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/nsp12 | 595 | Y595Y | Y4987Y | syn | taT | taC | 592 | 592 | 1 | 15223-15225 |
ORF1ab/nsp12 | 595 | Y595X | Y4987X | nonsyn | taT | taA | 103 | 101 | 0.980583 | 15223-15225 |
ORF1ab/nsp12 | 595 | Y595X | Y4987X | nonsyn | taT | taG | 103 | 2 | 0.0194175 | 15223-15225 |
ORF1ab/nsp12 | 595 | Y595del | Y4987del | del | TAT | --- | 39 | 39 | 1 | 15223-15225 |
ORF1ab/nsp12 | 595 | Y595C | Y4987C | nonsyn | tAt | tGt | 16 | 16 | 1 | 15223-15225 |
ORF1ab/nsp12 | 595 | Y595H | Y4987H | nonsyn | Tat | Cat | 13 | 13 | 1 | 15223-15225 |
ORF1ab/nsp12 | 595 | Y595del1 | Y4987del1 | del | Tat | -at | 6 | 5 | 0.833333 | 15223-15225 |
ORF1ab/nsp12 | 595 | Y595del1 | Y4987del1 | del | taT | ta- | 6 | 1 | 0.166667 | 15223-15225 |
ORF1ab/nsp12 | 595 | Y595F | Y4987F | nonsyn | tAt | tTt | 2 | 2 | 1 | 15223-15225 |
ORF1ab/nsp12 | 595 | Y595N | Y4987N | nonsyn | Tat | Aat | 2 | 2 | 1 | 15223-15225 |
ORF1ab/nsp12 | 595 | Y595S | Y4987S | nonsyn | tAt | tCt | 2 | 1 | 0.5 | 15223-15225 |
ORF1ab/nsp12 | 595 | Y595S | Y4987S | nonsyn | TAT | AGC | 2 | 1 | 0.5 | 15223-15225 |
ORF1ab/nsp12 | 595 | Y595D | Y4987D | nonsyn | TaT | GaC | 1 | 1 | 1 | 15223-15225 |
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/nsp12 | 595 | Y595Y | taT | taC | 592 | 592 | All | 0.000113 |
ORF1ab/nsp12 | 595 | Y595Y | taT | taC | 306 | 306 | AY.25 | 0.001841 |
ORF1ab/nsp12 | 595 | Y595X | taT | taA | 101 | 103 | All | 0.000019 |
ORF1ab/nsp12 | 595 | Y595X | taT | taG | 2 | 103 | All | 0 |
ORF1ab/nsp12 | 595 | Y595X | taT | taA | 62 | 63 | B.1.1.7 | 0.000056 |
ORF1ab/nsp12 | 595 | Y595X | taT | taG | 1 | 63 | B.1.1.7 | 0.000001 |
ORF1ab/nsp12 | 595 | Y595Y | taT | taC | 47 | 47 | AY.4 | 0.000073 |
ORF1ab/nsp12 | 595 | Y595del | TAT | --- | 39 | 39 | All | 0.000007 |
ORF1ab/nsp12 | 595 | Y595Y | taT | taC | 38 | 38 | AY.102 | 0.001008 |
ORF1ab/nsp12 | 595 | Y595Y | taT | taC | 26 | 26 | B.1.1.7 | 0.000023 |
ORF1ab/nsp12 | 595 | Y595del | TAT | --- | 20 | 20 | B.1.1.7 | 0.000018 |
ORF1ab/nsp12 | 595 | Y595Y | taT | taC | 19 | 19 | B.1.617.2 | 0.000072 |
ORF1ab/nsp12 | 595 | Y595Y | taT | taC | 18 | 18 | B.1.9.3 | 0.692308 |
ORF1ab/nsp12 | 595 | Y595C | tAt | tGt | 16 | 16 | All | 0.000003 |
ORF1ab/nsp12 | 595 | Y595Y | taT | taC | 14 | 14 | AY.39 | 0.000346 |
ORF1ab/nsp12 | 595 | Y595Y | taT | taC | 14 | 14 | B.1.177.21 | 0.001071 |
ORF1ab/nsp12 | 595 | Y595H | Tat | Cat | 13 | 13 | All | 0.000002 |
ORF1ab/nsp12 | 595 | Y595Y | taT | taC | 13 | 13 | AY.44 | 0.000079 |
ORF1ab/nsp12 | 595 | Y595Y | taT | taC | 10 | 10 | AY.5 | 0.000206 |
ORF1ab/nsp12 | 595 | Y595Y | taT | taC | 9 | 9 | B.1 | 0.000082 |
ORF1ab/nsp12 | 595 | Y595Y | taT | taC | 7 | 7 | AY.23 | 0.000488 |
ORF1ab/nsp12 | 595 | Y595del1 | Tat | -at | 5 | 6 | All | 0.000001 |
ORF1ab/nsp12 | 595 | Y595del1 | taT | ta- | 1 | 6 | All | 0 |
ORF1ab/nsp12 | 595 | Y595Y | taT | taC | 6 | 6 | AY.103 | 0.000037 |
ORF1ab/nsp12 | 595 | Y595X | taT | taA | 6 | 6 | AY.43 | 0.000027 |
ORF1ab/nsp12 | 595 | Y595Y | taT | taC | 6 | 6 | AY.43 | 0.000027 |
ORF1ab/nsp12 | 595 | Y595Y | taT | taC | 6 | 6 | B.1.2 | 0.000053 |
ORF1ab/nsp12 | 595 | Y595Y | taT | taC | 5 | 5 | B.1.1.519 | 0.000199 |
ORF1ab/nsp12 | 595 | Y595H | Tat | Cat | 4 | 4 | AY.4 | 0.000006 |
ORF1ab/nsp12 | 595 | Y595Y | taT | taC | 4 | 4 | C.37 | 0.000464 |
ORF1ab/nsp12 | 595 | Y595Y | taT | taC | 3 | 3 | AY.20 | 0.000117 |
ORF1ab/nsp12 | 595 | Y595del | TAT | --- | 3 | 3 | AY.4 | 0.000005 |
ORF1ab/nsp12 | 595 | Y595X | taT | taA | 3 | 3 | AY.4 | 0.000005 |
ORF1ab/nsp12 | 595 | Y595X | taT | taA | 3 | 3 | B.1 | 0.000027 |
ORF1ab/nsp12 | 595 | Y595del | TAT | --- | 3 | 3 | B.1.177 | 0.00004 |
ORF1ab/nsp12 | 595 | Y595Y | taT | taC | 3 | 3 | B.1.243 | 0.000209 |
ORF1ab/nsp12 | 595 | Y595Y | taT | taC | 3 | 3 | B.1.544 | 0.018072 |
ORF1ab/nsp12 | 595 | Y595C | tAt | tGt | 3 | 3 | B.1.617.2 | 0.000011 |
ORF1ab/nsp12 | 595 | Y595N | Tat | Aat | 2 | 2 | All | 0 |
ORF1ab/nsp12 | 595 | Y595F | tAt | tTt | 2 | 2 | All | 0 |
ORF1ab/nsp12 | 595 | Y595S | tAt | tCt | 1 | 2 | All | 0 |
ORF1ab/nsp12 | 595 | Y595S | TAT | AGC | 1 | 2 | All | 0 |
ORF1ab/nsp12 | 595 | Y595Y | taT | taC | 2 | 2 | AY.117 | 0.000169 |
ORF1ab/nsp12 | 595 | Y595Y | taT | taC | 2 | 2 | AY.118 | 0.000125 |
ORF1ab/nsp12 | 595 | Y595Y | taT | taC | 2 | 2 | AY.26 | 0.000057 |
ORF1ab/nsp12 | 595 | Y595X | taT | taA | 2 | 2 | AY.39 | 0.000049 |
ORF1ab/nsp12 | 595 | Y595X | taT | taA | 2 | 2 | AY.42 | 0.00008 |
ORF1ab/nsp12 | 595 | Y595Y | taT | taC | 2 | 2 | AY.46.4 | 0.000329 |
ORF1ab/nsp12 | 595 | Y595X | taT | taA | 2 | 2 | AY.46.6 | 0.000144 |
ORF1ab/nsp12 | 595 | Y595Y | taT | taC | 2 | 2 | AY.47 | 0.000062 |
ORF1ab/nsp12 | 595 | Y595Y | taT | taC | 2 | 2 | AY.9.2 | 0.000073 |
ORF1ab/nsp12 | 595 | Y595Y | taT | taC | 2 | 2 | AY.98 | 0.000158 |
ORF1ab/nsp12 | 595 | Y595X | taT | taA | 2 | 2 | B.1.1.121 | 0.004854 |
ORF1ab/nsp12 | 595 | Y595del1 | Tat | -at | 2 | 2 | B.1.1.7 | 0.000002 |
ORF1ab/nsp12 | 595 | Y595C | tAt | tGt | 2 | 2 | B.1.1.7 | 0.000002 |
ORF1ab/nsp12 | 595 | Y595X | taT | taA | 2 | 2 | B.1.117 | 0.025 |
ORF1ab/nsp12 | 595 | Y595Y | taT | taC | 2 | 2 | B.1.234 | 0.000264 |
ORF1ab/nsp12 | 595 | Y595C | tAt | tGt | 2 | 2 | B.1.429 | 0.000047 |
ORF1ab/nsp12 | 595 | Y595X | taT | taA | 2 | 2 | B.1.617.2 | 0.000008 |
ORF1ab/nsp12 | 595 | Y595C | tAt | tGt | 2 | 2 | D.2 | 0.00015 |
ORF1ab/nsp12 | 595 | Y595del | TAT | --- | 1 | 1 | AD.2 | 0.000219 |
ORF1ab/nsp12 | 595 | Y595Y | taT | taC | 1 | 1 | AE.8 | 0.000489 |
ORF1ab/nsp12 | 595 | Y595D | TaT | GaC | 1 | 1 | All | 0 |
ORF1ab/nsp12 | 595 | Y595Y | taT | taC | 1 | 1 | AY.100 | 0.000046 |
ORF1ab/nsp12 | 595 | Y595X | taT | taA | 1 | 1 | AY.103 | 0.000006 |
ORF1ab/nsp12 | 595 | Y595Y | taT | taC | 1 | 1 | AY.120 | 0.000037 |
ORF1ab/nsp12 | 595 | Y595Y | taT | taC | 1 | 1 | AY.120.1 | 0.000321 |
ORF1ab/nsp12 | 595 | Y595S | TAT | AGC | 1 | 1 | AY.120.1 | 0.000321 |
ORF1ab/nsp12 | 595 | Y595Y | taT | taC | 1 | 1 | AY.121 | 0.000135 |
ORF1ab/nsp12 | 595 | Y595N | Tat | Aat | 1 | 1 | AY.24 | 0.000431 |
ORF1ab/nsp12 | 595 | Y595C | tAt | tGt | 1 | 1 | AY.25 | 0.000006 |
ORF1ab/nsp12 | 595 | Y595X | taT | taA | 1 | 1 | AY.25 | 0.000006 |
ORF1ab/nsp12 | 595 | Y595Y | taT | taC | 1 | 1 | AY.29 | 0.000016 |
ORF1ab/nsp12 | 595 | Y595del | TAT | --- | 1 | 1 | AY.33 | 0.000067 |
ORF1ab/nsp12 | 595 | Y595Y | taT | taC | 1 | 1 | AY.36 | 0.000148 |
ORF1ab/nsp12 | 595 | Y595Y | taT | taC | 1 | 1 | AY.39.1 | 0.00004 |
ORF1ab/nsp12 | 595 | Y595C | tAt | tGt | 1 | 1 | AY.4 | 0.000002 |
ORF1ab/nsp12 | 595 | Y595del | TAT | --- | 1 | 1 | AY.4.5 | 0.000107 |
ORF1ab/nsp12 | 595 | Y595X | taT | taA | 1 | 1 | AY.41 | 0.000294 |
ORF1ab/nsp12 | 595 | Y595H | Tat | Cat | 1 | 1 | AY.42 | 0.00004 |
ORF1ab/nsp12 | 595 | Y595del | TAT | --- | 1 | 1 | AY.43 | 0.000004 |
ORF1ab/nsp12 | 595 | Y595H | Tat | Cat | 1 | 1 | AY.43 | 0.000004 |
ORF1ab/nsp12 | 595 | Y595H | Tat | Cat | 1 | 1 | AY.44 | 0.000006 |
ORF1ab/nsp12 | 595 | Y595C | tAt | tGt | 1 | 1 | AY.44 | 0.000006 |
ORF1ab/nsp12 | 595 | Y595X | taT | taA | 1 | 1 | AY.45 | 0.000122 |
ORF1ab/nsp12 | 595 | Y595Y | taT | taC | 1 | 1 | AY.46 | 0.000104 |
ORF1ab/nsp12 | 595 | Y595X | taT | taA | 1 | 1 | AY.46.4 | 0.000165 |
ORF1ab/nsp12 | 595 | Y595C | tAt | tGt | 1 | 1 | AY.47 | 0.000031 |
ORF1ab/nsp12 | 595 | Y595del | TAT | --- | 1 | 1 | AY.52 | 0.000814 |
ORF1ab/nsp12 | 595 | Y595X | taT | taA | 1 | 1 | AY.7.2 | 0.000559 |
ORF1ab/nsp12 | 595 | Y595Y | taT | taC | 1 | 1 | AY.75.1 | 0.00018 |
ORF1ab/nsp12 | 595 | Y595X | taT | taA | 1 | 1 | AY.98.1 | 0.000048 |
ORF1ab/nsp12 | 595 | Y595del | TAT | --- | 1 | 1 | AY.99.1 | 0.001553 |
ORF1ab/nsp12 | 595 | Y595C | tAt | tGt | 1 | 1 | AY.99.2 | 0.000092 |
ORF1ab/nsp12 | 595 | Y595N | Tat | Aat | 1 | 1 | B.1 | 0.000009 |
ORF1ab/nsp12 | 595 | Y595del1 | Tat | -at | 1 | 1 | B.1 | 0.000009 |
ORF1ab/nsp12 | 595 | Y595H | Tat | Cat | 1 | 1 | B.1 | 0.000009 |
ORF1ab/nsp12 | 595 | Y595X | taT | taA | 1 | 1 | B.1.1 | 0.000018 |
ORF1ab/nsp12 | 595 | Y595H | Tat | Cat | 1 | 1 | B.1.1.101 | 0.01 |
ORF1ab/nsp12 | 595 | Y595X | taT | taA | 1 | 1 | B.1.1.115 | 0.008929 |
ORF1ab/nsp12 | 595 | Y595F | tAt | tTt | 1 | 1 | B.1.1.138 | 0.006061 |
ORF1ab/nsp12 | 595 | Y595Y | taT | taC | 1 | 1 | B.1.1.216 | 0.00089 |
ORF1ab/nsp12 | 595 | Y595Y | taT | taC | 1 | 1 | B.1.1.288 | 0.001916 |
ORF1ab/nsp12 | 595 | Y595X | taT | taA | 1 | 1 | B.1.1.369 | 0.000446 |
ORF1ab/nsp12 | 595 | Y595F | tAt | tTt | 1 | 1 | B.1.1.4 | 0.002976 |
ORF1ab/nsp12 | 595 | Y595Y | taT | taC | 1 | 1 | B.1.1.448 | 0.002033 |
ORF1ab/nsp12 | 595 | Y595H | Tat | Cat | 1 | 1 | B.1.1.7 | 0.000001 |
ORF1ab/nsp12 | 595 | Y595del | TAT | --- | 1 | 1 | B.1.1.70 | 0.000341 |
ORF1ab/nsp12 | 595 | Y595del1 | taT | ta- | 1 | 1 | B.1.140 | 0.018868 |
ORF1ab/nsp12 | 595 | Y595del | TAT | --- | 1 | 1 | B.1.160 | 0.000031 |
ORF1ab/nsp12 | 595 | Y595del | TAT | --- | 1 | 1 | B.1.160.23 | 0.004831 |
ORF1ab/nsp12 | 595 | Y595X | taT | taG | 1 | 1 | B.1.165 | 0.011905 |
ORF1ab/nsp12 | 595 | Y595del | TAT | --- | 1 | 1 | B.1.177.16 | 0.000664 |
ORF1ab/nsp12 | 595 | Y595del | TAT | --- | 1 | 1 | B.1.177.54 | 0.000606 |
ORF1ab/nsp12 | 595 | Y595Y | taT | taC | 1 | 1 | B.1.177.57 | 0.000281 |
ORF1ab/nsp12 | 595 | Y595del | TAT | --- | 1 | 1 | B.1.177.81 | 0.000189 |
ORF1ab/nsp12 | 595 | Y595D | TaT | GaC | 1 | 1 | B.1.2 | 0.000009 |
ORF1ab/nsp12 | 595 | Y595C | tAt | tGt | 1 | 1 | B.1.2 | 0.000009 |
ORF1ab/nsp12 | 595 | Y595X | taT | taA | 1 | 1 | B.1.2 | 0.000009 |
ORF1ab/nsp12 | 595 | Y595Y | taT | taC | 1 | 1 | B.1.329 | 0.000608 |
ORF1ab/nsp12 | 595 | Y595H | Tat | Cat | 1 | 1 | B.1.336 | 0.002439 |
ORF1ab/nsp12 | 595 | Y595X | taT | taA | 1 | 1 | B.1.350 | 0.002933 |
ORF1ab/nsp12 | 595 | Y595Y | taT | taC | 1 | 1 | B.1.351 | 0.00003 |
ORF1ab/nsp12 | 595 | Y595X | taT | taA | 1 | 1 | B.1.398 | 0.002976 |
ORF1ab/nsp12 | 595 | Y595Y | taT | taC | 1 | 1 | B.1.429 | 0.000024 |
ORF1ab/nsp12 | 595 | Y595S | tAt | tCt | 1 | 1 | B.1.462 | 0.007246 |
ORF1ab/nsp12 | 595 | Y595C | tAt | tGt | 1 | 1 | B.1.497 | 0.000315 |
ORF1ab/nsp12 | 595 | Y595X | taT | taA | 1 | 1 | B.1.576 | 0.000907 |
ORF1ab/nsp12 | 595 | Y595del1 | Tat | -at | 1 | 1 | B.1.596 | 0.000087 |
ORF1ab/nsp12 | 595 | Y595H | Tat | Cat | 1 | 1 | B.1.596 | 0.000087 |
ORF1ab/nsp12 | 595 | Y595Y | taT | taC | 1 | 1 | B.1.597 | 0.00463 |
ORF1ab/nsp12 | 595 | Y595del1 | Tat | -at | 1 | 1 | B.1.617.2 | 0.000004 |
ORF1ab/nsp12 | 595 | Y595H | Tat | Cat | 1 | 1 | D.3 | 0.005917 |
ORF1ab/nsp12 | 595 | Y595Y | taT | taC | 1 | 1 | P.1 | 0.000016 |
ORF1ab/nsp12 | 595 | Y595X | taT | taA | 1 | 1 | P.1 | 0.000016 |
ORF1ab/nsp12 | 595 | Y595del | 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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