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Table 1 Cyprus specific mutations ordered by p-value for best fit according to our glm model

From: In depth analysis of Cyprus-specific mutations of SARS-CoV-2 strains using computational approaches

REFa

ALTa

GENEa

NT.POSa

REF.AAa

ALT.AAa

AA.POSa

CY

counts11

CY

counts02

Other

counts13

Other

counts04

P-value5

OR6

C

T

ORF1ab

18,440

S

F

6059

60

84

25

242,241

6.94E-180

6921.17

G

T

ORF1ab

11,557

E

D

3764

69

75

928

241,338

1.03E-124

239.26

C

T

E

26,313

F

F

23

69

75

1016

241,250

4.25E-122

218.45

C

T

ORF1ab

20,451

N

N

6729

76

68

2983

239,283

5.26E-104

89.65

T

C

M

26,972

R

R

150

77

67

3988

238,278

1.86E-96

68.67

T

C

S

24,910

T

T

1116

76

68

3967

238,299

8.45E-95

67.14

G

A

ORF1ab

15,598

V

I

5112

76

68

3973

238,293

9.45E-95

67.03

G

T

ORF1ab

12,988

M

I

4241

76

68

3976

238,290

1.00E-94

66.98

G

T

ORF1ab

18,028

A

S

5922

76

68

4020

238,246

2.27E-94

66.24

C

A

ORF7b

27,800

A

A

15

76

68

4431

237,835

3.13E-91

59.99

T

C

ORF1ab

7767

I

T

2501

77

67

5213

237,053

1.06E-87

52.26

C

T

ORF1ab

8047

Y

Y

2594

76

68

5199

237,067

4.44E-86

50.96

C

T

ORF1ab

17,104

H

Y

5614

76

68

5486

236,780

2.38E-84

48.24

C

A

S

22,879

N

K

439

76

68

5501

236,765

2.92E-84

48.10

A

G

ORF1ab

20,268

L

L

6668

83

61

16,967

225,299

4.21E-57

18.07

C

T

ORF1ab

14,408

P

L

4715

143

1

225,633

16,633

2.08E-04

10.54

C

T

ORF1ab

3037

F

F

924

143

1

225,640

16,626

2.08E-04

10.54

A

G

S

23,403

D

G

614

143

1

225,843

16,423

2.36E-04

10.40

  1. aREF reference nucleotide, ALT alternate nucleotide, GENE gene name, NT.POS nucleotide position in gene, REF.AA reference amino acid, ALT.AA alternate amino acid, AA.POS amino acid position in protein
  2. 1CY counts1 number of times ALT form of the S6059F mutation (value 1) was found in Cyprus strains
  3. 2CY counts0 number of times REF form of the S6059F mutation (value 0) was found in Cyprus strains
  4. 3Other counts1 number of times ALT form of the S6059F mutation (value 1) was found strains from other countries
  5. 4Other counts0 number of times REF form of the S6059F mutation (value 0) was found strains from other countries
  6. 5GLM p-value
  7. 6Odds ratio (OR) statistic