SNPs and Hox gene mapping in Ciona intestinalis

BMC Genomics

Table 3 Nucleotide polymorphisms in C. intestinalis sp. B 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	349	2	0	1	1	100	0	0	0	0	0	0	-	1	0	1	-	0.002	0.003	0.003	0.0028	0.0028
Hox2	530	5	3	3	6	75	0	1	0	1	2	25	3	8	7	24	0.3	0.008	0.015	0.045	0.0019	0.0021
Hox5	383	5	4	2	6	37	4	3	0	3	10	63	0.6	16	1	27	0.4	0.028	0.042	0.07	0.0267	0.0268
Hox10	537	2	5	0	5	83	0	1	0	0	1	17	5	6	9	17	0.3	0.011	0.011	0.032	0.0116	0.0207
Xlox	704	9	4	3	7	70	0	1	2	0	3	30	2.3	10	11	35	0.3	0.006	0.014	0.05	0.000002	0.0017
	2503	23	16	9	25	61	4	6	2	4	16	39	1.6	41	28	104	0.4		0.016	0.04
COI	515	5	5	5	10	100	0	0	0	0	0	0	-	10	1	12	0.8	0.009	0.019	0.025	0.0039	0.0048
Hox13	596	5	6	3	9	82	0	1	0	1	2	18	4.05	11	1	23	0.5	0.016	0.018	0.038	0.0067	0.0099
Tot	1111		11	8	19	90	0	1	0	1	2	10	9.5	21	2	35	0.6		0.019	0.031

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