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/nsp5A-B | 140 | F140F | F3403F | syn | ttC | ttT | 1505 | 1505 | 1 | 10472-10474 |
ORF1ab/nsp5A-B | 140 | F140del | F3403del | del | TTC | --- | 79 | 79 | 1 | 10472-10474 |
ORF1ab/nsp5A-B | 140 | F140L | F3403L | nonsyn | ttC | ttA | 24 | 15 | 0.625 | 10472-10474 |
ORF1ab/nsp5A-B | 140 | F140L | F3403L | nonsyn | Ttc | Ctc | 24 | 6 | 0.25 | 10472-10474 |
ORF1ab/nsp5A-B | 140 | F140L | F3403L | nonsyn | ttC | ttG | 24 | 3 | 0.125 | 10472-10474 |
ORF1ab/nsp5A-B | 140 | F140S | F3403S | nonsyn | tTc | tCc | 11 | 11 | 1 | 10472-10474 |
ORF1ab/nsp5A-B | 140 | F140C | F3403C | nonsyn | tTc | tGc | 9 | 8 | 0.888889 | 10472-10474 |
ORF1ab/nsp5A-B | 140 | F140C | F3403C | nonsyn | tTC | tGT | 9 | 1 | 0.111111 | 10472-10474 |
ORF1ab/nsp5A-B | 140 | F140V | F3403V | nonsyn | Ttc | Gtc | 3 | 2 | 0.666667 | 10472-10474 |
ORF1ab/nsp5A-B | 140 | F140del1 | F3403del1 | del | TtC | -tT | 3 | 1 | 0.333333 | 10472-10474 |
ORF1ab/nsp5A-B | 140 | F140del1 | F3403del1 | del | tTC | tC- | 3 | 1 | 0.333333 | 10472-10474 |
ORF1ab/nsp5A-B | 140 | F140V | F3403V | nonsyn | TtC | GtA | 3 | 1 | 0.333333 | 10472-10474 |
ORF1ab/nsp5A-B | 140 | F140del1 | F3403del1 | del | Ttc | -tc | 3 | 1 | 0.333333 | 10472-10474 |
ORF1ab/nsp5A-B | 140 | F140X | F3403X | nonsyn | tTC | tAG | 1 | 1 | 1 | 10472-10474 |
ORF1ab/nsp5A-B | 140 | F140T | F3403T | nonsyn | TTc | ACc | 1 | 1 | 1 | 10472-10474 |
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/nsp5A-B | 140 | F140F | ttC | ttT | 1505 | 1505 | All | 0.000288 |
ORF1ab/nsp5A-B | 140 | F140F | ttC | ttT | 585 | 585 | B.1.404 | 0.761719 |
ORF1ab/nsp5A-B | 140 | F140F | ttC | ttT | 148 | 148 | AY.39 | 0.003657 |
ORF1ab/nsp5A-B | 140 | F140F | ttC | ttT | 119 | 119 | B.1.36.17 | 0.058794 |
ORF1ab/nsp5A-B | 140 | F140F | ttC | ttT | 98 | 98 | B.1.1.7 | 0.000088 |
ORF1ab/nsp5A-B | 140 | F140del | TTC | --- | 79 | 79 | All | 0.000015 |
ORF1ab/nsp5A-B | 140 | F140F | ttC | ttT | 62 | 62 | AY.25 | 0.000373 |
ORF1ab/nsp5A-B | 140 | F140F | ttC | ttT | 54 | 54 | B.1 | 0.000495 |
ORF1ab/nsp5A-B | 140 | F140F | ttC | ttT | 50 | 50 | AY.26 | 0.001416 |
ORF1ab/nsp5A-B | 140 | F140F | ttC | ttT | 50 | 50 | B.1.1.368 | 0.154321 |
ORF1ab/nsp5A-B | 140 | F140F | ttC | ttT | 38 | 38 | B.1.351 | 0.00113 |
ORF1ab/nsp5A-B | 140 | F140del | TTC | --- | 33 | 33 | AZ.2 | 0.027094 |
ORF1ab/nsp5A-B | 140 | F140F | ttC | ttT | 31 | 31 | B.1.2 | 0.000273 |
ORF1ab/nsp5A-B | 140 | F140L | ttC | ttA | 15 | 24 | All | 0.000003 |
ORF1ab/nsp5A-B | 140 | F140L | Ttc | Ctc | 6 | 24 | All | 0.000001 |
ORF1ab/nsp5A-B | 140 | F140L | ttC | ttG | 3 | 24 | All | 0.000001 |
ORF1ab/nsp5A-B | 140 | F140F | ttC | ttT | 24 | 24 | AY.44 | 0.000146 |
ORF1ab/nsp5A-B | 140 | F140F | ttC | ttT | 20 | 20 | P.1 | 0.000315 |
ORF1ab/nsp5A-B | 140 | F140F | ttC | ttT | 18 | 18 | B.1.617.2 | 0.000068 |
ORF1ab/nsp5A-B | 140 | F140F | ttC | ttT | 17 | 17 | AY.4 | 0.000026 |
ORF1ab/nsp5A-B | 140 | F140del | TTC | --- | 17 | 17 | B.1.1.7 | 0.000015 |
ORF1ab/nsp5A-B | 140 | F140F | ttC | ttT | 14 | 14 | AY.29 | 0.000221 |
ORF1ab/nsp5A-B | 140 | F140F | ttC | ttT | 13 | 13 | AY.102 | 0.000345 |
ORF1ab/nsp5A-B | 140 | F140S | tTc | tCc | 11 | 11 | All | 0.000002 |
ORF1ab/nsp5A-B | 140 | F140F | ttC | ttT | 11 | 11 | AY.85 | 0.004699 |
ORF1ab/nsp5A-B | 140 | F140F | ttC | ttT | 11 | 11 | B.1.177 | 0.000145 |
ORF1ab/nsp5A-B | 140 | F140C | tTc | tGc | 8 | 9 | All | 0.000002 |
ORF1ab/nsp5A-B | 140 | F140C | tTC | tGT | 1 | 9 | All | 0 |
ORF1ab/nsp5A-B | 140 | F140F | ttC | ttT | 8 | 8 | AY.120 | 0.000297 |
ORF1ab/nsp5A-B | 140 | F140F | ttC | ttT | 8 | 8 | AY.3 | 0.00008 |
ORF1ab/nsp5A-B | 140 | F140L | ttC | ttA | 5 | 8 | B.1 | 0.000046 |
ORF1ab/nsp5A-B | 140 | F140L | Ttc | Ctc | 2 | 8 | B.1 | 0.000018 |
ORF1ab/nsp5A-B | 140 | F140L | ttC | ttG | 1 | 8 | B.1 | 0.000009 |
ORF1ab/nsp5A-B | 140 | F140F | ttC | ttT | 7 | 7 | AY.103 | 0.000043 |
ORF1ab/nsp5A-B | 140 | F140F | ttC | ttT | 7 | 7 | B.1.596 | 0.00061 |
ORF1ab/nsp5A-B | 140 | F140del | TTC | --- | 6 | 6 | 0.333333 | |
ORF1ab/nsp5A-B | 140 | F140F | ttC | ttT | 6 | 6 | AY.43 | 0.000027 |
ORF1ab/nsp5A-B | 140 | F140F | ttC | ttT | 6 | 6 | B.1.36 | 0.000875 |
ORF1ab/nsp5A-B | 140 | F140F | ttC | ttT | 5 | 5 | B.1.1 | 0.000091 |
ORF1ab/nsp5A-B | 140 | F140F | ttC | ttT | 5 | 5 | B.1.429 | 0.000118 |
ORF1ab/nsp5A-B | 140 | F140F | ttC | ttT | 4 | 4 | AY.4.2 | 0.000087 |
ORF1ab/nsp5A-B | 140 | F140F | ttC | ttT | 4 | 4 | B.1.160 | 0.000125 |
ORF1ab/nsp5A-B | 140 | F140F | ttC | ttT | 4 | 4 | P.1.14 | 0.000191 |
ORF1ab/nsp5A-B | 140 | F140V | Ttc | Gtc | 2 | 3 | All | 0 |
ORF1ab/nsp5A-B | 140 | F140del1 | tTC | tC- | 1 | 3 | All | 0 |
ORF1ab/nsp5A-B | 140 | F140del1 | TtC | -tT | 1 | 3 | All | 0 |
ORF1ab/nsp5A-B | 140 | F140del1 | Ttc | -tc | 1 | 3 | All | 0 |
ORF1ab/nsp5A-B | 140 | F140V | TtC | GtA | 1 | 3 | All | 0 |
ORF1ab/nsp5A-B | 140 | F140del | TTC | --- | 3 | 3 | AY.4 | 0.000005 |
ORF1ab/nsp5A-B | 140 | F140F | ttC | ttT | 3 | 3 | B | 0.000383 |
ORF1ab/nsp5A-B | 140 | F140S | tTc | tCc | 3 | 3 | B.1 | 0.000027 |
ORF1ab/nsp5A-B | 140 | F140F | ttC | ttT | 3 | 3 | B.1.1.361 | 0.136364 |
ORF1ab/nsp5A-B | 140 | F140F | ttC | ttT | 3 | 3 | B.1.1.39 | 0.001529 |
ORF1ab/nsp5A-B | 140 | F140F | ttC | ttT | 3 | 3 | B.1.177.53 | 0.007177 |
ORF1ab/nsp5A-B | 140 | F140F | ttC | ttT | 3 | 3 | B.1.234 | 0.000396 |
ORF1ab/nsp5A-B | 140 | F140F | ttC | ttT | 3 | 3 | B.1.241 | 0.002435 |
ORF1ab/nsp5A-B | 140 | F140F | ttC | ttT | 2 | 2 | AY.106 | 0.00067 |
ORF1ab/nsp5A-B | 140 | F140F | ttC | ttT | 2 | 2 | AY.117 | 0.000169 |
ORF1ab/nsp5A-B | 140 | F140F | ttC | ttT | 2 | 2 | AY.119 | 0.000071 |
ORF1ab/nsp5A-B | 140 | F140F | ttC | ttT | 2 | 2 | AY.3.1 | 0.000171 |
ORF1ab/nsp5A-B | 140 | F140L | ttC | ttA | 2 | 2 | AY.43 | 0.000009 |
ORF1ab/nsp5A-B | 140 | F140F | ttC | ttT | 2 | 2 | AY.58 | 0.001815 |
ORF1ab/nsp5A-B | 140 | F140F | ttC | ttT | 2 | 2 | AY.6 | 0.000082 |
ORF1ab/nsp5A-B | 140 | F140F | ttC | ttT | 2 | 2 | AY.62 | 0.000871 |
ORF1ab/nsp5A-B | 140 | F140del | TTC | --- | 2 | 2 | AY.70 | 0.000417 |
ORF1ab/nsp5A-B | 140 | F140C | tTc | tGc | 2 | 2 | AY.9.2 | 0.000073 |
ORF1ab/nsp5A-B | 140 | F140del | TTC | --- | 2 | 2 | B.1.1.51 | 0.003436 |
ORF1ab/nsp5A-B | 140 | F140C | tTC | tGT | 1 | 2 | B.1.1.7 | 0.000001 |
ORF1ab/nsp5A-B | 140 | F140C | tTc | tGc | 1 | 2 | B.1.1.7 | 0.000001 |
ORF1ab/nsp5A-B | 140 | F140L | ttC | ttA | 1 | 2 | B.1.1.7 | 0.000001 |
ORF1ab/nsp5A-B | 140 | F140L | Ttc | Ctc | 1 | 2 | B.1.1.7 | 0.000001 |
ORF1ab/nsp5A-B | 140 | F140F | ttC | ttT | 2 | 2 | B.1.146 | 0.008475 |
ORF1ab/nsp5A-B | 140 | F140F | ttC | ttT | 2 | 2 | B.1.324 | 0.00321 |
ORF1ab/nsp5A-B | 140 | F140F | ttC | ttT | 2 | 2 | B.1.427 | 0.000101 |
ORF1ab/nsp5A-B | 140 | F140F | ttC | ttT | 2 | 2 | B.1.466.2 | 0.000782 |
ORF1ab/nsp5A-B | 140 | F140F | ttC | ttT | 2 | 2 | B.1.561 | 0.000794 |
ORF1ab/nsp5A-B | 140 | F140C | tTc | tGc | 2 | 2 | B.1.617.1 | 0.000258 |
ORF1ab/nsp5A-B | 140 | F140L | ttC | ttA | 1 | 1 | A | 0.000387 |
ORF1ab/nsp5A-B | 140 | F140F | ttC | ttT | 1 | 1 | A.23.1 | 0.000704 |
ORF1ab/nsp5A-B | 140 | F140S | tTc | tCc | 1 | 1 | AD.2 | 0.000219 |
ORF1ab/nsp5A-B | 140 | F140X | tTC | tAG | 1 | 1 | All | 0 |
ORF1ab/nsp5A-B | 140 | F140T | TTc | ACc | 1 | 1 | All | 0 |
ORF1ab/nsp5A-B | 140 | F140L | Ttc | Ctc | 1 | 1 | AY.103 | 0.000006 |
ORF1ab/nsp5A-B | 140 | F140del | TTC | --- | 1 | 1 | AY.108 | 0.001103 |
ORF1ab/nsp5A-B | 140 | F140C | tTc | tGc | 1 | 1 | AY.118 | 0.000063 |
ORF1ab/nsp5A-B | 140 | F140C | tTc | tGc | 1 | 1 | AY.119 | 0.000035 |
ORF1ab/nsp5A-B | 140 | F140F | ttC | ttT | 1 | 1 | AY.14 | 0.000088 |
ORF1ab/nsp5A-B | 140 | F140F | ttC | ttT | 1 | 1 | AY.20 | 0.000039 |
ORF1ab/nsp5A-B | 140 | F140V | Ttc | Gtc | 1 | 1 | AY.24 | 0.000431 |
ORF1ab/nsp5A-B | 140 | F140del | TTC | --- | 1 | 1 | AY.25 | 0.000006 |
ORF1ab/nsp5A-B | 140 | F140X | tTC | tAG | 1 | 1 | AY.26 | 0.000028 |
ORF1ab/nsp5A-B | 140 | F140L | ttC | ttA | 1 | 1 | AY.3 | 0.00001 |
ORF1ab/nsp5A-B | 140 | F140S | tTc | tCc | 1 | 1 | AY.3 | 0.00001 |
ORF1ab/nsp5A-B | 140 | F140S | tTc | tCc | 1 | 1 | AY.33 | 0.000067 |
ORF1ab/nsp5A-B | 140 | F140F | ttC | ttT | 1 | 1 | AY.39.1 | 0.00004 |
ORF1ab/nsp5A-B | 140 | F140del | TTC | --- | 1 | 1 | AY.4.5 | 0.000107 |
ORF1ab/nsp5A-B | 140 | F140L | Ttc | Ctc | 1 | 1 | AY.41 | 0.000294 |
ORF1ab/nsp5A-B | 140 | F140F | ttC | ttT | 1 | 1 | AY.47 | 0.000031 |
ORF1ab/nsp5A-B | 140 | F140F | ttC | ttT | 1 | 1 | AY.51 | 0.000909 |
ORF1ab/nsp5A-B | 140 | F140L | ttC | ttA | 1 | 1 | AY.52 | 0.000814 |
ORF1ab/nsp5A-B | 140 | F140F | ttC | ttT | 1 | 1 | AY.61 | 0.000105 |
ORF1ab/nsp5A-B | 140 | F140F | ttC | ttT | 1 | 1 | AY.63 | 0.000387 |
ORF1ab/nsp5A-B | 140 | F140del | TTC | --- | 1 | 1 | AY.75 | 0.000056 |
ORF1ab/nsp5A-B | 140 | F140C | tTc | tGc | 1 | 1 | AY.75 | 0.000056 |
ORF1ab/nsp5A-B | 140 | F140del | TTC | --- | 1 | 1 | AY.75.1 | 0.00018 |
ORF1ab/nsp5A-B | 140 | F140F | ttC | ttT | 1 | 1 | AY.9.2 | 0.000037 |
ORF1ab/nsp5A-B | 140 | F140del | TTC | --- | 1 | 1 | AY.99 | 0.001049 |
ORF1ab/nsp5A-B | 140 | F140L | ttC | ttA | 1 | 1 | B | 0.000128 |
ORF1ab/nsp5A-B | 140 | F140V | Ttc | Gtc | 1 | 1 | B | 0.000128 |
ORF1ab/nsp5A-B | 140 | F140V | TtC | GtA | 1 | 1 | B.1 | 0.000009 |
ORF1ab/nsp5A-B | 140 | F140del1 | tTC | tC- | 1 | 1 | B.1 | 0.000009 |
ORF1ab/nsp5A-B | 140 | F140del | TTC | --- | 1 | 1 | B.1 | 0.000009 |
ORF1ab/nsp5A-B | 140 | F140L | ttC | ttG | 1 | 1 | B.1.1 | 0.000018 |
ORF1ab/nsp5A-B | 140 | F140S | tTc | tCc | 1 | 1 | B.1.1 | 0.000018 |
ORF1ab/nsp5A-B | 140 | F140del | TTC | --- | 1 | 1 | B.1.1 | 0.000018 |
ORF1ab/nsp5A-B | 140 | F140F | ttC | ttT | 1 | 1 | B.1.1.13 | 0.035714 |
ORF1ab/nsp5A-B | 140 | F140F | ttC | ttT | 1 | 1 | B.1.1.214 | 0.000055 |
ORF1ab/nsp5A-B | 140 | F140F | ttC | ttT | 1 | 1 | B.1.1.229 | 0.005747 |
ORF1ab/nsp5A-B | 140 | F140F | ttC | ttT | 1 | 1 | B.1.1.25 | 0.000569 |
ORF1ab/nsp5A-B | 140 | F140F | ttC | ttT | 1 | 1 | B.1.1.254 | 0.011236 |
ORF1ab/nsp5A-B | 140 | F140del | TTC | --- | 1 | 1 | B.1.1.315 | 0.008475 |
ORF1ab/nsp5A-B | 140 | F140L | ttC | ttG | 1 | 1 | B.1.1.326 | 0.001761 |
ORF1ab/nsp5A-B | 140 | F140F | ttC | ttT | 1 | 1 | B.1.1.348 | 0.000796 |
ORF1ab/nsp5A-B | 140 | F140F | ttC | ttT | 1 | 1 | B.1.1.402 | 0.011111 |
ORF1ab/nsp5A-B | 140 | F140del | TTC | --- | 1 | 1 | B.1.1.409 | 0.002833 |
ORF1ab/nsp5A-B | 140 | F140F | ttC | ttT | 1 | 1 | B.1.1.518 | 0.006329 |
ORF1ab/nsp5A-B | 140 | F140F | ttC | ttT | 1 | 1 | B.1.1.519 | 0.00004 |
ORF1ab/nsp5A-B | 140 | F140F | ttC | ttT | 1 | 1 | B.1.1.58 | 0.005376 |
ORF1ab/nsp5A-B | 140 | F140del1 | Ttc | -tc | 1 | 1 | B.1.1.7 | 0.000001 |
ORF1ab/nsp5A-B | 140 | F140del | TTC | --- | 1 | 1 | B.1.177 | 0.000013 |
ORF1ab/nsp5A-B | 140 | F140F | ttC | ttT | 1 | 1 | B.1.177.10 | 0.000878 |
ORF1ab/nsp5A-B | 140 | F140del | TTC | --- | 1 | 1 | B.1.177.4 | 0.000211 |
ORF1ab/nsp5A-B | 140 | F140F | ttC | ttT | 1 | 1 | B.1.177.81 | 0.000189 |
ORF1ab/nsp5A-B | 140 | F140F | ttC | ttT | 1 | 1 | B.1.177.9 | 0.001332 |
ORF1ab/nsp5A-B | 140 | F140F | ttC | ttT | 1 | 1 | B.1.243 | 0.00007 |
ORF1ab/nsp5A-B | 140 | F140F | ttC | ttT | 1 | 1 | B.1.258 | 0.000067 |
ORF1ab/nsp5A-B | 140 | F140S | tTc | tCc | 1 | 1 | B.1.258.17 | 0.000104 |
ORF1ab/nsp5A-B | 140 | F140L | ttC | ttA | 1 | 1 | B.1.301 | 0.005917 |
ORF1ab/nsp5A-B | 140 | F140L | Ttc | Ctc | 1 | 1 | B.1.336 | 0.002439 |
ORF1ab/nsp5A-B | 140 | F140del1 | TtC | -tT | 1 | 1 | B.1.351 | 0.00003 |
ORF1ab/nsp5A-B | 140 | F140del | TTC | --- | 1 | 1 | B.1.36.17 | 0.000494 |
ORF1ab/nsp5A-B | 140 | F140F | ttC | ttT | 1 | 1 | B.1.36.2 | 0.010753 |
ORF1ab/nsp5A-B | 140 | F140F | ttC | ttT | 1 | 1 | B.1.36.36 | 0.000602 |
ORF1ab/nsp5A-B | 140 | F140F | ttC | ttT | 1 | 1 | B.1.396 | 0.000706 |
ORF1ab/nsp5A-B | 140 | F140del | TTC | --- | 1 | 1 | B.1.415 | 0.014286 |
ORF1ab/nsp5A-B | 140 | F140F | ttC | ttT | 1 | 1 | B.1.525 | 0.000113 |
ORF1ab/nsp5A-B | 140 | F140F | ttC | ttT | 1 | 1 | B.1.526 | 0.000024 |
ORF1ab/nsp5A-B | 140 | F140F | ttC | ttT | 1 | 1 | B.1.567 | 0.003333 |
ORF1ab/nsp5A-B | 140 | F140F | ttC | ttT | 1 | 1 | B.1.582 | 0.000491 |
ORF1ab/nsp5A-B | 140 | F140T | TTc | ACc | 1 | 1 | B.1.617.2 | 0.000004 |
ORF1ab/nsp5A-B | 140 | F140del | TTC | --- | 1 | 1 | B.1.617.2 | 0.000004 |
ORF1ab/nsp5A-B | 140 | F140F | ttC | ttT | 1 | 1 | B.1.620 | 0.000946 |
ORF1ab/nsp5A-B | 140 | F140S | tTc | tCc | 1 | 1 | B.1.621 | 0.000089 |
ORF1ab/nsp5A-B | 140 | F140L | ttC | ttA | 1 | 1 | B.1.623 | 0.000536 |
ORF1ab/nsp5A-B | 140 | F140F | ttC | ttT | 1 | 1 | B.1.81 | 0.021277 |
ORF1ab/nsp5A-B | 140 | F140S | tTc | tCc | 1 | 1 | B.31 | 0.003731 |
ORF1ab/nsp5A-B | 140 | F140F | ttC | ttT | 1 | 1 | C.6 | 0.037037 |
ORF1ab/nsp5A-B | 140 | F140del | TTC | --- | 1 | 1 | N.4 | 0.004255 |
ORF1ab/nsp5A-B | 140 | F140S | tTc | tCc | 1 | 1 | P.1.1 | 0.000318 |
ORF1ab/nsp5A-B | 140 | F140L | ttC | ttA | 1 | 1 | P.1.15 | 0.000232 |
ORF1ab/nsp5A-B | 140 | F140F | ttC | ttT | 1 | 1 | P.2 | 0.000187 |
ORF1ab/nsp5A-B | 140 | F140F | ttC | ttT | 1 | 1 | Q.8 | 0.000165 |
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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