| Nsp2 |
G1397A |
C884T, C1093T, C1884T |
S5, S9 |
| Nsp3 |
C3037T, A7766G |
C6078T, C6198A, A6281G, A6282T, C6285A, C7528T, |
S1, S2, S4, S5, S7, S8, S10, S11 |
| Nsp4 |
C9118T |
G8653T, C8655T, A8658G, A8897T, T9860C, T9861G |
S2, S5, S7, S8, S9, S10, S11 |
| Nsp5 |
– |
C10074T, A10075T |
S7, S11 |
| Nsp6 |
G11083T |
– |
S5, S9 |
| Nsp8 |
– |
A12297T |
S10 |
| Nsp10 |
C13381T |
– |
S2, S8, S11 |
| Nsp12 |
C14408T |
G14369T, C14703T, C14724T, C14802T, C14993T |
S1, S2, S4, S7, S8, S10, S11 |
| Nsp13 |
– |
G16301T |
S7 |
| Nsp14 |
C18877T |
G18670T |
S1, S7 |
| Nsp15 |
– |
A19499C |
S7 |
| Spike (S) gene |
A23403G |
G22021T, T22092G |
S1, S2, S4, S7, S8, S9, S10, S11 |
| ORF3a |
G25563T, C25578T, C25609T |
C25611T, A25965G |
S1, S2, S5, S8, S9, S10, S11 |
| ORF7a |
– |
C27643T |
S11 |
| None-coding region |
– |
G27788A, T27789C |
S5, S9 |
| N gene |
T28688C, G28881A, G28882A, G28883C |
C28354T |
S4, S5, S8, S9 |
| None-coding region |
– |
G29543T |
S7 |
| 3′ UTR |
G29742T |
– |
S5, S7, S9 |
