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/nsp3 | 1159 | P1159L | P1977L | nonsyn | cCc | cTc | 4630 | 4619 | 0.997624 | 6194-6196 |
ORF1ab/nsp3 | 1159 | P1159L | P1977L | nonsyn | cCC | cTT | 4630 | 9 | 0.00194384 | 6194-6196 |
ORF1ab/nsp3 | 1159 | P1159L | P1977L | nonsyn | cCC | cTA | 4630 | 1 | 0.000215983 | 6194-6196 |
ORF1ab/nsp3 | 1159 | P1159L | P1977L | nonsyn | cCC | cTG | 4630 | 1 | 0.000215983 | 6194-6196 |
Details of the mutation P1159L 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/nsp3 | 1159 | P1159L | cCc | cTc | 4619 | 4630 | All | 0.000883 |
ORF1ab/nsp3 | 1159 | P1159L | cCC | cTT | 9 | 4630 | All | 0.000002 |
ORF1ab/nsp3 | 1159 | P1159L | cCC | cTG | 1 | 4630 | All | 0 |
ORF1ab/nsp3 | 1159 | P1159L | cCC | cTA | 1 | 4630 | All | 0 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 1349 | 1352 | AY.103 | 0.008376 |
ORF1ab/nsp3 | 1159 | P1159L | cCC | cTT | 3 | 1352 | AY.103 | 0.000019 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 671 | 671 | B.1.1.7 | 0.000601 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 448 | 448 | B.1.617.2 | 0.001687 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 273 | 273 | AY.5.4 | 0.07554 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 273 | 273 | B.1.177 | 0.003595 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 210 | 210 | B.1.22 | 0.27668 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 201 | 201 | AY.4 | 0.000313 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 138 | 138 | B.1.575 | 0.041869 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 100 | 100 | B.1.429 | 0.002353 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 67 | 67 | B.1.2 | 0.00059 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 65 | 65 | AY.26 | 0.00184 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 58 | 58 | AY.98 | 0.004582 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 57 | 57 | B.1.311 | 0.015651 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 48 | 48 | AY.25 | 0.000289 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 42 | 42 | B.1 | 0.000385 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 39 | 39 | AY.44 | 0.000237 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 37 | 37 | B.1.620 | 0.035005 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 32 | 32 | B.1.22.1 | 1 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 31 | 31 | AY.98.1 | 0.001501 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 28 | 28 | AY.35 | 0.006525 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 22 | 23 | AY.43 | 0.000097 |
ORF1ab/nsp3 | 1159 | P1159L | cCC | cTT | 1 | 23 | AY.43 | 0.000004 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 21 | 21 | B.1.160 | 0.000655 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 18 | 19 | B.1.1 | 0.000327 |
ORF1ab/nsp3 | 1159 | P1159L | cCC | cTT | 1 | 19 | B.1.1 | 0.000018 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 18 | 18 | B.1.369 | 0.005134 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 18 | 18 | B.1.526 | 0.000423 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 17 | 17 | AY.3 | 0.000169 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 16 | 16 | Q.8 | 0.002639 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 15 | 15 | P.1 | 0.000236 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 14 | 14 | AY.54 | 0.001335 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 14 | 14 | B.1.637 | 0.001023 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 13 | 13 | B.1.1.254 | 0.146067 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 11 | 11 | AY.120 | 0.000409 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 10 | 10 | B.1.160.20 | 0.089286 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 9 | 9 | AY.118 | 0.000564 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 9 | 9 | AY.45 | 0.001095 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 8 | 8 | AY.39 | 0.000198 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 7 | 7 | AY.106 | 0.002344 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 7 | 7 | AY.32 | 0.003727 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 6 | 7 | B.1.221 | 0.000426 |
ORF1ab/nsp3 | 1159 | P1159L | cCC | cTA | 1 | 7 | B.1.221 | 0.000071 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 7 | 7 | B.1.258.11 | 0.002774 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 6 | 6 | AY.119 | 0.000212 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 6 | 6 | AY.23 | 0.000418 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 6 | 6 | AY.9.2 | 0.00022 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 6 | 6 | B.1.576 | 0.00544 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 6 | 6 | C.37 | 0.000696 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 5 | 5 | AE.8 | 0.002445 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 2 | 4 | 0.111111 | |
ORF1ab/nsp3 | 1159 | P1159L | cCC | cTT | 1 | 4 | 0.055556 | |
ORF1ab/nsp3 | 1159 | P1159L | cCC | cTG | 1 | 4 | 0.055556 | |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 4 | 4 | AY.20 | 0.000155 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 4 | 4 | AY.5 | 0.000083 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 4 | 4 | AY.60 | 0.003752 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 4 | 4 | B.1.1.50 | 0.002716 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 4 | 4 | D.2 | 0.0003 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 3 | 3 | AY.100 | 0.000138 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 3 | 3 | AY.102 | 0.00008 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 3 | 3 | AY.109 | 0.002219 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 3 | 3 | AY.27 | 0.000194 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 3 | 3 | AY.3.1 | 0.000256 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 3 | 3 | AY.39.1 | 0.000119 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 3 | 3 | AY.4.2 | 0.000065 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 3 | 3 | AY.4.2.1 | 0.000447 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 3 | 3 | AY.46.4 | 0.000494 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 3 | 3 | AY.92 | 0.000862 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 3 | 3 | B.1.243 | 0.000209 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 3 | 3 | B.1.36 | 0.000438 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 3 | 3 | B.1.400 | 0.001287 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 3 | 3 | P.1.14 | 0.000143 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 3 | 3 | P.2 | 0.00056 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 2 | 2 | AY.121 | 0.000271 |
ORF1ab/nsp3 | 1159 | P1159L | cCC | cTT | 2 | 2 | AY.33 | 0.000134 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 2 | 2 | AY.6 | 0.000082 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 2 | 2 | AY.61 | 0.00021 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 2 | 2 | AY.69 | 0.000373 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 2 | 2 | AY.74 | 0.000231 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 2 | 2 | AY.75 | 0.000112 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 2 | 2 | AY.85 | 0.000854 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 2 | 2 | AY.9.1 | 0.000167 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 2 | 2 | B | 0.000256 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 2 | 2 | B.1.1.307 | 0.005063 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 2 | 2 | B.1.1.420 | 0.002012 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 2 | 2 | B.1.1.519 | 0.000079 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 2 | 2 | B.1.213 | 0.029851 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 2 | 2 | B.1.258 | 0.000133 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 2 | 2 | B.1.351 | 0.000059 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 2 | 2 | B.1.36.27 | 0.001527 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 2 | 2 | B.1.408 | 0.00738 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 2 | 2 | B.1.621 | 0.000177 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 2 | 2 | Q.1 | 0.000253 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 1 | 1 | A.21 | 0.00277 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 1 | 1 | AY.107 | 0.000466 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 1 | 1 | AY.116 | 0.000287 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 1 | 1 | AY.117 | 0.000085 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 1 | 1 | AY.29 | 0.000016 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 1 | 1 | AY.34.1 | 0.00051 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 1 | 1 | AY.46 | 0.000104 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 1 | 1 | AY.46.2 | 0.000635 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 1 | 1 | AY.5.3 | 0.000337 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 1 | 1 | AY.50 | 0.000799 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 1 | 1 | AY.53 | 0.000288 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 1 | 1 | AY.73 | 0.000665 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 1 | 1 | AY.82 | 0.001357 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 1 | 1 | AY.88 | 0.000884 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 1 | 1 | AY.90 | 0.000684 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 1 | 1 | B.1.1.1 | 0.000327 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 1 | 1 | B.1.1.101 | 0.01 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 1 | 1 | B.1.1.159 | 0.004673 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 1 | 1 | B.1.1.33 | 0.000421 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 1 | 1 | B.1.1.359 | 0.027778 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 1 | 1 | B.1.1.375 | 0.011905 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 1 | 1 | B.1.1.435 | 0.034483 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 1 | 1 | B.1.1.46 | 0.004367 |
ORF1ab/nsp3 | 1159 | P1159L | cCC | cTT | 1 | 1 | B.1.1.486 | 0.001577 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 1 | 1 | B.1.110.3 | 0.000718 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 1 | 1 | B.1.146 | 0.004237 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 1 | 1 | B.1.160.28 | 0.002924 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 1 | 1 | B.1.177.10 | 0.000878 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 1 | 1 | B.1.177.32 | 0.00135 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 1 | 1 | B.1.177.45 | 0.000381 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 1 | 1 | B.1.177.57 | 0.000281 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 1 | 1 | B.1.177.7 | 0.000165 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 1 | 1 | B.1.214.2 | 0.0006 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 1 | 1 | B.1.338 | 0.008621 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 1 | 1 | B.1.36.18 | 0.00042 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 1 | 1 | B.1.36.31 | 0.001751 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 1 | 1 | B.1.403 | 0.003268 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 1 | 1 | B.1.404 | 0.001302 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 1 | 1 | B.1.525 | 0.000113 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 1 | 1 | B.1.617.1 | 0.000129 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 1 | 1 | B.1.619 | 0.000871 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 1 | 1 | B.1.623 | 0.000536 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 1 | 1 | B.1.628 | 0.000352 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 1 | 1 | B.29 | 0.003509 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 1 | 1 | B.30 | 0.014706 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 1 | 1 | B.40 | 0.000364 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 1 | 1 | C.35 | 0.000774 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 1 | 1 | C.36 | 0.000911 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 1 | 1 | P.1.16 | 0.000374 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 1 | 1 | P.1.7 | 0.000319 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 1 | 1 | P.3 | 0.001595 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 1 | 1 | P.7 | 0.004367 |
ORF1ab/nsp3 | 1159 | P1159L | cCc | cTc | 1 | 1 | R.1 | 0.00009 |
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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