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 | 381 | Y381Y | Y3144Y | syn | taT | taC | 306 | 306 | 1 | 9695-9697 |
ORF1ab/nsp4 | 381 | Y381del | Y3144del | del | TAT | --- | 109 | 109 | 1 | 9695-9697 |
ORF1ab/nsp4 | 381 | Y381H | Y3144H | nonsyn | Tat | Cat | 8 | 8 | 1 | 9695-9697 |
ORF1ab/nsp4 | 381 | Y381F | Y3144F | nonsyn | tAt | tTt | 7 | 7 | 1 | 9695-9697 |
ORF1ab/nsp4 | 381 | Y381del2 | Y3144del2 | del | TAt | --t | 7 | 7 | 1 | 9695-9697 |
ORF1ab/nsp4 | 381 | Y381C | Y3144C | nonsyn | tAt | tGt | 7 | 7 | 1 | 9695-9697 |
ORF1ab/nsp4 | 381 | Y381X | Y3144X | nonsyn | taT | taA | 6 | 6 | 1 | 9695-9697 |
ORF1ab/nsp4 | 381 | Y381N | Y3144N | nonsyn | Tat | Aat | 4 | 3 | 0.75 | 9695-9697 |
ORF1ab/nsp4 | 381 | Y381del1 | Y3144del1 | del | Tat | -at | 4 | 2 | 0.5 | 9695-9697 |
ORF1ab/nsp4 | 381 | Y381del1 | Y3144del1 | del | tAt | t-t | 4 | 2 | 0.5 | 9695-9697 |
ORF1ab/nsp4 | 381 | Y381N | Y3144N | nonsyn | TaT | AaC | 4 | 1 | 0.25 | 9695-9697 |
ORF1ab/nsp4 | 381 | Y381L | Y3144L | nonsyn | tAT | tTA | 3 | 3 | 1 | 9695-9697 |
ORF1ab/nsp4 | 381 | Y381D | Y3144D | nonsyn | Tat | Gat | 3 | 3 | 1 | 9695-9697 |
ORF1ab/nsp4 | 381 | Y381E | Y3144E | nonsyn | TaT | GaG | 2 | 2 | 1 | 9695-9697 |
ORF1ab/nsp4 | 381 | Y381S | Y3144S | nonsyn | tAt | tCt | 2 | 2 | 1 | 9695-9697 |
ORF1ab/nsp4 | 381 | Y381A | Y3144A | nonsyn | TAt | GCt | 1 | 1 | 1 | 9695-9697 |
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/nsp4 | 381 | Y381Y | taT | taC | 306 | 306 | All | 0.000059 |
ORF1ab/nsp4 | 381 | Y381del | TAT | --- | 109 | 109 | All | 0.000021 |
ORF1ab/nsp4 | 381 | Y381Y | taT | taC | 73 | 73 | B.1.1.7 | 0.000065 |
ORF1ab/nsp4 | 381 | Y381del | TAT | --- | 51 | 51 | B.1.1.7 | 0.000046 |
ORF1ab/nsp4 | 381 | Y381Y | taT | taC | 48 | 48 | AY.4 | 0.000075 |
ORF1ab/nsp4 | 381 | Y381Y | taT | taC | 21 | 21 | AY.43 | 0.000093 |
ORF1ab/nsp4 | 381 | Y381Y | taT | taC | 20 | 20 | B.1.180 | 1 |
ORF1ab/nsp4 | 381 | Y381Y | taT | taC | 14 | 14 | B.1.617.2 | 0.000053 |
ORF1ab/nsp4 | 381 | Y381Y | taT | taC | 11 | 11 | AY.3 | 0.000109 |
ORF1ab/nsp4 | 381 | Y381Y | taT | taC | 9 | 9 | B.1.1.519 | 0.000357 |
ORF1ab/nsp4 | 381 | Y381H | Tat | Cat | 8 | 8 | All | 0.000002 |
ORF1ab/nsp4 | 381 | Y381del | TAT | --- | 8 | 8 | AY.4 | 0.000012 |
ORF1ab/nsp4 | 381 | Y381Y | taT | taC | 8 | 8 | B.1 | 0.000073 |
ORF1ab/nsp4 | 381 | Y381Y | taT | taC | 8 | 8 | B.1.177 | 0.000105 |
ORF1ab/nsp4 | 381 | Y381Y | taT | taC | 8 | 8 | B.1.177.86 | 0.001468 |
ORF1ab/nsp4 | 381 | Y381del2 | TAt | --t | 7 | 7 | All | 0.000001 |
ORF1ab/nsp4 | 381 | Y381C | tAt | tGt | 7 | 7 | All | 0.000001 |
ORF1ab/nsp4 | 381 | Y381F | tAt | tTt | 7 | 7 | All | 0.000001 |
ORF1ab/nsp4 | 381 | Y381del | TAT | --- | 7 | 7 | AY.4.5 | 0.000752 |
ORF1ab/nsp4 | 381 | Y381Y | taT | taC | 7 | 7 | B.1.160 | 0.000218 |
ORF1ab/nsp4 | 381 | Y381del | TAT | --- | 7 | 7 | B.1.177 | 0.000092 |
ORF1ab/nsp4 | 381 | Y381X | taT | taA | 6 | 6 | All | 0.000001 |
ORF1ab/nsp4 | 381 | Y381Y | taT | taC | 6 | 6 | P.1 | 0.000095 |
ORF1ab/nsp4 | 381 | Y381Y | taT | taC | 5 | 5 | AY.103 | 0.000031 |
ORF1ab/nsp4 | 381 | Y381N | Tat | Aat | 3 | 4 | All | 0.000001 |
ORF1ab/nsp4 | 381 | Y381del1 | Tat | -at | 2 | 4 | All | 0 |
ORF1ab/nsp4 | 381 | Y381del1 | tAt | t-t | 2 | 4 | All | 0 |
ORF1ab/nsp4 | 381 | Y381N | TaT | AaC | 1 | 4 | All | 0 |
ORF1ab/nsp4 | 381 | Y381del | TAT | --- | 4 | 4 | AY.43 | 0.000018 |
ORF1ab/nsp4 | 381 | Y381Y | taT | taC | 4 | 4 | AY.47 | 0.000124 |
ORF1ab/nsp4 | 381 | Y381Y | taT | taC | 4 | 4 | B.1.499 | 0.004202 |
ORF1ab/nsp4 | 381 | Y381Y | taT | taC | 4 | 4 | B.1.637 | 0.000292 |
ORF1ab/nsp4 | 381 | Y381F | tAt | tTt | 3 | 3 | 0.166667 | |
ORF1ab/nsp4 | 381 | Y381L | tAT | tTA | 3 | 3 | 0.166667 | |
ORF1ab/nsp4 | 381 | Y381X | taT | taA | 3 | 3 | 0.166667 | |
ORF1ab/nsp4 | 381 | Y381L | tAT | tTA | 3 | 3 | All | 0.000001 |
ORF1ab/nsp4 | 381 | Y381D | Tat | Gat | 3 | 3 | All | 0.000001 |
ORF1ab/nsp4 | 381 | Y381Y | taT | taC | 3 | 3 | AY.34 | 0.000291 |
ORF1ab/nsp4 | 381 | Y381Y | taT | taC | 3 | 3 | AY.44 | 0.000018 |
ORF1ab/nsp4 | 381 | Y381Y | taT | taC | 3 | 3 | B.1.221.3 | 0.0025 |
ORF1ab/nsp4 | 381 | Y381E | TaT | GaG | 2 | 2 | 0.111111 | |
ORF1ab/nsp4 | 381 | Y381S | tAt | tCt | 2 | 2 | All | 0 |
ORF1ab/nsp4 | 381 | Y381E | TaT | GaG | 2 | 2 | All | 0 |
ORF1ab/nsp4 | 381 | Y381Y | taT | taC | 2 | 2 | AY.102 | 0.000053 |
ORF1ab/nsp4 | 381 | Y381Y | taT | taC | 2 | 2 | AY.26 | 0.000057 |
ORF1ab/nsp4 | 381 | Y381Y | taT | taC | 2 | 2 | AY.39 | 0.000049 |
ORF1ab/nsp4 | 381 | Y381F | tAt | tTt | 2 | 2 | AY.4 | 0.000003 |
ORF1ab/nsp4 | 381 | Y381C | tAt | tGt | 2 | 2 | AY.4 | 0.000003 |
ORF1ab/nsp4 | 381 | Y381del | TAT | --- | 2 | 2 | B.1.1 | 0.000036 |
ORF1ab/nsp4 | 381 | Y381N | TaT | AaC | 1 | 2 | B.1.1 | 0.000018 |
ORF1ab/nsp4 | 381 | Y381N | Tat | Aat | 1 | 2 | B.1.1 | 0.000018 |
ORF1ab/nsp4 | 381 | Y381Y | taT | taC | 2 | 2 | B.1.1.318 | 0.000604 |
ORF1ab/nsp4 | 381 | Y381C | tAt | tGt | 2 | 2 | B.1.1.7 | 0.000002 |
ORF1ab/nsp4 | 381 | Y381del1 | Tat | -at | 2 | 2 | B.1.177 | 0.000026 |
ORF1ab/nsp4 | 381 | Y381del | TAT | --- | 2 | 2 | B.1.177.69 | 0.002967 |
ORF1ab/nsp4 | 381 | Y381del | TAT | --- | 2 | 2 | B.1.2 | 0.000018 |
ORF1ab/nsp4 | 381 | Y381del | TAT | --- | 2 | 2 | B.1.617.2 | 0.000008 |
ORF1ab/nsp4 | 381 | Y381C | tAt | tGt | 2 | 2 | B.1.617.2 | 0.000008 |
ORF1ab/nsp4 | 381 | Y381Y | taT | taC | 2 | 2 | P.1.14 | 0.000096 |
ORF1ab/nsp4 | 381 | Y381Y | taT | taC | 1 | 1 | A | 0.000387 |
ORF1ab/nsp4 | 381 | Y381A | TAt | GCt | 1 | 1 | All | 0 |
ORF1ab/nsp4 | 381 | Y381S | tAt | tCt | 1 | 1 | AY.102 | 0.000027 |
ORF1ab/nsp4 | 381 | Y381del | TAT | --- | 1 | 1 | AY.106 | 0.000335 |
ORF1ab/nsp4 | 381 | Y381Y | taT | taC | 1 | 1 | AY.110 | 0.000113 |
ORF1ab/nsp4 | 381 | Y381C | tAt | tGt | 1 | 1 | AY.118 | 0.000063 |
ORF1ab/nsp4 | 381 | Y381Y | taT | taC | 1 | 1 | AY.120.2 | 0.001285 |
ORF1ab/nsp4 | 381 | Y381del | TAT | --- | 1 | 1 | AY.19 | 0.00114 |
ORF1ab/nsp4 | 381 | Y381Y | taT | taC | 1 | 1 | AY.20 | 0.000039 |
ORF1ab/nsp4 | 381 | Y381Y | taT | taC | 1 | 1 | AY.25 | 0.000006 |
ORF1ab/nsp4 | 381 | Y381del2 | TAt | --t | 1 | 1 | AY.25 | 0.000006 |
ORF1ab/nsp4 | 381 | Y381H | Tat | Cat | 1 | 1 | AY.26 | 0.000028 |
ORF1ab/nsp4 | 381 | Y381Y | taT | taC | 1 | 1 | AY.27 | 0.000065 |
ORF1ab/nsp4 | 381 | Y381Y | taT | taC | 1 | 1 | AY.29 | 0.000016 |
ORF1ab/nsp4 | 381 | Y381del2 | TAt | --t | 1 | 1 | AY.3 | 0.00001 |
ORF1ab/nsp4 | 381 | Y381Y | taT | taC | 1 | 1 | AY.3.1 | 0.000085 |
ORF1ab/nsp4 | 381 | Y381Y | taT | taC | 1 | 1 | AY.32 | 0.000532 |
ORF1ab/nsp4 | 381 | Y381X | taT | taA | 1 | 1 | AY.4 | 0.000002 |
ORF1ab/nsp4 | 381 | Y381Y | taT | taC | 1 | 1 | AY.42 | 0.00004 |
ORF1ab/nsp4 | 381 | Y381H | Tat | Cat | 1 | 1 | AY.43 | 0.000004 |
ORF1ab/nsp4 | 381 | Y381del | TAT | --- | 1 | 1 | AY.44 | 0.000006 |
ORF1ab/nsp4 | 381 | Y381Y | taT | taC | 1 | 1 | AY.46 | 0.000104 |
ORF1ab/nsp4 | 381 | Y381del | TAT | --- | 1 | 1 | AY.46.2 | 0.000635 |
ORF1ab/nsp4 | 381 | Y381H | Tat | Cat | 1 | 1 | AY.46.2 | 0.000635 |
ORF1ab/nsp4 | 381 | Y381Y | taT | taC | 1 | 1 | AY.46.6 | 0.000072 |
ORF1ab/nsp4 | 381 | Y381Y | taT | taC | 1 | 1 | AY.5 | 0.000021 |
ORF1ab/nsp4 | 381 | Y381Y | taT | taC | 1 | 1 | AY.5.4 | 0.000277 |
ORF1ab/nsp4 | 381 | Y381Y | taT | taC | 1 | 1 | AY.55 | 0.000917 |
ORF1ab/nsp4 | 381 | Y381del | TAT | --- | 1 | 1 | AY.6 | 0.000041 |
ORF1ab/nsp4 | 381 | Y381Y | taT | taC | 1 | 1 | AY.61 | 0.000105 |
ORF1ab/nsp4 | 381 | Y381Y | taT | taC | 1 | 1 | AY.63 | 0.000387 |
ORF1ab/nsp4 | 381 | Y381del | TAT | --- | 1 | 1 | AY.68 | 0.000274 |
ORF1ab/nsp4 | 381 | Y381Y | taT | taC | 1 | 1 | AY.71 | 0.000475 |
ORF1ab/nsp4 | 381 | Y381Y | taT | taC | 1 | 1 | AY.81 | 0.001992 |
ORF1ab/nsp4 | 381 | Y381del | TAT | --- | 1 | 1 | AY.9 | 0.000068 |
ORF1ab/nsp4 | 381 | Y381Y | taT | taC | 1 | 1 | AY.9.2 | 0.000037 |
ORF1ab/nsp4 | 381 | Y381del | TAT | --- | 1 | 1 | AY.9.2 | 0.000037 |
ORF1ab/nsp4 | 381 | Y381X | taT | taA | 1 | 1 | AY.90 | 0.000684 |
ORF1ab/nsp4 | 381 | Y381Y | taT | taC | 1 | 1 | AY.98 | 0.000079 |
ORF1ab/nsp4 | 381 | Y381X | taT | taA | 1 | 1 | AY.98.1 | 0.000048 |
ORF1ab/nsp4 | 381 | Y381del | TAT | --- | 1 | 1 | AY.99 | 0.001049 |
ORF1ab/nsp4 | 381 | Y381del | TAT | --- | 1 | 1 | AY.99.1 | 0.001553 |
ORF1ab/nsp4 | 381 | Y381N | Tat | Aat | 1 | 1 | B.1 | 0.000009 |
ORF1ab/nsp4 | 381 | Y381del1 | tAt | t-t | 1 | 1 | B.1 | 0.000009 |
ORF1ab/nsp4 | 381 | Y381del | TAT | --- | 1 | 1 | B.1 | 0.000009 |
ORF1ab/nsp4 | 381 | Y381Y | taT | taC | 1 | 1 | B.1.1 | 0.000018 |
ORF1ab/nsp4 | 381 | Y381del | TAT | --- | 1 | 1 | B.1.1.139 | 0.022727 |
ORF1ab/nsp4 | 381 | Y381Y | taT | taC | 1 | 1 | B.1.1.176 | 0.000439 |
ORF1ab/nsp4 | 381 | Y381Y | taT | taC | 1 | 1 | B.1.1.220 | 0.001859 |
ORF1ab/nsp4 | 381 | Y381del | TAT | --- | 1 | 1 | B.1.1.236 | 0.006897 |
ORF1ab/nsp4 | 381 | Y381Y | taT | taC | 1 | 1 | B.1.1.372 | 0.000689 |
ORF1ab/nsp4 | 381 | Y381del2 | TAt | --t | 1 | 1 | B.1.1.7 | 0.000001 |
ORF1ab/nsp4 | 381 | Y381D | Tat | Gat | 1 | 1 | B.1.1.7 | 0.000001 |
ORF1ab/nsp4 | 381 | Y381del1 | tAt | t-t | 1 | 1 | B.1.1.7 | 0.000001 |
ORF1ab/nsp4 | 381 | Y381F | tAt | tTt | 1 | 1 | B.1.1.7 | 0.000001 |
ORF1ab/nsp4 | 381 | Y381del | TAT | --- | 1 | 1 | B.1.1.70 | 0.000341 |
ORF1ab/nsp4 | 381 | Y381F | tAt | tTt | 1 | 1 | B.1.139 | 0.000733 |
ORF1ab/nsp4 | 381 | Y381H | Tat | Cat | 1 | 1 | B.1.160.16 | 0.000929 |
ORF1ab/nsp4 | 381 | Y381del2 | TAt | --t | 1 | 1 | B.1.177 | 0.000013 |
ORF1ab/nsp4 | 381 | Y381del | TAT | --- | 1 | 1 | B.1.177.11 | 0.001698 |
ORF1ab/nsp4 | 381 | Y381Y | taT | taC | 1 | 1 | B.1.177.12 | 0.000152 |
ORF1ab/nsp4 | 381 | Y381del | TAT | --- | 1 | 1 | B.1.177.17 | 0.000821 |
ORF1ab/nsp4 | 381 | Y381del | TAT | --- | 1 | 1 | B.1.177.4 | 0.000211 |
ORF1ab/nsp4 | 381 | Y381del | TAT | --- | 1 | 1 | B.1.177.55 | 0.002331 |
ORF1ab/nsp4 | 381 | Y381del | TAT | --- | 1 | 1 | B.1.177.56 | 0.000668 |
ORF1ab/nsp4 | 381 | Y381del | TAT | --- | 1 | 1 | B.1.177.58 | 0.001332 |
ORF1ab/nsp4 | 381 | Y381del | TAT | --- | 1 | 1 | B.1.177.76 | 0.002494 |
ORF1ab/nsp4 | 381 | Y381H | Tat | Cat | 1 | 1 | B.1.2 | 0.000009 |
ORF1ab/nsp4 | 381 | Y381Y | taT | taC | 1 | 1 | B.1.2 | 0.000009 |
ORF1ab/nsp4 | 381 | Y381del2 | TAt | --t | 1 | 1 | B.1.2 | 0.000009 |
ORF1ab/nsp4 | 381 | Y381del2 | TAt | --t | 1 | 1 | B.1.206 | 0.000816 |
ORF1ab/nsp4 | 381 | Y381H | Tat | Cat | 1 | 1 | B.1.206 | 0.000816 |
ORF1ab/nsp4 | 381 | Y381del2 | TAt | --t | 1 | 1 | B.1.234 | 0.000132 |
ORF1ab/nsp4 | 381 | Y381Y | taT | taC | 1 | 1 | B.1.258 | 0.000067 |
ORF1ab/nsp4 | 381 | Y381Y | taT | taC | 1 | 1 | B.1.258.17 | 0.000104 |
ORF1ab/nsp4 | 381 | Y381D | Tat | Gat | 1 | 1 | B.1.332 | 0.003497 |
ORF1ab/nsp4 | 381 | Y381D | Tat | Gat | 1 | 1 | B.1.351 | 0.00003 |
ORF1ab/nsp4 | 381 | Y381A | TAt | GCt | 1 | 1 | B.1.351 | 0.00003 |
ORF1ab/nsp4 | 381 | Y381S | tAt | tCt | 1 | 1 | B.1.351 | 0.00003 |
ORF1ab/nsp4 | 381 | Y381del | TAT | --- | 1 | 1 | B.1.36.38 | 0.001642 |
ORF1ab/nsp4 | 381 | Y381Y | taT | taC | 1 | 1 | B.1.404 | 0.001302 |
ORF1ab/nsp4 | 381 | Y381Y | taT | taC | 1 | 1 | B.1.409 | 0.000781 |
ORF1ab/nsp4 | 381 | Y381Y | taT | taC | 1 | 1 | B.1.429 | 0.000024 |
ORF1ab/nsp4 | 381 | Y381Y | taT | taC | 1 | 1 | B.1.480 | 0.002488 |
ORF1ab/nsp4 | 381 | Y381Y | taT | taC | 1 | 1 | B.1.526 | 0.000024 |
ORF1ab/nsp4 | 381 | Y381H | Tat | Cat | 1 | 1 | B.1.532 | 0.006211 |
ORF1ab/nsp4 | 381 | Y381Y | taT | taC | 1 | 1 | B.1.577 | 0.000687 |
ORF1ab/nsp4 | 381 | Y381H | Tat | Cat | 1 | 1 | B.1.612 | 0.002653 |
ORF1ab/nsp4 | 381 | Y381Y | taT | taC | 1 | 1 | B.1.617.1 | 0.000129 |
ORF1ab/nsp4 | 381 | Y381N | Tat | Aat | 1 | 1 | B.1.617.1 | 0.000129 |
ORF1ab/nsp4 | 381 | Y381Y | taT | taC | 1 | 1 | P.1.10.1 | 0.00813 |
ORF1ab/nsp4 | 381 | Y381del | TAT | --- | 1 | 1 | Q.1 | 0.000126 |
ORF1ab/nsp4 | 381 | Y381del | TAT | --- | 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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