TABLE 5.
Sequence and structural homology-based prediction of non-synonymous substitution as hotspot mutations along with their protein structural stability for 71,038 global SARS-CoV-2 genomes.
| Change in | Change in | Mapped with | PolyPhen-2 | I-mutant 2.0 | ||
|---|---|---|---|---|---|---|
| Nucleotide | Amino acid | Coding regions | Prediction | Score | Stability | DDG (kcal/mol) |
| G28881A | R203 K | Nucleocapsid | Probably damaging | 0.969 | Decrease | −2.26 |
| G28881T | R203M | Nucleocapsid | Probably damaging | 0.998 | Decrease | −1.52 |
| G28883C | G204R | Nucleocapsid | Probably damaging | 1 | No change | 0 |
| C23604A | P681H | Spike | Not generated | Not generated | Decrease | −0.92 |
| C23604G | P681R | Spike | Not generated | Not generated | Decrease | −0.79 |
| G28280C | D3H | Nucleocapsid | Probably damaging | 1 | Increase | 0.34 |
| A23063T | N501Y | Spike | Benign | 0.145 | Decrease | −0.34 |
| C3267T | T183I | NSP3 | Not generated | Not generated | Decrease | -0.1 |
| G24914C | D1118H | Spike | Probably damaging | 0.998 | Decrease | −0.1 |
| T6954C | I1412T | NSP3 | Benign | 0.026 | Decrease | −2.78 |
| C28977T | S235F | Nucleocapsid | Probably damaging | 0.998 | Increase | 2.43 |
| T28282A | D3E | Nucleocapsid | Probably damaging | 0.997 | Decrease | −0.02 |
| G28048T | R52I | ORF8 | Probably damaging | 1 | Decrease | −0.09 |
| C23271A | A570D | Spike | Benign | 0.031 | Decrease | −1.32 |
| A28281T | D3V | Nucleocapsid | Probably damaging | 1 | Decrease | −0.22 |
| C5388A | A890D | NSP3 | Probably damaging | 1 | Decrease | −1.09 |
| A28111G | Y73C | ORF8 | Probably damaging | 0.994 | Increase | 1.04 |
| C23709T | T716I | Spike | Possibly damaging | 0.696 | Decrease | −0.95 |
| T24506G | S982A | Spike | Probably damaging | 0.996 | Decrease | −1.36 |
| C22227T | A222V | Spike | Benign | 0.001 | Increase | 0.48 |
| T26767G | I82S | Membrane | Possibly damaging | 0.951 | Decrease | −2 |
| C25469T | S26L | ORF3a | Benign | 0.017 | Increase | 0.92 |
| G29402T | D377Y | Nucleocapsid | Probably damaging | 1 | Increase | 0.51 |
| T22917G | L452R | Spike | Benign | 0.04 | Decrease | −1.4 |
| T27638C | V82A | ORF7a | Possibly damaging | 0.732 | Decrease | -2.18 |
| G25563T | Q57H | ORF3a | Probably damaging | 0.983 | Decrease | −1.12 |
| C28854T | S194L | Nucleocapsid | Probably damaging | 0.994 | Increase | 0.45 |
| G24410A | D950N | Spike | Possibly damaging | 0.731 | Increase | 0.15 |
| G21987A | G142D | Spike | Benign | 0.051 | Decrease | −1.17 |
| C21618G | T19R | Spike | Benign | 0.004 | Decrease | −0.12 |
| C27752T | T120I | ORF7a | Possibly damaging | 0.915 | Decrease | −0.26 |
| C22995A | T478K | Spike | Benign | 0 | Decrease | −0.09 |
| A28461G | D63G | Nucleocapsid | Benign | 0 | Decrease | −0.57 |
| G15451A | G671S | RdRp | Probably damaging | 1 | Decrease | −0.29 |
| G23012C | E484Q | Spike | Possibly damaging | 0.786 | Decrease | −0.48 |
| C16466T | P77L | Helicase | Probably damaging | 1 | Decrease | −1.03 |
| A11201G | T77A | NSP6 | Possibly damaging | 0.577 | Decrease | −0.7 |
| C5184T | P822L | NSP3 | Benign | 0.007 | Decrease | −0.54 |
| C5700A | A994D | NSP3 | Probably damaging | 0.972 | Decrease | −0.78 |
| A20396G | K259R | endoRNAse | Benign | 0 | Decrease | −0.49 |
| A24775T | Q1071H | Spike | Possibly damaging | 0.998 | Decrease | −1.19 |
| T11418C | V149A | NSP6 | Possibly damaging | 0.865 | Decrease | −3.43 |
| C9891T | A446V | NSP4 | Probably damaging | 0.999 | Increase | 0.64 |
| G17523T | M429I | Helicase | Possibly damaging | 0.649 | Decrease | −1.26 |
| C4965T | T749I | NSP3 | Probably damaging | 0.996 | Decrease | −0.92 |
| G22022A | E154 K | Spike | Not generated | Not Generated | Decrease | −1.4 |
| C1191T | P129L | NSP2 | Possibly damaging | 0.888 | Decrease | −0.53 |
| C21846T | T95I | Spike | Probably damaging | 0.999 | Decrease | −1.8 |