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/nsp4 | 428 | L428L | L3191L | syn | Cta | Tta | 1317 | 1246 | 0.94609 | 9836-9838 |
ORF1ab/nsp4 | 428 | L428L | L3191L | syn | ctA | ctG | 1317 | 53 | 0.040243 | 9836-9838 |
ORF1ab/nsp4 | 428 | L428L | L3191L | syn | ctA | ctT | 1317 | 14 | 0.0106302 | 9836-9838 |
ORF1ab/nsp4 | 428 | L428L | L3191L | syn | ctA | ctC | 1317 | 4 | 0.00303721 | 9836-9838 |
Details of the mutation L428L 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/nsp4 | 428 | L428L | Cta | Tta | 1246 | 1317 | All | 0.000238 |
ORF1ab/nsp4 | 428 | L428L | ctA | ctG | 53 | 1317 | All | 0.00001 |
ORF1ab/nsp4 | 428 | L428L | ctA | ctT | 14 | 1317 | All | 0.000003 |
ORF1ab/nsp4 | 428 | L428L | ctA | ctC | 4 | 1317 | All | 0.000001 |
ORF1ab/nsp4 | 428 | L428L | Cta | Tta | 664 | 680 | B.1.1.7 | 0.000594 |
ORF1ab/nsp4 | 428 | L428L | ctA | ctG | 15 | 680 | B.1.1.7 | 0.000013 |
ORF1ab/nsp4 | 428 | L428L | ctA | ctT | 1 | 680 | B.1.1.7 | 0.000001 |
ORF1ab/nsp4 | 428 | L428L | Cta | Tta | 67 | 67 | B.1.1.12 | 0.5 |
ORF1ab/nsp4 | 428 | L428L | Cta | Tta | 60 | 60 | B.1.2 | 0.000528 |
ORF1ab/nsp4 | 428 | L428L | Cta | Tta | 60 | 60 | P.1.1 | 0.01906 |
ORF1ab/nsp4 | 428 | L428L | Cta | Tta | 56 | 56 | AY.4 | 0.000087 |
ORF1ab/nsp4 | 428 | L428L | Cta | Tta | 40 | 42 | B.1.617.2 | 0.000151 |
ORF1ab/nsp4 | 428 | L428L | ctA | ctG | 2 | 42 | B.1.617.2 | 0.000008 |
ORF1ab/nsp4 | 428 | L428L | Cta | Tta | 24 | 26 | B.1 | 0.00022 |
ORF1ab/nsp4 | 428 | L428L | ctA | ctT | 1 | 26 | B.1 | 0.000009 |
ORF1ab/nsp4 | 428 | L428L | ctA | ctG | 1 | 26 | B.1 | 0.000009 |
ORF1ab/nsp4 | 428 | L428L | Cta | Tta | 13 | 23 | AY.29 | 0.000205 |
ORF1ab/nsp4 | 428 | L428L | ctA | ctG | 10 | 23 | AY.29 | 0.000158 |
ORF1ab/nsp4 | 428 | L428L | Cta | Tta | 21 | 21 | AY.44 | 0.000128 |
ORF1ab/nsp4 | 428 | L428L | Cta | Tta | 17 | 18 | AY.119 | 0.0006 |
ORF1ab/nsp4 | 428 | L428L | ctA | ctG | 1 | 18 | AY.119 | 0.000035 |
ORF1ab/nsp4 | 428 | L428L | Cta | Tta | 13 | 14 | AY.75 | 0.000728 |
ORF1ab/nsp4 | 428 | L428L | ctA | ctG | 1 | 14 | AY.75 | 0.000056 |
ORF1ab/nsp4 | 428 | L428L | Cta | Tta | 12 | 13 | AY.103 | 0.000075 |
ORF1ab/nsp4 | 428 | L428L | ctA | ctG | 1 | 13 | AY.103 | 0.000006 |
ORF1ab/nsp4 | 428 | L428L | Cta | Tta | 13 | 13 | B.1.1.33 | 0.005471 |
ORF1ab/nsp4 | 428 | L428L | Cta | Tta | 11 | 11 | B.1.1.519 | 0.000437 |
ORF1ab/nsp4 | 428 | L428L | Cta | Tta | 10 | 10 | B.1.582 | 0.004907 |
ORF1ab/nsp4 | 428 | L428L | Cta | Tta | 9 | 9 | AY.43 | 0.00004 |
ORF1ab/nsp4 | 428 | L428L | Cta | Tta | 8 | 8 | AY.47 | 0.000249 |
ORF1ab/nsp4 | 428 | L428L | Cta | Tta | 6 | 8 | B.1.1 | 0.000109 |
ORF1ab/nsp4 | 428 | L428L | ctA | ctT | 1 | 8 | B.1.1 | 0.000018 |
ORF1ab/nsp4 | 428 | L428L | ctA | ctC | 1 | 8 | B.1.1 | 0.000018 |
ORF1ab/nsp4 | 428 | L428L | Cta | Tta | 8 | 8 | B.1.177 | 0.000105 |
ORF1ab/nsp4 | 428 | L428L | Cta | Tta | 3 | 7 | B.1.221 | 0.000213 |
ORF1ab/nsp4 | 428 | L428L | ctA | ctT | 2 | 7 | B.1.221 | 0.000142 |
ORF1ab/nsp4 | 428 | L428L | ctA | ctG | 2 | 7 | B.1.221 | 0.000142 |
ORF1ab/nsp4 | 428 | L428L | ctA | ctT | 5 | 7 | B.1.429 | 0.000118 |
ORF1ab/nsp4 | 428 | L428L | Cta | Tta | 2 | 7 | B.1.429 | 0.000047 |
ORF1ab/nsp4 | 428 | L428L | Cta | Tta | 5 | 6 | AY.25 | 0.00003 |
ORF1ab/nsp4 | 428 | L428L | ctA | ctG | 1 | 6 | AY.25 | 0.000006 |
ORF1ab/nsp4 | 428 | L428L | ctA | ctT | 4 | 6 | B.1.160 | 0.000125 |
ORF1ab/nsp4 | 428 | L428L | ctA | ctC | 1 | 6 | B.1.160 | 0.000031 |
ORF1ab/nsp4 | 428 | L428L | ctA | ctG | 1 | 6 | B.1.160 | 0.000031 |
ORF1ab/nsp4 | 428 | L428L | Cta | Tta | 6 | 6 | B.1.526 | 0.000141 |
ORF1ab/nsp4 | 428 | L428L | Cta | Tta | 5 | 5 | A.1 | 0.001409 |
ORF1ab/nsp4 | 428 | L428L | Cta | Tta | 5 | 5 | AY.20 | 0.000194 |
ORF1ab/nsp4 | 428 | L428L | ctA | ctG | 3 | 5 | AY.5 | 0.000062 |
ORF1ab/nsp4 | 428 | L428L | Cta | Tta | 2 | 5 | AY.5 | 0.000041 |
ORF1ab/nsp4 | 428 | L428L | Cta | Tta | 5 | 5 | B.1.1.157 | 0.004566 |
ORF1ab/nsp4 | 428 | L428L | Cta | Tta | 5 | 5 | B.1.525 | 0.000566 |
ORF1ab/nsp4 | 428 | L428L | Cta | Tta | 4 | 4 | AY.27 | 0.000259 |
ORF1ab/nsp4 | 428 | L428L | Cta | Tta | 4 | 4 | AY.54 | 0.000381 |
ORF1ab/nsp4 | 428 | L428L | Cta | Tta | 4 | 4 | B.1.36.29 | 0.002069 |
ORF1ab/nsp4 | 428 | L428L | Cta | Tta | 2 | 3 | 0.111111 | |
ORF1ab/nsp4 | 428 | L428L | ctA | ctG | 1 | 3 | 0.055556 | |
ORF1ab/nsp4 | 428 | L428L | Cta | Tta | 3 | 3 | AY.3 | 0.00003 |
ORF1ab/nsp4 | 428 | L428L | Cta | Tta | 3 | 3 | AY.30 | 0.001187 |
ORF1ab/nsp4 | 428 | L428L | Cta | Tta | 3 | 3 | AY.38 | 0.001498 |
ORF1ab/nsp4 | 428 | L428L | Cta | Tta | 3 | 3 | AY.39 | 0.000074 |
ORF1ab/nsp4 | 428 | L428L | Cta | Tta | 3 | 3 | AY.45 | 0.000365 |
ORF1ab/nsp4 | 428 | L428L | Cta | Tta | 3 | 3 | AY.7.1 | 0.000338 |
ORF1ab/nsp4 | 428 | L428L | Cta | Tta | 3 | 3 | AY.75.1 | 0.000541 |
ORF1ab/nsp4 | 428 | L428L | Cta | Tta | 3 | 3 | AY.90 | 0.002053 |
ORF1ab/nsp4 | 428 | L428L | Cta | Tta | 3 | 3 | B.1.1.385 | 0.013393 |
ORF1ab/nsp4 | 428 | L428L | ctA | ctG | 3 | 3 | B.1.177.52 | 0.005272 |
ORF1ab/nsp4 | 428 | L428L | Cta | Tta | 3 | 3 | B.1.351 | 0.000089 |
ORF1ab/nsp4 | 428 | L428L | Cta | Tta | 3 | 3 | B.1.427 | 0.000151 |
ORF1ab/nsp4 | 428 | L428L | Cta | Tta | 3 | 3 | B.1.544 | 0.018072 |
ORF1ab/nsp4 | 428 | L428L | Cta | Tta | 3 | 3 | P.1 | 0.000047 |
ORF1ab/nsp4 | 428 | L428L | Cta | Tta | 2 | 2 | AY.99.2 | 0.000184 |
ORF1ab/nsp4 | 428 | L428L | ctA | ctG | 1 | 2 | B | 0.000128 |
ORF1ab/nsp4 | 428 | L428L | Cta | Tta | 1 | 2 | B | 0.000128 |
ORF1ab/nsp4 | 428 | L428L | ctA | ctG | 2 | 2 | B.1.305 | 0.004301 |
ORF1ab/nsp4 | 428 | L428L | Cta | Tta | 2 | 2 | B.1.409 | 0.001563 |
ORF1ab/nsp4 | 428 | L428L | Cta | Tta | 2 | 2 | B.1.617.1 | 0.000258 |
ORF1ab/nsp4 | 428 | L428L | Cta | Tta | 2 | 2 | B.1.621 | 0.000177 |
ORF1ab/nsp4 | 428 | L428L | Cta | Tta | 2 | 2 | N.1 | 0.033898 |
ORF1ab/nsp4 | 428 | L428L | Cta | Tta | 2 | 2 | R.1 | 0.00018 |
ORF1ab/nsp4 | 428 | L428L | ctA | ctG | 1 | 1 | A.2.5 | 0.000499 |
ORF1ab/nsp4 | 428 | L428L | Cta | Tta | 1 | 1 | AY.100 | 0.000046 |
ORF1ab/nsp4 | 428 | L428L | Cta | Tta | 1 | 1 | AY.102 | 0.000027 |
ORF1ab/nsp4 | 428 | L428L | Cta | Tta | 1 | 1 | AY.14 | 0.000088 |
ORF1ab/nsp4 | 428 | L428L | Cta | Tta | 1 | 1 | AY.28 | 0.00189 |
ORF1ab/nsp4 | 428 | L428L | Cta | Tta | 1 | 1 | AY.3.1 | 0.000085 |
ORF1ab/nsp4 | 428 | L428L | ctA | ctG | 1 | 1 | AY.36 | 0.000148 |
ORF1ab/nsp4 | 428 | L428L | Cta | Tta | 1 | 1 | AY.4.5 | 0.000107 |
ORF1ab/nsp4 | 428 | L428L | Cta | Tta | 1 | 1 | AY.6 | 0.000041 |
ORF1ab/nsp4 | 428 | L428L | Cta | Tta | 1 | 1 | AY.61 | 0.000105 |
ORF1ab/nsp4 | 428 | L428L | Cta | Tta | 1 | 1 | AY.9.1 | 0.000084 |
ORF1ab/nsp4 | 428 | L428L | ctA | ctG | 1 | 1 | AY.98 | 0.000079 |
ORF1ab/nsp4 | 428 | L428L | Cta | Tta | 1 | 1 | B.1.1.176 | 0.000439 |
ORF1ab/nsp4 | 428 | L428L | Cta | Tta | 1 | 1 | B.1.1.237 | 0.005405 |
ORF1ab/nsp4 | 428 | L428L | Cta | Tta | 1 | 1 | B.1.1.28 | 0.000311 |
ORF1ab/nsp4 | 428 | L428L | Cta | Tta | 1 | 1 | B.1.1.306 | 0.000438 |
ORF1ab/nsp4 | 428 | L428L | ctA | ctC | 1 | 1 | B.1.1.326 | 0.001761 |
ORF1ab/nsp4 | 428 | L428L | Cta | Tta | 1 | 1 | B.1.1.376 | 0.005952 |
ORF1ab/nsp4 | 428 | L428L | ctA | ctG | 1 | 1 | B.1.1.416 | 0.000905 |
ORF1ab/nsp4 | 428 | L428L | ctA | ctG | 1 | 1 | B.1.1.50 | 0.000679 |
ORF1ab/nsp4 | 428 | L428L | Cta | Tta | 1 | 1 | B.1.177.18 | 0.00116 |
ORF1ab/nsp4 | 428 | L428L | Cta | Tta | 1 | 1 | B.1.177.21 | 0.000076 |
ORF1ab/nsp4 | 428 | L428L | ctA | ctC | 1 | 1 | B.1.177.33 | 0.001645 |
ORF1ab/nsp4 | 428 | L428L | Cta | Tta | 1 | 1 | B.1.177.60 | 0.000218 |
ORF1ab/nsp4 | 428 | L428L | Cta | Tta | 1 | 1 | B.1.177.81 | 0.000189 |
ORF1ab/nsp4 | 428 | L428L | Cta | Tta | 1 | 1 | B.1.210 | 0.002132 |
ORF1ab/nsp4 | 428 | L428L | Cta | Tta | 1 | 1 | B.1.258 | 0.000067 |
ORF1ab/nsp4 | 428 | L428L | Cta | Tta | 1 | 1 | B.1.361 | 0.001289 |
ORF1ab/nsp4 | 428 | L428L | ctA | ctG | 1 | 1 | B.1.480 | 0.002488 |
ORF1ab/nsp4 | 428 | L428L | Cta | Tta | 1 | 1 | B.1.497 | 0.000315 |
ORF1ab/nsp4 | 428 | L428L | Cta | Tta | 1 | 1 | B.1.561 | 0.000397 |
ORF1ab/nsp4 | 428 | L428L | Cta | Tta | 1 | 1 | B.1.575 | 0.000303 |
ORF1ab/nsp4 | 428 | L428L | Cta | Tta | 1 | 1 | B.1.596 | 0.000087 |
ORF1ab/nsp4 | 428 | L428L | Cta | Tta | 1 | 1 | B.1.612 | 0.002653 |
ORF1ab/nsp4 | 428 | L428L | Cta | Tta | 1 | 1 | C.37 | 0.000116 |
ORF1ab/nsp4 | 428 | L428L | Cta | Tta | 1 | 1 | D.2 | 0.000075 |
ORF1ab/nsp4 | 428 | L428L | Cta | Tta | 1 | 1 | P.1.14 | 0.000048 |
ORF1ab/nsp4 | 428 | L428L | ctA | ctG | 1 | 1 | P.1.7 | 0.000319 |
ORF1ab/nsp4 | 428 | L428L | ctA | ctG | 1 | 1 | P.2 | 0.000187 |
ORF1ab/nsp4 | 428 | L428L | Cta | Tta | 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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