Table 1. Dengue virus serotype 2 (DENV-2) recombinant strains obtained using RDP4 package.

A total of 26 recombinant strains were identified using RDP4 with p-value < 0.00001. The breakpoint positions are reported according to the position in the respective recombinant sequence. The recombination is detected using at least two of the six recombination detection methods in RDP4 program namely RDP, GENCONV, BOOTSCAN, MAXCHI, CHIMAERA, SISCAN and 3SEQ and are represented as R, G, B, M, C, S and Q, respectively. The method showing comparatively lowest p-value is shown and is represented as bold and the corresponding p-value is also reported.

Serial number	Recombinant DENV-2 strain [Genotype_ GenBank-Accession]	Major Parent [Genotype_ GenBank-Accession]	Minor Parent [Genotype_ GenBank-Accession]	Breakpoint start	Breakpoint end	Methods: RGBMCSQ	Lowest p-value
1	AM_GQ398257	AM_GQ868600	AA_GQ398269	4,256	6,361	RGBMCSQ	3.70E−140
2	AM_JQ922552	AM_JQ922550	AM_JQ922549	6,081	6,535	RGBMCS	1.05E−20
3	AM_JQ922553	AM_JQ922552	C_JQ922551	7,448	8,410	RGBMCSQ	1.97E−36
4	AM_JQ922550	AM_JQ922552	C_JQ922551	7,448	8,410	RGBMCSQ	1.97E−36
5	AM_AF100467	AM_EU056811	AM_GQ868588	6,000	7,947	RGBQ	1.23E−18
6	C_EU179859	C_EU482640	Unknown	2,985	3,975	RGBMCSQ	3.56E−84
7	C_FJ196854	C_JN851128	A1_FJ196851	0*	773	RGBS	1.89E−28
		C_GQ398264	A1_FJ196851	10,200	10,498*	RGB	1.55E−14
8	C_ JQ922551	C_GQ398261	AM_JQ922552	1,544	1,824	RGB	5.428E−08
9	AA_GQ398269	AA_GQ398300	AAF204178	4,289	6,204	RGBMCS	4.51E−53
10	AA_JN819408	AA_GQ868553	Unknown	10,411	10,620*	RGBMC	1.41E−69
11	AA_EU482726	AA_EU596491	AA_EU482719	5,260	8,059	GBMCS	1.22E−38
12	AA_JF357906	AA_EU621672	Unknown	10,466	10,783*	RGBMCQ	1.60E−113
13	AA_FJ744708	AA_JF357906	Unknown	7,502	7,567	RB	2.97E−08
14	AA_JN819418	AA_M20558	Unknown	10,266	10,576*	RGBMC	8.77E−78
15	AA_AF100466	AA_GQ868540	A1_AF100463	0*	606	RGBSQ	6.77E−40
16	AI_FJ196851	AI_GQ868545	C_FJ196852	4,984	5,266	RGB	1.82E−22
		AI_GQ868545	C_FJ196853	8,294	9,438	RGBMCSQ	3.33E−44
17	AI_FJ687444	AI_FJ744721	Unknown	10,277	10,363*	RGB	6.92E−27
18	AI_EU482784	AI_EU482775	C_EU482640	2,726	3,751	RGBMCSQ	8.50E−73
		AI_FM210211	Unknown	9,970	10,679*	RGBMC	1.59E−19
19	AI_FJ410193	AI_FM210211	Unknown	0*	59	RGB	2.79E−08
20	AI_FM210211	AI_FJ687444	AA_EU482783	9,988	10,691*	RGBMCS	3.04E−29
21	AI_GU131924	AI_FM210211	Unknown	9,955	10,557*	RGBMC	1.59E−19
22	AI_JN368476	AI_GU131930	AI_GU131897	8,188	9,896	RGBS	1.14E−12
23	AI_FJ639717	Unknown	AI_GU131897	8,317	9,306*	RGBSQ	1.14E−12
24	AI_JF730047	Unknown	AI_GU131897	8,329	9,318*	RGBSQ	1.14E−12
25	AI_GU131930	Unknown	AI_GU131897	8,317	9,306*	RGBSQ	1.14E−12
26	AI_JF730048	Unknown	AI_GU131897	8,328	9,317	RGBSQ	1.14E−12

Notes.

^*Indicates that the actual breakpoint position is undetermined in subsequent recombination event.