Table 1.

Statistics of clean reads’ alignment with porcine reference genome (Sscrofa11.1/susScr11) and methylation rates in CpG, CHG, and CHH contexts.

Sample	Clean read pair	Uniquely aligned rate	Number of aligned site	Total number of analyzed cytosine	Cytosine methylation rate in CpG context	Cytosine methylation rate in CHG context	Cytosine methylation rate in CHH context
1	16,505,578	46%	6,555,417	210,492,580	49%	0.91%	0.61%
2	93,817,089	51%	11,786,693	1,458,034,594	53%	0.99%	0.69%
3	38,026,074	47%	8,350,750	507,968,318	46%	0.84%	0.58%
4	75,769,839	51%	11,024,632	1,161,664,236	52%	0.87%	0.62%
5	57,267,890	51%	10,230,855	994,282,472	50%	0.68%	0.52%
6	68,607,455	46%	8,427,406	881,065,710	46%	0.89%	0.64%
7	85,068,927	49%	8,799,356	1,220,798,901	49%	0.92%	0.67%
8	75,438,276	51%	9,259,657	1,194,394,820	51%	0.92%	0.67%
9	16,940,690	47%	6,619,706	214,465,154	50%	0.95%	0.66%
Mean	58,604,646	49%	9,006,052	871,462,976	50%	0.89%	0.63%
SD	28,617,798	2.3%	1,798,552	456,951,421	2.4%	0.09%	0.05%