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 |
S | 20 | T20N | nonsyn | aCc | aAc | 112479 | 112270 | 0.998142 | 21620-21622 | |
S | 20 | T20N | nonsyn | aCC | aAT | 112479 | 209 | 0.00185812 | 21620-21622 |
Details of the mutation T20N 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 |
S | 20 | T20N | aCc | aAc | 112270 | 112479 | All | 0.021473 |
S | 20 | T20N | aCC | aAT | 209 | 112479 | All | 0.00004 |
S | 20 | T20N | aCc | aAc | 61403 | 61537 | P.1 | 0.967342 |
S | 20 | T20N | aCC | aAT | 134 | 61537 | P.1 | 0.002111 |
S | 20 | T20N | aCc | aAc | 20820 | 20830 | P.1.14 | 0.99522 |
S | 20 | T20N | aCC | aAT | 10 | 20830 | P.1.14 | 0.000478 |
S | 20 | T20N | aCc | aAc | 6068 | 6069 | P.1.17 | 0.981559 |
S | 20 | T20N | aCC | aAT | 1 | 6069 | P.1.17 | 0.000162 |
S | 20 | T20N | aCc | aAc | 4205 | 4211 | P.1.15 | 0.976998 |
S | 20 | T20N | aCC | aAT | 6 | 4211 | P.1.15 | 0.001394 |
S | 20 | T20N | aCc | aAc | 3654 | 3660 | P.1.10 | 0.98464 |
S | 20 | T20N | aCC | aAT | 6 | 3660 | P.1.10 | 0.001617 |
S | 20 | T20N | aCc | aAc | 3090 | 3101 | P.1.7 | 0.98659 |
S | 20 | T20N | aCC | aAT | 11 | 3101 | P.1.7 | 0.003512 |
S | 20 | T20N | aCc | aAc | 2945 | 2948 | P.1.1 | 0.935515 |
S | 20 | T20N | aCC | aAT | 3 | 2948 | P.1.1 | 0.000953 |
S | 20 | T20N | aCc | aAc | 2522 | 2550 | P.1.16 | 0.943509 |
S | 20 | T20N | aCC | aAT | 28 | 2550 | P.1.16 | 0.010475 |
S | 20 | T20N | aCc | aAc | 1789 | 1793 | P.1.12 | 0.865924 |
S | 20 | T20N | aCC | aAT | 4 | 1793 | P.1.12 | 0.001936 |
S | 20 | T20N | aCc | aAc | 1141 | 1141 | P.1.17.1 | 0.99825 |
S | 20 | T20N | aCc | aAc | 1079 | 1079 | P.1.13 | 0.969452 |
S | 20 | T20N | aCc | aAc | 1017 | 1022 | P.1.4 | 0.993164 |
S | 20 | T20N | aCC | aAT | 5 | 1022 | P.1.4 | 0.004883 |
S | 20 | T20N | aCc | aAc | 856 | 856 | P.1.2 | 0.989595 |
S | 20 | T20N | aCc | aAc | 512 | 512 | P.1.6 | 0.996109 |
S | 20 | T20N | aCc | aAc | 208 | 208 | P.1.8 | 0.995215 |
S | 20 | T20N | aCc | aAc | 204 | 204 | P.1.9 | 0.980769 |
S | 20 | T20N | aCc | aAc | 106 | 106 | P.1.10.1 | 0.861789 |
S | 20 | T20N | aCc | aAc | 98 | 98 | P.1.11 | 1 |
S | 20 | T20N | aCc | aAc | 78 | 78 | B.1 | 0.000714 |
S | 20 | T20N | aCc | aAc | 64 | 65 | B.1.1.7 | 0.000057 |
S | 20 | T20N | aCC | aAT | 1 | 65 | B.1.1.7 | 0.000001 |
S | 20 | T20N | aCc | aAc | 50 | 50 | B.1.1 | 0.000907 |
S | 20 | T20N | aCc | aAc | 29 | 29 | B.1.497 | 0.009128 |
S | 20 | T20N | aCc | aAc | 29 | 29 | P.1.3 | 1 |
S | 20 | T20N | aCc | aAc | 28 | 28 | B.1.617.2 | 0.000105 |
S | 20 | T20N | aCc | aAc | 25 | 25 | B.1.1.528 | 0.120192 |
S | 20 | T20N | aCc | aAc | 24 | 24 | P.1.10.2 | 1 |
S | 20 | T20N | aCc | aAc | 21 | 21 | B.1.1.28 | 0.006536 |
S | 20 | T20N | aCc | aAc | 21 | 21 | C.37 | 0.002437 |
S | 20 | T20N | aCc | aAc | 15 | 15 | AY.43 | 0.000066 |
S | 20 | T20N | aCc | aAc | 14 | 14 | Q.1 | 0.001769 |
S | 20 | T20N | aCc | aAc | 13 | 13 | P.1.5 | 1 |
S | 20 | T20N | aCc | aAc | 9 | 9 | AY.103 | 0.000056 |
S | 20 | T20N | aCc | aAc | 9 | 9 | P.2 | 0.00168 |
S | 20 | T20N | aCc | aAc | 8 | 8 | AY.4 | 0.000012 |
S | 20 | T20N | aCc | aAc | 5 | 5 | AY.29 | 0.000079 |
S | 20 | T20N | aCc | aAc | 5 | 5 | AY.44 | 0.00003 |
S | 20 | T20N | aCc | aAc | 5 | 5 | B.1.596 | 0.000436 |
S | 20 | T20N | aCc | aAc | 4 | 4 | AY.20 | 0.000155 |
S | 20 | T20N | aCc | aAc | 4 | 4 | B.1.1.161 | 0.014134 |
S | 20 | T20N | aCc | aAc | 4 | 4 | B.1.621 | 0.000354 |
S | 20 | T20N | aCc | aAc | 4 | 4 | B.1.636 | 0.026846 |
S | 20 | T20N | aCc | aAc | 3 | 3 | AY.39 | 0.000074 |
S | 20 | T20N | aCc | aAc | 3 | 3 | B.1.1.348 | 0.002389 |
S | 20 | T20N | aCc | aAc | 3 | 3 | B.1.1.519 | 0.000119 |
S | 20 | T20N | aCc | aAc | 3 | 3 | B.1.351 | 0.000089 |
S | 20 | T20N | aCc | aAc | 3 | 3 | B.1.600 | 0.017544 |
S | 20 | T20N | aCc | aAc | 2 | 2 | A.2.5 | 0.000998 |
S | 20 | T20N | aCc | aAc | 2 | 2 | AY.102 | 0.000053 |
S | 20 | T20N | aCc | aAc | 2 | 2 | AY.23 | 0.000139 |
S | 20 | T20N | aCc | aAc | 2 | 2 | AY.45 | 0.000243 |
S | 20 | T20N | aCc | aAc | 2 | 2 | AY.67 | 0.000929 |
S | 20 | T20N | aCc | aAc | 2 | 2 | AY.9.2 | 0.000073 |
S | 20 | T20N | aCc | aAc | 2 | 2 | AY.99.2 | 0.000184 |
S | 20 | T20N | aCc | aAc | 2 | 2 | B.1.1.332 | 0.0625 |
S | 20 | T20N | aCc | aAc | 2 | 2 | B.1.177.73 | 0.001133 |
S | 20 | T20N | aCc | aAc | 2 | 2 | B.1.36.27 | 0.001527 |
S | 20 | T20N | aCc | aAc | 2 | 2 | B.1.369 | 0.00057 |
S | 20 | T20N | aCc | aAc | 2 | 2 | B.1.517 | 0.000854 |
S | 20 | T20N | aCc | aAc | 2 | 2 | B.1.526 | 0.000047 |
S | 20 | T20N | aCc | aAc | 2 | 2 | C.37.1 | 0.005236 |
S | 20 | T20N | aCc | aAc | 1 | 1 | AY.100 | 0.000046 |
S | 20 | T20N | aCc | aAc | 1 | 1 | AY.25 | 0.000006 |
S | 20 | T20N | aCc | aAc | 1 | 1 | AY.26 | 0.000028 |
S | 20 | T20N | aCc | aAc | 1 | 1 | AY.3 | 0.00001 |
S | 20 | T20N | aCc | aAc | 1 | 1 | AY.34.1 | 0.00051 |
S | 20 | T20N | aCc | aAc | 1 | 1 | AY.42 | 0.00004 |
S | 20 | T20N | aCc | aAc | 1 | 1 | AY.5.3 | 0.000337 |
S | 20 | T20N | aCc | aAc | 1 | 1 | AY.68 | 0.000274 |
S | 20 | T20N | aCc | aAc | 1 | 1 | AY.98 | 0.000079 |
S | 20 | T20N | aCc | aAc | 1 | 1 | AY.98.1 | 0.000048 |
S | 20 | T20N | aCc | aAc | 1 | 1 | B | 0.000128 |
S | 20 | T20N | aCc | aAc | 1 | 1 | B.1.1.117 | 0.009709 |
S | 20 | T20N | aCc | aAc | 1 | 1 | B.1.1.220 | 0.001859 |
S | 20 | T20N | aCc | aAc | 1 | 1 | B.1.1.236 | 0.006897 |
S | 20 | T20N | aCc | aAc | 1 | 1 | B.1.1.33 | 0.000421 |
S | 20 | T20N | aCc | aAc | 1 | 1 | B.1.1.39 | 0.00051 |
S | 20 | T20N | aCc | aAc | 1 | 1 | B.1.177 | 0.000013 |
S | 20 | T20N | aCc | aAc | 1 | 1 | B.1.177.31 | 0.011494 |
S | 20 | T20N | aCc | aAc | 1 | 1 | B.1.177.7 | 0.000165 |
S | 20 | T20N | aCc | aAc | 1 | 1 | B.1.177.86 | 0.000183 |
S | 20 | T20N | aCc | aAc | 1 | 1 | B.1.2 | 0.000009 |
S | 20 | T20N | aCc | aAc | 1 | 1 | B.1.214 | 0.003663 |
S | 20 | T20N | aCc | aAc | 1 | 1 | B.1.311 | 0.000275 |
S | 20 | T20N | aCc | aAc | 1 | 1 | B.1.349 | 0.000715 |
S | 20 | T20N | aCc | aAc | 1 | 1 | B.1.36.29 | 0.000517 |
S | 20 | T20N | aCc | aAc | 1 | 1 | B.1.375 | 0.00082 |
S | 20 | T20N | aCc | aAc | 1 | 1 | B.1.399 | 0.001934 |
S | 20 | T20N | aCc | aAc | 1 | 1 | B.1.415 | 0.014286 |
S | 20 | T20N | aCc | aAc | 1 | 1 | B.1.429 | 0.000024 |
S | 20 | T20N | aCc | aAc | 1 | 1 | B.1.525 | 0.000113 |
S | 20 | T20N | aCc | aAc | 1 | 1 | B.1.533 | 0.009615 |
S | 20 | T20N | aCc | aAc | 1 | 1 | B.1.577 | 0.000687 |
S | 20 | T20N | aCc | aAc | 1 | 1 | B.1.609 | 0.000479 |
S | 20 | T20N | aCc | aAc | 1 | 1 | B.1.620 | 0.000946 |
S | 20 | T20N | aCc | aAc | 1 | 1 | B.1.623 | 0.000536 |
S | 20 | T20N | aCc | aAc | 1 | 1 | B.11 | 0.005128 |
S | 20 | T20N | aCc | aAc | 1 | 1 | B.3 | 0.000831 |
S | 20 | T20N | aCc | aAc | 1 | 1 | C.16 | 0.00106 |
S | 20 | T20N | aCc | aAc | 1 | 1 | C.35 | 0.000774 |
S | 20 | T20N | aCc | aAc | 1 | 1 | P.7 | 0.004367 |
S | 20 | T20N | aCc | aAc | 1 | 1 | Q.3 | 0.000145 |
S | 20 | T20N | aCc | aAc | 1 | 1 | Q.4 | 0.000455 |
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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