Application of massive parallel sequencing to whole genome SNP discovery in the porcine genome

BMC Genomics

Table 2 Summary of in silico digest of reference genome and analysis of consensus sequences.

Chr	Total sequence length (bp) in silico	Total observed sequence length (bp)	Total observed sequence length (bp) per 1-Mb window		Nucleotide diversity		GC content (%)
			Mean	s.e.	Mean	s.e.	Mean	s.e.
1	1,942,512	2,167,060	8,738.15	204.29	0.0013	0.00007	31.72	0.11
2	564,894	704,052	8,912.05	430.80	0.0017	0.00015	31.82	0.21
3	396,990	510,151	7,971.11	337.50	0.0013	0.00011	32.60	0.22
4	931,194	988,690	7,724.14	286.62	0.0012	0.00009	32.26	0.16
5	541,200	589,399	7,805.12	417.18	0.0019	0.00012	32.29	0.24
6	263,538	354,332	7,874.04	508.06	0.0015	0.00013	32.65	0.24
7	263,538	831,673	6,253.18	283.95	0.0015	0.00010	32.62	0.17
8	590,700	732,338	10,930.42	338.24	0.0011	0.00013	31.36	0.22
9	582,384	763,287	9,541.09	406.33	0.0014	0.00014	32.06	0.18
10	292,842	367,327	8,959.20	380.01	0.0021	0.00019	32.44	0.21
11	527,274	584,831	9,137.98	370.76	0.0015	0.00013	31.85	0.30
12	135,894	174,581	6,020.03	462.41	0.0018	0.00015	33.71	0.36
13	924,396	1,177,791	9,897.40	293.47	0.0014	0.00009	31.64	0.14
14	874,500	952,048	6,476.52	265.24	0.0014	0.00008	32.83	0.17
15	822,822	974,572	10,185.12	326.63	0.0010	0.00009	31.47	0.14
16	402,270	500,390	10,007.80	481.24	0.0016	0.00013	31.97	0.26
17	280,434	303,111	5,511.11	367.98	0.0015	0.00011	33.22	0.24
18	256,806	314,098	9,518.12	593.62	0.0007	0.00010	32,45	0.29
X	495,726	386,932	5,300.44	181.11	0.0005	0.00009	31.77	0.20

ISSN: 1471-2164