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 | 728 | Y728Y | Y5120Y | syn | taT | taC | 399 | 399 | 1 | 15622-15624 |
ORF1ab/nsp12 | 728 | Y728del | Y5120del | del | TAT | --- | 42 | 42 | 1 | 15622-15624 |
ORF1ab/nsp12 | 728 | Y728F | Y5120F | nonsyn | tAt | tTt | 7 | 7 | 1 | 15622-15624 |
ORF1ab/nsp12 | 728 | Y728H | Y5120H | nonsyn | Tat | Cat | 5 | 5 | 1 | 15622-15624 |
ORF1ab/nsp12 | 728 | Y728S | Y5120S | nonsyn | tAt | tCt | 2 | 2 | 1 | 15622-15624 |
ORF1ab/nsp12 | 728 | Y728del2 | Y5120del2 | del | TAt | --t | 2 | 1 | 0.5 | 15622-15624 |
ORF1ab/nsp12 | 728 | Y728del2 | Y5120del2 | del | TAT | C-- | 2 | 1 | 0.5 | 15622-15624 |
ORF1ab/nsp12 | 728 | Y728C | Y5120C | nonsyn | tAT | tGC | 1 | 1 | 1 | 15622-15624 |
ORF1ab/nsp12 | 728 | Y728R | Y5120R | nonsyn | TAt | CGt | 1 | 1 | 1 | 15622-15624 |
ORF1ab/nsp12 | 728 | Y728X | Y5120X | nonsyn | taT | taA | 1 | 1 | 1 | 15622-15624 |
ORF1ab/nsp12 | 728 | Y728L | Y5120L | nonsyn | TAt | CTt | 1 | 1 | 1 | 15622-15624 |
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 | 728 | Y728Y | taT | taC | 399 | 399 | All | 0.000076 |
ORF1ab/nsp12 | 728 | Y728Y | taT | taC | 94 | 94 | B.1.423 | 0.959184 |
ORF1ab/nsp12 | 728 | Y728Y | taT | taC | 83 | 83 | B.1.1.7 | 0.000074 |
ORF1ab/nsp12 | 728 | Y728del | TAT | --- | 42 | 42 | All | 0.000008 |
ORF1ab/nsp12 | 728 | Y728Y | taT | taC | 37 | 37 | B.1 | 0.000339 |
ORF1ab/nsp12 | 728 | Y728Y | taT | taC | 29 | 29 | AY.4 | 0.000045 |
ORF1ab/nsp12 | 728 | Y728Y | taT | taC | 28 | 28 | AY.25 | 0.000168 |
ORF1ab/nsp12 | 728 | Y728Y | taT | taC | 14 | 14 | AY.120.1 | 0.004494 |
ORF1ab/nsp12 | 728 | Y728Y | taT | taC | 12 | 12 | AY.103 | 0.000075 |
ORF1ab/nsp12 | 728 | Y728del | TAT | --- | 12 | 12 | B.1.1.7 | 0.000011 |
ORF1ab/nsp12 | 728 | Y728Y | taT | taC | 10 | 10 | AY.3 | 0.000099 |
ORF1ab/nsp12 | 728 | Y728Y | taT | taC | 9 | 9 | AY.44 | 0.000055 |
ORF1ab/nsp12 | 728 | Y728Y | taT | taC | 9 | 9 | AY.98 | 0.000711 |
ORF1ab/nsp12 | 728 | Y728Y | taT | taC | 9 | 9 | B.1.617.2 | 0.000034 |
ORF1ab/nsp12 | 728 | Y728del | TAT | --- | 8 | 8 | 0.444444 | |
ORF1ab/nsp12 | 728 | Y728F | tAt | tTt | 7 | 7 | All | 0.000001 |
ORF1ab/nsp12 | 728 | Y728Y | taT | taC | 7 | 7 | B.1.221 | 0.000497 |
ORF1ab/nsp12 | 728 | Y728H | Tat | Cat | 5 | 5 | All | 0.000001 |
ORF1ab/nsp12 | 728 | Y728Y | taT | taC | 5 | 5 | AY.116.1 | 0.001557 |
ORF1ab/nsp12 | 728 | Y728Y | taT | taC | 5 | 5 | AY.75 | 0.00028 |
ORF1ab/nsp12 | 728 | Y728Y | taT | taC | 5 | 5 | P.1 | 0.000079 |
ORF1ab/nsp12 | 728 | Y728Y | taT | taC | 4 | 4 | AY.43 | 0.000018 |
ORF1ab/nsp12 | 728 | Y728Y | taT | taC | 4 | 4 | AY.46.4 | 0.000658 |
ORF1ab/nsp12 | 728 | Y728Y | taT | taC | 3 | 3 | B.1.36.8 | 0.003 |
ORF1ab/nsp12 | 728 | Y728Y | taT | taC | 3 | 3 | B.1.404 | 0.003906 |
ORF1ab/nsp12 | 728 | Y728S | tAt | tCt | 2 | 2 | All | 0 |
ORF1ab/nsp12 | 728 | Y728del2 | TAt | --t | 1 | 2 | All | 0 |
ORF1ab/nsp12 | 728 | Y728del2 | TAT | C-- | 1 | 2 | All | 0 |
ORF1ab/nsp12 | 728 | Y728Y | taT | taC | 2 | 2 | AY.113 | 0.000285 |
ORF1ab/nsp12 | 728 | Y728Y | taT | taC | 2 | 2 | AY.16 | 0.000759 |
ORF1ab/nsp12 | 728 | Y728Y | taT | taC | 2 | 2 | AY.26 | 0.000057 |
ORF1ab/nsp12 | 728 | Y728del | TAT | --- | 2 | 2 | AY.4 | 0.000003 |
ORF1ab/nsp12 | 728 | Y728del | TAT | --- | 2 | 2 | AY.4.5 | 0.000215 |
ORF1ab/nsp12 | 728 | Y728Y | taT | taC | 2 | 2 | AY.55 | 0.001835 |
ORF1ab/nsp12 | 728 | Y728del | TAT | --- | 2 | 2 | B.1 | 0.000018 |
ORF1ab/nsp12 | 728 | Y728del | TAT | --- | 2 | 2 | B.1.1 | 0.000036 |
ORF1ab/nsp12 | 728 | Y728del | TAT | --- | 2 | 2 | B.1.1.311 | 0.000716 |
ORF1ab/nsp12 | 728 | Y728del | TAT | --- | 2 | 2 | B.1.177 | 0.000026 |
ORF1ab/nsp12 | 728 | Y728Y | taT | taC | 2 | 2 | B.1.243 | 0.000139 |
ORF1ab/nsp12 | 728 | Y728Y | taT | taC | 2 | 2 | B.1.526 | 0.000047 |
ORF1ab/nsp12 | 728 | Y728del | TAT | --- | 2 | 2 | B.1.617.2 | 0.000008 |
ORF1ab/nsp12 | 728 | Y728X | taT | taA | 1 | 1 | All | 0 |
ORF1ab/nsp12 | 728 | Y728R | TAt | CGt | 1 | 1 | All | 0 |
ORF1ab/nsp12 | 728 | Y728C | tAT | tGC | 1 | 1 | All | 0 |
ORF1ab/nsp12 | 728 | Y728L | TAt | CTt | 1 | 1 | All | 0 |
ORF1ab/nsp12 | 728 | Y728Y | taT | taC | 1 | 1 | AY.117 | 0.000085 |
ORF1ab/nsp12 | 728 | Y728Y | taT | taC | 1 | 1 | AY.119 | 0.000035 |
ORF1ab/nsp12 | 728 | Y728Y | taT | taC | 1 | 1 | AY.120 | 0.000037 |
ORF1ab/nsp12 | 728 | Y728Y | taT | taC | 1 | 1 | AY.16.1 | 0.00047 |
ORF1ab/nsp12 | 728 | Y728F | tAt | tTt | 1 | 1 | AY.25 | 0.000006 |
ORF1ab/nsp12 | 728 | Y728F | tAt | tTt | 1 | 1 | AY.26 | 0.000028 |
ORF1ab/nsp12 | 728 | Y728del2 | TAT | C-- | 1 | 1 | AY.3 | 0.00001 |
ORF1ab/nsp12 | 728 | Y728del | TAT | --- | 1 | 1 | AY.43 | 0.000004 |
ORF1ab/nsp12 | 728 | Y728S | tAt | tCt | 1 | 1 | AY.44 | 0.000006 |
ORF1ab/nsp12 | 728 | Y728C | tAT | tGC | 1 | 1 | AY.44 | 0.000006 |
ORF1ab/nsp12 | 728 | Y728Y | taT | taC | 1 | 1 | AY.5 | 0.000021 |
ORF1ab/nsp12 | 728 | Y728Y | taT | taC | 1 | 1 | AY.58 | 0.000907 |
ORF1ab/nsp12 | 728 | Y728R | TAt | CGt | 1 | 1 | AY.67 | 0.000464 |
ORF1ab/nsp12 | 728 | Y728Y | taT | taC | 1 | 1 | AY.75.1 | 0.00018 |
ORF1ab/nsp12 | 728 | Y728del | TAT | --- | 1 | 1 | AY.9 | 0.000068 |
ORF1ab/nsp12 | 728 | Y728Y | taT | taC | 1 | 1 | AY.9.2 | 0.000037 |
ORF1ab/nsp12 | 728 | Y728F | tAt | tTt | 1 | 1 | B | 0.000128 |
ORF1ab/nsp12 | 728 | Y728H | Tat | Cat | 1 | 1 | B.1 | 0.000009 |
ORF1ab/nsp12 | 728 | Y728F | tAt | tTt | 1 | 1 | B.1 | 0.000009 |
ORF1ab/nsp12 | 728 | Y728S | tAt | tCt | 1 | 1 | B.1 | 0.000009 |
ORF1ab/nsp12 | 728 | Y728del2 | TAt | --t | 1 | 1 | B.1 | 0.000009 |
ORF1ab/nsp12 | 728 | Y728X | taT | taA | 1 | 1 | B.1.1 | 0.000018 |
ORF1ab/nsp12 | 728 | Y728F | tAt | tTt | 1 | 1 | B.1.1 | 0.000018 |
ORF1ab/nsp12 | 728 | Y728Y | taT | taC | 1 | 1 | B.1.1 | 0.000018 |
ORF1ab/nsp12 | 728 | Y728L | TAt | CTt | 1 | 1 | B.1.1.315 | 0.008475 |
ORF1ab/nsp12 | 728 | Y728H | Tat | Cat | 1 | 1 | B.1.1.39 | 0.00051 |
ORF1ab/nsp12 | 728 | Y728F | tAt | tTt | 1 | 1 | B.1.1.7 | 0.000001 |
ORF1ab/nsp12 | 728 | Y728del | TAT | --- | 1 | 1 | B.1.1.70 | 0.000341 |
ORF1ab/nsp12 | 728 | Y728H | Tat | Cat | 1 | 1 | B.1.160 | 0.000031 |
ORF1ab/nsp12 | 728 | Y728del | TAT | --- | 1 | 1 | B.1.177.19 | 0.001431 |
ORF1ab/nsp12 | 728 | Y728H | Tat | Cat | 1 | 1 | B.1.177.42 | 0.000894 |
ORF1ab/nsp12 | 728 | Y728del | TAT | --- | 1 | 1 | B.1.177.51 | 0.004566 |
ORF1ab/nsp12 | 728 | Y728Y | taT | taC | 1 | 1 | B.1.177.77 | 0.000726 |
ORF1ab/nsp12 | 728 | Y728del | TAT | --- | 1 | 1 | B.1.177.87 | 0.000728 |
ORF1ab/nsp12 | 728 | Y728Y | taT | taC | 1 | 1 | B.1.2 | 0.000009 |
ORF1ab/nsp12 | 728 | Y728del | TAT | --- | 1 | 1 | B.1.258 | 0.000067 |
ORF1ab/nsp12 | 728 | Y728H | Tat | Cat | 1 | 1 | B.1.284 | 0.013158 |
ORF1ab/nsp12 | 728 | Y728Y | taT | taC | 1 | 1 | B.1.351 | 0.00003 |
ORF1ab/nsp12 | 728 | Y728Y | taT | taC | 1 | 1 | B.1.370 | 0.008 |
ORF1ab/nsp12 | 728 | Y728Y | taT | taC | 1 | 1 | B.1.588 | 0.00091 |
ORF1ab/nsp12 | 728 | Y728Y | taT | taC | 1 | 1 | B.1.595 | 0.000261 |
ORF1ab/nsp12 | 728 | Y728Y | taT | taC | 1 | 1 | B.1.621 | 0.000089 |
ORF1ab/nsp12 | 728 | Y728Y | taT | taC | 1 | 1 | P.1.14 | 0.000048 |
ORF1ab/nsp12 | 728 | Y728del | TAT | --- | 1 | 1 | Q.1 | 0.000126 |
ORF1ab/nsp12 | 728 | Y728F | tAt | tTt | 1 | 1 | Q.3 | 0.000145 |
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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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