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 | 269 | T269T | syn | acG | acT | 2952 | 1970 | 0.667344 | 26197-26199 |
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 |
ORF3a | 269 | T269T | acG | acT | 1970 | 2952 | All | 0.000377 |
ORF3a | 269 | T269T | acG | acT | 247 | 555 | B.1.1.7 | 0.000221 |
ORF3a | 269 | T269T | acG | acT | 4 | 291 | B.1.1.519 | 0.000159 |
ORF3a | 269 | T269T | acG | acT | 199 | 222 | AY.4 | 0.00031 |
ORF3a | 269 | T269T | acG | acT | 187 | 187 | AY.16.1 | 0.087876 |
ORF3a | 269 | T269T | acG | acT | 94 | 120 | AY.3 | 0.000935 |
ORF3a | 269 | T269T | acG | acT | 97 | 108 | B.1.617.2 | 0.000365 |
ORF3a | 269 | T269T | acG | acT | 95 | 105 | AY.44 | 0.000578 |
ORF3a | 269 | T269T | acG | acT | 43 | 83 | B.1 | 0.000394 |
ORF3a | 269 | T269T | acG | acT | 71 | 82 | AY.43 | 0.000315 |
ORF3a | 269 | T269T | acG | acT | 78 | 78 | AY.29 | 0.00123 |
ORF3a | 269 | T269T | acG | acT | 56 | 64 | B.1.2 | 0.000493 |
ORF3a | 269 | T269T | acG | acT | 9 | 59 | B.1.240 | 0.00194 |
ORF3a | 269 | T269T | acG | acT | 52 | 55 | B.1.177 | 0.000685 |
ORF3a | 269 | T269T | acG | acT | 37 | 47 | AY.25 | 0.000223 |
ORF3a | 269 | T269T | acG | acT | 26 | 44 | B.1.1 | 0.000472 |
ORF3a | 269 | T269T | acG | acT | 39 | 39 | Q.3 | 0.005656 |
ORF3a | 269 | T269T | acG | acT | 29 | 38 | AY.103 | 0.00018 |
ORF3a | 269 | T269T | acG | acT | 2 | 38 | B.1.1.294 | 0.002532 |
ORF3a | 269 | T269T | acG | acT | 32 | 34 | P.1 | 0.000504 |
ORF3a | 269 | T269T | acG | acT | 31 | 31 | B.1.139 | 0.022727 |
ORF3a | 269 | T269T | acG | acT | 24 | 26 | AY.26 | 0.000679 |
ORF3a | 269 | T269T | acG | acT | 22 | 26 | AY.33 | 0.001469 |
ORF3a | 269 | T269T | acG | acT | 23 | 24 | B.1.429 | 0.000541 |
ORF3a | 269 | T269T | acG | acT | 19 | 23 | B.1.427 | 0.000959 |
ORF3a | 269 | T269T | acG | acT | 20 | 22 | AY.47 | 0.000622 |
ORF3a | 269 | T269T | acG | acT | 22 | 22 | B.1.243 | 0.001531 |
ORF3a | 269 | T269T | acG | acT | 20 | 21 | B.1.160 | 0.000624 |
ORF3a | 269 | T269T | acG | acT | 17 | 17 | B.1.1.222 | 0.003468 |
ORF3a | 269 | T269T | acG | acT | 17 | 17 | B.1.409 | 0.013281 |
ORF3a | 269 | T269T | acG | acT | 16 | 16 | B.1.416 | 0.020305 |
ORF3a | 269 | T269T | acG | acT | 11 | 15 | C.37 | 0.001277 |
ORF3a | 269 | T269T | acG | acT | 12 | 14 | AY.102 | 0.000318 |
ORF3a | 269 | T269T | acG | acT | 10 | 12 | AY.4.2 | 0.000217 |
ORF3a | 269 | T269T | acG | acT | 11 | 12 | AY.5 | 0.000227 |
ORF3a | 269 | T269T | acG | acT | 11 | 11 | AY.9.2 | 0.000404 |
ORF3a | 269 | T269T | acG | acT | 10 | 10 | AD.2 | 0.00219 |
ORF3a | 269 | T269T | acG | acT | 1 | 9 | AY.23 | 0.00007 |
ORF3a | 269 | T269T | acG | acT | 5 | 9 | B.1.351 | 0.000149 |
ORF3a | 269 | T269T | acG | acT | 8 | 8 | AY.54 | 0.000763 |
ORF3a | 269 | T269T | acG | acT | 3 | 8 | B.1.221 | 0.000213 |
ORF3a | 269 | T269T | acG | acT | 8 | 8 | B.1.621 | 0.000708 |
ORF3a | 269 | T269T | acG | acT | 4 | 7 | AY.99.2 | 0.000369 |
ORF3a | 269 | T269T | acG | acT | 7 | 7 | P.1.14 | 0.000335 |
ORF3a | 269 | T269T | acG | acT | 5 | 6 | AY.100 | 0.00023 |
ORF3a | 269 | T269T | acG | acT | 6 | 6 | AY.20 | 0.000233 |
ORF3a | 269 | T269T | acG | acT | 3 | 6 | AY.59 | 0.001589 |
ORF3a | 269 | T269T | acG | acT | 6 | 6 | B.1.1.368 | 0.018519 |
ORF3a | 269 | T269T | acG | acT | 6 | 6 | B.1.160.14 | 0.012712 |
ORF3a | 269 | T269T | acG | acT | 6 | 6 | B.1.526 | 0.000141 |
ORF3a | 269 | T269T | acG | acT | 2 | 5 | AY.61 | 0.00021 |
ORF3a | 269 | T269T | acG | acT | 5 | 5 | B.1.617.1 | 0.000645 |
ORF3a | 269 | T269T | acG | acT | 5 | 5 | P.1.7 | 0.001596 |
ORF3a | 269 | T269T | acG | acT | 4 | 4 | AY.115 | 0.020833 |
ORF3a | 269 | T269T | acG | acT | 4 | 4 | AY.37 | 0.001264 |
ORF3a | 269 | T269T | acG | acT | 4 | 4 | AY.39 | 0.000099 |
ORF3a | 269 | T269T | acG | acT | 4 | 4 | AY.42 | 0.000161 |
ORF3a | 269 | T269T | acG | acT | 4 | 4 | AY.46 | 0.000416 |
ORF3a | 269 | T269T | acG | acT | 4 | 4 | AY.75 | 0.000224 |
ORF3a | 269 | T269T | acG | acT | 2 | 4 | AY.85 | 0.000854 |
ORF3a | 269 | T269T | acG | acT | 4 | 4 | AY.95 | 0.003044 |
ORF3a | 269 | T269T | acG | acT | 4 | 4 | B.1.258 | 0.000266 |
ORF3a | 269 | T269T | acG | acT | 4 | 4 | B.1.403 | 0.013072 |
ORF3a | 269 | T269T | acG | acT | 4 | 4 | B.1.564 | 0.001704 |
ORF3a | 269 | T269T | acG | acT | 2 | 4 | B.1.637 | 0.000146 |
ORF3a | 269 | T269T | acG | acT | 3 | 3 | AY.117 | 0.000254 |
ORF3a | 269 | T269T | acG | acT | 2 | 3 | AY.118 | 0.000125 |
ORF3a | 269 | T269T | acG | acT | 3 | 3 | AY.119 | 0.000106 |
ORF3a | 269 | T269T | acG | acT | 3 | 3 | AY.121 | 0.000406 |
ORF3a | 269 | T269T | acG | acT | 3 | 3 | AY.27 | 0.000194 |
ORF3a | 269 | T269T | acG | acT | 2 | 3 | AY.3.1 | 0.000171 |
ORF3a | 269 | T269T | acG | acT | 3 | 3 | AY.36 | 0.000445 |
ORF3a | 269 | T269T | acG | acT | 3 | 3 | AY.45 | 0.000365 |
ORF3a | 269 | T269T | acG | acT | 3 | 3 | AY.6 | 0.000123 |
ORF3a | 269 | T269T | acG | acT | 3 | 3 | AY.9.1 | 0.000251 |
ORF3a | 269 | T269T | acG | acT | 1 | 3 | AY.98.1 | 0.000048 |
ORF3a | 269 | T269T | acG | acT | 3 | 3 | B.1.1.25 | 0.001706 |
ORF3a | 269 | T269T | acG | acT | 3 | 3 | B.1.1.28 | 0.000934 |
ORF3a | 269 | T269T | acG | acT | 3 | 3 | B.1.36.24 | 0.018519 |
ORF3a | 269 | T269T | acG | acT | 3 | 3 | B.1.517 | 0.001281 |
ORF3a | 269 | T269T | acG | acT | 3 | 3 | B.1.525 | 0.000339 |
ORF3a | 269 | T269T | acG | acT | 3 | 3 | B.1.631 | 0.010101 |
ORF3a | 269 | T269T | acG | acT | 2 | 3 | D.2 | 0.00015 |
ORF3a | 269 | T269T | acG | acT | 2 | 2 | AY.114 | 0.000462 |
ORF3a | 269 | T269T | acG | acT | 2 | 2 | AY.116.1 | 0.000623 |
ORF3a | 269 | T269T | acG | acT | 2 | 2 | AY.12 | 0.000632 |
ORF3a | 269 | T269T | acG | acT | 2 | 2 | AY.120 | 0.000074 |
ORF3a | 269 | T269T | acG | acT | 1 | 2 | AY.16 | 0.00038 |
ORF3a | 269 | T269T | acG | acT | 2 | 2 | AY.46.6 | 0.000144 |
ORF3a | 269 | T269T | acG | acT | 1 | 2 | AY.57 | 0.000656 |
ORF3a | 269 | T269T | acG | acT | 2 | 2 | AY.64 | 0.00119 |
ORF3a | 269 | T269T | acG | acT | 2 | 2 | AY.65 | 0.001066 |
ORF3a | 269 | T269T | acG | acT | 1 | 2 | AY.69 | 0.000187 |
ORF3a | 269 | T269T | acG | acT | 2 | 2 | AY.7 | 0.000392 |
ORF3a | 269 | T269T | acG | acT | 1 | 2 | B.1.1.176 | 0.000439 |
ORF3a | 269 | T269T | acG | acT | 2 | 2 | B.1.1.216 | 0.001781 |
ORF3a | 269 | T269T | acG | acT | 2 | 2 | B.1.1.241 | 0.004141 |
ORF3a | 269 | T269T | acG | acT | 2 | 2 | B.1.1.353 | 0.041667 |
ORF3a | 269 | T269T | acG | acT | 2 | 2 | B.1.1.409 | 0.005666 |
ORF3a | 269 | T269T | acG | acT | 2 | 2 | B.1.1.482 | 0.046512 |
ORF3a | 269 | T269T | acG | acT | 2 | 2 | B.1.1.523 | 0.003125 |
ORF3a | 269 | T269T | acG | acT | 1 | 2 | B.1.36 | 0.000146 |
ORF3a | 269 | T269T | acG | acT | 2 | 2 | B.1.399 | 0.003868 |
ORF3a | 269 | T269T | acG | acT | 2 | 2 | B.1.400 | 0.000858 |
ORF3a | 269 | T269T | acG | acT | 2 | 2 | B.1.621.1 | 0.001012 |
ORF3a | 269 | T269T | acG | acT | 2 | 2 | B.1.623 | 0.001073 |
ORF3a | 269 | T269T | acG | acT | 2 | 2 | B.1.628 | 0.000705 |
ORF3a | 269 | T269T | acG | acT | 2 | 2 | P.1.12 | 0.000968 |
ORF3a | 269 | T269T | acG | acT | 2 | 2 | P.1.15 | 0.000465 |
ORF3a | 269 | T269T | acG | acT | 2 | 2 | P.1.2 | 0.002312 |
ORF3a | 269 | T269T | acG | acT | 2 | 2 | P.2 | 0.000373 |
ORF3a | 269 | T269T | acG | acT | 2 | 2 | Q.8 | 0.00033 |
ORF3a | 269 | T269T | acG | acT | 1 | 1 | A.1 | 0.000282 |
ORF3a | 269 | T269T | acG | acT | 1 | 1 | A.2.5.3 | 0.010309 |
ORF3a | 269 | T269T | acG | acT | 1 | 1 | A.5 | 0.001923 |
ORF3a | 269 | T269T | acG | acT | 1 | 1 | AY.10 | 0.00053 |
ORF3a | 269 | T269T | acG | acT | 1 | 1 | AY.110 | 0.000113 |
ORF3a | 269 | T269T | acG | acT | 1 | 1 | AY.116 | 0.000287 |
ORF3a | 269 | T269T | acG | acT | 1 | 1 | AY.120.1 | 0.000321 |
ORF3a | 269 | T269T | acG | acT | 1 | 1 | AY.13 | 0.000161 |
ORF3a | 269 | T269T | acG | acT | 1 | 1 | AY.14 | 0.000088 |
ORF3a | 269 | T269T | acG | acT | 1 | 1 | AY.23.1 | 0.000417 |
ORF3a | 269 | T269T | acG | acT | 1 | 1 | AY.29.1 | 0.000221 |
ORF3a | 269 | T269T | acG | acT | 1 | 1 | AY.32 | 0.000532 |
ORF3a | 269 | T269T | acG | acT | 1 | 1 | AY.34 | 0.000097 |
ORF3a | 269 | T269T | acG | acT | 1 | 1 | AY.34.1 | 0.00051 |
ORF3a | 269 | T269T | acG | acT | 1 | 1 | AY.4.2.1 | 0.000149 |
ORF3a | 269 | T269T | acG | acT | 1 | 1 | AY.46.2 | 0.000635 |
ORF3a | 269 | T269T | acG | acT | 1 | 1 | AY.5.3 | 0.000337 |
ORF3a | 269 | T269T | acG | acT | 1 | 1 | AY.60 | 0.000938 |
ORF3a | 269 | T269T | acG | acT | 1 | 1 | AY.7.2 | 0.000559 |
ORF3a | 269 | T269T | acG | acT | 1 | 1 | AY.70 | 0.000209 |
ORF3a | 269 | T269T | acG | acT | 1 | 1 | AY.74 | 0.000116 |
ORF3a | 269 | T269T | acG | acT | 1 | 1 | AY.76 | 0.004831 |
ORF3a | 269 | T269T | acG | acT | 1 | 1 | AY.77 | 0.001127 |
ORF3a | 269 | T269T | acG | acT | 1 | 1 | AY.78 | 0.001541 |
ORF3a | 269 | T269T | acG | acT | 1 | 1 | AY.98 | 0.000079 |
ORF3a | 269 | T269T | acG | acT | 1 | 1 | B.1.1.231 | 0.003096 |
ORF3a | 269 | T269T | acG | acT | 1 | 1 | B.1.1.232 | 0.001815 |
ORF3a | 269 | T269T | acG | acT | 1 | 1 | B.1.1.302 | 0.002075 |
ORF3a | 269 | T269T | acG | acT | 1 | 1 | B.1.1.312 | 0.001912 |
ORF3a | 269 | T269T | acG | acT | 1 | 1 | B.1.1.33 | 0.000421 |
ORF3a | 269 | T269T | acG | acT | 1 | 1 | B.1.1.37 | 0.000193 |
ORF3a | 269 | T269T | acG | acT | 1 | 1 | B.1.119 | 0.010526 |
ORF3a | 269 | T269T | acG | acT | 1 | 1 | B.1.177.14 | 0.006098 |
ORF3a | 269 | T269T | acG | acT | 1 | 1 | B.1.177.20 | 0.001517 |
ORF3a | 269 | T269T | acG | acT | 1 | 1 | B.1.177.23 | 0.003236 |
ORF3a | 269 | T269T | acG | acT | 1 | 1 | B.1.177.35 | 0.000691 |
ORF3a | 269 | T269T | acG | acT | 1 | 1 | B.1.258.17 | 0.000104 |
ORF3a | 269 | T269T | acG | acT | 1 | 1 | B.1.438.1 | 0.000107 |
ORF3a | 269 | T269T | acG | acT | 1 | 1 | B.1.439 | 0.005917 |
ORF3a | 269 | T269T | acG | acT | 1 | 1 | B.1.459 | 0.004082 |
ORF3a | 269 | T269T | acG | acT | 1 | 1 | B.1.523 | 0.002451 |
ORF3a | 269 | T269T | acG | acT | 1 | 1 | B.1.567 | 0.003333 |
ORF3a | 269 | T269T | acG | acT | 1 | 1 | B.1.595 | 0.000261 |
ORF3a | 269 | T269T | acG | acT | 1 | 1 | B.1.619.1 | 0.000641 |
ORF3a | 269 | T269T | acG | acT | 1 | 1 | C.16 | 0.00106 |
ORF3a | 269 | T269T | acG | acT | 1 | 1 | C.36 | 0.000911 |
ORF3a | 269 | T269T | acG | acT | 1 | 1 | P.1.13 | 0.000898 |
ORF3a | 269 | T269T | acG | acT | 1 | 1 | P.1.17.1 | 0.000875 |
ORF3a | 269 | T269T | acG | acT | 1 | 1 | P.3 | 0.001595 |
ORF3a | 269 | T269T | acG | acT | 1 | 1 | Q.1 | 0.000126 |
ORF3a | 269 | T269T | acG | acT | 1 | 1 | R.1 | 0.00009 |
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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