Table 8.
The non-synonymous amino acid substitutions in ORF1ab protein with the predicted PROVEAN score and ΔΔG prediction value.
| Substitution | PROVEAN score | Type | ΔΔG prediction | RI | Freq. |
|---|---|---|---|---|---|
| G30S | −0.673 | Neutral | −1.15 | 8 | 1 |
| D33N | −0.733 | Neutral | −1.33 | 4 | 2 |
| V38F | −0.553 | Neutral | −1.48 | 9 | 1 |
| G112C | −1.223 | Neutral | −1.08 | 7 | 1 |
| D147E | −1.123 | Neutral | 0.01 | 4 | 1 |
| V169A | 0.027 | Neutral | −1.7 | 8 | 1 |
| G192D | −1.198 | Neutral | −1.23 | 8 | 1 |
| L204F | 0.327 | Neutral | −1.11 | 8 | 2 |
| S212L | 0.097 | Neutral | 0.24 | 1 | 1 |
| T265I | −0.693 | Neutral | −0.67 | 6 | 1 |
| T283I | −0.088 | Neutral | −0.57 | 7 | 2 |
| P309A | −0.135 | Neutral | −1.8 | 8 | 1 |
| P309L | 0.518 | Neutral | −0.72 | 5 | 1 |
| G327D | −1.072 | Neutral | −0.89 | 5 | 1 |
| K338R | −0.685 | Neutral | 0.05 | 2 | 1 |
| A339V | −0.465 | Neutral | 0.07 | 1 | 1 |
| E347D | −0.548 | Neutral | −0.39 | 6 | 1 |
| H417Y | 0.379 | Neutral | 0.26 | 7 | 1 |
| S443P | −0.678 | Neutral | −0.23 | 2 | 1 |
| G519S | −0.633 | Neutral | −1.2 | 8 | 4 |
| Q575R | −0.331 | Neutral | −0.49 | 6 | 3 |
| E633D | −0.233 | Neutral | −0.37 | 7 | 5 |
| E658K | −0.707 | Neutral | −0.44 | 7 | 1 |
| G662R | −1.425 | Neutral | −0.35 | 7 | 1 |
| Q676P | −0.531 | Neutral | −0.58 | 7 | 69 |
| V682L | 0.035 | Neutral | −1.02 | 7 | 1 |
| T882I | −0.691 | Neutral | −0.1 | 2 | 1 |
| P892S | 0.996 | Neutral | −1.35 | 7 | 1 |
| E940D | 0.515 | Neutral | −0.41 | 4 | 1 |
| G989V | 0.35 | Neutral | −0.36 | 5 | 1 |
| D1036G | −0.887 | Neutral | −1.54 | 8 | 1 |
| P1054L | −1.268 | Neutral | −0.44 | 0 | 2 |
| T1055I | −0.496 | Neutral | −0.38 | 2 | 3 |
| E1126D | −0.535 | Neutral | −0.52 | 6 | 1 |
| P1158S | −0.909 | Neutral | −1.75 | 9 | 5 |
| H1160Y | 0.734 | Neutral | 0.11 | 4 | 3 |
| V1211F | −0.667 | Neutral | −0.7 | 5 | 1 |
| E1251K | −0.511 | Neutral | −0.7 | 6 | 1 |
| A1268T | 0.092 | Neutral | −0.78 | 4 | 2 |
| A1283V | −0.232 | Neutral | −0.15 | 2 | 2 |
| A1298V | 0.22 | Neutral | −0.01 | 1 | 1 |
| T1429I | 0.457 | Neutral | −0.5 | 5 | 1 |
| A1432V | 0.864 | Neutral | 0.07 | 2 | 1 |
| S1534I | 0.319 | Neutral | 0.36 | 1 | 7 |
| I1551T | −0.057 | Neutral | −1.98 | 4 | 1 |
| T1573A | −2.402 | Neutral | −1.47 | 9 | 1 |
| M1588I | −0.746 | Neutral | −0.08 | 0 | 2 |
| D1625Y | −2.143 | Neutral | 0.01 | 2 | 2 |
| S1733G | −1.551 | Neutral | −1.07 | 8 | 2 |
| M1769I | −0.349 | Neutral | −0.11 | 5 | 3 |
| A1812D | −0.753 | Neutral | −0.63 | 3 | 6 |
| T1822I | −0.406 | Neutral | 0.1 | 0 | 1 |
| L1853F | −0.808 | Neutral | −1.19 | 6 | 1 |
| T1854A | −0.326 | Neutral | −1.28 | 8 | 1 |
| T1854I | −0.193 | Neutral | −0.25 | 3 | 1 |
| T1874I | −1.364 | Neutral | −0.16 | 3 | 1 |
| D1939G | −0.936 | Neutral | −1.28 | 6 | 1 |
| D1940Y | −0.872 | Neutral | −0.16 | 2 | 1 |
| Q1943H | −0.464 | Neutral | −0.78 | 6 | 1 |
| K1973R | −0.294 | Neutral | −0.37 | 1 | 1 |
| S2015R | −0.501 | Neutral | −0.17 | 0 | 5 |
| T2016K | −0.166 | Neutral | −0.86 | 4 | 10 |
| K2029E | −0.63 | Neutral | −0.5 | 6 | 1 |
| K2029N | −0.431 | Neutral | −0.64 | 2 | 1 |
| P2046L | −1.038 | Neutral | −0.65 | 5 | 3 |
| T2093I | 0.565 | Neutral | 0.1 | 4 | 1 |
| S2103F | −0.372 | Neutral | 0.24 | 6 | 1 |
| L2146P | −1.386 | Neutral | −1.61 | 7 | 1 |
| S2242P | 0.105 | Neutral | −0.06 | 3 | 1 |
| I2307T | −0.03 | Neutral | −2.34 | 8 | 1 |
| L2323V | −0.361 | Neutral | −1.47 | 8 | 1 |
| H2357Y | 0.301 | Neutral | 0.38 | 7 | 3 |
| S2488F | 2.899 | Neutral | −0.05 | 2 | 1 |
| K2511N | −0.966 | Neutral | −0.38 | 0 | 2 |
| H2520R | −0.243 | Neutral | −0.29 | 3 | 2 |
| A2593V | −1.178 | Neutral | −0.24 | 0 | 1 |
| A2732D | −3.463 | Deleterious | −0.68 | 6 | 3 |
| P2739L | −1.595 | Neutral | −0.62 | 4 | 1 |
| H2831Y | 3.17 | Neutral | 0.27 | 6 | 1 |
| A2891V | −0.835 | Neutral | 0 | 3 | 1 |
| D2980G | 0.071 | Neutral | −1.27 | 5 | 1 |
| A2994V | −1.769 | Neutral | −0.05 | 0 | 3 |
| T3058I | 1.463 | Neutral | −0.48 | 4 | 7 |
| G3072C | −5.058 | Deleterious | −1.07 | 6 | 2 |
| M3087I | 0.614 | Neutral | −0.56 | 5 | 3 |
| T3150I | 0.112 | Neutral | −0.43 | 1 | 2 |
| S3158G | −0.785 | Neutral | −1.35 | 7 | 1 |
| L3338F | −3.068 | Deleterious | −1.09 | 6 | 2 |
| K3353R | −1.343 | Neutral | −0.13 | 1 | 1 |
| V3377G | −6.124 | Deleterious | −2.51 | 9 | 1 |
| Q3390R | −0.324 | Neutral | −0.33 | 4 | 1 |
| N3405L | −4.454 | Deleterious | −0.05 | 0 | 5 |
| P3447S | −1.913 | Neutral | −1.7 | 9 | 1 |
| T3453A | −0.882 | Neutral | −0.83 | 7 | 1 |
| V3475F | −2.291 | Neutral | −1.42 | 9 | 1 |
| K3499R | −0.421 | Neutral | −0.25 | 2 | 5 |
| L3606F | −1.432 | Neutral | −1 | 6 | 14 |
| I3618T | −1.397 | Neutral | −1.49 | 7 | 1 |
| M3655I | 0.174 | Neutral | −0.75 | 7 | 1 |
| D3681N | −0.466 | Neutral | −1.11 | 7 | 1 |
| L3711F | −0.348 | Neutral | −1.21 | 7 | 2 |
| I3731T | −0.744 | Neutral | −2.36 | 9 | 2 |
| V3759F | −1.765 | Neutral | −1.52 | 9 | 1 |
| E3909G | −3.759 | Deleterious | −1.17 | 9 | 1 |
| E3962K | −0.041 | Neutral | −0.34 | 3 | 1 |
| S3983F | −2.722 | Deleterious | −0.34 | 7 | 2 |
| R3993C | −6.175 | Deleterious | −0.86 | 5 | 1 |
| R3993L | −5.422 | Deleterious | −0.3 | 7 | 1 |
| K4069T | −2.268 | Neutral | −0.48 | 6 | 1 |
| V4073I | −0.106 | Neutral | −0.55 | 8 | 1 |
| K4081R | −0.921 | Neutral | −0.33 | 7 | 1 |
| M4116I | −0.46 | Neutral | −0.74 | 5 | 1 |
| K4176N | 0.651 | Neutral | −0.36 | 3 | 1 |
| V4181I | −0.046 | Neutral | −0.7 | 7 | 1 |
| A4271V | −3.278 | Deleterious | −0.25 | 1 | 1 |
| A4273V | −3.349 | Deleterious | −0.23 | 1 | 1 |
| K4451N | −0.49 | Neutral | −0.65 | 2 | 2 |
| K4483N | −1.326 | Neutral | −0.42 | 4 | 1 |
| A4487V | 0.357 | Neutral | −0.24 | 2 | 1 |
| A4489V | −2.346 | Neutral | −0.31 | 1 | 10 |
| D4532G | −3.086 | Deleterious | −1.08 | 6 | 1 |
| A4577V | −1.878 | Neutral | −0.17 | 4 | 1 |
| M4588I | −1.074 | Neutral | −0.81 | 8 | 1 |
| I4593L | 0.213 | Neutral | −0.9 | 7 | 1 |
| E4670D | −0.609 | Neutral | −0.59 | 5 | 2 |
| P4715L | −0.446 | Neutral | −0.83 | 6 | 359 |
| L4721I | −1.085 | Neutral | −1.29 | 7 | 7 |
| V4746A | −2.528 | Deleterious | −2.01 | 9 | 1 |
| M4855I | −1.728 | Neutral | −0.81 | 8 | 3 |
| C4856F | −0.483 | Neutral | −0.21 | 3 | 1 |
| L5030F | −2.739 | Deleterious | −0.99 | 7 | 3 |
| T5035I | −0.622 | Neutral | −0.43 | 2 | 1 |
| T5036M | −1.529 | Neutral | −0.29 | 2 | 1 |
| M5060I | −0.117 | Neutral | −0.56 | 7 | 1 |
| A5091S | −1.821 | Neutral | −0.82 | 9 | 2 |
| Q5214H | 1.016 | Neutral | −0.77 | 6 | 2 |
| V5272I | −0.551 | Neutral | −0.17 | 2 | 18 |
| D5285Y | −1.381 | Neutral | 0.27 | 3 | 2 |
| T5300I | −0.542 | Neutral | −0.42 | 4 | 1 |
| S5305L | −2.332 | Neutral | 0.22 | 4 | 1 |
| P5377S | −0.897 | Neutral | −1.73 | 9 | 2 |
| H5488Y | 0.534 | Neutral | 0.19 | 7 | 1 |
| E5492Q | −2.053 | Neutral | −0.7 | 7 | 1 |
| G5530C | −2.742 | Deleterious | −0.82 | 4 | 4 |
| H5569R | 1.004 | Neutral | −0.1 | 5 | 1 |
| V5571F | −1.592 | Neutral | −1.62 | 8 | 2 |
| Y5577H | −0.845 | Neutral | −1.53 | 7 | 2 |
| S5583T | −0.858 | Neutral | −0.66 | 4 | 1 |
| P5624L | −5.36 | Deleterious | −0.63 | 7 | 2 |
| R5766Q | 0.366 | Neutral | −0.91 | 8 | 1 |
| F5823L | −3.989 | Deleterious | −1.17 | 5 | 1 |
| A5926S | 0.351 | Neutral | −1.08 | 10 | 1 |
| N5928H | −0.711 | Neutral | −0.77 | 9 | 1 |
| K5957R | −0.861 | Neutral | −0.09 | 0 | 1 |
| I5970K | −1.93 | Neutral | −2.18 | 9 | 1 |
| M5997I | −0.985 | Neutral | −0.96 | 8 | 1 |
| G6039V | −6.16 | Deleterious | −0.14 | 1 | 1 |
| A6044V | 2.2 | Neutral | 0.14 | 2 | 1 |
| P6065S | 0.176 | Neutral | −1.67 | 8 | 2 |
| L6082F | −0.771 | Neutral | −1.04 | 6 | 1 |
| R6088C | −5.465 | Deleterious | −1.2 | 7 | 3 |
| L6102F | −1.397 | Neutral | −1.05 | 4 | 67 |
| S6180R | −1.897 | Neutral | 0.16 | 4 | 1 |
| A6199S | −2.053 | Neutral | −0.62 | 8 | 1 |
| D6249Y | 0.823 | Neutral | −0.16 | 3 | 1 |
| K6274N | −0.353 | Neutral | −0.18 | 3 | 3 |
| T6297I | −0.448 | Neutral | −0.8 | 3 | 45 |
| N6313D | −3.422 | Deleterious | −0.62 | 7 | 1 |
| P6368L | −6.762 | Deleterious | −0.79 | 6 | 1 |
| V6385L | −0.789 | Neutral | −1.03 | 7 | 3 |
| K6464N | −1.404 | Neutral | −0.42 | 2 | 1 |
| T6500I | −1.557 | Neutral | −0.42 | 5 | 1 |
| A6533V | −0.465 | Neutral | −0.35 | 5 | 3 |
| D6580Y | −0.868 | Neutral | −0.59 | 5 | 1 |
| G6581D | −2.423 | Neutral | −1.12 | 7 | 2 |
| A6589V | −0.154 | Neutral | −0.17 | 3 | 1 |
| V6600A | −2.262 | Neutral | −1.84 | 9 | 4 |
| L6614F | −1.53 | Neutral | −1.28 | 7 | 1 |
| A6623T | 0.442 | Neutral | −0.76 | 6 | 1 |
| V6688I | −0.141 | Neutral | −0.49 | 4 | 1 |
| M6723I | −0.049 | Neutral | −0.85 | 6 | 1 |
| C6742Y | −0.068 | Neutral | −0.18 | 0 | 1 |
| D6900Y | −3.735 | Deleterious | −0.41 | 1 | 1 |
| L6909F | −0.541 | Neutral | −1.04 | 5 | 1 |
| A6914S | −0.017 | Neutral | −1.04 | 5 | 2 |
| A6914V | −0.428 | Neutral | −0.03 | 1 | 1 |
| K6958R | −0.492 | Neutral | −0.17 | 5 | 2 |
| P7034L | 0.713 | Neutral | −0.88 | 5 | 1 |
| N7083D | −1.153 | Neutral | −0.42 | 2 | 1 |
The substitutions with either high PROVEAN score (< − 2.5, type: deleterious) or large increase stability (ΔΔG < − 0.5) or both are shown in bold.