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 | 139 | P139del | del | CCA | --- | 943 | 943 | 1 | 21977-21979 |
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 |
S | 139 | P139del | CCA | --- | 943 | 943 | All | 0.00018 |
S | 139 | P139del | CCA | --- | 160 | 160 | AT.1 | 0.820513 |
S | 139 | P139del | CCA | --- | 100 | 100 | C.38 | 0.806452 |
S | 139 | P139del | CCA | --- | 98 | 98 | P.1 | 0.001544 |
S | 139 | P139del | CCA | --- | 63 | 63 | B.1.1.7 | 0.000056 |
S | 139 | P139del | CCA | --- | 60 | 60 | AY.4 | 0.000093 |
S | 139 | P139del | CCA | --- | 42 | 42 | B.1.429 | 0.000988 |
S | 139 | P139del | CCA | --- | 39 | 39 | AY.43 | 0.000173 |
S | 139 | P139del | CCA | --- | 22 | 22 | B.1 | 0.000202 |
S | 139 | P139del | CCA | --- | 22 | 22 | B.1.177 | 0.00029 |
S | 139 | P139del | CCA | --- | 21 | 21 | B.1.576 | 0.019039 |
S | 139 | P139del | CCA | --- | 16 | 16 | AY.4.2 | 0.000347 |
S | 139 | P139del | CCA | --- | 15 | 15 | AY.44 | 0.000091 |
S | 139 | P139del | CCA | --- | 13 | 13 | AY.25 | 0.000078 |
S | 139 | P139del | CCA | --- | 12 | 12 | AY.102 | 0.000318 |
S | 139 | P139del | CCA | --- | 11 | 11 | P.1.14 | 0.000526 |
S | 139 | P139del | CCA | --- | 10 | 10 | B.1.2 | 0.000088 |
S | 139 | P139del | CCA | --- | 10 | 10 | B.1.617.2 | 0.000038 |
S | 139 | P139del | CCA | --- | 9 | 9 | B.1.160 | 0.000281 |
S | 139 | P139del | CCA | --- | 8 | 8 | B.1.1 | 0.000145 |
S | 139 | P139del | CCA | --- | 7 | 7 | AY.42 | 0.000282 |
S | 139 | P139del | CCA | --- | 7 | 7 | AY.9 | 0.000473 |
S | 139 | P139del | CCA | --- | 7 | 7 | B.1.351 | 0.000208 |
S | 139 | P139del | CCA | --- | 6 | 6 | B.1.526 | 0.000141 |
S | 139 | P139del | CCA | --- | 5 | 5 | AY.29 | 0.000079 |
S | 139 | P139del | CCA | --- | 5 | 5 | AY.4.2.1 | 0.000745 |
S | 139 | P139del | CCA | --- | 5 | 5 | B.1.234 | 0.00066 |
S | 139 | P139del | CCA | --- | 4 | 4 | 0.222222 | |
S | 139 | P139del | CCA | --- | 4 | 4 | A.2.5 | 0.001996 |
S | 139 | P139del | CCA | --- | 4 | 4 | AY.103 | 0.000025 |
S | 139 | P139del | CCA | --- | 4 | 4 | AY.119 | 0.000141 |
S | 139 | P139del | CCA | --- | 4 | 4 | AY.3 | 0.00004 |
S | 139 | P139del | CCA | --- | 3 | 3 | AY.120 | 0.000112 |
S | 139 | P139del | CCA | --- | 3 | 3 | AY.34.1 | 0.00153 |
S | 139 | P139del | CCA | --- | 3 | 3 | AY.47 | 0.000093 |
S | 139 | P139del | CCA | --- | 3 | 3 | B.1.1.37 | 0.000579 |
S | 139 | P139del | CCA | --- | 3 | 3 | B.1.243 | 0.000209 |
S | 139 | P139del | CCA | --- | 3 | 3 | B.1.319 | 0.009146 |
S | 139 | P139del | CCA | --- | 3 | 3 | B.1.36 | 0.000438 |
S | 139 | P139del | CCA | --- | 3 | 3 | B.1.427 | 0.000151 |
S | 139 | P139del | CCA | --- | 3 | 3 | B.1.561 | 0.001191 |
S | 139 | P139del | CCA | --- | 3 | 3 | B.1.621 | 0.000266 |
S | 139 | P139del | CCA | --- | 3 | 3 | P.1.16 | 0.001122 |
S | 139 | P139del | CCA | --- | 2 | 2 | AY.108 | 0.002205 |
S | 139 | P139del | CCA | --- | 2 | 2 | AY.4.5 | 0.000215 |
S | 139 | P139del | CCA | --- | 2 | 2 | AY.46 | 0.000208 |
S | 139 | P139del | CCA | --- | 2 | 2 | AY.65 | 0.001066 |
S | 139 | P139del | CCA | --- | 2 | 2 | AY.74 | 0.000231 |
S | 139 | P139del | CCA | --- | 2 | 2 | AY.75 | 0.000112 |
S | 139 | P139del | CCA | --- | 2 | 2 | AY.99 | 0.002099 |
S | 139 | P139del | CCA | --- | 2 | 2 | AZ.5 | 0.007018 |
S | 139 | P139del | CCA | --- | 2 | 2 | B.1.1.311 | 0.000716 |
S | 139 | P139del | CCA | --- | 2 | 2 | B.1.177.12 | 0.000303 |
S | 139 | P139del | CCA | --- | 2 | 2 | B.1.177.57 | 0.000562 |
S | 139 | P139del | CCA | --- | 2 | 2 | B.1.241 | 0.001623 |
S | 139 | P139del | CCA | --- | 2 | 2 | B.1.36.38 | 0.003284 |
S | 139 | P139del | CCA | --- | 2 | 2 | B.1.595 | 0.000522 |
S | 139 | P139del | CCA | --- | 2 | 2 | B.1.596 | 0.000174 |
S | 139 | P139del | CCA | --- | 2 | 2 | B.1.620 | 0.001892 |
S | 139 | P139del | CCA | --- | 2 | 2 | C.36.3.1 | 0.005435 |
S | 139 | P139del | CCA | --- | 2 | 2 | C.37 | 0.000232 |
S | 139 | P139del | CCA | --- | 2 | 2 | P.1.10 | 0.000539 |
S | 139 | P139del | CCA | --- | 2 | 2 | P.1.15 | 0.000465 |
S | 139 | P139del | CCA | --- | 2 | 2 | P.1.17 | 0.000324 |
S | 139 | P139del | CCA | --- | 2 | 2 | P.3 | 0.00319 |
S | 139 | P139del | CCA | --- | 1 | 1 | A.1 | 0.000282 |
S | 139 | P139del | CCA | --- | 1 | 1 | AD.2 | 0.000219 |
S | 139 | P139del | CCA | --- | 1 | 1 | AY.106 | 0.000335 |
S | 139 | P139del | CCA | --- | 1 | 1 | AY.107 | 0.000466 |
S | 139 | P139del | CCA | --- | 1 | 1 | AY.109 | 0.00074 |
S | 139 | P139del | CCA | --- | 1 | 1 | AY.118 | 0.000063 |
S | 139 | P139del | CCA | --- | 1 | 1 | AY.12 | 0.000316 |
S | 139 | P139del | CCA | --- | 1 | 1 | AY.120.2 | 0.001285 |
S | 139 | P139del | CCA | --- | 1 | 1 | AY.121 | 0.000135 |
S | 139 | P139del | CCA | --- | 1 | 1 | AY.26 | 0.000028 |
S | 139 | P139del | CCA | --- | 1 | 1 | AY.27 | 0.000065 |
S | 139 | P139del | CCA | --- | 1 | 1 | AY.29.1 | 0.000221 |
S | 139 | P139del | CCA | --- | 1 | 1 | AY.33 | 0.000067 |
S | 139 | P139del | CCA | --- | 1 | 1 | AY.35 | 0.000233 |
S | 139 | P139del | CCA | --- | 1 | 1 | AY.36 | 0.000148 |
S | 139 | P139del | CCA | --- | 1 | 1 | AY.39 | 0.000025 |
S | 139 | P139del | CCA | --- | 1 | 1 | AY.4.1 | 0.000737 |
S | 139 | P139del | CCA | --- | 1 | 1 | AY.45 | 0.000122 |
S | 139 | P139del | CCA | --- | 1 | 1 | AY.5 | 0.000021 |
S | 139 | P139del | CCA | --- | 1 | 1 | AY.60 | 0.000938 |
S | 139 | P139del | CCA | --- | 1 | 1 | AY.62 | 0.000436 |
S | 139 | P139del | CCA | --- | 1 | 1 | AY.7.2 | 0.000559 |
S | 139 | P139del | CCA | --- | 1 | 1 | AY.73 | 0.000665 |
S | 139 | P139del | CCA | --- | 1 | 1 | AY.78 | 0.001541 |
S | 139 | P139del | CCA | --- | 1 | 1 | AY.84 | 0.000437 |
S | 139 | P139del | CCA | --- | 1 | 1 | AY.85 | 0.000427 |
S | 139 | P139del | CCA | --- | 1 | 1 | AY.9.2 | 0.000037 |
S | 139 | P139del | CCA | --- | 1 | 1 | AY.92 | 0.000287 |
S | 139 | P139del | CCA | --- | 1 | 1 | AY.98.1 | 0.000048 |
S | 139 | P139del | CCA | --- | 1 | 1 | AY.99.1 | 0.001553 |
S | 139 | P139del | CCA | --- | 1 | 1 | B.1.1.139 | 0.022727 |
S | 139 | P139del | CCA | --- | 1 | 1 | B.1.1.170 | 0.001247 |
S | 139 | P139del | CCA | --- | 1 | 1 | B.1.1.284 | 0.000107 |
S | 139 | P139del | CCA | --- | 1 | 1 | B.1.1.306 | 0.000438 |
S | 139 | P139del | CCA | --- | 1 | 1 | B.1.1.318 | 0.000302 |
S | 139 | P139del | CCA | --- | 1 | 1 | B.1.1.39 | 0.00051 |
S | 139 | P139del | CCA | --- | 1 | 1 | B.1.1.397 | 0.002252 |
S | 139 | P139del | CCA | --- | 1 | 1 | B.1.1.41 | 0.006329 |
S | 139 | P139del | CCA | --- | 1 | 1 | B.1.1.528 | 0.004808 |
S | 139 | P139del | CCA | --- | 1 | 1 | B.1.111 | 0.001175 |
S | 139 | P139del | CCA | --- | 1 | 1 | B.1.160.23 | 0.004831 |
S | 139 | P139del | CCA | --- | 1 | 1 | B.1.177.11 | 0.001698 |
S | 139 | P139del | CCA | --- | 1 | 1 | B.1.177.4 | 0.000211 |
S | 139 | P139del | CCA | --- | 1 | 1 | B.1.177.42 | 0.000894 |
S | 139 | P139del | CCA | --- | 1 | 1 | B.1.177.45 | 0.000381 |
S | 139 | P139del | CCA | --- | 1 | 1 | B.1.177.5 | 0.001242 |
S | 139 | P139del | CCA | --- | 1 | 1 | B.1.177.54 | 0.000606 |
S | 139 | P139del | CCA | --- | 1 | 1 | B.1.177.76 | 0.002494 |
S | 139 | P139del | CCA | --- | 1 | 1 | B.1.177.81 | 0.000189 |
S | 139 | P139del | CCA | --- | 1 | 1 | B.1.177.86 | 0.000183 |
S | 139 | P139del | CCA | --- | 1 | 1 | B.1.177.87 | 0.000728 |
S | 139 | P139del | CCA | --- | 1 | 1 | B.1.221 | 0.000071 |
S | 139 | P139del | CCA | --- | 1 | 1 | B.1.222 | 0.001692 |
S | 139 | P139del | CCA | --- | 1 | 1 | B.1.232 | 0.000537 |
S | 139 | P139del | CCA | --- | 1 | 1 | B.1.258.11 | 0.000396 |
S | 139 | P139del | CCA | --- | 1 | 1 | B.1.258.14 | 0.00098 |
S | 139 | P139del | CCA | --- | 1 | 1 | B.1.36.31 | 0.001751 |
S | 139 | P139del | CCA | --- | 1 | 1 | B.1.37 | 0.014706 |
S | 139 | P139del | CCA | --- | 1 | 1 | B.1.380 | 0.006623 |
S | 139 | P139del | CCA | --- | 1 | 1 | B.1.396 | 0.000706 |
S | 139 | P139del | CCA | --- | 1 | 1 | B.1.400 | 0.000429 |
S | 139 | P139del | CCA | --- | 1 | 1 | B.1.416 | 0.001269 |
S | 139 | P139del | CCA | --- | 1 | 1 | B.1.585 | 0.027778 |
S | 139 | P139del | CCA | --- | 1 | 1 | B.1.587 | 0.001898 |
S | 139 | P139del | CCA | --- | 1 | 1 | B.1.596.1 | 0.009346 |
S | 139 | P139del | CCA | --- | 1 | 1 | B.1.612 | 0.002653 |
S | 139 | P139del | CCA | --- | 1 | 1 | B.1.637 | 0.000073 |
S | 139 | P139del | CCA | --- | 1 | 1 | B.1.93 | 0.000934 |
S | 139 | P139del | CCA | --- | 1 | 1 | B.40 | 0.000364 |
S | 139 | P139del | CCA | --- | 1 | 1 | P.1.1 | 0.000318 |
S | 139 | P139del | CCA | --- | 1 | 1 | P.1.12 | 0.000484 |
S | 139 | P139del | CCA | --- | 1 | 1 | P.1.13 | 0.000898 |
S | 139 | P139del | CCA | --- | 1 | 1 | Q.7 | 0.001111 |
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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