Identification and analysis of Single Nucleotide Polymorphisms (SNPs) in the mosquito Anopheles funestus, malaria vector

Wondji, Charles S; Hemingway, Janet; Ranson, Hilary

doi:10.1186/1471-2164-8-5

Table 1 Nucleotide polymorphism in An. funestus genes

From: Identification and analysis of Single Nucleotide Polymorphisms (SNPs) in the mosquito Anopheles funestus, malaria vector

		Coding region																Non-coding region
		Polymorphic sites												Nucleotide diversity				Polymorphic sites				Nucleotide diversity
			Transition				Transversion
Gene	nHap	L (bp)	1st	2nd	3rd	Σ	1st	2nd	3rd	Σ	Syn	Rep	Σ	π	π_n	K_s	K_a	L(bp)	T_s	T_v	Σ	π
*4G17*	3	190	0	1	1	2	0	0	0	0	1	1	2	0.0052	0.0036	0.0200	0.0072	0	0	0	0	0.0000
*9K1*	23	199	3	1	3	7	1	0	1	2	5	4	9	0.0193	0.0107	0.1010	0.0270	0	0	0	0	0.0000
*4J10*	14	141	1	0	3	4	0	0	1	1	5	0	5	0.0116	0.0000	0.1300	0.0000	73	2	2	4	0.0157
*6P3*	18	0	0	0	0	0	0	0	0	0	0	0	0	0.0000	0.0000	0.0000	0.0000	179	6	2	8	0.0188
*6P4*	17	201	0	0	2	2	0	0	0	0	2	0	2	0.0041	0.0000	0.0450	0.0000	189	8	3	11	0.0233
*6P5*	5	189	0	0	1	1	0	0	0	0	1	0	1	0.0016	0.0000	0.0200	0.0000	112	2	0	2	0.0063
*6Z1*	14	444	1	0	5	6	0	0	5	5	8	3	11	0.0079	0.0022	0.0750	0.0088	29	1	0	1	0.0159
*6Z3*	14	453	1	0	13	14	1	0	5	6	18	2	20	0.0169	0.0011	0.1860	0.0057	0	0	0	0	0.0000
*9J12*	9	156	2	1	0	3	1	0	1	2	0	5	5	0.0117	0.0156	0.0000	0.0510	0	0	0	0	0.0000
*9J14*	14	174	0	0	3	3	2	0	0	2	3	2	5	0.0140	0.0077	0.0760	0.0150	0	0	0	0	0.0000
*BU01*	2	162	0	0	1	1	0	0	0	0	1	0	1	0.0011	0.0000	0.0230	0.0000	26	0	0	0	0.0000
*BU08*	12	394	0	0	2	2	2	1	2	5	4	3	7	0.0042	0.0026	0.0470	0.0098	16	0	0	0	0.0000
*Ache*	18	249	0	1	7	8	0	1	2	3	8	3	11	0.0149	0.0034	0.1460	0.0160	85	2	2	4	0.0180
*BU10*	16	294	1	0	3	4	0	0	2	2	5	1	6	0.0084	0.0024	0.0690	0.0045	245	3	1	4	0.0056
*BU11*	4	177	0	1	0	1	0	0	0	0	0	1	1	0.0029	0.0039	0.0000	0.0074	53	0	1	1	0.0099
*BU12*	7	504	1	1	1	3	0	1	1	2	3	2	5	0.0032	0.0011	0.0240	0.0053	38	0	0	0	0.0000
*BU13*	19	363	2	0	1	3	0	0	0	0	1	2	3	0.0026	0.0029	0.0110	0.0073	148	2	5	7	0.0133
*BU19*	22	526	3	1	4	8	0	1	1	2	6	4	10	0.0072	0.0035	0.0490	0.0100	0	0	0	0	0.0000
*BU021*	17	267	0	0	2	2	0	0	2	2	4	0	4	0.0044	0.0000	0.0610	0.0000	67	2	2	4	0.0164
*BU21*	16	417	0	1	2	3	1	0	2	3	4	2	6	0.0073	0.0018	0.0510	0.0077	81	4	1	5	0.0256
*BU25*	2	234	0	0	0	0	0	0	0	0	0	0	0	0.0000	0.0000	0.0000	0.0000	111	2	0	2	0.0036
*BU29*	11	258	0	0	2	2	0	0	2	2	3	1	4	0.0038	0.0008	0.0540	0.0049	152	0	2	2	0.0029
*BU34*	11	231	0	0	2	2	0	2	2	4	4	2	6	0.0101	0.0051	0.0740	0.0113	28	0	0	0	0.0000
*BU35*	12	264	0	0	7	7	0	0	1	1	8	0	8	0.0071	0.0000	0.1280	0.0000	108	1	1	1	0.0039
*BU40*	14	255	2	1	1	4	1	0	0	1	1	4	5	0.0074	0.0076	0.0170	0.0200	415	3	2	5	0.0016
*BU56*	4	156	0	1	2	3	1	0	2	3	3	3	6	0.0214	0.0132	0.0710	0.0263	126	5	2	7	0.0331
*BU58*	7	261	1	0	2	3	0	1	1	2	3	2	5	0.0053	0.0019	0.0446	0.0103	20	0	0	0	0.0000
*BU62*	22	213	0	0	1	1	0	0	0	0	1	0	1	0.0013	0.0000	0.0207	0.0000	260	7	5	12	0.0143
*BU66*	25	282	9	2	0	11	1	2	0	3	3	11	14	0.0174	0.0194	0.0503	0.0494	179	4	4	8	0.0099
*BU70*	5	228	0	0	2	2	0	0	2	2	2	2	4	0.0066	0.0015	0.0506	0.0059	62	0	1	1	0.0069
*BU71*	9	573	0	0	6	6	1	1	2	4	8	2	10	0.0044	0.0005	0.0615	0.0045	98	1	0	1	0.0051
*BU72*	20	354	2	1	2	5	2	1	1	4	3	6	9	0.0082	0.0062	0.0368	0.0220	195	1	1	2	0.0052
*BU73*	5	277	0	0	0	0	1	2	0	3	0	3	3	0.0039	0.0036	0.0000	0.0135	0	0	0	0	0.0000
*BU76*	15	330	0	0	7	7	1	1	1	3	9	1	10	0.0087	0.0008	0.1104	0.0041	154	3	3	6	0.0095
*BU77*	18	261	3	0	1	4	1	2	0	3	6	1	7	0.0125	0.0136	0.0166	0.0298	198	9	7	16	0.0345
*BU82*	13	228	0	0	2	2	0	2	0	2	2	2	4	0.0059	0.0025	0.0402	0.0112	88	2	2	4	0.0156
*BU85*	14	299	2	1	8	11	0	0	1	1	11	1	12	0.0108	0.0363	0.1155	0.0033	121	2	0	2	0.0087
*BU88*	16	441	2	0	12	14	0	0	2	2	16	0	16	0.0135	0.0000	0.1601	0.0000	212	9	4	13	0.0179
*BU90*	4	0	0	0	0	0	0	0	0	0	0	0	0	0.0000	0.0000	0.0000	0.0000	261	1	2	3	0.0021
*BU92*	11	345	3	1	3	7	1	1	1	3	5	5	10	0.0075	0.0031	0.0650	0.0186	110	5	3	8	0.0226
*BU93*	8	510	0	0	5	5	0	0	3	3	7	1	8	0.0035	0.0004	0.0626	0.0025	137	0	2	2	0.0023
*BU98*	4	369	0	0	5	5	0	0	2	2	7	0	7	0.0101	0.0000	0.0843	0.0000	158	2	6	8	0.0257
*BU883*	21	354	1	0	5	6	2	1	2	5	7	4	11	0.0120	0.0052	0.0913	0.0145	188	8	3	11	0.0189
*BU897*	19	303	0	0	2	2	3	1	2	6	3	5	8	0.0080	0.0078	0.0458	0.0210	167	4	3	7	0.0180
*BU901*	12	231	0	0	3	3	0	0	0	0	3	0	3	0.0035	0.0000	0.0552	0.0000	229	2	2	4	0.0065
*BU973*	5	471	1	1	0	2	0	0	0	0	2	0	2	0.0015	0.0019	0.0000	0.0054	67	1	0	1	0.0028
*BU974*	3	459	0	0	2	2	0	0	1	1	3	0	3	0.0036	0.0000	0.0265	0.0000	52	1	0	1	0.0096
*BU982*	4	240	0	1	1	2	0	0	0	0	1	1	2	0.0030	0.0016	0.0190	0.0053	51	1	0	1	0.0107
*BU996*	18	543	4	0	2	6	1	1	1	3	6	3	9	0.0073	0.0019	0.0518	0.0070	87	6	6	12	0.0312
*Kdr*	13	201	0	0	0	0	1	1	0	2	0	2	2	0.0020	0.0026	0.0000	0.0127	501	2	5	7	0.0039
Total		14671	45	17	139	201	25	23	54	102	206	97	303					5876	106	85	191
Average														0.0072	0.0041	0.0537	0.0097					0.0123

nHap, number of haplotypes; L, length of the nucleotide sequence; ∑, total; Syn, synonymous substitutions; Rep, replacement substitutions; π, average number of nucleotide substitution per site; π_n, average number of non-synonymous nucleotide substitution per site; K_s, average number of nucleotide substitution per synonymous site; K_a, per non-synonymous site; T_s, transitions; T_v, transversions.

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