Alignment Stats
| Sequences analysed in total |
3717864 |
| Single-end alignments with a unique best hit |
1214110 |
| Sequences without alignments under any condition |
2395981 |
| Sequences that did not map uniquely |
107773 |
| Genomic sequence context not extractable (edges of chromosomes) |
0 |
|
|
Cytosine Methylation
| Total C's analysed |
23829885 |
| Methylated C's in CpG context |
931396 |
| Methylated C's in CHG context |
445571 |
| Methylated C's in CHH context |
1547725 |
| Methylated C's in Unknown context |
42570 |
| Unmethylated C's in CpG context |
488061 |
| Unmethylated C's in CHG context |
5462613 |
| Unmethylated C's in CHH context |
14954519 |
| Unmethylated C's in Unknown context |
102435 |
| Percentage methylation (CpG context) |
65.6% |
| Percentage methylation (CHG context) |
7.5% |
| Percentage methylation (CHH context) |
9.4% |
| Methylated C's in Unknown context |
N/A% |
|
|
Alignment to Individual Bisulfite Strands
| OT |
317804 |
original top strand |
| CTOT |
289337 |
complementary to original top strand |
| CTOB |
289648 |
complementary to original bottom strand |
| OB |
317321 |
original bottom strand |
|
|
Deduplication
| Alignments analysed |
2448089 |
| Unique alignments |
1603212 |
| Duplicates removed |
844877 |
| Duplicated alignments were found at 486282 different positions |
|
|
Cytosine Methylation after Extraction
| Total C's analysed |
23937849 |
| Methylated C's in CpG context |
854198 |
| Methylated C's in CHG context |
66862 |
| Methylated C's in CHH context |
193754 |
| Unmethylated C's in CpG context |
478414 |
| Unmethylated C's in CHG context |
5978821 |
| Unmethylated C's in CHH context |
16365800 |
| Percentage methylation (CpG context) |
64.1% |
| Percentage methylation (CHG context) |
1.1% |
| Percentage methylation (CHH context) |
1.2% |
|
|
Nucleotide Coverage
| Nucleotide Class | Counts Sample | Counts Genome | % in Sample | % in Genome | fold coverage |
|---|
| A | 30287759 | 294005666 | 31.48 | 29.12 | 0.103 |
|---|
| T | 26045577 | 294285704 | 27.07 | 29.15 | 0.089 |
|---|
| C | 18909903 | 210594019 | 19.65 | 20.86 | 0.090 |
|---|
| G | 20973567 | 210590343 | 21.80 | 20.86 | 0.100 |
|---|
| AC | 5173541 | 52532529 | 5.43 | 5.20 | 0.098 |
|---|
| CA | 7522491 | 77472169 | 7.90 | 7.67 | 0.097 |
|---|
| TC | 4974557 | 60093701 | 5.22 | 5.95 | 0.083 |
|---|
| CT | 6149276 | 73354317 | 6.46 | 7.27 | 0.084 |
|---|
| CC | 3951882 | 48375161 | 4.15 | 4.79 | 0.082 |
|---|
| CG | 1069645 | 11392056 | 1.12 | 1.13 | 0.094 |
|---|
| GC | 4613470 | 49592331 | 4.84 | 4.91 | 0.093 |
|---|
| GG | 4776364 | 48349387 | 5.02 | 4.79 | 0.099 |
|---|
| AG | 7675200 | 73308184 | 8.06 | 7.26 | 0.105 |
|---|
| GA | 6493655 | 60059654 | 6.82 | 5.95 | 0.108 |
|---|
| TG | 7237190 | 77540413 | 7.60 | 7.68 | 0.093 |
|---|
| GT | 4881076 | 52588666 | 5.13 | 5.21 | 0.093 |
|---|
| TT | 7767085 | 96125962 | 8.16 | 9.52 | 0.081 |
|---|
| TA | 5779550 | 60525298 | 6.07 | 6.00 | 0.095 |
|---|
| AT | 6985441 | 72216445 | 7.34 | 7.15 | 0.097 |
|---|
| AA | 10180630 | 95948192 | 10.69 | 9.50 | 0.106 |
|---|
|
|
M-Bias Plot
