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 | 1018 | Y1018Y | Y1836Y | syn | taT | taC | 662 | 662 | 1 | 5771-5773 |
ORF1ab/nsp3 | 1018 | Y1018del | Y1836del | del | TAT | --- | 17 | 17 | 1 | 5771-5773 |
ORF1ab/nsp3 | 1018 | Y1018S | Y1836S | nonsyn | tAt | tCt | 14 | 14 | 1 | 5771-5773 |
ORF1ab/nsp3 | 1018 | Y1018D | Y1836D | nonsyn | Tat | Gat | 11 | 11 | 1 | 5771-5773 |
ORF1ab/nsp3 | 1018 | Y1018H | Y1836H | nonsyn | Tat | Cat | 7 | 6 | 0.857143 | 5771-5773 |
ORF1ab/nsp3 | 1018 | Y1018H | Y1836H | nonsyn | TaT | CaC | 7 | 1 | 0.142857 | 5771-5773 |
ORF1ab/nsp3 | 1018 | Y1018X | Y1836X | nonsyn | taT | taA | 5 | 3 | 0.6 | 5771-5773 |
ORF1ab/nsp3 | 1018 | Y1018X | Y1836X | nonsyn | taT | taG | 5 | 2 | 0.4 | 5771-5773 |
ORF1ab/nsp3 | 1018 | Y1018C | Y1836C | nonsyn | tAt | tGt | 4 | 4 | 1 | 5771-5773 |
ORF1ab/nsp3 | 1018 | Y1018del1 | Y1836del1 | del | taT | ta- | 2 | 2 | 1 | 5771-5773 |
ORF1ab/nsp3 | 1018 | Y1018del2 | Y1836del2 | del | TAt | --t | 2 | 2 | 1 | 5771-5773 |
ORF1ab/nsp3 | 1018 | Y1018N | Y1836N | nonsyn | TaT | AaC | 1 | 1 | 1 | 5771-5773 |
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 | 1018 | Y1018Y | taT | taC | 662 | 662 | All | 0.000127 |
ORF1ab/nsp3 | 1018 | Y1018Y | taT | taC | 207 | 207 | AY.49 | 0.661342 |
ORF1ab/nsp3 | 1018 | Y1018Y | taT | taC | 71 | 71 | B.1.1.7 | 0.000064 |
ORF1ab/nsp3 | 1018 | Y1018Y | taT | taC | 50 | 50 | B.1.258.15 | 0.943396 |
ORF1ab/nsp3 | 1018 | Y1018Y | taT | taC | 39 | 39 | B.1.596 | 0.003398 |
ORF1ab/nsp3 | 1018 | Y1018Y | taT | taC | 30 | 30 | AY.25 | 0.00018 |
ORF1ab/nsp3 | 1018 | Y1018Y | taT | taC | 27 | 27 | B.1.1.506 | 1 |
ORF1ab/nsp3 | 1018 | Y1018Y | taT | taC | 27 | 27 | B.1.429 | 0.000635 |
ORF1ab/nsp3 | 1018 | Y1018Y | taT | taC | 26 | 26 | B.1.617.2 | 0.000098 |
ORF1ab/nsp3 | 1018 | Y1018Y | taT | taC | 24 | 24 | AY.4 | 0.000037 |
ORF1ab/nsp3 | 1018 | Y1018Y | taT | taC | 21 | 21 | B.1.2 | 0.000185 |
ORF1ab/nsp3 | 1018 | Y1018Y | taT | taC | 18 | 18 | B.1.258 | 0.001198 |
ORF1ab/nsp3 | 1018 | Y1018del | TAT | --- | 17 | 17 | All | 0.000003 |
ORF1ab/nsp3 | 1018 | Y1018S | tAt | tCt | 14 | 14 | All | 0.000003 |
ORF1ab/nsp3 | 1018 | Y1018D | Tat | Gat | 11 | 11 | All | 0.000002 |
ORF1ab/nsp3 | 1018 | Y1018Y | taT | taC | 10 | 10 | AY.44 | 0.000061 |
ORF1ab/nsp3 | 1018 | Y1018Y | taT | taC | 9 | 9 | AY.103 | 0.000056 |
ORF1ab/nsp3 | 1018 | Y1018Y | taT | taC | 9 | 9 | AY.43 | 0.00004 |
ORF1ab/nsp3 | 1018 | Y1018Y | taT | taC | 9 | 9 | AY.54 | 0.000858 |
ORF1ab/nsp3 | 1018 | Y1018Y | taT | taC | 9 | 9 | B.1.1.176 | 0.003954 |
ORF1ab/nsp3 | 1018 | Y1018Y | taT | taC | 9 | 9 | B.1.177.81 | 0.001704 |
ORF1ab/nsp3 | 1018 | Y1018Y | taT | taC | 8 | 8 | B.1.177 | 0.000105 |
ORF1ab/nsp3 | 1018 | Y1018H | Tat | Cat | 6 | 7 | All | 0.000001 |
ORF1ab/nsp3 | 1018 | Y1018H | TaT | CaC | 1 | 7 | All | 0 |
ORF1ab/nsp3 | 1018 | Y1018Y | taT | taC | 6 | 6 | AY.102 | 0.000159 |
ORF1ab/nsp3 | 1018 | Y1018D | Tat | Gat | 6 | 6 | B.1.1.7 | 0.000005 |
ORF1ab/nsp3 | 1018 | Y1018X | taT | taA | 3 | 5 | All | 0.000001 |
ORF1ab/nsp3 | 1018 | Y1018X | taT | taG | 2 | 5 | All | 0 |
ORF1ab/nsp3 | 1018 | Y1018D | Tat | Gat | 5 | 5 | B.1.525 | 0.000566 |
ORF1ab/nsp3 | 1018 | Y1018C | tAt | tGt | 4 | 4 | All | 0.000001 |
ORF1ab/nsp3 | 1018 | Y1018Y | taT | taC | 4 | 4 | AY.101 | 0.001962 |
ORF1ab/nsp3 | 1018 | Y1018Y | taT | taC | 4 | 4 | AY.3 | 0.00004 |
ORF1ab/nsp3 | 1018 | Y1018del | TAT | --- | 4 | 4 | B.1.1.7 | 0.000004 |
ORF1ab/nsp3 | 1018 | Y1018S | tAt | tCt | 4 | 4 | B.1.160 | 0.000125 |
ORF1ab/nsp3 | 1018 | Y1018Y | taT | taC | 3 | 3 | B.1.1 | 0.000054 |
ORF1ab/nsp3 | 1018 | Y1018Y | taT | taC | 3 | 3 | B.1.119 | 0.031579 |
ORF1ab/nsp3 | 1018 | Y1018del1 | taT | ta- | 2 | 2 | All | 0 |
ORF1ab/nsp3 | 1018 | Y1018del2 | TAt | --t | 2 | 2 | All | 0 |
ORF1ab/nsp3 | 1018 | Y1018Y | taT | taC | 2 | 2 | AY.116 | 0.000574 |
ORF1ab/nsp3 | 1018 | Y1018Y | taT | taC | 2 | 2 | AY.120 | 0.000074 |
ORF1ab/nsp3 | 1018 | Y1018Y | taT | taC | 2 | 2 | AY.13 | 0.000322 |
ORF1ab/nsp3 | 1018 | Y1018Y | taT | taC | 2 | 2 | AY.22 | 0.004184 |
ORF1ab/nsp3 | 1018 | Y1018del1 | taT | ta- | 2 | 2 | B.1 | 0.000018 |
ORF1ab/nsp3 | 1018 | Y1018Y | taT | taC | 2 | 2 | B.1 | 0.000018 |
ORF1ab/nsp3 | 1018 | Y1018H | Tat | Cat | 2 | 2 | B.1 | 0.000018 |
ORF1ab/nsp3 | 1018 | Y1018Y | taT | taC | 2 | 2 | B.1.1.214 | 0.000111 |
ORF1ab/nsp3 | 1018 | Y1018S | tAt | tCt | 2 | 2 | B.1.177 | 0.000026 |
ORF1ab/nsp3 | 1018 | Y1018Y | taT | taC | 2 | 2 | B.1.177.86 | 0.000367 |
ORF1ab/nsp3 | 1018 | Y1018del | TAT | --- | 2 | 2 | B.1.36 | 0.000292 |
ORF1ab/nsp3 | 1018 | Y1018Y | taT | taC | 2 | 2 | B.1.466.2 | 0.000782 |
ORF1ab/nsp3 | 1018 | Y1018Y | taT | taC | 2 | 2 | P.1 | 0.000032 |
ORF1ab/nsp3 | 1018 | Y1018del | TAT | --- | 1 | 1 | A.2.2 | 0.001689 |
ORF1ab/nsp3 | 1018 | Y1018H | Tat | Cat | 1 | 1 | AH.3 | 0.003802 |
ORF1ab/nsp3 | 1018 | Y1018N | TaT | AaC | 1 | 1 | All | 0 |
ORF1ab/nsp3 | 1018 | Y1018Y | taT | taC | 1 | 1 | AY.114 | 0.000231 |
ORF1ab/nsp3 | 1018 | Y1018Y | taT | taC | 1 | 1 | AY.117 | 0.000085 |
ORF1ab/nsp3 | 1018 | Y1018Y | taT | taC | 1 | 1 | AY.118 | 0.000063 |
ORF1ab/nsp3 | 1018 | Y1018H | TaT | CaC | 1 | 1 | AY.119 | 0.000035 |
ORF1ab/nsp3 | 1018 | Y1018Y | taT | taC | 1 | 1 | AY.119 | 0.000035 |
ORF1ab/nsp3 | 1018 | Y1018C | tAt | tGt | 1 | 1 | AY.119 | 0.000035 |
ORF1ab/nsp3 | 1018 | Y1018Y | taT | taC | 1 | 1 | AY.23 | 0.00007 |
ORF1ab/nsp3 | 1018 | Y1018Y | taT | taC | 1 | 1 | AY.39 | 0.000025 |
ORF1ab/nsp3 | 1018 | Y1018Y | taT | taC | 1 | 1 | AY.46 | 0.000104 |
ORF1ab/nsp3 | 1018 | Y1018Y | taT | taC | 1 | 1 | AY.46.2 | 0.000635 |
ORF1ab/nsp3 | 1018 | Y1018Y | taT | taC | 1 | 1 | AY.46.4 | 0.000165 |
ORF1ab/nsp3 | 1018 | Y1018Y | taT | taC | 1 | 1 | AY.46.6 | 0.000072 |
ORF1ab/nsp3 | 1018 | Y1018X | taT | taG | 1 | 1 | AY.61 | 0.000105 |
ORF1ab/nsp3 | 1018 | Y1018Y | taT | taC | 1 | 1 | AY.61 | 0.000105 |
ORF1ab/nsp3 | 1018 | Y1018C | tAt | tGt | 1 | 1 | AY.62 | 0.000436 |
ORF1ab/nsp3 | 1018 | Y1018Y | taT | taC | 1 | 1 | AY.65 | 0.000533 |
ORF1ab/nsp3 | 1018 | Y1018del | TAT | --- | 1 | 1 | AY.85 | 0.000427 |
ORF1ab/nsp3 | 1018 | Y1018del | TAT | --- | 1 | 1 | B | 0.000128 |
ORF1ab/nsp3 | 1018 | Y1018S | tAt | tCt | 1 | 1 | B.1.1 | 0.000018 |
ORF1ab/nsp3 | 1018 | Y1018del | TAT | --- | 1 | 1 | B.1.1.139 | 0.022727 |
ORF1ab/nsp3 | 1018 | Y1018del | TAT | --- | 1 | 1 | B.1.1.142 | 0.017544 |
ORF1ab/nsp3 | 1018 | Y1018S | tAt | tCt | 1 | 1 | B.1.1.39 | 0.00051 |
ORF1ab/nsp3 | 1018 | Y1018Y | taT | taC | 1 | 1 | B.1.1.51 | 0.001718 |
ORF1ab/nsp3 | 1018 | Y1018C | tAt | tGt | 1 | 1 | B.1.1.519 | 0.00004 |
ORF1ab/nsp3 | 1018 | Y1018Y | taT | taC | 1 | 1 | B.1.1.519 | 0.00004 |
ORF1ab/nsp3 | 1018 | Y1018del | TAT | --- | 1 | 1 | B.1.1.63 | 0.000386 |
ORF1ab/nsp3 | 1018 | Y1018H | Tat | Cat | 1 | 1 | B.1.1.7 | 0.000001 |
ORF1ab/nsp3 | 1018 | Y1018S | tAt | tCt | 1 | 1 | B.1.160.16 | 0.000929 |
ORF1ab/nsp3 | 1018 | Y1018S | tAt | tCt | 1 | 1 | B.1.160.30 | 0.002976 |
ORF1ab/nsp3 | 1018 | Y1018X | taT | taA | 1 | 1 | B.1.177 | 0.000013 |
ORF1ab/nsp3 | 1018 | Y1018C | tAt | tGt | 1 | 1 | B.1.177 | 0.000013 |
ORF1ab/nsp3 | 1018 | Y1018X | taT | taA | 1 | 1 | B.1.177.32 | 0.00135 |
ORF1ab/nsp3 | 1018 | Y1018S | tAt | tCt | 1 | 1 | B.1.177.43 | 0.001477 |
ORF1ab/nsp3 | 1018 | Y1018S | tAt | tCt | 1 | 1 | B.1.177.44 | 0.000519 |
ORF1ab/nsp3 | 1018 | Y1018Y | taT | taC | 1 | 1 | B.1.177.54 | 0.000606 |
ORF1ab/nsp3 | 1018 | Y1018X | taT | taA | 1 | 1 | B.1.2 | 0.000009 |
ORF1ab/nsp3 | 1018 | Y1018H | Tat | Cat | 1 | 1 | B.1.2 | 0.000009 |
ORF1ab/nsp3 | 1018 | Y1018del2 | TAt | --t | 1 | 1 | B.1.2 | 0.000009 |
ORF1ab/nsp3 | 1018 | Y1018S | tAt | tCt | 1 | 1 | B.1.221 | 0.000071 |
ORF1ab/nsp3 | 1018 | Y1018del | TAT | --- | 1 | 1 | B.1.258 | 0.000067 |
ORF1ab/nsp3 | 1018 | Y1018Y | taT | taC | 1 | 1 | B.1.351 | 0.00003 |
ORF1ab/nsp3 | 1018 | Y1018Y | taT | taC | 1 | 1 | B.1.36.24 | 0.006173 |
ORF1ab/nsp3 | 1018 | Y1018X | taT | taG | 1 | 1 | B.1.416 | 0.001269 |
ORF1ab/nsp3 | 1018 | Y1018Y | taT | taC | 1 | 1 | B.1.526 | 0.000024 |
ORF1ab/nsp3 | 1018 | Y1018del2 | TAt | --t | 1 | 1 | B.1.596 | 0.000087 |
ORF1ab/nsp3 | 1018 | Y1018del | TAT | --- | 1 | 1 | B.1.617.2 | 0.000004 |
ORF1ab/nsp3 | 1018 | Y1018H | Tat | Cat | 1 | 1 | B.1.617.2 | 0.000004 |
ORF1ab/nsp3 | 1018 | Y1018Y | taT | taC | 1 | 1 | B.1.637 | 0.000073 |
ORF1ab/nsp3 | 1018 | Y1018del | TAT | --- | 1 | 1 | B.15 | 0.017544 |
ORF1ab/nsp3 | 1018 | Y1018del | TAT | --- | 1 | 1 | B.34 | 0.013699 |
ORF1ab/nsp3 | 1018 | Y1018S | tAt | tCt | 1 | 1 | C.16 | 0.00106 |
ORF1ab/nsp3 | 1018 | Y1018N | TaT | AaC | 1 | 1 | C.35 | 0.000774 |
ORF1ab/nsp3 | 1018 | Y1018del | TAT | --- | 1 | 1 | C.37 | 0.000116 |
ORF1ab/nsp3 | 1018 | Y1018Y | taT | taC | 1 | 1 | P.1.14 | 0.000048 |
ORF1ab/nsp3 | 1018 | Y1018Y | taT | taC | 1 | 1 | P.1.15 | 0.000232 |
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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