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/nsp2 | 525 | L525L | L705L | syn | ttA | ttG | 410 | 340 | 0.829268 | 2378-2380 |
ORF1ab/nsp2 | 525 | L525L | L705L | syn | Tta | Cta | 410 | 69 | 0.168293 | 2378-2380 |
ORF1ab/nsp2 | 525 | L525L | L705L | syn | TtA | CtG | 410 | 1 | 0.00243902 | 2378-2380 |
ORF1ab/nsp2 | 525 | L525del | L705del | del | TTA | --- | 105 | 105 | 1 | 2378-2380 |
ORF1ab/nsp2 | 525 | L525F | L705F | nonsyn | ttA | ttT | 27 | 20 | 0.740741 | 2378-2380 |
ORF1ab/nsp2 | 525 | L525F | L705F | nonsyn | ttA | ttC | 27 | 7 | 0.259259 | 2378-2380 |
ORF1ab/nsp2 | 525 | L525S | L705S | nonsyn | tTa | tCa | 17 | 16 | 0.941176 | 2378-2380 |
ORF1ab/nsp2 | 525 | L525S | L705S | nonsyn | tTA | tCT | 17 | 1 | 0.0588235 | 2378-2380 |
ORF1ab/nsp2 | 525 | L525V | L705V | nonsyn | Tta | Gta | 15 | 13 | 0.866667 | 2378-2380 |
ORF1ab/nsp2 | 525 | L525V | L705V | nonsyn | TtA | GtG | 15 | 1 | 0.0666667 | 2378-2380 |
ORF1ab/nsp2 | 525 | L525V | L705V | nonsyn | TtA | GtT | 15 | 1 | 0.0666667 | 2378-2380 |
ORF1ab/nsp2 | 525 | L525I | L705I | nonsyn | Tta | Ata | 11 | 10 | 0.909091 | 2378-2380 |
ORF1ab/nsp2 | 525 | L525I | L705I | nonsyn | TtA | AtT | 11 | 1 | 0.0909091 | 2378-2380 |
ORF1ab/nsp2 | 525 | L525X | L705X | nonsyn | tTa | tAa | 5 | 2 | 0.4 | 2378-2380 |
ORF1ab/nsp2 | 525 | L525X | L705X | nonsyn | tTa | tGa | 5 | 2 | 0.4 | 2378-2380 |
ORF1ab/nsp2 | 525 | L525X | L705X | nonsyn | tTA | tAG | 5 | 1 | 0.2 | 2378-2380 |
ORF1ab/nsp2 | 525 | L525T | L705T | nonsyn | TTa | ACa | 2 | 2 | 1 | 2378-2380 |
ORF1ab/nsp2 | 525 | L525del1 | L705del1 | del | ttA | tt- | 2 | 1 | 0.5 | 2378-2380 |
ORF1ab/nsp2 | 525 | L525del1 | L705del1 | del | TtA | Gt- | 2 | 1 | 0.5 | 2378-2380 |
ORF1ab/nsp2 | 525 | L525C | L705C | nonsyn | tTA | tGT | 1 | 1 | 1 | 2378-2380 |
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/nsp2 | 525 | L525L | ttA | ttG | 340 | 410 | All | 0.000065 |
ORF1ab/nsp2 | 525 | L525L | Tta | Cta | 69 | 410 | All | 0.000013 |
ORF1ab/nsp2 | 525 | L525L | TtA | CtG | 1 | 410 | All | 0 |
ORF1ab/nsp2 | 525 | L525del | TTA | --- | 105 | 105 | All | 0.00002 |
ORF1ab/nsp2 | 525 | L525L | ttA | ttG | 98 | 98 | AS.1 | 0.933333 |
ORF1ab/nsp2 | 525 | L525L | ttA | ttG | 62 | 62 | AY.103 | 0.000385 |
ORF1ab/nsp2 | 525 | L525L | ttA | ttG | 55 | 59 | B.1.1.7 | 0.000049 |
ORF1ab/nsp2 | 525 | L525L | Tta | Cta | 3 | 59 | B.1.1.7 | 0.000003 |
ORF1ab/nsp2 | 525 | L525L | TtA | CtG | 1 | 59 | B.1.1.7 | 0.000001 |
ORF1ab/nsp2 | 525 | L525L | ttA | ttG | 39 | 39 | AY.114 | 0.009013 |
ORF1ab/nsp2 | 525 | L525F | ttA | ttT | 20 | 27 | All | 0.000004 |
ORF1ab/nsp2 | 525 | L525F | ttA | ttC | 7 | 27 | All | 0.000001 |
ORF1ab/nsp2 | 525 | L525del | TTA | --- | 25 | 25 | B.1.1.7 | 0.000022 |
ORF1ab/nsp2 | 525 | L525L | ttA | ttG | 19 | 23 | B.1.617.2 | 0.000072 |
ORF1ab/nsp2 | 525 | L525L | Tta | Cta | 4 | 23 | B.1.617.2 | 0.000015 |
ORF1ab/nsp2 | 525 | L525L | ttA | ttG | 19 | 19 | AY.120.1 | 0.0061 |
ORF1ab/nsp2 | 525 | L525L | Tta | Cta | 18 | 18 | AY.43 | 0.00008 |
ORF1ab/nsp2 | 525 | L525S | tTa | tCa | 16 | 17 | All | 0.000003 |
ORF1ab/nsp2 | 525 | L525S | tTA | tCT | 1 | 17 | All | 0 |
ORF1ab/nsp2 | 525 | L525L | Tta | Cta | 14 | 17 | AY.4 | 0.000022 |
ORF1ab/nsp2 | 525 | L525L | ttA | ttG | 3 | 17 | AY.4 | 0.000005 |
ORF1ab/nsp2 | 525 | L525V | Tta | Gta | 13 | 15 | All | 0.000002 |
ORF1ab/nsp2 | 525 | L525V | TtA | GtT | 1 | 15 | All | 0 |
ORF1ab/nsp2 | 525 | L525V | TtA | GtG | 1 | 15 | All | 0 |
ORF1ab/nsp2 | 525 | L525L | ttA | ttG | 13 | 13 | B.1.1.317 | 0.005352 |
ORF1ab/nsp2 | 525 | L525I | Tta | Ata | 10 | 11 | All | 0.000002 |
ORF1ab/nsp2 | 525 | L525I | TtA | AtT | 1 | 11 | All | 0 |
ORF1ab/nsp2 | 525 | L525L | Tta | Cta | 9 | 11 | AY.44 | 0.000055 |
ORF1ab/nsp2 | 525 | L525L | ttA | ttG | 2 | 11 | AY.44 | 0.000012 |
ORF1ab/nsp2 | 525 | L525L | Tta | Cta | 11 | 11 | AY.98 | 0.000869 |
ORF1ab/nsp2 | 525 | L525del | TTA | --- | 8 | 8 | 0.444444 | |
ORF1ab/nsp2 | 525 | L525L | ttA | ttG | 7 | 8 | B.1 | 0.000064 |
ORF1ab/nsp2 | 525 | L525L | Tta | Cta | 1 | 8 | B.1 | 0.000009 |
ORF1ab/nsp2 | 525 | L525del | TTA | --- | 8 | 8 | B.1.617.2 | 0.00003 |
ORF1ab/nsp2 | 525 | L525del | TTA | --- | 7 | 7 | B.1 | 0.000064 |
ORF1ab/nsp2 | 525 | L525F | ttA | ttC | 6 | 6 | AY.4 | 0.000009 |
ORF1ab/nsp2 | 525 | L525X | tTa | tAa | 2 | 5 | All | 0 |
ORF1ab/nsp2 | 525 | L525X | tTa | tGa | 2 | 5 | All | 0 |
ORF1ab/nsp2 | 525 | L525X | tTA | tAG | 1 | 5 | All | 0 |
ORF1ab/nsp2 | 525 | L525V | Tta | Gta | 4 | 4 | AY.25 | 0.000024 |
ORF1ab/nsp2 | 525 | L525del | TTA | --- | 4 | 4 | AY.43 | 0.000018 |
ORF1ab/nsp2 | 525 | L525I | Tta | Ata | 4 | 4 | B.1.1.412 | 0.030534 |
ORF1ab/nsp2 | 525 | L525del | TTA | --- | 3 | 3 | AY.25 | 0.000018 |
ORF1ab/nsp2 | 525 | L525L | ttA | ttG | 2 | 3 | AY.3 | 0.00002 |
ORF1ab/nsp2 | 525 | L525L | Tta | Cta | 1 | 3 | AY.3 | 0.00001 |
ORF1ab/nsp2 | 525 | L525del | TTA | --- | 3 | 3 | B.1.1 | 0.000054 |
ORF1ab/nsp2 | 525 | L525del | TTA | --- | 3 | 3 | B.1.1.33 | 0.001263 |
ORF1ab/nsp2 | 525 | L525F | ttA | ttT | 2 | 3 | B.1.1.7 | 0.000002 |
ORF1ab/nsp2 | 525 | L525F | ttA | ttC | 1 | 3 | B.1.1.7 | 0.000001 |
ORF1ab/nsp2 | 525 | L525L | ttA | ttG | 2 | 3 | B.1.2 | 0.000018 |
ORF1ab/nsp2 | 525 | L525L | Tta | Cta | 1 | 3 | B.1.2 | 0.000009 |
ORF1ab/nsp2 | 525 | L525F | ttA | ttT | 3 | 3 | B.1.617.1 | 0.000387 |
ORF1ab/nsp2 | 525 | L525F | ttA | ttT | 2 | 2 | 0.111111 | |
ORF1ab/nsp2 | 525 | L525V | Tta | Gta | 1 | 2 | 0.055556 | |
ORF1ab/nsp2 | 525 | L525I | TtA | AtT | 1 | 2 | 0.055556 | |
ORF1ab/nsp2 | 525 | L525V | TtA | GtT | 1 | 2 | 0.055556 | |
ORF1ab/nsp2 | 525 | L525I | Tta | Ata | 1 | 2 | 0.055556 | |
ORF1ab/nsp2 | 525 | L525T | TTa | ACa | 2 | 2 | All | 0 |
ORF1ab/nsp2 | 525 | L525del1 | TtA | Gt- | 1 | 2 | All | 0 |
ORF1ab/nsp2 | 525 | L525del1 | ttA | tt- | 1 | 2 | All | 0 |
ORF1ab/nsp2 | 525 | L525L | Tta | Cta | 1 | 2 | AY.100 | 0.000046 |
ORF1ab/nsp2 | 525 | L525L | ttA | ttG | 1 | 2 | AY.100 | 0.000046 |
ORF1ab/nsp2 | 525 | L525F | ttA | ttT | 2 | 2 | AY.20 | 0.000078 |
ORF1ab/nsp2 | 525 | L525del | TTA | --- | 2 | 2 | AY.4 | 0.000003 |
ORF1ab/nsp2 | 525 | L525del | TTA | --- | 2 | 2 | AY.75 | 0.000112 |
ORF1ab/nsp2 | 525 | L525del | TTA | --- | 2 | 2 | AY.99 | 0.002099 |
ORF1ab/nsp2 | 525 | L525S | tTa | tCa | 2 | 2 | B.1 | 0.000018 |
ORF1ab/nsp2 | 525 | L525L | ttA | ttG | 2 | 2 | B.1.1 | 0.000036 |
ORF1ab/nsp2 | 525 | L525L | ttA | ttG | 2 | 2 | B.1.1.28 | 0.000622 |
ORF1ab/nsp2 | 525 | L525del | TTA | --- | 2 | 2 | B.1.1.348 | 0.001592 |
ORF1ab/nsp2 | 525 | L525S | tTa | tCa | 2 | 2 | B.1.1.7 | 0.000002 |
ORF1ab/nsp2 | 525 | L525V | Tta | Gta | 2 | 2 | B.1.1.7 | 0.000002 |
ORF1ab/nsp2 | 525 | L525X | tTa | tGa | 1 | 2 | B.1.1.7 | 0.000001 |
ORF1ab/nsp2 | 525 | L525X | tTa | tAa | 1 | 2 | B.1.1.7 | 0.000001 |
ORF1ab/nsp2 | 525 | L525L | Tta | Cta | 1 | 2 | B.1.177 | 0.000013 |
ORF1ab/nsp2 | 525 | L525L | ttA | ttG | 1 | 2 | B.1.177 | 0.000013 |
ORF1ab/nsp2 | 525 | L525I | Tta | Ata | 2 | 2 | B.1.2 | 0.000018 |
ORF1ab/nsp2 | 525 | L525del | TTA | --- | 2 | 2 | B.1.424 | 0.016129 |
ORF1ab/nsp2 | 525 | L525del | TTA | --- | 2 | 2 | B.1.429 | 0.000047 |
ORF1ab/nsp2 | 525 | L525del | TTA | --- | 2 | 2 | B.1.617.1 | 0.000258 |
ORF1ab/nsp2 | 525 | L525F | ttA | ttT | 2 | 2 | B.1.617.2 | 0.000008 |
ORF1ab/nsp2 | 525 | L525del | TTA | --- | 2 | 2 | B.1.621 | 0.000177 |
ORF1ab/nsp2 | 525 | L525del | TTA | --- | 2 | 2 | N.6 | 0.014184 |
ORF1ab/nsp2 | 525 | L525L | ttA | ttG | 2 | 2 | P.1 | 0.000032 |
ORF1ab/nsp2 | 525 | L525I | Tta | Ata | 1 | 1 | A.1 | 0.000282 |
ORF1ab/nsp2 | 525 | L525S | tTa | tCa | 1 | 1 | A.1 | 0.000282 |
ORF1ab/nsp2 | 525 | L525T | TTa | ACa | 1 | 1 | A.1 | 0.000282 |
ORF1ab/nsp2 | 525 | L525C | tTA | tGT | 1 | 1 | All | 0 |
ORF1ab/nsp2 | 525 | L525V | Tta | Gta | 1 | 1 | AY.100 | 0.000046 |
ORF1ab/nsp2 | 525 | L525del | TTA | --- | 1 | 1 | AY.108 | 0.001103 |
ORF1ab/nsp2 | 525 | L525del | TTA | --- | 1 | 1 | AY.113 | 0.000142 |
ORF1ab/nsp2 | 525 | L525del | TTA | --- | 1 | 1 | AY.117 | 0.000085 |
ORF1ab/nsp2 | 525 | L525del | TTA | --- | 1 | 1 | AY.120 | 0.000037 |
ORF1ab/nsp2 | 525 | L525L | ttA | ttG | 1 | 1 | AY.120.2 | 0.001285 |
ORF1ab/nsp2 | 525 | L525del | TTA | --- | 1 | 1 | AY.26 | 0.000028 |
ORF1ab/nsp2 | 525 | L525S | tTa | tCa | 1 | 1 | AY.29 | 0.000016 |
ORF1ab/nsp2 | 525 | L525F | ttA | ttT | 1 | 1 | AY.29 | 0.000016 |
ORF1ab/nsp2 | 525 | L525del | TTA | --- | 1 | 1 | AY.29.1 | 0.000221 |
ORF1ab/nsp2 | 525 | L525S | tTa | tCa | 1 | 1 | AY.39 | 0.000025 |
ORF1ab/nsp2 | 525 | L525L | ttA | ttG | 1 | 1 | AY.39.1 | 0.00004 |
ORF1ab/nsp2 | 525 | L525V | Tta | Gta | 1 | 1 | AY.4 | 0.000002 |
ORF1ab/nsp2 | 525 | L525S | tTa | tCa | 1 | 1 | AY.4.2 | 0.000022 |
ORF1ab/nsp2 | 525 | L525V | Tta | Gta | 1 | 1 | AY.43 | 0.000004 |
ORF1ab/nsp2 | 525 | L525T | TTa | ACa | 1 | 1 | AY.43 | 0.000004 |
ORF1ab/nsp2 | 525 | L525F | ttA | ttT | 1 | 1 | AY.43 | 0.000004 |
ORF1ab/nsp2 | 525 | L525V | Tta | Gta | 1 | 1 | AY.46 | 0.000104 |
ORF1ab/nsp2 | 525 | L525L | Tta | Cta | 1 | 1 | AY.46.2 | 0.000635 |
ORF1ab/nsp2 | 525 | L525del | TTA | --- | 1 | 1 | AY.46.6 | 0.000072 |
ORF1ab/nsp2 | 525 | L525L | Tta | Cta | 1 | 1 | AY.5 | 0.000021 |
ORF1ab/nsp2 | 525 | L525F | ttA | ttT | 1 | 1 | AY.55 | 0.000917 |
ORF1ab/nsp2 | 525 | L525L | Tta | Cta | 1 | 1 | AY.6 | 0.000041 |
ORF1ab/nsp2 | 525 | L525del | TTA | --- | 1 | 1 | AY.62 | 0.000436 |
ORF1ab/nsp2 | 525 | L525del | TTA | --- | 1 | 1 | AY.67 | 0.000464 |
ORF1ab/nsp2 | 525 | L525L | ttA | ttG | 1 | 1 | AY.75 | 0.000056 |
ORF1ab/nsp2 | 525 | L525del | TTA | --- | 1 | 1 | AY.75.1 | 0.00018 |
ORF1ab/nsp2 | 525 | L525del | TTA | --- | 1 | 1 | AY.84 | 0.000437 |
ORF1ab/nsp2 | 525 | L525S | tTa | tCa | 1 | 1 | AY.85 | 0.000427 |
ORF1ab/nsp2 | 525 | L525del1 | TtA | Gt- | 1 | 1 | AY.9.2 | 0.000037 |
ORF1ab/nsp2 | 525 | L525L | Tta | Cta | 1 | 1 | AY.92 | 0.000287 |
ORF1ab/nsp2 | 525 | L525X | tTA | tAG | 1 | 1 | AY.98.1 | 0.000048 |
ORF1ab/nsp2 | 525 | L525del | TTA | --- | 1 | 1 | AY.98.1 | 0.000048 |
ORF1ab/nsp2 | 525 | L525F | ttA | ttT | 1 | 1 | B.1.1 | 0.000018 |
ORF1ab/nsp2 | 525 | L525V | Tta | Gta | 1 | 1 | B.1.1 | 0.000018 |
ORF1ab/nsp2 | 525 | L525del | TTA | --- | 1 | 1 | B.1.1.137 | 0.0125 |
ORF1ab/nsp2 | 525 | L525del | TTA | --- | 1 | 1 | B.1.1.139 | 0.022727 |
ORF1ab/nsp2 | 525 | L525L | ttA | ttG | 1 | 1 | B.1.1.153 | 0.001095 |
ORF1ab/nsp2 | 525 | L525C | tTA | tGT | 1 | 1 | B.1.1.192 | 0.002309 |
ORF1ab/nsp2 | 525 | L525F | ttA | ttT | 1 | 1 | B.1.1.216 | 0.00089 |
ORF1ab/nsp2 | 525 | L525S | tTa | tCa | 1 | 1 | B.1.1.26 | 0.005236 |
ORF1ab/nsp2 | 525 | L525del1 | ttA | tt- | 1 | 1 | B.1.1.28 | 0.000311 |
ORF1ab/nsp2 | 525 | L525L | ttA | ttG | 1 | 1 | B.1.1.294 | 0.001266 |
ORF1ab/nsp2 | 525 | L525V | Tta | Gta | 1 | 1 | B.1.1.318 | 0.000302 |
ORF1ab/nsp2 | 525 | L525L | ttA | ttG | 1 | 1 | B.1.1.333 | 0.001076 |
ORF1ab/nsp2 | 525 | L525del | TTA | --- | 1 | 1 | B.1.1.416 | 0.000905 |
ORF1ab/nsp2 | 525 | L525del | TTA | --- | 1 | 1 | B.1.1.448 | 0.002033 |
ORF1ab/nsp2 | 525 | L525F | ttA | ttT | 1 | 1 | B.1.1.464 | 0.001473 |
ORF1ab/nsp2 | 525 | L525I | Tta | Ata | 1 | 1 | B.1.1.7 | 0.000001 |
ORF1ab/nsp2 | 525 | L525F | ttA | ttT | 1 | 1 | B.1.1.70 | 0.000341 |
ORF1ab/nsp2 | 525 | L525V | TtA | GtG | 1 | 1 | B.1.160 | 0.000031 |
ORF1ab/nsp2 | 525 | L525L | ttA | ttG | 1 | 1 | B.1.160 | 0.000031 |
ORF1ab/nsp2 | 525 | L525S | tTa | tCa | 1 | 1 | B.1.160 | 0.000031 |
ORF1ab/nsp2 | 525 | L525F | ttA | ttT | 1 | 1 | B.1.177 | 0.000013 |
ORF1ab/nsp2 | 525 | L525S | tTa | tCa | 1 | 1 | B.1.177.23 | 0.003236 |
ORF1ab/nsp2 | 525 | L525L | ttA | ttG | 1 | 1 | B.1.177.4 | 0.000211 |
ORF1ab/nsp2 | 525 | L525L | ttA | ttG | 1 | 1 | B.1.177.7 | 0.000165 |
ORF1ab/nsp2 | 525 | L525del | TTA | --- | 1 | 1 | B.1.179 | 0.003759 |
ORF1ab/nsp2 | 525 | L525S | tTa | tCa | 1 | 1 | B.1.2 | 0.000009 |
ORF1ab/nsp2 | 525 | L525I | Tta | Ata | 1 | 1 | B.1.214.2 | 0.0006 |
ORF1ab/nsp2 | 525 | L525L | ttA | ttG | 1 | 1 | B.1.232 | 0.000537 |
ORF1ab/nsp2 | 525 | L525del | TTA | --- | 1 | 1 | B.1.258 | 0.000067 |
ORF1ab/nsp2 | 525 | L525S | tTa | tCa | 1 | 1 | B.1.258.17 | 0.000104 |
ORF1ab/nsp2 | 525 | L525S | tTa | tCa | 1 | 1 | B.1.36.1 | 0.00114 |
ORF1ab/nsp2 | 525 | L525del | TTA | --- | 1 | 1 | B.1.416.1 | 0.001563 |
ORF1ab/nsp2 | 525 | L525L | ttA | ttG | 1 | 1 | B.1.525 | 0.000113 |
ORF1ab/nsp2 | 525 | L525del | TTA | --- | 1 | 1 | B.1.561 | 0.000397 |
ORF1ab/nsp2 | 525 | L525del | TTA | --- | 1 | 1 | B.1.595 | 0.000261 |
ORF1ab/nsp2 | 525 | L525S | tTa | tCa | 1 | 1 | B.1.596 | 0.000087 |
ORF1ab/nsp2 | 525 | L525X | tTa | tGa | 1 | 1 | B.1.609 | 0.000479 |
ORF1ab/nsp2 | 525 | L525X | tTa | tAa | 1 | 1 | B.1.617.2 | 0.000004 |
ORF1ab/nsp2 | 525 | L525L | Tta | Cta | 1 | 1 | B.1.628 | 0.000352 |
ORF1ab/nsp2 | 525 | L525S | tTA | tCT | 1 | 1 | B.4 | 0.002208 |
ORF1ab/nsp2 | 525 | L525del | TTA | --- | 1 | 1 | B.57 | 0.015152 |
ORF1ab/nsp2 | 525 | L525F | ttA | ttT | 1 | 1 | D.2 | 0.000075 |
ORF1ab/nsp2 | 525 | L525del | TTA | --- | 1 | 1 | P.1 | 0.000016 |
ORF1ab/nsp2 | 525 | L525del | TTA | --- | 1 | 1 | P.1.1 | 0.000318 |
ORF1ab/nsp2 | 525 | L525del | TTA | --- | 1 | 1 | P.2 | 0.000187 |
ORF1ab/nsp2 | 525 | L525del | TTA | --- | 1 | 1 | Q.2 | 0.000613 |
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
|