National Institute Of Genetic Engineering and Biotechnology

P.I:Mohammad-Ali Malboobi
Here we provide last mutation observed in Nucleocapsid gene of COVID-19 prevalent in Iran.
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Amino acid changes

How to read this table:
- Rows are reference amino acids and columns are changed amino acids. E.g. Row 'A' column 'E' indicates how many 'A' amino acids have been replaced by 'E' amino acids.
- Red background colors indicate that more changes happened (heat-map).
- Diagonals are indicated using grey background color
- WARNING: This table may include different translation codon tables (e.g. mamalian DNA and mitochondrial DNA).

  * - ? A C D F G H I K L M N P Q R S T V Y
*     2                         1          
-     112                                    
?                                          
A     6 2       1                   2   2  
C 1   3   1                       1        
D     3         1                       1 1
F     12   1   2     2   4           3      
G     3     1   2                          
H                                          
I     6               1 5 2       2   3 3  
K                                          
L     12       2     1   4     2   1        
M     6             4 1                 1  
N     16     3         1     5       2 1   4
P     3                 1     2     1 1    
Q 1   3           1     1                  
R 1   5   1     1 1 1 1 1     1   1 1      
S     6       1 1             1     2      
T     6             1     1           1    
V     11 3     1     2   3               6  
Y 1   9   2       3                       2

Nucleotide and amino acid mutations

Here we provide list of mutation observed in Nucleocapsid at gene and protein of COVID-19.
-The position column is nucleotide position in reference genome as NC_045512.2
-The Reference column indicate reference nucleotide in NC_045512.2
-The NS column indicate number of samples that this position have been observed
-The NSR column indicate number of samples with reference nucleotide. Therefore diffrenciate related to Ns indicate number of sample with mutated nucleotide
Contoury Position Reference Alt. NSR NS AAchange
0 USA 29558 A 87267 87267
1 USA 29559 T 87291 87290
2 USA 29560 G T,A 87299 87288 Met1?-p.Met1?
3 USA 29561 G 87301 87299
4 USA 29562 G A 87302 87296 Gly2Asp
5 USA 29563 C T,A 87305 87297 Gly2Gly-p.Gly2Gly
6 USA 29564 T C 87306 87301 Tyr3His
7 USA 29565 A G 87323 87318 Tyr3Cys
8 USA 29566 T C 87324 87320 Tyr3Tyr
9 USA 29567 A G,C,T 87326 86507 Ile4Leu-p.Ile4Leu
10 USA 29568 T C 87326 87322 Ile4Thr
11 USA 29569 A 87327 87324
12 USA 29570 A T,G 87327 87322 Asn5Tyr-p.Asn5Asp
13 USA 29571 A 87327 87272
14 USA 29572 C T 87329 87324 Asn5Asn
15 USA 29573 G 87330 87322
16 USA 29574 T 87331 87306
17 USA 29575 T C,G 87332 87308 Val6Val-p.Val6Val
18 USA 29576 T C 87333 87315 Phe7Leu
19 USA 29577 T C 87333 87309 Phe7Ser
20 USA 29578 C T,A 87341 87318 Phe7Leu-p.Phe7Phe
21 USA 29579 G T 87342 87315 Ala8Ser
22 USA 29580 C T,G 87343 87259 Ala8Val-p.Ala8Gly
23 USA 29581 T C 87343 87310 Ala8Ala
24 USA 29582 T A,C 87343 87321 Phe9Ile-p.Phe9Leu
25 USA 29583 T C 87343 87319 Phe9Ser
26 USA 29584 T 87343 87323
27 USA 29585 C T,A 87343 87216 Pro10Ser-p.Pro10Thr
28 USA 29586 C T 87348 87325 Pro10Leu
29 USA 29587 G A,T 87349 87312 Pro10Pro-p.Pro10Pro
30 USA 29588 T C 87348 87281 Phe11Leu
31 USA 29589 T 87351 87336
32 USA 29590 T C 87353 87336 Phe11Phe
33 USA 29591 A 87402 87397
34 USA 29592 C T 87410 87395 Thr12Met
35 USA 29593 G A 87412 87400 Thr12Thr
36 USA 29594 A T,G,C 87418 87333 Ile13Val-p.Ile13Leu
37 USA 29595 T C,G 87410 87387 Ile13Thr-p.Ile13Arg
38 USA 29596 A G 87416 87397 Ile13Met
39 USA 29597 T C 87416 87409 Tyr14His
40 USA 29598 A G 87416 87409 Tyr14Cys
41 USA 29599 T 87416 87413
42 USA 29600 A G 87414 87399 Ser15Gly
43 USA 29601 G 87428 87423
44 USA 29602 T C 87428 87422 Ser15Ser
45 USA 29603 C 87425 87417
46 USA 29604 T C 87421 87413 Leu16Pro
47 USA 29605 A G 87418 87409 Leu16Leu
48 USA 29606 C T 87417 87403 Leu17Phe
49 USA 29607 T 87417 87410
50 USA 29608 C 87420 87416
51 USA 29609 T 87408 87398
52 USA 29610 T 87387 87371
53 USA 29611 G A 87388 87366 Leu18Leu
54 USA 29612 T C 87387 87368 Cys19Arg
55 USA 29613 G 87388 87367
56 USA 29614 C T,A 87389 86831 Cys19*-p.Cys19Cys
57 USA 29615 A T,G 87381 87355 Arg20*-p.Arg20Gly
58 USA 29616 G T,A 87382 87309 Arg20Ile-p.Arg20Lys
59 USA 29617 A G 87381 87358 Arg20Arg
60 USA 29618 A G 87387 87366 Met21Val
61 USA 29619 T A 87387 87365 Met21Lys
62 USA 29620 G C,A 87385 87358 Met21Ile-p.Met21Ile
63 USA 29621 A G,T 87383 87354 Asn22Asp-p.Asn22Tyr
64 USA 29622 A G 87382 87361 Asn22Ser
65 USA 29623 T C 87380 87367 Asn22Asn
66 USA 29624 T C 87380 87350 Ser23Pro
67 USA 29625 C T 87372 87271 Ser23Phe
68 USA 29626 T C 87371 87353 Ser23Ser
69 USA 29627 C T,A 87372 87230 Arg24Cys-p.Arg24Ser
70 USA 29628 G T,C,A 87370 87101 Arg24Pro-p.Arg24His
71 USA 29629 T 87370 87350
72 USA 29630 A G 87369 87350 Asn25Asp
73 USA 29631 A G 87368 87350 Asn25Ser
74 USA 29632 C T 87370 87339 Asn25Asn
75 USA 29633 T C 87365 87348 Tyr26His
76 USA 29634 A 87363 87349
77 USA 29635 C T,A 87363 87301 Tyr26*-p.Tyr26Tyr
78 USA 29636 A G,T 87362 87344 Ile27Val-p.Ile27Leu
79 USA 29637 T C,A,G 87357 87316 Ile27Lys-p.Ile27Arg
80 USA 29638 A G 87346 87330 Ile27Met
81 USA 29639 G T 87343 87319 Ala28Ser
82 USA 29640 C T 87340 87241 Ala28Val
83 USA 29641 A G 87336 87313 Ala28Ala
84 USA 29642 C T 87336 87188 Gln29*
85 USA 29643 A T 87318 87300 Gln29Leu
86 USA 29644 A T 87318 87294 Gln29His
87 USA 29645 G T,C,A 87316 87192 Val30Leu-p.Val30Ile
88 USA 29646 T C 87313 87304 Val30Ala
89 USA 29647 A G 87306 87282 Val30Val
90 USA 29648 G T 87277 87222 Asp31Tyr
91 USA 29649 A T,G 87272 87256 Asp31Val-p.Asp31Gly
92 USA 29650 T 87268 87255
93 USA 29651 G T 87255 87234 Val32Leu
94 USA 29652 T C 87246 87232 Val32Ala
95 USA 29653 A G,T 87219 87188 Val32Val-p.Val32Val
96 USA 29654 G T,A 87218 87211 Val33Phe-p.Val33Ile
97 USA 29655 T C 87206 87193 Val33Ala
98 USA 29656 T C 87202 87193 Val33Val
99 USA 29657 A T 87180 87161 Asn34Tyr
100 USA 29658 A C 87175 87165 Asn34Thr
101 USA 29659 C T 87173 87105 Asn34Asn
102 USA 29660 T A 87165 87148 Phe35Ile
103 USA 29661 T C,G 87133 87120 Phe35Ser-p.Phe35Cys
104 USA 29662 T 87124 87120
105 USA 29663 A T 87116 87109 Asn36Tyr
106 USA 29664 A 87111 87108
107 USA 29665 T C,G 87080 87069 Asn36Lys-p.Asn36Asn
108 USA 29666 C T,A 86528 86353 Leu37Phe-p.Leu37Ile
109 USA 29667 T G,C 86497 86481 Leu37Arg-p.Leu37Pro
110 USA 29668 C T,A 86474 86101 Leu37Leu-p.Leu37Leu
111 USA 29669 A 86473 86455
112 USA 29670 C T 86470 86420 Thr38Ile
113 USA 29671 A 86463 86457
114 USA 29672 T C 86459 86303 Ter39Glnext*?
115 USA 29673 A 86444 86444
116 USA 29674 G 86418 86418