Table 1. Localization of the recombination breakpoints with different methods in RDP3 on an alignment of 28 full-length coding genomes, analyzed with Bonferroni correction and P-value <0.05.

Detection method	Daughter	Major parent	Minor parent	Av. P-Val	Start	End	Size
Genconv	LIV	SSEV	Neudoerfl	1.1×10−5	5787	5991	204
Bootscan	LIV	SSEV	Neudoerfl	3.2×10−6	5787	5991	204
Chimaera*	LIV	SSEV	Hypr	3.0×10−2	5675	6001	326
MaxChi*	LIV	SSEV	Hypr	5.0×10−3	5768	6048	280
RDP	LIV	SSEV	Neudoerfl	2.2×10−3	5787	5991	204
SiScan	LIV	SSEV	Neudoerfl	8.0×10−5	5787	5991	204

Sequences are numbered from the start of the ORF using Neudoerfl as reference.

*indicates that this method did not recover the general recombination signal in a simultaneous run. Instead, it found a different signal when used as a single primary detection method.