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 | 479 | P479S | nonsyn | Cct | Tct | 3363 | 3360 | 0.999108 | 22997-22999 | |
S | 479 | P479S | nonsyn | CcT | TcA | 3363 | 2 | 0.000594707 | 22997-22999 | |
S | 479 | P479S | nonsyn | CcT | TcC | 3363 | 1 | 0.000297354 | 22997-22999 |
Details of the mutation P479S 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 | 479 | P479S | Cct | Tct | 3360 | 3363 | All | 0.000643 |
S | 479 | P479S | CcT | TcA | 2 | 3363 | All | 0 |
S | 479 | P479S | CcT | TcC | 1 | 3363 | All | 0 |
S | 479 | P479S | Cct | Tct | 748 | 748 | AY.4 | 0.001164 |
S | 479 | P479S | Cct | Tct | 538 | 538 | AY.44 | 0.003275 |
S | 479 | P479S | Cct | Tct | 250 | 250 | B.1.1.7 | 0.000224 |
S | 479 | P479S | Cct | Tct | 193 | 193 | AY.3 | 0.00192 |
S | 479 | P479S | Cct | Tct | 180 | 180 | B.1.617.2 | 0.000678 |
S | 479 | P479S | Cct | Tct | 164 | 164 | AY.103 | 0.001018 |
S | 479 | P479S | Cct | Tct | 137 | 137 | B.1.1 | 0.002485 |
S | 479 | P479S | Cct | Tct | 109 | 109 | B.1.2 | 0.00096 |
S | 479 | P479S | Cct | Tct | 81 | 81 | B.1.142 | 0.234783 |
S | 479 | P479S | Cct | Tct | 74 | 74 | AY.43 | 0.000328 |
S | 479 | P479S | Cct | Tct | 62 | 62 | AY.119 | 0.002189 |
S | 479 | P479S | Cct | Tct | 59 | 59 | AY.58 | 0.053539 |
S | 479 | P479S | Cct | Tct | 55 | 55 | B.1 | 0.000504 |
S | 479 | P479S | Cct | Tct | 46 | 46 | AY.25 | 0.000277 |
S | 479 | P479S | Cct | Tct | 43 | 43 | AY.42 | 0.00173 |
S | 479 | P479S | Cct | Tct | 42 | 42 | AY.26 | 0.001189 |
S | 479 | P479S | Cct | Tct | 42 | 42 | B.1.1.384 | 1 |
S | 479 | P479S | Cct | Tct | 31 | 31 | AY.4.2 | 0.000672 |
S | 479 | P479S | Cct | Tct | 29 | 29 | AY.20 | 0.001127 |
S | 479 | P479S | Cct | Tct | 29 | 29 | AY.29 | 0.000457 |
S | 479 | P479S | Cct | Tct | 25 | 25 | AY.39 | 0.000618 |
S | 479 | P479S | Cct | Tct | 25 | 25 | AY.91 | 0.018262 |
S | 479 | P479S | Cct | Tct | 24 | 24 | AY.23 | 0.001674 |
S | 479 | P479S | Cct | Tct | 22 | 22 | AY.102 | 0.000583 |
S | 479 | P479S | Cct | Tct | 22 | 22 | C.39 | 0.415094 |
S | 479 | P479S | Cct | Tct | 21 | 21 | B.1.429 | 0.000494 |
S | 479 | P479S | Cct | Tct | 18 | 18 | AY.12 | 0.005689 |
S | 479 | P479S | Cct | Tct | 12 | 12 | AY.6 | 0.000494 |
S | 479 | P479S | Cct | Tct | 12 | 12 | P.1 | 0.000189 |
S | 479 | P479S | Cct | Tct | 11 | 11 | AY.98.1 | 0.000533 |
S | 479 | P479S | Cct | Tct | 9 | 9 | A.2.5 | 0.004491 |
S | 479 | P479S | Cct | Tct | 9 | 9 | AY.114 | 0.00208 |
S | 479 | P479S | Cct | Tct | 9 | 9 | AY.33 | 0.000601 |
S | 479 | P479S | Cct | Tct | 9 | 9 | AY.9.1 | 0.000754 |
S | 479 | P479S | Cct | Tct | 8 | 8 | AY.117 | 0.000676 |
S | 479 | P479S | Cct | Tct | 8 | 8 | AY.98 | 0.000632 |
S | 479 | P479S | Cct | Tct | 7 | 7 | AY.5 | 0.000145 |
S | 479 | P479S | Cct | Tct | 6 | 6 | B.1.177 | 0.000079 |
S | 479 | P479S | Cct | Tct | 5 | 5 | AY.118 | 0.000313 |
S | 479 | P479S | Cct | Tct | 5 | 5 | B.1.1.1 | 0.001633 |
S | 479 | P479S | Cct | Tct | 5 | 5 | B.1.1.174 | 0.016892 |
S | 479 | P479S | Cct | Tct | 2 | 4 | 0.111111 | |
S | 479 | P479S | CcT | TcA | 2 | 4 | 0.111111 | |
S | 479 | P479S | Cct | Tct | 4 | 4 | AY.13 | 0.000644 |
S | 479 | P479S | Cct | Tct | 4 | 4 | AY.3.1 | 0.000341 |
S | 479 | P479S | Cct | Tct | 4 | 4 | AY.32 | 0.00213 |
S | 479 | P479S | Cct | Tct | 4 | 4 | AY.34 | 0.000388 |
S | 479 | P479S | Cct | Tct | 4 | 4 | AY.46.4 | 0.000658 |
S | 479 | P479S | Cct | Tct | 4 | 4 | AY.5.3 | 0.00135 |
S | 479 | P479S | Cct | Tct | 4 | 4 | AY.54 | 0.000381 |
S | 479 | P479S | Cct | Tct | 4 | 4 | B.1.1.519 | 0.000159 |
S | 479 | P479S | Cct | Tct | 4 | 4 | B.1.416 | 0.005076 |
S | 479 | P479S | Cct | Tct | 4 | 4 | B.1.596 | 0.000349 |
S | 479 | P479S | Cct | Tct | 3 | 3 | AY.100 | 0.000138 |
S | 479 | P479S | Cct | Tct | 3 | 3 | AY.116 | 0.00086 |
S | 479 | P479S | Cct | Tct | 3 | 3 | AY.120 | 0.000112 |
S | 479 | P479S | Cct | Tct | 3 | 3 | AY.36 | 0.000445 |
S | 479 | P479S | Cct | Tct | 3 | 3 | AY.4.4 | 0.001227 |
S | 479 | P479S | Cct | Tct | 3 | 3 | AY.45 | 0.000365 |
S | 479 | P479S | Cct | Tct | 3 | 3 | AY.47 | 0.000093 |
S | 479 | P479S | Cct | Tct | 3 | 3 | AY.94 | 0.001328 |
S | 479 | P479S | Cct | Tct | 3 | 3 | AY.99.2 | 0.000276 |
S | 479 | P479S | Cct | Tct | 3 | 3 | B.1.1.50 | 0.002037 |
S | 479 | P479S | Cct | Tct | 3 | 3 | B.1.351 | 0.000089 |
S | 479 | P479S | Cct | Tct | 3 | 3 | C.18 | 0.007772 |
S | 479 | P479S | Cct | Tct | 3 | 3 | Q.8 | 0.000495 |
S | 479 | P479S | Cct | Tct | 2 | 2 | AY.107 | 0.000932 |
S | 479 | P479S | Cct | Tct | 2 | 2 | AY.111 | 0.000366 |
S | 479 | P479S | Cct | Tct | 2 | 2 | AY.120.1 | 0.000642 |
S | 479 | P479S | Cct | Tct | 2 | 2 | AY.38 | 0.000999 |
S | 479 | P479S | Cct | Tct | 2 | 2 | AY.39.1 | 0.000079 |
S | 479 | P479S | Cct | Tct | 2 | 2 | AY.4.5 | 0.000215 |
S | 479 | P479S | Cct | Tct | 2 | 2 | AY.55 | 0.001835 |
S | 479 | P479S | Cct | Tct | 2 | 2 | AY.61 | 0.00021 |
S | 479 | P479S | Cct | Tct | 2 | 2 | AY.65 | 0.001066 |
S | 479 | P479S | Cct | Tct | 2 | 2 | AY.68 | 0.000547 |
S | 479 | P479S | Cct | Tct | 2 | 2 | AY.75 | 0.000112 |
S | 479 | P479S | Cct | Tct | 2 | 2 | AY.75.1 | 0.000361 |
S | 479 | P479S | Cct | Tct | 2 | 2 | AY.84 | 0.000875 |
S | 479 | P479S | Cct | Tct | 2 | 2 | AY.9.2 | 0.000073 |
S | 479 | P479S | Cct | Tct | 2 | 2 | AY.92 | 0.000575 |
S | 479 | P479S | Cct | Tct | 2 | 2 | B.1.1.12 | 0.014925 |
S | 479 | P479S | Cct | Tct | 2 | 2 | B.1.1.178 | 0.083333 |
S | 479 | P479S | Cct | Tct | 2 | 2 | B.1.1.329 | 0.007692 |
S | 479 | P479S | Cct | Tct | 2 | 2 | B.1.1.374 | 0.004751 |
S | 479 | P479S | Cct | Tct | 2 | 2 | B.1.1.434 | 0.000697 |
S | 479 | P479S | Cct | Tct | 2 | 2 | B.1.221 | 0.000142 |
S | 479 | P479S | Cct | Tct | 2 | 2 | B.1.258 | 0.000133 |
S | 479 | P479S | Cct | Tct | 2 | 2 | B.1.525 | 0.000226 |
S | 479 | P479S | Cct | Tct | 1 | 1 | A | 0.000387 |
S | 479 | P479S | Cct | Tct | 1 | 1 | A.2 | 0.000662 |
S | 479 | P479S | Cct | Tct | 1 | 1 | AY.110 | 0.000113 |
S | 479 | P479S | Cct | Tct | 1 | 1 | AY.121 | 0.000135 |
S | 479 | P479S | Cct | Tct | 1 | 1 | AY.16.1 | 0.00047 |
S | 479 | P479S | Cct | Tct | 1 | 1 | AY.27 | 0.000065 |
S | 479 | P479S | Cct | Tct | 1 | 1 | AY.34.1 | 0.00051 |
S | 479 | P479S | Cct | Tct | 1 | 1 | AY.35 | 0.000233 |
S | 479 | P479S | Cct | Tct | 1 | 1 | AY.39.2 | 0.001541 |
S | 479 | P479S | Cct | Tct | 1 | 1 | AY.4.2.1 | 0.000149 |
S | 479 | P479S | Cct | Tct | 1 | 1 | AY.4.3 | 0.000842 |
S | 479 | P479S | Cct | Tct | 1 | 1 | AY.41 | 0.000294 |
S | 479 | P479S | Cct | Tct | 1 | 1 | AY.46 | 0.000104 |
S | 479 | P479S | Cct | Tct | 1 | 1 | AY.46.6 | 0.000072 |
S | 479 | P479S | Cct | Tct | 1 | 1 | AY.48 | 0.000465 |
S | 479 | P479S | Cct | Tct | 1 | 1 | AY.53 | 0.000288 |
S | 479 | P479S | Cct | Tct | 1 | 1 | AY.63 | 0.000387 |
S | 479 | P479S | Cct | Tct | 1 | 1 | AY.64 | 0.000595 |
S | 479 | P479S | Cct | Tct | 1 | 1 | AY.69 | 0.000187 |
S | 479 | P479S | Cct | Tct | 1 | 1 | AY.7.2 | 0.000559 |
S | 479 | P479S | Cct | Tct | 1 | 1 | AY.71 | 0.000475 |
S | 479 | P479S | Cct | Tct | 1 | 1 | AY.85 | 0.000427 |
S | 479 | P479S | Cct | Tct | 1 | 1 | AY.9 | 0.000068 |
S | 479 | P479S | Cct | Tct | 1 | 1 | B.1.1.258 | 0.003257 |
S | 479 | P479S | Cct | Tct | 1 | 1 | B.1.1.315 | 0.008475 |
S | 479 | P479S | Cct | Tct | 1 | 1 | B.1.1.33 | 0.000421 |
S | 479 | P479S | Cct | Tct | 1 | 1 | B.1.13 | 0.002375 |
S | 479 | P479S | Cct | Tct | 1 | 1 | B.1.206 | 0.000816 |
S | 479 | P479S | Cct | Tct | 1 | 1 | B.1.240 | 0.000216 |
S | 479 | P479S | Cct | Tct | 1 | 1 | B.1.243 | 0.00007 |
S | 479 | P479S | Cct | Tct | 1 | 1 | B.1.36.2 | 0.010753 |
S | 479 | P479S | Cct | Tct | 1 | 1 | B.1.396 | 0.000706 |
S | 479 | P479S | Cct | Tct | 1 | 1 | B.1.426 | 0.001009 |
S | 479 | P479S | Cct | Tct | 1 | 1 | B.1.456 | 0.003268 |
S | 479 | P479S | Cct | Tct | 1 | 1 | B.1.508 | 0.025641 |
S | 479 | P479S | Cct | Tct | 1 | 1 | B.1.526 | 0.000024 |
S | 479 | P479S | Cct | Tct | 1 | 1 | B.1.565 | 0.00081 |
S | 479 | P479S | Cct | Tct | 1 | 1 | B.1.567 | 0.003333 |
S | 479 | P479S | Cct | Tct | 1 | 1 | B.1.587 | 0.001898 |
S | 479 | P479S | Cct | Tct | 1 | 1 | B.1.597 | 0.00463 |
S | 479 | P479S | Cct | Tct | 1 | 1 | B.1.609 | 0.000479 |
S | 479 | P479S | Cct | Tct | 1 | 1 | C.1.2 | 0.004255 |
S | 479 | P479S | Cct | Tct | 1 | 1 | C.35 | 0.000774 |
S | 479 | P479S | Cct | Tct | 1 | 1 | D.2 | 0.000075 |
S | 479 | P479S | Cct | Tct | 1 | 1 | P.1.1 | 0.000318 |
S | 479 | P479S | Cct | Tct | 1 | 1 | P.1.14 | 0.000048 |
S | 479 | P479S | Cct | Tct | 1 | 1 | P.1.15 | 0.000232 |
S | 479 | P479S | CcT | TcC | 1 | 1 | P.1.17 | 0.000162 |
S | 479 | P479S | Cct | Tct | 1 | 1 | Q.1 | 0.000126 |
S | 479 | P479S | Cct | Tct | 1 | 1 | Q.7 | 0.001111 |
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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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