Table 3.
CpG coverage for reduced representation bisulfite sequencing (RRBS) and whole genome bisulfite sequencing (WGBS) when reduced amounts of sequence data are available.
| >Amount of sequencing (GB) | RRBS (total no. CpGs) | Sites covered relative to 30 GB (%) | RRBS (≥10X CpGs) | Sites covered relative to 30 GB (%) | WGBS (total no. CpGs) | Sites covered relative to 30 GB (%) | WGBS (≥10X CpGs) | Sites covered relative to 30 GB (%) |
|---|---|---|---|---|---|---|---|---|
| 30 | 2,599,828 | 100 | 1,765,542 | 100 | 9,719,824 | 100 | 2,840,025 | 100 |
| 25 | 2,566,252 | 98.7 | 1,697,946 | 96.2 | 9,545,383 | 98.2 | 2,037,927 | 71.8 |
| 18.5 | 2,504,492 | 96.3 | 1,584,743 | 89.8 | 9,207,310 | 94.7 | 1,083,324 | 38.1 |
| 12 | 2,399,624 | 92.3 | 1,400,619 | 79.3 | 6,315,859 | 65.0 | 8,059 | 0.3 |
| 5 | 2,128,539 | 81.9 | 961,329 | 54.4 | 5,851,814 | 60.2 | 4,074 | 0.1 |
| 2.5 | 1,853,981 | 71.3 | 645,386 | 36.6 | 4,101,353 | 42.2 | 1,065 | 0.0 |
Large sequence files (30 GB) obtained from sequencing RRBS and WGBS libraries over one lane of an Illumina HiSeq were randomly sampled resulting in sequentially smaller sequence files for comparison.