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/nsp7 | 3 | M3I | M3862I | nonsyn | atG | atT | 3959 | 3685 | 0.930791 | 11849-11851 |
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 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 3685 | 3959 | All | 0.000705 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 1129 | 1129 | B.1.367 | 0.894612 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 699 | 699 | B.1.1.269 | 0.945873 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 305 | 330 | B.1.1.7 | 0.000273 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 183 | 206 | AY.43 | 0.000811 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 160 | 184 | AY.4 | 0.000249 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 138 | 145 | B.1 | 0.001264 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 107 | 108 | B.1.1.70 | 0.036494 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 98 | 98 | AY.42 | 0.003943 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 66 | 69 | B.1.617.2 | 0.000249 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 63 | 65 | AY.103 | 0.000391 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 51 | 51 | B.1.177 | 0.000672 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 50 | 50 | B.1.326 | 0.378788 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 29 | 49 | AY.3 | 0.000288 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 40 | 42 | B.1.1 | 0.000726 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 38 | 39 | AY.86 | 0.031535 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 28 | 37 | AY.44 | 0.00017 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 29 | 35 | B.1.2 | 0.000255 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 32 | 32 | B.1.497 | 0.010072 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 29 | 29 | AA.1 | 0.210145 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 24 | 24 | AY.29 | 0.000379 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 6 | 22 | AY.119 | 0.000212 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 20 | 20 | B.1.160 | 0.000624 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 18 | 19 | AZ.2 | 0.014778 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 15 | 18 | B.1.221 | 0.001065 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 8 | 13 | B.1.258 | 0.000532 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 10 | 12 | B.1.351 | 0.000297 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 9 | 11 | AY.4.2 | 0.000195 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 7 | 11 | B.1.609 | 0.003356 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 11 | 11 | C.35 | 0.008514 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 7 | 11 | P.1 | 0.00011 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 8 | 10 | AY.25 | 0.000048 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 8 | 10 | B | 0.001022 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 9 | 9 | A.2.4 | 0.030303 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 9 | 9 | B.1.1.50 | 0.00611 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 7 | 7 | AY.102 | 0.000186 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 5 | 6 | AY.120 | 0.000186 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 6 | 6 | AY.98 | 0.000474 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 4 | 6 | B.1.526 | 0.000094 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 6 | 6 | C.37 | 0.000696 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 5 | 5 | AY.14 | 0.00044 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 2 | 5 | AY.23 | 0.000139 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 5 | 5 | AY.37 | 0.00158 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 5 | 5 | AY.39.1 | 0.000198 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 5 | 5 | AY.61 | 0.000524 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 5 | 5 | B.1.1.317 | 0.002058 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 5 | 5 | B.1.427 | 0.000252 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 5 | 5 | B.1.577 | 0.003436 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 3 | 4 | AY.20 | 0.000117 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 4 | 4 | AY.33 | 0.000267 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 4 | 4 | AY.52 | 0.003257 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 2 | 4 | AY.54 | 0.000191 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 2 | 4 | AY.6 | 0.000082 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 4 | 4 | B.1.1.222 | 0.000816 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 4 | 4 | B.1.1.28 | 0.001245 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 4 | 4 | B.1.1.372 | 0.002755 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 4 | 4 | B.1.177.77 | 0.002905 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 3 | 4 | B.1.234 | 0.000396 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 4 | 4 | B.1.596 | 0.000349 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 4 | 4 | B.1.617.1 | 0.000516 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 3 | 3 | AY.116 | 0.00086 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 3 | 3 | AY.29.1 | 0.000662 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 2 | 3 | AY.34 | 0.000194 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 3 | 3 | AY.38 | 0.001498 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 2 | 3 | AY.39 | 0.000049 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 2 | 3 | AY.45 | 0.000243 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 3 | 3 | AY.9.1 | 0.000251 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 3 | 3 | B.1.1.519 | 0.000119 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 3 | 3 | B.1.126 | 0.003827 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 3 | 3 | B.1.177.60 | 0.000655 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 3 | 3 | B.1.177.71 | 0.030303 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 3 | 3 | B.1.524 | 0.004219 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 3 | 3 | P.1.1 | 0.000953 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 3 | 3 | Q.1 | 0.000379 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 1 | 2 | AY.24 | 0.000431 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 2 | 2 | AY.35 | 0.000466 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 1 | 2 | AY.5 | 0.000021 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 2 | 2 | AY.67 | 0.000929 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 2 | 2 | AY.74 | 0.000231 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 2 | 2 | AY.98.1 | 0.000097 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 2 | 2 | B.1.177.19 | 0.002861 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 2 | 2 | B.1.177.78 | 0.019417 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 2 | 2 | B.1.311 | 0.000549 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 2 | 2 | B.1.36 | 0.000292 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 2 | 2 | B.1.36.29 | 0.001035 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 2 | 2 | B.1.429 | 0.000047 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 2 | 2 | B.1.529 | 0.111111 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 2 | 2 | B.1.617.3 | 0.00597 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 1 | 2 | B.40 | 0.000364 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 1 | 2 | D.2 | 0.000075 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 2 | 2 | P.1.14 | 0.000096 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 2 | 2 | P.2 | 0.000373 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 1 | 1 | A.2.2 | 0.001689 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 1 | 1 | A.23 | 0.010526 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 1 | 1 | A.3 | 0.002096 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 1 | 1 | AN.1 | 0.02 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 1 | 1 | AY.106 | 0.000335 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 1 | 1 | AY.110 | 0.000113 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 1 | 1 | AY.111 | 0.000183 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 1 | 1 | AY.117 | 0.000085 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 1 | 1 | AY.12 | 0.000316 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 1 | 1 | AY.121 | 0.000135 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 1 | 1 | AY.26 | 0.000028 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 1 | 1 | AY.27 | 0.000065 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 1 | 1 | AY.3.1 | 0.000085 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 1 | 1 | AY.30 | 0.000396 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 1 | 1 | AY.4.3 | 0.000842 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 1 | 1 | AY.4.5 | 0.000107 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 1 | 1 | AY.46 | 0.000104 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 1 | 1 | AY.46.6 | 0.000072 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 1 | 1 | AY.68 | 0.000274 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 1 | 1 | AY.75 | 0.000056 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 1 | 1 | AY.9 | 0.000068 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 1 | 1 | AY.9.2 | 0.000037 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 1 | 1 | AY.92 | 0.000287 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 1 | 1 | B.1.1.25 | 0.000569 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 1 | 1 | B.1.1.306 | 0.000438 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 1 | 1 | B.1.1.318 | 0.000302 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 1 | 1 | B.1.1.33 | 0.000421 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 1 | 1 | B.1.1.376 | 0.005952 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 1 | 1 | B.1.1.39 | 0.00051 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 1 | 1 | B.1.1.521 | 0.005348 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 1 | 1 | B.1.110.3 | 0.000718 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 1 | 1 | B.1.128 | 0.000635 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 1 | 1 | B.1.157 | 0.002985 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 1 | 1 | B.1.177.16 | 0.000664 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 1 | 1 | B.1.177.18 | 0.00116 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 1 | 1 | B.1.177.31 | 0.011494 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 1 | 1 | B.1.177.57 | 0.000281 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 1 | 1 | B.1.177.6 | 0.000977 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 1 | 1 | B.1.177.86 | 0.000183 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 1 | 1 | B.1.189 | 0.004292 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 1 | 1 | B.1.250 | 0.014493 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 1 | 1 | B.1.3 | 0.002618 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 1 | 1 | B.1.321 | 0.034483 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 1 | 1 | B.1.36.39 | 0.002217 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 1 | 1 | B.1.36.9 | 0.003215 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 1 | 1 | B.1.389 | 0.001002 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 1 | 1 | B.1.396 | 0.000706 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 1 | 1 | B.1.448 | 0.002625 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 1 | 1 | B.1.459 | 0.004082 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 1 | 1 | B.1.462 | 0.007246 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 1 | 1 | B.1.499 | 0.00105 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 1 | 1 | B.1.523 | 0.002451 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 1 | 1 | B.1.530 | 0.007143 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 1 | 1 | B.1.533 | 0.009615 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 1 | 1 | B.1.538 | 0.008065 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 1 | 1 | B.1.544 | 0.006024 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 1 | 1 | B.1.547 | 0.02439 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 1 | 1 | B.1.597 | 0.00463 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 1 | 1 | B.1.621 | 0.000089 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 1 | 1 | B.1.621.1 | 0.000506 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 1 | 1 | B.6 | 0.00091 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 1 | 1 | L.1 | 0.001905 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 1 | 1 | P.1.17.1 | 0.000875 |
ORF1ab/nsp7 | 3 | M3I | atG | atT | 1 | 1 | P.6 | 0.003145 |
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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