Alignment Stats
| Sequences analysed in total |
1296516 |
| Single-end alignments with a unique best hit |
825661 |
| Sequences without alignments under any condition |
416639 |
| Sequences that did not map uniquely |
54216 |
| Genomic sequence context not extractable (edges of chromosomes) |
0 |
|
|
Cytosine Methylation
| Total C's analysed |
19352171 |
| Methylated C's in CpG context |
619668 |
| Methylated C's in CHG context |
187701 |
| Methylated C's in CHH context |
495053 |
| Methylated C's in Unknown context |
12862 |
| Unmethylated C's in CpG context |
629431 |
| Unmethylated C's in CHG context |
4857372 |
| Unmethylated C's in CHH context |
12562946 |
| Unmethylated C's in Unknown context |
83718 |
| Percentage methylation (CpG context) |
49.6% |
| Percentage methylation (CHG context) |
3.7% |
| Percentage methylation (CHH context) |
3.8% |
| Methylated C's in Unknown context |
N/A% |
|
|
Alignment to Individual Bisulfite Strands
| OT |
169906 |
original top strand |
| CTOT |
244308 |
complementary to original top strand |
| CTOB |
242487 |
complementary to original bottom strand |
| OB |
168960 |
original bottom strand |
|
|
Deduplication
| Alignments analysed |
1639843 |
| Unique alignments |
1438295 |
| Duplicates removed |
201548 |
| Duplicated alignments were found at 166940 different positions |
|
|
Cytosine Methylation after Extraction
| Total C's analysed |
27535857 |
| Methylated C's in CpG context |
856749 |
| Methylated C's in CHG context |
193852 |
| Methylated C's in CHH context |
447461 |
| Unmethylated C's in CpG context |
810140 |
| Unmethylated C's in CHG context |
7011857 |
| Unmethylated C's in CHH context |
18215798 |
| Percentage methylation (CpG context) |
51.4% |
| Percentage methylation (CHG context) |
2.7% |
| Percentage methylation (CHH context) |
2.4% |
|
|
Nucleotide Coverage
| Nucleotide Class | Counts Sample | Counts Genome | % in Sample | % in Genome | fold coverage |
|---|
| A | 27280913 | 294005666 | 28.26 | 29.12 | 0.093 |
|---|
| T | 26515587 | 294285704 | 27.47 | 29.15 | 0.090 |
|---|
| C | 20486688 | 210594019 | 21.22 | 20.86 | 0.097 |
|---|
| G | 22247616 | 210590343 | 23.05 | 20.86 | 0.106 |
|---|
| AC | 4864353 | 52532529 | 5.09 | 5.20 | 0.093 |
|---|
| CA | 7440833 | 77472169 | 7.78 | 7.67 | 0.096 |
|---|
| TC | 5421407 | 60093701 | 5.67 | 5.95 | 0.090 |
|---|
| CT | 6870619 | 73354317 | 7.18 | 7.27 | 0.094 |
|---|
| CC | 4740948 | 48375161 | 4.96 | 4.79 | 0.098 |
|---|
| CG | 1233741 | 11392056 | 1.29 | 1.13 | 0.108 |
|---|
| GC | 5270211 | 49592331 | 5.51 | 4.91 | 0.106 |
|---|
| GG | 5370345 | 48349387 | 5.62 | 4.79 | 0.111 |
|---|
| AG | 7585648 | 73308184 | 7.93 | 7.26 | 0.103 |
|---|
| GA | 6200027 | 60059654 | 6.48 | 5.95 | 0.103 |
|---|
| TG | 7843461 | 77540413 | 8.20 | 7.68 | 0.101 |
|---|
| GT | 5201513 | 52588666 | 5.44 | 5.21 | 0.099 |
|---|
| TT | 7924738 | 96125962 | 8.29 | 9.52 | 0.082 |
|---|
| TA | 5069078 | 60525298 | 5.30 | 6.00 | 0.084 |
|---|
| AT | 6273888 | 72216445 | 6.56 | 7.15 | 0.087 |
|---|
| AA | 8317040 | 95948192 | 8.70 | 9.50 | 0.087 |
|---|
|
|
M-Bias Plot
