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 |
ORF7a | 61 | T61I | nonsyn | aCt | aTt | 5192 | 5181 | 0.997881 | 27574-27576 | |
ORF7a | 61 | T61I | nonsyn | aCT | aTC | 5192 | 7 | 0.00134823 | 27574-27576 | |
ORF7a | 61 | T61I | nonsyn | aCT | aTA | 5192 | 4 | 0.000770416 | 27574-27576 |
Details of the mutation T61I 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 |
ORF7a | 61 | T61I | aCt | aTt | 5181 | 5192 | All | 0.000991 |
ORF7a | 61 | T61I | aCT | aTC | 7 | 5192 | All | 0.000001 |
ORF7a | 61 | T61I | aCT | aTA | 4 | 5192 | All | 0.000001 |
ORF7a | 61 | T61I | aCt | aTt | 2583 | 2583 | B.1.1.7 | 0.002312 |
ORF7a | 61 | T61I | aCt | aTt | 618 | 618 | AY.3 | 0.006147 |
ORF7a | 61 | T61I | aCt | aTt | 367 | 367 | AY.4 | 0.000571 |
ORF7a | 61 | T61I | aCt | aTt | 207 | 207 | B.1.617.2 | 0.000779 |
ORF7a | 61 | T61I | aCt | aTt | 103 | 103 | AY.44 | 0.000627 |
ORF7a | 61 | T61I | aCt | aTt | 98 | 102 | AY.25 | 0.000589 |
ORF7a | 61 | T61I | aCT | aTC | 2 | 102 | AY.25 | 0.000012 |
ORF7a | 61 | T61I | aCT | aTA | 2 | 102 | AY.25 | 0.000012 |
ORF7a | 61 | T61I | aCt | aTt | 89 | 89 | AY.10 | 0.047165 |
ORF7a | 61 | T61I | aCt | aTt | 80 | 80 | AY.46.5 | 0.015873 |
ORF7a | 61 | T61I | aCt | aTt | 79 | 79 | P.1 | 0.001245 |
ORF7a | 61 | T61I | aCt | aTt | 57 | 57 | AY.43 | 0.000253 |
ORF7a | 61 | T61I | aCt | aTt | 52 | 52 | AY.118 | 0.003258 |
ORF7a | 61 | T61I | aCt | aTt | 49 | 49 | B.1.2 | 0.000431 |
ORF7a | 61 | T61I | aCt | aTt | 45 | 45 | B.1.177 | 0.000593 |
ORF7a | 61 | T61I | aCt | aTt | 44 | 44 | B.1.429 | 0.001035 |
ORF7a | 61 | T61I | aCt | aTt | 40 | 40 | B.1.427 | 0.00202 |
ORF7a | 61 | T61I | aCt | aTt | 37 | 37 | AY.103 | 0.00023 |
ORF7a | 61 | T61I | aCt | aTt | 30 | 30 | B.1.1.118 | 0.306122 |
ORF7a | 61 | T61I | aCt | aTt | 27 | 28 | B.1 | 0.000247 |
ORF7a | 61 | T61I | aCT | aTA | 1 | 28 | B.1 | 0.000009 |
ORF7a | 61 | T61I | aCt | aTt | 23 | 23 | AY.100 | 0.001058 |
ORF7a | 61 | T61I | aCt | aTt | 23 | 23 | B.1.1 | 0.000417 |
ORF7a | 61 | T61I | aCt | aTt | 21 | 22 | B.1.351 | 0.000624 |
ORF7a | 61 | T61I | aCT | aTA | 1 | 22 | B.1.351 | 0.00003 |
ORF7a | 61 | T61I | aCt | aTt | 20 | 20 | AY.20 | 0.000777 |
ORF7a | 61 | T61I | aCt | aTt | 17 | 17 | AY.48 | 0.007907 |
ORF7a | 61 | T61I | aCt | aTt | 15 | 15 | B.1.1.519 | 0.000596 |
ORF7a | 61 | T61I | aCt | aTt | 14 | 14 | AY.47 | 0.000435 |
ORF7a | 61 | T61I | aCt | aTt | 13 | 13 | AY.102 | 0.000345 |
ORF7a | 61 | T61I | aCt | aTt | 13 | 13 | AY.26 | 0.000368 |
ORF7a | 61 | T61I | aCt | aTt | 12 | 12 | AY.119 | 0.000424 |
ORF7a | 61 | T61I | aCt | aTt | 12 | 12 | B.1.526 | 0.000282 |
ORF7a | 61 | T61I | aCt | aTt | 11 | 11 | AY.62 | 0.004793 |
ORF7a | 61 | T61I | aCt | aTt | 11 | 11 | B.1.1.398 | 0.035484 |
ORF7a | 61 | T61I | aCt | aTt | 10 | 10 | AY.4.2 | 0.000217 |
ORF7a | 61 | T61I | aCt | aTt | 10 | 10 | B.1.177.12 | 0.001517 |
ORF7a | 61 | T61I | aCt | aTt | 10 | 10 | C.37 | 0.001161 |
ORF7a | 61 | T61I | aCt | aTt | 9 | 9 | AY.34 | 0.000873 |
ORF7a | 61 | T61I | aCt | aTt | 9 | 9 | AY.5 | 0.000186 |
ORF7a | 61 | T61I | aCt | aTt | 7 | 7 | AY.29 | 0.00011 |
ORF7a | 61 | T61I | aCt | aTt | 7 | 7 | B.1.177.81 | 0.001325 |
ORF7a | 61 | T61I | aCt | aTt | 7 | 7 | B.1.637 | 0.000512 |
ORF7a | 61 | T61I | aCt | aTt | 7 | 7 | P.1.14 | 0.000335 |
ORF7a | 61 | T61I | aCt | aTt | 7 | 7 | P.1.4 | 0.006836 |
ORF7a | 61 | T61I | aCt | aTt | 7 | 7 | Q.1 | 0.000884 |
ORF7a | 61 | T61I | aCt | aTt | 6 | 6 | AY.23 | 0.000418 |
ORF7a | 61 | T61I | aCt | aTt | 6 | 6 | AY.33 | 0.000401 |
ORF7a | 61 | T61I | aCt | aTt | 6 | 6 | AY.39.1 | 0.000238 |
ORF7a | 61 | T61I | aCt | aTt | 6 | 6 | AY.6 | 0.000247 |
ORF7a | 61 | T61I | aCt | aTt | 6 | 6 | AY.75 | 0.000336 |
ORF7a | 61 | T61I | aCt | aTt | 6 | 6 | B.1.525 | 0.000679 |
ORF7a | 61 | T61I | aCt | aTt | 5 | 5 | AY.4.2.1 | 0.000745 |
ORF7a | 61 | T61I | aCt | aTt | 5 | 5 | B.1.177.4 | 0.001055 |
ORF7a | 61 | T61I | aCT | aTC | 5 | 5 | B.1.214.2 | 0.002998 |
ORF7a | 61 | T61I | aCt | aTt | 5 | 5 | B.1.258 | 0.000333 |
ORF7a | 61 | T61I | aCt | aTt | 5 | 5 | R.1 | 0.00045 |
ORF7a | 61 | T61I | aCt | aTt | 4 | 4 | AY.117 | 0.000338 |
ORF7a | 61 | T61I | aCt | aTt | 4 | 4 | AY.120 | 0.000149 |
ORF7a | 61 | T61I | aCt | aTt | 4 | 4 | AY.13 | 0.000644 |
ORF7a | 61 | T61I | aCt | aTt | 4 | 4 | AY.70 | 0.000834 |
ORF7a | 61 | T61I | aCt | aTt | 4 | 4 | AY.71 | 0.0019 |
ORF7a | 61 | T61I | aCt | aTt | 4 | 4 | AY.9.1 | 0.000335 |
ORF7a | 61 | T61I | aCt | aTt | 4 | 4 | AY.98 | 0.000316 |
ORF7a | 61 | T61I | aCt | aTt | 4 | 4 | AY.99.2 | 0.000369 |
ORF7a | 61 | T61I | aCt | aTt | 4 | 4 | B.1.36 | 0.000584 |
ORF7a | 61 | T61I | aCt | aTt | 4 | 4 | P.1.15 | 0.000929 |
ORF7a | 61 | T61I | aCt | aTt | 4 | 4 | Q.8 | 0.00066 |
ORF7a | 61 | T61I | aCt | aTt | 3 | 3 | AY.106 | 0.001005 |
ORF7a | 61 | T61I | aCt | aTt | 3 | 3 | AY.114 | 0.000693 |
ORF7a | 61 | T61I | aCt | aTt | 3 | 3 | AY.3.1 | 0.000256 |
ORF7a | 61 | T61I | aCt | aTt | 3 | 3 | AY.34.1 | 0.00153 |
ORF7a | 61 | T61I | aCt | aTt | 3 | 3 | AY.5.3 | 0.001012 |
ORF7a | 61 | T61I | aCt | aTt | 3 | 3 | AY.61 | 0.000314 |
ORF7a | 61 | T61I | aCt | aTt | 3 | 3 | AY.91 | 0.002191 |
ORF7a | 61 | T61I | aCt | aTt | 3 | 3 | B.1.160 | 0.000094 |
ORF7a | 61 | T61I | aCt | aTt | 3 | 3 | B.1.177.21 | 0.000229 |
ORF7a | 61 | T61I | aCt | aTt | 3 | 3 | B.1.177.56 | 0.002003 |
ORF7a | 61 | T61I | aCt | aTt | 3 | 3 | B.1.232 | 0.001612 |
ORF7a | 61 | T61I | aCt | aTt | 3 | 3 | B.1.243 | 0.000209 |
ORF7a | 61 | T61I | aCt | aTt | 3 | 3 | B.1.258.22 | 0.008 |
ORF7a | 61 | T61I | aCt | aTt | 3 | 3 | B.1.596 | 0.000261 |
ORF7a | 61 | T61I | aCt | aTt | 3 | 3 | B.1.617.1 | 0.000387 |
ORF7a | 61 | T61I | aCt | aTt | 3 | 3 | B.1.621 | 0.000266 |
ORF7a | 61 | T61I | aCt | aTt | 3 | 3 | P.1.16 | 0.001122 |
ORF7a | 61 | T61I | aCt | aTt | 2 | 2 | A.29 | 0.010638 |
ORF7a | 61 | T61I | aCt | aTt | 2 | 2 | AY.1 | 0.000791 |
ORF7a | 61 | T61I | aCt | aTt | 2 | 2 | AY.101 | 0.000981 |
ORF7a | 61 | T61I | aCt | aTt | 2 | 2 | AY.120.2 | 0.002571 |
ORF7a | 61 | T61I | aCt | aTt | 2 | 2 | AY.121 | 0.000271 |
ORF7a | 61 | T61I | aCt | aTt | 2 | 2 | AY.14 | 0.000176 |
ORF7a | 61 | T61I | aCt | aTt | 2 | 2 | AY.16 | 0.000759 |
ORF7a | 61 | T61I | aCt | aTt | 2 | 2 | AY.36 | 0.000296 |
ORF7a | 61 | T61I | aCt | aTt | 2 | 2 | AY.39 | 0.000049 |
ORF7a | 61 | T61I | aCt | aTt | 2 | 2 | AY.42 | 0.00008 |
ORF7a | 61 | T61I | aCt | aTt | 2 | 2 | AY.45 | 0.000243 |
ORF7a | 61 | T61I | aCt | aTt | 2 | 2 | AY.73 | 0.001331 |
ORF7a | 61 | T61I | aCt | aTt | 2 | 2 | AY.75.1 | 0.000361 |
ORF7a | 61 | T61I | aCt | aTt | 2 | 2 | AY.79 | 0.002421 |
ORF7a | 61 | T61I | aCt | aTt | 2 | 2 | AY.85 | 0.000854 |
ORF7a | 61 | T61I | aCt | aTt | 2 | 2 | AY.88 | 0.001768 |
ORF7a | 61 | T61I | aCt | aTt | 2 | 2 | AY.9.2 | 0.000073 |
ORF7a | 61 | T61I | aCt | aTt | 2 | 2 | AY.99 | 0.002099 |
ORF7a | 61 | T61I | aCt | aTt | 2 | 2 | B.1.1.231 | 0.006192 |
ORF7a | 61 | T61I | aCt | aTt | 2 | 2 | B.1.177.7 | 0.00033 |
ORF7a | 61 | T61I | aCt | aTt | 2 | 2 | B.1.177.77 | 0.001452 |
ORF7a | 61 | T61I | aCt | aTt | 2 | 2 | B.1.177.82 | 0.000955 |
ORF7a | 61 | T61I | aCt | aTt | 2 | 2 | B.1.221 | 0.000142 |
ORF7a | 61 | T61I | aCt | aTt | 2 | 2 | B.1.221.4 | 0.008333 |
ORF7a | 61 | T61I | aCt | aTt | 2 | 2 | B.1.234 | 0.000264 |
ORF7a | 61 | T61I | aCt | aTt | 2 | 2 | B.1.438.1 | 0.000215 |
ORF7a | 61 | T61I | aCt | aTt | 2 | 2 | B.1.517 | 0.000854 |
ORF7a | 61 | T61I | aCt | aTt | 2 | 2 | N.3 | 0.011628 |
ORF7a | 61 | T61I | aCt | aTt | 1 | 1 | A.1 | 0.000282 |
ORF7a | 61 | T61I | aCt | aTt | 1 | 1 | AD.2 | 0.000219 |
ORF7a | 61 | T61I | aCt | aTt | 1 | 1 | AP.1 | 0.001502 |
ORF7a | 61 | T61I | aCt | aTt | 1 | 1 | AU.1 | 0.001266 |
ORF7a | 61 | T61I | aCt | aTt | 1 | 1 | AY.108 | 0.001103 |
ORF7a | 61 | T61I | aCt | aTt | 1 | 1 | AY.110 | 0.000113 |
ORF7a | 61 | T61I | aCt | aTt | 1 | 1 | AY.113 | 0.000142 |
ORF7a | 61 | T61I | aCt | aTt | 1 | 1 | AY.19 | 0.00114 |
ORF7a | 61 | T61I | aCt | aTt | 1 | 1 | AY.21 | 0.001898 |
ORF7a | 61 | T61I | aCt | aTt | 1 | 1 | AY.27 | 0.000065 |
ORF7a | 61 | T61I | aCt | aTt | 1 | 1 | AY.30 | 0.000396 |
ORF7a | 61 | T61I | aCt | aTt | 1 | 1 | AY.38 | 0.000499 |
ORF7a | 61 | T61I | aCt | aTt | 1 | 1 | AY.46 | 0.000104 |
ORF7a | 61 | T61I | aCt | aTt | 1 | 1 | AY.46.3 | 0.000934 |
ORF7a | 61 | T61I | aCt | aTt | 1 | 1 | AY.46.6 | 0.000072 |
ORF7a | 61 | T61I | aCt | aTt | 1 | 1 | AY.5.4 | 0.000277 |
ORF7a | 61 | T61I | aCt | aTt | 1 | 1 | AY.53 | 0.000288 |
ORF7a | 61 | T61I | aCt | aTt | 1 | 1 | AY.54 | 0.000095 |
ORF7a | 61 | T61I | aCt | aTt | 1 | 1 | AY.59 | 0.00053 |
ORF7a | 61 | T61I | aCt | aTt | 1 | 1 | AY.69 | 0.000187 |
ORF7a | 61 | T61I | aCt | aTt | 1 | 1 | AY.7 | 0.000196 |
ORF7a | 61 | T61I | aCt | aTt | 1 | 1 | AY.7.2 | 0.000559 |
ORF7a | 61 | T61I | aCt | aTt | 1 | 1 | AY.74 | 0.000116 |
ORF7a | 61 | T61I | aCt | aTt | 1 | 1 | AY.84 | 0.000437 |
ORF7a | 61 | T61I | aCt | aTt | 1 | 1 | AY.86 | 0.00083 |
ORF7a | 61 | T61I | aCt | aTt | 1 | 1 | AY.87 | 0.000833 |
ORF7a | 61 | T61I | aCt | aTt | 1 | 1 | AY.92 | 0.000287 |
ORF7a | 61 | T61I | aCt | aTt | 1 | 1 | AY.94 | 0.000443 |
ORF7a | 61 | T61I | aCt | aTt | 1 | 1 | AY.98.1 | 0.000048 |
ORF7a | 61 | T61I | aCt | aTt | 1 | 1 | B.1.1.128 | 0.007092 |
ORF7a | 61 | T61I | aCt | aTt | 1 | 1 | B.1.1.214 | 0.000055 |
ORF7a | 61 | T61I | aCt | aTt | 1 | 1 | B.1.1.222 | 0.000204 |
ORF7a | 61 | T61I | aCt | aTt | 1 | 1 | B.1.1.228 | 0.003049 |
ORF7a | 61 | T61I | aCt | aTt | 1 | 1 | B.1.1.265 | 0.003155 |
ORF7a | 61 | T61I | aCt | aTt | 1 | 1 | B.1.1.277 | 0.000759 |
ORF7a | 61 | T61I | aCt | aTt | 1 | 1 | B.1.1.279 | 0.001121 |
ORF7a | 61 | T61I | aCt | aTt | 1 | 1 | B.1.1.28 | 0.000311 |
ORF7a | 61 | T61I | aCt | aTt | 1 | 1 | B.1.1.300 | 0.010753 |
ORF7a | 61 | T61I | aCt | aTt | 1 | 1 | B.1.1.362 | 0.005618 |
ORF7a | 61 | T61I | aCt | aTt | 1 | 1 | B.1.1.397 | 0.002252 |
ORF7a | 61 | T61I | aCt | aTt | 1 | 1 | B.1.1.411 | 0.014706 |
ORF7a | 61 | T61I | aCt | aTt | 1 | 1 | B.1.1.50 | 0.000679 |
ORF7a | 61 | T61I | aCt | aTt | 1 | 1 | B.1.13 | 0.002375 |
ORF7a | 61 | T61I | aCt | aTt | 1 | 1 | B.1.139 | 0.000733 |
ORF7a | 61 | T61I | aCt | aTt | 1 | 1 | B.1.147 | 0.000756 |
ORF7a | 61 | T61I | aCt | aTt | 1 | 1 | B.1.160.11 | 0.005714 |
ORF7a | 61 | T61I | aCt | aTt | 1 | 1 | B.1.160.14 | 0.002119 |
ORF7a | 61 | T61I | aCt | aTt | 1 | 1 | B.1.177.50 | 0.004695 |
ORF7a | 61 | T61I | aCt | aTt | 1 | 1 | B.1.177.75 | 0.001041 |
ORF7a | 61 | T61I | aCt | aTt | 1 | 1 | B.1.177.86 | 0.000183 |
ORF7a | 61 | T61I | aCt | aTt | 1 | 1 | B.1.210 | 0.002132 |
ORF7a | 61 | T61I | aCt | aTt | 1 | 1 | B.1.236 | 0.002053 |
ORF7a | 61 | T61I | aCt | aTt | 1 | 1 | B.1.258.17 | 0.000104 |
ORF7a | 61 | T61I | aCt | aTt | 1 | 1 | B.1.258.9 | 0.005 |
ORF7a | 61 | T61I | aCt | aTt | 1 | 1 | B.1.346 | 0.001311 |
ORF7a | 61 | T61I | aCt | aTt | 1 | 1 | B.1.351.5 | 0.0006 |
ORF7a | 61 | T61I | aCt | aTt | 1 | 1 | B.1.36.27 | 0.000763 |
ORF7a | 61 | T61I | aCt | aTt | 1 | 1 | B.1.369 | 0.000285 |
ORF7a | 61 | T61I | aCt | aTt | 1 | 1 | B.1.389 | 0.001002 |
ORF7a | 61 | T61I | aCt | aTt | 1 | 1 | B.1.400 | 0.000429 |
ORF7a | 61 | T61I | aCt | aTt | 1 | 1 | B.1.459 | 0.004082 |
ORF7a | 61 | T61I | aCt | aTt | 1 | 1 | B.1.509 | 0.000866 |
ORF7a | 61 | T61I | aCt | aTt | 1 | 1 | B.1.520 | 0.021739 |
ORF7a | 61 | T61I | aCt | aTt | 1 | 1 | B.1.564 | 0.000426 |
ORF7a | 61 | T61I | aCt | aTt | 1 | 1 | B.1.575 | 0.000303 |
ORF7a | 61 | T61I | aCt | aTt | 1 | 1 | B.1.576 | 0.000907 |
ORF7a | 61 | T61I | aCt | aTt | 1 | 1 | B.1.580 | 0.004065 |
ORF7a | 61 | T61I | aCt | aTt | 1 | 1 | B.1.582 | 0.000491 |
ORF7a | 61 | T61I | aCt | aTt | 1 | 1 | B.1.612 | 0.002653 |
ORF7a | 61 | T61I | aCt | aTt | 1 | 1 | B.1.628 | 0.000352 |
ORF7a | 61 | T61I | aCt | aTt | 1 | 1 | B.1.630 | 0.005236 |
ORF7a | 61 | T61I | aCt | aTt | 1 | 1 | B.6 | 0.00091 |
ORF7a | 61 | T61I | aCt | aTt | 1 | 1 | C.36.2 | 0.034483 |
ORF7a | 61 | T61I | aCt | aTt | 1 | 1 | D.2 | 0.000075 |
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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