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/nsp2 | 394 | S394S | S574S | syn | tcA | tcG | 5998 | 5993 | 0.999166 | 1985-1987 |
ORF1ab/nsp2 | 394 | S394S | S574S | syn | tcA | tcT | 5998 | 4 | 0.000666889 | 1985-1987 |
ORF1ab/nsp2 | 394 | S394S | S574S | syn | tcA | tcC | 5998 | 1 | 0.000166722 | 1985-1987 |
ORF1ab/nsp2 | 394 | S394A | S574A | nonsyn | Tca | Gca | 203 | 201 | 0.990148 | 1985-1987 |
ORF1ab/nsp2 | 394 | S394A | S574A | nonsyn | TcA | GcG | 203 | 2 | 0.00985222 | 1985-1987 |
ORF1ab/nsp2 | 394 | S394del | S574del | del | TCA | --- | 54 | 54 | 1 | 1985-1987 |
ORF1ab/nsp2 | 394 | S394X | S574X | nonsyn | tCa | tAa | 15 | 15 | 1 | 1985-1987 |
ORF1ab/nsp2 | 394 | S394L | S574L | nonsyn | tCa | tTa | 14 | 14 | 1 | 1985-1987 |
ORF1ab/nsp2 | 394 | S394T | S574T | nonsyn | Tca | Aca | 7 | 7 | 1 | 1985-1987 |
ORF1ab/nsp2 | 394 | S394P | S574P | nonsyn | Tca | Cca | 2 | 2 | 1 | 1985-1987 |
ORF1ab/nsp2 | 394 | S394F | S574F | nonsyn | tCA | tTT | 1 | 1 | 1 | 1985-1987 |
ORF1ab/nsp2 | 394 | S394del1 | S574del1 | del | tcA | tc- | 1 | 1 | 1 | 1985-1987 |
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/nsp2 | 394 | S394S | tcA | tcG | 5993 | 5998 | All | 0.001146 |
ORF1ab/nsp2 | 394 | S394S | tcA | tcT | 4 | 5998 | All | 0.000001 |
ORF1ab/nsp2 | 394 | S394S | tcA | tcC | 1 | 5998 | All | 0 |
ORF1ab/nsp2 | 394 | S394S | tcA | tcG | 4713 | 4713 | B.1.177.4 | 0.994724 |
ORF1ab/nsp2 | 394 | S394S | tcA | tcG | 739 | 739 | B.1.177 | 0.009731 |
ORF1ab/nsp2 | 394 | S394S | tcA | tcG | 220 | 220 | B.1.177.2 | 1 |
ORF1ab/nsp2 | 394 | S394A | Tca | Gca | 201 | 203 | All | 0.000038 |
ORF1ab/nsp2 | 394 | S394A | TcA | GcG | 2 | 203 | All | 0 |
ORF1ab/nsp2 | 394 | S394S | tcA | tcG | 119 | 119 | B.1.177.3 | 0.908397 |
ORF1ab/nsp2 | 394 | S394A | Tca | Gca | 109 | 109 | AY.4 | 0.00017 |
ORF1ab/nsp2 | 394 | S394del | TCA | --- | 54 | 54 | All | 0.00001 |
ORF1ab/nsp2 | 394 | S394A | Tca | Gca | 53 | 53 | B.1.258.11 | 0.021007 |
ORF1ab/nsp2 | 394 | S394S | tcA | tcG | 38 | 39 | AY.4 | 0.000059 |
ORF1ab/nsp2 | 394 | S394S | tcA | tcT | 1 | 39 | AY.4 | 0.000002 |
ORF1ab/nsp2 | 394 | S394S | tcA | tcG | 29 | 30 | B.1.1.7 | 0.000026 |
ORF1ab/nsp2 | 394 | S394S | tcA | tcT | 1 | 30 | B.1.1.7 | 0.000001 |
ORF1ab/nsp2 | 394 | S394S | tcA | tcG | 23 | 23 | AY.3 | 0.000229 |
ORF1ab/nsp2 | 394 | S394S | tcA | tcG | 22 | 23 | B.1 | 0.000202 |
ORF1ab/nsp2 | 394 | S394S | tcA | tcT | 1 | 23 | B.1 | 0.000009 |
ORF1ab/nsp2 | 394 | S394A | Tca | Gca | 21 | 21 | AY.43 | 0.000093 |
ORF1ab/nsp2 | 394 | S394X | tCa | tAa | 15 | 15 | All | 0.000003 |
ORF1ab/nsp2 | 394 | S394L | tCa | tTa | 14 | 14 | All | 0.000003 |
ORF1ab/nsp2 | 394 | S394del | TCA | --- | 10 | 10 | B.1.1.7 | 0.000009 |
ORF1ab/nsp2 | 394 | S394S | tcA | tcG | 9 | 9 | AY.43 | 0.00004 |
ORF1ab/nsp2 | 394 | S394T | Tca | Aca | 7 | 7 | All | 0.000001 |
ORF1ab/nsp2 | 394 | S394S | tcA | tcG | 7 | 7 | AY.120 | 0.00026 |
ORF1ab/nsp2 | 394 | S394X | tCa | tAa | 7 | 7 | B.1 | 0.000064 |
ORF1ab/nsp2 | 394 | S394S | tcA | tcG | 7 | 7 | B.1.1 | 0.000127 |
ORF1ab/nsp2 | 394 | S394S | tcA | tcG | 7 | 7 | B.1.1.519 | 0.000278 |
ORF1ab/nsp2 | 394 | S394S | tcA | tcG | 7 | 7 | B.1.177.35 | 0.004838 |
ORF1ab/nsp2 | 394 | S394S | tcA | tcG | 6 | 6 | B.1.603 | 0.06383 |
ORF1ab/nsp2 | 394 | S394A | Tca | Gca | 5 | 6 | B.1.617.2 | 0.000019 |
ORF1ab/nsp2 | 394 | S394A | TcA | GcG | 1 | 6 | B.1.617.2 | 0.000004 |
ORF1ab/nsp2 | 394 | S394del | TCA | --- | 5 | 5 | B.1 | 0.000046 |
ORF1ab/nsp2 | 394 | S394L | tCa | tTa | 5 | 5 | B.1.1.7 | 0.000004 |
ORF1ab/nsp2 | 394 | S394A | Tca | Gca | 5 | 5 | P.1 | 0.000079 |
ORF1ab/nsp2 | 394 | S394S | tcA | tcG | 4 | 4 | AY.103 | 0.000025 |
ORF1ab/nsp2 | 394 | S394T | Tca | Aca | 4 | 4 | B.1.1.7 | 0.000004 |
ORF1ab/nsp2 | 394 | S394L | tCa | tTa | 3 | 3 | B.1 | 0.000027 |
ORF1ab/nsp2 | 394 | S394del | TCA | --- | 3 | 3 | B.1.1.33 | 0.001263 |
ORF1ab/nsp2 | 394 | S394del | TCA | --- | 3 | 3 | B.1.1.348 | 0.002389 |
ORF1ab/nsp2 | 394 | S394P | Tca | Cca | 2 | 2 | All | 0 |
ORF1ab/nsp2 | 394 | S394S | tcA | tcG | 2 | 2 | AY.29 | 0.000032 |
ORF1ab/nsp2 | 394 | S394del | TCA | --- | 2 | 2 | AY.4 | 0.000003 |
ORF1ab/nsp2 | 394 | S394del | TCA | --- | 2 | 2 | AY.4.5 | 0.000215 |
ORF1ab/nsp2 | 394 | S394S | tcA | tcG | 2 | 2 | AY.44 | 0.000012 |
ORF1ab/nsp2 | 394 | S394S | tcA | tcG | 2 | 2 | AY.47 | 0.000062 |
ORF1ab/nsp2 | 394 | S394S | tcA | tcC | 1 | 2 | AY.5 | 0.000021 |
ORF1ab/nsp2 | 394 | S394S | tcA | tcG | 1 | 2 | AY.5 | 0.000021 |
ORF1ab/nsp2 | 394 | S394S | tcA | tcG | 2 | 2 | AY.6 | 0.000082 |
ORF1ab/nsp2 | 394 | S394X | tCa | tAa | 2 | 2 | B | 0.000256 |
ORF1ab/nsp2 | 394 | S394L | tCa | tTa | 2 | 2 | B.1.1 | 0.000036 |
ORF1ab/nsp2 | 394 | S394P | Tca | Cca | 2 | 2 | B.1.1.7 | 0.000002 |
ORF1ab/nsp2 | 394 | S394del | TCA | --- | 2 | 2 | B.1.177 | 0.000026 |
ORF1ab/nsp2 | 394 | S394S | tcA | tcG | 2 | 2 | B.1.177.56 | 0.001335 |
ORF1ab/nsp2 | 394 | S394S | tcA | tcG | 2 | 2 | B.1.177.7 | 0.00033 |
ORF1ab/nsp2 | 394 | S394S | tcA | tcG | 2 | 2 | B.1.36 | 0.000292 |
ORF1ab/nsp2 | 394 | S394del | TCA | --- | 2 | 2 | B.1.424 | 0.016129 |
ORF1ab/nsp2 | 394 | S394S | tcA | tcG | 2 | 2 | B.1.525 | 0.000226 |
ORF1ab/nsp2 | 394 | S394del | TCA | --- | 2 | 2 | N.6 | 0.014184 |
ORF1ab/nsp2 | 394 | S394S | tcA | tcG | 2 | 2 | P.1.15 | 0.000465 |
ORF1ab/nsp2 | 394 | S394del | TCA | --- | 2 | 2 | P.2 | 0.000373 |
ORF1ab/nsp2 | 394 | S394del | TCA | --- | 2 | 2 | Q.1 | 0.000253 |
ORF1ab/nsp2 | 394 | S394L | tCa | tTa | 1 | 1 | A | 0.000387 |
ORF1ab/nsp2 | 394 | S394X | tCa | tAa | 1 | 1 | A | 0.000387 |
ORF1ab/nsp2 | 394 | S394F | tCA | tTT | 1 | 1 | All | 0 |
ORF1ab/nsp2 | 394 | S394del1 | tcA | tc- | 1 | 1 | All | 0 |
ORF1ab/nsp2 | 394 | S394del | TCA | --- | 1 | 1 | AY.103 | 0.000006 |
ORF1ab/nsp2 | 394 | S394del | TCA | --- | 1 | 1 | AY.111 | 0.000183 |
ORF1ab/nsp2 | 394 | S394S | tcA | tcG | 1 | 1 | AY.117 | 0.000085 |
ORF1ab/nsp2 | 394 | S394S | tcA | tcG | 1 | 1 | AY.120.1 | 0.000321 |
ORF1ab/nsp2 | 394 | S394del | TCA | --- | 1 | 1 | AY.16.1 | 0.00047 |
ORF1ab/nsp2 | 394 | S394S | tcA | tcG | 1 | 1 | AY.25 | 0.000006 |
ORF1ab/nsp2 | 394 | S394del | TCA | --- | 1 | 1 | AY.25 | 0.000006 |
ORF1ab/nsp2 | 394 | S394A | Tca | Gca | 1 | 1 | AY.39 | 0.000025 |
ORF1ab/nsp2 | 394 | S394S | tcA | tcG | 1 | 1 | AY.4.2 | 0.000022 |
ORF1ab/nsp2 | 394 | S394X | tCa | tAa | 1 | 1 | AY.43 | 0.000004 |
ORF1ab/nsp2 | 394 | S394del1 | tcA | tc- | 1 | 1 | AY.44 | 0.000006 |
ORF1ab/nsp2 | 394 | S394S | tcA | tcG | 1 | 1 | AY.46 | 0.000104 |
ORF1ab/nsp2 | 394 | S394T | Tca | Aca | 1 | 1 | AY.47 | 0.000031 |
ORF1ab/nsp2 | 394 | S394A | Tca | Gca | 1 | 1 | AY.5 | 0.000021 |
ORF1ab/nsp2 | 394 | S394X | tCa | tAa | 1 | 1 | AY.52 | 0.000814 |
ORF1ab/nsp2 | 394 | S394del | TCA | --- | 1 | 1 | AY.54 | 0.000095 |
ORF1ab/nsp2 | 394 | S394A | Tca | Gca | 1 | 1 | AY.54 | 0.000095 |
ORF1ab/nsp2 | 394 | S394L | tCa | tTa | 1 | 1 | AY.65 | 0.000533 |
ORF1ab/nsp2 | 394 | S394S | tcA | tcG | 1 | 1 | AY.7.1 | 0.000113 |
ORF1ab/nsp2 | 394 | S394S | tcA | tcG | 1 | 1 | AY.74 | 0.000116 |
ORF1ab/nsp2 | 394 | S394S | tcA | tcG | 1 | 1 | AY.75 | 0.000056 |
ORF1ab/nsp2 | 394 | S394A | TcA | GcG | 1 | 1 | AY.75 | 0.000056 |
ORF1ab/nsp2 | 394 | S394L | tCa | tTa | 1 | 1 | AY.75 | 0.000056 |
ORF1ab/nsp2 | 394 | S394del | TCA | --- | 1 | 1 | AY.75.1 | 0.00018 |
ORF1ab/nsp2 | 394 | S394T | Tca | Aca | 1 | 1 | AY.9 | 0.000068 |
ORF1ab/nsp2 | 394 | S394del | TCA | --- | 1 | 1 | AY.9.2 | 0.000037 |
ORF1ab/nsp2 | 394 | S394S | tcA | tcT | 1 | 1 | AY.98 | 0.000079 |
ORF1ab/nsp2 | 394 | S394F | tCA | tTT | 1 | 1 | B.1 | 0.000009 |
ORF1ab/nsp2 | 394 | S394del | TCA | --- | 1 | 1 | B.1.1 | 0.000018 |
ORF1ab/nsp2 | 394 | S394A | Tca | Gca | 1 | 1 | B.1.1 | 0.000018 |
ORF1ab/nsp2 | 394 | S394S | tcA | tcG | 1 | 1 | B.1.1.214 | 0.000055 |
ORF1ab/nsp2 | 394 | S394S | tcA | tcG | 1 | 1 | B.1.1.28 | 0.000311 |
ORF1ab/nsp2 | 394 | S394S | tcA | tcG | 1 | 1 | B.1.1.315 | 0.008475 |
ORF1ab/nsp2 | 394 | S394A | Tca | Gca | 1 | 1 | B.1.1.412 | 0.007634 |
ORF1ab/nsp2 | 394 | S394del | TCA | --- | 1 | 1 | B.1.1.416 | 0.000905 |
ORF1ab/nsp2 | 394 | S394A | Tca | Gca | 1 | 1 | B.1.1.519 | 0.00004 |
ORF1ab/nsp2 | 394 | S394A | Tca | Gca | 1 | 1 | B.1.1.7 | 0.000001 |
ORF1ab/nsp2 | 394 | S394X | tCa | tAa | 1 | 1 | B.1.177 | 0.000013 |
ORF1ab/nsp2 | 394 | S394del | TCA | --- | 1 | 1 | B.1.177.12 | 0.000152 |
ORF1ab/nsp2 | 394 | S394del | TCA | --- | 1 | 1 | B.1.177.18 | 0.00116 |
ORF1ab/nsp2 | 394 | S394S | tcA | tcG | 1 | 1 | B.1.177.53 | 0.002392 |
ORF1ab/nsp2 | 394 | S394S | tcA | tcG | 1 | 1 | B.1.177.6 | 0.000977 |
ORF1ab/nsp2 | 394 | S394S | tcA | tcG | 1 | 1 | B.1.177.60 | 0.000218 |
ORF1ab/nsp2 | 394 | S394del | TCA | --- | 1 | 1 | B.1.179 | 0.003759 |
ORF1ab/nsp2 | 394 | S394L | tCa | tTa | 1 | 1 | B.1.2 | 0.000009 |
ORF1ab/nsp2 | 394 | S394A | Tca | Gca | 1 | 1 | B.1.221 | 0.000071 |
ORF1ab/nsp2 | 394 | S394del | TCA | --- | 1 | 1 | B.1.234 | 0.000132 |
ORF1ab/nsp2 | 394 | S394S | tcA | tcG | 1 | 1 | B.1.258 | 0.000067 |
ORF1ab/nsp2 | 394 | S394X | tCa | tAa | 1 | 1 | B.1.301 | 0.005917 |
ORF1ab/nsp2 | 394 | S394S | tcA | tcG | 1 | 1 | B.1.351 | 0.00003 |
ORF1ab/nsp2 | 394 | S394S | tcA | tcG | 1 | 1 | B.1.36.37 | 0.002778 |
ORF1ab/nsp2 | 394 | S394S | tcA | tcG | 1 | 1 | B.1.36.39 | 0.002217 |
ORF1ab/nsp2 | 394 | S394del | TCA | --- | 1 | 1 | B.1.429 | 0.000024 |
ORF1ab/nsp2 | 394 | S394del | TCA | --- | 1 | 1 | B.1.439 | 0.005917 |
ORF1ab/nsp2 | 394 | S394del | TCA | --- | 1 | 1 | B.1.561 | 0.000397 |
ORF1ab/nsp2 | 394 | S394S | tcA | tcG | 1 | 1 | B.1.575 | 0.000303 |
ORF1ab/nsp2 | 394 | S394T | Tca | Aca | 1 | 1 | B.1.617.2 | 0.000004 |
ORF1ab/nsp2 | 394 | S394del | TCA | --- | 1 | 1 | B.1.617.2 | 0.000004 |
ORF1ab/nsp2 | 394 | S394X | tCa | tAa | 1 | 1 | B.1.623 | 0.000536 |
ORF1ab/nsp2 | 394 | S394del | TCA | --- | 1 | 1 | B.57 | 0.015152 |
ORF1ab/nsp2 | 394 | S394S | tcA | tcG | 1 | 1 | C.16 | 0.00106 |
ORF1ab/nsp2 | 394 | S394S | tcA | tcG | 1 | 1 | C.40 | 0.027778 |
ORF1ab/nsp2 | 394 | S394S | tcA | tcG | 1 | 1 | D.2 | 0.000075 |
ORF1ab/nsp2 | 394 | S394S | tcA | tcG | 1 | 1 | P.1 | 0.000016 |
ORF1ab/nsp2 | 394 | S394del | TCA | --- | 1 | 1 | P.1 | 0.000016 |
ORF1ab/nsp2 | 394 | S394S | tcA | tcG | 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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