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/nsp2 | 325 | S325S | S505S | syn | tcC | tcT | 1441 | 1340 | 0.92991 | 1778-1780 |
ORF1ab/nsp2 | 325 | S325S | S505S | syn | tcC | tcA | 1441 | 95 | 0.0659264 | 1778-1780 |
ORF1ab/nsp2 | 325 | S325S | S505S | syn | tcC | tcG | 1441 | 6 | 0.00416378 | 1778-1780 |
Details of the mutation S325S 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/nsp2 | 325 | S325S | tcC | tcT | 1340 | 1441 | All | 0.000256 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcA | 95 | 1441 | All | 0.000018 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcG | 6 | 1441 | All | 0.000001 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcT | 334 | 337 | B.1.617.2 | 0.001258 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcA | 3 | 337 | B.1.617.2 | 0.000011 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcT | 190 | 217 | B.1.1.7 | 0.00017 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcA | 26 | 217 | B.1.1.7 | 0.000023 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcG | 1 | 217 | B.1.1.7 | 0.000001 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcT | 170 | 170 | AY.39.1 | 0.006734 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcT | 70 | 70 | B.1.596 | 0.0061 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcT | 56 | 61 | AY.4 | 0.000087 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcA | 4 | 61 | AY.4 | 0.000006 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcG | 1 | 61 | AY.4 | 0.000002 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcT | 59 | 59 | AY.100 | 0.002714 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcT | 50 | 50 | C.37 | 0.005803 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcT | 34 | 38 | AY.44 | 0.000207 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcA | 4 | 38 | AY.44 | 0.000024 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcT | 33 | 33 | B.1.177.60 | 0.007208 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcT | 28 | 28 | AY.3 | 0.000278 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcT | 21 | 22 | AY.26 | 0.000595 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcA | 1 | 22 | AY.26 | 0.000028 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcT | 22 | 22 | B.1.1.424 | 1 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcT | 17 | 18 | P.1 | 0.000268 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcA | 1 | 18 | P.1 | 0.000016 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcT | 16 | 16 | B.1.177 | 0.000211 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcT | 14 | 15 | B.1.1 | 0.000254 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcA | 1 | 15 | B.1.1 | 0.000018 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcT | 13 | 14 | AY.43 | 0.000058 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcA | 1 | 14 | AY.43 | 0.000004 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcT | 14 | 14 | D.2 | 0.001051 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcT | 10 | 13 | B.1 | 0.000092 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcA | 3 | 13 | B.1 | 0.000027 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcT | 12 | 12 | B.1.429 | 0.000282 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcT | 10 | 10 | AY.25 | 0.00006 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcT | 9 | 9 | AY.20 | 0.00035 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcA | 7 | 9 | P.2 | 0.001306 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcT | 2 | 9 | P.2 | 0.000373 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcT | 4 | 8 | AY.103 | 0.000025 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcA | 4 | 8 | AY.103 | 0.000025 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcT | 8 | 8 | AY.39 | 0.000198 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcT | 8 | 8 | B.1.160 | 0.00025 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcT | 5 | 8 | B.1.351 | 0.000149 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcA | 3 | 8 | B.1.351 | 0.000089 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcA | 7 | 7 | AY.4.2.1 | 0.001043 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcT | 7 | 7 | B.1.1.519 | 0.000278 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcT | 6 | 6 | AY.84 | 0.002625 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcT | 4 | 5 | AY.29 | 0.000063 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcA | 1 | 5 | AY.29 | 0.000016 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcT | 5 | 5 | P.1.1 | 0.001588 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcT | 4 | 4 | AY.102 | 0.000106 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcT | 3 | 4 | B.1.2 | 0.000026 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcG | 1 | 4 | B.1.2 | 0.000009 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcT | 4 | 4 | B.28 | 0.013115 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcT | 3 | 3 | AY.118 | 0.000188 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcT | 2 | 3 | AY.3.1 | 0.000171 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcA | 1 | 3 | AY.3.1 | 0.000085 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcT | 3 | 3 | AY.45 | 0.000365 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcA | 3 | 3 | AY.46.4 | 0.000494 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcT | 3 | 3 | AY.46.6 | 0.000217 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcT | 2 | 3 | AY.9.2 | 0.000073 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcG | 1 | 3 | AY.9.2 | 0.000037 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcA | 3 | 3 | B.1.177.62 | 0.003576 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcA | 3 | 3 | B.1.177.83 | 0.004444 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcT | 2 | 3 | P.1.17 | 0.000324 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcA | 1 | 3 | P.1.17 | 0.000162 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcT | 3 | 3 | P.1.2 | 0.003468 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcA | 2 | 3 | Q.8 | 0.00033 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcT | 1 | 3 | Q.8 | 0.000165 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcA | 2 | 2 | 0.111111 | |
ORF1ab/nsp2 | 325 | S325S | tcC | tcT | 2 | 2 | AF.1 | 0.074074 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcT | 2 | 2 | AY.113 | 0.000285 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcT | 1 | 2 | AY.120 | 0.000037 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcA | 1 | 2 | AY.120 | 0.000037 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcT | 2 | 2 | AY.121 | 0.000271 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcT | 1 | 2 | AY.14 | 0.000088 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcA | 1 | 2 | AY.14 | 0.000088 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcT | 2 | 2 | AY.16.1 | 0.00094 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcT | 2 | 2 | AY.23 | 0.000139 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcT | 2 | 2 | AY.27 | 0.000129 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcT | 1 | 2 | AY.36 | 0.000148 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcA | 1 | 2 | AY.36 | 0.000148 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcT | 2 | 2 | AY.42 | 0.00008 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcT | 1 | 2 | AY.5 | 0.000021 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcG | 1 | 2 | AY.5 | 0.000021 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcT | 1 | 2 | AY.53 | 0.000288 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcG | 1 | 2 | AY.53 | 0.000288 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcT | 2 | 2 | AY.69 | 0.000373 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcT | 2 | 2 | AY.98 | 0.000158 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcA | 2 | 2 | AY.99.2 | 0.000184 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcA | 2 | 2 | B.1.1.214 | 0.000111 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcT | 2 | 2 | B.1.1.220 | 0.003717 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcT | 2 | 2 | B.1.1.28 | 0.000622 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcT | 2 | 2 | B.1.1.354 | 0.008772 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcT | 2 | 2 | B.1.1.372 | 0.001377 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcT | 2 | 2 | B.1.240 | 0.000431 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcT | 2 | 2 | B.1.311 | 0.000549 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcT | 2 | 2 | B.1.526 | 0.000047 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcT | 2 | 2 | B.1.617.1 | 0.000258 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcT | 2 | 2 | B.6.6 | 0.001778 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcT | 2 | 2 | P.1.7 | 0.000639 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcT | 1 | 1 | A | 0.000387 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcT | 1 | 1 | AD.2 | 0.000219 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcT | 1 | 1 | AY.101 | 0.00049 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcA | 1 | 1 | AY.11 | 0.001339 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcA | 1 | 1 | AY.119 | 0.000035 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcA | 1 | 1 | AY.16 | 0.00038 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcT | 1 | 1 | AY.24 | 0.000431 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcT | 1 | 1 | AY.38 | 0.000499 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcT | 1 | 1 | AY.4.2 | 0.000022 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcT | 1 | 1 | AY.47 | 0.000031 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcA | 1 | 1 | AY.61 | 0.000105 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcT | 1 | 1 | AY.75 | 0.000056 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcT | 1 | 1 | AY.75.1 | 0.00018 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcT | 1 | 1 | AY.79 | 0.001211 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcT | 1 | 1 | AY.9 | 0.000068 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcT | 1 | 1 | AY.9.1 | 0.000084 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcA | 1 | 1 | AY.99.1 | 0.001553 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcT | 1 | 1 | B | 0.000128 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcT | 1 | 1 | B.1.1.1 | 0.000327 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcT | 1 | 1 | B.1.1.109 | 0.04 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcT | 1 | 1 | B.1.1.170 | 0.001247 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcT | 1 | 1 | B.1.1.25 | 0.000569 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcT | 1 | 1 | B.1.1.258 | 0.003257 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcT | 1 | 1 | B.1.1.318 | 0.000302 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcT | 1 | 1 | B.1.1.368 | 0.003086 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcT | 1 | 1 | B.1.1.409 | 0.002833 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcT | 1 | 1 | B.1.177.69 | 0.001484 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcT | 1 | 1 | B.1.221 | 0.000071 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcA | 1 | 1 | B.1.236 | 0.002053 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcT | 1 | 1 | B.1.258 | 0.000067 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcT | 1 | 1 | B.1.367 | 0.000792 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcT | 1 | 1 | B.1.369 | 0.000285 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcT | 1 | 1 | B.1.428 | 0.00102 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcA | 1 | 1 | B.1.438.1 | 0.000107 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcT | 1 | 1 | B.1.443 | 0.004673 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcT | 1 | 1 | B.1.520 | 0.021739 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcT | 1 | 1 | B.1.525 | 0.000113 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcT | 1 | 1 | B.1.564 | 0.000426 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcT | 1 | 1 | B.1.621 | 0.000089 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcT | 1 | 1 | B.1.621.1 | 0.000506 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcT | 1 | 1 | P.1.14 | 0.000048 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcT | 1 | 1 | P.1.15 | 0.000232 |
ORF1ab/nsp2 | 325 | S325S | tcC | tcT | 1 | 1 | P.1.4 | 0.000977 |
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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