Sperm DNA methylation patterns at discrete CpGs and genes involved in embryonic development are related to bull fertility

Table 1 Library characterisation, mapping efficiency on the bovine genome (ARS-UCD1.2), coverage and average methylation in reduced representative bisulphite sequencing (RRBS) libraries

	Low-fertility bulls (n = 10)	High-fertility bulls (n = 10)
Sequence pairs analysed (10⁶)	28.5 ± 2.52	32.2 ± 2.93
All maps (%)	88.0 ± 0.51	88.0 ± 0.61
Unique maps (%)	34.0 ± 0.30	34.0 ± 0.32
Ambiguous maps (%)	54.0 ± 0.32	54.0 ± 0.48
Total number of CpGs analysed (10⁶)	3.3 ± 0.04	3.4 ± 0.05
Percentage of CpGs covered by ≥10 sequences (CpGs10)	55.9 ± 2.25	58.5 ± 1.78
Mean genomic coverage by CpGs	19.7 ± 1.67	21.6 ± 1.80
Average DNA methylation of CpGs10 (%)	46.9 ± 0.41	47.6 ± 0.29
Average DNA methylation of CpGs without filter (%)	50.0 ± 0.35	50.4 ± 0.20
Bisulphite conversion rate (%)	99.6 ± 0.06	99.6 ± 0.09

Values are presented as mean ± standard error. CpGs10 are CpGs covered by at least 10 uniquely mapped reads. There was no difference between fertility groups in any of the parameters investigated (t-test, p > 0.05)

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