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/nsp13 | 149 | Y149Y | Y5473Y | syn | taT | taC | 819 | 819 | 1 | 16681-16683 |
ORF1ab/nsp13 | 149 | Y149del | Y5473del | del | TAT | --- | 108 | 108 | 1 | 16681-16683 |
ORF1ab/nsp13 | 149 | Y149C | Y5473C | nonsyn | tAt | tGt | 60 | 58 | 0.966667 | 16681-16683 |
ORF1ab/nsp13 | 149 | Y149C | Y5473C | nonsyn | tAT | tGC | 60 | 2 | 0.0333333 | 16681-16683 |
ORF1ab/nsp13 | 149 | Y149H | Y5473H | nonsyn | Tat | Cat | 47 | 45 | 0.957447 | 16681-16683 |
ORF1ab/nsp13 | 149 | Y149H | Y5473H | nonsyn | TaT | CaC | 47 | 2 | 0.0425532 | 16681-16683 |
ORF1ab/nsp13 | 149 | Y149F | Y5473F | nonsyn | tAt | tTt | 38 | 37 | 0.973684 | 16681-16683 |
ORF1ab/nsp13 | 149 | Y149F | Y5473F | nonsyn | tAT | tTC | 38 | 1 | 0.0263158 | 16681-16683 |
ORF1ab/nsp13 | 149 | Y149D | Y5473D | nonsyn | Tat | Gat | 9 | 7 | 0.777778 | 16681-16683 |
ORF1ab/nsp13 | 149 | Y149D | Y5473D | nonsyn | TaT | GaC | 9 | 2 | 0.222222 | 16681-16683 |
ORF1ab/nsp13 | 149 | Y149E | Y5473E | nonsyn | TaT | GaA | 5 | 5 | 1 | 16681-16683 |
ORF1ab/nsp13 | 149 | Y149X | Y5473X | nonsyn | taT | taA | 4 | 4 | 1 | 16681-16683 |
ORF1ab/nsp13 | 149 | Y149Q | Y5473Q | nonsyn | TaT | CaA | 3 | 3 | 1 | 16681-16683 |
ORF1ab/nsp13 | 149 | Y149N | Y5473N | nonsyn | Tat | Aat | 3 | 3 | 1 | 16681-16683 |
ORF1ab/nsp13 | 149 | Y149del2 | Y5473del2 | del | TAT | --N | 3 | 1 | 0.333333 | 16681-16683 |
ORF1ab/nsp13 | 149 | Y149del2 | Y5473del2 | del | tAT | t-- | 3 | 1 | 0.333333 | 16681-16683 |
ORF1ab/nsp13 | 149 | Y149del2 | Y5473del2 | del | TAt | --t | 3 | 1 | 0.333333 | 16681-16683 |
ORF1ab/nsp13 | 149 | Y149K | Y5473K | nonsyn | TaT | AaA | 2 | 2 | 1 | 16681-16683 |
ORF1ab/nsp13 | 149 | Y149del1 | Y5473del1 | del | taT | ta- | 1 | 1 | 1 | 16681-16683 |
ORF1ab/nsp13 | 149 | Y149I | Y5473I | nonsyn | TAt | ATt | 1 | 1 | 1 | 16681-16683 |
ORF1ab/nsp13 | 149 | Y149S | Y5473S | nonsyn | tAt | tCt | 1 | 1 | 1 | 16681-16683 |
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/nsp13 | 149 | Y149Y | taT | taC | 819 | 819 | All | 0.000157 |
ORF1ab/nsp13 | 149 | Y149Y | taT | taC | 422 | 422 | B.1.1.7 | 0.000378 |
ORF1ab/nsp13 | 149 | Y149Y | taT | taC | 281 | 281 | AY.4 | 0.000437 |
ORF1ab/nsp13 | 149 | Y149del | TAT | --- | 108 | 108 | All | 0.000021 |
ORF1ab/nsp13 | 149 | Y149del | TAT | --- | 64 | 64 | B.1.1.7 | 0.000057 |
ORF1ab/nsp13 | 149 | Y149C | tAt | tGt | 58 | 60 | All | 0.000011 |
ORF1ab/nsp13 | 149 | Y149C | tAT | tGC | 2 | 60 | All | 0 |
ORF1ab/nsp13 | 149 | Y149H | Tat | Cat | 45 | 47 | All | 0.000009 |
ORF1ab/nsp13 | 149 | Y149H | TaT | CaC | 2 | 47 | All | 0 |
ORF1ab/nsp13 | 149 | Y149F | tAt | tTt | 37 | 38 | All | 0.000007 |
ORF1ab/nsp13 | 149 | Y149F | tAT | tTC | 1 | 38 | All | 0 |
ORF1ab/nsp13 | 149 | Y149F | tAt | tTt | 30 | 30 | AM.3 | 1 |
ORF1ab/nsp13 | 149 | Y149H | Tat | Cat | 29 | 29 | AY.45 | 0.003529 |
ORF1ab/nsp13 | 149 | Y149C | tAt | tGt | 19 | 19 | B.1.1.7 | 0.000017 |
ORF1ab/nsp13 | 149 | Y149Y | taT | taC | 18 | 18 | AY.113 | 0.002563 |
ORF1ab/nsp13 | 149 | Y149Y | taT | taC | 17 | 17 | B.1 | 0.000156 |
ORF1ab/nsp13 | 149 | Y149Y | taT | taC | 17 | 17 | B.1.2 | 0.00015 |
ORF1ab/nsp13 | 149 | Y149del | TAT | --- | 15 | 15 | B.1.177 | 0.000198 |
ORF1ab/nsp13 | 149 | Y149Y | taT | taC | 14 | 14 | B.1.617.2 | 0.000053 |
ORF1ab/nsp13 | 149 | Y149Y | taT | taC | 12 | 12 | AY.103 | 0.000075 |
ORF1ab/nsp13 | 149 | Y149D | Tat | Gat | 7 | 9 | All | 0.000001 |
ORF1ab/nsp13 | 149 | Y149D | TaT | GaC | 2 | 9 | All | 0 |
ORF1ab/nsp13 | 149 | Y149D | Tat | Gat | 5 | 7 | 0.277778 | |
ORF1ab/nsp13 | 149 | Y149D | TaT | GaC | 2 | 7 | 0.111111 | |
ORF1ab/nsp13 | 149 | Y149Y | taT | taC | 7 | 7 | B.1.221 | 0.000497 |
ORF1ab/nsp13 | 149 | Y149E | TaT | GaA | 5 | 5 | 0.277778 | |
ORF1ab/nsp13 | 149 | Y149H | Tat | Cat | 3 | 5 | 0.166667 | |
ORF1ab/nsp13 | 149 | Y149H | TaT | CaC | 2 | 5 | 0.111111 | |
ORF1ab/nsp13 | 149 | Y149E | TaT | GaA | 5 | 5 | All | 0.000001 |
ORF1ab/nsp13 | 149 | Y149C | tAt | tGt | 5 | 5 | B.1.236 | 0.010267 |
ORF1ab/nsp13 | 149 | Y149X | taT | taA | 4 | 4 | 0.222222 | |
ORF1ab/nsp13 | 149 | Y149del | TAT | --- | 4 | 4 | AD.2 | 0.000876 |
ORF1ab/nsp13 | 149 | Y149X | taT | taA | 4 | 4 | All | 0.000001 |
ORF1ab/nsp13 | 149 | Y149Y | taT | taC | 4 | 4 | AY.102 | 0.000106 |
ORF1ab/nsp13 | 149 | Y149C | tAt | tGt | 4 | 4 | B.1.36.29 | 0.002069 |
ORF1ab/nsp13 | 149 | Y149Q | TaT | CaA | 3 | 3 | 0.166667 | |
ORF1ab/nsp13 | 149 | Y149N | Tat | Aat | 3 | 3 | All | 0.000001 |
ORF1ab/nsp13 | 149 | Y149Q | TaT | CaA | 3 | 3 | All | 0.000001 |
ORF1ab/nsp13 | 149 | Y149del2 | TAt | --t | 1 | 3 | All | 0 |
ORF1ab/nsp13 | 149 | Y149del2 | TAT | --N | 1 | 3 | All | 0 |
ORF1ab/nsp13 | 149 | Y149del2 | tAT | t-- | 1 | 3 | All | 0 |
ORF1ab/nsp13 | 149 | Y149Y | taT | taC | 3 | 3 | AY.3 | 0.00003 |
ORF1ab/nsp13 | 149 | Y149C | tAt | tGt | 3 | 3 | AY.4 | 0.000005 |
ORF1ab/nsp13 | 149 | Y149C | tAt | tGt | 3 | 3 | AY.98.1 | 0.000145 |
ORF1ab/nsp13 | 149 | Y149C | tAt | tGt | 3 | 3 | B.1 | 0.000027 |
ORF1ab/nsp13 | 149 | Y149C | tAt | tGt | 3 | 3 | B.1.1 | 0.000054 |
ORF1ab/nsp13 | 149 | Y149del | TAT | --- | 3 | 3 | B.1.1 | 0.000054 |
ORF1ab/nsp13 | 149 | Y149Y | taT | taC | 3 | 3 | P.1 | 0.000047 |
ORF1ab/nsp13 | 149 | Y149Y | taT | taC | 2 | 2 | 0.111111 | |
ORF1ab/nsp13 | 149 | Y149C | tAT | tGC | 2 | 2 | 0.111111 | |
ORF1ab/nsp13 | 149 | Y149del | TAT | --- | 2 | 2 | 0.111111 | |
ORF1ab/nsp13 | 149 | Y149K | TaT | AaA | 2 | 2 | All | 0 |
ORF1ab/nsp13 | 149 | Y149F | tAt | tTt | 2 | 2 | AM.4 | 0.007143 |
ORF1ab/nsp13 | 149 | Y149H | Tat | Cat | 2 | 2 | AY.103 | 0.000012 |
ORF1ab/nsp13 | 149 | Y149Y | taT | taC | 2 | 2 | AY.25 | 0.000012 |
ORF1ab/nsp13 | 149 | Y149F | tAt | tTt | 2 | 2 | AY.4 | 0.000003 |
ORF1ab/nsp13 | 149 | Y149Y | taT | taC | 2 | 2 | AY.44 | 0.000012 |
ORF1ab/nsp13 | 149 | Y149Y | taT | taC | 2 | 2 | AY.75 | 0.000112 |
ORF1ab/nsp13 | 149 | Y149del | TAT | --- | 2 | 2 | B.1 | 0.000018 |
ORF1ab/nsp13 | 149 | Y149H | Tat | Cat | 2 | 2 | B.1 | 0.000018 |
ORF1ab/nsp13 | 149 | Y149K | TaT | AaA | 2 | 2 | B.1.1 | 0.000036 |
ORF1ab/nsp13 | 149 | Y149del | TAT | --- | 2 | 2 | B.1.1.315 | 0.016949 |
ORF1ab/nsp13 | 149 | Y149F | tAt | tTt | 2 | 2 | B.1.1.7 | 0.000002 |
ORF1ab/nsp13 | 149 | Y149C | tAt | tGt | 2 | 2 | B.1.2 | 0.000018 |
ORF1ab/nsp13 | 149 | Y149C | tAt | tGt | 2 | 2 | B.1.221 | 0.000142 |
ORF1ab/nsp13 | 149 | Y149C | tAt | tGt | 2 | 2 | B.1.429 | 0.000047 |
ORF1ab/nsp13 | 149 | Y149F | tAT | tTC | 1 | 2 | P.1 | 0.000016 |
ORF1ab/nsp13 | 149 | Y149F | tAt | tTt | 1 | 2 | P.1 | 0.000016 |
ORF1ab/nsp13 | 149 | Y149D | Tat | Gat | 1 | 1 | A.2.4 | 0.003367 |
ORF1ab/nsp13 | 149 | Y149del1 | taT | ta- | 1 | 1 | All | 0 |
ORF1ab/nsp13 | 149 | Y149I | TAt | ATt | 1 | 1 | All | 0 |
ORF1ab/nsp13 | 149 | Y149S | tAt | tCt | 1 | 1 | All | 0 |
ORF1ab/nsp13 | 149 | Y149C | tAt | tGt | 1 | 1 | AY.102 | 0.000027 |
ORF1ab/nsp13 | 149 | Y149H | Tat | Cat | 1 | 1 | AY.119 | 0.000035 |
ORF1ab/nsp13 | 149 | Y149del | TAT | --- | 1 | 1 | AY.121 | 0.000135 |
ORF1ab/nsp13 | 149 | Y149Y | taT | taC | 1 | 1 | AY.20 | 0.000039 |
ORF1ab/nsp13 | 149 | Y149del | TAT | --- | 1 | 1 | AY.24 | 0.000431 |
ORF1ab/nsp13 | 149 | Y149Y | taT | taC | 1 | 1 | AY.27 | 0.000065 |
ORF1ab/nsp13 | 149 | Y149H | Tat | Cat | 1 | 1 | AY.3 | 0.00001 |
ORF1ab/nsp13 | 149 | Y149C | tAt | tGt | 1 | 1 | AY.3 | 0.00001 |
ORF1ab/nsp13 | 149 | Y149H | Tat | Cat | 1 | 1 | AY.3.1 | 0.000085 |
ORF1ab/nsp13 | 149 | Y149del | TAT | --- | 1 | 1 | AY.4 | 0.000002 |
ORF1ab/nsp13 | 149 | Y149D | Tat | Gat | 1 | 1 | AY.42 | 0.00004 |
ORF1ab/nsp13 | 149 | Y149Y | taT | taC | 1 | 1 | AY.43 | 0.000004 |
ORF1ab/nsp13 | 149 | Y149Y | taT | taC | 1 | 1 | AY.46.2 | 0.000635 |
ORF1ab/nsp13 | 149 | Y149C | tAt | tGt | 1 | 1 | AY.47 | 0.000031 |
ORF1ab/nsp13 | 149 | Y149C | tAt | tGt | 1 | 1 | AY.5 | 0.000021 |
ORF1ab/nsp13 | 149 | Y149N | Tat | Aat | 1 | 1 | AY.59 | 0.00053 |
ORF1ab/nsp13 | 149 | Y149Y | taT | taC | 1 | 1 | AY.61 | 0.000105 |
ORF1ab/nsp13 | 149 | Y149Y | taT | taC | 1 | 1 | AY.92 | 0.000287 |
ORF1ab/nsp13 | 149 | Y149del | TAT | --- | 1 | 1 | AZ.2 | 0.000821 |
ORF1ab/nsp13 | 149 | Y149del2 | TAT | --N | 1 | 1 | AZ.2 | 0.000821 |
ORF1ab/nsp13 | 149 | Y149del2 | TAt | --t | 1 | 1 | B.1 | 0.000009 |
ORF1ab/nsp13 | 149 | Y149Y | taT | taC | 1 | 1 | B.1.1 | 0.000018 |
ORF1ab/nsp13 | 149 | Y149del | TAT | --- | 1 | 1 | B.1.1.231 | 0.003096 |
ORF1ab/nsp13 | 149 | Y149Y | taT | taC | 1 | 1 | B.1.1.251 | 0.007937 |
ORF1ab/nsp13 | 149 | Y149Y | taT | taC | 1 | 1 | B.1.1.297 | 0.002237 |
ORF1ab/nsp13 | 149 | Y149del | TAT | --- | 1 | 1 | B.1.1.305 | 0.003861 |
ORF1ab/nsp13 | 149 | Y149del | TAT | --- | 1 | 1 | B.1.1.306 | 0.000438 |
ORF1ab/nsp13 | 149 | Y149del | TAT | --- | 1 | 1 | B.1.1.44 | 0.00241 |
ORF1ab/nsp13 | 149 | Y149N | Tat | Aat | 1 | 1 | B.1.1.7 | 0.000001 |
ORF1ab/nsp13 | 149 | Y149del2 | tAT | t-- | 1 | 1 | B.1.1.7 | 0.000001 |
ORF1ab/nsp13 | 149 | Y149del | TAT | --- | 1 | 1 | B.1.160.17 | 0.001701 |
ORF1ab/nsp13 | 149 | Y149del | TAT | --- | 1 | 1 | B.1.160.23 | 0.004831 |
ORF1ab/nsp13 | 149 | Y149Y | taT | taC | 1 | 1 | B.1.177 | 0.000013 |
ORF1ab/nsp13 | 149 | Y149C | tAt | tGt | 1 | 1 | B.1.177.5 | 0.001242 |
ORF1ab/nsp13 | 149 | Y149del | TAT | --- | 1 | 1 | B.1.177.73 | 0.000566 |
ORF1ab/nsp13 | 149 | Y149del | TAT | --- | 1 | 1 | B.1.177.83 | 0.001481 |
ORF1ab/nsp13 | 149 | Y149H | Tat | Cat | 1 | 1 | B.1.2 | 0.000009 |
ORF1ab/nsp13 | 149 | Y149H | Tat | Cat | 1 | 1 | B.1.222 | 0.001692 |
ORF1ab/nsp13 | 149 | Y149del | TAT | --- | 1 | 1 | B.1.242 | 0.018868 |
ORF1ab/nsp13 | 149 | Y149I | TAt | ATt | 1 | 1 | B.1.351 | 0.00003 |
ORF1ab/nsp13 | 149 | Y149C | tAt | tGt | 1 | 1 | B.1.351 | 0.00003 |
ORF1ab/nsp13 | 149 | Y149del | TAT | --- | 1 | 1 | B.1.36 | 0.000146 |
ORF1ab/nsp13 | 149 | Y149Y | taT | taC | 1 | 1 | B.1.36.10 | 0.004785 |
ORF1ab/nsp13 | 149 | Y149H | Tat | Cat | 1 | 1 | B.1.369 | 0.000285 |
ORF1ab/nsp13 | 149 | Y149N | Tat | Aat | 1 | 1 | B.1.400 | 0.000429 |
ORF1ab/nsp13 | 149 | Y149C | tAt | tGt | 1 | 1 | B.1.427 | 0.00005 |
ORF1ab/nsp13 | 149 | Y149Y | taT | taC | 1 | 1 | B.1.429 | 0.000024 |
ORF1ab/nsp13 | 149 | Y149S | tAt | tCt | 1 | 1 | B.1.497 | 0.000315 |
ORF1ab/nsp13 | 149 | Y149del | TAT | --- | 1 | 1 | B.1.617.1 | 0.000129 |
ORF1ab/nsp13 | 149 | Y149del1 | taT | ta- | 1 | 1 | B.1.617.1 | 0.000129 |
ORF1ab/nsp13 | 149 | Y149C | tAt | tGt | 1 | 1 | B.1.617.2 | 0.000004 |
ORF1ab/nsp13 | 149 | Y149H | Tat | Cat | 1 | 1 | B.1.617.2 | 0.000004 |
ORF1ab/nsp13 | 149 | Y149H | Tat | Cat | 1 | 1 | B.1.621 | 0.000089 |
ORF1ab/nsp13 | 149 | Y149Y | taT | taC | 1 | 1 | B.1.623 | 0.000536 |
ORF1ab/nsp13 | 149 | Y149C | tAt | tGt | 1 | 1 | B.1.633 | 0.041667 |
ORF1ab/nsp13 | 149 | Y149C | tAt | tGt | 1 | 1 | B.3 | 0.000831 |
ORF1ab/nsp13 | 149 | Y149H | Tat | Cat | 1 | 1 | B.6 | 0.00091 |
ORF1ab/nsp13 | 149 | Y149C | tAt | tGt | 1 | 1 | L.1 | 0.001905 |
ORF1ab/nsp13 | 149 | Y149C | tAt | tGt | 1 | 1 | P.1 | 0.000016 |
ORF1ab/nsp13 | 149 | Y149del | TAT | --- | 1 | 1 | Q.1 | 0.000126 |
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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