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 |
S | 305 | S305S | syn | tcC | tcT | 1381 | 1280 | 0.926865 | 22475-22477 | |
S | 305 | S305S | syn | tcC | tcA | 1381 | 95 | 0.0687907 | 22475-22477 | |
S | 305 | S305S | syn | tcC | tcG | 1381 | 6 | 0.00434468 | 22475-22477 |
Details of the mutation S305S 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 |
S | 305 | S305S | tcC | tcT | 1280 | 1381 | All | 0.000245 |
S | 305 | S305S | tcC | tcA | 95 | 1381 | All | 0.000018 |
S | 305 | S305S | tcC | tcG | 6 | 1381 | All | 0.000001 |
S | 305 | S305S | tcC | tcT | 356 | 359 | B.1.617.2 | 0.00134 |
S | 305 | S305S | tcC | tcA | 2 | 359 | B.1.617.2 | 0.000008 |
S | 305 | S305S | tcC | tcG | 1 | 359 | B.1.617.2 | 0.000004 |
S | 305 | S305S | tcC | tcT | 171 | 184 | B.1.1.7 | 0.000153 |
S | 305 | S305S | tcC | tcA | 13 | 184 | B.1.1.7 | 0.000012 |
S | 305 | S305S | tcC | tcT | 168 | 168 | AY.43 | 0.000744 |
S | 305 | S305S | tcC | tcT | 145 | 152 | B.1 | 0.001328 |
S | 305 | S305S | tcC | tcA | 7 | 152 | B.1 | 0.000064 |
S | 305 | S305S | tcC | tcT | 49 | 66 | AY.4 | 0.000076 |
S | 305 | S305S | tcC | tcA | 17 | 66 | AY.4 | 0.000026 |
S | 305 | S305S | tcC | tcT | 65 | 65 | B.1.282 | 0.970149 |
S | 305 | S305S | tcC | tcT | 36 | 52 | AY.25 | 0.000217 |
S | 305 | S305S | tcC | tcA | 16 | 52 | AY.25 | 0.000096 |
S | 305 | S305S | tcC | tcT | 37 | 37 | AY.39 | 0.000914 |
S | 305 | S305S | tcC | tcT | 18 | 25 | B.1.2 | 0.000158 |
S | 305 | S305S | tcC | tcA | 7 | 25 | B.1.2 | 0.000062 |
S | 305 | S305S | tcC | tcT | 11 | 19 | AY.103 | 0.000068 |
S | 305 | S305S | tcC | tcA | 8 | 19 | AY.103 | 0.00005 |
S | 305 | S305S | tcC | tcT | 13 | 14 | AY.33 | 0.000868 |
S | 305 | S305S | tcC | tcG | 1 | 14 | AY.33 | 0.000067 |
S | 305 | S305S | tcC | tcT | 11 | 14 | B.1.1.519 | 0.000437 |
S | 305 | S305S | tcC | tcA | 3 | 14 | B.1.1.519 | 0.000119 |
S | 305 | S305S | tcC | tcT | 13 | 13 | B.1.526 | 0.000306 |
S | 305 | S305S | tcC | tcT | 10 | 10 | B.1.1 | 0.000181 |
S | 305 | S305S | tcC | tcT | 10 | 10 | B.1.1.54 | 0.030211 |
S | 305 | S305S | tcC | tcT | 7 | 7 | AY.44 | 0.000043 |
S | 305 | S305S | tcC | tcT | 6 | 7 | P.1 | 0.000095 |
S | 305 | S305S | tcC | tcA | 1 | 7 | P.1 | 0.000016 |
S | 305 | S305S | tcC | tcT | 7 | 7 | P.1.1 | 0.002224 |
S | 305 | S305S | tcC | tcT | 6 | 6 | B.1.234 | 0.000792 |
S | 305 | S305S | tcC | tcT | 6 | 6 | B.1.351.2 | 0.001815 |
S | 305 | S305S | tcC | tcT | 4 | 5 | AY.102 | 0.000106 |
S | 305 | S305S | tcC | tcG | 1 | 5 | AY.102 | 0.000027 |
S | 305 | S305S | tcC | tcT | 5 | 5 | AY.120 | 0.000186 |
S | 305 | S305S | tcC | tcT | 5 | 5 | AY.16 | 0.001898 |
S | 305 | S305S | tcC | tcT | 5 | 5 | AY.20 | 0.000194 |
S | 305 | S305S | tcC | tcT | 3 | 5 | AY.74 | 0.000347 |
S | 305 | S305S | tcC | tcA | 2 | 5 | AY.74 | 0.000231 |
S | 305 | S305S | tcC | tcA | 3 | 5 | B.1.177 | 0.00004 |
S | 305 | S305S | tcC | tcT | 2 | 5 | B.1.177 | 0.000026 |
S | 305 | S305S | tcC | tcT | 5 | 5 | B.1.596 | 0.000436 |
S | 305 | S305S | tcC | tcT | 4 | 5 | D.2 | 0.0003 |
S | 305 | S305S | tcC | tcA | 1 | 5 | D.2 | 0.000075 |
S | 305 | S305S | tcC | tcT | 4 | 4 | AY.61 | 0.000419 |
S | 305 | S305S | tcC | tcT | 4 | 4 | AY.9.1 | 0.000335 |
S | 305 | S305S | tcC | tcT | 4 | 4 | B.1.177.83 | 0.005926 |
S | 305 | S305S | tcC | tcT | 4 | 4 | B.1.330 | 0.114286 |
S | 305 | S305S | tcC | tcT | 4 | 4 | B.1.503 | 0.00995 |
S | 305 | S305S | tcC | tcT | 2 | 3 | AY.5 | 0.000041 |
S | 305 | S305S | tcC | tcA | 1 | 3 | AY.5 | 0.000021 |
S | 305 | S305S | tcC | tcT | 3 | 3 | B.1.258 | 0.0002 |
S | 305 | S305S | tcC | tcT | 3 | 3 | B.1.320 | 0.003736 |
S | 305 | S305S | tcC | tcT | 2 | 2 | 0.111111 | |
S | 305 | S305S | tcC | tcT | 2 | 2 | AY.116 | 0.000574 |
S | 305 | S305S | tcC | tcT | 2 | 2 | AY.3.1 | 0.000171 |
S | 305 | S305S | tcC | tcT | 1 | 2 | AY.34 | 0.000097 |
S | 305 | S305S | tcC | tcG | 1 | 2 | AY.34 | 0.000097 |
S | 305 | S305S | tcC | tcT | 2 | 2 | AY.42 | 0.00008 |
S | 305 | S305S | tcC | tcT | 2 | 2 | AY.46 | 0.000208 |
S | 305 | S305S | tcC | tcT | 2 | 2 | AY.46.6 | 0.000144 |
S | 305 | S305S | tcC | tcT | 1 | 2 | AY.47 | 0.000031 |
S | 305 | S305S | tcC | tcA | 1 | 2 | AY.47 | 0.000031 |
S | 305 | S305S | tcC | tcT | 2 | 2 | AY.54 | 0.000191 |
S | 305 | S305S | tcC | tcA | 2 | 2 | AY.99.2 | 0.000184 |
S | 305 | S305S | tcC | tcT | 1 | 2 | B.1.160 | 0.000031 |
S | 305 | S305S | tcC | tcA | 1 | 2 | B.1.160 | 0.000031 |
S | 305 | S305S | tcC | tcT | 2 | 2 | B.1.177.4 | 0.000422 |
S | 305 | S305S | tcC | tcT | 2 | 2 | B.1.177.54 | 0.001213 |
S | 305 | S305S | tcC | tcT | 2 | 2 | B.1.177.85 | 0.01087 |
S | 305 | S305S | tcC | tcG | 1 | 2 | B.1.221 | 0.000071 |
S | 305 | S305S | tcC | tcT | 1 | 2 | B.1.221 | 0.000071 |
S | 305 | S305S | tcC | tcT | 2 | 2 | B.1.36.8 | 0.002 |
S | 305 | S305S | tcC | tcT | 2 | 2 | B.1.398 | 0.005952 |
S | 305 | S305S | tcC | tcT | 2 | 2 | P.2 | 0.000373 |
S | 305 | S305S | tcC | tcT | 1 | 1 | A.21 | 0.00277 |
S | 305 | S305S | tcC | tcG | 1 | 1 | AT.1 | 0.005128 |
S | 305 | S305S | tcC | tcT | 1 | 1 | AY.104 | 0.001984 |
S | 305 | S305S | tcC | tcA | 1 | 1 | AY.117 | 0.000085 |
S | 305 | S305S | tcC | tcT | 1 | 1 | AY.119 | 0.000035 |
S | 305 | S305S | tcC | tcT | 1 | 1 | AY.14 | 0.000088 |
S | 305 | S305S | tcC | tcT | 1 | 1 | AY.16.1 | 0.00047 |
S | 305 | S305S | tcC | tcT | 1 | 1 | AY.26 | 0.000028 |
S | 305 | S305S | tcC | tcA | 1 | 1 | AY.27 | 0.000065 |
S | 305 | S305S | tcC | tcT | 1 | 1 | AY.3 | 0.00001 |
S | 305 | S305S | tcC | tcT | 1 | 1 | AY.32 | 0.000532 |
S | 305 | S305S | tcC | tcT | 1 | 1 | AY.35 | 0.000233 |
S | 305 | S305S | tcC | tcT | 1 | 1 | AY.36 | 0.000148 |
S | 305 | S305S | tcC | tcA | 1 | 1 | AY.37 | 0.000316 |
S | 305 | S305S | tcC | tcT | 1 | 1 | AY.39.1 | 0.00004 |
S | 305 | S305S | tcC | tcT | 1 | 1 | AY.4.2 | 0.000022 |
S | 305 | S305S | tcC | tcT | 1 | 1 | AY.45 | 0.000122 |
S | 305 | S305S | tcC | tcT | 1 | 1 | AY.46.5 | 0.000198 |
S | 305 | S305S | tcC | tcT | 1 | 1 | AY.48 | 0.000465 |
S | 305 | S305S | tcC | tcT | 1 | 1 | AY.5.4 | 0.000277 |
S | 305 | S305S | tcC | tcT | 1 | 1 | AY.59 | 0.00053 |
S | 305 | S305S | tcC | tcA | 1 | 1 | AY.67 | 0.000464 |
S | 305 | S305S | tcC | tcA | 1 | 1 | AY.68 | 0.000274 |
S | 305 | S305S | tcC | tcT | 1 | 1 | AY.75 | 0.000056 |
S | 305 | S305S | tcC | tcT | 1 | 1 | AY.98.1 | 0.000048 |
S | 305 | S305S | tcC | tcT | 1 | 1 | B | 0.000128 |
S | 305 | S305S | tcC | tcT | 1 | 1 | B.1.1.191 | 0.004762 |
S | 305 | S305S | tcC | tcT | 1 | 1 | B.1.1.222 | 0.000204 |
S | 305 | S305S | tcC | tcT | 1 | 1 | B.1.1.25 | 0.000569 |
S | 305 | S305S | tcC | tcT | 1 | 1 | B.1.1.284 | 0.000107 |
S | 305 | S305S | tcC | tcT | 1 | 1 | B.1.1.523 | 0.001563 |
S | 305 | S305S | tcC | tcT | 1 | 1 | B.1.1.63 | 0.000386 |
S | 305 | S305S | tcC | tcT | 1 | 1 | B.1.177.43 | 0.001477 |
S | 305 | S305S | tcC | tcT | 1 | 1 | B.1.243 | 0.00007 |
S | 305 | S305S | tcC | tcA | 1 | 1 | B.1.311 | 0.000275 |
S | 305 | S305S | tcC | tcT | 1 | 1 | B.1.316 | 0.111111 |
S | 305 | S305S | tcC | tcT | 1 | 1 | B.1.351 | 0.00003 |
S | 305 | S305S | tcC | tcT | 1 | 1 | B.1.36 | 0.000146 |
S | 305 | S305S | tcC | tcT | 1 | 1 | B.1.36.10 | 0.004785 |
S | 305 | S305S | tcC | tcT | 1 | 1 | B.1.36.18 | 0.00042 |
S | 305 | S305S | tcC | tcT | 1 | 1 | B.1.36.29 | 0.000517 |
S | 305 | S305S | tcC | tcT | 1 | 1 | B.1.366 | 0.004878 |
S | 305 | S305S | tcC | tcA | 1 | 1 | B.1.399 | 0.001934 |
S | 305 | S305S | tcC | tcT | 1 | 1 | B.1.551 | 0.00129 |
S | 305 | S305S | tcC | tcT | 1 | 1 | B.1.575 | 0.000303 |
S | 305 | S305S | tcC | tcT | 1 | 1 | B.1.577 | 0.000687 |
S | 305 | S305S | tcC | tcA | 1 | 1 | B.1.597 | 0.00463 |
S | 305 | S305S | tcC | tcT | 1 | 1 | B.1.609 | 0.000479 |
S | 305 | S305S | tcC | tcT | 1 | 1 | B.1.621 | 0.000089 |
S | 305 | S305S | tcC | tcT | 1 | 1 | B.1.628 | 0.000352 |
S | 305 | S305S | tcC | tcA | 1 | 1 | B.1.637 | 0.000073 |
S | 305 | S305S | tcC | tcT | 1 | 1 | B.4 | 0.002208 |
S | 305 | S305S | tcC | tcA | 1 | 1 | B.6 | 0.00091 |
S | 305 | S305S | tcC | tcT | 1 | 1 | R.1 | 0.00009 |
S | 305 | S305S | tcC | tcT | 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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