Table 1.

Recombination events detected with RDP4 from the alignment of whole genome and individual genes used for tree construction. The average P-value of detection methods are indicated.

Recombinant	Breakpoints	Major Parent	Minor Parent	Recombination Detection Methods (Av. P-alue)
				RDP	GENECONV	BootScan	MaxChi	Chimaera	SiScan	3Seq
WholeGenome
SH/2015/D187	184–1581	SH/2015/D381	NIVD103	2.91 × 10−09	5.11 × 10−07	2.81 × 10−09	4.83 × 10−03	4.04 × 10−02	3.67 × 10−05	—
SH/2015/D16	19659–29993	NIVD103	Unkown	4.65 × 10−05	2.58 × 10−05	5.44 × 10−04	2.21 × 10−10	1.19 × 10−08	3.69 × 10−31	1.62 × 10−05
SH/2015/D240	19659–29993	NIVD103	Unknown	4.65 × 10−05	2.58 × 10−05	5.44 × 10−04	2.21 × 10−10	1.19 × 10−08	3.69 × 10−31	1.62 × 10−05
SH/2015/D363	31–1085	SH/2015/D381	NIVD103	—	1.01 × 10−05	2.99 × 10−06	4.42 × 10−02	—	1.64 × 10−18	3.11 × 10−04
	10012–12520	NY/2010/4845	NIVD103	4.64 × 10−03	1.21 × 10−02	5.59 × 10−03	1.96 × 10−02	1.96 × 10−02	3.48 × 10−06	1.03 × 10−02
	17719–19568	NY/2010/4845	NIVD103	—	3.69 × 10−11	2.41 × 10−15	4.24 × 10−13	1.26 × 10−11	5.48 × 10−09	—
	26452–29139	Unknown	NY/2010/4845	3.89 × 10−03	—	—	—	—	2.18 × 10−05	2.28 × 10−03
	31194–31825	NY/2010/4845	Unknown	8.42 × 10−07	2.72 × 10−06	5.19 × 10−07	7.22 × 10−03	—	—	1.39 × 10−03
	31826–33318	NY/2010/4845	NIVD103	—	1.28 × 10−10	—	7.53 × 10−09	—	—	1.37 × 10−02
Long fiber
SH/2015/D363	1492–1538	NIVD103	Unknown	—	4.89 × 10−06	1.61 × 10−06	2.53 × 10−02	—	—	4.87 × 10−04
Hexon										—
SH/2015/D16	293–2067	D31	Tak	—	—	—	—	—	8.32 × 10−17	2.19 × 10−02
SH/2015/D240	293–2067	D31	Tak	—	—	—	—	—	8.32 × 10−17	2.19 × 10−02
SH/2015/D363	292–1976	D31	Tak	—	—	—	—	—	8.32 × 10−17	2.19 × 10−02