TABLE 3.

An overview of basic statistic for RRBS libraries constructed based on the gel-free protocol.

Sample ID	Total reads	Clean reads after trimming	Read coverage (X)	Unique mapping efficiency (%)	Global CpG methylation (%)	Number of covered CpGs	Bisulfite conversion rate (%)
14 A	8,092,814	7,424,375	15.3	32.3	40.4	4,287,779	99.2
17 A	8,769,052	8,037,908	16.2	29.2	38.4	4,161,727	99.2
14 B	8,187,841	7,514,351	15.4	30.5	38.0	3,867,873	99.2
17 B	7,916,740	7,242,150	15.0	30.2	37.6	3,941,237	99.2
14 C	9,235,837	8,452,463	17.4	33.3	40.3	4,792,957	99.2
17 C	8,208,151	7,515,657	15.3	33.0	39.9	4,267,681	99.2
14 D	8,608,751	7,932,141	15.6	33.3	39.6	4,529,706	99.3
17 D	6,947,434	6,395,163	12.4	32.6	39.6	3,918,954	99.2
14 E	7,745,029	7,098,249	14.6	33.9	40.2	4,230,165	99.2
17 E	8,179,041	7,538,949	15.7	34.4	40.7	4,384,431	99.2
14 F	9,561,827	8,631,458	18.2	33.9	41.2	4,855,729	99.0
17 F	11,204,211	10,288,338	21.6	34.8	41.4	5,383,672	98.9
14 G	6,739,955	6,197,336	13.1	35.2	40.7	3,947,850	98.8
17 G	8,406,205	7,643,950	16.4	37.0	42.7	4,819,724	98.7

Libraries were constructed from sperm DNA collected from the same young Norwegian red bulls (n = 7) at two different ages. Letters A to G prefixed by 14 or 17, indicating different bulls of age 14 and 17 months, respectively. Clean reads were obtained after adapter and low-quality trimming of Illumina sequencing reads (total reads). Read coverage was calculated by number of bp in the clean reads/number of bp at in silico MspI-digested bosTau9 genome. Mapping efficiency shows the percentage of uniquely mapped clean reads with the reference genome. CpG methylation shows the percentage of global methylation in clean reads. Downstream analyses were performed based on all covered CpGs. Bisulfite conversion rate shows the proportion of Cs, which converted to uracil during bisulfite conversion process.