Table 4.
Distribution of SNPs across different proteins.
| S No | Gene/Protein | No of Variable Sites | Sum of Mutations Incidence | Mutations affecting Protein (N = N2 + N3; D = D2 + D3) | Neutral by Three (N3) | Disease by One/Neutral by Two (N2) | Disease by Two/Neutral by One (D2) | Disease by Three (D3) |
|---|---|---|---|---|---|---|---|---|
| 1 | 5′UTR | 8 | 16 | – | ||||
| 2 | ORF1a | 231 | 578 | 127 | ||||
| NSP1 | 14 | 19 | 7 (N = 6; D = 1) |
H81Y, G137C, D147E, V169A |
R24C; V38F | R124C | ||
| NSP2 | 29 | 46 | 15 (N = 14; D = 1) |
Y196H, L204F, K338R, I616F, Y621S, E633D, V682L, T708I, I739V, P765S |
G192D; P626T; I671T; V710F | T592I | ||
| NSP3 | 101 | 284 | 63 (N = 54; D = 9) |
A872T, T882I, Y925C, E940D, P971S, G989V, S1029I, P1054L, M1083I, H1141Y, A1268T, S1534I, T1543K, T1567I, M1588I, V1629A, S1733G, T1761I, G1861S, T1822I, T1854A, T1854I, N1871T, K1973R, S2103F, K2029E, G2035E, P2144S, L2146F, A2249V, V2372I, T2274I, T2300I, L2323V, P2480L, H2520Y, A2593V, S2625F, S2661F |
D930G, D1036G, A1298V, A1649S S1515F, A1812D S1978P, P2046L P2079L, S2015K S2015R, G2118C S2303Y, V2613F V2629A |
A1306V P1472S D1625V L2146P S2242P |
G1069E Y1675C C2691S A2732D |
|
| NSP4 | 26 | 109 | 14 (N = 11; D = 3) |
W2769L, M2796I, H2831Y, A2994V, F3031Y, D3042N A3143V, L3161I | T2777I T3058I Y3160H |
L2781P F3071Y | T3223I | |
| NSP5 | 20 | 41 | 9 (N = 4; D = 5) |
T3453A, Q3390R, P3395S | N3405L | S3386P | L3338F A3379V Y3472H S3517F |
|
| NSP6 | 17 | 30 | 7 (N = 6; D = 1) |
Q3826H Q3826R |
I3731T, P3613L, D3681N, I3835T, | I3731F | ||
| NSP7 | 2 | 5 | 0 | |||||
| NSP8 | 11 | 26 | 6 (N = 3; D = 3) |
K4081R | E3962K, K4069T | M4032S, L4033F |
R3993C | |
| NSP9 | 6 | 11 | 3 (N = 2; D = 1) |
V4181I, V4242I | T4249I | |||
| NSP10 | 4 | 4 | 2 (N = 0; D = 2) |
A4271V A4273V |
||||
| NSP12a | 1 | 3 | 1 (N = 1; D = 0) |
S4398L | ||||
| 3 | ORF1ab | 103 | 182 | 60 | ||||
| NSP12b | 43 | 84 | 22 (N = 12; D = 10) |
A4487V, I4593L, S4621G, A4645G, T4685I, A4798V S5305L |
K4451N, R4565H M4588I, E4670D, L4721I | K4483N, D4532G, A4577V,D4676Y, S4710T, M5148I, V5272I |
D5076G G5200E T4801I |
|
| NSP13 | 30 | 49 | 21 (N = 8; D = 14) |
P5377S, S5490A, K5669R, M5798V, V5894L I5899V, T5923I |
A5770V | K5364R, E5492Q, I5617V, A5620S, P5624L, V5820L, N5827K, A5833G. M5900I |
W5830C Y5865C P5726S |
|
| NSP14 | 15 | 20 | 7 (N = 7; D = 0) |
A5926S, P5971L, M5974I, K6274N | L5952I, T5930A S6180I | |||
| NSP15 | 8 | 17 | 5 (N = 3; D = 2) |
V6518L, A6533T | G6581D | D6491Y K6486T |
||
| NSP16 | 7 | 12 | 5 (N = 4; D = 1) |
P6805S, L6909F, A6914S | K6958R | G6837C | ||
| 4 | S | 74 | 227 | 49 (N = 36; D = 13) |
L54F, N148Y, E156D, A243S, S255F, G261S, Q271R, T299I, T323I, E471Q, A520S, T572I, E583D, T602I, V622I, Q677H, A706S, T761S, G769V, T827I, A831S, A879S, T1027I, H1101Y, V1104L, G1124V, K1181R, K1191N, G1251V, Q1201K |
I434K, S494P, D574Y, A892V H1083Q, P1263L |
T723I, F797C, L828P, T941K, V1068F, D1153Y, C1243F |
G857C A930T A930V S1021F I1179N C1250F |
| 5 | ORF3a | 31 | 178 | 22 (N = 9; D = 13) |
V13L, G18V, S74A, V77F, T175I | L41F, S74F, S171L, T190I | I62T, L83F, T176I | I35T, L46F, L53F, Q57H, C81F, L85F, L86W, G172C, G196V, G251V |
| 6 | E | 5 | 8 | 1 (N = 0; D = 1) |
V29S | |||
| 7 | M | 10 | 136 | 5 (N = 5; D = 0) |
D3G, A68S, H125Y | A69S, V70F | ||
| 8 | ORF6 | 6 | 17 | 2 (N = 1; D = 1) |
I60V | D61L | ||
| 9 | ORF7a | 2 | 2 | 2 (N = 0; D = 2) |
P45L | G38V | ||
| 10 | ORF7b | 1 | 1 | 0 | ||||
| 11 | ORF8 | – | – | – | ||||
| 12 | N | 20 | 38 | 13 (N = 12; D = 1) |
S37L, L139F, A152S |
P6T, P13L, G18V, G30V, S33I, D63N, D144Y, A156S, Q160P |
R92S | |
| 13 | ORF10 | – | – | – | ||||
| 14 | 3′UTR | 2 | 3 | 0 | ||||
| 281 |