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 | S248R | S428R | nonsyn | Agc | Cgc | 2251 | 2145 | 0.95291 | 1547-1549 |
ORF1ab/nsp2 | 248 | S248R | S428R | nonsyn | agC | agA | 2251 | 102 | 0.0453132 | 1547-1549 |
ORF1ab/nsp2 | 248 | S248R | S428R | nonsyn | agC | agG | 2251 | 4 | 0.00177699 | 1547-1549 |
Details of the mutation S248R 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 | S248R | Agc | Cgc | 2145 | 2251 | All | 0.00041 |
ORF1ab/nsp2 | 248 | S248R | agC | agA | 102 | 2251 | All | 0.00002 |
ORF1ab/nsp2 | 248 | S248R | agC | agG | 4 | 2251 | All | 0.000001 |
ORF1ab/nsp2 | 248 | S248R | Agc | Cgc | 642 | 647 | B.1.1.7 | 0.000575 |
ORF1ab/nsp2 | 248 | S248R | agC | agA | 5 | 647 | B.1.1.7 | 0.000004 |
ORF1ab/nsp2 | 248 | S248R | Agc | Cgc | 337 | 338 | AY.43 | 0.001493 |
ORF1ab/nsp2 | 248 | S248R | agC | agA | 1 | 338 | AY.43 | 0.000004 |
ORF1ab/nsp2 | 248 | S248R | Agc | Cgc | 293 | 296 | B.1.617.2 | 0.001103 |
ORF1ab/nsp2 | 248 | S248R | agC | agA | 3 | 296 | B.1.617.2 | 0.000011 |
ORF1ab/nsp2 | 248 | S248R | Agc | Cgc | 112 | 112 | AY.75.1 | 0.020195 |
ORF1ab/nsp2 | 248 | S248R | Agc | Cgc | 101 | 101 | AY.4.5 | 0.010857 |
ORF1ab/nsp2 | 248 | S248R | Agc | Cgc | 95 | 96 | AY.4 | 0.000148 |
ORF1ab/nsp2 | 248 | S248R | agC | agA | 1 | 96 | AY.4 | 0.000002 |
ORF1ab/nsp2 | 248 | S248R | Agc | Cgc | 49 | 49 | AY.46.6 | 0.003538 |
ORF1ab/nsp2 | 248 | S248R | Agc | Cgc | 48 | 48 | AY.98.1 | 0.002325 |
ORF1ab/nsp2 | 248 | S248R | Agc | Cgc | 42 | 42 | AY.41 | 0.012346 |
ORF1ab/nsp2 | 248 | S248R | agC | agA | 42 | 42 | B.1.2 | 0.00037 |
ORF1ab/nsp2 | 248 | S248R | Agc | Cgc | 40 | 40 | B.1.258.17 | 0.004159 |
ORF1ab/nsp2 | 248 | S248R | Agc | Cgc | 36 | 36 | AY.9.1 | 0.003014 |
ORF1ab/nsp2 | 248 | S248R | Agc | Cgc | 34 | 34 | AY.5 | 0.000702 |
ORF1ab/nsp2 | 248 | S248R | Agc | Cgc | 30 | 30 | Q.1 | 0.00379 |
ORF1ab/nsp2 | 248 | S248R | Agc | Cgc | 25 | 25 | B.1 | 0.000229 |
ORF1ab/nsp2 | 248 | S248R | Agc | Cgc | 23 | 23 | AY.42 | 0.000925 |
ORF1ab/nsp2 | 248 | S248R | agC | agA | 12 | 17 | B.1.351 | 0.000357 |
ORF1ab/nsp2 | 248 | S248R | Agc | Cgc | 5 | 17 | B.1.351 | 0.000149 |
ORF1ab/nsp2 | 248 | S248R | Agc | Cgc | 14 | 14 | AY.46 | 0.001457 |
ORF1ab/nsp2 | 248 | S248R | agC | agA | 13 | 13 | AY.4.2 | 0.000282 |
ORF1ab/nsp2 | 248 | S248R | Agc | Cgc | 13 | 13 | AY.7.1 | 0.001465 |
ORF1ab/nsp2 | 248 | S248R | Agc | Cgc | 13 | 13 | AY.9.2 | 0.000477 |
ORF1ab/nsp2 | 248 | S248R | Agc | Cgc | 11 | 11 | AY.4.4 | 0.004501 |
ORF1ab/nsp2 | 248 | S248R | Agc | Cgc | 9 | 10 | B.1.1 | 0.000163 |
ORF1ab/nsp2 | 248 | S248R | agC | agG | 1 | 10 | B.1.1 | 0.000018 |
ORF1ab/nsp2 | 248 | S248R | Agc | Cgc | 9 | 9 | AY.9 | 0.000608 |
ORF1ab/nsp2 | 248 | S248R | Agc | Cgc | 9 | 9 | AY.98 | 0.000711 |
ORF1ab/nsp2 | 248 | S248R | Agc | Cgc | 7 | 7 | AY.106 | 0.002344 |
ORF1ab/nsp2 | 248 | S248R | Agc | Cgc | 7 | 7 | AY.95 | 0.005327 |
ORF1ab/nsp2 | 248 | S248R | Agc | Cgc | 4 | 7 | P.1 | 0.000063 |
ORF1ab/nsp2 | 248 | S248R | agC | agA | 2 | 7 | P.1 | 0.000032 |
ORF1ab/nsp2 | 248 | S248R | agC | agG | 1 | 7 | P.1 | 0.000016 |
ORF1ab/nsp2 | 248 | S248R | Agc | Cgc | 6 | 6 | AY.116 | 0.001721 |
ORF1ab/nsp2 | 248 | S248R | Agc | Cgc | 6 | 6 | AY.4.3 | 0.005051 |
ORF1ab/nsp2 | 248 | S248R | Agc | Cgc | 6 | 6 | AY.68 | 0.001642 |
ORF1ab/nsp2 | 248 | S248R | Agc | Cgc | 6 | 6 | B.1.258 | 0.000399 |
ORF1ab/nsp2 | 248 | S248R | Agc | Cgc | 6 | 6 | Q.4 | 0.002729 |
ORF1ab/nsp2 | 248 | S248R | Agc | Cgc | 4 | 4 | AY.111 | 0.000733 |
ORF1ab/nsp2 | 248 | S248R | Agc | Cgc | 4 | 4 | AY.23 | 0.000279 |
ORF1ab/nsp2 | 248 | S248R | Agc | Cgc | 4 | 4 | AY.33 | 0.000267 |
ORF1ab/nsp2 | 248 | S248R | Agc | Cgc | 4 | 4 | AY.34 | 0.000388 |
ORF1ab/nsp2 | 248 | S248R | Agc | Cgc | 4 | 4 | AY.70 | 0.000834 |
ORF1ab/nsp2 | 248 | S248R | Agc | Cgc | 4 | 4 | B | 0.000511 |
ORF1ab/nsp2 | 248 | S248R | agC | agA | 4 | 4 | B.1.427 | 0.000202 |
ORF1ab/nsp2 | 248 | S248R | Agc | Cgc | 4 | 4 | C.36.3 | 0.002269 |
ORF1ab/nsp2 | 248 | S248R | Agc | Cgc | 3 | 3 | AT.1 | 0.015385 |
ORF1ab/nsp2 | 248 | S248R | Agc | Cgc | 3 | 3 | AY.120 | 0.000112 |
ORF1ab/nsp2 | 248 | S248R | Agc | Cgc | 3 | 3 | AY.24 | 0.001293 |
ORF1ab/nsp2 | 248 | S248R | Agc | Cgc | 3 | 3 | AY.25 | 0.000018 |
ORF1ab/nsp2 | 248 | S248R | agC | agA | 2 | 3 | AY.36 | 0.000296 |
ORF1ab/nsp2 | 248 | S248R | Agc | Cgc | 1 | 3 | AY.36 | 0.000148 |
ORF1ab/nsp2 | 248 | S248R | Agc | Cgc | 3 | 3 | AY.46.4 | 0.000494 |
ORF1ab/nsp2 | 248 | S248R | Agc | Cgc | 3 | 3 | AY.6 | 0.000123 |
ORF1ab/nsp2 | 248 | S248R | Agc | Cgc | 3 | 3 | AY.60 | 0.002814 |
ORF1ab/nsp2 | 248 | S248R | Agc | Cgc | 3 | 3 | AY.7.2 | 0.001678 |
ORF1ab/nsp2 | 248 | S248R | agC | agA | 3 | 3 | B.1.243 | 0.000209 |
ORF1ab/nsp2 | 248 | S248R | Agc | Cgc | 2 | 2 | AY.118 | 0.000125 |
ORF1ab/nsp2 | 248 | S248R | Agc | Cgc | 2 | 2 | AY.3 | 0.00002 |
ORF1ab/nsp2 | 248 | S248R | Agc | Cgc | 2 | 2 | AY.45 | 0.000243 |
ORF1ab/nsp2 | 248 | S248R | Agc | Cgc | 2 | 2 | AY.58 | 0.001815 |
ORF1ab/nsp2 | 248 | S248R | Agc | Cgc | 2 | 2 | AY.71 | 0.00095 |
ORF1ab/nsp2 | 248 | S248R | Agc | Cgc | 2 | 2 | AY.84 | 0.000875 |
ORF1ab/nsp2 | 248 | S248R | Agc | Cgc | 2 | 2 | AY.91 | 0.001461 |
ORF1ab/nsp2 | 248 | S248R | Agc | Cgc | 2 | 2 | AY.92 | 0.000575 |
ORF1ab/nsp2 | 248 | S248R | Agc | Cgc | 2 | 2 | B.1.1.363 | 0.011976 |
ORF1ab/nsp2 | 248 | S248R | Agc | Cgc | 2 | 2 | B.1.160 | 0.000062 |
ORF1ab/nsp2 | 248 | S248R | Agc | Cgc | 2 | 2 | B.1.527 | 0.007407 |
ORF1ab/nsp2 | 248 | S248R | Agc | Cgc | 2 | 2 | B.1.91 | 0.004149 |
ORF1ab/nsp2 | 248 | S248R | agC | agA | 2 | 2 | B.40 | 0.000729 |
ORF1ab/nsp2 | 248 | S248R | Agc | Cgc | 2 | 2 | Q.8 | 0.00033 |
ORF1ab/nsp2 | 248 | S248R | agC | agG | 1 | 1 | 0.055556 | |
ORF1ab/nsp2 | 248 | S248R | Agc | Cgc | 1 | 1 | AY.102 | 0.000027 |
ORF1ab/nsp2 | 248 | S248R | agC | agA | 1 | 1 | AY.103 | 0.000006 |
ORF1ab/nsp2 | 248 | S248R | Agc | Cgc | 1 | 1 | AY.108 | 0.001103 |
ORF1ab/nsp2 | 248 | S248R | agC | agA | 1 | 1 | AY.109 | 0.00074 |
ORF1ab/nsp2 | 248 | S248R | Agc | Cgc | 1 | 1 | AY.113 | 0.000142 |
ORF1ab/nsp2 | 248 | S248R | agC | agA | 1 | 1 | AY.120.1 | 0.000321 |
ORF1ab/nsp2 | 248 | S248R | Agc | Cgc | 1 | 1 | AY.26 | 0.000028 |
ORF1ab/nsp2 | 248 | S248R | agC | agA | 1 | 1 | AY.39 | 0.000025 |
ORF1ab/nsp2 | 248 | S248R | Agc | Cgc | 1 | 1 | AY.46.5 | 0.000198 |
ORF1ab/nsp2 | 248 | S248R | Agc | Cgc | 1 | 1 | AY.5.4 | 0.000277 |
ORF1ab/nsp2 | 248 | S248R | Agc | Cgc | 1 | 1 | AY.53 | 0.000288 |
ORF1ab/nsp2 | 248 | S248R | Agc | Cgc | 1 | 1 | AY.73 | 0.000665 |
ORF1ab/nsp2 | 248 | S248R | Agc | Cgc | 1 | 1 | AY.97 | 0.001701 |
ORF1ab/nsp2 | 248 | S248R | Agc | Cgc | 1 | 1 | B.1.1.194 | 0.00495 |
ORF1ab/nsp2 | 248 | S248R | Agc | Cgc | 1 | 1 | B.1.1.317 | 0.000412 |
ORF1ab/nsp2 | 248 | S248R | Agc | Cgc | 1 | 1 | B.1.1.433 | 0.001425 |
ORF1ab/nsp2 | 248 | S248R | Agc | Cgc | 1 | 1 | B.1.1.523 | 0.001563 |
ORF1ab/nsp2 | 248 | S248R | Agc | Cgc | 1 | 1 | B.1.1.58 | 0.005376 |
ORF1ab/nsp2 | 248 | S248R | Agc | Cgc | 1 | 1 | B.1.1.70 | 0.000341 |
ORF1ab/nsp2 | 248 | S248R | Agc | Cgc | 1 | 1 | B.1.146 | 0.004237 |
ORF1ab/nsp2 | 248 | S248R | Agc | Cgc | 1 | 1 | B.1.149 | 0.003425 |
ORF1ab/nsp2 | 248 | S248R | Agc | Cgc | 1 | 1 | B.1.177 | 0.000013 |
ORF1ab/nsp2 | 248 | S248R | Agc | Cgc | 1 | 1 | B.1.177.51 | 0.004566 |
ORF1ab/nsp2 | 248 | S248R | Agc | Cgc | 1 | 1 | B.1.177.60 | 0.000218 |
ORF1ab/nsp2 | 248 | S248R | Agc | Cgc | 1 | 1 | B.1.177.79 | 0.002342 |
ORF1ab/nsp2 | 248 | S248R | Agc | Cgc | 1 | 1 | B.1.177.83 | 0.001481 |
ORF1ab/nsp2 | 248 | S248R | Agc | Cgc | 1 | 1 | B.1.221 | 0.000071 |
ORF1ab/nsp2 | 248 | S248R | agC | agA | 1 | 1 | B.1.239 | 0.001221 |
ORF1ab/nsp2 | 248 | S248R | agC | agA | 1 | 1 | B.1.265 | 0.001271 |
ORF1ab/nsp2 | 248 | S248R | agC | agA | 1 | 1 | B.1.36 | 0.000146 |
ORF1ab/nsp2 | 248 | S248R | agC | agA | 1 | 1 | B.1.396 | 0.000706 |
ORF1ab/nsp2 | 248 | S248R | agC | agG | 1 | 1 | B.1.417 | 0.028571 |
ORF1ab/nsp2 | 248 | S248R | Agc | Cgc | 1 | 1 | B.1.482 | 0.083333 |
ORF1ab/nsp2 | 248 | S248R | agC | agA | 1 | 1 | B.1.515 | 0.014493 |
ORF1ab/nsp2 | 248 | S248R | agC | agA | 1 | 1 | B.1.526 | 0.000024 |
ORF1ab/nsp2 | 248 | S248R | Agc | Cgc | 1 | 1 | B.1.625 | 0.002353 |
ORF1ab/nsp2 | 248 | S248R | Agc | Cgc | 1 | 1 | B.55 | 0.00295 |
ORF1ab/nsp2 | 248 | S248R | agC | agA | 1 | 1 | C.37 | 0.000116 |
ORF1ab/nsp2 | 248 | S248R | Agc | Cgc | 1 | 1 | P.1.1 | 0.000318 |
ORF1ab/nsp2 | 248 | S248R | agC | agA | 1 | 1 | P.2 | 0.000187 |
ORF1ab/nsp2 | 248 | S248R | Agc | Cgc | 1 | 1 | Q.2 | 0.000613 |
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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