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/nsp3 | 389 | P389S | P1207S | nonsyn | Cct | Tct | 4559 | 4557 | 0.999561 | 3884-3886 |
Details of the mutation no 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/nsp3 | 389 | P389S | Cct | Tct | 4557 | 4559 | All | 0.000872 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 2787 | 2787 | B.1.628 | 0.98203 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 346 | 346 | AY.4 | 0.000539 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 228 | 228 | B.1.1.7 | 0.000204 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 196 | 196 | B.1.523 | 0.480392 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 190 | 190 | B.1.2 | 0.001673 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 98 | 98 | B.1 | 0.000898 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 93 | 93 | B.1.617.2 | 0.00035 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 76 | 76 | B.1.1.222 | 0.015504 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 41 | 41 | B.1.243 | 0.002853 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 40 | 40 | AY.103 | 0.000248 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 36 | 36 | P.1 | 0.000567 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 33 | 33 | AY.25 | 0.000198 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 22 | 22 | B.1.406 | 0.133333 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 19 | 19 | AY.100 | 0.000874 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 19 | 19 | AY.44 | 0.000116 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 17 | 17 | B.1.324 | 0.027287 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 13 | 13 | AY.98 | 0.001027 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 12 | 12 | B.1.218 | 0.061856 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 11 | 11 | B.1.1 | 0.0002 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 11 | 11 | B.1.1.519 | 0.000437 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 11 | 11 | P.1.12 | 0.005324 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 10 | 10 | AY.23 | 0.000697 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 10 | 10 | AY.39 | 0.000247 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 9 | 9 | B.1.526 | 0.000212 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 8 | 8 | AY.2 | 0.002849 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 8 | 8 | AY.43 | 0.000035 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 8 | 8 | B.1.221 | 0.000568 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 7 | 7 | B.1.427 | 0.000353 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 7 | 7 | B.1.621 | 0.00062 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 5 | 6 | AY.119 | 0.000177 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 6 | 6 | AY.120 | 0.000223 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 6 | 6 | AY.46.6 | 0.000433 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 6 | 6 | B.1.177.7 | 0.000989 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 6 | 6 | B.1.36.1 | 0.006842 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 6 | 6 | B.1.438.1 | 0.000644 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 6 | 6 | P.1.2 | 0.006936 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 5 | 5 | AY.102 | 0.000133 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 5 | 5 | AY.42 | 0.000201 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 5 | 5 | AY.46.4 | 0.000823 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 5 | 5 | AY.47 | 0.000156 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 5 | 5 | B.1.429 | 0.000118 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 4 | 4 | AY.113 | 0.00057 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 4 | 4 | AY.16.1 | 0.00188 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 4 | 4 | AY.41 | 0.001176 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 4 | 4 | B.1.177 | 0.000053 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 4 | 4 | B.1.177.86 | 0.000734 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 4 | 4 | B.1.627 | 0.008081 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 3 | 3 | AY.116 | 0.00086 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 3 | 3 | AY.33 | 0.0002 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 3 | 3 | AY.6 | 0.000123 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 3 | 3 | C.37 | 0.000348 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 3 | 3 | P.1.1 | 0.000953 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 3 | 3 | P.2 | 0.00056 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 3 | 3 | R.1 | 0.00027 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 1 | 2 | 0.055556 | |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 2 | 2 | AY.117 | 0.000169 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 2 | 2 | AY.29 | 0.000032 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 2 | 2 | AY.30 | 0.000791 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 2 | 2 | AY.36 | 0.000296 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 2 | 2 | AY.4.2 | 0.000043 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 2 | 2 | AY.70 | 0.000417 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 2 | 2 | B.1.1.28 | 0.000622 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 2 | 2 | B.1.177.16 | 0.001329 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 2 | 2 | B.1.36.29 | 0.001035 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 2 | 2 | B.1.596 | 0.000174 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 2 | 2 | B.1.637 | 0.000146 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 2 | 2 | C.2 | 0.032258 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 2 | 2 | D.2 | 0.00015 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 2 | 2 | W.3 | 0.010526 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 2 | 2 | Z.1 | 0.00578 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 1 | 1 | A.2.4 | 0.003367 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 1 | 1 | AY.111 | 0.000183 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 1 | 1 | AY.114 | 0.000231 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 1 | 1 | AY.118 | 0.000063 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 1 | 1 | AY.20 | 0.000039 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 1 | 1 | AY.26 | 0.000028 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 1 | 1 | AY.3 | 0.00001 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 1 | 1 | AY.3.1 | 0.000085 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 1 | 1 | AY.34 | 0.000097 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 1 | 1 | AY.4.2.1 | 0.000149 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 1 | 1 | AY.4.5 | 0.000107 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 1 | 1 | AY.46 | 0.000104 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 1 | 1 | AY.5 | 0.000021 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 1 | 1 | AY.58 | 0.000907 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 1 | 1 | AY.61 | 0.000105 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 1 | 1 | AY.62 | 0.000436 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 1 | 1 | AY.63 | 0.000387 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 1 | 1 | AY.7.2 | 0.000559 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 1 | 1 | AY.75 | 0.000056 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 1 | 1 | AY.77 | 0.001127 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 1 | 1 | AY.9.2 | 0.000037 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 1 | 1 | AY.98.1 | 0.000048 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 1 | 1 | B | 0.000128 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 1 | 1 | B.1.1.117 | 0.009709 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 1 | 1 | B.1.1.214 | 0.000055 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 1 | 1 | B.1.1.216 | 0.00089 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 1 | 1 | B.1.1.294 | 0.001266 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 1 | 1 | B.1.103 | 0.019231 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 1 | 1 | B.1.160 | 0.000031 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 1 | 1 | B.1.177.56 | 0.000668 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 1 | 1 | B.1.177.6 | 0.000977 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 1 | 1 | B.1.232 | 0.000537 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 1 | 1 | B.1.234 | 0.000132 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 1 | 1 | B.1.258.17 | 0.000104 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 1 | 1 | B.1.351 | 0.00003 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 1 | 1 | B.1.36 | 0.000146 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 1 | 1 | B.1.36.16 | 0.001425 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 1 | 1 | B.1.36.8 | 0.001 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 1 | 1 | B.1.367 | 0.000792 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 1 | 1 | B.1.408 | 0.00369 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 1 | 1 | B.1.428 | 0.00102 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 1 | 1 | B.1.544 | 0.006024 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 1 | 1 | B.1.561 | 0.000397 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 1 | 1 | B.1.580 | 0.004065 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 1 | 1 | B.1.633 | 0.041667 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 1 | 1 | P.1.14 | 0.000048 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 1 | 1 | Q.1 | 0.000126 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 1 | 1 | Q.4 | 0.000455 |
ORF1ab/nsp3 | 389 | P389S | Cct | Tct | 1 | 1 | U.3 | 0.003861 |
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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