Alignment Stats
| Sequences analysed in total |
258905 |
| Single-end alignments with a unique best hit |
184288 |
| Sequences without alignments under any condition |
59688 |
| Sequences that did not map uniquely |
14929 |
| Genomic sequence context not extractable (edges of chromosomes) |
0 |
|
|
Cytosine Methylation
| Total C's analysed |
3872882 |
| Methylated C's in CpG context |
109451 |
| Methylated C's in CHG context |
38334 |
| Methylated C's in CHH context |
97020 |
| Methylated C's in Unknown context |
1684 |
| Unmethylated C's in CpG context |
103816 |
| Unmethylated C's in CHG context |
950259 |
| Unmethylated C's in CHH context |
2574002 |
| Unmethylated C's in Unknown context |
13484 |
| Percentage methylation (CpG context) |
51.3% |
| Percentage methylation (CHG context) |
3.9% |
| Percentage methylation (CHH context) |
3.6% |
| Methylated C's in Unknown context |
N/A% |
|
|
Alignment to Individual Bisulfite Strands
| OT |
41295 |
original top strand |
| CTOT |
50970 |
complementary to original top strand |
| CTOB |
50938 |
complementary to original bottom strand |
| OB |
41085 |
original bottom strand |
|
|
Deduplication
| Alignments analysed |
351712 |
| Unique alignments |
345330 |
| Duplicates removed |
6382 |
| Duplicated alignments were found at 6233 different positions |
|
|
Cytosine Methylation after Extraction
| Total C's analysed |
5940239 |
| Methylated C's in CpG context |
164022 |
| Methylated C's in CHG context |
44190 |
| Methylated C's in CHH context |
108737 |
| Unmethylated C's in CpG context |
150017 |
| Unmethylated C's in CHG context |
1476663 |
| Unmethylated C's in CHH context |
3996610 |
| Percentage methylation (CpG context) |
52.2% |
| Percentage methylation (CHG context) |
2.9% |
| Percentage methylation (CHH context) |
2.6% |
|
|
Nucleotide Coverage
| Nucleotide Class | Counts Sample | Counts Genome | % in Sample | % in Genome | fold coverage |
|---|
| A | 6545983 | 294005666 | 28.93 | 29.12 | 0.022 |
|---|
| T | 6360908 | 294285704 | 28.11 | 29.15 | 0.022 |
|---|
| C | 4710621 | 210594019 | 20.82 | 20.86 | 0.022 |
|---|
| G | 5010763 | 210590343 | 22.14 | 20.86 | 0.024 |
|---|
| AC | 1162536 | 52532529 | 5.19 | 5.20 | 0.022 |
|---|
| CA | 1755510 | 77472169 | 7.84 | 7.67 | 0.023 |
|---|
| TC | 1281424 | 60093701 | 5.72 | 5.95 | 0.021 |
|---|
| CT | 1601480 | 73354317 | 7.15 | 7.27 | 0.022 |
|---|
| CC | 1056582 | 48375161 | 4.72 | 4.79 | 0.022 |
|---|
| CG | 247884 | 11392056 | 1.11 | 1.13 | 0.022 |
|---|
| GC | 1163491 | 49592331 | 5.19 | 4.91 | 0.023 |
|---|
| GG | 1155676 | 48349387 | 5.16 | 4.79 | 0.024 |
|---|
| AG | 1749564 | 73308184 | 7.81 | 7.26 | 0.024 |
|---|
| GA | 1433218 | 60059654 | 6.40 | 5.95 | 0.024 |
|---|
| TG | 1805469 | 77540413 | 8.06 | 7.68 | 0.023 |
|---|
| GT | 1209634 | 52588666 | 5.40 | 5.21 | 0.023 |
|---|
| TT | 1941456 | 96125962 | 8.67 | 9.52 | 0.020 |
|---|
| TA | 1267035 | 60525298 | 5.66 | 6.00 | 0.021 |
|---|
| AT | 1546538 | 72216445 | 6.90 | 7.15 | 0.021 |
|---|
| AA | 2025728 | 95948192 | 9.04 | 9.50 | 0.021 |
|---|
|
|
M-Bias Plot
