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 |
N | 314 | F314F | syn | ttC | ttT | 1479 | 1479 | 1 | 29213-29215 | |
N | 314 | F314L | nonsyn | ttC | ttA | 75 | 63 | 0.84 | 29213-29215 | |
N | 314 | F314L | nonsyn | Ttc | Ctc | 75 | 8 | 0.106667 | 29213-29215 | |
N | 314 | F314L | nonsyn | ttC | ttG | 75 | 4 | 0.0533333 | 29213-29215 | |
N | 314 | F314del | del | TTC | --- | 36 | 36 | 1 | 29213-29215 | |
N | 314 | F314S | nonsyn | tTc | tCc | 6 | 6 | 1 | 29213-29215 | |
N | 314 | F314del1 | del | ttC | tt- | 4 | 4 | 1 | 29213-29215 | |
N | 314 | F314V | nonsyn | Ttc | Gtc | 4 | 4 | 1 | 29213-29215 | |
N | 314 | F314C | nonsyn | tTc | tGc | 2 | 2 | 1 | 29213-29215 | |
N | 314 | F314I | nonsyn | Ttc | Atc | 2 | 2 | 1 | 29213-29215 | |
N | 314 | F314Y | nonsyn | tTc | tAc | 2 | 2 | 1 | 29213-29215 | |
N | 314 | F314W | nonsyn | tTC | tGG | 1 | 1 | 1 | 29213-29215 | |
N | 314 | F314X | nonsyn | tTC | tAA | 1 | 1 | 1 | 29213-29215 |
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 |
N | 314 | F314F | ttC | ttT | 1479 | 1479 | All | 0.000283 |
N | 314 | F314F | ttC | ttT | 307 | 307 | B.1.1.7 | 0.000275 |
N | 314 | F314F | ttC | ttT | 219 | 219 | B.1.617.2 | 0.000825 |
N | 314 | F314F | ttC | ttT | 203 | 203 | AE.8 | 0.099267 |
N | 314 | F314F | ttC | ttT | 86 | 86 | B.1.177.67 | 0.656489 |
N | 314 | F314L | ttC | ttA | 63 | 75 | All | 0.000012 |
N | 314 | F314L | Ttc | Ctc | 8 | 75 | All | 0.000002 |
N | 314 | F314L | ttC | ttG | 4 | 75 | All | 0.000001 |
N | 314 | F314F | ttC | ttT | 65 | 65 | B.1.471 | 0.177596 |
N | 314 | F314F | ttC | ttT | 54 | 54 | AY.92 | 0.015513 |
N | 314 | F314F | ttC | ttT | 50 | 50 | AY.13 | 0.008049 |
N | 314 | F314F | ttC | ttT | 45 | 45 | AY.22 | 0.094142 |
N | 314 | F314F | ttC | ttT | 40 | 40 | P.1 | 0.00063 |
N | 314 | F314F | ttC | ttT | 37 | 37 | AY.25 | 0.000223 |
N | 314 | F314F | ttC | ttT | 37 | 37 | B.1.2 | 0.000326 |
N | 314 | F314del | TTC | --- | 36 | 36 | All | 0.000007 |
N | 314 | F314F | ttC | ttT | 36 | 36 | AY.98 | 0.002844 |
N | 314 | F314F | ttC | ttT | 33 | 33 | B.1.1.421 | 1 |
N | 314 | F314L | ttC | ttA | 25 | 25 | AY.4 | 0.000039 |
N | 314 | F314F | ttC | ttT | 21 | 21 | B.1.526 | 0.000494 |
N | 314 | F314F | ttC | ttT | 18 | 18 | AY.4 | 0.000028 |
N | 314 | F314L | ttC | ttA | 18 | 18 | AY.4.5 | 0.001935 |
N | 314 | F314F | ttC | ttT | 17 | 17 | AY.43 | 0.000075 |
N | 314 | F314F | ttC | ttT | 14 | 14 | B.1.36.18 | 0.005882 |
N | 314 | F314F | ttC | ttT | 12 | 12 | B.1 | 0.00011 |
N | 314 | F314F | ttC | ttT | 11 | 11 | AY.39 | 0.000272 |
N | 314 | F314F | ttC | ttT | 11 | 11 | AY.44 | 0.000067 |
N | 314 | F314F | ttC | ttT | 10 | 10 | AY.23 | 0.000697 |
N | 314 | F314F | ttC | ttT | 9 | 9 | AY.16.1 | 0.004229 |
N | 314 | F314F | ttC | ttT | 8 | 8 | P.1.14 | 0.000382 |
N | 314 | F314F | ttC | ttT | 7 | 7 | B.1.396 | 0.00494 |
N | 314 | F314S | tTc | tCc | 6 | 6 | All | 0.000001 |
N | 314 | F314F | ttC | ttT | 6 | 6 | AY.48 | 0.002791 |
N | 314 | F314F | ttC | ttT | 6 | 6 | AY.98.1 | 0.000291 |
N | 314 | F314F | ttC | ttT | 6 | 6 | B.1.1 | 0.000109 |
N | 314 | F314L | ttC | ttA | 5 | 5 | AY.9 | 0.000338 |
N | 314 | F314del | TTC | --- | 5 | 5 | B.1.1.7 | 0.000004 |
N | 314 | F314F | ttC | ttT | 5 | 5 | B.1.177 | 0.000066 |
N | 314 | F314F | ttC | ttT | 5 | 5 | P.1.1 | 0.001588 |
N | 314 | F314F | ttC | ttT | 5 | 5 | Q.8 | 0.000825 |
N | 314 | F314V | Ttc | Gtc | 4 | 4 | All | 0.000001 |
N | 314 | F314del1 | ttC | tt- | 4 | 4 | All | 0.000001 |
N | 314 | F314F | ttC | ttT | 4 | 4 | AY.119 | 0.000141 |
N | 314 | F314L | ttC | ttA | 4 | 4 | AY.8 | 0.002424 |
N | 314 | F314F | ttC | ttT | 4 | 4 | B.1.1.63 | 0.001543 |
N | 314 | F314del | TTC | --- | 4 | 4 | B.1.177 | 0.000053 |
N | 314 | F314F | ttC | ttT | 4 | 4 | B.1.588 | 0.00364 |
N | 314 | F314F | ttC | ttT | 4 | 4 | P.1.15 | 0.000929 |
N | 314 | F314F | ttC | ttT | 3 | 3 | AY.102 | 0.00008 |
N | 314 | F314F | ttC | ttT | 3 | 3 | AY.113 | 0.000427 |
N | 314 | F314F | ttC | ttT | 3 | 3 | AY.68 | 0.000821 |
N | 314 | F314L | ttC | ttA | 2 | 3 | B.1 | 0.000018 |
N | 314 | F314L | Ttc | Ctc | 1 | 3 | B.1 | 0.000009 |
N | 314 | F314del | TTC | --- | 3 | 3 | B.1.1 | 0.000054 |
N | 314 | F314del | TTC | --- | 3 | 3 | B.1.617.2 | 0.000011 |
N | 314 | F314F | ttC | ttT | 3 | 3 | B.1.621 | 0.000266 |
N | 314 | F314L | ttC | ttG | 2 | 2 | 0.111111 | |
N | 314 | F314Y | tTc | tAc | 2 | 2 | 0.111111 | |
N | 314 | F314Y | tTc | tAc | 2 | 2 | All | 0 |
N | 314 | F314I | Ttc | Atc | 2 | 2 | All | 0 |
N | 314 | F314C | tTc | tGc | 2 | 2 | All | 0 |
N | 314 | F314F | ttC | ttT | 2 | 2 | AY.103 | 0.000012 |
N | 314 | F314F | ttC | ttT | 2 | 2 | AY.108 | 0.002205 |
N | 314 | F314F | ttC | ttT | 2 | 2 | AY.26 | 0.000057 |
N | 314 | F314F | ttC | ttT | 2 | 2 | AY.29 | 0.000032 |
N | 314 | F314F | ttC | ttT | 2 | 2 | AY.3 | 0.00002 |
N | 314 | F314F | ttC | ttT | 2 | 2 | AY.4.2 | 0.000043 |
N | 314 | F314F | ttC | ttT | 2 | 2 | AY.75 | 0.000112 |
N | 314 | F314F | ttC | ttT | 2 | 2 | AY.87 | 0.001665 |
N | 314 | F314S | tTc | tCc | 2 | 2 | B.1 | 0.000018 |
N | 314 | F314V | Ttc | Gtc | 2 | 2 | B.1 | 0.000018 |
N | 314 | F314L | ttC | ttA | 2 | 2 | B.1.1 | 0.000036 |
N | 314 | F314L | ttC | ttA | 1 | 2 | B.1.1.7 | 0.000001 |
N | 314 | F314L | Ttc | Ctc | 1 | 2 | B.1.1.7 | 0.000001 |
N | 314 | F314L | Ttc | Ctc | 2 | 2 | B.1.177 | 0.000026 |
N | 314 | F314F | ttC | ttT | 2 | 2 | B.1.177.60 | 0.000437 |
N | 314 | F314F | ttC | ttT | 2 | 2 | B.1.177.81 | 0.000379 |
N | 314 | F314F | ttC | ttT | 2 | 2 | B.1.177.86 | 0.000367 |
N | 314 | F314F | ttC | ttT | 2 | 2 | B.1.258 | 0.000133 |
N | 314 | F314F | ttC | ttT | 2 | 2 | B.1.36 | 0.000292 |
N | 314 | F314F | ttC | ttT | 2 | 2 | B.1.36.29 | 0.001035 |
N | 314 | F314F | ttC | ttT | 2 | 2 | B.1.422 | 0.001625 |
N | 314 | F314F | ttC | ttT | 2 | 2 | B.1.596 | 0.000174 |
N | 314 | F314F | ttC | ttT | 2 | 2 | P.2 | 0.000373 |
N | 314 | F314V | Ttc | Gtc | 1 | 1 | 0.055556 | |
N | 314 | F314W | tTC | tGG | 1 | 1 | All | 0 |
N | 314 | F314X | tTC | tAA | 1 | 1 | All | 0 |
N | 314 | F314F | ttC | ttT | 1 | 1 | AY.100 | 0.000046 |
N | 314 | F314del | TTC | --- | 1 | 1 | AY.102 | 0.000027 |
N | 314 | F314F | ttC | ttT | 1 | 1 | AY.12 | 0.000316 |
N | 314 | F314F | ttC | ttT | 1 | 1 | AY.120 | 0.000037 |
N | 314 | F314L | ttC | ttA | 1 | 1 | AY.120 | 0.000037 |
N | 314 | F314L | ttC | ttA | 1 | 1 | AY.17 | 0.008197 |
N | 314 | F314F | ttC | ttT | 1 | 1 | AY.19 | 0.00114 |
N | 314 | F314del | TTC | --- | 1 | 1 | AY.20 | 0.000039 |
N | 314 | F314F | ttC | ttT | 1 | 1 | AY.20 | 0.000039 |
N | 314 | F314V | Ttc | Gtc | 1 | 1 | AY.23 | 0.00007 |
N | 314 | F314S | tTc | tCc | 1 | 1 | AY.25 | 0.000006 |
N | 314 | F314del | TTC | --- | 1 | 1 | AY.25 | 0.000006 |
N | 314 | F314F | ttC | ttT | 1 | 1 | AY.33 | 0.000067 |
N | 314 | F314del | TTC | --- | 1 | 1 | AY.34 | 0.000097 |
N | 314 | F314L | Ttc | Ctc | 1 | 1 | AY.36 | 0.000148 |
N | 314 | F314F | ttC | ttT | 1 | 1 | AY.36 | 0.000148 |
N | 314 | F314del | TTC | --- | 1 | 1 | AY.4 | 0.000002 |
N | 314 | F314F | ttC | ttT | 1 | 1 | AY.4.4 | 0.000409 |
N | 314 | F314F | ttC | ttT | 1 | 1 | AY.42 | 0.00004 |
N | 314 | F314del | TTC | --- | 1 | 1 | AY.43 | 0.000004 |
N | 314 | F314F | ttC | ttT | 1 | 1 | AY.47 | 0.000031 |
N | 314 | F314del | TTC | --- | 1 | 1 | AY.5 | 0.000021 |
N | 314 | F314F | ttC | ttT | 1 | 1 | AY.5 | 0.000021 |
N | 314 | F314F | ttC | ttT | 1 | 1 | AY.53 | 0.000288 |
N | 314 | F314F | ttC | ttT | 1 | 1 | AY.55 | 0.000917 |
N | 314 | F314I | Ttc | Atc | 1 | 1 | AY.57 | 0.000656 |
N | 314 | F314L | ttC | ttA | 1 | 1 | AY.58 | 0.000907 |
N | 314 | F314del1 | ttC | tt- | 1 | 1 | AY.61 | 0.000105 |
N | 314 | F314del | TTC | --- | 1 | 1 | AY.67 | 0.000464 |
N | 314 | F314F | ttC | ttT | 1 | 1 | AY.69 | 0.000187 |
N | 314 | F314del | TTC | --- | 1 | 1 | AY.75 | 0.000056 |
N | 314 | F314F | ttC | ttT | 1 | 1 | AY.77 | 0.001127 |
N | 314 | F314del | TTC | --- | 1 | 1 | AY.78 | 0.001541 |
N | 314 | F314F | ttC | ttT | 1 | 1 | AY.86 | 0.00083 |
N | 314 | F314L | ttC | ttA | 1 | 1 | AY.87 | 0.000833 |
N | 314 | F314del1 | ttC | tt- | 1 | 1 | B | 0.000128 |
N | 314 | F314del | TTC | --- | 1 | 1 | B.1 | 0.000009 |
N | 314 | F314F | ttC | ttT | 1 | 1 | B.1.1.121 | 0.002427 |
N | 314 | F314L | ttC | ttG | 1 | 1 | B.1.1.139 | 0.022727 |
N | 314 | F314F | ttC | ttT | 1 | 1 | B.1.1.161 | 0.003534 |
N | 314 | F314F | ttC | ttT | 1 | 1 | B.1.1.214 | 0.000055 |
N | 314 | F314F | ttC | ttT | 1 | 1 | B.1.1.222 | 0.000204 |
N | 314 | F314F | ttC | ttT | 1 | 1 | B.1.1.265 | 0.003155 |
N | 314 | F314L | ttC | ttG | 1 | 1 | B.1.1.27 | 0.00565 |
N | 314 | F314F | ttC | ttT | 1 | 1 | B.1.1.279 | 0.001121 |
N | 314 | F314del | TTC | --- | 1 | 1 | B.1.1.279 | 0.001121 |
N | 314 | F314C | tTc | tGc | 1 | 1 | B.1.1.318 | 0.000302 |
N | 314 | F314F | ttC | ttT | 1 | 1 | B.1.1.519 | 0.00004 |
N | 314 | F314del1 | ttC | tt- | 1 | 1 | B.1.1.7 | 0.000001 |
N | 314 | F314F | ttC | ttT | 1 | 1 | B.1.160 | 0.000031 |
N | 314 | F314L | Ttc | Ctc | 1 | 1 | B.1.177.31 | 0.011494 |
N | 314 | F314X | tTC | tAA | 1 | 1 | B.1.177.63 | 0.002703 |
N | 314 | F314del | TTC | --- | 1 | 1 | B.1.177.83 | 0.001481 |
N | 314 | F314L | Ttc | Ctc | 1 | 1 | B.1.2 | 0.000009 |
N | 314 | F314del | TTC | --- | 1 | 1 | B.1.2 | 0.000009 |
N | 314 | F314S | tTc | tCc | 1 | 1 | B.1.221 | 0.000071 |
N | 314 | F314F | ttC | ttT | 1 | 1 | B.1.221 | 0.000071 |
N | 314 | F314F | ttC | ttT | 1 | 1 | B.1.232 | 0.000537 |
N | 314 | F314F | ttC | ttT | 1 | 1 | B.1.241 | 0.000812 |
N | 314 | F314del | TTC | --- | 1 | 1 | B.1.258 | 0.000067 |
N | 314 | F314del | TTC | --- | 1 | 1 | B.1.258.16 | 0.001637 |
N | 314 | F314F | ttC | ttT | 1 | 1 | B.1.260 | 0.003344 |
N | 314 | F314F | ttC | ttT | 1 | 1 | B.1.319 | 0.003049 |
N | 314 | F314F | ttC | ttT | 1 | 1 | B.1.36.2 | 0.010753 |
N | 314 | F314W | tTC | tGG | 1 | 1 | B.1.36.29 | 0.000517 |
N | 314 | F314F | ttC | ttT | 1 | 1 | B.1.369 | 0.000285 |
N | 314 | F314del | TTC | --- | 1 | 1 | B.1.427 | 0.00005 |
N | 314 | F314F | ttC | ttT | 1 | 1 | B.1.429 | 0.000024 |
N | 314 | F314L | Ttc | Ctc | 1 | 1 | B.1.466.2 | 0.000391 |
N | 314 | F314C | tTc | tGc | 1 | 1 | B.1.466.2 | 0.000391 |
N | 314 | F314L | ttC | ttA | 1 | 1 | B.1.599 | 0.00365 |
N | 314 | F314del | TTC | --- | 1 | 1 | B.1.610 | 0.003546 |
N | 314 | F314S | tTc | tCc | 1 | 1 | B.1.612 | 0.002653 |
N | 314 | F314del | TTC | --- | 1 | 1 | B.1.617.1 | 0.000129 |
N | 314 | F314L | ttC | ttA | 1 | 1 | B.1.617.2 | 0.000004 |
N | 314 | F314del | TTC | --- | 1 | 1 | B.1.617.3 | 0.002985 |
N | 314 | F314del1 | ttC | tt- | 1 | 1 | B.1.628 | 0.000352 |
N | 314 | F314del | TTC | --- | 1 | 1 | B.1.630 | 0.005236 |
N | 314 | F314I | Ttc | Atc | 1 | 1 | B.6 | 0.00091 |
N | 314 | F314S | tTc | tCc | 1 | 1 | D.2 | 0.000075 |
N | 314 | F314F | ttC | ttT | 1 | 1 | D.2 | 0.000075 |
N | 314 | F314F | ttC | ttT | 1 | 1 | P.1.12 | 0.000484 |
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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