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 | 54 | L54L | syn | ttG | ttA | 2370 | 1611 | 0.679747 | 21722-21724 | |
S | 54 | L54L | syn | Ttg | Ctg | 2370 | 756 | 0.318987 | 21722-21724 | |
S | 54 | L54L | syn | TtG | CtT | 2370 | 2 | 0.000843882 | 21722-21724 | |
S | 54 | L54L | syn | TtG | CtA | 2370 | 1 | 0.000421941 | 21722-21724 |
Details of the mutation L54L 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 | 54 | L54L | ttG | ttA | 1611 | 2370 | All | 0.000308 |
S | 54 | L54L | Ttg | Ctg | 756 | 2370 | All | 0.000145 |
S | 54 | L54L | TtG | CtT | 2 | 2370 | All | 0 |
S | 54 | L54L | TtG | CtA | 1 | 2370 | All | 0 |
S | 54 | L54L | ttG | ttA | 706 | 706 | B.1.1.294 | 0.893671 |
S | 54 | L54L | ttG | ttA | 302 | 302 | B.1.177.7 | 0.049786 |
S | 54 | L54L | Ttg | Ctg | 224 | 278 | B.1.1.7 | 0.000201 |
S | 54 | L54L | ttG | ttA | 54 | 278 | B.1.1.7 | 0.000048 |
S | 54 | L54L | Ttg | Ctg | 227 | 245 | B.1.617.2 | 0.000855 |
S | 54 | L54L | ttG | ttA | 18 | 245 | B.1.617.2 | 0.000068 |
S | 54 | L54L | ttG | ttA | 182 | 184 | AY.3 | 0.00181 |
S | 54 | L54L | Ttg | Ctg | 2 | 184 | AY.3 | 0.00002 |
S | 54 | L54L | Ttg | Ctg | 143 | 143 | AY.20 | 0.005558 |
S | 54 | L54L | ttG | ttA | 59 | 60 | B.1.258 | 0.003926 |
S | 54 | L54L | Ttg | Ctg | 1 | 60 | B.1.258 | 0.000067 |
S | 54 | L54L | ttG | ttA | 33 | 47 | AY.4 | 0.000051 |
S | 54 | L54L | Ttg | Ctg | 14 | 47 | AY.4 | 0.000022 |
S | 54 | L54L | Ttg | Ctg | 35 | 44 | B.1.1 | 0.000635 |
S | 54 | L54L | ttG | ttA | 9 | 44 | B.1.1 | 0.000163 |
S | 54 | L54L | ttG | ttA | 43 | 43 | M.1 | 1 |
S | 54 | L54L | Ttg | Ctg | 13 | 18 | AY.43 | 0.000058 |
S | 54 | L54L | ttG | ttA | 5 | 18 | AY.43 | 0.000022 |
S | 54 | L54L | ttG | ttA | 16 | 16 | AY.25 | 0.000096 |
S | 54 | L54L | Ttg | Ctg | 7 | 13 | AY.44 | 0.000043 |
S | 54 | L54L | ttG | ttA | 6 | 13 | AY.44 | 0.000037 |
S | 54 | L54L | ttG | ttA | 13 | 13 | M.3 | 1 |
S | 54 | L54L | ttG | ttA | 9 | 12 | AY.5 | 0.000186 |
S | 54 | L54L | Ttg | Ctg | 3 | 12 | AY.5 | 0.000062 |
S | 54 | L54L | ttG | ttA | 11 | 12 | B.1.429 | 0.000259 |
S | 54 | L54L | Ttg | Ctg | 1 | 12 | B.1.429 | 0.000024 |
S | 54 | L54L | ttG | ttA | 12 | 12 | M.2 | 1 |
S | 54 | L54L | Ttg | Ctg | 8 | 11 | AY.117 | 0.000676 |
S | 54 | L54L | ttG | ttA | 3 | 11 | AY.117 | 0.000254 |
S | 54 | L54L | Ttg | Ctg | 7 | 9 | AY.39 | 0.000173 |
S | 54 | L54L | ttG | ttA | 2 | 9 | AY.39 | 0.000049 |
S | 54 | L54L | Ttg | Ctg | 8 | 8 | AY.45 | 0.000973 |
S | 54 | L54L | ttG | ttA | 7 | 8 | B.1.177 | 0.000092 |
S | 54 | L54L | Ttg | Ctg | 1 | 8 | B.1.177 | 0.000013 |
S | 54 | L54L | ttG | ttA | 7 | 7 | AY.98.1 | 0.000339 |
S | 54 | L54L | ttG | ttA | 7 | 7 | B.1.480 | 0.017413 |
S | 54 | L54L | ttG | ttA | 6 | 6 | AY.47 | 0.000187 |
S | 54 | L54L | ttG | ttA | 5 | 6 | B.1 | 0.000046 |
S | 54 | L54L | Ttg | Ctg | 1 | 6 | B.1 | 0.000009 |
S | 54 | L54L | ttG | ttA | 5 | 6 | B.1.2 | 0.000044 |
S | 54 | L54L | Ttg | Ctg | 1 | 6 | B.1.2 | 0.000009 |
S | 54 | L54L | ttG | ttA | 3 | 5 | AY.103 | 0.000019 |
S | 54 | L54L | Ttg | Ctg | 2 | 5 | AY.103 | 0.000012 |
S | 54 | L54L | ttG | ttA | 5 | 5 | AY.9 | 0.000338 |
S | 54 | L54L | Ttg | Ctg | 3 | 4 | 0.166667 | |
S | 54 | L54L | TtG | CtT | 1 | 4 | 0.055556 | |
S | 54 | L54L | ttG | ttA | 4 | 4 | AY.100 | 0.000184 |
S | 54 | L54L | ttG | ttA | 4 | 4 | AY.26 | 0.000113 |
S | 54 | L54L | Ttg | Ctg | 4 | 4 | B.1.1.216 | 0.003562 |
S | 54 | L54L | ttG | ttA | 4 | 4 | B.1.1.28 | 0.001245 |
S | 54 | L54L | TtG | CtA | 1 | 4 | B.1.1.409 | 0.002833 |
S | 54 | L54L | TtG | CtT | 1 | 4 | B.1.1.409 | 0.002833 |
S | 54 | L54L | ttG | ttA | 1 | 4 | B.1.1.409 | 0.002833 |
S | 54 | L54L | Ttg | Ctg | 1 | 4 | B.1.1.409 | 0.002833 |
S | 54 | L54L | ttG | ttA | 4 | 4 | B.1.258.17 | 0.000416 |
S | 54 | L54L | ttG | ttA | 4 | 4 | B.1.565 | 0.003241 |
S | 54 | L54L | ttG | ttA | 4 | 4 | C.36 | 0.003643 |
S | 54 | L54L | Ttg | Ctg | 2 | 4 | P.1 | 0.000032 |
S | 54 | L54L | ttG | ttA | 2 | 4 | P.1 | 0.000032 |
S | 54 | L54L | Ttg | Ctg | 3 | 3 | AY.118 | 0.000188 |
S | 54 | L54L | Ttg | Ctg | 3 | 3 | AY.36 | 0.000445 |
S | 54 | L54L | Ttg | Ctg | 3 | 3 | AY.48 | 0.001395 |
S | 54 | L54L | Ttg | Ctg | 2 | 3 | AY.53 | 0.000575 |
S | 54 | L54L | ttG | ttA | 1 | 3 | AY.53 | 0.000288 |
S | 54 | L54L | ttG | ttA | 2 | 3 | AY.6 | 0.000082 |
S | 54 | L54L | Ttg | Ctg | 1 | 3 | AY.6 | 0.000041 |
S | 54 | L54L | ttG | ttA | 2 | 3 | AY.65 | 0.001066 |
S | 54 | L54L | Ttg | Ctg | 1 | 3 | AY.65 | 0.000533 |
S | 54 | L54L | ttG | ttA | 3 | 3 | AY.85 | 0.001282 |
S | 54 | L54L | ttG | ttA | 3 | 3 | B | 0.000383 |
S | 54 | L54L | ttG | ttA | 3 | 3 | B.1.1.1 | 0.00098 |
S | 54 | L54L | ttG | ttA | 2 | 3 | B.1.351 | 0.000059 |
S | 54 | L54L | Ttg | Ctg | 1 | 3 | B.1.351 | 0.00003 |
S | 54 | L54L | ttG | ttA | 3 | 3 | B.1.623 | 0.001609 |
S | 54 | L54L | ttG | ttA | 3 | 3 | P.1.14 | 0.000143 |
S | 54 | L54L | Ttg | Ctg | 1 | 2 | AY.119 | 0.000035 |
S | 54 | L54L | ttG | ttA | 1 | 2 | AY.119 | 0.000035 |
S | 54 | L54L | ttG | ttA | 1 | 2 | AY.23.1 | 0.000417 |
S | 54 | L54L | Ttg | Ctg | 1 | 2 | AY.23.1 | 0.000417 |
S | 54 | L54L | ttG | ttA | 2 | 2 | AY.29 | 0.000032 |
S | 54 | L54L | ttG | ttA | 2 | 2 | AY.46 | 0.000208 |
S | 54 | L54L | Ttg | Ctg | 2 | 2 | AY.55 | 0.001835 |
S | 54 | L54L | Ttg | Ctg | 2 | 2 | AY.77 | 0.002255 |
S | 54 | L54L | Ttg | Ctg | 2 | 2 | AY.84 | 0.000875 |
S | 54 | L54L | ttG | ttA | 2 | 2 | AY.9.2 | 0.000073 |
S | 54 | L54L | Ttg | Ctg | 2 | 2 | AY.98 | 0.000158 |
S | 54 | L54L | ttG | ttA | 2 | 2 | B.1.1.464 | 0.002946 |
S | 54 | L54L | ttG | ttA | 2 | 2 | B.1.160 | 0.000062 |
S | 54 | L54L | ttG | ttA | 2 | 2 | B.1.324 | 0.00321 |
S | 54 | L54L | ttG | ttA | 2 | 2 | B.1.445 | 0.023529 |
S | 54 | L54L | Ttg | Ctg | 2 | 2 | B.1.469 | 0.00722 |
S | 54 | L54L | Ttg | Ctg | 2 | 2 | B.1.526 | 0.000047 |
S | 54 | L54L | ttG | ttA | 2 | 2 | P.2 | 0.000373 |
S | 54 | L54L | Ttg | Ctg | 1 | 1 | AY.102 | 0.000027 |
S | 54 | L54L | Ttg | Ctg | 1 | 1 | AY.108 | 0.001103 |
S | 54 | L54L | Ttg | Ctg | 1 | 1 | AY.120 | 0.000037 |
S | 54 | L54L | ttG | ttA | 1 | 1 | AY.23 | 0.00007 |
S | 54 | L54L | ttG | ttA | 1 | 1 | AY.27 | 0.000065 |
S | 54 | L54L | Ttg | Ctg | 1 | 1 | AY.35 | 0.000233 |
S | 54 | L54L | ttG | ttA | 1 | 1 | AY.39.1 | 0.00004 |
S | 54 | L54L | Ttg | Ctg | 1 | 1 | AY.39.2 | 0.001541 |
S | 54 | L54L | Ttg | Ctg | 1 | 1 | AY.41 | 0.000294 |
S | 54 | L54L | Ttg | Ctg | 1 | 1 | AY.42 | 0.00004 |
S | 54 | L54L | Ttg | Ctg | 1 | 1 | AY.46.1 | 0.001027 |
S | 54 | L54L | Ttg | Ctg | 1 | 1 | AY.46.2 | 0.000635 |
S | 54 | L54L | Ttg | Ctg | 1 | 1 | AY.46.6 | 0.000072 |
S | 54 | L54L | Ttg | Ctg | 1 | 1 | AY.7 | 0.000196 |
S | 54 | L54L | Ttg | Ctg | 1 | 1 | AY.71 | 0.000475 |
S | 54 | L54L | Ttg | Ctg | 1 | 1 | AY.73 | 0.000665 |
S | 54 | L54L | Ttg | Ctg | 1 | 1 | AY.82 | 0.001357 |
S | 54 | L54L | ttG | ttA | 1 | 1 | AY.87 | 0.000833 |
S | 54 | L54L | ttG | ttA | 1 | 1 | AY.92 | 0.000287 |
S | 54 | L54L | Ttg | Ctg | 1 | 1 | AY.93 | 0.000273 |
S | 54 | L54L | ttG | ttA | 1 | 1 | B.1.1.205 | 0.003717 |
S | 54 | L54L | Ttg | Ctg | 1 | 1 | B.1.1.214 | 0.000055 |
S | 54 | L54L | ttG | ttA | 1 | 1 | B.1.177.21 | 0.000076 |
S | 54 | L54L | Ttg | Ctg | 1 | 1 | B.1.177.65 | 0.000665 |
S | 54 | L54L | Ttg | Ctg | 1 | 1 | B.1.232 | 0.000537 |
S | 54 | L54L | Ttg | Ctg | 1 | 1 | B.1.258.16 | 0.001637 |
S | 54 | L54L | ttG | ttA | 1 | 1 | B.1.311 | 0.000275 |
S | 54 | L54L | ttG | ttA | 1 | 1 | B.1.36.36 | 0.000602 |
S | 54 | L54L | ttG | ttA | 1 | 1 | B.1.362 | 0.001541 |
S | 54 | L54L | ttG | ttA | 1 | 1 | B.1.409 | 0.000781 |
S | 54 | L54L | ttG | ttA | 1 | 1 | B.1.577 | 0.000687 |
S | 54 | L54L | Ttg | Ctg | 1 | 1 | B.1.595 | 0.000261 |
S | 54 | L54L | ttG | ttA | 1 | 1 | B.1.617.1 | 0.000129 |
S | 54 | L54L | ttG | ttA | 1 | 1 | P.1.15 | 0.000232 |
S | 54 | L54L | ttG | ttA | 1 | 1 | P.1.7 | 0.000319 |
S | 54 | L54L | ttG | ttA | 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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