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Table 3 Summary of possible recombination events in TBTV isolates identified by RDP4

From: Phylogenetic and recombination analysis of Tobacco bushy top virus in China

Event number

Recombinant Sequence(s)

Breakpoint position

Parental sequence (s)

Recombinant score

P-Value for the six detection methods in RDP4

Begin/End

Minor/Major

 

RDP

GENECONV

BootScan

MaxChi

Chimaera

SiScan

1

TBTV-JC

616/965

YYXi/MD-II

0.472

NS

NS

NS

8.76E-03

1.68E-02

4.07E-03

2

TBTV-MD-I

241/1464

JC/YYXi

0.469

2.71E-02

1.06E-02

1.11E-02

1.93E-05

4.78E-04

1.19E-09

3

TBTV-MD-I

616/965

YYXi/MD-II

0.472

NS

NS

NS

8.76E-03

1.68E-02

4.07E-03

4

TBTV-MD-I

629/3207

JC/YYXi

0.608

3.07E-02

NS

2.97E-02

1.65E-03

6.97E-03

5.17E-08

5

TBTV-MD-II

279/519

JC/Unknown (YYXi)

0.482

1.81E-03

NS

1.95E-02

3.48E-05

7.87E-06

3.56E-05

6

TBTV-MD-II

2716/3511

YWDu/Unknown (YYXi)

0.426

7.26E-04

NS

1.11E-02

1.22E-06

3.49E-06

NS

7

TBTV-Ch

210/618

MD-I/YYXi

0.426

NS

3.18E-02

2.76E-02

7.31E-03

3.32E-02

4.49E-06

8

TBTV-Ch

211/652

JC/YYXi

0.482

1.81E-03

NS

1.95E-02

3.48E-05

7.87E-06

3.56E-05

9

TBTV-Ch

253/385

MD-II/YLLi

0.419

NS

NS

NS

3.24E-02

NS

NS

10

TBTV-Ch

652/3207

YYXi/JC

0.608

3.07E-02

NS

2.97E-02

1.65E-03

6.97E-03

5.17E-08

11

TBTV-Ch

3574/142

YYXi/MD-I

0.461

1.23E-02

NS

1.37E-02

1.37E-02

1.62E-04

NS

12

TBTV-YWSh

211/793

JC/YYXi

0.483

1.04E-02

NS

1.00E-02

4.09E-02

1.23E-02

1.09E-06

13

TBTV-YWSh

253/385

MD-II/YLLi

0.419

NS

NS

NS

3.24E-02

NS

NS

14

TBTV-YWSh

384/666

MD-I/YYXi

0.426

NS

3.18E-02

2.76E-02

7.31E-03

3.32E-02

4.49E-06

15

TBTV-YWSh

652/3207

YYXi/JC

0.608

3.07E-02

NS

2.97E-02

1.65E-03

6.97E-03

5.17E-08

16

TBTV-YYXi

183/2070

MD-II/JC

0.593

2.95E-03

3.16E-02

8.25E-05

NS

NS

6.63E-05

17

TBTV-YYXi

1355/1687

YWSh/Unknown (MD-II)

0.420

NS

1.41E-02

NS

4.78E-02

NS

6.90E-06

18

TBTV-YYXi

2571/3508

Unknown (MD-II)/Ch

0.443

NS

NS

NS

1.53E-04

NS

NS

19

TBTV-YYXi

3155/3603

Unknown (MD-II)/ YLLi

0.615

1.03E-02

4.02E-04

2.49E-04

9.70E-04

7.29E-04

4.44E-05

20

TBTV-YYXi

3207/3514

Unknown(JC)/YWDu

0.841

3.26E-04

2.37E-02

NS

6.50E-04

1.63E-02

NS

21

TBTV-YYXi

3538/209

Ch/Unknown(MD-I)

0.534

NS

NS

NS

7.38E-06

4.47E-04

NS

22

TBTV-YLLi

211/1515

JC/YYXi

0.608

3.07E-02

NS

2.97E-02

1.65E-03

6.97E-03

5.17E-08

23

TBTV-YLLi

616/965

YYXi/MD-II

0.472

NS

NS

NS

8.76E-03

1.68E-02

4.07E-03

24

TBTV-YLLi

1533/1986

MD-II/MD-I

0.741

1.21E-08

3.18E-04

9.88E-09

8.14E-04

5.48E-04

NS

25

TBTV-YLLi

1533/2480

YYXi/MD-I

0.731

1.31E-03

NS

2.93E-02

3.86E-08

3.61E-05

NS

26

TBTV-YLLi

1554/1971

Ch/MD-I

0.611

NS

NS

3.56E-04

1.26E-03

NS

NS

27

TBTV-YWDu

2027/11

Ch/Unknown(MD-II)

0.632

3.34E-42

6.13E-42

1.08E-39

5.51E-19

7.16E-19

2.38E-23

28

TBTV-YWDu

2042/3170

Ch/Unknown(MD-II)

0.601

5.12E-23

1.81E-23

7.17E-25

3.99E-09

3.28E-11

1.92E-09

29

TBTV-YWDu

3171/4140

Ch/Unknown(MD-II)

0.545

3.34E-42

6.13E-42

1.08E-39

5.42E-06

5.80E-06

1.13E-14

  1. NS: not significant