Table 7.

Comparison of substitutions and InDels in four Stephania species

Comparative analyses of substitutions
Species	Region	Transition Substitutions	Transversion Substitutions					Total Number of SNP sites	Ts/Tv
		A/G	C/T	A/T	A/C	C/G	G/T
S. tetrandra voucher ZJ	Large single copy	158	173	13	61	15	35	455	2.6
S. tetrandra voucher JX		177	207	20	64	19	40	527	2.7
S. japonica		242	245	28	69	26	60	670	2.5
S. kwangsiensis		228	239	39	87	25	61	679	2.2
S. tetrandra voucher ZJ	Inverted repeat	8	9	0	3	2	1	23	2.1
S. tetrandra voucher JX		10	7	1	5	1	3	27	1.7
S. japonica		10	11	1	4	2	5	33	1.9
S. kwangsiensis		9	13	1	5	1	5	34	1.8
S. tetrandra voucher ZJ	Small single copy	43	38	5	19	4	18	127	2.0
S. tetrandra voucher JX		64	61	15	21	9	10	180	2.2
S. japonica		68	92	21	25	11	21	238	2.2
S. kwangsiensis		73	66	13	27	7	24	210	1.9
Comparative analyses of InDels sites
Species	Large single copy		Inverted repeat				Small single copy
	No’s of Indels	InDel average length	No’s of Indels		InDel average length		No’s of Indels	InDel average length
S. tetrandra voucher ZJ	11	88.636	5		104.400		5	28.200
S. tetrandra voucher JX	13	42.581	2		87.300		5	28.200
S. japonica	19	37.421	6		89.500		5	28.200
S. kwangsiensis	21	34.571	4		134.250		5	23.400