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/nsp2 | 248 | S248S | S428S | syn | agC | agT | 1362 | 1360 | 0.998532 | 1547-1549 |
ORF1ab/nsp2 | 248 | S248S | S428S | syn | AGc | TCc | 1362 | 1 | 0.000734214 | 1547-1549 |
ORF1ab/nsp2 | 248 | S248S | S428S | syn | AGC | TCT | 1362 | 1 | 0.000734214 | 1547-1549 |
Details of the mutation S248S 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/nsp2 | 248 | S248S | agC | agT | 1360 | 1362 | All | 0.00026 |
ORF1ab/nsp2 | 248 | S248S | AGC | TCT | 1 | 1362 | All | 0 |
ORF1ab/nsp2 | 248 | S248S | AGc | TCc | 1 | 1362 | All | 0 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 223 | 223 | B.1.1.7 | 0.0002 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 202 | 202 | AY.4 | 0.000314 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 131 | 131 | B.1.617.2 | 0.000493 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 102 | 102 | AY.44 | 0.000621 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 62 | 62 | B.1.2 | 0.000546 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 45 | 45 | AY.117 | 0.003803 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 39 | 39 | AY.43 | 0.000173 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 36 | 36 | B.1.221.3 | 0.03 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 33 | 33 | B.1.177 | 0.000435 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 31 | 31 | B.1 | 0.000284 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 24 | 24 | P.1 | 0.000378 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 22 | 22 | AY.42 | 0.000885 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 22 | 22 | AY.98 | 0.001738 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 18 | 18 | AY.103 | 0.000112 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 18 | 18 | B.1.429 | 0.000424 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 16 | 16 | AY.23 | 0.001116 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 15 | 15 | AY.25 | 0.00009 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 14 | 14 | B.1.177.81 | 0.002651 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 14 | 14 | B.1.621 | 0.001239 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 13 | 13 | AY.102 | 0.000345 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 13 | 13 | AY.39 | 0.000321 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 13 | 13 | B.1.619 | 0.011324 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 11 | 11 | B.1.526 | 0.000259 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 11 | 11 | B.1.623 | 0.005901 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 9 | 9 | AY.26 | 0.000255 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 8 | 8 | AY.3 | 0.00008 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 8 | 8 | AY.33 | 0.000534 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 7 | 7 | AY.14 | 0.000616 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 7 | 7 | AY.57 | 0.004593 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 7 | 7 | B.1.577 | 0.004811 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 6 | 6 | B.1.1.519 | 0.000238 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 3 | 5 | 0.166667 | |
ORF1ab/nsp2 | 248 | S248S | AGC | TCT | 1 | 5 | 0.055556 | |
ORF1ab/nsp2 | 248 | S248S | AGc | TCc | 1 | 5 | 0.055556 | |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 5 | 5 | AY.54 | 0.000477 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 5 | 5 | AY.99 | 0.005247 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 4 | 4 | AY.29 | 0.000063 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 4 | 4 | AY.47 | 0.000124 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 4 | 4 | AY.5 | 0.000083 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 4 | 4 | AY.9 | 0.00027 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 4 | 4 | AY.91 | 0.002922 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 4 | 4 | B.1.1 | 0.000073 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 4 | 4 | B.1.1.63 | 0.001543 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 4 | 4 | B.1.177.82 | 0.001909 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 4 | 4 | B.1.243 | 0.000278 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 4 | 4 | B.1.36 | 0.000584 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 4 | 4 | B.1.369 | 0.001141 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 4 | 4 | B.1.621.1 | 0.002023 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 4 | 4 | P.1.14 | 0.000191 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 3 | 3 | AY.4.2 | 0.000065 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 3 | 3 | AY.9.2 | 0.00011 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 3 | 3 | B.1.160 | 0.000094 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 3 | 3 | B.1.177.73 | 0.001699 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 3 | 3 | B.1.36.18 | 0.001261 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 3 | 3 | D.2 | 0.000225 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 3 | 3 | P.2 | 0.00056 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 3 | 3 | Q.8 | 0.000495 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 2 | 2 | A.1 | 0.000564 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 2 | 2 | AY.100 | 0.000092 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 2 | 2 | AY.106 | 0.00067 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 2 | 2 | AY.113 | 0.000285 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 2 | 2 | AY.39.1 | 0.000079 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 2 | 2 | AY.59 | 0.001059 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 2 | 2 | AY.9.1 | 0.000167 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 2 | 2 | B.1.1.222 | 0.000408 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 2 | 2 | B.1.1.50 | 0.001358 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 2 | 2 | B.1.147 | 0.001512 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 2 | 2 | B.1.177.4 | 0.000422 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 2 | 2 | B.1.177.60 | 0.000437 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 2 | 2 | B.1.258 | 0.000133 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 2 | 2 | B.1.258.14 | 0.001961 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 2 | 2 | B.1.351 | 0.000059 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 2 | 2 | B.1.404 | 0.002604 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 2 | 2 | B.1.427 | 0.000101 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 2 | 2 | Q.1 | 0.000253 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 1 | 1 | A.23.1 | 0.000704 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 1 | 1 | AY.116 | 0.000287 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 1 | 1 | AY.118 | 0.000063 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 1 | 1 | AY.119 | 0.000035 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 1 | 1 | AY.120.1 | 0.000321 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 1 | 1 | AY.121 | 0.000135 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 1 | 1 | AY.20 | 0.000039 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 1 | 1 | AY.21 | 0.001898 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 1 | 1 | AY.3.1 | 0.000085 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 1 | 1 | AY.30 | 0.000396 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 1 | 1 | AY.32 | 0.000532 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 1 | 1 | AY.34 | 0.000097 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 1 | 1 | AY.38 | 0.000499 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 1 | 1 | AY.4.5 | 0.000107 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 1 | 1 | AY.45 | 0.000122 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 1 | 1 | AY.46 | 0.000104 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 1 | 1 | AY.46.1 | 0.001027 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 1 | 1 | AY.46.6 | 0.000072 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 1 | 1 | AY.48 | 0.000465 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 1 | 1 | AY.6 | 0.000041 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 1 | 1 | AY.68 | 0.000274 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 1 | 1 | AY.70 | 0.000209 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 1 | 1 | AY.80 | 0.001129 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 1 | 1 | AY.84 | 0.000437 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 1 | 1 | AY.95 | 0.000761 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 1 | 1 | B.1.1.111 | 0.014706 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 1 | 1 | B.1.1.214 | 0.000055 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 1 | 1 | B.1.1.317 | 0.000412 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 1 | 1 | B.1.1.318 | 0.000302 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 1 | 1 | B.1.1.328 | 0.016949 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 1 | 1 | B.1.1.37 | 0.000193 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 1 | 1 | B.1.1.372 | 0.000689 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 1 | 1 | B.1.1.381 | 0.04 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 1 | 1 | B.1.1.39 | 0.00051 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 1 | 1 | B.1.1.419 | 0.007407 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 1 | 1 | B.1.160.22 | 0.006757 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 1 | 1 | B.1.177.32 | 0.00135 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 1 | 1 | B.1.177.33 | 0.001645 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 1 | 1 | B.1.177.55 | 0.002331 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 1 | 1 | B.1.177.57 | 0.000281 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 1 | 1 | B.1.177.65 | 0.000665 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 1 | 1 | B.1.258.3 | 0.001675 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 1 | 1 | B.1.329 | 0.000608 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 1 | 1 | B.1.336 | 0.002439 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 1 | 1 | B.1.400 | 0.000429 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 1 | 1 | B.1.422 | 0.000812 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 1 | 1 | B.1.525 | 0.000113 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 1 | 1 | B.1.574 | 0.002151 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 1 | 1 | B.1.617.1 | 0.000129 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 1 | 1 | B.1.637 | 0.000073 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 1 | 1 | B.1.93 | 0.000934 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 1 | 1 | P.1.15 | 0.000232 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 1 | 1 | P.1.6 | 0.001946 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 1 | 1 | P.7 | 0.004367 |
ORF1ab/nsp2 | 248 | S248S | agC | agT | 1 | 1 | Z.1 | 0.00289 |
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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