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 | 242 | L242del | del | CTT | --- | 39205 | 39205 | 1 | 22286-22288 |
Details of the mutation L242del 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 | 242 | L242del | CTT | --- | 39205 | 39205 | All | 0.007498 |
S | 242 | L242del | CTT | --- | 30216 | 30216 | B.1.351 | 0.898216 |
S | 242 | L242del | CTT | --- | 3136 | 3136 | B.1.351.2 | 0.948865 |
S | 242 | L242del | CTT | --- | 1390 | 1390 | B.1.351.5 | 0.833333 |
S | 242 | L242del | CTT | --- | 1035 | 1035 | B.1.351.3 | 0.907099 |
S | 242 | L242del | CTT | --- | 1012 | 1012 | B.1.620 | 0.957427 |
S | 242 | L242del | CTT | --- | 649 | 649 | AY.4 | 0.00101 |
S | 242 | L242del | CTT | --- | 371 | 371 | B.1.1.7 | 0.000332 |
S | 242 | L242del | CTT | --- | 307 | 307 | B.1 | 0.002812 |
S | 242 | L242del | CTT | --- | 126 | 126 | B.1.415.1 | 0.954545 |
S | 242 | L242del | CTT | --- | 55 | 55 | B.1.617.2 | 0.000207 |
S | 242 | L242del | CTT | --- | 48 | 48 | B.1.1 | 0.000871 |
S | 242 | L242del | CTT | --- | 41 | 41 | AY.25 | 0.000247 |
S | 242 | L242del | CTT | --- | 40 | 40 | AY.103 | 0.000248 |
S | 242 | L242del | CTT | --- | 40 | 40 | AY.43 | 0.000177 |
S | 242 | L242del | CTT | --- | 36 | 36 | AY.44 | 0.000219 |
S | 242 | L242del | CTT | --- | 31 | 31 | B.1.2 | 0.000273 |
S | 242 | L242del | CTT | --- | 26 | 26 | AY.3 | 0.000259 |
S | 242 | L242del | CTT | --- | 26 | 26 | B.1.160 | 0.000811 |
S | 242 | L242del | CTT | --- | 25 | 25 | B.1.177 | 0.000329 |
S | 242 | L242del | CTT | --- | 24 | 24 | B.1.526 | 0.000564 |
S | 242 | L242del | CTT | --- | 23 | 23 | P.1 | 0.000362 |
S | 242 | L242del | CTT | --- | 21 | 21 | B.1.429 | 0.000494 |
S | 242 | L242del | CTT | --- | 20 | 20 | AY.119 | 0.000706 |
S | 242 | L242del | CTT | --- | 19 | 19 | P.3 | 0.030303 |
S | 242 | L242del | CTT | --- | 17 | 17 | B.1.636 | 0.114094 |
S | 242 | L242del | CTT | --- | 16 | 16 | C.37 | 0.001857 |
S | 242 | L242del | CTT | --- | 13 | 13 | B.1.221 | 0.000923 |
S | 242 | L242del | CTT | --- | 12 | 12 | B.1.177.7 | 0.001978 |
S | 242 | L242del | CTT | --- | 11 | 11 | AY.26 | 0.000311 |
S | 242 | L242del | CTT | --- | 10 | 10 | B.1.177.86 | 0.001835 |
S | 242 | L242del | CTT | --- | 10 | 10 | P.1.15 | 0.002323 |
S | 242 | L242del | CTT | --- | 9 | 9 | AY.102 | 0.000239 |
S | 242 | L242del | CTT | --- | 9 | 9 | AY.23 | 0.000628 |
S | 242 | L242del | CTT | --- | 9 | 9 | AY.4.2 | 0.000195 |
S | 242 | L242del | CTT | --- | 9 | 9 | B | 0.00115 |
S | 242 | L242del | CTT | --- | 9 | 9 | B.1.525 | 0.001018 |
S | 242 | L242del | CTT | --- | 9 | 9 | B.1.554 | 0.039648 |
S | 242 | L242del | CTT | --- | 8 | 8 | B.1.177.73 | 0.00453 |
S | 242 | L242del | CTT | --- | 8 | 8 | B.1.595 | 0.002088 |
S | 242 | L242del | CTT | --- | 7 | 7 | AY.39 | 0.000173 |
S | 242 | L242del | CTT | --- | 7 | 7 | AY.5 | 0.000145 |
S | 242 | L242del | CTT | --- | 7 | 7 | AY.56 | 0.011236 |
S | 242 | L242del | CTT | --- | 7 | 7 | AY.75 | 0.000392 |
S | 242 | L242del | CTT | --- | 7 | 7 | AY.98.1 | 0.000339 |
S | 242 | L242del | CTT | --- | 7 | 7 | B.1.1.432 | 0.008861 |
S | 242 | L242del | CTT | --- | 7 | 7 | Q.1 | 0.000884 |
S | 242 | L242del | CTT | --- | 6 | 6 | AY.33 | 0.000401 |
S | 242 | L242del | CTT | --- | 5 | 5 | AY.46.6 | 0.000361 |
S | 242 | L242del | CTT | --- | 5 | 5 | AY.75.1 | 0.000902 |
S | 242 | L242del | CTT | --- | 4 | 4 | AY.120 | 0.000149 |
S | 242 | L242del | CTT | --- | 4 | 4 | AY.14 | 0.000352 |
S | 242 | L242del | CTT | --- | 4 | 4 | AY.20 | 0.000155 |
S | 242 | L242del | CTT | --- | 4 | 4 | B.1.1.389 | 0.024242 |
S | 242 | L242del | CTT | --- | 4 | 4 | B.1.258 | 0.000266 |
S | 242 | L242del | CTT | --- | 4 | 4 | B.1.609 | 0.001918 |
S | 242 | L242del | CTT | --- | 4 | 4 | B.1.621 | 0.000354 |
S | 242 | L242del | CTT | --- | 4 | 4 | P.5 | 0.054795 |
S | 242 | L242del | CTT | --- | 3 | 3 | AY.1 | 0.001187 |
S | 242 | L242del | CTT | --- | 3 | 3 | AY.100 | 0.000138 |
S | 242 | L242del | CTT | --- | 3 | 3 | AY.106 | 0.001005 |
S | 242 | L242del | CTT | --- | 3 | 3 | AY.116.1 | 0.000934 |
S | 242 | L242del | CTT | --- | 3 | 3 | AY.29 | 0.000047 |
S | 242 | L242del | CTT | --- | 3 | 3 | AY.36 | 0.000445 |
S | 242 | L242del | CTT | --- | 3 | 3 | AY.4.5 | 0.000322 |
S | 242 | L242del | CTT | --- | 3 | 3 | AY.42 | 0.000121 |
S | 242 | L242del | CTT | --- | 3 | 3 | AY.45 | 0.000365 |
S | 242 | L242del | CTT | --- | 3 | 3 | AY.47 | 0.000093 |
S | 242 | L242del | CTT | --- | 3 | 3 | B.1.1.519 | 0.000119 |
S | 242 | L242del | CTT | --- | 3 | 3 | B.1.170 | 0.012931 |
S | 242 | L242del | CTT | --- | 3 | 3 | B.1.240 | 0.000647 |
S | 242 | L242del | CTT | --- | 3 | 3 | B.1.336 | 0.007317 |
S | 242 | L242del | CTT | --- | 3 | 3 | B.1.416 | 0.003807 |
S | 242 | L242del | CTT | --- | 3 | 3 | B.1.427 | 0.000151 |
S | 242 | L242del | CTT | --- | 3 | 3 | B.1.596 | 0.000261 |
S | 242 | L242del | CTT | --- | 3 | 3 | B.1.617.1 | 0.000387 |
S | 242 | L242del | CTT | --- | 2 | 2 | 0.111111 | |
S | 242 | L242del | CTT | --- | 2 | 2 | AY.105 | 0.001286 |
S | 242 | L242del | CTT | --- | 2 | 2 | AY.114 | 0.000462 |
S | 242 | L242del | CTT | --- | 2 | 2 | AY.118 | 0.000125 |
S | 242 | L242del | CTT | --- | 2 | 2 | AY.13 | 0.000322 |
S | 242 | L242del | CTT | --- | 2 | 2 | AY.3.1 | 0.000171 |
S | 242 | L242del | CTT | --- | 2 | 2 | AY.46 | 0.000208 |
S | 242 | L242del | CTT | --- | 2 | 2 | AY.5.3 | 0.000675 |
S | 242 | L242del | CTT | --- | 2 | 2 | AY.63 | 0.000774 |
S | 242 | L242del | CTT | --- | 2 | 2 | AY.70 | 0.000417 |
S | 242 | L242del | CTT | --- | 2 | 2 | AY.95 | 0.001522 |
S | 242 | L242del | CTT | --- | 2 | 2 | AY.98 | 0.000158 |
S | 242 | L242del | CTT | --- | 2 | 2 | AY.99.2 | 0.000184 |
S | 242 | L242del | CTT | --- | 2 | 2 | B.1.1.222 | 0.000408 |
S | 242 | L242del | CTT | --- | 2 | 2 | B.1.1.28 | 0.000622 |
S | 242 | L242del | CTT | --- | 2 | 2 | B.1.1.294 | 0.002532 |
S | 242 | L242del | CTT | --- | 2 | 2 | B.1.1.318 | 0.000604 |
S | 242 | L242del | CTT | --- | 2 | 2 | B.1.1.375 | 0.02381 |
S | 242 | L242del | CTT | --- | 2 | 2 | B.1.1.507 | 0.017391 |
S | 242 | L242del | CTT | --- | 2 | 2 | B.1.1.528 | 0.009615 |
S | 242 | L242del | CTT | --- | 2 | 2 | B.1.177.16 | 0.001329 |
S | 242 | L242del | CTT | --- | 2 | 2 | B.1.177.2 | 0.009091 |
S | 242 | L242del | CTT | --- | 2 | 2 | B.1.177.31 | 0.022989 |
S | 242 | L242del | CTT | --- | 2 | 2 | B.1.177.54 | 0.001213 |
S | 242 | L242del | CTT | --- | 2 | 2 | B.1.177.81 | 0.000379 |
S | 242 | L242del | CTT | --- | 2 | 2 | B.1.243 | 0.000139 |
S | 242 | L242del | CTT | --- | 2 | 2 | B.1.258.11 | 0.000793 |
S | 242 | L242del | CTT | --- | 2 | 2 | B.1.258.3 | 0.00335 |
S | 242 | L242del | CTT | --- | 2 | 2 | B.1.351.1 | 0.076923 |
S | 242 | L242del | CTT | --- | 2 | 2 | B.1.36 | 0.000292 |
S | 242 | L242del | CTT | --- | 2 | 2 | B.1.576 | 0.001813 |
S | 242 | L242del | CTT | --- | 2 | 2 | B.1.623 | 0.001073 |
S | 242 | L242del | CTT | --- | 2 | 2 | B.1.637 | 0.000146 |
S | 242 | L242del | CTT | --- | 2 | 2 | C.16 | 0.002121 |
S | 242 | L242del | CTT | --- | 2 | 2 | C.36.3 | 0.001134 |
S | 242 | L242del | CTT | --- | 2 | 2 | P.1.12 | 0.000968 |
S | 242 | L242del | CTT | --- | 2 | 2 | Q.2 | 0.001227 |
S | 242 | L242del | CTT | --- | 2 | 2 | Q.4 | 0.00091 |
S | 242 | L242del | CTT | --- | 2 | 2 | Q.8 | 0.00033 |
S | 242 | L242del | CTT | --- | 1 | 1 | A | 0.000387 |
S | 242 | L242del | CTT | --- | 1 | 1 | A.19 | 0.009434 |
S | 242 | L242del | CTT | --- | 1 | 1 | A.2 | 0.000662 |
S | 242 | L242del | CTT | --- | 1 | 1 | A.2.5 | 0.000499 |
S | 242 | L242del | CTT | --- | 1 | 1 | A.23 | 0.010526 |
S | 242 | L242del | CTT | --- | 1 | 1 | A.27 | 0.001656 |
S | 242 | L242del | CTT | --- | 1 | 1 | A.29 | 0.005319 |
S | 242 | L242del | CTT | --- | 1 | 1 | AD.2 | 0.000219 |
S | 242 | L242del | CTT | --- | 1 | 1 | AU.3 | 0.00211 |
S | 242 | L242del | CTT | --- | 1 | 1 | AY.101 | 0.00049 |
S | 242 | L242del | CTT | --- | 1 | 1 | AY.111 | 0.000183 |
S | 242 | L242del | CTT | --- | 1 | 1 | AY.113 | 0.000142 |
S | 242 | L242del | CTT | --- | 1 | 1 | AY.117 | 0.000085 |
S | 242 | L242del | CTT | --- | 1 | 1 | AY.121 | 0.000135 |
S | 242 | L242del | CTT | --- | 1 | 1 | AY.2 | 0.000356 |
S | 242 | L242del | CTT | --- | 1 | 1 | AY.30 | 0.000396 |
S | 242 | L242del | CTT | --- | 1 | 1 | AY.37 | 0.000316 |
S | 242 | L242del | CTT | --- | 1 | 1 | AY.39.1 | 0.00004 |
S | 242 | L242del | CTT | --- | 1 | 1 | AY.4.2.1 | 0.000149 |
S | 242 | L242del | CTT | --- | 1 | 1 | AY.40 | 0.000964 |
S | 242 | L242del | CTT | --- | 1 | 1 | AY.46.1 | 0.001027 |
S | 242 | L242del | CTT | --- | 1 | 1 | AY.5.4 | 0.000277 |
S | 242 | L242del | CTT | --- | 1 | 1 | AY.50 | 0.000799 |
S | 242 | L242del | CTT | --- | 1 | 1 | AY.51 | 0.000909 |
S | 242 | L242del | CTT | --- | 1 | 1 | AY.54 | 0.000095 |
S | 242 | L242del | CTT | --- | 1 | 1 | AY.58 | 0.000907 |
S | 242 | L242del | CTT | --- | 1 | 1 | AY.59 | 0.00053 |
S | 242 | L242del | CTT | --- | 1 | 1 | AY.6 | 0.000041 |
S | 242 | L242del | CTT | --- | 1 | 1 | AY.61 | 0.000105 |
S | 242 | L242del | CTT | --- | 1 | 1 | AY.65 | 0.000533 |
S | 242 | L242del | CTT | --- | 1 | 1 | AY.7.2 | 0.000559 |
S | 242 | L242del | CTT | --- | 1 | 1 | AY.73 | 0.000665 |
S | 242 | L242del | CTT | --- | 1 | 1 | AY.74 | 0.000116 |
S | 242 | L242del | CTT | --- | 1 | 1 | AY.78 | 0.001541 |
S | 242 | L242del | CTT | --- | 1 | 1 | AY.89 | 0.004902 |
S | 242 | L242del | CTT | --- | 1 | 1 | AY.9 | 0.000068 |
S | 242 | L242del | CTT | --- | 1 | 1 | AY.91 | 0.00073 |
S | 242 | L242del | CTT | --- | 1 | 1 | B.1.1.148 | 0.008772 |
S | 242 | L242del | CTT | --- | 1 | 1 | B.1.1.159 | 0.004673 |
S | 242 | L242del | CTT | --- | 1 | 1 | B.1.1.192 | 0.002309 |
S | 242 | L242del | CTT | --- | 1 | 1 | B.1.1.214 | 0.000055 |
S | 242 | L242del | CTT | --- | 1 | 1 | B.1.1.217 | 0.003636 |
S | 242 | L242del | CTT | --- | 1 | 1 | B.1.1.284 | 0.000107 |
S | 242 | L242del | CTT | --- | 1 | 1 | B.1.1.298 | 0.000862 |
S | 242 | L242del | CTT | --- | 1 | 1 | B.1.1.323 | 0.014085 |
S | 242 | L242del | CTT | --- | 1 | 1 | B.1.1.352 | 0.03125 |
S | 242 | L242del | CTT | --- | 1 | 1 | B.1.1.356 | 0.008547 |
S | 242 | L242del | CTT | --- | 1 | 1 | B.1.1.369 | 0.000446 |
S | 242 | L242del | CTT | --- | 1 | 1 | B.1.1.372 | 0.000689 |
S | 242 | L242del | CTT | --- | 1 | 1 | B.1.1.39 | 0.00051 |
S | 242 | L242del | CTT | --- | 1 | 1 | B.1.1.409 | 0.002833 |
S | 242 | L242del | CTT | --- | 1 | 1 | B.1.1.448 | 0.002033 |
S | 242 | L242del | CTT | --- | 1 | 1 | B.1.1.464 | 0.001473 |
S | 242 | L242del | CTT | --- | 1 | 1 | B.1.1.486 | 0.001577 |
S | 242 | L242del | CTT | --- | 1 | 1 | B.1.110.3 | 0.000718 |
S | 242 | L242del | CTT | --- | 1 | 1 | B.1.111 | 0.001175 |
S | 242 | L242del | CTT | --- | 1 | 1 | B.1.139 | 0.000733 |
S | 242 | L242del | CTT | --- | 1 | 1 | B.1.160.7 | 0.002079 |
S | 242 | L242del | CTT | --- | 1 | 1 | B.1.177.18 | 0.00116 |
S | 242 | L242del | CTT | --- | 1 | 1 | B.1.177.28 | 0.007407 |
S | 242 | L242del | CTT | --- | 1 | 1 | B.1.177.4 | 0.000211 |
S | 242 | L242del | CTT | --- | 1 | 1 | B.1.177.44 | 0.000519 |
S | 242 | L242del | CTT | --- | 1 | 1 | B.1.177.51 | 0.004566 |
S | 242 | L242del | CTT | --- | 1 | 1 | B.1.177.60 | 0.000218 |
S | 242 | L242del | CTT | --- | 1 | 1 | B.1.177.62 | 0.001192 |
S | 242 | L242del | CTT | --- | 1 | 1 | B.1.177.69 | 0.001484 |
S | 242 | L242del | CTT | --- | 1 | 1 | B.1.177.77 | 0.000726 |
S | 242 | L242del | CTT | --- | 1 | 1 | B.1.177.82 | 0.000477 |
S | 242 | L242del | CTT | --- | 1 | 1 | B.1.177.85 | 0.005435 |
S | 242 | L242del | CTT | --- | 1 | 1 | B.1.177.87 | 0.000728 |
S | 242 | L242del | CTT | --- | 1 | 1 | B.1.22 | 0.001318 |
S | 242 | L242del | CTT | --- | 1 | 1 | B.1.237 | 0.004975 |
S | 242 | L242del | CTT | --- | 1 | 1 | B.1.258.14 | 0.00098 |
S | 242 | L242del | CTT | --- | 1 | 1 | B.1.258.17 | 0.000104 |
S | 242 | L242del | CTT | --- | 1 | 1 | B.1.36.20 | 0.016949 |
S | 242 | L242del | CTT | --- | 1 | 1 | B.1.36.37 | 0.002778 |
S | 242 | L242del | CTT | --- | 1 | 1 | B.1.367 | 0.000792 |
S | 242 | L242del | CTT | --- | 1 | 1 | B.1.369 | 0.000285 |
S | 242 | L242del | CTT | --- | 1 | 1 | B.1.375 | 0.00082 |
S | 242 | L242del | CTT | --- | 1 | 1 | B.1.399 | 0.001934 |
S | 242 | L242del | CTT | --- | 1 | 1 | B.1.400 | 0.000429 |
S | 242 | L242del | CTT | --- | 1 | 1 | B.1.409 | 0.000781 |
S | 242 | L242del | CTT | --- | 1 | 1 | B.1.416.1 | 0.001563 |
S | 242 | L242del | CTT | --- | 1 | 1 | B.1.417 | 0.028571 |
S | 242 | L242del | CTT | --- | 1 | 1 | B.1.438.1 | 0.000107 |
S | 242 | L242del | CTT | --- | 1 | 1 | B.1.441 | 0.009615 |
S | 242 | L242del | CTT | --- | 1 | 1 | B.1.497 | 0.000315 |
S | 242 | L242del | CTT | --- | 1 | 1 | B.1.517 | 0.000427 |
S | 242 | L242del | CTT | --- | 1 | 1 | B.1.561 | 0.000397 |
S | 242 | L242del | CTT | --- | 1 | 1 | B.1.582 | 0.000491 |
S | 242 | L242del | CTT | --- | 1 | 1 | B.1.599 | 0.00365 |
S | 242 | L242del | CTT | --- | 1 | 1 | B.1.8 | 0.001972 |
S | 242 | L242del | CTT | --- | 1 | 1 | B.6 | 0.00091 |
S | 242 | L242del | CTT | --- | 1 | 1 | C.1.1 | 0.076923 |
S | 242 | L242del | CTT | --- | 1 | 1 | C.1.2 | 0.004255 |
S | 242 | L242del | CTT | --- | 1 | 1 | C.36 | 0.000911 |
S | 242 | L242del | CTT | --- | 1 | 1 | P.1.1 | 0.000318 |
S | 242 | L242del | CTT | --- | 1 | 1 | P.1.14 | 0.000048 |
S | 242 | L242del | CTT | --- | 1 | 1 | P.1.6 | 0.001946 |
S | 242 | L242del | CTT | --- | 1 | 1 | Q.3 | 0.000145 |
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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