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 | 575 | A575A | syn | gcT | gcC | 8083 | 7935 | 0.98169 | 23285-23287 | |
S | 575 | A575A | syn | gcT | gcA | 8083 | 115 | 0.0142274 | 23285-23287 | |
S | 575 | A575A | syn | gcT | gcG | 8083 | 33 | 0.00408264 | 23285-23287 |
Details of the mutation A575A 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 | 575 | A575A | gcT | gcC | 7935 | 8083 | All | 0.001518 |
S | 575 | A575A | gcT | gcA | 115 | 8083 | All | 0.000022 |
S | 575 | A575A | gcT | gcG | 33 | 8083 | All | 0.000006 |
S | 575 | A575A | gcT | gcC | 3282 | 3282 | B.1.1.318 | 0.990344 |
S | 575 | A575A | gcT | gcC | 1205 | 1205 | AZ.2 | 0.989327 |
S | 575 | A575A | gcT | gcC | 1139 | 1139 | AZ.1 | 0.987858 |
S | 575 | A575A | gcT | gcC | 655 | 655 | AZ.3 | 0.995441 |
S | 575 | A575A | gcT | gcC | 294 | 298 | AY.43 | 0.001303 |
S | 575 | A575A | gcT | gcA | 3 | 298 | AY.43 | 0.000013 |
S | 575 | A575A | gcT | gcG | 1 | 298 | AY.43 | 0.000004 |
S | 575 | A575A | gcT | gcC | 298 | 298 | AZ.4 | 1 |
S | 575 | A575A | gcT | gcC | 284 | 284 | AZ.5 | 0.996491 |
S | 575 | A575A | gcT | gcC | 123 | 123 | AZ.2.1 | 1 |
S | 575 | A575A | gcT | gcC | 119 | 119 | AZ.6 | 1 |
S | 575 | A575A | gcT | gcC | 48 | 86 | B.1.1.7 | 0.000043 |
S | 575 | A575A | gcT | gcA | 34 | 86 | B.1.1.7 | 0.00003 |
S | 575 | A575A | gcT | gcG | 4 | 86 | B.1.1.7 | 0.000004 |
S | 575 | A575A | gcT | gcC | 68 | 68 | B.1.221 | 0.00483 |
S | 575 | A575A | gcT | gcC | 53 | 53 | B.1.1 | 0.000961 |
S | 575 | A575A | gcT | gcC | 41 | 48 | B.1.617.2 | 0.000154 |
S | 575 | A575A | gcT | gcA | 6 | 48 | B.1.617.2 | 0.000023 |
S | 575 | A575A | gcT | gcG | 1 | 48 | B.1.617.2 | 0.000004 |
S | 575 | A575A | gcT | gcA | 34 | 39 | B.1.177 | 0.000448 |
S | 575 | A575A | gcT | gcC | 4 | 39 | B.1.177 | 0.000053 |
S | 575 | A575A | gcT | gcG | 1 | 39 | B.1.177 | 0.000013 |
S | 575 | A575A | gcT | gcC | 19 | 29 | P.1 | 0.000299 |
S | 575 | A575A | gcT | gcG | 5 | 29 | P.1 | 0.000079 |
S | 575 | A575A | gcT | gcA | 5 | 29 | P.1 | 0.000079 |
S | 575 | A575A | gcT | gcC | 28 | 28 | A.1 | 0.007892 |
S | 575 | A575A | gcT | gcC | 23 | 23 | AY.39 | 0.000568 |
S | 575 | A575A | gcT | gcC | 14 | 22 | AY.4 | 0.000022 |
S | 575 | A575A | gcT | gcA | 8 | 22 | AY.4 | 0.000012 |
S | 575 | A575A | gcT | gcC | 17 | 20 | AY.102 | 0.000451 |
S | 575 | A575A | gcT | gcA | 3 | 20 | AY.102 | 0.00008 |
S | 575 | A575A | gcT | gcC | 18 | 18 | AY.4.5 | 0.001935 |
S | 575 | A575A | gcT | gcC | 10 | 15 | AY.44 | 0.000061 |
S | 575 | A575A | gcT | gcA | 5 | 15 | AY.44 | 0.00003 |
S | 575 | A575A | gcT | gcC | 13 | 13 | AY.46.4 | 0.002139 |
S | 575 | A575A | gcT | gcC | 11 | 11 | AY.99 | 0.011542 |
S | 575 | A575A | gcT | gcC | 11 | 11 | B.1 | 0.000101 |
S | 575 | A575A | gcT | gcC | 8 | 10 | AY.103 | 0.00005 |
S | 575 | A575A | gcT | gcA | 2 | 10 | AY.103 | 0.000012 |
S | 575 | A575A | gcT | gcC | 9 | 10 | AY.23 | 0.000628 |
S | 575 | A575A | gcT | gcA | 1 | 10 | AY.23 | 0.00007 |
S | 575 | A575A | gcT | gcC | 10 | 10 | AY.5 | 0.000206 |
S | 575 | A575A | gcT | gcG | 10 | 10 | B.1.1.139 | 0.227273 |
S | 575 | A575A | gcT | gcC | 9 | 10 | B.1.617.1 | 0.001161 |
S | 575 | A575A | gcT | gcA | 1 | 10 | B.1.617.1 | 0.000129 |
S | 575 | A575A | gcT | gcC | 8 | 9 | B.1.2 | 0.00007 |
S | 575 | A575A | gcT | gcA | 1 | 9 | B.1.2 | 0.000009 |
S | 575 | A575A | gcT | gcC | 7 | 7 | AT.1 | 0.035897 |
S | 575 | A575A | gcT | gcC | 5 | 5 | AY.25 | 0.00003 |
S | 575 | A575A | gcT | gcC | 5 | 5 | B.1.1.28 | 0.001556 |
S | 575 | A575A | gcT | gcC | 5 | 5 | B.1.1.409 | 0.014164 |
S | 575 | A575A | gcT | gcG | 5 | 5 | B.1.291 | 0.096154 |
S | 575 | A575A | gcT | gcA | 3 | 4 | AY.4.2 | 0.000065 |
S | 575 | A575A | gcT | gcC | 1 | 4 | AY.4.2 | 0.000022 |
S | 575 | A575A | gcT | gcC | 4 | 4 | AY.72 | 0.005442 |
S | 575 | A575A | gcT | gcC | 4 | 4 | B.1.1.411 | 0.058824 |
S | 575 | A575A | gcT | gcC | 4 | 4 | B.1.1.448 | 0.00813 |
S | 575 | A575A | gcT | gcC | 4 | 4 | B.1.110.3 | 0.002874 |
S | 575 | A575A | gcT | gcC | 4 | 4 | B.1.234 | 0.000528 |
S | 575 | A575A | gcT | gcC | 3 | 3 | A | 0.001161 |
S | 575 | A575A | gcT | gcC | 3 | 3 | AY.114 | 0.000693 |
S | 575 | A575A | gcT | gcC | 2 | 3 | AY.20 | 0.000078 |
S | 575 | A575A | gcT | gcG | 1 | 3 | AY.20 | 0.000039 |
S | 575 | A575A | gcT | gcC | 3 | 3 | AY.3 | 0.00003 |
S | 575 | A575A | gcT | gcC | 3 | 3 | AY.30 | 0.001187 |
S | 575 | A575A | gcT | gcC | 2 | 3 | B.1.351 | 0.000059 |
S | 575 | A575A | gcT | gcG | 1 | 3 | B.1.351 | 0.00003 |
S | 575 | A575A | gcT | gcC | 3 | 3 | B.1.525 | 0.000339 |
S | 575 | A575A | gcT | gcC | 3 | 3 | B.1.576 | 0.00272 |
S | 575 | A575A | gcT | gcC | 3 | 3 | B.1.596 | 0.000261 |
S | 575 | A575A | gcT | gcC | 3 | 3 | B.1.621 | 0.000266 |
S | 575 | A575A | gcT | gcA | 1 | 2 | A.2.5 | 0.000499 |
S | 575 | A575A | gcT | gcC | 1 | 2 | A.2.5 | 0.000499 |
S | 575 | A575A | gcT | gcC | 1 | 2 | AY.34 | 0.000097 |
S | 575 | A575A | gcT | gcA | 1 | 2 | AY.34 | 0.000097 |
S | 575 | A575A | gcT | gcC | 2 | 2 | AY.39.1 | 0.000079 |
S | 575 | A575A | gcT | gcC | 2 | 2 | AY.46.6 | 0.000144 |
S | 575 | A575A | gcT | gcC | 2 | 2 | AY.47 | 0.000062 |
S | 575 | A575A | gcT | gcC | 1 | 2 | B | 0.000128 |
S | 575 | A575A | gcT | gcG | 1 | 2 | B | 0.000128 |
S | 575 | A575A | gcT | gcC | 2 | 2 | B.1.1.484 | 0.2 |
S | 575 | A575A | gcT | gcA | 2 | 2 | B.1.396 | 0.001411 |
S | 575 | A575A | gcT | gcA | 1 | 2 | B.1.526 | 0.000024 |
S | 575 | A575A | gcT | gcG | 1 | 2 | B.1.526 | 0.000024 |
S | 575 | A575A | gcT | gcA | 2 | 2 | B.1.561 | 0.000794 |
S | 575 | A575A | gcT | gcC | 2 | 2 | B.1.575 | 0.000607 |
S | 575 | A575A | gcT | gcG | 2 | 2 | B.23 | 0.005848 |
S | 575 | A575A | gcT | gcC | 2 | 2 | N.5 | 0.003534 |
S | 575 | A575A | gcT | gcC | 1 | 1 | AY.110 | 0.000113 |
S | 575 | A575A | gcT | gcC | 1 | 1 | AY.119 | 0.000035 |
S | 575 | A575A | gcT | gcA | 1 | 1 | AY.13 | 0.000161 |
S | 575 | A575A | gcT | gcC | 1 | 1 | AY.14 | 0.000088 |
S | 575 | A575A | gcT | gcC | 1 | 1 | AY.26 | 0.000028 |
S | 575 | A575A | gcT | gcC | 1 | 1 | AY.27 | 0.000065 |
S | 575 | A575A | gcT | gcC | 1 | 1 | AY.29 | 0.000016 |
S | 575 | A575A | gcT | gcC | 1 | 1 | AY.36 | 0.000148 |
S | 575 | A575A | gcT | gcC | 1 | 1 | AY.42 | 0.00004 |
S | 575 | A575A | gcT | gcC | 1 | 1 | AY.59 | 0.00053 |
S | 575 | A575A | gcT | gcC | 1 | 1 | AY.67 | 0.000464 |
S | 575 | A575A | gcT | gcC | 1 | 1 | AY.71 | 0.000475 |
S | 575 | A575A | gcT | gcC | 1 | 1 | AY.75 | 0.000056 |
S | 575 | A575A | gcT | gcC | 1 | 1 | AY.75.1 | 0.00018 |
S | 575 | A575A | gcT | gcC | 1 | 1 | AY.9.2 | 0.000037 |
S | 575 | A575A | gcT | gcC | 1 | 1 | B.1.1.142 | 0.017544 |
S | 575 | A575A | gcT | gcC | 1 | 1 | B.1.1.222 | 0.000204 |
S | 575 | A575A | gcT | gcC | 1 | 1 | B.1.1.307 | 0.002532 |
S | 575 | A575A | gcT | gcA | 1 | 1 | B.1.160 | 0.000031 |
S | 575 | A575A | gcT | gcC | 1 | 1 | B.1.177.16 | 0.000664 |
S | 575 | A575A | gcT | gcC | 1 | 1 | B.1.177.57 | 0.000281 |
S | 575 | A575A | gcT | gcC | 1 | 1 | B.1.177.7 | 0.000165 |
S | 575 | A575A | gcT | gcC | 1 | 1 | B.1.218 | 0.005155 |
S | 575 | A575A | gcT | gcC | 1 | 1 | B.1.369 | 0.000285 |
S | 575 | A575A | gcT | gcC | 1 | 1 | B.1.429 | 0.000024 |
S | 575 | A575A | gcT | gcC | 1 | 1 | B.1.470 | 0.001404 |
S | 575 | A575A | gcT | gcC | 1 | 1 | B.1.620 | 0.000946 |
S | 575 | A575A | gcT | gcC | 1 | 1 | B.58 | 0.010204 |
S | 575 | A575A | gcT | gcC | 1 | 1 | D.2 | 0.000075 |
S | 575 | A575A | gcT | gcC | 1 | 1 | P.1.7 | 0.000319 |
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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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