Alignment Stats
| Sequences analysed in total |
48325 |
| Single-end alignments with a unique best hit |
35468 |
| Sequences without alignments under any condition |
10232 |
| Sequences that did not map uniquely |
2625 |
| Genomic sequence context not extractable (edges of chromosomes) |
0 |
|
|
Cytosine Methylation
| Total C's analysed |
773678 |
| Methylated C's in CpG context |
22988 |
| Methylated C's in CHG context |
2472 |
| Methylated C's in CHH context |
7632 |
| Methylated C's in Unknown context |
320 |
| Unmethylated C's in CpG context |
21338 |
| Unmethylated C's in CHG context |
196394 |
| Unmethylated C's in CHH context |
522854 |
| Unmethylated C's in Unknown context |
2974 |
| Percentage methylation (CpG context) |
51.9% |
| Percentage methylation (CHG context) |
1.2% |
| Percentage methylation (CHH context) |
1.4% |
| Methylated C's in Unknown context |
N/A% |
|
|
Alignment to Individual Bisulfite Strands
| OT |
7060 |
original top strand |
| CTOT |
10675 |
complementary to original top strand |
| CTOB |
10847 |
complementary to original bottom strand |
| OB |
6886 |
original bottom strand |
|
|
Deduplication
| Alignments analysed |
68320 |
| Unique alignments |
68079 |
| Duplicates removed |
241 |
| Duplicated alignments were found at 237 different positions |
|
|
Cytosine Methylation after Extraction
| Total C's analysed |
1240767 |
| Methylated C's in CpG context |
36570 |
| Methylated C's in CHG context |
3233 |
| Methylated C's in CHH context |
9012 |
| Unmethylated C's in CpG context |
32631 |
| Unmethylated C's in CHG context |
316549 |
| Unmethylated C's in CHH context |
842772 |
| Percentage methylation (CpG context) |
52.8% |
| Percentage methylation (CHG context) |
1.0% |
| Percentage methylation (CHH context) |
1.1% |
|
|
Nucleotide Coverage
| Nucleotide Class | Counts Sample | Counts Genome | % in Sample | % in Genome | fold coverage |
|---|
| A | 1291898 | 294005666 | 28.78 | 29.12 | 0.004 |
|---|
| T | 1252552 | 294285704 | 27.91 | 29.15 | 0.004 |
|---|
| C | 940393 | 210594019 | 20.95 | 20.86 | 0.004 |
|---|
| G | 1003700 | 210590343 | 22.36 | 20.86 | 0.005 |
|---|
| AC | 229384 | 52532529 | 5.16 | 5.20 | 0.004 |
|---|
| CA | 347273 | 77472169 | 7.82 | 7.67 | 0.004 |
|---|
| TC | 253054 | 60093701 | 5.69 | 5.95 | 0.004 |
|---|
| CT | 318148 | 73354317 | 7.16 | 7.27 | 0.004 |
|---|
| CC | 212245 | 48375161 | 4.78 | 4.79 | 0.004 |
|---|
| CG | 52521 | 11392056 | 1.18 | 1.13 | 0.005 |
|---|
| GC | 236155 | 49592331 | 5.31 | 4.91 | 0.005 |
|---|
| GG | 232257 | 48349387 | 5.23 | 4.79 | 0.005 |
|---|
| AG | 347974 | 73308184 | 7.83 | 7.26 | 0.005 |
|---|
| GA | 286255 | 60059654 | 6.44 | 5.95 | 0.005 |
|---|
| TG | 360631 | 77540413 | 8.12 | 7.68 | 0.005 |
|---|
| GT | 239294 | 52588666 | 5.39 | 5.21 | 0.005 |
|---|
| TT | 379275 | 96125962 | 8.54 | 9.52 | 0.004 |
|---|
| TA | 246437 | 60525298 | 5.55 | 6.00 | 0.004 |
|---|
| AT | 303575 | 72216445 | 6.83 | 7.15 | 0.004 |
|---|
| AA | 399107 | 95948192 | 8.98 | 9.50 | 0.004 |
|---|
|
|
M-Bias Plot
