 | 788 | Y788S | tAt | tCt | 2 | 3 | All | 0 |
ORF1ab/nsp12 | 788 | Y788S | TAt | AGt | 1 | 3 | All | 0 |
ORF1ab/nsp12 | 788 | Y788Y | taT | taC | 3 | 3 | AY.33 | 0.0002 |
ORF1ab/nsp12 | 788 | Y788Y | taT | taC | 3 | 3 | AY.6 | 0.000123 |
ORF1ab/nsp12 | 788 | Y788Y | taT | taC | 3 | 3 | B.1.1.317 | 0.001235 |
ORF1ab/nsp12 | 788 | Y788Y | taT | taC | 3 | 3 | B.1.1.519 | 0.000119 |
ORF1ab/nsp12 | 788 | Y788Y | taT | taC | 3 | 3 | B.1.1.63 | 0.001157 |
ORF1ab/nsp12 | 788 | Y788del | TAT | --- | 3 | 3 | B.1.1.7 | 0.000003 |
ORF1ab/nsp12 | 788 | Y788Y | taT | taC | 3 | 3 | C.37 | 0.000348 |
ORF1ab/nsp12 | 788 | Y788L | tAT | tTA | 2 | 2 | 0.111111 | |
ORF1ab/nsp12 | 788 | Y788Y | taT | taC | 2 | 2 | A.2 | 0.001324 |
ORF1ab/nsp12 | 788 | Y788L | tAT | tTA | 2 | 2 | All | 0 |
ORF1ab/nsp12 | 788 | Y788D | Tat | Gat | 2 | 2 | All | 0 |
ORF1ab/nsp12 | 788 | Y788Y | taT | taC | 2 | 2 | AY.39.1 | 0.000079 |
ORF1ab/nsp12 | 788 | Y788H | Tat | Cat | 2 | 2 | B.1 | 0.000018 |
ORF1ab/nsp12 | 788 | Y788Y | taT | taC | 2 | 2 | B.1.177.21 | 0.000153 |
ORF1ab/nsp12 | 788 | Y788Y | taT | taC | 2 | 2 | B.1.429 | 0.000047 |
ORF1ab/nsp12 | 788 | Y788N | Tat | Aat | 1 | 1 | 0.055556 | |
ORF1ab/nsp12 | 788 | Y788S | TAt | AGt | 1 | 1 | 0.055556 | |
ORF1ab/nsp12 | 788 | Y788S | tAt | tCt | 1 | 1 | A.6 | 0.005128 |
ORF1ab/nsp12 | 788 | Y788E | TaT | GaA | 1 | 1 | All | 0 |
ORF1ab/nsp12 | 788 | Y788G | TAT | GGG | 1 | 1 | All | 0 |
ORF1ab/nsp12 | 788 | Y788R | TAt | CGt | 1 | 1 | All | 0 |
ORF1ab/nsp12 | 788 | Y788N | Tat | Aat | 1 | 1 | All | 0 |
ORF1ab/nsp12 | 788 | Y788K | TaT | AaG | 1 | 1 | All | 0 |
ORF1ab/nsp12 | 788 | Y788Y | taT | taC | 1 | 1 | AY.113 | 0.000142 |
ORF1ab/nsp12 | 788 | Y788Y | taT | taC | 1 | 1 | AY.116 | 0.000287 |
ORF1ab/nsp12 | 788 | Y788del | TAT | --- | 1 | 1 | AY.118 | 0.000063 |
ORF1ab/nsp12 | 788 | Y788Y | taT | taC | 1 | 1 | AY.120 | 0.000037 |
ORF1ab/nsp12 | 788 | Y788Y | taT | taC | 1 | 1 | AY.16 | 0.00038 |
ORF1ab/nsp12 | 788 | Y788Y | taT | taC | 1 | 1 | AY.20 | 0.000039 |
ORF1ab/nsp12 | 788 | Y788X | taT | taA | 1 | 1 | AY.3 | 0.00001 |
ORF1ab/nsp12 | 788 | Y788Y | taT | taC | 1 | 1 | AY.38 | 0.000499 |
ORF1ab/nsp12 | 788 | Y788Y | taT | taC | 1 | 1 | AY.39.1.1 | 0.000725 |
ORF1ab/nsp12 | 788 | Y788del | TAT | --- | 1 | 1 | AY.4.5 | 0.000107 |
ORF1ab/nsp12 | 788 | Y788del1 | taT | ta- | 1 | 1 | AY.43 | 0.000004 |
ORF1ab/nsp12 | 788 | Y788del | TAT | --- | 1 | 1 | AY.43 | 0.000004 |
ORF1ab/nsp12 | 788 | Y788S | tAt | tCt | 1 | 1 | AY.44 | 0.000006 |
ORF1ab/nsp12 | 788 | Y788R | TAt | CGt | 1 | 1 | AY.44 | 0.000006 |
ORF1ab/nsp12 | 788 | Y788Y | taT | taC | 1 | 1 | AY.47 | 0.000031 |
ORF1ab/nsp12 | 788 | Y788Y | taT | taC | 1 | 1 | AY.53 | 0.000288 |
ORF1ab/nsp12 | 788 | Y788Y | taT | taC | 1 | 1 | AY.61 | 0.000105 |
ORF1ab/nsp12 | 788 | Y788del1 | taT | ta- | 1 | 1 | AY.67 | 0.000464 |
ORF1ab/nsp12 | 788 | Y788Y | taT | taC | 1 | 1 | AY.71 | 0.000475 |
ORF1ab/nsp12 | 788 | Y788Y | taT | taC | 1 | 1 | AY.75.1 | 0.00018 |
ORF1ab/nsp12 | 788 | Y788Y | taT | taC | 1 | 1 | AY.9.2 | 0.000037 |
ORF1ab/nsp12 | 788 | Y788G | TAT | GGG | 1 | 1 | AY.99 | 0.001049 |
ORF1ab/nsp12 | 788 | Y788Y | taT | taC | 1 | 1 | AZ.2 | 0.000821 |
ORF1ab/nsp12 | 788 | Y788Y | taT | taC | 1 | 1 | B | 0.000128 |
ORF1ab/nsp12 | 788 | Y788del1 | tAt | t-t | 1 | 1 | B.1 | 0.000009 |
ORF1ab/nsp12 | 788 | Y788del | TAT | --- | 1 | 1 | B.1.1 | 0.000018 |
ORF1ab/nsp12 | 788 | Y788Y | taT | taC | 1 | 1 | B.1.1 | 0.000018 |
ORF1ab/nsp12 | 788 | Y788Y | taT | taC | 1 | 1 | B.1.1.28 | 0.000311 |
ORF1ab/nsp12 | 788 | Y788Y | taT | taC | 1 | 1 | B.1.1.306 | 0.000438 |
ORF1ab/nsp12 | 788 | Y788H | Tat | Cat | 1 | 1 | B.1.1.409 | 0.002833 |
ORF1ab/nsp12 | 788 | Y788K | TaT | AaG | 1 | 1 | B.1.1.7 | 0.000001 |
ORF1ab/nsp12 | 788 | Y788E | TaT | GaA | 1 | 1 | B.1.1.7 | 0.000001 |
ORF1ab/nsp12 | 788 | Y788D | Tat | Gat | 1 | 1 | B.1.128 | 0.000635 |
ORF1ab/nsp12 | 788 | Y788Y | taT | taC | 1 | 1 | B.1.177.10 | 0.000878 |
ORF1ab/nsp12 | 788 | Y788Y | taT | taC | 1 | 1 | B.1.177.23 | 0.003236 |
ORF1ab/nsp12 | 788 | Y788Y | taT | taC | 1 | 1 | B.1.177.55 | 0.002331 |
ORF1ab/nsp12 | 788 | Y788Y | taT | taC | 1 | 1 | B.1.177.60 | 0.000218 |
ORF1ab/nsp12 | 788 | Y788del | TAT | --- | 1 | 1 | B.1.177.83 | 0.001481 |
ORF1ab/nsp12 | 788 | Y788del1 | taT | ta- | 1 | 1 | B.1.2 | 0.000009 |
ORF1ab/nsp12 | 788 | Y788D | Tat | Gat | 1 | 1 | B.1.222 | 0.001692 |
ORF1ab/nsp12 | 788 | Y788Y | taT | taC | 1 | 1 | B.1.329 | 0.000608 |
ORF1ab/nsp12 | 788 | Y788Y | taT | taC | 1 | 1 | B.1.351.2 | 0.000303 |
ORF1ab/nsp12 | 788 | Y788Y | taT | taC | 1 | 1 | B.1.36.35 | 0.002604 |
ORF1ab/nsp12 | 788 | Y788Y | taT | taC | 1 | 1 | B.1.499 | 0.00105 |
ORF1ab/nsp12 | 788 | Y788Y | taT | taC | 1 | 1 | B.1.576 | 0.000907 |
ORF1ab/nsp12 | 788 | Y788H | Tat | Cat | 1 | 1 | B.1.580 | 0.004065 |
ORF1ab/nsp12 | 788 | Y788del1 | taT | ta- | 1 | 1 | B.1.617.2 | 0.000004 |
ORF1ab/nsp12 | 788 | Y788Y | taT | taC | 1 | 1 | P.1.1 | 0.000318 |
ORF1ab/nsp12 | 788 | Y788Y | taT | taC | 1 | 1 | P.1.2 | 0.001156 |
ORF1ab/nsp12 | 788 | Y788Y | taT | taC | 1 | 1 | P.2 | 0.000187 |
ORF1ab/nsp12 | 788 | Y788del | TAT | --- | 1 | 1 | Q.1 | 0.000126 |
ORF1ab/nsp12 | 788 | Y788Y | taT | taC | 1 | 1 | R.1 | 0.00009 |
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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