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 | 9 | T9T | syn | acC | acT | 2369 | 2296 | 0.969185 | 26547-26549 | |
M | 9 | T9T | syn | acC | acA | 2369 | 68 | 0.0287041 | 26547-26549 | |
M | 9 | T9T | syn | acC | acG | 2369 | 5 | 0.0021106 | 26547-26549 |
Details of the mutation T9T 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 | 9 | T9T | acC | acT | 2296 | 2369 | All | 0.000439 |
M | 9 | T9T | acC | acA | 68 | 2369 | All | 0.000013 |
M | 9 | T9T | acC | acG | 5 | 2369 | All | 0.000001 |
M | 9 | T9T | acC | acT | 411 | 423 | AY.4 | 0.00064 |
M | 9 | T9T | acC | acA | 12 | 423 | AY.4 | 0.000019 |
M | 9 | T9T | acC | acT | 354 | 361 | B.1.1.7 | 0.000317 |
M | 9 | T9T | acC | acA | 7 | 361 | B.1.1.7 | 0.000006 |
M | 9 | T9T | acC | acT | 259 | 259 | B.1.599 | 0.945255 |
M | 9 | T9T | acC | acT | 218 | 218 | B.1.2 | 0.00192 |
M | 9 | T9T | acC | acT | 159 | 162 | B.1.617.2 | 0.000599 |
M | 9 | T9T | acC | acA | 3 | 162 | B.1.617.2 | 0.000011 |
M | 9 | T9T | acC | acT | 98 | 98 | B.1.530 | 0.7 |
M | 9 | T9T | acC | acT | 80 | 80 | B.1 | 0.000733 |
M | 9 | T9T | acC | acT | 72 | 72 | AY.36 | 0.010671 |
M | 9 | T9T | acC | acT | 49 | 49 | P.1.7 | 0.015645 |
M | 9 | T9T | acC | acT | 32 | 47 | AY.103 | 0.000199 |
M | 9 | T9T | acC | acA | 15 | 47 | AY.103 | 0.000093 |
M | 9 | T9T | acC | acT | 47 | 47 | AY.44 | 0.000286 |
M | 9 | T9T | acC | acT | 40 | 40 | AY.120.1 | 0.012841 |
M | 9 | T9T | acC | acT | 32 | 32 | AY.43 | 0.000142 |
M | 9 | T9T | acC | acT | 29 | 29 | B.1.234 | 0.003826 |
M | 9 | T9T | acC | acT | 28 | 28 | B.1.243 | 0.001948 |
M | 9 | T9T | acC | acT | 25 | 25 | B.1.429 | 0.000588 |
M | 9 | T9T | acC | acT | 18 | 22 | B.1.351 | 0.000535 |
M | 9 | T9T | acC | acA | 4 | 22 | B.1.351 | 0.000119 |
M | 9 | T9T | acC | acT | 14 | 16 | AY.26 | 0.000396 |
M | 9 | T9T | acC | acA | 2 | 16 | AY.26 | 0.000057 |
M | 9 | T9T | acC | acT | 12 | 15 | AY.29 | 0.000189 |
M | 9 | T9T | acC | acA | 3 | 15 | AY.29 | 0.000047 |
M | 9 | T9T | acC | acT | 15 | 15 | AY.4.2 | 0.000325 |
M | 9 | T9T | acC | acT | 15 | 15 | AY.98 | 0.001185 |
M | 9 | T9T | acC | acT | 12 | 12 | AY.46 | 0.001249 |
M | 9 | T9T | acC | acT | 12 | 12 | B.1.36.29 | 0.006208 |
M | 9 | T9T | acC | acT | 10 | 10 | AY.16 | 0.003797 |
M | 9 | T9T | acC | acT | 9 | 10 | B.1.526 | 0.000212 |
M | 9 | T9T | acC | acA | 1 | 10 | B.1.526 | 0.000024 |
M | 9 | T9T | acC | acT | 9 | 9 | AY.23 | 0.000628 |
M | 9 | T9T | acC | acT | 7 | 9 | AY.25 | 0.000042 |
M | 9 | T9T | acC | acA | 2 | 9 | AY.25 | 0.000012 |
M | 9 | T9T | acC | acT | 9 | 9 | AY.39 | 0.000222 |
M | 9 | T9T | acC | acT | 9 | 9 | AY.42 | 0.000362 |
M | 9 | T9T | acC | acT | 8 | 9 | B.1.1 | 0.000145 |
M | 9 | T9T | acC | acA | 1 | 9 | B.1.1 | 0.000018 |
M | 9 | T9T | acC | acT | 8 | 8 | B.1.177 | 0.000105 |
M | 9 | T9T | acC | acT | 7 | 7 | AY.59 | 0.003708 |
M | 9 | T9T | acC | acT | 7 | 7 | B.4 | 0.015453 |
M | 9 | T9T | acC | acA | 7 | 7 | P.1.10 | 0.001886 |
M | 9 | T9T | acC | acT | 6 | 6 | AY.3 | 0.00006 |
M | 9 | T9T | acC | acT | 6 | 6 | B.1.177.21 | 0.000459 |
M | 9 | T9T | acC | acT | 6 | 6 | B.1.311 | 0.001647 |
M | 9 | T9T | acC | acG | 3 | 6 | B.1.36 | 0.000438 |
M | 9 | T9T | acC | acT | 3 | 6 | B.1.36 | 0.000438 |
M | 9 | T9T | acC | acT | 6 | 6 | B.6.6 | 0.005333 |
M | 9 | T9T | acC | acT | 6 | 6 | P.1 | 0.000095 |
M | 9 | T9T | acC | acT | 5 | 5 | AY.102 | 0.000133 |
M | 9 | T9T | acC | acT | 5 | 5 | AY.119 | 0.000177 |
M | 9 | T9T | acC | acT | 5 | 5 | B.1.1.25 | 0.002843 |
M | 9 | T9T | acC | acT | 5 | 5 | B.1.1.58 | 0.026882 |
M | 9 | T9T | acC | acT | 5 | 5 | B.1.258.17 | 0.00052 |
M | 9 | T9T | acC | acA | 2 | 4 | AY.4.5 | 0.000215 |
M | 9 | T9T | acC | acT | 2 | 4 | AY.4.5 | 0.000215 |
M | 9 | T9T | acC | acA | 2 | 4 | AY.5 | 0.000041 |
M | 9 | T9T | acC | acG | 1 | 4 | AY.5 | 0.000021 |
M | 9 | T9T | acC | acT | 1 | 4 | AY.5 | 0.000021 |
M | 9 | T9T | acC | acA | 2 | 4 | AY.75 | 0.000112 |
M | 9 | T9T | acC | acT | 2 | 4 | AY.75 | 0.000112 |
M | 9 | T9T | acC | acT | 4 | 4 | B.1.596 | 0.000349 |
M | 9 | T9T | acC | acT | 3 | 3 | 0.166667 | |
M | 9 | T9T | acC | acT | 3 | 3 | AY.110 | 0.000338 |
M | 9 | T9T | acC | acT | 3 | 3 | AY.118 | 0.000188 |
M | 9 | T9T | acC | acT | 3 | 3 | AY.120 | 0.000112 |
M | 9 | T9T | acC | acT | 3 | 3 | AY.14 | 0.000264 |
M | 9 | T9T | acC | acT | 3 | 3 | AY.9.2 | 0.00011 |
M | 9 | T9T | acC | acT | 3 | 3 | B.1.177.7 | 0.000495 |
M | 9 | T9T | acC | acT | 3 | 3 | B.1.466.2 | 0.001174 |
M | 9 | T9T | acC | acT | 3 | 3 | D.2 | 0.000225 |
M | 9 | T9T | acC | acT | 3 | 3 | Q.8 | 0.000495 |
M | 9 | T9T | acC | acT | 2 | 2 | AY.115 | 0.010417 |
M | 9 | T9T | acC | acT | 2 | 2 | AY.13 | 0.000322 |
M | 9 | T9T | acC | acT | 2 | 2 | AY.27 | 0.000129 |
M | 9 | T9T | acC | acT | 2 | 2 | AY.34.1 | 0.00102 |
M | 9 | T9T | acC | acT | 2 | 2 | AY.4.2.1 | 0.000298 |
M | 9 | T9T | acC | acT | 1 | 2 | AY.45 | 0.000122 |
M | 9 | T9T | acC | acA | 1 | 2 | AY.45 | 0.000122 |
M | 9 | T9T | acC | acT | 1 | 2 | AY.47 | 0.000031 |
M | 9 | T9T | acC | acA | 1 | 2 | AY.47 | 0.000031 |
M | 9 | T9T | acC | acT | 2 | 2 | AY.74 | 0.000231 |
M | 9 | T9T | acC | acT | 2 | 2 | AZ.2 | 0.001642 |
M | 9 | T9T | acC | acT | 2 | 2 | B.1.1.214 | 0.000111 |
M | 9 | T9T | acC | acT | 2 | 2 | B.1.1.453 | 0.016949 |
M | 9 | T9T | acC | acT | 2 | 2 | B.1.177.60 | 0.000437 |
M | 9 | T9T | acC | acT | 2 | 2 | B.1.218 | 0.010309 |
M | 9 | T9T | acC | acT | 2 | 2 | B.1.221 | 0.000142 |
M | 9 | T9T | acC | acT | 2 | 2 | B.1.369 | 0.00057 |
M | 9 | T9T | acC | acA | 1 | 2 | P.1.1 | 0.000318 |
M | 9 | T9T | acC | acG | 1 | 2 | P.1.1 | 0.000318 |
M | 9 | T9T | acC | acT | 2 | 2 | P.1.17 | 0.000324 |
M | 9 | T9T | acC | acT | 2 | 2 | R.1 | 0.00018 |
M | 9 | T9T | acC | acT | 1 | 1 | A | 0.000387 |
M | 9 | T9T | acC | acT | 1 | 1 | AY.10 | 0.00053 |
M | 9 | T9T | acC | acT | 1 | 1 | AY.100 | 0.000046 |
M | 9 | T9T | acC | acT | 1 | 1 | AY.104 | 0.001984 |
M | 9 | T9T | acC | acT | 1 | 1 | AY.107 | 0.000466 |
M | 9 | T9T | acC | acT | 1 | 1 | AY.111 | 0.000183 |
M | 9 | T9T | acC | acT | 1 | 1 | AY.117 | 0.000085 |
M | 9 | T9T | acC | acT | 1 | 1 | AY.12 | 0.000316 |
M | 9 | T9T | acC | acT | 1 | 1 | AY.29.1 | 0.000221 |
M | 9 | T9T | acC | acT | 1 | 1 | AY.32 | 0.000532 |
M | 9 | T9T | acC | acT | 1 | 1 | AY.33 | 0.000067 |
M | 9 | T9T | acC | acT | 1 | 1 | AY.34 | 0.000097 |
M | 9 | T9T | acC | acT | 1 | 1 | AY.38 | 0.000499 |
M | 9 | T9T | acC | acT | 1 | 1 | AY.46.4 | 0.000165 |
M | 9 | T9T | acC | acT | 1 | 1 | AY.5.4 | 0.000277 |
M | 9 | T9T | acC | acT | 1 | 1 | AY.6 | 0.000041 |
M | 9 | T9T | acC | acT | 1 | 1 | AY.68 | 0.000274 |
M | 9 | T9T | acC | acT | 1 | 1 | AY.71 | 0.000475 |
M | 9 | T9T | acC | acT | 1 | 1 | AY.72 | 0.001361 |
M | 9 | T9T | acC | acT | 1 | 1 | AY.75.1 | 0.00018 |
M | 9 | T9T | acC | acA | 1 | 1 | AY.79 | 0.001211 |
M | 9 | T9T | acC | acT | 1 | 1 | AY.9 | 0.000068 |
M | 9 | T9T | acC | acT | 1 | 1 | AY.92 | 0.000287 |
M | 9 | T9T | acC | acT | 1 | 1 | B.1.1.232 | 0.001815 |
M | 9 | T9T | acC | acT | 1 | 1 | B.1.1.284 | 0.000107 |
M | 9 | T9T | acC | acT | 1 | 1 | B.1.1.306 | 0.000438 |
M | 9 | T9T | acC | acT | 1 | 1 | B.1.1.37 | 0.000193 |
M | 9 | T9T | acC | acT | 1 | 1 | B.1.1.434 | 0.000349 |
M | 9 | T9T | acC | acT | 1 | 1 | B.1.1.526 | 0.003546 |
M | 9 | T9T | acC | acT | 1 | 1 | B.1.139 | 0.000733 |
M | 9 | T9T | acC | acT | 1 | 1 | B.1.177.32 | 0.00135 |
M | 9 | T9T | acC | acT | 1 | 1 | B.1.177.45 | 0.000381 |
M | 9 | T9T | acC | acA | 1 | 1 | B.1.222 | 0.001692 |
M | 9 | T9T | acC | acT | 1 | 1 | B.1.240 | 0.000216 |
M | 9 | T9T | acC | acT | 1 | 1 | B.1.302 | 0.013333 |
M | 9 | T9T | acC | acT | 1 | 1 | B.1.324 | 0.001605 |
M | 9 | T9T | acC | acT | 1 | 1 | B.1.332 | 0.003497 |
M | 9 | T9T | acC | acT | 1 | 1 | B.1.351.1 | 0.038462 |
M | 9 | T9T | acC | acT | 1 | 1 | B.1.367 | 0.000792 |
M | 9 | T9T | acC | acT | 1 | 1 | B.1.380 | 0.006623 |
M | 9 | T9T | acC | acT | 1 | 1 | B.1.400 | 0.000429 |
M | 9 | T9T | acC | acT | 1 | 1 | B.1.417 | 0.028571 |
M | 9 | T9T | acC | acT | 1 | 1 | B.1.427 | 0.00005 |
M | 9 | T9T | acC | acT | 1 | 1 | B.1.438 | 0.006536 |
M | 9 | T9T | acC | acT | 1 | 1 | B.1.567 | 0.003333 |
M | 9 | T9T | acC | acT | 1 | 1 | B.1.582 | 0.000491 |
M | 9 | T9T | acC | acT | 1 | 1 | B.1.595 | 0.000261 |
M | 9 | T9T | acC | acT | 1 | 1 | B.1.617.1 | 0.000129 |
M | 9 | T9T | acC | acT | 1 | 1 | B.1.78 | 0.008547 |
M | 9 | T9T | acC | acT | 1 | 1 | B.1.9.5 | 0.005682 |
M | 9 | T9T | acC | acT | 1 | 1 | C.37.1 | 0.002618 |
M | 9 | T9T | acC | acT | 1 | 1 | P.1.15 | 0.000232 |
M | 9 | T9T | acC | acT | 1 | 1 | P.2 | 0.000187 |
M | 9 | T9T | acC | acT | 1 | 1 | P.3 | 0.001595 |
M | 9 | T9T | acC | acT | 1 | 1 | Q.7 | 0.001111 |
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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