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 | 90 | V90del | del | GTT | --- | 657 | 657 | 1 | 21830-21832 |
Details of the mutation V90del 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 | 90 | V90del | GTT | --- | 657 | 657 | All | 0.000126 |
S | 90 | V90del | GTT | --- | 121 | 121 | B.1.617.2 | 0.000456 |
S | 90 | V90del | GTT | --- | 84 | 84 | AY.43 | 0.000372 |
S | 90 | V90del | GTT | --- | 53 | 53 | AY.4 | 0.000082 |
S | 90 | V90del | GTT | --- | 52 | 52 | B.1.1.7 | 0.000047 |
S | 90 | V90del | GTT | --- | 31 | 31 | AY.4.2 | 0.000672 |
S | 90 | V90del | GTT | --- | 26 | 26 | AY.25 | 0.000156 |
S | 90 | V90del | GTT | --- | 24 | 24 | AY.44 | 0.000146 |
S | 90 | V90del | GTT | --- | 22 | 22 | AY.9 | 0.001487 |
S | 90 | V90del | GTT | --- | 18 | 18 | AY.102 | 0.000477 |
S | 90 | V90del | GTT | --- | 10 | 10 | AY.4.2.1 | 0.00149 |
S | 90 | V90del | GTT | --- | 9 | 9 | AY.34.1 | 0.004589 |
S | 90 | V90del | GTT | --- | 8 | 8 | AY.39 | 0.000198 |
S | 90 | V90del | GTT | --- | 8 | 8 | AY.4.5 | 0.00086 |
S | 90 | V90del | GTT | --- | 8 | 8 | AY.9.2 | 0.000294 |
S | 90 | V90del | GTT | --- | 7 | 7 | AY.33 | 0.000467 |
S | 90 | V90del | GTT | --- | 7 | 7 | AY.61 | 0.000733 |
S | 90 | V90del | GTT | --- | 7 | 7 | B.1.177 | 0.000092 |
S | 90 | V90del | GTT | --- | 6 | 6 | AY.121 | 0.000812 |
S | 90 | V90del | GTT | --- | 6 | 6 | AY.3 | 0.00006 |
S | 90 | V90del | GTT | --- | 6 | 6 | B.1 | 0.000055 |
S | 90 | V90del | GTT | --- | 6 | 6 | B.1.1 | 0.000109 |
S | 90 | V90del | GTT | --- | 5 | 5 | AY.103 | 0.000031 |
S | 90 | V90del | GTT | --- | 5 | 5 | AY.46.6 | 0.000361 |
S | 90 | V90del | GTT | --- | 4 | 4 | 0.222222 | |
S | 90 | V90del | GTT | --- | 4 | 4 | AY.42 | 0.000161 |
S | 90 | V90del | GTT | --- | 4 | 4 | AY.46 | 0.000416 |
S | 90 | V90del | GTT | --- | 4 | 4 | AY.5 | 0.000083 |
S | 90 | V90del | GTT | --- | 4 | 4 | AY.98.1 | 0.000194 |
S | 90 | V90del | GTT | --- | 4 | 4 | P.1 | 0.000063 |
S | 90 | V90del | GTT | --- | 3 | 3 | AY.108 | 0.003308 |
S | 90 | V90del | GTT | --- | 3 | 3 | AY.20 | 0.000117 |
S | 90 | V90del | GTT | --- | 3 | 3 | AY.26 | 0.000085 |
S | 90 | V90del | GTT | --- | 3 | 3 | AY.29 | 0.000047 |
S | 90 | V90del | GTT | --- | 3 | 3 | AY.47 | 0.000093 |
S | 90 | V90del | GTT | --- | 3 | 3 | AY.54 | 0.000286 |
S | 90 | V90del | GTT | --- | 3 | 3 | AY.70 | 0.000626 |
S | 90 | V90del | GTT | --- | 3 | 3 | AY.75 | 0.000168 |
S | 90 | V90del | GTT | --- | 3 | 3 | AY.85 | 0.001282 |
S | 90 | V90del | GTT | --- | 3 | 3 | C.38 | 0.024194 |
S | 90 | V90del | GTT | --- | 2 | 2 | AY.118 | 0.000125 |
S | 90 | V90del | GTT | --- | 2 | 2 | AY.120 | 0.000074 |
S | 90 | V90del | GTT | --- | 2 | 2 | AY.34 | 0.000194 |
S | 90 | V90del | GTT | --- | 2 | 2 | AY.45 | 0.000243 |
S | 90 | V90del | GTT | --- | 2 | 2 | AY.60 | 0.001876 |
S | 90 | V90del | GTT | --- | 2 | 2 | AY.68 | 0.000547 |
S | 90 | V90del | GTT | --- | 2 | 2 | AY.7.2 | 0.001119 |
S | 90 | V90del | GTT | --- | 2 | 2 | AY.75.1 | 0.000361 |
S | 90 | V90del | GTT | --- | 2 | 2 | AY.99 | 0.002099 |
S | 90 | V90del | GTT | --- | 2 | 2 | B.1.2 | 0.000018 |
S | 90 | V90del | GTT | --- | 2 | 2 | B.1.429 | 0.000047 |
S | 90 | V90del | GTT | --- | 2 | 2 | B.1.525 | 0.000226 |
S | 90 | V90del | GTT | --- | 2 | 2 | B.1.621 | 0.000177 |
S | 90 | V90del | GTT | --- | 2 | 2 | P.1.10 | 0.000539 |
S | 90 | V90del | GTT | --- | 2 | 2 | R.1 | 0.00018 |
S | 90 | V90del | GTT | --- | 1 | 1 | AY.101 | 0.00049 |
S | 90 | V90del | GTT | --- | 1 | 1 | AY.111 | 0.000183 |
S | 90 | V90del | GTT | --- | 1 | 1 | AY.119 | 0.000035 |
S | 90 | V90del | GTT | --- | 1 | 1 | AY.24 | 0.000431 |
S | 90 | V90del | GTT | --- | 1 | 1 | AY.29.1 | 0.000221 |
S | 90 | V90del | GTT | --- | 1 | 1 | AY.3.1 | 0.000085 |
S | 90 | V90del | GTT | --- | 1 | 1 | AY.30 | 0.000396 |
S | 90 | V90del | GTT | --- | 1 | 1 | AY.36 | 0.000148 |
S | 90 | V90del | GTT | --- | 1 | 1 | AY.38 | 0.000499 |
S | 90 | V90del | GTT | --- | 1 | 1 | AY.4.4 | 0.000409 |
S | 90 | V90del | GTT | --- | 1 | 1 | AY.5.4 | 0.000277 |
S | 90 | V90del | GTT | --- | 1 | 1 | AY.51 | 0.000909 |
S | 90 | V90del | GTT | --- | 1 | 1 | AY.52 | 0.000814 |
S | 90 | V90del | GTT | --- | 1 | 1 | AY.53 | 0.000288 |
S | 90 | V90del | GTT | --- | 1 | 1 | AY.59 | 0.00053 |
S | 90 | V90del | GTT | --- | 1 | 1 | AY.64 | 0.000595 |
S | 90 | V90del | GTT | --- | 1 | 1 | AY.67 | 0.000464 |
S | 90 | V90del | GTT | --- | 1 | 1 | AY.71 | 0.000475 |
S | 90 | V90del | GTT | --- | 1 | 1 | AY.72 | 0.001361 |
S | 90 | V90del | GTT | --- | 1 | 1 | AY.94 | 0.000443 |
S | 90 | V90del | GTT | --- | 1 | 1 | AY.99.1 | 0.001553 |
S | 90 | V90del | GTT | --- | 1 | 1 | B.1.1.159 | 0.004673 |
S | 90 | V90del | GTT | --- | 1 | 1 | B.1.1.236 | 0.006897 |
S | 90 | V90del | GTT | --- | 1 | 1 | B.1.1.306 | 0.000438 |
S | 90 | V90del | GTT | --- | 1 | 1 | B.1.1.311 | 0.000358 |
S | 90 | V90del | GTT | --- | 1 | 1 | B.1.1.318 | 0.000302 |
S | 90 | V90del | GTT | --- | 1 | 1 | B.1.1.434 | 0.000349 |
S | 90 | V90del | GTT | --- | 1 | 1 | B.1.1.523 | 0.001563 |
S | 90 | V90del | GTT | --- | 1 | 1 | B.1.160 | 0.000031 |
S | 90 | V90del | GTT | --- | 1 | 1 | B.1.177.17 | 0.000821 |
S | 90 | V90del | GTT | --- | 1 | 1 | B.1.177.18 | 0.00116 |
S | 90 | V90del | GTT | --- | 1 | 1 | B.1.177.21 | 0.000076 |
S | 90 | V90del | GTT | --- | 1 | 1 | B.1.177.51 | 0.004566 |
S | 90 | V90del | GTT | --- | 1 | 1 | B.1.177.55 | 0.002331 |
S | 90 | V90del | GTT | --- | 1 | 1 | B.1.179 | 0.003759 |
S | 90 | V90del | GTT | --- | 1 | 1 | B.1.258.16 | 0.001637 |
S | 90 | V90del | GTT | --- | 1 | 1 | B.1.36.18 | 0.00042 |
S | 90 | V90del | GTT | --- | 1 | 1 | B.1.561 | 0.000397 |
S | 90 | V90del | GTT | --- | 1 | 1 | B.1.620 | 0.000946 |
S | 90 | V90del | GTT | --- | 1 | 1 | C.35 | 0.000774 |
S | 90 | V90del | GTT | --- | 1 | 1 | C.36.3 | 0.000567 |
S | 90 | V90del | GTT | --- | 1 | 1 | P.1.1 | 0.000318 |
S | 90 | V90del | GTT | --- | 1 | 1 | Q.1 | 0.000126 |
S | 90 | V90del | GTT | --- | 1 | 1 | Q.8 | 0.000165 |
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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