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Table 1 Nucleic acid and amino acid mutations observed in seventeen SARS-CoV-2 virus genomes collected from Yogyakarta and Central Java provinces between June and September 2020

From: Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters

No. NA position* Gene/ Region Number of SNP NA change (SNP) Type of base change Entropy values Frequency Type of mutation AA changes (position)#
1 1154 NSP2 7 C → T Transition 0.21456 2 Missense A205V
2 1280    C → T Transition 0.34883 2 Missense V247A
3 1307    C → T Transition 0.45056 3 Missense T256I
4 1501    C → A Transversion 0.34883 2 Missense Q321K
5 1845    C → T Transition 0.21456 1 Synonymous N435N
6 1998    C → T Transition 0.21456 1 Synonymous T486T
7 2247    A → G Transition 0.21456 1 Synonymous R569R
8 2772 NSP3 13 C → T Transition 0.45056 15 Synonymous F106F
9 3264    T → C Transition 0.21456 1 Synonymous D270D
10 3350    T → C Transition 0.21456 1 Synonymous V299A
11 3819    C → T Transition 0.52971 4 Synonymous G443G
12 4489    C → T Transition 0.21456 1 Missense P679S
13 4919    C → T Transition 0.66825 13 Missense P822L
14 5519    C → T Transition 0.21456 1 Missense T1022I
15 5541    C → T Transition 0.34883 2 Synonymous C1029C
16 5990    C → T Transition 0.21456 1 Missense A1179V
17 6047    C → A Transversion 0.21456 1 Missense T1198K
18 6515    T → G Transversion 0.21456 1 Missense F1354C
19 7374    C → T Transition 0.21456 1 Synonymous F1640F
20 7448    C → T Transition 0.21456 1 Missense P1665L
21 8981 NSP4 1 C → T Transition 0.21456 1 Missense A231V
22 9824 NSP5 4 A → G Transition 0.52971 4 Missense K12R
23 9936    G → T Transversion 0.21456 1 Missense M49I
24 10242    C → T Transition 0.68696 8 Synonymous N151N
25 10339    C → T Transition 0.21456 1 Missense P184S
26 10818 NSP6 1 G → T Transversion 0.21456 1 Missense L37F
27 11887 NSP8 2 G → A Transition 0.21456 1 Missense A21T
28 12174    C → T Transition 0.21456 1 Synonymous P116P
29 12544 NSP9 1 C → T Transition 0.21456 1 Missense L42F
30 13465 NSP12 (RdRp) 12 C → T Transition 0.21456 1 Missense A97V
31 13790    G → T Transversion 0.21456 1 Synonymous L205L
32 13855    C → T Transition 0.21456 1 Missense P227L
33 13918    C → T Transition 0.52971 3 Missense T248I
34 14027    C → T Transition 0.21456 1 Synonymous D284D
35 14143    C → T Transition 0.45056 15 Missense P323L
36 14429    C → T Transition 0.21456 1 Synonymous D418D
37 15141    G → T Transversion 0.21456 1 Missense A656S
38 15278    G → T Transversion 0.21456 1 Synonymous T701T
39 15500    A → G Transition 0.21456 1 Synonymous L775L
40 15849    C → T Transition 0.34883 2 Missense H892Y
41 15891    A → G Transition 0.21456 1 Missense M906V
42 16130 NSP13 8 A → T Transversion 0.45056 3 Synonymous P53P
43 16196    C → T Transition 0.21456 1 Synonymous H75H
44 16351    C → T Transition 0.21456 1 Missense T127I
45 16382    G → T Transversion 0.52971 4 Synonymous T137T
46 16429    C → T Transition 0.21456 1 Missense T153I
47 16476    G → T Transversion 0.21456 1 Missense V169F
48 16745    C → T Transition 0.21456 1 Synonymous I258I
49 17699    G → T Transversion 0.21456 1 Missense M576I
50 18382 NSP14 4 C → T Transition 0.21456 1 Missense P203L
51 18479    C → T Transition 0.68696 8 Synonymous Y235Y
52 18612    C → T Transition 0.59084 14 Synonymous L280L
53 18737    A → G Transition 0.21456 1 Synonymous L321L
54 19859 NSP15 2 T → C Transition 0.21456 1 Synonymous I168I
55 20364    C → T Transition 0.21456 1 Missense H337Y
56 20843 NSP16 2 C → T Transition 0.21456 1 Synonymous F150F
57 21058    A → G Transition 0.21456 2 Missense Y222C
58 21310 Spike (S) 12 C → T Transition 0.34883 2 Missense L5F
59 21387    T → C Transition 0.21456 1 Synonymous N30N
60 21477    C → T Transition 0.52971 4 Synonymous S60S
61 21483    T → C Transition 0.21456 1 Synonymous V62V
62 21544    G → C Transversion 0.21456 1 Missense V83L
63 21935    T → C Transition 0.52971 4 Missense V213A
64 22069    T → C Transition 0.21456 1 Missense W258R
65 23138    A → G Transition 0.34883 16 Missense D614G
66 23328    G → T Transversion 0.21456 1 Missense Q677H
67 23664    C → T Transition 0.21456 1 Synonymous Y789Y
68 23729    A → T Transversion 0.21456 1 Missense N811I
69 23928    G → T Transversion 0.21456 1 Synonymous L877L
70 25288 NS3 6 C → T Transition 0.21456 1 Missense A54V
71 25298    G → T Transversion 0.59084 14 Missense Q57H
72 25349    C → T Transition 0.34883 2 Synonymous S74S
73 25422    G → T Transversion 0.21456 1 Missense A99S
74 25579    C → T Transition 0.21456 1 Missense T151I
75 25791    G → T Transversion 0.21456 1 Missense D222Y
76 26470 M 3 C → T Transition 0.59084 14 Synonymous Y71Y
77 26536    C → A Transversion 0.34883 2 Synonymous L93L
78 26602    A → G Transition 0.66825 7 Synonymous E115E
79 27345 NS7a 1 C → T Transition 0.21456 1 Missense H73Y
80 27808 NS8 1 G → A Transition 0.21456 1 Synonymous L60L
81 28046 N 14 C → T Transition 0.21456 1 Missense P13L
82 28363    G → T Transversion 0.52971 4 Missense A119S
83 28470    T → C Transition 0.21456 1 Synonymous N154N
84 28479    C → T Transition 0.21456 1 Synonymous I157I
85 28487    A → G Transition 0.21456 1 Missense Q160R
86 28586    G → T Transversion 0.52971 4 Missense S193I
87 28593    A → T Transversion 0.21456 1 Missense R195S
88 28603    C → T Transition 0.21456 1 Missense P199S
89 28616    G → A Transition 0.34883 2 Missense R203K
90 28617    G → A Transition 0.34883 2   
91 28618    G → C Transversion 0.34883 2 Missense G204R
92 28710    G → T Transversion 0.21456 1 Missense M234I
93 28944    A → G Transition 0.21456 1 Synonymous S312S
94 29094    A → T Transversion 0.34883 2 Synonymous T362T
  1. Bold indicates non-synonymous substitutions
  2. *Nucleic acid numbering starting from ORF1ab start codon (ATG)
  3. #Amino acid numbering starting from start codon of each gene