Table 1 Characterization, mapping efficiency on the bovine reference genome (ARS-UCD2.1) and on a Repbase artificial genome, coverage and average methylation in RRBS libraries
| Â | Main cohort | Independent cohort | ||
|---|---|---|---|---|
Fertile (n = 57) | Subfertile (n = 43) | Fertile (n = 16) | Subfertile (n = 4) | |
Sequencing parameters | ||||
Number of read pairs (million) | 32.9 ± 5.6 | 33.9 ± 5.4 | 35.5 ± 5.6 | 33.9 ± 2.5 |
Average quality score (Phred score) | 38.2 ± 0.3 | 38.4 ± 0.3 | 39.0 ± 0.3 | 38.9 ± 0.4 |
Bisulfite conversion rate (%) | 99.0 ± 0.4 | 99.0 ± 0.4 | 99.3 ± 0.6 | 99.1 ± 0.6 |
Alignment on ARS-UCD2.1 | ||||
Uniquely mapped reads (%) | 33.9 ± 1.5 | 34.3 ± 1.6 | 35.8 ± 2 | 35.0 ± 3.1 |
Number of covered CpGs (million) | 3.2 ± 0.1 | 3.2 ± 0.09 | 3.3 ± 0.1 | 3.3 ± 0.1 |
Average coverage per CpG | 23.2 ± 3.6 | 24.0 ± 3.5 | 24.1 ± 3 | 22.9 ± 1.8 |
Percentage of CpGs10 | 60.2 ± 3.9 | 60.9 ± 3.5 | 62.2 ± 2.9 | 60.3 ± 1.9 |
Average DNA methylation at CpGs10 (%) | 46.2 ± 1.6 | 46.5 ± 1.2 | 47.5 ± 1.7 | 47.8 ± 1.8 |
Percentage of hypomethylated CpGs10 | 50.9 ± 2 | 50.4 ± 1.2 | 49.3 ± 2 | 49.0 ± 2.1 |
Percentage of intermediate CpGs10 | 6.0 ± 1.1 | 6.0 ± 0.4 | 5.8 ± 0.6 | 6.1 ± 0.2 |
Percentage of hypermethylated CpGs10 | 43.4 ± 2.4 | 43.7 ± 1.1 | 44.9 ± 1.7 | 44.9 ± 1.9 |
Alignment on RepBase | ||||
Uniquely mapped reads (%) | 20.6 ± 1.7 | 20.4 ± 1.2 | 21.6 ± 1.9 | 22.4 ± 1.6 |
Number of covered CpGs (million) | 1104 ± 72 | 1124 ± 85 | 1080 ± 38 | 1048 ± 4 |
Average coverage per CpG | 36,996 ± 6451 | 37,722 ± 6606 | 43,479 ± 8507 | 43,603 ± 6136 |
Percentage of CpGs10 | 70.8 ± 3 | 70.8 ± 3.1 | 73.5 ± 2 | 73.3 ± 2 |
Average DNA methylation at CpGs10 (%) | 30.8 ± 3 | 31.1 ± 3.2 | 31.3 ± 2.1 | 30.6 ± 2.9 |
Percentage of hypomethylated CpGs10 | 50.4 ± 2.7 | 49.5 ± 2.9 | 49.7 ± 2.9 | 48.4 ± 5.4 |
Percentage of intermediate CpGs10 | 41.3 ± 2 | 42.1 ± 1.8 | 40.8 ± 2.5 | 43.1 ± 5.4 |
Percentage of hypermethylated CpGs10 | 8.2 ± 1.9 | 8.5 ± 2.4 | 9.4 ± 1.7* | 8.5 ± 1.5* |