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 |
ORF3a | 62 | I62T | nonsyn | aTc | aCc | 4091 | 4085 | 0.998533 | 25576-25578 | |
ORF3a | 62 | I62T | nonsyn | aTC | aCT | 4091 | 6 | 0.00146663 | 25576-25578 |
Details of the mutation I62T 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 |
ORF3a | 62 | I62T | aTc | aCc | 4085 | 4091 | All | 0.000781 |
ORF3a | 62 | I62T | aTC | aCT | 6 | 4091 | All | 0.000001 |
ORF3a | 62 | I62T | aTc | aCc | 2481 | 2482 | B.1.561 | 0.984915 |
ORF3a | 62 | I62T | aTC | aCT | 1 | 2482 | B.1.561 | 0.000397 |
ORF3a | 62 | I62T | aTc | aCc | 539 | 539 | B.1.438.1 | 0.057814 |
ORF3a | 62 | I62T | aTc | aCc | 206 | 206 | B.1.1.294 | 0.260759 |
ORF3a | 62 | I62T | aTc | aCc | 177 | 180 | B.1.1.7 | 0.000158 |
ORF3a | 62 | I62T | aTC | aCT | 3 | 180 | B.1.1.7 | 0.000003 |
ORF3a | 62 | I62T | aTc | aCc | 85 | 85 | B.1 | 0.000779 |
ORF3a | 62 | I62T | aTc | aCc | 80 | 82 | B.1.177 | 0.001053 |
ORF3a | 62 | I62T | aTC | aCT | 2 | 82 | B.1.177 | 0.000026 |
ORF3a | 62 | I62T | aTc | aCc | 47 | 47 | B.1.617.2 | 0.000177 |
ORF3a | 62 | I62T | aTc | aCc | 38 | 38 | AY.4 | 0.000059 |
ORF3a | 62 | I62T | aTc | aCc | 34 | 34 | B.1.2 | 0.000299 |
ORF3a | 62 | I62T | aTc | aCc | 33 | 33 | AY.47 | 0.001026 |
ORF3a | 62 | I62T | aTc | aCc | 27 | 27 | B.1.1 | 0.00049 |
ORF3a | 62 | I62T | aTc | aCc | 23 | 23 | B.3 | 0.019103 |
ORF3a | 62 | I62T | aTc | aCc | 16 | 16 | AY.39 | 0.000395 |
ORF3a | 62 | I62T | aTc | aCc | 15 | 15 | AY.9 | 0.001014 |
ORF3a | 62 | I62T | aTc | aCc | 14 | 14 | AY.44 | 0.000085 |
ORF3a | 62 | I62T | aTc | aCc | 12 | 12 | AY.102 | 0.000318 |
ORF3a | 62 | I62T | aTc | aCc | 11 | 11 | AY.103 | 0.000068 |
ORF3a | 62 | I62T | aTc | aCc | 11 | 11 | AY.25 | 0.000066 |
ORF3a | 62 | I62T | aTc | aCc | 8 | 8 | AY.39.1 | 0.000317 |
ORF3a | 62 | I62T | aTc | aCc | 8 | 8 | AY.48 | 0.003721 |
ORF3a | 62 | I62T | aTc | aCc | 8 | 8 | P.1 | 0.000126 |
ORF3a | 62 | I62T | aTc | aCc | 8 | 8 | P.1.14 | 0.000382 |
ORF3a | 62 | I62T | aTc | aCc | 7 | 7 | AY.23 | 0.000488 |
ORF3a | 62 | I62T | aTc | aCc | 7 | 7 | AY.43 | 0.000031 |
ORF3a | 62 | I62T | aTc | aCc | 7 | 7 | AY.92 | 0.002011 |
ORF3a | 62 | I62T | aTc | aCc | 7 | 7 | B.1.232 | 0.003761 |
ORF3a | 62 | I62T | aTc | aCc | 6 | 6 | B.1.577 | 0.004124 |
ORF3a | 62 | I62T | aTc | aCc | 5 | 5 | AY.3 | 0.00005 |
ORF3a | 62 | I62T | aTc | aCc | 5 | 5 | AY.42 | 0.000201 |
ORF3a | 62 | I62T | aTc | aCc | 5 | 5 | AY.75 | 0.00028 |
ORF3a | 62 | I62T | aTc | aCc | 5 | 5 | B.1.1.519 | 0.000199 |
ORF3a | 62 | I62T | aTc | aCc | 5 | 5 | B.1.241 | 0.004058 |
ORF3a | 62 | I62T | aTc | aCc | 5 | 5 | B.1.281 | 0.108696 |
ORF3a | 62 | I62T | aTc | aCc | 5 | 5 | B.1.582 | 0.002453 |
ORF3a | 62 | I62T | aTc | aCc | 5 | 5 | B.1.618 | 0.020161 |
ORF3a | 62 | I62T | aTc | aCc | 4 | 4 | AY.110 | 0.000451 |
ORF3a | 62 | I62T | aTc | aCc | 4 | 4 | AY.116 | 0.001147 |
ORF3a | 62 | I62T | aTc | aCc | 4 | 4 | AY.5 | 0.000083 |
ORF3a | 62 | I62T | aTc | aCc | 4 | 4 | B.1.221 | 0.000284 |
ORF3a | 62 | I62T | aTc | aCc | 4 | 4 | B.1.525 | 0.000453 |
ORF3a | 62 | I62T | aTc | aCc | 4 | 4 | B.1.526 | 0.000094 |
ORF3a | 62 | I62T | aTc | aCc | 4 | 4 | B.1.596 | 0.000349 |
ORF3a | 62 | I62T | aTc | aCc | 4 | 4 | P.1.15 | 0.000929 |
ORF3a | 62 | I62T | aTc | aCc | 3 | 3 | AY.16 | 0.001139 |
ORF3a | 62 | I62T | aTc | aCc | 3 | 3 | AY.26 | 0.000085 |
ORF3a | 62 | I62T | aTc | aCc | 3 | 3 | AY.34.1 | 0.00153 |
ORF3a | 62 | I62T | aTc | aCc | 3 | 3 | B.1.1.413 | 0.02069 |
ORF3a | 62 | I62T | aTc | aCc | 3 | 3 | B.1.351 | 0.000089 |
ORF3a | 62 | I62T | aTc | aCc | 3 | 3 | B.1.369 | 0.000856 |
ORF3a | 62 | I62T | aTc | aCc | 3 | 3 | Q.8 | 0.000495 |
ORF3a | 62 | I62T | aTc | aCc | 3 | 3 | R.1 | 0.00027 |
ORF3a | 62 | I62T | aTc | aCc | 2 | 2 | AY.119 | 0.000071 |
ORF3a | 62 | I62T | aTc | aCc | 2 | 2 | AY.29 | 0.000032 |
ORF3a | 62 | I62T | aTc | aCc | 2 | 2 | AY.3.1 | 0.000171 |
ORF3a | 62 | I62T | aTc | aCc | 2 | 2 | AY.4.2 | 0.000043 |
ORF3a | 62 | I62T | aTc | aCc | 2 | 2 | AY.54 | 0.000191 |
ORF3a | 62 | I62T | aTc | aCc | 2 | 2 | AY.76 | 0.009662 |
ORF3a | 62 | I62T | aTc | aCc | 2 | 2 | B.1.1.318 | 0.000604 |
ORF3a | 62 | I62T | aTc | aCc | 2 | 2 | B.1.160 | 0.000062 |
ORF3a | 62 | I62T | aTc | aCc | 2 | 2 | B.1.177.35 | 0.001382 |
ORF3a | 62 | I62T | aTc | aCc | 2 | 2 | B.1.258 | 0.000133 |
ORF3a | 62 | I62T | aTc | aCc | 2 | 2 | B.1.311 | 0.000549 |
ORF3a | 62 | I62T | aTc | aCc | 2 | 2 | B.1.445 | 0.023529 |
ORF3a | 62 | I62T | aTc | aCc | 2 | 2 | B.1.470 | 0.002809 |
ORF3a | 62 | I62T | aTc | aCc | 2 | 2 | B.1.555 | 0.044444 |
ORF3a | 62 | I62T | aTc | aCc | 2 | 2 | B.1.617.1 | 0.000258 |
ORF3a | 62 | I62T | aTc | aCc | 2 | 2 | B.1.621 | 0.000177 |
ORF3a | 62 | I62T | aTc | aCc | 1 | 1 | A.23.1 | 0.000704 |
ORF3a | 62 | I62T | aTc | aCc | 1 | 1 | AY.100 | 0.000046 |
ORF3a | 62 | I62T | aTc | aCc | 1 | 1 | AY.14 | 0.000088 |
ORF3a | 62 | I62T | aTc | aCc | 1 | 1 | AY.20 | 0.000039 |
ORF3a | 62 | I62T | aTc | aCc | 1 | 1 | AY.27 | 0.000065 |
ORF3a | 62 | I62T | aTc | aCc | 1 | 1 | AY.29.1 | 0.000221 |
ORF3a | 62 | I62T | aTc | aCc | 1 | 1 | AY.30 | 0.000396 |
ORF3a | 62 | I62T | aTc | aCc | 1 | 1 | AY.4.4 | 0.000409 |
ORF3a | 62 | I62T | aTc | aCc | 1 | 1 | AY.46.4 | 0.000165 |
ORF3a | 62 | I62T | aTc | aCc | 1 | 1 | AY.55 | 0.000917 |
ORF3a | 62 | I62T | aTc | aCc | 1 | 1 | AY.57 | 0.000656 |
ORF3a | 62 | I62T | aTc | aCc | 1 | 1 | AY.6 | 0.000041 |
ORF3a | 62 | I62T | aTc | aCc | 1 | 1 | AY.61 | 0.000105 |
ORF3a | 62 | I62T | aTc | aCc | 1 | 1 | AY.62 | 0.000436 |
ORF3a | 62 | I62T | aTc | aCc | 1 | 1 | AY.84 | 0.000437 |
ORF3a | 62 | I62T | aTc | aCc | 1 | 1 | B.1.1.316 | 0.000925 |
ORF3a | 62 | I62T | aTc | aCc | 1 | 1 | B.1.1.70 | 0.000341 |
ORF3a | 62 | I62T | aTc | aCc | 1 | 1 | B.1.139 | 0.000733 |
ORF3a | 62 | I62T | aTc | aCc | 1 | 1 | B.1.177.73 | 0.000566 |
ORF3a | 62 | I62T | aTc | aCc | 1 | 1 | B.1.177.77 | 0.000726 |
ORF3a | 62 | I62T | aTc | aCc | 1 | 1 | B.1.221.3 | 0.000833 |
ORF3a | 62 | I62T | aTc | aCc | 1 | 1 | B.1.240 | 0.000216 |
ORF3a | 62 | I62T | aTc | aCc | 1 | 1 | B.1.243 | 0.00007 |
ORF3a | 62 | I62T | aTc | aCc | 1 | 1 | B.1.247 | 0.014925 |
ORF3a | 62 | I62T | aTc | aCc | 1 | 1 | B.1.277 | 0.02381 |
ORF3a | 62 | I62T | aTc | aCc | 1 | 1 | B.1.284 | 0.013158 |
ORF3a | 62 | I62T | aTc | aCc | 1 | 1 | B.1.335 | 0.010309 |
ORF3a | 62 | I62T | aTc | aCc | 1 | 1 | B.1.36 | 0.000146 |
ORF3a | 62 | I62T | aTc | aCc | 1 | 1 | B.1.36.17 | 0.000494 |
ORF3a | 62 | I62T | aTc | aCc | 1 | 1 | B.1.408 | 0.00369 |
ORF3a | 62 | I62T | aTc | aCc | 1 | 1 | B.1.424 | 0.008065 |
ORF3a | 62 | I62T | aTc | aCc | 1 | 1 | B.1.427 | 0.00005 |
ORF3a | 62 | I62T | aTc | aCc | 1 | 1 | B.1.429 | 0.000024 |
ORF3a | 62 | I62T | aTc | aCc | 1 | 1 | B.1.459 | 0.004082 |
ORF3a | 62 | I62T | aTc | aCc | 1 | 1 | B.1.460 | 0.017857 |
ORF3a | 62 | I62T | aTc | aCc | 1 | 1 | B.1.610 | 0.003546 |
ORF3a | 62 | I62T | aTc | aCc | 1 | 1 | B.1.621.1 | 0.000506 |
ORF3a | 62 | I62T | aTc | aCc | 1 | 1 | B.1.628 | 0.000352 |
ORF3a | 62 | I62T | aTc | aCc | 1 | 1 | B.40 | 0.000364 |
ORF3a | 62 | I62T | aTc | aCc | 1 | 1 | B.6 | 0.00091 |
ORF3a | 62 | I62T | aTc | aCc | 1 | 1 | C.36.3 | 0.000567 |
ORF3a | 62 | I62T | aTc | aCc | 1 | 1 | P.1.10 | 0.000269 |
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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