Alignment Stats
| Sequences analysed in total |
524825 |
| Single-end alignments with a unique best hit |
375912 |
| Sequences without alignments under any condition |
106062 |
| Sequences that did not map uniquely |
42851 |
| Genomic sequence context not extractable (edges of chromosomes) |
0 |
|
|
Cytosine Methylation
| Total C's analysed |
7328139 |
| Methylated C's in CpG context |
225656 |
| Methylated C's in CHG context |
107232 |
| Methylated C's in CHH context |
242386 |
| Methylated C's in Unknown context |
3305 |
| Unmethylated C's in CpG context |
222253 |
| Unmethylated C's in CHG context |
1810079 |
| Unmethylated C's in CHH context |
4720533 |
| Unmethylated C's in Unknown context |
26931 |
| Percentage methylation (CpG context) |
50.4% |
| Percentage methylation (CHG context) |
5.6% |
| Percentage methylation (CHH context) |
4.9% |
| Methylated C's in Unknown context |
N/A% |
|
|
Alignment to Individual Bisulfite Strands
| OT |
81045 |
original top strand |
| CTOT |
106784 |
complementary to original top strand |
| CTOB |
107238 |
complementary to original bottom strand |
| OB |
80845 |
original bottom strand |
|
|
Deduplication
| Alignments analysed |
717564 |
| Unique alignments |
712915 |
| Duplicates removed |
4649 |
| Duplicated alignments were found at 4397 different positions |
|
|
Cytosine Methylation after Extraction
| Total C's analysed |
11138095 |
| Methylated C's in CpG context |
336737 |
| Methylated C's in CHG context |
122546 |
| Methylated C's in CHH context |
270466 |
| Unmethylated C's in CpG context |
317259 |
| Unmethylated C's in CHG context |
2798815 |
| Unmethylated C's in CHH context |
7292272 |
| Percentage methylation (CpG context) |
51.5% |
| Percentage methylation (CHG context) |
4.2% |
| Percentage methylation (CHH context) |
3.6% |
|
|
Nucleotide Coverage
| Nucleotide Class | Counts Sample | Counts Genome | % in Sample | % in Genome | fold coverage |
|---|
| A | 12478537 | 294005666 | 28.39 | 29.12 | 0.042 |
|---|
| T | 12139641 | 294285704 | 27.62 | 29.15 | 0.041 |
|---|
| C | 9260662 | 210594019 | 21.07 | 20.86 | 0.044 |
|---|
| G | 10081404 | 210590343 | 22.93 | 20.86 | 0.048 |
|---|
| AC | 2214098 | 52532529 | 5.09 | 5.20 | 0.042 |
|---|
| CA | 3376862 | 77472169 | 7.77 | 7.67 | 0.044 |
|---|
| TC | 2466426 | 60093701 | 5.67 | 5.95 | 0.041 |
|---|
| CT | 3111645 | 73354317 | 7.16 | 7.27 | 0.042 |
|---|
| CC | 2121969 | 48375161 | 4.88 | 4.79 | 0.044 |
|---|
| CG | 541710 | 11392056 | 1.25 | 1.13 | 0.048 |
|---|
| GC | 2357260 | 49592331 | 5.42 | 4.91 | 0.048 |
|---|
| GG | 2388503 | 48349387 | 5.49 | 4.79 | 0.049 |
|---|
| AG | 3457530 | 73308184 | 7.95 | 7.26 | 0.047 |
|---|
| GA | 2844868 | 60059654 | 6.54 | 5.95 | 0.047 |
|---|
| TG | 3578479 | 77540413 | 8.23 | 7.68 | 0.046 |
|---|
| GT | 2383283 | 52588666 | 5.48 | 5.21 | 0.045 |
|---|
| TT | 3633279 | 96125962 | 8.36 | 9.52 | 0.038 |
|---|
| TA | 2321750 | 60525298 | 5.34 | 6.00 | 0.038 |
|---|
| AT | 2880362 | 72216445 | 6.63 | 7.15 | 0.040 |
|---|
| AA | 3798123 | 95948192 | 8.74 | 9.50 | 0.040 |
|---|
|
|
M-Bias Plot
