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 | 17 | F17L | F2780L | nonsyn | Ttc | Ctc | 45068 | 44980 | 0.998047 | 8603-8605 |
ORF1ab/nsp4 | 17 | F17L | F2780L | nonsyn | TtC | CtT | 45068 | 44 | 0.000976302 | 8603-8605 |
ORF1ab/nsp4 | 17 | F17L | F2780L | nonsyn | ttC | ttA | 45068 | 39 | 0.000865359 | 8603-8605 |
ORF1ab/nsp4 | 17 | F17L | F2780L | nonsyn | ttC | ttG | 45068 | 4 | 0.0000887548 | 8603-8605 |
ORF1ab/nsp4 | 17 | F17L | F2780L | nonsyn | TtC | CtA | 45068 | 1 | 0.0000221887 | 8603-8605 |
Details of the mutation F17L 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 | 17 | F17L | Ttc | Ctc | 44980 | 45068 | All | 0.008603 |
ORF1ab/nsp4 | 17 | F17L | TtC | CtT | 44 | 45068 | All | 0.000008 |
ORF1ab/nsp4 | 17 | F17L | ttC | ttA | 39 | 45068 | All | 0.000007 |
ORF1ab/nsp4 | 17 | F17L | ttC | ttG | 4 | 45068 | All | 0.000001 |
ORF1ab/nsp4 | 17 | F17L | TtC | CtA | 1 | 45068 | All | 0 |
ORF1ab/nsp4 | 17 | F17L | Ttc | Ctc | 44259 | 44299 | B.1.1.7 | 0.039622 |
ORF1ab/nsp4 | 17 | F17L | TtC | CtT | 39 | 44299 | B.1.1.7 | 0.000035 |
ORF1ab/nsp4 | 17 | F17L | TtC | CtA | 1 | 44299 | B.1.1.7 | 0.000001 |
ORF1ab/nsp4 | 17 | F17L | Ttc | Ctc | 392 | 397 | Q.8 | 0.064644 |
ORF1ab/nsp4 | 17 | F17L | TtC | CtT | 5 | 397 | Q.8 | 0.000825 |
ORF1ab/nsp4 | 17 | F17L | Ttc | Ctc | 78 | 83 | AY.44 | 0.000475 |
ORF1ab/nsp4 | 17 | F17L | ttC | ttA | 5 | 83 | AY.44 | 0.00003 |
ORF1ab/nsp4 | 17 | F17L | Ttc | Ctc | 47 | 48 | B.1.1 | 0.000853 |
ORF1ab/nsp4 | 17 | F17L | ttC | ttA | 1 | 48 | B.1.1 | 0.000018 |
ORF1ab/nsp4 | 17 | F17L | Ttc | Ctc | 38 | 43 | B.1 | 0.000348 |
ORF1ab/nsp4 | 17 | F17L | ttC | ttA | 3 | 43 | B.1 | 0.000027 |
ORF1ab/nsp4 | 17 | F17L | ttC | ttG | 2 | 43 | B.1 | 0.000018 |
ORF1ab/nsp4 | 17 | F17L | Ttc | Ctc | 35 | 35 | AY.9.1 | 0.00293 |
ORF1ab/nsp4 | 17 | F17L | Ttc | Ctc | 22 | 22 | AY.9.2 | 0.000808 |
ORF1ab/nsp4 | 17 | F17L | ttC | ttA | 7 | 11 | AY.4 | 0.000011 |
ORF1ab/nsp4 | 17 | F17L | Ttc | Ctc | 4 | 11 | AY.4 | 0.000006 |
ORF1ab/nsp4 | 17 | F17L | Ttc | Ctc | 7 | 11 | B.1.221 | 0.000497 |
ORF1ab/nsp4 | 17 | F17L | ttC | ttA | 4 | 11 | B.1.221 | 0.000284 |
ORF1ab/nsp4 | 17 | F17L | Ttc | Ctc | 9 | 9 | AY.103 | 0.000056 |
ORF1ab/nsp4 | 17 | F17L | Ttc | Ctc | 8 | 8 | B.1.177 | 0.000105 |
ORF1ab/nsp4 | 17 | F17L | Ttc | Ctc | 5 | 5 | AY.25 | 0.00003 |
ORF1ab/nsp4 | 17 | F17L | Ttc | Ctc | 3 | 5 | B.1.617.2 | 0.000011 |
ORF1ab/nsp4 | 17 | F17L | ttC | ttA | 2 | 5 | B.1.617.2 | 0.000008 |
ORF1ab/nsp4 | 17 | F17L | Ttc | Ctc | 5 | 5 | Q.1 | 0.000632 |
ORF1ab/nsp4 | 17 | F17L | Ttc | Ctc | 4 | 4 | B.1.1.157 | 0.003653 |
ORF1ab/nsp4 | 17 | F17L | Ttc | Ctc | 4 | 4 | Q.5 | 0.067797 |
ORF1ab/nsp4 | 17 | F17L | Ttc | Ctc | 2 | 3 | AY.43 | 0.000009 |
ORF1ab/nsp4 | 17 | F17L | ttC | ttA | 1 | 3 | AY.43 | 0.000004 |
ORF1ab/nsp4 | 17 | F17L | Ttc | Ctc | 3 | 3 | B.1.177.73 | 0.001699 |
ORF1ab/nsp4 | 17 | F17L | Ttc | Ctc | 3 | 3 | B.1.438.1 | 0.000322 |
ORF1ab/nsp4 | 17 | F17L | Ttc | Ctc | 3 | 3 | B.1.526 | 0.000071 |
ORF1ab/nsp4 | 17 | F17L | Ttc | Ctc | 3 | 3 | Q.4 | 0.001364 |
ORF1ab/nsp4 | 17 | F17L | Ttc | Ctc | 3 | 3 | Q.6 | 0.019868 |
ORF1ab/nsp4 | 17 | F17L | ttC | ttA | 2 | 2 | AY.13 | 0.000322 |
ORF1ab/nsp4 | 17 | F17L | ttC | ttA | 1 | 2 | AY.23 | 0.00007 |
ORF1ab/nsp4 | 17 | F17L | Ttc | Ctc | 1 | 2 | AY.23 | 0.00007 |
ORF1ab/nsp4 | 17 | F17L | ttC | ttA | 1 | 2 | AY.39 | 0.000025 |
ORF1ab/nsp4 | 17 | F17L | ttC | ttG | 1 | 2 | AY.39 | 0.000025 |
ORF1ab/nsp4 | 17 | F17L | Ttc | Ctc | 2 | 2 | B.1.1.519 | 0.000079 |
ORF1ab/nsp4 | 17 | F17L | Ttc | Ctc | 2 | 2 | B.1.576 | 0.001813 |
ORF1ab/nsp4 | 17 | F17L | Ttc | Ctc | 2 | 2 | P.1 | 0.000032 |
ORF1ab/nsp4 | 17 | F17L | ttC | ttA | 1 | 1 | 0.055556 | |
ORF1ab/nsp4 | 17 | F17L | Ttc | Ctc | 1 | 1 | A.2 | 0.000662 |
ORF1ab/nsp4 | 17 | F17L | Ttc | Ctc | 1 | 1 | A.2.4 | 0.003367 |
ORF1ab/nsp4 | 17 | F17L | ttC | ttA | 1 | 1 | AY.110 | 0.000113 |
ORF1ab/nsp4 | 17 | F17L | Ttc | Ctc | 1 | 1 | AY.119 | 0.000035 |
ORF1ab/nsp4 | 17 | F17L | Ttc | Ctc | 1 | 1 | AY.3 | 0.00001 |
ORF1ab/nsp4 | 17 | F17L | Ttc | Ctc | 1 | 1 | AY.3.1 | 0.000085 |
ORF1ab/nsp4 | 17 | F17L | Ttc | Ctc | 1 | 1 | AY.34.1 | 0.00051 |
ORF1ab/nsp4 | 17 | F17L | ttC | ttA | 1 | 1 | AY.47 | 0.000031 |
ORF1ab/nsp4 | 17 | F17L | Ttc | Ctc | 1 | 1 | AY.54 | 0.000095 |
ORF1ab/nsp4 | 17 | F17L | Ttc | Ctc | 1 | 1 | AY.60 | 0.000938 |
ORF1ab/nsp4 | 17 | F17L | ttC | ttA | 1 | 1 | AY.65 | 0.000533 |
ORF1ab/nsp4 | 17 | F17L | Ttc | Ctc | 1 | 1 | AY.98 | 0.000079 |
ORF1ab/nsp4 | 17 | F17L | Ttc | Ctc | 1 | 1 | B.1.1.181 | 0.004545 |
ORF1ab/nsp4 | 17 | F17L | Ttc | Ctc | 1 | 1 | B.1.1.220 | 0.001859 |
ORF1ab/nsp4 | 17 | F17L | ttC | ttA | 1 | 1 | B.1.1.222 | 0.000204 |
ORF1ab/nsp4 | 17 | F17L | Ttc | Ctc | 1 | 1 | B.1.1.286 | 0.002899 |
ORF1ab/nsp4 | 17 | F17L | Ttc | Ctc | 1 | 1 | B.1.1.317 | 0.000412 |
ORF1ab/nsp4 | 17 | F17L | ttC | ttA | 1 | 1 | B.1.1.33 | 0.000421 |
ORF1ab/nsp4 | 17 | F17L | ttC | ttA | 1 | 1 | B.1.1.349 | 0.010309 |
ORF1ab/nsp4 | 17 | F17L | ttC | ttA | 1 | 1 | B.1.1.48 | 0.002874 |
ORF1ab/nsp4 | 17 | F17L | Ttc | Ctc | 1 | 1 | B.1.1.525 | 0.005464 |
ORF1ab/nsp4 | 17 | F17L | Ttc | Ctc | 1 | 1 | B.1.111 | 0.001175 |
ORF1ab/nsp4 | 17 | F17L | Ttc | Ctc | 1 | 1 | B.1.177.15 | 0.000631 |
ORF1ab/nsp4 | 17 | F17L | Ttc | Ctc | 1 | 1 | B.1.177.19 | 0.001431 |
ORF1ab/nsp4 | 17 | F17L | Ttc | Ctc | 1 | 1 | B.1.177.58 | 0.001332 |
ORF1ab/nsp4 | 17 | F17L | ttC | ttA | 1 | 1 | B.1.2 | 0.000009 |
ORF1ab/nsp4 | 17 | F17L | ttC | ttA | 1 | 1 | B.1.210 | 0.002132 |
ORF1ab/nsp4 | 17 | F17L | Ttc | Ctc | 1 | 1 | B.1.243 | 0.00007 |
ORF1ab/nsp4 | 17 | F17L | Ttc | Ctc | 1 | 1 | B.1.258 | 0.000067 |
ORF1ab/nsp4 | 17 | F17L | ttC | ttA | 1 | 1 | B.1.351 | 0.00003 |
ORF1ab/nsp4 | 17 | F17L | Ttc | Ctc | 1 | 1 | B.1.36 | 0.000146 |
ORF1ab/nsp4 | 17 | F17L | Ttc | Ctc | 1 | 1 | B.1.369 | 0.000285 |
ORF1ab/nsp4 | 17 | F17L | Ttc | Ctc | 1 | 1 | B.1.375 | 0.00082 |
ORF1ab/nsp4 | 17 | F17L | Ttc | Ctc | 1 | 1 | B.1.393 | 0.028571 |
ORF1ab/nsp4 | 17 | F17L | Ttc | Ctc | 1 | 1 | B.1.427 | 0.00005 |
ORF1ab/nsp4 | 17 | F17L | ttC | ttA | 1 | 1 | B.1.429 | 0.000024 |
ORF1ab/nsp4 | 17 | F17L | Ttc | Ctc | 1 | 1 | B.1.462 | 0.007246 |
ORF1ab/nsp4 | 17 | F17L | Ttc | Ctc | 1 | 1 | B.1.466.2 | 0.000391 |
ORF1ab/nsp4 | 17 | F17L | Ttc | Ctc | 1 | 1 | B.1.517 | 0.000427 |
ORF1ab/nsp4 | 17 | F17L | Ttc | Ctc | 1 | 1 | B.1.596 | 0.000087 |
ORF1ab/nsp4 | 17 | F17L | Ttc | Ctc | 1 | 1 | B.1.609 | 0.000479 |
ORF1ab/nsp4 | 17 | F17L | Ttc | Ctc | 1 | 1 | B.1.619 | 0.000871 |
ORF1ab/nsp4 | 17 | F17L | Ttc | Ctc | 1 | 1 | B.1.619.1 | 0.000641 |
ORF1ab/nsp4 | 17 | F17L | Ttc | Ctc | 1 | 1 | B.1.623 | 0.000536 |
ORF1ab/nsp4 | 17 | F17L | ttC | ttG | 1 | 1 | D.2 | 0.000075 |
ORF1ab/nsp4 | 17 | F17L | Ttc | Ctc | 1 | 1 | P.1.1 | 0.000318 |
ORF1ab/nsp4 | 17 | F17L | Ttc | Ctc | 1 | 1 | P.1.10 | 0.000269 |
ORF1ab/nsp4 | 17 | F17L | Ttc | Ctc | 1 | 1 | P.1.12 | 0.000484 |
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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