TABLE 1.
Library characterization, mapping efficiency on the bovine genome (UMD3.1), coverage and average methylation in RRBS libraries.
| HM15 (n = 9) | MM15 (n = 7) | MM16 (n = 9) | |
| Number of read pairs (million) | 35.1 ± 6.1 | 36.5 ± 7.0 | 39.4 ± 7.5 |
| Average quality score (Phred score) | 38.3 ± 0.2 | 38.2 ± 0.3 | 38.2 ± 0.1 |
| Uniquely mapped reads (%) | 35.5 ± 3.1 | 35.3 ± 2.4 | 35.0 ± 2.9 |
| Ambiguous reads (%) | 52.6 ± 2.8 | 52.5 ± 3.0 | 52.7 ± 2.8 |
| Unmapped reads (%) | 11.9 ± 1.0 | 12.2 ± 0.9 | 12.2 ± 0.8 |
| Bisulfite conversion rate (%) | 99.3 ± 0.7 | 99.4 ± 0.7 | 99.5 ± 0.6 |
| Number of covered CpGs (million) | 3.05 ± 0.1 | 3.08 ± 0.2 | 3.08 ± 0.1 |
| Average coverage per CpG | 24.8 ± 4.6 | 25.1 ± 4.4 | 26.8 ± 4.0 |
| Percentage of CpGs10 | 56.7 ± 5.0 | 57.8 ± 4.7 | 59.8 ± 3.3 |
| Average DNA methylation at CpGs10 (%) | 50.3 ± 1.0 | 50.1 ± 0.9 | 50.5 ± 0.6 |
| Percentage of CpGs10 hypermethylated (DNA methylation > 80%) | 47.1 ± 1.4 | 46.9 ± 0.7 | 47.5 ± 0.6 |
| Percentage of intermediate CpGs10 (DNA methylation in [20%; 80%]) | 7.1 ± 0.5 | 7.3 ± 0.3 | 7.1 ± 0.4 |
| Percentage of CpGs10 hypomethylated (DNA methylation < 20%) | 45.8 ± 1.1 | 45.8 ± 0.8 | 45.5 ± 0.5 |
Values are mean ± standard error of the means. CpGs10: CpGs covered by at least 10 uniquely mapped reads. Hypermethylated, intermediate and hypomethylated CpGs10 indicate CpGs10 with average methylation percentage >80%, [20%; 80%], and <20%, respectively.