Table 4.
Characteristics of non-synonymous signature SNPs for Global Dataset without India (Dataset A) and exclusive Indian (Dataset B) SARS-CoV-2 genomes.
| Non-synonymous signature SNPs for Global excluding India sequences | ||||||||
|---|---|---|---|---|---|---|---|---|
| Clade | Change in | Mapped with | PROVEAN |
PolyPhen-2 |
I-Mutant 2.0 |
|||
| Amino Acid | Coding Regions | Prediction | Score | Prediction | Score | Stability | DDG | |
| L37F | NSP6 | Neutral | -1.369 | Benign | 0.027 | Decrease | -0.05 | |
| G251D | ORF3a | Deleterious | -6.933 | Probably Damaging | 1.000 | Increase | 0.02 | |
| G251V | ORF3a | Deleterious | −8.581 | Probably Damaging | 1.000 | Decrease | −0.54 | |
| 19A | P585S | NSP2 | Neutral | 0.442 | Benign | 0.005 | Decrease | −1.58 |
| I559V | NSP2 | Neutral | 0.444 | Benign | 0.003 | Decrease | −0.28 | |
| L84S | ORF8 | Neutral | 2.333 | Benign | 0.002 | Decrease | −2.87 | |
| G212D | NSP2 | Neutral | 0.704 | Benign | 0.013 | Decrease | −1.15 | |
| L84S | ORF8 | Neutral | 2.333 | Benign | 0.002 | Decrease | −2.87 | |
| Y541C | Helicase | Deleterious | -8.863 | Probably Damaging | 1.000 | Increase | 0.67 | |
| 19B | P504L | Helicase | Deleterious | -8.158 | Probably Damaging | 0.993 | Increase | 0.16 |
| F308Y | NSP4 | Deleterious | −2.663 | Probably Damaging | 0.998 | Decrease | −0.68 | |
| S197L | Nucleocapsid | Neutral | -2.221 | Probably Damaging | 0.994 | Increase | 0.26 | |
| G196V | ORF3a | Deleterious | −6.581 | Probably Damaging | 1.000 | Decrease | −0.80 | |
| P323H | RdRp | Neutral | 1.146 | Benign | 0.005 | Decrease | −2.09 | |
| P323L | RdRp | Neutral | -0.865 | Benign | 0.005 | Decrease | −0.80 | |
| 20A | D614G | Spike | Neutral | 0.598 | Benign | 0.004 | Decrease | −1.94 |
| A222V | Spike | Neutral | -0.096 | Benign | 0.000 | Increase | 0.48 | |
| V30L | ORF10 | Deleterious | -3.000 | Not Generated | Not Generated | Decrease | −1.31 | |
| A220V | Nucleocapsid | Neutral | -0.140 | Probably Damaging | 0.999 | Increase | 0.76 | |
| D614G | Spike | Neutral | 0.598 | Benign | 0.004 | Decrease | −1.94 | |
| R203S | Nucleocapsid | Neutral | -2.374 | Probably Damaging | 0.994 | Decrease | −2.10 | |
| G204R | Nucleocapsid | Neutral | -1.656 | Probably Damaging | 1.000 | No change | 0.00 | |
| R203K | Nucleocapsid | Neutral | -1.604 | Probably Damaging | 0.969 | Decrease | −2.26 | |
| 20B | R203M | Nucleocapsid | Deleterious | −3.305 | Probably Damaging | 0.998 | Decrease | −1.52 |
| P323H | RdRp | Neutral | 1.146 | Benign | 0.005 | Decrease | −2.09 | |
| P323L | RdRp | Neutral | -0.865 | Benign | 0.005 | Decrease | −0.80 | |
| I120F | NSP2 | Neutral | -1.333 | Benign | 0.393 | Decrease | −1.85 | |
| S477N | Spike | Neutral | -0.034 | Benign | 0.014 | Increase | 0.01 | |
| S477I | Spike | Neutral | -1.310 | Probably Damaging | 0.531 | Increase | 0.34 | |
| S477T | Spike | Neutral | -0.336 | Benign | 0.066 | Decrease | −0.49 | |
| T85I | NSP2 | Deleterious | −4.090 | Probably Damaging | 0.998 | Decrease | −1.71 | |
| P323H | RdRp | Neutral | 1.146 | Benign | 0.005 | Decrease | −2.09 | |
| 20C | P323L | RdRp | Neutral | -0.865 | Benign | 0.005 | Decrease | −0.80 |
| D614G | Spike | Neutral | 0.598 | Benign | 0.004 | Decrease | −1.94 | |
| Q57H | ORF3a | Deleterious | −3.286 | Probably Damaging | 0.966 | Decrease | −1.12 | |
| S24L | ORF8 | Neutral | -1.833 | Benign | 0.013 | Increase | 0.53 | |
| S25L | NSP7 | Deleterious | -4.272 | Probably Damaging | 0.600 | Increase | 0.21 | |
| Non-synonymous signature SNPs for Indian sequences | ||||||||
| Clade | Change in | Mapped with | PROVEAN |
PolyPhen-2 |
I-Mutant 2.0 |
|||
| Amino Acid | Coding Regions | Prediction | Score | Prediction | Score | Stability | DDG | |
| A97V | RdRp | Deleterious | −3.611 | Probably Damaging | 0.990 | Decrease | −0.53 | |
| L37F | NSP6 | Neutral | -1.369 | Benign | 0.027 | Decrease | -0.05 | |
| P13L | Nucleocapsid | Neutral | -1.230 | Probably Damaging | 1.000 | Increase | 0.11 | |
| T1198I | NSP3 | Neutral | -0.085 | Probably Damaging | 0.998 | Decrease | -0.72 | |
| 19A | T1198K | NSP3 | Neutral | -0.353 | Not generated | Not generated | Decrease | -1.37 |
| S1197R | NSP3 | Neutral | -0.835 | Not generated | Not generated | Decrease | -0.88 | |
| G339S | NSP2 | Deleterious | −3.130 | Probably Damaging | 1.000 | Decrease | −1.57 | |
| G339C | NSP2 | Deleterious | −4.874 | Probably Damaging | 1.000 | Decrease | −1.91 | |
| V198I | NSP2 | Neutral | 0.307 | Benign | 0.006 | Increase | 0.18 | |
| L84S | ORF8 | Neutral | 2.333 | Benign | 0.002 | Decrease | -2.87 | |
| S202N | Nucleocapsid | Neutral | -0.404 | Probably Damaging | 0.994 | Decrease | -0.80 | |
| 19B | S202I | Nucleocapsid | Deleterious | -3.308 | Probably Damaging | 0.998 | Increase | 0.22 |
| S202T | Nucleocapsid | Neutral | −1.428 | Probably Damaging | 0.986 | Decrease | -0.53 | |
| T634A | NSP2 | Neutral | -0.004 | Benign | 0.106 | Decrease | -1.13 | |
| V354L | RdRp | Deleterious | -2.581 | Probably Damaging | 0.997 | Decrease | -1.95 | |
| D614G | Spike | Neutral | 0.598 | Benign | 0.004 | Decrease | -1.94 | |
| 20A | P323L | RdRp | Neutral | -0.865 | Benign | 0.005 | Decrease | -0.80 |
| Q57H | ORF3a | Deleterious | −3.286 | Probably Damaging | 0.966 | Decrease | −1.12 | |
| S194L | Nucleocapsid | Deleterious | -4.272 | Probably Damaging | 0.994 | Increase | 0.45 | |
| D614G | Spike | Neutral | 0.598 | Benign | 0.004 | Decrease | -1.94 | |
| R203K | Nucleocapsid | Neutral | -1.604 | Probably Damaging | 0.969 | Decrease | -2.26 | |
| 20B | R203M | Nucleocapsid | Deleterious | −3.305 | Probably Damaging | 0.998 | Decrease | −1.52 |
| G204R | Nucleocapsid | Neutral | -1.656 | Probably Damaging | 1.000 | No change | 0.00 | |
| P323L | RdRp | Neutral | -0.865 | Benign | 0.005 | Decrease | -0.80 | |
| A994D | NSP3 | Neutral | -1.103 | Not generated | Not generated | Decrease | -0.78 | |
| T85I | NSP2 | Deleterious | −4.090 | Probably Damaging | 0.998 | Decrease | −1.71 | |
| P323L | RdRp | Neutral | -0.865 | Benign | 0.005 | Decrease | -0.80 | |
| 20C | D614G | Spike | Neutral | 0.598 | Benign | 0.004 | Decrease | -1.94 |
| Q57H | ORF3a | Deleterious | −3.286 | Probably Damaging | 0.966 | Decrease | −1.12 | |
| S183Y | Nucleocapsid | Deleterious | -2.750 | Probably Damaging | 0.998 | No change | 0.00 | |
| A262S | Spike | Neutral | 0.154 | Not generated | Not generated | Decrease | -0.95 | |