Alignment Stats
| Sequences analysed in total |
73117 |
| Single-end alignments with a unique best hit |
45305 |
| Sequences without alignments under any condition |
25781 |
| Sequences that did not map uniquely |
2031 |
| Genomic sequence context not extractable (edges of chromosomes) |
0 |
|
|
Cytosine Methylation
| Total C's analysed |
1055444 |
| Methylated C's in CpG context |
29103 |
| Methylated C's in CHG context |
45836 |
| Methylated C's in CHH context |
110896 |
| Methylated C's in Unknown context |
672 |
| Unmethylated C's in CpG context |
23466 |
| Unmethylated C's in CHG context |
216452 |
| Unmethylated C's in CHH context |
629691 |
| Unmethylated C's in Unknown context |
3571 |
| Percentage methylation (CpG context) |
55.4% |
| Percentage methylation (CHG context) |
17.5% |
| Percentage methylation (CHH context) |
15.0% |
| Methylated C's in Unknown context |
N/A% |
|
|
Alignment to Individual Bisulfite Strands
| OT |
9544 |
original top strand |
| CTOT |
13176 |
complementary to original top strand |
| CTOB |
12935 |
complementary to original bottom strand |
| OB |
9650 |
original bottom strand |
|
|
Deduplication
| Alignments analysed |
90602 |
| Unique alignments |
43913 |
| Duplicates removed |
46689 |
| Duplicated alignments were found at 43903 different positions |
|
|
Cytosine Methylation after Extraction
| Total C's analysed |
666703 |
| Methylated C's in CpG context |
17998 |
| Methylated C's in CHG context |
24523 |
| Methylated C's in CHH context |
59275 |
| Unmethylated C's in CpG context |
14055 |
| Unmethylated C's in CHG context |
139694 |
| Unmethylated C's in CHH context |
411158 |
| Percentage methylation (CpG context) |
56.2% |
| Percentage methylation (CHG context) |
14.9% |
| Percentage methylation (CHH context) |
12.6% |
|
|
Nucleotide Coverage
| Nucleotide Class | Counts Sample | Counts Genome | % in Sample | % in Genome | fold coverage |
|---|
| A | 754425 | 294005666 | 29.65 | 29.12 | 0.003 |
|---|
| T | 741218 | 294285704 | 29.13 | 29.15 | 0.003 |
|---|
| C | 505493 | 210594019 | 19.87 | 20.86 | 0.002 |
|---|
| G | 543092 | 210590343 | 21.35 | 20.86 | 0.003 |
|---|
| AC | 131064 | 52532529 | 5.20 | 5.20 | 0.002 |
|---|
| CA | 190817 | 77472169 | 7.57 | 7.67 | 0.002 |
|---|
| TC | 145982 | 60093701 | 5.79 | 5.95 | 0.002 |
|---|
| CT | 176436 | 73354317 | 7.00 | 7.27 | 0.002 |
|---|
| CC | 109262 | 48375161 | 4.33 | 4.79 | 0.002 |
|---|
| CG | 24344 | 11392056 | 0.97 | 1.13 | 0.002 |
|---|
| GC | 114600 | 49592331 | 4.54 | 4.91 | 0.002 |
|---|
| GG | 123347 | 48349387 | 4.89 | 4.79 | 0.003 |
|---|
| AG | 191002 | 73308184 | 7.58 | 7.26 | 0.003 |
|---|
| GA | 161361 | 60059654 | 6.40 | 5.95 | 0.003 |
|---|
| TG | 199482 | 77540413 | 7.91 | 7.68 | 0.003 |
|---|
| GT | 138902 | 52588666 | 5.51 | 5.21 | 0.003 |
|---|
| TT | 234431 | 96125962 | 9.30 | 9.52 | 0.002 |
|---|
| TA | 154360 | 60525298 | 6.12 | 6.00 | 0.003 |
|---|
| AT | 184868 | 72216445 | 7.33 | 7.15 | 0.003 |
|---|
| AA | 241206 | 95948192 | 9.57 | 9.50 | 0.003 |
|---|
|
|
M-Bias Plot
