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 | 9 | P9L | nonsyn | cCa | cTa | 2956 | 2955 | 0.999662 | 21587-21589 |
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 |
S | 9 | P9L | cCa | cTa | 2955 | 2956 | All | 0.000565 |
S | 9 | P9L | cCa | cTa | 999 | 999 | B.1.1.7 | 0.000894 |
S | 9 | P9L | cCa | cTa | 345 | 345 | B.1.427 | 0.017422 |
S | 9 | P9L | cCa | cTa | 218 | 218 | C.1.2 | 0.92766 |
S | 9 | P9L | cCa | cTa | 194 | 194 | P.3 | 0.30941 |
S | 9 | P9L | cCa | cTa | 183 | 183 | B.1.630 | 0.958115 |
S | 9 | P9L | cCa | cTa | 178 | 178 | AT.1 | 0.912821 |
S | 9 | P9L | cCa | cTa | 105 | 105 | C.38 | 0.846774 |
S | 9 | P9L | cCa | cTa | 80 | 80 | B.1 | 0.000733 |
S | 9 | P9L | cCa | cTa | 46 | 46 | B.1.1 | 0.000834 |
S | 9 | P9L | cCa | cTa | 44 | 44 | B.1.2 | 0.000387 |
S | 9 | P9L | cCa | cTa | 42 | 42 | B.1.1.524 | 0.875 |
S | 9 | P9L | cCa | cTa | 31 | 31 | B.1.177 | 0.000408 |
S | 9 | P9L | cCa | cTa | 30 | 30 | N.10 | 0.882353 |
S | 9 | P9L | cCa | cTa | 27 | 27 | C.36.3.1 | 0.07337 |
S | 9 | P9L | cCa | cTa | 22 | 22 | A.2.5 | 0.010978 |
S | 9 | P9L | cCa | cTa | 22 | 22 | B.1.576 | 0.019946 |
S | 9 | P9L | cCa | cTa | 22 | 22 | C.39 | 0.415094 |
S | 9 | P9L | cCa | cTa | 20 | 20 | B.1.351 | 0.000595 |
S | 9 | P9L | cCa | cTa | 19 | 19 | B.1.214.2 | 0.011391 |
S | 9 | P9L | cCa | cTa | 19 | 19 | B.1.637 | 0.001388 |
S | 9 | P9L | cCa | cTa | 16 | 16 | B.1.177.81 | 0.003029 |
S | 9 | P9L | cCa | cTa | 15 | 15 | B.1.149 | 0.05137 |
S | 9 | P9L | cCa | cTa | 12 | 12 | B.1.160 | 0.000374 |
S | 9 | P9L | cCa | cTa | 10 | 10 | B.1.1.1 | 0.003267 |
S | 9 | P9L | cCa | cTa | 10 | 10 | B.1.1.33 | 0.004209 |
S | 9 | P9L | cCa | cTa | 9 | 9 | B.1.1.519 | 0.000357 |
S | 9 | P9L | cCa | cTa | 9 | 9 | B.1.617.1 | 0.001161 |
S | 9 | P9L | cCa | cTa | 9 | 9 | C.37 | 0.001045 |
S | 9 | P9L | cCa | cTa | 8 | 8 | B.1.429 | 0.000188 |
S | 9 | P9L | cCa | cTa | 7 | 7 | AY.4 | 0.000011 |
S | 9 | P9L | cCa | cTa | 7 | 7 | AY.45 | 0.000852 |
S | 9 | P9L | cCa | cTa | 7 | 7 | B.1.1.214 | 0.000388 |
S | 9 | P9L | cCa | cTa | 7 | 7 | B.1.526 | 0.000165 |
S | 9 | P9L | cCa | cTa | 6 | 6 | B.1.258 | 0.000399 |
S | 9 | P9L | cCa | cTa | 6 | 6 | B.1.588 | 0.00546 |
S | 9 | P9L | cCa | cTa | 5 | 5 | B.1.258.17 | 0.00052 |
S | 9 | P9L | cCa | cTa | 5 | 5 | D.2 | 0.000375 |
S | 9 | P9L | cCa | cTa | 4 | 4 | B.1.1.434 | 0.001394 |
S | 9 | P9L | cCa | cTa | 4 | 4 | B.1.617.2 | 0.000015 |
S | 9 | P9L | cCa | cTa | 4 | 4 | Q.8 | 0.00066 |
S | 9 | P9L | cCa | cTa | 3 | 3 | AZ.2.1 | 0.02439 |
S | 9 | P9L | cCa | cTa | 3 | 3 | B.1.1.28 | 0.000934 |
S | 9 | P9L | cCa | cTa | 3 | 3 | B.1.1.318 | 0.000905 |
S | 9 | P9L | cCa | cTa | 3 | 3 | B.1.1.50 | 0.002037 |
S | 9 | P9L | cCa | cTa | 3 | 3 | B.1.110.3 | 0.002155 |
S | 9 | P9L | cCa | cTa | 3 | 3 | B.1.234 | 0.000396 |
S | 9 | P9L | cCa | cTa | 3 | 3 | B.1.240 | 0.000647 |
S | 9 | P9L | cCa | cTa | 3 | 3 | B.1.369 | 0.000856 |
S | 9 | P9L | cCa | cTa | 3 | 3 | B.1.404 | 0.003906 |
S | 9 | P9L | cCa | cTa | 2 | 3 | B.1.525 | 0.000226 |
S | 9 | P9L | cCa | cTa | 3 | 3 | B.1.595 | 0.000783 |
S | 9 | P9L | cCa | cTa | 2 | 2 | AD.2 | 0.000438 |
S | 9 | P9L | cCa | cTa | 2 | 2 | AY.44 | 0.000012 |
S | 9 | P9L | cCa | cTa | 2 | 2 | B.1.1.207 | 0.002364 |
S | 9 | P9L | cCa | cTa | 2 | 2 | B.1.1.265 | 0.006309 |
S | 9 | P9L | cCa | cTa | 2 | 2 | B.1.1.37 | 0.000386 |
S | 9 | P9L | cCa | cTa | 2 | 2 | B.1.1.525 | 0.010929 |
S | 9 | P9L | cCa | cTa | 2 | 2 | B.1.177.33 | 0.003289 |
S | 9 | P9L | cCa | cTa | 2 | 2 | B.1.221 | 0.000142 |
S | 9 | P9L | cCa | cTa | 2 | 2 | B.1.311 | 0.000549 |
S | 9 | P9L | cCa | cTa | 2 | 2 | B.1.36.35 | 0.005208 |
S | 9 | P9L | cCa | cTa | 2 | 2 | B.1.39 | 0.007812 |
S | 9 | P9L | cCa | cTa | 2 | 2 | B.1.396 | 0.001411 |
S | 9 | P9L | cCa | cTa | 2 | 2 | B.1.466.2 | 0.000782 |
S | 9 | P9L | cCa | cTa | 2 | 2 | B.1.621 | 0.000177 |
S | 9 | P9L | cCa | cTa | 2 | 2 | C.1 | 0.004785 |
S | 9 | P9L | cCa | cTa | 2 | 2 | C.23 | 0.011628 |
S | 9 | P9L | cCa | cTa | 2 | 2 | P.2 | 0.000373 |
S | 9 | P9L | cCa | cTa | 2 | 2 | P.5 | 0.027397 |
S | 9 | P9L | cCa | cTa | 1 | 1 | A | 0.000387 |
S | 9 | P9L | cCa | cTa | 1 | 1 | A.2 | 0.000662 |
S | 9 | P9L | cCa | cTa | 1 | 1 | A.2.5.1 | 0.004808 |
S | 9 | P9L | cCa | cTa | 1 | 1 | AU.1 | 0.001266 |
S | 9 | P9L | cCa | cTa | 1 | 1 | AY.102 | 0.000027 |
S | 9 | P9L | cCa | cTa | 1 | 1 | AY.103 | 0.000006 |
S | 9 | P9L | cCa | cTa | 1 | 1 | AY.11 | 0.001339 |
S | 9 | P9L | cCa | cTa | 1 | 1 | AY.13 | 0.000161 |
S | 9 | P9L | cCa | cTa | 1 | 1 | AY.16.1 | 0.00047 |
S | 9 | P9L | cCa | cTa | 1 | 1 | AY.23.1 | 0.000417 |
S | 9 | P9L | cCa | cTa | 1 | 1 | AY.25 | 0.000006 |
S | 9 | P9L | cCa | cTa | 1 | 1 | AY.3 | 0.00001 |
S | 9 | P9L | cCa | cTa | 1 | 1 | AY.30 | 0.000396 |
S | 9 | P9L | cCa | cTa | 1 | 1 | AY.42 | 0.00004 |
S | 9 | P9L | cCa | cTa | 1 | 1 | AY.43 | 0.000004 |
S | 9 | P9L | cCa | cTa | 1 | 1 | AY.53 | 0.000288 |
S | 9 | P9L | cCa | cTa | 1 | 1 | AY.7.1 | 0.000113 |
S | 9 | P9L | cCa | cTa | 1 | 1 | AY.75 | 0.000056 |
S | 9 | P9L | cCa | cTa | 1 | 1 | AY.75.1 | 0.00018 |
S | 9 | P9L | cCa | cTa | 1 | 1 | B.1.1.176 | 0.000439 |
S | 9 | P9L | cCa | cTa | 1 | 1 | B.1.1.185 | 0.076923 |
S | 9 | P9L | cCa | cTa | 1 | 1 | B.1.1.189 | 0.001513 |
S | 9 | P9L | cCa | cTa | 1 | 1 | B.1.1.192 | 0.002309 |
S | 9 | P9L | cCa | cTa | 1 | 1 | B.1.1.25 | 0.000569 |
S | 9 | P9L | cCa | cTa | 1 | 1 | B.1.1.277 | 0.000759 |
S | 9 | P9L | cCa | cTa | 1 | 1 | B.1.1.311 | 0.000358 |
S | 9 | P9L | cCa | cTa | 1 | 1 | B.1.1.317 | 0.000412 |
S | 9 | P9L | cCa | cTa | 1 | 1 | B.1.1.337 | 0.003597 |
S | 9 | P9L | cCa | cTa | 1 | 1 | B.1.1.369 | 0.000446 |
S | 9 | P9L | cCa | cTa | 1 | 1 | B.1.1.377 | 0.001381 |
S | 9 | P9L | cCa | cTa | 1 | 1 | B.1.1.397 | 0.002252 |
S | 9 | P9L | cCa | cTa | 1 | 1 | B.1.1.402 | 0.011111 |
S | 9 | P9L | cCa | cTa | 1 | 1 | B.1.1.432 | 0.001266 |
S | 9 | P9L | cCa | cTa | 1 | 1 | B.1.1.44 | 0.00241 |
S | 9 | P9L | cCa | cTa | 1 | 1 | B.1.1.448 | 0.002033 |
S | 9 | P9L | cCa | cTa | 1 | 1 | B.1.1.463 | 0.0625 |
S | 9 | P9L | cCa | cTa | 1 | 1 | B.1.1.48 | 0.002874 |
S | 9 | P9L | cCa | cTa | 1 | 1 | B.1.1.53 | 0.013699 |
S | 9 | P9L | cCa | cTa | 1 | 1 | B.1.111 | 0.001175 |
S | 9 | P9L | cCa | cTa | 1 | 1 | B.1.128 | 0.000635 |
S | 9 | P9L | cCa | cTa | 1 | 1 | B.1.177.12 | 0.000152 |
S | 9 | P9L | cCa | cTa | 1 | 1 | B.1.177.21 | 0.000076 |
S | 9 | P9L | cCa | cTa | 1 | 1 | B.1.177.3 | 0.007634 |
S | 9 | P9L | cCa | cTa | 1 | 1 | B.1.177.4 | 0.000211 |
S | 9 | P9L | cCa | cTa | 1 | 1 | B.1.177.44 | 0.000519 |
S | 9 | P9L | cCa | cTa | 1 | 1 | B.1.177.57 | 0.000281 |
S | 9 | P9L | cCa | cTa | 1 | 1 | B.1.177.9 | 0.001332 |
S | 9 | P9L | cCa | cTa | 1 | 1 | B.1.210 | 0.002132 |
S | 9 | P9L | cCa | cTa | 1 | 1 | B.1.239 | 0.001221 |
S | 9 | P9L | cCa | cTa | 1 | 1 | B.1.241 | 0.000812 |
S | 9 | P9L | cCa | cTa | 1 | 1 | B.1.252 | 0.006623 |
S | 9 | P9L | cCa | cTa | 1 | 1 | B.1.323 | 0.020833 |
S | 9 | P9L | cCa | cTa | 1 | 1 | B.1.324 | 0.001605 |
S | 9 | P9L | cCa | cTa | 1 | 1 | B.1.335 | 0.010309 |
S | 9 | P9L | cCa | cTa | 1 | 1 | B.1.36.29 | 0.000517 |
S | 9 | P9L | cCa | cTa | 1 | 1 | B.1.361 | 0.001289 |
S | 9 | P9L | cCa | cTa | 1 | 1 | B.1.380 | 0.006623 |
S | 9 | P9L | cCa | cTa | 1 | 1 | B.1.399 | 0.001934 |
S | 9 | P9L | cCa | cTa | 1 | 1 | B.1.416 | 0.001269 |
S | 9 | P9L | cCa | cTa | 1 | 1 | B.1.433 | 0.003195 |
S | 9 | P9L | cCa | cTa | 1 | 1 | B.1.459 | 0.004082 |
S | 9 | P9L | cCa | cTa | 1 | 1 | B.1.486 | 0.111111 |
S | 9 | P9L | cCa | cTa | 1 | 1 | B.1.499.1 | 0.111111 |
S | 9 | P9L | cCa | cTa | 1 | 1 | B.1.501 | 0.007353 |
S | 9 | P9L | cCa | cTa | 1 | 1 | B.1.529 | 0.055556 |
S | 9 | P9L | cCa | cTa | 1 | 1 | B.1.596 | 0.000087 |
S | 9 | P9L | cCa | cTa | 1 | 1 | B.1.609 | 0.000479 |
S | 9 | P9L | cCa | cTa | 1 | 1 | B.1.618 | 0.004032 |
S | 9 | P9L | cCa | cTa | 1 | 1 | B.1.619.1 | 0.000641 |
S | 9 | P9L | cCa | cTa | 1 | 1 | B.1.623 | 0.000536 |
S | 9 | P9L | cCa | cTa | 1 | 1 | B.1.93 | 0.000934 |
S | 9 | P9L | cCa | cTa | 1 | 1 | B.31 | 0.003731 |
S | 9 | P9L | cCa | cTa | 1 | 1 | B.4 | 0.002208 |
S | 9 | P9L | cCa | cTa | 1 | 1 | B.40 | 0.000364 |
S | 9 | P9L | cCa | cTa | 1 | 1 | B.6 | 0.00091 |
S | 9 | P9L | cCa | cTa | 1 | 1 | C.35 | 0.000774 |
S | 9 | P9L | cCa | cTa | 1 | 1 | C.4 | 0.01 |
S | 9 | P9L | cCa | cTa | 1 | 1 | P.1 | 0.000016 |
S | 9 | P9L | cCa | cTa | 1 | 1 | P.1.1 | 0.000318 |
S | 9 | P9L | cCa | cTa | 1 | 1 | Q.1 | 0.000126 |
S | 9 | P9L | cCa | cTa | 1 | 1 | Q.3 | 0.000145 |
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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