SNPs and Hox gene mapping in Ciona intestinalis

BMC Genomics

Table 1 Nucleotide polymorphisms in C. intestinalis sp. A loci.

Gene	bp	nH	Ts				Tv						Ts/Tv	∑_SNPs(ts+tv)	1 bp indel	∑_PS	∑_SNPs/_PS	π	f_SNPs	f_∑PS	T93	L'sP
			AG	CT	∑_Ts	%	AC	AT	GC	GT	∑_Tv	%
Hox1	573	4	1	3	4	40	2	3	1	0	6	60	0.67	10	4	16	0.62	0.017	0.020	0.03	0.007	0.012
Hox2	531	3	1	0	1	50	0	1	0	0	1	50	0.5	2	1	3	0.67	0.002	0.004	0.005	0.000002	0.000066
Hox4	357	3	0	0	0	0	0	1	0	0	1	100	0	1	1	2	1	0.002	0.006	0.006	0.0028	0.0062
Hox5	481	11	10	8	18	72	1	6	0	0	7	28	2.57	25	3	45	0.55	0.024	0.052	0.093	0.004	0.004
Hox10	531	8	10	5	15	43	1	15	0	4	20	57	0.75	35	8	61	0.57	0.038	0.066	0.115	0.004	0.003
EvxA	569	3	0	0	0	0	0	2	0	0	2	100	0	2	1	3	0.67	0.002	0.003	0.005	0.0035	0.0039
Xlox	707	5	3	2	5	55	0	1	3	0	4	45	1.25	9	1	16	0.56	0.006	0.013	0.022	0.000002	0.0018
Gsx	186	6	1	1	2	100	0	0	0	0	0	0	0	2	0	15	0.13	0.012	0.01	0.08	0.0035	0.003706
Wd-40	1340	4	2	0	2	28	3	1	0	1	5	72	0.4	7	3	30	0.23	0.008	0.005	0.028	0.0084	0.231
ci0100134706	678	4	6	6	12	70	0	2	0	3	5	30	2.4	17	7	38	0.45	0.019	0.025	0.056	0.03	0.04
	5953		34	25	59	54	7	32	4	8	51	46	1.18	110	29	229	0.48		0.019	0.038
Gsx	897	4	5	8	13	87	0	2	0	0	2	13	6.5	15	0	15	1	0.011	0.017	0.017	0.00452	0.004575
Hox13	601	2	1	1	2	67	0	0	0	1	1	33	2	3	3	11	0.27	0.008	0.005	0.025	0.01188	0.016926
COI	515	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
	2013		6	9	15	83	0	2	0	1	3	17	5.0	18	3	26	0.69		0.009	0.013

Abbreviations: bp, length of the amplified sequence; nH, number of haplotypes; Ts, transition; Tv, transversion; ∑, total; PS, polymorphic sites; π, nucleotide diversity; f, frequency; T93, Tamura-Nei genetic distance (1993); L'sP, Lake's paralinear genetic distance.

ISSN: 1471-2164