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/nsp12 | 249 | R249R | R4641R | syn | agG | agA | 14415 | 14310 | 0.992716 | 14185-14187 |
ORF1ab/nsp12 | 249 | R249R | R4641R | syn | Agg | Cgg | 14415 | 105 | 0.00728408 | 14185-14187 |
Details of the mutation R249R 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/nsp12 | 249 | R249R | agG | agA | 14310 | 14415 | All | 0.002737 |
ORF1ab/nsp12 | 249 | R249R | Agg | Cgg | 105 | 14415 | All | 0.00002 |
ORF1ab/nsp12 | 249 | R249R | agG | agA | 9825 | 9825 | AY.54 | 0.936785 |
ORF1ab/nsp12 | 249 | R249R | agG | agA | 1455 | 1455 | B.1.2 | 0.012812 |
ORF1ab/nsp12 | 249 | R249R | agG | agA | 1073 | 1077 | B.1.617.2 | 0.00404 |
ORF1ab/nsp12 | 249 | R249R | Agg | Cgg | 4 | 1077 | B.1.617.2 | 0.000015 |
ORF1ab/nsp12 | 249 | R249R | agG | agA | 598 | 598 | B.1.1.7 | 0.000535 |
ORF1ab/nsp12 | 249 | R249R | agG | agA | 362 | 362 | B.1.396 | 0.255469 |
ORF1ab/nsp12 | 249 | R249R | agG | agA | 246 | 250 | AY.4 | 0.000383 |
ORF1ab/nsp12 | 249 | R249R | Agg | Cgg | 4 | 250 | AY.4 | 0.000006 |
ORF1ab/nsp12 | 249 | R249R | agG | agA | 149 | 149 | C.30.1 | 1 |
ORF1ab/nsp12 | 249 | R249R | agG | agA | 116 | 116 | AY.103 | 0.00072 |
ORF1ab/nsp12 | 249 | R249R | agG | agA | 100 | 101 | B.1 | 0.000916 |
ORF1ab/nsp12 | 249 | R249R | Agg | Cgg | 1 | 101 | B.1 | 0.000009 |
ORF1ab/nsp12 | 249 | R249R | Agg | Cgg | 87 | 90 | B.1.1.214 | 0.004825 |
ORF1ab/nsp12 | 249 | R249R | agG | agA | 3 | 90 | B.1.1.214 | 0.000166 |
ORF1ab/nsp12 | 249 | R249R | agG | agA | 27 | 27 | AY.25 | 0.000162 |
ORF1ab/nsp12 | 249 | R249R | agG | agA | 20 | 20 | B.1.1.306 | 0.008768 |
ORF1ab/nsp12 | 249 | R249R | agG | agA | 19 | 19 | AY.44 | 0.000116 |
ORF1ab/nsp12 | 249 | R249R | agG | agA | 18 | 18 | AY.62 | 0.007843 |
ORF1ab/nsp12 | 249 | R249R | agG | agA | 17 | 17 | P.1 | 0.000268 |
ORF1ab/nsp12 | 249 | R249R | agG | agA | 16 | 16 | B.1.596 | 0.001394 |
ORF1ab/nsp12 | 249 | R249R | agG | agA | 13 | 13 | AY.43 | 0.000058 |
ORF1ab/nsp12 | 249 | R249R | agG | agA | 13 | 13 | AY.75 | 0.000728 |
ORF1ab/nsp12 | 249 | R249R | agG | agA | 13 | 13 | B.1.429 | 0.000306 |
ORF1ab/nsp12 | 249 | R249R | agG | agA | 11 | 11 | B.1.1 | 0.0002 |
ORF1ab/nsp12 | 249 | R249R | agG | agA | 11 | 11 | B.1.1.519 | 0.000437 |
ORF1ab/nsp12 | 249 | R249R | agG | agA | 11 | 11 | B.1.351 | 0.000327 |
ORF1ab/nsp12 | 249 | R249R | agG | agA | 10 | 10 | AY.39 | 0.000247 |
ORF1ab/nsp12 | 249 | R249R | agG | agA | 10 | 10 | AY.7.1 | 0.001127 |
ORF1ab/nsp12 | 249 | R249R | agG | agA | 9 | 9 | AY.16 | 0.003417 |
ORF1ab/nsp12 | 249 | R249R | agG | agA | 9 | 9 | B.1.177 | 0.000119 |
ORF1ab/nsp12 | 249 | R249R | agG | agA | 9 | 9 | B.1.526 | 0.000212 |
ORF1ab/nsp12 | 249 | R249R | Agg | Cgg | 5 | 7 | AY.119 | 0.000177 |
ORF1ab/nsp12 | 249 | R249R | agG | agA | 2 | 7 | AY.119 | 0.000071 |
ORF1ab/nsp12 | 249 | R249R | agG | agA | 6 | 6 | AY.61 | 0.000629 |
ORF1ab/nsp12 | 249 | R249R | agG | agA | 5 | 5 | AY.117 | 0.000423 |
ORF1ab/nsp12 | 249 | R249R | agG | agA | 5 | 5 | AY.52 | 0.004072 |
ORF1ab/nsp12 | 249 | R249R | agG | agA | 4 | 4 | AY.39.1 | 0.000158 |
ORF1ab/nsp12 | 249 | R249R | agG | agA | 4 | 4 | AY.45 | 0.000487 |
ORF1ab/nsp12 | 249 | R249R | agG | agA | 4 | 4 | AY.9.2 | 0.000147 |
ORF1ab/nsp12 | 249 | R249R | agG | agA | 4 | 4 | B.1.160.16 | 0.003717 |
ORF1ab/nsp12 | 249 | R249R | agG | agA | 4 | 4 | B.1.221 | 0.000284 |
ORF1ab/nsp12 | 249 | R249R | Agg | Cgg | 3 | 4 | B.1.258 | 0.0002 |
ORF1ab/nsp12 | 249 | R249R | agG | agA | 1 | 4 | B.1.258 | 0.000067 |
ORF1ab/nsp12 | 249 | R249R | agG | agA | 4 | 4 | P.1.15 | 0.000929 |
ORF1ab/nsp12 | 249 | R249R | agG | agA | 3 | 3 | AY.3 | 0.00003 |
ORF1ab/nsp12 | 249 | R249R | agG | agA | 3 | 3 | AY.46.4 | 0.000494 |
ORF1ab/nsp12 | 249 | R249R | agG | agA | 3 | 3 | AY.51 | 0.002727 |
ORF1ab/nsp12 | 249 | R249R | agG | agA | 3 | 3 | AZ.1 | 0.002602 |
ORF1ab/nsp12 | 249 | R249R | agG | agA | 3 | 3 | B.1.1.219 | 0.015 |
ORF1ab/nsp12 | 249 | R249R | agG | agA | 3 | 3 | B.1.210 | 0.006397 |
ORF1ab/nsp12 | 249 | R249R | agG | agA | 3 | 3 | B.1.311 | 0.000824 |
ORF1ab/nsp12 | 249 | R249R | agG | agA | 2 | 2 | AY.120 | 0.000074 |
ORF1ab/nsp12 | 249 | R249R | agG | agA | 2 | 2 | AY.16.1 | 0.00094 |
ORF1ab/nsp12 | 249 | R249R | agG | agA | 2 | 2 | AY.20 | 0.000078 |
ORF1ab/nsp12 | 249 | R249R | agG | agA | 2 | 2 | AY.23.1 | 0.000835 |
ORF1ab/nsp12 | 249 | R249R | agG | agA | 2 | 2 | AY.93 | 0.000546 |
ORF1ab/nsp12 | 249 | R249R | agG | agA | 2 | 2 | B.1.1.317 | 0.000823 |
ORF1ab/nsp12 | 249 | R249R | agG | agA | 2 | 2 | B.1.1.416 | 0.00181 |
ORF1ab/nsp12 | 249 | R249R | agG | agA | 2 | 2 | B.1.1.528 | 0.009615 |
ORF1ab/nsp12 | 249 | R249R | agG | agA | 2 | 2 | B.1.234 | 0.000264 |
ORF1ab/nsp12 | 249 | R249R | agG | agA | 2 | 2 | B.1.243 | 0.000139 |
ORF1ab/nsp12 | 249 | R249R | agG | agA | 2 | 2 | B.1.258.11 | 0.000793 |
ORF1ab/nsp12 | 249 | R249R | agG | agA | 2 | 2 | B.1.284 | 0.026316 |
ORF1ab/nsp12 | 249 | R249R | agG | agA | 2 | 2 | B.1.369 | 0.00057 |
ORF1ab/nsp12 | 249 | R249R | agG | agA | 2 | 2 | B.1.538 | 0.016129 |
ORF1ab/nsp12 | 249 | R249R | agG | agA | 2 | 2 | B.1.580 | 0.00813 |
ORF1ab/nsp12 | 249 | R249R | agG | agA | 2 | 2 | B.1.595 | 0.000522 |
ORF1ab/nsp12 | 249 | R249R | agG | agA | 2 | 2 | B.1.617.1 | 0.000258 |
ORF1ab/nsp12 | 249 | R249R | agG | agA | 2 | 2 | B.1.621 | 0.000177 |
ORF1ab/nsp12 | 249 | R249R | agG | agA | 1 | 1 | 0.055556 | |
ORF1ab/nsp12 | 249 | R249R | agG | agA | 1 | 1 | A.6 | 0.005128 |
ORF1ab/nsp12 | 249 | R249R | agG | agA | 1 | 1 | AU.1 | 0.001266 |
ORF1ab/nsp12 | 249 | R249R | agG | agA | 1 | 1 | AY.116 | 0.000287 |
ORF1ab/nsp12 | 249 | R249R | agG | agA | 1 | 1 | AY.14 | 0.000088 |
ORF1ab/nsp12 | 249 | R249R | agG | agA | 1 | 1 | AY.26 | 0.000028 |
ORF1ab/nsp12 | 249 | R249R | agG | agA | 1 | 1 | AY.34 | 0.000097 |
ORF1ab/nsp12 | 249 | R249R | agG | agA | 1 | 1 | AY.37 | 0.000316 |
ORF1ab/nsp12 | 249 | R249R | agG | agA | 1 | 1 | AY.4.1 | 0.000737 |
ORF1ab/nsp12 | 249 | R249R | agG | agA | 1 | 1 | AY.4.5 | 0.000107 |
ORF1ab/nsp12 | 249 | R249R | agG | agA | 1 | 1 | AY.46 | 0.000104 |
ORF1ab/nsp12 | 249 | R249R | agG | agA | 1 | 1 | AY.46.6 | 0.000072 |
ORF1ab/nsp12 | 249 | R249R | agG | agA | 1 | 1 | AY.47 | 0.000031 |
ORF1ab/nsp12 | 249 | R249R | agG | agA | 1 | 1 | AY.5 | 0.000021 |
ORF1ab/nsp12 | 249 | R249R | agG | agA | 1 | 1 | AY.5.4 | 0.000277 |
ORF1ab/nsp12 | 249 | R249R | agG | agA | 1 | 1 | AY.53 | 0.000288 |
ORF1ab/nsp12 | 249 | R249R | agG | agA | 1 | 1 | AY.75.1 | 0.00018 |
ORF1ab/nsp12 | 249 | R249R | agG | agA | 1 | 1 | AY.98 | 0.000079 |
ORF1ab/nsp12 | 249 | R249R | agG | agA | 1 | 1 | AY.98.1 | 0.000048 |
ORF1ab/nsp12 | 249 | R249R | agG | agA | 1 | 1 | B | 0.000128 |
ORF1ab/nsp12 | 249 | R249R | agG | agA | 1 | 1 | B.1.1.1 | 0.000327 |
ORF1ab/nsp12 | 249 | R249R | agG | agA | 1 | 1 | B.1.1.16 | 0.055556 |
ORF1ab/nsp12 | 249 | R249R | agG | agA | 1 | 1 | B.1.1.189 | 0.001513 |
ORF1ab/nsp12 | 249 | R249R | agG | agA | 1 | 1 | B.1.1.194 | 0.00495 |
ORF1ab/nsp12 | 249 | R249R | agG | agA | 1 | 1 | B.1.1.329 | 0.003846 |
ORF1ab/nsp12 | 249 | R249R | agG | agA | 1 | 1 | B.1.1.33 | 0.000421 |
ORF1ab/nsp12 | 249 | R249R | agG | agA | 1 | 1 | B.1.1.37 | 0.000193 |
ORF1ab/nsp12 | 249 | R249R | agG | agA | 1 | 1 | B.1.1.50 | 0.000679 |
ORF1ab/nsp12 | 249 | R249R | agG | agA | 1 | 1 | B.1.139 | 0.000733 |
ORF1ab/nsp12 | 249 | R249R | agG | agA | 1 | 1 | B.1.177.15 | 0.000631 |
ORF1ab/nsp12 | 249 | R249R | agG | agA | 1 | 1 | B.1.177.21 | 0.000076 |
ORF1ab/nsp12 | 249 | R249R | agG | agA | 1 | 1 | B.1.177.33 | 0.001645 |
ORF1ab/nsp12 | 249 | R249R | agG | agA | 1 | 1 | B.1.258.20 | 0.015873 |
ORF1ab/nsp12 | 249 | R249R | agG | agA | 1 | 1 | B.1.265 | 0.001271 |
ORF1ab/nsp12 | 249 | R249R | agG | agA | 1 | 1 | B.1.281 | 0.021739 |
ORF1ab/nsp12 | 249 | R249R | agG | agA | 1 | 1 | B.1.36 | 0.000146 |
ORF1ab/nsp12 | 249 | R249R | Agg | Cgg | 1 | 1 | B.1.36.18 | 0.00042 |
ORF1ab/nsp12 | 249 | R249R | agG | agA | 1 | 1 | B.1.362 | 0.001541 |
ORF1ab/nsp12 | 249 | R249R | agG | agA | 1 | 1 | B.1.381 | 0.007812 |
ORF1ab/nsp12 | 249 | R249R | agG | agA | 1 | 1 | B.1.427 | 0.00005 |
ORF1ab/nsp12 | 249 | R249R | agG | agA | 1 | 1 | B.1.525 | 0.000113 |
ORF1ab/nsp12 | 249 | R249R | agG | agA | 1 | 1 | B.1.561 | 0.000397 |
ORF1ab/nsp12 | 249 | R249R | agG | agA | 1 | 1 | B.1.577 | 0.000687 |
ORF1ab/nsp12 | 249 | R249R | agG | agA | 1 | 1 | B.1.588 | 0.00091 |
ORF1ab/nsp12 | 249 | R249R | agG | agA | 1 | 1 | B.1.597 | 0.00463 |
ORF1ab/nsp12 | 249 | R249R | agG | agA | 1 | 1 | B.1.628 | 0.000352 |
ORF1ab/nsp12 | 249 | R249R | agG | agA | 1 | 1 | B.40 | 0.000364 |
ORF1ab/nsp12 | 249 | R249R | agG | agA | 1 | 1 | C.37 | 0.000116 |
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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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