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 | 1403 | P1403S | P2221S | nonsyn | Cct | Tct | 3430 | 3429 | 0.999708 | 6926-6928 |
ORF1ab/nsp3 | 1403 | P1403S | P2221S | nonsyn | CcT | TcC | 3430 | 1 | 0.000291545 | 6926-6928 |
Details of the mutation P1403S 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 | 1403 | P1403S | Cct | Tct | 3429 | 3430 | All | 0.000656 |
ORF1ab/nsp3 | 1403 | P1403S | CcT | TcC | 1 | 3430 | All | 0 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 694 | 694 | AY.5 | 0.014331 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 524 | 524 | L.1 | 0.998095 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 400 | 400 | B.1.1.7 | 0.000358 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 339 | 339 | B.1.2 | 0.002985 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 252 | 252 | AY.4 | 0.000392 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 214 | 214 | B.1.617.2 | 0.000806 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 71 | 71 | B.1 | 0.00065 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 62 | 62 | AY.103 | 0.000385 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 58 | 58 | AY.44 | 0.000353 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 45 | 46 | AY.43 | 0.000199 |
ORF1ab/nsp3 | 1403 | P1403S | CcT | TcC | 1 | 46 | AY.43 | 0.000004 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 45 | 45 | B.1.621 | 0.003983 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 43 | 43 | B.1.1 | 0.00078 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 38 | 38 | P.1 | 0.000599 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 35 | 35 | B.1.258.22 | 0.093333 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 33 | 33 | B.1.234 | 0.004354 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 30 | 30 | B.1.1.519 | 0.001191 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 28 | 28 | B.1.1.10 | 0.031215 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 20 | 20 | B.1.177 | 0.000263 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 20 | 20 | C.36.3 | 0.011344 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 20 | 20 | R.1 | 0.0018 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 16 | 16 | AY.102 | 0.000424 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 16 | 16 | AY.16 | 0.006074 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 16 | 16 | B.1.1.216 | 0.014248 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 16 | 16 | B.1.177.81 | 0.003029 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 14 | 14 | AY.3 | 0.000139 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 14 | 14 | B.1.160 | 0.000437 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 12 | 12 | AY.29 | 0.000189 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 12 | 12 | AY.4.2 | 0.00026 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 11 | 11 | B.1.351 | 0.000327 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 11 | 11 | C.36 | 0.010018 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 10 | 10 | AY.23 | 0.000697 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 10 | 10 | AY.25 | 0.00006 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 10 | 10 | B.1.1.318 | 0.003018 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 10 | 10 | B.1.243 | 0.000696 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 9 | 9 | B.1.36 | 0.001313 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 8 | 8 | AY.27 | 0.000518 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 8 | 8 | AY.33 | 0.000534 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 8 | 8 | AY.39 | 0.000198 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 8 | 8 | B.1.429 | 0.000188 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 7 | 7 | B.1.258.17 | 0.000728 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 7 | 7 | Q.8 | 0.001154 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 6 | 6 | AY.100 | 0.000276 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 6 | 6 | AY.3.1 | 0.000512 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 6 | 6 | AY.36 | 0.000889 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 6 | 6 | B.1.1.25 | 0.003411 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 5 | 5 | AY.118 | 0.000313 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 5 | 5 | AY.47 | 0.000156 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 5 | 5 | B.1.541 | 0.022124 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 5 | 5 | B.1.575 | 0.001517 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 4 | 4 | AY.6 | 0.000165 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 4 | 4 | AY.75.1 | 0.000721 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 4 | 4 | AY.9.2 | 0.000147 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 4 | 4 | B.1.1.28 | 0.001245 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 4 | 4 | B.1.351.2 | 0.00121 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 4 | 4 | B.1.524 | 0.005626 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 3 | 3 | A.23.1 | 0.002113 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 3 | 3 | AY.13 | 0.000483 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 3 | 3 | AY.34 | 0.000291 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 3 | 3 | AY.4.2.1 | 0.000447 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 3 | 3 | AY.42 | 0.000121 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 3 | 3 | AY.98 | 0.000237 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 3 | 3 | B.1.1.306 | 0.001315 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 3 | 3 | B.1.1.311 | 0.001074 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 3 | 3 | B.1.177.12 | 0.000455 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 3 | 3 | B.1.427 | 0.000151 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 3 | 3 | B.1.517 | 0.001281 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 3 | 3 | B.1.526 | 0.000071 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 3 | 3 | B.1.596 | 0.000261 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 3 | 3 | C.37 | 0.000348 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 2 | 2 | AY.110 | 0.000225 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 2 | 2 | AY.121 | 0.000271 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 2 | 2 | AY.26 | 0.000057 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 2 | 2 | AY.46.6 | 0.000144 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 2 | 2 | AY.75 | 0.000112 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 2 | 2 | AY.85 | 0.000854 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 2 | 2 | AY.88 | 0.001768 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 2 | 2 | AY.92 | 0.000575 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 2 | 2 | AY.95 | 0.001522 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 2 | 2 | AY.98.1 | 0.000097 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 2 | 2 | B.1.1.149 | 0.032787 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 2 | 2 | B.1.1.161 | 0.007067 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 2 | 2 | B.1.1.277 | 0.001517 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 2 | 2 | B.1.1.356 | 0.017094 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 2 | 2 | B.1.177.32 | 0.002699 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 2 | 2 | B.1.177.54 | 0.001213 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 2 | 2 | B.1.177.86 | 0.000367 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 2 | 2 | B.1.221 | 0.000142 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 2 | 2 | B.1.258 | 0.000133 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 2 | 2 | B.1.36.29 | 0.001035 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 2 | 2 | B.1.362 | 0.003082 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 2 | 2 | B.1.367 | 0.001585 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 2 | 2 | B.1.564 | 0.000852 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 2 | 2 | B.1.617.1 | 0.000258 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 2 | 2 | C.14 | 0.008658 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 2 | 2 | C.16 | 0.002121 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 2 | 2 | P.1.4 | 0.001953 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 1 | 1 | A | 0.000387 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 1 | 1 | AE.8 | 0.000489 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 1 | 1 | AY.104 | 0.001984 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 1 | 1 | AY.115 | 0.005208 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 1 | 1 | AY.117 | 0.000085 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 1 | 1 | AY.23.1 | 0.000417 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 1 | 1 | AY.24 | 0.000431 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 1 | 1 | AY.29.1 | 0.000221 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 1 | 1 | AY.34.1 | 0.00051 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 1 | 1 | AY.39.1 | 0.00004 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 1 | 1 | AY.45 | 0.000122 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 1 | 1 | AY.46.2 | 0.000635 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 1 | 1 | AY.46.4 | 0.000165 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 1 | 1 | AY.5.3 | 0.000337 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 1 | 1 | AY.5.4 | 0.000277 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 1 | 1 | AY.51 | 0.000909 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 1 | 1 | AY.55 | 0.000917 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 1 | 1 | AY.58 | 0.000907 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 1 | 1 | AY.59 | 0.00053 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 1 | 1 | AY.61 | 0.000105 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 1 | 1 | AY.62 | 0.000436 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 1 | 1 | AY.67 | 0.000464 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 1 | 1 | AY.84 | 0.000437 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 1 | 1 | AY.96 | 0.002075 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 1 | 1 | AY.99.2 | 0.000092 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 1 | 1 | B.1.1.163 | 0.007634 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 1 | 1 | B.1.1.176 | 0.000439 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 1 | 1 | B.1.1.222 | 0.000204 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 1 | 1 | B.1.1.236 | 0.006897 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 1 | 1 | B.1.1.253 | 0.002506 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 1 | 1 | B.1.1.312 | 0.001912 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 1 | 1 | B.1.1.409 | 0.002833 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 1 | 1 | B.1.1.432 | 0.001266 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 1 | 1 | B.1.1.448 | 0.002033 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 1 | 1 | B.1.1.57 | 0.011494 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 1 | 1 | B.1.1.70 | 0.000341 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 1 | 1 | B.1.110.3 | 0.000718 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 1 | 1 | B.1.160.16 | 0.000929 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 1 | 1 | B.1.160.22 | 0.006757 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 1 | 1 | B.1.177.44 | 0.000519 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 1 | 1 | B.1.177.60 | 0.000218 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 1 | 1 | B.1.177.7 | 0.000165 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 1 | 1 | B.1.177.77 | 0.000726 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 1 | 1 | B.1.177.82 | 0.000477 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 1 | 1 | B.1.222 | 0.001692 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 1 | 1 | B.1.241 | 0.000812 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 1 | 1 | B.1.351.5 | 0.0006 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 1 | 1 | B.1.36.18 | 0.00042 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 1 | 1 | B.1.441 | 0.009615 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 1 | 1 | B.1.466.2 | 0.000391 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 1 | 1 | B.1.525 | 0.000113 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 1 | 1 | B.1.538 | 0.008065 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 1 | 1 | B.1.577 | 0.000687 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 1 | 1 | B.1.609 | 0.000479 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 1 | 1 | D.2 | 0.000075 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 1 | 1 | P.1.1 | 0.000318 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 1 | 1 | P.1.14 | 0.000048 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 1 | 1 | P.1.15 | 0.000232 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 1 | 1 | P.2 | 0.000187 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 1 | 1 | P.6 | 0.003145 |
ORF1ab/nsp3 | 1403 | P1403S | Cct | Tct | 1 | 1 | Q.1 | 0.000126 |
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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