Alignment Stats
| Sequences analysed in total |
84606 |
| Single-end alignments with a unique best hit |
43426 |
| Sequences without alignments under any condition |
38812 |
| Sequences that did not map uniquely |
2368 |
| Genomic sequence context not extractable (edges of chromosomes) |
0 |
|
|
Cytosine Methylation
| Total C's analysed |
988745 |
| Methylated C's in CpG context |
27977 |
| Methylated C's in CHG context |
46136 |
| Methylated C's in CHH context |
111272 |
| Methylated C's in Unknown context |
685 |
| Unmethylated C's in CpG context |
23469 |
| Unmethylated C's in CHG context |
201457 |
| Unmethylated C's in CHH context |
578434 |
| Unmethylated C's in Unknown context |
3211 |
| Percentage methylation (CpG context) |
54.4% |
| Percentage methylation (CHG context) |
18.6% |
| Percentage methylation (CHH context) |
16.1% |
| Methylated C's in Unknown context |
N/A% |
|
|
Alignment to Individual Bisulfite Strands
| OT |
9214 |
original top strand |
| CTOT |
12575 |
complementary to original top strand |
| CTOB |
12393 |
complementary to original bottom strand |
| OB |
9244 |
original bottom strand |
|
|
Deduplication
| Alignments analysed |
86844 |
| Unique alignments |
42082 |
| Duplicates removed |
44762 |
| Duplicated alignments were found at 42072 different positions |
|
|
Cytosine Methylation after Extraction
| Total C's analysed |
615438 |
| Methylated C's in CpG context |
17340 |
| Methylated C's in CHG context |
24805 |
| Methylated C's in CHH context |
59267 |
| Unmethylated C's in CpG context |
13871 |
| Unmethylated C's in CHG context |
128390 |
| Unmethylated C's in CHH context |
371765 |
| Percentage methylation (CpG context) |
55.6% |
| Percentage methylation (CHG context) |
16.2% |
| Percentage methylation (CHH context) |
13.8% |
|
|
Nucleotide Coverage
| Nucleotide Class | Counts Sample | Counts Genome | % in Sample | % in Genome | fold coverage |
|---|
| A | 679063 | 294005666 | 29.36 | 29.12 | 0.002 |
|---|
| T | 668788 | 294285704 | 28.92 | 29.15 | 0.002 |
|---|
| C | 461299 | 210594019 | 19.95 | 20.86 | 0.002 |
|---|
| G | 503613 | 210590343 | 21.78 | 20.86 | 0.002 |
|---|
| AC | 116760 | 52532529 | 5.10 | 5.20 | 0.002 |
|---|
| CA | 172048 | 77472169 | 7.51 | 7.67 | 0.002 |
|---|
| TC | 132773 | 60093701 | 5.79 | 5.95 | 0.002 |
|---|
| CT | 160358 | 73354317 | 7.00 | 7.27 | 0.002 |
|---|
| CC | 101149 | 48375161 | 4.41 | 4.79 | 0.002 |
|---|
| CG | 23406 | 11392056 | 1.02 | 1.13 | 0.002 |
|---|
| GC | 106355 | 49592331 | 4.64 | 4.91 | 0.002 |
|---|
| GG | 116336 | 48349387 | 5.08 | 4.79 | 0.002 |
|---|
| AG | 175354 | 73308184 | 7.65 | 7.26 | 0.002 |
|---|
| GA | 148999 | 60059654 | 6.50 | 5.95 | 0.002 |
|---|
| TG | 183832 | 77540413 | 8.02 | 7.68 | 0.002 |
|---|
| GT | 127180 | 52588666 | 5.55 | 5.21 | 0.002 |
|---|
| TT | 210115 | 96125962 | 9.17 | 9.52 | 0.002 |
|---|
| TA | 135608 | 60525298 | 5.92 | 6.00 | 0.002 |
|---|
| AT | 164805 | 72216445 | 7.19 | 7.15 | 0.002 |
|---|
| AA | 216271 | 95948192 | 9.44 | 9.50 | 0.002 |
|---|
|
|
M-Bias Plot
