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 | 39 | L39L | L219L | syn | ctG | ctA | 11141 | 2555 | 0.229333 | 920-922 |
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 | 39 | L39L | ctG | ctA | 2555 | 11141 | All | 0.000489 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctA | 75 | 1898 | B.1.1.7 | 0.000067 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctA | 1305 | 1305 | B.1.36.27 | 0.996183 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctA | 99 | 627 | AY.4 | 0.000154 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctA | 23 | 418 | AY.44 | 0.00014 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctA | 108 | 411 | B.1.617.2 | 0.000407 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctA | 14 | 403 | B.1.429 | 0.000329 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctA | 312 | 323 | B.1.36 | 0.045521 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctA | 18 | 318 | AY.103 | 0.000112 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctA | 45 | 266 | P.1 | 0.000709 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctA | 1 | 248 | B.1.258 | 0.000067 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctA | 16 | 228 | B.1.2 | 0.000141 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctA | 11 | 212 | B.1.177 | 0.000145 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctA | 20 | 179 | B.1 | 0.000183 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctA | 3 | 141 | AY.3 | 0.00003 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctA | 2 | 117 | B.1.637 | 0.000146 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctA | 8 | 115 | AY.43 | 0.000035 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctA | 1 | 114 | B.1.596 | 0.000087 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctA | 19 | 102 | B.1.1 | 0.000345 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctA | 1 | 71 | AY.20 | 0.000039 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctA | 62 | 66 | B.1.1.214 | 0.003438 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctA | 1 | 65 | B.1.609 | 0.000479 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctA | 62 | 62 | A | 0.023994 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctA | 1 | 55 | AY.39 | 0.000025 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctA | 55 | 55 | AY.7.1 | 0.006199 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctA | 12 | 54 | AY.39.1 | 0.000475 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctA | 5 | 51 | AY.25 | 0.00003 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctA | 4 | 50 | B.1.526 | 0.000094 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctA | 3 | 49 | AY.102 | 0.00008 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctA | 18 | 49 | AY.99.2 | 0.001659 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctA | 2 | 48 | AY.47 | 0.000062 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctA | 3 | 44 | B.1.621 | 0.000266 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctA | 1 | 39 | AY.5 | 0.000021 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctA | 25 | 38 | AY.100 | 0.00115 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctA | 32 | 34 | AY.9.1 | 0.002679 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctA | 28 | 33 | AY.29 | 0.000442 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctA | 2 | 33 | B.1.351 | 0.000059 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctA | 1 | 30 | AY.61 | 0.000105 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctA | 1 | 29 | AY.33 | 0.000067 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctA | 13 | 26 | B.1.1.519 | 0.000516 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctA | 8 | 26 | B.1.427 | 0.000404 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctA | 18 | 22 | AY.121 | 0.002436 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctA | 3 | 21 | AY.4.2 | 0.000065 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctA | 3 | 16 | B.1.1.28 | 0.000934 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctA | 1 | 15 | B.1.1.317 | 0.000412 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctA | 12 | 13 | AY.14 | 0.001056 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctA | 3 | 12 | AY.9.2 | 0.00011 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctA | 5 | 11 | AY.42 | 0.000201 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctA | 1 | 11 | C.37 | 0.000116 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctA | 2 | 9 | AY.29.1 | 0.000441 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctA | 7 | 9 | B.1.177.44 | 0.003633 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctA | 8 | 9 | B.1.470 | 0.011236 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctA | 1 | 8 | AY.12 | 0.000316 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctA | 1 | 7 | AY.119 | 0.000035 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctA | 2 | 7 | AY.34 | 0.000194 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctA | 1 | 7 | AY.46 | 0.000104 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctA | 1 | 7 | AY.5.4 | 0.000277 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctA | 1 | 7 | AY.6 | 0.000041 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctA | 1 | 6 | AY.118 | 0.000063 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctA | 6 | 6 | B.1.468 | 0.034286 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctA | 1 | 5 | AY.117 | 0.000085 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctA | 1 | 5 | B.1.1.25 | 0.000569 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctA | 1 | 5 | B.1.177.7 | 0.000165 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctA | 1 | 5 | C.36 | 0.000911 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctA | 1 | 4 | AY.24 | 0.000431 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctA | 4 | 4 | AY.69 | 0.000747 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctA | 1 | 4 | AY.77 | 0.001127 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctA | 2 | 4 | B.1.234 | 0.000264 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctA | 1 | 4 | P.2 | 0.000187 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctA | 1 | 3 | AY.109 | 0.00074 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctA | 1 | 3 | AY.114 | 0.000231 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctA | 1 | 3 | AY.13 | 0.000161 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctA | 2 | 3 | AY.98 | 0.000158 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctA | 2 | 3 | B.1.1.33 | 0.000842 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctA | 3 | 3 | B.1.260 | 0.010033 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctA | 1 | 3 | B.1.595 | 0.000261 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctA | 2 | 2 | AY.79 | 0.002421 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctA | 2 | 2 | AY.80 | 0.002257 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctA | 1 | 2 | AY.84 | 0.000437 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctA | 2 | 2 | B.1.142 | 0.005797 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctA | 2 | 2 | B.1.36.16 | 0.002849 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctA | 2 | 2 | B.1.466 | 0.046512 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctA | 1 | 2 | B.1.480 | 0.002488 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctA | 1 | 1 | A.28 | 0.002646 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctA | 1 | 1 | AY.1 | 0.000396 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctA | 1 | 1 | AY.32 | 0.000532 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctA | 1 | 1 | AY.54 | 0.000095 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctA | 1 | 1 | B.1.1.286 | 0.002899 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctA | 1 | 1 | B.1.1.318 | 0.000302 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctA | 1 | 1 | B.1.160.23 | 0.004831 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctA | 1 | 1 | B.1.177.15 | 0.000631 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctA | 1 | 1 | B.1.177.65 | 0.000665 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctA | 1 | 1 | B.1.190 | 0.01 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctA | 1 | 1 | B.1.22 | 0.001318 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctA | 1 | 1 | B.1.332 | 0.003497 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctA | 1 | 1 | B.1.36.22 | 0.001208 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctA | 1 | 1 | B.1.36.34 | 0.021277 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctA | 1 | 1 | B.1.408 | 0.00369 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctA | 1 | 1 | B.1.416 | 0.001269 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctA | 1 | 1 | B.1.456 | 0.003268 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctA | 1 | 1 | B.1.546 | 0.003704 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctA | 1 | 1 | B.1.588 | 0.00091 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctA | 1 | 1 | B.1.590 | 0.004545 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctA | 1 | 1 | C.26 | 0.007353 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctA | 1 | 1 | P.1.12 | 0.000484 |
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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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