Complete chloroplast genome of Stephania tetrandra (Menispermaceae) from Zhejiang Province: insights into molecular structures, comparative genome analysis, mutational hotspots and phylogenetic relationships

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
Species	Region	A/G	C/T	A/T	A/C	C/G	G/T	Total Number of SNP sites	Ts/Tv
*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
Species	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

ISSN: 1471-2164