Table 3 An overview of basic RRBS statistics. Boar ejaculates (n = 18) from seven different individuals (boar A – G) after Day 4 of liquid preservation at 18 °C, based on their DFI value were divided into low (L), medium (M) and high (H) groups (six ejaculates each)
From: DNA methylation patterns vary in boar sperm cells with different levels of DNA fragmentation
DFI group | DFI (%) | Sample ID | Boar ID | Total reads | Clean reads after trimming | Read coverage (X) | Mapping efficiency (%) | CpG methylation (%) | Number of CpGs (10X) | Bisulphite conversion rate (%) |
|---|---|---|---|---|---|---|---|---|---|---|
Low (L) | 0.4 | L 1 | A | 16,442,959 | 16,372,832 | 20.5 | 60.5 | 12.4 | 1,136,877 | 99.9 |
0.5 | L 2 | A | 19,490,143 | 19,164,300 | 20.1 | 46.7 | 42.2 | 797,270 | 98.9 | |
0.6 | L 3 | A | 21,720,429 | 21,600,109 | 27.3 | 57.0 | 41.5 | 1,261,660 | 98.9 | |
0.6 | L 4 | A | 13,374,736 | 13,313,871 | 16.7 | 58.8 | 9.8 | 971,589 | 99.9 | |
0.7 | L 5 | B | 12,614,151 | 12,582,707 | 15.7 | 63.3 | 42.8 | 438,273 | 99.9 | |
0.9 | L 6 | B | 16,423,268 | 16,286,276 | 20.5 | 57.3 | 38.8 | 951,776 | 99.9 | |
Medium (M) | 5.8 | M 1 | C | 13,193,208 | 13,168,643 | 16.5 | 62.6 | 44.1 | 475,564 | 99.9 |
6.9 | M 2 | D | 12,551,543 | 12,528,289 | 15.7 | 62.4 | 39.1 | 453,421 | 99.9 | |
6.9 | M 3 | C | 10,703,251 | 10,679,744 | 13.4 | 64.2 | 47.0 | 287,489 | 99.9 | |
7.0 | M 4 | C | 15,460,504 | 15,025,860 | 18.9 | 50.1 | 40.4 | 769,498 | 99.9 | |
7.5 | M 5 | D | 14,215,843 | 14,142,428 | 17.7 | 56.5 | 12.1 | 975,707 | 99.9 | |
8.1 | M 6 | E | 15,162,760 | 15,122,630 | 18.7 | 62.0 | 41.1 | 545,567 | 99.9 | |
High (H) | 15.8 | H 1 | F | 17,995,363 | 17,939,071 | 22.6 | 62.2 | 13.1 | 1,183,512 | 99.9 |
18.5 | H 2 | D | 17,139,869 | 16,928,292 | 21.3 | 45.6 | 38.3 | 725,755 | 99.9 | |
21.3 | H 3 | F | 16,767,296 | 16,670,788 | 20.8 | 61.2 | 7.9 | 1,145,606 | 99.8 | |
26.0 | H 4 | G | 11,580,556 | 11,547,471 | 14.2 | 63.6 | 48.2 | 152,219 | 99.9 | |
27.4 | H 5 | F | 21,075,288 | 20,855,183 | 26.3 | 50.7 | 30.8 | 1,188,854 | 99.9 | |
28.4 | H 6 | G | 17,655,261 | 17,614,978 | 21.8 | 64.3 | 50.1 | 496,490 | 99.9 |