Integrated analyses using RNA-Seq data reveal viral genomes, single nucleotide variations, the phylogenetic relationship, and recombination for Apple stem grooving virus

Table 4 Recombination analysis of 21 ASGV genomes using RDP4 program

	In alignment		In recombinant sequence		Relative to CTLV_Lily					Detection methods
Event Number	Begin	End	Begin	End	Begin	End	Recombinant sequence(s)	Minor parental sequence(s)	Major parental sequence(s)	RDP	GENECONV	Bootscan	Maxchi	Chimaera	SiSscan	PhylPro	LARD	3Seq
1	6492	1926	6487	1924	6488	1925	ASGV_YTG	Unknown (ASGV_HH), Unknown (ASGV_CHN)	ASGV_Fuji	1.30E-31	3.39E-09	8.78E-30	1.16E-10	9.12E-16	9.16E-27	NS	NS	3.17E-17
2	6492	2488	6488	2487	6488	2487	ASGV_HH, ASGV_CHN, CTLV_MTH[P]	ASGV_Fuji, CTLV_MTH	ASGV_Li-23, CTLV_Lily	3.40E-19	3.89E-04	1.47E-16	1.29E-16	1.83E-10	1.06E-27	NS	NS	1.48E-13
3	4112	4552	4110	4550	4110	4550	PBNLSV	ASGV_Li-23, CTLV_Lily	ASGV_KFP	1.20E-12	2.22E-08	8.19E-11	2.20E-05	2.75E-05	1.41E-10	NS	NS	NS
4	5844	6224	5842	6221	5842	6221	PBNLSV	ASGV_Li-23, CTLV_Lily	Unknown (CTLV_Pk), Unknown (CTLV_Kumquat1), Unknown (CTLV_LCd-NA-1), Unknown (CTLV_SO), Unknown (CTLV_XHC), Unknown (ASGV_Matsuco)	6.90E-07	1.12E-08	1.61E-07	6.45E-04	6.44E-04	1.30E-06	NS	NS	NS
5	5819	6412^a	5816	6408^a	5817	6409^a	ASGV_YTG	ASGV_HH, ASGV_CHN	ASGV_P-209, ASGV_T47	2.42E-08	2.14E-03	1.58E-09	2.89E-03	1.65E-02	1.97E-07	NS	NS	NS
6	4412	4946	4409	4943	4410	4944	CTLV_LCd-NA-1	CTLV_SO, CTLV_Kumquat1, CTLV_XHC	Unknown (ASGV_Matsuco)	1.20E-02	2.91E-04	1.01E-02	4.02E-04	5.76E-03	4.04E-03	NS	NS	NS

Minor Parent Parent contributing smaller fraction of sequence, Major Parent Parent contributing larger fraction of sequence, Unknown Only one parent and a recombinant need be in the alignment for a recombination event to be detectable. The sequence listed as unknown was used to infer the existence of a missing parental sequence, NS No significant P-value was recorded for this recombination event using this method
^aThe actual breakpoint position is undetermined (it was most likely overprinted by a subsequent recombination event)

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