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 |
ORF7a | 59 | F59L | nonsyn | ttT | ttA | 301 | 173 | 0.574751 | 27568-27570 | |
ORF7a | 59 | F59L | nonsyn | Ttt | Ctt | 301 | 107 | 0.355482 | 27568-27570 | |
ORF7a | 59 | F59L | nonsyn | ttT | ttG | 301 | 13 | 0.0431894 | 27568-27570 | |
ORF7a | 59 | F59L | nonsyn | TtT | CtG | 301 | 3 | 0.00996678 | 27568-27570 | |
ORF7a | 59 | F59L | nonsyn | TtT | CtA | 301 | 3 | 0.00996678 | 27568-27570 | |
ORF7a | 59 | F59L | nonsyn | TtT | CtC | 301 | 2 | 0.00664452 | 27568-27570 |
Details of the mutation F59L 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 |
ORF7a | 59 | F59L | ttT | ttA | 173 | 301 | All | 0.000033 |
ORF7a | 59 | F59L | Ttt | Ctt | 107 | 301 | All | 0.00002 |
ORF7a | 59 | F59L | ttT | ttG | 13 | 301 | All | 0.000002 |
ORF7a | 59 | F59L | TtT | CtA | 3 | 301 | All | 0.000001 |
ORF7a | 59 | F59L | TtT | CtG | 3 | 301 | All | 0.000001 |
ORF7a | 59 | F59L | TtT | CtC | 2 | 301 | All | 0 |
ORF7a | 59 | F59L | ttT | ttA | 38 | 51 | B.1.1.7 | 0.000034 |
ORF7a | 59 | F59L | Ttt | Ctt | 12 | 51 | B.1.1.7 | 0.000011 |
ORF7a | 59 | F59L | ttT | ttG | 1 | 51 | B.1.1.7 | 0.000001 |
ORF7a | 59 | F59L | ttT | ttA | 19 | 26 | AY.25 | 0.000114 |
ORF7a | 59 | F59L | Ttt | Ctt | 2 | 26 | AY.25 | 0.000012 |
ORF7a | 59 | F59L | ttT | ttG | 2 | 26 | AY.25 | 0.000012 |
ORF7a | 59 | F59L | TtT | CtA | 1 | 26 | AY.25 | 0.000006 |
ORF7a | 59 | F59L | TtT | CtC | 1 | 26 | AY.25 | 0.000006 |
ORF7a | 59 | F59L | TtT | CtG | 1 | 26 | AY.25 | 0.000006 |
ORF7a | 59 | F59L | Ttt | Ctt | 14 | 25 | AY.44 | 0.000085 |
ORF7a | 59 | F59L | ttT | ttA | 10 | 25 | AY.44 | 0.000061 |
ORF7a | 59 | F59L | ttT | ttG | 1 | 25 | AY.44 | 0.000006 |
ORF7a | 59 | F59L | ttT | ttA | 16 | 24 | AY.43 | 0.000071 |
ORF7a | 59 | F59L | Ttt | Ctt | 7 | 24 | AY.43 | 0.000031 |
ORF7a | 59 | F59L | ttT | ttG | 1 | 24 | AY.43 | 0.000004 |
ORF7a | 59 | F59L | Ttt | Ctt | 12 | 22 | B.1.617.2 | 0.000045 |
ORF7a | 59 | F59L | ttT | ttA | 8 | 22 | B.1.617.2 | 0.00003 |
ORF7a | 59 | F59L | TtT | CtG | 1 | 22 | B.1.617.2 | 0.000004 |
ORF7a | 59 | F59L | ttT | ttG | 1 | 22 | B.1.617.2 | 0.000004 |
ORF7a | 59 | F59L | ttT | ttA | 18 | 18 | AY.103 | 0.000112 |
ORF7a | 59 | F59L | Ttt | Ctt | 13 | 17 | AY.3 | 0.000129 |
ORF7a | 59 | F59L | ttT | ttA | 4 | 17 | AY.3 | 0.00004 |
ORF7a | 59 | F59L | ttT | ttA | 6 | 10 | AY.4 | 0.000009 |
ORF7a | 59 | F59L | Ttt | Ctt | 3 | 10 | AY.4 | 0.000005 |
ORF7a | 59 | F59L | ttT | ttG | 1 | 10 | AY.4 | 0.000002 |
ORF7a | 59 | F59L | Ttt | Ctt | 10 | 10 | B.1.177 | 0.000132 |
ORF7a | 59 | F59L | ttT | ttA | 7 | 9 | B.1.2 | 0.000062 |
ORF7a | 59 | F59L | Ttt | Ctt | 2 | 9 | B.1.2 | 0.000018 |
ORF7a | 59 | F59L | Ttt | Ctt | 5 | 6 | AY.102 | 0.000133 |
ORF7a | 59 | F59L | ttT | ttA | 1 | 6 | AY.102 | 0.000027 |
ORF7a | 59 | F59L | Ttt | Ctt | 3 | 5 | B.1 | 0.000027 |
ORF7a | 59 | F59L | ttT | ttA | 2 | 5 | B.1 | 0.000018 |
ORF7a | 59 | F59L | ttT | ttA | 4 | 4 | AY.5 | 0.000083 |
ORF7a | 59 | F59L | ttT | ttA | 3 | 4 | B.1.177.21 | 0.000229 |
ORF7a | 59 | F59L | TtT | CtA | 1 | 4 | B.1.177.21 | 0.000076 |
ORF7a | 59 | F59L | TtT | CtA | 1 | 4 | B.1.351 | 0.00003 |
ORF7a | 59 | F59L | ttT | ttA | 1 | 4 | B.1.351 | 0.00003 |
ORF7a | 59 | F59L | TtT | CtC | 1 | 4 | B.1.351 | 0.00003 |
ORF7a | 59 | F59L | Ttt | Ctt | 1 | 4 | B.1.351 | 0.00003 |
ORF7a | 59 | F59L | ttT | ttA | 3 | 4 | P.1 | 0.000047 |
ORF7a | 59 | F59L | Ttt | Ctt | 1 | 4 | P.1 | 0.000016 |
ORF7a | 59 | F59L | ttT | ttA | 3 | 3 | AY.118 | 0.000188 |
ORF7a | 59 | F59L | ttT | ttA | 2 | 3 | AY.120 | 0.000074 |
ORF7a | 59 | F59L | Ttt | Ctt | 1 | 3 | AY.120 | 0.000037 |
ORF7a | 59 | F59L | ttT | ttA | 3 | 3 | B.1.1.37 | 0.000579 |
ORF7a | 59 | F59L | Ttt | Ctt | 2 | 2 | 0.111111 | |
ORF7a | 59 | F59L | Ttt | Ctt | 2 | 2 | AD.2 | 0.000438 |
ORF7a | 59 | F59L | Ttt | Ctt | 2 | 2 | AY.29 | 0.000032 |
ORF7a | 59 | F59L | ttT | ttG | 1 | 2 | AY.39 | 0.000025 |
ORF7a | 59 | F59L | ttT | ttA | 1 | 2 | AY.39 | 0.000025 |
ORF7a | 59 | F59L | Ttt | Ctt | 1 | 2 | AY.54 | 0.000095 |
ORF7a | 59 | F59L | ttT | ttG | 1 | 2 | AY.54 | 0.000095 |
ORF7a | 59 | F59L | ttT | ttG | 1 | 2 | B.1.1 | 0.000018 |
ORF7a | 59 | F59L | Ttt | Ctt | 1 | 2 | B.1.1 | 0.000018 |
ORF7a | 59 | F59L | ttT | ttA | 2 | 2 | B.1.160 | 0.000062 |
ORF7a | 59 | F59L | ttT | ttA | 2 | 2 | B.1.415.1 | 0.015152 |
ORF7a | 59 | F59L | ttT | ttA | 1 | 2 | B.40 | 0.000364 |
ORF7a | 59 | F59L | ttT | ttG | 1 | 2 | B.40 | 0.000364 |
ORF7a | 59 | F59L | ttT | ttA | 1 | 1 | AY.1 | 0.000396 |
ORF7a | 59 | F59L | Ttt | Ctt | 1 | 1 | AY.116 | 0.000287 |
ORF7a | 59 | F59L | ttT | ttA | 1 | 1 | AY.117 | 0.000085 |
ORF7a | 59 | F59L | ttT | ttA | 1 | 1 | AY.121 | 0.000135 |
ORF7a | 59 | F59L | Ttt | Ctt | 1 | 1 | AY.23 | 0.00007 |
ORF7a | 59 | F59L | ttT | ttA | 1 | 1 | AY.26 | 0.000028 |
ORF7a | 59 | F59L | Ttt | Ctt | 1 | 1 | AY.27 | 0.000065 |
ORF7a | 59 | F59L | ttT | ttA | 1 | 1 | AY.4.2 | 0.000022 |
ORF7a | 59 | F59L | ttT | ttA | 1 | 1 | AY.42 | 0.00004 |
ORF7a | 59 | F59L | ttT | ttA | 1 | 1 | AY.46.4 | 0.000165 |
ORF7a | 59 | F59L | ttT | ttA | 1 | 1 | AY.61 | 0.000105 |
ORF7a | 59 | F59L | Ttt | Ctt | 1 | 1 | AY.65 | 0.000533 |
ORF7a | 59 | F59L | ttT | ttA | 1 | 1 | AY.74 | 0.000116 |
ORF7a | 59 | F59L | ttT | ttA | 1 | 1 | AY.75 | 0.000056 |
ORF7a | 59 | F59L | ttT | ttA | 1 | 1 | AY.9 | 0.000068 |
ORF7a | 59 | F59L | Ttt | Ctt | 1 | 1 | AY.99.2 | 0.000092 |
ORF7a | 59 | F59L | ttT | ttA | 1 | 1 | B.1.1.214 | 0.000055 |
ORF7a | 59 | F59L | ttT | ttG | 1 | 1 | B.1.1.225 | 0.007194 |
ORF7a | 59 | F59L | ttT | ttG | 1 | 1 | B.1.1.303 | 0.002762 |
ORF7a | 59 | F59L | ttT | ttA | 1 | 1 | B.1.1.317 | 0.000412 |
ORF7a | 59 | F59L | Ttt | Ctt | 1 | 1 | B.1.1.377 | 0.001381 |
ORF7a | 59 | F59L | Ttt | Ctt | 1 | 1 | B.1.1.409 | 0.002833 |
ORF7a | 59 | F59L | ttT | ttA | 1 | 1 | B.1.1.50 | 0.000679 |
ORF7a | 59 | F59L | Ttt | Ctt | 1 | 1 | B.1.149 | 0.003425 |
ORF7a | 59 | F59L | ttT | ttA | 1 | 1 | B.1.177.12 | 0.000152 |
ORF7a | 59 | F59L | TtT | CtG | 1 | 1 | B.1.177.63 | 0.002703 |
ORF7a | 59 | F59L | ttT | ttA | 1 | 1 | B.1.258 | 0.000067 |
ORF7a | 59 | F59L | Ttt | Ctt | 1 | 1 | B.1.258.11 | 0.000396 |
ORF7a | 59 | F59L | Ttt | Ctt | 1 | 1 | B.1.36 | 0.000146 |
ORF7a | 59 | F59L | Ttt | Ctt | 1 | 1 | B.1.389 | 0.001002 |
ORF7a | 59 | F59L | Ttt | Ctt | 1 | 1 | B.1.398 | 0.002976 |
ORF7a | 59 | F59L | ttT | ttA | 1 | 1 | B.1.429 | 0.000024 |
ORF7a | 59 | F59L | ttT | ttA | 1 | 1 | B.1.630 | 0.005236 |
ORF7a | 59 | F59L | Ttt | Ctt | 1 | 1 | D.2 | 0.000075 |
ORF7a | 59 | F59L | ttT | ttA | 1 | 1 | P.1.4 | 0.000977 |
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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