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/nsp4 | 408 | S408S | S3171S | syn | tcC | tcT | 2287 | 2196 | 0.96021 | 9776-9778 |
ORF1ab/nsp4 | 408 | S408S | S3171S | syn | tcC | tcA | 2287 | 88 | 0.0384784 | 9776-9778 |
ORF1ab/nsp4 | 408 | S408S | S3171S | syn | tcC | tcG | 2287 | 3 | 0.00131176 | 9776-9778 |
Details of the mutation S408S 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/nsp4 | 408 | S408S | tcC | tcT | 2196 | 2287 | All | 0.00042 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcA | 88 | 2287 | All | 0.000017 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcG | 3 | 2287 | All | 0.000001 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 389 | 389 | AY.3 | 0.003869 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 187 | 204 | B.1.1.7 | 0.000167 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcA | 16 | 204 | B.1.1.7 | 0.000014 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcG | 1 | 204 | B.1.1.7 | 0.000001 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 193 | 193 | AY.26 | 0.005464 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 176 | 176 | AT.1 | 0.902564 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 162 | 167 | B.1 | 0.001484 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcA | 5 | 167 | B.1 | 0.000046 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 138 | 138 | B.1.9.4 | 0.846626 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 111 | 113 | AY.25 | 0.000668 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcA | 2 | 113 | AY.25 | 0.000012 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 91 | 97 | AY.4 | 0.000142 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcA | 6 | 97 | AY.4 | 0.000009 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 62 | 72 | B.1.617.2 | 0.000233 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcA | 10 | 72 | B.1.617.2 | 0.000038 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 39 | 39 | AY.75 | 0.002185 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 37 | 38 | AY.43 | 0.000164 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcA | 1 | 38 | AY.43 | 0.000004 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 36 | 38 | B.1.2 | 0.000317 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcA | 2 | 38 | B.1.2 | 0.000018 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 34 | 34 | AY.103 | 0.000211 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 26 | 30 | B.1.1 | 0.000472 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcA | 4 | 30 | B.1.1 | 0.000073 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 25 | 25 | AY.44 | 0.000152 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 25 | 25 | B.1.526 | 0.000588 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 25 | 25 | P.1 | 0.000394 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 24 | 24 | B.1.351 | 0.000713 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 19 | 21 | AY.102 | 0.000504 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcA | 2 | 21 | AY.102 | 0.000053 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 18 | 18 | B.1.1.519 | 0.000715 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 17 | 17 | B.1.399 | 0.032882 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 16 | 16 | B.1.427 | 0.000808 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 16 | 16 | B.1.91 | 0.033195 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 14 | 14 | AY.9 | 0.000946 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 12 | 12 | AY.9.1 | 0.001005 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcA | 7 | 11 | AY.119 | 0.000247 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 4 | 11 | AY.119 | 0.000141 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 11 | 11 | B.1.429 | 0.000259 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 11 | 11 | B.1.637 | 0.000804 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcA | 5 | 10 | AY.29 | 0.000079 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 4 | 10 | AY.29 | 0.000063 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcG | 1 | 10 | AY.29 | 0.000016 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 10 | 10 | AY.39.1 | 0.000396 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 10 | 10 | B.1.349 | 0.007148 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcA | 8 | 8 | B.1.1.170 | 0.009975 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 7 | 7 | AY.47 | 0.000218 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 7 | 7 | B.1.1.28 | 0.002179 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 7 | 7 | B.1.177 | 0.000092 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 7 | 7 | B.1.36.18 | 0.002941 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcA | 7 | 7 | B.1.438.1 | 0.000751 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 7 | 7 | B.1.9 | 0.04321 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 6 | 6 | AY.39 | 0.000148 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 6 | 6 | AY.5.4 | 0.00166 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 6 | 6 | B.1.243 | 0.000418 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 5 | 6 | B.1.525 | 0.000566 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcG | 1 | 6 | B.1.525 | 0.000113 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 6 | 6 | P.1.14 | 0.000287 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 5 | 5 | AY.5 | 0.000103 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 5 | 5 | AY.61 | 0.000524 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 5 | 5 | B.1.416.1 | 0.007812 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 5 | 5 | B.1.609 | 0.002397 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcA | 4 | 4 | AY.101 | 0.001962 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 4 | 4 | AY.117 | 0.000338 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 3 | 4 | AY.4.2 | 0.000065 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcA | 1 | 4 | AY.4.2 | 0.000022 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 3 | 4 | AY.46 | 0.000312 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcA | 1 | 4 | AY.46 | 0.000104 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 4 | 4 | AY.54 | 0.000381 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 4 | 4 | AY.9.2 | 0.000147 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 4 | 4 | B.1.361 | 0.005155 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 4 | 4 | B.1.425 | 0.011976 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 4 | 4 | B.1.617.1 | 0.000516 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 4 | 4 | B.1.9.5 | 0.022727 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 4 | 4 | P.1.5 | 0.307692 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 4 | 4 | P.1.7 | 0.001277 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 3 | 3 | A.23.1 | 0.002113 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 3 | 3 | AY.118 | 0.000188 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 3 | 3 | AY.33 | 0.0002 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 3 | 3 | AY.42 | 0.000121 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 3 | 3 | AY.83 | 0.005172 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcA | 2 | 3 | B | 0.000256 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 1 | 3 | B | 0.000128 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 2 | 3 | B.1.160 | 0.000062 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcA | 1 | 3 | B.1.160 | 0.000031 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 3 | 3 | B.1.234 | 0.000396 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 3 | 3 | B.1.258 | 0.0002 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 3 | 3 | B.1.36.1 | 0.003421 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 3 | 3 | B.1.595.2 | 0.12 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 3 | 3 | D.2 | 0.000225 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 3 | 3 | P.1.4 | 0.00293 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 2 | 2 | A.2 | 0.001324 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 2 | 2 | A.29 | 0.010638 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 2 | 2 | AE.8 | 0.000978 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 2 | 2 | AY.100 | 0.000092 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 2 | 2 | AY.20 | 0.000078 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 2 | 2 | AY.4.3 | 0.001684 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 2 | 2 | AY.72 | 0.002721 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 2 | 2 | AY.93 | 0.000546 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 2 | 2 | AY.98 | 0.000158 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 2 | 2 | AY.99.2 | 0.000184 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 2 | 2 | B.1.1.397 | 0.004505 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 2 | 2 | B.1.177.15 | 0.001262 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 1 | 2 | B.1.177.73 | 0.000566 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcA | 1 | 2 | B.1.177.73 | 0.000566 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 2 | 2 | B.1.177.87 | 0.001456 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 2 | 2 | B.1.311 | 0.000549 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 2 | 2 | B.1.324 | 0.00321 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 2 | 2 | B.1.36.29 | 0.001035 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 2 | 2 | B.1.36.35 | 0.005208 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 2 | 2 | B.1.429.1 | 0.024096 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 2 | 2 | C.1 | 0.004785 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 2 | 2 | C.37 | 0.000232 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 1 | 1 | A.2.5 | 0.000499 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 1 | 1 | AH.3 | 0.003802 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 1 | 1 | AY.106 | 0.000335 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 1 | 1 | AY.116.1 | 0.000311 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 1 | 1 | AY.120 | 0.000037 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 1 | 1 | AY.22 | 0.002092 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 1 | 1 | AY.23 | 0.00007 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcA | 1 | 1 | AY.3.1 | 0.000085 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 1 | 1 | AY.34 | 0.000097 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 1 | 1 | AY.45 | 0.000122 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 1 | 1 | AY.46.3 | 0.000934 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 1 | 1 | AY.46.6 | 0.000072 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 1 | 1 | AY.65 | 0.000533 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 1 | 1 | AY.68 | 0.000274 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 1 | 1 | AY.70 | 0.000209 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 1 | 1 | AY.71 | 0.000475 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 1 | 1 | AY.82 | 0.001357 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 1 | 1 | AY.91 | 0.00073 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 1 | 1 | AY.92 | 0.000287 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 1 | 1 | AY.98.1 | 0.000048 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 1 | 1 | AZ.2 | 0.000821 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcA | 1 | 1 | B.1.1.141 | 0.002012 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 1 | 1 | B.1.1.196 | 0.005714 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 1 | 1 | B.1.1.294 | 0.001266 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 1 | 1 | B.1.1.306 | 0.000438 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 1 | 1 | B.1.1.370 | 0.012658 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 1 | 1 | B.1.1.61 | 0.008772 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 1 | 1 | B.1.128 | 0.000635 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 1 | 1 | B.1.157 | 0.002985 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 1 | 1 | B.1.177.54 | 0.000606 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 1 | 1 | B.1.177.86 | 0.000183 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 1 | 1 | B.1.187 | 0.033333 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 1 | 1 | B.1.221 | 0.000071 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 1 | 1 | B.1.241 | 0.000812 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 1 | 1 | B.1.323 | 0.020833 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcA | 1 | 1 | B.1.36 | 0.000146 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 1 | 1 | B.1.36.17 | 0.000494 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 1 | 1 | B.1.36.34 | 0.021277 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 1 | 1 | B.1.367 | 0.000792 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 1 | 1 | B.1.369 | 0.000285 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 1 | 1 | B.1.400 | 0.000429 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 1 | 1 | B.1.436 | 0.001029 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 1 | 1 | B.1.450 | 0.011364 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 1 | 1 | B.1.497 | 0.000315 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 1 | 1 | B.1.595 | 0.000261 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 1 | 1 | B.1.596 | 0.000087 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 1 | 1 | B.1.623 | 0.000536 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 1 | 1 | B.23 | 0.002924 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 1 | 1 | B.4 | 0.002208 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 1 | 1 | P.1.15 | 0.000232 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 1 | 1 | P.1.6 | 0.001946 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 1 | 1 | P.2 | 0.000187 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 1 | 1 | Q.8 | 0.000165 |
ORF1ab/nsp4 | 408 | S408S | tcC | tcT | 1 | 1 | R.1 | 0.00009 |
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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