Table 1.
Summary of detected nucleotide and amino acid mutations in SARS‐CoV‐2
| Genome region | Protein/peptide chain | Domain | Nucleotide position | Reference | Allele | Frequency | Relative frequency | AA position | Amino acid mutation | Type of AA change/mutation |
|---|---|---|---|---|---|---|---|---|---|---|
| 5ʹ‐UTR | N/A | N/A | 4 | A | T | 1 | 0.67 | N/A | N/A | N/A |
| 26 | A | ‐ | 2 | 1.33 | ||||||
| 28 | C | T | 2 | 1.33 | ||||||
| 31 | A | T | 1 | 0.67 | ||||||
| 34 | A | T | 1 | 0.67 | ||||||
| 35 | A | T | 2 | 1.33 | ||||||
| 36 | C | T | 2 | 1.33 | ||||||
| 75 | C | A | 1 | 0.67 | ||||||
| 104 | T | A | 1 | 0.67 | ||||||
| 111 | T | C | 1 | 0.67 | ||||||
| 112 | T | G | 1 | 0.67 | ||||||
| 119 | C | G | 1 | 0.67 | ||||||
| 120 | T | C | 1 | 0.67 | ||||||
| 124 | G | A | 1 | 0.67 | ||||||
| 186 | C | T | 2 | 1.33 | ||||||
| 241 | C | T | 24 | 16.00 | ||||||
| 254 | C | T | 2 | 1.33 | ||||||
| ORF1ab | Leader protein/nsp1 | Leader protein/nsp2 | 270 | A | G | 1 | 0.01 | 2 | E>G | Charged<>Neutral |
| 313 | C | T | 3 | 2.00 | 16 | Silent | Silent | |||
| 490 | T | A | 4 | 0.03 | 75 | D>E | Similar Charge | |||
| 508 | TGGTCATGTTATGGT | ‐ | 2 | 0.01 | 82 | G82_V86del | Deletion | |||
| 514 | T | C | 1 | 0.67 | 83 | Silent | Silent | |||
| 565 | T | C | 1 | 0.67 | 100 | Silent | Silent | |||
| 614 | G | A | 1 | 0.01 | 117 | A>T | Polar<>Neutral | |||
| 618 | A | G | 1 | 0.01 | 118 | Y>C | Polar<>Neutral | |||
| 654 | G | A | 1 | 0.01 | 130 | G>E | Charged<>Neutral | |||
| 686 | AAGTCATTT | ‐ | 1 | 0.01 | 141 | Deletion | Deletion | |||
| 721 | T | C | 1 | 0.67 | 152 | Silent | Silent | |||
| nsp2 | nsp3 | 884 | C | T | 1 | 0.01 | 207 | R>C | Charged<>Polar | |
| 1059 | C | T | 6 | 0.04 | 265 | T>I | Polar<>Neutral | |||
| 1076 | C | T | 1 | 0.01 | 271 | P>S | Polar<>Neutral | |||
| 1102 | C | T | 1 | 0.67 | 279 | Silent | Silent | |||
| 1385 | C | T | 1 | 0.01 | 374 | H>Y | Charged<>Neutral | |||
| 1397 | G | A | 3 | 0.02 | 378 | V>I | Similar Charge | |||
| 1431 | ATG | ‐ | 1 | 0.01 | 389 | Deletion | Deletion | |||
| 1548 | G | A | 1 | 0.01 | 428 | S>N | Similar Charge | |||
| 1623 | T | C | 1 | 0.01 | 453 | I>T | Polar<>Neutral | |||
| 1691 | A | G | 1 | 0.01 | 476 | I>V | Similar Charge | |||
| 1895 | G | T | 1 | 0.01 | 544 | V>L | Similar Charge | |||
| 2091 | C | T | 1 | 0.01 | 609 | T>I | Polar<>Neutral | |||
| 2269 | A | T | 1 | 0.67 | 668 | Silent | Silent | |||
| 2277 | T | C | 1 | 0.01 | 671 | I>T | Polar<>Neutral | |||
| 2388 | C | T | 1 | 0.01 | 708 | T>I | Polar<>Neutral | |||
| 2416 | C | T | 2 | 1.33 | 717 | Silent | Silent | |||
| 2446 | T | C | 1 | 0.67 | 727 | Silent | Silent | |||
| 2472 | C | T | 7 | 4.67 | 736 | Silent | Silent | |||
| 2717 | G | A | 1 | 0.01 | 818 | G>S | Polar<>Neutral | |||
| nsp3 | nsp3 chain | 2875 | G | A | 1 | 0.67 | 870 | Silent | Silent | |
| 2971 | G | T | 1 | 0.01 | 902 | M>I | Similar Charge | |||
| Nsp3 N‐terminal/DUF3655 (domain with unknown function) | 3037 | C | T | 23 | 15.33 | 924 | Silent | Silent | ||
| 3099 | C | T | 2 | 0.01 | 945 | T>I | Polar<>Neutral | |||
| 3177 | C | T | 4 | 0.03 | 971 | P>L | Similar Charge | |||
| nsp3 chain | 3259 | G | T | 1 | 0.01 | 998 | Q>H | Charged<>Polar | ||
| Macro domain | 3299 | T | C | 1 | 0.67 | 1012 | Silent | Silent | ||
| 3333 | TTG | ‐ | 1 | 0.01 | 1023 | Deletion | ||||
| 3411 | C | T | 1 | 0.01 | 1049 | A>V | Similar Charge | |||
| 3518 | G | T | 1 | 0.01 | 1085 | V>F | Similar Charge | |||
| 3738 | C | T | 1 | 0.01 | 1158 | P>L | Similar Charge | |||
| nsp3 chain | 3778 | A | G | 1 | 0.67 | 1171 | Silent | Silent | ||
| Nsp3 ss‐polyA binding domain | 4234 | C | T | 1 | 0.67 | 1323 | Silent | Silent | ||
| 4402 | T | C | 6 | 4.00 | 1379 | Silent | Silent | |||
| PL2Pro domain | 4780 | C | T | 1 | 0.67 | 1505 | Silent | Silent | ||
| Papain‐like viral protease | 4946 | T | C | 1 | 0.01 | 1561 | S>P | Polar<>Neutral | ||
| 5062 | G | T | 6 | 0.04 | 1599 | L>F | Similar Charge | |||
| 5084 | A | G | 1 | 0.01 | 1607 | I>V | Similar Charge | |||
| Papain‐like viral protease/peptidase C16 | 5572 | G | T | 1 | 0.01 | 1769 | M>I | Similar Charge | ||
| 5608 | A | G | 1 | 0.67 | 1781 | Silent | Silent | |||
| 5784 | C | T | 1 | 0.01 | 1840 | T>I | Polar<>Neutral | |||
| 5845 | A | T | 1 | 0.01 | 1860 | K>N | Charged<>Polar | |||
| Nucleic acid‐binding domain | 6026 | C | T | 1 | 0.01 | 1921 | P>S | Polar<>Neutral | ||
| 6031 | C | T | 1 | 0.67 | 1922 | Silent | Silent | |||
| 6035 | A | G | 1 | 0.01 | 1924 | S>G | Polar<>Neutral | |||
| 6040 | C | T | 2 | 1.33 | 1925 | Silent | Silent | |||
| 6312 | C | A | 2 | 0.01 | 2016 | T>K | Charged<>Polar | |||
| nsp3 chain | 6501 | C | T | 1 | 0.01 | 2079 | P>L | Similar Charge | ||
| 6636 | C | T | 1 | 0.01 | 2124 | T>I | Polar<>Neutral | |||
| 6695 | C | T | 1 | 0.01 | 2144 | P>S | Polar<>Neutral | |||
| 6819 | G | T | 2 | 0.01 | 2185 | S>I | Polar<>Neutral | |||
| 6968 | C | A | 1 | 0.01 | 2235 | L>I | Similar Charge | |||
| 6996 | T | C | 2 | 0.01 | 2244 | I>T | Polar<>Neutral | |||
| 7016 | G | A | 1 | 0.01 | 2251 | G>S | Polar<>Neutral | |||
| 7105 | C | T | 1 | 0.67 | 2280 | Silent | Silent | |||
| 7488 | C | T | 1 | 0.01 | 2408 | T>I | Polar<>Neutral | |||
| 7866 | G | T | 1 | 0.01 | 2534 | G>V | Similar Charge | |||
| 8001 | A | C | 1 | 0.01 | 2579 | D>A | Charged<>Neutral | |||
| 8388 | A | G | 1 | 0.01 | 2708 | N>S | Similar Charge | |||
| nsp4 | nsp4 | 8653 | G | T | 1 | 0.01 | 2796 | M>I | Similar Charge | |
| 8728 | A | G | 1 | 0.67 | 2821 | Silent | Silent | |||
| 8782 | C | T | 43 | 28.67 | 2839 | Silent | Silent | |||
| 8945 | A | G | 1 | 0.01 | 2894 | N>D | Charged<>Polar | |||
| 8987 | T | A | 1 | 0.01 | 2908 | F>I | Similar Charge | |||
| 9034 | A | G | 1 | 0.67 | 2923 | Silent | Silent | |||
| 9157 | T | C | 1 | 0.67 | 2964 | Silent | Silent | |||
| 9274 | A | G | 1 | 0.67 | 3003 | Silent | Silent | |||
| 9430 | C | T | 1 | 0.67 | 3055 | Silent | Silent | |||
| 9474 | C | T | 1 | 0.01 | 3070 | A>V | Similar Charge | |||
| 9477 | T | A | 3 | 0.02 | 3071 | F>Y | Similar Charge | |||
| 9491 | C | T | 1 | 0.01 | 3076 | H>Y | Charged<>Neutral | |||
| 9534 | C | T | 1 | 0.01 | 3090 | T>I | Polar<>Neutral | |||
| 9561 | C | T | 1 | 0.01 | 3099 | S>L | Polar<>Neutral | |||
| 9924 | C | T | 1 | 0.01 | 3220 | A>V | Similar Charge | |||
| 10015 | C | T | 1 | 0.67 | 3250 | Silent | Silent | |||
| 3C‐like proteinase | Peptidase C30 domain | 10036 | C | T | 1 | 0.67 | 3257 | Silent | Silent | |
| 10232 | C | T | 2 | 0.01 | 3323 | R>C | Charged<>Polar | |||
| nsp6 | nsp6 | 10507 | C | T | 1 | 0.67 | 3414 | Silent | Silent | |
| 11075 | ‐ | TTT | 1 | 0.01 | 3605_3606 | F_LinsF | Insertion | |||
| 11083 | G | C | 1 | 0.01 | 3606 | L>F | Similar Charge | |||
| 11083 | G | T | 16 | 0.11 | 3606 | L>F | Similar Charge | |||
| 11101 | A | G | 1 | 0.67 | 3612 | Silent | Silent | |||
| 11410 | G | A | 2 | 1.33 | 3715 | Silent | Silent | |||
| 11750 | C | T | 1 | 0.01 | 3829 | L>F | Similar Charge | |||
| 11752 | C | T | 1 | 0.67 | 3829 | Silent | Silent | |||
| nsp7 | nsp7 | 11764 | T | A | 1 | 0.01 | 3833 | N>K | Charged<>Polar | |
| 11916 | C | T | 3 | 0.02 | 3884 | S>L | Polar<>Neutral | |||
| 11937 | G | A | 1 | 0.01 | 3891 | C>Y | Polar<>Neutral | |||
| nsp8 | nsp8 | 11956 | C | T | 1 | 0.67 | 3897 | Silent | Silent | |
| 12102 | C | T | 1 | 0.01 | 3946 | S>L | Polar<>Neutral | |||
| 12115 | C | T | 1 | 0.67 | 3950 | Silent | Silent | |||
| 12473 | C | T | 1 | 0.67 | 4070 | Silent | Silent | |||
| 12478 | G | A | 2 | 0.01 | 4071 | M>I | Similar Charge | |||
| nsp9 | nsp9 | 12534 | C | T | 1 | 0.01 | 4090 | T>I | Polar<>Neutral | |
| nsp10 | nsp10 | 13072 | C | T | 1 | 0.67 | 4269 | Silent | Silent | |
| 13225 | C | G | 1 | 0.01 | 4321 | F>L | Similar Charge | |||
| 13226 | T | C | 1 | 0.67 | 4321 | Silent | Silent | |||
| RNA‐dependent RNA polymerase | RNA‐dependent RNA polymerase N‐terminal | 13620 | C | T | 1 | 0.67 | 4452 | Silent | Silent | |
| 13730 | C | T | 2 | 0.01 | 4489 | A>V | Similar Charge | |||
| 14408 | C | T | 26 | 0.17 | 4715 | P>L | Similar Charge | |||
| RdRp chain | 14657 | C | T | 1 | 0.01 | 4798 | A>V | Similar Charge | ||
| 14786 | C | T | 1 | 0.01 | 4841 | A>V | Similar Charge | |||
| 14805 | C | T | 6 | 4.00 | 4847 | Silent | Silent | |||
| 14849 | T | G | 1 | 0.01 | 4862 | L>R | Charged<>Neutral | |||
| 14856 | A | T | 1 | 0.67 | 4864 | Silent | Silent | |||
| 14858 | T | A | 1 | 0.01 | 4865 | V>D | Charged<>Neutral | |||
| RdRp catalytic | 15324 | C | T | 4 | 2.67 | 5020 | Silent | Silent | ||
| 15418 | G | T | 1 | 0.01 | 5052 | A>S | Polar<>Neutral | |||
| 15597 | T | C | 1 | 0.67 | 5111 | Silent | Silent | |||
| 15607 | T | C | 1 | 0.67 | 5115 | Silent | Silent | |||
| RdRp Chain | 15910 | G | T | 1 | 0.01 | 5216 | D>Y | Charged<>Neutral | ||
| 15960 | C | T | 1 | 0.67 | 5232 | Silent | Silent | |||
| Helicase | CoVi ZnBD | 16272 | T | G | 1 | 0.67 | 5336 | Silent | Silent | |
| 16293 | C | T | 1 | 0.67 | 5343 | Silent | Silent | |||
| 16325 | G | C | 1 | 0.01 | 5354 | C>S | Similar Charge | |||
| 16467 | A | G | 1 | 0.67 | 5401 | Silent | Silent | |||
| Helicase chain | 16877 | C | T | 1 | 0.01 | 5538 | T>I | Polar<>Neutral | ||
| 17000 | C | T | 1 | 0.01 | 5579 | T>I | Polar<>Neutral | |||
| (+) RNA virus Helicase ATP‐binding domain | 17141 | C | A | 1 | 0.01 | 5626 | A>D | Charged<>Neutral | ||
| 17247 | T | C | 2 | 1.33 | 5661 | Silent | Silent | |||
| 17249 | C | T | 1 | 0.01 | 5662 | A>V | Similar Charge | |||
| 17280 | G | T | 1 | 0.67 | 5672 | Silent | Silent | |||
| 17373 | C | T | 5 | 3.33 | 5703 | Silent | Silent | |||
| 17376 | A | G | 1 | 0.67 | 5704 | Silent | Silent | |||
| 17410 | C | T | 1 | 0.01 | 5716 | R>C | Similar Charge | |||
| 17423 | A | G | 1 | 0.01 | 5720 | Y>C | Polar<>Neutral | |||
| 17470 | C | T | 1 | 0.67 | 5736 | Silent | Silent | |||
| (+) RNA virus Helicase C‐terminal domain | 17747 | C | T | 9 | 0.06 | 5828 | P>L | Similar Charge | ||
| 17825 | C | T | 1 | 0.01 | 5854 | T>I | Polar<>Neutral | |||
| 17858 | A | G | 10 | 0.07 | 5865 | Y>C | Polar<>Neutral | |||
| 17894 | C | T | 1 | 0.01 | 5877 | A>V | Similar Charge | |||
| Guanine‐N7 methyltransferase | Guanine‐N7 methyltransferase | 18060 | C | T | 11 | 7.33 | 5932 | Silent | Silent | |
| 18115 | C | T | 1 | 0.01 | 5951 | H>Y | Charged<>Neutral | |||
| 18126 | T | C | 1 | 0.67 | 5954 | Silent | Silent | |||
| 18603 | T | C | 1 | 0.67 | 6113 | Silent | Silent | |||
| 18736 | T | C | 3 | 0.02 | 6158 | F>L | Similar Charge | |||
| 18744 | C | T | 1 | 0.67 | 6160 | Silent | Silent | |||
| 18788 | C | T | 1 | 0.01 | 6175 | T>I | Polar<>Neutral | |||
| 18814 | C | T | 1 | 0.67 | 6184 | Silent | Silent | |||
| 18975 | T | A | 1 | 0.67 | 6273 | Silent | Silent | |||
| 18996 | T | C | 1 | 0.67 | 6244 | Silent | Silent | |||
| 18998 | C | T | 2 | 0.01 | 6245 | A>V | Similar Charge | |||
| 19065 | T | C | 1 | 0.67 | 6267 | Silent | Silent | |||
| 19175 | A | C | 1 | 0.01 | 6304 | D>A | Charged<>Neutral | |||
| 19610 | C | T | 1 | 0.01 | 6449 | T>I | Polar<>Neutral | |||
| N‐Endo, uridylate‐specific endoribonuclease | N‐Endo, uridylate‐specific endoribonuclease | 19684 | G | T | 1 | 0.01 | 6474 | V>L | Similar Charge | |
| 20268 | A | G | 1 | 0.67 | 6668 | Silent | Silent | |||
| 20281 | T | C | 1 | 0.01 | 6673 | F>L | Similar Charge | |||
| 20298 | ATT | ‐ | 1 | 0.01 | 6679 | Deletion | Deletion | |||
| 20437 | A | T | 1 | 0.01 | 6725 | S>C | Similar Charge | |||
| 20449 | A | T | 1 | 0.01 | 6729 | N>Y | Polar<>Neutral | |||
| 2ʹ‐O‐Ribose methyltransferase | 2′‐O‐Ribose methyltransferase | 20692 | C | T | 3 | 0.02 | 6810 | P>S | Polar<>Neutral | |
| 20936 | C | T | 1 | 0.01 | 6891 | T>M | Polar<>Neutral | |||
| 20995 | G | A | 1 | 0.01 | 6911 | G>S | Polar<>Neutral | |||
| 21137 | A | G | 1 | 0.01 | 6958 | K>R | Similar Charge | |||
| 21147 | T | C | 1 | 0.67 | 6961 | Silent | Silent | |||
| 21316 | G | A | 1 | 0.01 | 7018 | D>N | Charged<>Polar | |||
| 21384 | ‐ | T | 1 | 0.01 | 7041 | Insertion | Insertion | |||
| 21386 | C | T | 1 | 0.01 | 7041 | S>F | Polar<>Neutral | |||
| 21387 | ‐ | TT | 1 | 0.01 | 7042 | Insertion | Insertion | |||
| 21426 | T | G | 1 | 0.67 | 7054 | Silent | Silent | |||
| S | Spike protein S1/surface glycoprotein S1 | Spike protein S1/surface glycoprotein S1 chain | 21595 | C | T | 1 | 0.67 | 11 | Silent | Silent |
| Spike protein S1 N‐terminus | 21644 | T | A | 1 | 0.01 | 28 | Y>N | Polar<>Neutral | ||
| 21691 | C | T | 1 | 0.67 | 43 | Silent | Silent | |||
| 21707 | C | T | 2 | 0.01 | 49 | H>Y | Charged<>Neutral | |||
| 21711 | C | T | 1 | 0.01 | 50 | S>L | Polar<>Neutral | |||
| 21784 | T | A | 1 | 0.01 | 74 | N>K | Charged<>Polar | |||
| 21830 | G | T | 1 | 0.01 | 90 | V>F | Similar Charge | |||
| 21906 | A | G | 1 | 0.01 | 115 | Q>R | Charged<>Polar | |||
| 21991 | TTA | ‐ | 1 | 0.01 | 145 | Deletion | Deletion | |||
| 22033 | C | A | 1 | 0.01 | 157 | F>L | Similar Charge | |||
| 22104 | G | T | 1 | 0.01 | 181 | G>V | Similar Charge | |||
| 22151 | A | G | 1 | 0.01 | 197 | I>V | Similar Charge | |||
| 22224 | C | G | 1 | 0.01 | 221 | S>W | Polar<>Neutral | |||
| 22303 | T | G | 1 | 0.01 | 247 | S>R | Charged<>Polar | |||
| 22432 | C | T | 1 | 0.67 | 290 | Silent | Silent | |||
| 22468 | G | T | 1 | 0.67 | 302 | Silent | Silent | |||
| Spike receptor binding domain/spike protein S1 C‐terminal domain | 22785 | G | T | 1 | 0.01 | 408 | R>I | Charged<>Neutral | ||
| Spike receptor binding domain | 23185 | C | T | 1 | 0.67 | 541 | Silent | Silent | ||
| 23271 | C | T | 1 | 0.01 | 570 | A>V | Similar Charge | |||
| Spike protein S1/surface glycoprotein S1 chain | 23403 | A | G | 26 | 0.17 | 614 | D>G | Charged<>Neutral | ||
| 23520 | C | T | 1 | 0.01 | 653 | A>V | Similar Charge | |||
| 23613 | C | T | 1 | 0.01 | 684 | A>V | Similar Charge | |||
| Spike protein S2/surface glycoprotein S2 | Spike protein S2 chain | 23876 | G | A | 1 | 0.01 | 772 | V>I | Similar Charge | |
| 23929 | C | T | 2 | 1.33 | 789 | Silent | Silent | |||
| 23952 | T | G | 1 | 0.01 | 797 | F>C | Polar<>Neutral | |||
| Spike protein S2′ chain/fusion peptide 1 | 24022 | T | C | 1 | 0.67 | 820 | Silent | Silent | ||
| 24023 | C | T | 1 | 0.67 | 821 | Silent | Silent | |||
| Spike protein S2′ chain/heptad repeat 1 | 24325 | A | G | 3 | 2.00 | 921 | Silent | Silent | ||
| 24351 | C | T | 1 | 0.01 | 930 | A>V | Similar Charge | |||
| 24370 | C | T | 1 | 0.67 | 936 | Silent | Silent | |||
| Spike protein S2′ chain | 24694 | A | T | 2 | 1.33 | 1044 | Silent | Silent | ||
| 24789 | C | T | 1 | 0.01 | 1076 | T>I | Polar<>Neutral | |||
| 24862 | A | G | 1 | 0.67 | 1100 | Silent | Silent | |||
| Spike protein S2′ chain/heptad repeat 2 | 25156 | C | T | 1 | 0.67 | 1198 | Silent | Silent | ||
| ORF3a | ORF3a protein | ORF3a protein | 25433 | C | T | 1 | 0.01 | 14 | T>I | Polar<>Neutral |
| 25533 | T | A | 1 | 0.67 | 47 | Silent | Silent | |||
| 25534 | G | T | 1 | 0.01 | 48 | V>F | Similar Charge | |||
| 25563 | G | T | 5 | 0.03 | 57 | Q>H | Charged<>Polar | |||
| 25672 | C | A | 1 | 0.01 | 94 | L>I | Similar Charge | |||
| 25687 | G | T | 1 | 0.01 | 99 | A>S | Polar<>Neutral | |||
| 25771 | C | A | 1 | 0.01 | 127 | L>I | Similar Charge | |||
| 25775 | G | T | 1 | 0.01 | 128 | W>L | Similar Charge | |||
| 25806 | A | T | 1 | 0.67 | 138 | Silent | Silent | |||
| 25810 | C | G | 1 | 0.01 | 140 | L>V | Similar Charge | |||
| 25979 | G | T | 3 | 0.02 | 196 | G>V | Similar Charge | |||
| 26048 | T | G | 1 | 0.01 | 219 | L>W | Similar Charge | |||
| 26088 | C | T | 1 | 0.67 | 232 | Silent | Silent | |||
| 26144 | G | T | 10 | 0.07 | 251 | G>V | Similar Charge | |||
| E | Envelope protein | Envelope protein | 26326 | C | T | 2 | 1.33 | 28 | Silent | Silent |
| 26354 | T | A | 1 | 0.01 | 37 | L>H | Charged<>Neutral | |||
| M | Membrane glycoprotein | Membrane glycoprotein | 26526 | G | T | 1 | 0.01 | 2 | A>S | Polar<>Neutral |
| 26530 | A | G | 1 | 0.01 | 3 | D>G | Charged<>Neutral | |||
| 26729 | T | C | 5 | 3.33 | 69 | Silent | Silent | |||
| 26849 | G | T | 1 | 0.01 | 109 | M>I | Similar Charge | |||
| 27046 | C | T | 1 | 0.01 | 175 | T>M | Polar<>Neutral | |||
| ORF6 | ORF6 protein | ORF6 protein | 27225 | G | T | 1 | 0.01 | 8 | Q>H | Charged<>Polar |
| 27299 | T | C | 1 | 0.01 | 33 | I>T | Polar<>Neutral | |||
| 27384 | T | C | 1 | 0.67 | 61 | Silent | Silent | |||
| ORF7a | ORF7a protein | SARS coronavirus X4 like | 27635 | C | T | 1 | 0.01 | 81 | S>L | Polar<>Neutral |
| ORF8 | ORF 8 protein | ORF 8 protein | 27925 | C | T | 1 | 0.01 | 11 | T>I | Polar<>Neutral |
| 27964 | C | T | 1 | 0.01 | 24 | S>L | Polar<>Neutral | |||
| 28077 | G | C | 5 | 0.03 | 62 | V>L | Similar Charge | |||
| 28144 | T | C | 43 | 0.29 | 84 | L>S | Polar<>Neutral | |||
| N | Nucleocapsid phosphoprotein | Nucleocapsid phosphoprotein | 28311 | C | T | 1 | 0.01 | 13 | P>L | Similar Charge |
| 28378 | G | T | 2 | 1.33 | 35 | Silent | Silent | |||
| 28409 | C | T | 1 | 0.01 | 46 | P>S | Polar<>Neutral | |||
| 28657 | C | T | 3 | 2.00 | 128 | Silent | Silent | |||
| 28688 | T | C | 3 | 2.00 | 139 | Silent | Silent | |||
| 28792 | A | T | 1 | 0.67 | 173 | Silent | Silent | |||
| 28854 | C | T | 2 | 0.01 | 194 | S>L | Polar<>Neutral | |||
| 28857 | G | T | 1 | 0.01 | 195 | R>I | Charged<>Neutral | |||
| 28863 | C | T | 3 | 0.02 | 197 | S>L | Polar<>Neutral | |||
| 28878 | G | A | 1 | 0.01 | 202 | S>N | Similar Charge | |||
| 28881 | G | A | 10 | 0.07 | 203 | R>K | Similar Charge | |||
| 28882 | G | A | 10 | 0.07 | 204 | G>R | Charged<>Neutral | |||
| 28883 | G | C | 10 | 0.07 | 204 | G>R | Charged<>Neutral | |||
| 28887 | C | T | 1 | 0.01 | 205 | T>I | Polar<>Neutral | |||
| 28896 | C | G | 2 | 0.01 | 208 | A>G | Similar Charge | |||
| 28916 | G | A | 1 | 0.01 | 215 | G>S | Polar<>Neutral | |||
| 28985 | G | T | 1 | 0.01 | 238 | G>C | Polar<>Neutral | |||
| 29029 | T | C | 1 | 0.67 | 252 | Silent | Silent | |||
| 29095 | C | T | 5 | 3.33 | 274 | Silent | Silent | |||
| 29140 | G | T | 1 | 0.01 | 289 | Q>H | Charged<>Polar | |||
| 29148 | T | C | 1 | 0.01 | 292 | I>T | Polar<>Neutral | |||
| 29230 | C | T | 1 | 0.67 | 319 | Silent | Silent | |||
| 29301 | A | T | 1 | 0.01 | 343 | A>V | Similar Charge | |||
| 29303 | C | T | 2 | 0.01 | 344 | P>S | Polar<>Neutral | |||
| 29527 | G | A | 2 | 1.33 | 418 | Silent | Silent | |||
| Between N and ORF10 non coding region | N/A | N/A | 29540 | G | A | 2 | 1.33 | |||
| ORF10 | ORF10 protein | ORF10 protein | 29563 | C | T | 1 | 0.67 | 2 | Silent | Silent |
| 29573 | G | A | 1 | 0.01 | 6 | V>I | Similar Charge | |||
| ORF10, stem loop | N/A | N/A | 29635 | C | T | 1 | 0.67 | N/A | N/A | N/A |
| 3′ UTR: 3′ UTR | N/A | N/A | 29695 | A | G | 1 | 0.67 | N/A | N/A | N/A |
| 29700 | A | G | 3 | 2.00 | ||||||
| 29736 | G | T | 3 | 2.00 | ||||||
| 29742 | G | A | 1 | 0.67 | ||||||
| 29742 | G | T | 2 | 1.33 | ||||||
| 29750 | CGATCGAGTG | ‐ | 1 | 0.67 | ||||||
| 29751 | G | C | 2 | 1.33 | ||||||
| 29786 | G | C | 1 | 0.67 | ||||||
| 29844 | A | G | 1 | 0.67 | ||||||
| 29845 | T | G | 2 | 1.33 | ||||||
| 29846 | T | A | 1 | 0.67 | ||||||
| 29847 | T | G | 1 | 0.67 | ||||||
| 29848 | T | G | 1 | 0.67 | ||||||
| 29861 | G | A | 2 | 1.33 | ||||||
| 29864 | G | A | 1 | 0.67 | ||||||
| 29867 | T | A | 2 | 1.33 | ||||||
| 29868 | G | A | 2 | 1.33 | ||||||
| 29868 | G | C | 5 | 3.33 | ||||||
| 29870 | C | A | 5 | 3.33 | ||||||
| 29873 | A | T | 1 | 0.67 |
Abbreviations: E, envelope; M, membrane glycoprotein; N, nucleocapsid; S, spike; SARS‐CoV‐2, severe acute respiratory syndrome coronavirus 2; UTR, untranslated region.