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 | 1 | A1A | A181A | syn | gcA | gcT | 1382 | 743 | 0.537627 | 806-808 |
ORF1ab/nsp2 | 1 | A1A | A181A | syn | gcA | gcG | 1382 | 618 | 0.447178 | 806-808 |
ORF1ab/nsp2 | 1 | A1A | A181A | syn | gcA | gcC | 1382 | 21 | 0.0151954 | 806-808 |
Details of the mutation A1A 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 | 1 | A1A | gcA | gcT | 743 | 1382 | All | 0.000142 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcG | 618 | 1382 | All | 0.000118 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcC | 21 | 1382 | All | 0.000004 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcT | 537 | 543 | AY.25 | 0.00323 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcG | 6 | 543 | AY.25 | 0.000036 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcG | 194 | 228 | B.1.1.7 | 0.000174 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcT | 31 | 228 | B.1.1.7 | 0.000028 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcC | 3 | 228 | B.1.1.7 | 0.000003 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcG | 66 | 66 | AY.33 | 0.004407 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcG | 28 | 55 | AY.4 | 0.000044 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcT | 27 | 55 | AY.4 | 0.000042 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcG | 38 | 38 | B.1.517 | 0.016225 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcG | 26 | 32 | AY.103 | 0.000161 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcT | 6 | 32 | AY.103 | 0.000037 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcG | 30 | 30 | AY.118 | 0.001879 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcT | 12 | 26 | B.1.617.2 | 0.000045 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcG | 11 | 26 | B.1.617.2 | 0.000041 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcC | 3 | 26 | B.1.617.2 | 0.000011 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcG | 12 | 24 | AY.3 | 0.000119 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcT | 11 | 24 | AY.3 | 0.000109 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcC | 1 | 24 | AY.3 | 0.00001 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcG | 23 | 24 | B.1.525 | 0.002603 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcC | 1 | 24 | B.1.525 | 0.000113 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcT | 10 | 19 | AD.2 | 0.00219 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcG | 9 | 19 | AD.2 | 0.001971 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcG | 17 | 17 | B.1.351.2 | 0.005144 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcT | 13 | 16 | B.1 | 0.000119 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcG | 3 | 16 | B.1 | 0.000027 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcG | 13 | 13 | AY.121 | 0.001759 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcT | 13 | 13 | B.1.134 | 0.071038 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcC | 6 | 12 | AY.29 | 0.000095 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcG | 6 | 12 | AY.29 | 0.000095 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcG | 8 | 11 | AY.102 | 0.000212 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcT | 2 | 11 | AY.102 | 0.000053 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcC | 1 | 11 | AY.102 | 0.000027 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcG | 8 | 11 | AY.43 | 0.000035 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcT | 2 | 11 | AY.43 | 0.000009 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcC | 1 | 11 | AY.43 | 0.000004 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcT | 8 | 11 | B.1.177 | 0.000105 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcG | 3 | 11 | B.1.177 | 0.00004 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcT | 6 | 11 | B.1.2 | 0.000053 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcG | 4 | 11 | B.1.2 | 0.000035 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcC | 1 | 11 | B.1.2 | 0.000009 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcG | 10 | 10 | B.1.177.9 | 0.013316 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcG | 8 | 9 | AY.45 | 0.000973 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcT | 1 | 9 | AY.45 | 0.000122 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcG | 6 | 7 | AY.44 | 0.000037 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcT | 1 | 7 | AY.44 | 0.000006 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcT | 5 | 6 | AY.113 | 0.000712 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcC | 1 | 6 | AY.113 | 0.000142 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcG | 6 | 6 | AY.119 | 0.000212 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcG | 6 | 6 | AY.81 | 0.011952 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcT | 4 | 6 | B.1.1 | 0.000073 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcG | 2 | 6 | B.1.1 | 0.000036 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcG | 5 | 6 | B.1.221 | 0.000355 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcT | 1 | 6 | B.1.221 | 0.000071 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcG | 4 | 5 | AY.100 | 0.000184 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcT | 1 | 5 | AY.100 | 0.000046 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcT | 5 | 5 | B.1.177.21 | 0.000382 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcT | 5 | 5 | B.1.596 | 0.000436 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcG | 3 | 4 | AY.39 | 0.000074 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcC | 1 | 4 | AY.39 | 0.000025 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcT | 4 | 4 | AY.75 | 0.000224 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcT | 4 | 4 | Q.3 | 0.00058 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcG | 2 | 3 | AY.23 | 0.000139 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcT | 1 | 3 | AY.23 | 0.00007 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcG | 2 | 3 | AY.3.1 | 0.000171 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcT | 1 | 3 | AY.3.1 | 0.000085 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcT | 3 | 3 | AY.47 | 0.000093 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcT | 3 | 3 | B.1.1.279 | 0.003363 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcG | 3 | 3 | B.1.1.28 | 0.000934 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcG | 3 | 3 | B.1.1.306 | 0.001315 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcG | 3 | 3 | B.1.1.369 | 0.001339 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcG | 3 | 3 | B.1.243 | 0.000209 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcG | 3 | 3 | B.1.336 | 0.007317 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcT | 2 | 2 | A | 0.000774 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcG | 2 | 2 | AY.108 | 0.002205 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcG | 2 | 2 | AY.20 | 0.000078 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcG | 2 | 2 | AY.4.2 | 0.000043 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcG | 1 | 2 | AY.5 | 0.000021 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcT | 1 | 2 | AY.5 | 0.000021 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcG | 2 | 2 | AY.9 | 0.000135 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcG | 1 | 2 | AY.98.1 | 0.000048 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcT | 1 | 2 | AY.98.1 | 0.000048 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcG | 2 | 2 | B.1.1.189 | 0.003026 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcT | 2 | 2 | B.1.1.33 | 0.000842 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcG | 2 | 2 | B.1.1.519 | 0.000079 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcG | 2 | 2 | B.1.177.60 | 0.000437 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcT | 2 | 2 | B.1.369 | 0.00057 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcG | 2 | 2 | B.1.429 | 0.000047 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcG | 1 | 2 | P.1.7 | 0.000319 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcT | 1 | 2 | P.1.7 | 0.000319 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcG | 2 | 2 | P.3 | 0.00319 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcT | 2 | 2 | R.1 | 0.00018 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcC | 1 | 1 | 0.055556 | |
ORF1ab/nsp2 | 1 | A1A | gcA | gcT | 1 | 1 | AY.11 | 0.001339 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcG | 1 | 1 | AY.111 | 0.000183 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcT | 1 | 1 | AY.116 | 0.000287 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcT | 1 | 1 | AY.120 | 0.000037 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcG | 1 | 1 | AY.14 | 0.000088 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcT | 1 | 1 | AY.26 | 0.000028 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcG | 1 | 1 | AY.28 | 0.00189 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcG | 1 | 1 | AY.4.1 | 0.000737 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcG | 1 | 1 | AY.42 | 0.00004 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcT | 1 | 1 | AY.46 | 0.000104 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcT | 1 | 1 | AY.46.3 | 0.000934 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcT | 1 | 1 | AY.46.4 | 0.000165 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcG | 1 | 1 | AY.46.5 | 0.000198 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcT | 1 | 1 | AY.46.6 | 0.000072 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcT | 1 | 1 | AY.48 | 0.000465 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcG | 1 | 1 | AY.5.3 | 0.000337 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcG | 1 | 1 | AY.6 | 0.000041 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcG | 1 | 1 | AY.62 | 0.000436 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcG | 1 | 1 | AY.76 | 0.004831 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcG | 1 | 1 | AY.95 | 0.000761 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcC | 1 | 1 | B.1.1.257 | 0.009709 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcG | 1 | 1 | B.1.1.317 | 0.000412 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcG | 1 | 1 | B.1.1.348 | 0.000796 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcT | 1 | 1 | B.1.1.420 | 0.001006 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcT | 1 | 1 | B.1.177.83 | 0.001481 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcT | 1 | 1 | B.1.234 | 0.000132 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcT | 1 | 1 | B.1.265 | 0.001271 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcG | 1 | 1 | B.1.36.29 | 0.000517 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcG | 1 | 1 | B.1.36.7 | 0.004 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcG | 1 | 1 | B.1.375 | 0.00082 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcT | 1 | 1 | B.1.495 | 0.009091 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcG | 1 | 1 | B.1.609 | 0.000479 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcG | 1 | 1 | B.1.636 | 0.006711 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcG | 1 | 1 | B.1.83 | 0.015385 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcT | 1 | 1 | B.23 | 0.002924 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcG | 1 | 1 | C.37 | 0.000116 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcG | 1 | 1 | P.1.12 | 0.000484 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcG | 1 | 1 | P.2 | 0.000187 |
ORF1ab/nsp2 | 1 | A1A | gcA | gcG | 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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