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 E.g. Row 'A' column 'E' indicates how many 'A' amino acids have been replaced by 'E' amino acids.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 E F G H I K L M N P Q R S T V W Y
*     2                                        
-     179                                        
?                                              
A     3 2                                 1    
C                                              
D     12     3     2 2         2           1   4
E 3   16     6 4   4     2         1       1    
F     9         2         4           3   1   1
G                                              
H     3     1       1     1         1         1
I     30         1     7   6 4       1   8 7    
K 1   11       2       1 3     4     2   1      
L     22         4   1 1   12     4   2 1   1    
M     8               7   2         1   1 1    
N     11     1       3   4     3       3 2      
P     3                   1     1              
Q 3   9             2   1 1       2 1          
R     3                 1   1       2 1     1  
S     10 3       3         1     1     9 1      
T     9 2             3       2         3      
V     9 1       3     1   1               3    
W     3   1               1         2          
Y 1   6   1     2   2                         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 27202 A 87954 87954
1 USA 27203 T 87956 87956
2 USA 27204 G T,C,A 87959 87939 Met1?-p.Met1?
3 USA 27205 T C,G 87960 87954 Phe2Leu-p.Phe2Val
4 USA 27206 T C 87961 87945 Phe2Ser
5 USA 27207 T C 87961 87951 Phe2Phe
6 USA 27208 C T,G 87963 87935 His3Tyr-p.His3Asp
7 USA 27209 A G,T 87965 87962 His3Arg-p.His3Leu
8 USA 27210 T C 87965 87946 His3His
9 USA 27211 C T 87969 87965 Leu4Phe
10 USA 27212 T C,G,A 87969 87619 Leu4Arg-p.Leu4His
11 USA 27213 C T 87970 87825 Leu4Leu
12 USA 27214 G T,A 87970 87937 Val5Phe-p.Val5Ile
13 USA 27215 T 87970 87969
14 USA 27216 T A 87972 87970 Val5Val
15 USA 27217 G T,A 87974 87957 Asp6Tyr-p.Asp6Asn
16 USA 27218 A 87974 87974
17 USA 27219 C T 87975 87960 Asp6Asp
18 USA 27220 T C 87978 87972 Phe7Leu
19 USA 27221 T C 87978 87972 Phe7Ser
20 USA 27222 T C,G 87979 87962 Phe7Leu-p.Phe7Phe
21 USA 27223 C T 87979 87962 Gln8*
22 USA 27224 A G 87979 87969 Gln8Arg
23 USA 27225 G T,A 87979 87969 Gln8His-p.Gln8Gln
24 USA 27226 G T 87980 87955 Val9Phe
25 USA 27227 T C 87980 87971 Val9Ala
26 USA 27228 T A,C 87981 87957 Val9Val-p.Val9Val
27 USA 27229 A 87981 87974
28 USA 27230 C T 87984 87954 Thr10Ile
29 USA 27231 T C,A 87984 87979 Thr10Thr-p.Thr10Thr
30 USA 27232 A T 87984 87980 Ile11Leu
31 USA 27233 T C,G 87984 87978 Ile11Thr-p.Ile11Arg
32 USA 27234 A T 87982 87975 Ile11Ile
33 USA 27235 G 87980 87972
34 USA 27236 C T 87979 87969 Ala12Val
35 USA 27237 A G,T 87980 87970 Ala12Ala-p.Ala12Ala
36 USA 27238 G A 87980 87970 Glu13Lys
37 USA 27239 A 87979 87970
38 USA 27240 G T,C 87980 87943 Glu13Asp-p.Glu13Asp
39 USA 27241 A G 87978 87961 Ile14Val
40 USA 27242 T C 87978 87832 Ile14Thr
41 USA 27243 A G 87978 87965 Ile14Met
42 USA 27244 T C 87978 87962 Leu15Leu
43 USA 27245 T C 87978 87966 Leu15Ser
44 USA 27246 A G,C 87976 87953 Leu15Phe-p.Leu15Leu
45 USA 27247 C T 87976 87880 Leu16Leu
46 USA 27248 T C 87975 87964 Leu16Pro
47 USA 27249 A 87970 87953
48 USA 27250 A C,T 87966 87925 Ile17Leu-p.Ile17Phe
49 USA 27251 T C 87967 87954 Ile17Thr
50 USA 27252 T C 87967 87951 Ile17Ile
51 USA 27253 A G 87966 87942 Ile18Val
52 USA 27254 T 87964 87952
53 USA 27255 T G 87962 87951 Ile18Met
54 USA 27256 A G 87962 87951 Met19Val
55 USA 27257 T C,G 87962 87945 Met19Thr-p.Met19Arg
56 USA 27258 G T,A 87963 87931 Met19Ile-p.Met19Ile
57 USA 27259 A T,C 87964 87944 Arg20Trp-p.Arg20Arg
58 USA 27260 G T,A 87965 87920 Arg20Met-p.Arg20Lys
59 USA 27261 G T,A 87964 87869 Arg20Ser-p.Arg20Arg
60 USA 27262 A G 87920 87886 Thr21Ala
61 USA 27263 C T,A 87920 87859 Thr21Ile-p.Thr21Asn
62 USA 27264 T 87918 87885
63 USA 27265 T 87918 87882
64 USA 27266 T C,A 87918 87879 Phe22Ser-p.Phe22Tyr
65 USA 27267 T A 87917 87877 Phe22Leu
66 USA 27268 A T,G 87917 87876 Lys23*-p.Lys23Glu
67 USA 27269 A C,G 87918 87874 Lys23Thr-p.Lys23Arg
68 USA 27270 A G 87916 87872 Lys23Lys
69 USA 27271 G T,C 87917 87865 Val24Phe-p.Val24Leu
70 USA 27272 T 87914 87857
71 USA 27273 T 87913 87858
72 USA 27274 T G,A 87913 87858 Ser25Ala-p.Ser25Thr
73 USA 27275 C T 87912 87852 Ser25Phe
74 USA 27276 C T,A,G 87912 87809 Ser25Ser-p.Ser25Ser
75 USA 27277 A G 87913 87848 Ile26Val
76 USA 27278 T 87912 87859
77 USA 27279 T G 87911 87804 Ile26Met
78 USA 27280 T C,A 87911 87857 Trp27Arg-p.Trp27Arg
79 USA 27281 G T 87909 87787 Trp27Leu
80 USA 27282 G T 87910 87865 Trp27Cys
81 USA 27283 A G,C 87912 87873 Asn28Asp-p.Asn28His
82 USA 27284 A 87913 87879
83 USA 27285 T C 87914 87878 Asn28Asn
84 USA 27286 C T,G,A 87916 87875 Leu29Val-p.Leu29Ile
85 USA 27287 T 87916 87883
86 USA 27288 T C 87917 87882 Leu29Leu
87 USA 27289 G C,T 87917 87872 Asp30His-p.Asp30Tyr
88 USA 27290 A 87916 87886
89 USA 27291 T 87916 87890
90 USA 27292 T C 87912 87880 Tyr31His
91 USA 27293 A T,G 87911 87887 Tyr31Phe-p.Tyr31Cys
92 USA 27294 C T 87911 87762 Tyr31Tyr
93 USA 27295 A G 87907 87877 Ile32Val
94 USA 27296 T C 87906 87883 Ile32Thr
95 USA 27297 C T 87896 87715 Ile32Ile
96 USA 27298 A T,G 87896 87878 Ile33Leu-p.Ile33Val
97 USA 27299 T C 87896 87777 Ile33Thr
98 USA 27300 A G,T 87895 87872 Ile33Met-p.Ile33Ile
99 USA 27301 A C 87895 87876 Asn34His
100 USA 27302 A G 87894 87864 Asn34Ser
101 USA 27303 C A 87895 87876 Asn34Lys
102 USA 27304 C T 87895 87868 Leu35Phe
103 USA 27305 T G,C 87889 87847 Leu35Arg-p.Leu35Pro
104 USA 27306 C T,A 87889 87840 Leu35Leu-p.Leu35Leu
105 USA 27307 A G,T 87888 87840 Ile36Val-p.Ile36Leu
106 USA 27308 T C 87888 87839 Ile36Thr
107 USA 27309 A T 87887 87834 Ile36Ile
108 USA 27310 A C 87887 87842 Ile37Leu
109 USA 27311 T C 87887 87836 Ile37Thr
110 USA 27312 T 87883 87825
111 USA 27313 A 87883 87824
112 USA 27314 A 87884 87828
113 USA 27315 A T 87884 87828 Lys38Asn
114 USA 27316 A 87884 87830
115 USA 27317 A G,C 87884 87825 Asn39Ser-p.Asn39Thr
116 USA 27318 T A,C 87884 87808 Asn39Lys-p.Asn39Asn
117 USA 27319 T C 87882 87817 Leu40Leu
118 USA 27320 T 87881 87823
119 USA 27321 A G 87881 87814 Leu40Leu
120 USA 27322 T G,C 87931 87899 Ser41Ala-p.Ser41Pro
121 USA 27323 C T 87931 87885 Ser41Phe
122 USA 27324 T C 87931 87897 Ser41Ser
123 USA 27325 A 87931 87893
124 USA 27326 A 87931 87895
125 USA 27327 G T,C,A 87933 87850 Lys42Asn-p.Lys42Lys
126 USA 27328 T G 87932 87897 Ser43Ala
127 USA 27329 C T 87931 87903 Ser43Leu
128 USA 27330 A G,T,C 87930 87899 Ser43Ser-p.Ser43Ser
129 USA 27331 C T 87929 87897 Leu44Leu
130 USA 27332 T C 87927 87897 Leu44Pro
131 USA 27333 A T 87927 87898 Leu44Leu
132 USA 27334 A G 87927 87895 Thr45Ala
133 USA 27335 C A,T 87927 87858 Thr45Asn-p.Thr45Ile
134 USA 27336 T C 87924 87888 Thr45Thr
135 USA 27337 G 87924 87895
136 USA 27338 A G 87922 87883 Glu46Gly
137 USA 27339 G T,A 87923 87896 Glu46Asp-p.Glu46Glu
138 USA 27340 A C 87922 87900 Asn47His
139 USA 27341 A C,G 87922 87896 Asn47Thr-p.Asn47Ser
140 USA 27342 T C,A,G 87923 87899 Asn47Lys-p.Asn47Asn
141 USA 27343 A G 87923 87896 Lys48Glu
142 USA 27344 A T,G 87923 87901 Lys48Ile-p.Lys48Arg
143 USA 27345 A T,G 87922 87897 Lys48Asn-p.Lys48Lys
144 USA 27346 T C 87923 87901 Tyr49His
145 USA 27347 A T 87922 87902 Tyr49Phe
146 USA 27348 T C,G 87922 87891 Tyr49*-p.Tyr49Tyr
147 USA 27349 T 87922 87905
148 USA 27350 C T 87922 87900 Ser50Phe
149 USA 27351 T C,G 87922 87902 Ser50Ser-p.Ser50Ser
150 USA 27352 C T,A 87925 87903 Gln51*-p.Gln51Lys
151 USA 27353 A T 87925 87904 Gln51Leu
152 USA 27354 A G 87924 87904 Gln51Gln
153 USA 27355 T C 87925 87910 Leu52Leu
154 USA 27356 T 87925 87918
155 USA 27357 A 87925 87920
156 USA 27358 G T,A 87926 87904 Asp53Tyr-p.Asp53Asn
157 USA 27359 A G,T 87926 87870 Asp53Gly-p.Asp53Val
158 USA 27360 T C 87926 87924 Asp53Asp
159 USA 27361 G T,A 87926 87918 Glu54*-p.Glu54Lys
160 USA 27362 A G 87926 87925 Glu54Gly
161 USA 27363 A G,C 87926 87921 Glu54Asp-p.Glu54Glu
162 USA 27364 G T,C 87924 87874 Glu55*-p.Glu55Gln
163 USA 27365 A G 87919 87889 Glu55Gly
164 USA 27366 G T,A 87917 87880 Glu55Asp-p.Glu55Glu
165 USA 27367 C T 87915 87897 Gln56*
166 USA 27368 A 87914 87908
167 USA 27369 A T 87914 87907 Gln56His
168 USA 27370 C 87914 87904
169 USA 27371 C T 87914 87842 Pro57Leu
170 USA 27372 A T 87913 87904 Pro57Pro
171 USA 27373 A T,C 87913 87905 Met58Leu-p.Met58Leu
172 USA 27374 T 87913 87910
173 USA 27375 G T,A 87911 87900 Met58Ile-p.Met58Ile
174 USA 27376 G T 87909 87896 Glu59*
175 USA 27377 A T,G 87907 87900 Glu59Val-p.Glu59Gly
176 USA 27378 G A,T 87906 87886 Glu59Asp-p.Glu59Glu
177 USA 27379 A G,C 87904 87894 Ile60Val-p.Ile60Leu
178 USA 27380 T C 87902 87895 Ile60Thr
179 USA 27381 T A,C 87901 87892 Ile60Ile-p.Ile60Ile
180 USA 27382 G T,C 87862 87812 Asp61Tyr-p.Asp61His
181 USA 27383 A G 87860 87807 Asp61Gly
182 USA 27384 T C 87860 87152 Asp61Asp
183 USA 27385 T 87860 87860
184 USA 27386 A 87848 87846
185 USA 27387 A 87848 87848