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 |
M | 66 | V66V | syn | gtG | gtA | 5381 | 3063 | 0.569225 | 26718-26720 | |
M | 66 | V66V | syn | gtG | gtT | 5381 | 2264 | 0.42074 | 26718-26720 | |
M | 66 | V66V | syn | gtG | gtC | 5381 | 54 | 0.0100353 | 26718-26720 |
Details of the mutation V66V 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 |
M | 66 | V66V | gtG | gtA | 3063 | 5381 | All | 0.000586 |
M | 66 | V66V | gtG | gtT | 2264 | 5381 | All | 0.000433 |
M | 66 | V66V | gtG | gtC | 54 | 5381 | All | 0.00001 |
M | 66 | V66V | gtG | gtA | 1474 | 2010 | AY.4 | 0.002294 |
M | 66 | V66V | gtG | gtT | 536 | 2010 | AY.4 | 0.000834 |
M | 66 | V66V | gtG | gtA | 1249 | 1249 | AY.90 | 0.854894 |
M | 66 | V66V | gtG | gtT | 793 | 802 | B.1.160 | 0.024732 |
M | 66 | V66V | gtG | gtA | 9 | 802 | B.1.160 | 0.000281 |
M | 66 | V66V | gtG | gtA | 114 | 186 | B.1.1.7 | 0.000102 |
M | 66 | V66V | gtG | gtT | 72 | 186 | B.1.1.7 | 0.000064 |
M | 66 | V66V | gtG | gtT | 176 | 176 | B.1.177.12 | 0.026699 |
M | 66 | V66V | gtG | gtA | 52 | 91 | B.1.617.2 | 0.000196 |
M | 66 | V66V | gtG | gtT | 39 | 91 | B.1.617.2 | 0.000147 |
M | 66 | V66V | gtG | gtT | 40 | 67 | B.1 | 0.000366 |
M | 66 | V66V | gtG | gtA | 26 | 67 | B.1 | 0.000238 |
M | 66 | V66V | gtG | gtC | 1 | 67 | B.1 | 0.000009 |
M | 66 | V66V | gtG | gtT | 66 | 66 | B.1.160.27 | 1 |
M | 66 | V66V | gtG | gtT | 49 | 51 | B.1.429 | 0.001153 |
M | 66 | V66V | gtG | gtA | 2 | 51 | B.1.429 | 0.000047 |
M | 66 | V66V | gtG | gtC | 48 | 48 | B.4 | 0.10596 |
M | 66 | V66V | gtG | gtT | 47 | 47 | AY.39 | 0.001161 |
M | 66 | V66V | gtG | gtT | 36 | 39 | B.1.258 | 0.002396 |
M | 66 | V66V | gtG | gtA | 3 | 39 | B.1.258 | 0.0002 |
M | 66 | V66V | gtG | gtT | 21 | 34 | B.1.1 | 0.000381 |
M | 66 | V66V | gtG | gtA | 12 | 34 | B.1.1 | 0.000218 |
M | 66 | V66V | gtG | gtC | 1 | 34 | B.1.1 | 0.000018 |
M | 66 | V66V | gtG | gtT | 31 | 31 | B.1.351 | 0.000922 |
M | 66 | V66V | gtG | gtT | 15 | 27 | B.1.177 | 0.000198 |
M | 66 | V66V | gtG | gtA | 12 | 27 | B.1.177 | 0.000158 |
M | 66 | V66V | gtG | gtT | 25 | 26 | AY.44 | 0.000152 |
M | 66 | V66V | gtG | gtA | 1 | 26 | AY.44 | 0.000006 |
M | 66 | V66V | gtG | gtT | 18 | 26 | B.1.2 | 0.000158 |
M | 66 | V66V | gtG | gtA | 8 | 26 | B.1.2 | 0.00007 |
M | 66 | V66V | gtG | gtT | 20 | 25 | AY.43 | 0.000089 |
M | 66 | V66V | gtG | gtA | 5 | 25 | AY.43 | 0.000022 |
M | 66 | V66V | gtG | gtT | 20 | 21 | AY.103 | 0.000124 |
M | 66 | V66V | gtG | gtA | 1 | 21 | AY.103 | 0.000006 |
M | 66 | V66V | gtG | gtT | 21 | 21 | AY.20 | 0.000816 |
M | 66 | V66V | gtG | gtT | 16 | 19 | AY.113 | 0.002278 |
M | 66 | V66V | gtG | gtA | 3 | 19 | AY.113 | 0.000427 |
M | 66 | V66V | gtG | gtT | 15 | 16 | AY.25 | 0.00009 |
M | 66 | V66V | gtG | gtA | 1 | 16 | AY.25 | 0.000006 |
M | 66 | V66V | gtG | gtT | 12 | 15 | B.1.221 | 0.000852 |
M | 66 | V66V | gtG | gtA | 3 | 15 | B.1.221 | 0.000213 |
M | 66 | V66V | gtG | gtT | 10 | 14 | AY.5 | 0.000206 |
M | 66 | V66V | gtG | gtA | 4 | 14 | AY.5 | 0.000083 |
M | 66 | V66V | gtG | gtT | 9 | 11 | AY.102 | 0.000239 |
M | 66 | V66V | gtG | gtA | 2 | 11 | AY.102 | 0.000053 |
M | 66 | V66V | gtG | gtT | 10 | 11 | P.1 | 0.000158 |
M | 66 | V66V | gtG | gtA | 1 | 11 | P.1 | 0.000016 |
M | 66 | V66V | gtG | gtT | 9 | 10 | B | 0.00115 |
M | 66 | V66V | gtG | gtC | 1 | 10 | B | 0.000128 |
M | 66 | V66V | gtG | gtT | 9 | 9 | AY.42 | 0.000362 |
M | 66 | V66V | gtG | gtT | 6 | 8 | AY.3 | 0.00006 |
M | 66 | V66V | gtG | gtA | 2 | 8 | AY.3 | 0.00002 |
M | 66 | V66V | gtG | gtT | 7 | 8 | B.1.1.404 | 0.111111 |
M | 66 | V66V | gtG | gtA | 1 | 8 | B.1.1.404 | 0.015873 |
M | 66 | V66V | gtG | gtT | 7 | 7 | AY.56 | 0.011236 |
M | 66 | V66V | gtG | gtT | 7 | 7 | B.1.459 | 0.028571 |
M | 66 | V66V | gtG | gtT | 2 | 6 | 0.111111 | |
M | 66 | V66V | gtG | gtC | 2 | 6 | 0.111111 | |
M | 66 | V66V | gtG | gtA | 2 | 6 | 0.111111 | |
M | 66 | V66V | gtG | gtT | 5 | 5 | AY.3.1 | 0.000426 |
M | 66 | V66V | gtG | gtA | 4 | 5 | AY.9 | 0.00027 |
M | 66 | V66V | gtG | gtT | 1 | 5 | AY.9 | 0.000068 |
M | 66 | V66V | gtG | gtT | 5 | 5 | B.1.466.2 | 0.001956 |
M | 66 | V66V | gtG | gtT | 4 | 4 | AY.29 | 0.000063 |
M | 66 | V66V | gtG | gtT | 4 | 4 | AY.54 | 0.000381 |
M | 66 | V66V | gtG | gtT | 4 | 4 | AY.9.2 | 0.000147 |
M | 66 | V66V | gtG | gtA | 4 | 4 | B.1.160.12 | 0.025641 |
M | 66 | V66V | gtG | gtT | 4 | 4 | B.1.189 | 0.017167 |
M | 66 | V66V | gtG | gtT | 4 | 4 | P.1.16 | 0.001496 |
M | 66 | V66V | gtG | gtT | 3 | 3 | AY.111 | 0.000549 |
M | 66 | V66V | gtG | gtT | 2 | 3 | AY.120 | 0.000074 |
M | 66 | V66V | gtG | gtA | 1 | 3 | AY.120 | 0.000037 |
M | 66 | V66V | gtG | gtT | 2 | 3 | AY.34 | 0.000194 |
M | 66 | V66V | gtG | gtA | 1 | 3 | AY.34 | 0.000097 |
M | 66 | V66V | gtG | gtT | 3 | 3 | AY.4.2 | 0.000065 |
M | 66 | V66V | gtG | gtT | 3 | 3 | AY.5.3 | 0.001012 |
M | 66 | V66V | gtG | gtT | 3 | 3 | AY.98 | 0.000237 |
M | 66 | V66V | gtG | gtA | 3 | 3 | B.1.1.14 | 0.051724 |
M | 66 | V66V | gtG | gtA | 3 | 3 | B.1.1.372 | 0.002066 |
M | 66 | V66V | gtG | gtA | 3 | 3 | B.1.160.16 | 0.002788 |
M | 66 | V66V | gtG | gtA | 3 | 3 | B.1.177.43 | 0.004431 |
M | 66 | V66V | gtG | gtA | 3 | 3 | B.1.177.7 | 0.000495 |
M | 66 | V66V | gtG | gtT | 3 | 3 | B.1.627 | 0.006061 |
M | 66 | V66V | gtG | gtT | 3 | 3 | B.23 | 0.008772 |
M | 66 | V66V | gtG | gtT | 3 | 3 | Q.8 | 0.000495 |
M | 66 | V66V | gtG | gtA | 2 | 2 | A.2 | 0.001324 |
M | 66 | V66V | gtG | gtT | 2 | 2 | A.2.5 | 0.000998 |
M | 66 | V66V | gtG | gtT | 2 | 2 | AY.119 | 0.000071 |
M | 66 | V66V | gtG | gtT | 2 | 2 | AY.12 | 0.000632 |
M | 66 | V66V | gtG | gtT | 1 | 2 | AY.16 | 0.00038 |
M | 66 | V66V | gtG | gtA | 1 | 2 | AY.16 | 0.00038 |
M | 66 | V66V | gtG | gtT | 2 | 2 | AY.23 | 0.000139 |
M | 66 | V66V | gtG | gtT | 2 | 2 | AY.26 | 0.000057 |
M | 66 | V66V | gtG | gtT | 2 | 2 | AY.64 | 0.00119 |
M | 66 | V66V | gtG | gtA | 2 | 2 | AY.98.1 | 0.000097 |
M | 66 | V66V | gtG | gtA | 2 | 2 | B.1.1.301 | 0.002358 |
M | 66 | V66V | gtG | gtT | 2 | 2 | B.1.1.306 | 0.000877 |
M | 66 | V66V | gtG | gtT | 1 | 2 | B.1.1.37 | 0.000193 |
M | 66 | V66V | gtG | gtA | 1 | 2 | B.1.1.37 | 0.000193 |
M | 66 | V66V | gtG | gtA | 2 | 2 | B.1.1.83 | 0.00542 |
M | 66 | V66V | gtG | gtA | 2 | 2 | B.1.177.81 | 0.000379 |
M | 66 | V66V | gtG | gtA | 2 | 2 | B.1.235 | 0.005038 |
M | 66 | V66V | gtG | gtA | 1 | 2 | B.1.260 | 0.003344 |
M | 66 | V66V | gtG | gtT | 1 | 2 | B.1.260 | 0.003344 |
M | 66 | V66V | gtG | gtA | 1 | 2 | B.1.526 | 0.000024 |
M | 66 | V66V | gtG | gtT | 1 | 2 | B.1.526 | 0.000024 |
M | 66 | V66V | gtG | gtT | 2 | 2 | B.1.609 | 0.000959 |
M | 66 | V66V | gtG | gtT | 2 | 2 | P.1.7 | 0.000639 |
M | 66 | V66V | gtG | gtA | 2 | 2 | S.1 | 0.009901 |
M | 66 | V66V | gtG | gtT | 1 | 1 | AY.118 | 0.000063 |
M | 66 | V66V | gtG | gtT | 1 | 1 | AY.14 | 0.000088 |
M | 66 | V66V | gtG | gtA | 1 | 1 | AY.16.1 | 0.00047 |
M | 66 | V66V | gtG | gtT | 1 | 1 | AY.27 | 0.000065 |
M | 66 | V66V | gtG | gtT | 1 | 1 | AY.33 | 0.000067 |
M | 66 | V66V | gtG | gtT | 1 | 1 | AY.36 | 0.000148 |
M | 66 | V66V | gtG | gtT | 1 | 1 | AY.39.1 | 0.00004 |
M | 66 | V66V | gtG | gtT | 1 | 1 | AY.41 | 0.000294 |
M | 66 | V66V | gtG | gtT | 1 | 1 | AY.45 | 0.000122 |
M | 66 | V66V | gtG | gtT | 1 | 1 | AY.46 | 0.000104 |
M | 66 | V66V | gtG | gtA | 1 | 1 | AY.47 | 0.000031 |
M | 66 | V66V | gtG | gtA | 1 | 1 | AY.58 | 0.000907 |
M | 66 | V66V | gtG | gtT | 1 | 1 | AY.63 | 0.000387 |
M | 66 | V66V | gtG | gtT | 1 | 1 | AY.7.1 | 0.000113 |
M | 66 | V66V | gtG | gtT | 1 | 1 | AY.74 | 0.000116 |
M | 66 | V66V | gtG | gtT | 1 | 1 | AY.79 | 0.001211 |
M | 66 | V66V | gtG | gtT | 1 | 1 | AY.85 | 0.000427 |
M | 66 | V66V | gtG | gtA | 1 | 1 | AY.89 | 0.004902 |
M | 66 | V66V | gtG | gtT | 1 | 1 | AY.92 | 0.000287 |
M | 66 | V66V | gtG | gtA | 1 | 1 | B.1.1.170 | 0.001247 |
M | 66 | V66V | gtG | gtA | 1 | 1 | B.1.1.217 | 0.003636 |
M | 66 | V66V | gtG | gtT | 1 | 1 | B.1.1.222 | 0.000204 |
M | 66 | V66V | gtG | gtT | 1 | 1 | B.1.1.25 | 0.000569 |
M | 66 | V66V | gtG | gtT | 1 | 1 | B.1.1.318 | 0.000302 |
M | 66 | V66V | gtG | gtT | 1 | 1 | B.1.1.326 | 0.001761 |
M | 66 | V66V | gtG | gtT | 1 | 1 | B.1.1.348 | 0.000796 |
M | 66 | V66V | gtG | gtT | 1 | 1 | B.1.1.385 | 0.004464 |
M | 66 | V66V | gtG | gtA | 1 | 1 | B.1.1.39 | 0.00051 |
M | 66 | V66V | gtG | gtA | 1 | 1 | B.1.1.43 | 0.014925 |
M | 66 | V66V | gtG | gtA | 1 | 1 | B.1.1.45 | 0.014085 |
M | 66 | V66V | gtG | gtA | 1 | 1 | B.1.1.47 | 0.005348 |
M | 66 | V66V | gtG | gtT | 1 | 1 | B.1.1.526 | 0.003546 |
M | 66 | V66V | gtG | gtA | 1 | 1 | B.1.1.70 | 0.000341 |
M | 66 | V66V | gtG | gtA | 1 | 1 | B.1.1.72 | 0.030303 |
M | 66 | V66V | gtG | gtA | 1 | 1 | B.1.160.11 | 0.005714 |
M | 66 | V66V | gtG | gtT | 1 | 1 | B.1.160.15 | 0.00495 |
M | 66 | V66V | gtG | gtA | 1 | 1 | B.1.160.9 | 0.007194 |
M | 66 | V66V | gtG | gtA | 1 | 1 | B.1.165 | 0.011905 |
M | 66 | V66V | gtG | gtA | 1 | 1 | B.1.177.23 | 0.003236 |
M | 66 | V66V | gtG | gtA | 1 | 1 | B.1.177.44 | 0.000519 |
M | 66 | V66V | gtG | gtA | 1 | 1 | B.1.177.53 | 0.002392 |
M | 66 | V66V | gtG | gtA | 1 | 1 | B.1.177.77 | 0.000726 |
M | 66 | V66V | gtG | gtT | 1 | 1 | B.1.177.84 | 0.006667 |
M | 66 | V66V | gtG | gtT | 1 | 1 | B.1.177.87 | 0.000728 |
M | 66 | V66V | gtG | gtT | 1 | 1 | B.1.214.1 | 0.02 |
M | 66 | V66V | gtG | gtC | 1 | 1 | B.1.221.1 | 0.002907 |
M | 66 | V66V | gtG | gtA | 1 | 1 | B.1.223 | 0.002778 |
M | 66 | V66V | gtG | gtT | 1 | 1 | B.1.234 | 0.000132 |
M | 66 | V66V | gtG | gtT | 1 | 1 | B.1.258.14 | 0.00098 |
M | 66 | V66V | gtG | gtA | 1 | 1 | B.1.351.2 | 0.000303 |
M | 66 | V66V | gtG | gtT | 1 | 1 | B.1.36 | 0.000146 |
M | 66 | V66V | gtG | gtA | 1 | 1 | B.1.36.35 | 0.002604 |
M | 66 | V66V | gtG | gtT | 1 | 1 | B.1.36.8 | 0.001 |
M | 66 | V66V | gtG | gtA | 1 | 1 | B.1.391 | 0.001127 |
M | 66 | V66V | gtG | gtT | 1 | 1 | B.1.396 | 0.000706 |
M | 66 | V66V | gtG | gtA | 1 | 1 | B.1.40 | 0.019608 |
M | 66 | V66V | gtG | gtA | 1 | 1 | B.1.418 | 0.015873 |
M | 66 | V66V | gtG | gtT | 1 | 1 | B.1.438.1 | 0.000107 |
M | 66 | V66V | gtG | gtT | 1 | 1 | B.1.465 | 0.003802 |
M | 66 | V66V | gtG | gtT | 1 | 1 | B.1.470 | 0.001404 |
M | 66 | V66V | gtG | gtT | 1 | 1 | B.1.492 | 0.007042 |
M | 66 | V66V | gtG | gtA | 1 | 1 | B.1.525 | 0.000113 |
M | 66 | V66V | gtG | gtT | 1 | 1 | B.1.561 | 0.000397 |
M | 66 | V66V | gtG | gtT | 1 | 1 | B.1.564 | 0.000426 |
M | 66 | V66V | gtG | gtA | 1 | 1 | B.1.582 | 0.000491 |
M | 66 | V66V | gtG | gtA | 1 | 1 | B.1.617.1 | 0.000129 |
M | 66 | V66V | gtG | gtT | 1 | 1 | B.1.628 | 0.000352 |
M | 66 | V66V | gtG | gtA | 1 | 1 | B.1.637 | 0.000073 |
M | 66 | V66V | gtG | gtA | 1 | 1 | B.28 | 0.003279 |
M | 66 | V66V | gtG | gtA | 1 | 1 | B.40 | 0.000364 |
M | 66 | V66V | gtG | gtA | 1 | 1 | B.6 | 0.00091 |
M | 66 | V66V | gtG | gtT | 1 | 1 | C.1 | 0.002392 |
M | 66 | V66V | gtG | gtA | 1 | 1 | C.3 | 0.007634 |
M | 66 | V66V | gtG | gtT | 1 | 1 | P.1.12 | 0.000484 |
M | 66 | V66V | gtG | gtT | 1 | 1 | P.2 | 0.000187 |
M | 66 | V66V | gtG | gtT | 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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