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 | 556 | T556T | T4948T | syn | acC | acT | 1865 | 1707 | 0.915281 | 15106-15108 |
ORF1ab/nsp12 | 556 | T556T | T4948T | syn | acC | acA | 1865 | 150 | 0.080429 | 15106-15108 |
ORF1ab/nsp12 | 556 | T556T | T4948T | syn | acC | acG | 1865 | 8 | 0.00428954 | 15106-15108 |
Details of the mutation T556T 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 | 556 | T556T | acC | acT | 1707 | 1865 | All | 0.000326 |
ORF1ab/nsp12 | 556 | T556T | acC | acA | 150 | 1865 | All | 0.000029 |
ORF1ab/nsp12 | 556 | T556T | acC | acG | 8 | 1865 | All | 0.000002 |
ORF1ab/nsp12 | 556 | T556T | acC | acT | 510 | 519 | AY.4 | 0.000794 |
ORF1ab/nsp12 | 556 | T556T | acC | acA | 9 | 519 | AY.4 | 0.000014 |
ORF1ab/nsp12 | 556 | T556T | acC | acT | 192 | 198 | B.1.1.7 | 0.000172 |
ORF1ab/nsp12 | 556 | T556T | acC | acA | 5 | 198 | B.1.1.7 | 0.000004 |
ORF1ab/nsp12 | 556 | T556T | acC | acG | 1 | 198 | B.1.1.7 | 0.000001 |
ORF1ab/nsp12 | 556 | T556T | acC | acT | 171 | 171 | B.1.503 | 0.425373 |
ORF1ab/nsp12 | 556 | T556T | acC | acT | 110 | 130 | B.1.429 | 0.002588 |
ORF1ab/nsp12 | 556 | T556T | acC | acA | 20 | 130 | B.1.429 | 0.000471 |
ORF1ab/nsp12 | 556 | T556T | acC | acT | 108 | 111 | AY.25 | 0.00065 |
ORF1ab/nsp12 | 556 | T556T | acC | acA | 3 | 111 | AY.25 | 0.000018 |
ORF1ab/nsp12 | 556 | T556T | acC | acT | 99 | 99 | B.1.1.222 | 0.020196 |
ORF1ab/nsp12 | 556 | T556T | acC | acT | 59 | 59 | AY.26 | 0.00167 |
ORF1ab/nsp12 | 556 | T556T | acC | acA | 50 | 50 | B.1.1.316 | 0.046253 |
ORF1ab/nsp12 | 556 | T556T | acC | acT | 42 | 47 | B.1 | 0.000385 |
ORF1ab/nsp12 | 556 | T556T | acC | acA | 5 | 47 | B.1 | 0.000046 |
ORF1ab/nsp12 | 556 | T556T | acC | acT | 24 | 41 | AY.103 | 0.000149 |
ORF1ab/nsp12 | 556 | T556T | acC | acA | 17 | 41 | AY.103 | 0.000106 |
ORF1ab/nsp12 | 556 | T556T | acC | acT | 40 | 40 | AY.5.4 | 0.011068 |
ORF1ab/nsp12 | 556 | T556T | acC | acT | 39 | 39 | B.1.1.519 | 0.001549 |
ORF1ab/nsp12 | 556 | T556T | acC | acT | 36 | 39 | B.1.617.2 | 0.000136 |
ORF1ab/nsp12 | 556 | T556T | acC | acA | 3 | 39 | B.1.617.2 | 0.000011 |
ORF1ab/nsp12 | 556 | T556T | acC | acT | 31 | 31 | AY.43 | 0.000137 |
ORF1ab/nsp12 | 556 | T556T | acC | acT | 24 | 28 | AY.44 | 0.000146 |
ORF1ab/nsp12 | 556 | T556T | acC | acA | 4 | 28 | AY.44 | 0.000024 |
ORF1ab/nsp12 | 556 | T556T | acC | acT | 22 | 22 | N.7 | 0.647059 |
ORF1ab/nsp12 | 556 | T556T | acC | acA | 10 | 18 | B.1.177 | 0.000132 |
ORF1ab/nsp12 | 556 | T556T | acC | acT | 8 | 18 | B.1.177 | 0.000105 |
ORF1ab/nsp12 | 556 | T556T | acC | acT | 13 | 13 | AY.29 | 0.000205 |
ORF1ab/nsp12 | 556 | T556T | acC | acT | 13 | 13 | B.1.631 | 0.043771 |
ORF1ab/nsp12 | 556 | T556T | acC | acT | 9 | 12 | AY.39 | 0.000222 |
ORF1ab/nsp12 | 556 | T556T | acC | acA | 3 | 12 | AY.39 | 0.000074 |
ORF1ab/nsp12 | 556 | T556T | acC | acT | 11 | 12 | P.1 | 0.000173 |
ORF1ab/nsp12 | 556 | T556T | acC | acA | 1 | 12 | P.1 | 0.000016 |
ORF1ab/nsp12 | 556 | T556T | acC | acT | 7 | 7 | AY.37 | 0.002212 |
ORF1ab/nsp12 | 556 | T556T | acC | acT | 5 | 7 | B.1.1 | 0.000091 |
ORF1ab/nsp12 | 556 | T556T | acC | acA | 2 | 7 | B.1.1 | 0.000036 |
ORF1ab/nsp12 | 556 | T556T | acC | acT | 6 | 7 | B.1.160 | 0.000187 |
ORF1ab/nsp12 | 556 | T556T | acC | acA | 1 | 7 | B.1.160 | 0.000031 |
ORF1ab/nsp12 | 556 | T556T | acC | acG | 6 | 6 | AY.45 | 0.00073 |
ORF1ab/nsp12 | 556 | T556T | acC | acT | 6 | 6 | B.1.1.33 | 0.002525 |
ORF1ab/nsp12 | 556 | T556T | acC | acT | 6 | 6 | P.1.14 | 0.000287 |
ORF1ab/nsp12 | 556 | T556T | acC | acT | 5 | 5 | B.1.2 | 0.000044 |
ORF1ab/nsp12 | 556 | T556T | acC | acT | 4 | 4 | B.1.214.2 | 0.002398 |
ORF1ab/nsp12 | 556 | T556T | acC | acT | 4 | 4 | B.1.36 | 0.000584 |
ORF1ab/nsp12 | 556 | T556T | acC | acT | 4 | 4 | B.1.621.1 | 0.002023 |
ORF1ab/nsp12 | 556 | T556T | acC | acT | 4 | 4 | B.1.635 | 0.070175 |
ORF1ab/nsp12 | 556 | T556T | acC | acT | 2 | 3 | AY.120 | 0.000074 |
ORF1ab/nsp12 | 556 | T556T | acC | acA | 1 | 3 | AY.120 | 0.000037 |
ORF1ab/nsp12 | 556 | T556T | acC | acT | 3 | 3 | AY.29.1 | 0.000662 |
ORF1ab/nsp12 | 556 | T556T | acC | acT | 3 | 3 | AY.3 | 0.00003 |
ORF1ab/nsp12 | 556 | T556T | acC | acT | 3 | 3 | AY.33 | 0.0002 |
ORF1ab/nsp12 | 556 | T556T | acC | acT | 3 | 3 | AY.62 | 0.001307 |
ORF1ab/nsp12 | 556 | T556T | acC | acT | 3 | 3 | B.1.427 | 0.000151 |
ORF1ab/nsp12 | 556 | T556T | acC | acT | 3 | 3 | B.1.564 | 0.001278 |
ORF1ab/nsp12 | 556 | T556T | acC | acT | 3 | 3 | P.1.1 | 0.000953 |
ORF1ab/nsp12 | 556 | T556T | acC | acT | 1 | 2 | AY.119 | 0.000035 |
ORF1ab/nsp12 | 556 | T556T | acC | acA | 1 | 2 | AY.119 | 0.000035 |
ORF1ab/nsp12 | 556 | T556T | acC | acT | 1 | 2 | AY.20 | 0.000039 |
ORF1ab/nsp12 | 556 | T556T | acC | acA | 1 | 2 | AY.20 | 0.000039 |
ORF1ab/nsp12 | 556 | T556T | acC | acT | 2 | 2 | AY.23 | 0.000139 |
ORF1ab/nsp12 | 556 | T556T | acC | acA | 2 | 2 | AY.34 | 0.000194 |
ORF1ab/nsp12 | 556 | T556T | acC | acT | 1 | 2 | AY.42 | 0.00004 |
ORF1ab/nsp12 | 556 | T556T | acC | acA | 1 | 2 | AY.42 | 0.00004 |
ORF1ab/nsp12 | 556 | T556T | acC | acT | 2 | 2 | AY.46.6 | 0.000144 |
ORF1ab/nsp12 | 556 | T556T | acC | acT | 2 | 2 | AY.9 | 0.000135 |
ORF1ab/nsp12 | 556 | T556T | acC | acT | 2 | 2 | B.1.1.158 | 0.02439 |
ORF1ab/nsp12 | 556 | T556T | acC | acA | 1 | 2 | B.1.1.39 | 0.00051 |
ORF1ab/nsp12 | 556 | T556T | acC | acT | 1 | 2 | B.1.1.39 | 0.00051 |
ORF1ab/nsp12 | 556 | T556T | acC | acT | 2 | 2 | B.1.1.434 | 0.000697 |
ORF1ab/nsp12 | 556 | T556T | acC | acT | 2 | 2 | B.1.234 | 0.000264 |
ORF1ab/nsp12 | 556 | T556T | acC | acT | 2 | 2 | B.1.351 | 0.000059 |
ORF1ab/nsp12 | 556 | T556T | acC | acA | 2 | 2 | B.1.369 | 0.00057 |
ORF1ab/nsp12 | 556 | T556T | acC | acT | 2 | 2 | B.1.526 | 0.000047 |
ORF1ab/nsp12 | 556 | T556T | acC | acT | 2 | 2 | B.1.546 | 0.007407 |
ORF1ab/nsp12 | 556 | T556T | acC | acT | 2 | 2 | B.1.621 | 0.000177 |
ORF1ab/nsp12 | 556 | T556T | acC | acT | 2 | 2 | Q.2 | 0.001227 |
ORF1ab/nsp12 | 556 | T556T | acC | acA | 1 | 1 | 0.055556 | |
ORF1ab/nsp12 | 556 | T556T | acC | acT | 1 | 1 | A | 0.000387 |
ORF1ab/nsp12 | 556 | T556T | acC | acT | 1 | 1 | A.11 | 0.058824 |
ORF1ab/nsp12 | 556 | T556T | acC | acT | 1 | 1 | AY.102 | 0.000027 |
ORF1ab/nsp12 | 556 | T556T | acC | acT | 1 | 1 | AY.117 | 0.000085 |
ORF1ab/nsp12 | 556 | T556T | acC | acT | 1 | 1 | AY.14 | 0.000088 |
ORF1ab/nsp12 | 556 | T556T | acC | acT | 1 | 1 | AY.2 | 0.000356 |
ORF1ab/nsp12 | 556 | T556T | acC | acT | 1 | 1 | AY.4.2 | 0.000022 |
ORF1ab/nsp12 | 556 | T556T | acC | acT | 1 | 1 | AY.46 | 0.000104 |
ORF1ab/nsp12 | 556 | T556T | acC | acT | 1 | 1 | AY.46.2 | 0.000635 |
ORF1ab/nsp12 | 556 | T556T | acC | acT | 1 | 1 | AY.47 | 0.000031 |
ORF1ab/nsp12 | 556 | T556T | acC | acA | 1 | 1 | AY.5.3 | 0.000337 |
ORF1ab/nsp12 | 556 | T556T | acC | acT | 1 | 1 | AY.54 | 0.000095 |
ORF1ab/nsp12 | 556 | T556T | acC | acT | 1 | 1 | AY.85 | 0.000427 |
ORF1ab/nsp12 | 556 | T556T | acC | acT | 1 | 1 | AY.9.2 | 0.000037 |
ORF1ab/nsp12 | 556 | T556T | acC | acT | 1 | 1 | AY.99 | 0.001049 |
ORF1ab/nsp12 | 556 | T556T | acC | acT | 1 | 1 | AY.99.2 | 0.000092 |
ORF1ab/nsp12 | 556 | T556T | acC | acT | 1 | 1 | AZ.4 | 0.003356 |
ORF1ab/nsp12 | 556 | T556T | acC | acT | 1 | 1 | B.1.1.129 | 0.009174 |
ORF1ab/nsp12 | 556 | T556T | acC | acA | 1 | 1 | B.1.1.25 | 0.000569 |
ORF1ab/nsp12 | 556 | T556T | acC | acT | 1 | 1 | B.1.1.28 | 0.000311 |
ORF1ab/nsp12 | 556 | T556T | acC | acT | 1 | 1 | B.1.1.298 | 0.000862 |
ORF1ab/nsp12 | 556 | T556T | acC | acT | 1 | 1 | B.1.1.306 | 0.000438 |
ORF1ab/nsp12 | 556 | T556T | acC | acT | 1 | 1 | B.1.1.385 | 0.004464 |
ORF1ab/nsp12 | 556 | T556T | acC | acT | 1 | 1 | B.1.1.397 | 0.002252 |
ORF1ab/nsp12 | 556 | T556T | acC | acA | 1 | 1 | B.1.1.416 | 0.000905 |
ORF1ab/nsp12 | 556 | T556T | acC | acT | 1 | 1 | B.1.1.70 | 0.000341 |
ORF1ab/nsp12 | 556 | T556T | acC | acT | 1 | 1 | B.1.177.23 | 0.003236 |
ORF1ab/nsp12 | 556 | T556T | acC | acT | 1 | 1 | B.1.177.4 | 0.000211 |
ORF1ab/nsp12 | 556 | T556T | acC | acT | 1 | 1 | B.1.177.53 | 0.002392 |
ORF1ab/nsp12 | 556 | T556T | acC | acA | 1 | 1 | B.1.177.60 | 0.000218 |
ORF1ab/nsp12 | 556 | T556T | acC | acT | 1 | 1 | B.1.240 | 0.000216 |
ORF1ab/nsp12 | 556 | T556T | acC | acT | 1 | 1 | B.1.258 | 0.000067 |
ORF1ab/nsp12 | 556 | T556T | acC | acT | 1 | 1 | B.1.258.21 | 0.007752 |
ORF1ab/nsp12 | 556 | T556T | acC | acA | 1 | 1 | B.1.260 | 0.003344 |
ORF1ab/nsp12 | 556 | T556T | acC | acT | 1 | 1 | B.1.311 | 0.000275 |
ORF1ab/nsp12 | 556 | T556T | acC | acT | 1 | 1 | B.1.36.29 | 0.000517 |
ORF1ab/nsp12 | 556 | T556T | acC | acT | 1 | 1 | B.1.36.38 | 0.001642 |
ORF1ab/nsp12 | 556 | T556T | acC | acT | 1 | 1 | B.1.367 | 0.000792 |
ORF1ab/nsp12 | 556 | T556T | acC | acG | 1 | 1 | B.1.416 | 0.001269 |
ORF1ab/nsp12 | 556 | T556T | acC | acT | 1 | 1 | B.1.438.1 | 0.000107 |
ORF1ab/nsp12 | 556 | T556T | acC | acT | 1 | 1 | B.1.466.2 | 0.000391 |
ORF1ab/nsp12 | 556 | T556T | acC | acA | 1 | 1 | B.1.468 | 0.005714 |
ORF1ab/nsp12 | 556 | T556T | acC | acT | 1 | 1 | B.1.521 | 0.004975 |
ORF1ab/nsp12 | 556 | T556T | acC | acT | 1 | 1 | B.1.597 | 0.00463 |
ORF1ab/nsp12 | 556 | T556T | acC | acT | 1 | 1 | B.1.617.1 | 0.000129 |
ORF1ab/nsp12 | 556 | T556T | acC | acT | 1 | 1 | B.3 | 0.000831 |
ORF1ab/nsp12 | 556 | T556T | acC | acT | 1 | 1 | C.1 | 0.002392 |
ORF1ab/nsp12 | 556 | T556T | acC | acT | 1 | 1 | C.36 | 0.000911 |
ORF1ab/nsp12 | 556 | T556T | acC | acT | 1 | 1 | D.2 | 0.000075 |
ORF1ab/nsp12 | 556 | T556T | acC | acA | 1 | 1 | P.1.12 | 0.000484 |
ORF1ab/nsp12 | 556 | T556T | acC | acT | 1 | 1 | P.1.15 | 0.000232 |
ORF1ab/nsp12 | 556 | T556T | acC | acT | 1 | 1 | P.1.8 | 0.004785 |
ORF1ab/nsp12 | 556 | T556T | acC | acT | 1 | 1 | Q.8 | 0.000165 |
ORF1ab/nsp12 | 556 | T556T | acC | acT | 1 | 1 | R.1 | 0.00009 |
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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