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/nsp3 | 702 | S702F | S1520F | nonsyn | tCt | tTt | 2336 | 2335 | 0.999572 | 4823-4825 |
ORF1ab/nsp3 | 702 | S702F | S1520F | nonsyn | tCT | tTC | 2336 | 1 | 0.000428082 | 4823-4825 |
Details of the mutation S702F 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/nsp3 | 702 | S702F | tCt | tTt | 2335 | 2336 | All | 0.000447 |
ORF1ab/nsp3 | 702 | S702F | tCT | tTC | 1 | 2336 | All | 0 |
ORF1ab/nsp3 | 702 | S702F | tCt | tTt | 1022 | 1022 | AY.4 | 0.001591 |
ORF1ab/nsp3 | 702 | S702F | tCt | tTt | 375 | 375 | B.1.1.7 | 0.000336 |
ORF1ab/nsp3 | 702 | S702F | tCt | tTt | 276 | 276 | B.1.1.337 | 0.992806 |
ORF1ab/nsp3 | 702 | S702F | tCt | tTt | 48 | 48 | B.1 | 0.00044 |
ORF1ab/nsp3 | 702 | S702F | tCt | tTt | 45 | 45 | B.1.634 | 0.15411 |
ORF1ab/nsp3 | 702 | S702F | tCt | tTt | 43 | 43 | B.1.160 | 0.001341 |
ORF1ab/nsp3 | 702 | S702F | tCt | tTt | 43 | 43 | B.1.617.2 | 0.000162 |
ORF1ab/nsp3 | 702 | S702F | tCt | tTt | 41 | 41 | AY.34 | 0.003976 |
ORF1ab/nsp3 | 702 | S702F | tCt | tTt | 31 | 31 | AY.102 | 0.000822 |
ORF1ab/nsp3 | 702 | S702F | tCt | tTt | 26 | 27 | AY.44 | 0.000158 |
ORF1ab/nsp3 | 702 | S702F | tCT | tTC | 1 | 27 | AY.44 | 0.000006 |
ORF1ab/nsp3 | 702 | S702F | tCt | tTt | 26 | 26 | B.1.1 | 0.000472 |
ORF1ab/nsp3 | 702 | S702F | tCt | tTt | 24 | 24 | AY.103 | 0.000149 |
ORF1ab/nsp3 | 702 | S702F | tCt | tTt | 24 | 24 | B.1.2 | 0.000211 |
ORF1ab/nsp3 | 702 | S702F | tCt | tTt | 23 | 23 | B.1.1.306 | 0.010083 |
ORF1ab/nsp3 | 702 | S702F | tCt | tTt | 13 | 13 | AY.3 | 0.000129 |
ORF1ab/nsp3 | 702 | S702F | tCt | tTt | 12 | 12 | AY.25 | 0.000072 |
ORF1ab/nsp3 | 702 | S702F | tCt | tTt | 12 | 12 | P.1 | 0.000189 |
ORF1ab/nsp3 | 702 | S702F | tCt | tTt | 11 | 11 | AY.43 | 0.000049 |
ORF1ab/nsp3 | 702 | S702F | tCt | tTt | 9 | 9 | AY.74 | 0.001041 |
ORF1ab/nsp3 | 702 | S702F | tCt | tTt | 8 | 8 | AY.98.1 | 0.000387 |
ORF1ab/nsp3 | 702 | S702F | tCt | tTt | 8 | 8 | B.1.1.222 | 0.001632 |
ORF1ab/nsp3 | 702 | S702F | tCt | tTt | 7 | 7 | AY.23 | 0.000488 |
ORF1ab/nsp3 | 702 | S702F | tCt | tTt | 7 | 7 | AY.42 | 0.000282 |
ORF1ab/nsp3 | 702 | S702F | tCt | tTt | 7 | 7 | B.1.177 | 0.000092 |
ORF1ab/nsp3 | 702 | S702F | tCt | tTt | 7 | 7 | C.37 | 0.000812 |
ORF1ab/nsp3 | 702 | S702F | tCt | tTt | 7 | 7 | P.2 | 0.001306 |
ORF1ab/nsp3 | 702 | S702F | tCt | tTt | 6 | 6 | AY.113 | 0.000854 |
ORF1ab/nsp3 | 702 | S702F | tCt | tTt | 6 | 6 | B.1.1.267 | 0.060606 |
ORF1ab/nsp3 | 702 | S702F | tCt | tTt | 6 | 6 | B.1.1.28 | 0.001867 |
ORF1ab/nsp3 | 702 | S702F | tCt | tTt | 6 | 6 | B.1.221 | 0.000426 |
ORF1ab/nsp3 | 702 | S702F | tCt | tTt | 6 | 6 | B.1.400 | 0.002574 |
ORF1ab/nsp3 | 702 | S702F | tCt | tTt | 5 | 5 | AY.39 | 0.000124 |
ORF1ab/nsp3 | 702 | S702F | tCt | tTt | 5 | 5 | AY.99.2 | 0.000461 |
ORF1ab/nsp3 | 702 | S702F | tCt | tTt | 5 | 5 | B.1.1.519 | 0.000199 |
ORF1ab/nsp3 | 702 | S702F | tCt | tTt | 5 | 5 | B.1.429 | 0.000118 |
ORF1ab/nsp3 | 702 | S702F | tCt | tTt | 4 | 4 | AY.110 | 0.000451 |
ORF1ab/nsp3 | 702 | S702F | tCt | tTt | 4 | 4 | AY.26 | 0.000113 |
ORF1ab/nsp3 | 702 | S702F | tCt | tTt | 4 | 4 | AY.39.1 | 0.000158 |
ORF1ab/nsp3 | 702 | S702F | tCt | tTt | 4 | 4 | B.1.609 | 0.001918 |
ORF1ab/nsp3 | 702 | S702F | tCt | tTt | 3 | 3 | AY.100 | 0.000138 |
ORF1ab/nsp3 | 702 | S702F | tCt | tTt | 3 | 3 | AY.117 | 0.000254 |
ORF1ab/nsp3 | 702 | S702F | tCt | tTt | 3 | 3 | AY.46.6 | 0.000217 |
ORF1ab/nsp3 | 702 | S702F | tCt | tTt | 3 | 3 | B.1.351 | 0.000089 |
ORF1ab/nsp3 | 702 | S702F | tCt | tTt | 3 | 3 | B.1.36.29 | 0.001552 |
ORF1ab/nsp3 | 702 | S702F | tCt | tTt | 3 | 3 | B.1.409 | 0.002344 |
ORF1ab/nsp3 | 702 | S702F | tCt | tTt | 3 | 3 | B.1.526 | 0.000071 |
ORF1ab/nsp3 | 702 | S702F | tCt | tTt | 3 | 3 | B.1.621 | 0.000266 |
ORF1ab/nsp3 | 702 | S702F | tCt | tTt | 3 | 3 | B.1.628 | 0.001057 |
ORF1ab/nsp3 | 702 | S702F | tCt | tTt | 3 | 3 | D.2 | 0.000225 |
ORF1ab/nsp3 | 702 | S702F | tCt | tTt | 2 | 2 | AY.119 | 0.000071 |
ORF1ab/nsp3 | 702 | S702F | tCt | tTt | 2 | 2 | AY.4.2 | 0.000043 |
ORF1ab/nsp3 | 702 | S702F | tCt | tTt | 2 | 2 | AY.45 | 0.000243 |
ORF1ab/nsp3 | 702 | S702F | tCt | tTt | 2 | 2 | AY.61 | 0.00021 |
ORF1ab/nsp3 | 702 | S702F | tCt | tTt | 2 | 2 | AY.7.1 | 0.000225 |
ORF1ab/nsp3 | 702 | S702F | tCt | tTt | 2 | 2 | AY.75 | 0.000112 |
ORF1ab/nsp3 | 702 | S702F | tCt | tTt | 2 | 2 | AY.9 | 0.000135 |
ORF1ab/nsp3 | 702 | S702F | tCt | tTt | 2 | 2 | AY.9.2 | 0.000073 |
ORF1ab/nsp3 | 702 | S702F | tCt | tTt | 2 | 2 | B.1.1.161 | 0.007067 |
ORF1ab/nsp3 | 702 | S702F | tCt | tTt | 2 | 2 | B.1.1.207 | 0.002364 |
ORF1ab/nsp3 | 702 | S702F | tCt | tTt | 2 | 2 | B.1.1.214 | 0.000111 |
ORF1ab/nsp3 | 702 | S702F | tCt | tTt | 2 | 2 | B.1.1.300 | 0.021505 |
ORF1ab/nsp3 | 702 | S702F | tCt | tTt | 2 | 2 | B.1.1.343 | 0.041667 |
ORF1ab/nsp3 | 702 | S702F | tCt | tTt | 2 | 2 | B.1.234 | 0.000264 |
ORF1ab/nsp3 | 702 | S702F | tCt | tTt | 2 | 2 | B.1.258 | 0.000133 |
ORF1ab/nsp3 | 702 | S702F | tCt | tTt | 2 | 2 | B.1.36.8 | 0.002 |
ORF1ab/nsp3 | 702 | S702F | tCt | tTt | 2 | 2 | B.1.587 | 0.003795 |
ORF1ab/nsp3 | 702 | S702F | tCt | tTt | 2 | 2 | P.1.14 | 0.000096 |
ORF1ab/nsp3 | 702 | S702F | tCt | tTt | 1 | 1 | A.2.2 | 0.001689 |
ORF1ab/nsp3 | 702 | S702F | tCt | tTt | 1 | 1 | A.2.4 | 0.003367 |
ORF1ab/nsp3 | 702 | S702F | tCt | tTt | 1 | 1 | A.2.5 | 0.000499 |
ORF1ab/nsp3 | 702 | S702F | tCt | tTt | 1 | 1 | AY.114 | 0.000231 |
ORF1ab/nsp3 | 702 | S702F | tCt | tTt | 1 | 1 | AY.120 | 0.000037 |
ORF1ab/nsp3 | 702 | S702F | tCt | tTt | 1 | 1 | AY.16.1 | 0.00047 |
ORF1ab/nsp3 | 702 | S702F | tCt | tTt | 1 | 1 | AY.19 | 0.00114 |
ORF1ab/nsp3 | 702 | S702F | tCt | tTt | 1 | 1 | AY.29 | 0.000016 |
ORF1ab/nsp3 | 702 | S702F | tCt | tTt | 1 | 1 | AY.29.1 | 0.000221 |
ORF1ab/nsp3 | 702 | S702F | tCt | tTt | 1 | 1 | AY.33 | 0.000067 |
ORF1ab/nsp3 | 702 | S702F | tCt | tTt | 1 | 1 | AY.34.1 | 0.00051 |
ORF1ab/nsp3 | 702 | S702F | tCt | tTt | 1 | 1 | AY.36 | 0.000148 |
ORF1ab/nsp3 | 702 | S702F | tCt | tTt | 1 | 1 | AY.47 | 0.000031 |
ORF1ab/nsp3 | 702 | S702F | tCt | tTt | 1 | 1 | AY.9.1 | 0.000084 |
ORF1ab/nsp3 | 702 | S702F | tCt | tTt | 1 | 1 | AY.93 | 0.000273 |
ORF1ab/nsp3 | 702 | S702F | tCt | tTt | 1 | 1 | B.1.1.101 | 0.01 |
ORF1ab/nsp3 | 702 | S702F | tCt | tTt | 1 | 1 | B.1.1.220 | 0.001859 |
ORF1ab/nsp3 | 702 | S702F | tCt | tTt | 1 | 1 | B.1.1.244 | 0.015385 |
ORF1ab/nsp3 | 702 | S702F | tCt | tTt | 1 | 1 | B.1.1.25 | 0.000569 |
ORF1ab/nsp3 | 702 | S702F | tCt | tTt | 1 | 1 | B.1.1.419 | 0.007407 |
ORF1ab/nsp3 | 702 | S702F | tCt | tTt | 1 | 1 | B.1.1.432 | 0.001266 |
ORF1ab/nsp3 | 702 | S702F | tCt | tTt | 1 | 1 | B.1.147 | 0.000756 |
ORF1ab/nsp3 | 702 | S702F | tCt | tTt | 1 | 1 | B.1.167 | 0.007812 |
ORF1ab/nsp3 | 702 | S702F | tCt | tTt | 1 | 1 | B.1.177.12 | 0.000152 |
ORF1ab/nsp3 | 702 | S702F | tCt | tTt | 1 | 1 | B.1.177.21 | 0.000076 |
ORF1ab/nsp3 | 702 | S702F | tCt | tTt | 1 | 1 | B.1.177.60 | 0.000218 |
ORF1ab/nsp3 | 702 | S702F | tCt | tTt | 1 | 1 | B.1.177.73 | 0.000566 |
ORF1ab/nsp3 | 702 | S702F | tCt | tTt | 1 | 1 | B.1.258.16 | 0.001637 |
ORF1ab/nsp3 | 702 | S702F | tCt | tTt | 1 | 1 | B.1.258.22 | 0.002667 |
ORF1ab/nsp3 | 702 | S702F | tCt | tTt | 1 | 1 | B.1.323 | 0.020833 |
ORF1ab/nsp3 | 702 | S702F | tCt | tTt | 1 | 1 | B.1.351.2 | 0.000303 |
ORF1ab/nsp3 | 702 | S702F | tCt | tTt | 1 | 1 | B.1.36 | 0.000146 |
ORF1ab/nsp3 | 702 | S702F | tCt | tTt | 1 | 1 | B.1.36.17 | 0.000494 |
ORF1ab/nsp3 | 702 | S702F | tCt | tTt | 1 | 1 | B.1.361 | 0.001289 |
ORF1ab/nsp3 | 702 | S702F | tCt | tTt | 1 | 1 | B.1.377 | 0.004566 |
ORF1ab/nsp3 | 702 | S702F | tCt | tTt | 1 | 1 | B.1.390 | 0.010638 |
ORF1ab/nsp3 | 702 | S702F | tCt | tTt | 1 | 1 | B.1.427 | 0.00005 |
ORF1ab/nsp3 | 702 | S702F | tCt | tTt | 1 | 1 | B.1.561 | 0.000397 |
ORF1ab/nsp3 | 702 | S702F | tCt | tTt | 1 | 1 | B.1.564 | 0.000426 |
ORF1ab/nsp3 | 702 | S702F | tCt | tTt | 1 | 1 | B.1.596 | 0.000087 |
ORF1ab/nsp3 | 702 | S702F | tCt | tTt | 1 | 1 | B.1.600 | 0.005848 |
ORF1ab/nsp3 | 702 | S702F | tCt | tTt | 1 | 1 | B.1.619.1 | 0.000641 |
ORF1ab/nsp3 | 702 | S702F | tCt | tTt | 1 | 1 | B.12 | 0.00641 |
ORF1ab/nsp3 | 702 | S702F | tCt | tTt | 1 | 1 | B.6.1 | 0.026316 |
ORF1ab/nsp3 | 702 | S702F | tCt | tTt | 1 | 1 | C.36.3 | 0.000567 |
ORF1ab/nsp3 | 702 | S702F | tCt | tTt | 1 | 1 | L.2 | 0.011364 |
ORF1ab/nsp3 | 702 | S702F | tCt | tTt | 1 | 1 | Q.8 | 0.000165 |
ORF1ab/nsp3 | 702 | S702F | tCt | tTt | 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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