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 |
N | 312 | S312S | syn | tcA | tcG | 859 | 471 | 0.548312 | 29207-29209 | |
N | 312 | S312S | syn | tcA | tcT | 859 | 329 | 0.383004 | 29207-29209 | |
N | 312 | S312S | syn | tcA | tcC | 859 | 59 | 0.0686845 | 29207-29209 | |
N | 312 | S312L | nonsyn | tCa | tTa | 34 | 32 | 0.941176 | 29207-29209 | |
N | 312 | S312L | nonsyn | TCA | CTT | 34 | 1 | 0.0294118 | 29207-29209 | |
N | 312 | S312L | nonsyn | tCA | tTG | 34 | 1 | 0.0294118 | 29207-29209 | |
N | 312 | S312del | del | TCA | --- | 29 | 29 | 1 | 29207-29209 | |
N | 312 | S312P | nonsyn | Tca | Cca | 5 | 5 | 1 | 29207-29209 | |
N | 312 | S312A | nonsyn | Tca | Gca | 4 | 4 | 1 | 29207-29209 | |
N | 312 | S312del2 | del | TCA | --N | 4 | 2 | 0.5 | 29207-29209 | |
N | 312 | S312del2 | del | tCA | t-- | 4 | 1 | 0.25 | 29207-29209 | |
N | 312 | S312del2 | del | TCa | --a | 4 | 1 | 0.25 | 29207-29209 | |
N | 312 | S312del1 | del | tcA | tc- | 2 | 2 | 1 | 29207-29209 | |
N | 312 | S312X | nonsyn | tCa | tAa | 2 | 2 | 1 | 29207-29209 | |
N | 312 | S312T | nonsyn | TcA | AcC | 2 | 1 | 0.5 | 29207-29209 | |
N | 312 | S312T | nonsyn | Tca | Aca | 2 | 1 | 0.5 | 29207-29209 | |
N | 312 | S312F | nonsyn | tCA | tTC | 2 | 1 | 0.5 | 29207-29209 | |
N | 312 | S312F | nonsyn | tCA | tTT | 2 | 1 | 0.5 | 29207-29209 | |
N | 312 | S312K | nonsyn | TCa | AAa | 1 | 1 | 1 | 29207-29209 |
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 |
N | 312 | S312S | tcA | tcG | 471 | 859 | All | 0.00009 |
N | 312 | S312S | tcA | tcT | 329 | 859 | All | 0.000063 |
N | 312 | S312S | tcA | tcC | 59 | 859 | All | 0.000011 |
N | 312 | S312S | tcA | tcT | 171 | 251 | B.1.1.7 | 0.000153 |
N | 312 | S312S | tcA | tcG | 80 | 251 | B.1.1.7 | 0.000072 |
N | 312 | S312S | tcA | tcG | 81 | 81 | B.1.1.461 | 0.975904 |
N | 312 | S312S | tcA | tcG | 41 | 74 | AY.4 | 0.000064 |
N | 312 | S312S | tcA | tcT | 25 | 74 | AY.4 | 0.000039 |
N | 312 | S312S | tcA | tcC | 8 | 74 | AY.4 | 0.000012 |
N | 312 | S312S | tcA | tcG | 65 | 73 | B.1.160 | 0.002027 |
N | 312 | S312S | tcA | tcT | 8 | 73 | B.1.160 | 0.00025 |
N | 312 | S312S | tcA | tcG | 35 | 35 | B.1.526 | 0.000823 |
N | 312 | S312L | tCa | tTa | 32 | 34 | All | 0.000006 |
N | 312 | S312L | TCA | CTT | 1 | 34 | All | 0 |
N | 312 | S312L | tCA | tTG | 1 | 34 | All | 0 |
N | 312 | S312S | tcA | tcC | 17 | 31 | AY.44 | 0.000103 |
N | 312 | S312S | tcA | tcG | 12 | 31 | AY.44 | 0.000073 |
N | 312 | S312S | tcA | tcT | 2 | 31 | AY.44 | 0.000012 |
N | 312 | S312del | TCA | --- | 29 | 29 | All | 0.000006 |
N | 312 | S312S | tcA | tcC | 16 | 29 | AY.103 | 0.000099 |
N | 312 | S312S | tcA | tcT | 7 | 29 | AY.103 | 0.000043 |
N | 312 | S312S | tcA | tcG | 6 | 29 | AY.103 | 0.000037 |
N | 312 | S312S | tcA | tcG | 24 | 25 | B.1 | 0.00022 |
N | 312 | S312S | tcA | tcT | 1 | 25 | B.1 | 0.000009 |
N | 312 | S312S | tcA | tcT | 11 | 23 | B.1.617.2 | 0.000041 |
N | 312 | S312S | tcA | tcG | 11 | 23 | B.1.617.2 | 0.000041 |
N | 312 | S312S | tcA | tcC | 1 | 23 | B.1.617.2 | 0.000004 |
N | 312 | S312S | tcA | tcT | 19 | 22 | AY.102 | 0.000504 |
N | 312 | S312S | tcA | tcG | 3 | 22 | AY.102 | 0.00008 |
N | 312 | S312S | tcA | tcT | 13 | 17 | AY.25 | 0.000078 |
N | 312 | S312S | tcA | tcG | 4 | 17 | AY.25 | 0.000024 |
N | 312 | S312S | tcA | tcG | 13 | 13 | AY.118 | 0.000814 |
N | 312 | S312S | tcA | tcT | 13 | 13 | AY.39 | 0.000321 |
N | 312 | S312S | tcA | tcG | 10 | 12 | P.1 | 0.000158 |
N | 312 | S312S | tcA | tcT | 2 | 12 | P.1 | 0.000032 |
N | 312 | S312S | tcA | tcT | 11 | 11 | AY.98.1 | 0.000533 |
N | 312 | S312S | tcA | tcC | 7 | 9 | B.1.2 | 0.000062 |
N | 312 | S312S | tcA | tcG | 2 | 9 | B.1.2 | 0.000018 |
N | 312 | S312L | tCa | tTa | 7 | 8 | B.1 | 0.000064 |
N | 312 | S312L | tCA | tTG | 1 | 8 | B.1 | 0.000009 |
N | 312 | S312S | tcA | tcG | 6 | 7 | AY.3 | 0.00006 |
N | 312 | S312S | tcA | tcT | 1 | 7 | AY.3 | 0.00001 |
N | 312 | S312S | tcA | tcG | 4 | 6 | B.1.1 | 0.000073 |
N | 312 | S312S | tcA | tcT | 2 | 6 | B.1.1 | 0.000036 |
N | 312 | S312S | tcA | tcG | 5 | 5 | AD.2 | 0.001095 |
N | 312 | S312P | Tca | Cca | 5 | 5 | All | 0.000001 |
N | 312 | S312S | tcA | tcG | 4 | 5 | AY.43 | 0.000018 |
N | 312 | S312S | tcA | tcT | 1 | 5 | AY.43 | 0.000004 |
N | 312 | S312S | tcA | tcG | 5 | 5 | B.1.177.77 | 0.003631 |
N | 312 | S312L | tCa | tTa | 5 | 5 | D.2 | 0.000375 |
N | 312 | S312A | Tca | Gca | 4 | 4 | All | 0.000001 |
N | 312 | S312del2 | TCA | --N | 2 | 4 | All | 0 |
N | 312 | S312del2 | TCa | --a | 1 | 4 | All | 0 |
N | 312 | S312del2 | tCA | t-- | 1 | 4 | All | 0 |
N | 312 | S312S | tcA | tcC | 4 | 4 | AY.100 | 0.000184 |
N | 312 | S312S | tcA | tcG | 4 | 4 | AY.20 | 0.000155 |
N | 312 | S312S | tcA | tcG | 4 | 4 | AY.4.2 | 0.000087 |
N | 312 | S312del | TCA | --- | 4 | 4 | B.1.177 | 0.000053 |
N | 312 | S312S | tcA | tcG | 4 | 4 | B.1.243 | 0.000278 |
N | 312 | S312S | tcA | tcT | 3 | 3 | AY.113 | 0.000427 |
N | 312 | S312S | tcA | tcT | 2 | 3 | AY.14 | 0.000176 |
N | 312 | S312S | tcA | tcG | 1 | 3 | AY.14 | 0.000088 |
N | 312 | S312S | tcA | tcG | 3 | 3 | AY.23 | 0.000209 |
N | 312 | S312S | tcA | tcG | 3 | 3 | AY.27 | 0.000194 |
N | 312 | S312S | tcA | tcG | 2 | 3 | AY.46 | 0.000208 |
N | 312 | S312S | tcA | tcT | 1 | 3 | AY.46 | 0.000104 |
N | 312 | S312S | tcA | tcG | 3 | 3 | AY.70 | 0.000626 |
N | 312 | S312S | tcA | tcG | 3 | 3 | AY.75 | 0.000168 |
N | 312 | S312S | tcA | tcT | 3 | 3 | B.1.1.369 | 0.001339 |
N | 312 | S312S | tcA | tcT | 3 | 3 | B.1.177.4 | 0.000633 |
N | 312 | S312S | tcA | tcT | 3 | 3 | B.1.206 | 0.002447 |
N | 312 | S312del | TCA | --- | 2 | 2 | 0.111111 | |
N | 312 | S312del1 | tcA | tc- | 2 | 2 | All | 0 |
N | 312 | S312X | tCa | tAa | 2 | 2 | All | 0 |
N | 312 | S312T | TcA | AcC | 1 | 2 | All | 0 |
N | 312 | S312F | tCA | tTT | 1 | 2 | All | 0 |
N | 312 | S312T | Tca | Aca | 1 | 2 | All | 0 |
N | 312 | S312F | tCA | tTC | 1 | 2 | All | 0 |
N | 312 | S312S | tcA | tcG | 1 | 2 | AY.119 | 0.000035 |
N | 312 | S312S | tcA | tcT | 1 | 2 | AY.119 | 0.000035 |
N | 312 | S312S | tcA | tcG | 2 | 2 | AY.13 | 0.000322 |
N | 312 | S312L | tCa | tTa | 2 | 2 | AY.25 | 0.000012 |
N | 312 | S312S | tcA | tcG | 2 | 2 | AY.36 | 0.000296 |
N | 312 | S312L | tCa | tTa | 2 | 2 | AY.4 | 0.000003 |
N | 312 | S312S | tcA | tcG | 2 | 2 | AY.4.4 | 0.000818 |
N | 312 | S312S | tcA | tcT | 2 | 2 | AY.66 | 0.002139 |
N | 312 | S312S | tcA | tcT | 2 | 2 | AY.7.2 | 0.001119 |
N | 312 | S312S | tcA | tcT | 2 | 2 | AY.9.1 | 0.000167 |
N | 312 | S312S | tcA | tcG | 2 | 2 | AY.99.2 | 0.000184 |
N | 312 | S312del | TCA | --- | 2 | 2 | B.1.1 | 0.000036 |
N | 312 | S312A | Tca | Gca | 2 | 2 | B.1.1 | 0.000036 |
N | 312 | S312T | TcA | AcC | 1 | 2 | B.1.1.39 | 0.00051 |
N | 312 | S312T | Tca | Aca | 1 | 2 | B.1.1.39 | 0.00051 |
N | 312 | S312del1 | tcA | tc- | 2 | 2 | B.1.1.7 | 0.000002 |
N | 312 | S312del | TCA | --- | 2 | 2 | B.1.1.7 | 0.000002 |
N | 312 | S312del2 | tCA | t-- | 1 | 2 | B.1.1.7 | 0.000001 |
N | 312 | S312del2 | TCA | --N | 1 | 2 | B.1.1.7 | 0.000001 |
N | 312 | S312L | tCa | tTa | 2 | 2 | B.1.160 | 0.000062 |
N | 312 | S312L | tCa | tTa | 2 | 2 | B.1.2 | 0.000018 |
N | 312 | S312S | tcA | tcT | 2 | 2 | B.1.375 | 0.001639 |
N | 312 | S312S | tcA | tcT | 2 | 2 | B.1.415.1 | 0.015152 |
N | 312 | S312S | tcA | tcG | 1 | 2 | B.1.621 | 0.000089 |
N | 312 | S312S | tcA | tcC | 1 | 2 | B.1.621 | 0.000089 |
N | 312 | S312S | tcA | tcG | 1 | 2 | P.1.14 | 0.000048 |
N | 312 | S312S | tcA | tcT | 1 | 2 | P.1.14 | 0.000048 |
N | 312 | S312S | tcA | tcT | 2 | 2 | P.1.7 | 0.000639 |
N | 312 | S312S | tcA | tcT | 1 | 1 | A.2.4 | 0.003367 |
N | 312 | S312S | tcA | tcG | 1 | 1 | A.21 | 0.00277 |
N | 312 | S312K | TCa | AAa | 1 | 1 | All | 0 |
N | 312 | S312del | TCA | --- | 1 | 1 | AY.102 | 0.000027 |
N | 312 | S312L | tCa | tTa | 1 | 1 | AY.119 | 0.000035 |
N | 312 | S312S | tcA | tcT | 1 | 1 | AY.2 | 0.000356 |
N | 312 | S312del | TCA | --- | 1 | 1 | AY.20 | 0.000039 |
N | 312 | S312F | tCA | tTC | 1 | 1 | AY.23 | 0.00007 |
N | 312 | S312del | TCA | --- | 1 | 1 | AY.25 | 0.000006 |
N | 312 | S312A | Tca | Gca | 1 | 1 | AY.25 | 0.000006 |
N | 312 | S312S | tcA | tcG | 1 | 1 | AY.26 | 0.000028 |
N | 312 | S312S | tcA | tcT | 1 | 1 | AY.33 | 0.000067 |
N | 312 | S312del | TCA | --- | 1 | 1 | AY.34 | 0.000097 |
N | 312 | S312S | tcA | tcG | 1 | 1 | AY.37 | 0.000316 |
N | 312 | S312L | tCa | tTa | 1 | 1 | AY.39.1 | 0.00004 |
N | 312 | S312del | TCA | --- | 1 | 1 | AY.4 | 0.000002 |
N | 312 | S312S | tcA | tcT | 1 | 1 | AY.4.1 | 0.000737 |
N | 312 | S312del | TCA | --- | 1 | 1 | AY.43 | 0.000004 |
N | 312 | S312L | tCa | tTa | 1 | 1 | AY.43 | 0.000004 |
N | 312 | S312S | tcA | tcT | 1 | 1 | AY.46.4 | 0.000165 |
N | 312 | S312L | tCa | tTa | 1 | 1 | AY.48 | 0.000465 |
N | 312 | S312S | tcA | tcG | 1 | 1 | AY.54 | 0.000095 |
N | 312 | S312del | TCA | --- | 1 | 1 | AY.67 | 0.000464 |
N | 312 | S312S | tcA | tcT | 1 | 1 | AY.69 | 0.000187 |
N | 312 | S312del | TCA | --- | 1 | 1 | AY.75 | 0.000056 |
N | 312 | S312K | TCa | AAa | 1 | 1 | AY.79 | 0.001211 |
N | 312 | S312X | tCa | tAa | 1 | 1 | AY.84 | 0.000437 |
N | 312 | S312S | tcA | tcC | 1 | 1 | AY.85 | 0.000427 |
N | 312 | S312S | tcA | tcG | 1 | 1 | AY.9 | 0.000068 |
N | 312 | S312F | tCA | tTT | 1 | 1 | AY.9.1 | 0.000084 |
N | 312 | S312S | tcA | tcG | 1 | 1 | AY.9.2 | 0.000037 |
N | 312 | S312S | tcA | tcG | 1 | 1 | B | 0.000128 |
N | 312 | S312del | TCA | --- | 1 | 1 | B.1 | 0.000009 |
N | 312 | S312L | tCa | tTa | 1 | 1 | B.1.1 | 0.000018 |
N | 312 | S312X | tCa | tAa | 1 | 1 | B.1.1 | 0.000018 |
N | 312 | S312P | Tca | Cca | 1 | 1 | B.1.1 | 0.000018 |
N | 312 | S312S | tcA | tcG | 1 | 1 | B.1.1.139 | 0.022727 |
N | 312 | S312S | tcA | tcG | 1 | 1 | B.1.1.153 | 0.001095 |
N | 312 | S312S | tcA | tcT | 1 | 1 | B.1.1.180 | 0.010753 |
N | 312 | S312S | tcA | tcG | 1 | 1 | B.1.1.200 | 0.007463 |
N | 312 | S312S | tcA | tcT | 1 | 1 | B.1.1.25 | 0.000569 |
N | 312 | S312L | TCA | CTT | 1 | 1 | B.1.1.27 | 0.00565 |
N | 312 | S312S | tcA | tcT | 1 | 1 | B.1.1.277 | 0.000759 |
N | 312 | S312del | TCA | --- | 1 | 1 | B.1.1.279 | 0.001121 |
N | 312 | S312L | tCa | tTa | 1 | 1 | B.1.1.311 | 0.000358 |
N | 312 | S312S | tcA | tcC | 1 | 1 | B.1.1.33 | 0.000421 |
N | 312 | S312L | tCa | tTa | 1 | 1 | B.1.1.369 | 0.000446 |
N | 312 | S312del2 | TCA | --N | 1 | 1 | B.1.1.37 | 0.000193 |
N | 312 | S312S | tcA | tcT | 1 | 1 | B.1.1.374 | 0.002375 |
N | 312 | S312S | tcA | tcC | 1 | 1 | B.1.1.39 | 0.00051 |
N | 312 | S312S | tcA | tcG | 1 | 1 | B.1.1.409 | 0.002833 |
N | 312 | S312S | tcA | tcG | 1 | 1 | B.1.1.434 | 0.000349 |
N | 312 | S312S | tcA | tcG | 1 | 1 | B.1.1.519 | 0.00004 |
N | 312 | S312P | Tca | Cca | 1 | 1 | B.1.1.7 | 0.000001 |
N | 312 | S312P | Tca | Cca | 1 | 1 | B.1.160 | 0.000031 |
N | 312 | S312S | tcA | tcT | 1 | 1 | B.1.177 | 0.000013 |
N | 312 | S312L | tCa | tTa | 1 | 1 | B.1.177 | 0.000013 |
N | 312 | S312del2 | TCa | --a | 1 | 1 | B.1.177.63 | 0.002703 |
N | 312 | S312S | tcA | tcG | 1 | 1 | B.1.177.7 | 0.000165 |
N | 312 | S312del | TCA | --- | 1 | 1 | B.1.177.83 | 0.001481 |
N | 312 | S312del | TCA | --- | 1 | 1 | B.1.258 | 0.000067 |
N | 312 | S312del | TCA | --- | 1 | 1 | B.1.258.16 | 0.001637 |
N | 312 | S312S | tcA | tcG | 1 | 1 | B.1.351 | 0.00003 |
N | 312 | S312S | tcA | tcT | 1 | 1 | B.1.351.3 | 0.000876 |
N | 312 | S312S | tcA | tcG | 1 | 1 | B.1.36 | 0.000146 |
N | 312 | S312L | tCa | tTa | 1 | 1 | B.1.36.29 | 0.000517 |
N | 312 | S312L | tCa | tTa | 1 | 1 | B.1.369 | 0.000285 |
N | 312 | S312S | tcA | tcC | 1 | 1 | B.1.400 | 0.000429 |
N | 312 | S312del | TCA | --- | 1 | 1 | B.1.427 | 0.00005 |
N | 312 | S312S | tcA | tcC | 1 | 1 | B.1.548 | 0.035714 |
N | 312 | S312S | tcA | tcG | 1 | 1 | B.1.561 | 0.000397 |
N | 312 | S312del | TCA | --- | 1 | 1 | B.1.610 | 0.003546 |
N | 312 | S312del | TCA | --- | 1 | 1 | B.1.617.1 | 0.000129 |
N | 312 | S312S | tcA | tcG | 1 | 1 | B.1.617.1 | 0.000129 |
N | 312 | S312del | TCA | --- | 1 | 1 | B.1.617.2 | 0.000004 |
N | 312 | S312A | Tca | Gca | 1 | 1 | B.1.617.2 | 0.000004 |
N | 312 | S312P | Tca | Cca | 1 | 1 | B.1.617.2 | 0.000004 |
N | 312 | S312del | TCA | --- | 1 | 1 | B.1.617.3 | 0.002985 |
N | 312 | S312S | tcA | tcG | 1 | 1 | B.1.625 | 0.002353 |
N | 312 | S312del | TCA | --- | 1 | 1 | B.1.630 | 0.005236 |
N | 312 | S312L | tCa | tTa | 1 | 1 | B.4.7 | 0.010101 |
N | 312 | S312L | tCa | tTa | 1 | 1 | C.37 | 0.000116 |
N | 312 | S312P | Tca | Cca | 1 | 1 | D.2 | 0.000075 |
N | 312 | S312S | tcA | tcG | 1 | 1 | D.2 | 0.000075 |
N | 312 | S312S | tcA | tcG | 1 | 1 | P.1.15 | 0.000232 |
N | 312 | S312S | tcA | tcG | 1 | 1 | Q.3 | 0.000145 |
N | 312 | S312S | tcA | tcT | 1 | 1 | Q.8 | 0.000165 |
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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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