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 | P139P | syn | ccA | ccT | 1152 | 584 | 0.506944 | 21977-21979 | |
S | 139 | P139P | syn | ccA | ccG | 1152 | 522 | 0.453125 | 21977-21979 | |
S | 139 | P139P | syn | ccA | ccC | 1152 | 46 | 0.0399306 | 21977-21979 | |
S | 139 | P139del | del | CCA | --- | 943 | 943 | 1 | 21977-21979 | |
S | 139 | P139S | nonsyn | Cca | Tca | 144 | 140 | 0.972222 | 21977-21979 | |
S | 139 | P139S | nonsyn | CcA | TcC | 144 | 3 | 0.0208333 | 21977-21979 | |
S | 139 | P139S | nonsyn | CcA | TcT | 144 | 1 | 0.00694444 | 21977-21979 | |
S | 139 | P139L | nonsyn | cCa | cTa | 75 | 70 | 0.933333 | 21977-21979 | |
S | 139 | P139L | nonsyn | cCA | cTC | 75 | 3 | 0.04 | 21977-21979 | |
S | 139 | P139L | nonsyn | CCa | TTa | 75 | 1 | 0.0133333 | 21977-21979 | |
S | 139 | P139L | nonsyn | cCA | cTT | 75 | 1 | 0.0133333 | 21977-21979 | |
S | 139 | P139T | nonsyn | Cca | Aca | 27 | 26 | 0.962963 | 21977-21979 | |
S | 139 | P139T | nonsyn | CcA | AcT | 27 | 1 | 0.037037 | 21977-21979 | |
S | 139 | P139Q | nonsyn | cCa | cAa | 16 | 16 | 1 | 21977-21979 | |
S | 139 | P139del2 | del | cCA | c-- | 12 | 5 | 0.416667 | 21977-21979 | |
S | 139 | P139del2 | del | CCa | --a | 12 | 4 | 0.333333 | 21977-21979 | |
S | 139 | P139del2 | del | CCA | --N | 12 | 3 | 0.25 | 21977-21979 | |
S | 139 | P139del1 | del | ccA | cc- | 11 | 5 | 0.454545 | 21977-21979 | |
S | 139 | P139del1 | del | Cca | -ca | 11 | 3 | 0.272727 | 21977-21979 | |
S | 139 | P139del1 | del | CCA | -NN | 11 | 2 | 0.181818 | 21977-21979 | |
S | 139 | P139del1 | del | CCa | -Aa | 11 | 1 | 0.0909091 | 21977-21979 | |
S | 139 | P139R | nonsyn | cCa | cGa | 7 | 6 | 0.857143 | 21977-21979 | |
S | 139 | P139R | nonsyn | cCA | cGG | 7 | 1 | 0.142857 | 21977-21979 | |
S | 139 | P139A | nonsyn | Cca | Gca | 5 | 4 | 0.8 | 21977-21979 | |
S | 139 | P139A | nonsyn | CcA | GcT | 5 | 1 | 0.2 | 21977-21979 | |
S | 139 | P139H | nonsyn | cCA | cAT | 4 | 4 | 1 | 21977-21979 | |
S | 139 | P139X | nonsyn | CCa | TAa | 2 | 1 | 0.5 | 21977-21979 | |
S | 139 | P139X | nonsyn | CCA | TAG | 2 | 1 | 0.5 | 21977-21979 | |
S | 139 | P139F | nonsyn | CCA | TTC | 1 | 1 | 1 | 21977-21979 | |
S | 139 | P139Y | nonsyn | CCA | TAT | 1 | 1 | 1 | 21977-21979 | |
S | 139 | P139I | nonsyn | CCa | ATa | 1 | 1 | 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 | P139P | ccA | ccT | 584 | 1152 | All | 0.000112 |
S | 139 | P139P | ccA | ccG | 522 | 1152 | All | 0.0001 |
S | 139 | P139P | ccA | ccC | 46 | 1152 | All | 0.000009 |
S | 139 | P139del | CCA | --- | 943 | 943 | All | 0.00018 |
S | 139 | P139P | ccA | ccT | 339 | 354 | AY.4 | 0.000528 |
S | 139 | P139P | ccA | ccG | 15 | 354 | AY.4 | 0.000023 |
S | 139 | P139P | ccA | ccT | 121 | 192 | B.1.1.7 | 0.000108 |
S | 139 | P139P | ccA | ccG | 71 | 192 | B.1.1.7 | 0.000064 |
S | 139 | P139del | CCA | --- | 160 | 160 | AT.1 | 0.820513 |
S | 139 | P139S | Cca | Tca | 140 | 144 | All | 0.000027 |
S | 139 | P139S | CcA | TcC | 3 | 144 | All | 0.000001 |
S | 139 | P139S | CcA | TcT | 1 | 144 | All | 0 |
S | 139 | P139P | ccA | ccG | 106 | 106 | B.1.177.81 | 0.020068 |
S | 139 | P139del | CCA | --- | 100 | 100 | C.38 | 0.806452 |
S | 139 | P139del | CCA | --- | 98 | 98 | P.1 | 0.001544 |
S | 139 | P139P | ccA | ccG | 93 | 93 | AY.3 | 0.000925 |
S | 139 | P139L | cCa | cTa | 70 | 75 | All | 0.000013 |
S | 139 | P139L | cCA | cTC | 3 | 75 | All | 0.000001 |
S | 139 | P139L | CCa | TTa | 1 | 75 | All | 0 |
S | 139 | P139L | cCA | cTT | 1 | 75 | All | 0 |
S | 139 | P139P | ccA | ccG | 66 | 66 | AY.75 | 0.003697 |
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 | P139P | ccA | ccC | 23 | 33 | B.1 | 0.000211 |
S | 139 | P139P | ccA | ccT | 5 | 33 | B.1 | 0.000046 |
S | 139 | P139P | ccA | ccG | 5 | 33 | B.1 | 0.000046 |
S | 139 | P139S | Cca | Tca | 33 | 33 | B.1.1.7 | 0.00003 |
S | 139 | P139P | ccA | ccT | 29 | 29 | P.1.3 | 1 |
S | 139 | P139T | Cca | Aca | 26 | 27 | All | 0.000005 |
S | 139 | P139T | CcA | AcT | 1 | 27 | All | 0 |
S | 139 | P139P | ccA | ccG | 24 | 24 | AY.3.1 | 0.002046 |
S | 139 | P139P | ccA | ccG | 23 | 24 | AY.44 | 0.00014 |
S | 139 | P139P | ccA | ccT | 1 | 24 | AY.44 | 0.000006 |
S | 139 | P139P | ccA | ccG | 15 | 23 | B.1.617.2 | 0.000056 |
S | 139 | P139P | ccA | ccT | 8 | 23 | B.1.617.2 | 0.00003 |
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 | P139L | cCa | cTa | 20 | 20 | B.1.1.7 | 0.000018 |
S | 139 | P139S | Cca | Tca | 18 | 18 | AY.4 | 0.000028 |
S | 139 | P139P | ccA | ccT | 16 | 18 | B.1.177 | 0.000211 |
S | 139 | P139P | ccA | ccG | 2 | 18 | B.1.177 | 0.000026 |
S | 139 | P139Q | cCa | cAa | 16 | 16 | All | 0.000003 |
S | 139 | P139del | CCA | --- | 16 | 16 | AY.4.2 | 0.000347 |
S | 139 | P139del | CCA | --- | 15 | 15 | AY.44 | 0.000091 |
S | 139 | P139P | ccA | ccG | 13 | 14 | AY.43 | 0.000058 |
S | 139 | P139P | ccA | ccT | 1 | 14 | AY.43 | 0.000004 |
S | 139 | P139del | CCA | --- | 13 | 13 | AY.25 | 0.000078 |
S | 139 | P139del2 | cCA | c-- | 5 | 12 | All | 0.000001 |
S | 139 | P139del2 | CCa | --a | 4 | 12 | All | 0.000001 |
S | 139 | P139del2 | CCA | --N | 3 | 12 | All | 0.000001 |
S | 139 | P139del | CCA | --- | 12 | 12 | AY.102 | 0.000318 |
S | 139 | P139P | ccA | ccC | 6 | 12 | AY.26 | 0.00017 |
S | 139 | P139P | ccA | ccG | 5 | 12 | AY.26 | 0.000142 |
S | 139 | P139P | ccA | ccT | 1 | 12 | AY.26 | 0.000028 |
S | 139 | P139P | ccA | ccT | 11 | 12 | B.1.429 | 0.000259 |
S | 139 | P139P | ccA | ccG | 1 | 12 | B.1.429 | 0.000024 |
S | 139 | P139del1 | ccA | cc- | 5 | 11 | All | 0.000001 |
S | 139 | P139del1 | Cca | -ca | 3 | 11 | All | 0.000001 |
S | 139 | P139del1 | CCA | -NN | 2 | 11 | All | 0 |
S | 139 | P139del1 | CCa | -Aa | 1 | 11 | All | 0 |
S | 139 | P139P | ccA | ccG | 7 | 11 | B.1.2 | 0.000062 |
S | 139 | P139P | ccA | ccT | 4 | 11 | B.1.2 | 0.000035 |
S | 139 | P139S | Cca | Tca | 11 | 11 | B.1.429 | 0.000259 |
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 | P139P | ccA | ccC | 4 | 9 | AY.103 | 0.000025 |
S | 139 | P139P | ccA | ccT | 3 | 9 | AY.103 | 0.000019 |
S | 139 | P139P | ccA | ccG | 2 | 9 | AY.103 | 0.000012 |
S | 139 | P139del | CCA | --- | 9 | 9 | B.1.160 | 0.000281 |
S | 139 | P139del | CCA | --- | 8 | 8 | B.1.1 | 0.000145 |
S | 139 | P139P | ccA | ccC | 5 | 8 | B.1.177.21 | 0.000382 |
S | 139 | P139P | ccA | ccT | 3 | 8 | B.1.177.21 | 0.000229 |
S | 139 | P139P | ccA | ccG | 6 | 8 | B.1.351 | 0.000178 |
S | 139 | P139P | ccA | ccC | 1 | 8 | B.1.351 | 0.00003 |
S | 139 | P139P | ccA | ccT | 1 | 8 | B.1.351 | 0.00003 |
S | 139 | P139P | ccA | ccT | 8 | 8 | B.1.36 | 0.001167 |
S | 139 | P139R | cCa | cGa | 6 | 7 | All | 0.000001 |
S | 139 | P139R | cCA | cGG | 1 | 7 | All | 0 |
S | 139 | P139S | Cca | Tca | 7 | 7 | AY.4.2 | 0.000152 |
S | 139 | P139del | CCA | --- | 7 | 7 | AY.42 | 0.000282 |
S | 139 | P139del | CCA | --- | 7 | 7 | AY.9 | 0.000473 |
S | 139 | P139P | ccA | ccG | 7 | 7 | B.1.1.416 | 0.006335 |
S | 139 | P139T | Cca | Aca | 7 | 7 | B.1.1.7 | 0.000006 |
S | 139 | P139del | CCA | --- | 7 | 7 | B.1.351 | 0.000208 |
S | 139 | P139P | ccA | ccC | 3 | 7 | P.1 | 0.000047 |
S | 139 | P139P | ccA | ccG | 2 | 7 | P.1 | 0.000032 |
S | 139 | P139P | ccA | ccT | 2 | 7 | P.1 | 0.000032 |
S | 139 | P139L | cCa | cTa | 6 | 6 | AY.4 | 0.000009 |
S | 139 | P139S | Cca | Tca | 6 | 6 | AY.44 | 0.000037 |
S | 139 | P139S | Cca | Tca | 6 | 6 | AY.68 | 0.001642 |
S | 139 | P139L | cCa | cTa | 6 | 6 | B.1.429 | 0.000141 |
S | 139 | P139del | CCA | --- | 6 | 6 | B.1.526 | 0.000141 |
S | 139 | P139A | Cca | Gca | 4 | 5 | All | 0.000001 |
S | 139 | P139A | CcA | GcT | 1 | 5 | All | 0 |
S | 139 | P139del | CCA | --- | 5 | 5 | AY.29 | 0.000079 |
S | 139 | P139T | Cca | Aca | 5 | 5 | AY.4 | 0.000008 |
S | 139 | P139del | CCA | --- | 5 | 5 | AY.4.2.1 | 0.000745 |
S | 139 | P139del1 | ccA | cc- | 3 | 5 | B.1.1.7 | 0.000003 |
S | 139 | P139del1 | CCA | -NN | 1 | 5 | B.1.1.7 | 0.000001 |
S | 139 | P139del1 | Cca | -ca | 1 | 5 | B.1.1.7 | 0.000001 |
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 | P139H | cCA | cAT | 4 | 4 | All | 0.000001 |
S | 139 | P139del | CCA | --- | 4 | 4 | AY.103 | 0.000025 |
S | 139 | P139P | ccA | ccG | 4 | 4 | AY.117 | 0.000338 |
S | 139 | P139del | CCA | --- | 4 | 4 | AY.119 | 0.000141 |
S | 139 | P139P | ccA | ccG | 4 | 4 | AY.25 | 0.000024 |
S | 139 | P139del | CCA | --- | 4 | 4 | AY.3 | 0.00004 |
S | 139 | P139P | ccA | ccG | 4 | 4 | AY.62 | 0.001743 |
S | 139 | P139Q | cCa | cAa | 4 | 4 | B.1 | 0.000037 |
S | 139 | P139S | Cca | Tca | 4 | 4 | B.1.1 | 0.000073 |
S | 139 | P139P | ccA | ccG | 4 | 4 | B.1.1 | 0.000073 |
S | 139 | P139P | ccA | ccG | 3 | 4 | B.1.1.222 | 0.000612 |
S | 139 | P139P | ccA | ccT | 1 | 4 | B.1.1.222 | 0.000204 |
S | 139 | P139L | cCA | cTT | 1 | 4 | B.1.221 | 0.000071 |
S | 139 | P139L | CCa | TTa | 1 | 4 | B.1.221 | 0.000071 |
S | 139 | P139L | cCA | cTC | 1 | 4 | B.1.221 | 0.000071 |
S | 139 | P139L | cCa | cTa | 1 | 4 | B.1.221 | 0.000071 |
S | 139 | P139L | cCa | cTa | 4 | 4 | B.1.351 | 0.000119 |
S | 139 | P139L | cCa | cTa | 4 | 4 | B.1.427 | 0.000202 |
S | 139 | P139S | Cca | Tca | 4 | 4 | B.1.427 | 0.000202 |
S | 139 | P139P | ccA | ccT | 3 | 4 | N.5 | 0.0053 |
S | 139 | P139P | ccA | ccG | 1 | 4 | N.5 | 0.001767 |
S | 139 | P139L | cCa | cTa | 3 | 3 | AY.111 | 0.000549 |
S | 139 | P139del | CCA | --- | 3 | 3 | AY.120 | 0.000112 |
S | 139 | P139P | ccA | ccT | 2 | 3 | AY.23 | 0.000139 |
S | 139 | P139P | ccA | ccG | 1 | 3 | AY.23 | 0.00007 |
S | 139 | P139S | Cca | Tca | 3 | 3 | AY.25 | 0.000018 |
S | 139 | P139S | Cca | Tca | 3 | 3 | AY.3 | 0.00003 |
S | 139 | P139del | CCA | --- | 3 | 3 | AY.34.1 | 0.00153 |
S | 139 | P139R | cCa | cGa | 2 | 3 | AY.4 | 0.000003 |
S | 139 | P139R | cCA | cGG | 1 | 3 | AY.4 | 0.000002 |
S | 139 | P139del | CCA | --- | 3 | 3 | AY.47 | 0.000093 |
S | 139 | P139P | ccA | ccT | 3 | 3 | AY.6 | 0.000123 |
S | 139 | P139P | ccA | ccT | 3 | 3 | B.1.1.189 | 0.004539 |
S | 139 | P139del | CCA | --- | 3 | 3 | B.1.1.37 | 0.000579 |
S | 139 | P139P | ccA | ccG | 3 | 3 | B.1.1.456 | 0.166667 |
S | 139 | P139Q | cCa | cAa | 3 | 3 | B.1.1.7 | 0.000003 |
S | 139 | P139L | cCa | cTa | 3 | 3 | B.1.177 | 0.00004 |
S | 139 | P139S | CcA | TcC | 2 | 3 | B.1.221 | 0.000142 |
S | 139 | P139P | ccA | ccG | 2 | 3 | B.1.221 | 0.000142 |
S | 139 | P139P | ccA | ccC | 1 | 3 | B.1.221 | 0.000071 |
S | 139 | P139S | Cca | Tca | 1 | 3 | B.1.221 | 0.000071 |
S | 139 | P139del | CCA | --- | 3 | 3 | B.1.243 | 0.000209 |
S | 139 | P139P | ccA | ccG | 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 | P139T | Cca | Aca | 3 | 3 | B.1.525 | 0.000339 |
S | 139 | P139P | ccA | ccG | 3 | 3 | B.1.526 | 0.000071 |
S | 139 | P139del | CCA | --- | 3 | 3 | B.1.561 | 0.001191 |
S | 139 | P139S | Cca | Tca | 3 | 3 | B.1.617.2 | 0.000011 |
S | 139 | P139L | cCa | cTa | 2 | 3 | B.1.617.2 | 0.000008 |
S | 139 | P139L | cCA | cTC | 1 | 3 | B.1.617.2 | 0.000004 |
S | 139 | P139del | CCA | --- | 3 | 3 | B.1.621 | 0.000266 |
S | 139 | P139S | Cca | Tca | 3 | 3 | D.2 | 0.000225 |
S | 139 | P139S | Cca | Tca | 2 | 3 | P.1 | 0.000032 |
S | 139 | P139S | CcA | TcT | 1 | 3 | P.1 | 0.000016 |
S | 139 | P139del | CCA | --- | 3 | 3 | P.1.16 | 0.001122 |
S | 139 | P139P | ccA | ccT | 1 | 2 | 0.055556 | |
S | 139 | P139P | ccA | ccG | 1 | 2 | 0.055556 | |
S | 139 | P139X | CCa | TAa | 1 | 2 | All | 0 |
S | 139 | P139X | CCA | TAG | 1 | 2 | All | 0 |
S | 139 | P139S | Cca | Tca | 2 | 2 | AY.103 | 0.000012 |
S | 139 | P139del | CCA | --- | 2 | 2 | AY.108 | 0.002205 |
S | 139 | P139P | ccA | ccG | 1 | 2 | AY.34 | 0.000097 |
S | 139 | P139P | ccA | ccT | 1 | 2 | AY.34 | 0.000097 |
S | 139 | P139del | CCA | --- | 2 | 2 | AY.4.5 | 0.000215 |
S | 139 | P139del2 | cCA | c-- | 1 | 2 | AY.43 | 0.000004 |
S | 139 | P139del2 | CCa | --a | 1 | 2 | AY.43 | 0.000004 |
S | 139 | P139R | cCa | cGa | 2 | 2 | AY.44 | 0.000012 |
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 | P139P | ccA | ccT | 2 | 2 | AY.98 | 0.000158 |
S | 139 | P139del | CCA | --- | 2 | 2 | AY.99 | 0.002099 |
S | 139 | P139del | CCA | --- | 2 | 2 | AZ.5 | 0.007018 |
S | 139 | P139L | cCa | cTa | 2 | 2 | B.1 | 0.000018 |
S | 139 | P139S | Cca | Tca | 2 | 2 | B.1 | 0.000018 |
S | 139 | P139T | Cca | Aca | 1 | 2 | B.1 | 0.000009 |
S | 139 | P139T | CcA | AcT | 1 | 2 | B.1 | 0.000009 |
S | 139 | P139del | CCA | --- | 2 | 2 | B.1.1.311 | 0.000716 |
S | 139 | P139S | Cca | Tca | 2 | 2 | B.1.177 | 0.000026 |
S | 139 | P139del | CCA | --- | 2 | 2 | B.1.177.12 | 0.000303 |
S | 139 | P139P | ccA | ccT | 1 | 2 | B.1.177.44 | 0.000519 |
S | 139 | P139P | ccA | ccC | 1 | 2 | B.1.177.44 | 0.000519 |
S | 139 | P139del | CCA | --- | 2 | 2 | B.1.177.57 | 0.000562 |
S | 139 | P139S | Cca | Tca | 2 | 2 | B.1.2 | 0.000018 |
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 | P139P | ccA | ccT | 2 | 2 | B.1.416.1 | 0.003125 |
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 | P139S | Cca | Tca | 2 | 2 | B.1.621 | 0.000177 |
S | 139 | P139S | Cca | Tca | 1 | 2 | B.1.9 | 0.006173 |
S | 139 | P139S | CcA | TcC | 1 | 2 | B.1.9 | 0.006173 |
S | 139 | P139T | Cca | Aca | 2 | 2 | B.6 | 0.00182 |
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 | P139A | Cca | Gca | 1 | 1 | A | 0.000387 |
S | 139 | P139del | CCA | --- | 1 | 1 | A.1 | 0.000282 |
S | 139 | P139del2 | CCA | --N | 1 | 1 | AC.1 | 0.037037 |
S | 139 | P139del | CCA | --- | 1 | 1 | AD.2 | 0.000219 |
S | 139 | P139F | CCA | TTC | 1 | 1 | All | 0 |
S | 139 | P139Y | CCA | TAT | 1 | 1 | All | 0 |
S | 139 | P139I | CCa | ATa | 1 | 1 | All | 0 |
S | 139 | P139P | ccA | ccG | 1 | 1 | AY.100 | 0.000046 |
S | 139 | P139del2 | cCA | c-- | 1 | 1 | AY.101 | 0.00049 |
S | 139 | P139del2 | CCA | --N | 1 | 1 | AY.102 | 0.000027 |
S | 139 | P139T | Cca | Aca | 1 | 1 | AY.102 | 0.000027 |
S | 139 | P139P | ccA | ccG | 1 | 1 | AY.102 | 0.000027 |
S | 139 | P139del | CCA | --- | 1 | 1 | AY.106 | 0.000335 |
S | 139 | P139del | CCA | --- | 1 | 1 | AY.107 | 0.000466 |
S | 139 | P139S | Cca | Tca | 1 | 1 | AY.108 | 0.001103 |
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 | P139P | ccA | ccT | 1 | 1 | AY.120 | 0.000037 |
S | 139 | P139del | CCA | --- | 1 | 1 | AY.120.2 | 0.001285 |
S | 139 | P139del | CCA | --- | 1 | 1 | AY.121 | 0.000135 |
S | 139 | P139P | ccA | ccT | 1 | 1 | AY.14 | 0.000088 |
S | 139 | P139T | Cca | Aca | 1 | 1 | AY.19 | 0.00114 |
S | 139 | P139P | ccA | ccG | 1 | 1 | AY.2 | 0.000356 |
S | 139 | P139S | Cca | Tca | 1 | 1 | AY.20 | 0.000039 |
S | 139 | P139L | cCa | cTa | 1 | 1 | AY.20 | 0.000039 |
S | 139 | P139del2 | CCA | --N | 1 | 1 | AY.21 | 0.001898 |
S | 139 | P139T | Cca | Aca | 1 | 1 | AY.21 | 0.001898 |
S | 139 | P139S | Cca | Tca | 1 | 1 | AY.23 | 0.00007 |
S | 139 | P139del2 | cCA | c-- | 1 | 1 | AY.25 | 0.000006 |
S | 139 | P139del | CCA | --- | 1 | 1 | AY.26 | 0.000028 |
S | 139 | P139del | CCA | --- | 1 | 1 | AY.27 | 0.000065 |
S | 139 | P139P | ccA | ccG | 1 | 1 | AY.29.1 | 0.000221 |
S | 139 | P139del | CCA | --- | 1 | 1 | AY.29.1 | 0.000221 |
S | 139 | P139S | Cca | Tca | 1 | 1 | AY.33 | 0.000067 |
S | 139 | P139del | CCA | --- | 1 | 1 | AY.33 | 0.000067 |
S | 139 | P139del1 | CCa | -Aa | 1 | 1 | AY.34 | 0.000097 |
S | 139 | P139del | CCA | --- | 1 | 1 | AY.35 | 0.000233 |
S | 139 | P139P | ccA | ccG | 1 | 1 | AY.36 | 0.000148 |
S | 139 | P139del | CCA | --- | 1 | 1 | AY.36 | 0.000148 |
S | 139 | P139del | CCA | --- | 1 | 1 | AY.39 | 0.000025 |
S | 139 | P139del1 | CCA | -NN | 1 | 1 | AY.39 | 0.000025 |
S | 139 | P139S | Cca | Tca | 1 | 1 | AY.39.1 | 0.00004 |
S | 139 | P139del2 | cCA | c-- | 1 | 1 | AY.4 | 0.000002 |
S | 139 | P139del | CCA | --- | 1 | 1 | AY.4.1 | 0.000737 |
S | 139 | P139del1 | ccA | cc- | 1 | 1 | AY.4.2.1 | 0.000149 |
S | 139 | P139P | ccA | ccT | 1 | 1 | AY.4.4 | 0.000409 |
S | 139 | P139L | cCa | cTa | 1 | 1 | AY.4.5 | 0.000107 |
S | 139 | P139S | Cca | Tca | 1 | 1 | AY.4.5 | 0.000107 |
S | 139 | P139S | Cca | Tca | 1 | 1 | AY.42 | 0.00004 |
S | 139 | P139T | Cca | Aca | 1 | 1 | AY.43 | 0.000004 |
S | 139 | P139X | CCA | TAG | 1 | 1 | AY.43 | 0.000004 |
S | 139 | P139L | cCa | cTa | 1 | 1 | AY.44 | 0.000006 |
S | 139 | P139T | Cca | Aca | 1 | 1 | AY.44 | 0.000006 |
S | 139 | P139P | ccA | ccG | 1 | 1 | AY.45 | 0.000122 |
S | 139 | P139del | CCA | --- | 1 | 1 | AY.45 | 0.000122 |
S | 139 | P139P | ccA | ccG | 1 | 1 | AY.46.6 | 0.000072 |
S | 139 | P139P | ccA | ccG | 1 | 1 | AY.47 | 0.000031 |
S | 139 | P139del2 | CCa | --a | 1 | 1 | AY.5 | 0.000021 |
S | 139 | P139S | Cca | Tca | 1 | 1 | AY.5 | 0.000021 |
S | 139 | P139del | CCA | --- | 1 | 1 | AY.5 | 0.000021 |
S | 139 | P139P | ccA | ccG | 1 | 1 | AY.5 | 0.000021 |
S | 139 | P139Q | cCa | cAa | 1 | 1 | AY.53 | 0.000288 |
S | 139 | P139H | cCA | cAT | 1 | 1 | AY.55 | 0.000917 |
S | 139 | P139Q | cCa | cAa | 1 | 1 | AY.58 | 0.000907 |
S | 139 | P139Q | cCa | cAa | 1 | 1 | AY.6 | 0.000041 |
S | 139 | P139del | CCA | --- | 1 | 1 | AY.60 | 0.000938 |
S | 139 | P139del | CCA | --- | 1 | 1 | AY.62 | 0.000436 |
S | 139 | P139P | ccA | ccT | 1 | 1 | AY.63 | 0.000387 |
S | 139 | P139A | CcA | GcT | 1 | 1 | AY.69 | 0.000187 |
S | 139 | P139del | CCA | --- | 1 | 1 | AY.7.2 | 0.000559 |
S | 139 | P139L | cCa | cTa | 1 | 1 | AY.70 | 0.000209 |
S | 139 | P139del | CCA | --- | 1 | 1 | AY.73 | 0.000665 |
S | 139 | P139I | CCa | ATa | 1 | 1 | AY.74 | 0.000116 |
S | 139 | P139del | CCA | --- | 1 | 1 | AY.78 | 0.001541 |
S | 139 | P139P | ccA | ccT | 1 | 1 | AY.8 | 0.000606 |
S | 139 | P139del | CCA | --- | 1 | 1 | AY.84 | 0.000437 |
S | 139 | P139L | cCA | cTC | 1 | 1 | AY.85 | 0.000427 |
S | 139 | P139del | CCA | --- | 1 | 1 | AY.85 | 0.000427 |
S | 139 | P139del | CCA | --- | 1 | 1 | AY.9.2 | 0.000037 |
S | 139 | P139P | ccA | ccG | 1 | 1 | AY.9.2 | 0.000037 |
S | 139 | P139A | Cca | Gca | 1 | 1 | AY.90 | 0.000684 |
S | 139 | P139P | ccA | ccT | 1 | 1 | AY.92 | 0.000287 |
S | 139 | P139del | CCA | --- | 1 | 1 | AY.92 | 0.000287 |
S | 139 | P139del | CCA | --- | 1 | 1 | AY.98.1 | 0.000048 |
S | 139 | P139Q | cCa | cAa | 1 | 1 | AY.98.1 | 0.000048 |
S | 139 | P139del | CCA | --- | 1 | 1 | AY.99.1 | 0.001553 |
S | 139 | P139P | ccA | ccT | 1 | 1 | AY.99.2 | 0.000092 |
S | 139 | P139S | Cca | Tca | 1 | 1 | B | 0.000128 |
S | 139 | P139del2 | CCa | --a | 1 | 1 | B.1.1 | 0.000018 |
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 | P139S | Cca | Tca | 1 | 1 | B.1.1.176 | 0.000439 |
S | 139 | P139P | ccA | ccG | 1 | 1 | B.1.1.216 | 0.00089 |
S | 139 | P139P | ccA | ccT | 1 | 1 | B.1.1.25 | 0.000569 |
S | 139 | P139P | ccA | ccG | 1 | 1 | B.1.1.28 | 0.000311 |
S | 139 | P139del | CCA | --- | 1 | 1 | B.1.1.284 | 0.000107 |
S | 139 | P139P | ccA | ccG | 1 | 1 | B.1.1.298 | 0.000862 |
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 | P139Q | cCa | cAa | 1 | 1 | B.1.1.326 | 0.001761 |
S | 139 | P139S | Cca | Tca | 1 | 1 | B.1.1.369 | 0.000446 |
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 | P139S | Cca | Tca | 1 | 1 | B.1.1.423 | 0.0625 |
S | 139 | P139S | Cca | Tca | 1 | 1 | B.1.1.445 | 0.037037 |
S | 139 | P139L | cCa | cTa | 1 | 1 | B.1.1.519 | 0.00004 |
S | 139 | P139L | cCa | cTa | 1 | 1 | B.1.1.524 | 0.020833 |
S | 139 | P139del | CCA | --- | 1 | 1 | B.1.1.528 | 0.004808 |
S | 139 | P139H | cCA | cAT | 1 | 1 | B.1.1.7 | 0.000001 |
S | 139 | P139del | CCA | --- | 1 | 1 | B.1.111 | 0.001175 |
S | 139 | P139P | ccA | ccG | 1 | 1 | B.1.13 | 0.002375 |
S | 139 | P139del | CCA | --- | 1 | 1 | B.1.160.23 | 0.004831 |
S | 139 | P139del1 | Cca | -ca | 1 | 1 | B.1.177 | 0.000013 |
S | 139 | P139T | Cca | Aca | 1 | 1 | B.1.177 | 0.000013 |
S | 139 | P139del | CCA | --- | 1 | 1 | B.1.177.11 | 0.001698 |
S | 139 | P139L | cCa | cTa | 1 | 1 | B.1.177.16 | 0.000664 |
S | 139 | P139S | Cca | Tca | 1 | 1 | B.1.177.17 | 0.000821 |
S | 139 | P139L | cCa | cTa | 1 | 1 | B.1.177.30 | 0.002513 |
S | 139 | P139del | CCA | --- | 1 | 1 | B.1.177.4 | 0.000211 |
S | 139 | P139P | ccA | ccG | 1 | 1 | B.1.177.41 | 0.0025 |
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 | P139P | ccA | ccG | 1 | 1 | B.1.177.57 | 0.000281 |
S | 139 | P139P | ccA | ccG | 1 | 1 | B.1.177.60 | 0.000218 |
S | 139 | P139P | ccA | ccG | 1 | 1 | B.1.177.62 | 0.001192 |
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 | P139S | Cca | Tca | 1 | 1 | B.1.177.81 | 0.000189 |
S | 139 | P139L | cCa | cTa | 1 | 1 | B.1.177.86 | 0.000183 |
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 | P139L | cCa | cTa | 1 | 1 | B.1.2 | 0.000009 |
S | 139 | P139L | cCa | cTa | 1 | 1 | B.1.206 | 0.000816 |
S | 139 | P139F | CCA | TTC | 1 | 1 | B.1.221 | 0.000071 |
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 | P139A | Cca | Gca | 1 | 1 | B.1.234 | 0.000132 |
S | 139 | P139P | ccA | ccG | 1 | 1 | B.1.234 | 0.000132 |
S | 139 | P139S | Cca | Tca | 1 | 1 | B.1.237 | 0.004975 |
S | 139 | P139L | cCa | cTa | 1 | 1 | B.1.243 | 0.00007 |
S | 139 | P139S | Cca | Tca | 1 | 1 | B.1.243 | 0.00007 |
S | 139 | P139S | Cca | Tca | 1 | 1 | B.1.258 | 0.000067 |
S | 139 | P139L | cCa | cTa | 1 | 1 | B.1.258 | 0.000067 |
S | 139 | P139del | CCA | --- | 1 | 1 | B.1.258.11 | 0.000396 |
S | 139 | P139S | Cca | Tca | 1 | 1 | B.1.258.12 | 0.007874 |
S | 139 | P139del | CCA | --- | 1 | 1 | B.1.258.14 | 0.00098 |
S | 139 | P139L | cCa | cTa | 1 | 1 | B.1.279 | 0.000514 |
S | 139 | P139L | cCa | cTa | 1 | 1 | B.1.298 | 0.002114 |
S | 139 | P139T | Cca | Aca | 1 | 1 | B.1.311 | 0.000275 |
S | 139 | P139S | Cca | Tca | 1 | 1 | B.1.351 | 0.00003 |
S | 139 | P139P | ccA | ccG | 1 | 1 | B.1.36.29 | 0.000517 |
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 | P139L | cCa | cTa | 1 | 1 | B.1.396 | 0.000706 |
S | 139 | P139del | CCA | --- | 1 | 1 | B.1.400 | 0.000429 |
S | 139 | P139R | cCa | cGa | 1 | 1 | B.1.407 | 0.035714 |
S | 139 | P139S | Cca | Tca | 1 | 1 | B.1.409 | 0.000781 |
S | 139 | P139del | CCA | --- | 1 | 1 | B.1.416 | 0.001269 |
S | 139 | P139P | ccA | ccT | 1 | 1 | B.1.424 | 0.008065 |
S | 139 | P139P | ccA | ccG | 1 | 1 | B.1.427 | 0.00005 |
S | 139 | P139R | cCa | cGa | 1 | 1 | B.1.429 | 0.000024 |
S | 139 | P139Q | cCa | cAa | 1 | 1 | B.1.429 | 0.000024 |
S | 139 | P139S | Cca | Tca | 1 | 1 | B.1.465 | 0.003802 |
S | 139 | P139P | ccA | ccT | 1 | 1 | B.1.499 | 0.00105 |
S | 139 | P139L | cCa | cTa | 1 | 1 | B.1.526 | 0.000024 |
S | 139 | P139del2 | cCA | c-- | 1 | 1 | B.1.526 | 0.000024 |
S | 139 | P139P | ccA | ccT | 1 | 1 | B.1.575 | 0.000303 |
S | 139 | P139P | ccA | ccG | 1 | 1 | B.1.582 | 0.000491 |
S | 139 | P139del | CCA | --- | 1 | 1 | B.1.585 | 0.027778 |
S | 139 | P139del | CCA | --- | 1 | 1 | B.1.587 | 0.001898 |
S | 139 | P139del1 | Cca | -ca | 1 | 1 | B.1.595 | 0.000261 |
S | 139 | P139Q | cCa | cAa | 1 | 1 | B.1.596 | 0.000087 |
S | 139 | P139del | CCA | --- | 1 | 1 | B.1.596.1 | 0.009346 |
S | 139 | P139P | ccA | ccG | 1 | 1 | B.1.597 | 0.00463 |
S | 139 | P139del | CCA | --- | 1 | 1 | B.1.612 | 0.002653 |
S | 139 | P139Q | cCa | cAa | 1 | 1 | B.1.617.1 | 0.000129 |
S | 139 | P139A | Cca | Gca | 1 | 1 | B.1.617.1 | 0.000129 |
S | 139 | P139H | cCA | cAT | 1 | 1 | B.1.617.2 | 0.000004 |
S | 139 | P139P | ccA | ccT | 1 | 1 | B.1.630 | 0.005236 |
S | 139 | P139S | Cca | Tca | 1 | 1 | B.1.637 | 0.000073 |
S | 139 | P139del | CCA | --- | 1 | 1 | B.1.637 | 0.000073 |
S | 139 | P139P | ccA | ccC | 1 | 1 | B.1.9 | 0.006173 |
S | 139 | P139del | CCA | --- | 1 | 1 | B.1.93 | 0.000934 |
S | 139 | P139del | CCA | --- | 1 | 1 | B.40 | 0.000364 |
S | 139 | P139P | ccA | ccG | 1 | 1 | C.36.1 | 0.004149 |
S | 139 | P139L | cCa | cTa | 1 | 1 | D.2 | 0.000075 |
S | 139 | P139del2 | CCa | --a | 1 | 1 | P.1 | 0.000016 |
S | 139 | P139H | cCA | cAT | 1 | 1 | P.1 | 0.000016 |
S | 139 | P139Y | CCA | TAT | 1 | 1 | P.1 | 0.000016 |
S | 139 | P139Q | cCa | cAa | 1 | 1 | P.1 | 0.000016 |
S | 139 | P139X | CCa | TAa | 1 | 1 | P.1 | 0.000016 |
S | 139 | P139P | ccA | ccC | 1 | 1 | P.1.1 | 0.000318 |
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 | P139S | Cca | Tca | 1 | 1 | P.1.14 | 0.000048 |
S | 139 | P139T | Cca | Aca | 1 | 1 | P.3 | 0.001595 |
S | 139 | P139del1 | ccA | cc- | 1 | 1 | Q.2 | 0.000613 |
S | 139 | P139L | cCa | cTa | 1 | 1 | Q.3 | 0.000145 |
S | 139 | P139del | CCA | --- | 1 | 1 | Q.7 | 0.001111 |
S | 139 | P139P | ccA | ccG | 1 | 1 | R.1 | 0.00009 |
S | 139 | P139S | Cca | Tca | 1 | 1 | Z.1 | 0.00289 |
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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